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July 13, 2020
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https://www.sciencedaily.com/releases/2020/07/200713165558.htm
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Artificial energy source for muscle
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A chemist and kinesiologist got on a bus, but this isn't the set-up to a joke. Instead, kinesiologist and lead author Ned Debold and chemist Dhandapani Venkataraman, "DV," began talking on their bus commute to the University of Massachusetts Amherst and discovered their mutual interest in how energy is converted from one form to another -- for Debold, in muscle tissue and for DV, in solar cells.
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Debold told the chemist how researchers have been seeking an alternative energy source to replace the body's usual one, a molecule called adenosine triphosphate (ATP). Such a source could control muscle activity, and might lead to new muscle spasm-calming treatments in cerebral palsy, for example, or activate or enhance skeletal muscle function in MS, ALS and chronic heart failure.All are highly debilitating because the body has no way to fix them, says muscle physiologist Debold. It doesn't have good mechanisms to control -- either inhibit or boost -- myosin function, the molecular motor that drives movement.As DV notes, the usual approach to seeking a new compound is to systematically test each one among millions until one seems worth followup -- the classic "needle in a haystack" approach. He says, "At one point I suggested to Ned, 'Why don't we build the needle ourselves instead?' That started us on this interesting project that put together people who would otherwise never work together."The two soon saw that they would need someone to model interactions between the molecules DV was making and the myosin molecules Debold was using to test them. They invited computational chemist Jianhan Chen.Chen explains, "We did computer modeling because experimentally it is difficult to know how myosin might be using the molecules DV was synthesizing. We can use computer simulation to provide a detailed picture at the molecular level to understand why these compounds might have certain effects. This can provide insight into not only how myosin interacts with the current set of compounds, but also it can provide a roadmap for DV to use to design new compounds that are even more effective at altering myosin function."This month, the researchers report in the By using different isomers -- molecules with atoms in different arrangements -- they were able to "effectively modulate, and even inhibit, the activity of myosin," suggesting that changing the isomer may offer a simple yet powerful approach to control molecular motor function. With three isomers of the new ATP substitute, they show that myosin's force- and motion-generating capacity can be dramatically altered. "By correlating our experimental results with computation, we show that each isomer exerts intrinsic control by affecting distinct steps in myosin's mechano-chemical cycle."DV recalls, "My lab had never made such types of compounds before, we had to learn a new chemistry; my student Eric Ostrander worked on the synthesis." The new chemistry involves sticking three phosphate groups onto a light-sensitive molecule, azobenzene, making what the researchers now call Azobenzene triphosphate, he adds.The next stage for the trio will be to map the process at various points in myosin's biochemical cycle, Debold says. "In the muscle research field, we still don't fully understand how myosin converts energy gain from the food we eat into mechanical work. It's a question that lies at the heart of understanding how muscles contract. By feeding myosin carefully designed alternative energy sources, we can understand how this complex molecular motor works. And along the way we are likely to reveal novel targets and approaches to address a host of muscle related diseases."
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Biotechnology
| 2,020 |
July 13, 2020
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https://www.sciencedaily.com/releases/2020/07/200713144410.htm
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Uncovering the architecture of natural photosynthetic machinery
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Biological membranes play important roles in shaping the cell, sensing the external environment, molecule transport, and generating energy for life. One of the most significant biological membranes are the thylakoid membranes produced in plants, algae and cyanobacteria, which carry out the light reactions of photosynthesis.
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Researchers at the University of Liverpool have uncovered the molecular architecture and organisational landscape of thylakoid membranes from a model cyanobacterium in unprecedented detail. The study, which is published in Professor Luning Liu, who led the study, explained: "Cyanobacteria perform plant-like photosynthesis. Hence, thylakoid membranes from laboratory-grown cyanobacteria are the ideal model system for studying and tuning plant photosynthesis."The researchers used state-of-the-art atomic force microscopy (AFM) to probe the structures and organisation of photosynthetic proteins within the thylakoid membranes. The results reveal how thylakoid membranes modulate the abundance of different photosynthetic proteins and form structurally variable complexes to adapt to the changing environments.Dr Longsheng Zhao, the first author of this paper, said: "We observed that different protein complexes have their specific locations in the thylakoid membranes. We also visualised that distinct photosynthetic complexes can be close to each other, indicating that these photosynthetic complexes can form 'supercomplex' structures to facilitate electron transport between these protein complexes."Professor Luning Liu, added: "The development of structural biology approaches has greatly improved our understanding of individual photosynthetic complexes. However, these techniques have limitations for studying membrane multi-protein assembly and interactions in their native membrane environment. Our research has proved the power and potential of AFM in exploring complex, dynamic membrane structures and transient protein assembly."The researchers hope their ongoing work could help find solutions to modulate the photosynthetic efficiency of crop plants to boost plant growth and productivity.
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Biotechnology
| 2,020 |
July 13, 2020
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https://www.sciencedaily.com/releases/2020/07/200713104334.htm
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Engineered llama antibodies neutralize COVID-19 virus
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Antibodies derived from llamas have been shown to neutralise the SARS-CoV-2 virus in lab tests, UK researchers announced today.
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The team involves researchers from the Rosalind Franklin Institute, Oxford University, Diamond Light Source and Public Health England. They hope the antibodies -- known as nanobodies due to their small size -- could eventually be developed as a treatment for patients with severe COVID-19. The peer reviewed findings are published in Llamas, camels and alpacas naturally produce quantities of small antibodies with a simpler structure, that can be turned into nanobodies. The team engineered their new nanobodies using a collection of antibodies taken from llama blood cells. They have shown that the nanobodies bind tightly to the spike protein of the SARS-CoV-2 virus, blocking it from entering human cells and stopping infection.Using advanced imaging with X-rays and electrons at Diamond Light Source and Oxford University, the team also identified that the nanobodies bind to the spike protein in a new and different way to other antibodies already discovered.There is currently no cure or vaccine for COVID-19. However, transfusion of critically ill patients with serum from convalesced individuals, which contain human antibodies against the virus, has been shown to greatly improve clinical outcome. This process, known as passive immunisation, has been used for over 100 years, but it is not straightforward to identify the right individuals with the right antibodies and to give such a blood product safely. A lab-based product which can be made on demand would have considerable advantages and could be used earlier in the disease where it is likely to be more effective.Professor James Naismith, Director of The Rosalind Franklin Institute and Professor of Structural Biology at Oxford University said: "These nanobodies have the potential to be used in a similar way to convalescent serum, effectively stopping progression of the virus in patients who are ill. We were able to combine one of the nanobodies with a human antibody and show the combination was even more powerful than either alone. Combinations are particularly useful since the virus has to change multiple things at the same time to escape; this is very hard for the virus to do. The nanobodies also have potential as a powerful diagnostic."Professor Ray Owens from Oxford University, who leads the nanobody program at the Franklin, said: "This research is a great example of team work in science, as we have created, analysed and tested the nanobodies in 12 weeks. This has seen the team carry out experiments in just a few days, that would typically take months to complete. We are hopeful that we can push this breakthrough on into pre-clinical trials."Professor David Stuart, from Diamond Light Source and Oxford University said: "The electron microscopy structures showed us that the three nanobodies can bind to the virus spike, essentially covering up the portions that the virus uses to enter human cells."The team started from a lab-based library of llama antibodies. They are now screening antibodies from Fifi, one of the 'Franklin llamas' based at the University of Reading, taken after she was immunised with harmless purified virus proteins.The team are investigating preliminary results which show that Fifi's immune system has produced different antibodies from those already identified, which will enable cocktails of nanobodies to be tested against the virus.The Rosalind Franklin Institute is a new research institute funded through UK Research and Innovation's Engineering and Physical Sciences Research Council. The Franklin is leading the UK's work in the innovative field of nanobodies, whose tiny size and specificity make them perfect tools for scientific research, usually used to stabilise proteins for imaging. The Institute is named for the researcher Rosalind Franklin, who was born 100 years ago this year. Although famous for her contribution to the discovery of DNA, Franklin's later career turned to imaging virus structures, including polio.Professor Naismith said: "2020 marks the centenary of Franklin's birth. As an institute named for a pioneer of biological imaging, we are proud to follow in her footsteps and continue her work in viruses, applied here to an unprecedented global pandemic. Franklin's work transformed biology, and our projects aspire to that same transformational effect."
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Biotechnology
| 2,020 |
July 10, 2020
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https://www.sciencedaily.com/releases/2020/07/200710131520.htm
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Fast-spreading mutation helps common flu subtype escape immune response
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Strains of a common subtype of influenza virus, H3N2, have almost universally acquired a mutation that effectively blocks antibodies from binding to a key viral protein, according to a study from researchers at Johns Hopkins Bloomberg School of Public Health.
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The results have implications for flu vaccine design, according to the researchers. Current flu vaccines, which are "seasonal vaccines" designed to protect against recently circulating flu strains, induce antibody responses mostly against a different viral protein called hemagglutinin.The new mutation, described in the study published online June 29 in The mutation alters a viral protein called neuraminidase, and the researchers found in their study that this alteration paradoxically reduces the ability of flu virus to replicate in a type of human nasal cell that it normally infects. However, the researchers also found evidence that the mutation more than compensates for this deficit by setting up a physical barrier that hinders antibodies from binding to neuraminidase."These findings tell us that flu vaccines focusing on the hemagglutinin protein are leaving the virus openings to evolve and evade other types of immunity," says study senior author Andrew Pekosz, PhD, professor and vice chair of the Department of Molecular Microbiology and Immunology at the Bloomberg School.Every year, influenza viruses sicken millions of people around the world, killing several hundred thousands. The diversity of flu strains and their ability to mutate rapidly -- two strains infecting the same host can even swap genes -- have made flu viruses an especially difficult target for vaccine designers. Although scientists are working towards a universal vaccine that will protect long-term against most flu variants, current flu vaccines are designed to protect against only a short list of recently circulating strains. Any mutation that occurs in these circulating strains and appears to improve their ability to spread is naturally of interest to flu virologists.The goal of the study was to understand better the workings of the new H3N2 mutation. Scientists have known that it alters the flu virus's neuraminidase protein in a way that provides an attachment point, close to neuraminidase's active site, for a sugar-like molecule called a glycan. But how the presence of a glycan at that location on the neuraminidase protein improves the virus's ability to infect hosts and spread hasn't been clear.Pekosz and first author Harrison Powell, PhD, a graduate student in his laboratory at the time of the study, compared the growth, in laboratory cells, of typical H3N2 strains that have the glycan-attachment mutation to the growth of the same flu strains without the mutation. They found that the mutant versions grew markedly more slowly in human cells from the lining of the nasal passages -- a cell type that a flu virus would initially infect.The researchers found the likely reason for this slower growth: the glycan-attracting mutation hinders the activity of neuraminidase. The protein is known to serve as a crucial flu enzyme whose functions include clearing a path for the virus through airway mucus, and enhancing the release of new virus particles from infected cells.It wasn't entirely unexpected that the addition of a moderately bulky glycan molecule near the enzyme's active site would have this effect. But it left unexplained how that would benefit the virus.The scientists solved the mystery by showing that the glycan blocks antibodies that would otherwise bind to or near the active site of the neuraminidase enzyme.Neuraminidase, especially its active site, is considered one of the most important targets for the immune response to a flu infection. It is also the target of flu drugs such as Tamiflu (oseltamivir). Thus it makes sense that a mutation protecting that target confers a net benefit to the virus, even if it means that the neuraminidase enzyme itself works less efficiently.The finding highlights the potential for flu viruses to evade therapies, seasonal vaccines, and the ordinary immune response, Pekosz says, and points to the need for targeting multiple sites on the virus to reduce the chance that single mutations can confer such resistance.The researchers have been following up their findings with studies of how the new mutation affects the severity of flu, how it has spread so rapidly among H3N2 strains, and how these altered flu strains have adapted with further mutations.The study was supported by the National Institute of Allergy and Infectious Diseases (CEIRS HHSN272201400007C) and the National Institutes of Health (T32 AI007417).
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Biotechnology
| 2,020 |
July 10, 2020
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https://www.sciencedaily.com/releases/2020/07/200710100940.htm
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Researchers solve a 50-year-old enzyme mystery
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Advanced herbicides and treatments for infection may result from the unravelling of a 50-year-old mystery by University of Queensland researchers.
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The research team, led by UQ's Professor Luke Guddat, revealed the complete three-dimensional structure of an enzyme, providing the first step in the biosynthesis of three essential amino acids -- leucine, valine and isoleucine."This is a major scientific advance, which has been pursued globally by chemists for half a century," Professor Guddat said."This information provides new insights into an important enzyme -- acetohydroxyacid synthase -- a target for more than 50 commercial herbicides."It's also a potential target for new drugs to treat infections such as tuberculosis and invasive Candida infections."Using advanced techniques such as cryo-electron microscopy and X-ray crystallography, the team deciphered the structure of the plant and fungal versions of the enzyme."We identified how this highly complex structure is assembled, which is the highly unusual shape of a Maltese Cross," Professor Guddat said."Coincidently, the Maltese Cross also features as a part of UQ's logo."Professor Guddat said the discovery could have big implications for global agriculture."Sulfometuron is a herbicide that targets this enzyme, and was widely used in the 1990s for wheat crop protection throughout Australia," he said."But today it is completely ineffective due to the development of resistance."With this new insight, we will be able to make changes to existing herbicides, restoring options for future herbicide application."Professor Guddat said the enzyme was only found in plants and microbes, not in humans."For this reason, the herbicides and drugs that it targets are likely to be safe and non-toxic to all mammals," he said."And another surprising finding of the research was the role that the molecule known as ATP plays in the regulation of the enzyme."Normally ATP plays a role in providing energy to all living cells," Professor Guddat said."However, here it is acting like a piece of glue to hold the structure together.""They're fascinating findings for us, and we're excited for new opportunities for targeted design of next-gen herbicides and antimicrobial agents."
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Biotechnology
| 2,020 |
July 9, 2020
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https://www.sciencedaily.com/releases/2020/07/200709150118.htm
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Biologists trace plants' steady mitochondrial genomes to a gene found in viruses, bacteria
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One could say that mitochondria, the energy-producing organelles inside every human cell, dance to their own beat. After all, they have their own genome - a set of DNA-containing chromosomes -- completely separate from the genome of the cell's nucleus.
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Mitochondria are essential to life because they power the cell's biochemical reactions, but they make a lot of missteps -- that is, their genomes do. Human mitochondrial genomes are notoriously prone to mutation, which is why so many genetic disorders -- from diabetes mellitus to mitochondrial myopathy -- are linked to malfunctioning genes in this organelle.Seeking to understand why human mitochondrial genomes mess up so much, Colorado State University biologist Dan Sloan thinks we have a lot to learn from our very distant evolutionary cousins -- plants. Like us, plants maintain a separate mitochondrial genome, but unlike us, plant mitochondrial genomes have some of the slowest known mutation rates of any living thing -- about one mutation at each DNA position in a billion years. Just how they keep their genetic sequences on lockdown, while we don't, has long been a mystery for many biologists.Sloan is funded by a grant from the National Institutes of Health to investigate why plants have such stable mitochondrial genomes, and his lab has recently come across a tantalizing lead. They have traced this stability to a particular gene -- MSH1 -- that plants have but animals (including us) don't. Their experiments, described in "Understanding how some systems have been able to maintain these really accurate, low mutation rates, sets up the opportunity for understanding the flip side of the coin -- how it is that humans suffer such high mitochondrial mutation rates," said Sloan, associate professor in the Department of Biology. "It's not as simple as just the nasty chemistry going on inside these mitochondrial compartments, as some have thought. It probably comes down to more differences between organisms' error correction machinery. That's one of the punchlines that comes out of this research."The researchers tested several plant genes they thought might be responsible for mitochondrial genomic stability. They found that disrupting the MSH1 gene in a common plant, Arabidopsis thaliana, led to massive increases in frequency of point mutations and changes to the mitochondrial DNA. MSH1, it turns out, contains molecular features that may make it able to recognize mismatches of nucleotide base pairings during the process of DNA copying. They researchers plan to follow up on this hypothesis in later studies.The MSH1 gene exists in plants, but not animals, which offers a good explanation for why human mitochondrial genomes mutate so often. The researchers then asked, where did this gene come from?To find an answer, undergraduate researcher and paper co-author Connor King set out to explore the distribution of the gene across the tree of life. He computationally mined nucleotide and protein sequence repositories to find what species have the gene. He found evidence of the gene not only in plants but also in many lineages of complex organisms, including single-celled eukaryotic organisms, as well as some prokaryotic and viral species.King's analysis raises the possibility that the gene came from so-called giant viruses that have genomes almost the size of bacteria, and are much more complex than typical viruses. They may have been shared with other organisms via an ancient horizontal gene transfer, in which one species transfers DNA into another."Connor's results pretty clearly tell us that this gene has been transferred around different parts of the tree of life," Sloan said. This insight would be consistent with the idea that some organisms manage to borrow machinery from viruses and replace it with their own.The study was made possible by advanced DNA sequencing, in which huge amounts of DNA can be mined to find very rare mutations. A key enabling innovation was led by graduate student and co-author Gus Waneka, who customized a technique called duplex sequencing to increase its accuracy within the margin of error the team needed to draw their conclusions.
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Biotechnology
| 2,020 |
July 9, 2020
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https://www.sciencedaily.com/releases/2020/07/200709141619.htm
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Safer CRISPR gene editing with fewer off-target hits
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The CRISPR system is a powerful tool for the targeted editing of genomes, with significant therapeutic potential, but runs the risk of inappropriately editing "off-target" sites. However, a new study publishing July 9, 2020 in the open-access journal
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The CRISPR system employs an enzyme called Cas9 to cleave DNA. Cas9 will cut almost any DNA sequence. Its specificity comes from its interaction with a "guide RNA" (gRNA) whose sequence allows it to bind with the target DNA through base-pair matching. Once it does, the enzyme is activated and the DNA is cut.The CRISPR system is found in multiple bacterial species; among those commonly used in research, that from Staphylococcus aureus has the advantage of size -- unlike some others, its gene is small enough to fit inside a versatile and harmless gene therapy vector called adeno-associated virus, making it attractive for therapeutic purposes.A key limitation of any of the CRISPR systems, including that from S. aureus, is off-target cleavage of DNA. A guide RNA may bind weakly to a site whose sequence is a close but imperfect match; depending on how close the match is and how tightly the enzyme interacts with the paired gRNA-DNA complex, the enzyme may become activated and cut the DNA wrongly, with potentially harmful consequences.To explore whether the S. aureus Cas9 could be modified to cleave with higher fidelity to the intended target, the authors generated a range of novel Cas9 mutants and tested their ability to discriminate against imperfect matches while retaining high activity at the intended site. They found one such mutant, which distinguished and rejected single base-pair mismatches between gRNA and DNA, regardless of the target, increasing the fidelity up to 93-fold over the original enzyme. They showed that the mutation affected part of the recognition domain, the region of the enzyme that coordinates contacts between the enzyme and the gRNA-DNA complex. The mutation had the likely effect of weakening those contacts, thus ensuring that only the strongest pairing -- which would come from a perfect sequence match -- would trigger enzyme activity."Avoidance of off-target cleavage is a crucial challenge for development of CRISPR for medical interventions, such as correcting genetic diseases or targeting cancer cells," Gu said. "Our results point the way to developing potentially safer gene therapy strategies."
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Biotechnology
| 2,020 |
July 9, 2020
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https://www.sciencedaily.com/releases/2020/07/200709092502.htm
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New clues from fruit flies about the critical role of sex hormones in stem cell control
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In one of the first studies addressing the role of sex hormones' impact on stem cells in the gut, scientists outline new insights showing how a steroidal sex hormone, that is structurally and functionally similar to human steroid hormones, drastically alters the way intestinal stem cells behave, ultimately affecting the overarching structure and function of this critical organ. The authors found that ecdysone, a steroid hormone produced by fruit flies, stimulates intestinal stem cell growth and causes the gut of the female fruit fly to grow in size, and induces other critical changes. The study also provides a mechanism to account for sex-specific roles for intestinal stem cells in normal gut function. Moreover, the research presents evidence that gut hormones may accelerate tumor development. The findings, reported jointly by Huntsman Cancer Institute (HCI) at the University of Utah (U of U) and the German Cancer Research Center (DKFZ), are published today in the journal
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Bruce Edgar, PhD, a stem cell biologist at HCI and professor of oncological sciences at the U of U, together with Aurelio Teleman, PhD, division head at DKFZ and professor at Heidelberg University jointly led the work. They asked whether sex hormones affect intestinal stem cells' ability to multiply and contribute to gut growth. "My lab and many others around the world have studied the Drosophila gut for some time to better understand how stem cells are regulated," says Edgar. "We knew that male and female fruit flies exhibited differences in their intestine -- for example, the female's intestine is larger than the male's, and females develop intestinal tumors much more readily than males -- but we didn't know why." This study adds significant insights into these differences, and how they arise.The Edgar and Teleman teams found that ecdysone, a sex-specific hormone, can drastically alter the growth properties of stem cells in an organ that, remarkably, is not directly involved in reproduction. They found that these changes affect the structure and function of the entire organ. They discovered that subjecting male flies to ecdysone caused their otherwise slow dividing stem cells to divide as fast as in females, leading to intestinal growth in males as well. This suggests that the limiting difference between the division of stem cells in male and female flies is the circulating levels of the hormone.This process confers both advantages and disadvantages to the female fruit fly during the course of its life. Initially, more ecdysone in females helps with the evolutionarily critical processes of reproduction. It promotes gut enlargement, facilitating nutrient absorption, which helps the fly lay more eggs. But later in life, the ecdysone hormone, produced by the ovaries, eventually causes gut disfunction that can shorten the lifespan in female fruit flies by creating an environment that favors tumor growth. While humans don't produce ecdysone, they do have related steroid hormones such as estrogen, progesterone and testosterone, which have similar mechanisms of action.The experimental work on this study was performed primarily by Sara Ahmed, a joint PhD student between the Edgar and Teleman labs at the Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) and the DKFZ. Ahmed designed experiments utilizing various genetic tools to switch genes on and off in different cell types in the fly's intestine and in its ovaries, which produce ecdysone. "Our study provides conclusive evidence that sex hormones alter the behavior of non-sex organs like the intestine," says Ahmed. She further speculates that long-term implications of this research may include exploration of new paths to treating human cancers.According to the researchers, understanding whether a similar stem cell-hormone relationship operates in human organs will require further studies. They plan to explore this in the future. In addition to the critical role played by sex hormones in intestinal stem cell behavior, the authors believe this study in Drosophila potentially unveils a new mechanism that may play out in human physiology and pathology. Insights from this study add to a growing body of work showing that the incidence cancers of non-reproductive organs, including colon and gastric cancers, are different in males and females.This study was supported by the National Institutes of Health including the National Cancer Institute P30 CA01420114, the National Institute of General Medical Sciences R01 124434, the European Research Council AdG268515, DKFZ, and Huntsman Cancer Foundation.
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Biotechnology
| 2,020 |
July 8, 2020
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https://www.sciencedaily.com/releases/2020/07/200708150606.htm
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How good gut bacteria help reduce the risk for heart disease
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Scientists have discovered that one of the good bacteria found in the human gut has a benefit that has remained unrecognized until now: the potential to reduce the risk for heart disease.
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The bacteria's activity in the intestines reduces production of a chemical that has been linked to the development of clogged arteries. After it's manufactured in the gut, the chemical enters the bloodstream and travels to the liver, where it is converted into its most harmful form.The Ohio State University researchers have traced the bacteria's behavior to a family of proteins that they suspect could explain other ways that good gut organisms can contribute to human health. In essence, these microbes compete with bad bacteria for access to the same nutrients in the gut -- and if the good bacteria win, they may prevent health problems that can result from how the body metabolizes food.Much more work is ahead, but the scientists see potential for this microbe, Eubacterium limosum, to be used for therapeutic purposes in the future. Previous research has already shown the bacterium is "good" because it calms inflammation in the gut."Over the last decade, it has become apparent that bacteria in the human gut influence our health in many ways. The organism we studied affects health by preventing a problematic compound from becoming a worse one," said Joseph Krzycki, professor of microbiology at Ohio State and senior author of the study. "It's too soon to say whether this bacterium could have therapeutic value. But that's what we're working toward."The research appears online and will be published in a future edition of the The chemical linked to the clogged arteries that characterize atherosclerosis is called trimethylamine, or TMA. It is produced during metabolism when some intestinal microbes -- generally the bacteria considered unhelpful to humans -- interact with certain nutrients from food. Among those nutrients is L-carnitine, a chemical compound found in meat and fish that is also used as a nutritional supplement to improve recovery after exercise.Krzycki and his colleagues discovered that E. limosum interacts with L-carnitine in a different way in the gut, and that interaction eliminates L-carnitine's role in production of TMA (other nutrients also participate in TMA production in the gut).The researchers attribute the bacteria's beneficial behavior to a protein called MtcB, an enzyme that cuts specific molecules off of compounds to help bacteria generate energy and survive. The process is called demethylation, and involves the removal of one methyl group -- a carbon atom surrounded by three hydrogen atoms -- to change a compound's structure or function."The bacterium does this for its own benefit, but it has the downstream effect of reducing the toxicity of TMA," Krzycki said. "Up until now, the only known gut microbial reactions with L-carnitine involved converting it into its bad form. We've discovered that a bacterium known to be beneficial could remove a methyl group and send the resulting product down another pathway without making any other harmful compounds in the process."In these interactions, L-carnitine functions as a growth substrate -- a compound consumed so the organism can live and grow, and also a target for enzyme activity. In the study, the researchers fed E. limosum cultures an assortment of potential substrates, including L-carnitine. Only when offered L-carnitine did the microbe synthesize the MtcB protein specifically to lop off L-carnitine's methyl group -- in essence, MtcB is part of the bacteria's natural way to consume the nutrient.Krzycki said finding this one significant health benefit in one species of gut bacteria suggests there is still a lot to learn about how gut bacteria can influence health outcomes associated with human metabolism."MtcB is part of a family of proteins with thousands of representatives that may use different compounds and change what nutrients bacteria consume in the gut," he said. "These proteins may behave very similarly chemically, but using different compounds obviously can create big changes as far as biology goes."This work was supported by grants from the National Institutes of Health.
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Biotechnology
| 2,020 |
July 8, 2020
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https://www.sciencedaily.com/releases/2020/07/200708150601.htm
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How bacteria build essential carbon-fixing machinery
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Scientists from the University of Liverpool have revealed new insight into how cyanobacteria construct the organelles that are essential for their ability to photosynthesise. The research, which carried out in collaboration with the University of Science and Technology of China, has been published in
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Cyanobacteria are an ancient group of photosynthetic microbes that occur in the ocean and most inland waters. They have evolved a protein organelle, called the carboxysome, to convert environmental carbon dioxide into sugar in an efficient way.A key step of this conversion is catalysed by a carbon-fixing enzyme Rubisco. However, Rubisco is poorly 'designed' because it is inefficient in fixing CO"It is a mystery how cyanobacterial cells generate the complex carboxysome structure and pack Rubisco enzymes in the organelle to have biological functions," said Luning Liu, a Professor at the University of Liverpool, and a senior author on this paper. "My research group has interest in addressing the key questions in this biological process."The formation of the Rubisco complex involves a few 'helping' proteins called chaperones, including a protein named Rubisco assembly factor 1 (Raf1). To understand the exact roles of Raf1, the team used state-of-the-art microscopies, such as confocal fluorescence microscopy, electron microscopy, and cryo-electron microscopy, combined with molecular biology and biochemical techniques, to study how Raf1 interacts with Rubisco subunits to promote the assembly of Rubisco, and how carboxysome formation is affected when cells do not produce Raf1.The researchers proved that Raf1 is vital for building the Rubisco complex. Without Raf1, the Rubisco complexes are less efficiently assembled and cannot be densely packed inside the carboxysomes. This could greatly affect the construction of carboxysomes and therefor the growth of cyanobacterial cells."This is the first time that we have determined the function of Rubisco assembly chaperones in the biosynthesis of carboxysomes in cyanobacterial cells," said Dr Fang Huang, a Leverhulme Trust Early Career Fellow, and the first author on this paper. "We are very excited about this finding. It also allowed us to propose a new working model of carboxysome biogenesis, which teach us in detail how Rubisco complexes are generated, how Raf1 drive Rubisco packing, and how the entire carboxysome structure is constructed."Currently, there is a tremendous interest in transferring carboxysomes into crop plants to improve crop yields and food production. This study may provide important information required for producing intact and functional carbon-fixing machinery.
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Biotechnology
| 2,020 |
July 8, 2020
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https://www.sciencedaily.com/releases/2020/07/200708110013.htm
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Fluorescent peptide nanoparticles, in every color of the rainbow
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The discovery of green fluorescent protein (GFP), which is made by a jellyfish, transformed cell biology. It allowed scientists to stitch the GFP sequence to proteins from other organisms to trace their movements and interactions in living cells. Now, researchers reporting in
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Scientists have tried to mimic the fluorescence of GFP in small molecules such as chromophore-containing polymers or fluorescent peptide nanostructures. Peptides, which are small pieces of proteins, are attractive because of their structural simplicity and biocompatibility. However, previous fluorescent peptide nanomaterials glow in only one color, which limits their use. Yuefei Wang and colleagues wanted to make peptides that can fluoresce in a rainbow of colors.The researchers designed 12 peptides that contained 1-3 copies of the amino acids phenylalanine, tyrosine, tryptophan or histidine, all of which are weakly fluorescent in the visible range. They added a hydrophobic ferrocene group to one end of the peptide, which caused multiple peptides to assemble into spherical fluorescent nanoparticles. The ferrocene group also changed the emission properties, or colors, of the peptides. The researchers found that each peptide nanoparticle could glow in more than one color, and together, the 12-peptide palette encompassed all colors in the visible region of light. The peptide colors were photostable and showed no toxicity when added to human cells. These results indicate that the peptide nanoprobes could be substituted for fluorescent proteins, such as GFP, in biomedical imaging, although the fluorescence quantum yield is not as high, the researchers say.
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Biotechnology
| 2,020 |
July 8, 2020
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https://www.sciencedaily.com/releases/2020/07/200708105955.htm
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Spider silk made by photosynthetic bacteria
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Spiders produce amazingly strong and lightweight threads called draglines that are made from silk proteins. Although they can be used to manufacture a number of useful materials, getting enough of the protein is difficult because only a small amount can be produced by each tiny spider. In a new study published in
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In addition to being tough and lightweight, silks derived from arthropod species are biodegradable and biocompatible. In particular, spider silk is ultra-lightweight and is as tough as steel. "Spider silk has the potential to be used in the manufacture of high-performance and durable materials such as tear-resistant clothing, automobile parts, and aerospace components," explains Choon Pin Foong, who conducted this study. "Its biocompatibility makes it safe for use in biomedical applications such as drug delivery systems, implant devices, and scaffolds for tissue engineering." Because only a trace amount can be obtained from one spider, and because breeding large numbers of spiders is difficult, attempts have been made to produce artificial spider silk in a variety of species.The CSRS team focused on the marine photosynthetic bacterium Rhodovulum sulfidophilum. This bacterium is ideal for establishing a sustainable bio-factory because it grows in seawater, requires carbon dioxide and nitrogen in the atmosphere, and uses solar energy, all of which are abundant and inexhaustible.The researchers genetically engineered the bacterium to produce MaSp1 protein, the main component of the Nephila spider dragline which is thought to play an important role in the strength of the spider silk. Optimization of the gene sequence that they inserted into the bacterium's genome was able to maximize the amount of silk that could be produced. They also found that a simple recipe -- artificial seawater, bicarbonate salt, nitrogen gas, yeast extract, and irradiation with near-infrared light -- allows R. sulfidophilum to grow well and produce the silk protein efficiently. Further observations confirmed that the surface and internal structures of the fibers produced in the bacteria were very similar to those produced naturally by spiders."Our current study shows the initial proof of concept for producing spider silk in photosynthetic bacteria. We are now working to mass produce spider-silk dragline proteins at higher molecular weights in our photosynthetic system," Numata says. "The photosynthetic microbial cell factories, which produce bio-based and bio-degradable materials via a carbon neutral bioprocess, could help us in accomplishing some of the Sustainable Development Goals (SDGs) adopted by the United Nations such as Goal #12 'Responsible Production and Consumption, and Goal #13 'Climate Action'. Our results will help provide feasible solutions for energy, water and food crises, solid waste problems, and global warming."
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Biotechnology
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July 7, 2020
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https://www.sciencedaily.com/releases/2020/07/200707183922.htm
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Strain of E. coli may offer protections against its more malevolent cousins
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Typically, there aren't a lot of positive thoughts when
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But for more than a century, one strain of the bacteria, Now researchers at the University of Cincinnati College of Medicine say Alison Weiss, PhD, professor, and Suman Pradhan, PhD, research associate, both in in the UC Department of Molecular Genetics, Biochemistry and Microbiology, used stem cell-derived human intestinal organoid tissues to evaluate the safety of Nissle and its ability to protect from pathogenic They found that human intestinal tissues (HIO) were not harmed by the Nissle bacteria introduced into human intestinal organoids while pathogenic The study's findings are available online in "Nissle did not kill pathogenic "There are all sorts of flavors of Weiss says they hope to learn more about the abilities of Nissle in order to develop a treatment of "Right now there is no cure for an "The study conducted by Weiss and Pradhan was supported by National Institutes of Health grants U19-AI116491 and R01AI139027 and by the National Institute of Diabetes and Digestive and Kidney Diseases grant P30 DK078392.
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Biotechnology
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July 7, 2020
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https://www.sciencedaily.com/releases/2020/07/200707134208.htm
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RNA key in helping stem cells know what to become
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Look deep inside our cells, and you'll find that each has an identical genome -a complete set of genes that provides the instructions for our cells' form and function.
