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In organic chemistry, the Le Bel–Van t Hoff rule states that the number of stereoisomers of an organic compound containing no internal planes of symmetry is 2, where n represents the number of asymmetric carbon atoms. Joseph Achille Le Bel and Jacobus Henricus van t Hoff both announced this hypothesis in 1874 and that this accounted for all molecular asymmetry known at the time.
As an example, four of the carbon atoms of the aldohexose class of molecules are asymmetric, therefore the Le Bel–Van 't Hoff rule gives a calculation of 2 = 16 stereoisomers. This is indeed the case: these chemicals are two enantiomers each of eight different diastereomers: allose, altrose, glucose, mannose, gulose, idose, galactose, and talose. | 4 | Stereochemistry |
Since glycans play an important role in intercellular interactions and protein, they serve as viable targets for various therapeutic interactions. Multiple current therapeutics aim to take advantage of their role in signaling pathways, and target their biosynthesis or engineer related glycoproteins. These interactions can be controlled by encouraging or inhibiting the presence of those glycans that mediate signaling, which is the mechanism of action for a number of extant drugs, including heparin, erythropoietin, the antivirals oseltamivir and zanamivir, and the Hib vaccine. Furthermore, the glycans themselves can serve as drugs and there is ongoing research and development to engineer more effective ones. | 1 | Biochemistry |
The decomposition process starts after death and can proceed in the water column as the gelatinous organisms are sinking. Decay happens faster in the tropics than in temperate and subpolar waters as a result of warmer temperatures. In the tropics, a jelly-fall may take less than 2 days to decay in warmer, surface water, but as many as 25 days when it is lower than 1000 m deep. However, lone gelatinous organisms may spend less time on the sea floor as one study found that jellies could be decomposed by scavengers in the Norwegian deep sea in under two and a half hours.
Decomposition of jelly-falls is largely aided by these kinds of scavengers. In general, echinoderms, such as sea stars, have emerged as the primary consumer of jelly-falls, followed by crustaceans and fish. However, which scavengers find their way to jelly-falls is highly reliant on each ecosystem. For example, in an experiment in the Norwegian deep sea, hagfish were the first scavengers to find the traps of decaying jellies, followed by squat lobsters, and finally decapod shrimp. Photographs taken off the coast of Norway on natural jelly-falls also revealed caridean shrimp feeding on jelly carcasses.
With increased populations and blooms becoming more common, with favorable conditions and a lack of other filter feeders in the area to consume plankton, environments with jellies present will have carbon pumps be more primarily supplied with jelly-falls. This could lead to issues of habitats with established biological pumps succumbing to nonequilibrium as the presence of jellies would change the food web as well as changes to the amount of carbon deposited into the sediment.
Finally, decomposition is aided by the microbial community. In a case study on the Black Sea, the number of bacteria increased in the presence of jelly-falls, and the bacteria were shown to preferentially use nitrogen released from decaying jelly carcasses while mostly leaving carbon. In a study conducted by Andrew Sweetman in 2016, it was discovered using core samples of the sediment in Norwegian fjords, the presence of jelly-falls significantly impacted the biochemical process of these benthic communities. Bacteria consume jelly carcasses rapidly, removing opportunities of acquiring sustenance for bottoming feeding macrofauna, which has impacts traveling up the trophic levels. In addition, with the exclusion of scavengers, jelly-falls develop a white layer of bacteria over the decaying carcasses and emit a black residue over the surrounding area, which is from sulfide. This high level of microbial activity requires a lot of oxygen, which can lead zones around jelly-falls to become hypoxic and inhospitable to larger scavengers. | 9 | Geochemistry |
Protocol databases correlate results from bioassays to their metadata about experimental conditions and protocol designs. | 1 | Biochemistry |
As a scientific tool, CrysTBox suite is freely available for academic purposes, it supports file formats widely used in the community and offers interconnection with other scientific software. | 3 | Analytical Chemistry |
Assimilation is the process of absorption of vitamins, minerals, and other chemicals from food as part of the nutrition of an organism. In humans, this is always done with a chemical breakdown (enzymes and acids) and physical breakdown (oral mastication and stomach churning). Chemical alteration of substances in the bloodstream by the liver or cellular secretions. Although a few similar compounds can be absorbed in digestion bio assimilation, the bioavailability of many compounds is dictated by this second process since both the liver and cellular secretions can be very specific in their metabolic action (see chirality). This second process is where the absorbed food reaches the cells via the liver.
Most foods are composed of largely indigestible components depending on the enzymes and effectiveness of an animal's digestive tract. The most well-known of these indigestible compounds is cellulose; the basic chemical polymer in the makeup of plant cell walls. Most animals, however, do not produce cellulase; the enzyme needed to digest cellulose. However, some animals and species have developed symbiotic relationships with cellulase-producing bacteria (see termites and metamonads.) This allows termites to use the energy-dense cellulose carbohydrate. Other such enzymes are known to significantly improve bio-assimilation of nutrients. Because of the use of bacterial derivatives, enzymatic dietary supplements now contain such enzymes as amylase, glucoamylase, protease, invertase, peptidase, lipase, lactase, phytase, and cellulase. | 1 | Biochemistry |
The Antique Gas & Steam Engine Museum (AGSEM) is a living history museum founded in 1969. It is located on of county-owned land at 2040 N Santa Fe Ave. on the outskirts of Vista, California. The museum is a non-profit 501c(3) organization, run by several paid employees along with volunteer help.
