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August 24, 2020
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https://www.sciencedaily.com/releases/2020/08/200824165628.htm
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Biologists discover gene critical to development of columbines' iconic spurs
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Once in a while, over the history of life, a new trait evolves that leads to an explosion of diversity in a group of organisms. Take wings, for instance. Every group of animals that evolved them has spun off into a host of different species -- birds, bats, insects and pterosaurs. Scientists call these "key innovations."
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Understanding the development of key innovations is critical to understanding the evolution of the amazing array of organisms on Earth. Most of these happened deep in the distant past, making them difficult to study from a genetic perspective. Fortunately, one group of plants has acquired just such a trait in the past few million years.Columbines, with their elegant nectar spurs, promise scientists an opportunity to investigate the genetic changes that underpin a key innovation. After much research, UC Santa Barbara professor Scott Hodges, research associate Evangeline Ballerini, and their coauthors at Harvard University have identified a gene critical to the development of these structures. And to their knowledge, this is among the first key innovations for which a critical developmental gene has been identified. Their findings appear in the journal The researchers named the gene after Gregg Popovich, head coach of the San Antonio Spurs basketball team. "This gene is a transcription factor, which means it controls spur development in columbines by regulating the activity of other genes," explained Ballerini. "So I chose the name POPOVICH because as coach, Popovich controls San Antonio Spurs development, in a sense, by regulating the activity of his players."The evolution of spurs in columbines' ancestors seems to have led to rapid expansion in the genus. Around 70 species evolved over the past 5 to 7 million years, compared to its spurless sister genus, which counts only four species among its members.And columbines aren't the only flowers with spurs. The trait evolved independently in many different plants, including nasturtiums, larkspurs and impatiens. "And in each of those groups, the ones that have spurs have far more species than their closest relatives that don't have spurs," said Hodges."We think that diversity is linked to the evolution of this spur because the spur produces nectar, which attracts animal pollinators," Ballerini said. Changing the length or shape of the spur changes the animals that can pollinate the flower. "Bees are only moving pollen between bee flowers, hummingbirds are only moving pollen between hummingbird flowers, so you're not exchanging genes between those two different populations." Eventually, the two can split into different species.The question the researchers were trying to answer was how innovations like these develop in the first place. "If we can find genes that are important in the development of a key innovation, that will help us understand this kind of process," said Hodges."In most of these cases -- like in the wing example with birds, bats and insects -- those evolved so long ago that it's hard to find a particular gene that was critical for evolving that trait," he added. "Here we have a fairly recent origin of a key innovation, only 5 to 7 million years ago, and it's a fairly simple trait, so it's a little more straightforward."Since columbines evolved so recently, most of them can form fertile hybrids with each other. In the 1950s and '60s, a Polish geneticist crossed a spurless species -- appropriately named the spurless columbine -- with its spurred cousins. She found that in the first generation of offspring all had spurs, but self-pollinating these yielded a second generation where spurlessness reappeared in a quarter of the plants.That ratio was crucial to Hodges and Ballerini's work some half a century later. This simple fraction suggested that a single gene controlled the development of spurs. But columbines have roughly 30,000 genes, and only one was the gene they were looking for.Following in the footsteps of his predecessor, Hodges also crossed the spurless columbine with a spurred species, and then self-pollinated the offspring. But unlike in the previous experiment, Ballerini and Hodges now had the tools to search the plants' genetic code.Ballerini sequenced the genome of each of the nearly 300 second generation plants and looked for instances in which the spurless plants had inherited two copies from their spurless grandparent. This narrowed the search to around 1,100 genes on one of the plants' chromosomes.Still, 1,100 genes are a lot to sort through. "There was no guarantee that these methods would lead us to the gene we were looking for," Ballerini said. "There was definitely quite a bit of work that went into all of the experiments and analyses, but in the end there was a bit of luck too."Ballerini examined the expression of genes during five stages of early petal development in the spurless columbine and three other spurred species. She sequenced all the genes that were turned on in each stage and looked for consistent differences between the spurless and spurred plants. Eventually, with input from one of her collaborators at Harvard, Ballerini suspected she had identified the right gene. It was always turned off in the spurless species, turned on in the spurred species and was one of the 1,100 genes previously identified as associated with spurless flowers in the genetic cross. Now it was time to test her hypothesis.She used a genetically modified virus to knock down the expression of the gene in question as well as a gene critical for producing red pigment. This way they could tell which petals were affected just by looking at the color.Wherever POPOVICH was sidelined, the flowers developed diminutive spurs. But spur length depends both on the number and the size of cells. So the researchers worked with collaborators to count the number and measure the length of each cell making up these diminutive spurs."The longer spurs had more cells, and the shorter spurs had fewer cells," Hodges noted. "So the gene must have been acting by affecting how many cells were produced."Ballerini remembers sitting in her office after finishing her final analyses. She began throwing out potential gene names to graduate student Zac Cabin, a fellow sports enthusiast. "At the same time Zac and I turned to each other and both said 'POPOVICH!'" she recalled. The name seemed a perfect fit. "And it leaves open the possibility that, if we identify other genes at play in spur development, we can name them after some of the players on the Spurs."While identifying POPOVICH is certainly an achievement, the true value of the discovery lies in what it reveals about the evolution of key innovations. Before this work, none of the plant groups that had well-known genomes also made spurs. "We had no idea where to start," said Hodges. "This discovery provides us a foothold.""Once we identify one gene -- like this gene, which seems to be key in the process of forming spurs -- then we can start to figure out all of the components," he added. The team can now begin investigating which genes POPOVICH regulates, and which genes regulate POPOVICH. "This is a place to start to understand the whole system."While the researchers don't know how POPOVICH functions in other groups of plants, it appears to influence the number of leaflets that grow on bur clovers. Columbines also express the gene in their leaves; perhaps it was recruited from the leaves into petal development, Ballerini suggested.Novel adaptations don't appear out of nowhere, she explained. "When you're evolving a new structure, usually you're not evolving a whole brand new gene." Generally, organisms repurpose or add a purpose to an existing gene.The authors are also interested in identifying genes involved in the second phase of spur formation: the elongation of the cells in the spur cup."These are things that we will want to do now that we've identified this gene," Hodges said. "And since it's a transcription factor, it must have particular genes that it's affecting. The next logical step would be to identify the targets of this gene, and that would tell us a lot more about how it functions."The researchers expressed their gratitude toward Harvey Karp, who generously funded the Karp Discovery Award that made their research possible. "We really couldn't have done this project without it," Ballerini said.
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Zoology
| 2,020 |
August 24, 2020
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https://www.sciencedaily.com/releases/2020/08/200824120040.htm
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Beam me up: Researchers use 'behavioral teleporting' to study social interactions
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Teleporting is a science fiction trope often associated with
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The team, led by Maurizio Porfiri, Institute Professor at NYU Tandon, devised a novel approach to getting physically separated fish to interact with each other, leading to insights about what kinds of cues influence social behavior.The innovative system, called "behavioral teleporting" -- the transfer of the complete inventory of behaviors and actions (ethogram) of a live zebrafish onto a remotely located robotic replica -- allowed the investigators to independently manipulate multiple factors underpinning social interactions in real-time. The research, "Behavioral teleporting of individual ethograms onto inanimate robots: experiments on social interactions in live zebrafish," appears in the Cell Press journal The team, including Mert Karakaya, a Ph.D. candidate in the Department of Mechanical and Aerospace Engineering at NYU Tandon, and Simone Macrì of the Centre for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità, Rome, devised a setup consisting of two separate tanks, each containing one fish and one robotic replica. Within each tank, the live fish of the pair swam with the zebrafish replica matching the morphology and locomotory pattern of the live fish located in the other tank.An automated tracking system scored each of the live subjects' locomotory patterns, which were, in turn, used to control the robotic replica swimming in the other tank via an external manipulator. Therefore, the system allowed the transfer of the complete ethogram of each fish across tanks within a fraction of a second, establishing a complex robotics-mediated interaction between two remotely-located live animals. By independently controlling the morphology of these robots, the team explored the link between appearance and movements in social behavior.The investigators found that the replica teleported the fish motion in almost all trials (85% of the total experimental time), with a 95% accuracy at a maximum time lag of less than two-tenths of a second. The high accuracy in the replication of fish trajectory was confirmed by equivalent analysis on speed, turn rate, and acceleration.Porfiri explained that the behavioral teleporting system avoids the limits of typical modeling using robots."Since existing approaches involve the use of a mathematical representation of social behavior for controlling the movements of the replica, they often lead to unnatural behavioral responses of live animals," he said. "But because behavioral teleporting 'copy/pastes' the behavior of a live fish onto robotic proxies, it confers a high degree of precision with respect to such factors as position, speed, turn rate, and acceleration."Porfiri's previous research proving robots are viable as behavior models for zebrafish showed that schools of zebrafish could be made to follow the lead of their robotic counterparts."In humans, social behavior unfolds in actions, habits, and practices that ultimately define our individual life and our society," added Macrì. "These depend on complex processes, mediated by individual traits -- baldness, height, voice pitch, and outfit, for example -- and behavioral feedback, vectors that are often difficult to isolate. This new approach demonstrates that we canisolate influences on the quality of social interaction and determine which visual features really matterThe research included experiments to understand the asymmetric relationship between large and small fish and identify leader/follower roles, in which a large fish swam with a small replica that mirrored the behavior of the small fish positioned in the other tank and vice-versa.Karakaya said the team was surprised to find that the smaller -- not larger -- fish "led" the interactions."There are no strongly conclusive results on why that could be, but one reason might be due to the 'curious' nature of the smaller individuals to explore a novel space," he said. "In known environments, large fish tend to lead; however, in new environments larger and older animals can be cautious in their approach, whereas the smaller and younger ones could be 'bolder.'"The method also led to the discovery that interaction between fish was not determined by locomotor patterns alone, but also by appearance."It is interesting to see that, as is the case with our own species, there is a relationship between appearance and social interaction," he added.Karakaya added that this could serve as an important tool for human interactions in the near future, whereby, through the closed-loop teleporting, people could use robots as proxies of themselves."One example would be the colonies on Mars, where experts from Earth could use humanoid robots as an extension of themselves to interact with the environment and people there. This would provide easier and more accurate medical examination, improve human contact, and reduce isolation. Detailed studies on the behavioral and psychological effects of these proxies must be completed to better understand how these techniques can be implemented into daily life."This work was supported by the National Science Foundation, the National Institute on Drug Abuse, and the Office of Behavioral and Social Sciences Research.
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Zoology
| 2,020 |
August 24, 2020
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https://www.sciencedaily.com/releases/2020/08/200820164209.htm
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Downstream effects: Sturgeon lifespan, fertility vary strikingly with river conditions
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As he discussed how the pallid sturgeon has responded to differing conditions along the Missouri River, the mind of soft-spoken fish ecologist Mark Pegg drifted to a Def Leppard lyric inspired by Neil Young.
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"What is the old song? 'It's better to burn out than to fade away?' In this case, I'm not sure that's true," said Pegg, a professor with the University of Nebraska-Lincoln's School of Natural Resources.Pegg was referring not to the existential fate of the shovel-nosed, long-lived endangered species, but to the life cycles of individual specimens. He was talking about the impressive developmental flexibility, but also the troubling developmental deficits, that some specimens have shown in the face of human intervention on the Missouri -- the power of nurture, or lack thereof, revealed by an unprecedented new study.The study found that pallid sturgeon stocked around the lower basin of Nebraska, Iowa and Missouri live an average of just 19.8 years -- nearly three times shorter than in the upper basin of Montana and North Dakota, where the average was an estimated 56.4 years.Combined with the fact that females in the lower basin weighed an average of seven times less than in the upper basin, that altered trajectory also seemed to dramatically influence reproduction. The shorter-lived female specimens appeared to compensate by reaching sexual maturity at around age 10, compared with age 17 in their longer-lived counterparts. Despite the head start, though, their looming demise caught up with them: The lower-basin females spawned between three and 11 times, well below the range of 13-20 times among females in the upper basin. According to the estimates of the research team, the lower-basin females consequently laid about 10 times fewer eggs over their lifetimes.The researchers, led by the University of Georgia's Martin Hamel, came to the striking conclusions by analyzing existing data gathered from both wild and hatchery-raised sturgeon -- more than 1,200 in total. In the mid-2000s, a cadre of agencies began regularly measuring and monitoring the age, size and fertility of wild specimens in an effort to learn more about threats to the endangered species. But an even earlier effort, begun in the mid-1990s, sought to supplement the species' declining numbers."So they grabbed whatever fish they could that were of reproductive size and age and started making little sturgeon," Pegg said.The sturgeon they initially grabbed and set to spawning in hatcheries came from the upper basin in Montana. When it came time to release those offspring into the Missouri River, the agencies stocked them across both the upper basin, where their parents had lived, and the lower basin.Years later, that decision would manifest as a boon for Hamel, Pegg and their colleagues, Kirk Steffensen of the Nebraska Game and Parks Commission and Jonathan Spurgeon of the University of Arkansas at Pine Bluff. Because of it, the researchers had access to an exceedingly rare dataset: substantial numbers of genetically similar specimens left to grow and mature in two environments separated by more than a thousand miles. Any major differences in their development, then, would almost certainly arise from differences in those environments -- an ichthyological analog of studying identical human twins raised in different households."Replicating that (approach) is horribly difficult, especially in Mother Nature's lab," Pegg said. "We just don't have the space, time or resources to really do that. So this was more of a moment of serendipity than any real planning on our part."We knew where the fish were coming from, and we could start to look at how they were actually responding to their new environment."Pegg said the extreme developmental differences the team discovered between the upper- and lower-basin populations probably speak to at least two major differences in their environments: depth and currents. Though the upper basin has undergone some human-related change over the past few centuries, it more closely resembles the relatively shallow, slow-moving river it was before the arrival of white colonialists. Even where it is deeper and faster, he said, it still offers some slower-flowing refuges where larvae and finger-length juveniles can settle and grow without much stress. Those refuges also house food, from algae to minnows, that make life easier for larvae and adults alike.The lower basin, by contrast, features more reservoirs and deeper channels that were carved into the river to promote currents and ease the conveyance of ships down the river. The success of those efforts, Pegg said, has probably forced the sturgeon to invest an inordinate amount of time and energy essentially swimming in place -- investments that likely slow growth among juveniles and keep females from putting on the weight that is strongly tied to fertility."They have to spend a lot of energy maintaining position, as opposed to up in Montana ... where they have the ability to get bigger because they're not spending a lot of energy keeping themselves in the water column."We're sort of shortchanging the fish down here in a lot of different ways."The team's study follows in the wake of others that have demonstrated the ability of organisms, including fish, to adjust their development and behavior in response to their environments -- and on timelines far too short for genetic-based evolution to explain. Some research, for instance, has tracked the fates of largemouth bass that were transported from Florida to bodies of water farther north. But from what Pegg has seen, no prior studies have examined the phenomenon on such a wide scale, either geographically or numerically."To my knowledge, this is the one and only that's covering literally 2,500 miles of river or so," he said of the study, published in the journal "Most of the other (similar studies) were dealing with tanks of fish or, at best, a pond of fish with maybe a few hundred. But we're talking about -- at least in the lower part of the river, where we really saw that change -- literally thousands of individuals. So I think from the magnitude of sample size, our effect is pretty large, in terms of what we can say about the results."And what they can say, according to Pegg, is that the findings make a dramatic and literal case for the downstream effects of environmental change. While those effects may not be solely responsible for the species' endangered status, they probably account for some of the difficulty in resuscitating its population, he said. But they might also point the way to more successful conservation efforts, and more careful planning, down the line."What it really highlights is that we do need to be careful about just willy-nilly stocking or reintroducing fish or birds or mammals into places they may or may not be well-adapted to," he said. "At least in this case, (the sturgeon) seem to be holding on and maybe have adjusted to their new environments a little better than some other places. But we aren't necessarily producing a viable population based on those original stockings (to the extent) that we'd hoped for. So taking care to properly think through and plan with the best science we have available to us is certainly one of the big take-home messages."
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Zoology
| 2,020 |
August 21, 2020
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https://www.sciencedaily.com/releases/2020/08/200821094836.htm
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Meet hedge fund managers of avian world
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In uncertain times, it makes sense to manage risk in your endeavors -- whether it's investing in money-making opportunities or deciding where to lay your eggs.
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Brood parasites are birds that are known to lay their eggs in other birds' nests. Cowbirds and cuckoos are among the most famous examples of this group.New research from Washington University in St. Louis finds that brood parasites living in more variable and unpredictable habitats tend to parasitize -- or squat and drop their eggs in -- the nests of a greater variety and number of hosts. The study is published Aug. 21 in "When brood parasites face increased ecological risks -- for example, greater climatic uncertainty in their environment, or greater uncertainty with regards to the availability or behavior of their hosts -- they turn to bet-hedging," said Carlos Botero, assistant professor of biology in Arts & Sciences and the study's senior author."In other words, when it is difficult to predict the ideal host, parasites literally lay their few precious eggs in more than one basket," he said. "This means increasing not just the number of different host species they use, but also expanding the diversity of taxonomic families that they choose as hosts."A birder himself, Botero says that he is fascinated by things animals do that fall outside the boundaries of what some think of as "typical" -- like brood parasitism."Parasite mothers can't really do much about the behaviors that their hosts will display as surrogate parents," Botero said. "With bet-hedging in the choice of hosts, parasites are at least able to increase the chances that one -- or a few -- of the surrogate parents they choose will end up behaving in the optimal way.Botero and his colleagues at the University of Illinois Urbana-Champaign and Columbia University observed a pattern that they considered striking.The researchers aggregated environmental, parasite and host species data associated with 84 species of obligate avian brood parasites from 19 genera and five different bird families. Their list covered approximately 86% of all known brood parasitic species.For all of these birds, host behavior is critical when it comes to countering environmental threats. Even small differences in the nest architecture, habitat selection, breeding timing or incubation behavior of the chosen surrogate parents can have life or death implications for young parasitic chicks.A brood parasite's properly "hedged" portfolio must include a reasonable diversity of host types to ensure that at least some reproductive success is achieved -- no matter what environmental conditions are experienced in any given year.But bet-hedging does come at a cost, the researchers said."A bet-hedging strategy involves making some or sometimes even many 'wrong' choices," Botero said. "For example, for years in which the behaviors, timing and nest type of a given host clearly work better than those of other species, it would be clearly ideal to stick with that option and avoid wasting eggs on others."The problem is, parasites that live in variable and unpredictable environments cannot know at the onset which option will work best that year."Parasitic mothers that diversify their egg-laying choices may not contribute as many offspring to any given generation as they would have if they had chosen the best host type that year," Botero said. "But, over time, they will end up contributing a much larger total number of offspring to future generations by fledging some offspring every year.""It is this long-term vision that allows bet-hedging lineages to prevail and to steer the course of evolution so that in the end, everyone in their species bet-hedges."
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Zoology
| 2,020 |
August 19, 2020
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https://www.sciencedaily.com/releases/2020/08/200819170221.htm
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This cuttlefish is flamboyant on special occasions only!
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The flashy Flamboyant Cuttlefish is among the most famous of the cephalopods (octopus, squid, and cuttlefish) -- but it is widely misunderstood by its legions of fans.
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A new paper from the Roger Hanlon laboratory at the Marine Biological Laboratory, Woods Hole, sets the record straight."This animal is well known in the Internet community, has been on TV many times, and is popular in public aquariums," Hanlon says. "In almost all cases, [its skin] is showing this brilliantly colorful flamboyant display."But Hanlon's field studies in Indonesia, reported here, tell a different and richer story. "It turns out in nature, flamboyant cuttlefish are camouflaged nearly all of the time. They are nearly impossible to find," he says. In the blink of an eye, they can switch from some of "best camouflage known in the cephalopods" to their dazzling flamboyant display. But they only use this display on certain occasions: For elaborate male courtship rituals; or when males are fighting over a female; or to flash briefly at a threatening object when it approaches too close, presumably to scare it away."The flamboyant display is common when a diver approaches close enough to photograph, which is why the public may think this species always looks so colorful," Hanlon says. "But it is rare to see this species in flamboyant display in the wild."The courtship displays by male flamboyant cuttlefish (Males, which tend to be significantly smaller than females, approach and court a camouflaged female with flamboyant displays and elaborate rituals, which include "waves" (rapidly waving three pairs of arms while displaying "passing cloud") and "kisses" (male darts forward and briefly, gently touches his arms to hers).Females generally ignore males while they are courting; they stay camouflaged and motionless or just keep on foraging and hunting. Male courtship goes on non-stop for prolonged periods (6 to 52 minutes observed in this study).In three observations, two males competed simultaneously for a female. Males can display flamboyant courtship signaling on one side of the body while flashing white (signaling aggression) on the other side toward the rival male.In one case, male competition ended abruptly when one of the males, while facing the female and waving and kissing, backed into a camouflaged scorpionfish and was eaten! "Sex can have a real cost," Hanlon notes.Females were choosy and often rejected courting males. Female receptivity was obvious when she widely spread her first three pairs of arms (while standing on the fourth pair of arms). The male would then swim within the arm crown and quickly deposit spermatophores in the buccal region where the seminal receptacle is located. Average duration of mating was only 2.89 seconds.After fertilization, the successful male guarded the female for a while but not, curiously, up to egg laying, as is common with other cuttlefish. When another male was present, mate guarding was aggressive.The female lays her eggs while camouflaged and staying still. She then pushes her eggs under a coconut shell and affixes them to the inside of the shell. When the hatchlings exit the egg case and jet away, they are fully formed and capable of camouflage and signaling.The primary mode of defense for both male and female The vibrant colors (white, yellow, red and brown) of the flamboyant display are combined with apparent "waves" of dark brown color that produce a dazzling and dizzying kaleidoscope of motion, color, and patterning. The fast neural control of many thousands of chromatophore organs in the skin enable this unique signaling capability -- all turned on or off in less than a second, and changed depending on the behavioral context of the courtship, or in the case of defense, the fish predators that discover them."Birds are renowned for highly evolved visual displays that depend partly on dramatic postural changes (with wings of different color and pattern, in particular), yet this invertebrate cuttlefish species has evolved equally dramatic and complex displays mainly with its skin coloration," Hanlon says.Video:
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Zoology
| 2,020 |
August 19, 2020
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https://www.sciencedaily.com/releases/2020/08/200819155723.htm
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Lungfish fins reveal how limbs evolved
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The evolution of limbs with functional digits from fish fins happened approximately 400 million years ago in the Devonian. This morphological transition allowed vertebrates to leave the water to conquer land and gave rise to all four-legged animals or tetrapods -- the evolutionary lineage that includes all amphibians, reptiles, birds and mammals (including humans). Since the nineteenth century several theories based on both fossils and embryos have been put forward trying to explain how this transformation unfolded. Yet, exactly how hands with digits originated from fish fins remained unknown.
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An international team of biologists based at the University of Konstanz (Germany), Macquarie University in Sydney (Australia) and the Stazione Zoologica Anton Dohrn in Naples (Italy) has determined how limbs have evolved from fins using embryos of the Australian lungfish (Neoceratodus forsteri) for their study. The Australian lungfish is the closest living fish relative of tetrapods and is often considered a "living fossil" as it still resembles the fishes that were around at the time when the first four-limbed vertebrates began to walk on land. For these reasons the fins of lungfish provide a better reference to study the evolutionary transition of fins into limbs than any other extant fish species.The team's research, which is reported in the latest issue of To solve the puzzle of how limbs emerged from fins during evolution researchers have focused on embryonic development. "During embryogenesis, a suite of 'architect' genes shapes an amorphous group of precursor cells into fully grown limbs," explains Dr. Joost Woltering, first author on the study and an assistant professor in the Evolutionary Biology group at the University of Konstanz led by Professor Axel Meyer. The very same "architect" genes also drive fin development. However, because evolutionary changes have occurred in the activity of these genes, the developmental process produces fins in fish and limbs in tetrapods.To compare this process in fins and limbs, the team studied such "architect" genes in the embryos of the Australian lungfish. "Amazingly, what we discovered is that the gene specifying the hand in limbs (hoxa13) is activated in a similar skeletal region in lungfish fins," explains Woltering. Importantly, this domain has never been observed in the fins of other fish that are more distantly related to tetrapods. "This finding clearly indicates that a primitive hand was already present in the ancestors of land animals."The lungfish "hand," in spite of this modern genetic signature, only partially resembles the anatomy of tetrapod hands because it lacks fingers or toes. To understand the genetic basis for this difference the team went on to analyse additional genes known to be associated with the formation of digits, finding that one gene important for the formation of fingers and toes (hoxd13 -- a "sister gene" to the above-mentioned hoxa13) appeared to be switched on differently in fins.During tetrapod limb development, the hoxd13 gene is switched on in a dynamic manner. It first becomes activated in the developing pinky finger and then expands all the way throughout the future hand towards the thumb. This process coordinates the correct formation of all five fingers. While Joost Woltering's team observed a similar activation pattern of this gene in lungfish fins, it did not show this expansion but only remained activated in exactly one half of the fin. Additional differences were found for genes that are normally switched off in digits. In lungfish fins these genes remain active, but on the opposite side of the domain where hoxd13 is activated."All of this goes to show that while lungfish fins unexpectedly have a primitive hand in common with tetrapods, the fins of our ancestors also needed an evolutionary 'finishing touch' to produce limbs. In this sense it looks as if the hand was there first, only to be complemented with digits later during evolution," says Woltering. One influential hypothesis regarding the evolution of limbs first put forward by early 20th-century palaeontologists Thomas Westoll and William Gregory, and in the 1980s famously developed further by Neil Shubin, postulates that fingers and toes arose through an expansion of the skeletal elements on one side of the fins of the tetrapod ancestor. This inferred expansion of fin elements corresponds exactly to the differences the team found in the expansion of the digit genes between lungfish fins and tetrapod limbs. The team's observations on the activation and deactivation of limb "architect" genes in lungfish fins thus provides evidence in support of this classical transformational model.In the future, to fully understand what causes this domain to expand, making our limbs so different from fish fins, the researchers plan to conduct further analyses on the development of fins and limbs, using lungfish but also more modern fish species such as cichlids as their embryos are easier to investigate using techniques like CRISPR. "To complete the picture of what happened in our fish ancestors that crawled onto land hundreds of millions of years ago, we really rely on currently living species to see how their embryos grow fins and limbs so differently," concludes Woltering.- A new study by an international team of researchers from the University of Konstanz (Germany), Macquarie University in Sydney (Australia) and the Stazione Zoologica Anton Dohrn in Naples (Italy) provides an evolutionary model of how hands with digits emerged from fish fins.- Studying the embryos of Australian lungfish (Neoceratodus forsteri), the closest extant fish relative of tetrapods, the researchers identified similarities and differences in the way lungfish fins and tetrapod limbs form during embryonic development.- The presence of a primitive hand domain common to fins and limbs is revealed by the expression of a gene responsible for the specification of the hand in limbs (hoxa13). This gene becomes activated in similar skeletal domains in tetrapods and lungfish.- One of the main morphological differences between fins and limbs, namely the absence of digits, can be explained by differences in the activation (hoxd13) and de-activation (alx4, pax9) of genes involved in digit development. This suggests that limbs with digits evolved from fish fins through changes in the activation of digit specific genes within a primitive hand domain.
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Zoology
| 2,020 |
August 19, 2020
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https://www.sciencedaily.com/releases/2020/08/200819120716.htm
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Team creates better tool to aid COVID-19 diagnosis
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An LSU Health New Orleans radiologist and evolutionary anatomist have teamed up to show the same techniques used for research on reptile and bird lungs can be used to help confirm the diagnosis of COVID-19 in patients. Their paper published in
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Emma R. Schachner, PhD, Associate Professor of Cell Biology & Anatomy, and Bradley Spieler, MD, Vice Chairman of Radiology Research and Associate Professor of Radiology, Internal Medicine, Urology, & Cell Biology and Anatomy at LSU Health New Orleans School of Medicine, created 3D digital models from CT scans of patients hospitalized with symptoms associated with severe acute respiratory syndrome coronavirus (SARS-CoV-2).Three patients who were suspected of having COVID-19 underwent contrast enhanced thoracic CT when their symptoms worsened. Two had tested positive for SARS-CoV-2, but one was reverse transcription chain reaction (RT-PCR) negative. But because this patient had compelling clinical and imaging, the result was presumed to be a false negative."An array of RT-PCR sensitivities has been reported, ranging from 30-91%," notes Dr. Spieler. "This may be the result of relatively lower viral loads in individuals who are asymptomatic or experience only mild symptoms when tested. Tests performed when symptoms were resolving have also resulted in false negatives, which seemed to be the result in this case."Given diagnostic challenges with respect to false negative results by RT-PCR, the gold standard for COVID-19 diagnostic screening, CT can be helpful in establishing this diagnosis. Importantly, these CT features can range in form and structure and appear to correlate with disease progression. This allows for 3D segmentation of the data in which lung tissue can be volumetrically quantified or airflow patterns could be modeled.The CT scans were all segmented into 3D digital surface models using the scientific visualization program Avizo (Thermofisher Scientific) and techniques that the Schachner Lab uses for evolutionary anatomy research."The full effect of COVID-19 on the respiratory system remains unknown, but the 3D digital segmented models provide clinicians a new tool to evaluate the extent and distribution of the disease in one encapsulated view," adds Spieler. "This is especially useful in the case where RT-PCR for SARS-CoV-2 is negative but there is strong clinical suspicion for COVID-19."To date, there haven't been good models of what COVID is doing to the lungs. So, this project focused on the visualization of the lung damage in the 3D models as compared to previous methods that have been published -- volume-rendered models and straight 2D screen shots of CT scans and radiographs."Previously published 3D models of lungs with COVID-19 have been created using automated volume rendering techniques," says Dr. Schachner. "Our method is more challenging and time consuming, but results in a highly accurate and detailed anatomical model where the layers can be pulled apart, volumes quantified, and it can be 3D printed."The three models all show varying degrees of COVID-19 related infection in the respiratory tissues -- particularly along the back of the lungs, and bottom sections. They more clearly show COVID-19-related infection in the respiratory system compared to radiographs (X-rays), CT scans, or RT-PCR testing alone.Schachner and Spieler are now segmenting more models for a larger follow up project.
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Zoology
| 2,020 |
August 18, 2020
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https://www.sciencedaily.com/releases/2020/08/200818175411.htm
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Songbirds, like people, sing better after warming up
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If you've ever been woken up before sunrise by the trilling and chirping of birds outside your window, you may have wondered: why do birds sing so loud, so early in the morning?
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Researchers at Duke University say there may be a good reason why birds are most vocal at first light. By singing early and often, a new study suggests, birds perform better during the day.The morning cacophony is mostly males, whose songs are meant to impress potential mates and rivals."It's like they're warming up backstage, before the sun comes up and the curtain rises," said co-author Stephen Nowicki, a biology professor at Duke.Scientists have proposed various hypotheses for why birds do their most vigorous singing in the early morning hours. One idea is that it's the best time to broadcast, since there's little wind to distort their sound. Others have suggested that the dim light makes it difficult to do much else, like hunt for insects.But a study in the journal To test the "warm-up hypothesis," Nowicki and Duke biologist Susan Peters recorded 11 male swamp sparrows between 2 a.m. and noon for two to three mornings each.The song of the swamp sparrow is a simple trill of up to five notes, repeated around 5 to 10 times a second. "It sounds a bit like a melodious police whistle," Nowicki said.Birdsong may look effortless, but it requires balancing competing demands of speed and dexterity, said first author Jason Dinh, a biology Ph.D. student who did the study while still an undergraduate at Duke.Birds switch from one note to the next by opening and closing their beaks. To go from low to high and back down again in rapid-fire succession, a bird must precisely coordinate the movements of their beak and voice box with each breath.To monitor the birds' performance, the researchers measured each bird's trill rate and vocal range over the course of the morning.For swamp sparrows, the concert can start as early at 2:30 a.m. But they don't wake up singing like virtuosos, the study found.Statistical analysis of the recordings revealed that they start off taking it easy; singing slower, or with a more limited range. They only start to nail their songs -- picking up the tempo and reaching for higher and lower pitch -- just after dawn, after hundreds of takes.The more they warmed up, the better they got. "They're able to perform more difficult songs later in the morning," Dinh said.While it's hard to make direct comparisons to the physiological effects in humans, Dinh said, the warm-up up may help get their blood flowing and temperature rising to meet the physical demands of singing.Previous playback experiments by this research team have shown that a well-sung song, compared to a rusty one, is a bigger turn-on for females and more threatening to eavesdropping males, Peters said.If male swamp sparrows see improvements in their singing within hours, the researchers say, the next step is to find out if females take note. If so, then males that sing early and often may have an advantage in attracting a mate.This research was supported by the National Science Foundation (IBN-0315377).
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Zoology
| 2,020 |
August 18, 2020
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https://www.sciencedaily.com/releases/2020/08/200818094019.htm
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New gene therapy approach eliminates at least 90% latent herpes simplex virus 1
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Infectious disease researchers at Fred Hutchinson Cancer Research Center have used a gene editing approach to remove latent herpes simplex virus 1, or HSV-1, also known as oral herpes. In animal models, the findings show at least a 90 percent decrease in the latent virus, enough researchers expect that it will keep the infection from coming back.
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The study, published August 18 in "This is the first time that scientists have been able to go in and actually eliminate most of the herpes in a body," said senior author Dr. Keith Jerome, professor in the Vaccine and Infectious Disease Division at Fred Hutch. "We are targeting the root cause of the infection: the infected cells where the virus lies dormant and are the seeds that give rise to repeat infections."Most research on herpes has focused on suppressing the recurrence of painful symptoms, and Jerome said that his team is taking a completely different approach by focusing on how to cure the disease."The big jump here is from doing this in test tubes to doing this in an animal," said Jerome, who also leads the Virology Division at UW Medicine. "I hope this study changes the dialog around herpes research and opens up the idea that we can start thinking about cure, rather than just control of the virus."Two-thirds of the world population under the age of 50 have HSV-1, according to the World Health Organization. The infection primarily causes cold sores and is lifelong.In the study, the researchers used two types of genetic scissors to cut the DNA of the herpes virus. They found that when using just one pair of the scissors the virus DNA can be repaired in the infected cell. But by combining two scissors -- two sets of gene-cutting proteins called meganucleases that zero in on and cut a segment of herpes DNA -- the virus fell apart."We use a dual meganuclease that targets two sites on the virus DNA," said first author Martine Aubert, a senior staff scientist at Fred Hutch. "When there are two cuts, the cells seem to say that the virus DNA is too damaged to be repaired and other molecular players come in to remove it from the cell body."The dual genetic scissors are introduced into the target cells by delivering the gene coding for the gene-cutting proteins with a vector, which is a harmless deactivated virus that can slip into infected cells. The researchers injected the delivery vector into a mouse model of HSV-1 infection, and it finds its way to the target cells after entering the nerve pathways.The researchers found a 92% reduction in the virus DNA present in the superior cervical ganglia, the nerve tissue where the virus lies dormant. The reductions remained for at least a month after the treatment and is enough the researchers say to keep the virus from reactivating.The team did other comparisons to fine-tune the gene editing approach:- Refining the vector delivery mechanism, they found the adeno-associated virus (AAV) vector that was the most efficient at getting the gene edits to cells infected with the virus.The researchers are pursuing a similar strategy for herpes simplex 2, which causes genital herpes. They expect it to take at least 3 years to move toward clinical trials."This is a curative approach for both oral and genital HSV infection," Aubert said. "I see it going into clinical trials in the near future."
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Zoology
| 2,020 |
August 17, 2020
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https://www.sciencedaily.com/releases/2020/08/200817191739.htm
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Penguins are Aussies: Or are they Kiwis?
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From the four-foot-tall emperor penguin to the aptly named foot-long little penguin, these unique flightless birds have invaded habitats from Antarctica to the equator, not to mention the hearts of the public.
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A comparison of the full genomes of 18 recognized species of penguins provides clues to how they achieved this success -- though not their adorability -- over tens of millions of years, through warm and cold climate swings. It also cautions that today's rapidly changing climate may be too much for them."We are able to show how penguins have been able to diversify to occupy the incredibly different thermal environments they live in today, going from 9 degrees Celsius (48 F) in the waters around Australia and New Zealand, down to negative temperatures in Antarctica and up to 26 degrees (79 F) in the Galápagos Islands," said Rauri Bowie, professor of integrative biology at the University of California, Berkeley, and curator in the Museum of Vertebrate Zoology (MVZ) at Berkeley. "But we want to make the point that it has taken millions of years for penguins to be able to occupy such diverse habitats, and at the rate that oceans are warming, penguins are not going to be able to adapt fast enough to keep up with changing climate."The researchers established conclusively that penguins arose in the cool coastal regions of Australia and New Zealand, not frigid Antarctica, as many scientists thought, and they pinpoint the origin of penguins at about 22 million years ago.Despite their success in spreading widely throughout the Southern Hemisphere, many penguin populations are now threatened. Breeding colonies of emperor penguins in Antarctica have had to relocate because of receding sea ice, while last year saw mass mortality of Adélie penguin chicks on the continent. Galápagos penguin populations are declining as warm El Niño events become more common. In New Zealand, populations of little and yellow-eyed penguins must be fenced off to protect them from the depredations of feral cats, while African penguin populations are declining drastically as the waters off southern Africa warm."We saw, over millions of years, that the diversification of penguins decreased with increasing temperature, but that was over a longtime scale," said Juliana Vianna, associate professor of ecosystems and environment at the Pontifical Catholic University of Chile in Santiago. "Right now, changes in the climate and environment are going too fast for some species to respond to the climate change."Vianna is first author of a paper with Bowie and other colleagues describing their findings that will be published online this week in the journal For the study, Vianna, Bowie and colleagues at museums and universities around the world gathered blood and tissue samples from 22 penguins representing 18 species and then sequenced and analyzed their whole genomes to chart penguin movement and diversification over the millennia.Their conclusions resolve several long-standing questions: in particular, where penguins originated -- along the coasts of Australia, New Zealand and nearby islands of the South Pacific -- and when -- 22 million years ago. The genetic evidence indicates that the ancestors of the king and emperor penguins, the two largest species, soon split off from the other penguins and moved to sub-Antarctic and Antarctic waters, respectively, presumably to take advantage of abundant food resources. This scenario is consistent with the contested hypothesis that the emperor and king penguins -- the only two species in the genus Aptenodytes -- are the sister group to all other penguin lineages."It was very satisfying to be able to resolve the phylogeny, which has been debated for a long time," Bowie said. "The debate hinged on where, exactly, the emperor and king penguins were placed in the family tree, whether they are nested inside the tree closer to other lineages of penguins or whether they are sisters to all the other penguins, which is what our phylogeny showed and some other previous studies had suggested. And it fits with the rich fossil history of penguins."The other penguins diversified and spread widely across the southern oceans, after the Drake's Passage between Antarctica and the southern tip of South America fully opened about 12 million years ago. The opening revved up the clockwise-moving Antarctic Circumpolar Current allowed these flightless birds to swim with the ocean currents throughout the southern ocean, populating both the cold sub-Antarctic islands and the warmer coastal areas of South America and Africa, where they populated to coastlines and remote islands with cold, upwelling, nutrient-rich water.Today, penguins are found in Australia and New Zealand (yellow-eyed, little and other crested penguins), Antarctica (emperor, Adélie, gentoo and chinstrap), the tropical west coast of South America (Galápagos and Humboldt), the southern coasts of South America (Magellanic and southern rockhopper), the South Atlantic (Magellanic and Macaroni), southern Africa (African) and some in the sub-Antarctic (king, gentoo and Macaroni), Indian Ocean islands (eastern rockhopper) and sub-tropical regions (northern rockhopper).Using powerful analysis techniques, some developed recently to analyze historical interactions among humans and our Neanderthal and Denisovan relatives, the researchers were able to determine that several groups of penguins have interbred over the course of their evolutionary history. Through exchange of genetic material, penguins may have shared genetic traits that facilitated the diversification of penguins across the steep thermal and salinity gradients encountered in the southern oceans. The most hybridized are the rockhopper penguins and their close relatives, which experienced at least four introgressions, or transfers of genetic information, over the course of millions of years.The team also pinpointed genetic adaptions that allowed penguins to thrive in new and challenging environments, including changes in genes responsible for regulating body temperature, which allowed them to adapt to subzero Antarctic temperatures, as well as tropical temperatures near the equator; oxygen consumption that permitted deeper dives; and osmoregulation, so they could survive on seawater without the need to find fresh water.New analytical tools helped the researchers to infer the sizes of ancient penguin populations going back about 1 million years. Most penguin species, they found, increased to their greatest numbers as the world cooled 40,000 to 70,000 years ago during the last glaciation -- many species prefer to breed on snow and ice -- and some had a bump in population during the previous glaciation period 140,000 years ago.Two species -- the gentoo and the Galápagos -- seem to have been declining in populations for at least the past 1 million years.Vianna has long-running research projects on penguins in Chile and Antarctica and, for this study, obtained blood samples from many species in those areas. Colleagues in France, Norway, Brazil, Australia, the United States and South Africa supplied blood from some remote species -- Norwegian colleagues provided blood from the chinstrap penguin of the Bouvet islands, for example -- while Vianna and Bowie obtained blood samples from an African penguin in a colony at the California Academy of Sciences in San Francisco.But some species were harder to locate. The researchers were forced to rely on tissue from a preserved specimen of the yellow-eyed penguin in UC Berkeley's MVZ, while the American Museum of Natural History in New York supplied tissue from preserved erect-crested and Fiordland penguins.Each genome was sequenced 30 times by Illumina shotgun sequencing, which produced tiny pieces -- about 150 base pairs long -- of the entire genome. Vianna, who at the time was working with Bowie at UC Berkeley on a sabbatical, painstakingly aligned each piece along a reference genome that had previously been sequenced -- that of the emperor penguin -- as a scaffold."Having a reference genome is like using the cover of a puzzle box to assemble a jigsaw puzzle: You can take all your super little pieces and align them to that reference genome," Bowie said. "We did that with each of these penguin genomes."The genome comparisons told them that penguins arose between 21 million and 22 million years ago, narrowing down the 10-to-40-million-year window determined previously from fossil penguins.They also disproved a paper published last year that suggested that the closely related king and emperor penguins were a sister group to the gentoo and Adélie penguins. Instead, they found that the king and emperor penguins are the sister group to all other penguins.Vianna and Bowie now have genome sequences of 300 individual penguins and are diving more deeply into the genetic variations within and among disparate penguin populations. They recently discovered a new lineage of penguin that awaits scientific description."Penguins are very charismatic, certainly," Vianna said. "But I hope these studies also lead to better conservation."The work was supported by the Chilean Antarctic Institute, Fondecyt Project, GAB PIA CONICYT (ACT172065) and the U.S. National Science Foundation (DEB-1441652). Among the paper's co-authors are Ke Bi and Cynthia Wang-Claypool of UC Berkeley and Daly Noll of Pontifical Catholic University of Chile.