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But if each blueprint is identical, why does an eye cell look and act differently than a skin cell or brain cell? How does a stem cell -- the raw material with which our organ and tissue cells are made -- know what to become?In a study published July 8, University of Colorado Boulder researchers come one step closer to answering that fundamental question, concluding that the molecular messenger RNA (ribonucleic acid) plays an indispensable role in cell differentiation, serving as a bridge between our genes and the so-called "epigenetic" machinery that turns them on and off.When that bridge is missing or flawed, the researchers report in the journal The paper comes at a time when pharmaceutical companies are taking unprecedented interest in RNA. And, while the research is young, it could ultimately inform development of new RNA-targeted therapies, from cancer treatments to therapies for cardiac abnormalities."All genes are not expressed all the time in all cells. Instead, each tissue type has its own epigenetic program that determines which genes get turned on or off at any moment," said co-senior author Thomas Cech, a Nobel laureate and distinguished professor of biochemistry. "We determined in great detail that RNA is a master regulator of this epigenetic silencing and that in the absence of RNA, this system cannot work. It is critical for life."Scientists have known for decades that while each cell has identical genes, cells in different organs and tissues express them differently. Epigenetics, or the machinery that switches genes on or off, makes this possible.But just how that machinery works has remained unclear.In 2006, John Rinn, now a professor of biochemistry at CU Boulder and co-senior-author on the new paper, proposed for the first time that RNA -- the oft-overlooked sibling of DNA (deoxyribonucleic acid) -- might be key.In a landmark paper in Cell, Rinn showed that inside the nucleus, RNA attaches itself to a folded cluster of proteins called polycomb repressive complex (PRC2), which is believed to regulate gene expression. Numerous other studies have since found the same and added that different RNAs also bind to different protein complexes.The hotly debated question: Does this actually matter in determining a cell's fate?No fewer than 502 papers have been published since. Some determined RNA is key in epigenetics; others dismissed its role as tangential at best.So, in 2015, Yicheng Long, a biochemist and postdoctoral researcher in Cech's lab, set out to ask the question again using the latest available tools. After a chance meeting in a breakroom at the BioFrontiers Institute where both their labs are housed, Long bumped into Taeyoung Hwang, a computational biologist in Rinn's lab.A unique partnership was born."We were able to use data science approaches and high-powered computing to understand molecular patterns and evaluate RNA's role in a novel, quantitative way," said Hwang, who along with Long is co-first-author on the new paper.In the lab, the team then used a simple enzyme to remove all RNA in cells to understand whether the epigenetic machinery still found its way to DNA to silence genes. The answer was 'no.'"RNA seemed to be playing the role of air traffic controller, guiding the plane -- or protein complex -- to the right spot on the DNA to land and silence genes," said Long.For a third step, they used the gene-editing technology known as CRISPR to develop a line of stem cells destined to become human heart muscle cells but in which the protein complex, PRC2, was incapable of binding to RNA. In essence, the plane couldn't connect with air-traffic control and lost its way, and the process fell apart.By day 7, the normal stem cells had begun to look and act like heart cells. But the mutant cells didn't beat. Notably, when normal PRC2 was restored, they began to behave more normally."We can now say, unequivocally, that RNA is critical in this process of cell differentiation," said Long.Previous research has already shown that genetic mutations in humans that disrupt RNA's ability to bind to these proteins boost risk of certain cancers and fetal heart abnormalities. Ultimately, the researchers envision a day when RNA-targeted therapies could be used to address such problems."These findings will set a new scientific stage showing an inextricable link between epigenetics and RNA biology," said Rinn. "They could have broad implications for understanding, and addressing, human disease going forward."
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Biotechnology
| 2,020 |
July 7, 2020
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https://www.sciencedaily.com/releases/2020/07/200707113255.htm
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Research reveals regulatory features of maize genome during early reproductive development
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Growth and development of all organisms depends on coordinated regulation of gene expression in time and space, and this is largely controlled by non-coding sequences in the genome. A major challenge in genomics-enabled crop improvement is functional annotation of cis-regulatory elements in crop genomes and the ability to harness these sequences, either through breeding or biotechnology, to fine-tune target pathways with minimal disruption to the complex networks in which they reside.
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A team of researchers led by Andrea Eveland, Ph.D., assistant member, Donald Danforth Plant Science Center, has mapped out the non-coding, 'functio nal' genome in maize during an early developmental window critical to formation of pollen-bearing tassels and grain-bearing ears.Integrating information on chromatin structure, transcript profiles, and genome-wide association studies, their analyses provide a comprehensive look into the regulation of inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential. This study by Parvathaneni and Bertolini et al., "The regulatory landscape of early maize inflorescence development," was published on July 6, 2020 in the journal, "We have a good idea of the major controllers of inflorescence development in maize from years of classical genetics studies" said Eveland. "But simply removing their function or expressing them constitutively usually does not result in higher-yielding corn. We need to learn how to adjust their expression precisely in space and time to achieve optimal outputs. This study serves as a foundation for doing that."Over the past century, hybrid-based breeding and improvement in maize has led to selection of smaller tassels that intercept less light and sequester less resources, and larger, more productive ears. Since the tassel and ear develop by a common developmental program, further improvement of ear traits will require decoupling of this program, for example, by tassel- or ear-specific regulatory elements. Understanding how the same genes are regulated differently in tassel and ear, and using this specificity to control one over the other, will enhance breeding efforts in maize.Eveland's research focuses on the developmental mechanisms that control plant architecture traits in cereal crops. Specifically, she investigates how plant organs are formed from stem cells, and how variation in the underlying gene regulatory networks can precisely modulate plant form. Her team integrates both computational and experimental approaches to explore how perturbations to these gene networks can alter morphology, both within a species and across the grasses, with the ultimate goal of defining targets for improving grain yield in cereals.In addition to Eveland's team, co-authors include researchers from Florida State University, the University of California at Davis, and the University of Illinois Urbana-Champaign. The collaborative research was funded by the National Science Foundation PGRP in awards to Eveland and co-author Alexander Lipka, Ph.D. (UIUC) to identify regulatory variation for improving maize yield traits, and to Hank Bass, Ph.D. (FSU) to apply techniques in chromatin profiling to important agronomic crop species.
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Biotechnology
| 2,020 |
July 7, 2020
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https://www.sciencedaily.com/releases/2020/07/200707113215.htm
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Sensory neurons outside the brain drive autistic social behaviors, study suggests
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A new study from Penn Medicine lends further evidence that the social behaviors tied to autism spectrum disorders (ASD) emerge from abnormal function of sensory neurons outside the brain. It's an important finding, published today in the journal
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In the fruit fly "These data raise the exciting possibility that the root of the problem doesn't begin with errors in the brain itself. It's the disrupted flow of information from the periphery to the brain we should be taking a closer look at," said senior author Matthew Kayser, MD, PhD, an assistant professor in the department of Psychiatry in the Perelman School of Medicine at the University of Pennsylvania. "The findings should help guide the field toward sensory processing therapeutic targets that, if effective, could be transformative for patients suffering from these disorders."In humans, a loss of neurofibromin 1 is associated with neurofibromatosis type 1 (NF1), a neurodevelopmental disorder with high rates of ASD, but how that loss leads to social deficits is unknown. Past studies have also shown a link between the peripheral sensory system and social deficits; however, this is the first study to implicate neurofibromin's function.Up to 50 percent of children with NF1 fall on the autism spectrum, and are 13 times more likely to exhibit highly elevated ASD symptoms, including social and communicative disabilities, increased isolation and bullying, difficulties on social tasks, and sensitivities to sound or light. Those symptoms are all tied to difficulties with processing sensory information. Face and gaze processing, for example, makes a social gesture like eye contact exceedingly difficult.The team, led by Penn postdoctoral scientist Emilia Moscato, PhD, used genetically manipulated flies to show that a loss of neurofibromin led to diminished social courtship behavior and errors in gustatory sensory neurons called ppk23, which are known to coordinate such behaviors. These behavioral deficits stem from an ongoing role for neurofibromin in coordinating social functions in adults, as opposed to guiding development of social behavioral neural circuits.More specifically, in vivo monitoring of neural activity in the mutant flies showed decreased sensory neuron activation in response to specific pheromonal cues, which then disrupted proper function of downstream brain neurons that direct social decisions. The disruption also led to persistent changes in behavior of the flies beyond the social interaction itself, suggesting a brief sensory error can have long-lasting consequences on behavior.Next, the researchers aim to better understand how this mutation translates to disruption in brain activity and ultimately behaviors associated with ASD and NF1. They also hope to test different drugs in animal models to identify novel compounds that can restore social behaviors."Sensory processing is a readily testable entry-point into social behavioral dysfunction," Kayser said, "so findings from these experiments have potential to rapidly impact the clinical setting."Co-authors of the study include Penn's Moscato and Christine Dubowy, as well as James A. Walker of Massachusetts General Hospital.This work was supported by a McMorris Autism Early Intervention Initiative Fund Pilot Study Award, a Burroughs Wellcome Career Award for Medical Scientists, a National Institutes of Health grant (DP2 NS111996), and an NIH New Program Development Award of the Intellectual and Developmental Disabilities Research Center at Children's Hospital of Philadelphia/Penn (U54 HD086984).
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Biotechnology
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July 6, 2020
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https://www.sciencedaily.com/releases/2020/07/200706173451.htm
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When it comes to DNA repair, it's not one tool fits all
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Our cells are constantly dividing, and as they do, the DNA molecule -- our genetic code -- sometimes gets broken. DNA has twin strands, and a break in both is considered especially dangerous. This kind of double-strand break can lead to genome rearrangements that are hallmarks of cancer cells, said James Daley, PhD, of the Long School of Medicine at The University of Texas Health Science Center at San Antonio.
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Dr. Daley is first author of research, published June 18 in the journal "What's exciting about this work is that it answers a long-held mystery among scientists," Dr. Daley said. "For a decade we have known that resection enzymes are at the forefront of homologous recombination. What we didn't know is why so many of these enzymes are involved, and why we need three or four different enzymes that seem to accomplish the same task in repairing double-strand breaks.""On the surface of it, there seems to be quite a bit of redundancy," said Dr. Sung, who holds the Robert A. Welch Distinguished Chair in Chemistry at UT Health San Antonio. "Our study is significant in showing that the perceived redundancy is really a very naïve notion."DNA resection pathways actually are highly specific, the findings show."It's like an engine mechanic who has a set of tools at his disposal," Dr. Sung said. "The tool he uses depends on the issue that needs to be repaired. In like fashion, each DNA repair tool in our cells is designed to repair a distinctive type of break in our DNA."The research team studied complex breaks that featured double-strand breaks with other kinds of DNA damage nearby -- such complex breaks are more relevant physiologically, Dr. Daley said. Studies in the field of DNA repair usually tend to look at simpler versions of double-strand breaks, he said. Dr. Daley found that each resection enzyme is tailored to deal with a specific type of complex break, which explains why a diverse toolkit of resection enzymes has evolved over millennia.Dr. Burma, the Mays Family Foundation Distinguished Chair in Oncology at UT Health San Antonio MD Anderson Cancer Center, said the fundamental understandings gleaned from this research could one day lead to improved cancer treatments."The cancer therapeutic implications are immense," Dr. Burma said. "This research by our team is timely because a new type of radiation therapy, called carbon ion therapy, is now being considered in the U.S. While being much more precisely aimed at tumors, this therapy is likely to induce exactly the sort of complex DNA damage that we studied. Understanding how specific enzymes repair complex damage could lead to strategies to dramatically increase the efficacy of cancer therapy."Part of the research is funded by NASA. "These kinds of complex DNA breaks are also induced by space radiation," Dr. Burma said. "Therefore, the research is relevant not just to cancer therapy, but also to cancer risks inherent to space exploration."
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Biotechnology
| 2,020 |
July 6, 2020
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https://www.sciencedaily.com/releases/2020/07/200706140848.htm
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Biological factories: How do bacteria build up natural products?
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The active agents of many drugs are natural products, so called because often only microorganisms are able to produce the complex structures. Similar to the production line in a factory, large enzyme complexes put these active agent molecules together. A team of the Technical University of Munich (TUM) and the Goethe University Frankfurt has now succeeded in investigating the basic mechanisms of one of these molecular factories.
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Many important drugs such as antibiotics or active agents against cancer are natural products which are built up by microorganisms for example bacteria or fungi. In the laboratory, these natural products can often be not produced at all or only with great effort. The starting point of a large number of such compounds are polyketides, which are carbon chains where every second atom has a double bound to an oxygen atom.In a microbial cell such as in the Photorhabdus luminescens bacterium, they are produced with the help of polyketide synthases (PKS). In order to build up the desired molecules step by step, in the first stage of PKS type II systems, four proteins work together in changing "teams."In a second stage, they are then modified to the desired natural product by further enzymes. Examples of bacterial natural products which are produced that way are, inter alia, the clinically used Tetracyclin antibiotics or Doxorubicin, an anti-cancer drug.While the modified steps of the second stage are well studied for many active agents, there have up to now hardly been any insights into the general functioning of the first stage of these molecular factories where the highly reactive polyketide intermediate product is bound to the enzyme complex and protected so that it cannot react spontaneously.This gap is now closed by the results of the cooperation between the working groups of Michael Groll, professor of biochemistry at the Technical University of Munich, and Helge Bode, professor of molecular biotechnology at Goethe University Frankfurt, which are published in the scientific journal "In the context of this work, we were for the first time able to analyze complexes of the different partner proteins of type II polyketide synthase with the help of X-ray structure analysis and now understand the complete catalytic cycle in detail," Michael Groll explains."Based on these findings, it will be possible in the future to manipulate the central biochemical processes in a targeted manner and thus change the basic structures instead of being restricted to the decorating enzymes," Helge Bode adds.Although it is a long way to develop improved antibiotics and other drugs, both groups are optimistic that now also the structure and the mechanism of the missing parts of the molecular factory can be explained. "We already have promising data of the further protein complexes," says Maximilian Schmalhofer, who was involved in the study as a doctoral candidate in Munich.
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Biotechnology
| 2,020 |
July 6, 2020
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https://www.sciencedaily.com/releases/2020/07/200706140845.htm
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Physics: Bubbling and burping droplets of DNA
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Liquid droplets formed from DNA display a peculiar response to enzymes. An international collaboration between Ludwig-Maximilians-Universitaet (LMU) in Munich and UCSB has now been able to explain the mechanisms behind bubble formation.
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A watched pot never boils ... but researchers from Ludwig-Maximilians University (LMU), Munich, and University of California in Santa Barbara (UCSB) and found that's not the case when watching liquids formed from DNA. Recent advances in cellular biology have found that the molecular components of living cells (such as DNA and proteins) can bind each other and form liquid droplets that appear similar to oil droplets in shaken salad dressing. These cellular droplets interact with other components to carry out basic processes critical to life, yet little is known about how those interactions function. To gain insight into this fundamental process, the LMU/UCSB team used modern methods of nanotechnology to engineer a model system, a liquid droplet formed from particles of DNA, and watched those droplets as they interacted with a DNA-cleaving enzyme.Surprisingly, they found, in certain cases, addition of the enzyme would cause the DNA droplets to suddenly start bubbling, appearing just like boiling water. "The bizarre thing about the bubbling DNA is that we didn't heat the system -- it's as if a pot of water started boiling even though you forgot to turn on the stove," says Professor Omar Saleh from UCSB, co-leader of the project. However, the bubbling behavior didn't always occur -- sometimes adding the enzyme would cause the droplets to smoothly shrink away, and it was unclear why one response or the other would occur.To get to the bottom of this mystery, the team carried out a rigorous set of precision experiments quantifying the shrinking and bubbling behaviors. They found that there were two types of shrinking behavior, the first cause by enzymes cutting the DNA only on the droplet surface, and the second caused by enzymes penetrating inside the droplet. "This observation was critical to unraveling the behavior, as it put it into our heads that the enzyme could start nibbling away at the droplets from the inside," notes co-leader Tim Liedl, Professor at the LMU, where the experiments were conducted.By comparing the droplet response to the DNA particle design, the team cracked the case: they found that bubbling and penetration-based shrinking occurred together, and only happened when the DNA particles were only lightly bound together, whereas strongly-bound DNA particles would keep the enzyme on the outside. Saleh notes: "It's like trying to walk through a crowd -- if the crowd is tightly holding hands, you wouldn't be able to get through."The bubbles, then, happen only in the lightly-bound systems, when the enzyme can get through the crowded DNA particles to the interior of the droplet, and begin to eat away at the droplet from the inside. The chemical fragments created by the enzyme lead to an osmotic effect, where water is drawn in from the outside, causing a swelling phenomenon that produces the bubbles. The bubbles grow, reach the droplet surface, then release the fragments in a burp-like gaseous outburst. "It is quite striking to watch, as the bubbles swell and pop over and over," says Liedl.The work demonstrates a complex relationship between the basic material properties of a biomolecular liquid, and its interactions with external components. The team believes the insight gained from studying the bubbling process will lead to both better models of living processes, and enhanced abilities to engineer liquid droplets for use as synthetic bioreactors.The research was enabled by an award to Professor Saleh from the Alexander von Humboldt Foundation, which enabled him to visit Munich and work directly with Tim Liedl on this project. "These types of international collaborations are extremely productive," says Saleh.
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Biotechnology
| 2,020 |
July 6, 2020
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https://www.sciencedaily.com/releases/2020/07/200706140843.htm
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Researchers develop software to find drug-resistant bacteria
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Washington State University researchers have developed an easy-to-use software program to identify drug-resistant genes in bacteria.
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The program could make it easier to identify the deadly antimicrobial resistant bacteria that exist in the environment. Such microbes annually cause more than 2.8 million difficult-to-treat pneumonia, bloodstream and other infections and 35,000 deaths in the U.S. The researchers, including PhD computer science graduate Abu Sayed Chowdhury, Shira Broschat in the School of Electrical Engineering and Computer Science, and Douglas Call in the Paul G. Allen School for Global Animal Health, report on their work in the journal Antimicrobial resistance (AMR) occurs when bacteria or other microorganisms evolve or acquire genes that encode drug-resistance mechanisms. Bacteria that cause staph or strep infections or diseases such as tuberculosis and pneumonia have developed drug-resistant strains that make them increasingly difficult and sometimes impossible to treat. The problem is expected to worsen in future decades in terms of increased infections, deaths, and health costs as bacteria evolve to "outsmart" a limited number of antibiotic treatments."We need to develop tools to easily and efficiently predict antimicrobial resistance that increasingly threatens health and livelihoods around the world," said Chowdhury, lead author on the paper.As large-scale genetic sequencing has become easier, researchers are looking for AMR genes in the environment. Researchers are interested in where microbes are living in soil and water and how they might spread and affect human health. While they are able to identify genes that are similar to known AMR-resistant genes, they are probably missing genes for resistance that look very unique from a protein sequence perspective.The WSU research team developed a machine-learning algorithm that uses features of AMR proteins rather than the similarity of gene sequences to identify AMR genes. The researchers used game theory, a tool that is used in several fields, especially economics, to model strategic interactions between game players, which in turn helps identify AMR genes. Using their machine learning algorithm and game theory approach, the researchers looked at the interactions of several features of the genetic material, including its structure and the physiochemical and composition properties of protein sequences rather than simply sequence similarity."Our software can be employed to analyze metagenomic data in greater depth than would be achieved by simple sequence matching algorithms," Chowdhury said. "This can be an important tool to identify novel antimicrobial resistance genes that eventually could become clinically important.""The virtue of this program is that we can actually detect AMR in newly sequenced genomes," Broschat said. "It's a way of identifying AMR genes and their prevalence that might not otherwise have been found. That's really important."The WSU team considered resistance genes found in species of They have developed a software package that can be easily downloaded and used by other researchers to look for AMR in large pools of genetic material. The software can also be improved over time. While it's trained on currently available data, researchers will be able to re-train the algorithm as more data and sequences become available."You can bootstrap and improve the software as more positive data becomes available," Broschat said.The work was funded in part by the Carl M. Hansen Foundation.
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Biotechnology
| 2,020 |
July 2, 2020
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https://www.sciencedaily.com/releases/2020/07/200702144729.htm
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New technique in which drugs make bacteria glow could help fight antibiotic resistance
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New technique in which drugs make bacteria glow could help fight antibiotic resistance.
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A new technique could help reduce antibiotic prescribing by predicting which drugs could be effective in fighting bacteria within minutes.Scientists at the University of Exeter have developed the method, which allows users to see whether a bacterium is likely to respond to antibiotics. The research is currently in early stages of development, and the team hope the miniaturised devices they use for this research could one day be based in clinics, reducing the number of different antibiotics prescribed to patients.The technique works by examining whether fluorescent qualities of the antibiotics are taken up by bacteria. If so, the bacteria glow brighter under the microscope, revealing that the antibiotic has infiltrated the membrane and could be effective. The research, published in the journal Antibiotic resistance is recognised as a major global threat. As these drugs increasingly fail to work, around 10 million people are predicted to die annually of infections by 2050.The new technique uses a special microscope and a miniaturised device into which a sample of the bacteria is injected, along with the antibiotic. To date, the team has used the antibiotic ofloxacin, which glows fluorescent under ultraviolet light. Bacteria also glow when the antibiotic is taken up. However, if they remain dark, the antibiotic has no chance of working and killing the bacteria.Dr Stefano Pagliara, a biophysicist in the Living Systems Institute, leading this research at the University of Exeter, said: "We're really excited about the potential for this technique to make a meaningful reduction in prescribing, helping to fight the global threat of antibiotic resistance. At the moment, it can take days for clinicians to get a lab result, which involves growing bacteria, but there is still some guess work involved. Our technique could reduce the use of multiple antibiotics to try and fight a bacterial infection."Dr Jehangir Cama, an industry research fellow at the Living Systems Institute, who performed the experimental work of this research, said: "Our next step is to further develop this exciting new method by combining it with more advanced microscopy techniques, to see where exactly the antibiotics go when they enter the bacteria."The team is now working on expanding the technique, by manipulating the fluorescent qualities of other forms of antibiotics so they can work in the same way. Further research in this area has been funded by QUEX, a partnership between the University of Exeter and The University of Queensland in Australia. The Queensland team, led by Dr Mark Blaskovich, Director of the Centre for Superbug Solutions at the Institute for Molecular Bioscience, is developing fluorescent versions of other antibiotics so they can be tested in a similar manner. Blaskovich adds "I am enthused about the opportunities to improve our fundamental understanding of the interactions between antibiotics and bacteria and how this leads to antimicrobial resistance, by combining our novel antibiotic-derived probes with the cutting edge single cell analysis capabilities of the Exeter group."
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Biotechnology
| 2,020 |
July 2, 2020
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https://www.sciencedaily.com/releases/2020/07/200702144059.htm
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Moss protein corrects genetic defects of other plants
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Almost all land plants employ an army of molecular editors who correct errors in their genetic information. Together with colleagues from Hanover, Ulm and Kyoto (Japan), researchers from the University of Bonn have now transferred one of these proofreaders from the moss Physcomitrium patens (previously known as Physcomitrella patens) into a flowering plant. Surprisingly, it performs its work there as reliably as in the moss itself. The strategy could be suitable for investigating certain functions of the plant energy metabolism in more detail. It may also be valuable for developing more efficient crops. The study will be published in the journal
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Plants differ from animals in that they are capable of photosynthesis. They do this in specialized "mini-organs" (biologists speak of organelles), the chloroplasts. Chloroplasts produce sugar with the help of sunlight, which in turn is used in other organelles, the mitochondria, to produce energy.Both chloroplasts and mitochondria have their own genetic material. And in both of them this genome contains a lot of errors. "At least that is the case with almost all land plants," explains Dr. Mareike Schallenberg-Rüdinger. The researcher heads a junior research group at the University of Bonn in the Department of Molecular Evolution under Prof. Volker Knoop. "They have to correct these errors so their power supply does not collapse."In fact, land plants do the same, and in a very complicated way: They do not correct the errors in the genome itself. Instead, they correct the RNA copies that the cell makes of these DNA blueprints, which it then uses to produce certain enzymes, for example. So instead of correcting the original, it only irons out the inaccuracies afterwards in the copies.Functional despite 400 million years of evolutionary historyMolecular proofreaders, the so-called PPR proteins, are responsible for this. Most of them are specialists for only one particular error in the many gene copies that the cell produces around the clock. These errors occur when, in the course of evolution, a certain chemical building block of DNA (a letter, if you like, in the genetic blueprint) is swapped for another. When the PPR proteins find such a swap, they convert the wrong letter in the RNA copy (the building block cytidine, abbreviated C) into the correct version (uridine, abbreviated U)."We have now taken a gene for a PPR protein from the moss Physcomitrium patens and transferred it into a flowering plant, the thale cress Arabidopsis thaliana," explains Schallenberg-Rüdinger. "The protein then recognized and corrected the same error there for which it was also responsible in the moss." This is astonishing, since there are more than 400 million years of evolutionary history between Physcomitrium and Arabidopsis. The PPR proteins can therefore also differ significantly in their structure.For instance, the thale cress contains PPR proteins that can identify errors but still require a separate "white-out" enzyme to correct them. In contrast, the PPR proteins of the moss Physcomitrium perform both tasks simultaneously. "In these cases, the transfer from moss to thale cress works, but the thale cress gene remains inactive in the moss," explains Bastian Oldenkott, doctoral student and lead author of the study. The macadamia nut appeared in evolution a little earlier than Arabidopsis. Its PPR protein being investigated is more similar to that of Physcomitrium. Once introduced into the moss, it therefore performs its service there without any problems.The study may open up a new way to modify the genetic material of chloroplasts and mitochondria. "Especially for plant mitochondria, this is not yet possible at all," emphasizes Schallenberg-Rüdinger. Using special "designer" PPR genes, for example, one might specifically render certain genome transcripts unusable and test how this affects the plant. In the medium term, this may also result in new findings for breeding particularly high-yielding, high-performance varieties. First, however, the researchers hope to gain insights into the complex interaction of genes in the functioning of chloroplasts and mitochondria.The research carried out by co-authors Prof. Hans-Peter Braun and Dr. Jennifer Senkler from the University of Hanover proves that this approach can actually work. They were able to clarify what the PPR protein from the moss is needed for: If it is missing, the plant is no longer able to correctly assemble the machinery for the so-called respiratory chain in the mitochondria, which is used to generate energy. The work in the thale cress was carried out in cooperation with Matthias Burger (University of Ulm) and Prof. Mizuki Takenaka (University of Kyoto), a fine example of successful international cooperation.
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Biotechnology
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July 2, 2020
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https://www.sciencedaily.com/releases/2020/07/200702144052.htm
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Tiny mineral particles are better vehicles for promising gene therapy
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University of Wisconsin-Madison researchers have developed a safer and more efficient way to deliver a promising new method for treating cancer and liver disorders and for vaccination.
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The technology relies on inserting into cells pieces of carefully designed messenger RNA (mRNA), a strip of genetic material that human cells typically transcribe from a person's DNA in order to make useful proteins and go about their business. Problems delivering mRNA safely and intact without running afoul of the immune system have held back mRNA-based therapy, but UW-Madison researchers are making tiny balls of minerals that appear to do the trick in mice."These microparticles have pores on their surface that are on the nanometer scale that allow them to pick up and carry molecules like proteins or messenger RNA," says William Murphy, a UW-Madison professor of biomedical engineering and orthopedics. "They mimic something commonly seen in archaeology, when we find intact protein or DNA on a bone sample or an eggshell from thousands of years ago. The mineral components helped to stabilize those molecules for all that time."Murphy and UW-Madison collaborators used the mineral-coated microparticles (MCMs) -- which are 5 to 10 micrometers in diameter, about the size of a human cell -- in a series of experiments to deliver mRNA to cells surrounding wounds in diabetic mice. Wounds healed faster in MCM-treated mice, and cells in related experiments showed much more efficient pickup of the mRNA molecules than other delivery methods.The researchers described their findings today in the journal In a healthy cell, DNA is transcribed into mRNA, and mRNA serves as the instructions the cell's machinery uses to make proteins. A strip of mRNA created in a lab can be substituted into the process to tell a cell to make something new. If that something is a certain kind of antigen, a molecule that alerts the immune system to the presence of a potentially harmful virus, the mRNA has done the job of a vaccine.The UW-Madison researchers coded mRNA with instructions directing cell ribosomes to pump out a growth factor, a protein that prompts healing processes that are otherwise slow to unfold or nonexistent in the diabetic mice (and many severely diabetic people).mRNA is short-lived in the body, though, so to deliver enough to cells typically means administering large and frequent doses in which the mRNA strands are carried by containers made of molecules called cationic polymers."Oftentimes the cationic component is toxic. The more mRNA you deliver, the more therapeutic effect you get, but the more likely it is that you're going to see toxic effect, too. So, it's a trade-off," Murphy says. What we found is when we deliver from the MCMs, we don't see that toxicity. And because MCM delivery protects the mRNA from degrading, you can get more mRNA where you want it while mitigating the toxic effects."The new study also paired mRNA with an immune-system-inhibiting protein, to make sure the target cells didn't pick the mRNA out as a foreign object and destroy or eject it.Successful mRNA delivery usually keeps a cell working on new instructions for about 24 hours, and the molecules they produce disperse throughout the body. That's enough for vaccines and the antigens they produce. To keep lengthy processes like growing replacement tissue to heal skin or organs, the proteins or growth factors produced by the cells need to hang around for much longer."What we've seen with the MCMs is, once the cells take up the mRNA and start making protein, that protein will bind right back within the MCM particle," Murphy says. "Then it gets released over the course of weeks. We're basically taking something that would normally last maybe hours or even a day, and we're making it last for a long time."And because the MCMs are large enough that they don't enter the bloodstream and float away, they stay right where they are needed to keep releasing helpful therapy. In the mice, that therapeutic activity kept going for more than 20 days."They are made of minerals similar to tooth enamel and bone, but designed to be reabsorbed by the body when they're not useful anymore," says Murphy, whose work is supported by the Environmental Protection Agency, the National Institutes of Health and the National Science Foundation and a donation from UW-Madison alums Michael and Mary Sue Shannon."We can control their lifespan by adjusting the way they're made, so they dissolve harmlessly when we want."The technology behind the microparticles was patented with the help of the Wisconsin Alumni Research Foundation and is licensed to Dianomi Therapeutics, a company Murphy co-founded.The researchers are now working on growing bone and cartilage and repairing spinal cord injuries with mRNA delivered by MCMs.This research was supported by grants from the Environmental Protection Agency (S3.TAR grant 83573701), the National Institutes of Health (R01AR059916, R21EB019558, NIH 5 T32 GM008349) and the National Science Foundation (DMR 1105591, DGE-1256259).
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Biotechnology
| 2,020 |
July 2, 2020
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https://www.sciencedaily.com/releases/2020/07/200702115032.htm
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New sequencing technology will help scientists decipher disease mechanisms
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New technologies capable of sequencing single molecules in fine detail will help scientists better understand the mechanisms of rare nucleotides thought to play an important role in the progression of some diseases.
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A review paper, led by a scientist at the University of Birmingham, describes how emerging sequencing technologies will transform our understanding of these molecules, ultimately leading to new drug targets. The paper is published in the journal Expression of genes to make protein involves making a messenger RNA molecule. Although RNA, like DNA consist of the four nucleotides, some of them carry decorations called the epitranscriptome. These modified nucleotides are important additions to the genetic code whose functions are little understood, but have been linked to disease such as obesity, cancer and neurological disorders.Although the importance of the epitranscriptome is recognized, its detection is difficult and comes with high error rates.Scientist have been interested in these rare modified nucleotides since their discovery more than 40 years ago, but they had been very difficult to examine in specific genes due to technical difficulties. However, their importance has been recognized, because many human parasites and viruses have them. Even more, some viruses including coronavirus SARS-CoV2 have their own RNA modification enzymes, originally acquired from their hosts, but then adapted to their needs.Until recently, the study of these modified nucleotides has been limited because they occur so rarely, and existing technologies have not been sufficiently fine-tuned to detect the modifications.The new technology, developed by Oxford Nanopore Technologies, is promising to overcome current sequencing limitations, with highly selective sequencing capabilities. By identifying specific nucleotide targets associated with particular diseases, drug developers will be able to start to investigate inhibitor drugs that can interfere with the molecules and influence the progression of the disease.Lead author of this multinational study, Dr Matthias Soller from the University of Birmingham, UK, says: "These modified nucleotides are particularly hard to detect and previously it was impossible to examine their occurrence in the entire genome with high confidence."First author and Schmidt Science Fellow Dr Ina Anreiter, University of Toronto, Canada, adds: "Previously, it was only possible to look at one modification at a time, but there a more than just one and they likely hiding a yet to discover code."This new technology will really enable a step-change in how we approach modified nucleotides, giving us a 'real-time' topographic map of where the molecules are within the genome, and how frequently they occur. This will be really important in instructing further research into their function and providing us with new insights into how these molecules lead to human disease."Dr Soller added: "There is plenty of work still to be done to further develop these sequencing devices, including improving the machine-learning capability for interpreting the sequencing signals, but progress is happening rapidly and I think we will be seeing some very exciting results emerging from this technology."
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Biotechnology
| 2,020 |
July 2, 2020
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https://www.sciencedaily.com/releases/2020/07/200702113731.htm
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Marine algae from the Kiel Fjord discovered as a remedy against infections and skin cancer
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Healing with the help of marine organisms is no utopia. Already 12 life-saving drugs, e.g. against cancer, have been developed from marine organisms and their symbiotic microbiota. Their high potential for drug development is hampered by the lengthy and costly discovery process. The research group of the Marine Natural Product Chemistry Research Unit at GEOMAR Helmholtz Centre for Ocean Research Kiel, supported by computer-aided automated approaches, has now successfully discovered marine molecules as potential remedies against infections and skin cancer in an alga and its fungal symbiont originating from the Kiel Fjord.
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The search process for marine active ingredients starts with the extraction of marine macro- and microorganisms, followed by the purification and characterization of their novel and bioactive chemical constituents, which are intended to be used for the development of new therapeutics. "One of the biggest pitfalls in drug research is the isolation of already described natural molecules, using the 'classical' bioactivity-guided isolation process," explains Prof. Dr. Deniz Tasdemir, head of Research Unit Marine Natural Product Chemistry at GEOMAR and GEOMAR Centre for Marine Biotechnology. "This approach is complicated and often prone to failures," Dr. Tasdemir continues.In her research group, she addressed this problem through automated, computer-based approaches in combination with bioactivity screenings. In a one-year study, it was found that the brown alga Fucus vesiculosus (bladder wrack) from the Kiel Fjord, inhibits the pathogenic bacterium Methicillin-resistant Staphylococcus aureus (MRSA), which causes hospital infections."Algorithm-based bioinformatics strategies and machine learning tools have enabled us to map the massive metabolome of brown alga and at the same time predict the molecular clusters responsible for their antibiotic activity," said Dr. Larissa Büdenbender, a former postdoctoral fellow in Prof. Tasdemir's group and first author of one of the two articles now published in the journal "In nature, bladder wrack is often under strong pressure from fouling and biofilm formation by millions of microorganisms found in seawater. Therefore, membrane-bound compounds, as we identified in this study, are of high ecological importance for self-protection of the alga. Such molecules, which perform a critical function in natural space, often display related activities against human pathogens. Since bladder wrack is an edible seaweed, such activities make it an attractive candidate not only as a source of drugs, but also for food supplements or food protection," says Prof. Tasdemir. Next, we will be investigating the application potential of bladder wrack in food industry.Many fungi also live in symbiosis on the surfaces and inside of seaweed. These are also promising sources for the discovery and development of new drugs. Bicheng Fan, a PhD student of Professor Tasdemir, has isolated more than 120 symbiotic fungi from bladder wrack and has studied the fungus Pyrenochaetopsis sp. in detail, as it efficiently kills melanoma-type skin cancer cells with low cytotoxicity and has a very rich chemical inventory. Bicheng also used computer-aided automated approaches to isolate special molecules with a rare chemical scaffold. The study was also recently published in According to Prof Tasdemir, this is only the second chemical study on the previously completely unexplored fungal genus Pyrenochaetopsis. "Fungi, which we isolated from bladder wrack and fermented in optimized laboratory conditions, are an established source of natural anti-cancer agents. We have found several novel natural products here, which we named as pyrenosetins A and B, that have a high potential for fighting skin cancer," the chemist continues."Nature is the source of more than half of all modern medicines that we use today. Access to the revolutionary genomics, metabolomics, bioinformatics and machine learning tools will enable, in an unprecedented way, new and rapid discovery of marine compounds, and more rational and efficient use for subsequent drug development with industrial partners"," Professor Tasdemir concludes.