The museum is open almost every day of the year and has two bi-annual shows, on the 3rd and 4th weekends of June and October. The museum also has other public and private events throughout the year.
Exhibits at the museum include: | 8 | Metallurgy |
Many specialized methods have been developed for forming unsymmetrical disulfides. Reagents that deliver the equivalent of "" react with thiols to give asymmetrical disulfides:
where is the phthalimido group.
Bunte salts, derivatives of the type are also used to generate unsymmetrical disulfides: | 0 | Organic Chemistry |
In the recent years, fluid inclusion research has been extensively applied to understand the role of fluids in the deep crust and crust-mantle interface. Fluid inclusions trapped within granulite facies rocks have provided important clues on the petrogenesis of dry granulite facies rocks through the influx of CO-rich fluids from sub-lithospheric sources. CO-rich fluid inclusions were also recorded from a number of ultra high temperature granulite facies terranes, suggesting the involvement of CO in extreme crustal metamorphism. Some recent studies speculate that CO derived by sub-solidus decarbonation reactions during extreme metamorphism has contributed to the deglaciation of the snowball Earth. | 9 | Geochemistry |
Common side effects include vomiting, diarrhea, headaches, and a rash. Severe side effects requiring hospitalization are rare, but include mental health problems such as depression, hallucinations, anxiety and neurological side effects such as poor balance, seizures, and ringing in the ears. Mefloquine is therefore not recommended in people with a history of psychiatric disorders or epilepsy. | 4 | Stereochemistry |
The Heck–Matsuda (HM) reaction is an organic reaction and a type of palladium catalysed arylation of olefins that uses arenediazonium salts as an alternative to aryl halides and triflates.
The use of arenediazonium salts presents some advantages over traditional aryl halide electrophiles, for example, the use of phosphines as ligand are not required and thus negating the requirement for anaerobic conditions, which makes the reaction more practical and easier to handle. Additionally, the reaction can be performed with or without a base and is often faster than traditional Heck protocols.
Allylic alcohols, conjugated alkenes, unsaturated heterocycles and unactivated alkenes are capable of being arylated with arenediazonium salts using simple catalysts such as palladium acetate (Pd(OAc)) or tris(dibenzylideneacetone)dipalladium(0) (Pddba) at room temperature in air, and in benign and conventional solvents.
In addition to the intermolecular variant of the HM reaction, intramolecular cyclization processes have also been developed for the construction of a range of oxygen and nitrogen heterocycles.
The catalytic cycle for the Heck-Matsuda arylation reaction has four main steps: oxidative addition, migratory insertion or carbopalladation, syn β-elimination and reductive elimination. The proposed Heck catalytic cycle involving cationic palladium with diazonium salts was reinforced by studies with mass spectrometry (ESI) by Correia and co-workers. These results also show the complex interactions that occur in the coordination sphere of palladium during the Heck reaction with arenediazonium salt.
A related reaction is the Meerwein arylation that precedes the Heck reaction. Meerwein arylation often use copper salts, but may in some cases be done without a transition metal. | 0 | Organic Chemistry |
At low concentrations of TNP-ATP (≤1 μM), fluorescent intensity is proportional to the concentration of TNP added. However, at concentrations exceeding 1 μM, inner filter effects cause this relationship to no longer be linear. To correct this, researchers must determine the ratio of the predicted theoretical fluorescence intensity (assuming linearity) to the observed fluorescence intensity and then apply this correction factor. However, in most cases, researchers will try to keep the concentration of TNP to lower than 1 μM.
To determine binding affinities, TNP-ATP is added to a solution and then titrated with protein. This produces a saturation curve from which the binding affinity can be determined. The number of binding sites may also be determined through this saturation curve by looking to see if there are sudden changes in slope. One can also titrate a fixed amount of protein with increasing additions of TNP-ATP to obtain a saturation curve. To do so, however, may get complicated due to the inner filter effects that will need to be corrected for.
To determine dissociation constants, TNP-ATP can be competed off of a protein with ATP. The value of the dissociation constant K for a single-site binding can then be obtained by applying the Langmuir equation for a curve fit:
where RFU is relative fluorescent units, RFU is the fluorescence observed, RFU is the fluorescence of free TNP-ATP, and RFU is the fluorescence of TNP-ATP when completely bound to a protein.
To measure an ATP competitor, one can add competitor to pre-incubated samples of protein:TNP-ATP. The fraction of TNP-ATP bound to the protein can be calculated via:
where θ is that fraction, and RFU is the value of fluorescence intensity at saturation, meaning when 100% of TNP-ATP is bound.