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Zoology
| 2,020 |
August 17, 2020
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https://www.sciencedaily.com/releases/2020/08/200817191737.htm
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Cashew shell compound appears to mend damaged nerves
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In laboratory experiments, a chemical compound found in the shell of the cashew nut promotes the repair of myelin, a team from Vanderbilt University Medical Center reports today in the
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Myelin is a protective sheath surrounding nerves. Damage to this covering -- demyelination -- is a hallmark of multiple sclerosis and related diseases of the central nervous system."We see this as an exciting finding, suggesting a new avenue in the search for therapies to correct the ravages of MS and other demyelinating diseases," said the paper's senior author, Subramaniam Sriram, MBBS, William C. Weaver III Professor of Neurology and chief of the Division of Neuroimmunology.Previous work led by Sriram showed that a protein called interleukin 33, or IL-33, induced myelin formation. IL-33 is, among other things, an immune response regulator, and multiple sclerosis is an autoimmune disorder.The cashew shell compound is called anacardic acid. Sriram and team grew interested in it because it's known to inhibit an enzyme involved in gene expression called histone acetyltransferase, or HAT, and the team had discovered that whatever inhibits HAT induces production of IL-33.The report includes a range of new findings that point to potential therapeutic use of anacardic acid for demyelinating diseases:"These are striking results that clearly urge further study of anarcardic acid for demyelinating diseases," Sriram said.Joining Sriram for the study were Asa Ljunggren-Rose, Chandramohan Natarajan, Pranathi Matta, Akansha Pandey and Isha Upender.
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Zoology
| 2,020 |
August 12, 2020
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https://www.sciencedaily.com/releases/2020/08/200812161320.htm
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Time-shifted inhibition helps electric fish ignore their own signals
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Electric fish generate electric pulses to communicate with other fish and sense their surroundings. Some species broadcast shorter electric pulses, while others send out long ones. But all that zip-zapping in the water can get confusing. The fish need to filter out their own pulses so they can identify external messages and only respond to those signals.
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A solution to this problem is a brain function called a corollary discharge. It's sort of like a negative copy of the original message -- something that tells the fish: Ignore this.But an animal's brain doesn't have to block sensory inputs during the entire message to effectively ignore its own signal, according to new research from biologists at Washington University in St. Louis.Instead, the inhibitory signal -- that call to ignore -- is delayed in fish that communicate using longer electric pulses, versus those using shorter pulses."In fish that communicate with longer pulses, sensory responses to their own pulse are delayed," said Bruce Carlson, professor of biology in Arts & Sciences. "Thus, a delayed corollary discharge optimally blocks electrosensory responses to the fish's own signal."Carlson and Matasaburo Fukutomi, a postdoctoral fellow in his laboratory, published their new research on African mormyrid weakly electric fish in the A brief, well-defined period of inhibition keeps electric fish from missing out on other important external signals, Carlson said.Scientists have known about corollary discharges since the 1950s. In the decades since, corollary discharges have been found in many different species and sensory systems, but it remained unknown how corollary discharges were modified as communication signals evolved.Previous work on corollary discharge in electric fish had been done with species that communicate using short-duration electric pulses, those lasting less than 1 millisecond.For their new study, Carlson and Fukutomi included these fish and five additional species that communicate using electrical pulses ranging in duration from 0.1 to 10 milliseconds."We found the sensory neurons respond with spikes in a narrow time window regardless of pulse duration," Fukutomi said. "These spikes occurred in a specific part of the self-generated pulse, the first peak of the pulse. In addition, we compared the time courses between the corollary discharge inhibition and the pulse and found that the time-shifted inhibition overlapped the first peak of the electric pulse."Time-shifted inhibition is a reasonable change because longer-lasting inhibition would result in an unnecessarily long insensitive period," he said. "I am impressed that there is a solution that makes more sense in real organisms than we might have expected."The new findings have broader implications for understanding the evolution of brains."Despite the complexity of sensory and motor systems working together to deal with the problem of separating self-generated from external signals, it seems like the principle is very simple," Carlson said. "The systems talk to each other. Somehow, they adjust to even widespread, dramatic changes in signals over short periods of evolutionary time."As part of continuing research, Carlson and Fukutomi are working to pinpoint the place in the brain circuit where the delay is adjusted, and how that adjustment is made. They are also investigating how the inhibition delay changes over the individual lifetime of a fish.The researchers also recently co-authored a new review paper on the contributions of electric fish to the study of corollary discharge in Even though humans aren't able to generate electric fields, research on corollary discharge in electric fish has provided insights that are important in medical science as well as basic science. Dysfunction of corollary discharge may be related to psychiatric diseases such as schizophrenia in humans, for example."I love strange creatures, including electric fish," Fukutomi said. "We can only feel electricity as pain, but we never sense electricity as the fish does."Surprisingly, electrosensory systems share a lot of general features with other sensory systems," he said. "I am very excited to be studying these fish."
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Zoology
| 2,020 |
August 11, 2020
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https://www.sciencedaily.com/releases/2020/08/200811125040.htm
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'Insect apocalypse' may not be happening in US
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Scientists have been warning about an "insect apocalypse" in recent years, noting sharp declines in specific areas -- particularly in Europe. A new study shows these warnings may have been exaggerated and are not representative of what's happening to insects on a larger scale.
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University of Georgia professor of agroecology Bill Snyder sought to find out if the so-called "insect apocalypse" is really going to happen, and if so, had it already begun. Some scientists say it might be only 30 years before all insects are extinct, so this is a really important and timely question for agriculture and conservation.Snyder and a team of researchers from UGA, Hendrix College and the U.S. Department of Agriculture used more than 5,300 data points for insects and other arthropods -- collected over four to 36 years at monitoring sites representing 68 natural and managed areas -- to search for evidence of declines across the United States.Some groups and sites showed increases or decreases in abundance and diversity, but many remained unchanged, yielding net abundance and biodiversity trends generally indistinguishable from zero. This lack of overall increase or decline was consistent across arthropod feeding groups, and was similar for heavily disturbed versus relatively natural sites. These results were recently published in The idea for the study started last year with a cross-country road trip for Snyder from Washington state to his new home in Georgia."I had the same observation a lot of people had. We had our drive across the country -- you don't see as many insects squished on your car or windshield."When he got to his home in Bishop, Georgia, it seemed like a different story."I noticed the lights outside were full of insects, as many as I remember as a kid," he said. "People have this notion -- there seems like [there are] fewer insects -- but what is the evidence?"There is some alarming evidence that European honey bees have problems, but Snyder was curious if insects everywhere are in decline. "We depend on insects for so many things," he said. "If insects disappear it would be really, really bad. Maybe the end of human existence."He was discussing the topic with another biologist and friend, Matthew Moran at Hendrix College, and they recalled the U.S. National Science Foundation's network of Long-Term Ecological Research (LTER) sites, which were established in 1980 and encompass a network of 25 monitoring locations across each of the country's major ecoregions.The NSF's LTER data is publicly available, but has not previously been gathered into a single dataset to be examined for evidence of broad-scale density and biodiversity change through time until now.Arthropod data sampled by the team included grasshoppers in the Konza Prairie in Kansas; ground arthropods in the Sevilleta desert/grassland in New Mexico; mosquito larvae in Baltimore, Maryland; macroinvertebrates and crayfish in North Temperate Lakes in Wisconsin; aphids in the Midwestern U.S.; crab burrows in Georgia coastal ecosystems; ticks in Harvard Forest in Massachusetts; caterpillars in Hubbard Brook in New Hampshire; arthropods in Phoenix, Arizona; and stream insects in the Arctic in Alaska.The team compared the samples with human footprint index data, which includes multiple factors like insecticides, light pollution and built environments to see if there were any overall trends."No matter what factor we looked at, nothing could explain the trends in a satisfactory way," said Michael Crossley, a postdoctoral researcher in the UGA department of entomology and lead author of the study. "We just took all the data and, when you look, there are as many things going up as going down. Even when we broke it out in functional groups there wasn't really a clear story like predators are decreasing or herbivores are increasing.""This is an implication for conservation and one for scientists, who have been calling for more data due to under-sampling in certain areas or certain insects. We took this opportunity to use this wealth of data that hasn't been used yet," explained Crossley, an agricultural entomologist who uses molecular and geospatial tools to understand pest ecology and evolution and to improve management outcomes. "There's got to be even more data sets that we don't even know about. We want to continue to canvass to get a better idea about what's going on."To answer Snyder's broad question of, "Are there overall declines?" No, according to the study. "But we're not going to ignore small changes," Snyder said. "It's worthwhile to differentiate between the two issues."Particular insect species that we rely on for the key ecosystem services of pollination, natural pest control and decomposition remain unambiguously in decline in North America, the authors note.In Europe, where studies have found dramatic insect declines, there may be a bigger, longer-term impact on insects than the U.S., which has a lower population density, according to Snyder."It's not the worst thing in the world to take a deep breath," suggested Snyder. "There's been a lot of environmental policies and changes. A lot of the insecticides used in agriculture now are narrow-acting. Some of those effects look like they may be working."When it comes to conservation, there's always room for everyone to pitch in and do their part."It's hard to tell when you're a single homeowner if you're having an effect when you plant more flowers in your garden," he said. "Maybe some of these things we're doing are starting to have a beneficial impact. This could be a bit of a hopeful message that things that people are doing to protect bees, butterflies and other insects are actually working."
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Zoology
| 2,020 |
August 11, 2020
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https://www.sciencedaily.com/releases/2020/08/200811120215.htm
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Most close relatives of birds neared the potential for powered flight but few crossed its thresholds
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Uncertainties in the evolutionary tree of birds and their closest relatives have impeded deeper understanding of early flight in theropods, the group of dinosaurs that includes birds. To help address this, an international study led by HKU Research Assistant Professor Dr. Michael Pittman (Vertebrate Palaeontology Laboratory, Division of Earth and Planetary Science & Department of Earth Sciences) and co-first-authored by his former Postdoctoral Fellow Dr. Rui Pei (now an Associate Professor at the Institute of Vertebrate Paleontology and Paleoanthropology, Beijing), produced an updated evolutionary tree of early birds and their closest relatives to reconstruct powered flight potential, showing it evolved at least three times. Many ancestors of the closest bird relatives neared the thresholds of powered flight potential, suggesting broad experimentation with wing-assisted locomotion before flight evolved.
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"Our revised evolutionary tree supports the traditional relationship of dromaeosaurid ("raptors") and troodontid theropods as the closest relatives of birds. It also supports the status of the controversial anchiornithine theropods as the earliest birds," said Dr. Pei. With this improved evolutionary tree, the team reconstructed the potential of bird-like theropods for power flight, using proxies borrowed from the study flight in living birds. The team found that the potential for powered flight evolved at least three times in theropods: once in birds and twice in dromaeosaurids. "The capability for gliding flight in some dromaeosaurids is well established so us finding at least two origins of powered flight potential among dromaeosaurids is really exciting," said Dr. Pittman. Crucially, the team found that many ancestors of bird relatives neared the thresholds of powered flight potential. "This suggests that theropod dinosaurs broadly experimented with the use of their feathered wings before flight evolved, overturning the paradigm that this was limited to a much more exclusive club," added Dr. Pittman.This study is the latest in the Vertebrate Palaeontology Laboratory's long-term research into the evolution of early birds and their closest relatives (see Notes). Asked about future plans, Dr. Pittman replied: "We have helped to better constrain the broader functional landscape of theropods just before flight evolved and in its earliest stages. We plan to now focus on the dromaeosaurids and early birds that we have shown to have the potential for powered flight to improve our understanding of what it took to fly and why."
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Zoology
| 2,020 |
August 10, 2020
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https://www.sciencedaily.com/releases/2020/08/200810140949.htm
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Biology blurs line between sexes, behaviors
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Biological sex is typically understood in binary terms: male and female. However, there are many examples of animals that are able to modify sex-typical biological and behavioral features and even change sex. A new study, which appears in the journal
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The research -- led by Douglas Portman, Ph.D., an associate professor in the University of Rochester Department of Biomedical Genetics and the Del Monte Institute for Neuroscience -was conducted in C. elegans, a microscopic roundworm that has been used in labs for decades to understand the nervous system. Many of the discoveries made using C. elegans apply throughout the animal kingdom and this research has led to a broader understanding of human biology. C. elegans is the only animal whose nervous system has been completely mapped, providing a wiring diagram -- or connectome -- that is helping researchers understand how brain circuits integrate information, make decisions, and control behavior.There are two sexes of C. elegans, males and hermaphrodites. Though the hermaphrodites are able to self-fertilize, they are also mating partners for males, and are considered to be modified females. A single gene, TRA-1, determines the sex of these roundworms. If a developing worm has two X chromosomes, this gene is activated and the worm will develop into a female. If there is only one X chromosome, TRA-1 is inactivated, causing the worm to become a male.The new study shows that the TRA-1 gene doesn't go completely silent in males, as had been previously thought. Instead, it can go into action when circumstances compel males to act more like females. Typically, C. elegans males prefer searching for mates over eating, in part because they can't smell food as well as females do. But if a male goes too long without eating, it will dial up its ability to detect food and acts more like a female. The new research shows that TRA-1 is necessary for this switch, and without it hungry males can't enhance their sense of smell and stay locked in the default, food-insensitive mate-searching mode. TRA-1 does the same job in juvenile males -- it activates efficient food detection in males that are too young to search for mates."These findings indicate that, at the molecular level, sex isn't binary or static, but rather dynamic and flexible," said Portman. "The new results suggest that aspects of the male nervous system might transiently take on a female 'state,' allowing male behavior to be flexible according to internal and external conditions."A separate study appearing Additional co-authors of the study include Hannah Lawson, Leigh Wexler, and Hayley Wnuk with the University of Rochester. The research was supported with funding from the National Institute of General Medical Sciences.
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Zoology
| 2,020 |
August 7, 2020
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https://www.sciencedaily.com/releases/2020/08/200807111935.htm
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Scientists use CRISPR to knock down gene messages early in development
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Since its discovery, scientists have been using the much-lauded gene editing tool CRISPR to alter the DNA of model organisms and uncover the functions of thousands of genes. Now, researchers at the Stowers Institute for Medical Research in Kansas City, Missouri, and the Andalusian Center of Developmental Biology at Pablo de Olavide University in Seville, Spain, have harnessed the technology to target gene messages (messenger RNA) involved in early vertebrate development.
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By disrupting gene messages (RNA) instead of the underlying genes (DNA), researchers can study genes that might previously have been difficult or impossible to manipulate because they were essential to life or involved in a critical stage of biological development. This approach also allows targeting of maternally-contributed gene RNAs, which are deposited in the egg to kick off the earliest genetic programs.The study, which appears online August 7, 2020, in the journal "The exciting thing about this study is not just what we found, but what we can do," says Ariel Bazzini, PhD, an assistant investigator at the Stowers Institute and co-leader of the study. "We still don't understand how genes jumpstart the earliest stages of development. Now we can find out by targeting their RNA messages, one by one.""We are also very excited about the the low cost of the technique," Bazzini says. "Any lab working with zebrafish or other animal embryos could use this method. Indeed, we have already distributed the reagents and protocol to several labs around the world."Before development even begins, egg must first meet sperm. The resulting embryo carries half the genes from the mother and half from the father. In addition to its genome, the embryo has components such as RNA and proteins provided by the mother."That maternal contribution is a mystery that many of us want to solve," says Bazzini. However, attempts to systematically target RNA in zebrafish, the model organism of choice for many developmental biologists, have been unsuccessful. The aptly-named RNA interference method, which has been a mainstay in studies of gene function, does not work in zebrafish, or other fish or frogs. Other methods using synthetics strips of genetic code known as morpholinos or antisense oligonucleotides have sometimes been associated with toxicity and off-target effects.So when Bazzini and his collaborator and friend Miguel A. Moreno-Mateos, PhD, a professor at Pablo de Olavide University, noticed reports that CRISPR technology had been employed to degrade RNA in yeast, plants, and mammalian cells, they were eager to give it a try. Moreno-Mateos was a postdoc in Antonio Giraldez's lab at Yale University at the same time as Bazzini, and is considered an expert on the optimization of CRISPR-Cas technology in vivo.The CRISPR-Cas13 system depends on two ingredients -- a short RNA sequence known as a "guide" RNA, and an enzyme called Cas13 (part of the Cas, or CRISPR-associated, family of proteins) that cuts any RNA messages in the cell that could line up and bind to that guide sequence. The researchers tested four different Cas13 proteins that had been successfully used in previous studies. They found that the Cas13 proteins were either inefficient or toxic to the developing zebrafish, except for one protein, called RfxCas13d.They then examined whether targeting RNA with CRISPR-RfxCas13d in zebrafish embryos could recreate the same defects as altering the organism's underlying DNA. For example, when they targeted the RNA of the tbxta gene, which is necessary for growing a tail, the zebrafish embryos were tailless.The researchers went on to show that the CRISPR system could efficiently target a variety of RNAs, both those provided by the mother as well as those produced by the embryo, decreasing RNA levels by an average of 76%. Collaborators within and outside of Stowers helped derive that statistic, and showed that the technique also works in killifish, medaka, and mouse embryos."The CRISPR-RfxCas13d system is an efficient, specific and inexpensive method that can be used in animal embryos in a comprehensive manner," says Moreno-Mateos, who is also co-leader of the study. "With this tool we will help to understand fundamental questions in biology and biomedicine."One of the fundamental questions the researchers hope to pursue is the role that RNA plays in the earliest hours of development. The RNAs left behind by the mother have to be removed at precisely the same time that the genome of the embryo comes online; otherwise, the embryo never develops."We think this tool could have a profound effect on our understanding of infertility and developmental problems in general," says Bazzini."The Stowers facilities and collaborative environment have allowed us to test CRISPR technology in other animal model systems," Bazzini says. "When I joined Stowers about four years ago, I would have never predicted that my lab would be doing experiments in mouse or killifish models. It's been a fun adventure!"Other coauthors from the Stowers Institute include Gopal Kushawah, PhD, Michelle DeVore, Huzaifa Hassan, Wei Wang, PhD, Timothy J. Corbin, Andrea M. Moran, and Alejandro Sánchez Alvarado, PhD.This research was funded by the Stowers Institute for Medical Research, Pablo de Olavide University, Consejo Superior de Investigaciones Cientificas, and Junta de Andalucia. Additional support included the Ramon y Cajal program (RyC-2017-23041) and grants (BFU2017-86339-P, PGC2018-097260-B-I00, and MDM-2016-0687) from the Spanish Ministerio de Ciencia, Innovación y Universidades; the Springboard program from Centro Andaluz de Biología del Desarrollo; Genome Engineer Innovation 2019 Grant from Synthego; the Pew Innovation Fund; Innovate Peru (grant 168-PNICP-PIAP-2015); and FONDECYT (travel grant 043-2019).
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Zoology
| 2,020 |
August 6, 2020
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https://www.sciencedaily.com/releases/2020/08/200804190711.htm
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Monarch butterflies raised in captivity may be worse at migrating than wild monarchs raised outdoors
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A hallmark of summer, monarch butterflies are a familiar sight in the Midwest, and many butterfly enthusiasts are eager to do what they can to support the declining monarch population. A new study at the University of Chicago provides new insight into the effects that raising monarchs in captivity might have on their ability to migrate south at the end of the summer, and cautions that some methods could have a detrimental impact on the population.
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Recognizable by their lacy orange and black wings, monarch butterflies are famous for their seasonal migration. Each fall, millions of monarchs fly from Canada and the northern U.S. south to California and Mexico, where they overwinter before returning north in the spring.UChicago's Ayşe Tenger-Trolander and Marcus Kronforst, PhD, have been looking into how environmental triggers and genetic variation affect migration behavior. In a 2019 study, they, along with other members of the Kronforst lab, found that a group of commercially bred monarch butterflies seemed to be worse at orienting south than their wild-bred counterparts, spelling trouble for their ability to migrate correctly. What's more, they found that these commercial monarchs had a completely different genetic profile than the wild ones -- likely because commercial-bred monarchs don't have to face the selective pressure of that annual migration.But that led to more questions. "We published the paper, and other people pointed out that when they tagged commercially bred monarchs before releasing them into the wild, some of them would show up in the overwintering grounds in Mexico," said Kronforst, a professor in the Department of Ecology and Evolution. "We wanted to know what that meant, and at the same time, we wanted to see if we could figure out what environmental cues were necessary to tell monarchs that it's time to start flying south."The new study, published in Using a new strategy of testing the flight behavior of commercially derived butterflies repeatedly, Tenger-Trolander noticed something interesting. "We discovered that it's not that all individuals in the population have completely lost the ability to orient south," said the graduate student. "We found that if you repeatedly test the same individuals over and over again, a proportion of the population do repeatedly fly south. What this means is that while the population on average doesn't seem to show the same drive to fly south, some individuals do still have that response."The researchers say that these results should provoke caution from the monarch-rearing community when it comes to raising and releasing commercially derived butterflies. "These results indicate that mass-rearing butterflies as a response to the declining monarch population may not be the best approach," Tenger-Trolander said. "Breeding monarchs in large facilities could be having unintended effects on their genetics that makes it harder for the butterflies to fly south, and we should be careful about introducing that trait into the wild population."But what about wild-bred monarch butterflies? Could eggs and caterpillars taken from a wild environment, as opposed to a commercial producer, be better for the population?Previous research had found that simply raising monarchs in an environmental chamber that mimicked early fall weather wasn't enough to trigger proper migratory behavior; even monarchs that were sourced from the wild population had a hard time orienting south.To further pick apart the cues that trigger migration, the researchers opted to raise the wild monarchs in a greenhouse, where the butterflies were exposed to true sunlight throughout the day, as well as raising the insects in the lab near a south-facing window and in a large outdoor cage.To their surprise, the natural light wasn't enough to trigger the appropriate orienting behavior. Compared to the monarch butterflies raised in the outdoor cages, the ones raised in the greenhouse were worse at flying south."This isn't what we expected to happen," Tenger-Trolander said. "This shows us that even if you're working with wild-derived butterflies and providing them with the same environmental and sunlight conditions they would be exposed to outdoors, they still require some unknown cues that we haven't been able to replicate indoors."While the researchers are stumped for the moment, they have plans to continue working on this question to see if they can determine what environmental conditions are necessary to tell monarch butterflies when to migrate."In the fall, you have a lot of potential cues telling the butterflies it's time to go," said Tenger-Trolander. "Is it the sunlight, is it the location of the sun in the sky, is it a change in the plants or in the temperature? Is one of those cues the most critical, or is it a combination? Is there a critical period during the monarch's life cycle for these cues to have the right effect? We just don't know."Kronforst said they're still trying to figure out what cues are necessary for this behavior and to see if they can dissect which genes are controlling it. "And then the next big question will be, can we rewire a monarch that doesn't want to migrate so that it will orient south properly?"The researchers say that these results can help inform best practices for those at-home monarch enthusiasts who want to raise the butterflies themselves."Raising monarchs can be so educational," said Tenger-Trolander. "Kids get to see this weird, magical process happening right in front of their eyes. It creates a lot of people who are interested in conservation and science, who then go on to become activists for maintaining important habitats for many different species. But the big unanswered question is whether breeding monarchs in captivity or rearing wild caterpillars at home bad for the wild population.""There are a lot of pros to having people raise monarchs, and it's something a lot of people like to do," Kronforst said. "These results lend support to the idea that if people are interested in raising these butterflies, they should try and keep those conditions as natural as possible, because it's going to lead to healthier insects that are more likely to become migratory, and to make the migration successfully."
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Zoology
| 2,020 |
August 5, 2020
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https://www.sciencedaily.com/releases/2020/08/200805160921.htm
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Warming climate may trigger more West Nile outbreaks in Southern California
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As climate change brings hotter weather to Southern California, coastal populations from San Diego to Santa Barbara may face an increased risk of contracting West Nile virus and other mosquito-borne diseases, suggests a new study led by researchers at the University of California, Berkeley.
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West Nile virus is America's deadliest mosquito-borne disease and has been a threat to the Los Angeles metropolitan area since it arrived in 2003. The virus is harbored by mosquitos and birds and is most commonly spread to humans through the bite of an infected mosquito.The study team analyzed data on nearly 2 million mosquitoes that had been captured and tested for West Nile in Los Angeles between 2006 and 2016. They then used machine learning to identify the landscape and climate conditions that influenced mosquito infection in different neighborhoods.They found that infection among captured mosquitoes was strongly associated with the average temperature in the neighborhood."Our data revealed a sharp transition, where -- as temperatures shift between 70 to around 73 degrees Fahrenheit -- the likelihood of capturing infected mosquitoes in L.A. neighborhoods increases dramatically," said Nicholas Skaff, the lead author of the study and a former postdoctoral scholar in environmental health sciences at UC Berkeley's School of Public Health. "Above this range, conditions become consistently favorable for transmission, and below this range, conditions are consistently unfavorable."The results, published today (Wednesday, Aug. 5) in the journal With significant warming expected over the coming decades, a greater number of West Nile cases may be expected along the Southern California coast, said Justin Remais, associate professor of environmental health sciences at UC Berkeley."Coastal L.A. appears to be vulnerable to the expected warming of California's climate by mid-century, which will push coastal climates more consistently into the favorable zone," Remais said. "Inland L.A. may not be as susceptible to these shifts, as the climate is already favorable. Yet, as climate warming progresses towards the century's end, it is possible that temperatures become too hot in these areas."The researchers emphasize that one or a few particularly hot days do not appear to increase transmission risk significantly. Rather, it is sustained warm temperatures over the course of weeks that give mosquitoes time to acquire the infection and pass it on to bird host species like the house finch."Our research suggests that, rather than focusing on daily weather reports, it's important to examine temperatures over the long haul," Skaff said. "If coastal Los Angeles experiences a month or two of warm temperatures during the summer or early fall, it's probably a good time to be extra careful to avoid mosquito bites. Inland parts of L.A. are almost always sufficiently hot during the summer, so other factors end up determining whether intense transmission occurs there."And while the data indicate that temperature plays a very important role, the researchers emphasize that many factors ultimately determine whether a West Nile outbreak will occur."You can think of the favorable temperature range we identified as a prerequisite -- if other things don't go right for the vector or the virus, transmission may still not occur, even when temperatures are favorable," Skaff said. "For example, if most of the susceptible birds in the region were infected during the previous year or two because a large outbreak occurred, herd immunity will be high, and the risk to people will be limited.""Predicting the transmission of infectious diseases carried by animal hosts and vectors represents a complex puzzle," added Remais, "and machine learning can pick up patterns in vast epidemiological and ecological datasets that help us understand why certain people and neighborhoods are at the highest risk, as well as what the future holds."
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Zoology
| 2,020 |
August 5, 2020
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https://www.sciencedaily.com/releases/2020/08/200805102023.htm
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Scientists discover the switch that makes human brown fat burn energy
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An international research team have discovered how to activate brown fat in humans, which may lead to new treatments for type 2 diabetes and obesity. The results of the collaboration between the Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS) and the Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR) at the University of Copenhagen were published today in Cell Metabolism.
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Brown fat burns energy and generates heat -- a process called thermogenesis -- after being activated by cold temperature or chemical signals. Humans have small deposits of brown fat, and scientists have long hypothesized that finding alternative ways to pharmacologically activate the fat could help improve metabolism.Scientists have now discovered that beta2-adrenergic receptors (b2-AR) in brown fat cells are responsible for stimulating thermogenesis. According to Dr. Denis Blondin from CRCHUS, the finding could explain why most clinical trials, which have attempted to induce BAT to burn energy, have performed poorly."We show that perhaps we were aiming for the wrong target all along. In contrast to rodents, human BAT is activated through the stimulation of the beta2-adrenergic receptor, the same receptor responsible for the release of fat from our white adipose tissue."According to Associate Professor Camilla Schéele at CBMR, this finding has clear therapeutic applications. "Activation of brown fat burns calories, improves insulin sensitivity and even affects appetite regulation. Our data reveals a previously unknown key to unlocking these functions in humans, which would potentially be of great gain for people living with obesity or type 2 diabetes."A second phase of research will begin in the autumn, which will attempt to validate the finding by activating brown fat with drugs that target b2-AR, explains Professor André Carpentier from CRCHUS:"Our next step will be to use a drug that specifically activate that target on brown fat and determine how much it could be of use to burn fat and calories in humans. Once this is done, studies in patients with type 2 diabetes will start to determine if this approach can be useful to improve the metabolic control of the disease."
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Zoology
| 2,020 |
August 4, 2020
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https://www.sciencedaily.com/releases/2020/08/200804170423.htm
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Tool could improve success in translating drugs from animal studies to humans
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About 50% of people who take the drug infliximab for inflammatory bowel diseases, such as Crohn's disease, end up becoming resistant or unresponsive to it.
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Scientists might be able to catch problems like this one earlier in the drug development process, when drugs move from testing in animals to clinical trials, with a new computational model developed by researchers from Purdue University and Massachusetts Institute of Technology.The researchers call the model "TransComp-R." In a study published in Such a mechanism is hard to catch in preclinical testing of new drugs because animal models of human diseases may have different biological processes driving disease or a response to therapy. This makes it difficult to translate observations from animal experiments to human biological contexts."This model could help better determine which drugs should move from animal testing to humans," said Doug Brubaker, a Purdue assistant professor of biomedical engineering, who led the development and testing of this model as a postdoctoral associate at MIT."If there is a reason why the drug would fail, such as a resistance mechanism that wasn't obvious from the animal studies, then this model would also potentially detect that and help guide how a clinical trial should be set up," he said.TransComp-R consolidates thousands of measurements from an animal model to just a few data coordinates for comparing with humans. The dwindled-down data explain the most relevant sources of biological differences between the animal model and humans.From there, scientists could train other sets of models to predict a human's response to therapy in terms of those data coordinates from an animal model.For infliximab, data from a mouse model and human hadn't matched up because they were different types of biological measurements. The mouse model data came in the form of intestinal proteins, whereas data from patients were only available in the form of expressed genes, a discrepancy TransComp-R was able to address.TransComp-R helped Brubaker's team to find links in the data pointing toward a resistance mechanism in humans.The team collaborated with researchers from Vanderbilt University to test the predicted mechanism in intestinal biopsies from a Crohn's disease patient and then with experiments in human immune cells.The researchers used single-cell sequencing of a sample from an infliximab-resistant Crohn's disease patient to identify the cell types expressing the genes related to the resistance mechanism predicted by TransComp-R.They then treated immune cells with infliximab and an inhibitor of the receptor identified by the model to be part of the resistance mechanism. The experiment showed that inhibiting the receptor enhanced the anti-inflammatory effects of infliximab, enabling the drug to be more effective because it could better control inflammation.With additional testing to figure out a way to more precisely measure the markers of this resistance mechanism, doctors could use information about the drug response to determine if a patient needs a different course of treatment.Since this study, Brubaker has been working with his former research group at MIT to apply the mathematical framework behind TransComp-R to identify mouse models predictive of Alzheimer's disease biology and immune signatures of vaccine effectiveness in animal studies of COVID-19 vaccine candidates."The modeling framework itself can be repurposed to different kinds of animals, different disease areas and different questions," Brubaker said. "Figuring out when what we see in animals doesn't track with what's happening in humans could save a lot of time, cost and effort in the drug development process overall."
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Zoology
| 2,020 |
August 4, 2020
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https://www.sciencedaily.com/releases/2020/08/200804111524.htm
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Nanostructures modeled on moth eyes effective for anti-icing
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Researchers have been working for decades on improving the anti-icing performance of functional surfaces. Ice accumulation on aircraft wings, for instance, can reduce lifting force, block moving parts and cause disastrous problems.
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Research in the journal The researchers fabricated the moth eye nanostructure on a quartz substrate that was covered with a paraffin layer to isolate it from a cold and humid environment. Paraffin wax was chosen as a coating material due to its low thermal conductivity, easy coating and original water repellency."We evaluated the anti-icing properties of this unique nanostructure covered with paraffin in terms of adhesion strength, freezing time and mimicking rain sustainability," said Nguyen Ba Duc, one of the authors.Ice accumulation on energy transmission systems, vehicles and ships in a harsh environment often leads to massive destruction and contributes to serious accidents.The researchers found the moth eyes nanostructure surface coated in paraffin exhibited greatly improved anti-icing performance, indicating the advantage of combining original water repellency and a unique heat-delaying structure. The paraffin interfered in the icing process in both water droplet and freezing rain experiments.The number of air blocks trapped inside the nanostructure also contributed to delaying heat transfer, leading to an increase in freezing time of the attached water droplets."We also determined this unique nanostructure sample is suitable for optical applications, such as eyeglasses, as it has high transparency and anti-reflective properties," said Ba Duc.The high transparency and anti-reflective effects were due to the nanostructure being modeled on moth eyes, which have these transparent and anti-reflective properties.
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Zoology
| 2,020 |
August 4, 2020
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https://www.sciencedaily.com/releases/2020/08/200804085903.htm
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Humans and flies employ very similar mechanisms for brain development and function
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With these new findings scientists can potentially better understand the subtle changes that can occur in genes and brain circuits that can lead to mental health disorders such as anxiety and autism spectrum disorders.
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Although physically very different, research has found that the brains of flies, mice and humans are similar in how they form and how they function. Data has shown that the genetic mechanisms that underlie the brain development of insects and mammals are very similar but this can be interpreted in two different ways, where some believe it provides evidence of one single ancestor for both mammals and insects and others think it could support the theory that brains evolved multiple times independently.Published in the journal Most strikingly they have demonstrated that when these regulatory mechanisms are inhibited or impaired in insects and mammals they experience very similar behavioural problems. This indicates that the same building blocks that control the activity of genes are essential to both the formation of brain circuits and the behaviour-related functions they perform. According to the researchers this provides evidence that these mechanisms have been established in one common ancestor.Senior author on the study, Dr Frank Hirth from the Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London said: 'To my knowledge this is the first study that provides evidence of the source of similarities between human and fly brains, how they form and how they function. Our research shows that the brain circuits essential for coordinated behaviour are put in place by similar mechanisms in humans, flies and mice. This indicates that the evolution of their very different brains can be traced back to a common ancestral brain more than a half billion years ago.'Nicholas Strausfeld, Regents Professor of Neuroscience at the University of Arizona and a co-author on the study said: 'The jigsaw puzzle of how the brain evolved still lacks an image on the box, but the pieces currently being added suggest a very early origin of essential circuits that, over an immense span of time have been maintained, albeit with modification, across the great diversity of brains we see today.'The study focussed on those areas of the brain known as the deutocerebral-tritocerebral boundary (DTB) in flies and the midbrain-hindbrain boundary (MHB) in vertebrates including humans. Using genomic data, researchers identified the genes that play a major role in the formation of the brain circuits that are responsible for basic motion in the DTB in flies and MHB in humans. They then ascertained the parts of the genome that control when and where these genes are expressed, otherwise known as cis-regulatory elements.The researchers found that these cis-regulatory elements are very similar in flies, mice and humans, indicating that they share the same fundamental genetic mechanism by which these brain areas develop. By manipulating the relevant genomic regions in flies so they no longer regulate the genes appropriately, the researchers showed a subsequent impairment in behaviour. This corresponds to findings from research with people where mutations in gene regulatory sequences or the regulated genes themselves have been associated with behavioural problems including anxiety and autism spectrum disorders.Dr Hirth commented: 'For many years researchers have been trying to find the mechanistic basis behind behaviour and I would say that we have discovered a crucial part of the jigsaw puzzle by identifying these basic genetic regulatory mechanisms required for midbrain circuit formation and function. If we can understand these very small, very basic building blocks, how they form and function, this will help find answers to what happens when things go wrong at a genetic level to cause these disorders.'
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Zoology
| 2,020 |
August 3, 2020
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https://www.sciencedaily.com/releases/2020/08/200803160504.htm
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Your hair knows what you eat and how much your haircut costs
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Millimeter by millimeter, your hair is building a record of your diet. As hair strands are built from amino acids that come from your food, they preserve the chemical traces of the protein in that food. It's a strong enough record to show whether you prefer veggie burgers or double bacon cheeseburgers.