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Biotechnology
| 2,020 |
July 2, 2020
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https://www.sciencedaily.com/releases/2020/06/200630111502.htm
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Buzzing to rebuild broken bone
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Healing broken bones could get easier with a device that provides both a scaffold for the bone to grow on and electrical stimulation to urge it forward, UConn engineers reported on June 27 in the Journal of
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Although minor bone breaks usually heal on their own, large fractures with shattered or missing chunks of bone are more difficult to repair. Applying a tiny electrical field to the site of the fracture to mimic the body's natural electrical field helps the cells regenerate. But the medical devices that do this are usually bulky, rely on electrical wires or toxic batteries, require invasive removal surgery, and can't do much for serious injuries.Now, a group of biomedical engineers from UConn have developed a scaffold of non-toxic polymer that also generates a controllable electrical field to encourage bone growth. The scaffold helps the body bridge large fractures. Although many scientists are exploring the use of scaffolding to encourage bone growth, pairing it with electrical stimulation is new.The team demonstrated the device in mice with skull fractures.The electrical voltage the scaffold generates is very small, just a few millivolts. And uniquely for this type of device, the voltage is generated via remotely-controlled ultrasound. The ultrasound vibrates the polymer scaffolding, which then creates an electrical field (materials that create electricity from vibration, or vice versa, are called piezoelectric.) To help heal a thigh fracture, for example, the polymer scaffold can be implanted across the broken bone. Later, the person with the broken bone can wave the ultrasound wand over their own thigh themselves. No need for batteries, and no need for invasive removal surgery once the bone is healed."The electrical field relates to the natural signal generated by your body at the injury location. We can sustain that voltage, on demand and reversible," for however long is needed using ultrasound, says UConn biomedical engineer Thanh Nguyen. The piezoelectric polymer Nguyen and his colleagues use to build the scaffold is called poly(L-lactic acid), or PLLA. In addition to being non-toxic and piezoelectric, PLLA gradually dissolves in the body over time, disappearing as the new bone grows."The electric field created by the piezoelectric PLLA scaffold seems to attract bone cells to the site of the fracture and promote stem cells to evolve into bone cells. This technology can possibly be combined with other factors to facilitate regeneration of other tissues, like cartilage, muscles or nerves," says Ritopa Das, a graduate student in Nguyen group and the first author of the published paper.Currently Nguyen and his colleagues are working to make the polymer more favorable to bone growth, so that it heals a large fracture more quickly. They are also trying to understand why electrical fields encourage bone growth at all. Bone itself is somewhat piezoelectric, generating a surface charge when the bone is stressed by everyday life activities. That surface charge encourages more bone to grow. But scientists don't know whether it's because it helps cells stick to the surface of the bone, or whether it makes the cells themselves more active."Once we understand the mechanism, we can devise a better way to improve the material and the whole approach of tissue stimulation," Nguyen says.This work was supported by the National Institutes of Health.
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Biotechnology
| 2,020 |
July 1, 2020
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https://www.sciencedaily.com/releases/2020/07/200701125429.htm
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Smart structures: Structural cells of the body control immune function
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The immune system protects our body from constant attack by viruses, bacteria, and other pathogens. Much of this protection is provided by hematopoietic immune cells, which are derived from the bone marrow and specialize in fighting pathogens. They include macrophages, which remove pathogens; T cells, which kill infected virus-producing cells; and B cells producing antibodies that neutralize pathogens. However, immune functions are not restricted to these "specialists," and many more cell types are able to sense when they are infected and contribute to the immune response against pathogens.
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Structural cells provide essential building blocks of the body and play an important role in shaping the structure of tissue and organs. Most notably, epithelial cells constitute the surface of the skin, while also separating tissues and organs from each other; endothelial cells coat the inside of all blood vessels; and fibroblast provide the connective tissue that keeps tissues and organs in shape. Structural cells are often regarded as simple and rather uninteresting components of the body, despite their well-established roles in autoimmune diseases (such as rheumatoid arthritis and inflammatory bowel disease) and in cancer. In their new study, Thomas Krausgruber, Nikolaus Fortelny and colleagues in Christoph Bock's laboratory at CeMM focused on elucidating the role of structural cells in immune regulation by pursuing a systematic, genome-wide analysis of epigenetic and transcriptional regulation of structural cells in the body.To that end, the CeMM researchers established a comprehensive catalog of immune gene activity in structural cells, applying high-throughput sequencing technology (RNA-seq, ATAC-seq, ChIPmentation) to three types of structural cells (epithelium, endothelium, fibroblasts) from twelve different organs of healthy mice. This dataset uncovered widespread expression of immune genes in structural cells as well as highly cell-type-specific and organ-specific patterns of gene regulation. Bioinformatic analysis detected genes that control a complex network of interactions between structural cells and hematopoietic immune cells, indicating potential mechanisms by which structural cells contribute to the response to pathogens.Interestingly, many immune genes showed epigenetic signatures that are normally associated with high gene expression, while the observed expression in structural cells obtained from healthy mice was lower than expected based on their epigenetic signatures. CeMM researchers therefore hypothesized that these genes are epigenetically pre-programmed for rapid upregulation when their activity is needed -- for example in response to a pathogen. To test this hypothesis, they joined forces with Andreas Bergthaler's laboratory at CeMM, capitalizing on their expertise in viral immunology and infection biology.When the mice were infected with a virus (LCMV) that triggers a broad immune response, many of those genes that were epigenetically poised for activation became upregulated and contributed to the transcriptional changes that structural cells showed in response to viral infection. These results suggest that structural cells implement an "epigenetic potential" that pre-programs them to engage in rapid immune responses. As an additional validation, the researchers triggered an artificial immune response by injecting cytokines into mice, and they indeed found that many of the same genes were upregulated.The new study has uncovered a striking complexity of immune gene regulation in structural cells. These results highlight that structural cells are not only essential building blocks of the body, but also contribute extensively to its defense against pathogens. Moreover, the presented data constitute an important first step toward understanding what "structural immunity" might mean for the immune system, and it may help develop innovative therapies for some of the many diseases that involve the immune system.
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Biotechnology
| 2,020 |
July 9, 2020
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https://www.sciencedaily.com/releases/2020/07/200709113513.htm
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Unraveling the mystery of wheat herbicide tolerance
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Genetically speaking, the loaf of bread you stress-baked during the COVID-19 shutdown is more complex than you think. Wheat's 16 billion genes, organized in not one but three semi-independent genomes, can overlap or substitute for one another, making things extremely tricky for geneticists trying to enhance desirable traits in the world's most widely grown crop.
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One of those traits is herbicide tolerance. Many cereal crops, including wheat, have a natural ability to detoxify certain herbicides applied to weeds in their midst. Under optimal conditions, weeds die, but the crops stand tall. If scientists can identify the genes involved, they could potentially amplify expression of those genes to make the detoxification process more effective under a range of environmental conditions.In a new University of Illinois study published in "In the 1950s, scientists came up with a process called 'alien substitution' where you can replace chromosomes from one of the three wheat genomes with chromosomes from a wheat relative, such as Aegilops searsii. The chromosomes are similar enough that the plant can still grow and still looks pretty much like wheat," explains Dean Riechers, professor in the Department of Crop Sciences at Illinois and co-author on the study. "The benefit is that the relative might not have the same traits as wheat, so the alien substitution line will help pinpoint where genes of interest are located."The method is now so commonplace in wheat research that scientists can simply obtain seeds for wheat plants with Aegilops searsii chromosomes, denoted as the S genome, subbing in for each of the seven wheat chromosomes across all three of its genomes (A, B, and D). These are known as alien substitution lines, and Riechers and doctoral student Olivia Obenland used them to determine that synthetic auxin tolerance in wheat likely resides somewhere on chromosome 5A."Although the method is common for finding genes for pathogen resistance and other useful genes in wheat, ours is the only research group to have used this method to search for herbicide tolerance," Riechers says. "We've basically shortened the list from 21 chromosomes down to one, so now we know where to focus our future gene discovery efforts."Obenland grew all 21 alien substitution lines in the greenhouse, along with wheat cultivar 'Chinese Spring' and Aegilops searsii, and sprayed them all with high rates of the synthetic auxin herbicide halauxifen-methyl. She then compared the biomass of the treated plants to untreated controls.The researchers expected and observed minimal injury in 'Chinese Spring,' thanks to its ability to naturally detoxify the chemical. But Aegilops searsii turned out to be highly sensitive to halauxifen-methyl, as were wheat plants with alien substitutions at chromosome 5A."By subbing 5A with the 5S chromosome of the alien species, we took away wheat's natural halauxifen-methyl tolerance and made it sensitive," Obenland says.Plants with the substitution at chromosome 5B also showed some sensitivity, but only when the herbicide was applied at the highest rate. Although this means 5B likely possesses genes involved in synthetic auxin detoxification as well, the results so far point to 5A as the key player. Interestingly, chromosome 5D in wheat's third (D) genome doesn't seem to play a major role, according to the research.The next step is to scour chromosome 5A for specific genes that could be involved in herbicide tolerance. Obenland and Riechers are already working on it, and although they've identified some interesting genes related to those they've found in resistant waterhemp, they're not ready to release those results without further molecular tests."Ultimately, we hope to broaden and deepen our understanding of wheat's natural tolerance to halauxifen-methyl, as well as other synthetic auxin herbicides, and this is a great first step. And it is very satisfying to apply existing genetic tools to address a new scientific problem," Riechers says.
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Genetically Modified
| 2,020 |
June 29, 2020
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https://www.sciencedaily.com/releases/2020/06/200629120225.htm
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Genomic variation causing common autoinflammatory disease may increase resilience to bubonic plague
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Researchers have discovered that Mediterranean populations may be more susceptible to an autoinflammatory disease because of evolutionary pressure to survive the bubonic plague. The study, carried out by scientists at the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health, determined that specific genomic variants that cause a disease called familial Mediterranean fever (FMF) may also confer increased resilience to the plague.
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The researchers suggest that because of this potential advantage, FMF-causing genomic variants have been positively selected for in Mediterranean populations over centuries. The findings were published in the journal Over centuries, a biological arms race has been fought between humans and microbial pathogens. This evolutionary battle is between the human immune system and microorganisms trying to invade our bodies. Microbes affect the human genome in many ways. For example, they can influence some of the genomic variation that accumulates in human populations over time."In this era of a new pandemic, understanding the interplay between microbes and humans is ever critical," said Dr. Dan Kastner, NHGRI scientific director and a co-author on the paper. "We can witness evolution playing out before our very eyes."One such microbe is FMF, like the plague, is an ancient disease. It is the most common periodic fever syndrome, and symptoms of FMF include recurrent fevers, arthritis, rashes and inflammation of the tissues that line the heart, lungs, and abdominal organs. FMF may also lead to renal failure and death without treatment. The disease appears across the Mediterranean region and mostly affects Turkish, Jewish, Armenian and Arab populations.Genomic variants in the In contrast, FMF patients produce abnormal pyrin because of genomic variants (mutations) in the The Despite the lower survival rate, almost 10% of Turks, Jews, Arabs and Armenians carry at least one copy of an FMF-causing genomic variant. If chance were the only factor, that percentage would be much lower.The researchers proposed that this higher percentage was a consequence of positive natural selection, which is an evolutionary process that drives an increase in specific genomic variants and traits that are advantageous in some way."Just like sickle cell trait is positively selected for because it protects against malaria, we speculated that the mutant pyrin in FMF might be helping the Mediterranean population in some way," said Jae Jin Chae, Ph.D., senior author of the paper and a staff scientist in NHGRI's Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch. "The mutant pyrin may be protecting them from some fatal infection."The team turned to It turns out "Inflammation is a process in which white blood cells protect the body from infection. From the host's point of view, inflammation helps us survive. From the bacteria's point of view, inflammation is something to be evaded by any means available," said Daniel Shriner, Ph.D., staff scientist in the Center for Research on Genomics and Global Health at NHGRI.Researchers were struck by the fact that The idea that evolution would push for one disease in a group to fight another may seem counterintuitive. But it comes down to what is the least bad option.The average mortality rate of people with bubonic plague over centuries has been as high as 66%, while, even with a carrier frequency of 10%, less than 1% of the population has FMF. Theoretically, the evolutionary odds are in the latter's favor.But first, the team had to verify if two of the genomic variants that cause FMF had indeed undergone positive selection in Mediterranean populations.For this, they performed genetic analysis on a large cohort of 2,313 Turkish individuals. They also examined genomes from 352 ancient archaeological samples, including 261 from before the Christian era. The researchers tested for the presence of two FMF-causing genomic variants in both groups of samples. They also used population genetics principles and mathematical modeling to predict how the frequency of FMF-causing genomic variants changed over generations."We found that both FMF-causing genomic variants arose more than 2,000 years ago, before the Justinian Plague and the Black Death. Both variants were associated with evidence of positive selection," said Elaine Remmers, Ph.D., associate investigator in NHGRI's Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch.Researchers then studied how The team found that The researchers thought that if To test this hypothesis, the researchers genetically engineered mice with FMF-causing genomic variants. They infected both healthy and genetically engineered mice with These findings, in combination, indicate that over centuries, FMF-causing genomic variants positively selected in Turkish populations play a role in providing resistance to
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Genetically Modified
| 2,020 |
June 10, 2020
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https://www.sciencedaily.com/releases/2020/06/200610135015.htm
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COVID-19 mouse model will speed search for drugs, vaccines
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The global effort to quickly develop drugs and vaccines for COVID-19 has been hampered by limited numbers of laboratory mice that are susceptible to infection with SARS-CoV-2, the virus that causes COVID-19. Now, researchers at Washington University School of Medicine in St. Louis report they have developed a mouse model of COVID-19 that replicates the illness in people. Further, the same approach could be adopted easily by other scientists to dramatically accelerate the testing of experimental COVID-19 treatments and preventives.
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The mouse model is described in a paper published online June 10 in the journal "There's been a huge push to develop vaccines and therapeutics as quickly as possible, and since animal models have been limited, these investigational drugs and vaccines have been put directly into humans, and many of them haven't panned out," said principal investigator Michael S. Diamond, MD, PhD, the Herbert S. Gasser Professor of Medicine and an expert on viral infections. "Mice are useful because you can study a large number of them and observe the course of the disease and the immune response in a way that is hard to do in people. It would be more cost-effective and efficient and safer for people if we could get more information about how these potential drugs and vaccines work and how effective they are before we move to more challenging non-human primate and ultimately human studies."Mice do not naturally get infected with the virus that causes COVID-19. To infect people, the virus latches onto a protein called angiotensin converting enzyme-2 (ACE2) on the surface of cells in the respiratory tract. But the human ACE2 protein is different from the mouse ACE2 protein, and the virus is unable to attach to the mouse version.The virus that caused the SARS epidemic in 2003 is closely related to the one causing the COVID-19 pandemic, and the SARS virus also infects cells by latching onto the human ACE2 protein. During the SARS epidemic, researchers created a strain of genetically modified mice with the human ACE2 protein so they could study SARS. After the epidemic ended, however, interest in SARS waned and the mouse colonies were closed. The emergence of COVID-19 earlier this year triggered a frantic rush to begin breeding the mice again, but even now there are not nearly enough mice for all of the researchers who want to study the disease and to test potential vaccines and therapeutics.Diamond, who previously had led an effort to develop a mouse model of Zika infection, realized they needed a faster way to obtain mice that could be used for COVID-19 studies. Diamond and colleagues -- including co-first authors Ahmed Hassan, DVM, PhD, and Brett Case, PhD, both postdoctoral researchers, and Emma Winkler, an MD/PhD graduate student, as well as several other key members of the COVID-19 team from Diamond's laboratory -- decided to introduce the human ACE2 protein into mice temporarily. To accomplish this, they inserted the gene for human ACE2 into a mild respiratory virus known as an adenovirus. They also removed genes that the adenovirus needs to replicate, so the virus could infect cells once but not multiply. Then, the researchers infected mice with the modified adenovirus. The animals produced human ACE2 in their respiratory tracts for a few days, making them vulnerable to infection with the virus that causes COVID-19.To see whether mice develop an illness similar to the one in people, the researchers infected mice with the modified adenovirus, and then five days later gave them the COVID-19 virus through the nose. The virus quickly spread along the respiratory tract and especially to the lungs, where it replicated to high numbers and caused pneumonia with marked inflammation, much as it does in people. The researchers also found lower levels of virus in the heart, spleen and brain -- all organs that can be targets of the virus in people. The mice lost 10% to 25% of their body weight during their illnesses but ultimately recovered."The mice develop a similar lung disease to what we see in humans," said Diamond, who is also a professor of molecular microbiology, and of pathology and immunology. "They get quite sick for a while but eventually recover, like the vast majority of people who get COVID-19. You can use this technique with almost any strain of laboratory mouse to make them susceptible to SARS-CoV-2 and then do whatever kind of study you want: test vaccines or drugs, study the immune response, and many other things related to how the virus causes disease."The model also can be used to better understand the factors that put some people at risk of severe COVID-19 disease. Advanced age, male sex, and conditions such as obesity, diabetes, and heart, kidney or lung disease all increase risk of severe COVID-19 for reasons that are not fully understood."It would be easy to study, for example, older mice or obese mice and see how they respond to infection," Diamond said. "I'd expect that they would do substantially worse, but the real question is why. Do they have more virus in the early stages? Is their condition weakening the immune response, or perhaps exacerbating a detrimental inflammatory response? With this model, we can begin to look at some of those factors that are very hard to study in people."
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Genetically Modified
| 2,020 |
June 2, 2020
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https://www.sciencedaily.com/releases/2020/06/200602183419.htm
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Scientists engineer human cells with squid-like transparency
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Octopuses, squids and other sea creatures can perform a disappearing act by using specialized tissues in their bodies to manipulate the transmission and reflection of light, and now researchers at the University of California, Irvine have engineered human cells to have similar transparent abilities.
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In a paper published today in "For millennia, people have been fascinated by transparency and invisibility, which have inspired philosophical speculation, works of science fiction, and much academic research," said lead author Atrouli Chatterjee, a UCI doctoral student in chemical & biomolecular engineering. "Our project -- which is decidedly in the realm of science -- centers on designing and engineering cellular systems and tissues with controllable properties for transmitting, reflecting and absorbing light."Chatterjee works in the laboratory of Alon Gorodetsky, UCI associate professor of chemical & biomolecular engineering, who has a long history of exploring how cephalopods' color-changing capabilities can be mimicked to develop unique technologies to benefit people. His team's bioinspired research has led to breakthrough developments in infrared camouflage and other advanced materials.For this study, the group drew inspiration from the way female Doryteuthis opalescens squids can evade predators by dynamically switching a stripe on their mantle from nearly transparent to opaque white. The researchers then borrowed some of the intercellular protein-based particles involved in this biological cloaking technique and found a way to introduce them into human cells to test whether the light-scattering powers are transferable to other animals.This species of squid has specialized reflective cells called leucophores which can alter the how they scatter light. Within these cells are leucosomes, membrane-bound particles which are composed of proteins known as reflectins, which can produce iridescent camouflage.In their experiments, the researchers cultured human embryonic kidney cells and genetically engineered them to express reflectin. They found that the protein would assemble into particles in the cells' cytoplasm in a disordered arrangement. They also saw through optical microscopy and spectroscopy that the introduced reflectin-based structures caused the cells to change their scattering of light."We were amazed to find that the cells not only expressed reflectin but also packaged the protein in spheroidal nanostructures and distributed them throughout the cells' bodies," said Gorodetsky, a co-author on this study. "Through quantitative phase microscopy, we were able to determine that the protein structures had different optical characteristics when compared to the cytoplasm inside the cells; in other words, they optically behaved almost as they do in their native cephalopod leucophores."In another important part of the study, the team tested whether the reflectance could potentially be toggled on and off through external stimuli. They sandwiched cells in between coated glass plates and applied different concentrations of sodium chloride. Measuring the amount of light that was transmitted by the cells, they found that the ones exposed to higher sodium levels scattered more light and stood out more from the surroundings."Our experiments showed that these effects appeared in the engineered cells but not in cells that lacked the reflectin particles, demonstrating a potential valuable method for tuning light-scattering properties in human cells," Chatterjee said.While invisible humans are still firmly in the realm of science fiction, Gorodetsky said his group's research can offer some tangible benefits in the near term."This project showed that it's possible to develop human cells with stimuli-responsive optical properties inspired by leucophores in celphalopods, and it shows that these amazing reflectin proteins can maintain their properties in foreign cellular environments," he said.He said the new knowledge also could open the possibility of using reflectins as a new type of biomolecular marker for medical and biological microscopy applications.This project, which received support from Defense Applied Research Projects Agency and the Air Force Office of Scientific Research, also involved researchers from the University of California, San Diego and Hamamatsu Photonics in Japan.
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Genetically Modified
| 2,020 |
May 27, 2020
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https://www.sciencedaily.com/releases/2020/05/200527123332.htm
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Mouse model mimics SARS-CoV-2 infection in humans
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A mouse model of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reproduces features observed in human patients, researchers report May 26 in the journal
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"A small animal model that reproduces the clinical course and pathology observed in COVID-19 patients is highly needed," says co-senior study author You-Chun Wang of the National Institutes for Food and Drug Control (NIFDC) in Beijing, China. "The animal model described here provides a useful tool for studying SARS-CoV-2 infection and transmission."Wang and his collaborators used CRIPSR/Cas9 to generate a mouse model that could express hACE2. According to the authors, their mouse model has several advantages compared with other genetically engineered mice that express hACE2 for modeling SARS-CoV-2 infection. Instead of being randomly inserted, hACE2 is inserted precisely into a specific site on the X chromosome, and it completely replaces the mouse version of the protein. In addition, this is a genetically stable model, with few differences among individuals. Moreover, the viral RNA loads in the lung are much higher, and the resulting distribution of hACE2 in various tissues better matches that observed in humans.After being infected with SARS-CoV-2 through the nose, the genetically engineered mice showed evidence of robust viral RNA replication in the lung, trachea, and brain. "The presence of viral RNAs in brain was somewhat unexpected, as only a few COVID-19 patients have developed neurological symptoms," says co-senior study author Cheng-Feng Qin of the Academy of Military Medical Sciences (AMMS) in Beijing, China.SARS-CoV-2 S protein, which binds to hACE2 to enter host cells, was also present in the lung tissue and brain cells. Moreover, the researchers identified the major airway cells targeted by SARS-CoV-2 as Clara cells that produce the protein CC10. "Our result provides the first line of evidence showing the major target cells of SARS-CoV-2 in the lung," says co-senior study author Yu-Sen Zhou of AMMS.In addition, the mice developed interstitial pneumonia, which affects the tissue and space around the air sacs of the lungs, causing the infiltration of inflammatory cells, the thickening of the structure that separates air sacs, and blood vessel damage. Compared with young mice, older mice showed more severe lung damage and increased production of signaling molecules called cytokines. Taken together, these features recapitulate those observed in COVID-19 patients.When the researchers administered SARS-CoV-2 into the stomach, two of the three mice showed high levels of viral RNA in the trachea and lung. The S protein was also present in lung tissue, which showed signs of inflammation. According to the authors, these findings are consistent with the observation that patients with COVID-19 sometimes experience gastrointestinal symptoms such as diarrhea, abdominal pain, and vomiting. But 10 times the dose of SARS-CoV-2 was required to establish infection through the stomach than through the nose.Future studies using this mouse model may shed light on how SARS-CoV-2 invades the brain and how the virus survives the gastrointestinal environment and invades the respiratory tract. "The hACE2 mice described in our manuscript provide a small animal model for understanding unexpected clinical manifestations of SARS-CoV-2 infection in humans," says co-senior study author Chang-Fa Fan of NIFDC. "This model will also be valuable for testing vaccines and therapeutics to combat SARS-CoV-2."This work was primarily supported by the National Key Research and Development Project of China, the National Science and Technology Major Project of China, the National Natural Science Foundation of China, and the Guangdong Pearl River talent plan.
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Genetically Modified
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May 21, 2020
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https://www.sciencedaily.com/releases/2020/05/200521102056.htm
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The ins and outs of sex change in medaka fish
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Larval nutrition plays a role in determining the sexual characteristics of Japanese rice fish, also called medaka (Oryzias latipes), report a team of researchers led by Nagoya University. The findings, published in the journal
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Decades ago, scientists found that medaka fish often undergo sex reversal in the wild. This involves genetically female larvae (meaning they have two X chromosomes) going on to develop male characteristics, or vice versa. This has made medaka fish a model organism for studying environmental sex development and other biological processes they have in common with vertebrates.Now, Nagoya University reproductive biologist Minoru Tanaka and colleagues in Japan have gained further insight into the factors that affect medaka sex reversal, potentially providing direction for future research into similar conditions in other species.Scientists had already discovered that environmental factors, such as temperature changes in the brackish and fresh waters where medaka fish live, are likely involved in their sex reversal. Tanaka and his team wanted to know if nutrition also played a role.They starved medaka larvae for five days. This was enough time to affect their metabolism without killing them. Three to four months later, the team examined the fish and found that 20% of the genetically female medaka had developed testes and characteristically male fins. The same did not occur in larvae that were not starved.Further tests showed that sex reversal in the fish was associated with reduced fatty acid synthesis and lipid levels. Specifically, starvation suppressed a metabolic pathway that synthesizes an enzyme called CoA, and disrupted a gene called "Overall, our findings showed that the sex of medaka fish is affected by both the external environment and internal metabolism," Tanaka says. "We believe lipids may represent a novel sex regulation system that responds to nutritional conditions."The team next plans on identifying other internal factors involved in medaka sex reversal. Future research should try to find the tissues or organs that sense changes in the internal environment and then produce key metabolites to regulate sex differentiation.
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Genetically Modified
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May 19, 2020
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https://www.sciencedaily.com/releases/2020/05/200519140416.htm
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Rapid screening method targets fatty acids in yeast; Key to sustainable bioproducts
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Scientists engineering valuable microbes for renewable fuels and bioproducts have developed a fast, efficient way to identify the most promising varieties.
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Researchers at the University of Illinois at Urbana-Champaign developed a novel mass spectrometry-based screening technique to rapidly profile medium-chain fatty acids produced in yeast -- part of a larger group of free fatty acids that are key components in essential nutrients, soaps, industrial chemicals, and fuels. They also identified seven new genetically engineered mutants of the yeast The study is detailed in a paper published in the journal Zhao's group genetically engineers tiny yeast cells to increase production of fatty acids, crucial components of biodiesel, fatty alcohols, waxes and olefins -- the building blocks for detergents, adhesives, and plastics. CABBI's goal is to develop robust yeasts that can convert renewable plant biomass to fuels and chemicals, as an environmentally friendly and sustainable alternative to petroleum-based chemical manufacturing processes.Scientists can create a large library of engineered yeast strains, or mutants, producing various MCFAs very quickly, Xue said. But their ability to control the exact composition of MCFAs produced in these microbial cell factories is limited, with no "high-throughput" way to quickly analyze large numbers of samples.To overcome this limitation, Xue and other researchers worked with Sweedler's group to develop a high-throughput screening tool, a chemical characterization approach based on MALDI-ToF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry). Mass spectrometry is an information-rich way to analyze complex samples by measuring their mass-to-charge ratio of ions. A laser is shot at a colony of yeast on a slide; the instrument measures the molecular masses of the lipids in the yeast, and thus is able to identify them.Most existing processes for detecting or analyzing free fatty acids rely on more complex gas or liquid chromatography-mass spectrometry, considered the gold standard methods. But those methods have limitations when dealing with a large pool of variations, and preparing samples is time-consuming and labor-intensive.The overall approach using the MALDI-ToF MS system is faster and has been used successfully with proteins and peptides. The ToF mass analyzer is fast, relatively low cost and has a large detection window, well-suited for screening complex biological targets.But medium-chain fatty acids are highly volatile and lightweight, making them harder to detect and quantify with this approach. Moreover, the thick cell wall of yeast creates another challenge for researchers to decompose cellular compositions efficiently.So the CABBI researchers optimized the sample preparation steps with various solvents and matrices. And instead of trying to directly detect the MCFAs, they used a proxy: membrane lipids in yeast cells. They hypothesized that increased levels of membrane lipids with shorter acyl chain phosphatidylcholines (PCs), a class of phospholipids, would correlate with a greater capacity to produce MCFAs, which are shorter in length than the abundant fatty acids commonly found in To validate that hypothesis, U of I scientists compared the MALDI-ToF MS profile of the naturally occurring yeast with two genetically engineered strains previously found to produce higher levels of MCFAs. The data showed that these two mutants had more of the shorter acyl chain PCs than the naturally occurring yeast. Those preliminary findings were then confirmed by the more exact liquid chromatography and fragment mass spectrometry processes.With their established screening method in hand, CABBI team members set out to find more mutant strains with higher production of MCFAs. They found two prominent peaks on the mass spectrum that were correlated with the phospholipids, an indication of fatty acids. Those were then used as a sign of MCFA production.As Sweedler points out, "the mass spectrometry measurement is fast -- analyzing up to 2,000 yeast colonies per hour (approximately one sample every two seconds) compared to 30 minutes per sample under traditional methods." The processing time is also significantly shortened: two to three minutes vs. three to four hours per sample. Overall, the MALDI-ToF MS screening tool allows scientists to quickly identify strains that warrant more detailed analysis."Our method allows us to screen tons of mutants in a short time. We can identify the good candidates for further study," Xue said.In the future, the method can be modified and used for high-throughput screening of other types of products, such as longer-chain fatty acids or fatty alcohols, saving time and labor.The researchers hope to build on their work at CABBI's iBioFAB -- the Illinois Biological Foundry for Advanced Biomanufacturing. Its robotic system can speed up sample preparation and provide faster, more accurate results, helping scale up the project to test many more mutant strains, Xue said. With about 6,000 genes in Beyond science, these C6 to C12 fatty acids are important in human health, providing critical nutrients and useful products, such as Omega-3 fatty acids."In the future if we can directly generate biofuels and bioproducts such as fatty acids from microbial cells like yeast in large scale, that means we don't need to use petrol," Xue said. "We can save the environment and save a lot of money as well."
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Genetically Modified
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May 11, 2020
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https://www.sciencedaily.com/releases/2020/05/200511112605.htm
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A 'consciousness conductor' synchronizes and connects mouse brain areas
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For scientists searching for the brain's 'control room', an area called the claustrum has emerged as a compelling candidate. This little-studied deep brain structure is thought to be the place where multiple senses are brought together, attention is controlled, and consciousness arises. Observations in mice now support the role of the claustrum as a hub for coordinating activity across the brain. New research from the RIKEN Center for Brain Science (CBS) shows that slow-wave brain activity, a characteristic of sleep and resting states, is controlled by the claustrum. The synchronization of silent and active states across large parts of the brain by these slow waves could contribute to consciousness.
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A serendipitous discovery actually led Yoshihiro Yoshihara, team leader at CBS, to investigate the claustrum. His lab normally studies the sense of smell and the detection of pheromones, but they chanced upon a genetically engineered mouse strain with a specific population of brain cells that was present only in the claustrum. These neurons could be turned on using optogenetic technology or selectively silenced through genetic manipulation, thus enabling the study of what turned out to be a vast, claustrum-controlled network. The study by Yoshihara and colleagues was published in They started out by mapping the claustrum's inputs and outputs and found that many higher-order brain areas send connections to the claustrum, such as those involved in sensation and motor control. Outgoing connections from the claustrum were broadly distributed across the brain, reaching numerous brain areas such as prefrontal, orbital, cingulate, motor, insular, and entorhinal cortices. "The claustrum is at the center of a widespread brain network, covering areas that are involved in cognitive processing," says co-first author Kimiya Narikiyo. "It essentially reaches all higher brain areas and all types of neurons, making it a potential orchestrator of brain-wide activity."Indeed, this is what the researchers found when they manipulated claustrum neurons optogenetically. Neural firing in the claustrum closely correlated with the slow-wave activity in many brain regions that receive input from the claustrom. When they artificially activated the claustrum by optogenetic light stimulation, it silenced brain activity across the cortex -- a phenomenon known as a "Down state," which can be seen when mice are asleep or at rest. Up and Down states are known to be synchronized across the cortex by slow waves of activity that travel from the front of the brain to the back. "The slow wave is especially important during sleep because it promotes homeostasis of synapses across the brain and consolidates memories from the preceding awake period," comments Yoshihara.The claustrum turns out to be vital for generating this slow-wave activity. Genetically removing the claustrum neurons significantly reduced slow waves in the frontal cortex. "We think the claustrum plays a pivotal role in triggering the down states during slow-wave activity, through its widespread inputs to many cortical areas," says Yoshihara. When these areas subsequently enter an up state and fire synchronously, this serves to 'replay' memories, transfer information between areas, and consolidate long-term memories, "all functions that may contribute indirectly to a conscious state," Yoshihara observes. "The claustrum is a coordinator of global slow-wave activity, and it is so exciting that we are getting closer to linking specific brain connections and actions with the ultimate puzzle of consciousness."
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Genetically Modified
| 2,020 |
May 7, 2020
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https://www.sciencedaily.com/releases/2020/05/200507094807.htm
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The EU not ready for the release of Gene drive organisms into the environment
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Within the last decades, new genetic engineering tools for manipulating genetic material in plants, animals and microorganisms are getting large attention from the international community, bringing new challenges and possibilities. While genetically modified organisms (GMO) have been known and used for quite a while now, gene drive organisms (GDO) are yet at the consideration and evaluation stage.
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The difference between these two technologies, where both are meant to replace certain characters in animals or plants with ones that are more favourable for the human population, is that, even though in GDO there is also foreign "synthetic" DNA being introduced, the inheritance mode differs. In GDO, the genome's original base arrangements are changed, using CRISPR/Cas-9 genome editing. Once the genome is changed, its alterations are carried down the organism's offspring and subsequent generations.In their study, published in the open-access journal The research team also points to current regulations addressing invasive alien species and biocontrol agents, and finds that the GMO regulations are, in principle, also a useful starting point for GDO.There are three main areas suggested to benefit from gene drive systems: public health (e.g. vector control of human pathogens), agriculture (e.g. weed and pest control), environmental protection and nature conservation (e.g. control of harmful non-native species).In recent years, a range of studies have shown the feasibility of synthetic CRISPR-based gene drives in different organisms, such as yeast, the common fruit fly, mosquitoes and partly in mammals.Given the results of previous research, the gene drive approach can even be used as prevention for some zoonotic diseases and, hence, possible future pandemics. For example, laboratory tests showed that the release of genetically modified mosquitoes can drastically reduce the number of malaria vectors. Nevertheless, potential environment and health implications, related to the release of GDO, remain unclear. Only a few potential applications have so far progressed to the research and development stage."The potential of GDOs for unlimited spread throughout wild populations, once released, and the apparently inexhaustible possibilities of multiple and rapid modifications of the genome in a vast variety of organisms, including higher organisms such as vertebrates, pose specific challenges for the application of adequate risk assessment methodologies," shares the lead researcher Mrs. Dolezel.In the sense of genetic engineering being a fastly developing science, every novel feature must be taken into account, while preparing evaluations and guidance, and each of them provides extra challenges.Today, the scientists present three key differences of gene drives compared to the classical GMO:1. Introducing novel modifications to wild populations instead of "familiar" crop species, which is a major difference between "classic" GMOs and GDOs."The goal of gene drive applications is to introduce a permanent change in the ecosystem, either by introducing a phenotypic change or by drastically reducing or eradicating a local population or a species. This is a fundamental difference to GM crops for which each single generation of hybrid seed is genetically modified, released and removed from the environment after a relatively short period," shares Dolezel.2. Intentional and potentially unlimited spread of synthetic genes in wild populations and natural ecosystems.Gene flow of synthetic genes to wild organisms can have adverse ecological impact on the genetic diversity of the targeted population. It could change the weediness or invasiveness of certain plants, but also threaten with extinction the species in the wild.Possibility for long-term risks to populations and ecosystems.Key and unique features of GDOs are the potential long-term changes in populations and large-scale spread across generations.In summary, the research team points out that, most of all, gene drive organisms must be handled extremely carefully, and that the environmental risks related to their release must be assessed under rigorous scrutiny. The standard requirements before the release of GDOs need to also include close post-release monitoring and risk management measures.It is still hard to assess with certainty the potential risks and impact of gene drive applications on the environment, human and animal health. That's why highly important questions need to be addressed, and the key one is whether genetically driven organisms are to be deliberately released into the environment in the European Union. The High Level Group of the European Commission's Scientific Advice Mechanism highlights that within the current regulatory frameworks those risks may not be covered.The research group recommends the institutions to evaluate whether the regulatory oversight of GMOs in the EU is accomodate to cover the novel risks and challenges posed by gene drive applications."The final decision to release GDOs into the environment will, however, not be a purely scientific question, but will need some form of broader stakeholder engagement and the commitment to specific protection goals for human health and the environment," concludes Dolezel.