The dissociation constants for TNP and competitor can then be calculated through the equation:
For reasons not yet fully understood, TNP-ATP typically binds the ATP binding sites of proteins and enzymes anywhere from one to three times tighter than regular ATP. The dissociation constants are usually around 0.3–50 μM. | 7 | Physical Chemistry |
Levich is one of the pioneers in induced-charge electrokinetic field. He calculated the perturbed slip profile around a conducting particle in contact with electrolyte. He also theoretically predicted that vortices induced around this particle once the electric filed is applied. | 7 | Physical Chemistry |
Iridium-catalyzed transfer-hydrogenative carbonyl allylation method has been applied to the synthesis of polyketide natural products. Some examples are shown below. In every case, the target compound was prepared in significantly fewer steps than was previously achieved. For example, total syntheses of roxaticin, bryostatin and cryptocaryol were accomplished via double Krische allylation of 1,3-propane diol. This method was also used in the synthesis of mandelalide A.
The Krische bisallylation has been applied to the synthesis of psymberin in 17 LLS and 32 total steps. Through the use of the Krische allylation, this synthesis was accomplished via a much shorter route than previous syntheses. The Krische allylation to his synthesis of callyspongiolide using the chiral SEGPHOS catalyst complex. ] In 2018, Harran also prepared callyspongiolide using the Krische allylation as a convergent method for fragment union. Double crotylation was used by Krische to prepare 6-deoxyerythronolide B and swinholide A. | 0 | Organic Chemistry |
In 1931, Peirce, still president of the Baltimore Copper Smelting & Rolling Co., as well as being President of the Peirce-Smith Converter Company and vice president of the American Smelting & Refining Company, is awarded of the James Douglas medal, for "his numerous improvements in devices for smelting, refining, and rolling copper". | 8 | Metallurgy |
Saltatory conduction in myelinated axons requires organization of the nodes of Ranvier, whereas voltage-gated sodium channels are highly populated. Studies show that αII-Spectrin, a component of the cytoskeleton is enriched at the nodes and paranodes at early stages and as the nodes mature, the expression of this molecule disappears. It is also proven that αII-Spectrin in the axonal cytoskeleton is absolutely vital for stabilizing sodium channel clusters and organizing the mature node of Ranvier. | 1 | Biochemistry |
Optimal eastern meadow vole habitat consists of moist, dense grassland with substantial amounts of plant litter. Habitat selection is largely influenced by relative ground cover of grasses and forbs; soil temperature, moisture, sodium, potassium, and pH levels; humidity; and interspecific competition. Eastern meadow voles are most commonly associated with sites having high soil moisture. They are often restricted to the wetter microsites when they occur in sympatry with prairie voles (Microtus ochrogaster) or montane voles.
In eastern Massachusetts, eastern meadow vole density on a mosaic of grassy fields and mixed woods was positively correlated with decreasing vertical woody stem density and decreasing shrub cover. Density was highest on plots with more forbs and grasses and less with woody cover; eastern meadow voles preferred woody cover over sparse vegetation where grassy cover was not available.
In West Virginia, the only forested habitats in which eastern meadow voles were captured were seedling stands.
In Pennsylvania, three subadult eastern meadow voles were captured at least 1.6 miles (2.6 km) from the nearest appreciable suitable eastern meadow vole habitat, suggesting they are adapted to long-distance dispersal.
In Ohio, the effects of patch shape and proportion of edge were investigated by mowing strips between study plots. The square plots were 132 feet per side (40 m x 40 m), and the rectangular patches were 52.8 feet by 330 feet (16 m x 100 m). Square habitat patches were not significantly different from rectangular patches in eastern meadow vole density. Edge effects in patches of this size were not found, suggesting eastern meadow voles are edge-tolerant. Habitat patch shape did affect dispersal and space use behaviors. In rectangular patches, home ranges were similar in size to those in square patches, but were elongated.
Eastern meadow voles tend to remain in home ranges and defend at least a portion of their home ranges from conspecifics. Home ranges overlap and have irregular shapes. Home range size depends on season, habitat, and population density: ranges are larger in summer than winter, those in marshes are larger than in meadows, and are smaller at higher population densities. Home ranges vary in size from 0.08 to 2.3 hectares (0.32-0.9 ac). Females have smaller home ranges than males, but are more highly territorial than males; often, juveniles from one litter are still present in the adult female's home range when the next litter is born. Female territoriality tends to determine density in suboptimal habitats; the amount of available forage may be the determining factor in female territory size, so determines reproductive success. | 2 | Environmental Chemistry |
The Northwest Territories Legislative Assembly moved into its new building, designed to preserve as much of the original shoreline and vegetation as possible, on the north shore of the lake in 1993. By then, all recreational use of the lake itself had ended. Many residents were too leery of leeches, which thrived in the lake in the absence of fish preying on them, to enter the water. Instead, the lake became the focus of the Frame Lake Trail, a partially paved path around the entire shoreline, which soon became popular for walking and jogging.