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A study led by University of Utah researchers finds that this record reveals a divergence in diet according to socioeconomic status (SES), with lower-SES areas displaying higher proportions of protein coming from cornfed animals. It's a way, the authors write, to assess a community's diet and their health risks. The study is published in "This information can be used to quantify dietary trends in ways that surveys cannot capture," says distinguished professor Jim Ehleringer, of the U's School of Biological Sciences. "We would like to see the health community begin to assess dietary patterns using hair isotope surveys, especially across different economic groups within the US."Beginning in the 1990s, Ehleringer, distinguished professors Denise Dearing and Thure Cerling and colleagues started looking into the ways that traces of mammal diets could be reflected in their hair. Different food sources have different ratios of stable isotopes, or atoms of the same element with slightly different weights. As food breaks down into amino acids, the isotopes present in our food, including those of carbon and nitrogen, find their way into all parts of our bodies -- including our hair.Water, which varies in its oxygen and isotope ratios according to geography, works the same way. So, in 2008, Ehleringer, Cerling and colleagues published results showing that the isotopic composition of hair could trace a person's travels, by virtue of the isotopes in the water they drink. (Read how Gabe Bowen, U professor and co-author on this paper, continued this work in 2019 during a solo 10-day flight, cross-country, to sample water isotopes.)"We then began consideration of what we could learn from carbon and nitrogen isotopes in the hair," Ehleringer says.For livestock raised in concentrated animal feeding operations, the corn that they eat is incorporated into their tissues. Corn is in a group of plants called CSo if you eat protein that ate corn, the amino acids that comprise your hair will have isotope ratios more like corn. If your protein comes more from plant sources or from animals who ate CThose are the principles of hair isotope analysis, but this study is about the applications -- and for that, we'll need some samples of hair.To collect samples, the researchers went -- where else? -- to barbershops and hair salons in 65 cities across the United States. They also collected samples from 29 ZIP codes in the Salt Lake Valley to intensively study a single urban area.Barbers and salon owners were supportive, Ehleringer says. "They would then let us go to the trash bin and pull out a handful or two of hair, which we then sort into identifiable clusters representing individuals." This sampling technique was blind, he adds, to the individual's age, gender, income, health status or any other factor, except for the isotope record. All together, they collected samples representing nearly 700 people.The results showed variations in hair isotope ratios, both locally and nationally, but within a relatively narrow range. Within that variation, the researchers found, carbon isotope values correlated with the cost of living in the ZIP codes where the samples were collected. Previous studies provided the expected isotope values from the ends of the diet spectrum, from vegans to meat-prominent omnivores.The samples collected from the Salt Lake Valley offered an opportunity to examine in greater detail the factors behind the isotope variation. Surprisingly, carbon isotopes in hair correlated with the price of the haircut at the sampling location. "We had not imagined that it might be possible to estimate the average cost an individual had paid for their haircut knowing [carbon isotope] values," the authors wrote.With an eye toward diet, the authors found corn-like isotope signatures more predominant among lower SES areas, and that the predominantly meat-eaters in the samples got their protein from cornfed animals, likely from concentrated animal feeding operations.They went a step further. Using driver's license data to calculate trends in body mass index for particular ZIP codes, the authors found that the isotope ratios also correlated with obesity rates. This, they write, draws potential connections between diet, SES and health.Hair isotope analysis, Ehleringer says, can be a tool for assessing a community's health risks."This measure is not biased by personal recollections, or mis-recollections, that would be reflected in dietary surveys," he says. "As an integrated, long-term measure of an individual's diet, the measurement can be used to understand dietary choices among different age groups and different socioeconomic groups."
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Zoology
| 2,020 |
July 28, 2020
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https://www.sciencedaily.com/releases/2020/07/200728150639.htm
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For rufous hummingbirds, migration looks different depending on age and sex
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Plucky, beautiful and declining in numbers at about a 2% annual rate, the rufous hummingbird makes its long annual migration in different timing and route patterns based the birds' age and sex, new research by Oregon State University shows.
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The findings, published in the journal "Different age-sex categories of rufous hummingbirds use alternative routes and differ in migration cycles and distributions," said the study's corresponding author, Jose?e Rousseau, a Ph.D. candidate in the OSU College of Forestry. "Our results seem to indicate that the age-sex categories could be affected in different ways by things like habitat loss and climate during migration. If we keep that in mind, we can make conservation efforts that help these amazingly feisty little creatures -- and I describe them that way with the utmost respect -- have the resources they need during their migration across the landscape."With a reputation as one of the continent's most determined and assertive birds, the rufous hummingbird, scientifically known as Selasphorus rufus, weighs less than a nickel and tops out at about 3 inches long. Based on its body length, its migratory journey is one of the world's longest -- the hummingbirds that travel the full extent of the range, from Alaska to Mexico, migrate almost 80 million body lengths, or 3,900 miles.By comparison, an arctic tern covers about 51 million body lengths on the 13-inch bird's one-way flight of 11,000 miles.Rufous hummingbirds live in open woodlands, nest in trees and eat nectar. A common visitor to bird feeders, the extremely territorial rufous hummingbird will chase away much larger species of hummingbirds, and they'll even drive squirrels away from their nesting areas.Equipped with excellent memories, rufous hummingbirds will visit the same feeders over multiple years, even looking for food at former locations of feeders that have been moved.The study by scientists in the Oregon State University College of Forestry and at the Klamath Bird Observatory in Ashland looked at 15 years' worth of fall migration banding data involving nearly 30,000 hummingbird captures at more than 450 locations.The research showed that adult females tended to have a southbound migration route that was parallel to and between those of young and adult males, Rousseau said."Also, a greater number of young birds migrated south through California in comparison to adult females and adult males," she said. "Our results suggest that the migration of each age-sex category is separated by about two weeks, with adult males migrating first, followed by adult females, and then the young of both sexes. Interestingly, though, migration speed was not statistically different among the categories."The adult males were captured within a smaller geographic distribution during any given week of migration compared with adult females and young birds, she added.Collaborating with Rousseau on the study were Matt Betts of the OSU College of Forestry and John Alexander of the Klamath Bird Observatory.The Natural Sciences and Engineering Research Council, the National Science Foundation, the Western Hummingbird Partnership, the U.S. Forest Service and the OSU Richardson Family Graduate Fellowship supported the research.
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Zoology
| 2,020 |
July 28, 2020
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https://www.sciencedaily.com/releases/2020/07/200728113627.htm
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Eavesdropping on trout building their nests
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Steelhead trout (
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To lay their eggs, trout use their caudal fins to dig pits up to three metres long on each side and ten centimetres deep into the river bed. The aim of the researchers was to locate these spawning pits and to analyze the chronological sequence of the construction process. To this end, the researchers set up a network of seismic stations on a 150-meter section of the Mashel River in the US state of Washington. The geophones embedded in the earth are highly sensitive and detect the slightest vibrations in the ground. Small stones moved by the fish caused short frequency pulses in the range of 20 to 100 hertz and could be distinguished from background frequencies of flowing water, raindrops and even the pulses of passing airplanes. "The same signal arrives at each of the stations slightly delayed. This enabled us to determine where the seismic wave was generated," says Dietze, first author of the study.The researchers listened to the construction of four spawning pits for almost four weeks from the end of April to the end of May. The geophones revealed that the trout were mostly busy building their nests within eleven days of the measurement period. The fish preferably started at sunrise and were active until early noon, followed by another period in the early evening. The trout dug in the sediment for between one and twenty minutes, typically at two- to three-minute intervals with 50 to 100 tail strokes. This was followed by a break of about the same length."Normally, the nest-building behaviour of the trout was recorded only very irregularly, at most weekly. We can now resolve this to the millisecond. In the future, we want to extend the method to the behaviour of other species, for example animals that dig along the banks and destabilize them," explains Dietze. The new measurement method might support fish and behavioural biology and provide a more accurate picture of the biotic and abiotic contribution of sediment transport in rivers. "Fish can move as much sediment as a normal spring flood. The biological component can therefore play a very important role," said Dietze.
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Zoology
| 2,020 |
July 27, 2020
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https://www.sciencedaily.com/releases/2020/07/200727145424.htm
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Return of the zombie cicadas: Manipulative qualities of fungal-infected flyers
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Cicadas infected with the parasitic fungus
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It's a recent discovery into the bizarre world of cicadas plagued by a psychedelic fungus that contains chemicals including those found in hallucinogenic mushrooms. The research, "Behavioral betrayal: How select fungal parasites enlist living insects to do their bidding," was published in the journal "Essentially, the cicadas are luring others into becoming infected because their healthy counterparts are interested in mating," said Brian Lovett, study co-author and post-doctoral researcher with the Davis College of Agriculture, Natural Resources and Design. "The bioactive compounds may manipulate the insect to stay awake and continue to transmit the pathogen for longer."These actions persist amid a disturbing display of B-horror movie proportions: Lovett compared the transmission of the behavior-modifying virus to rabies.Both rabies and entomopathogenic fungi (parasites that destroy insects) enlist their living hosts for successful "active host transmission," Lovett said."When you're infected with rabies, you become aggressive, you become afraid of water and you don't swallow," Lovett said. "The virus is passed through saliva and all of those symptoms essentially turn you into a rabies-spreading machine where you're more likely to bite people."In that sense, we're all very familiar with active host transmission. Since we are also animals like insects, we like to think we have complete control over our decisions and we take our freewill for granted. But when these pathogens infect cicadas, it's very clear that the pathogen is pulling the behavioral levers of the cicada to cause it to do things which are not in the interest of the cicada but is very much in the interest of the pathogen."Lovett's colleague and paper co-author, Matthew Kasson, associate professor of plant pathology and mycology, helped first discover the existence of psychoactive compounds in "Our previous literature always mentioned the strange behaviors associated with Kasson noted that it's generally accepted that cicada nymphs encounter "The fungus could more or less lay in wait inside its host for the next 17 years until something awakens it, perhaps a hormone cue, where it possibly lays dormant and asymptomatic in its cicada host," Kasson said.Working alongside Lovett and Kasson was doctoral student Angie Macias, who believes their research will lead to a better overall understanding of insects."These discoveries are not only super cool but also have a lot of potential in helping us understand insects better, and perhaps learn better ways to control pest species using fungi that manipulate host behaviors," she said. "It is almost certain that there are undiscovered The team managed to research cicada broods earlier this year in southeastern West Virginia.Lovett also explained why we're seeing cicadas emerging again so soon."Different broods come out at different time spans," he said. "There's our periodical cicadas that come out every 13 years and there are other periodical cicadas that come out every 17 years. The timing is staggered in different states."And, as grotesque as an infected decaying cicada sounds, they're generally harmless to humans, he said. They also reproduce at such a rate that the fungi's extermination of hordes of cicadas has little effect on their overall population."They're very docile," Lovett said. "You can walk right up to one, pick it up to see if it has the fungus (a white to yellowish plug on its back end) and set it back down. They're not a major pest in any way. They're just a really interesting quirky insect that's developed a bizarre lifestyle."
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Zoology
| 2,020 |
July 23, 2020
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https://www.sciencedaily.com/releases/2020/07/200723143642.htm
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Shifts seen in breeding times and duration for 73 boreal bird species over 40 years
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In a new study out this week, a team including forest ecologist Malcolm Itter at the University of Massachusetts Amherst reports finding "clear evidence of a contraction of the breeding period" among boreal birds in Finland over a 43-year span for which good quality data were available.
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The study was run by researchers within the Research Centre for Ecological Change (RCEC) at the University of Helsinki, led by Maria Hällfors with Itter and Laura Antão, all postdoctoral researchers at the time. They were joined by additional researchers at the Swedish University of Agricultural Sciences and the Finnish Museum of Natural History. Details appear in Itter says that for most of the 73 species studied, "we saw an advance in the beginning of the breeding period," an average 4.6 days, and the breeding period ending earlier, an average of 6.3 days. The average breeding period contracted by 1.7 days over the period with a breeding period contraction in roughly 31 percent of all species.The researchers report that "this pattern was most common among resident and short-distance migrating species." This suggests that residents and short-distance migrants "may be better able to respond to increased temperatures in the spring and thus take better advantage of the earlier food and resource availability," while "long-distance migrants that arrive later may not be able to do so," Itter explains.This study is unusual, as researchers looked not only at the onset of the breeding period, but also its end, and duration. They used "unique and extensive long-term bird-banding data" collected over 43 breeding seasons by a small army of experienced, dedicated banders -- called ringers in Europe. Tits, thrushes, crows, owls and gulls showed the greatest changes in breeding period. "Any species that had a contraction had an earlier end to the breeding season," Itter notes.The authors state, "Our findings highlight the importance of quantifying phenological change across species and over the entire season to reveal shifts in the community-level distribution of bird reproduction." And, "most importantly, our study suggests that evaluating changes throughout the season is crucial, as earlier and shorter breeding periods in birds may alter community-wide patterns of species co-occurrence and trophic relations across the boreal region."Hällfors, Itter and colleagues' main hypothesis was that as conditions warm, they should see food and other resources become available earlier in the year, and because temperature is the cue for favorable conditions to rear chicks, warmer springs may cause the breeding period to shift forward.They used a creative combination of techniques for data analysis, including a modeling framework developed for natural community data and primarily to predict species' range shifts. The model framework was applied in this case to jointly estimate changes in the breeding period of a boreal bird community -- breeding beginning, end and duration.The model included evolutionary history information; the study found that species that shared evolutionary history shared similar breeding shifts. "From a methodological perspective, our study illustrates that a focus on quantifying phenological advances alone may mask important patterns of phenology change across the season," authors noteItter says the team expected to see differences in breeding period linked to distinct ecological zones across a latitudinal gradient in Finland, but found instead that "ecological zone didn't seem to matter, changes in the beginning, duration and end of breeding did not vary strongly by ecological zone for a given species."This work was supported by the Jane and Aatos Erkko Foundation through the RCEC at the University of Helsinki and the Academy of Finland.
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Zoology
| 2,020 |
July 23, 2020
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https://www.sciencedaily.com/releases/2020/07/200723115902.htm
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Wide awake: Light pollution keeps magpies and pigeons tossing and turning
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Researchers are urging city-dwellers to switch off their garden lights at night-time after a study of magpies and pigeons revealed the harmful impact artificial light is having on the birds' sleep patterns.
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The study by La Trobe University and University of Melbourne, published today in The researchers looked at how birds' sleep was affected by artificial white light and the apparently more "sleep-friendly" amber light.They found light comparable in intensity to street lighting can disrupt the length, structure and intensity of sleep in magpies and pigeons, regardless of the light's colour.Utilising miniature sensors to measure magpie and pigeon brain activity, researchers found their non-rapid eye movement (NREM) and REM sleep cycles were altered when exposed to white and amber lighting at night, but that the magnitude of these effects differed between the species.La Trobe University sleep expert Dr John Lesku said that while magpie sleep is more disrupted under white light compared to amber light, both types of light are equally disruptive for sleep in pigeons."Both magpies and pigeons average 10 hours of sleep per night. We found that magpies lost more NREM sleep under white light than amber light. By comparison, pigeons lost around 4 hours of sleep under both white and amber light," Dr Lesku said."Interestingly, neither species fully recovered sleep lost to white or amber light exposure."University of Melbourne and La Trobe University researcher Dr Anne Aulsebrook said changes to sleeping patterns in birds, caused by human light pollution, is concerning."We know sleep is important for animals to not only function, but thrive," Dr Aulsebrook said."While amber lighting appears to have a less damaging impact than white light on magpies, our findings suggest the relative impacts of light pollution on birds may be species-specific. Amber lighting can reduce sleep disruption in some birds, but it is not a solution for all species."Additionally, disrupted sleeping patterns that force birds to catch up on sleep in the daytime could impact their ability to forage for food, fight off predators and search for mates."University of Melbourne and La Trobe University graduate researcher Farley Connelly recommended further research into avian circadian rhythms and the implementation of short-term solutions."We should think about using artificial light only as and where it's needed," Mr Connelly said."Switch off that porch light, install sensor lights, remove decorative lights from trees, balconies and other outdoor settings, and keep street and park lights directed to the ground or shielded where possible."And if you're ever woken by the early call of a magpie, remember it could be just as sleep deprived as you are."
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Zoology
| 2,020 |
July 23, 2020
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https://www.sciencedaily.com/releases/2020/07/200723092638.htm
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Mammal cells could struggle to fight space germs
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The immune systems of mammals -- including humans -- might struggle to detect and respond to germs from other planets, new research suggests.
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Microorganisms (such as bacteria and viruses) could exist beyond Earth, and there are plans to search for signs of them on Mars and some of Saturn and Jupiter's moons.Such organisms might be based on different amino acids (key building blocks of all life) than lifeforms on Earth.Scientists from the universities of Aberdeen and Exeter tested how mammal immune cells responded to peptides (combinations of amino acids) containing two amino acids that are rare on Earth but are commonly found on meteorites.The immune response to these "alien" peptides was "less efficient" than the reaction to those common on Earth.The study -- conducted in mice, whose immune cells function in a similar way to those of humans -- suggests extra-terrestrial microorganisms could pose a threat to space missions, and on Earth if they were brought back."The world is now only too aware of the immune challenge posed by the emergence of brand new pathogens," said Professor Neil Gow, Deputy Vice-Chancellor (Research and Impact) at the University of Exeter."As a thought experiment, we wondered what would happen if we were to be exposed to a microorganism that had been retrieved from another planet or moon where life had evolved."Some very unusual organic building blocks exist outside of the planet Earth, and these could be used to make up the cells of such alien microbes."Would our immune system be able to detect proteins made from these non-terrestrial building blocks if such organisms were discovered and were brought back to Earth and then accidently escaped?"Our paper addresses this hypothetical event."The study was led by scientists at the MRC Centre for Medical Mycology, which moved from Aberdeen to Exeter last year.Researchers examined the reaction of T cells, which are key to immune responses, to peptides containing amino acids commonly found on meteorites: isovaline and ?-aminoisobutyric acid.The response was less efficient, with activation levels of 15% and 61% -- compared to 82% and 91% when exposed to peptides made entirely of amino acids that are common on Earth."Life on Earth relies on essential 22 amino acids," said lead author Dr Katja Schaefer, of the University of Exeter."We hypothesised that lifeforms that evolved in an environment of different amino acids might contain them in their structure."We chemically synthetised 'exo-peptides' containing amino acids that are rare on Earth, and tested whether a mammal immune system could detect them."Our investigation showed that these exo-peptides were still processed, and T cells were still activated, but these responses were less efficient than for 'ordinary' Earth peptides."We therefore speculate that contact with extra-terrestrial microorganisms might pose an immunological risk for space missions aiming to retrieve organisms from exoplanets and moons."The discovery of liquid water at several locations in the solar system raises the possibility that microbial life may have evolved outside Earth, and could therefore be accidently introduced into the Earth's ecosystem.
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Zoology
| 2,020 |
July 22, 2020
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https://www.sciencedaily.com/releases/2020/07/200722142730.htm
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Lahontan Cutthroat Trout thrive at Paiute's Summit Lake in far northern Nevada
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Summit Lake in remote northwest Nevada is home to the only self-sustaining, robust, lake population of Lahontan Cutthroat Trout, North America's largest freshwater native trout species. Research to understand the reasons why this population continues to thrive, where others have not, will be used to protect the fish and its habitat -- as well as to apply the knowledge to help restore other Nevada lakes that once had bountiful numbers of the iconic fish that historically reached 60 pounds.
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A team of researchers from the University of Nevada, Reno and the Summit Lake Paiute Tribe has been studying the watershed ecosystem and recently authored two papers published in scientific journals describing their findings about the relatively small desert terminal lake.This project is part of a 9-year collaboration to conserve habitats and promote a healthy ecosystem for the lake. University researchers Sudeep Chandra and Zeb Hogan -- as well as students from their aquatics ecosystems lab and Global Water Center -- work with the tribe's Natural Resources Department, formerly led by fish biologist William Cowan before he retired from the U.S. Fish and Wildlife Service."An objective to implement holistic management at Summit Lake is to blend science with traditional knowledge to protect and conserve natural ecologic processes, species diversity and tribal cultural practices," Cowan said. "The partnership with the Global Water Center, as well as many other researchers, agencies, and organizations has complemented this objective by implementing science-based research and technological advances to investigate the viability of trout in the Summit Lake watershed."Monitoring data, including climate, hydrology, fish and wildlife population trends and habitat integrity, is used to develop, revise or validate the tribe's management plans and regulations. This approach is a stark contrast to when the lake ecosystem and associated resources were at risk of irreversible impacts caused by non-point source pollution, irrigation diversions, livestock grazing, and the unknown affects caused by exporting trout eggs for establishment or supplementation of other populations."Our team at the University wants to support the efforts initiated by the Summit Lake Tribe," Chandra, a professor in the College of Science, said. "Our goals are to assist them in developing their science-based program to protect Nevada's only strong, self sustaining lake population of Lahontan Cutthroat Trout. We believe that investigations in this robust ecosystem like Summit, where there is little human impact, could improve recovery efforts in other lake systems that are less fortunate and that have lost their trout like the Walker and Tahoe. Surprisingly there are still few comparative investigations of these lake ecosystems and how they could support trout during a time for increasing global changes."The Lahontan Cutthroat Trout, with its crimson red-orange slash marks on the throat under the jaw and black spots scattered over steel gray to olive green scales, is Nevada's state fish and holds a cultural significance to the Summit Lake Paiute Tribe while providing the tribe with bountiful food and fish resources.As an important traditional food source, Lahontan Cutthroat Trout composed a large part of Tribal member's diets and were the focus of many gatherings held to honor the fish and to learn oral history, traditional practices, and cultural resources from elders of the tribe."The tribe has exercised their sovereignty to protect, manage and enhance tribal homelands, including the lake ecosystem and associated resources by working with federal agencies and other organizations that enable the tribe to holistically manage and protect the land, water and resources that fish, wildlife and tribal members depend on for survival," Cowan said.The lake is about one square mile of surface area, has a mean depth of 20 feet with the southern end generally deeper with about 50 feet of depth at the deepest. The lake elevation decreased about 13 feet during the severe drought in the western United States that lasted from 2012 to 2016."One thing we learned is that the climatically induced drought can change the hydrology, or flow of water and connections of stream to lake, but even with these changes, the trout populations remain relatively stable in the lake," Chandra said. "They look for the opportunity to spawn every year and likely wait for better conditions with higher flows for better access to upstream spawning grounds."So it is critical to support the tribe's efforts to protect the watershed and understand how the long term changes in water resources, like the flow of water, will change with pending climate change projections for the Great Basin."James Simmons, doctoral student with the Ecology, Evolution and Conservation Biology program at the University said the population appears resilient to today's climate disturbances/drought, which is very positive, but should the frequency and severity of drought increase in the future, will the population remain resilient in the face of continued low abundance, survival, spawners and a skewed sex ratio."I think the key going forward will be for the tribe to try to understand how the long-term flow of water in the watershed will be impacted by the future changing climate in the Great Basin -- so that the tribe can formulate a game plan to get ahead of any potential negative repercussions," he said. "Like cutthroat populations across the western U.S., this population faces unknown impacts from climate change."Declining abundance and diverging male and female abundance under changing drought cycles and conditions may have negative long term consequences. The prediction of increased frequency, severity and duration of drought and an increased percentage of rain may decrease abundance, reduce the effective population size and skew the sex ratio at Summit Lake."The research team found that connections between the upper watershed and the lake are essential for maintaining a healthy population during a drought. During the drought of 2012-2016, Summit Lake had a strong, stable population of naturally reproducing Lahontan Cutthroat Trout. The numbers of trout spawning up Mahogany Creek, one of the lake's only inflow streams, was also relatively stable in number. Some of the trout in the lake migrated all the way to the upper watershed, about eight miles."Lahontan Cutthroat Trout can live in streams and lakes," Chandra said. "The trout that live in lakes need rivers to spawn to keep their populations healthy. The numbers do show with little to no major changes to the watershed by human development, there is still a highly variable amount of spawning from lake to stream."Adequate stream flow is necessary for spawning and movement to the lake-dwelling component of the population. In rivers where flow is regulated, enough flow must be preserved in the spring to allow "lake spawners" to come upstream and in the fall to allow juveniles to migrate to the lake."Healthy habitat and ecological connectivity between habitats, such as no man-made migration barriers and adequate stream flow, should be preserved throughout as much of the watershed as possible (and of course between the stream and the lake) to facilitate movement for both stream- and lake-dwelling fish, and to support a robust overall population," Teresa Campbell, a biologist and staff researcher in the University's Global Water Center and lead author of one of the scientific papers, said."Strong connectivity between healthy stream and lake habitats is crucially important to the long-term survival of the Summit Lake Lahontan Cutthroat Trout because it seems that the exchange of individual fish across habitats contributes to the resilience and vitality of the population as a whole."The study also found that in drought-prone systems, streams should have adequate pool habitat and cover such as trees and woody debris to provide a refuge area from the drought and cooler temperatures for trout."During the drought, in the stream, these refuge pools with structure in the form of wood, cobbles, or boulders supported higher densities of stream-dwelling trout," Campbell said. "Therefore, this habitat type is an important component of healthy stream habitat for trout."Forward thinking on the part of the tribe led to early habitat protections for the stream and the lake that now contribute to the success of this population. The tribe took measures to protect much of the stream habitat, erecting grazing enclosures in the 70s that prevented cattle from trampling the stream and allowed the stream to recover into the healthy habitat it is now. This is one of the reasons that trout are thriving here."The lake and surface water on the Reservation are further protected by restricting public access and monitoring resources necessary to sustain endemic species diversity in the area," Cowan said.The Summit Lake Paiute Tribe Reservation is the most remote Native American reservation in Nevada. Located in the northwest corner of Nevada, the reservation is 50 miles south of the Oregon border and 70 miles east of the California border.
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Zoology
| 2,020 |
July 22, 2020
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https://www.sciencedaily.com/releases/2020/07/200722142724.htm
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Is it a bird, a plane? Not superman, but a flapping wing drone
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A drone prototype that mimics the aerobatic manoeuvres of one of the world's fastest birds, the swift, is being developed by an international team of engineers in the latest example of biologically inspired flight.
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A research team from Singapore, Australia, China and Taiwan has designed a 26 gram ornithopter (flapping wing aircraft) which can hover, dart, glide, brake and dive just like a swift, making them more versatile, safer and quieter than the existing quadcopter drones.Weighing the equivalent of two tablespoons of flour, the flapping wing drone has been optimised to fly in cluttered environments near humans, with the ability to glide, hover at very low power, and stop quickly from fast speeds, avoiding collisions -- all things that quadcopters can't do.National University of Singapore research scientist, Dr Yao-Wei Chin, who has led the project published today in "Unlike common quadcopters that are quite intrusive and not very agile, biologically-inspired drones could be used very successfully in a range of environments," Dr Chin says.The surveillance applications are clear, but novel applications include pollination of indoor vertical farms without damaging dense vegetation, unlike the rotary-propelled quadcopters whose blades risk shredding crops.Because of their stability in strong winds, the ornithopter drone could also be used to chase birds away from airports, reducing the risk of them getting sucked into jet engines.University of South Australia (UniSA) aerospace engineer, Professor Javaan Chahl, says copying the design of birds, like swifts, is just one strategy to improve the flight performance of flapping wing drones."There are existing ornithopters that can fly forward and backward as well as circling and gliding, but until now, they haven't been able to hover or climb. We have overcome these issues with our prototype, achieving the same thrust generated by a propeller," Dr Chahl says."The triple roles of flapping wings for propulsion, lift and drag enable us to replicate the flight patterns of aggressive birds by simple tail control. Essentially, the ornithopter drone is a combination of a paraglider, aeroplane and helicopter."There are currently no commercialised ornithopters being used for surveillance, but this could change with the latest breakthrough, researchers claim.By improving the design so ornithopters can now produce enough thrust to hover and to carry a camera and accompanying electronics, the flapping wing drone could be used for crowd and traffic monitoring, information gathering and surveying forests and wildlife."The light weight and the slow beating wings of the ornithopter poses less danger to the public than quadcopter drones in the event of a crash and given sufficient thrust and power banks it could be modified to carry different payloads depending on what is required," Dr Chin says.One area that requires more research is how birds will react to a mechanical flying object resembling them in size and shape. Small, domesticated birds are easily scared by drones but large flocks and much bigger birds have been known to attack ornithopters.And while the bio-inspired breakthrough is impressive, we are a long way from replicating biological flight, Dr Chin says."Although ornithopters are the closest to biological flight with their flapping wing propulsion, birds and insects have multiple sets of muscles which enable them to fly incredibly fast, fold their wings, twist, open feather slots and save energy."Their wing agility allows them to turn their body in mid-air while still flapping at different speeds and angles."Common swifts can cruise at a maximum speed of 31 metres a second, equivalent to 112 kilometres per hour or 90 miles per hour."At most, I would say we are replicating 10 per cent of biological flight," he says.
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Zoology
| 2,020 |
July 20, 2020
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https://www.sciencedaily.com/releases/2020/07/200720145915.htm
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Mutant zebrafish reveals a turning point in spine's evolution
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A chance mutation that led to spinal defects in a zebrafish has opened a little window into our own fishy past.
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Rising fifth-year Duke graduate student Brianna Peskin, who started the project during her first-year rotation in Michel Bagnat's cell biology lab and "kinda kept coming back to it," was merely trying to figure out why this one mutation led to developmental issues in a zebrafish's spine.What she found is that embryos of the mutant fish have a single-letter change in their DNA that alters the way they build the bones and other structures that make up their spine, leaving them with a shorter body and a tortured looking spine that contains clefts dividing their vertebrae in half.The mutant fish are named spondo, short for spondylos which is Greek for spine, and also a reference to dispondyly, a condition where each vertebra has two bony arches not one.But that's not the end of the story.When Bagnat's research colleague Matthew Harris of Harvard Medical School showed some pictures of the mutant fish spine to a colleague in fish paleontology, Gloria Arratia at the University of Kansas, she immediately spotted that the mutants look a lot like fossil specimens of ancestral fish whose style of spine has gone out of fashion in most living fishes."And then they both got really excited because they were noticing these similarities between ancestral fossil specimens and our mutant," Peskin said.The tiny mutation showed that both recipes for spine development are still to be found in the fish genome.In the bony fish, known as teleosts, building the spine relies on a tube-like structure running the length of the developing embryo called the notochord. The notochord sets up the patterns that lead to articulated bones and cartilage in the developing spine by sending chemical signals that attract different molecules and cell types to different regions -- bone parts here, cartilage parts there.Human embryos start with a notochord too, but it doesn't pattern the bony vertebrae the way it does in teleosts; it ends up building the cartilage pucks between the bones, the intervertebral discs.The gene that is mutated in spondo fish is unique to teleosts and the mutant fish's notochord doesn't set up the patterning the way it does in other fish. Rather, its patterning reverts to an ancestral form. So, this tiny difference in DNA may be where land animals like us parted company with our fish ancestors a very, very, very long time ago.While the zebrafish (But not anymore. The research team's new paper, which appears July 20 in And that, in turn, gives them the insight to study human spinal defects with these fast-growing, translucent fish, because the spondo mutants are sensitive to factors known to cause congenital scoliosis in human children, a curvature of the spine."This work not only gave us a glimpse into spine evolution, but also made us understand how the spine is put together in mammals," said Bagnat, who is an associate professor of Cell Biology in the Duke School of Medicine. "Moving forward, we'll be able to use mutations like spondo to unravel the complex genetics of scoliosis and other spine defects that are rooted in the biology of the notochord and have been intractable until now.""Overall, what this study means is that notochord signals are key to establishing the spine. These signals have changed over evolutionary time and account for differences that exist in spine patterning strategies across vertebrates," Peskin said. "So we are all fish after all."
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Zoology
| 2,020 |
July 20, 2020
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https://www.sciencedaily.com/releases/2020/07/200720112220.htm
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European sea bass absorb virtually no microplastic in their muscle tissue
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In a new laboratory study, experts from the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI) investigated how many microplastic particles would be absorbed in the muscle tissue of young European sea bass after being given feed with extremely high microplastic particle content for a period of four months. At least with regard to this particular food fish, their findings are good news: only an extremely small percentage of the plastic particles ingested found their way into the fish fillets; the majority were excreted. The experts take this finding as a first indication that fish fillets can still be safe for human consumption, even if the fish eaten are subjected to extreme microplastic pollution. Their study has now been published in the July issue of the journal
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By now, fish are subjected to microplastic particles in all of their habitats -- in rivers, lakes and seas, as well as aquaculture. Further, it has been confirmed that the animals ingest these tiny particles together with their food. In a new study conducted at the Centre for Aquaculture Research, part of the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI) in Bremerhaven, scientists have for the first time investigated how many of the ingested particles make their way from the sea bass' digestive tract to the bloodstream, and subsequently to the muscle tissue. "This question is relevant for us human beings, especially because, as a rule, we don't eat the whole fish, including its innards, but only the fillets," explains Dr Sinem Zeytin, an AWI biologist and first author of the study.For the laboratory experiment, adolescent European sea bass (Dicentrarchus labrax) were fed pellets consisting of fish meal, wheat bran, vitamins and fish oil, which the scientists had laced with a powder of yellow-orange fluorescing microplastic particles, for 16 weeks. The particles had a diameter of one to five micrometres (thousandths of a millimetre), so as to be representative of the smallest size category for microplastic. In the course of the experiment, every sea bass ingested roughly 163 million of these microscopically small plastic particles. Once the experiment was over, the experts filleted the fish to measure the particle content, while also gathering samples from their blood, gills, intestinal tract and internal organs like the liver for subsequent analysis. They heated part of the fillets in caustic potash, which completely dissolved the muscle tissue. The resultant fluid was then pressed through a filter that captured all of the plastic. They counted the number of particles present using a fluorescence microscope -- first manually, and then using an automated technique.The results came as a pleasant surprise to the researchers. "Even though we subjected the sea bass to extremely high microplastic pollution in comparison to their natural setting, in the end there were only 1 or 2 particles in every five grams of their fillets," Sinem Zeytin reports. "This, along with the fact that the fish grew very well and were in perfect health, tells us that the fish can apparently isolate and excrete these particles before they have a chance to penetrate their tissues. For everyone who enjoys eating sea bass, that's very good news," adds Dr Matthew Slater, Head of the Aquaculture Research Group at the AWI.As Slater explains, due to the nature of the study, it's also possible that those microplastic particles detected weren't actually in the muscle cells, but instead in the tiny amounts of residual blood in the fillets. "In fact, during our study we found virtually no indications that the particles pass from the blood into the muscle cells," the AWI expert explains. That being said, initial analyses of other tissues confirmed that the particles do pass from the digestive tract to the bloodstream.But how do the microplastic particles get from the digestive tract to the bloodstream? According to Sinem Zeytin, "So far, we have identified two ways: either the microscopically small plastic fragments manage to squeeze between two cells in the intestinal wall, or special transporter cells actively separate the particles from the remainder of the feed and pass them on, just like they do with minerals and nutrients."Which of these two processes is predominant, whether there are other processes, and just how particle transport works in each one are questions the experts will seek to answer in future experiments.The study was a joint project involving experts from the Alfred Wegener Institute, the University of Bremen, and the laboratory IBEN GmbH in Bremerhaven. The cultivation and killing of the sea bass for research purposes were done with prior written consent from the Office for Consumer Protection, Veterinary Medicine and Plant Protection, part of Bremen's Senatorial Authorities for Science, Health and Consumer Protection.
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Zoology
| 2,020 |
July 17, 2020
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https://www.sciencedaily.com/releases/2020/07/200717101024.htm
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Predicting the biodiversity of rivers
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Biodiversity is severely threatened both in Switzerland and worldwide, and numerous organisms are facing massive declines -- particularly in freshwater ecosystems. All the species living in rivers -- including fish, bacteria and many different aquatic invertebrates, such as mayflies, stoneflies and caddisflies -- are crucial for the functioning of these ecosystems. But many species are under threat due to habitat homogenization, pollution by pesticides and nutrients, and the spread of non-native species. In order to understand and protect riverine ecosystems, assessing their biodiversity is essential.
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In a new study, the research group of Florian Altermatt, professor at the Department of Evolutionary Biology and Environmental Studies of the University of Zurich (UZH) and the Swiss Federal Institute of Aquatic Science and Technology (Eawag), developed a novel approach to predict biodiversity patterns in river ecosystems. "For the first time, we combined the use of environmental DNA with hydrological models in order to make predictions on the state of biodiversity at a very fine resolution across catchments of hundreds of square kilometers," says Altermatt.All organisms constantly shed their DNA into the environment. By collecting water samples and extracting and sequencing the so-called environmental DNA (eDNA), the biodiversity can be determined faster, less invasively and more comprehensively than by identifying the organisms themselves. Since the DNA in rivers can be transported downstream by stream flow for many kilometers, information on the occurrence of organisms in the upstream catchment is also received. Using mathematical models based on hydrological principles, the scientists were able to reconstruct biodiversity patterns for the whole 740 square kilometer basin of the Thur in north-eastern Switzerland with a resolution of stream sections of one kilometer. "Our model matches the direct observation of aquatic insects' local occurrence with an unprecedented accuracy of 57 to 100%," says Luca Carraro, first author of the study.The Thur catchment is representative of many land-use types, including forest, agriculture and settlements. It thus serves as a generalizable example for many riverine ecosystems. Furthermore, the new method can be used for large-scale and high-resolution assessments of biodiversity state and change even with minimal prior knowledge of the riverine ecosystem. "Specifically, the approach enables biodiversity hotspots to be identified that might be otherwise overlooked, thus enabling focused conservation strategies to be implemented," adds Altermatt.Many countries are currently establishing aquatic biomonitoring using eDNA, and could profit from the novel method. According to Florian Altermatt, Switzerland has a leading role in this field: "The transfer from scientific findings to application is very rapid. We are now finalizing guidelines for the Federal Office for the Environment on how to use eDNA in standard biodiversity monitoring." This will make it easier to describe and monitor biodiversity for the whole network of Swiss rivers and streams, which is about 65,000 kilometers in total.
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Zoology
| 2,020 |
July 16, 2020
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https://www.sciencedaily.com/releases/2020/07/200716163031.htm
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When power is toxic: Dominance reduces influence in groups
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New study by researchers from the University of Konstanz, the co-located Max Planck Institute of Animal Behavior (both in Germany) and the University of Texas at Austin finds that groups led by subordinate males outperform those led by dominant and aggressive males
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Being the strongest, biggest and most aggressive individual in a group might make you dominant, but it doesn't mean you make all the decisions.A new study of fish behaviour published in the "The same traits that make you powerful in one context can actively reduce your influence in others, especially contexts in which individuals are free to choose who to follow," says senior author Alex Jordan, a group leader at the Max Planck Institute of Animal Behavior and at the University of Konstanz's Cluster of Excellence "Centre for the Advanced Study of Collective Behaviour.""Dominant individuals can force their will on the group by being pushy, but that also makes them socially aversive. When it comes to bringing peers to consensus during more sophisticated tasks, it is the least aggressive individuals that exert the greatest influence. Our results illustrate that although domineering individuals most often ascend to positions of power, they can in fact create the least effective influence structures at the same time."To disentangle the effects of dominance and influence, the researchers studied groups of a social cichlid fish, Astatotilpia burtoni. "This species form groups with strict social hierarchies, in which dominant males control resources, territory, and space," says Mariana Rodriguez-Santiago, co-first author on the study and a doctoral student in the lab of co-corresponding author Hans Hofmann at UT Austin."We ask if the colourful dominant males, which are aggressive, central in their social networks, and control resources, are most influential? Or if drab subordinate males wield the greatest influence, despite being passive, non-territorial, and having little or no control over resources."The researchers separated the effects of social dominance from social influence by examining how information flows between either dominant or subordinate males and their groups in two different contexts: routine social behaviour, or a more complex social learning task. In the more complex social learning task, dominant or subordinate male fish were trained that a certain coloured light on one side of the tank meant food would soon arrive at that location. These "informed" individuals were then placed into new groups of uninformed individuals and researchers asked which group -- those with informed dominant or subordinate males -- more quickly learned to associate a coloured light with food.The researchers observed the movement of the fish and found that in routine social interactions the dominant males exerted the greatest influential by chasing and pushing the group around. But in the more complex task, where influence was not forced on the group, but rather individuals had a choice about who to follow, it was subordinate males who wielded the greatest influence in their social groups. In groups with a subordinate male as demonstrator, fish quickly came to a consensus about which light to follow, moving together as a coherent unit to succeed in the task. With a dominant male as the informant, groups were far slower to reach consensus, if they did at all.By using additional machine-learning based animal tracking, employing cutting edge techniques developed in the computer sciences, researchers were able to break down the behavioural differences between dominant and subordinate males: dominant males were central in behavioural social networks (they frequently interacted with others) but they occupied peripheral locations in spatial networks (they were avoided by others). The technology provided insights never before available, revealing the mechanisms of influence as well as the outcome."By capturing behavioural data that are impossible to be measured with the naked eye, our automated tracking methods revealed that it was not the difference in social position between dominant and subordinate per se, but rather in the way they moved and interacted with others," says co-first author Paul Nührenberg, a doctoral student at the Cluster of Excellence "Centre for the Advanced Study of Collective Behaviour" at the University of Konstanz. "These behavioural differences lead directly to differences in social influence."This result touches on the evolution of animal societies as well as leadership structures in organisations. "In many societies, whether animal or human, individuals in positions of power all possess a similar suite of traits, which are aggression, intimidation and coercion," says Jordan. "But effective communication requires the presence of a diversity of voices, not just the loudest. Our results from a natural system show that allowing alternative pathways to positions of power may be useful in creating stronger advisory, governmental, and educational structures."
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Zoology
| 2,020 |
July 16, 2020
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https://www.sciencedaily.com/releases/2020/07/200716111636.htm
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Ultra-black skin allows some fish to lurk unseen
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If there were a stagehand of the sea, wearing black to disappear into the darkness backstage, it might be the dragonfish. Or the common fangtooth.