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Genetically Modified
| 2,020 |
April 27, 2020
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https://www.sciencedaily.com/releases/2020/04/200427125154.htm
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Rapid evolution in fish: Genomic changes within a generation
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Evolution is usually viewed as a slow process, with changes in traits emerging over thousands of generations only. Over the recent years, however, research has indicated that adaptation in specific traits can occur more quickly. However, very few studies outside microorganisms were able to demonstrate empirically how quickly natural selection shapes the whole genome.
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A research team led by Dr. Daniel Berner at the University of Basel's Department of Environmental Sciences has now provided evidence for rapid evolution within a single generation, using threespine stickleback fish as model organism. The five-year study combined lab work, field experiments, mathematical modeling and genomic analysis.In the Lake Constance area, stickleback have adapted to ecologically different habitats -- lakes and rivers. To examine how quickly adaptation occurs across the genome, lake- and river-dwelling fish were crossed in the laboratory over several generations. The genomes of the two ecotypes were thus mixed, resulting in a genetically diverse experimental population.In a second step, the researchers released thousands of these experimental fish into a natural river habitat without resident stickleback, exposing them to natural selection. After a year, the remaining fish were recaptured and examined genetically."The hypothesis of this experiment was that in the river habitat in which the experimental animals had to survive, genetic variants of the original river population would increase in frequency," says Berner. "However, we had no idea whether this would be measurable within a single generation."To record potential changes in the genome, the researchers first had to identify the DNA regions most likely to be targeted by natural selection. To do so, they compared the original lake and river populations based on DNA sequence data. This revealed hundreds of regions in the genome likely important for adapting to the lake and river conditions. In precisely these regions, the experimental population's DNA sequence data from before and after the field experiment were then compared to identify changes in the frequency of genetic variants.The result supported the hypothesis: on average, the frequency of the river variants increased by around 2.5% at the expense of the lake variants. "This difference might appear small at first glance, but is truly substantial when extrapolated over a few dozen generations," says Berner. The experiment demonstrates that evolution can occur very quickly right in front of our eyes -- and not only in microorganisms. "Such rapid evolution may help some organisms to cope with the current rapid environmental changes caused by humans," Berner concludes.
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Genetically Modified
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April 23, 2020
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https://www.sciencedaily.com/releases/2020/04/200423154209.htm
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Researchers are making recombinant-protein drugs cheaper
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The mammalian cell lines that are engineered to produce high-value recombinant-protein drugs also produce unwanted proteins that push up the overall cost to manufacture these drugs. These same proteins can also lower drug quality. In a new paper in
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With the team's CRISPR-Cas mediated gene editing approach, the researchers demonstrate a significant decrease in purification demands across the mammalian cell lines they investigated. This work could lead to both lower production costs and higher quality drugs.Recombinant proteins currently account for the majority of the top drugs by sales, including drugs for treating complex diseases ranging from arthritis to cancer and even combating infectious diseases such as COVID-19 by neutralizing antibodies. However, the cost of these drugs puts them out of reach of much of the world population. The high cost is due in part to the fact that they are produced in cultured cells in the laboratory. One of the major costs is purification of these drugs, which can account for up to 80 percent of the manufacturing costs.In an international collaboration, researchers at the University of California San Diego and the Technical University of Denmark recently demonstrated the potential to protect the quality of recombinant protein drugs while substantially increasing their purity prior to purification, as reported in the study entitled "Multiplex secretome engineering enhances recombinant protein production and purity" published in April 2020 in the journal "Cells, such as Chinese hamster ovary (CHO) cells, are cultured and used to produce many leading drugs," explained Nathan E. Lewis, Associate Professor of Pediatrics and Bioengineering at the University of California San Diego, and Co-Director of the CHO Systems Biology Center at UC San Diego. "However, in addition to the medications we want, the cells also produce and secrete at least hundreds of their own proteins into the broth. The problem is that some of these proteins can degrade the quality of the drugs or could elicit negative side effects in a patient. That's why there are such strict rules for purification, since we want the safest and most effective medications possible."These host cell proteins (HCPs) that are secreted are carefully removed from every batch of drug, but before they are removed, they can degrade the quality and potency of the drugs. The various steps of purification can remove or further damage the drugs."Already at an early stage of our research program, we wondered how many of these secreted contaminating host cell proteins could be removed," recounted Director Bjorn Voldborg, Head of the CHO Core facility at the Center of Biosustainability at the Technical University of Denmark.In 2012 the Novo Nordisk Foundation awarded a large grant, which has funded ground-breaking work in genomics, systems biology and large scale genome editing for research and technology development of CHO cells at the Center for Biosustainability at the Danish Technical University (DTU) and the University of California San Diego. This funded the first publicly accessible genome sequences for CHO cells, and has provided a unique opportunity to combine synthetic and systems biology to rationally engineer CHO cells for biopharmaceutical production."Host cell proteins can be problematic if they pose a significant metabolic demand, degrade product quality, or are maintained throughout downstream purification," explained Stefan Kol, lead author on the study who performed this research while at DTU. "We hypothesized that with multiple rounds of CRISPR-Cas mediated gene editing, we could decrease host cell protein levels in a stepwise fashion. At this point, we did not expect to make a large impact on HCP secretion considering that there are thousands of individual HCPs that have been previously identified."This work builds on promising computational work published earlier in 2020.Researchers at UC San Diego had developed a computational model of recombinant protein production in CHO cells, published earlier this year in These modifications can be combined with additional advantageous genetic modifications being identified by the team in an effort to obtain higher quality medications at lower costs.
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Genetically Modified
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April 23, 2020
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https://www.sciencedaily.com/releases/2020/04/200423082238.htm
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Ocean microbes' role in climate effects
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A new study shows that "hotspots" of nutrients surrounding phytoplankton -- which are tiny marine algae producing approximately half of the oxygen we breathe every day -- play an outsized role in the release of a gas involved in cloud formation and climate regulation.
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The new research quantifies the way specific marine bacteria process a key chemical called dimethylsulfoniopropionate (DMSP), which is produced in enormous amounts by phytoplankton. This chemical plays a pivotal role in the way sulfur and carbon get consumed by microorganisms in the ocean and released into the atmosphere.The work is reported in the journal More than a billion tons of DMSP is produced annually by microorganisms in the oceans, accounting for 10 percent of the carbon that gets taken up by phytoplankton -- a major "sink" for carbon dioxide, without which the greenhouse gas would be building up even faster in the atmosphere. But exactly how this compound gets processed and how its different chemical pathways figure into global carbon and sulfur cycles had not been well-understood until now, Gao says."DMSP is a major nutrient source for bacteria," she says. "It satisfies up to 95 percent of bacterial sulfur demand and up to 15 percent of bacterial carbon demand in the ocean. So given the ubiquity and the abundance of DMSP, we expect that these microbial processes would have a significant role in the global sulfur cycle."Gao and her co-workers genetically modified a marine bacterium called Ruegeria pomeroyi, causing it to fluoresce when one of two different pathways for processing DMSP was activated, allowing the relative expression of the processes to be analyzed under a variety of conditions.One of the two pathways, called demethylation, produces carbon and sulfur based nutrients that the microbes can use to sustain their growth. The other pathway, called cleavage, produces a gas called dimethylsulfide (DMS), which Gao explains "is the compound that's responsible for the smell of the sea. I actually smelled the ocean a lot in the lab when I was experimenting."DMS is the gas responsible for most of the biologically derived sulfur that enters the atmosphere from the oceans. Once in the atmosphere, sulfur compounds are a key source of condensation for water molecules, so their concentration in the air affects both rainfall patterns and the overall reflectivity of the atmosphere through cloud generation. Understanding the process responsible for much of that production could be important in multiple ways for refining climate models.Those climate implications are "why we're interested in knowing when bacteria decide to use the cleavage pathway versus the demethylation pathway," in order to better understand how much of the important DMS gets produced under what conditions, Gao says. "This has been an open question for at least two decades."The new study found that the concentration of DMSP in the vicinity regulates which pathway the bacteria use. Below a certain concentration, demethylation was dominant, but above a level of about 10 micromoles, the cleavage process dominated."What was really surprising to us was, upon experimentation with the engineered bacteria, we found that the concentrations of DMSP in which the cleavage pathway dominates is higher than expected -- orders of magnitude higher than the average concentration in the ocean," she says.That suggests that this process hardly takes place under typical ocean conditions, the researchers concluded. Rather, microscale "hotspots" of elevated DMSP concentration are probably responsible for a highly disproportionate amount of global DMS production. These microscale "hotspots" are areas surrounding certain phytoplankton cells where extremely high amounts of DMSP are present at about a thousand times greater than average oceanic concentration."We actually did a co-incubation experiment between the engineered bacteria and a DMSP-producing phytoplankton," Gao says. The experiment showed "that indeed, bacteria increased their expression of the DMS-producing pathway, closer to the phytoplankton."The new analysis should help researchers understand key details of how these microscopic marine organisms, through their collective behavior, are affecting global-scale biogeochemical and climatic processes, the researchers say.The research team included MIT and ETH Zurich postdocs Vicente Fernandez and Kang Soo Lee, graduate student Simona Fenizia, and Professor Georg Pohnert at Friedrich Schiller University in Germany. The work was supported by the Gordon and Betty Moore Foundation, the Simons Foundation, the National Science Foundation, and the Australian Research Council.
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Genetically Modified
| 2,020 |
April 16, 2020
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https://www.sciencedaily.com/releases/2020/04/200416135853.htm
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New universal Ebola vaccine may fight all four virus species that infect humans
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Infectious disease scientists report early development of a potential universal vaccine for Ebola viruses that preclinical tests show might neutralize all four species of these deadly viruses infecting people in recent outbreaks, mainly in Africa.
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Scientists at Cincinnati Children's Hospital Medical Center report their preclinical results in the Although still in early preclinical testing, researchers report that their data indicate that the prospective vaccine has potential to be a stand-alone protection from Ebola. It also could broaden and extend the durability of protective immunity induced by current live vaccines already being tested in clinical trials against individual Ebola virus species, said Karnail Singh, PhD, the study's co-principal investigator in the Division of Infectious Diseases."This could be a significant advancement in the global effort to prevent or manage Ebola outbreaks, especially if this vaccine used alone or in combination with another Ebola vaccine results in long-term and durable protective immunity against different Ebola viruses," Singh said.A deadly Ebola outbreak in West Africa between 2013 and 2016 accelerated international efforts to develop vaccines for these highly infectious and harmful viruses. This led to development of recombinant Ebola vaccines in which glycoprotein from Zaire Ebola virus is engineered into another modified live viral vector. When administered, these live vaccines induce immune responses against the Ebola glycoprotein that, in turn, protect against any subsequent attack by the Ebola virus.Singh and colleagues report that while the live-vector vaccines are producing encouraging results in clinical trials, until the current study none of the new vaccines under development have been shown to induce immune responses that cross-react against multiple Ebola virus species that cause the deadly disease in humans.The new vaccine takes a novel approach, according to the study. The researchers designed a bivalent, spherical Ebola virus-like particle (VLP) that incorporates two genetically diverse glycoproteins (one each from the Zaire Ebola virus and Sudan Ebola virus) on a spherical core.This approach will not cause illness in the recipient as the VLPs lack the genetic material and do not multiply. The vaccine works by stimulating immune responses against Ebola that generate virus-fighting antibodies to attack the different virus species.When the researchers administered their new Ebola VLP vaccine to appropriate animal models, it produced robust immune responses against Ebola virus species known to be pathogenic in humans.Although the new vaccine uses glycoproteins from two Ebola virus species, Singh said it might work against all four known pathogenic Ebola viruses as responses to one of the glycoproteins generates cross-reactive responses against two other Ebola virus species.The researchers emphasize that extensive additional preclinical testing of the prospective Ebola VLP vaccine is needed before it could potentially be tested in clinical trials.A key collaborator on the multi-institutional study -- which included the University of Cincinnati College of Medicine, the Emory University School of Medicine, and the University of Louisiana's New Iberia Research Center -- was Paul Spearman, MD, Division Director of Infectious Diseases at Cincinnati Children's.Spearman said at the moment, vaccine challenge experiments are in the planning stages. They will involve working in collaboration with an institution that has Level 4 biosafety facilities and will require additional external funding to move this promising research forward."If the data from those studies is equally encouraging, the vaccine should be ready to progress to generation of clinical grade material for human trials," he said.The study was funded in part by a pilot grant to Singh and Spearman by Innovation Ventures, the technology commercialization arm of Cincinnati Children's, the Cincinnati Children's Research Foundation and support from the New Iberia Research Center, University of Louisiana at Lafayette. Partial support for the study's use of virus-like-particle (VLP) platforms to conduct Ebola vaccine research was provided by the National Institutes of Health.
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Genetically Modified
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April 10, 2020
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https://www.sciencedaily.com/releases/2020/04/200410162452.htm
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Moving closer to producing heparin in the lab
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In a recent study published in the
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In particular, the researchers found a critical gene in heparin biosynthesis: ZNF263 (zinc-finger protein 263). The researchers believe this gene regulator is a key discovery on the way to industrial heparin production. The idea would be to control this regulator in industrial cell lines using genetic engineering, paving the way for safe industrial production of heparin in well-controlled cell culture.Heparin is currently produced by extracting the drug from pig intestines, which is a concern for safety, sustainability, and security reasons. Millions of pigs are needed each year to meet our needs, and most manufacturing is done outside the USA. Furthermore, ten years ago, contaminants from the pig preparations led to dozens of deaths. Thus, there is a need to develop sustainable recombinant production. The work in PNAS provides new insights on exactly how cells control synthesis of heparin.Heparin is a special subtype of a more general class of carbohydrates, called heparan sulfates, that are produced by a wide range of cells, both in the human body, as well as in cell culture. Yet, heparin is exclusively produced in a special type of blood cells called mast cells. To this day, heparin cannot be successfully produced in cell culture.Researchers at UC San Diego reasoned that heparin synthesis must be under the control of certain gene regulators (called transcription factors), whose tissue-specific occurrence might give mast cells the unique ability to produce heparin.Since regulators for heparin were not known, a research team led by UC San Diego professors Jeffrey Esko and Nathan Lewis used bioinformatic software to scan the genes encoding enzymes involved in heparin production and specifically look for sequence elements that could represent binding sites for transcription factors. The existence of such a binding site could indicate that the respective gene is regulated by a corresponding gene regulator protein, i.e. a transcription factor."One DNA sequence that stood out the most is preferred by a transcription factor called ZNF263 (zinc-finger protein 263)," explains UC San Diego professor Nathan E. Lewis, who holds appointments in the UC San Diego School of Medicine's Department of Pediatrics and in the UC San Diego Jacobs School of Engineering's Department of Bioengineering."While some research has been done on this gene regulator, this is the first major regulator involved in heparin synthesis," said Lewis. He is also Co-Director of the CHO Systems Biology Center at the UC San Diego Jacobs School of Engineering.Using the gene-editing technology, CRISPR/Cas9, the UC San Diego researchers mutated ZNF263 in a human cell line that normally does not produce heparin. They found that the heparan sulfate that this cell line would normally produce was now chemically altered and showed a reactivity that was closer to heparin.Experiments further showed that ZNF263 represses key genes involved in heparin production. Interestingly, analysis of gene expression data from human white blood cells showed suppression of ZNF263 in mast cells (which produce heparin in vivo) and basophils, which are related to mast cells. The researchers report that ZNF263 appears to be an active repressor of heparin biosynthesis throughout most cell types, and mast cells are enabled to produce heparin because ZNF263 is suppressed in these cells.This finding could have important relevance in biotechnology. Cell lines used in industry (such as CHO cells that normally are unable to produce heparin) could be genetically modified to inactivate ZNF263 which could enable them to produce heparin, like mast cells do.Philipp Spahn, a project scientist in Nathan Lewis' lab in the Departments of Pediatrics and Bioengineering at UC San Diego, described further directions the team is pursuing: "Our bioinformatic analysis revealed several additional potential gene regulators which can also contribute to heparin production and are now exciting objects of further study."
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Genetically Modified
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April 10, 2020
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https://www.sciencedaily.com/releases/2020/04/200410162404.htm
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A model for better predicting the unpredictable byproducts of genetic modification
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Researchers are interested in genetically modifying trees for a variety of applications, from biofuels to paper production. They also want to steer clear of modifications with unintended consequences. These consequences can arise when intended modifications to one gene results in unexpected changes to other genes. A new model aims to predict these changes, helping to avoid unintended consequences, and hopefully paving the way for more efficient research in the fields of genetic modification and forestry.
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The research at issue focuses on lignin, a complex material found in trees that helps to give trees their structure. It is, in effect, what makes wood feel like wood."Whether you want to use wood as a biofuel source or to create pulp and paper products, there is a desire to modify the chemical structure of lignin by manipulating lignin-specific genes, resulting in lignin that is easier to break down," says Cranos Williams, corresponding author of a paper on the work and an associate professor of electrical and computer engineering at NC State. "However, you don't want to make changes to a tree's genome that compromise its ability to grow or thrive."The researchers focused on a tree called "Previous research generated models that predict how independent changes to the expression of lignin genes impacted lignin characteristics," says Megan Matthews, first author of the paper, a former Ph.D. student at NC State and a current postdoc at the University of Illinois. "These models, however, do not account for cross-regulatory influences between the genes. So, when we modify a targeted gene, the existing models do not accurately predict the changes we see in how non-targeted genes are being expressed. Not capturing these changes in expression of non-targeted genes hinders our ability to develop accurate gene-modification strategies, increasing the possibility of unintended outcomes in lignin and wood traits."To address this challenge, we developed a model that was able to predict the direct and indirect changes across all of the lignin genes, capturing the effects of multiple types of regulation. This allows us to predict how the expression of the non-targeted genes is impacted, as well as the expression of the targeted genes," Matthews says."Another of the key merits of this work, versus other models of gene regulation, is that previous models only looked at how the RNA is impacted when genes are modified," Matthews says. "Those models assume the proteins will be impacted in the same way, but that's not always the case. Our model is able to capture some of the changes to proteins that aren't seen in the RNA, or vice versa."This model could be incorporated into larger, multi-scale models, providing a computational tool for exploring new approaches to genetically modifying tree species to improve lignin traits for use in a variety of industry sectors."In other words, by changing one gene, researchers can accidentally mess things up with other genes, creating trees that aren't what they want. The new model can help researchers figure out how to avoid that.This work was supported by the National Science Foundation Grant DBI-0922391 to Chiang and by a National Physical Science Consortium Graduate Fellowship to Matthews.
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Genetically Modified
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April 9, 2020
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https://www.sciencedaily.com/releases/2020/04/200409140019.htm
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Identical mice, different gut bacteria, different levels of cancer
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Researchers at the University of Michigan Rogel Cancer Center are shedding new light on the way microorganisms that live in the gastrointestinal tract can affect the development of colorectal cancer.
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Some types of gut bacteria are better than others at stimulating certain immune cells, specifically CD8+ T cells, in the body, they found. And while these CD8+ T cells normally help protect the body against cancer, overstimulating them may promote inflammation and exhaust the T cells -- which can actually increase susceptibility to cancer, according to new mouse model study published in The work will help scientists pinpoint which populations of bacteria are tumor suppressive or tumor promoting and how, says study first author Amy Yu, a doctoral candidate in immunology at U-M."There has also been a lot of excitement about the role bacteria may play in improving the effectiveness of immunotherapy," says senior study author Grace Chen, M.D., Ph.D., an associate professor of hematology/oncology at Michigan Medicine and member of the Rogel Cancer Center. "This work suggests it may be a double edged sword -- and that promoting T cell exhaustion is something researchers need to watch out for."In the U.S., colorectal cancer is the third-leading cause of cancer-related death in both men and women, according to the American Cancer Society.The current study builds on previous work from Chen's group, which found that disturbances of the gut microbiome can directly contribute to the development of cancer.The group found that mice from two different research colonies had vastly different susceptibility to colorectal cancer when they were exposed to a carcinogen as well as an agent that promotes gastrointestinal inflammation.The mice from the first colony grew an average of five tumors, while the mice from the second colony developed 15 tumors and had a more significant inflammatory response.When the researchers sequenced fecal bacteria from the two different colonies, they found they had distinct microbiomes composed of different types of bacteria."This was exciting because my lab is very interested in which bacteria have the biggest impact on colorectal cancer risk, and by what mechanisms," Chen says.To better understand what was causing the differences the researchers were seeing in the two different colonies of mice, they transplanted gut bacteria from each of the two colonies into genetically identical mice that had been bred in a bacteria free environment. Once again, mice with bacteria from the second colony fared far worse."This showed that the different gut microbiota directly contributed to tumor development," Yu notes. "Our data ultimately revealed nine different bacterial populations that may have tumor-suppressive or tumor-promoting activity."Investigating mechanismsThe team next conducted experiments to better understand what was driving the increased inflammation and tumor growth associated with the bacteria from the second mouse colony.Through immune cell profiling, they found that there were more T cells in the colon tissue of mice with bacteria from the second colony, and many more of a type of cell called CD8+."It's a little counter intuitive, since T cells and CD8+ cells are usually associated with better outcomes in colorectal cancer patients," Chen says. "We hypothesized that these cells get over-activated in the presence of certain bacteria and then exhausted, leaving them less capable of killing tumor cells."When the bacteria from the second mouse colony were transplanted into mice that were engineered to lack CD8+ T cells, fewer tumors developed, supporting T cells' role in promoting the growth of the cancer in the presence of certain bacteria, Chen notes.Meanwhile, the lab continues to build on the research as it investigates the mechanisms by which different bacteria may contribute to promoting or protecting against the development of colorectal cancer.
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Genetically Modified
| 2,020 |
April 7, 2020
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https://www.sciencedaily.com/releases/2020/04/200407170742.htm
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It's now or never: Visual events have 100 milliseconds to hit brain target or go unnoticed
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Researchers at the National Eye Institute (NEI) have defined a crucial window of time that mice need to key in on visual events. As the brain processes visual information, an evolutionarily conserved region known as the superior colliculus notifies other regions of the brain that an event has occurred. Inhibiting this brain region during a specific 100-millisecond window inhibited event perception in mice. Understanding these early visual processing steps could have implications for conditions that affect perception and visual attention, like schizophrenia and attention deficit hyperactivity disorder (ADHD). The study was published online in the
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"One of the most important aspects of vision is fast detection of important events, like detecting threats or the opportunity for a reward. Our result shows this depends on visual processing in the midbrain, not only the visual cortex," said Richard Krauzlis, Ph.D., chief of the Section on Eye Movements and Visual Selection at NEI and senior author of the study.Visual perception -- one's ability to know that one has seen something -- depends on the eye and the brain working together. Signals generated in the retina travel via retinal ganglion cell nerve fibers to the brain. In mice, 85% of retinal ganglion cells connect to the superior colliculus. The superior colliculus provides the majority of early visual processing in these animals. In primates, a highly complex visual cortex takes over more of this visual processing load, but 10% of retinal ganglion cells still connect to the superior colliculus, which manages basic but necessary perceptual tasks.One of these tasks is detecting that a visual event has occurred. The superior colliculus takes in information from the retina and cortex, and when there is sufficient evidence that an event has taken place in the visual field, neurons in the superior colliculus fire. Classical experiments into perceptual decision-making involve having a subject, like a person or a monkey, look at an image of vertical grating (a series of blurry vertical black and white lines) and decide if or when the grating rotates slightly. In 2018, Krauzlis and Wang adapted these classic experiments for mice, opening up new avenues for research."Although we have to be cautious translating data from mice to humans, because of the difference in visual systems, mice have many of the same basic mechanisms for event detection and visual attention as humans. The genetic tools available for mice allow us to study how specific genes and neurons are involved in controlling perception," said Lupeng Wang, Ph.D., first author of the study.In this study, Wang and colleagues used a technique called optogenetics to tightly control the activity of the superior colliculus over time. They used genetically modified mice so that they could turn neurons in the superior colliculus on or off using a beam of light. This on-off switch could be timed precisely, enabling the researchers to determine exactly when the neurons of the superior colliculus were required for detecting visual events. The researchers trained their mice to lick a spout when they'd seen a visual event (a rotation in the vertical grating), and to avoid licking the spout otherwise.Inhibiting the cells of the superior colliculus made the mice less likely to report that they'd seen an event, and when they did, their decision took longer. The inhibition had to occur within a 100 millisecond (one-tenth of a second) interval after the visual event. If the inhibition was outside that 100-millisecond timeframe, the mouse's decisions were mostly unaffected. The inhibition was side-specific: because the retinal cells cross over and connect to the superior colliculus on the opposite side of the head (the left eye is connected to the right superior colliculus and vice versa), inhibiting the right side of the superior colliculus depressed responses to stimuli on the left side, but not on the right."The ability to temporarily block the transmission of neural signals with such precise timing is one of the great advantages of using optogenetics in mice and reveals exactly when the crucial signals pass through the circuit," said Wang.Interestingly, the researchers found that the deficits with superior colliculus inhibition were much more pronounced when the mice were forced to ignore things happening elsewhere in their visual field. Essentially, without the activity of the superior colliculus, the mice were unable to ignore distracting visual events. This ability to ignore visual events, called visual attention, is critical for navigating the complex visual environments of the real world."The superior colliculus is a good target for probing these functions because it has a neatly organized map of the visual world. And it is connected to less neatly organized regions, like the basal ganglia, which are directly implicated in a wide range of neuropsychiatric disorders in humans," said Krauzlis. "It's sort of like holding the hand of a friend as you reach into the unknown."
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Genetically Modified
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April 7, 2020
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https://www.sciencedaily.com/releases/2020/04/200407072712.htm
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Engineered virus might be able to block coronavirus infections, mouse study shows
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No vaccines exist that protect people against infections by coronaviruses, including SARS-CoV-2, which causes COVID-19, or the ones that cause SARS and MERS. As COVID-19 continues to wreak havoc, many labs around the world have developed a laser-like focus on understanding the virus and finding the best strategy for stopping it.
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This week in In the new paper, the researchers suggest that the approach they took for a MERS virus vaccine may also work against SARS-CoV-2. The vaccine's delivery method is an RNA virus called parainfluenza virus 5 (PIV5), which is believed to cause a condition known as kennel cough in dogs but appears harmless to people. The researchers added an extra gene to the virus so that infected cells would produce the S, or spike, glycoprotein known to be involved in MERS infections."We know people have been exposed to PIV5, but it seems to be an innocuous virus in humans," said pediatric pulmonologist and coronavirus expert Paul McCray, M.D., at the University of Iowa, in Iowa City, who co-led the new study with virologist Biao He, Ph.D., at the University of Georgia, in Athens. "PIV5 doesn't seem to cause a cytopathic effect." The MERS virus cannot replicate in mice, so to test the vaccine McCray developed a mouse model that mimics human infections. The mice had been genetically engineered to express DPP4, the protein used by the MERS virus as an entry point for human cells.Lab tests showed that a single dose of the vaccine, given intranasally, effectively caused infected cells to produce the S protein, which in turn triggered immune responses against the protein in the animal host.Four weeks after the mice received the vaccine, they were exposed to a strain of the MERS virus, adapted to the mice to cause a lethal infection. The MERS virus was also given to groups of mice that had received a different PIV5 vaccine -- one without the genes for the S protein -- or an intramuscular vaccine with inactivated MERS virus.All the mice immunized with the modified PIV5 virus survived MERS virus infection. In contrast, all the mice immunized with the PIV5 without S died from the infection. The intramuscular vaccine of inactivated MERS virus only protected 25% of the mice from a lethal infection. The mice that received inactivated MERS virus showed above-average levels of eosinophils, white blood cells that indicate infection or inflammation. This connection raises a safety concern for inactivated MERS virus as a potential vaccine, said He. The study demonstrates that an intranasal, PIV5-based vaccine is effective against MERS in mice, said He, and should be investigated for its potential against other dangerous coronaviruses, including SARS-CoV-2."We're quite interested in using viruses as gene delivery vehicles," said McCray, who has also investigated similar strategies as a way to treat cystic fibrosis. Now, like colleagues around the world, McCray and He have both focused their research efforts on SARS-CoV-2, taking a similar tack to working with mouse models of infection and testing vaccines.Finding an effective vaccine against the coronavirus that causes COVID-19 is a race against time, McCray said. "One hundred percent of the population is not going to be exposed to the virus the first time around, which means there will be more people to infect when it comes again," he said. "We don't know yet if people get lasting immunity from the SARS-CoV-2 infection, so it's important to think about ways to protect the population."
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Genetically Modified
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March 30, 2020
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https://www.sciencedaily.com/releases/2020/03/200330152124.htm
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'Living drug factories' might treat diabetes and other diseases
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One promising way to treat diabetes is with transplanted islet cells that produce insulin when blood sugar levels get too low. However, patients who receive such transplants must take drugs to prevent their immune systems from rejecting the transplanted cells, so the treatment is not often used.
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To help make this type of therapy more feasible, MIT researchers have now devised a way to encapsulate therapeutic cells in a flexible protective device that prevents immune rejection while still allowing oxygen and other critical nutrients to reach the cells. Such cells could pump out insulin or other proteins whenever they are needed."The vision is to have a living drug factory that you can implant in patients, which could secrete drugs as-needed in the patient. We hope that technology like this could be used to treat many different diseases, including diabetes," says Daniel Anderson, an associate professor of chemical engineering, a member of MIT's Koch Institute for Integrative Cancer Research and Institute for Medical Engineering and Science, and the senior author of the work.In a study of mice, the researchers showed that genetically engineered human cells remained viable for at least five months, and they believe they could last longer to achieve long-term treatment of chronic diseases such as diabetes or hemophilia, among others.Suman Bose, a research scientist at the Koch Institute, is the lead author of the paper, which appears today in Patients with type 1 diabetes usually have to inject themselves with insulin several times a day to keep their blood sugar levels within a healthy range. Since 1999, a small number of diabetes patients have received transplanted islet cells, which can take over for their nonfunctioning pancreas. While the treatment is often effective, the immunosuppressant drugs that these patients have to take make them vulnerable to infection and can have other serious side effects.For several years, Anderson's lab has been working on ways to protect transplanted cells from the host's immune system, so that immunosuppressant drugs would not be necessary."We want to be able to implant cells into patients that can secrete therapeutic factors like insulin, but prevent them from being rejected by the body," Anderson says. "If you could build a device that could protect those cells and not require immune suppression, you could really help a lot of people."To protect the transplanted cells from the immune system, the researchers housed them inside a device built out of a silicon-based elastomer (polydimethylsiloxane) and a special porous membrane. "It's almost the same stiffness as tissue, and you make it thin enough so that it can wrap around organs," Bose says.They then coated the outer surface of the device with a small-molecule drug called THPT. In a previous study, the researchers had discovered that this molecule can help prevent fibrosis, a buildup of scar tissue that results when the immune system attacks foreign objects.The device contains a porous membrane that allows the transplanted cells obtain nutrients and oxygen from the bloodstream. These pores must be large enough to allow nutrients and insulin to pass through, but small enough so that immune cells such as T cells can't get in and attack the transplanted cells.In this study, the researchers tested polymer coatings with pores ranging from 400 nanometers to 3 micrometers in diameter, and found that a size range of 800 nanometers to 1 micrometer was optimal. At this size, small molecules and oxygen can pass through, but not T cells. Until now, it had been believed that 1-micrometer pores would be too large to stop cellular rejection.In a study of diabetic mice, the researchers showed that transplanted rat islets inside microdevices maintained normal blood glucose levels in the mice for more than 10 weeks.The researchers also tested this approach with human embryonic kidney cells that were engineered to produce erythropoietin (EPO), a hormone that promotes red blood cell production and is used to treat anemia. These therapeutic human cells survived in mice for at least the 19-week duration of the experiment."The cells in the device act as a factory and continuously produce high levels of EPO. This led to an increase in the red blood cell count in the animals for as long as we did the experiment," Anderson says.In addition, the researchers showed that they could program the transplanted cells to produce a protein only in response to treatment with a small molecule drug. Specifically, the transplanted engineered cells produced EPO when mice were given the drug doxycycline. This strategy could allow for on-demand production of a protein or hormone only when it is needed.This type of "living drug factory" could be useful for treating any kind of chronic disease that requires frequent doses of a protein or hormone, the researchers say. They are currently focusing on diabetes and are working on ways to extend the lifetime of transplanted islet cells."This is the eighth Nature journal paper our team has published in the past four-plus years elucidating key fundamental aspects of biocompatibility of implants. We hope and believe these findings will lead to new super-biocompatible implants to treat diabetes and many other diseases in the years to come," says Robert Langer, the David H. Koch Institute Professor at MIT and an author of the paper.
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Genetically Modified
| 2,020 |
March 19, 2020
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https://www.sciencedaily.com/releases/2020/03/200319141028.htm
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Scientists program cells to carry out gene-guided construction projects
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Stanford researchers have developed a technique that reprograms cells to use synthetic materials, provided by the scientists, to build artificial structures able to carry out functions inside the body.