In 2007, a conservation report prepared for the city named Frame Lake its top priority and suggested enacting special nature-preservation zoning to protect it. During the following decade, residents began to rediscover Frame Lake. "As a city, weve largely disengaged from this little jewel in our midst", wrote Matthew Mallon in YK_Edge', a local weekly newspaper. Newer residents, he said, were incredulous at his recollections of swimming and sailing on the lake in his childhood. In 2013 another local resident organized a Canada Day cleanup and swim in the lake, saying concerns about arsenic and leeches in the water were exaggerated.
The Carleton study carried out under a grant from Tides Canada and the Royal Bank of Canada in 2015 established that the lake had declined more precipitously since 1970, and described how. It will continue to measure the degradation of the lake on an annual basis to form a basis for policy recommendations to revitalize the lake. Currently researchers believe that either dredging rotten sediments off the lake bottom or aeration would best restore the water quality of the lake's early years. | 2 | Environmental Chemistry |
Scandium has the smallest atomic and ionic (3+) radii (1.62 and 0.885 Å, respectively) among the rare-earth elements. It forms several icosahedron-based borides which are not found for other rare-earth elements; however, most of them are ternary Sc-B-C compounds. There are many boron-rich phases in the boron-rich corner of Sc-B-C phase diagram, as shown in figure 17. A slight variation of the composition can produce ScB, ScBC, ScBC and ScBC; their crystal structures are unusual for borides and are very different from each other. | 3 | Analytical Chemistry |
Damage repair is the conversion of a damaged metabolite back to its original state via one or more enzymatic reactions; the concept is similar to DNA repair and protein repair. For example, the promiscuous activity of malate dehydrogenase causes reduction of alpha-ketoglutarate to L-2-hydroxyglutarate. This compound is a dead-end metabolite and is not a substrate for any other enzyme in central metabolism, and its accumulation in humans causes L-2-Hydroxyglutaric aciduria. The repair enzyme L-2-hydroxyglutarate dehydrogenase oxidizes L-2-hydroxyglutarate back to alpha-ketoglutarate, thus repairing this metabolite. In humans, L-2-hydroxyglutarate dehydrogenase uses FAD as the cofactor, while the E. coli enzyme reduces molecular oxygen. | 1 | Biochemistry |
Chemical decomposition, or chemical breakdown, is the process or effect of simplifying a single chemical entity (normal molecule, reaction intermediate, etc.) into two or more fragments. Chemical decomposition is usually regarded and defined as the exact opposite of chemical synthesis. In short, the chemical reaction in which two or more products are formed from a single reactant is called a decomposition reaction.
The details of a decomposition process are not always well defined. Nevertheless, some activation energy is generally needed to break the involved bonds and as such, higher temperatures generally accelerates decomposition. The net reaction can be an endothermic process, or in the case of spontaneous decompositions, an exothermic process.
The stability of a chemical compound is eventually limited when exposed to extreme environmental conditions such as heat, radiation, humidity, or the acidity of a solvent. Because of this chemical decomposition is often an undesired chemical reaction. However chemical decomposition can be desired, such as in various waste treatment processes.
For example, this method is employed for several analytical techniques, notably mass spectrometry, traditional gravimetric analysis, and thermogravimetric analysis. Additionally decomposition reactions are used today for a number of other reasons in the production of a wide variety of products. One of these is the explosive breakdown reaction of sodium azide [(NaN)] into nitrogen gas (N) and sodium (Na). It is this process which powers the life-saving airbags present in virtually all of today's automobiles.
Decomposition reactions can be generally classed into three categories; thermal, electrolytic, and photolytic decomposition reactions. | 0 | Organic Chemistry |
In another setting, the chambers are connected side by side horizontally (Zigmond chamber) or as concentric rings on a slide (Dunn chamber) Concentration gradient develops on a narrow connecting bridge between the chambers and the number of migrating cells is also counted on the surface of the bridge by light microscope. In some cases the bridge between the two chambers is filled with agar and cells have to "glide" in this semisolid layer. | 1 | Biochemistry |
Aflatoxin total synthesis concerns the total synthesis of a group of organic compounds called aflatoxins. These compounds occur naturally in several fungi. As with other chemical compound targets in organic chemistry, the organic synthesis of aflatoxins serves various purposes. Traditionally it served to prove the structure of a complex biocompound in addition to evidence obtained from spectroscopy. It also demonstrates new concepts in organic chemistry (reagents, reaction types) and opens the way to molecular derivatives not found in nature. And for practical purposes, a synthetic biocompound is a commercial alternative to isolating the compound from natural resources. Aflatoxins in particular add another dimension because it is suspected that they have been mass-produced in the past from biological sources as part of a biological weapons program.