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These fish live in the ocean's inky depths where there is nowhere to take cover. Even beyond the reach of sunlight, they can still be caught in the glow of bioluminescent organisms that illuminate the water to hunt. So they evade detection with a trick of their own: stealth wear.Scientists report that at least 16 species of deep-sea fish have evolved ultra-black skin that absorbs more than 99.5% of the light that hits them, making them nearly impossible to pick out from the shadows.These fish owe their disappearing act to tiny packets of pigment within their skin cells called melanosomes. The melanosomes of ultra-black fish are differently shaped and arranged, on a microscopic level, compared with regular black fish, says a study led by Duke University and the Smithsonian National Museum of Natural History.The researchers say the work could lead to new light-trapping materials for use in applications ranging from solar panels to telescopes.For the paper, to be published July 16 in the journal Using a spectrometer to measure the amount of light reflected off the fishes' skin, the researchers identified 16 species that reflected less than 0.5% of light, making them some 20 times darker and less reflective than everyday black objects."Ultra-black arose more than once across the fish family tree," said first author Alexander Davis, a biology Ph.D. student in Sonke Johnsen's lab at Duke.The darkest species they found, a tiny anglerfish not much longer than a golf tee, soaks up so much light that almost none -- 0.04% -- bounces back to the eye. Only one other group of black animals, the birds-of-paradise of Papua New Guinea with their ultra-dark plumage, are known to match them.Getting decent photos of these fish onboard the ship was tough; their features kept getting lost. "It didn't matter how you set up the camera or lighting -- they just sucked up all the light," said research zoologist Karen Osborn of the Smithsonian National Museum of Natural History.The team found that, when magnified thousands of times under electron microscopes, normal black skin and ultra-black skin look very different. Both have tiny structures within their cells that contain melanin -- the same pigment that lends human skin its color. What sets ultra-black fish apart, they say, is the shape and arrangement of these melanosomes.Other cold-blooded animals with normal black skin have tiny pearl-shaped melanosomes, while ultra-black ones are larger, more tic-tac-shaped. And ultra-black skin has melanosomes that are more tightly packed together, forming a continuous sheet around the body, whereas normal black skin contains unpigmented gaps.The researchers ran some computer models, simulating fish skin containing different sizes and shapes of melanosomes, and found that ultra-black melanosomes have the optimal geometry for swallowing light.Melanosomes are packed into the skin cells "like a tiny gumball machine, where all of the gumballs are of just the right size and shape to trap light within the machine," Davis said.Their ultra-black camouflage could be the difference between eating and getting eaten, Davis says. By being blacker than black, these fish manage to avoid detection even at six-fold shorter ranges.
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Zoology
| 2,020 |
July 15, 2020
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https://www.sciencedaily.com/releases/2020/07/200715142253.htm
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A GoPro for beetles: Researchers create a robotic camera backpack for insects
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In the movie "Ant-Man," the title character can shrink in size and travel by soaring on the back of an insect. Now researchers at the University of Washington have developed a tiny wireless steerable camera that can also ride aboard an insect, giving everyone a chance to see an Ant-Man view of the world.
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The camera, which streams video to a smartphone at 1 to 5 frames per second, sits on a mechanical arm that can pivot 60 degrees. This allows a viewer to capture a high-resolution, panoramic shot or track a moving object while expending a minimal amount of energy. To demonstrate the versatility of this system, which weighs about 250 milligrams -- about one-tenth the weight of a playing card -- the team mounted it on top of live beetles and insect-sized robots.The results will be published July 15 in "We have created a low-power, low-weight, wireless camera system that can capture a first-person view of what's happening from an actual live insect or create vision for small robots," said senior author Shyam Gollakota, a UW associate professor in the Paul G. Allen School of Computer Science & Engineering. "Vision is so important for communication and for navigation, but it's extremely challenging to do it at such a small scale. As a result, prior to our work, wireless vision has not been possible for small robots or insects."Typical small cameras, such as those used in smartphones, use a lot of power to capture wide-angle, high-resolution photos, and that doesn't work at the insect scale. While the cameras themselves are lightweight, the batteries they need to support them make the overall system too big and heavy for insects -- or insect-sized robots -- to lug around. So the team took a lesson from biology."Similar to cameras, vision in animals requires a lot of power," said co-author Sawyer Fuller, a UW assistant professor of mechanical engineering. "It's less of a big deal in larger creatures like humans, but flies are using 10 to 20% of their resting energy just to power their brains, most of which is devoted to visual processing. To help cut the cost, some flies have a small, high-resolution region of their compound eyes. They turn their heads to steer where they want to see with extra clarity, such as for chasing prey or a mate. This saves power over having high resolution over their entire visual field."To mimic an animal's vision, the researchers used a tiny, ultra-low-power black-and-white camera that can sweep across a field of view with the help of a mechanical arm. The arm moves when the team applies a high voltage, which makes the material bend and move the camera to the desired position. Unless the team applies more power, the arm stays at that angle for about a minute before relaxing back to its original position. This is similar to how people can keep their head turned in one direction for only a short period of time before returning to a more neutral position."One advantage to being able to move the camera is that you can get a wide-angle view of what's happening without consuming a huge amount of power," said co-lead author Vikram Iyer, a UW doctoral student in electrical and computer engineering. "We can track a moving object without having to spend the energy to move a whole robot. These images are also at a higher resolution than if we used a wide-angle lens, which would create an image with the same number of pixels divided up over a much larger area."The camera and arm are controlled via Bluetooth from a smartphone from a distance up to 120 meters away, just a little longer than a football field.The researchers attached their removable system to the backs of two different types of beetles -- a death-feigning beetle and a Pinacate beetle. Similar beetles have been known to be able to carry loads heavier than half a gram, the researchers said."We made sure the beetles could still move properly when they were carrying our system," said co-lead author Ali Najafi, a UW doctoral student in electrical and computer engineering. "They were able to navigate freely across gravel, up a slope and even climb trees."The beetles also lived for at least a year after the experiment ended."We added a small accelerometer to our system to be able to detect when the beetle moves. Then it only captures images during that time," Iyer said. "If the camera is just continuously streaming without this accelerometer, we could record one to two hours before the battery died. With the accelerometer, we could record for six hours or more, depending on the beetle's activity level."The researchers also used their camera system to design the world's smallest terrestrial, power-autonomous robot with wireless vision. This insect-sized robot uses vibrations to move and consumes almost the same power as low-power Bluetooth radios need to operate.The team found, however, that the vibrations shook the camera and produced distorted images. The researchers solved this issue by having the robot stop momentarily, take a picture and then resume its journey. With this strategy, the system was still able to move about 2 to 3 centimeters per second -- faster than any other tiny robot that uses vibrations to move -- and had a battery life of about 90 minutes.While the team is excited about the potential for lightweight and low-power mobile cameras, the researchers acknowledge that this technology comes with a new set of privacy risks."As researchers we strongly believe that it's really important to put things in the public domain so people are aware of the risks and so people can start coming up with solutions to address them," Gollakota said.Applications could range from biology to exploring novel environments, the researchers said. The team hopes that future versions of the camera will require even less power and be battery free, potentially solar-powered."This is the first time that we've had a first-person view from the back of a beetle while it's walking around. There are so many questions you could explore, such as how does the beetle respond to different stimuli that it sees in the environment?" Iyer said. "But also, insects can traverse rocky environments, which is really challenging for robots to do at this scale. So this system can also help us out by letting us see or collect samples from hard-to-navigate spaces."This research was funded by a Microsoft fellowship and the National Science Foundation.Video:
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Zoology
| 2,020 |
July 14, 2020
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https://www.sciencedaily.com/releases/2020/07/200714111730.htm
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Experts' high-flying study reveals secrets of soaring birds
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New research has revealed when it comes to flying the largest of birds don't rely on flapping to move around. Instead they make use of air currents to keep them airborne for hours at a time.
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The Andean condor -- the world's heaviest soaring bird which can weigh in at up to 15kg -- actually flaps its wings for one per cent of its flight time.The study is part of a collaboration between Swansea University's Professor Emily Shepard and Dr Sergio Lambertucci in Argentina, that uses high-tech flight-recorders on Andean condors. These log each and every wingbeat and twist and turn in flight as condors search for food.The team wanted to find out more about how birds' flight efforts vary depending on environmental conditions. Their findings will help to improve understanding about large birds' capacity for soaring and the specific circumstances that make flight costly.During the study, the researchers discovered that more than 75 per cent of the condors' flapping was associated with take-off.However, once in the sky condors can sustain soaring for long periods in a wide range of wind and thermal conditions -- one bird managed to clock up five hours without flapping, covering around 172 km or more than 100 miles.The findings are revealed in a new paper Physical limits of flight performance in the heaviest soaring bird, which has just been published by Dr Hannah Williams, now at the Max Planck Institute for Animal Behaviour, said: "Watching birds from kites to eagles fly, you might wonder if they ever flap."This question is important, because by the time birds are as big as condors, theory tells us they are dependent on soaring to get around."Our results revealed the amount the birds flapped didn't change substantially with the weather."This suggests that decisions about when and where to land are crucial, as not only do condors need to be able to take off again, but unnecessary landings will add significantly to their overall flight costs."Professor Shepard, who is part of Swansea Lab for Animal Movement, said as all the birds they studied were immature, it demonstrated that low investment in flight is possible even in the early years of a condor's life.Closer examination showed the challenges the birds faced as they moved between weak thermals. The condors were seen to flap more as they reached the end of the glides between thermals when they were likely to be closer to the ground.Dr Lambertucci explained: "This is a critical time as birds need to find rising air to avoid an unplanned landing. These risks are higher when moving between thermal updrafts."Thermals can behave like lava lamps, with bubbles of air rising intermittently from the ground when the air is warm enough. Birds may therefore arrive in the right place for a thermal, but at the wrong time.""This is a nice example of where the behaviour of the birds can provide insight into the behaviour of the air."
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Zoology
| 2,020 |
July 14, 2020
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https://www.sciencedaily.com/releases/2020/07/200714101255.htm
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Avian speciation: Uniform vs. particolored plumage
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Although carrion crows and hooded crows are almost indistinguishable genetically, they avoid mating with each other. Researchers from Ludwig-Maximlian-Universitaet (LMU) in Munich have now identified a mutation that appears to contribute to this instance of reproductive isolation.
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The carrion crow and the hooded crow are genetically closely related, but they are distinguishable on the basis of the color of their plumage. The carrion crow's feathers are soot-black, while the hooded crow's plumage presents a particolored combination of black and light gray. Although crosses between the two forms can produce fertile offspring, the region of overlap between their geographical distributions in Europe is strikingly narrow. For this reason, the two forms have become a popular model for the elucidation of the processes that lead to species divergence. LMU evolutionary biologist Jochen Wolf and his team are studying the factors that contribute to the divergence of the two populations at the molecular level. Genetic analyses have already suggested that differences in the color of the plumage play an important role in limiting the frequency of hybridization between carrion and hooded crows. The scientists have now identified a crucial mutation that affects this character. Their findings appear in the online journal The ancestral population of crows in Europe began to diverge during the Late Pleistocene, at a time when the onset of glaciation in Central Europe forced the birds to retreat to refuge zones in Iberia and the Balkans. When the climate improved at the end of the last glacial maximum, they were able to recolonize their original habitats. However, during the period of their isolation, the populations in Southwestern and Southeastern Europe had diverged from each other to such an extent that they no longer interbred at the same rate, i.e. became reproductively isolated. In evolutionary terms, the two populations thereafter went their separate ways. The Western European population became the carrion crow, while their counterparts in Eastern Europe gave rise to the hooded crow. The zone in which the two now come into contact (the 'hybrid zone') is only 20 to 50 km wide, and in Germany it essentially follows the course of the Elbe River. "Within this narrow zone, there is a low incidence of interbreeding. The progeny of such crosses have plumage of an intermediate color," Wolf explains. "The fact that this zone is so clearly defined implies that hybrid progeny are subjected to negative selection."Wolf wants to understand the genetic basis of this instance of reproductive isolation. In previous work, he and his group had demonstrated that the two populations differ genetically from each other only in segments of their genomes that determine plumage color. Moreover, population genetic studies have strongly suggested that mate selection is indeed based on this very character -- the two forms preferentially choose mating partners that closely resemble themselves. These earlier studies were based on the investigation of single-base variation, i.e. differences between individuals at single sites (base-pairs) within the genomic DNA. "However, we have never been able to directly determine the functional effects of such single-base variations on plumage color," says Matthias Weissensteiner, the lead author of the study. "Even when we find an association between a single-base variant and plumage color, the mutation actually responsible for the color change might be located thousands of base-pairs away."To tackle this problem, the researchers have used a technically demanding method to search for interspecific differences that affect longer stretches of DNA. These 'structural' variations include deletions, insertions or inversions of sequence blocks. "Up until recently, high-throughput sequencing technologies could only sequence segments of DNA on the order of 100 bp in length, which is not long enough to capture large-scale structural mutations," says Wolf. "Thanks to the new methods, we can now examine very long stretches of DNA comprising up to 150,000 base pairs."The team applied this technology to DNA obtained from about two dozen birds, and searched for structural variations that differentiate carrion crows from hooded crows. The data not only confirmed the results of the single-base analyses, they also uncovered an insertion mutation in a gene which is known to determine plumage color by interacting with a second gene elsewhere in the genome. In addition, phylogenetic analysis of DNA from related species revealed that their common ancestor carried the black variant of the first of these genes. The variant found in the hooded crow represents a new mutation, which first appeared about half a million years ago. "The new color variant seems to be quite attractive, because it was able to establish itself very quickly, and therefore must have been positively selected," says Wolf. How the variant accomplished this feat is not yet clear. The evidence suggests that it first appeared in the region which now encompasses Iran and Iraq, and there are some indications that the lighter plumage confers a selective advantage in hot regions, because it effectively reflects sunlight. This supports the idea that the mutation might have initially been favored by natural selection. "Once it had reached a certain frequency within the local population, it would have been able to spread because parental imprinting, which enables nestlings to recognize their parents, also causes mature birds to choose mates that resemble their parents in appearance," Wolf explains. However, other possible scenarios, such as random genetic drift in small populations or the involvement of selfish genes (which promote their own propagation), are also conceivable and have yet to be ruled out.
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Zoology
| 2,020 |
July 14, 2020
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https://www.sciencedaily.com/releases/2020/07/200714082838.htm
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Predation by Caspian terns on young steelhead means fewer return as adults
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Caspian terns feeding on young fish have a significant impact on runs of steelhead in the Columbia River, research by Oregon State University suggests.
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Through detailed analysis of steelhead survival and Caspian tern predation rates, the researchers found that the birds are not only preying on fish that would perish for some other reason, but are adding to the annual death toll by eating steelhead smolts that would have survived without tern pressure.In scientific terms, the findings indicate that the terns are having an "additive" effect on prey mortality rather than a "compensatory" one.The study was published in In the Columbia Basin, 13 of 20 populations of anadromous salmon and steelhead are listed as threatened or endangered under the Endangered Species Act. Caspian terns, a protected migratory bird species native to the region, have been the object of predator management in the Columbia Basin in an effort to protect smolts, especially steelhead smolts, from being eaten before they can swim downstream to the ocean.The largest breeding colony of Caspian terns in the world was formerly on a small island in the lower Columbia River estuary between Oregon and Washington. It hosted more than 10,000 breeding pairs in 2008, just prior to implementation of nonlethal management to reduce colony size to between 3,125 and 4,375 breeding pairs."There has been little research, however, into whether reduced predation actually results in greater overall salmonid survival, either at the smolt stage, where the predation is taking place, or across the lifetime of the fish," said Oregon State's Dan Roby, professor emeritus in the Department of Fisheries and Wildlife of the College of Agricultural Sciences. "Without clear evidence that reduced predation means greater survival to adulthood, management to reduce predator impacts would be a waste of time and resources."To tackle the question, Roby and collaborators at Real Time Research, Inc., of Bend and the University of Washington looked at 11 years' worth of mark-recapture-recovery data for almost 80,000 steelhead trout smolts from the Upper Columbia population that were tagged and released to continue their out-migration to the ocean.After release, the tagged fish were exposed to predation throughout multiple stretches of river on their journey toward the Pacific. The tag-recovery data made possible estimates of the weekly probability of steelhead survival, mortality from being eaten by birds and death from other causes."This approach allowed us to directly measure the connection between smolt survival and tern predation," Roby said.Estimates of tern predation on steelhead were substantial for most of the years studied, he said. And increases in tern predation probabilities were connected with statistically significant decreases in steelhead survival for all of the years evaluated and both of the fish life stages studied: smolt out-migration and smolt-to-adult returns."Our results provide the first evidence that predation by Caspian terns may have been a super additive source of mortality during the smolt stage and a partially additive source in the smolt-to-adult life stage," Roby said. "A persistent pattern was clear: For each additional 10 steelhead smolts successfully consumed by Caspian terns, about 14 fewer smolts from each cohort survived out-migration."Another pattern: On average, for every 10 steelhead smolts eaten by terns, one fewer individual from each cohort returned to the Columbia Basin as an adult."Our model shows that mortality from tern predation was primarily additive and therefore has a credible, significant impact on prey survival," Roby said. "Predator-prey models need to consider additive effects of predation across life stages to avoid exaggerating potential benefits from management actions aimed at reducing predator populations to enhance prey populations. The primary value of the study is by analyzing the true effects of natural predators on populations of their prey, and thereby assessing the conservation value to prey of managing predators."Roby notes that the study by OSU, Real Time Research, and the University of Washington contradicts recently published research by scientists with the U.S. Fish and Wildlife Service and the Fish Passage Center, who found that steelhead mortality due to tern predation is compensatory.That paper, in the
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Zoology
| 2,020 |
July 13, 2020
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https://www.sciencedaily.com/releases/2020/07/200713154956.htm
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Design of insect-inspired fans offers wide-ranging applications
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A highly sophisticated folding mechanism employed by a group of insects for at least 280 million years is set to become available for a wide range of applications, thanks to a design method developed and tested through multidisciplinary research by engineers and palaeobiologists.
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According to an article published in the The hind wings of earwigs fold automatically under small leathery forewings when the animal is not in flight, employing a specialised folding pattern that reduces surface area ten to 15 times or more depending on the species. This is the most compact wing folding found in insects and gives earwigs unparalleled ground mobility for a flying insect. With the wings protected and their abdomens fully flexible, earwigs are able to wriggle into the soil and other narrow spaces, as well as use their characteristic rear pincers.Despite the outstanding potential for engineering of the earwig wing and its unique properties, a method for designing their complex folding patterns had not been resolved, hindering practical applications."The method to design our earwig-inspired fan is based on the flat-foldability in the origami model, a mathematical theorem that explains how crease patterns may be folded to form a flat figure," explains lead author Dr Kazuya Saito, an engineer from Kyushu University's Faculty of Design who specialises in bioinspired deployable structures. "Our earwig fan can be designed using classic drawing techniques, but we have also developed and released software that can automatise the process depending on the application requirements."The geometrical requirements for the new design method were informed by tomographic imaging in folded earwig hind wings.Researchers predict that their earwig-inspired fan will see multiple applications for folding structures, of variable sizes and materials, into highly compact shapes that can be efficiently transported and deployed. These may include daily-use articles such as fans or umbrellas, as well as multiple structures for use in architecture,mechanical engineering, and the aerospace industry, such as drone wings, antennae reflectors, or energy-absorbing panels.On the other hand, the research provides new insights into evolutionary biology, as the new design method can also recreate the wing-folding mechanism of 280 million-year-old earwig relatives."The wings of modern earwigs show little variation across their approximately2,000 living species, with shape and folding patterns remaining remarkably stable through evolution because of their specialised function," says Dr Ricardo Pérez-de la Fuente, an insect palaeobiologist from Oxford University Museum of Natural History and co-author of the work. "However, a group of long-extinct insects -- the protelytropterans -- possessed fan-like wings similar to those of earwigs, but different enough to test the consistency of the new design method. Our work shows how palaeontology can be of interest for practical applications."The new method defines the geometrical constraints for the fan-like wings of both earwigs and their deep-time protelytropteran relatives to remain functional. This allowed the researchers to project extinct, hypothetical intermediate forms between the two groups, shedding light on possible evolutionary pathways that could have led to the sophisticated wings of modern earwigs.This research represents a multidisciplinary effort between engineers and evolutionary biologists from Japan and the United Kingdom. Specimens from Oxford University Museum of Natural History and the Museum of Comparative Zoology (Harvard University) provided data to build and test the geometrical method, highlighting the value that natural history collections harbour, including for state-of-the-art applications."Nature has consistently been an everlasting source of inspiration," says Prof Zhong You, from Oxford University's Department of Engineering Science and co-author of the work. "Bioinspired technologies keep offering some of the most efficient and sustainable ways to meet many of the challenges of the future."
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Zoology
| 2,020 |
July 9, 2020
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https://www.sciencedaily.com/releases/2020/07/200709141606.htm
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Scientists trace the origin of our teeth from the most primitive jawed fish
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The origin of our teeth goes back more than 400 million years back in time, to the period when strange armoured fish first developed jaws and began to catch live prey. We are the descendants of these fish, as are all the other 60,000 living species of jawed vertebrates -- sharks, bony fish, amphibians, reptiles, birds and mammals. An international team of scientists led by Uppsala University (Sweden), in collaboration with the ESRF, the European Synchrotron (France), the brightest X-ray source, has digitally 'dissected', for the first time, the most primitive jawed fish fossils with teeth found near Prague more than 100 years ago. The results, published today in
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Teeth in current jawed vertebrates reveal some consistent patterns: for example, new teeth usually develop on the inner side of the old ones and then move outwards to replace them (in humans this pattern has been modified so that new teeth develop below the old ones, deep inside the jawbone). There are, however, several differences between bony fish (and their descendants the land animals) and sharks; for example the fact that sharks have no bones at all, their skeleton is made of cartilage, and neither the dentine scales nor the true teeth in the mouth attach to it; they simply sit in the skin. In bony fish and land animals, the teeth are always attached to jaw bones. In addition, whilst sharks shed their worn-out teeth entire, simply by detaching them from the skin, bony fish and land animals shed theirs by dissolving away the tooth bases.This diversity raises many questions about the origin of teeth. Until now, researchers have focused on fossils of a group of ancient fish that lived about 430 to 360 million years ago, called the arthrodires, which were the only stem jawed vertebrates in which teeth were known. However, they struggled to understand how they could have evolved into the teeth of modern vertebrates, as arthrodire teeth are so different in position and mode of tooth addition in comparison to bony fish and sharks.A team from Uppsala University, Charles University (Czech Republic), Natural History Museum in London (UK), National Museum in Prague (Czech Republic) and the ESRF, the European Synchrotron (France) set out to determine whether this peculiar type of dentition was really ancestral to ours, or just a specialised offshoot off the lineage leading towards modern jawed vertebrates.With this aim, they turned to the acanthothoracids, another early fish group that are believed to be more primitive than the arthrodires and closely related to the very first jawed vertebrates. The problem with acanthothoracids is that their fossils are rare and always incomplete. The very finest of them come from the Prague Basin in the Czech Republic, from rocks that are just over 400 million years old, and were collected at the turn of the last century. They have proved difficult to study by conventional techniques because the bones cannot be freed from the enclosing rock, and have therefore never been investigated in detail.The researchers used the unique properties of the ESRF, the world's brightest X-ray source and the synchrotron microtomography ID19's beamline, to visualise the internal structure of the fossils in 3D without damaging them. At the ESRF, an 844 metre-ring of electrons travelling at the speed of light emits high-powered X-ray beams that can be used to non-destructively scan matter, including fossils."The results were truly remarkable, including well-preserved dentitions that nobody expected to be there" says Valéria Vaškaninová, lead author of the study and scientist from Uppsala University. Follow-up scans at higher resolution allowed the researchers to visualize the growth pattern and even the perfectly preserved cell spaces inside the dentine of these ancient teeth.Like arthrodires, the acanthothoracid dentitions are attached to bones. This indicates that bony fish and land animals retain the ancestral condition in this regard, whereas sharks are specialized in having teeth that are only attached to the skin -- in contrast to the common perception that sharks are primitive living vertebrates. Again, like arthrodires, the teeth of acanthothoracids were not shed.In other ways, however, acanthothoracid dentitions are fundamentally different from those of arthrodires. Like sharks, bony fish and land animals, acanthothoracids only added new teeth on the inside; the oldest teeth were located right at the jaw margin. In this respect, the acanthothoracid dentitions look remarkably modern."To our surprise, the teeth perfectly matched our expectations of a common ancestral dentition for cartilaginous and bony vertebrates." explains Vaškaninová.The tooth-bearing bones also carry small non-biting dentine elements of the skin on their outer surfaces, a character shared with primitive bony fish but not with arthrodires. This is an important difference because it shows that acanthothoracid jaw bones were located right at the edge of the mouth, whereas arthrodire jaw bones lay further in. Uniquely, one acanthothoracid (Kosoraspis) shows a gradual shape transition from these dentine elements to the neighboring true teeth, while another (Radotina) has true teeth almost identical to its skin dentine elements in shape. This may be evidence that the true teeth had only recently evolved from dentine elements on the skin."These findings change our whole understanding of the origin of teeth" says co-author Per Ahlberg, professor at Uppsala University. And he adds: "Even though acanthothoracids are among the most primitive of all jawed vertebrates, their teeth are in some ways far more like modern ones than arthrodire dentitions. Their jawbones resemble those of bony fish and seem to be directly ancestral to our own. When you grin at the bathroom mirror in the morning, the teeth that grin back at you can trace their origins right back to the first jawed vertebrates."
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Zoology
| 2,020 |
July 9, 2020
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https://www.sciencedaily.com/releases/2020/07/200709105114.htm
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Fishing for a theory of emergent behavior
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Researchers at the University of Tsukuba used advanced metrics from information theory to describe the collective behavior of small schools of ayu fish. They found that the overall dynamics were noticeably different for groups of three or more, compared with smaller groups, even over very short timescales. This work may help shed light on fundamental problems in complexity theory and assist in the development of cooperative biomimetic swarming robots.
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Some of the most difficult questions in science today deal with the same fundamental question: How can complex dynamics arise from simple, local interactions? For example, schools of fish and flocks of birds can move and turn in near perfect synchrony without any top-down control from a leader. To try to make progress on this question, integrated information theory (IIT) has been used to provide a mathematical framework for measuring how information passes back and forth from individuals to the group as a whole.A team including Professor Takayuki Niizato at the University of Tsukuba studied the swimming of Ayu, which are small fish related to smelts. Ayu were randomly chosen and placed in a tank in groups of 2, 3, 4, or 5 fish.Explains Professor Niizato, "The trajectory of each fish was tracked, and a computer calculated three binary parameters for every fish at each time step. These parameters were as follows: if the subject fish was close to another fish, if the fish was turning, and if another fish was in its field of view. We found that, over times ranging from 40 milliseconds to one second, a grouping of three fish acted very differently than a pair."In this study, "integrated information" quantified the extent to which the cause and effect in a system can be explained by the repertoires of its components. And "integrated conceptual information" was used as an expression of the fish school's group collective action, roughly how much the behavior of individual members is dependent on the behavior of the group."The aim of IIT is to try to shift the paradigm from 'what a system does' to 'what a system is.' The former tries to analyze the system on the basis of observable behavior, while the latter tries to determine its intrinsic causal structure," says Professor Niizato.This work may help make inroads in some truly difficult questions surrounding group dynamics that emerge naturally when simple components join to form a complex group. This may also aid in the development of "swarming" robots that, like schools of fish or ant colonies, make use of this principle to achieve complicated goals.
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Zoology
| 2,020 |
July 9, 2020
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https://www.sciencedaily.com/releases/2020/07/200709085310.htm
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Extreme rainfall events cause top-heavy aquatic food webs
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An expansive, multi-site ecology study led by UBC has uncovered new insights into the effects of climate change on the delicate food webs of the neotropics.
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In research recently outlined in "This has knock-on effects for all parts of the rainforest system, because the larval insects in the bromeliads are destined to become winged adults that then are part of the forest ecosystem around them," said co-author Diane Srivastava, professor of zoology in UBC's faculty of science, who established the Bromeliad Working Group, an international consortium of researchers who conducted the research.To attain their results, scientists in sites spread across Argentina, Brazil, Columbia, Costa Rica, French Guiana and Puerto Rico performed identical experiments on bromeliads -- large flowering tropical plants that trap water and provide a habitat for many aquatic insects and larvae. The bromeliads were covered with rain shelters, and researchers watered them on strict schedules to replicate 30 different rainfall patterns in each site."This is the first study, to my knowledge, where we have a replicated study of how precipitation patterns affect an entire food web in multiple sites," said Srivastava. "Every day we'd run around with a watering can with a list of how much water each bromeliad should get on each day. We had a customized rainfall schedule for each bromeliad in every field site."While the researchers found that extreme rainfall patterns resulted in top-heavy food webs, the opposite was true when rainfall was delivered on an even schedule, with similar amounts of water delivered to the plants every day. Under those conditions, there were fewer predators and more prey among the larval insects."We were actually expecting to see the opposite pattern," said Srivastava. "We often think of predators being the most sensitive to environmental change, but we got the opposite result. One reason may be that, when the water level in the bromeliad went down during drier days, there was less aquatic habitat, so the prey was condensed into a small amount of water together with their predators. This can really benefit predators and disadvantage prey."These findings can be extrapolated to other rainfall-dependent aquatic ecosystems, said Srivastava. "In any small pond or lake which is primarily determined by rainfall, we can expect to see a similar effect. We should be concerned about these findings, because we've shown that these extreme perturbations in rainfall really do affect the flow of energy through the food web."
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Zoology
| 2,020 |
July 8, 2020
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https://www.sciencedaily.com/releases/2020/07/200708110019.htm
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Evolutionary biologists find several fish adapt in the same way to toxic water
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Several species of fish have adapted to harsh environments using the same mechanism, which brings to question evolutionary chance, according to a study by Kansas State University and Washington State University.
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Michi Tobler, associate professor, Ryan Greenway, May 2019 doctoral graduate, and Nick Barts, doctoral student, all in the Division of Biology; Joanna Kelley, associate professor at Washington State University; and many additional collaborators recently published an article about repeated adaptations to extreme environments in "We are trying to understand how evolution and adaptation work," Tobler said. "We stumbled across these fish living in this highly toxic water. It is so toxic that it kills most other living things by binding to an enzyme in the mitochondria -- the powerhouse of cells -- and shuts off energy production at the cellular level."The streams have high concentrations of hydrogen sulfide, a gas that is naturally dissolved in the water. Tobler and his collaborators found at least 10 different lineages of fish that have adapted to live in the extreme environment."Whether or not populations take the same path to adapting to novel environments is a long-standing question in evolutionary biology," Kelly said. "Our research shows that the same pathways have been modified in multiple different species of hydrogen sulfide adapted fishes."All 10 adapted, regardless of location, using the same mechanism: tweaking the enzyme so the toxicant can't bind to it."The cool thing about these enzymes is all organisms have them," Tobler said. "We have them. Fungi have them. Plants have them. It's the universal way to make energy. Yet, it is this ancient pathway that has been conserved for so long that is modified in these fish."According to Tobler, the fish also ramped up an existing detoxification mechanism inside the mitochondria so they can get rid of the hydrogen sulfide faster and survive when other non-adapted fish in the same species can't survive in the toxic water. The multiple lineages of fish with this capability brings to question a view proposed by evolutionary biologist Stephen Gould, that if evolution repeated itself, it would lead to different outcomes every time."Thirty years ago, Gould said 'if you could rewind the tape of life, you would get a different outcome every single time,' meaning that evolution would not find the same adaptive solutions every time," Tobler said. "What we actually found in all these lineages -- where the tape of life has been replayed as they were exposed to the same sources of selection -- is that evolution actually unfolds in very similar ways. I think it tells us something very fundamental about how organisms adapt and that adaptive solutions are possibly limited."The researchers are able to compare the fish with the adaptation living the toxic water with ancestors that live in the normal environment because there is not a barrier between habitats. Tobler said as a consequence of the fish adapting to the toxic environment, they are actually evolving into a new species. His graduate students have further research pending.Tobler's lab is funded by the National Science Foundation and the U.S. Army Research Office.
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Zoology
| 2,020 |
July 8, 2020
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https://www.sciencedaily.com/releases/2020/07/200708105900.htm
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Glowing worms provide live-action movies of the body's internal scaffolding
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Duke University researchers have made the first time-lapse movies of the sheet-like latticework that surrounds and supports most animal tissues.
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A thin layer of extracellular matrix known as the basement membrane lines many surfaces of the body such as the skin, blood vessels and urinary tract; and it surrounds muscles, fat, and peripheral nerves. While basement membranes play key roles in development, tissue function, and human disease, visualizing them in living organisms has been difficult to do, until now.By genetically modifying C. elegans worms to create basement membrane proteins that glow under fluorescent light, the researchers say it's possible to see for the first time how basement membranes are assembled during development, and how they change and regenerate throughout life. The work may help to pinpoint what might be going wrong in human diseases ranging from kidney disease to invasive cancer."We wouldn't be here without basement membranes," said Duke biology professor David Sherwood, who led the research.Basement membranes have been around for more than 600 million years, since the first multicellular animals evolved from their single-celled ancestors.They're the Scotch tape that helps attach cells together to form tissues, maintaining healthy skin. They're the molecular sieves that filter blood in the kidneys, protect blood vessels and muscles from stretching and compression, and harbor growth factors that tell cells where to go, what to become, and when to divide.But because most basement membranes lie deep within the body, beyond the reach of light microscopes, visualizing them in living tissues is hard to do in humans.So Sherwood's team looked at them in millimeter-long transparent worms, using a gene-editing technique called CRISPR to label 29 basement membrane proteins with green glowing tags to see when and where each protein is found using time-lapse microscopy.Getting a glimpse of these proteins in action inside a live animal offers a much more complete picture than previous experiments that looked at dissected and fixed tissues, which only provide a snapshot of proteins frozen in time, said postdoctoral fellow Eric Hastie."As a result, they have generally been thought of as 'boring' static structures," Hastie said.In some movies, the researchers tracked fluorescent proteins moving within the basement membrane lining the worm's throat. In others, they watched the rapid remodeling of the basement membrane surrounding the worm's gonad as it grew more than 90-fold in size.Surprisingly, the movies show that most basement membrane proteins don't stay put after they're deposited. While some core components are static, the scientists were surprised to see that many proteins moved within this stable scaffolding."Our findings suggest basement membranes quickly change their properties to support mechanically active tissues and they may act as highways that allow growth factors to rapidly travel," Sherwood said."We've just started getting to play with this tool kit," Hastie said. But the team says their work offers a new way to study the basement membrane defects underlying tissue degeneration during aging, and diseases ranging from diabetes to muscular dystrophy.This research was supported by the American Cancer Society (129351-PF-16-024-01-CSM) and the National Institutes of Health (F31 HD097901, F32GM103148, R35GM118049, R21HD084290).
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Zoology
| 2,020 |
July 7, 2020
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https://www.sciencedaily.com/releases/2020/07/200707084012.htm
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Community science birding data does not yet capture global bird trends
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Binoculars in hand, birders around the world contribute every day to a massive database of bird sightings worldwide. But while community science observations of birds can be useful data, it may not be enough to fill the data gaps in developing countries where professional bird surveys are insufficient or absent.
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Ornithologists at the University of Utah say that community science bird data shows different trends in bird populations than professional bird surveys do, especially in developing countries. Researchers look for trends to know whether the number of individuals in a species is increasing, stable or decreasing -- with the latter as a warning sign that the species is in trouble. Their results are published in Biological Conservation. More observations are needed, the researchers say, both by birders and professionals."We hope that this study will encourage birdwatchers to be more conscientious in their recording," says Monte Neate-Clegg, doctoral student and lead author of the study, "to think of these data not just as a personal record but as contributing to a wider cause."Birding is a long tradition, but as paper guidebooks and life lists have given way to digital records and mobile apps, birders have become more connected, compiling their data into near real-time global snapshots of where and when birders are seeing species. For this study, the authors accessed data from eBird.Developed by the Cornell Lab of Ornithology, eBird is the world's largest biodiversity-related community science project, the lab says, with more than 100 million bird sightings contributed each year. Birders submit sightings and checklists to eBird, which reaches out to birding experts when a sighting seems out of the ordinary.U ornithologist Ça?an ?ekercio?lu is a world-class eBirder, currently ranked fifth in the world for spotting more than 8,000 bird species -- more than 76% of all the species that eBirders have ever reported.In 2018, former ?ekercio?lu lab member JJ Horns found that eBird trend data matched the U.S. Breeding Bird Survey to within 0.4%. The results of the three-year project were encouraging -- maybe eBird, they hoped, could serve to accurately fill in data for countries that didn't have the same level of governmental or professional surveys.So, to compare eBird trends with worldwide trends, they turned to BirdLife International, an independent global partnership of conservation organizations."BirdLife amasses data and expert opinion across the world," Neate-Clegg says. Their methods for assessing bird populations and trends vary, though. "Some estimates are based on complete population counts or interpolated surveys," he says. "Most are indirectly assessed via changes in habitat or other impacts, such as hunting or wildlife trade."Downloading and analyzing eBird data is not an Excel-scale task. The U's Center for High Performance Computing assisted in processing the data, which includes more than 800 million records. Using observations from the past 20 years, Neate-Clegg further filtered the data to focus on the best-quality observations and to match the list of species with those reported by BirdLife International. Calculating the trends in bird counts over time, Neate-Clegg rated them as increasing, decreasing or stable.For the final list of 8,121 species, BirdLife listed 624 (7.7%) as increasing, 3,616 (44.5%) as stable and 3,881 (47.8%) as decreasing. The eBird trends differed: 1,974 (24.3%) species were rated as increasing, 4,942 (60.9%) as stable, and 1,205 (14.8%) as decreasing. Only a little more than a third of the species displayed trends that agreed between the two data sources. Unfortunately, that's not much better than would have been expected by chance."This isn't particularly reassuring," Neate-Clegg says.Part of the disagreement is due to the different experience of birdwatching in the tropics as compared to the U.S."Birdwatchers in the tropics tend to be more targeted in their approach," Neate-Clegg says, "meaningfully searching for particular species. This may mean that, although a species is declining, eBirders are still finding them reliably and so we do not detect that decline in the eBird data.""In some cases," ?ekercio?lu adds, "the rarer bird species can be seen more often by birders who may overlook the common species nearby that they have already seen before."Some results of the study were encouraging, though.As in the earlier study, Neate-Clegg's study shows that the rate of agreement with BirdLife trends for a species increases as the number of eBird checklists for that species increases. "This suggests that our accuracy will increase as more people gather data in the tropics," he says. The rate of agreement is also higher for species where population trends are directly estimated rather than indirectly inferred. "This suggests that we still need in situ population trend estimation by experts to validate eBird trends," he adds.Neate-Clegg says that the results of this study are far from the end of the story. "It is really important that we carry out studies such as these to validate the use of eBird data," he says. "It would be great to get to the point where we can successfully leverage what will soon exceed 1 billion bird records to estimate population trends."With a need for more quality data, Neate-Clegg encourages eBirders to include as much additional information in their checklists as possible. For example, he says, eBirders have the option of recording all species seen or counts of every species, as well as associated metadata such as the duration of the birdwatching period and the distance traveled."All of these data are important for maximizing the number of checklists we can use while controlling for variation in effort," he says.Birding in many different places, and not just hotspots with high species numbers, is also important. "You should be birding everywhere you go," ?ekercio?lu says, "which also has the personal satisfaction of being a pioneer as you are adding data from places with little or no bird data."In other words, keep watching the skies. And the trees. And the wetlands. Birders' efforts do not go unnoticed. The researchers express their gratitude to the Cornell Lab of Ornithology, BirdLife International and the millions of birders who contribute to eBird and other community science efforts like iNaturalist. "The centuries-long symbiosis between birdwatchers and ornithologists is the best example of the collaboration of community scientists, professional scientists and conservationists," ?ekercio?lu says.
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Zoology
| 2,020 |
July 3, 2020
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https://www.sciencedaily.com/releases/2020/07/200703094920.htm
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Does DNA in the water tell us how many fish are there?
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River water, lake water, and seawater contain DNA belonging to organisms such as animals and plants. Ecologists have begun to actively analyze such DNA molecules, called environmental DNA, to assess the distribution of macro-organisms. Challenges yet remain, however, in quantitative applications of environmental DNA.