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"We turned cells into chemical engineers of a sort, that use materials we provide to construct functional polymers that change their behaviors in specific ways," said Karl Deisseroth, professor of bioengineering and of psychiatry and behavioral sciences, who co-led the work.In the March 20 edition of Study co-leader Zhenan Bao, professor and chair of chemical engineering, said that while the current experiments focused mainly on brain cells or neurons, GTCA should also work with other cell types. "We've developed a technology platform that can tap into the biochemical processes of cells throughout the body," Bao said.The researchers began by genetically reprogramming the cells they wanted to affect. They did this by using standard bioengineering techniques to deliver instructions for adding an enzyme, called APEX2, into specific neurons.Next, the scientists immersed the worms and other experimental tissues in a solution with two active ingredients -- an extremely low, non-lethal dose of hydrogen peroxide, and billions of molecules of the raw material they wanted the cells to use for their building projects.Contact between the hydrogen peroxide and the neurons with the APEX2 enzyme triggered a series of chemical reactions that fused the raw-material molecules together into a chain known as a polymer to form a mesh-like material. In this way, the researchers were able to weave artificial nets with either insulative or conductive properties around only the neurons they wanted.The polymers changed the properties of the neurons. Depending on which polymer was formed, the neurons fired faster or slower, and when these polymers were created in cells of In the mammalian cell experiments, the researchers ran similar polymer-forming experiments on living slices from mouse brains and on cultured neurons from rat brains, and verified the conducting or insulating properties of the synthesized polymers. Finally, they injected a low-concentration hydrogen peroxide solution along with millions of the raw-material molecules into the brains of live mice to verify that these elements were not toxic together.Rather than a medical application, Deisseroth says, "what we have are tools for exploration." But these tools could be used to study how multiple sclerosis, caused by the fraying of myelin insulation around nerves, might respond if diseased cells could be induced to form insulating polymers as replacements. Researchers might also explore whether forming conductive polymers atop misfiring neurons in autism or epilepsy might modify those conditions.Going forward, the researchers would like to explore variants of their cell-targeted technology. GTCA could be used to produce a wide range of functional materials, implemented by diverse chemical signals. "We're imagining a whole world of possibilities at this new interface of chemistry and biology," Deisseroth said.
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Genetically Modified
| 2,020 |
March 18, 2020
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https://www.sciencedaily.com/releases/2020/03/200318104435.htm
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Loss of protein disturbs intestinal homeostasis and can drive cancer
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Colorectal carcinoma (CRC), the most common form of intestinal cancer, is the second leading cause of cancer related death worldwide. While some patients have a genetic predisposition to the disease, the majority of cases are sporadic and largely influenced by the ever-increasing "Western lifestyle," which includes obesity, poor diet and physical inactivity.
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A recently published study now sheds new light on how this disease develops: Through the use of genetically modified mice, an international team of researchers was able to demonstrate that the protein MCL1 is essential for maintaining intestinal homeostasis and thus protecting against intestinal cancer formation. The research project was led by Achim Weber, professor at the Institute of Molecular Cancer Research at the University of Zurich and at the Institute of Pathology and Molecular Pathology of the University Hospital Zurich, in collaboration with researchers from the German Cancer Research Center in Heidelberg and the Beatson Institute in Glasgow, Scotland.For their study, the researchers modified the genetic makeup of mice so that the animals' intestinal cells would no longer produce the MCL1 protein. This protein normally prevents the death of cells and thus maintains the right balance of dying and new cells in the intestinal mucosa. The loss of MCL1 resulted in irreparable damage to the intestine and the subsequent formation of intestinal tumors. Similar changes can also be observed in the intestine of humans suffering from chronic intestinal inflammation, who also carry an elevated risk of developing intestinal cancer.Microbiota-driven chronic intestinal inflammation has long been considered essential in the development of intestinal cancer. "What's remarkable, however, is that the loss of MCL1 can drive intestinal cancer even without bacteria-driven inflammation," says Weber. This was demonstrated by experiments in which mice without the MCL1 protein were held in a germfree environment. "This means that the loss of certain genes is apparently enough to cause intestinal cancer -- even in the absence of inflammation. This groundbreaking finding significantly furthers our understanding of the critical early steps associated with intestinal cancer development," says Weber.This study also reveals a second surprising result: In some types of tumor -- including colorectal carcinoma -- there is too much MCL1, rather than too little. Researchers assume that these tumors ramp up the production of MCL1 to gain an advantage for survival and enable them to better resist conventional treatment methods. As a result, a number of new therapies are currently being trialled to interfere with and reduce MCL1 function.However, the study's findings show that not only the overexpression, but also the loss of MCL1 can be detrimental. It is possible that the loss of MCL1 function -- even only temporarily -- may trigger a disturbance of the intestinal mucosa and the initial steps of tumor development. "The regulation of this protein is like walking a tightrope," warns Marc Healy, first author of the study. "Our study therefore urges an element of caution when it comes to using MCL1 inhibition in cancer therapy."
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Genetically Modified
| 2,020 |
March 12, 2020
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https://www.sciencedaily.com/releases/2020/03/200312114150.htm
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Statins starve cancer cells to death
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More than 35 million Americans take statin drugs daily to lower their blood cholesterol levels. Now, in experiments with human cells in the laboratory, researchers at Johns Hopkins Medicine have added to growing evidence that the ubiquitous drug may kill cancer cells and have uncovered clues to how they do it.
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The findings, say the researchers, enhance previous evidence that statins could be valuable in combating some forms of cancer. In unrelated studies, other Johns Hopkins Medicine researchers have studied how statins may cut the risk for aggressive prostate cancer."There have been epidemiological indications that people who take statins long term have fewer and less aggressive cancers, and that statins can kill cancer cells in the laboratory, but our research was not initially designed to investigate possible biological causes of these observations," says Peter Devreotes, Ph.D., Issac Morris and Lucille Elizabeth Hay Professor of Cell Biology.Results of the new research appeared Feb. 12 in the Devreotes and his team began the new study with an unbiased screen of about 2,500 drugs approved by the U.S. Food and Drug Administration (FDA) to see which ones had the best kill rate of cells genetically engineered to have a mutation in a cancer gene called PTEN. The gene codes for an enzyme that suppresses tumor growth. Among the thousands of drugs, statins and in particular pitavastatin, emerged as a top contender in cancer-killing ability. Most of the other drugs had no effect or killed normal and engineered cells at the same rate. Equal concentrations of pitavastatin caused cell death in nearly all of the engineered cells, but very in few normal cells.Devreotes and his team then looked at the molecular pathways that statins were likely to affect. It's well known, for example, that statins block a liver enzyme that makes cholesterol, but the drug also blocks the creation of a small molecule called geranylgeranyl pyrophosphate, or GGPP, which is responsible for connecting cellular proteins to cellular membranes.When the researchers added pitavastatin and GGPP to human cancer cells with PTEN mutations, the researchers found that GGPP prevented the statin's killing effects and the cancer cells survived, suggesting that GGPP may be a key ingredient to cancer cell survival.Next, looking under a microscope at cells engineered to lack the enzyme that makes GGPP, Devreotes and his team saw that as the cells began to die, they stopped moving. Under normal circumstances, cancer cells are a bundle of moving energy, consuming massive amounts of nutrients to maintain their unchecked growth. They maintain this breakneck pace by creating straw-like protrusions from their surface to drink up nutrients from the surrounding environment.Suspecting that the non-moving cancer cells were literally "starving to death," Devreotes says, the scientists then measured the statin-treated cells' intake by adding a fluorescent tag to proteins in the cells' environment.Normal human cells glowed brightly with the fluorescent tag, suggesting that these cells ingested protein from their surroundings regardless of whether the scientists added statins to the mix of nutrients and cells. However, human cancer cells with PTEN mutations took in almost no glowing proteins after the scientists added statins. The inability of the statin-treated cancer cells to make the protrusions needed take up proteins leads to their starvation.Devreotes says his team plans further research on the effects of statins in people with cancer and compounds that block GGPP.
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Genetically Modified
| 2,020 |
March 5, 2020
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https://www.sciencedaily.com/releases/2020/03/200305132134.htm
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City fox and country fox
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For wildlife, cities can present new opportunities as well as threats. Researchers from the Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW) and the Luxembourg National Museum of Natural History (NMNH) analysed genetic material of red foxes (Vulpes vulpes) inhabiting Berlin and its surroundings. They identified two genetically distinct, adjacent "urban" and "rural" fox populations and revealed that physical barriers such as rivers or human-made structures reduce the exchange between these populations but also differences in human activity in these landscapes play a major role. The researchers suggest that avoidance of sites of human activity may drive foxes into costly trade-offs as they prefer to disperse along potentially dangerous transportation infrastructures. The study was recently published in the scientific journal
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The red fox is a physically highly mobile and ecologically opportunistic omnivore, successfully adjusting to very different and dynamic environments. Cities are an attractive novel habitat for red foxes as they offer an abundance of food with an apparently reduced predation risk. Red foxes were first recorded in Berlin in the 1950s, and by the 1990s they were distributed across the entire city. Using the example of urban Berlin and neighbouring rural Brandenburg, the scientists analysed the genetic make-up of red foxes inhabiting the urban and adjacent rural areas based on material collected from more than 370 red foxes from both areas. They identified two genetically distinct clusters, broadly coinciding with the areas of urban conurbation and the adjacent rural countryside.The researchers also studied the factors limiting the gene flow between both populations. Landscape barriers such as large rivers and water bodies prevented foxes to some extent from mixing but were insufficient to explain maintenance of genetic differentiation and population structure. "The boundary between adjacent urban and rural areas, which is particularly characterized by increased human activity as well as denser housing, was a key factor," Sophia Kimmig, lead author of the study explains. The results of the study showed that Berlin foxes should be considered to be living on an "urban island" because of differences in behavioural responses of "city" and "country" foxes to human activity: Foxes from the city population are bolder than their relatives from the countryside, who are reluctant to cross the border into the city. Although "Berlin" foxes are more courageous in that they cope better with human activities ("city life"), they still prefer to use accident-prone motorways and railway lines -- areas of little human pedestrian activity -- to disperse within the city than taking potentially safer but busier public paths.People have hunted foxes for times immemorial. Even nowadays, fox hunting remains a legalised "recreational" activity in several countries. The scientists argue that this may have exerted sufficient selection pressures on foxes to be wary of people, encouraging a preference for avoiding people and sites of centres of human activity. Such a risk management might explain why "country" foxes only rarely venture across the rural-urban boundary, and why urban foxes chose to face the real risk of being hit by a train or a car and avoid sites of increased human activity.
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Genetically Modified
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March 3, 2020
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https://www.sciencedaily.com/releases/2020/03/200303175308.htm
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Improved CRISPR gene drive solves problems of old tech
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Gene drives use genetic engineering to create a desired mutation in a few individuals that then spreads via mating throughout a population in fewer than 10 generations.
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In theory, such a mechanism could be used to prevent malarial mosquitoes from transmitting disease, or possibly to wipe out an invasive species by disabling its ability to reproduce.Though scientists have had success proving the concept in the lab, they have found that wild populations invariably adapt and develop resistance to the scheme. And when gene drives work, they are all or nothing -- without nuance -- they spread to all individuals, which can be a drawback.Now, a Cornell study, "A Toxin-Antidote CRISPR Gene Drive System for Regional Population Modification," published Feb. 27 in the journal "Those are two things that this new drive that we developed here addresses to some extent," said Philipp Messer, an assistant professor of computational biology, and the paper's senior author. Jackson Champer, a postdoctoral researcher in Messer's lab, is the first author.In a classic gene drive, called a homing drive, an offspring inherits one set of genes, or genome, from the mother and another from the father. If an offspring inherits a gene with a drive from one parent and not the other, the drive copies itself into the genome from the parent without the drive."Now that individual has that drive in both of its genomes and it will pass it on to every offspring," Messer said.The drives are engineered with CRISPR-Cas9 gene-editing technology, so when the drive copies itself into a new genome, the CRISPR machinery makes a cut into the chromosome without the drive, and pastes in the new code. But sometimes, cells will repair the incision and, in doing so, randomly delete DNA letters. When this happens, the CRISPR gene drive can no longer find a genetic sequence it recognizes in order to make the incision, which creates a resistance and stops the gene drive from spreading.Natural genetic variation -- another source of changes in DNA sequences -- can also create resistance, since CRISPR gene drives must recognize short genetic sequences in order to make incisions."We were among the first labs to show that this is a tremendous problem," Messer said.The paper describes a new gene drive, called TARE (Toxin-Antidote Recessive Embryo), which works by targeting a gene that is essential for an organism to function. At the same time, the organism can survive with only one intact copy of this essential gene. Instead of cutting and pasting DNA as homing drives do, the TARE drive simply cuts the other parent's gene, disabling it.Meanwhile, the engineered TARE drive gene has a DNA sequence that has been recoded; the gene works but it won't be recognized or cut in future generations. If an offspring inherits two disabled genes, those individuals won't survive, thereby removing those copies from the population. Meanwhile, as viable individuals mate, more and more surviving offspring will carry TARE drive genes.Just a few individuals with homing drives can spread a trait through an entire population. TARE drives, on the other hand, do not cut and paste a drive into a target gene; instead they destroy one of the target gene copies in the offspring. Because of this, the drive requires a higher frequency of engineered individuals in the population to spread. For this reason, TARE drives are less likely to transfer from one distinct population to another.In lab experiments, when fruit flies with TARE gene drives were released in cages of wild-type fruit flies, all the flies in the cage had the TARE drive in just six generations.The researchers pointed out that resistance can indeed evolve with a TARE drive in the wild, especially in very large populations, but they believe it will take longer and evolve at a much lower rate, Messer said.Also contributing was Andrew Clark, professor of computational biology and molecular biology and genetics. The research was funded by the National Institutes of Health.
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Genetically Modified
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March 3, 2020
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https://www.sciencedaily.com/releases/2020/03/200303140158.htm
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Molecule found in oranges could reduce obesity and prevent heart disease and diabetes
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Researchers at Western University are studying a molecule found in sweet oranges and tangerines called nobiletin, which they have shown to drastically reduce obesity in mice and reverse its negative side-effects.
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But why it works remains a mystery.New research published in the "We went on to show that we can also intervene with nobiletin," said Murray Huff, PhD, a Professor at Western's Schulich School of Medicine & Dentistry who has been studying nobiletin's effects for over a decade. "We've shown that in mice that already have all the negative symptoms of obesity, we can use nobelitin to reverse those symptoms, and even start to regress plaque build-up in the arteries, known as atherosclerosis."But Huff says he and his team at Robarts Research Institute at Western still haven't been able to pinpoint exactly how nobiletin works. The researchers hypothesized that the molecule was likely acting on the pathway that regulates how fat is handled in the body. Called AMP Kinase, this regulator turns on the machinery in the body that burns fats to create energy, and it also blocks the manufacture of fats.However, when the researchers studied nobiletin's effects on mice that had been genetically modified to remove AMP Kinase, the effects were the same."This result told us that nobiletin is not acting on AMP Kinase, and is bypassing this major regulator of how fat is used in the body," said Huff. "What it still leaves us with is the question -- how is nobiletin doing this?"Huff says while the mystery remains, this result is still clinically important because it shows that nobiletin won't interfere with other drugs that act on the AMP Kinase system. He says current therapeutics for diabetes like metformin for example, work through this pathway.The next step is to move these studies into humans to determine if nobiletin has the same positive metabolic effects in human trials."Obesity and its resulting metabolic syndromes are a huge burden to our health care system, and we have very few interventions that have been shown to work effectively," said Huff. "We need to continue this emphasis on the discovery of new therapeutics."
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Genetically Modified
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March 2, 2020
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https://www.sciencedaily.com/releases/2020/03/200302113330.htm
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CRISPR-HOT: A new tool to 'color' specific genes and cells
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Researchers from the group of Hans Clevers at the Hubrecht Institute have developed a new genetic tool to label specific genes in human organoids, or mini organs. They used this new method, called CRISPR-HOT, to investigate how hepatocytes divide and how abnormal cells with too much DNA appear. By disabling the cancer gene TP53, they showed that unstructured divisions of abnormal hepatocytes were more frequent, which may contribute to cancer development. Their results were described and published in the scientific journal
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Organoids are mini organs that can be grown in the lab. These mini-organs grow from a very small piece of tissue, and this is possible for various organs. The ability to genetically altering these organoids would help a great deal in studying biological processes and modelling diseases. So far however, the generation of genetically altered human organoids has been proven difficult due to the lack of easy genome engineering methods.A few years ago, researchers discovered that CRISPR/Cas9, which acts like tiny molecular scissors, can precisely cut at a specific place in the DNA. This new technology greatly helped and simplified genetic engineering. "The little wound in the DNA can activate two different mechanisms of repair in the cells, that can both be used by researchers to coerce the cells to take up a new part of DNA, at the place of the wound" says Delilah Hendriks (Hubrecht Institute). One of these methods, called non-homologous end joining, was thought to make frequent mistakes and therefore until now not often used to insert new pieces of DNA. "Since some earlier work in mice indicated that new pieces of DNA can be inserted via non-homologous end joining, we set out to test this in human organoids" says Benedetta Artegiani (Hubrecht Institute). Artegiani and Hendriks then discovered that inserting whatever piece of DNA into human organoids through non-homologous end joining is actually more efficient and robust than the other method that has been used until now. They named their new method CRISPR-HOT.The researchers then used CRISPR-HOT to insert fluorescent labels into the DNA of human organoids, in such a way that these fluorescent labels were attached to specific genes they wanted to study. First, the researchers marked specific types of cells that are very rare in the intestine: the enteroendocrine cells. These cells produce hormones to regulate for example glucose levels, food intake, and stomach emptying. Because these cells are so rare, they are difficult to study. However, with CRISPR-HOT, the researchers easily "painted" these cells in different colors, after which they easily identified and analyzed them. Second, the researchers painted organoids derived from a specific cell type in the liver, the biliary ductal cells. Using CRISPR-HOT they visualized keratins, proteins involved in the skeleton of cells. Now that they could look at these keratins in detail and at high resolution, the researchers uncovered their organization in an ultra-structural way. These keratins also change expression when cells specialize, or differentiate. Therefore, the researchers anticipate that CRISPR-HOT may be useful to study cell fate and differentiation.Within the liver, there are many hepatocytes that contain two (or even more) times the DNA of a normal cell. It is unclear how these cells are formed and whether they are able to divide because of this abnormal quantity of DNA. Older adults contain more of these abnormal hepatocytes, but it is unclear if they are related to diseases such as cancer. Artegiani and Hendriks used CRISPR-HOT to label specific components of the cell division machinery in hepatocyte organoids and studied the process of cell division. Artegiani: "We saw that "normal" hepatocytes divide very orderly, always splitting into two daughter cells in a certain direction." Hendriks: "We also found several divisions in which an abnormal hepatocyte was formed. For the first time we saw how a "normal" hepatocyte turns into an abnormal one." In addition to this, the researchers studied the effects of a mutation often found in liver cancer, in the gene TP53, on abnormal cell division in hepatocytes. Without TP53 these abnormal hepatocytes were dividing much more often. This may be one of the ways that TP53 contributes to cancer development.The researchers believe that CRISPR-HOT can be applied to many types of human organoids, to visualize any gene or cell type, and to study many developmental and disease related questions.
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Genetically Modified
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January 31, 2020
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https://www.sciencedaily.com/releases/2020/01/200131114743.htm
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Efficient cryopreservation of genetically modified rat spermatozoa
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Rat spermatozoa are two to four times larger than that of other animal species and are easily damaged by changes in pH, osmotic pressure, and temperature. Because these animals are very frequently used in medical research, a cryopreservation method was developed nearly 20 years ago. However, rat spermatozoa motility after thawing is extremely poor, and unless artificial insemination is performed at night (10:00-11:00 pm) no offspring will be produced. Furthermore, the number of offspring produced after successful artificial insemination is often lower than normal so the cryopreservation of rat sperm is not typically considered practical.
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To improve cryopreservation methods, Professor Nakagata and Dr. Takeo of the Center for Animal Resources and Development (CARD) at Kumamoto University, Japan have been searching for methods to retain sperm mobility after thawing. They knew that the freezing process significantly reduced sperm motility, so they attempted to chill the sperm first to reduce movement as much as possible before freezing.They tested their cryopreservation method on a type of genetically modified rat (EGFP rat) sperm that emits green fluorescence and then used it for in vitro fertilization. Surprisingly, the fertilization rate exceeded 80% and the experiment successfully produced over 300 offspring from the sperm of one male rat.Sperm cryopreservation is easier than the cryopreservation of fertilized eggs, and many cells (50 -- 100 million) can be obtained from a single male rat. In recent years, genetically modified rats useful for human disease research have been produced using genome editing technology. This indicates that there is a need for an efficient technique to preserve genetically modified rat strains. The cryopreservation technology developed here can provide an efficient storage method of genetically modified rats and could accelerate the development of treatments for intractable diseases. "Compared to mice, rats are about ten times the size, require a larger housing space, and simply cost more to keep. There is a need to reduce the amount of space they take up and their cost for research labs," said Professor Nakagata. "Our cryopreservation technique is likely to be very useful in the preservation of genetically modified rat strains. We believe that it could become a new global standard for research resources."
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Genetically Modified
| 2,020 |
January 29, 2020
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https://www.sciencedaily.com/releases/2020/01/200129143339.htm
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Unique new antiviral treatment made using sugar
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New antiviral materials made from sugar have been developed to destroy viruses on contact and may help in the fight against viral outbreaks.
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This new development from a collaborative team of international scientists shows promise for the treatment of herpes simplex (cold sore virus), respiratory syncytial virus, hepatitis C, HIV, and Zika virus to name a few. The team have demonstrated success treating a range of viruses in the lab -- including respiratory infections to genital herpes.The research is a result of a collaboration between scientists from The University of Manchester, the University of Geneva (UNIGE) and the EPFL in Lausanne, Switzerland. Although at a very early stage of development, the broad spectrum activity of this new approach could also be effective against newly prevalent viral diseases such as the recent coronavirus outbreak.So called 'virucidal' substances, such as bleach, are typically capable of destroying viruses on contact but are extremely toxic to humans and so cannot be taken or applied to the human body without causing severe harm. Developing virucides from sugar has allowed for the advent of a new type of antiviral drug, which destroys viruses yet is non-toxic to humans.Current antiviral drugs work by inhibiting virus growth, but they are not always reliable as viruses can mutate and become resistant to these treatments.Using modified sugar molecules the team showed that the outer shell of a virus can be disrupted, thereby destroying the infectious particles on contact, as oppose to simply restricting its growth. This new approach has also been shown to defend against drug resistance.Publishing their work in the journal Dr Samuel Jones, from The University of Manchester and a member of the Henry Royce Institute for Advanced Materials, jointly led the pioneering research with Dr Valeria Cagno from the University of Geneva. "We have successfully engineered a new molecule, which is a modified sugar that shows broad-spectrum antiviral properties. The antiviral mechanism is virucidal meaning that viruses struggle to develop resistance. As this is a new type of antiviral and one of the first to ever show broad-spectrum efficacy, it has potential to be a game changer in treating viral infections." said Sam.Professor Caroline Tapparel from the University of Geneva and Prof Francesco Stellacci from EPFL were both also senior authors of the study. Prof Tapparel declared: "We developed a powerful molecule able to work against very different viruses, therefore, we think this could be game changing also for emerging infections."The molecule is patented and a spin-out company is being set up to continue pushing this new antiviral towards real-world use. With further testing the treatment could find a use in creams, ointments and nasal sprays or other similar treatments for viral infections. This exciting new material can work to break down multiple viruses making for cost-effective new treatments even for resistant viruses.
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Genetically Modified
| 2,020 |
January 29, 2020
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https://www.sciencedaily.com/releases/2020/01/200129131428.htm
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A host's genes likely influence the spread of antibiotic resistance
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In the gastrointestinal tract of host animals, bacteria can exchange the genes responsible for antibiotic resistance (AR) via small, circular chunks of DNA called plasmids. However, the process in this complex environment isn't completely understood, and AR has become a public health menace. Every year, according to the CDC, more than 2.8 million people are diagnosed with infections resistant to antibiotic treatment, and 35,000 people die.
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"The human gut has millions of bacteria," said microbiologist Melha Mellata, Ph.D., at Iowa State University in Ames, Iowa. "If an AR plasmid is introduced into our gut through contaminated food or by another means, it will quickly spread to other gut bacteria, which will generate bacteria resistant to treatments with antibiotics." To stop that from happening, she said, researchers need to know what factors trigger or reduce the transfer of plasmids.This week in The researchers found that the plasmids transferred successfully in some mice but not in others, which meant that AR didn't spread in the same way in all groups. That observation led the researchers to run further analyses, which suggested that the microbial transactions could be attributed to genetic factors in the mice themselves, as well as the complexity of the gut microbiota."There is something in the host's genes that can amplify this transfer," said Mellata, who led the study.Mellata and her colleagues used a strain of Salmonella known to harbor large plasmids that make the bacterium resistant to treatment with streptomycin and tetracycline, two common antibiotics. Previous studies by other researchers have confirmed that these plasmids can transfer to Escherichia coli.But those previous experiments were conducted in bacterial cultures. For the new study, Mellata's group studied how the plasmids spread to E. coli in the animals themselves. A better understanding of how resistance spreads requires examining what's going on in the host gastrointestinal tract, she said. "We need to study this issue through the lens of the host's complex environment, since in reality this is how this phenomenon happens."Mellata's research at Iowa State focuses on understanding large plasmids -- which may contain many AR-related genes -- and developing vaccines for strains of E. coli that are resistant to antibiotic treatment. Previous work by her group showed that mouse strains with a limited set of known gut microbes are more susceptible to infections than conventional mice. That observation led them to investigate how the genetic background of the animal itself -- and not just the microbial community -- might have some influence on the transfer of plasmids.Mellata's group is now following up on the experiment by trying to identify the specific genetic host factors that can trigger the plasmid transfer. She hopes those findings can lead to a new way to stop the spread of antibiotic resistance. "If we can target those specific host factors, we can reduce the plasmid transfer, which will prevent the emergence of new antibiotic-resistant strains," she said."People are dying from bacterial infections," she said. "They should not be dying from bacteria like E. coli. The emergence of bacteria resistant to last-resort antibiotics is happening really fast, and we want to discover what's making that happen."
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Genetically Modified
| 2,020 |
January 22, 2020
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https://www.sciencedaily.com/releases/2020/01/200122080604.htm
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A heart-healthy protein from bran of cereal crop
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Foxtail millet is an annual grass grown widely as a cereal crop in parts of India, China and Southeast Asia. Milling the grain removes the hard outer layer, or bran, from the rest of the seed. Now, researchers have identified a protein in this bran that can help stave off atherosclerosis in mice genetically prone to the disease. They report their results in ACS'
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Atherosclerosis, or narrowing of the arteries because of plaque buildup, is the leading cause of heart disease and stroke. Plaques form when immune cells called monocytes take up oxidized low-density lipoprotein cholesterol (ox-LDL) in the artery wall. These cells then secrete pro-inflammatory cytokines, causing aortic smooth muscle cells to migrate to the site. Eventually, a plaque made up of cholesterol, cells and other substances forms. Drugs called statins can treat atherosclerosis by lowering LDL levels, but some people suffer from side effects. Zhuoyu Li and colleagues previously identified a protein in foxtail millet bran that inhibits the migration of colon cancer cells. They wondered if the protein, called foxtail millet bran peroxidase (FMBP), could also help prevent atherosclerosis.To find out, the researchers treated human aortic smooth muscle cells and monocytes in petri dishes with FMBP. The millet protein reduced the uptake of lipids by both cell types and reduced the migration of smooth muscle cells. In monocytes, FMBP treatment blocked the expression of two key proteins involved in atherosclerosis. Next, the team fed mice that were genetically predisposed to atherosclerosis a high-fat diet. Mice that were then treated with either FMBP or a statin had far fewer plaques than untreated mice. The FMBP-treated mice also had elevated blood levels of high-density lipoprotein cholesterol (HDL), the "good cholesterol." Based on these results, FMBP is a natural product with great potential in the prevention and treatment of atherosclerosis, the researchers say.
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Genetically Modified
| 2,020 |
January 17, 2020
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https://www.sciencedaily.com/releases/2020/01/200117080827.htm
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America's most widely consumed oil causes genetic changes in the brain
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New UC Riverside research shows soybean oil not only leads to obesity and diabetes, but could also affect neurological conditions like autism, Alzheimer's disease, anxiety, and depression.
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Used for fast food frying, added to packaged foods, and fed to livestock, soybean oil is by far the most widely produced and consumed edible oil in the U.S., according to the U.S. Department of Agriculture. In all likelihood, it is not healthy for humans.It certainly is not good for mice. The new study, published this month in the journal The same UCR research team found in 2015 that soybean oil induces obesity, diabetes, insulin resistance, and fatty liver in mice. Then in a 2017 study, the same group learned that if soybean oil is engineered to be low in linoleic acid, it induces less obesity and insulin resistance.However, in the study released this month, researchers did not find any difference between the modified and unmodified soybean oil's effects on the brain. Specifically, the scientists found pronounced effects of the oil on the hypothalamus, where a number of critical processes take place."The hypothalamus regulates body weight via your metabolism, maintains body temperature, is critical for reproduction and physical growth as well as your response to stress," said Margarita Curras-Collazo, a UCR associate professor of neuroscience and lead author on the study.The team determined a number of genes in mice fed soybean oil were not functioning correctly. One such gene produces the "love" hormone, oxytocin. In soybean oil-fed mice, levels of oxytocin in the hypothalamus went down.The research team discovered roughly 100 other genes also affected by the soybean oil diet. They believe this discovery could have ramifications not just for energy metabolism, but also for proper brain function and diseases such as autism or Parkinson's disease. However, it is important to note there is no proof the oil causes these diseases.Additionally, the team notes the findings only apply to soybean oil -- not to other soy products or to other vegetable oils."Do not throw out your tofu, soymilk, edamame, or soy sauce," said Frances Sladek, a UCR toxicologist and professor of cell biology. "Many soy products only contain small amounts of the oil, and large amounts of healthful compounds such as essential fatty acids and proteins."A caveat for readers concerned about their most recent meal is that this study was conducted on mice, and mouse studies do not always translate to the same results in humans.Also, this study utilized male mice. Because oxytocin is so important for maternal health and promotes mother-child bonding, similar studies need to be performed using female mice.One additional note on this study -- the research team has not yet isolated which chemicals in the oil are responsible for the changes they found in the hypothalamus. But they have ruled out two candidates. It is not linoleic acid, since the modified oil also produced genetic disruptions; nor is it stigmasterol, a cholesterol-like chemical found naturally in soybean oil.Identifying the compounds responsible for the negative effects is an important area for the team's future research."This could help design healthier dietary oils in the future," said Poonamjot Deol, an assistant project scientist in Sladek's laboratory and first author on the study."The dogma is that saturated fat is bad and unsaturated fat is good. Soybean oil is a polyunsaturated fat, but the idea that it's good for you is just not proven," Sladek said.Indeed, coconut oil, which contains saturated fats, produced very few changes in the hypothalamic genes."If there's one message I want people to take away, it's this: reduce consumption of soybean oil," Deol said about the most recent study.
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Genetically Modified
| 2,020 |
January 10, 2020
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https://www.sciencedaily.com/releases/2020/01/200110073736.htm
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Dynamic interplay between genome and environment in pearl oysters
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Since the late 19th century, pearl aquaculture has been a revered industry in Japan, enabling widespread cultivation and commercialization of beautiful pearls. From a genetic and evolutionary perspective, scientists have known little about the source of these pearls -- the Japanese pearl oyster,
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Researchers in the Marine Genomics Unit at the Okinawa Institute of Science and Technology Graduate University (OIST), in collaboration with scientists from Mie Prefecture, Japan, have, using genome-wide genetic data from specimens collected across the western Pacific, elucidated how pearl oyster populations vary genetically and geographically. Their analyses provide insight into how these pearl oysters have adapted to environmental changes over time. Understanding the genetic structure of these populations will be crucial for developing effective and targeted conservation strategies for the species in light of climate change, the researchers said."In particular we wanted to understand the population structure of After a century of success, Japanese pearl production plummeted during the 1990s due to detrimental algal blooms and an outbreak of bacterial disease, both of which damaged pearl oyster populations. Additionally, during this time, pearl farmers introduced Chinese pearl oysters into Japanese waters, threatening the genetic diversity of the To better understand and conserve these animals, the scientists analyzed about 200 individual Takeuchi and his colleagues found that pearl oysters in mainland Japan (the northern population) are genetically distant from the southern population in the Nansei Islands, China, and Cambodia.However, the researchers could not understand why pearl oysters in the Japanese mainland and Nansei Islands were genetically distinct, since they weren't separated by a land barrier. Due to the strong Kuroshio Current, the oysters could easily be propelled from Nansei to the mainland, mixing the populations.To solve this mystery, the scientists looked at environmental factors that might influence genetic diversification, including sea surface temperature, oxygen, carbon dioxide, phosphate, and nitrate levels in the water, as well as ocean salinity.Through statistical analyses, they found that sea surface temperature and oxygen concentration strongly correlated with genetic variation. The mainland and Nansei populations are likely distinct because they adapted to local environmental conditions, the researchers said.These findings then helped the researchers piece together Moving forward, the researchers hope to continue studying the pearl oysters' genes, since climate change and increasing ocean temperatures may affect "Using genome-wide data, we revealed population structure of the pearl oyster in the western Pacific," said Takeuchi. "We are now developing DNA markers to distinguish the Japanese population from others. This will be useful for conserving the unique genetic resources of the Japanese pearl oysters," said Takeuchi.
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Genetically Modified
| 2,020 |
December 30, 2019
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https://www.sciencedaily.com/releases/2019/12/191230084802.htm
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How cells learn to 'count'
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One of the wonders of cell biology is its symmetry. Mammalian cells have one nucleus and one cell membrane, and most humans have 23 pairs of chromosomes. Trillions of mammalian cells achieve this uniformity -- but some consistently break this mold to fulfill unique functions. Now, a team of Johns Hopkins Medicine researchers have found how these outliers take shape.
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In experiments with genetically engineered mice, a research team has ruled out a mechanism that scientists have long believed controls the number of hairlike structures, called cilia, protruding on the outside of each mammalian cell. They concluded that control of the cilia count might rely instead on a process more commonly seen in non-mammalian species.The experiments, described Dec. 2 in Cilia are ancient structures that first appeared on single-celled organisms as small hairlike "fingers" that act as motors to move the cell or antennae to sense the environment. Nearly all human cells have at least one cilium that senses physical or chemical cues. However, some specialized cell types in humans, such as those lining the respiratory and reproductive tracts, have hundreds of cilia on their surface that beat in waves to move fluids through the system."Our main question was how these multicilliated cells become so dramatically different than the rest of the cells in our body," says Holland. "Most cells make exactly one cilium per cell, but these highly specialized cells give up on this tight numerical control and make hundreds of cilia."In an effort to answer the question, Holland and his team took a closer look at the base of cilia, the place where the organelles attach and grow from the surface of the cell. This base is a microscopic, cylinder-shaped structure called a centriole.In single-ciliated cells, Holland says, centrioles are created before a cell divides. A cell contains two-parent centrioles that each duplicate so that both new cells gets one pair of centrioles -- the oldest of these two centrioles then goes on to form the base of the cilium. However, multicilliated cells create unique structures, called deuterosomes, that act as a copy machine to enable the production of tens to hundreds of centrioles, allowing these cells to create many cilia."Deuterosomes are only present in multicilliated cells, and scientists have long thought they are central for determining how many centrioles and cilia are formed," says Holland.To test this, Holland and his team developed a mouse model that lacked the gene that creates deuterosomes. Then, they analyzed the tissues that carry multicilliated cells and counted their cilia.The researchers were surprised to find that the genetically engineered mice had the same number of cilia on cells as the mice with deuterosomes, ruling out the central role of deuterosomes in controlling the number of cilia. For example, the multicilliated cells lining the trachea all had 200-300 cillia per cell. The researchers also found that cells without deuterosomes could make new centrioles just as quickly as cells with them.With this surprising result in hand, the researchers engineered mouse cells that lacked both deuterosomes and parent centrioles, and then counted the number of cilia formed in multicilliated cells."We figured that with no parent centrioles and no deuterosomes, the multicilliated cells would be unable to create the proper number of new cilia," says Holland.Remarkably, Holland says, even the lack of parent centrioles had no effect on the final cilia number. Most cells in both normal and genetically engineered groups created between 50 and 90 cilia."This finding changes the dogma of what we believed to be the driving force behind centriole assembly," explains Holland. "Instead of needing a platform to grow on, centrioles can be created spontaneously."While uncommon in mammals, the so-called de novo generation of centrioles is not new to the animal kingdom. Some species, such as the small flatworm planaria, lack parent centrioles entirely, and rely on de novo centriole generation to create the cilia they use to move.In further experiments on genetically engineered mice, Holland found that all the spontaneously created centrioles were assembled within a region of the cell rich with fibrogranular material -- the protein components necessary to build a centriole.He says he suspects that proteins found in that little-understood area of the cell contain the essential elements necessary to construct centrioles and ultimately control the number of cilia that are formed. Everything else, the deuterosomes and even the parent centrioles, are "not strictly necessary," he says."We think that the deuterosomes function to relieve pressure on the parent centrioles from the demands of making many new centrioles, freeing up parent centrioles to fulfill other functions," says Holland.A better understanding of mechanisms that limit cilia number in human cells could potentially advance efforts to treat cilia-related disorders, he said, by identifying targets for drugs.