The synthesis of racemic aflatoxin B1 has been reported by Buechi et al. in 1967 and that of racemic aflatoxin B2 by Roberts et al. in 1968 The group of Barry Trost of Stanford University is responsible for the enantioselective total synthesis of (+)-Aflatoxin B and B in 2003. In 2005 the group of E. J. Corey of Harvard University presented the enantioselective synthesis of Aflatoxin B. | 0 | Organic Chemistry |
Various classification schemes can be applied. A commonly used scheme is based on the number of carbons and was devised by Jeffrey Harborne and Simmonds in 1964 and published in 1980:
C-C-C Diarylheptanoids are not included in this Harborne classification.
They can also be classified on the basis of their number of phenol groups. They can therefore be called simple phenols or monophenols, with only one phenolic group, or di- (bi-), tri- and oligophenols, with two, three or several phenolic groups respectively.
A diverse family natural phenols are the flavonoids, which include several thousand compounds, among them the flavonols, flavones, flavan-3ol (catechins), flavanones, anthocyanidins, and isoflavonoids.
The phenolic unit can be found dimerized or further polymerized, creating a new class of polyphenol. For example, ellagic acid is a dimer of gallic acid and forms the class of ellagitannins, or a catechin and a gallocatechin can combine to form the red compound theaflavin, a process that also results in the large class of brown thearubigins in tea.
Two natural phenols from two different categories, for instance a flavonoid and a lignan, can combine to form a hybrid class like the flavonolignans.
Nomenclature of polymers: | 0 | Organic Chemistry |
Dynamic kinetic resolution has also been applied to the total synthesis of a variety of natural products. After Bäckvall's discoveries in 2007, he employed another enzyme-metal coupled reaction to synthesize the natural product (R)-Bufuralol.
The key step that the literature points out utilizes DKR to convert the chlorohydrin into the (S)-acetate by means of a lipase and a ruthenium catalyst.
The lipase PS-C “Amano” II has been reported in the literature to be particularly enantioselective for the 1-phenyl-2-chloroethanol motif. The enzyme, along with the ruthenium catalyst, allows for rapid racemization of the chlorohydrin with a selective binding to the (S) isomer for the acetylation reaction. Here isopropenyl acetate is used as the acyl donor. The product is achieved in excellent yield (96%) and near-perfect enantiomeric excess (>99%). | 4 | Stereochemistry |
Hydrogen sulfide (HS) is a weak electrolyte. It is partially ionized when in aqueous solution, therefore there exists an equilibrium between un-ionized molecules and constituent ions in an aqueous medium as follows:
:HS H + HS
By applying the law of mass action, we have
Hydrochloric acid (HCl) is a strong electrolyte, which nearly completely ionizes as
:HCl → H + Cl
If HCl is added to the HS solution, H a common ion and creates a common ion effect. Due to the increase in concentration of H ions from the added HCl, the equilibrium of the dissociation of HS shifts to the left and keeps the value of K constant. Thus the dissociation of HS decreases, the concentration of un-ionized HS increases, and as a result, the concentration of sulfide ions decreases. | 7 | Physical Chemistry |
Cobalt oleate can be synthesized by heating a solution of sodium oleate and cobalt(II) chloride to 70 °C. | 0 | Organic Chemistry |
Homeostatic control can change the PCO2| and hence the pH of the arterial plasma within a few seconds. The partial pressure of carbon dioxide in the arterial blood is monitored by the central chemoreceptors of the medulla oblongata. These chemoreceptors are sensitive to the levels of carbon dioxide and pH in the cerebrospinal fluid.
The central chemoreceptors send their information to the respiratory centers in the medulla oblongata and pons of the brainstem. The respiratory centres then determine the average rate of ventilation of the alveoli of the lungs, to keep the in the arterial blood constant. The respiratory center does so via motor neurons which activate the muscles of respiration (in particular, the diaphragm). A rise in the in the arterial blood plasma above reflexly causes an increase in the rate and depth of breathing. Normal breathing is resumed when the partial pressure of carbon dioxide has returned to 5.3 kPa. The converse happens if the partial pressure of carbon dioxide falls below the normal range. Breathing may be temporally halted, or slowed down to allow carbon dioxide to accumulate once more in the lungs and arterial blood.
The sensor for the plasma HCO concentration is not known for certain. It is very probable that the renal tubular cells of the distal convoluted tubules are themselves sensitive to the pH of the plasma. The metabolism of these cells produces CO, which is rapidly converted to H and HCO through the action of carbonic anhydrase. When the extracellular fluids tend towards acidity, the renal tubular cells secrete the H ions into the tubular fluid from where they exit the body via the urine. The HCO ions are simultaneously secreted into the blood plasma, thus raising the bicarbonate ion concentration in the plasma, lowering the carbonic acid/bicarbonate ion ratio, and consequently raising the pH of the plasma. The converse happens when the plasma pH rises above normal: bicarbonate ions are excreted into the urine, and hydrogen ions into the plasma. These combine with the bicarbonate ions in the plasma to form carbonic acid (H + HCO HCO), thus raising the carbonic acid:bicarbonate ratio in the extracellular fluids, and returning its pH to normal.