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In a research article published online in DNA molecules are released from organisms present, are transported by the flow of water, and are eventually degraded. In a natural environment, these processes can operate in a complex way."This complicates and limits the traditional approach of population quantification based on environmental DNA where the presence of a definite relationship between the concentration of environmental DNA and population abundance has been critical, "explained Keiichi Fukaya, research associate at the National Institute for Environmental Studies and the lead author of the paper."We thought that these fundamental processes of environmental DNA, the shedding, transport, and degradation, should be accounted for, when we estimate population abundance through environmental DNA," he said.The authors implemented this idea by adopting a numerical hydrodynamic model that explicitly accounts for the processes to simulate the distribution of environmental DNA concentrations within an aquatic area. "By solving this model in the 'inverse direction', we can estimate fish population abundance based on the observed distribution of environmental DNA concentrations," Fukaya explained.A case study conducted in Maizuru Bay, Japan, confirmed that the estimate of the population abundance of Japanese jack mackerel ("The idea and framework presented in this study forms a cornerstone towards quantitative monitoring of ecosystems through environmental DNA analysis. By combining field observation, techniques of molecular biology, and mathematical/statistical modeling, the scope of the environmental DNA analysis will be broadened beyond the determination of the presence or absence of target species," explained Professor Michio Kondoh from Tohoku University, who led the 5.5-year environmental DNA research project, funded by the Japan Science and Technology Agency (CREST).This work was supported by JST CREST Grant Number JPMJCR13A2, Japan.
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Zoology
| 2,020 |
July 2, 2020
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https://www.sciencedaily.com/releases/2020/07/200702113711.htm
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Twenty-year study tracks a sparrow song that went 'viral
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Most bird species are slow to change their tune, preferring to stick with tried-and-true songs to defend territories and attract females. Now, with the help of citizen scientists, researchers have tracked how one rare sparrow song went "viral" across Canada, traveling over 3,000 kilometers between 2000 and 2019 and wiping out a historic song ending in the process. The study, publishing July 2 in the journal
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"As far as we know, it's unprecedented," says senior author Ken Otter, a biology professor at the University of Northern British Columbia. "We don't know of any other study that has ever seen this sort of spread through cultural evolution of a song type." Although it's well known that some bird species change their songs over time, these cultural evolutions tend to stay in local populations, becoming regional dialects rather than the norm for the species. This is how the two-note ending got its start.In the 1960s, white-throated sparrows across the country whistled a song that ended in a repeated three-note triplet, but by the time Otter moved to western Canada in the late 1990s and began listening to the local bird songs, the new two-note ending had already invaded local sparrow populations. "When I first moved to Prince George in British Columbia, they were singing something atypical from what was the classic white-throated sparrow song across all of eastern Canada," he says. Over the course of 40 years, songs ending in two notes, or doublet-ending songs, had become universal west of the Rocky Mountains.Otter and his team used the large network of citizen scientist birders across North America who had uploaded recordings of white-throated sparrow songs to online databases to track the new doublet-ending song. They found that the song was not only more popular west of the Rocky Mountains, but was also spreading rapidly across Canada beyond these western populations. "Originally, we measured the dialect boundaries in 2004 and it stopped about halfway through Alberta," he says. "By 2014, every bird we recorded in Alberta was singing this western dialect, and we started to see it appearing in populations as far away as Ontario, which is 3,000 kilometers from us."The scientists predicted that the sparrows' overwintering grounds were playing a role in the rapid spread of the two-note ending. "We know that birds sing on the wintering grounds, so juvenile males may be able to pick up new song types if they overwinter with birds from other dialect areas. This would allow males to learn new song types in the winter and take them to new locations when they return to breeding grounds, helping explain how the song type could spread," Otter says.So the researchers harnessed sparrows with geolocators -- what Otter calls "tiny backpacks" -- to see if western sparrows who knew the new song might share overwintering grounds with eastern populations that would later adopt it. They found that they did. And not only did it appear that this rare song was spreading across the continent from these overwintering grounds, but it was also completely replacing the historic triple-note ending that had persisted for so many decades -- something almost unheard of in male songbirds.Otter and his team found that the new song didn't give male birds a territorial advantage over male counterparts, but still want to study whether female birds have a preference between the two songs. "In many previous studies, the females tend to prefer whatever the local song type is," says Otter. "But in white-throated sparrows, we might find a situation in which the females actually like songs that aren't typical in their environment. If that's the case, there's a big advantage to any male who can sing a new song type."Now, another new song has appeared in a western sparrow population whose early spread may mirror that of the doublet-note ending. Otter and his team are excited to continue their work and see how this song shifts in real time with more help from citizen scientists. "By having all these people contribute their private recordings that they just make when they go bird watching, it's giving us a much more complete picture of what's going on throughout the continent," he says. "It's allowing us to do research that was never possible before."
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Zoology
| 2,020 |
July 1, 2020
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https://www.sciencedaily.com/releases/2020/07/200701125504.htm
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Different tracks, same dinosaurs: Researchers dig deeper into dinosaur movements
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When picturing dinosaur tracks, most people imagine a perfectly preserved mold of a foot on firm layer of earth. But what if that dinosaur was running through mud, sinking several inches -- or even up to their ankles -- into the ground as it moved?
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Using sophisticated X-ray-based technology, a team of Brown University researchers tracked the movements of guineafowl to investigate how their feet move below ground through various substrates and what those findings could mean for understanding fossil records left behind by dinosaurs.They found that regardless of the variability in substrates, or the guineafowl moving at different speeds, sinking at different depths or engaging in different behaviors, the birds' overall foot movement remained the same: The toes spread as they stepped onto the substrate surface, remained spread as the foot sank, collapsed and drew back as they were lifted from the substrate, and exited the substrate in front of the point of entry, creating a looping pattern as they walked.And part of what that means is that fossilized dinosaur tracks that look distinct from each other, and appear to be from different species, might instead come from the same dinosaurs."This is the first study that's really shown how the bird foot is moving below ground, showing the patterns of this subsurface foot motion and allowing us to break down the patterns that we're seeing in a living animal that has feet similar to those of a dinosaur," said Morgan Turner, a Ph.D. candidate at Brown in ecology and evolutionary biology and lead author of the research. "Below ground, or even above ground, they're responding to these soft substrates in a very similar way, which has potentially important implications for our ability to study the movement of these animals that we can't observe directly anymore."The findings were published on Wednesday, July 1, in the Royal Society journal To make the observations, Turner and her colleagues, Professor of Biology and Medical Science Stephen Gatesy and Peter Falkingham, now at Liverpool John Moores University, used a 3D-imaging technology developed at Brown called X-ray Reconstruction of Moving Morphology (XROMM). The technology combines CT scans of a skeleton with high-speed X-ray video, aided by tiny implanted metal markers, to create visualizations of how bones and muscles move inside humans and animals. In the study, the team used XROMM to watch guineafowl move through substrates of different hydration and compactness, analyzing how their feet moved underground and the tracks left behind.Sand, typically a dense combination of quartz and silica, does not lend itself well to X-ray imaging, so the team used poppy seeds to emulate sand. Muds were made using small glass bubbles, adding various amount of clay and water across 107 trials to achieve different consistencies and realistic tracks.They added metal markers underneath the claws of the guineafowl to allow for tracking in 3D space. It's these claw tips that the researchers think are least disturbed by mud flow and other variables that can impact and distort the form of the track.Despite the variation, the researchers observed a consistent looping pattern."The loops by themselves I don't think are that interesting," Gatesy said. "People are like, 'That's nice. Birds do this underground. So what?' It was only when [Turner] went back into it and said, 'What if we slice those motion trails at different depths as if they were footprints?' Then we made the nice connection to the fossils."By "slicing" through the 3D images of the movement patterns at different depths, the researchers found similarities between the guineafowl tracks and fossilized dinosaur tracks."We don't know what these dinosaurs were doing, we don't know what they were walking through exactly, we don't know how big they were or how deep they were sinking, but we can make this really strong connection between how they were moving and some level of context for where this track is being sampled from within that movement," Turner said.By recognizing the movement patterns, as well as the entry and exit point of the foot through various substrates, the team says they're able to gain a better understanding of what a dinosaur track could look like."You end up generating this big diversity of track shapes from a very simple foot shape because you're sampling at different depths and it's moving in complicated ways," Gatesy said. "Do we really have 40 different kinds of creatures, each with a differently shaped foot, or are we looking at some more complicated interaction that leaves behind these remnants that are partly anatomical and partly motion and partly depth?"To further their research, the team spent time at the Beneski Museum of Natural History at Amherst College in Massachusetts, which is home to an expansive collection of penetrative tracks discovered in the 1800s by geologist Edward Hitchcock.Hitchcock originally believed that his collection housed fossil tracks from over 100 distinct animals. Because of the team's work with XROMM, Gatesy now thinks it's possible that at least half of those tracks are actually from the same dinosaurs, just moving their feet in slightly different ways or sampled at slightly different depths."Going to museum together and being able to pick out these features and say, 'We think this track is low in the loop and we think this one is high,' that was the biggest moment of insight for me," Turner said.Turner says she hopes their research can lead to a greater interest in penetrative tracks, even if they seem a little less pretty or polished than the tracks people are used to seeing in museums."They have so much information in them," Turner said, "and I hope that this gives people a lens, a new way to view these footprints and appreciate the movement preserved within in them."This work was supported by the US National Science Foundation (EAR 1452119 to SMG and PLF; IOS 0925077 to SMG), a Marie Curie International Outgoing Fellowship within the 7th European Framework Programme to PLF, and the Bushnell Research and Education Fund to MLT.
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Zoology
| 2,020 |
July 1, 2020
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https://www.sciencedaily.com/releases/2020/07/200701100019.htm
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Why do arteries age? Study explores link to gut bacteria, diet
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A compound produced in the gut when we eat red meat damages our arteries and may play a key role in boosting risk of heart disease as we get older, according to new University of Colorado Boulder research.
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The study, published this month in the American Heart Association journal "Our work shows for the first time that not only is this compound directly impairing artery function, it may also help explain the damage to the cardiovascular system that naturally occurs with age," said first author Vienna Brunt, a postdoctoral researcher in the Department of Integrative Physiology.Eat a slab of steak or a plate of scrambled eggs, and your resident gut bacteria get to work immediately to break it down. As they metabolize the amino acids L-carnitine and choline, they churn out a metabolic byproduct called trimethylamine, which the liver converts to trimethylamine-N-Oxide (TMAO) and sends coursing through your bloodstream.Previous studies have shown that people with higher blood levels of TMAO are more than twice as likely to have a heart attack or stroke and tend to die earlier.But to date, scientists haven't completely understood why.Drawing on animal and human experiments, Brunt and her team set out to answer three questions: Does TMAO somehow damage our vascular system? If so, how? And could it be one reason why cardiovascular health gets worse -- even among people who exercise and don't smoke -- as we get older?The researchers measured the blood and arterial health of 101 older adults and 22 young adults and found that TMAO levels significantly rise with age. (This falls in line with a previous study in mice, showing the gut microbiome -- or your collection of intestinal bacteria -- changes with age, breeding more bacteria that help produce TMAO).Adults with higher blood levels of TMAO had significantly worse artery function, the new study found, and showed greater signs of oxidative stress, or tissue damage, in the lining of their blood vessels.When the researchers fed TMAO directly to young mice, their blood vessels swiftly aged."Just putting it in their diet made them look like old mice," said Brunt. She noted that 12-month-old mice (the equivalent of humans about 35 years old) looked more like 27-month-old mice (age 80 in people) after eating TMAO for several months.Preliminary data also show that mice with higher levels of TMAO exhibit decreases in learning and memory, suggesting the compound could also play a role in age-related cognitive decline.On the flip side, old mice that ate a compound called dimethyl butanol, (found in trace amounts in olive oil, vinegar and red wine) saw their vascular dysfunction reverse. Scientists believe that this compound prevents the production of TMAO.Brunt notes that everyone -- even a young vegan -- produces some TMAO. But over time, eating a lot of animal products may take a toll."The more red meat you eat, the more you are feeding those bacteria that produce it," she said.Senior author Doug Seals, director of the Integrative Physiology of Aging Laboratory, said the study is an important breakthrough because it sheds light on why our arteries erode with age, even in the healthiest people."Aging is the single greatest risk factor for cardiovascular disease, primarily as a result of oxidative stress to our arteries," said Seals. "But what causes oxidative stress to develop in our arteries as we age? That has been the big unkown. This study identifies what could be a very important driver."The research team is now further exploring compounds that might block production of TMAO to prevent age-related vascular decline.For now, they said, a plant-based diet may also keep levels in check.
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Zoology
| 2,020 |
June 30, 2020
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https://www.sciencedaily.com/releases/2020/06/200630092209.htm
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Research reveals fishing pressures affect tropical and temperate reefs differently
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In a study published recently in
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There has been much debate about the degree to which ocean ecosystems are impacted by fishing, also termed "top-down forcing" because such changes occur when predators at the top of the food web are removed, versus the availability of nutrients and other resources in an ecosystem, termed "bottom-up forcing.""Examples from a variety of marine systems of exploitation-induced, top-down forcing have led to a general view that human-induced predator perturbations can disrupt entire marine food webs, yet other studies that have found no such evidence provide a counterpoint," said Madin.Madin worked with an amazing team of marine ecologists from all over the world, particularly those from the Australian Institute of Marine Science (AIMS) and the University of Tasmania (UTas). Using time?series data for 104 reef communities spanning tropical to temperate Australia from 1992 to 2013, they aimed to quantify relationships among populations of predators, prey, and algae at the base of the food web; latitude; and exploitation status over a continental scale.As expected, no-take marine reserves -- where fishing is prohibited -- led to long-term increases in predator population sizes."This is good news for fishers, because as populations increase, the fish don't recognize the reserve boundaries and are likely to 'spill over' into adjacent areas where fishing is allowed, creating a kind of insurance policy whereby marine reserves ensure the ability of fishers to catch fish into the future," said Madin.Surprisingly though, the team found that in the tropics, the system tends to be driven predominantly by bottom-up forcing, whereas colder, temperate ecosystems are more driven by top-down forcing."I assumed at the start of the project that in places where fishing pressure was high and predators were depleted, we would see consequent increases in the population sizes of the predators' prey species, and the decreases in the prey's prey species," explained Madin. "However, in the tropical part of our study system, that is, Australia's Great Barrier Reef, this simply wasn't the case. This result had me scratching my head for quite some time, until I realized that this type of domino effect, called a trophic cascade, is simply a real, but rare, phenomenon in the tropics."These kinds of continent-scale analyses are only possible with large, long-term datasets.This study relied on data from the AIMS long-term coral reef monitoring program and the UTas Australian Temperate Reef Collaboration -- creating one enormous, continental-scale reef dataset."Only by looking at the very big picture, it turned out, were we able to find these trends," said Madin.Predator loss is now a globally pervasive phenomenon that touches nearly every marine ecosystem on the planet. Ecosystem destabilization is a widely-assumed consequence of predator loss. However, the extent to which top-down versus bottom-up forcing predominates in different types of marine systems is not definitively understood."Understanding how our fisheries are likely to impact other parts of the food web is important in making the best possible decisions in terms of how we manage our fisheries," said Madin. "By understanding how coral reef food webs are likely to respond to fishing pressure, or conversely to marine reserves, we can make more informed decisions about how much fishing our reefs can safely handle. Likewise, this knowledge gives us a better idea of what will happen when we create marine reserves designed to serve as an insurance policy so communities can continue to catch fish long into the future."
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Zoology
| 2,020 |
June 30, 2020
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https://www.sciencedaily.com/releases/2020/06/200630155747.htm
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New Zealand's ancient monster penguins had northern hemisphere doppelgangers
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New Zealand's monster penguins that lived 62 million years ago had doppelgangers in Japan, the USA and Canada, a study published today in the
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Scientists have identified striking similarities between the penguins' fossilised bones and those of a group of much younger Northern Hemisphere birds, the plotopterids.These similarities suggest plotopterids and ancient penguins looked very similar and might help scientists understand how birds started using their wings to swim instead of fly.Around 62 million years ago, the earliest known penguins swam in tropical seas that almost submerged the land that is now New Zealand. Palaeontologists have found the fossilised bones of these ancient waddlers at Waipara, North Canterbury. They have identified nine different species, ranging in size from small penguins, the size of today's Yellow-Eyed Penguin, to 1.6 metre-high monsters.Plotopterids developed in the Northern Hemisphere much later than penguins, with the first species appearing between 37 and 34 million years ago. Their fossils have been found at a number of sites in North America and Japan. Like penguins, they used their flipper-like wings to swim through the sea. Unlike penguins, which have survived into the modern era, the last plotopterid species became extinct around 25 million years ago.The scientists -- Dr Gerald Mayr of the Senckenberg Research Institute and Natural History Museum, Frankfurt; James Goedert of the Burke Museum of Natural History and Culture and University of Washington, USA; and Canterbury Museum Curators Dr Paul Scofield and Dr Vanesa De Pietri -- compared the fossilised bones of plotopterids with fossil specimens of the giant penguin species Waimanu, Muriwaimanu and Sequiwaimanu from Canterbury Museum's collection.They found plotopterids and the ancient penguins had similar long beaks with slit-like nostrils, similar chest and shoulder bones, and similar wings. These similarities suggest both groups of birds were strong swimmers that used their wings to propel them deep underwater in search of food.Some species of both groups could grow to huge sizes. The largest known plotopterids were over 2 metres long, while some of the giant penguins were up to 1.6 metres tall.Despite sharing a number of physical features with penguins both ancient and modern, plotopterids are more closely related to boobies, gannets and cormorants than they are to penguins."What's remarkable about all this is that plotopterids and ancient penguins evolved these shared features independently," says Dr De Pietri. "This is an example of what we call convergent evolution, when distantly related organisms develop similar morphological traits under similar environmental conditions."Dr Scofield says some large plotopterid species would have looked very similar to the ancient penguins. "These birds evolved in different hemispheres, millions of years apart, but from a distance you would be hard pressed to tell them apart," he says. "Plotopterids looked like penguins, they swam like penguins, they probably ate like penguins -- but they weren't penguins."Dr Mayr says the parallels in the evolution of the bird groups hint at an explanation for why birds developed the ability to swim with their wings."Wing-propelled diving is quite rare among birds; most swimming birds use their feet. We think both penguins and plotodopterids had flying ancestors that would plunge from the air into the water in search of food. Over time these ancestor species got better at swimming and worse at flying."Fossils from New Zealand's giant penguins, including Waimanu and Sequiwaimanu are currently on display alongside life-sized models of the birds in Canterbury Museum's exhibition Ancient New Zealand: Squawkzilla and the Giants, extended until 16 August 2020.This research was partly supported by the Royal Society of New Zealand's Marsden Fund.
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Zoology
| 2,020 |
June 29, 2020
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https://www.sciencedaily.com/releases/2020/06/200629090007.htm
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Researchers print, tune graphene sensors to monitor food freshness, safety
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Researchers dipped their new, printed sensors into tuna broth and watched the readings.
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It turned out the sensors -- printed with high-resolution aerosol jet printers on a flexible polymer film and tuned to test for histamine, an allergen and indicator of spoiled fish and meat -- can detect histamine down to 3.41 parts per million.The U.S. Food and Drug Administration has set histamine guidelines of 50 parts per million in fish, making the sensors more than sensitive enough to track food freshness and safety.Making the sensor technology possible is graphene, a supermaterial that's a carbon honeycomb just an atom thick and known for its strength, electrical conductivity, flexibility and biocompatibility. Making graphene practical on a disposable food-safety sensor is a low-cost, aerosol-jet-printing technology that's precise enough to create the high-resolution electrodes necessary for electrochemical sensors to detect small molecules such as histamine."This fine resolution is important," said Jonathan Claussen, an associate professor of mechanical engineering at Iowa State University and one of the leaders of the research project. "The closer we can print these electrode fingers, in general, the higher the sensitivity of these biosensors."Claussen and the other project leaders -- Carmen Gomes, an associate professor of mechanical engineering at Iowa State; and Mark Hersam, the Walter P. Murphy Professor of Materials Science and Engineering at Northwestern University in Evanston, Illinois -- have recently reported their sensor discovery in a paper published online by the journal The National Science Foundation, the U.S. Department of Agriculture, the Air Force Research Laboratory and the National Institute of Standards and Technology have supported the project.The paper describes how graphene electrodes were aerosol jet printed on a flexible polymer and then converted to histamine sensors by chemically binding histamine antibodies to the graphene. The antibodies specifically bind histamine molecules.The histamine blocks electron transfer and increases electrical resistance, Gomes said. That change in resistance can be measured and recorded by the sensor."This histamine sensor is not only for fish," Gomes said. "Bacteria in food produce histamine. So it can be a good indicator of the shelf life of food."The researchers believe the concept will work to detect other kinds of molecules, too."Beyond the histamine case study presented here, the (aerosol jet printing) and functionalization process can likely be generalized to a diverse range of sensing applications including environmental toxin detection, foodborne pathogen detection, wearable health monitoring, and health diagnostics," they wrote in their research paper.For example, by switching the antibodies bonded to the printed sensors, they could detect salmonella bacteria, or cancers or animal diseases such as avian influenza, the researchers wrote.Claussen, Hersam and other collaborators (see sidebar) have demonstrated broader application of the technology by modifying the aerosol-jet-printed sensors to detect cytokines, or markers of inflammation. The sensors, as reported in a recent paper published by ACS Applied Materials & Interfaces, can monitor immune system function in cattle and detect deadly and contagious paratuberculosis at early stages.Claussen, who has been working with printed graphene for years, said the sensors have another characteristic that makes them very useful: They don't cost a lot of money and can be scaled up for mass production."Any food sensor has to be really cheap," Gomes said. "You have to test a lot of food samples and you can't add a lot of cost."Claussen and Gomes know something about the food industry and how it tests for food safety. Claussen is chief scientific officer and Gomes is chief research officer for NanoSpy Inc., a startup company based in the Iowa State University Research Park that sells biosensors to food processing companies.They said the company is in the process of licensing this new histamine and cytokine sensor technology.It, after all, is what they're looking for in a commercial sensor. "This," Claussen said, "is a cheap, scalable, biosensor platform."
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Zoology
| 2,020 |
June 25, 2020
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https://www.sciencedaily.com/releases/2020/06/200625144904.htm
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Mountain meadow restoration can bring birds back
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In a new study led by scientists at Point Blue Conservation Science and in collaboration with The Institute for Bird Populations, authors evaluated the successes of mountain meadow restorations by analyzing eight years of bird data collected by field biologists. The authors concluded that, when "pond and plug" and similar techniques were followed, the number of birds of many species increased over time as habitat conditions improved.
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The paper, published in "This paper is the culmination of many years of work monitoring meadows. And it definitely increases the amount of evidence we have that one of the most commonly used approaches n is having the effects we want," says Brent Campos, a lead author of the study.Restoration of degraded meadows and their streams aims to increase the amount of water flowing out of the stream channel during spring runoff and elevate groundwater levels in the dry season. Currently there are major efforts being made to restore meadows across the Sierra Nevada that have been degraded from overgrazing, agricultural use, or deliberate stream channel modifications. Evaluations of meadow restoration are needed to ensure objectives -- such as increased biodiversity -- are being met and identify modifications that may improve outcomes.The study authors evaluated the expectation that meadow birds would increase in abundance following restoration. From 2009 to 2017 biologists sampled birds at 31 montane meadows in California previously restored using a common technique: partially filling the over-sized stream channel with meadow soils. The authors then assessed how the abundance of 12 species of meadow-associated birds changed from 1 to 18 years after restoration, and whether the amount of deciduous shrubs and trees (an indicator of bird habitat quality) at the time of restoration affected the rate of bird response.According to the research, six of the twelve species studied increased in abundance after restoration, while five stayed roughly the same and one may have decreased. The amount of deciduous trees and shrubs at the restoration site at the time of restoration was a strong predictor of bird abundance. The study's authors concluded that both hydrologic measures (partially filling in degraded stream channels) and vegetative measures (planting shrubs and trees such as willows and cottonwoods at restoration sites) were helpful in creating habitat for birds, with the latter approach accelerating the positive impacts of restoration."Having access to one of the longest term datasets around for bird monitoring and meadow restoration was really essential to this paper," said Helen Loffland, a meadow bird specialist with The Institute for Bird Populations, and one of the paper's co-authors. "And it was heartening to see such positive responses from the birds in areas where both hydrologic and vegetative restoration measures were used.""We know that restoration practitioners are out there trying to do the best job possible with limited funding," said Campos. "We hope that this new research will help them in their work restoring meadows' key functions of fostering biodiversity, reducing downstream flooding, purifying water, and storing carbon."The study sites included areas throughout the Sierra including the Perazzo Meadows restoration site near Truckee, Red Clover Valley near Portola, and a restoration site in Tasmam Koyom (Humbug Valley) in Plumas County."It is pretty incredible to visit the Tasmam Koyom site, which is only 6 years out from the restoration completion and see such an abundance of birds," said Ryan Burnet, another co-author. "To see so many more song sparrows or yellow warblers is really encouraging. Normally, you'd need to wait 10 or even 20 years to see a biological response like that."
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Zoology
| 2,020 |
June 25, 2020
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https://www.sciencedaily.com/releases/2020/06/200625144815.htm
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MicroCT reveals detailed head morphology of arthropod, Leanchoilia illecebrosa
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The Chengjiang biota in the Yunnan Province of China contains one of the most species-rich and well-preserved fossiliferous deposits for the early Cambrian (ca. 518 million years old), including numerous arthropod species. However, several Chengjiang arthropods have an unfamiliar morphology, are extremely rare, or are incompletely preserved, which often leads to many of these species being problematic, poorly known, or often both, thus hindering their contribution towards reconstructing the evolution of this major animal group.
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Javier Ortega-Hernández, Assistant Professor in the Department of Organismic and Evolutionary Biology and Curator of Invertebrate Paleontology in the Museum of Comparative Zoology at Harvard University, and Yu Liu, Professor of Paleobiology, Yunnan University, China have collaborated for years in the study of Chengjiang arthropods and their evolutionary significance. Their latest paper in Ortega-Hernández and Liu used microCT, a technique that uses X-rays to visualize features that are not easily observable on the surface of the fossils, to study the organization of the head in small juveniles of "The biggest surprise came when studying structures close to the mouth," said Ortega-Hernández. "Until now, the very existence of a labrum in megacheirans, and its position relative to the mouth, have been the source of heated debate. In living arthropods the labrum is considered an important feature of the head because of its precise origin during embryonic development. The 3D data on Leanchoilia allowed us to show for the first time and with great clarity that this animal indeed had a labrum. This is a useful discovery because researchers have argued with each other whether a labrum was present or not in this and other closely related species, which has prompted very different interpretations about their evolution and affinities."The paper is the fifth in a series of publications that represent an ongoing collaboration between the research groups led by Ortega-Hernández and Liu. This study along with others in "With microCT we can discern between the iron-rich fossils and the iron-depleted rock matrix to produce highly detailed and informative virtual models in 3D that reveal their affinities, ecology and evolutionary significance," said Ortega-Hernández. "Although each publication is a bit different and tells a distinct story for the early evolution of arthropods, they all follow the same overall goal and structure, and use similar techniques and methodology.""We have several ongoing projects as part of this collaboration, including many new and exciting species, as well as re-descriptions of some old favorites," said Ortega-Hernández. "There are certainly a few pleasant surprises, and we expect that this collaboration will continue yielding high-quality morphological information for several years, as we have only started to scratch the surface." The ongoing project is partially funded by the Harvard China Fund.
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Zoology
| 2,020 |
June 25, 2020
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https://www.sciencedaily.com/releases/2020/06/200623111328.htm
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Long-tailed tits avoid harmful inbreeding by recognising the calls of relatives
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Long-tailed tits actively avoid harmful inbreeding by discriminating between the calls of close family members and non-family members, according to new research from the University of Sheffield.
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Inbred animals typically suffer from reduced survival and reproductive success, so inbreeding is usually avoided. But, in species where young stay close to where they were born, relatives are often encountered as potential mates, increasing the risk of harmful inbreeding.Long-tailed tits often breed close to home, allowing kin to help raise each other's chicks, but also incurring a risk of inbreeding that reduces the reproductive success of offspring. The research, led by Dr Amy Leedale from the University of Sheffield's Department of Animal and Plant Science, found that despite this risk, close relatives are actively avoided when pairs form each spring.Long-tailed tits use distinctive calls to recognise close relatives so that they can help raise their offspring. The authors suggest that these calls also explain how the birds avoid inbreeding.Dr Amy Leedale, who led the research as a PhD student at the University of Sheffield, said: "We recorded the calls of males and females in many pairs of long-tailed tits and found that the calls of breeding pairs were less similar than the calls of close relatives that they could have bred with. Call similarity within breeding pairs was, instead, similar to that observed among distant relatives or unrelated birds."Long-tailed tit calls are learned in the nest, when parents, offspring and siblings are closely associated. Call similarity can therefore act as a reliable indicator of close relatedness in adulthood. This study reveals a potential mechanism by which long-tailed tits can avoid harmful inbreeding as well as gaining benefits from cooperating with kin.Professor Ben Hatchwell, who has led the long-tailed tit project at the University of Sheffield for more than 25 years, said: "This study demonstrates the value of long-term studies of wild animals, allowing us to build pedigrees of known individuals over many generations, and to measure the consequences of behavioural decisions for their reproductive success."
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Zoology
| 2,020 |
June 24, 2020
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https://www.sciencedaily.com/releases/2020/06/200624151603.htm
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Resident parasites influence appearance, evolution of barn swallows
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Barn swallows live almost everywhere on the planet, recognizable by their forked tail and agility in the air. Yet while they share these characteristics, these little birds often look slightly different in each place they live -- with some so distinct they're splitting off to become new species.
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Researchers at CU Boulder think that local parasites are influencing why barn swallows in Europe, the Middle East and Colorado are choosing their mates differently. Their new research, published in "It's possible we haven't appreciated just how important parasites might be in shaping the evolution of their hosts," said lead author Amanda Hund, who conducted the research as a doctoral candidate in the Ecology and Evolutionary Biology Department.Every organism, including humans, has co-evolved with a unique community of parasites, that by definition live at the expense of their host. While they are not beneficial to us like many other microbes are, parasites have shaped our own immune system, pheromones and even our mate selection, previous research has shown.Hund set out to characterize as many parasite communities as she could in barn swallows, to find out if they could be influencing their mate selection, and therefore the male birds' physical traits and the creation of new species.Hund and her colleagues studied barn swallows at sites in Colorado, the Czech Republic and Israel over four years. They measured the number and types of parasites on them, in their nests and in their blood and tracked who they chose to mate with in a given breeding season, their sexual signals -- breast color, throat color and tail shape -- and their health and the survival rate of their offspring.In all but one population in the study, the most "attractive" males had fewer parasites. Somehow the male birds' breast color, throat color and tail shape allowed females to make informed choices about their health and the likelihood of reproductive success with that partner.Many birds also had multiple parasites with connections to the same physical trait. For example, in Colorado, males with darker breast color are less likely to have mites, but more likely to have malaria. Nest mites are detrimental to the nestlings' survival -- whereas malaria only impacts the male bird."Males are investing in traits to attract females, and it looks like that comes at a cost -- where they are more attractive, but also more susceptible to malaria," said Hund, now a postdoctoral fellow at the University of Minnesota. "It is a tradeoff."Researchers who study the origin of biodiversity, or why the Earth has so many different species, often examine which traits animals are choosing in their partners. But the real question is: Why are they choosing those specific combinations of traits?To answer that question requires a very detailed type of scientific research, looking at the full reproductive cycle, health and survival rate of a population, in order to create a rich data set that unpacks how evolution is working between closely related populations."Most people are really good at characterizing the pattern. But Amanda's work is very special in terms of trying to unpack the process," said Rebecca Safran, associate professor in the Department of Ecology and Evolutionary Biology and co-author on the study.Many factors affect the divergent evolution of species. But as opposed to something like the weather, parasites are evolving as rapidly as their host species -- leading to a co-evolutionary relationship. While this has been studied in other animals, it has only previously been studied in one barn swallow population in Europe.Barn swallows make a great study specimen: they're ubiquitous and charismatic."These birds have evolved alongside humans for thousands of years. Every culture that we've visited seems to have its own unique story or relationship with this bird," said Safran.But because they nest almost exclusively in human made structures -- barns, bridges, culverts and the like -- barn swallows often live on private land. It turns out that winning the trust of landowners is as much a part of the work as catching the birds."Public relations is a very large part of barn swallow research," said Hund.Safran has been working with dozens of collaborators all over the world for over a decade. Hund built off these connections to do this research in Europe and the Middle East, facing unique circumstances and language barriers along the way.In Israel Hund lived on a Kibbutz, a collective community, in order to complete her research over several months. In the Czech Republic, Hund used award-winning skills from her childhood and rode horses at an equestrian center to build trust and gain access to an important nesting site.And here in Colorado, there were landowners who were unsure or suspicious of the project at the start of the breeding season. "But by the end, they were having us over for dinner," said Hund.The work doesn't stop here. The researchers are already trying to answer the next big question: why are local parasites and certain sexual traits linked?"And once you really figure that out, you can export that knowledge and our study methods to other populations and actually watch mate selection decisions and the associated reproductive consequences unfold," said Safran. "It's like watching evolution in action."
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Zoology
| 2,020 |
June 24, 2020
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https://www.sciencedaily.com/releases/2020/06/200624151533.htm
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Better way to keep birds from hitting power lines
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Suspended, rotating devices known as "flappers" may be the key to fewer birds flying into power lines, a study by Oregon State University suggests.
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The findings by researchers in OSU's College of Agricultural Sciences are important because around the globe both the number of power lines and concern over bird fatalities are on the rise.Research has documented more than 300 species of birds dying from hitting power lines, with one study estimating that more than 170 million perish annually in the United States and another estimating the global death toll to be 1 billion per year. There's also the problem of power outages that bird strikes can cause.Conservation managers and utilities many years ago developed flight diverters, basically regularly spaced devices that make the lines more visible, as a step toward reducing the number of birds flying into the lines.The most common type are the PVC spirals, which are durable and easy to install, but how well they actually work isn't well understood. Though they've been in use for nearly four decades, strike rates remain high for a number of species.OSU researchers Virginia Morandini and Ryan Baumbusch were part of an international collaboration that compared the effectiveness of three types of flight diverters: yellow PVC spiral; orange PVC spiral; and a flapper model with three orange and red polypropylene blades with reflective stickers.The flapper hangs from a power line and its blades, 21 centimeters by 6.2 centimeters, rotate around a vertical axis.The three-year study took place in southern Spain, and almost 54 kilometers of power lines were used in the research. Ten kilometers were marked with yellow spirals, 13 kilometers were marked with orange spirals, another 13 had flappers, and 16 kilometers had no markers, thus serving as a control. All three flight diverter types were spaced every 10 meters.Field workers combed the area under the lines every 40 days for evidence of birds killed by power lines and found a total of 131 such birds representing 32 species.The research suggested the flappers were responsible for a 70% lower average death rate compared to the control. The findings also showed the spirals were better than no diverters, but significantly less effective than the flappers."Colored PVC spiral is the most commonly used flight diverter by far, but the flapper diverter was the one showing the largest reduction in mortality with the lowest variation across different power lines, habitats and bird communities," Morandini said. "We suggest to consider the flapper as the first choice when installing bird flight diverters, recommending to increase future research in testing its material durability and resistance against vibrations and color loss."The flappers and PVC spirals have comparable materials and production costs, researchers say, with flappers being easier and faster to install.That's important because power companies must keep a line discharged during the diverter installation process -- losing money because electricity is not flowing through the line -- so the time required to install diverters is the most important factor when considering costs.
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Zoology
| 2,020 |
June 23, 2020
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https://www.sciencedaily.com/releases/2020/06/200623145339.htm
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Size matters in the sex life of salmon
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Every summer, tens of thousands of Atlantic salmon migrate from the Barents Sea to the Teno River, Finland, to spawn in the streams where they were born. This journey is a feat of endurance: salmon stop feeding and must navigate fast flowing water, leap over obstacles, and avoid predators, hooks, and fishing nets to arrive at their spawning grounds.
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The marathon doesn't stop there though: once they arrive at their spawning grounds, they must fight for the possibility to mate with members of the opposite sex. Who are the winners of this evolutionary competition? It turns out that the largest fish produce the most offspring, but there are far fewer of these fish on the spawning ground battling for reproductive success than their younger -- and smaller -- competitors, according to researchers at the University of Helsinki and the Natural Resources Institute Finland.The study, recently published in the scientific journal "Great care was taken to not harm the fish," explains Dr. Kenyon Mobley, lead author of the article. "In fact, we have recaptured adults returning to spawn several years later and juveniles returning to spawn as adults."Most salmon in Teno River spend between one and four years at sea before migrating back to breed. The more time salmon spend at sea, the larger they grow. Females generally take between 2-3 years to mature, but most males return after just one year at sea.Mobley's study showed that for every year spent at sea, females gain over 4 kilograms of body weight and produce 60% more offspring. Males, on the other hand, gain nearly 5 kilograms of body weight and produce 200% more offspring for every year they spend at sea.However, spending more time at sea comes with a significant cost. Very few of these older larger fish return to spawn. "This is presumably because spending more time at sea exposes fish longer to predators, fishing, and diseases, and thus a higher risk of death before having a chance to spawn," explains Mobley."Knowing the reproductive contributions of different sized fish in this river section can help us to develop more accurate models of offspring production. These are needed for developing Teno salmon management guidelines," says Professor Jaakko Erkinaro from Natural Resources Institute Finland. "It also helps our ongoing research aimed at predicting how many large adults may survive at sea to return to spawn," Mobley adds.Like most animals in nature, salmon are not monogamous and can have up to eight mating partners, the study shows. Having more mating partners ensures successful fertilization of eggs and passing on their genes to the next generation.Nearly all females captured in the study produced offspring, mating on average with more than two males, and gained 35% more mates for each year they spent at sea. Males have, on average, less than one mate, indicating that many males are excluded from mating presumably through strong competition by bigger males. For each year spent at sea, males gain 60% more mates. This means that larger salmon, in particular males, have a distinct advantage when it comes to finding mates.In the study population, females are a rare commodity. There are up to seven males for every female at the spawning ground near the entrance of the Utsjoki River. This pattern is consistent across all years of the study. Having a high number of males likely increases fights among males for opportunities to mate with the few available females. Why so few females return to this particular site remains a mystery, as other locations in the Teno River have a more balanced mix of males and females.Prior to entering the sea, juvenile salmon usually spend between 3-5 years in freshwater. The researchers were surprised to find that the longer the females stay in freshwater, the fewer years they spend at sea, and return to spawn at a much smaller size. Because these females are smaller, they have fewer eggs and produce less offspring. Males, on the other hand, do not seem to be affected by spending more time in freshwater."These results show how overlooked aspects of salmon life-history are important to the long-term conservation of these fish," said Mobley.
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Zoology
| 2,020 |
June 22, 2020
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https://www.sciencedaily.com/releases/2020/06/200622133022.htm
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300-million-year-old fish resembles a sturgeon but took a different evolutionary path
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Sturgeon, a long-lived, bottom-dwelling fish, are often described as "living fossils," owing to the fact that their form has remained relatively constant, despite hundreds of millions of years of evolution.