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Genetically Modified
| 2,019 |
December 19, 2019
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https://www.sciencedaily.com/releases/2019/12/191219142646.htm
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Gene drives work faster than non-drive approaches to control problem insects
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When controlling mosquitoes that spread malaria, gene drives, which force genetic changes to proliferate in a population, are faster and more efficient than simply releasing mosquitoes that are immune to the parasite, according to a new study published December 19th in
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Genetic approaches are the latest strategy for controlling mosquito populations that spread the malaria parasite and viruses like dengue, chikungunya fever, yellow fever and Zika. In the lab, scientists have attempted to control the numbers of mosquitoes that can transmit these infections by introducing insects engineered to carry anti-disease genes and through gene drives, where engineered individuals also carry genes that change the rules of inheritance, increasing the odds that the changes are passed on and spread throughout the entire population.In the current study, researchers simulated non-drive and gene-drive mosquito releases using small cage trials to explore the efficacy of delivering anti-malaria genes to a mosquito species that commonly carries the parasite. They demonstrated that both approaches are effective, but the gene drive was more efficient because it needed only a single release of a small number of insects. In contrast, the non-drive simulation required repeated, larger releases. The drive system targets a gene that affects female mosquito survival after it feeds on blood, and drove mosquito populations to extinction, except in one simulation where mutations popped up that prevented the engineered genes from being passed on effectively."The results may seem obvious to those working in this field, but it is important to get empirical evidence to support predictions, especially in this newly-emerging science," says Dr. James. "Gene drives are expected to reduce costs of mosquito control and contribute towards the eradication of some of the vector-borne diseases. Having an effective delivery system in hand is a big step forward, now we need to make sure that the 'cargo', the genes that interfere with the pathogens, function as designed, and that is what we are working on now."The findings suggest that gene drives will be the most efficient and affordable genetic approach for controlling mosquito populations, assuming that they are approved for use in the wild. The study also demonstrates that preliminary laboratory cage trials can help scientists to test and improve the design of engineered insects before they are released. The researchers point out that future gene drive experiments focused on malaria prevention should also involve mosquitoes infected with the parasite to better simulate actual conditions.
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Genetically Modified
| 2,019 |
December 17, 2019
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https://www.sciencedaily.com/releases/2019/12/191217141529.htm
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Disruption of glycine receptors to study embryonic development and brain function
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Glycine receptors are one of the most widely distributed inhibitory receptors in the central nervous system and have important roles in a variety of physiological processes. Researchers from Max Planck Florida Institute for Neuroscience (MPFI), University of Toyama, Yamagata University, Cairo University, RIKEN Center for Integrative Medical Sciences and Setsunan University joined forces to further study glycine receptors, particularly glycine receptor alpha-4 (Glra4), during development. In a recent publication in the journal
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Hirofumi Nishizono first author of this publication and research associate of Yasuda Lab, explained that in order to fully understand the function of a specific gene, it is necessary to study a condition where this gene is deleted. By applying in vitro fertilization in combination with CRISPR/Cas9 genome editing system to mouse embryos, the team generated a genetically modified mouse in which the Glra4 gene has been disrupted. One of the remarkable results show that Glra4 plays a critical role in the early development of fertilized eggs, facilitating the development of the blastocyst, a structure formed in the early development of mammals, maintaining embryo quality and litter size in mice. Interestingly, they have also shown that different types of glycine receptors are expressed not only in mouse fertilized eggs but also in fertilized eggs of humans and bovine, suggesting that the role of these receptors in early embryonic development is conserved across species. Moreover, while Glra4 is a pseudogene in humans, they use a different type of glycine receptors (GLRA2), which are active in humans, for this process.Nishizono is currently investigating the effects of the disruption of glycine receptors in the brain. He is conducting behavioral tests to evaluate if the deletion of Glra4 affects brain function of mice. Some preliminary data indicate that the deletion of Glra4 is associated with phenotypes related to psychiatric disorders. Yasuda Lab will continue to produce genetically modified mice to investigate the role of different molecules involved in learning and memory as well as various brain disorders.
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Genetically Modified
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December 10, 2019
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https://www.sciencedaily.com/releases/2019/12/191210111719.htm
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New viral strategy to escape detection
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University of Otago researchers have discovered how viruses that specifically kill bacteria can outwit bacteria by hiding from their defences, findings which are important for the development of new antimicrobials based on viruses and provide a significant advance in biological knowledge.
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Lead researcher Professor Peter Fineran explains that the rise in multi-drug resistant bacteria is leading to the development of alternative therapeutics, including viruses that specifically kill bacteria, called bacteriophages, often referred to as "phages." However, bacteria can become resistant to phages.Phages are the most abundant biological entities on the planet and are important for global ecosystems, but they can also be used to kill bacterial pathogens. To defend themselves from the phage invasion, bacteria have developed CRISPR-Cas defence systems -- immune systems within the bacteria. But the phages have come up with many ways to avoid these bacterial defences.In the study published today in PhD student in the Department of Microbiology and Immunology and first author of the study, Lucia Malone says it made the researchers question how this phage escapes recognition."We had molecular and genetic evidence for what was happening, but we really needed to see directly inside these tiny bacteria, which if 100 lined up side-by-side would be the width of a human hair," Ms Malone says.This was made possible using a new spinning disk confocal microscope for high-resolution imaging of live cells -- the only one with this capability in New Zealand -- that was recently set up by Dr Laura Gumy, a new group leader at the University of Otago."When phages infected the bacteria, we could see their DNA was encased by a physical 'shield' and hidden from the CRISPR-Cas defence systems that couldn't gain access," Dr Gumy explains.However, bacteria have another trick up their sleeve. To take over the host, the phages must produce RNA messages that leave this protective compartment. "This is the Achilles heel of these phages and can be destroyed by a special group of CRISPR-Cas defences that recognise RNA messages," Ms Malone says.Dr Fineran explains the study broadens the knowledge of intricate phage-host interactions and demonstrates that "jumbo" phages are less susceptible to bacterial defence systems than some other phages."From a biological perspective, our results provide exciting new insights into how phages evade bacterial defence systems."This is important because the rise of the multi-drug resistant bacteria is an issue of global concern, which has led to a renewed interest in using phages as anti-bacterials and jumbo phages may provide excellent therapeutics."
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Genetically Modified
| 2,019 |
December 9, 2019
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https://www.sciencedaily.com/releases/2019/12/191209110519.htm
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RNA modification: Methylation and mopping up
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Ludwig-Maximilian-Universitaet (LMU) in Munich researchers have discovered a novel type of chemical modification in bacterial RNAs. The modification is apparently attached to molecules only when cells are under stress, and is rapidly removed during recovery.
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Ribonucleic acid (RNA) is chemically closely related to the DNA that serves as the carrier of hereditary information in all cells. Indeed, RNA itself plays a central role in the process that converts the genetic messages into proteins, which catalyze chemical transformations and serve as structural elements in cells and organisms. Like DNA, RNA molecules are made up of sequences of four different types of subunits called nucleobases, which are connected to each other by means of sugar-phosphate links. In all organisms, these subunits can be selectively modified in order to regulate their interactions and functions. Now Dr. Stefanie Kellner, who heads an Emmy Noether Junior Research Group in the Department of Chemistry, in cooperation with Kirsten Jung (Professor of Microbiology at LMU), has identified a novel -- and biochemically rather unusual -- modification in bacterial RNAs. The modification is attached when microorganisms are subjected to stress, and can be promptly removed when conditions return to normal. The new findings appear in the online journal Both DNA and RNA can be modified by methylation, i.e. the attachment of methyl (CH3) substituents to nucleotides. In addition, bacteria modify RNAs with functional groups that contain sulfur atoms as a means of regulating protein synthesis. One such modification replaces the oxygen at position 2 in the cytidine base. In the rod-shaped bacterium Escherichia coli, Kellner and her colleagues have now identified a previously unknown form of this modified sulfur-containing base. "In this case, the bacteria are methylated at the sulfur of cytidine," says Kellner. "Coupling via a sulfur substituent converts the cytidine into a 2-methylthiocytidine, or ms2C for short."Further experiments revealed that ms2C appears in RNA mainly when the bacteria are placed under stress, by the addition of deleterious chemicals or antibiotics to the growth medium. Although the damage negatively impacts protein translation, it is not a death sentence to the bacteria.Interestingly, the bacterium possesses an enzyme that can subsequently remove the methylation damage. The team succeeded in characterizing the repair mechanism directly with the aid of a relatively new analytical technique called NAIL-MS (Nucleic Acid Isotope Labeling coupled Mass Spectrometry). This involves labeling of the sample with a heavy isotope prior to analysis by high-sensitivity mass spectrometry, which enables one to follow the fate of the modified RNAs after the stressor has been removed. "In this way, we were able to show, in living cells, that the modified RNA is not degraded.Instead, it is repaired by enzymatic detachment of the methyl group," as Kellner explains.Since the repair process is completed within 1-2 hours after modification of the RNA, the researchers believe that the cell is already 'prepared' to deal with the damage. It is conceivable that the sulfur-containing RNA bases act as scavengers of free methyl groups that are produced as a direct result of stress, thus preventing them from modifying the DNA or other proteins. Since bacterial cells are full of RNA molecules, these could function as an efficient detoxification mechanism to mop up reactive chemical groups.
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Genetically Modified
| 2,019 |
December 5, 2019
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https://www.sciencedaily.com/releases/2019/12/191205113148.htm
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New marker for insecticide resistance in malaria-carrying mosquitoes
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Researchers at LSTM have genetically modified malaria carrying mosquitoes in order to demonstrate the role of particular genes in conferring insecticide resistance.
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For the first time the team characterised three genes (Cyp6m2, Cyp6p3 and Gste2) most often associated with insecticide resistance directly by their overproduction in genetically modified Anopheles gambiae. LSTM's Dr Gareth Lycett is senior author on a paper published today in the journal To help find the causes of this increased resistance first author, Dr Adriana Adolfi, and her colleagues at LSTM generated genetically modified mosquitoes that overproduce specific enzymes that previous work at LSTM had identified as potential candidates in this process of acquiring insecticide resistance. This breakthrough work has found that increased production of just these three genes can between them cause the mosquitoes to become resistant to all four classes of public health insecticides currently being used in malaria control.Dr Lycett continued: "These data validate the particular genes as excellent markers for resistance, giving us much needed tools to monitor the growing problem effectively through molecular testing. The super-resistant mosquitoes generated are now also being used test new insecticides to find compounds that escape the activity of these enzymes and so can successfully to be incorporated in next generation bednets to again provide effective protection for users and the wider community."
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Genetically Modified
| 2,019 |
December 4, 2019
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https://www.sciencedaily.com/releases/2019/12/191204145756.htm
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Brewing beer that tastes fresh longer
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Unlike wine, which generally improves with time, beer does not age well. Usually within a year of bottling, the beverage starts to develop an unpleasant papery or cardboard-like flavor that drinkers describe as "stale." Now, researchers reporting in ACS'
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Scientists have linked stale beer flavors to aldehyde compounds, such as (The researchers used a genetic technique called "overexpression," in which they artificially increased the levels of various genes related to NADH production. With this method, they identified four genes that, when overexpressed, increased NADH levels. The team found that beer from the overexpressing yeast contained 26.3-47.3% less acetaldehyde than control beer, as well as decreased levels of other aldehydes. In addition, the modified strains produced more sulfur dioxide, a natural antioxidant that also helps reduce staling. Other flavor components were marginally changed. This approach could be useful for improving the flavor stability and prolonging the shelf life of beer, the researchers say.
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Genetically Modified
| 2,019 |
November 27, 2019
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https://www.sciencedaily.com/releases/2019/11/191127090148.htm
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Bad news for Nemo: Clownfish can't adapt to rapid environmental changes
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The beloved anemone fish popularized by the movies "Finding Nemo" and "Finding Dory" don't have the genetic capacity to adapt to rapid changes in their environment, according to a new study by France's National Centre for Scientific Research (CNRS), Woods Hole Oceanographic Institution (WHOI) and colleagues. Their findings published Nov. 27, 2019, in the journal
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An international team of researchers monitored clownfish in the lagoons of Kimbe Bay -- a biodiversity hot spot in Papua New Guinea -- for more than a decade. Using genetic analysis of the population's DNA, the researchers were able to calculate their potential to adapt to habitat changes and renew their population. They found that big families of clownfish that extended over many generations were linked to high-quality habitats, rather than to shared genes."The findings reported here were made possible by a huge sampling and DNA sequencing effort that had not been attempted for any marine species before," says WHOI biologist Simon Thorrold, a coauthor of the paper. "The biggest surprise to us was also the most troubling: conservation efforts cannot rely on genetic adaptation to protect clownfish from the effects of climate change. It seems that Nemo won't be able to save himself."The quality of the anemone that provides a home to clownfish contributes significantly -- on average 50 percent -- to its ability to survive and renew its population. If high-quality anemones remain healthy, the clownfish population will persist. However, if the anemones and coral reefs they call home are impacted by climate warming, the clownfish are in trouble."Nemo is thus at the mercy of a habitat that is degrading more and more every year," says Benoit Pujol, an evolutionary geneticist at CNRS. To expect a clownfish to genetically adapt at pace which would allow it to persist in the lagoons would be unreasonable, and thus the ability of these fish to remain in the lagoons over time will depend on our ability to maintain the quality of its habitat."
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Genetically Modified
| 2,019 |
November 20, 2019
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https://www.sciencedaily.com/releases/2019/11/191120131336.htm
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Slowing down -- Is aging caused by decreased cellular metabolism?
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Throughout history, humans have been obsessed with finding a way to prevent aging and prolong life. Although the mechanisms have long eluded us, modern science is revealing more and more about the aging process. Now, researchers from Japan have uncovered new information about the genetic processes that may trigger age-related disorders, including low energy production and low cellular growth.
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In a study published this month in "In a previous study, we proposed that the age-associated downregulation, or decrease in expression, of nuclear-encoded genes including SHMT2 impacts mitochondrial respiration" says lead author of the study Haruna Tani. "However, the mechanisms underlying this process were not clear. To address this in the present study, we tested the effects of impaired SHMT2 expression on a variety of cellular functions."To do this, the researchers used mouse embryos that had been genetically modified to lack the SHMT2 gene. This strain of mice, termed Shmt2-knockout mice, had impaired mitochondrial respiration and growth retardation in the liver but not the brain. The liver was found to exhibit downregulation in the metabolic pathways that generate taurine, which is necessary for mitochondrial respiration, as well as nucleotides, which are molecules that are implicated in cell division. These insufficiencies were also linked to anemia in the Shmt2-knockout E13.5 embryos."Although some researchers have proposed that human aging and age-related defects in mitochondrial respiration are caused by the accumulation of mutations in mitochondrial DNA," study senior author Jun-Ichi Hayashi says, "our data support an alternative explanation: age-related defects in mitochondrial respiration may be triggered by changes in the activity of metabolic pathways that are caused by epigenetic downregulation, but not by mutations, of specific genes associated with mitochondrial function."Understanding the mechanisms by which epigenetic processes impact cellular activity could provide insight regarding the processes associated with aging and illness. This could then lead to new treatments for conditions caused by genetic abnormalities, or even a way to extend life itself.
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Genetically Modified
| 2,019 |
November 14, 2019
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https://www.sciencedaily.com/releases/2019/11/191114180027.htm
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Genetics may determine who benefits from broccoli's effects on kidney health
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New research indicates that the benefits of a dietary compound on kidney health may depend on an individual's genetics. The findings, which appear in an upcoming issue of JASN, may be helpful for tailoring interventions to prevent or treat kidney disease.
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Glutathione S-transferase mu-1 (GSTM1) is an enzyme that plays a role in ridding the body of toxins and combatting oxidative stress. Many individuals carry a variant in the GSTM1 gene that prevents the gene's expression (called a null variant) and therefore they lack production of the enzyme. A team led by Thu H. Le, MD (University of Rochester Medical Center) previously showed that individuals carrying this variant face a higher risk of experiencing kidney function decline.In their latest study, the investigators found that deletion of the gene increases kidney injury in mice with hypertension and kidney disease. Supplementing the diet with broccoli powder (which is rich in an antioxidant-activating compound) significantly lessened kidney injury in the genetically altered mice, but not in normal mice with kidney disease."We speculate that the GSTM1 enzyme may be involved in the breakdown of antioxidant-promoting compounds, and therefore deficiency in the enzyme may increase the bioavailability of protective compounds relevant in kidney disease," said Dr. Le.When the researchers examined information from a large clinical trial, they found that high consumption of broccoli and other cruciferous vegetables was linked with a lower risk of kidney failure, primarily in participants with the GSTM1 null variant."Our study highlights diet-gene interactions in kidney disease and illustrates that response to the disease-modifying effect of diet is influenced by genetics," said Dr. Le. "In the context of personalized and precision medicine, increased consumption of cruciferous vegetables may be protective, particularly in those lacking GSTM1 who are genetically most at risk for kidney disease progression. Furthermore, our study suggests that knowing an individual's genetic information enables tailoring an intervention to prevent or delay kidney disease progression among those who would respond based on their genetic makeup."
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Genetically Modified
| 2,019 |
November 11, 2019
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https://www.sciencedaily.com/releases/2019/11/191111124746.htm
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Scientists map mouse personality
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Scientists at the Max Planck Institute of Psychiatry in Munich, Germany, together with colleagues at the Weizmann Institute of Sciencein Israel have developed a computational method to objectively measure the personality of mice living in a semi-natural, group environment.
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Just like humans, every mouse is different. Some are quick to explore a new environment while others prefer to stay within the comfort of their nest. Some prefer to stay close to their cage-mates, while others prefer to be alone. These unique characteristics of an individual remain fairly stable through life and define their personality. In humans, personality can be measured using multiple-choice questionnaires to derive personality scores but how can one measure personality in animals?Oren Forkosh and Stoyo Karamihalev, together with other colleagues collected huge amounts of data by analyzing video footage taken of groups of mice. To do this, they dyed the fur of each mouse a different color allowing them to track the groups of mice behaving undisturbed. Each video was analyzed for a repertoire of 60 behaviors, such as how close a mouse stays to other mice, if they chase one another or run away, or the time spent in the nest or eating.The scientists developed a mathematical algorithm that sought stable traits that were able to discriminate individuals based on differences in behavior. This method works somewhat in the same way as personality tests in humans in which people are often assessed on five dimensions, however it specifically searches for traits that are consistent over time. In mice, the algorithm identified four trait-like dimensions that could capture and describe the behavior of mice. To test that these traits were stable, the researchers mixed up the groups and found that while some of the behaviors had changed, the personalities of the mice were still stable. Using advanced RNA-sequencing tools and genetically modified mouse strains, the researchers were also able to show that individual differences captured in these traits corresponded to a variety of differences in gene expression in the mouse brain and could identify mice with different genetic makeup."This method has the potential to greatly advance our knowledge beyond what is possible using the current simplified methods for assessing behavior and toward stable and consistent differences in personality. It opens up the possibility to study how personality is affected by genes, drugs, aging, etc., how it is represented and maintained by the brain, and how it contributes to mental health and disease," explains Karamihalev, together with Oren Forkosh one of the first authors of the study. "This is a good first step in the direction of better pre-clinical methods for assessing individual differences in behavior and physiology," says Alon Chen, the principal investigator for this study. "Our hope is that such approaches will aid in the effort toward a more personalized psychiatry."
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Genetically Modified
| 2,019 |
November 4, 2019
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https://www.sciencedaily.com/releases/2019/11/191104112907.htm
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New possibilities for gene therapies with spin of the Sleeping Beauty transposase
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Scientists have developed a new variant of the Sleeping Beauty transposase. It has dramatically improved biochemical features, including enhanced stability and intrinsic cell penetrating properties. This transposase can be used for genome engineering of stem cells and therapeutic T cells. As such it is extremely valuable for use in regenerative medicine and cancer immunotherapy. The underlying genome engineering procedures will in the future also reduce costs and improve the safety of genome modifications.
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The team, comprising researchers from the European Molecular Biology Laboratory, the Universitätsklinikum Würzburg and the Paul-Ehrlich-Institut, managed to design a new variant of the Sleeping Beauty transposase with dramatically improved biochemical properties, enabling the direct use of the transposase protein for genome modifications. "The protein we developed can be delivered into mammalian cells and remains fully functional, enabling efficient and stable genome modifications in target cells on demand," explains Orsolya Barabas, group leader at EMBL Heidelberg.The delivery and efficient genetic engineering can be used on different types of cells, including human stem cells and T lymphocytes. The latter can be genetically modified to produce an artificial chimeric antigen receptor (CAR) for use in cancer immunotherapy. The new type of Sleeping Beauty transposase developed by the researchers not only enables direct protein delivery, but also penetrates cells autonomously. The latter feature was not planned for the new variant and was only discovered when it was studied in action. This was a pleasant surprise, as it is the first of its kind with this characteristic. "All these features open new avenues for CAR-T cell production and other gene therapies," explains Irma Querques, PhD student at EMBL and a lead author of the paper. As such, this is a breakthrough compared to other existing variants of the Sleeping Beauty transposase.The Sleeping Beauty transposon system consists of a transposase and a transposon to insert specific sequences of DNA into the genomes of animals.A transposase is a protein that binds to the ends of a transposon -- a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity -- and catalyses its movement to another part of the genome.The transposase can be encoded either within the transposon or can be supplied by another source, in which case the transposon becomes a non-autonomous element. Non-autonomous transposons are most useful as genetic tools, because after insertion they cannot independently continue to excise and re-insert themselves. All of the DNA transposons identified in the human genome and other mammalian genomes are non-autonomous because, even though they contain transposase genes, these genes are non-functional and unable to generate a transposase that can mobilise the transposon.The Sleeping Beauty transposase was resurrected from inactive copies in fish genomes by Zoltan Ivics and his colleagues in 1997, creating the first transposon tool that worked efficiently in vertebrate cells. Since then it has been used for many applications in genetics, including gene therapy.While EMBL researchers generally focus on fundamental research, these results lead to a direct medical application. "The new transposase and the genome engineering procedures we developed will find direct use in therapeutic cell engineering," highlights Michael Hudecek from the Universitätsklinikum Würzburg the importance of the results. "Already in this first study, we demonstrate the utility of our method for CAR-T cell production and its efficacy in a mouse model." Now Hudecek and his colleagues will continue research with the transposase for use in human patients."Our method further offers attractive use in stem cell engineering and I am sure it will find its applications in regenerative medicine and associated research. One of the most outstanding advantages of the novel technology is that it enables industrial-scale, pharmaceutical production of the transposase, making the Sleeping Beauty gene delivery system even more attractive for companies for future therapeutic applications," explains Zoltán Ivics, from the Paul-Ehrlich-Institut.The design principles of the transposase and protocols developed by the EMBL group will also help to create similar strategies for other transposon systems. The team is curious to further explore the mechanisms behind the cell penetrating property of the Sleeping Beauty transposase and whether these mechanisms can be transferred to other proteins as well. "The availability of our new Sleeping Beauty variant will also facilitate research towards understanding its molecular mechanisms, which in turn will promote the rational design of more advanced transposon tools," adds Cecilia Zuliani from EMBL; another lead author of the paper.While this will require further work, Barabas highlights one immediate impact: "For now, our new cell engineering procedure will lead to reduced costs and -- through improved fidelity and control of the method -- improved safety of medically relevant genome modifications."
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Genetically Modified
| 2,019 |
November 4, 2019
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https://www.sciencedaily.com/releases/2019/11/191104112838.htm
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Synthetic phages with programmable specificity
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Bacteriophages ("phages" for short) are viruses that infect bacteria. Phages are highly host-specific and will typically only infect and kill an individual species or even subspecies of bacteria. Compared to conventional antibiotics, phages do not indiscriminately kill bacteria. Therefore when used as a therapeutic, phages do not cause collateral damage to beneficial "good" bacteria living in the gut. This ability to target only disease-causing bacteria has led to phages being seen as potential "magic bullets" in the fight against bacterial infections, especially against bacteria that have developed antibiotic resistance.
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However, the high specificity of phages is also a disadvantage: Clinicians have to administer different combinations of phages to be sure the right phage is present to target a single bacterial infection. Not only does this approach limit the chances of phage therapy becoming a standardized treatment option, but also finding a phage, or combination of phages, for every infection becomes a time-consuming and labor-intensive task. Until now, phages had to be first isolated from their natural environment, tested against the bacterial strain(s) in question, and -- most importantly -- have their genomes sequenced to ensure they are safe for use in humans.Under the direction of Samuel Kilcher, an "Ambizione" fellow funded by the Swiss National Science Foundation, researchers from the Institute of Food, Nutrition and Health (IFNH) at ETH Zurich have genetically reprogrammed phages to produce synthetic phages that recognize and attack a broader range of bacterial strains beyond their natural host. The researchers reported their findings in the journal On the bottoms of phage tails are specialized receptor binding proteins that recognize specific receptors on the exposed cell walls of a target bacterium. "Using X-ray crystallography, we cracked the atomic structure of the first receptor binding protein from a Listeria phage, providing the structural blueprint for re-engineering our phages," says lead author Matthew Dunne.Akin to building with Lego blocks, the researchers assembled new receptor binding proteins by fitting together protein components derived from different phages to provide different host specificities. Finally, the researchers genetically modified Listeria phages with their designer receptor binding proteins, resulting in phages that recognize and kill new strains of the target bacterium. Although these designer phages attack different new hosts, they all share the same genome, except for the gene encoding their receptor binding proteins.A mixture of such phage variants could now be used to treat patients. "We could cover a broad range of hosts by administering several synthetically produced phages in a single cocktail," Kilcher explains. The difference to a wild-type phage cocktail is that the synthetic ones could be developed, produced and adapted in a much more targeted fashion. Cultivating artificial phages in pure culture is neither expensive nor labor-intensive. "We can program them accordingly for almost every specific purpose," he adds.Alongside therapeutic applications, the researchers could also use the synthetic phages as diagnostic markers of specific molecular structures, such as for detecting pathogenic strains among a mixed bacterial population.There are still many hurdles to overcome before therapies with genetically modified phages enter clinical practice. The present study is merely a proof-of-concept relating to Listeria as a model bacterium, which occurs in food and can cause severe infections in people with weak immune systems.The researchers are now planning to create artificial phages to combat other pathogens that are often difficult to treat with conventional therapy as a result of antibiotic resistance. Examples include Staphylococcus aureus, Klebsiella pneumoniae, and Enterococcus species. The methods for engineering such phages are yet to be developed. "Every phage and every host organism harbor particular challenges," emphasizes ETH Professor Martin Loessner, co-author of the study and director of the Laboratory of Food Microbiology at IFNH. However, he thinks it is just a matter of time before a workbench is also developed for such pathogens.Much hope is invested in phage therapies. Genetically modified phages have already been used therapeutically in one case. A few months ago, American researchers reported in the journal Nature Medicine on a case in which a 15-year-old who suffers from cystic fibrosis was administered phages in order to heal a severe infection caused by mycobacteria. The treatment worked. But broad-based clinical trials are still needed before any phage therapies can be approved.
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Genetically Modified
| 2,019 |
October 29, 2019
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https://www.sciencedaily.com/releases/2019/10/191029080744.htm
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Red algae thrive despite ancestor's massive loss of genes
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You'd think that losing 25 percent of your genes would be a big problem for survival. But not for red algae, including the seaweed used to wrap sushi.
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An ancestor of red algae lost about a quarter of its genes roughly one billion years ago, but the algae still became dominant in near-shore coastal areas around the world, according to Rutgers University-New Brunswick Professor Debashish Bhattacharya, who co-authored a study in the journal The research may assist in the creation of genetically altered seaweeds that could be used as crops, help to predict the spread of seaweed pests and -- as the climate warms and pollution possibly increases -- control invasive seaweeds that blanket shorelines.Scientists believe the 25 percent loss in genetic material resulted from adaptation by the red algal ancestor to an extreme environment, such as hot springs or a low-nutrient habitat. That's when the genome of these algae became smaller and more specialized. So, how did they manage to escape these challenging conditions to occupy so many different habitats?"It is a story akin to Phoenix rising from the ashes, and the study answers an important question in evolution," said Bhattacharya, a distinguished professor in the Department of Biochemistry and Microbiology in the School of Environmental and Biological Sciences. "This lineage has an amazing evolutionary history and the algae now thrive in a much more diverse environment than hot springs."Red algae include phytoplankton and seaweeds. Nori and other red seaweeds are major crops in Japan, Korea and China, where they serve as sushi wrap, among other uses. Red seaweeds are also used as food thickeners and emulsifiers and in molecular biology experiments. Meanwhile, seaweed pests and invasive species are becoming a common threat to coastlines, sometimes inundating them.The scientists hypothesized that the red algal ancestor was able to adapt to widely varying light environments by developing flexible light-harvesting apparatuses. And their results strongly support this hypothesis. They generated a high-quality genome sequence from Porphyridium, a unicellular red alga. They found that many duplicated as well as diversified gene families are associated with phycobilisomes -- proteins that capture and transfer light energy to photosystem II (a protein complex that absorbs light) to split water, the critical first step in photosynthesis that powers our planet.A key component of phycobilisomes are "linker proteins" that help assemble and stabilize this protein complex. The results show a major diversification of linker proteins that could have enhanced photosynthetic ability and may explain how the algae now thrive in diverse environments, from near-shore areas to coral reefs.
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Genetically Modified
| 2,019 |
October 23, 2019
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https://www.sciencedaily.com/releases/2019/10/191023104604.htm
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Immune response to influenza
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It is estimated that influenza (flu) results in 31.4 million outpatient visits each year. New research from the University of Minnesota Medical School provides insights into how the body can protect itself from immunopathology during flu.
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"One of the reasons people feel bad during flu and some people die from flu isn't actually the virus replication itself, but it is the immune system's attempt to control the virus that causes that damage," said lead author Ryan Langlois, PhD, assistant professor of Microbiology and Immunology at the Medical School. "That immune response, called immunopathology, is a very serious complication of flu."Many people who get the flu recover in under two weeks because the immune system is able to clear the virus, leaving no trace of it in the body. Traditional theory thought this was accomplished by T cell-mediated killing of all infected cells. Several years ago, however, Langlois genetically engineered a flu virus that could permanently label infected cells, which led to the discovery that some infected cells do survive clearance.The new study published in After clearance, no virus exists in the lung, but the cells that used to be infected remain. The team found that those "survivor cells" actually divide and replenish themselves at a faster rate than uninfected cells."One can imagine that if T cells killed every infected cell, like people once thought they did, whole airways could be lost," Langlois said. "This study lends more data to the idea that preventing immunopathology is incredibly important, and it allows us to better understand the basic mechanisms of how the body regulates itself to prevent it."
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Genetically Modified
| 2,019 |
October 19, 2019
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https://www.sciencedaily.com/releases/2019/10/191019154003.htm
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Researchers quantify Cas9-caused off-target mutagenesis in mice
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Scientists are finding new ways to improve the use of the CRISPR enzyme Cas9 and reduce the chances of off-target mutations in laboratory mice, according to new results from a research collaboration including Lauryl Nutter, PhD, Senior Director, Science and Technology Development at The Centre for Phenogenomics at The Hospital for Sick Children (SickKids) in Toronto. The findings, which help scientists contextualize a common concern related to gene editing and identify new strategies to improve its precision, were presented as a featured plenary abstract at the American Society of Human Genetics 2019 Annual Meeting in Houston.
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Dr. Nutter and her collaborators from the multi-institution Knockout Mouse Phenotyping Project (KOMP2) regularly use Cas9 and gene editing to produce lines of laboratory mice with specific mutations. In this work, they often encounter questions about the likelihood of off-target mutagenesis -- unintended genetic mutations introduced by the gene editing process -- in their mouse lines."We wanted to know: to what extent do we need to worry about off-target mutagenesis?" Dr. Nutter explained. By demonstrating the degree of the problem in mice, the researchers hoped to be better able to evaluate it in human cell lines being studied in the laboratory, as well as generate new ways to improve the precision of Cas9-based gene editing.To answer these questions, Dr. Nutter's team performed 58 genome editing experiments in mouse embryos with Cas9 and guide RNAs configured to induce a specific, targeted mutation in a different gene, which would be passed down to its descendants. Two to four guides were used for each experiment for a total of 175 different guide RNAs. They then sequenced each mouse's whole genome to search for any additional mutations that may have resulted. To get a baseline rate of mutation, the whole genomes of Cas9-treated mouse lines were compared to those of 25 untreated control mice.In 31 of the Cas9-treated mouse lines, the researchers found zero off-target mutations, and in the remaining 20 lines, they found an average of 2.3 off-target mutations. In comparison, among both the treated and untreated mouse lines, they found an average of 3,500 naturally occurring, unique mutations in each animal."Surprisingly, these results show that the number of naturally-occurring mutations far exceeded those introduced by Cas9," Dr. Nutter said. "They also show that when guide RNAs are properly designed, off-target mutagenesis is quite rare."The results also add context to the use of inbred laboratory mouse lines in genetics research and the assumptions that scientists make when using them."Historically, we have used inbred mouse lines to study genetics in mice because their genomes differed only at certain, defined places, and we've assumed that any difference between the mice is due to those differences," Dr. Nutter explained. "However, we found that even among mice in the same litter, there could be thousands of naturally-occurring genetic differences.""Our results highlight the need to be cognizant of using Cas9 and other tools in a genome that may not be as well defined as we think," she added.As next steps, Dr. Nutter and her collaborators plan to explore whether enzymes that inhibit or enhance DNA repair can affect the rate at which new mutations arise. They also plan to examine the tradeoff between improving the efficiency of Cas9 mutagenesis and improving its precision. Given their focus on the production of laboratory mouse lines, the researchers hope their findings will inform the development of better guide RNAs, the short pieces of RNA that enable Cas9 to bind to its intended target and induce the intended mutation.More broadly, they hope their findings will lead to better use of control groups and a more informed perspective on experimental design. They noted that this knowledge will be particularly important in gene editing research with potential therapeutic applications, including studies of the safety and efficacy of genetics-based therapies.Reference: L Nutter
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October 18, 2019
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https://www.sciencedaily.com/releases/2019/10/191018112136.htm
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Lifestyle is a threat to gut bacteria: Ötzi proves it, study shows
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The intestinal microbiome is a delicate ecosystem made up of billions and billions of microorganisms, bacteria in particular, that support our immune system, protect us from viruses and pathogens, and help us absorb nutrients and produce energy.