In general, metabolism produces more waste acids than bases. Urine produced is generally acidic and is partially neutralized by the ammonia (NH) that is excreted into the urine when glutamate and glutamine (carriers of excess, no longer needed, amino groups) are deaminated by the distal renal tubular epithelial cells. Thus some of the "acid content" of the urine resides in the resulting ammonium ion (NH) content of the urine, though this has no effect on pH homeostasis of the extracellular fluids. | 7 | Physical Chemistry |
The resonance structures below show the 1,3-dipole contribution, in which the two carbon atoms adjacent to the nitrogen have a negative or positive charge. The most common representation of azomethine ylides is that in which the nitrogen is positively charged, and the negative charge is shared between the two carbon atoms. The relative contributions of the different resonance structures depend on the substituents on each atom. The carbon containing electron-withdrawing substituents will have a more partial negative charge, due to the ability of the nearby electron-withdrawing group to stabilize the negative charge.
Three different ylide shapes are possible, each leading to different stereochemistry in the products of 1,3-dipolar cycloaddition reactions. W-shaped, U-shaped, and S-shaped ylides are possible. The W- and U-shaped ylides, in which the R substituents are on the same side, result in syn cycloaddition products, whereas S-shaped ylides result in anti products. In the examples below, where the R substituent ends up in the product depends on the substituent's steric and electronic nature (see regioselectivity of 1,3 dipolar cycloadditions). The stereochemistry of R and R in the cycloaddition product is derived from the dipole. The stereochemistry of R is derived from the dipolarophile—if the dipolarophile is more than mono-substituted (and prochiral), up to four new stereocenters can result in the product. | 0 | Organic Chemistry |
Vinyl and aryl Grignard reagents couple with primary alkyl halides in the presence of a catalytic amount of a copper(I) halide salt. The use of LiCuCl rather than simple copper(I) halide salts (CuX) improves yields of these coupling reactions.
The addition of Grignard reagents to alkynes is facilitated by a catalytic amount of copper halide. Transmetalation to copper and carbocupration are followed by transmetalation of the product alkene back to magnesium. The addition is syn unless a coordinating group is nearby in the substrate, in which case the addition becomes anti and yields improve. | 0 | Organic Chemistry |
In analytical chemistry, biomonitoring is the measurement of the body burden of toxic chemical compounds, elements, or their metabolites, in biological substances. Often, these measurements are done in blood and urine. Biomonitoring is performed in both environmental health, and in occupational safety and health as a means of exposure assessment and workplace health surveillance.
The two best established environmental biomonitoring programs in representative samples of the general population are those of the United States and Germany, although population-based programs exist in a few other countries. In 2001, the U.S. Centers for Disease Control and Prevention (CDC) began to publish its biennial National Report on Human Exposure to Environmental Chemicals, which reports a statistically representative sample of the U.S. population. | 2 | Environmental Chemistry |
LiHMDS is commercially available, but it can also be prepared by the deprotonation of bis(trimethylsilyl)amine with n-butyllithium. This reaction can be performed in situ.
Once formed, the compound can be purified by sublimation or distillation. | 0 | Organic Chemistry |
Discovered by Tillett and Francis in 1930, it was initially thought that CRP might be a pathogenic secretion since it was elevated in a variety of illnesses, including cancer. The later discovery of hepatic synthesis (made in the liver) demonstrated that it is a native protein. Initially, CRP was measured using the quellung reaction which gave a positive or a negative result. More precise methods nowadays use dynamic light scattering after reaction with CRP-specific antibodies.
CRP was so named because it was first identified as a substance in the serum of patients with acute inflammation that reacted with the cell wall polysaccharide (C-polysaccharide) of pneumococcus. | 1 | Biochemistry |
The sweetening properties of Synsepalum dulcificum berries were first noted by des Marchais during expeditions to West Africa in the 18th century. The term miraculin derived from experiments to isolate and purify the active glycoprotein that gave the berries their sweetening effects, results that were published simultaneously by Japanese and Dutch scientists working independently in the 1960s (the Dutch team called the glycoprotein mieraculin). The word miraculin was in common use by the mid-1970s. | 1 | Biochemistry |
In addition to a reduction in the rate of protein synthesis, it appears that some species of hypoxia-tolerant fish conserve energy by employing Hochachka's ion channel arrest hypothesis. This hypothesis makes two predictions:
# Hypoxia-tolerant animals naturally have low membrane permeabilities
# Membrane permeability decreases even more during hypoxic conditions (ion channel arrest)
The first prediction holds true. When membrane permeability to Na+ and K+ ions was compared between reptiles and mammals, reptile membranes were discovered to be five times less leaky. The second prediction has been more difficult to prove experimentally, however, indirect measures have showed a decrease in Na+/K+-ATPase activity in eel and trout hepatocytes during hypoxic conditions. Results seem to be tissue-specific, as crucian carp exposed to hypoxia do not undergo a reduction in Na+/K+ ATPase activity in their brain. Although evidence is limited, ion channel arrest enables organisms to maintain ion channel concentration gradients and membrane potentials without consuming large amounts of ATP. | 9 | Geochemistry |
P-substituted heavier group 14 analogues (Si, Ge, Sn, Pb) of diaminocarbenes are less established. It has been suggested this is due to a high energetic barrier associated with achieving a planar configuration at phosphorus, which would enable p(π)-p(π) overlap between the P lone pair and the empty p orbital of the group 14 center. Differences in donation ability of phosphorus versus nitrogen likely do not play a role in achieving p(π)-p(π) overlap because calculations indicate that the π donor capacity of phosphorus is similar to that of nitrogen. Consequently, all P atoms in reports on diphosphatetrylenes previous to ((Dipp)P)Ge contain pyramidal P with Ge-P bonds of exclusively σ character. By utilizing sterically encumbered (Dipp)P ligands, p(π)-p(π) in diphosphagermylene was achieved. This compound crystallizes as discrete monomers and is the first crystallographically characterized diphosphagermylene with a two-coordinate Ge center.