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In a new study in the The find indicates that, although ancient, the features that enabled Tanyrhinichthys to thrive in its environment arose multiple times in different fish lineages, a burst of innovation that was not previously fully appreciated for fish in this time period."Sturgeon are considered a 'primitive' species, but what we're showing is that the sturgeon lifestyle is something that's been selected for in certain conditions and has evolved over and over again," says Sallan, senior author on the work."Fish are very good at finding solutions to ecological problems," says Stack, first author on the study, who worked on the research as a Penn undergraduate and is now a graduate student at Michigan State University. "This shows the degree of both innovation and convergence that's possible in fishes. Once their numbers got up large enough, they started producing brand new morphologies that we now see have evolved numerous times through the history of fishes, under similar ecological conditions. "The first fossil of Tanyrhinichthys was found in 1984 in a fossil-rich area called the Kinney Brick Quarry, about a half hour east of Albuquerque. The first paleontologist to describe the species was Michael Gottfried, a Michigan State faculty member who now serves as Stack's advisor for his master's degree."The specimen looks like someone found a fish and just pulled on the front of its skull," Stack says. Many modern fish species, from the swordfish to the sailfish, have protuberant snouts that extend out in front of them, often aiding in their ability to lunge at prey. But this characteristic is much rarer in ancient fishes. In the 1980s when Gottfried described the initial specimen, he posited that the fish resembled a pike, an ambush predator with a longer snout.During the last decade, however, several more specimens of Tanyrhinichthys have been found in the same quarry. "Those finds were an impetus for this project, now that we had better information on this enigmatic and strange fish," Stack says.At the time that Tanyrhinichthys roamed the waters, Earth's continents were joined in the massive supercontinent called Pangea, surrounded by a single large ocean. But it was an ice age as well, with ice at both poles. Just before this period, the fossil record showed that ray-finned fishes, which now dominate the oceans, were exploding in diversity. Yet 300 million years ago, "it was like someone hit the pause button," Sallan says. "There's an expectation that there would be more diversity, but not much has been found, likely owing to the fact that there just hasn't been enough work on this time period, especially in the United States, and particularly in the Western United States."Aiming to fill in some of these gaps by further characterizing Tanyrhinichthys, Stack, Sallan, and colleagues closely examined the specimens in detail and studied other species that dated to this time period. "This sounds really simple, but it's obviously difficult in execution," Stack notes, as fossils are compressed flat when they are preserved. The researchers inferred a three-dimensional anatomy using the forms of modern fishes to guide them.What they noticed cast doubt on the conception of Tanyrhinichthys as resembling a pike. While a pike has an elongated snout with its jaws at the end of it, allowing it to rush its prey head-on, Tanyrhinichthys has an elongated snout with its jaws at the bottom."The whole form of this fish is similar to other bottom dwellers," Stack says. Sallan also noticed canal-like structures on its snout concentrated in the top of its head, suggestive of the locations where sensory organs would attach. "These would have detected vibrations to allow the fish to consume its prey," says Sallan.The researchers noted that many of the species that dwelled in similar environments possessed longer snouts, which Sallan called "like an antenna for your face.""This also makes sense because it was an estuary environment," Sallan says, "with large rivers feeding into it, churning up the water, and making it murky. Rather than using your eyesight, you have to use these other sensory organs to detect prey."Despite this, other features of the different ancient fishes' morphology were so different from Tanyrhinichthys that they do not appear to have shared a lineage with one another, nor do modern sturgeon descend from Tanyrhinichthys. Instead the long snouts appear to be an example of convergent evolution, or many different lineages all arriving at the same innovation to adapt well to their environment."Our work, and paleontology in general, shows that the diversity of life forms that are apparent today has roots that extend back into the past," says Stack.
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Zoology
| 2,020 |
June 22, 2020
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https://www.sciencedaily.com/releases/2020/06/200622095008.htm
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Biologists unravel tangled mystery of plant cell growth
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When cells don't divide into proper copies of themselves, living things fail to grow as they should. For the first time, scientists now understand how a protein called TANGLED1 can lead to accurate cell division in plants.
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Inside cells are structures called microtubules, which act like highways for moving proteins and organelles. They're also critical for separating DNA after it has been duplicated to eventually make two cells from one."You can't live without microtubules, and plants can't either," said Carolyn Rasmussen, an assistant professor of plant cell biology at UC Riveride. "Because they're so important, where they go and how they move has to be carefully controlled."Rasmussen and colleagues discovered that the TANGLED1 protein performs this microtubule controlling function by binding the microtubules together like glue. Their description of how TANGLED1 operates was published today in the By adding together microtubules and TANGLED1 in a test tube, the team saw surprising interactions between them. Often, proteins can only bundle microtubules at very specific angles -- 40 degrees or less. TANGLED1 can grab microtubules from any angle and link them together."To the best of my knowledge, this is the first plant protein observed in vitro with this characteristic," Rasmussen said.The protein's ability to capture and stabilize microtubules is likely critical for being able to separate daughter cells properly. Cell divisions at the wrong angle lead to big problems such as the formation of tumors.Animal cells normally need to remain attached to a surface, and their division is controlled to ensure the cells remain there. If a cell becomes unattached to the surface after division, that could mark the beginning of a tumor.Rasmussen's team included Pablo Martinez, Sean O'Leary, and Antonia Zhang from UC Riverside; biochemists Ram Dixit and Rachappa Balkunde from Washington University; and mathematician Kenneth Brakke from Susquehanna University.Now that the team has seen TANGLED1 at work in vitro, the next step is to observe it in a living cell. If they can gain a deeper understanding of the genes that control plant cell division, these genes might be manipulated to produce higher yield crops, such as bigger ears of corn or more grain.An additional benefit of this research is the insight it could yield into human cellular processes. When there are defects in the cell's ability to move material around on microtubules, diseases such as Alzheimer's disease or cancer could follow.Research on these diseases is often conducted on human cell lines or animal models. However, there are similarities between the microtubule bundling behavior of TANGLED1 in plants and microtubule binding proteins in humans, making it easier to learn more by characterizing both at the same time."People say plants don't get cancer, which is generally true," Rasmussen said. "But sometimes when you have a different perspective on a related question -- in this case, what controls the spatial positioning of cell division -- you can see things that are hard to see in other model systems."
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Zoology
| 2,020 |
June 19, 2020
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https://www.sciencedaily.com/releases/2020/06/200619104308.htm
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The wind beneath their wings: Albatrosses fine-tuned to wind conditions
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A new study of albatrosses has found that wind plays a bigger role in their decision to take flight than previously thought, and due to their differences in body size, males and females differ in their response to wind.
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With a wingspan of over three meters -- the largest of any bird alive today -- the wandering albatross can fly thousands of miles, even around the world, gliding for long periods in search of fish or squid. Birds search for prey in flight and capture it after landing on the sea surface. Due to their long wings, taking off from the sea surface is by far their most energetically demanding activity, requiring four times more energy than gliding flight.Now, research by University of Liverpool scientists published in the Using GPS loggers, researchers tracked the flight patterns of over 300 albatrosses from two major populations in the Southern Ocean, one of the windiest areas on the planet.By combining tracking data with computer modelling, they found that the seabirds wait on the sea surface for winds to pick up before attempting to fly again. They also found that males, which are 20% bigger than females, wait for stronger winds to help them take off from the ocean surface and sustain their flight.University of Liverpool seabird ecologist and lead author of the study, Dr Tommy Clay, said: "Albatrosses are the oceans' great voyagers and are well-known for their ability to glide on winds with barely a flap of their wings."Our study reveals that albatross behaviour is fine-tuned to the winds they encounter. In order to save energy, birds rely on strong winds for take-off, males more so than females."Ongoing changes to wind patterns as a result of climate change may pose different risks to males and females. In recent years, increases in wind speeds have led to higher breeding success, but as winds become less predictable, birds may be unable to adapt."Changing wind patterns around Antarctica have seen reductions in wind speeds in more northerly areas, where females are more likely to feed, and increases in southerly areas, where males are more common, which could affect how far they can travel to find food and their body condition.These changes are more likely to benefit males. However, more research is needed to determine the long-term effects on populations.The fieldwork was conducted over a seven year period in the remote sub-Antarctic islands of South Georgia in the south-west Atlantic Ocean and Crozet in the south-west Indian Ocean.The analysis was led by researchers at the University of Liverpool in collaboration with an international and highly interdisciplinary team.This involved researchers at the University of Florida (USA), Centre National de la Recherche Scientifique (CNRS, France), British Antarctic Survey (UK), Royal Netherlands Meteorological Institute and Delft University of Technology (Netherlands), and Stellenbosch University (South Africa). The project was funded by the Human Frontiers Research Program.
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Zoology
| 2,020 |
June 18, 2020
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https://www.sciencedaily.com/releases/2020/06/200618120209.htm
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Antioxidant-rich diet reduces stress response during bird migration
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A research team led by a University of Rhode Island ornithologist had birds fly in a wind tunnel to simulate migration and found that birds that consume dietary antioxidants before and during fall migration can reduce the endocrine stress response triggered by long-duration flights.
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The results, published this week in the "This reduction in the endocrine stress response may be a major benefit birds gain in fall by eating fruits at stopover sites during migration," said Scott McWilliams, URI professor of natural resources science, noting that many species of birds select berries containing anthocyanins, a type of dietary antioxidant present in purple-colored berries. "We know birds prefer certain berries that have lots of antioxidants."During long-distance flights that push birds to their physiological limits, levels of metabolic hormones called glucocorticoids become elevated to provide ready-to-use fuel to satisfy high energy demands, according to McWilliams. But prolonged exposure to glucocorticoids is detrimental and can lead to chronic stress response. The research concluded that the consumption of anthocyanin-rich food attenuates the potential stress triggered by the secretion of high levels of glucocorticoids."We always thought that glucocorticoids were important for birds preparing for migration, and antioxidants were there to mop up the free radicals associated with high metabolism during migration," said McWilliams. "We tested the hypothesis that antioxidants and glucocorticoids were metabolically complementary, that is if the birds ate anthocyanins before flying then the increase in glucocorticoids to support metabolism would be reduced."The study was conducted at a wind tunnel at the Max Planck Institute for Ornithology in Seewisen, Germany. Scientists from URI, the Institute, Jagellonian University in Poland and Sacred Heart University in Connecticut collaborated on the project. Funding was provided by the National Science Foundation and European grants.The researchers chose as their study subjects European starlings, a common species in Germany that migrates to southern Italy. The test subjects were collected from nest boxes, hand-raised adjacent to the wind tunnel, and put through endurance training for two weeks prior to the experiment. Physiological measurements were then taken before and after the birds' long-duration flights, some of which lasted up to six hours."The birds that ate anthocyanins prior to flying increased the level of glucocorticoids in their circulation by only about half as much as those that did not eat dietary antioxidants," said McWilliams.Equally important, he said, is that the birds that ate the anthocyanins "showed no other effects on their flight performance. The birds could fly for just as long, they used just as much fat, and everything else was similar. Their performance was the same, but they accomplished that performance while reducing their glucocorticoid response. The antioxidants attenuated the negative effects of the glucocorticoids."McWilliams believes that many species of birds benefit from feeding on berries high in antioxidants during fall migration."We know that lots of other species of birds switch to feeding on fruits in fall and show the same kind of preferences for certain fruits high in antioxidants," he said. For this reason, land management and conservation efforts for migratory songbirds, especially in the eastern U.S., focuses on providing habitat with an abundance of fruiting shrubs.While many varieties of anthocyanin-containing berries are available to birds during the fall migration season, few are available during spring migration, and little is known about how the birds cope with the high levels of glucocorticoids during their northbound flights."We don't know where they get those antioxidants in spring, or if they do," McWilliams said. "All animals have an endogenous antioxidant system, so perhaps when dietary antioxidants are less available, they rely more on this internal endogenous system."
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Zoology
| 2,020 |
June 17, 2020
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https://www.sciencedaily.com/releases/2020/06/200617150022.htm
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Fighting fish synchronize their combat moves and their gene expression
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When two betta fish are fighting for dominance, not only do their attacks mirror each other, but the gene expression in their brain cells also starts to align. The new findings, published June 17th in
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The fighting fish Betta splendens is famous for its aggression, but opponents typically stop fighting after assessing the other's abilities to avoid any serious injuries. The small freshwater fish is commonly used to study aggression in the lab, and it employs a handful of standard tactics like mouth-locking, bites, strikes and swimming to the surface to gulp air. In the new study, researchers observed that during a fight, two male opponents modify their actions to match the aggressive behavior of the other, leading to tightly synchronized battles. Furthermore, when the researchers analyzed the brains of both opponents, they observed that the fish also synchronized which genes were turned on or off in brain cells. The fighting pair had similar changes in gene activity related to learning, memory, synapse function and ion transport across cell membranes. The synchronization was specific to a fighting pair and became stronger after fighting for an hour compared to a 20-minute fight, suggesting that the degree of synchronization was driven by fighting interactions.The new study takes a neurogenomic approach to the old question of how animals synchronize their behavior. Similar mirrored behaviors also occur during mating, foraging and cooperative hunting, and these behaviors may also trigger synchronized brain changes in the pairs of animals. "One of my future plans is to elucidate what happens in the male-female interaction of fish on the molecular level," said author Norihiro Okada.The findings suggest that even though the betta fish are fighting each other, sometimes to the death, their brains may be cooperating at the molecular level.
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Zoology
| 2,020 |
June 17, 2020
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https://www.sciencedaily.com/releases/2020/06/200617091011.htm
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How fish got onto land, and stayed there
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Research on blennies, a family of fish that have repeatedly left the sea for land, suggests that being a 'jack of all trades' allows species to make the dramatic transition onto land but adapting into a 'master of one' allows them to stay there. The findings are published in the British Ecological Society journal
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Researchers from University of New South Wales and the University of Minnesota pooled data on hundreds of species of blennies, a diverse family of fish where some are aquatic and others have left the water completely. They found that a flexible diet and behaviour were likely to be instrumental in the transition to land.However, once out of the water, restrictions on the type of food available triggered major evolutionary changes, particularly to their teeth, as land dwelling blennies have become specialists in scraping algae and detritus from rocks.Dr Terry Ord, lead author of the research, said: "The implications of our findings are that having a broad diet or being behaviourally flexible can help you move into a new habitat. But once there, this flexibility becomes eroded by natural selection. This presumably means those highly specialised species are less likely to be able to make further transitions, or cope with abrupt environment changes in their existing habitat."The scenario of fish colonising land has obvious parallels with the origin of all land vertebrates. "Fossils can give us important insights into how that transition might have unfolded, and the types of evolutionary adaptations it required or produced. But having a contemporary example of fish making similar ecological transitions can also help us understand the general challenges that are faced by fish out of the water" said Dr Ord.Blennies are a remarkable family of fish with different species occupying strikingly different environments. Some are aquatic. Others spend time in and out of the water in the intertidal zone, an extreme environment with fluctuating water levels and pools that can rapidly change in temperature and oxygen levels.Some species of blenny are terrestrial and spend almost their entire lives out of the water in the splash zone and must keep moist in order to breathe through their skin and gills. Despite these challenges, blennies have been incredibly successful in repeatedly making these dramatic transitions.Because of this diversity, different blenny fish species represent clearly defined stages of the invasion process between two completely different environments. This makes them a unique group of animals to study.Dr Ord explained the origin of the study with his co-author Dr Peter Hundt: "We both had extensive data collected on many different species of blenny from across the world. Peter had detailed information on diet and teeth morphology, while I had lots of data on behaviour and frequency of different species emerging from water for brief or extended periods on land."We threw a set of complex evolutionary statistical models at this combined data and we were able to reveal the sequence of events that likely allowed aquatic marine fishes to ultimately evolve into fishes that could leave water and then colonise land. Our study also showed how those species on land adaptively changed to better suit the specialised diet needed to survive on land."The authors caution that although the observational data suggests a flexible diet and behaviour allows a transition to new environments to occur, it cannot confirm causality. "Ideally we would perform some type of experimental investigation to try to establish casualty. What this experimental study might be is hard to imagine at this stage, but we're working on it." Said Dr Ord.The authors are also looking to further investigate how the invasion of land has impacted other aspects of blenny fish behaviour, ecology and bodies. "Terrestrial blennies are really agile out of water, and I suspect they've adapted their body shape to allow them to hop about the rocks so freely. Which in turn implies they might not be able to go back to the water" said Dr Ord, "It would also be exciting to know how their sensory systems might have adapted out of the water as well, given vision and smell would probably work quite differently in these environments."
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Zoology
| 2,020 |
June 17, 2020
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https://www.sciencedaily.com/releases/2020/06/200617100432.htm
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Tracking Australia's gigantic carnivorous dinosaurs
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North America had the T. rex, South America had the Giganotosaurus and Africa the Spinosaurus -- now evidence shows Australia had gigantic predatory dinosaurs.
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The discovery came in University of Queensland research, led by palaeontologist Dr Anthony Romilio, which analysed southern Queensland dinosaur footprint fossils dated to the latter part of the Jurassic Period, between 165 and 151 million-year-ago."I've always wondered, where were Australia's big carnivorous dinosaurs?" Dr Romilio said."But I think we've found them, right here in Queensland."The specimens of these gigantic dinosaurs were not fossilised bones, which are the sorts of things that are typically housed at museums."Rather, we looked at footprints, which -- in Australia -- are much more abundant."These tracks were made by dinosaurs walking through the swamp-forests that once occupied much of the landscape of what is now southern Queensland."Most of the tracks used in the study belong to theropods, the same group of dinosaurs that includes Australovenator, Velociraptor, and their modern-day descendants, birds.Dr Romilio said these were clearly not bird tracks."Most of these footprints are around 50 to 60 centimetres in length, with some of the really huge tracks measuring nearly 80 centimetres," he said."We estimate these tracks were made by large-bodied carnivorous dinosaurs, some of which were up to three metres high at the hips and probably around 10 metres long."To put that into perspective, T. rex got to about 3.25 metres at the hips and attained lengths of 12 to 13 metres long, but it didn't appear until 90 million years after our Queensland giants."The Queensland tracks were probably made by giant carnosaurs -- the group that includes the Allosaurus."At the time, these were probably some of the largest predatory dinosaurs on the planet."Despite the study providing important new insights into Australia's natural heritage, the fossils are not a recent discovery."The tracks have been known for more than half a century," Dr Romilio said."They were discovered in the ceilings of underground coal mines from Rosewood near Ipswich, and Oakey just north of Toowoomba, back in the 1950s and 1960s."Most hadn't been scientifically described, and were left for decades in museum drawers waiting to be re-discovered."Finding these fossils has been our way of tracking down the creatures from Australia's Jurassic Park."
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Zoology
| 2,020 |
May 3, 2021
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https://www.sciencedaily.com/releases/2021/05/210503151306.htm
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Intranasal influenza vaccine enhances immune response and offers broad protection
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An influenza vaccine that is made of nanoparticles and administered through the nose enhances the body's immune response to influenza virus infection and offers broad protection against different viral strains, according to researchers in the Institute for Biomedical Sciences at Georgia State University.
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Recurring seasonal flu epidemics and potential pandemics are among the most severe threats to public health. Current seasonal influenza vaccines induce strain-specific immunity and are less effective against mismatched strains. Broadly protective influenza vaccines are urgently needed.Intranasal vaccines are a promising strategy for combatting infectious respiratory diseases, such as influenza. They are more effective than vaccines injected into a muscle because they can induce mucosal immune responses in respiratory tracts, preventing infection at the portal of virus entry. They can also stimulate systemic immune responses throughout the body.Scientists can overcome vaccine safety concerns and the long production phase of virus-based influenza vaccines by constructing intranasal vaccines with recombinant proteins or peptides. However, these vaccines are poor at producing immune responses, so it's necessary to have potent mucosal adjuvants, substances that enhance the body's immune response to antigens (the molecular structures on pathogens). The absence of appropriate mucosal adjuvants currently hinders the development of such a vaccine.In this study, the researchers developed an intranasal influenza vaccine using recombinant hemagglutinin (HA), a protein found on the surface of influenza viruses, as the antigen component of the vaccine. HA is integral to the ability of influenza virus to cause infection.They also created a two-dimensional nanomaterial (polyethyleneimine-functionalized graphene oxide nanoparticles) and found that it displayed potent adjuvant (immunoenhancing) effects on influenza vaccines delivered intranasally. The findings are published in the journal "Conventional flu vaccines predominantly induce antibody responses," said Dr. Baozhong Wang, senior author of the study, principal investigator of the National Institutes of Health grant supporting the study and a professor in the Institute for Biomedical Sciences. "However, recent research demonstrates that lung resident memory T cell responses are indispensable for optimal cross-protection against pulmonary influenza infection. The development of lung resident T cell responses requires vaccination by a respiratory route or influenza virus infection. Our research opens a new path for the development of needle-free and logistically simplified intranasal flu vaccines for cross-protection.""In our study, we reported for the first time that two-dimensional graphene oxide nanomaterials had a potent adjuvant effect in boosting the immune responses of intranasal hemagglutinin (HA) vaccines," said Dr. Chunhong Dong, lead author of the study and a postdoctoral research Fellow in Dr. Baozhong Wang's lab in the Institute for Biomedical Sciences."This study gives new insights into developing high performance intranasal vaccine systems with two-dimensional sheet-like nanoparticles," Dong said. "The graphene oxide nanoparticles have extraordinary attributes for drug delivery or vaccine development, such as the ultra-large surface area for high-density antigen loading, and the vaccine showed superior immunoenhancing properties in vitro and in vivo. The nanoplatform could be easily adapted for constructing mucosal vaccines for different respiratory pathogens."The study, conducted in mice and cell culture, found the nanoparticles significantly enhanced immune responses at mucosal surfaces and throughout the body in mice. The robust immune responses conferred immune protection against influenza virus challenges by homologous (same) virus strains and heterologous (different) virus strains.The results are also promising because needle-free, intranasal influenza vaccines possess superior logistical advantages over traditional injectable vaccines, such as easy administration with high acceptance for recipients and the avoidance of biohazardous waste.Co-authors of the study include Dr. Chunhong Dong, Ye Wang, Gilbert Gonzalez, Yao Ma, Yufeng Song, Dr. Sang-Moo Kang and Dr. Baozhong Wang of the Institute for Biomedical Sciences at Georgia State and Shelly Wang and Dr. Richard W. Compans of Emory University School of Medicine.The study was funded by the National Institutes of Health's National Institute of Allergy and Infectious Diseases.
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Biotechnology
| 2,021 |
April 28, 2021
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https://www.sciencedaily.com/releases/2021/04/210428132944.htm
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Two compounds can make chocolate smell musty and moldy
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Chocolate is a beloved treat, but sometimes the cocoa beans that go into bars and other sweets have unpleasant flavors or scents, making the final products taste bad. Surprisingly, only a few compounds associated with these stinky odors are known. Now, researchers reporting in ACS'
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Cocoa beans, when fermented correctly, have a pleasant smell with sweet and floral notes. But they can have an off-putting scent when fermentation goes wrong, or when storage conditions aren't quite right and microorganisms grow on them. If these beans make their way into the manufacturing process, the final chocolate can smell unpleasant, leading to consumer complaints and recalls. So, sensory professionals smell fermented cocoa beans before they are roasted, detecting any unwanted musty, moldy, smoky or mushroom-like odors. Even with this testing in place, spoiled beans can evade human noses and ruin batches of chocolate, so a more objective assessment is needed for quality control. In previous studies, researchers used molecular techniques to identify the compounds that contribute to undesirable smoky flavors, but a similar method has not clarified other volatile scent compounds. So, Martin Steinhaus and colleagues wanted to determine the principal compounds that cause musty and moldy odors in tainted cocoa beans.The researchers identified 57 molecules that made up the scent profiles of both normal and musty/moldy smelling cocoa beans using gas chromatography in combination with olfactometry and mass spectrometry. Of these compounds, four had higher concentrations in off-smelling samples. Then, these four compounds were spiked into unscented cocoa butter, and the researchers conducted smell tests with 15-20 participants. By comparing the results of these tests with the molecular content of nine samples of unpleasant fermented cocoa beans and cocoa liquors, the team determined that (-)-geosmin -- associated with moldy and beetroot odors -- and 3-methyl-1
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Biotechnology
| 2,021 |
April 19, 2021
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https://www.sciencedaily.com/releases/2021/04/210419135731.htm
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DNA robots designed in minutes instead of days
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Someday, scientists believe, tiny DNA-based robots and other nanodevices will deliver medicine inside our bodies, detect the presence of deadly pathogens, and help manufacture increasingly smaller electronics.
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Researchers took a big step toward that future by developing a new tool that can design much more complex DNA robots and nanodevices than were ever possible before in a fraction of the time.In a paper published today (April 19, 2021) in the journal The software helps researchers design ways to take tiny strands of DNA and combine them into complex structures with parts like rotors and hinges that can move and complete a variety of tasks, including drug delivery.Researchers have been doing this for a number of years with slower tools with tedious manual steps, said Carlos Castro, co-author of the study and associate professor of mechanical and aerospace engineering at Ohio State."But now, nanodevices that may have taken us several days to design before now take us just a few minutes," Castro said.And now researchers can make much more complex -- and useful -- nanodevices."Previously, we could build devices with up to about six individual components and connect them with joints and hinges and try to make them execute complex motions," said study co-author Hai-Jun Su, professor of mechanical and aerospace engineering at Ohio State."With this software, it is not hard to make robots or other devices with upwards of 20 components that are much easier to control. It is a huge step in our ability to design nanodevices that can perform the complex actions that we want them to do."The software has a variety of advantages that will help scientists design better, more helpful nanodevices and -- researchers hope -- shorten the time before they are in everyday use.One advantage is that it allows researchers to carry out the entire design truly in 3D. Earlier design tools only allowed creation in 2D, forcing researchers to map their creations into 3D. That meant designers couldn't make their devices too complex.The software also allows designers to build DNA structures "bottom up" or "top down."In "bottom up" design, researchers take individual strands of DNA and decide how to organize them into the structure they want, which allows fine control over local device structure and properties.But they can also take a "top down" approach where they decide how their overall device needs to be shaped geometrically and then automate how the DNA strands are put together.Combining the two allows for increasing complexity of the overall geometry while maintaining precise control over individual component properties, Castro said.Another key element of the software is that it allows simulations of how designed DNA devices would move and operate in the real world."As you make these structures more complex, it is difficult to predict exactly what they are going to look like and how they are going to behave," Castro said."It is critical to be able to simulate how our devices will actually operate. Otherwise, we waste a lot of time."As a demonstration of the software's ability, co-author Anjelica Kucinic, a doctoral student in chemical and biomolecular engineering at Ohio State, led the researchers in making and characterizing many nanostructures designed by the software.Some of the devices they created included robot arms with claws that can pick up smaller items, and a hundred nanometer-sized structure that looks like an airplane (The "airplane" is 1000 times smaller than the width of a human hair).The ability to make more complex nanodevices means that they can do more useful things and even carry out multiple tasks with one device, Castro said.For example, it is one thing to have a DNA robot that, after injection into the bloodstream, can detect a certain pathogen."But a more complex device may not only detect that something bad is happening, but can also react by releasing a drug or capturing the pathogen," he said."We want to be able to design robots that respond in a particular way to a stimulus or move in a certain way."Castro said he expects that for the next few years, the MagicDNA software will be used at universities and other research labs. But its use could expand in the future."There is getting to be more and more commercial interest in DNA nanotechnology," he said. "I think in the next five to 10 years we will start seeing commercial applications of DNA nanodevices and we are optimistic that this software can help drive that."
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Biotechnology
| 2,021 |
April 7, 2021
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https://www.sciencedaily.com/releases/2021/04/210407093228.htm
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Eucalyptus trees can be genetically modified not to invade native ecosystems
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Eucalyptus, a pest-resistant evergreen valued for its hardy lumber and wellness-promoting oil, can be genetically modified not to reproduce sexually, a key step toward preventing the global tree plantation staple from invading native ecosystems.
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Oregon State University's Steve Strauss led an international collaboration that showed the CRISPR Cas9 gene editing technique could be used with nearly 100% efficiency to knock out LEAFY, the master gene behind flower formation."The flowers never developed to the point where ovules, pollen or fertile seeds were observed," Strauss said. "And there was no detectable negative effect on tree growth or form. A field study should be the next step to take a more careful look at stability of the vegetative and floral sterility traits, but with physical gene mutation we expect high reliability over the life of the trees."Findings were published in Strauss, Ph.D. student Estefania Elorriaga and research assistant Cathleen Ma teamed up with scientists at the University of Colorado, Beijing Forestry University and the University of Pretoria on the research. The greenhouse study involved a hybrid of two species, Eucalyptus grandis and E. urophylla, that is widely planted in the Southern Hemisphere; there are more than 700 species of eucalyptus, most of them native to Australia."Roughly 7% of the world's forests are plantations, and 25% of that plantation area contains nonnative species and hybrids," said Elorriaga, now a postdoctoral researcher at North Carolina State. "Eucalyptus is one of the most widely planted genera of forest trees, particularly the 5.7 million hectares of eucalyptus in Brazil, the 4.5 million hectares in China and 3.9 million hectares in India."Those plantings, the scientists note, can lead to undesirable mingling with native ecosystems. Thus eliminating those trees' ability to sexually reproduce without affecting other characteristics would be an effective way to greatly reduce the potential for invasive spreading in areas where that is considered an important ecological or economic problem."This was the first successful application of CRISPR to solve a commercial problem in forest trees," Elorriaga said. "Research with CRISPR in forest trees to modify different traits is ongoing in many laboratories around the world. Global warming is having large impacts on forests of all kinds, and gene editing may be an important new breeding tool to supplement conventional methods."Strauss points out that despite the promising findings, trees genetically modified as they were in this research could not legally be planted in Brazil, a nation with some of the largest economic value from eucalyptus tree farming."The trait could not be used there due to laws against modifying plant reproduction with recombinant DNA methods," he said. "It would also be disallowed for field research or commercial use under sustainable forest management certification in many parts of the world -- something scientists have come together to severely criticize in recent years."A little more than two years ago, Strauss was part of a coalition of forestry researchers to call for a review of what they see as overly restrictive policies regarding biotech research."Hopefully, studies like this one, that show how precise and safe the technology can be in modifying traits, and that help to promote ecological safety, will help to change regulations and certification rules," he said. "Happily, such discussions are well underway in many nations."
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Biotechnology
| 2,021 |
March 21, 2021
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https://www.sciencedaily.com/releases/2021/03/210321215434.htm
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Eating processed meat could increase dementia risk, researchers say
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Scientists from the University's Nutritional Epidemiology Group used data from 500,000 people, discovering that consuming a 25g serving of processed meat a day, the equivalent to one rasher of bacon, is associated with a 44% increased risk of developing the disease.
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But their findings also show eating some unprocessed red meat, such as beef, pork or veal, could be protective, as people who consumed 50g a day were 19% less likely to develop dementia. The researchers were exploring whether there is a link between consumption of meat and development of dementia, a health condition which affects 5%-8% of over 60s worldwide.Their results, titled Meat consumption and risk of incident dementia: cohort study of 493,888 UK Biobank participants, are published today in the Lead researcher Huifeng Zhang, a PhD student from Leeds' School of Food Science and Nutrition, said: "Worldwide, the prevalence of dementia is increasing and diet as a modifiable factor could play a role."Our research adds to the growing body of evidence linking processed meat consumption to increased risk of a range of non-transmissible diseases." The research was supervised by Professors Janet Cade and Laura Hardie, both at Leeds.The team studied data provided by UK Biobank, a database containing in-depth genetic and health information from half a million UK participants aged 40 to 69, to investigate associations between consuming different types of meat and risk of developing dementia. The data included how often participants consumed different kinds of meat, with six options from never to once or more daily, collected in 2006-2010 by the UK Biobank. The study did not specifically assess the impact of a vegetarian or vegan diet on dementia risk, but it included data from people who said they did not eat red meat. Among the participants, 2,896 cases of dementia emerged over an average of eight years of follow up. These people were generally older, more economically deprived, less educated, more likely to smoke, less physically active, more likely to have stroke history and family dementia history, and more likely to be carriers of a gene which is highly associated with dementia. More men than women were diagnosed with dementia in the study population. Some people were three to six times more likely to develop dementia due to well established genetic factors, but the findings suggest the risks from eating processed meat were the same whether or not a person was genetically predisposed to developing the disease. Those who consumed higher amounts of processed meat were more likely to be male, less educated, smokers, overweight or obese, had lower intakes of vegetables and fruits, and had higher intakes of energy, protein, and fat (including saturated fat). Meat consumption has previously been associated with dementia risk, but this is believed to be the first large-scale study of participants over time to examine a link between specific meat types and amounts, and the risk of developing the disease. There are around 50 million dementia cases globally, with around 10 million new cases diagnosed every year. Alzheimer's Disease makes up 50% to 70% of cases, and vascular dementia around 25%. Its development and progression are associated with both genetic and environmental factors, including diet and lifestyle. Ms Zhang said: "Further confirmation is needed, but the direction of effect is linked to current healthy eating guidelines suggesting lower intakes of unprocessed red meat could be beneficial for health."Professor Cade said: "Anything we can do to explore potential risk factors for dementia may help us to reduce rates of this debilitating condition. This analysis is a first step towards understanding whether what we eat could influence that risk."
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Biotechnology
| 2,021 |
March 10, 2021
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https://www.sciencedaily.com/releases/2021/03/210310132343.htm
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Study of mosquito protein could lead to treatments against life-threatening viruses
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The mosquito protein AEG12 strongly inhibits the family of viruses that cause yellow fever, dengue, West Nile, and Zika and weakly inhibits coronaviruses, according to scientists at the National Institutes of Health (NIH) and their collaborators. The researchers found that AEG12 works by destabilizing the viral envelope, breaking its protective covering. Although the protein does not affect viruses that do not have an envelope, such as those that cause pink eye and bladder infections, the findings could lead to therapeutics against viruses that affect millions of people around the world. The research was published online in
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Scientists at the National Institute of Environmental Health Sciences (NIEHS), part of NIH, used X-ray crystallography to solve the structure of AEG12. Senior author Geoffrey Mueller, Ph.D., head of the NIEHS Nuclear Magnetic Resonance Group, said at the molecular level, AEG12 rips out the lipids, or the fat-like portions of the membrane that hold the virus together."It is as if AEG12 is hungry for the lipids that are in the virus membrane, so it gets rid of some of the lipids it has and exchanges them for the ones it really prefers," Mueller said. "The protein has high affinity for viral lipids and steals them from the virus."As a result, Mueller says the AEG12 protein has great killing power over some viruses. While the researchers demonstrated that AEG12 was most effective against flaviviruses, the family of viruses to which Zika, West Nile, and others belong, it is possible AEG12 could be effective against SARS-CoV-2, the coronavirus that causes COVID-19. But, Mueller said it will take years of bioengineering to make AEG12 a viable therapy for COVID-19. Part of the problem is AEG12 also breaks opens red blood cells, so researchers will have to identify compounds that will make the protein target viruses only.Alexander Foo, Ph.D., an NIEHS visiting fellow and lead author of the paper, explained that mosquitoes produce AEG12 when they take a blood meal or become infected with flaviviruses. Like humans, mosquitoes mount a vigorous immune response against these viruses, with AEG12 bursting their viral covering. But, at the beginning of the project, Foo and his colleagues knew little about the function of AEG12."The prospect of studying a new protein is exciting, yet daunting," Foo said. "Thankfully, we had enough clues and access to a wide range of expertise at NIEHS to piece it together."Co-author and crystallography expert Lars Pedersen, Ph.D., is leader of the NIEHS Structure Function Group. He routinely uses information about a molecule's physical makeup in his work and encourages more scientists to consider using this data in their studies. He said, "Our research shows that understanding the structure of a protein can be important in figuring out what it does and how it could help treat disease."
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Biotechnology
| 2,021 |
March 1, 2021
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https://www.sciencedaily.com/releases/2021/03/210301095936.htm
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Protein kinases significantly contribute to the immunodeficiency in HIV patients
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HIV infections are treated with antiviral drugs which effectively prevent the disease from developing. While pharmacological HIV therapy has advanced considerably, the virus cannot be entirely eliminated from the body with currently available drugs.
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However, in roughly one-fifth of HIV patients the immune system does not recover as expected: the quantity of CD4 T cells, reflecting the status of the immune system, remains low even when the quantity of HI viruses in blood is suppressed to very low levels or below the measurement threshold. In such patients, indications of chronic immune activation, which erodes the immune system, can be detected.In cooperation with the University of Erlangen-Nuremberg in Germany, researchers at the University of Helsinki have already shown that the Nef protein, a central factor associated with the HI virus, can continue low-level production in the patient's tissues for a long time even after viral multiplication is successfully suppressed. Important to this immunity-eroding activity are extracellular vesicles generated by Nef, circulating in blood and promoting chronic immune activation.In a new study, Professor Kalle Saksela's research group has discovered an intracellular mechanism through which the chain of events associated with immune activation is initiated.The study was published in the "The new findings demonstrate that the Nef protein kicks off this harmful chain of events via cellular signalling: it activates protein kinases of the Src family, which leads to the activation of Raf and MAPK protein kinases. As these two protein kinases are activated, the production of extracellular vesicles, mediated by them, begins," Saksela explains.Pharmaceutical agents that inhibit Src, Raf and MAPK protein kinases are already in clinical use, and the researchers at the University of Helsinki investigated their utility as well.Studying the drugs in tissue cultures, they observed that it was possible to entirely prevent the production of inflammatory extracellular vesicles caused by the Nef protein using the same drug levels as in the current clinical use of protein kinase inhibitors."Our findings make it possible to explore novel therapies without delay in patients whose immunodeficiency is not reversed to a sufficient degree with current antiretroviral therapies. The repurposing of kinase inhibitors for treating HIV infection appears to be a very promising way of solving this significant medical challenge," Professor Saksela states.In recent years, roughly 150 new HIV infections have been diagnosed in Finland annually. Throughout the 2000s, the number of new infections per year has remained under 200. In 2018 approximately 38 million people were estimated to be HIV positive, most of them in Africa.
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Biotechnology
| 2,021 |
December 29, 2020
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https://www.sciencedaily.com/releases/2020/12/201229104510.htm
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Sugars influence cell-to-surface adhesion
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How can cells adhere to surfaces and move on them? This is a question which was investigated by an international team of researchers headed by Prof. Michael Hippler from the University of Münster and Prof. Kaiyao Huang from the Institute of Hydrobiology (Chinese Academy of Sciences, Wuhan, China). The researchers used the green alga Chlamydomonas reinhardtii as their model organism. They manipulated the alga by altering the sugar modifications in proteins on the cell surface. As a result, they were able to alter the cellular surface adhesion, also known as adhesion force. The results have now been published in the open access scientific journal
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In order to move, the green alga has two thread-like flagella on its cell surface. The alga actually uses these flagella for swimming, but it can also use them to adhere to surfaces and glide along them. The researchers now wanted to find out how movement and adhesion on the part of the alga can be manipulated. "We discovered that proteins on cell surfaces that are involved in this process are modified by certain sugars. If these sugar chains on the proteins are altered, this enables their properties to be altered," explains Michael Hippler from the Institute of the Biology and Biotechnology of Plants at Münster University. Experts then describe such proteins as being N-glycosylated -- a modification in which carbohydrates are docked onto amino groups. Alterations to these sugar modifications by genetically manipulating the algae showed that the adhesion force of the algae and, as a result, any adhesion to surfaces were reduced. At the same time, there was no change in the cells gliding on the surface. The much-reduced force with which the mutants adhere to surfaces is therefore still sufficient, under laboratory conditions, to enable gliding to take place.In order to study these processes, the researchers first used so-called insertional mutagenesis and the CRISPR/Cas9 method to deactivate genes which encode enzymes relevant to the N-glycosylation process. "The next step was to analyse the sugar modifications of these genetically altered algae strains using mass spectrometry methods," says Michael Hippler, explaining the team's approach. In order to visualise the cell-gliding, the researchers used a special method of optical microscopy -- total internal reflection fluorescence microscopy (TIRF). This method is frequently used to carry out examinations of structures which are located very close to a surface. For this purpose, a fluorescent protein was expressed in the flagella of the algae in order to make the flagella and the cell-gliding visible.In order to measure how much force was used in adhering the individual cells to the surface, atomic force microscopy was used and micropipette adhesion measurements were undertaken in collaboration with groups at the University of Liverpool (UK) and the Max Planck Institute of Dynamics and Self-Organization in Göttingen. "This enabled us to verify that adhesion forces in the nanometre range are reduced by altering the protein sugar modifications," adds Kaiyao Huang.The two flagella on the green alga resemble for example not only the flagella of sperm but also other movable flagella. These are usually called 'cilia' and are also found in the human body -- for example in the respiratory tracts. "If we transfer our findings to human cells, sugar-modified proteins could be used to change the interaction of sperm or cilia with all sorts of surfaces," say Kaiyao Huang and Michael Hippler.