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The industrialization process in Western countries had a huge impact on its content. This was confirmed by a study on the bacteria found in the intestine of Ötzi, the Iceman who, in 1991, emerged from the ice of the Ötztal Alps, where Italy borders with Austria. Scientists of Eurac Research examined samples of the mummy's bacteria, confirming the findings of the researchers of the University of Trento who had analyzed the genome of intestinal microorganisms of over 6500 individuals from all continents.Previous studies by the University of Trento had demonstrated that there is a connection between the microbiome's bacterial content and the increase, in Western countries, of obesity, autoimmune and gastrointestinal diseases, allergies and other complex conditions. In the study that appeared today in That may have been caused by the Westernization process. Changes in diet, which is now higher in fat and low in fibers, a sedentary lifestyle in an urban setting, the development of new hygiene habits and the widespread use of antibiotics and other medical products have, with no doubt, made our life safer, but impacted the delicate balance of our microbiome.The scientists of Eurac Research in Bolzano/Bozen sequenced the Iceman's DNA and were able to identify his set of bacteria, while the researchers of the University of Trento compared it with the microbiome of contemporary non-Westernized populations (from Tanzania and Ghana in particular), which are not used to processed food and have non-Westernized hygiene practices and lifestyle. Their findings were surprising.The study focused, in particular, on "First of all, we found out that "Through these 'ancient' samples," continued Tett, "we were able to study the evolution of these clades and now we know that they genetically delineated with the human species and before the initial human migrations out of the African continent."The study is the result of close collaboration with the research group of Albert Zink and Frank Maixner at Eurac Research in Bolzano/Bozen. Their team was responsible for the collection and pre-analysis of the Iceman's DNA samples. "The relation between the evolution of the human species and the diversity of intestinal microorganisms, as a field of research, is still rather unexplored, but can yield important results in the future through the analysis of ancient DNA. For this reason, finding more advanced and less invasive techniques to obtain and analyze DNA from human remains is one of the major areas of research at Eurac" concluded the microbiologist of Eurac Research Frank Maixner.
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October 15, 2019
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https://www.sciencedaily.com/releases/2019/10/191015131622.htm
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Protein that triggers plant defences to light stress identified
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A newly discovered protein turns on plants' cellular defence to excessive light and other stress factors caused by a changing climate, according to a new study published in
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Plants play a crucial role in supporting life on earth by using energy from sunlight to convert carbon dioxide and water into sugars and oxygen -- a process called photosynthesis. This provides a crucial food supply for humans and animals, and makes the atmosphere more hospitable to living creatures. Understanding how plants respond to stressors may allow scientists to develop ways of protecting crops from increasingly harsh climate conditions.Tiny compartments in plant cells called chloroplasts house the molecular machinery of photosynthesis. This machinery is made up of proteins that must be assembled and maintained. Harsh conditions such as excessive light can push this machinery into overdrive and damage the proteins. When this happens, a protective response kicks in called the chloroplast unfolded protein response (cpUPR). "Until now, it was not known how cells evaluate the balance of healthy and damaged proteins in the chloroplast and trigger this protective response," says co-senior author Silvia Ramundo, Postdoctoral Fellow in the Walter Lab at the University of California, San Francisco (UCSF), US.To learn more, the UCSF team genetically engineered an alga called Chlamydomonas reinhardtii to produce fluorescent cells in response to damaged chloroplast proteins. They then searched for mutants in the cells that would no longer fluoresce, meaning they were unable to activate the cpUPR.These experiments led the team to identify a gene called Mutant Affected in Retrograde Signaling (MARS1) that is essential for turning on the cpUPR. "Importantly, we found that mutant cells in MARS1 are more sensitive to excessive light, are unable to turn on the cpUPR, and die as a result," explains lead author Karina Perlaza, a graduate student in the Walter lab. Restoring MARS1, or artificially turning on the cpUPR, protected the algae's cells from the harmful effects of excess light on chloroplast proteins."Our results underscore the important protective role of the cpUPR," says co-senior author Peter Walter, Professor of Biochemistry and Biophysics at UCSF, and a Howard Hughes Medical Institute investigator. "The findings suggest that this response could be harnessed in agriculture to enhance crop endurance to harsh climates, or to increase the production of proteins in plants called antigens that are commonly used in vaccines."
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October 3, 2019
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https://www.sciencedaily.com/releases/2019/10/191003114034.htm
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Engineered viruses could fight drug resistance
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In the battle against antibiotic resistance, many scientists have been trying to deploy naturally occurring viruses called bacteriophages that can infect and kill bacteria.
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Bacteriophages kill bacteria through different mechanisms than antibiotics, and they can target specific strains, making them an appealing option for potentially overcoming multidrug resistance. However, quickly finding and optimizing well-defined bacteriophages to use against a bacterial target is challenging.In a new study, MIT biological engineers showed that they could rapidly program bacteriophages to kill different strains of E. coli by making mutations in a viral protein that binds to host cells. These engineered bacteriophages are also less likely to provoke resistance in bacteria, the researchers found."As we're seeing in the news more and more now, bacterial resistance is continuing to evolve and is increasingly problematic for public health," says Timothy Lu, an MIT associate professor of electrical engineering and computer science and of biological engineering. "Phages represent a very different way of killing bacteria than antibiotics, which is complementary to antibiotics, rather than trying to replace them."The researchers created several engineered phages that could kill E. coli grown in the lab. One of the newly created phages was also able to eliminate two E. coli strains that are resistant to naturally occurring phages from a skin infection in mice.Lu is the senior author of the study, which appears in the Oct. 3 issue of The Food and Drug Administration has approved a handful of bacteriophages for killing harmful bacteria in food, but they have not been widely used to treat infections because finding naturally occurring phages that target the right kind of bacteria can be a difficult and time-consuming process.To make such treatments easier to develop, Lu's lab has been working on engineered viral "scaffolds" that can be easily repurposed to target different bacterial strains or different resistance mechanisms."We think phages are a good toolkit for killing and knocking down bacteria levels inside a complex ecosystem, but in a targeted way," Lu says.In 2015, the researchers used a phage from the T7 family, which naturally kills E.coli, and showed that they could program it to target other bacteria by swapping in different genes that code for tail fibers, the protein that bacteriophages use to latch onto receptors on the surfaces of host cells.While that approach did work, the researchers wanted to find a way to speed up the process of tailoring phages to a particular type of bacteria. In their new study, they came up with a strategy that allows them to rapidly create and test a much greater number of tail fiber variants.From previous studies of tail fiber structure, the researchers knew that the protein consists of segments called beta sheets that are connected by loops. They decided to try systematically mutating only the amino acids that form the loops, while preserving the beta sheet structure."We identified regions that we thought would have minimal effect on the protein structure, but would be able to change its binding interaction with the bacteria," Yehl says.They created phages with about 10,000,000 different tail fibers and tested them against several strains of E. coli that had evolved to be resistant to the nonengineered bacteriophage. One way that E. coli can become resistant to bacteriophages is by mutating "LPS" receptors so that they are shortened or missing, but the MIT team found that some of their engineered phages could kill even strains of E. coli with mutated or missing LPS receptors.Lu and Yehl now plan to apply this approach to targeting other resistance mechanisms used by E. coli, and they also hope to develop phages that can kill other types of harmful bacteria. "This is just the beginning, as there are many other viral scaffolds and bacteria to target," Yehl says. The researchers are also interested in using bacteriophages as a tool to target specific strains of bacteria that live in the human gut and cause health problems."Being able to selectively hit those nonbeneficial strains could give us a lot of benefits in terms of human clinical outcomes," Lu says.The research was funded by the Defense Threat Reduction Agency, the National Institutes of Health, the U.S. Army Research Laboratory/Army Research Office through the MIT Institute for Soldier Nanotechnologies, and the Koch Institute Support (core) Grant from the National Cancer Institute.
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October 3, 2019
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https://www.sciencedaily.com/releases/2019/10/191003111751.htm
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New method to purify cell types to high purity
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Researchers from the group of Alexander van Oudenaarden at the Hubrecht Institute (KNAW) have developed GateID, a new method that can highly purify a cell type of interest from a tissue, without the use of antibodies or a genetic reporter. Thereby, GateID allows to isolate a variety of cell types, such as stem cells, in order to study them in more detail. The researchers have published their results in the scientific journal
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Our bodies are made up of millions of cells, among which are many different cell types and subtypes carrying out different tasks in the body. For example, stem cells are a rare subtype of cells crucial for organ formation and maintenance. Additionally, tumors consist of different cell types, each one potentially responding differently to treatment. Overall, studying individual cell types and subtypes is important to obtain a better understanding of their properties and function in health and disease.Until now, single cells that belong to a certain cell type of interest, such as stem cells, are purified based on specific markers present on the outside of the cell. For the purification, researchers use fluorescent antibodies able to bind these markers or generate genetically modified organisms where the cells of interest are fluorescently labelled. In both cases, the fluorescent cells can be detected and specifically purified by a flow cytometer. While powerful, these approaches are not always available. For example, genetic modifications are impossible in humans and antibody availability are not always available. Therefore, certain cell types remain inaccessible to researchers due to the lack of purification solutions.Researchers at the Hubrecht Institute have developed a new tool, called GateID, that enables the purification of cell types purely based on the native characteritics of the cells. GateID uses characteristics such as shape, size and granularity that can be measured by a flow cytometer, the same equipment used for cell type purification based on the above-mentioned antibodies and genetic markers. This new approach makes it possible to purify a cell type of choice without having to resort to genetically modified organisms or commercially available antibodies.GateID uses two types of information: information from inside and outside the cell. First, researchers generate a dataset by collecting single cells from the organ or tissue of choice. For each single cell, both the native characteristics of the cells (how they look from the outside) and their specific gene expression profiles (how they look on the inside) are measured. The researchers then identify the cell type of each single cell through their gene expression profiles. The native characteristics are then coupled to the identified cell type. Next, GateID is able to select the best native characteristics to purify the desired cell type in many subsequent experiments. The researchers show that GateID allows for the isolation of several cell types to high purities.In their study, the researchers used GateID to purify four cell types from the zebrafish immune system, including blood stem cells and progenitor cells, and alpha and beta cells from the human pancreas. In the future, researchers will be able to use GateID to purify and study any cell type of choice, from stem cells to tumor cells.
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September 25, 2019
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https://www.sciencedaily.com/releases/2019/09/190925083802.htm
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Engineered protein crystals make cells magnetic
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If scientists could give living cells magnetic properties, they could perhaps manipulate cellular activities with external magnetic fields. But previous attempts to magnetize cells by producing iron-containing proteins inside them have resulted in only weak magnetic forces. Now, researchers reporting in ACS'
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The new area of magnetogenetics seeks to use genetically encoded proteins that are sensitive to magnetic fields to study and manipulate cells. Many previous approaches have featured a natural iron-storage protein called ferritin, which can self-assemble into a "cage" that holds as many as 4,500 iron atoms. But even with this large iron-storage capacity, ferritin cages in cells generate magnetic forces that are millions of times too small for practical applications. To drastically increase the amount of iron that a protein assembly can store, Bianxiao Cui and colleagues wanted to combine the iron-binding ability of ferritin with the self-assembly properties of another protein, called Inkabox-PAK4cat, that can form huge, spindle-shaped crystals inside cells. The researchers wondered if they could line the hollow interiors of the crystals with ferritin proteins to store larger amounts of iron that would generate substantial magnetic forces.To make the new crystals, the researchers fused genes encoding ferritin and Inkabox-PAK4cat and expressed the new protein in human cells in a petri dish. The resulting crystals, which grew to about 45 microns in length (or about half the diameter of a human hair) after 3 days, did not affect cell survival. The researchers then broke open the cells, isolated the crystals and added iron, which enabled them to pull the crystals around with external magnets. Each crystal contained about five billion iron atoms and generated magnetic forces that were nine orders of magnitude stronger than single ferritin cages. By introducing crystals that were pre-loaded with iron to living cells, the researchers could move the cells around with a magnet. However, they were unable to magnetize the cells by adding iron to crystals already growing in cells, possibly because the iron levels in cells were too low. This is an area that requires further investigation, the researchers say.
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September 18, 2019
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https://www.sciencedaily.com/releases/2019/09/190918105631.htm
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CBD may alleviate seizures, benefit behaviors in people with neurodevelopmental conditions
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A marijuana plant extract, also known as cannabidiol (CBD), is being commonly used to improve anxiety, sleep problems, pain, and many other neurological conditions. Now UNC School of Medicine researchers show it may alleviate seizures and normalize brain rhythms in Angelman syndrome, a rare neurodevelopmental condition.
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Published in the "There is an unmet need for better treatments for kids with Angelman syndrome to help them live fuller lives and to aid their families and caregivers," said Ben Philpot, PhD, Kenan Distinguished Professor of Cell Biology and Physiology and associate director of the UNC Neuroscience Center. "Our results show CBD could help the medical community safely meet this need."CBD, which is a major phytocannabinoid constituent of cannabis, has already shown to have anti-epileptic, anti-anxiety, and anti-psychotic effects. And in 2018, the FDA approved CBD for the treatment of seizures associated with two rare forms of epilepsy, but little is known about the potential anti-seizure and behavioral effects of CBD on Angelman symptom.The Philpot lab is a leader in the creation of genetically modified mouse models of neurodevelopmental disorders, and they use these models to identify new treatments for various diseases, such as Rett, Pitt-Hopkins, and Angelman syndromes.In experiments led by first author Bin Gu, PhD, a postdoctoral fellow in the Philpot lab, the UNC-Chapel Hill researchers systematically tested the beneficial effects of CBD on seizures, motor deficits, and brain activity abnormalities -- as measured by EEG -- in mice that genetically model Angelman syndrome, with the expectation that this information could guide eventual clinical use.The researchers found that a single injection of CBD substantially lessened seizure severity in mice when the seizures were experimentally triggered by elevated body temperature or loud sounds. A typical anti-convulsant dose of CBD (100 mg/kg) caused mild sedation in mice but had little effect on motor coordination or balance. CBD also restored the normal brain rhythms which are commonly impaired in Angelman syndrome."We're confident our study provides the preclinical framework necessary to better guide the rational development of CBD as a therapy to help lessen seizures associated with Angelman syndrome and other neurodevelopmental disorders," Gu said.Philpot and Gu added that patients and families should always seek advice from their physician before taking any CBD products, and that a human clinical trial is needed to fully understand its efficacy and safety.
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September 16, 2019
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https://www.sciencedaily.com/releases/2019/09/190916144006.htm
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Genetically engineered plasmid can be used to fight antimicrobial resistance
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Researchers have engineered a plasmid to remove an antibiotic resistance gene from the
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In vitro, and in mouse models, the engineered plasmid removed the antibiotic resistance gene from "Our concern with organisms that cause hospital-acquired infections that are resistant to many clinical antibiotic therapies motivated the research," said co-senior author Breck A. Duerkop, PhD, Assistant Professor of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz Medical Center, Aurora.The mechanism used to remove antibiotic resistance genes is the specialized protein, CRISPR-Cas9. It can make cuts just about anywhere in DNA.Along with CRISPR-Cas9, RNA sequences homologous to DNA within the antibiotic resistance gene have been added to the engineered plasmid. These RNAs guide the CRISPR-Cas9 to make the cuts in the right places.Previous work in animal models by co-senior investigator Kelli L. Palmer, PhD, found that CRISPR-Cas9 could prevent intestinal The delivery vehicle for the engineered plasmid is a particular strain of "Nonetheless, Dr. Duerkop cautioned that it remained possible that
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Genetically Modified
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September 10, 2019
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https://www.sciencedaily.com/releases/2019/09/190910134315.htm
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Studying vision in pitch-darkness shines light on how a mammal's brain drives behavior
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New work from Finland has been able to link mammalian behavior to its underlying neural code. The work examined how mammals' brains interpret signals from the eyes at low light levels.
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The new study shines light on a route to solve the two broad goals of neuroscience. The first goal is to read nerve signals and interpret what they mean to our brains, and the second is to work out how our brain takes these signals and decides what to do -- predicting how we behave based on what we see.All the information the body sends to the brain -- like what we can see, hear, smell and feel -- gets sent through nerves as electrical impulses called spike trains.The rulebook for how the brain decodes spike trains is unknown, and working it out is made harder by the fact that the nervous system often carries the same message in many different ways. When the different versions of the same message reach the brain, it interprets all these signals together to decide how to behave. Professor Petri Ala-Laurila and his teams at Aalto University and the University of Helsinki have now been able to link behaviour in a mouse to specific spike-trains originating in its eyes.The mice had been trained swim towards an extremely faint light in a pitch-dark maze, and the team measured how effective the mice were at finding it. Darkness had to be used because it critically reduces the number of relevant spike trains to the two most sensitive ones to dim light: one called the ON channel and one called the OFF channel. By creating a scenario where there are a limited number of spike trains getting sent for a specific input, the team were able to isolate which individual spike train controlled behaviour.It is very difficult to carry out precise science experiments in complete darkness, so the team developed a unique repertoire of state-of-the-art techniques. They had to design ways to measure electrical signals originating from single photons through the neural tissue of the eye -- the retina -- and linked these signals to mouse behavior in the maze. One of the breakthroughs is that the team can track mice in the dark using night-vision cameras and their deep-learning based software so accurately that they are able to predict with unprecedented resolution where photons land on each mouse's retinas.The light the mouse was trying to find was made dimmer each time, to the point that in the last few attempts only a few photons at a time were entering the mouse's eyes.The team compared two types of mice. The first group of mice that did the task were ordinary laboratory mice. The second group had been genetically modified so that their most sensitive ON channel needs 10 times more light to send a spike train than the most sensitive OFF channel. These modified mice turned out to be 10 times worse at seeing the light than their unmodified cousins. Therefore, the researchers were able to prove their important discovery: individual spike trains going through the ON channel were responsible for the mouse seeing the light.This result is the first time anyone has linked visual behavior with this resolution to precise spike-codes coming from the retina. "This is like trying to translate a language," Professor Petri Ala-Laurila explains. "Previously we were using a phrasebook: we knew what whole sentences meant but not the meaning of individual words. Now that we can link precise codes consisting of individual nerve impulses to behavior, we are getting closer to understanding individual 'words'."The result is highly relevant to researchers working on vision, but also broadly relevant to all neuroscientists working on perception, because of a surprising aspect of the result that overturned previously held beliefs in neurology. For 70 years, researchers have been using information theory to model how the brain handles different signals. One of the assumptions was that if the brain has to choose between two competing codes, it will rely on the signal that contains more information. In the case of the ON and OFF channels in vision in the genetically modified mice, the ON channel -- which the team showed was key in controlling behavior -- contains less information. The ON channel increases the amount of nerve impulses it sends to the brain when it detects photons, whereas the OFF channel decreases its impulse rate, and the researchers show that behaviour relies only on messages that are encoded in increased impulse rate rather than decreased impulse rate. "This discovery is really exciting for all of neuroscience because it's experimental proof of the brain prioritizing information encoded in spikes rather than in the absence of spikes" says Lina Smeds, the PhD student at University of Helsinki who is first author of the paper.The next steps for the Finnish groups are to measure if the same principles apply to more neural circuits and behavioral paradigms and to see if they also follow the same rules. Professor Ala-Laurila compares the discovery to that of the Rosetta Stone in terms of its applicability. "When the Rosetta Stone was discovered, it didn't mean we could immediately understand Ancient Egyptian: but it gave researchers a tool that they used over the next 2 decades to finally translate Hieroglyphics. Likewise, this discovery doesn't mean we can immediately predict behavior from sensory nerve signals, but it will mean we can now start to study what individual signals mean to the brain."
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Genetically Modified
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September 9, 2019
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https://www.sciencedaily.com/releases/2019/09/190909121115.htm
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New way to test for drug resistant infections
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Scientists have developed a method to test whether an infection is resistant to common antibiotics.
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Beta-lactam antibiotics (such as penicillin) are one of the most important classes of antibiotics, but resistance to them has grown to such an extent that doctors often avoid prescribing them in favour of stronger drugs.Scientists from the University of York modified an antibiotic from the beta-lactam family so that it can be attached to a sensor, enabling them to detect the presence of bacteria resistant to treatment.The new method could lead to clinicians being able to rapidly detect whether an infection is treatable with common antibiotics, reserving stronger alternatives for the patients that need them most.Antimicrobial resistance (AMR) is a major global threat accelerated by the inappropriate use of antibiotics.Co-author of the study, Callum Silver, a PhD student from the Department of Electronic Engineering, said: "If we continue to use antibiotics in the way we currently do, we may find ourselves in a situation where we can no longer use antibiotics to treat patients -- resulting in millions of deaths per year."This study paves the way for the development of tests which will give doctors important information on the bacteria they are dealing with so that common antibiotics can be used whenever possible. Resistance to new antibiotics can emerge very quickly after they come into use and so we need to reserve them for when they are really needed."The discovery may also help to identify and isolate resistant bacteria, reducing the chances of large outbreaks."One of the major ways in which bacteria become resistant to treatment is through the production of enzymes that can break down beta-lactam antibiotics, rendering them ineffective.The researchers were able to test for the presence of these resistance enzymes by attaching the modified antibiotic to a sensor surface which enabled them to see whether or not the drug was broken down.The researchers used multiple techniques to show that the drug is still accessible to the enzyme, meaning the modified antibiotic could be used to develop things like urine tests for AMR bacteria in patients.Callum Silver added: "The lack of diagnostic techniques to inform doctors whether or not they are dealing with resistant bacteria contributes to the problem of AMR.""This modified antibiotic could be applied to a variety of different biosensing devices for use at the point-of-care."Dr Steven Johnson, Reader in the University's Department of Electronic Engineering, said: "This important study is the result of a close collaboration between physical, chemical and biological scientists at the University of York and lays the foundation for a new diagnostic test for drug resistant infections."We are now working with clinicians at York Teaching Hospital NHS Foundation Trust to integrate this modified antibiotic into a rapid diagnostic test for antimicrobial resistance in urinary tract infections."
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Genetically Modified
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August 29, 2019
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https://www.sciencedaily.com/releases/2019/08/190829150828.htm
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Study of bile acids links individual's genetics and microbial gut community
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In a new study published 29th August in
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The complex assortment of microbes that live in the intestines are the result of poorly understood interactions between a person's individual genetics and environmental influences like diet and drugs. One factor that links these two are bile acids, which the body produces to help absorb vitamins and fat in the small intestine, and which encourage some bacterial populations and suppress others. Additionally, bacteria metabolize bile acids to create secondary bile acids, which the body also uses for digestion. To identify genetic variants that affect bile acid levels and the microbial community in the gut, researchers profiled a population of 400 genetically diverse mice. The analysis pointed to a gene that codes for the ileal bile acid transporter, a protein that takes up bile acids from the final section of the small intestine for recycling back to the liver. Genetic variants in this transporter not only affect the abundance of bacterial species belonging to a group called Turicibacter but also alter levels of a bile metabolite that the researchers detected in the blood.This study reveals novel interactions between Turicibacter species and bile acids and is the first to use genetic mapping to integrate the community of microbes living in the gut with the profile of bile acid metabolites. "We are interested in identifying the microbial functions that are under host genetic control," said author Federico Rey, "and future studies will integrate additional metabolomic, metagenomic and transcriptional data derived from the host intestine."More broadly, the work shows the power of systems genetics to identify novel interactions between microbes and metabolites in the intestine. It also provides multiple leads on host-microbe-metabolite interactions that with additional study can help dissect the complex factors that shape microbial communities in the gut.
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Genetically Modified
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August 27, 2019
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https://www.sciencedaily.com/releases/2019/08/190827170600.htm
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Vaccine against deadly superbug Klebsiella effective in mice
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Scientists have produced and tested, in mice, a vaccine that protects against a worrisome superbug: a hypervirulent form of the bacteria Klebsiella pneumoniae. And they've done so by genetically manipulating a harmless form of
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Klebsiella pneumoniae causes a variety of infections including rare but life-threatening liver, respiratory tract, bloodstream and other infections. Little is known about how exactly people become infected, and the bacteria are unusually adept at acquiring resistance to antibiotics. The prototype vaccine, details of which are published online Aug. 27 in "For a long time, Klebsiella was primarily an issue in the hospital setting, so even though drug resistance was a real problem in treating these infections, the impact on the public was limited," said co-author David A. Rosen, MD, PhD, an assistant professor of pediatrics and of molecular microbiology at Washington University. "But now we're seeing Klebsiella strains that are virulent enough to cause death or severe disease in healthy people in the community. And in the past five years, the really resistant bugs and the really virulent bugs have begun to merge so we're beginning to see drug-resistant, hypervirulent strains. And that's very scary."Hypervirulent strains of Klebsiella caused tens of thousands of infections in China, Taiwan and South Korea last year, and the bacteria are spreading around the world. About half of people infected with hypervirulent, drug-resistant Klebsiella die. Two types in particular -- known as K1 and K2 -- are responsible for 70 percent of the cases.Rosen; senior author Christian Harding, PhD, a co-founder of VaxNewMo; first author Mario Feldman, PhD, an associate professor of molecular microbiology at Washington University and a co-founder of VaxNewMo; and colleagues decided to create a vaccine against the two most common strains of hypervirulent Klebsiella. The bacterium's outer surface is coated with sugars so the researchers designed a glycoconjugate vaccine composed of these sugars linked to a protein that helps make the vaccine more effective. Similar vaccines have proven highly successful at protecting people against deadly diseases such as bacterial meningitis and a kind of pneumonia."Glycoconjugate vaccines are among the most effective, but traditionally they've involved a lot of chemical synthesis, which is slow and expensive," Harding said. "We've replaced chemistry with biology by engineering The researchers genetically modified a harmless strain of To test the vaccine, the researchers gave groups of 20 mice three doses of the vaccine or a placebo at two-week intervals. Then they challenged the mice with about 50 bacteria of either the K1 or the K2 type. Previous studies had shown that just 50 hypervirulent Klebsiella bacteria are enough to kill a mouse. In contrast, it takes tens of millions of classical Klebsiella -- the kind that affects hospitalized people -- to be similarly lethal.Of the mice that received the placebo, 80 percent infected with the K1 type and 30 percent infected with the K2 type died. In contrast, of the vaccinated mice, 80 percent infected with K1 and all of those infected with K2 survived."We are very happy with how effective this vaccine was," Feldman said. "We're working on scaling up production and optimizing the protocol so we can be ready to take the vaccine into clinical trials soon."The goal is to get a vaccine ready for human use before the hypervirulent strains start causing disease in even larger numbers of people."As a pediatrician, I want to see people get immunity to this bug as early as possible," Rosen said. "It's still rare in the United States, but given the high likelihood of dying or having severe debilitating disease, I think you could argue for vaccinating everybody. And soon we may not have a choice. The number of cases is increasing, and we're going to get to the point that we'll need to vaccinate everybody."
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August 27, 2019
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https://www.sciencedaily.com/releases/2019/08/190827095047.htm
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The making of 'Fancy Mouse'
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For the past few hundred years, the colorful hair and unique patterns of the so-called "Fancy Mouse" have made them the stars of pet shows in Japan and beyond. Now, scientists have finally revealed the true cause of the genetic mutation responsible for the iconic black pigmentation in the popular East Asian pet.
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Their findings were published on August 2, 2019 in All mammals possess an "agouti gene," which controls the distribution of melanin pigment that determines the color of hair, skin and eyes. The dominant A allele -- the variant form of a gene that gives rise to specific physical traits -- restricts black pigmentation, and its presence in wild mice results in an "agouti mouse" with a coat comprised of black and yellow banded hairs. "Nonagouti mice," by contrast, possess two a/a alleles due to a hypomorphic mutation of the agouti gene. This mutation causes an almost entirely loss of gene function, resulting in the mouse's coat consisting of only black hair.In addition to being popular pets, nonagouti mice have been used for a variety of studies into the mechanism and role of pigmentation and the production, storage and distribution of melanin, as well as the link between coat color and behavior."Nonagouti mutation is one of the most famous, classical mutations in mouse genetics. Until now, it has been thought that the insertion of a single retrovirus, called VL30, into the gene responsible for expressing hair color is the cause of the nonagouti mutation that results in black coat color in East Asian mice," said study co-author, Tsuyushi Koide, an associate professor in the Mouse Genomics Resource Laboratory at the National Institute of Genetics (NIG), and the Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies) in Japan."In our paper, we clarified the true cause of the nonagouti mutation and showed its historical origin. These findings provide a clearer understanding of one of the most well-known mutations in mice," said Koide, who adds that a better understanding of the cause of nonagouti mutation could be useful for many research fields.In the study, another endogenous retrovirus, known as β4, was found in VL3, and β4, but not VL30, interrupts the agouti gene expression. The researchers used a genome editing technique whereby the genome DNA sequence is efficiently inserted or removed to effect a change or mutation. By using these 'molecular technique' to precisely target and delete the β4 retrovirus located within the VL30 virus on the DNA strand of fertilized mouse eggs that were then inserted into pseudopregnant female mice, the coat color of the neonatal pups was changed from nonagouti (black hairs) to agouti (black and yellow banded hairs). These results show that insertion of a new type of retrovirus β4 into the VL30 retrovirus is the true cause of black coat color, and not the VL30 alone.After analyzing DNA samples from black (nonagouti) mice as well as a series of wild-derived strains, the researchers also found that the nonagouti trait originated from a line of East Asian mice that were most likely related to Japanese fancy mice."We found that the insertion of the β4 retrovirus into VL30 occurred in the lineage of Japanese fancy mice," said Koide. "This mutation was then introduced into a variety of laboratory mice including a standard strain in the early days of mouse genetics."According to Koide, the insertion of the β4 retrovirus is also found in the gene that causes another type of classical mutation -- piebald coloration -- in mice. "The piebald mutation was also found in the Japanese fancy mice and is known to cause the characteristic black and white piebald pattern," said Koide.The authors speculated that the β4 retrovirus actively spread within the founder group of Japanese fancy mice. "It will be important to understand when and how β4 was infected into the mouse DNA and the genetic consequences of it amplifying and spreading into several genes that form part of the genetic makeup of the mouse," said Koide.
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Genetically Modified
| 2,019 |
August 14, 2019
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https://www.sciencedaily.com/releases/2019/08/190814144455.htm
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Helping bacteria be better friends
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Bacteria, like people, have complicated relationships: they can either be friendly, neutral, or antagonistic toward each other, and those relationships can change depending on the situations in which they find themselves. As interest in identifying the bacterial species present in the human microbiome that contribute to health and disease has exploded in recent years, so too have efforts to understand how different species of bacteria interact. This knowledge could enable the creation of bacteria-based therapies and tools that could be used to improve human health, produce valuable substances, or repair microbial ecosystems. However, teasing out the relationships that occur simultaneously between multiple species within a consortium of bacteria in a complex environment like the human gut has proven to be a herculean challenge.
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Now, science is one major step closer to that goal, thanks to the efforts of a team of researchers from the Wyss Institute for Biologically Inspired Engineering, Harvard Medical School (HMS), and Brigham and Women's Hospital (BWH). In a new paper published last week in "Whenever there are multiple species coexisting in the same space and using the same resources, they are likely to be antagonistic toward each other because they are both trying to be the one that survives," said first author Marika Ziesack, Ph.D., a Postdoctoral Researcher at the Wyss Institute and HMS. "By pushing the bacteria toward more mutually beneficial interactions, we can ultimately make the whole consortium of species more robust and resilient, and could hopefully one day develop synthetic consortia that are optimally tuned for various applications in human gut health and bioproduction."To get the bacteria to play nicely with each other, the researchers modified their genomes so that each species was unable to produce three of the amino acids it needs to function and overproduced a fourth amino acid. Each species could therefore only thrive if the other three species were present in the community and producing the amino acids it lacked, which encouraged the bacteria to adopt a more live-and-let-live approach.Such metabolite cross-feeding between species is common in nature -- humans cannot produce nine of the 20 amino acids we need to maintain our bodies, so we have to consume a varied diet to get those essential building blocks. Many bacteria also depend on other species for compounds that they lack the ability to make, and such co-dependence is thought to help make bacterial consortia more diverse, which in turn helps them resist dominance by any one species or loss of a crucial member that could lead the consortium to collapse.The four bacterial species the team chose to create their artificial consortium are all found in the mammalian gut: E. coli, S. Typhimurium, B. thetaiotaomicron, and B. fragilis. Each strain was genetically modified to overproduce either methionine, histidine, tryptophan, or arginine, and its ability to produce the other three amino acids was knocked out.To evaluate whether each strain was able to "rescue" the other strains that were deficient in the amino acid that it overproduced, the researchers sequentially isolated the compounds secreted by each strain and grew the other strains in the presence of those compounds. Compared with a control group in which compounds from a non-overproducing strain were added, each of the overproducers was able to rescue the other strains to varying degrees, depending on how much of a given amino acid each strain needed to grow.To see how the four modified strains interacted collectively as a consortium, the researchers cultured them all together and found that they grew in roughly the same proportions but at lower total numbers than non-engineered versions of the same strains grown together, showing that all of the deficient strains were able to get enough amino acids from the others to survive and reproduce. The team then repeated this experiment multiple times, each time reducing the starting population of one strain ten-fold to see how the consortium would react to losing one member. They found that in consortia of non-engineered bacteria the knocked down strain did not recover, while in consortia of engineered bacteria both S. Typhimurium and B. theta regrew to their normal levels after knockdown. Neither E. coli nor B. fragilis was able to recover after knockdown, and the loss of B. fragilis caused the whole consortium to grow to only half its normal size.The knockdown experiments also revealed the relationships between the different strains in both non-engineered and engineered consortia. In the non-engineered consortium, the absence of certain strains resulted in the overgrowth of others, indicating that those strains are naturally in competition with each other. However, in the engineered consortium, knockdown of one species did not significantly alter the proportions of the remaining species, and in fact, the knockdown of B. fragilis had a negative impact on both S. Typhimurium and E. coli, indicating that the presence of B. fragilis had become beneficial to those species.The researchers also found that the consortia of engineered bacteria displayed greater evenness -- roughly similar amounts of each species -- than non-engineered consortia, both in vitro and when the consortia were inoculated into the guts of bacteria-free mice. This trend was also present when the bacteria were grown in low-amino-acid environments, indicating that the engineered bacteria were successfully able to cross-feed each other amino acids to create a stable community."As expected in a complex network of species, not all of the bacterial strains interacted with each other equally; the engineered E. coli and S. Typhimurium seem to 'mooch' off of the Bacteroides species without providing as much of a benefit back to the other members, so future research could focus on optimizing how much each species overproduces its given amino acid and consumes others, to improve the overall fitness of the consortium without compromising species evenness," said co-corresponding author Pamela Silver, Ph.D., a Founding Core Faculty member of the Wyss Institute who is also the Elliot T. and Onie H. Adams Professor of Biochemistry and Systems Biology at HMS.Other potential directions for this research include introducing cascades of interactions so that each bacterial strain takes in a compound from another strain, modifies it, and "passes it on" to another strain for further processing, to create a more efficient bioproduction assembly line to create chemicals of pharmaceutical or industrial interest."We're ultimately interested in rationally designing consortia of beneficial bacteria that can function in complex environments, including the human gut, for medical applications. Introducing 'friendly' interactions among bacteria is an important step toward being able to control these consortia so that they don't exhibit overgrowth behaviors or losses of species and can carry out their intended functions," said co-corresponding author Georg Gerber, M.D., Ph.D., who is also chief of the Division of Computational Pathology at Brigham and Women's Hospital and an Assistant Professor at HMS, as well as co-director of the Massachusetts Host-Microbiome Center at the Brigham."Being able to convert one type of bacterial consortium into another stable community is one of the major challenges in microbiome-related medicine today, and this work by Pam Silver and her collaborators represents a major first step toward developing ways to engineer this switch in a controlled way," said Wyss Institute Founding Director Donald Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at HMS and the Vascular Biology Program at Boston Children's Hospital, as well as Professor of Bioengineering at Harvard's John A. Paulson School of Engineering and Applied Sciences SEAS.Additional authors of the paper include Wyss Institute Senior Staff Scientist Jeffrey Way, Ph.D.; former Wyss Institute members John Oliver, Ph.D., Andrew Shumaker, Ph.D., and David Riglar, Ph.D.; former HMS Research Fellow Tobias Giessen, Ph.D.; HMS Postdoctoral Fellow Bryan Hsu, Ph.D.; and Travis Gibson, Ph.D., Nicholas DiBenedetto, and Lynn Bry, M.D., Ph.D. from the Massachusetts Host-Microbiome Center at Brigham & Women's Hospital and HMS.This research was supported by DARPA, the National Institutes of Health, the Harvard Digestive Diseases Center, and the Wyss Institute for Biologically Inspired Engineering at Harvard University.