By crystal structure analysis, the bond lengths of the two germanium-phosphorus bonds are 2.2337 Å (P1-Ge) and 2.3823 Å (P2-Ge). While the phosphorus center of P1-Ge is pyramidal, the P2-Ge phosphorus is trigonal planar. Moreover, the planes of P1-Ge-P2 and C-P1-Ge are nearly in coincident. These results are consistent with multiple bond character between a trigonal planar phosphorus (P1) and Ge. It has been suggested that only one P of the diphosphagermylene is planar because there is competition between the two phosphorus lone pairs and the empty P orbitals at the Ge center if both phosphorus atoms are planar. This would result in a weaker P-Ge interaction that would not be sufficient to overcome the energy of planarizing both P atoms.
In addition, ((Dipp)P)Ge was modified such that an iPr groups was added to the para position of (Dipp)P, to make (Tripp)P. The donating effect of an additional iPr group has little effect on the bonding and structure of the diphosphagermylene. | 0 | Organic Chemistry |
When writing a Clar structure, the following rules must be satisfied:
#each vertex of the molecular graph representing the polycyclic aromatic hydrocarbon either belongs to a double bond or a circle;
# such double bonds and circles never join;
# there are no rings with three double bonds, since they are always represented by circles; moreover, the number of circles in the graph is maximized;
#when a ring with a circle is adjacent to a ring with two double bonds, an arrow is drawn from the former to the latter ring.
Some observations about these rules are worth to be put into evidence. Following Clar, rules at points 1 and 2 imply that circles can never be in adjacent rings; rule at point 3 means that only four options are viable for rings, namely (i) having only one double bond, (ii) having two double bonds, (iii) having a circle, or (iv) being empty, i.e. having no double bonds; finally, the arrow mentioned in the rule at point 4 can be interpreted in terms of mobility of π-sextets (in this case we speak of migrating π-sextets) or, equivalently, of a quantum-mechanical resonance between different Clar structures. | 7 | Physical Chemistry |
Another useful imaging mode is differential interference contrast (DIC), which is usually obtained with a system designed by the Polish physicist Georges Nomarski. This system gives the best detail. DIC converts minor height differences on the plane-of-polish, invisible in BF, into visible detail. The detail in some cases can be quite striking and very useful. If an ST filter is used along with a Wollaston prism, color is introduced. The colors are controlled by the adjustment of the Wollaston prism, and have no specific physical meaning, per se. But, visibility may be better. | 8 | Metallurgy |
Utilitarian objects; objects of personal adornment
#Casas Grandes, Chihuahua
#Chalchihuites, Zacatecas
#Hervideros, Durango
#La Quemada, Zacatecas
#Navocoyán, Durango
#Chihuahua, Chihuahua
#Schroeder site, Durango
#Venis Meicis, San Luis Potosí
#Zape, Durango
#Babicora, Chihuahua
#Rancho San Miguiel, Chihuahua
#Santa Maria R., Chihuahua | 8 | Metallurgy |
Biological activities of metal ion-binding compounds can be changed in response to the increment of the metal concentration, and based on the latter compounds can be classified as "metal ionophores", "metal chelators" or "metal shuttles". If the biological effect is augmented by increasing the metal concentration, it is classified as a "metal ionophore". If the biological effect is decreased or reversed by increasing the metal concentration, it is classified as a "metal chelator". If the biological effect is not affected by increasing the metal concentration, and the compound-metal complex enters the cell, it is classified as a "metal shuttle". The term ionophore (from Greek ion carrier or ion bearer) was proposed by Berton Pressman in 1967 when he and his colleagues were investigating the antibiotic mechanisms of valinomycin and nigericin.
Many ionophores are produced naturally by a variety of microbes, fungi and plants, and act as a defense against competing or pathogenic species. Multiple synthetic membrane-spanning ionophores have also been synthesized.