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Biotechnology
| 2,020 |
December 29, 2020
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https://www.sciencedaily.com/releases/2020/12/201229080253.htm
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Protein twist and squeeze confers cancer drug resistance
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In 1986, cellular biochemist Kazumitsu Ueda, currently at Kyoto University's Institute for Integrated Cell-Material Sciences (iCeMS), discovered that a protein called ABCB1 could transport multiple chemotherapeutics out of some cancer cells, making them resistant to treatment. How it did this has remained a mystery for the past 35 years. Now, his team has published a review in the journal
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ABC transporter proteins are very similar across species and have various transportation roles: importing nutrients into cells, exporting toxic compounds outside them, and regulating lipid concentrations within cell membranes.ABCB1 is one of these proteins, and is responsible for exporting toxic compounds out of the cell in vital organs such as the brain, testes, and placenta. Sometimes, though, it can also export chemotherapeutic drugs from cancer cells, making them resistant to treatment. The protein lies across the cell membrane, with one end reaching into the cell and the other poking out into the surrounding space. Even though scientists have known its roles and structure for years, exactly how it functions has been unclear.Ueda and his team crystalized the ABCB1 protein before and after it exported a compound. They then conducted X-ray tests to determine the differences between the two structures. They also conducted analyses using ABCB1 fused with fluorescent proteins to monitor the conformational changes during transport.They found that compounds destined for export access ABCB1's cavity through a gate in the part of the protein lying inside of the cell membrane. The compound rests at the top of the cavity, where it attaches to molecules, triggering a structural change in the protein. This change requires energy, which is derived from the energy-carrying molecule adenosine triphosphate (ATP). When magnesium ions bind to ATP, the part of ABCB1 inside the cell packs tightly in on itself and tilts, causing its cavity to shrink and then close. This opens the protein's exit gate. ATP is also involved in making ABCB1 progressively rigid from its bottom to its top, leading to a twist and squeeze motion that expels the compound into the extracellular space."This mechanism is distinct from those of other transporter proteins," says Ueda. "We expect our work will facilitate the study of other ABC proteins, such as those involved in cholesterol homeostasis."
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Biotechnology
| 2,020 |
December 28, 2020
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https://www.sciencedaily.com/releases/2020/12/201228095424.htm
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High-speed atomic force microscopy takes on intrinsically disordered proteins
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Our understanding of biological proteins does not always correlate with how common or important they are. Half of all proteins, molecules that play an integral role in cell processes, are intrinsically disordered, which means many of the standard techniques for probing biomolecules don't work on them. Now researchers at Kanazawa University in Japan have shown that their home-grown high-speed atomic force microscopy technology can provide information not just on the structures of these proteins but also their dynamics.
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Understanding how a protein is put together provides valuable clues to its functions. The development of protein crystallography in the 1930s and 1950s brought several protein structures into view for the first time, but it gradually became apparent that a large fraction of proteins lack a single set structure making them intractable to xray crystallography. As they are too thin for electron microscopy, the only viable alternatives for many of these intrinsically disorderd proteins (IDPs) are nuclear magnetic resonance imaging and small angle xray scattering. Data collected from these techniques are averaged over ensembles and so give no clear indication of individual protein conformations or how often they occur. Atomic force microscopy on the other hand is capable of nanoscale resolution biological imaging at high-speed, so it can capture dynamics as well as protein structures.In this latest work researchers at Kanazawa University alongside collaborators in Japan, France and Italy applied the technique to the study of several IDPs and identified parameters defining the shape, size and chain length of protein regions, as well as a power law relating the protein size to the protein length, and a quantitative description of the effect of the mica surface on protein dimensions. The dynamics of the protein conformations captured thanks to the high-speed capabilities of the technique revealed globules that appear and disappear, and transformations between fully unstructured and loosely folded conformations in segments up to 160 amino acids long.Studies of the measles virus nucleoprotein in particular helped identify not just the shape and dimensions but also characteristics of the order-disorder transitions in the region responsible for molecular recognition, which allows viruses to identify host factors so that they can reproduce. They could also determine larger scale structures of the virus's phosphoprotein that are not accessible to nuclear magnetic resonance (which can only give an indication of distances between amino acides separated by less than 2 nm). The researchers suggest that the formation of certain compact shapes observed may explain the resistance to proteolysis -- protein breakdown.In their report of the work, the researchers highlight that as well as a powerful tool in its own right, "When all molecular features revealed by HS-AFM are combined with the folded local structure given by NMR, the combined information allows a quantitative delineation of the structural and dynamic characters of IDPs, in a more realistic manner compared to the pictures depicted individually, as demonstrated for PNT [measles virus phosphoprotein]."Atomic force microscopy was developed in the 1980s and brought the atomic scale resolution achieved by scanning tunnelling microscopy (which won the 1986 Nobel Prize for Physics) to non-conducting samples. It works using a tiny cantilever with a nanoscale tip at the end, which either feels the surface much like a vinyl record needle or taps it. Whether by adjusting the tip height or the resonant frequency of the tapping, the interactions between tip and surface provide a signal that can be used to generate an image.While AFM images brought huge benefits to biological research, these studies were able to move up a gear again when Toshio Ando and his team at Kanazawa University reported an atomic force microscope that operated at high speed. Atomic scale resolution images became movies bringing not just structures but also dynamics within grasp. Previous work on ordered proteins, which are reasonably well understood, as well as the IDP facilitates chromatin transcription (FACT) protein, has established that the technique can be used to image these biomolecules without effects from contact between tip and sample distorting the data.The arrival of xray crystallography gave researchers a clear view of vast numbers of biomolecule structures for the first time. But with the hundreds of thousands of biomolecule structures analysed using protein crystallography since the technique first came into use in the 1930s and 1950s, a mounting body of evidence began to build that not all proteins have a single set structure. The observations ran counter to the prevailing paradigm of protein function determined by a fixed structure.Over the past ten to twenty years the ubiquity of these intrinsically disorderd proteins and their importance in cell functions from signalling to the regulation of transcription and subsequent translation has become widely recognized. In the current work the researchers study IDPs including polyglutamine tract binding protein-1 (PQBP-1, involved in different processes, such as pre-mRNA splicing, transcription regulation, innate immunity and neuron development), autophagy proteins (which are invovolved in removing dysfunctional cell components) containing intrinsically disordered regions (IDRs) and the measles virus nucleoprotein.
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Biotechnology
| 2,020 |
December 28, 2020
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https://www.sciencedaily.com/releases/2020/12/201228095422.htm
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Chemists develop a new drug discovery strategy for 'undruggable' drug targets
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A research team led by Dr Xiaoyu LI from the Research Division for Chemistry, Faculty of Science, in collaboration with Professor Yizhou LI from School of Pharmaceutical Sciences, Chongqing University and Professor Yan CAO from School of Pharmacy, Second Military Medical University in Shanghai has developed a new drug discovery method targeting membrane proteins on live cells.
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Membrane proteins play important roles in biology, and many of them are high-value targets that are being intensively pursued in the pharmaceutical industry. The method developed by Dr Li's team provides an efficient way to discover novel ligands and inhibitors against membrane proteins, which remain largely intractable to traditional approaches. The development of the methodology and its applications are now published in Membrane proteins on the cell surface perform a myriad of biological functions that are vital to the survival of cells and organisms. Not surprisingly, numerous human diseases are associated with aberrant membrane protein functions. Indeed, membrane proteins account for over 60% of the targets of all FDA-approved small-molecule drugs. The G-protein coupled receptor (GPCR) superfamily alone, as the largest class of cell-surface receptors, are the targets of ~34% of all clinical drugs. However, despite the significance, drug discovery against membrane proteins is notoriously challenging, mainly due to the special property of their natural habitat: the cell membrane. Moreover, membrane proteins are also difficult to study in an isolated form, as they tend to lose essential cellular feature and may be deactivated. In fact, membrane proteins have long been considered as a type of "undruggable" targets in the pharmaceutical industry.In recent years, DNA-encoded chemical library (DEL) has emerged and become a powerful drug screening technology. To simplify, we can use a book library as an example. In a library, each book is indexed with a catalogue number and spatially encoded with a specific location on a bookshelf. Analogously, in a DEL, each chemical compound is attached with a unique DNA tag, which serves as the "catalogue number" recording the structural information of the compound. With DNA encoding, all library compounds can be mixed and screened against the target simultaneously to discover the ones that can modulate the biological functions of the target, e.g. inhibiting the proteins that are aberrantly active in malignant cancers. DELs can contain astonishingly large numbers of test compounds (billions or even trillions), and DEL screening can be conducted in just a few hours in a regular chemistry lab. Today, DEL has been widely adopted by nearly all major pharmaceutical industry worldwide. However, DEL also had encountered significant difficulties in interrogate membrane proteins on live cells.There are two hurdles that the team has overcome to enable the application of DEL on live cells. First, cell surface is not a smooth convex shape like a balloon; it is extremely complex with hundreds of different biomolecules with a rugged topology; thus, locating the desired target on the cells surface is like finding a single tree in a thick tropical forest. The team has overcome this "target specificity" problem by using a method they previously developed: DNA-programmed affinity labelling (DPAL). This method utilises a DNA-based probe system that can specifically deliver a DNA tag to the desired protein on live cells, and the DNA tag serves as a beacon to direct target-specific DEL screening. In other words, the team first installed a "tracker" on the target to achieve screening specificity.The second challenge is target abundance. Typically, membrane proteins exist in nanomolar to low micromolar concentration, which is far below the high micromolar concentration needed to capture the tiny fraction of binders among billions of non-binders in a library. To solve this problem, the team employed a novel strategy by using complementary sequences in the DNA tag on the target protein and the actual library, so that the library can hybridise close to the target, thereby "boosting" the effective concentration of the target protein. In other words, the "tracker" can not only help the library locate the target, but also create an attractive force to concentrate the library around the target, not being distracted by the non-binding population.In the publication, the team reports their detailed methodology development, and they also demonstrate the generality and performance of this method by screening a 30.42-million-compound library against folate receptor (FR), carbonic anhydrase 12 (CA-12), and epidermal growth factor receptor (EGFR) on live cells, all are important targets in anti-cancer drug discovery. This approach is expected to broadly applicable to many membrane proteins. For example, classical drug targets, such as GPCRs and ion channels, may be revisited in a live cell setting to identify new drug discovery opportunities by harnessing the power of DEL."We expect to the utility of this method is not limited to drug discovery, but also in academic research to explore challenging biological systems, such as oligomeric membrane protein complexes and cell-cell communications," said Dr Xiaoyu Li.Co-corresponding author Professor Yizhou Li from Chongqing University said: "This method has the potential to facilitate drug discovery for membrane proteins with the power of large and complex chemical diversity from DNA-encoded chemical libraries." Co-corresponding author Professor Yan Cao from Second Military Medical University in Shanghai added: "This technology is an effective tool for characterising ligand-target interaction; it will cast new light on the development of high throughput screening methods, and thus facilitate the fishing of ligands targeting membrane proteins."
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Biotechnology
| 2,020 |
December 28, 2020
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https://www.sciencedaily.com/releases/2020/12/201228095419.htm
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Switching DNA functions on and off by means of light
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Biochemists have developed a new strategy for controlling the biological functions of DNA (deoxyribonucleic acid) by means of light and therefore provide a tool to investigate processes which take place in cells.
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DNA (deoxyribonucleic acid) is the basis of life on earth. The function of DNA is to store all the genetic information, which an organism needs to develop, function and reproduce. It is essentially a biological instruction manual found in every cell. Biochemists at the University of Münster have now developed a strategy for controlling the biological functions of DNA with the aid of light. This enables researchers to better understand and control the different processes which take place in the cell -- for example epigenetics, the key chemical change and regulatory lever in DNA. The results have been published in the journal The cell's functions depend on special molecules, the enzymes. Enzymes are proteins, which carry out chemical reactions in the cell. They help to synthesize metabolic products, make copies of the DNA molecules, convert energy for the cell's activities, change DNA epigenetically and break down certain molecules. A team of researchers headed by Prof. Andrea Rentmeister from the Institute of Biochemistry at the University of Münster used a so-called enzymatic cascade reaction in order to understand and track these functions better. This sequence of successive reaction steps involving different enzymesmakes it possible to transfer so-called photocaging groups -- chemical groups, which can be removed by means of irradiation with light -- to DNA. Previously, studies had shown that only small residues (small modifications such as methyl groups) could be transferred very selectively to DNA, RNA (ribonucleic acid) or proteins. "As a result of our work, it is now possible to transfer larger residues or modifications such as the photocaging groups just mentioned," explains Nils Klöcker, one of the lead authors of the study and a PhD student at the Institute of Biochemistry. Working together with structural biologist Prof. Daniel Kümmel, who also works at the Institute of Biochemistry, it was also possible to explain the basis for the changed activity at a molecular level.Using so-called protein engineering -- a method for which a Nobel prize was awarded in 2018 -- the Münster researchers engineered one enzyme in the cascade, making it possible to switch DNA functions on and off by means of light. With the aid of protein design, it was possible to expand the substrate spectrum of enzymes -- in this case, methionine adenosyltransferases (MATs). In their work, the researchers examined two MATs. The modifications carried out offer a starting point for developing other MATs with an expanded substrate spectrum. "Combining these MATs with other enzymes has potential for future cellular applications. This is an important step for implementing in-situ generated, non-natural substances for other enzymes in epigenetic studies," says Andrea Rentmeister.
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Biotechnology
| 2,020 |
December 28, 2020
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https://www.sciencedaily.com/releases/2020/12/201228095428.htm
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Discovery boosts theory that life on Earth arose from RNA-DNA mix
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Chemists at Scripps Research have made a discovery that supports a surprising new view of how life originated on our planet.
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In a study published in the chemistry journal The finding is the latest in a series of discoveries, over the past several years, pointing to the possibility that DNA and its close chemical cousin RNA arose together as products of similar chemical reactions, and that the first self-replicating molecules -- the first life forms on Earth -- were mixes of the two.The discovery may also lead to new practical applications in chemistry and biology, but its main significance is that it addresses the age-old question of how life on Earth first arose. In particular, it paves the way for more extensive studies of how self-replicating DNA-RNA mixes could have evolved and spread on the primordial Earth and ultimately seeded the more mature biology of modern organisms."This finding is an important step toward the development of a detailed chemical model of how the first life forms originated on Earth," says study senior author Ramanarayanan Krishnamurthy, PhD, associate professor of chemistry at Scripps Research.The finding also nudges the field of origin-of-life chemistry away from the hypothesis that has dominated it in recent decades: The "RNA World" hypothesis posits that the first replicators were RNA-based, and that DNA arose only later as a product of RNA life forms.Krishnamurthy and others have doubted the RNA World hypothesis in part because RNA molecules may simply have been too "sticky" to serve as the first self-replicators.A strand of RNA can attract other individual RNA building blocks, which stick to it to form a sort of mirror-image strand -- each building block in the new strand binding to its complementary building block on the original, "template" strand. If the new strand can detach from the template strand, and, by the same process, start templating other new strands, then it has achieved the feat of self-replication that underlies life.But while RNA strands may be good at templating complementary strands, they are not so good at separating from these strands. Modern organisms make enzymes that can force twinned strands of RNA -- or DNA -- to go their separate ways, thus enabling replication, but it is unclear how this could have been done in a world where enzymes didn't yet exist.Krishnamurthy and colleagues have shown in recent studies that "chimeric" molecular strands that are part DNA and part RNA may have been able to get around this problem, because they can template complementary strands in a less-sticky way that permits them to separate relatively easily.The chemists also have shown in widely cited papers in the past few years that the simple ribonucleoside and deoxynucleoside building blocks, of RNA and DNA respectively, could have arisen under very similar chemical conditions on the early Earth.Moreover, in 2017 they reported that the organic compound DAP could have played the crucial role of modifying ribonucleosides and stringing them together into the first RNA strands. The new study shows that DAP under similar conditions could have done the same for DNA."We found, to our surprise, that using DAP to react with deoxynucleosides works better when the deoxynucleosides are not all the same but are instead mixes of different DNA 'letters' such as A and T, or G and C, like real DNA," says first author Eddy Jiménez, PhD, a postdoctoral research associate in the Krishnamurthy lab."Now that we understand better how a primordial chemistry could have made the first RNAs and DNAs, we can start using it on mixes of ribonucleoside and deoxynucleoside building blocks to see what chimeric molecules are formed -- and whether they can self-replicate and evolve," Krishnamurthy says.He notes that the work may also have broad practical applications. The artificial synthesis of DNA and RNA -- for example in the "PCR" technique that underlies COVID-19 tests -- amounts to a vast global business, but depends on enzymes that are relatively fragile and thus have many limitations. Robust, enzyme-free chemical methods for making DNA and RNA may end up being more attractive in many contexts, Krishnamurthy says.
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Biotechnology
| 2,020 |
December 24, 2020
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https://www.sciencedaily.com/releases/2020/12/201224113114.htm
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Protein tells developing cells to stick together
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Tohoku University scientists have, for the first time, provided experimental evidence that cell stickiness helps them stay sorted within correct compartments during development. How tightly cells clump together, known as cell adhesion, appears to be enabled by a protein better known for its role in the immune system. The findings were detailed in the journal
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Scientists have long observed that not-yet-specialized cells move in a way that ensures that cell groups destined for a specific tissue stay together. In 1964, American biologist Malcolm Steinberg proposed that cells with similar adhesiveness move to come in contact with each other to minimize energy use, producing a thermodynamically stable structure. This is known as the differential adhesion hypothesis."Many other theoretical works have emphasized the importance of differences in cell-to-cell adhesion for separating cell populations and maintaining the boundaries between them, but this had not yet been demonstrated in living animal epithelial tissues," says Erina Kuranaga of Tohoku University's Laboratory for Histogenetic Dynamics, who led the investigations. "Our study showed, for the first time, that cell sorting is regulated by changes in adhesion."Kuranaga and her team conducted experiments in fruit fly pupae, finding that a gene, called Toll-1, played a major role in this adhesion process.As fruit flies develop from the immature larval stage into the mature adult, epithelial tissue-forming cells, called histoblasts, cluster together into several 'nests' in the abdomen. Each nest contains an anterior and a posterior compartment. Histoblasts are destined to replace larval cells to form the adult epidermis, the outermost layer that covers the flies. The cells in each compartment form discrete cell populations, so they need to stick together, with a distinct boundary forming between them.Using fluorescent tags, Kuranaga and her team observed the Toll-1 protein is expressed mainly in the posterior compartment. Its fluorescence also showed a sharp boundary between the two compartments.Further investigations showed Toll-1 performs the function of an adhesion molecule, encouraging similar cells to stick together. This process keeps the boundary between the two compartments straight, correcting distortions that arise as the cells divide to increase the number.Interestingly, Toll proteins are best known for recognizing invading pathogens, and little is known about their work beyond the immune system. "Our work improves understanding of the non-immune roles of Toll proteins," says Kuranaga. She and her team next plan to study the function of other Toll genes in fruit fly epithelial cells.
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Biotechnology
| 2,020 |
December 23, 2020
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https://www.sciencedaily.com/releases/2020/12/201223125759.htm
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New class of antibiotics active against a wide range of bacteria
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Wistar Institute scientists have discovered a new class of compounds that uniquely combine direct antibiotic killing of pan drug-resistant bacterial pathogens with a simultaneous rapid immune response for combatting antimicrobial resistance (AMR). These finding were published today in
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The World Health Organization (WHO) has declared AMR as one of the top 10 global public health threats against humanity. It is estimated that by 2050, antibiotic-resistant infections could claim 10 million lives each year and impose a cumulative $100 trillion burden on the global economy. The list of bacteria that are becoming resistant to treatment with all available antibiotic options is growing and few new drugs are in the pipeline, creating a pressing need for new classes of antibiotics to prevent public health crises."We took a creative, double-pronged strategy to develop new molecules that can kill difficult-to-treat infections while enhancing the natural host immune response," said Farokh Dotiwala, M.B.B.S., Ph.D., assistant professor in the Vaccine & Immunotherapy Center and lead author of the effort to identify a new generation of antimicrobials named dual-acting immuno-antibiotics (DAIAs).Existing antibiotics target essential bacterial functions, including nucleic acid and protein synthesis, building of the cell membrane, and metabolic pathways. However, bacteria can acquire drug resistance by mutating the bacterial target the antibiotic is directed against, inactivating the drugs or pumping them out."We reasoned that harnessing the immune system to simultaneously attack bacteria on two different fronts makes it hard for them to develop resistance," said Dotiwala.He and colleagues focused on a metabolic pathway that is essential for most bacteria but absent in humans, making it an ideal target for antibiotic development. This pathway, called methyl-D-erythritol phosphate (MEP) or non-mevalonate pathway, is responsible for biosynthesis of isoprenoids -- molecules required for cell survival in most pathogenic bacteria. The lab targeted the IspH enzyme, an essential enzyme in isoprenoid biosynthesis, as a way to block this pathway and kill the microbes. Given the broad presence of IspH in the bacterial world, this approach may target a wide range of bacteria.Researchers used computer modeling to screen several million commercially available compounds for their ability to bind with the enzyme, and selected the most potent ones that inhibited IspH function as starting points for drug discovery.Since previously available IspH inhibitors could not penetrate the bacterial cell wall, Dotiwala collaborated with Wistar's medicinal chemist Joseph Salvino, Ph.D., professor in The Wistar Institute Cancer Center and a co-senior author on the study, to identify and synthesize novel IspH inhibitor molecules that were able to get inside the bacteria.The team demonstrated that the IspH inhibitors stimulated the immune system with more potent bacterial killing activity and specificity than current best-in-class antibiotics when tested in vitro on clinical isolates of antibiotic-resistant bacteria, including a wide range of pathogenic gram negative and gram positive bacteria. In preclinical models of gram negative bacterial infection, the bactericidal effects of the IspH inhibitors outperformed traditional pan antibiotics. All compounds tested were shown to be nontoxic to human cells."Immune activation represents the second line of attack of the DAIA strategy," said Kumar Singh, Ph.D., Dotiwala lab postdoctoral fellow and first author of the study."We believe this innovative DAIA strategy may represent a potential landmark in the world's fight against AMR, creating a synergy between the direct killing ability of antibiotics and the natural power of the immune system," echoed Dotiwala.Co-authors: Rishabh Sharma, Poli Adi Narayana Reddy, Prashanthi Vonteddu, Madeline Good, Anjana Sundarrajan, Hyeree Choi, Kar Muthumani, Andrew Kossenkov, Aaron R. Goldman, Hsin-Yao Tang, Joel Cassel, Maureen E. Murphy, Rajasekharan Somasundaram, and Meenhard Herlyn from Wistar; and Maxim Totrov from Molsoft LLC.Work supported by: The G. Harold and Leila Y. Mathers Foundation, funds from the Commonwealth Universal Research Enhancement (CURE) Program and the Wistar Science Discovery Fund; The Pew Charitable Trusts supported Farokh Dotiwala with a Wistar Institute recruitment grant; Additional support was provided by the Adelson Medical Research Foundation and the Department of Defense. Support for The Wistar Institute facilities was provided by Cancer Center Support Grant P30 CA010815 and National Institutes of Health instrument grant S10 OD023586.
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Biotechnology
| 2,020 |
December 23, 2020
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https://www.sciencedaily.com/releases/2020/12/201223125747.htm
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The ABCs of species evolution
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A transporter protein that regulates cell membrane cholesterol likely played an important role in vertebrate evolution, according to a review published by iCeMS researchers in the journal
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Almost four decades of research have led scientists at Japan's Institute for Integrated Cell-Material Sciences (iCeMS) to propose that a family of transporter proteins has played an important role in species evolution. One protein in particular, called ABCA1, was likely crucial for vertebrate evolution by helping regulate when signals involved in cell proliferation, differentiation and migration enter a cell. This process was necessary for vertebrates to develop into more complex organisms with sophisticated body structures.The ATP-binding cassette proteins (ABC) are very similar across species, including in bacteria, plants and animals. There are different types of ABC proteins with different transportation roles, importing nutrients into cells, exporting toxic compounds outside them, and regulating lipid concentrations within cell membranes.iCeMS cellular biochemist Kazumitsu Ueda has studied human ABC proteins for 35 years, ever since he and his colleagues identified the first eukaryote ABC protein gene."We believe ABC proteins must have played important roles in evolution," Ueda says. "By transporting lipids, they enabled plants and animals to thrive on land by protecting them from water loss and pathogen infection. They are also assumed to have accelerated vertebrate evolution by allowing cholesterol to function as an intra-membrane signalling molecule."Organisms that existed early in Earth's history were probably formed of DNA and proteins surrounded by a leaky lipid membrane. As the organisms evolved, their membranes were fortified to protect them from the external environment. But this meant only organisms that evolved special ABC transporters capable of carrying nutrients across the membrane survived. The ABC proteins also played important roles in generating an outer membrane that protected cells from external stresses and in removing harmful substances from inside.Recently, Ueda and his team studied the roles of ABCA1, gaining deeper insight into how it regulates cholesterol. Specifically, they found that ABCA1 exports cellular phospholipids and cholesterol outside the cell for generating high-density lipoproteins, popularly called good cholesterol.They also found that ABCA1 constantly flops cholesterol from the cell membrane's inner leaflet to its outer leaflet, maintaining a lower concentration on the inner side. This flopping is temporarily suppressed when the cell is exposed to an external stimulus, like growth hormone. The resultant accumulation of cholesterol in the inner leaflet triggers the recruitment of proteins to the membrane and modulates the signal transduction. Ueda and his team suggest that ABCA1 allowed vertebrates to evolve complicated biological processes and sophisticated bodies."ABCA1 is very unique and its functions surprised us," says Ueda. "Cholesterol's role was thought to focus mainly on physically strengthening the cell membrane and reducing its permeability to ions. Our research suggests it played a more important role in vertebrates, accelerating their evolution."
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Biotechnology
| 2,020 |
December 23, 2020
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https://www.sciencedaily.com/releases/2020/12/201223125728.htm
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New mammal reference genome helps ID genetic variants for human health
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The rhesus macaque is the most widely studied nonhuman primate in biomedical research. A genome sequencing project for this species, led by researchers at Baylor College of Medicine, the University of Missouri and the University of Washington, has created a new framework for study of this important primate. Research published in the journal
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"This is a major step forward in the amount of information we have about genetic variation in the rhesus macaque," said Dr. Jeffrey Rogers, associate professor at the Human Genome Sequencing Center and Department of Molecular and Human Genetics at Baylor and one of the corresponding authors of the study. "We have actually identified thousands of new mutations in the population of research animals. Now colleagues all over the country who are investigating various aspects of health and disease using rhesus macaques can begin to make use of that information."Dr. Wesley C. Warren at the University of Missouri and Dr. Evan Eichler at the University of Washington, both corresponding authors of the study, used a combination of several advanced technologies to substantially improve the rhesus macaque reference genome assembly first created in 2007. The new reference genome published today provides a more complete and accurate picture of the rhesus macaque DNA sequence. This improvement can support more sophisticated and more detailed analyses of fundamental questions in molecular genetics, cell biology and physiology."When we coupled this higher quality genome reference with a broader sequencing of expressed genes, our team discovered gene structures unique to macaque as well as specific repeat sequences undergoing deletions that suggest evolutionary competition to suppress these elements from expanding continues today," said Warren, professor at the University of Missouri's Bond Life Sciences Center.Researchers at Baylor's Human Genome Sequencing Center sequenced the genomes of 853 rhesus macaque from research institutions around the country and compared them to the new reference genome. The genome analysis showed that rhesus macaque have more genetic variants per individual than humans. Among the millions of genetic variants identified, researchers found several damaging mutations in genes known to cause genetic disorders in humans, including autism, inherited blindness and several others."We can find naturally occurring models of genetic disorders by surveying the rhesus macaque population," Rogers said. "We will find animals that naturally carry interesting and useful genetic mutations that can help us understand genetic variation and susceptibility to disease in humans. Rhesus macaques are also widely studied by primatologists and evolutionary biologists, so this new reference genome will also provide new insight into the evolution of the nonhuman primate and human genomes."
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Biotechnology
| 2,020 |
December 22, 2020
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https://www.sciencedaily.com/releases/2020/12/201222132115.htm
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A powerful computational tool for efficient analysis of cell division 4D image data
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A joint research team co-led by City University of Hong Kong (CityU) has developed a novel computational tool that can reconstruct and visualise three-dimensional (3D) shapes and temporal changes of cells, speeding up the analysing process from hundreds of hours by hand to a few hours by the computer. Revolutionising the way biologists analyse image data, this tool can advance further studies in developmental and cell biology, such as the growth of cancer cells.
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The interdisciplinary study was co-led by Professor Yan Hong, Chair Professor of Computer Engineering and Wong Chung Hong Professor of Data Engineering in the Department of Electrical Engineering (EE) at CityU, together with biologists from Hong Kong Baptist University (HKBU) and Peking University. Their findings have been published in the scientific journal The tool developed by the team is called "CShaper." "It is a powerful computational tool that can segment and analyse cell images systematically at the single-cell level, which is much needed for the study of cell division, and cell and gene functions," described Professor Yan.Biologists have been investigating how animals grow from a single cell, a fertilised egg, into organs and the whole body through countless cell divisions. In particular, they want to know the gene functions, such as the specific genes involved in cell divisions for forming different organs, or what causes the abnormal cell divisions leading to tumourous growth.A way to find the answer is to use the gene knockout technique. With all genes present, researchers first obtain cell images and the lineage tree. Then they "knock out" (remove) a gene from the DNA sequence, and compare the two lineage trees to analyse changes in the cells and infer gene functions. Then they repeat the experiment with other genes being knocked out.In the study, the collaborating biologist team used Caenorhabditis elegans (C. elegans) embryos to produce terabytes of data for Professor Yan's team to perform computational analysis. C. elegans is a type of worm which share many essential biological characteristics with humans and provide a valuable model for studying the tumour growth process in humans."With estimated 20,000 genes in C. elegans, it means nearly 20,000 experiments would be needed if knocking out one gene at a time. And there would be an enormous amount of data. So it is essential to use an automated image analysis system. And this drives us to develop a more efficient one," he said.Cell images are usually obtained by laser beam scanning. The existing image analysis systems can only detect cell nucleus well with a poor cell membrane image quality, hampering reconstruction of cell shapes. Also, there is a lack of reliable algorithm for the segmentation of time-lapsed 3D images (i.e. 4D images) of cell division. Image segmentation is a critical process in computer vision that involves dividing a visual input into segments to simplify image analysis. But researchers have to spend hundreds of hours labelling many cell images manually.The breakthrough in CShaper is that it can detect cell membranes, build up cell shapes in 3D, and more importantly, automatically segment the cell images at the cell level. "Using CShaper, biologists can decipher the contents of these images within a few hours. It can characterise cell shapes and surface structures, and provide 3D views of cells at different time points," said To achieve this, the deep-learning-based model DMapNet developed by the team plays a key role in the CShaper system. "By learning to capture multiple discrete distances between image pixels, DMapNet extracts the membrane contour while considering shape information, rather than just intensity features. Therefore CShaper achieved a 95.95% accuracy of identifying the cells, which outperformed other methods substantially," he explained.With CShaper, the team generated a time-lapse 3D atlas of cell morphology for the C. elegans embryo from the 4- to 350-cell stages, including cell shape, volume, surface area, migration, nucleus position and cell-cell contact with confirmed cell identities."To the best of our knowledge, CShaper is the first computational system for segmenting and analysing the images of C. elegans embryo systematically at the single-cell level," said Mr Cao. "Through close collaborations with biologists, we proudly developed a useful computer tool for automated analysis of a massive amount of cell image data. We believe it can promote further studies in developmental and cell biology, in particular in understanding the origination and growth of cancer cells," Professor Yan added.They also tested CShaper on plant tissue cells, showing promising results. They believe the computer tool can be adopted to other biological studies.
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Biotechnology
| 2,020 |
December 22, 2020
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https://www.sciencedaily.com/releases/2020/12/201222132032.htm
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How a large protein complex assembles in a cell
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Cells produce a great number of different protein complexes, each of which is made up of many individual proteins. These protein complexes, like ribosomes for example, are what regulate almost all of a cell's life-sustaining biological functions.
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Biologists have succeeded in determining the structure of many of these complexes, but there is less research so far on how the individual proteins assemble and then change over time. Conventional approaches have thus far proved insufficient for studying the exact course that these reactions in cells take, especially where large complexes are concerned.A group of ETH researchers led by Karsten Weis and research associate Evgeny Onischenko at ETH Zurich's Institute of Biochemistry are now presenting a new approach. Their method makes it possible to track the dynamics of protein complex assemblies, even for very large ones, with high temporal resolution. The study has just been published in the journal The ETH researchers call their new approach KARMA, which stands for kinetic analysis of incorporation rates in macromolecular assemblies and is based on methods for investigating metabolic processes. Scientists researching metabolism have long used radioactive carbon in their work, e.g., to label glucose molecules, which cells then take up and metabolise. The radioactive labelling enables researchers to track where and at what point in time the glucose molecules or their metabolites appear."This type of research inspired us to apply a similar principle in exploring the reactions that take place in the assembly of protein complexes," Weis explains. In their approach, the ETH researchers work with labelled amino acids, the fundamental building blocks of proteins, which contain heavier carbon and nitrogen isotopes. In a culture of yeast cells, the team replaces the lightweight amino acids with their heavier counterparts. The yeast uses these heavy amino acids in protein synthesis, which shifts the molecular weight of all newly produced proteins.To isolate protein complexes, the researchers remove yeast cells from the cultures at regular intervals and employ mass spectrometry to measure the tiny weight difference between molecules with heavier amino acids and those without. This indicates the age of a protein in a complex. Basically, the older the protein, the earlier it was incorporated into the complex. Based on these age differences, the researchers apply kinetic state models to ultimately reconstruct the precise assembly sequence of a given protein complex.As a case study to validate their method, Weis and his team chose the nuclear pore complex in yeast cells. This structure has some 500 to 1,000 elements composed of about 30 different proteins each in multiple copies, thus making it one of the largest known protein complexes.Using KARMA, the ETH biochemists were able to obtain a detailed map of which modules are integrated into the structure and when. One of their findings was a hierarchical principle: individual proteins form subunits within a very short time, which then assemble from the centre out to the periphery in a specific sequence."We've demonstrated for the first time that some proteins are used very quickly in the assembly of the pore complex, while others are incorporated only after about an hour. That's an incredibly long time," Weis says. A yeast cell divides every 90 minutes, which means it would take almost a whole generation to complete assembly of this vital pore complex. Precisely why the assembly of new pores takes so long in relation to the yeast reproduction cycle is not known.The ETH researchers also show that once assembly of the pore is complete, parts of the complex are highly stable and durable -- in the inner scaffold, for example, hardly any components are replaced during its lifetime. By contrast, proteins at the periphery of the nuclear pore complex are frequently replaced.Nuclear pores are some of the most important protein complexes in cells, as they are responsible for the exchange of substances and molecules between the cell nucleus and cytoplasm. For example, they transport messenger RNA from the nucleus to the cellular machinery outside the nucleus, which needs these molecules as blueprints for new proteins.Moreover, nuclear pores play direct and indirect roles in human disease. Accordingly, changes in the nuclear pore and its proteins can impact the development of conditions like leukaemia, diabetes or neurodegenerative diseases such as Alzheimer's. "Generally speaking, though, the reasons why pore defects cause these disease patterns are not well understood," Weis says, explaining that KARMA might help to gain deeper insight into such issues in the future."Although we applied KARMA to only one protein complex in this study, we're excited about its future applications. Our method will now enable us to decipher the sequence of a whole host of biological processes," Weis says. Their technique can be used, for example, to study molecular events that occur during the infection cycle of viruses such as COVID-19 and potentially help to find new drug candidates that break that cycle.The new method can also be applied to other biological molecules besides proteins, such as RNA or lipids.
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Biotechnology
| 2,020 |
December 22, 2020
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https://www.sciencedaily.com/releases/2020/12/201222132016.htm
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Brain gene expression patterns predict behavior of individual honey bees
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An unusual study that involved bar coding and tracking the behavior of thousands of individual honey bees in six queenless bee hives and analyzing gene expression in their brains offers new insights into how gene regulation contributes to social behavior.
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The study, reported in the journal "If the queen in a colony dies and the workers fail to rear a replacement queen, some worker bees activate their ovaries and begin to lay eggs," said Beryl Jones, a former graduate student at the University of Illinois Urbana-Champaign who led the study with entomology professor Gene Robinson, the director of the Carl R. Woese Institute for Genomic Biology at the U. of I.; and Sriram Chandrasekaran, a professor of biomedical engineering at the University of Michigan. Jones is a postdoctoral researcher at Princeton University."This is an example of 'behavioral plasticity,' the ability to change behavior in response to the environment," Jones said. "We know that behavioral plasticity is influenced by the activity of genes in the brain, but we do not know how genes in the brain work together to regulate these behavioral differences.""We wanted to compare egg-laying and foraging behaviors because they are quintessential examples of selfish and cooperative behaviors," Robinson said.Under typical conditions, queens lay eggs and workers forage. Studies that focus on differences in the brains and behavior of queens and foragers must contend with the fact that queens are fed and nurtured differently during development than worker bees, making any differences in gene regulation difficult to interpret. By studying queenless colonies, the researchers were able to analyze only worker bees and could therefore avoid this complication."Another challenge in studying how genes influence behavior is that behavior varies over time and also between individuals," Robinson said. "Hence, we automatically tracked the behavior of thousands of individual bees, 24/7, using small bar codes and computer vision to generate an unusually large dataset to help answer our questions."The scientists used computational algorithms to look for patterns of brain gene activity in the bees. They found consistent differences in gene regulation between bees that devoted themselves to foraging and those primarily focused on egg-laying. These patterns of transcription-factor regulation were so distinct that the researchers could use them to predict whether individual bees were foragers or egg-layers.The analysis revealed that a small number of egg-laying worker bees also engaged in foraging. These "generalist" bees had an intermediate gene-expression profile between the foraging specialists and the egg-laying specialists."We identified 15 transcription factors that best explained the behavioral differences in the bees," Jones said. The findings suggest that changes in the activity of a small number of influential transcription factors can lead to strikingly different behavior, she said."Some of the transcription factors we identified as important for honey bee behavior were previously identified as influencing the evolution of social behavior in other species," Robinson said. "This suggests our findings will aid in understanding how social behavior evolved and is regulated in multiple species, including, perhaps, humans."
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Biotechnology
| 2,020 |
December 22, 2020
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https://www.sciencedaily.com/releases/2020/12/201222081302.htm
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Frozen: Cutting-edge technology reveals structures within cells
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The cells in our body are in motion. Some migrate from A to B to heal wounds or fight pathogens. They do so with the help of small "feet" at the leading edge of migrating cells, so-called lamellipodia. These thin extensions are pushed forward and bind to the surface while the rest of the cell is pulled along. Inside these feet is a dense network of interwoven protein threads, called actin filaments, which form the cell's cytoskeleton. So far, it was unclear how the Arp2/3 complex, an assembly of seven proteins central for cell motility, sprouts off new actin filaments from pre-existing ones and thus generates dense, branched networks providing the required protrusive forces to the cell.