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Genetically Modified
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August 12, 2019
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https://www.sciencedaily.com/releases/2019/08/190812140351.htm
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Bacteria made to mimic cells, form communities
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Rice University scientists have found a way to engineer a new kind of cell differentiation in bacteria, inspired by a naturally occurring process in stem cells.
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They have created a genetic circuit able to produce genetically distinguished cells of Rice synthetic biologist Matthew Bennett and Sara Molinari, a former student in the university's Systems, Synthetic and Physical Biology Ph.D. program, led the project to show how manipulating the genetic code of plasmids -- free-floating pieces of circular DNA in cells -- can be used to obtain stem cell-like differentiation in bacteria."Stem cells have the remarkable ability to divide asymmetrically," Bennett said. "Upon division, the original stem cell stays the same, but the new daughter cell has a completely new phenotype. That's asymmetric cell division, and multicellular organisms use it to help control their cellular makeup."As a synthetic biologist, I think a lot about creating and controlling differentiated cell types within a multicellular population," he said. "Here, we've taken what we know about stem cells and engineered the means to do it in bacteria."The researchers reported the development, which they call asymmetric plasmid partitioning (APP), in Molinari first discovered how to force plasmids in She then expanded the synthetic circuit to induce the simultaneous asymmetric partitioning of two plasmid species in a single cell, resulting in four genetically distinct "When we started, we were thinking about creating materials that have to be able to sense and adapt to an environment," said Molinari, who recently earned her doctorate at Rice. "We thought if we could mimic this feature of higher-order tissues, we would increase the robustness of our colonies and their ability to perform tasks. The challenge was to engineer a population of bacteria that becomes something else whenever it's needed."Molinari and her colleagues hit the jackpot on their first try with "But there was something we couldn't completely figure out about the system," Molinari said. "It took two years to find out I made a cloning mistake when I got this protein and put it in my plasmid. I had randomly added 17 amino acids at the beginning of the protein, and that made the whole system work."With that knowledge, she proceeded to improve upon the hydrophobic proteins that cluster in cells while they bind to target plasmids, holding them in place.Bennett noted natural processes either load enough plasmids into a cell to ensure some land in each daughter cell or actively pull plasmids into each of the new cells to ensure they remain identical. "We have shown we can outcompete those processes," he said.APP could turn simple organisms into complicated systems that enhance understanding of multicellular life. "We're pretty good at designing bacteria," Bennett said. "We've been doing that for years now. I think the field has evolved to the point where we can do amazing things with bacteria and people are asking what else we can do."The new discovery, he said, provides a path forward."There are three main hallmarks to multicellular life," he said. "One is differentiation through asymmetric cell division. Another is intercellular communication, which synthetic biologists have been engineering for years. And the third is cell adhesion, so cells stay where they're supposed to and stick to each other. If we can control all those things together, we can talk about engineering interesting multicellular lifeforms."It starts to feel a bit like science fiction, for sure," he said.
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Genetically Modified
| 2,019 |
August 7, 2019
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https://www.sciencedaily.com/releases/2019/08/190807131941.htm
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Bermuda's baitfish populations
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Small fishes play an important role in the marine food chain, providing food for larger fishes and water birds, but they are also caught for use as bait in both commercial and recreational fisheries. Over the past thirty years, a decline has been noted in some species of baitfish, leading scientists and resource managers to look more closely at the population dynamics of these important fish. However, baitfish tend to congregate in large schools containing multiple species, making it difficult to study individual populations.
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In 2017, a team of researchers, with funding from a Darwin Plus grant through the United Kingdom's Department of Environment, Food and Rural Affairs (DEFRA), set out to characterize Bermuda's baitfish populations, with the goal of providing data to improve the management of these species. Currently, regulations are in place that restrict the size of nets that may be used to catch baitfish, while net fishing is prohibited altogether in four inshore bays around the island: Coot Pond, Whalebone Bay, and Shelly Bay in the east end, and Somerset Long Bay in the west end. However, one important question remaining for the research team was whether similar protected bays need to be more evenly distributed around the island.Gretchen Goodbody-Gringley, a coral reef ecologist at BIOS, and Joanna Pitt, marine resources officer for the Bermuda Government Department of Environment and Natural Resources, led the project, which also included Emma Strand, a former BIOS Research Experiences for Undergraduates (REU) student and a current doctoral student at the University of Rhode Island. Their findings were recently published as a paper in the peer-reviewed scientific journal "Baitfish depend on shallow inshore areas that are often modified and threatened by a variety of human activities, such as overfishing, pollution, and coastal development," Strand said. "It's important to understand the composition of baitfish assemblages and the distribution of the various species around the island."During June and July of 2017, the team collected baitfish from ten locations around Bermuda, including both the east and west ends and north and south shores. Using physical characteristics, they identified five of the most common baitfish species in Bermuda: the reef silverside (Hypoatherina harringtonensis), the Bermuda anchovy (Anchoa choerostoma), the dwarf herring (Jenkinsia lamprotaenia), the red ear herring (Harengula humeralis), and the round sardinella or Spanish sardine (Sardinella aurita).DNA samples were extracted from the muscle of the collected fish and then sequenced, allowing the researchers to look at the genetic makeup of the baitfish populations. The team looked at specific DNA markers found in mitochondria, which are the parts of a cell responsible for converting food into energy. Analysis of mitochondrial DNA helps shed light on how genetically diverse each fish species is at the local level, as well as how genetically connected (or similar) Bermuda's local populations are to populations elsewhere. It also serves as a method for confirming the initial identification of each species, which increases the accuracy of the results.Based on these genetic analyses, the team realized that the samples included a sixth species, the Atlantic thread, or threadfin, herring (Opisthonema oglinum), highlighting the importance of conducting DNA analyses when characterizing multispecies baitfish assemblages."For all six of the species we examined, our results showed a high degree of genetic diversity both within and between baitfish assemblages from different locations around Bermuda," Goodbody-Gringley said. "This tells us that, in terms of management, we should consider Bermuda's baitfish species as highly mixed populations in which individuals from all around the island contribute to a single gene pool."However, the results also indicated that gene flow, and therefore exchange of individuals, between populations of these species in Bermuda and those in other regions of the Caribbean and Western Atlantic is limited, suggesting that the Bermuda populations are largely locally maintained. From a management perspective, this means that local baitfish populations are not likely to be replenished from populations in the Caribbean or other areas of the Tropical West Atlantic."As a resource manager, it's important to be able to balance the ecological sustainability of baitfish populations and their role in commercial and recreational fishing," Pitt said. "In practical terms, these two pieces of information mean that we need to work to conserve our baitfish stocks, but that we don't need to worry about the exact placement of protected areas."She added that studies such as this demonstrate the value of population genetics for informing and adapting fishery management measures.
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Genetically Modified
| 2,019 |
July 26, 2019
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https://www.sciencedaily.com/releases/2019/07/190726131649.htm
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Mouse genetics influences the microbiome more than environment
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Genetics has a greater impact on the microbiome than maternal birth environment, at least in mice, according to a study published this week in
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"The powerful effect of genetics, as compared to environment, was surprising," said Yechezkel Kashi, Head of the Applied Genomics and Microbiology Lab, Technion -- Israel Institute of Technology. "It was also disappointing since it suggested that the benefits of probiotics might last only as long as one takes them."In the study, the investigators determined the microbiomes of two different inbred laboratory strains of mice, black mice (C57BL/6J), and white mice (BALB/c). The investigators then crossed the black and white mice. In one set of crosses, the mother was black, while in the other the mother was white. In both cases, the offspring were the same shade of gray, and had similar genetics, regardless of which parent was black and which was white.The crosses were conducted because in mammals, during birth, mothers transfer microbes from their birth canals to offspring. Thus, during birth, black mothers and white mothers would pass different microbiota to their offspring. The maternal environmental influence on the microbiomes of the offspring turned out to be trivial. The microbiomes of the offspring were similar to each other regardless of whether their mothers were black or white, showing that the maternal seeding during birth didn't take.A third experiment tested a different environmental influence -- food source -- on microbiome. In this experiment, black mice and white mice were kept together."Mice are coprophages," explained coauthor Hila Korach-Rechtman, PhD, Senior Scientist, The Applied Genomics and Microbiology Lab, Technion -- Israel Institute of Technology, Haifa. "They eat feces, and in captivity, they eat their cage mates' feces." Since feces contain the microbiome, in this experiment white mice were exposed to black mice' microbes, and vice versa.This made some difference in the microbiomes, but that difference persisted only as long as the mice occupied the same cages. Once the different strains of mice were separated, their microbiomes reverted to their original composition, said Dr. Korach-Rechtman."Obviously, we can't imply that the same model would apply to humans," said Dr. Kashi. Nonetheless, other evidence supports that hypothesis. Studies have found that in both mice and humans, certain genetic loci, or genes correlate with specific microbial species.Genetic variation could influence the gut microbiome through mechanisms such as "differences in the mucosal gut structure... differences in metabolism such as bile acids secretion... potentially olfactory receptor activity... and antimicrobial peptides and other genetic determinants of the immune system," the investigators wrote.To analyze the influence of both the mother's strain, and of the coprophagy, the investigators collected feces from the different inbred mouse lines, and analyzed their microbiomes using DNA extraction and sequencing, and bioinformatics analysis of the resulting sequences. The conclusion from both experiments: genetics had major influence on microbiome. Maternal environment and coprophagy had only minor influence.
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Genetically Modified
| 2,019 |
July 25, 2019
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https://www.sciencedaily.com/releases/2019/07/190725150944.htm
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Hidden genetic variations power evolutionary leaps
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Laboratory populations that quietly amass 'cryptic' genetic variants are capable of surprising evolutionary leaps, according to a paper in the July 26 issue of
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Genetic variation -- that is, accumulated mutations in the DNA -- is the fuel for all evolutionary change: the more genetic variation, the faster evolution works and the more possibilities for novel adaptive solutions.But one kind of genetic variation -- hidden, or "cryptic," variation -- doesn't alter the appearance or behavior of an organism in its usual environment."It's an underappreciated kind of genetic variation," says corresponding author Andreas Wagner, an evolutionary biologist at the University of Zurich and external professor at the Santa Fe Institute, "and it plays an important role in evolution."Previous work has shown that cryptic variation in natural populations promotes rapid evolutionary adaptation. But the underlying molecular mechanisms were unclear.To explore those mechanisms, Wagner's team worked with populations of the gut bacterium During stage 2, the team changed the selection rules and began selecting for In the experiment, says co-author Joshua Payne (ETH Zurich), cryptic variation did more than drive evolutionary adaptation faster. Cell lines with deep reserves of cryptic variation evolved greener YFP proteins, forms of the protein that were inaccessible to regular bacteria, and they evolved by multiple unique routes not available to regular Current laboratory directed evolution often leads to the same evolutionary outcomes each time. The new work shows how amassing cryptic variation can open doors to otherwise inaccessible regions of protein sequence space, says first author Jia Zheng, a postdoctoral researcher at the University of Zurich.In the wild, cryptic variation helps fish adapt to life in caves. In the lab, cryptic variation might help a biomolecule bind a new receptor. "Our work can help develop new directed evolution strategies to find innovative biomolecules for biotechnological and medical applications," says Zheng.Like a fat savings account, cryptic variation is a store of variation that becomes available in an emergency to fuel rapid evolutionary change critical to the survival of a lineage and useful for molecular biologists.
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Genetically Modified
| 2,019 |
July 25, 2019
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https://www.sciencedaily.com/releases/2019/07/190725150401.htm
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These gut bacteria prevent mice from becoming obese -- what could that mean for us?
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Researchers at University of Utah Health have identified a specific class of bacteria from the gut that prevents mice from becoming obese, suggesting these same microbes may similarly control weight in people. The beneficial bacteria, called Clostridia, are part of the microbiome -- collectively trillions of bacteria and other microorganisms that inhabit the intestine.
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Published online in the journal June Round, Ph.D., an associate professor of pathology at U of U Health, is the study's co-senior author along with U of U Health research assistant professor W. Zac Stephens, Ph.D. Charisse Petersen, Ph.D., a graduate student at the time, led the research."Now that we've found the minimal bacteria responsible for this slimming effect, we have the potential to really understand what the organisms are doing and whether they have therapeutic value," Round says.Results from this study are already pointing in that direction. Petersen and colleagues found that Clostridia prevents weight gain by blocking the intestine's ability to absorb fat. Mice experimentally treated so that Clostridia were the only bacteria living in their gut were leaner with less fat than mice that had no microbiome at all. They also had lower levels of a gene, CD36, that regulates the body's uptake of fatty acids.These insights could lead to a therapeutic approach, Round says, with advantages over the fecal transplants and probiotics that are now being widely investigated as ways to restore a healthy microbiota. Therapeutics such as these, that are based on transferring living microbiome to the gut, won't work for everyone due to differences in diet and other factors that influence which bacteria can survive and thrive.The current study found that one or more molecules produced by Clostridia prevented the gut from absorbing fat. The next step is to isolate these molecules and further characterize how they work to determine whether they could inspire focused treatments for obesity, type 2 diabetes, and other related metabolic disorders."These bacteria have evolved to live with us and benefit us," Petersen says. "We have a lot to learn from them."Finding that mice with a compromised immune system couldn't help but become obese was a discovery that almost didn't happen. Serendipity brought Petersen into the lab at the right time to see that mice genetically engineered to lack myd88, a gene central to the immune response, were "as fat as pancakes." She had let the rodents age longer than usual, revealing an unappreciated link between immunity and obesity.Still, the observation didn't answer the question why the animals became overweight.Based on previous research she had carried out in the Round lab, she suspected the microbiome was involved. She had helped demonstrate that one role of the immune system is to maintain balance among the diverse array of bacteria in the gut. Impairing the body's defenses can cause certain bacterial species to dominate over others. Sometimes, the shift negatively impacts health.Following a similar logic, Petersen and colleagues determined that the obesity observed in immune-compromised mice stemmed from the failure of the body's defense system to appropriately recognize bacteria. These mice produced fewer of the antibodies that ordinarily latch onto the microbiome like target-seeking missiles. This change made the gut less hospitable for Clostridia, leading to more fat absorption and excessive weight gain. Over time, the mice also developed signs of type 2 diabetes.Round points out that research by others have shown that people who are obese similarly lack Clostridia, mirroring the situation in these mice. There are also some indications that people who are obese or have type 2 diabetes may have a suboptimal immune response. The hope is that understanding these connections will provide new insights into preventing and treating these pervasive health conditions."We've stumbled onto a relatively unexplored aspect of type 2 diabetes and obesity," Round says. "This work will open new investigations on how the immune response regulates the microbiome and metabolic disease."
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Genetically Modified
| 2,019 |
July 25, 2019
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https://www.sciencedaily.com/releases/2019/07/190725092510.htm
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Bacteria-killing gel heals itself while healing you
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McMaster researchers have developed a novel new gel made entirely from bacteria-killing viruses.
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The anti-bacterial gel, which can be targeted to attack specific forms of bacteria, holds promise for numerous beneficial applications in medicine and environmental protection.Among many possibilities, it could be used as an antibacterial coating for implants and artificial joints, as a sterile growth scaffold for human tissue, or in environmental cleanup operations, says chemical engineer Zeinab Hosseini-Doust.Her lab, which specializes in developing engineering solutions for infectious disease, grew, extracted and packed together so many of the viruses -- called bacteriophages, or simply phages -- that they assembled themselves spontaneously into liquid crystals and, with the help of a chemical binder, formed into a gelatin-like substance that can heal itself when cut.Yellow in colour and resembling Jell-O, a single millilitre of the antibacterial gel contains 300 trillion phages, which are the most numerous organisms on Earth, outnumbering all other organisms combined, including bacteria."Phages are all around us, including inside our bodies," explains Hosseini-Doust. "Phages are bacteria's natural predators. Wherever there are bacteria, there are phages. What is unique here is the concentration we were able to achieve in the lab, to create a solid material."The field of phage research is growing rapidly, especially as the threat of antimicrobial resistance grows."We need new ways to kill bacteria, and bacteriophages are one of the promising alternatives," says Lei Tan, a PhD student in Hosseini-Doust's lab and a co-author on the paper describing the research, published today in the journal Hosseini-Doust says the DNA of phages can readily be modified to target specific cells, including cancer cells. Through a Nobel Prize-winning technology called phage display, it's even possible to find phages that target plastics or environmental pollutants.Being able to shape phages into solid form opens new vistas of possibility, just as their utility in fighting diseases is being realized, she says.
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Genetically Modified
| 2,019 |
July 24, 2019
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https://www.sciencedaily.com/releases/2019/07/190724103812.htm
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Genome research shows that the body controls the integrity of heritable genomes
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Scientists have presented new findings that challenge established concepts of genetic inheritance. They have proven that somatic cells of the roundworm C. elegans influence heredity.
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Scientists at the CECAD Cluster of Excellence in Aging Research of the University of Cologne have discovered that body cells which are in direct contact with the germ cells in the nematode Caenorhabditis elegans are responsible for controlling the stability of the genome in primordial germ cells (PGCs). All germ cells, including sperm and eggs, originate from primordial germ cells that form during early embryo development. Professor Dr. Björn Schumacher and his team at the UoC's Institute for Genome Stability in Aging and at CECAD discovered that somatic niche cells that surround the PGCs control their response to DNA damage. The study 'Somatic niche cells regulate the CEP-1/p53-mediated DNA damage response in primordial germ cells,' has now been published in For more than hundred years, inheritance of genetic information was thought to be autonomously controlled by the germ cells, explaining why acquired traits cannot be genetically inherited. Scientists believed that mutations occurring only in germ cells were responsible for any heritable genetic changes -- be it during evolution or as cause of genetic disorders. Schumacher and his team now challenge this assertion.The DNA of an organism constantly gets damaged. Not only environmental influences, but also by-products of the body's energy metabolism damage the molecular structure of the genome in every cell. The scientists investigated how the genome integrity of PGCs is controlled. PGCs need to survey their genomes particularly rigorously because they give rise to all sperm or eggs of the organism. Damaged PGCs are particularly dangerous because they are hereditary and can lead to serious genetic disorders. PGCs thus need to stop dividing when their genomes are damaged until the DNA is repaired. Special niche cells are responsible for signalling to the PGCs that they need to stop dividing and repair before generating further germ cells. If they fail to do so, the PGCs might pass on dangerous mutations to the next generation.To fulfil this important function, the niche cells are in intimate contact with the PGCs and instruct them whether to divide and generate germ cells or whether to stay inactive. 'This means that the body is responsible for controlling the integrity of heritable genomes,' Schumacher remarked. 'The parental body thus has somatic control over the integrity of PGC genomes, controlling the quality of the heritable genetic information.' Since studying PGCs in mammals is a complicated endeavour, Schumacher's team used These new insights open up new perspectives for understanding inheritance and causes of infertility.
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Genetically Modified
| 2,019 |
July 9, 2019
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https://www.sciencedaily.com/releases/2019/07/190709141243.htm
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Scientists identify new virus-killing protein
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A new protein called KHNYN has been identified as a missing piece in a natural antiviral system that kills viruses by targeting a specific pattern in viral genomes, according to new findings published today in
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Studying the body's natural defenses to viruses and how viruses evolve to evade them is crucial to developing new vaccines, drugs and anticancer treatments.The genetic information that makes up the genomes for many viruses is comprised of building blocks called RNA nucleotides. Recently, it was discovered that a protein called ZAP binds to a specific sequence of RNA nucleotides: a cytosine followed by a guanosine, or CpG for short.The human immunodeficiency virus (HIV) normally escapes being inhibited by ZAP because it has evolved to have few CpGs in its genome. However, when CpGs are added back to the virus, ZAP promotes its destruction. This helps us understand why HIV with more CpGs multiplies less successfully, and likely explains why many strains of HIV have evolved to have few CpGs. But a mystery remained because ZAP is unable to break down the viral RNA by itself."As ZAP can't degrade RNA on its own, we believed that it must recruit other proteins to the viral RNA to destroy it," says lead author Mattia Ficarelli, a PhD student in Chad Swanson's Lab, Department of Infectious Diseases, King's College London. "So, in the current study, we set out to identify new human proteins that are essential for ZAP to target viral RNAs for destruction."After discovering that KHNYN interacts with ZAP, the team tested what happens when they increased the amount of KHNYN produced in cells infected with a typical HIV that has few CpGs, or an HIV genetically engineered to have many CpGs. Increasing KHNYN production in the cells reduced the typical HIV's ability to multiply about five-fold and decreased the ability of the CpG-enriched HIV to multiply by about 400-fold.To figure out if KHNYN and ZAP work together, the team repeated the same experiments in cells without ZAP and found that KHNYN did not inhibit the ability of CpG-enriched HIV to multiply. They then looked at what happened in cells genetically engineered to lack KHNYN, and found that both CpG-enriched HIV and a mouse leukemia virus that has many CpGs were no longer inhibited by ZAP."We have identified that KHNYN is required for ZAP to prevent HIV from multiplying when it is enriched for CpGs," explains co-corresponding author Professor Stuart Neil, Department of Infectious Diseases, King's College London. He adds that KHNYN is likely an enzyme that cuts up the viral RNA that ZAP binds to."An interesting potential application of this work is to make new vaccines or treat cancer," adds senior author and lecturer Chad Swanson, from the same department. "Since some cancer cells have low levels of ZAP, it may be possible to develop CpG-enriched, cancer-killing viruses that would not harm healthy cells. But much more research is necessary to learn more about how ZAP and KHNYN recognise and destroy viral RNA before we can move on to explore such applications."
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Genetically Modified
| 2,019 |
July 8, 2019
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https://www.sciencedaily.com/releases/2019/07/190708140032.htm
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First proof-of-concept demonstrates genetic sex selection in mammals
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Certain plants, insects, crustaceans and fish possess the uncanny ability to change the sex of their offspring before they are born. Mammals have never before demonstrated this genetic skill, until now.
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A new Tel Aviv University study reveals a genetic system in mammals that enables two animals to mate and produce only females. A similar system based on identical principles would produce only males.Research for the breakthrough study was led by Prof. Udi Qimron, Dr. Ido Yosef and Dr. Motti Gerlic and conducted by Dr. Liat Edry-Botzer, Rea Globus, Inbar Shlomovitz and Prof. Ariel Munitz, all of the Department of Clinical Microbiology and Immunology at TAU's Sackler School of Medicine. The research was published on July 1 in "The research provides the world's first proof-of-concept for mammals to genetically produce only female progeny," says Prof. Qimron. "We proved the concept in mouse models, but the concept could also be demonstrated in cattle, swine, goats, chickens and other animals."The current approach uses sex-sorted cattle semen to control the sex of their offspring," Prof. Qimron explains. "Farmers in the dairy and layer-poultry industries obviously prefer female calves and chicks, but to date, there was no accessible genetic way to regulate the sex ratio, which is naturally left around 50-50. We approached this problem in an innovative way, using genetic engineering."The researchers crossed two types of genetically engineered mice. The maternal mouse encoded a Cas9 protein, a CRISPR-protein that is inactive unless guided by special "guide-RNAs." The paternal mouse encoded these guide-RNAs on the Y-sex chromosome, a sex chromosome present only in males. After fertilization, the guide-RNAs from the paternal sperm and the Cas9 protein from the maternal egg were combined in the male mouse embryos, but not in the female embryos (because the females lack the Y chromosome). The combination of guide-RNAs with Cas9 results in a complex that eliminates the male embryos."We showed that Cas9 was specifically activated only in male embryos," says Prof. Qimron. "Our results pave the way for a genetic system that allows biased sex production. When two transgenic types of mice encoding Cas9 or Y-chromosome-encoded guide-RNAs are crossed, lethality of males occurs because Cas9 is guided from the Y chromosome to target essential genes. This does not happen in females because the Y chromosome is not transferred to them. This cross thus halts embryonic development of males without affecting the development of females."Importantly, the system can also be used to produce only males. Engineering the guide-RNAs on the paternal X-sex chromosome should result in the exclusive elimination of females, resulting in males-only progeny, which are more beneficial in the beef industry."The research presents a first-of-its-kind approach to determining mammalian sex through genetic means, Prof. Qimron says. "We believe that the producers of cattle, swine and chicken may benefit greatly from the technology."
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Genetically Modified
| 2,019 |
July 8, 2019
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https://www.sciencedaily.com/releases/2019/07/190708112408.htm
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Transformed tobacco fields could cuts costs for medical proteins
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A new Cornell University-led study describes the first successful rearing of engineered tobacco plants in order to produce medical and industrial proteins outdoors in the field, a necessity for economic viability, so they can be grown at large scales.
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The market for such biologically derived proteins is forecast to reach $300 billion in the near future. Industrial enzymes and other proteins are currently made in large, expensive fermenting reactors, but making them in plants grown outdoors could reduce production costs by three times.Researchers from Cornell and University of Illinois have engineered plants capable of making proteins not native to the plant itself. "We knew these plants grew well in the greenhouse, but we just never had the opportunity to test them out in the field," said Beth Ahner, professor of biological and environmental engineering and senior author of "Field-grown tobacco plants maintain robust growth while accumulating large quantities of a bacterial cellulase in chloroplasts," published in the journal That opportunity came when University of Illinois plant biology professor Stephen Long obtained a permit from the U.S. Department of Agriculture to grow the genetically modified plants in the field.Conventional wisdom suggested that the burden of asking plants to turn 20 percent of the proteins they have in their cells into something the plant can't use would greatly stunt growth."When you put plants in the field, they have to face large transitions, in terms of drought or temperature or light, and they're going to need all the protein that they have," Ahner said. "But we show that the plant still is able to function perfectly normally in the field [while producing nonnative proteins]. That was really the breakthrough."Jennifer Schmidt, a graduate student in Ahner's lab, and Justin McGrath, a research scientist in Long's lab, are co-first authors of the paper. Maureen Hanson, the Liberty Hyde Bailey Professor in the Department of Molecular Biology and Genetics, is also a co-author.The study was funded by the USDA.Cornell University has dedicated television and audio studios available for media interviews supporting full HD, ISDN and web-based platforms.
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Genetically Modified
| 2,019 |
June 28, 2019
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https://www.sciencedaily.com/releases/2019/06/190628120435.htm
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Take two E. coli and call me in the morning
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Millions of people take capsules of probiotics with the goal of improving their digestion, but what if those bacteria were also able to detect diseases in the gut and indicate when something is awry? New research from the Wyss Institute at Harvard University and Harvard Medical School (HMS) has created an effective, non-invasive way to quickly identify new bacterial biosensors that can recognize and report the presence of various disease triggers in the gut, helping set the stage for a new frontier of digestive health monitoring and treatment. The paper is published in
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"Our understanding of how the human gut microbiome behaves is still in its early stages, which has hindered large-scale research into creating biosensors out of living bacteria," said David Riglar, Ph.D., a former postdoc at the Wyss Institute and HMS who now leads a research group as a Sir Henry Dale Fellow at Imperial College London. "This work provides a high-throughput platform for identifying genetic elements in bacteria that respond to different signals in the gut, putting us one step closer to engineering complex signaling pathways in bacteria that allow them to detect and even treat diseases long-term."The new platform builds on previous work from the lab of Wyss Founding Core Faculty member Pamela Silver, Ph.D. that designed a genetic circuit consisting of a "memory element" derived from a virus and a synthetic "trigger element" that together can detect and record the presence of a given stimulus -- originally, a deactivated version of the antibiotic tetracycline. The synthetic circuit was integrated into the genomes of E. coli bacteria, which were introduced into live mice that were then given tetracycline. The antibiotic caused the trigger element in the bacterial circuit to activate the memory element, which "flipped" like a switch that remained "on" for up to a week so that the bacteria "remembered" the presence of the tetracycline. The "on" signal was then easily read by non-invasively analyzing the animals' excrement.The team next demonstrated that the circuit could be tweaked to detect and report tetrathionate (a naturally occurring molecule that indicates the presence of inflammation) in the intestine of living mice for up to six months after being introduced into the animals, showing that their system could be used to monitor signals that would be useful for diagnosing disease states in the gut long-term.But tetrathionate is just one molecule; in order to develop new bacteria-based diagnostics, the researchers needed a way to rapidly test different potential trigger elements to see if they could respond to more disease signals.First, they modified the genetic circuit by adding an antibiotic-resistance gene that is activated when the memory element is flipped into its "on" state, allowing bacteria that "remember" a trigger to survive exposure to the antibiotic spectinomycin. To test their updated circuit against a wide variety of molecular signals, they created a library of different strains of E. coli that each contained the memory element and a unique trigger element in its genome. This library of bacterial strains was then introduced into the guts of live mice to see if any of the trigger elements were activated by substances in the mice's intestines. When they grew bacteria from mouse fecal samples in a medium laced with spectinomycin, they found that a number of strains grew, indicating that their memory elements had been turned on during passage through the mice. Two of the strains in particular showed consistent activation, even when given to mice in isolation, indicating that they were activated by conditions inside the mice's gut and could serve as sensors of gut-specific signals.The researchers repeated the experiment using a smaller library of E. coli strains whose trigger elements were genetic sequences thought to be associated with inflammation, ten of which were activated during transit through the mice. When this library was administered to mice that had intestinal inflammation, one particular strain displayed a stronger memory response in mice with inflammation compared to healthy mice, confirming that it was able to successfully record the presence of inflammatory biomolecules in the mouse gut and thus could serve as a living monitor of gastrointestinal health."The beauty of this method is that it allows us to identify biosensors that already exist in nature that we wouldn't be able to design ourselves, because so much of the function and regulation of bacterial genomes is still unknown," said first author Alexander Naydich, who recently completed his Ph.D. in the Silver lab. "We're really taking advantage of the incredible genetic diversity of the microbiome to home in on potential solutions quickly and effectively."Additional features of the system include the ability to record signals that occur either chronically or transiently in the gut, as well as adjustable sensitivity in the form of synthetic ribosome binding site (RBS) sequences engineered into the trigger elements that can control the rate at which the promoters can induce an "on" memory state in response to a signal. These capabilities allow for the fine-tuning of bacterial biosensors to detect specific conditions within the gut over a long time span."We have been able to advance this technology from a tool that tests for one thing to a tool that can test for multiple things concurrently, which is not only useful for identifying new potential biosensors, but could one day be developed into a probiotic-like pill containing sophisticated collections of bacteria that sense and record several signals at once, allowing clinicians to 'fingerprint' a disease and have greater confidence in making a diagnosis," said Pamela Silver, who is also the Elliot T. and Onie H. Adams Professor of Biochemistry and Systems Biology at HMS."The continuing advances made by the Silver team in the development of living cellular devices based on the genetic reengineering of microbiome represents an entirely new approach to low-cost diagnostics. This approach has the potential to radically transform how we interact with and control biological systems, including our own bodies," said Wyss Founding Director Donald Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at HMS and the Vascular Biology Program at Boston Children's Hospital, as well as Professor of Bioengineering at Harvard's John A. Paulson School of Engineering and Applied Sciences.
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Genetically Modified
| 2,019 |
June 26, 2019
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https://www.sciencedaily.com/releases/2019/06/190626160316.htm
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Robot arm tastes with engineered bacteria
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A robotic gripping arm that uses engineered bacteria to "taste" for a specific chemical has been developed by engineers at the University of California, Davis, and Carnegie Mellon University. The gripper is a proof-of-concept for biologically-based soft robotics.
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"Our long-term vision is about building a synthetic microbiota for soft robots that can help with repair, energy generation or biosensing of the environment," said Cheemeng Tan, assistant professor of biomedical engineering at UC Davis. The work was published June 26 in the journal Soft robotics uses lightweight, flexible and soft materials to create machines that match the versatility of living things, and soft robot designs often draw inspiration form nature. Adding actual living cells to soft robots brings scientists another step closer to creating biological-mechanical hybrid machines."By combining our work in flexible electronics and robotic skin with synthetic biology, we are closer to future breakthroughs like soft biohybrid robots that can adapt their abilities to sense, feel and move in response to changes in their environmental conditions," said Carmel Majidi, a co-author and associate professor of mechanical engineering at CMU.Biosensing with engineered bacteriaThe new device uses a biosensing module based on E. coli bacteria engineered to respond to the chemical IPTG by producing a fluorescent protein. The bacterial cells reside in wells with a flexible, porous membrane that allows chemicals to enter but keeps the cells inside. This biosensing module is built into the surface of a flexible gripper on a robotic arm, so the gripper can "taste" the environment through its fingers.When IPTG crosses the membrane into the chamber, the cells fluoresce and electronic circuits inside the module detect the light. The electrical signal travels to the gripper's control unit, which can decide whether to pick something up or release it.As a test, the gripper was able to check a laboratory water bath for IPTG then decide whether or not to place an object in the bath.So far, this biohybrid bot can only taste one thing and it's difficult to design systems that can detect changing concentrations, Tan said. Another challenge is to maintain a stable population of microbes in, or on, a robot -- comparable to the microbiome or ecosystem of bacteria and fungi that live in or on our own bodies and carry out many useful functions for us.Biohybrid systems potentially offer more flexibility than conventional robotics, he said. Bacteria could be engineered for different functions on the robot: detecting chemicals, making polymers for repairs or generating energy, for example.
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Genetically Modified
| 2,019 |
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