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Until now, scientists had to decide when they wanted to analyze the structure of the Arp2/3 complex: One option was to study it in isolation, where the protein complex is in an inactive conformation and hence does not allow understanding of how the network is formed. In order to become fully activated, however, the Arp2/3 complex needs to be bound to actin filaments. This requires using a method called electron tomography, which comes at the cost of considerably lower resolution. "Previous electron tomography data of Arp2/3 complexes bound to actin filaments in a test-tube environment was too imprecise, making it impossible to unambiguously tell where the individual elements of the complex must be located," explains Florian Fäßler, a postdoc in the group of IST Austria professor Florian Schur.For more than two years, he has been looking for a way to depict the protein complex in its natural environment in such a way that the individual structures can be analyzed precisely. Now he has succeeded. He imaged the complex within lamellipodia of mouse cells in its active actin-bound conformation. "We said to ourselves: Okay, we are going into the cell, where the environment is much more intricate because there is not only the protein complex and actin filaments but all sorts of other things as well. But this was the only way we were able to maintain this network in such a way that we could determine its structure," says molecular biologist Florian Schur.This was made possible by temperatures of minus 196 degrees Celsius. Within milliseconds, the researchers froze the samples -- too quickly to allow ice crystals to form that would have destroyed the cell's fine structures. They then used one of the most powerful cryo-electron microscopes available -- and the only one of its kind in Austria -- to image cells from different angles using cryo-electron tomography. Doing so, the team collected enough data for the 3D reconstruction of over 10,000 Arp2/3 complexes in their active state. Combined with advanced image processing, they then generated a 3D model of the Arp2/3 complex at a resolution of less than one nanometer. For comparison: human hair is about 50,000 nanometers thick. "We are now able to describe relatively precisely the structure of the protein complex and its subunits and how they form the actin filament network inside the lamellipodium of previously living cells," says Florian Fäßler. "Five years ago, probably no one would have thought that this could be done," adds Schur.Due to the advanced methodology, the team could refute an earlier model that had assumed much larger area connections between Arp2/3 complex and actin filaments. However, the scientists confirmed other aspects of how this complex is regulated and forms new actin filaments. With this knowledge, other scientists can now better understand this important protein complex's regulation and activity in its multiple roles beyond cell motility and the development of disease. "What we have done is to go as far as is currently possible with such complex samples in terms of methodology and resolution. With the current resolution, we have gained new biological insights, but it was also a methodological advance to show: It is possible," Schur says enthusiastically. Florian Fäßler now wants to improve the method even further to visualize other proteins and explore how far the method allows us to see inside a cell. "We are just starting to realize the full potential of cryo-electron tomography," says Schur.Video:
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Biotechnology
| 2,020 |
December 22, 2020
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https://www.sciencedaily.com/releases/2020/12/201222081257.htm
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Neuroscientists isolate promising mini antibodies against COVID-19 from a llama
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National Institutes of Health researchers have isolated a set of promising, tiny antibodies, or "nanobodies," against SARS-CoV-2 that were produced by a llama named Cormac. Preliminary results published in
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The study was led by a pair of neuroscientists, Thomas J. "T.J." Esparza, B.S., and David L. Brody, M.D., Ph.D., who work in a brain imaging lab at the NIH's National Institute of Neurological Disorders and Stroke (NINDS)."For years TJ and I had been testing out how to use nanobodies to improve brain imaging. When the pandemic broke, we thought this was a once in a lifetime, all-hands-on-deck situation and joined the fight," said Dr. Brody, who is also a professor at Uniformed Services University for the Health Sciences and the senior author of the study. "We hope that these anti-COVID-19 nanobodies may be highly effective and versatile in combating the coronavirus pandemic."A nanobody is a special type of antibody naturally produced by the immune systems of camelids, a group of animals that includes camels, llamas, and alpacas. On average, these proteins are about a tenth the weight of most human antibodies. This is because nanobodies isolated in the lab are essentially free-floating versions of the tips of the arms of heavy chain proteins, which form the backbone of a typical Y-shaped human IgG antibody. These tips play a critical role in the immune system's defenses by recognizing proteins on viruses, bacteria, and other invaders, also known as antigens.Because nanobodies are more stable, less expensive to produce, and easier to engineer than typical antibodies, a growing body of researchers, including Mr. Esparza and Dr. Brody, have been using them for medical research. For instance, a few years ago scientists showed that humanized nanobodies may be more effective at treating an autoimmune form of thrombotic thrombocytopenic purpura, a rare blood disorder, than current therapies.Since the pandemic broke, several researchers have produced llama nanobodies against the SARS-CoV-2 spike protein that may be effective at preventing infections. In the current study, the researchers used a slightly different strategy than others to find nanobodies that may work especially well."The SARS-CoV-2 spike protein acts like a key. It does this by opening the door to infections when it binds to a protein called the angiotensin converting enzyme 2 (ACE2) receptor, found on the surface of some cells," said Mr. Esparza, the lead author of the study. "We developed a method that would isolate nanobodies that block infections by covering the teeth of the spike protein that bind to and unlock the ACE2 receptor."To do this, the researchers immunized Cormac five times over 28 days with a purified version of the SARS-CoV-2 spike protein. After testing hundreds of nanobodies they found that Cormac produced 13 nanobodies that might be strong candidates.Initial experiments suggested that one candidate, called NIH-CoVnb-112, could work very well. Test tube studies showed that this nanobody bound to the ACE2 receptor 2 to 10 times stronger than nanobodies produced by other labs. Other experiments suggested that the NIH nanobody stuck directly to the ACE2 receptor binding portion of the spike protein.Then the team showed that the NIH-CoVnB-112 nanobody could be effective at preventing coronavirus infections. To mimic the SARS-CoV-2 virus, the researchers genetically mutated a harmless "pseudovirus" so that it could use the spike protein to infect cells that have human ACE2 receptors. The researchers saw that relatively low levels of the NIH-CoVnb-112 nanobodies prevented the pseudovirus from infecting these cells in petri dishes.Importantly, the researchers showed that the nanobody was equally effective in preventing the infections in petri dishes when it was sprayed through the kind of nebulizer, or inhaler, often used to help treat patients with asthma."One of the exciting things about nanobodies is that, unlike most regular antibodies, they can be aerosolized and inhaled to coat the lungs and airways," said Dr. Brody.The team has applied for a patent on the NIH-CoVnB-112 nanobody."Although we have a lot more work ahead of us, these results represent a promising first step," said Mr. Esparza. "With support from the NIH we are quickly moving forward to test whether these nanobodies could be safe and effective preventative treatments for COVID-19. Collaborators are also working to find out whether they could be used for inexpensive and accurate testing."
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Biotechnology
| 2,020 |
December 21, 2020
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https://www.sciencedaily.com/releases/2020/12/201221160430.htm
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New 3D maps reveal inner workings of immune cell gene expression
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The COVID-19 pandemic has highlighted how our small genetic differences can have a tremendous effect on how our bodies respond to disease.
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"The difference is within us," says Vivek Chandra, Ph.D., an instructor at La Jolla Institute for Immunology (LJI). "We can get infected by the same bacteria or viruses, but the ways our diseases progress can be very different."Genetic variations are important, but there's more to the puzzle. To truly understand how genes affect health, researchers need to track down the switches (also called "enhancers") that control when and where a gene is expressed in the body.Now researchers at La Jolla Institute for Immunology (LJI) have created 3D maps of how enhancer sequences and genes interact in several types of immune cells. Their new study in Nature Genetics opens the door to understanding individual risk for diseases from asthma to cancer."Nobody has done this mapping, either technically or analytically, to this precision in immune cells," says LJI Associate Professor Pandurangan Vijayanand M.D., Ph.D., co-senior author of the new study."Going forward, we can apply this framework to understand cell types involved in many different diseases," says study co-senior author Ferhat Ay, Ph.D., the Institute Leadership assistant professor of computational biology at LJI and an assistant adjunct professor at the UC San Diego School of Medicine.The work, published Dec. 21, 2020, is part of LJI's DICE Cis-Regulatory Interactome Project.Many of us are taught that a cell has machinery that hums along the genetic code, "reading" genes and making proteins. But there are two key genetic players with hidden roles in this process.First are "promoters." These are the DNA sequences that sit in the genetic code in front of genes. For a gene to be noticed, it needs to have a promoter. In 2018, the Vijayanand Laboratory published a seminal Cell study that revealed the impact of genetic variants in a set of human immune cells. This work gave Vijayanand's team a window into which genetic variants are important in which immune cells.For the new study, Chandra and LJI Bioinformatics Postdoctoral Fellow Sourya Bhattacharyya, Ph.D., worked together to map the target genes for important DNA sequences called "enhancers." An enhancer serves as a specific switch to turn a gene on in a cell-specific manner."People have found a lot of these switches, but it hasn't been easy to know which switch is connected to which gene," Vijayanand says.The researchers compare the situation to moving into a new house where you don't know which light switch controls which light -- but on a much bigger scale. There could be a million switches, and the lights they control could be a mile away."We really want to figure out the wiring," says Ay.The scientists used a genome-wide mapping technique to finally see the wiring between the lights and switches. They knew that no matter how far away an enhancer was in the DNA code, it would need to find a way to be physically near the promoter it controls. The team's new 3D maps showed how enhancers on one part of a DNA strand actually loop around to meet promoters.To their surprise, the researchers linked genes to enhancers very far away in the DNA sequences. Thinking at a molecular scale, for some of the genes, the enhancers appear miles away. "To date, fewer than a handful examples of such ultra-long distance connections have been discovered and validated" says Dr. Chandra, who performed genome editing experiments (CRISPR) that validated some of the discoveries in the paper.Of course, the enhancer sequences are also made up of DNA letters. The new study shows that variations in the enhancer sequences can actually disable the "switch" -- or impair the "wiring" -- leading to problems in turning on the right gene in the right cell type. With their new maps, researchers can predict whether DNA sequence changes in these switches will increase disease risk in a person.As with everything in genetics, even the promoters are more complex than scientists had realized. The new work shows that some "turned off" promoter sequences -- previously thought to do nothing -- are actually switching on genes far away in the DNA sequence. "They might be connected to other genes that you would never expect," says Ay.This discovery means that researchers may need to change how they think of gene regulation. When researchers uncover a genetic variant linked to a disease, they usually go looking for the nearby gene. Now, they'll need to use different tools to hunt for potential target genes scattered through the genome."People working on all kinds of diseases are completely rethinking how they find variants and the genes they associate with," says Ferhat.The LJI team will be helping though. Their findings in immune cells will be openly available online through the DICE (Database of Immune Cell Expression, Expression of quantitative trait loci and Epigenomics) database.The new study also shows how this same approach can be used on other cell types. "The next steps are endless," says Vijayanand.The study, titled "Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants," included authors Benjamin J. Schmiedel, Ariel Madrigal, Cristian Gonzalez-Colin, Stephanie Fotsing, Austin Crinklaw, Gregory Seumois, Pejman Mohammadi, Mitchell Kronenberg, Bjoern Peters.This research was supported by the National Institutes of Health (grants R24-AI108564, R35-GM128938) and the William K. Bowes Jr Foundation.
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Biotechnology
| 2,020 |
December 21, 2020
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https://www.sciencedaily.com/releases/2020/12/201221121749.htm
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Fungal RNA viruses: Unexpected complexity affecting more than your breakfast omelet
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We've all suffered from viruses, but did you know that they are also a problem for mushrooms and molds? Mycoviruses are viruses that specifically infect fungi and have the potential to impact ecology, agriculture, food security, and public health. Understanding the nature of these viruses, including their number and evolution, can help us understand their origins and inform our understanding of viruses in general.
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Previous research into RNA mycoviruses has relied on their sequence similarity to viruses that have already been described. However, this approach leaves viruses with different genetic structures or sequences undiscovered. Using an advanced technological approach called Fragmented and Primer Ligated Double Stranded RNA sequencing, or FLDS for short, researchers from the University of Tsukuba were able to identify viral sequences that were previously overlooked.Summarizing the importance of this work, Professor Hagiwara said: "The current approaches used to identify RNA viruses mean that their genetic diversity has been underestimated. Using FLDS, we were able to study RNA viruses without relying on sequence similarity, which allows us to identify RNA viral sequences that are dissimilar to those previously identified."Using FLDS, Professors Urayama and Hagiwara, and their colleagues, identified 19 RNA viruses in a fungus called Aspergillus. Highlighting the value of this approach, 9 of the 19 viruses identified had been undetected using conventional methods of examination. Moreover, 42% of identified viruses had genomes that were segmented, or spread throughout the host genome, and others identified had novel genome architectures.RNA-dependent RNA polymerase (RdRp) is an essential gene found in all RNA viruses and allows RNA genome replication from an RNA template. It was commonly understood that all RNA viruses encode RdRp as a single, continuous gene."Unexpectedly, we found that viruses within a certain clade of Narnaviridae encode an RdRp gene lacking the catalytic domains," Professor Urayama explains, "but we also found a different open reading frame containing the missing domains." Although some RdRp sequences lacking the catalytic domains have been described previously, those viral genomes also lack the catalytic domains and produce imperfect RdRp proteins. The functional, yet divided, RdRp described by Professors Urayama and Hagiwara, and their colleagues, indicates that researchers should reconsider the structural plasticity of RdRp.
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Biotechnology
| 2,020 |
December 21, 2020
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https://www.sciencedaily.com/releases/2020/12/201221101155.htm
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Targeting the deadly coils of Ebola
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In the midst of a global pandemic with COVID-19, it's hard to appreciate how lucky those outside of Africa have been to avoid the deadly Ebola virus disease. It incapacitates its victims soon after infection with massive vomiting or diarrhea, leading to death from fluid loss in about 50 percent of the afflicted. The Ebola virus transmits only through bodily fluids, marking a key difference from the COVID-19 virus and one that has helped contain Ebola's spread.
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Ebola outbreaks continue to flare up in West Africa, although a vaccine developed in December 2019 and improvements in care and containment have helped keep Ebola in check. Supercomputer simulations by a University of Delaware team that included an undergraduate supported by the XSEDE EMPOWER program are adding to the mix and helping to crack the defenses of Ebola's coiled genetic material. This new research could help lead to breakthroughs in treatment and improved vaccines for Ebola and other deadly viral diseases such as COVID-19."Our main findings are related to the stability of the Ebola nucleocapsid," said Juan R. Perilla, an assistant professor in the Department of Chemistry and Biochemistry at the University of Delaware. Perilla co-authored a study published in October 2020 in the AIP "What we've found is that the Ebola virus has evolved to regulate the stability of the nucleocapsid by forming electrostatic interactions with its RNA, its genetic material," Perilla said. "There is an interplay between the RNA and the nucleocapsid that keeps it together."Like coronaviruses, the Ebola virus depends on a rod-like and helically-shaped nucleocapsid to complete its life cycle. In particular, structural proteins called nucleoproteins assemble in a helical arrangement to encapsulate the single-stranded viral RNA genome (ssRNA) that forms the nucleocapsid.The study by Perilla and his science team sought the molecular determinants of the nucleocapsid stability, such as how the ssRNA genetic material is packaged, the electrostatic potential of the system, and the residue arrangement in the helical assembly. This knowledge is essential for developing new therapeutics against Ebola. Yet these insights remain out of reach even by the world's best experimental labs. Computer simulations, however, can and did fill that gap."You can think of simulation work as a theoretical extension of experimental work," said study co-author Tanya Nesterova, an undergraduate researcher in the Perilla Lab. "We found that RNA is highly negatively charged and helps stabilize the nucleocapsid through electrostatic interaction with the mostly positively charged nucleoproteins," she said.Nesterova was awarded funding through an XSEDE Expert Mentoring Producing Opportunities for Work, Education, and Research (EMPOWER) scholarship in 2019, which supports undergrads participate in the actual work of XSEDE."It was an effective program," she said. "We used computational resources such as Bridges this summer. We also had regular communication with the coordinator to keep our progress on track."The team developed a molecular dynamics simulation of the Ebola nucleocapsid, a system that contains 4.8 million atoms. They used the cryo-electron microscopy structure of the Ebola virus published in Nature in October of 2018 for their data in building the model."We built two systems," said study co-author Chaoyi Xu, a PhD student in the Perilla Lab. "One system is the Ebola nucleocapsid with the RNA. And the other one is just the nucleocapsid as a control.""After we built the whole tube, we put each nucleocapsid in an environment that is similar to the cell," Xu explained. They basically added sodium chloride ions, and then adjusted the concentration to match that found in the cytoplasm. They also put a water box inside around the nucleocapsid. "And then we ran a very powerful simulation," Xu added.The NSF-funded Extreme Science and Engineering Discovery Environment (XSEDE) awarded the team supercomputing allocations on the Stampede2 system at the Texas Advanced Computing Center and the Bridges system of the Pittsburgh Supercomputing Center."We are very thankful for the supercomputer resources provided by XSEDE that allowed this work to be possible. XSEDE also provided training through online courses that was helpful," Xu said."On Stampede2, we have access to run simulations on hundreds or even thousands of nodes," Xu continued. "This makes it possible for us to run simulations of larger systems, for example, the Ebola nucleocapsid. This simulation is impossible to finish locally. That's very important," he said."I like how with Bridges, when you run a simulation, you can be up to date on when it completes and when it started," Nesterova added. She said that was helpful for creating Slurm scripts, which help manage and schedule jobs on compute clusters."We just started using Frontera for the Ebola project," Xu added. Frontera is the NSF flagship Tier 1 system at TACC, ranked #9 in the world by Top500. "It's more powerful because it has the latest CPU architecture. And it's very fast," he said."Frontera is part of the TACC infrastructure," Perilla said. "We knew what developmental tools were going to be there, and also the queueing system and other intricacies of these machines. That helped a lot. In terms of architecture, we're familiar with Stampede2, although this is a different machine. Our experience with Stampede2 allowed us to move quickly to start using Frontera," he said.The science team simulated the interaction of the atoms in the Ebola virus nucleocapsid and measured how they change in time, yielding useful information about the atomic interactions. One of the things they found was that without the RNA, the Ebola virus nucleocapsid kept its tube-like shape. But the packing of the nucleoprotein monomers became disordered, and its helical symmetry was lost. With the RNA, it kept its helix. Their results showed that the RNA binding stabilized the helix and preserved the structure of the Ebola virus nucleocapsid.The team also found important interactions between the nucleoprotein residues and the ssRNA, and also interactions between two nucleoproteins."There's two kinds of interfaces between the pairs of nucleoproteins that form the helical arrangement. We figured out which of these interfaces plays a more important role. We can either target that interface to destabilize the helical arrangement or stabilize the helical arrangement to a large extent such that the virus nucleocapsid is unable to disassemble," said study co-author Nidhi Katyal, a postdoctoral researcher in the Perilla Lab.The Ebola virus is one tough organism because it tightly regulates its macromolecular assembly. Perilla suggested that instead of trying to devise drugs that destroy the nucleocapsid, a good strategy might be to do the opposite."If you make it too stable, that's enough to kill the virus," he said. Borrowing a strategy from his background in HIV research, he wants to find targets for drugs to over-stabilize the Ebola virus and keep it from releasing its genetic material, a key step in its replication.Perilla suggested a similar strategy for other pathogens that are tightly regulated, such as coronaviruses and hepatitis B viruses. "They're a sweet spot, so to speak. We know what confers stability. Other teams can look to see if maybe this is a good druggable site for making it hypostable or making it hyperstable," Perilla said.Looking ahead, Perilla indicated his lab will be looking more closely at the specifics of ssRNA sequence and whether it confers stability to the Ebola virus nucleocapsid tube. If it does, then some regions might be exposed and might be transcribed first, similar to what happens in the nucleus of the cell. Perilla said it would be "unheard of in a virus," and extremely advanced behavior in terms of the RNA regulating transcription.Said Perilla: "We know that there will be more pathogens that just keep coming, particularly with coronaviruses now, and they can stop the world. It's beneficial to society having the ability to study not only one virus, but taking these techniques to study a new virus, something like coronaviruses. In addition, the ability to train new students, like Tanya, provides the taxpayers their money's worth in terms of training the next generation, transferring knowledge from other viruses, and fighting the current problems."
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Biotechnology
| 2,020 |
December 21, 2020
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https://www.sciencedaily.com/releases/2020/12/201221101219.htm
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How cancers hurt themselves to hurt immune cells more
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Cancers like melanoma are hard to treat, not least because they have a varied bag of tricks for defeating or evading treatments. A combined research effort by scientists at the Weizmann Institute of Science and researchers in the Netherlands Cancer Institute in Amsterdam and the University of Oslo, Norway, shows exactly how tumors, in their battles to survive, will go so far as to starve themselves in order to keep the immune cells that would eradicate them from functioning.
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The immunotherapies currently administered for melanomas work by removing obstacles that keep immune cells called T cells from identifying and killing tumor cells. Recent research suggested that in melanoma, another blocker could assist the T cells -- this one to stop an enzyme called IDO1 that is overproduced by the cancer cells. IDO1 breaks down an essential amino acid, tryptophan, which is needed to make proteins, in the process leaving behind tryptophan breakdown byproducts that suppress the immune response. But IDO1 blockers did not fare well in clinical trials, suggesting more knowledge was needed -- including how the cancer cells, which also require tryptophan, can function after they have destroyed this resource.The research team, including the group of Prof. Yardena Samuels of Weizmann's Molecular Cell Biology Department, members of the lab of Prof. Reuven Agami of the Netherlands Cancer Institute; Dr. Noam Stern-Ginossar of the Weizmann Institute's Molecular Genetics Department; Dr. Yishai Levin and his group at the Nancy and Stephen Grand Israel National Center for Personalized Medicine on the Institute campus; and the group of Prof. Johanna Olweus of the University of Oslo, investigated the mystery of the missing tryptophan in melanoma cells.Agami and his team had, in previous research shown that in normal cells, when an amino acid like tryptophan is missing, this causes a sort of logjam in the protein production process. The ribosomes -- protein production units -- make their way down a strand of messenger RNA (mRNA), translating three-letter "words" known as codons into amino acids, which they grab and add to the expanding protein chain. When an amino acid is missing, the ribosomes stop working until one can be found, causing a pile-up in the ribosomes coming up the mRNA strand from behind.But that is not what happens in melanoma cells. The group found that some ribosomes manage to keep going, past the codons encoding the missing tryptophan. What was going on?It turned out that the melanoma ribosomes were engaging in a ruse known as "frameshifting." That is, they simply moved up or down one letter in the RNA strand. In the economical gene code -- based on just four letters -- the next three spelled the name of a different amino acid and the ribosomes continued down the mRNA strand, assembling protein chains. Of course, the frames of subsequent codon triplets shifted as well, so that the resultant proteins were quite abnormal. The cancer cells then displayed them on their outer membranes, where immune cells could pick up on the aberrant protein structures.Such frameshifting had been seen before in viruses and bacteria, but not in human cells. Previous studies have missed these proteins because they do not arise from genetic mutations (of which there are hundreds in melanoma), but from a sort of calculated blip in the production process. Agami, whose lab is now investigating exactly how this frameshifting is initiated and whether it occurs in other cancers, says: "This flexibility in mRNA translation might stimulate tumor growth and aggressive behavior by using an emergency program for scarcity."Dr. Osnat Bartok, in Samuels's group: "When things get stressful in the tumor's microenvironment, it can affect protein production, harming immune cells but also adding to the immune cells' clues for identifying cancer." Samuels adds: "These findings add to our knowledge of immune system interactions with cancer as well as the landscape immune cells encounter in a tumor. They suggest exciting ways we might regulate and therapeutically target the presentation of defective immune-reactive peptides on the cell surface."
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Biotechnology
| 2,020 |
December 18, 2020
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https://www.sciencedaily.com/releases/2020/12/201218133704.htm
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Scientists get the most realistic view yet of a coronavirus spike's protein structure
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Coronaviruses like the one that causes COVID-19 are studded with protein "spikes" that bind with receptors on the cells of their victims -- the first step in infection. Now scientists have made the first detailed images of those spikes in their natural state, while still attached to the virus and without using chemical fixatives that might distort their shape.
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They say their method, which combines cryogenic electron microscopy (cryo-EM) and computation, should produce quicker and more realistic snapshots of the infection apparatus in various strains of coronavirus, a critical step in designing therapeutic drugs and vaccines."The advantage of doing it this way is that when you purify a spike protein and study it in isolation, you lose important biological context: How does it look in an intact virus particle? It could possibly have a different structure there," said Wah Chiu, a professor at DOE's SLAC National Accelerator Laboratory and Stanford University and senior author of the study. They described their results in Seven strains of coronaviruses are known to infect humans. Four cause relatively mild illnesses; the other three -- including SARS-CoV-2, the virus that causes COVID-19 -- can be deadly, said co-author Jing Jin, an expert in the molecular biology of viruses at Vitalant Research Institute in San Francisco. Scientists at Vitalant hunt for viruses in blood and stool samples from humans and animals, screen blood samples during outbreaks like the current pandemic, and study interactions between viruses and their hosts.The virus that causes COVID-19 is so virulent that there are only a few cryo-EM labs in the world that can study it with a high enough level of biosafety controls, Jin said. So for this study, the research team looked at a much milder coronavirus strain called NL63, which causes common cold symptoms and is responsible for about 10% of human respiratory disease each year. It's thought to attach to the same receptors on the surfaces of human cells as the COVID-19 virus does.Rather than chemically removing and purifying NL63's spike proteins, the researchers flash-froze whole, intact viruses into a glassy state that preserves the natural arrangement of their components. Then they made thousands of detailed images of randomly oriented viruses using cryo-EM instruments at the Stanford-SLAC Cryo-EM Facilities, digitally extracted the bits that contained spike proteins, and combined them to get high-resolution pictures."The structure we saw had exactly the same structure as it does on the virus surface, free of chemical artifacts," Jin said. "This had not been done before."The team also identified places where sugar molecules attach to the spike protein in a process called glycosylation, which plays an important role in the virus's life cycle and in its ability to evade the immune system. Their map included three glycosylation sites that had been predicted but never directly seen before.Although a German group has used a similar method to digitally extract images of the spike protein from SARS-CoV-2, Jin said, they had to fix the virus in formaldehyde first so there would be no danger of it infecting anyone, and this treatment may cause chemical changes that interfere with seeing the true structure.Going forward, she said, the team would like to find out how the part of the spike that binds to receptors on human cells is activated, and also use the same technique to study spike proteins from the virus that causes COVID-19, which would require specialized biohazard containment facilities.The research was funded by the National Institutes of Health and by the DOE Office of Science through the National Virtual Biotechnology Laboratory, a consortium of DOE national laboratories focused on response to COVID-19, with funding provided by the Coronavirus CARES Act.
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Biotechnology
| 2,020 |
December 18, 2020
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https://www.sciencedaily.com/releases/2020/12/201218112458.htm
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New mechanism of force transduction in muscle cells discovered
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The ability of cells to sense and respond to their mechanical environment is critical for many cellular processes but the molecular mechanisms underlying cellular mechanosensitivity are still unclear. Researchers at the University of Münster have now discovered how the muscle-specific adhesion molecule metavinculin modulates mechanical force transduction on the molecular level. The research results have just been published in the journal
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The interaction of cells with their environment is mediated by specialized adhesion structures, which transduce mechanical forces inwards and out of cells. As cellular adhesions consist of hundreds of different proteins, it is still unclear how the mechanical information is transmitted on the molecular level. To study these processes in more detail, the Grashoff laboratory at the WWU Münster develops biosensors that allow the detection of piconewton-scale forces propagated across individual molecules in cells. In their most recent study, the authors applied their microscopy-based technique to the adhesion protein metavinculin, which is expressed in muscle cells and associated with cardiomyopathy, a heart muscle disease.By analyzing a range of genetically modified cells, the authors demonstrate that the presence of metavinculin changes how mechanical forces are transduced in cell adhesion complexes. "Our data indicate that metavinculin could function as a molecular dampener, helping to resist high peak forces observed in muscle tissues," explains Prof. Dr. Carsten Grashoff, principal investigator of the study. "This is a very interesting example of how the presence of a single protein can change the way mechanical information is processed in cells."Surprisingly, the authors did not observe any indications of cardiomyopathy in mice lacking metavinculin. This suggests that the pathophysiological role of metavinculin is more complex than previously assumed.
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Biotechnology
| 2,020 |
December 18, 2020
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https://www.sciencedaily.com/releases/2020/12/201218084115.htm
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Cell atlas of tropical disease parasite may hold key to new treatments
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The first cell atlas of an important life stage of Schistosoma mansoni, a parasitic worm that poses a risk to hundreds of millions of people each year, has been developed by researchers at the Wellcome Sanger Institute and their collaborators.
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The study, published today (18 December 2020) in S. mansoni has a complex life cycle that begins when larval forms of the parasite emerge from snails into rivers and lakes. These larvae then enter humans through the skin after contact with infested water. Once inside the body, the parasite begins what is known as the intra-mammalian stage of its life cycle, undergoing a series of developmental transitions as it matures to adulthood.Adult worms live in human blood vessels and reproduce, releasing eggs that pass from the body into water to continue the life cycle. But some eggs remain trapped in the body, leading to the disease schistosomiasis.Schistosomiasis is a debilitating long-term illness that can lead to the inability to work, organ damage and death. It affects hundreds of millions of people each year, primarily in sub-Saharan Africa,* and is listed by the World Health Organisation (WHO) as one of the most Neglected Tropical Diseases. Currently, only one drug is available to treat the disease, but this is inappropriate for use in very young children and there are fears that overreliance on a single treatment will allow the parasites to develop resistance to the drug.Researchers have been looking at ways to find new drug targets, but until now there has been no high-resolution understanding of the parasite's biology.This new study sought to map all of the cells in the first intra-mammalian stage of the parasite using single-cell technology, which identifies different cell types present in an organism or tissue.The early-stage parasites were broken apart into individual cells that were characterised by single-cell RNA sequencing by scientists at the Wellcome Sanger Institute. The data were then analysed to identify cell types according to the genes expressed by individual cells, and where in the body these cells were located.The team identified 13 distinct cell types, including previously unknown cell types in the nervous system and parenchymal system**. Individual fluorescent probes were made for genes specifically expressed by each cell type. Scientists at the Morgridge Institute for Research in the USA then used these probes to confirm the position of the discovered cells within whole parasites under the microscope.Dr Carmen Diaz Soria, a first author of the study from the Wellcome Sanger Institute, said: "Though significant advances in our understanding of Schistosoma mansoni have been made in recent years, we have yet to identify targets leading to a viable vaccine. Single-cell RNA sequencing provides a whole new level of biological detail, including previously unidentified cell types, that will allow us to better understand each cell population in the parasite."To identify new drug targets, researchers most often look for differences between a pathogen and its human host. However, S. mansoni is far closer to us in evolutionary terms than most major parasites, such as those that cause malaria. It is hoped that these findings will reveal areas of the parasite's genetic code that are sufficiently different from our own to be viable treatment targets.Dr Jayhun Lee, a first author of the study from the Morgridge Institute for Research, Wisconsin USA, said: "We found genes in the muscular system of Schistosoma mansoni that might be specific to schistosomes. Because they are found in these parasites but not in humans, they are one possible treatment target identified by the study. The muscle allows the parasite to travel through our bodies, so if we were able to hinder that ability, we may be able to halt its life cycle before reproduction takes place."The authors also shed light on the parenchymal tissue of S. mansoni, the 'filler' tissue that connects all the tissues of the parasite together. Previous studies had found it difficult to isolate parenchymal cells for analysis. The cell atlas found that some genes that are important for the parasite to digest food are also associated with the parenchymal tissue. Disrupting how the parasite feeds by targeting these cells could be another avenue for therapies.Dr Matt Berriman, senior author of the paper from the Wellcome Sanger Institute, said: "Schistosomiasis is one of the most serious neglected parasitic diseases and gaining a deeper understanding of the parasite's biology will help to expose vulnerabilities that could one day be targeted by new treatments. We hope that this cell atlas for the first intra-mammalian stage of Schistosoma mansoni will provide researchers with valuable clues to help accelerate the development of new treatments and eliminate this parasite from the lives of hundreds of millions of affected people each year."
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Biotechnology
| 2,020 |
December 18, 2020
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https://www.sciencedaily.com/releases/2020/12/201218094512.htm
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New insights into cholera microbe and chances of pandemic strain
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Researchers at The City College of New York have uncovered a novel way in which
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The finding was revealed by examining the type VI secretion system, or T6SS for short, a secretion system used by "We wanted to look at how a harmless environmental strain of Stefan Pukatzki, lead author of the CCNY study, added, "Even though we may not have a cure for cholera, this research contributes to our understanding of how these pathogens evolve and become pandemic."The study, "Pandemic Both Santoriello and Pukatzki have affiliation with the University of Colorado Denver's Department of Immunology and Microbiology.
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Biotechnology
| 2,020 |
December 18, 2020
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https://www.sciencedaily.com/releases/2020/12/201218094510.htm
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Engineers reveal molecular secrets of cephalopod powers
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Reflectins, the unique structural proteins that give squids and octopuses the ability to change colors and blend in with their surroundings, are thought to have great potential for innovations in areas as diverse as electronics, optics and medicine. Scientists and inventors have been stymied in their attempts to fully utilize the powers of these biomolecules due to their atypical chemical composition and high sensitivity to subtle environmental changes.
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In a study published recently in the "My laboratory at UCI has for a long time worked to mimic the light-scattering and light-reflecting powers of cephalopods with the goal of inventing new classes of adaptive thermoregulatory fabrics and other everyday technologies," said co-author Alon Gorodetsky, UCI associate professor of chemical and biomolecular engineering. "With this research, we have focused on developing a detailed fundamental understanding of how reflectins function at a molecular level."Gorodetsky said scientists are attracted to reflectins because, similar to other protein-based materials, they offer many advantageous attributes such as controllable self-assembly, stimuli-responsiveness, customizable functionality and compatibility with other biological systems. The model biomaterials have also shown their usefulness for modifying the refractive index of human cells and supporting the growth of neural stem cells.In their laboratory in UCI's Henry Sameuli School of Engineering, Gorodetsky and his collaborators used bioinformatics predictions to select a reflectin variant, produced the protein in bacteria and developed solution conditions for maintaining it in a stable state.The researchers then used a variety of tools for analysis of the protein and its solutions, including molecular dynamics simulations, small-angle x-ray scattering, and nuclear magnetic resonance spectroscopy. They also probed the assembled multimeric protein ensembles with techniques such as atomic force microscopy and three-dimensional holotomographic microscopy. These methods enabled the team to assess a full range of qualities and properties for the reflectin variant."Through our synergistic computational and experimental approaches, we were able to elucidate the three-dimensional structure of the reflectin variant, thereby establishing a direct correlation between the protein's structural characteristics and intrinsic optical properties," said Gorodetsky. "This research can be viewed as a valuable conceptual framework for using this class of proteins in bioengineering applications."Gorodetsky said his team's work will enable new techniques for processing reflectin-based materials and points to new avenues for custom tailoring films of the protein at the nano- and micro-meter scales, which would be beneficial for biophotonic and bioelectronic applications as well as for inspiring the design of polymeric materials with sophisticated light-scattering capabilities. He also said the approach used in this project could help better understand the mechanisms underpinning cephalopods' ability to change color.
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Biotechnology
| 2,020 |
December 17, 2020
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https://www.sciencedaily.com/releases/2020/12/201217145210.htm
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Scientists set a path for field trials of gene drive organisms
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The modern rise of gene drive research, accelerated by CRISPR-Cas9 gene editing technology, has led to transformational waves rippling across science.
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Gene drive organisms (GDOs), developed with select traits that are genetically engineered to spread through a population, have the power to dramatically alter the way society develops solutions to a range of daunting health and environmental challenges, from controlling dengue fever and malaria to protecting crops against plant pests.But before these gene drive organisms move from the laboratory to testing in the field, scientists are proposing a course for responsible testing of this powerful technology. These issues are addressed in a new Policy Forum article on biotechnology governance, "Core commitments for field trials of gene drive organisms," published Dec. 18, 2020 in "The research has progressed so rapidly with gene drive that we are now at a point when we really need to take a step back and think about the application of it and how it will impact humanity," said Akbari, the senior author of the article and an associate professor in the UC San Diego Division of Biological Sciences. "The new commitments that address field trials are to ensure that the trials are safely implemented, transparent, publicly accountable and scientifically, politically and socially robust."A multidisciplinary group of gene drive organism developers, ecologists and con¬servation biologists joined experts in social science, ethics and policy to outline several commitments that they deem "critical for responsible conduct of a field trial and to ensure that these technologies, if they are introduced, serve the public interest." Twelve core commitments were developed under the following broad categories: fair partnership and transparency; product efficacy and safety; regulatory evaluation and risk/benefit assessment; and monitoring and mitigation."Our intent is to contribute to public policy decisions on whether and how to proceed with GDOs, based on evaluations conducted in fair and effective partnerships with relevant authori-ties and other stakeholders," the authors write in the article. A signatory page for those supporting this effort will be available here."This will be an influential piece for the field given the number and diversity of co-authors and will help set a course toward open and transparent research," said article co-author Cinnamon Bloss, an associate professor at UC San Diego's Herbert Wertheim School of Public Health and Human Longevity "As the authors point out, more needs to be done," Bloss said. "In particular, my co-authors and I represent a largely North American viewpoint, and thus, stakeholders in other countries that might be more likely to serve as trial sites need to be brought into this conversation."Article co-author Robert Friedman, vice president for policy and university relations at the J. Craig Venter Institute, said a defining factor behind the effort was to merge disparate GDO viewpoints into a cohesive voice."The diversity of perspectives, background and engagement on the issue is really very impressive," said Friedman. "This paper includes a multidisciplinary group of developers, ecologists, ethicists and policy experts, and thus includes a broader set of commitments than might have otherwise been developed. This is, of course, appropriate and necessary for the significant next step, moving from the laboratory to a confined field trial."Other coauthors from UC San Diego's Division of Biological Sciences include Associate Professor Kimberly Cooper and Assistant Research Scientist Valentino Gantz."I believe the process of working together over the past few months itself has been valuable and hope that this effort to define our shared commitments will lead to even more cross-disciplinary collaboration in the gene drive field," said first-author Kanya Long, assistant adjunct professor at UC San Diego's Herbert Wertheim School of Public Health and Human Longevity Science.What exactly is a gene drive?Relatedly, on Dec. 8, Akbari and several co-authors published an opinion article in the Proceedings of the National Academy of Sciences (PNAS) on the need to standardize the core definition of gene drive and related terms.Surprising to those outside of science, the accelerated rise of gene drive technologies in recent years has emerged without a broadly accepted set of definitions. Without common agreement on gene drive-related terms, confusion and disagreement can emerge as gene drive policies and regulations are being developed. For example, the authors note, "gene drive" has been used both to describe a process (the biological activity of gene drive spreading in a population) and to describe an object (the development of a "gene drive" engineering tool)."There are multiple flavors of gene drives so it's really hard for a non-specialist to understand what we are talking about," said Akbari, who joined with world gene drive leaders Luke Alphey (PirBright) and Andrea Crisanti (Imperial College London), alongside Filippo (Fil) Randazzo (Leverage Science), to develop the definitions. "The point of the PNAS article was to bring leading experts together to define gene drive to provide a consistent and common language that can be used for communication."Working through the Foundation for the National Institutes of Health (FNIH), Akbari noted that individuals and organizations that agree with the new standard of definitions are becoming signatories in support of these definitions.
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Biotechnology
| 2,020 |
December 17, 2020
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https://www.sciencedaily.com/releases/2020/12/201217135336.htm
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Seeking to avoid 'full lockdown,' cells monitor ribosome collisions
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Ribosomes are the machines in the cell that use instructions from mRNA to synthesize functional proteins. There are hundreds of thousands of ribosomes in each cell, and they mostly process their instructions faithfully. But sometimes ribosomes get stuck or stall on roadblocks along defective mRNA molecules.
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New research from Washington University in St. Louis shows that cells monitor for ribosome collisions to determine the severity of the problem and how best to respond when things start to go awry.The research from the laboratory of Hani Zaher, associate professor of biology in Arts & Sciences, is published online Dec. 17 in the journal "The cell has two methods of stress response that are triggered by this very same signal of ribosomes running into each other," Zaher said. "However, the quality control mechanism of ribosome rescue and mRNA degradation responds more swiftly -- to resolve the problems and to prevent premature activation of the integrated stress response."Only after cells have exhausted the capacity of the quality control system do they move to shut down the entire translation system by activating the stress response," Zaher said.Leo Yan, a graduate student in biology and the first author of the study, used an analogy relevant to human experience during the COVID-19 pandemic."Integrated stress response is like a city going through full lockdown," Yan said. "If you only have 10 cases, you don't want to come out and tell the city, 'Let's just hunker down and not do anything,' or shut down all the productivity. You want the city to have a system to evaluate the severity of the stress -- and to deal with it according to its severity."The value of our paper is in describing the dynamic within the system that the cell can use to evaluate the level of stress -- from local, individual events, to events that require shutdown of the entire translation machinery," he said.Yan and Zaher discovered that cells are using ribosomes like sensors to alert them about changes in their environment.The scientists used drugs and genetic manipulations to alter ribosome speed and density, providing compelling evidence that both major kinds of stress response are activated in response to ribosome collisions.When ribosomes are evenly distributed, rarely running into each other, cells know that conditions are good. When some ribosomes run into each other, cells recognize that there are problems -- and call on quality control factors to resolve the collisions. When many ribosomes are colliding with each other, cells go on high alert and shut things down."There's a communication between these two pathways," Zaher said. "And the reason for that is that, even though the integrated stress response is a pro-survival pathway, it comes at a cost of shutting the cell down. You don't want to activate it prematurely, unless you're certain that there is a problem."The researchers made their observations using a yeast model system, but the findings are applicable to mammal cells, too, they said. In humans, dysregulation of integrated stress response signaling has been linked to diseases including diabetes, cancer and neurodegenerative disorders such as Alzheimer's and Parkinson's disease.
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Biotechnology
| 2,020 |
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