The two broad classifications of ionophores synthesized by microorganisms are:
*Carrier ionophores that bind to a particular ion and shield its charge from the surrounding environment. This makes it easier for the ion to pass through the hydrophobic interior of the lipid membrane. However, these ionophores become unable to transport ions under very low temperatures. An example of a carrier ionophore is valinomycin, a molecule that transports a single potassium cation. Carrier ionophores may be proteins or other molecules.
*Channel formers that introduce a hydrophilic pore into the membrane, allowing ions to pass through without coming into contact with the membrane's hydrophobic interior. Channel forming ionophores are usually large proteins. This type of ionophores can maintain their ability to transfer ions at low temperatures, unlike carrier ionophores. Examples of channel-forming ionophores are gramicidin A and nystatin.
Ionophores that transport hydrogen ions (H, i.e. protons) across the cell membrane are called protonophores. Iron ionophores and chelating agents are collectively called siderophores. | 7 | Physical Chemistry |
In organic chemistry, Nef synthesis is the addition of sodium acetylides to aldehydes and ketones to yield propargyl alcohols. It is named for John Ulric Nef, who discovered the reaction in 1899.
This process is often erroneously referred to as the Nef reaction, which is an unrelated chemical transformation discovered by the same chemist. | 0 | Organic Chemistry |
Jean Lynch-Stieglitz is a paleoceanographer known for her research on reconstructing changes in ocean circulation over the last 100,000 years. | 9 | Geochemistry |
Electrode potential appears at the interface between an electrode and electrolyte due to the transfer of charged species across the interface, specific adsorption of ions at the interface, and specific adsorption/orientation of polar molecules, including those of the solvent.
In an electrochemical cell, the cathode and the anode have certain electrode potentials independently and the difference between them is the cell potential:
The electrode potential may be either that at equilibrium at the working electrode ("reversible potential"), or a potential with a non-zero net reaction on the working electrode but zero net current ("corrosion potential", "mixed potential"), or a potential with a non-zero net current on the working electrode (like in galvanic corrosion or voltammetry). Reversible potentials can be sometimes converted to the standard electrode potential for a given electroactive species by extrapolation of the measured values to the standard state.
The value of the electrode potential under non-equilibrium depends on the nature and composition of the contacting phases, and on the kinetics of electrode reactions at the interface (see Butler–Volmer equation).
An operational assumption for determinations of the electrode potentials with the standard hydrogen electrode involves this reference electrode with hydrogen ion in an ideal solution having is "zero potential at all temperatures" equivalently to standard enthalpy of formation of hydrogen ion is also "zero at all temperatures". | 7 | Physical Chemistry |
When light leaves one material and enters another it bends, or refracts. The refractive index of a material is a measure of how much light bends when it enters. Differential refractometers contain a flow cell with two parts: one for the sample and one for the reference solvent. The detector measures the refractive index of both components. When only solvent is passing through the sample component the measured refractive index of both components is the same, but when an analyte passes through the flow cell the two measured refractive index are different. The difference appears as a peak in the chromatogram. | 3 | Analytical Chemistry |
Sirtuin-activating compounds (STAC) are chemical compounds having an effect on sirtuins, a group of enzymes that use NAD+ to remove acetyl groups from proteins. They are caloric restriction mimetic compounds that may be helpful in treating various aging-related diseases. | 1 | Biochemistry |
Defined by a cycle of transfers into and out of a system, a cyclic process is described by the quantities transferred in the several stages of the cycle. The descriptions of the staged states of the system may be of little or even no interest. A cycle is a sequence of a small number of thermodynamic processes that indefinitely often, repeatedly returns the system to its original state. For this, the staged states themselves are not necessarily described, because it is the transfers that are of interest. It is reasoned that if the cycle can be repeated indefinitely often, then it can be assumed that the states are recurrently unchanged. The condition of the system during the several staged processes may be of even less interest than is the precise nature of the recurrent states. If, however, the several staged processes are idealized and quasi-static, then the cycle is described by a path through a continuous progression of equilibrium states. | 7 | Physical Chemistry |
Several efficient techniques are available to detect the presence of distonic ions; the most appropriate method will depend on the ions internal energy and lifespan. Collisions between ions and uncharged molecules allow one to detect the location of the radical and charge site in order to confirm that the ion is not just a regular radical ion. When a molecule is ionized and can structurally be classified as a distonic ion, the molecules kinetics and thermodynamic properties have been greatly altered. However, additional chemical properties are based on the reactions of the central excited ions. Mass spectrometry techniques are used to study their chemistry. | 7 | Physical Chemistry |
Microdialysis is a minimally-invasive sampling technique that is used for continuous measurement of free, unbound analyte concentrations in the extracellular fluid of virtually any tissue. Analytes may include endogenous molecules (e.g. neurotransmitter, hormones, glucose, etc.) to assess their biochemical functions in the body, or exogenous compounds (e.g. pharmaceuticals) to determine their distribution within the body. The microdialysis technique requires the insertion of a small microdialysis catheter (also referred to as microdialysis probe) into the tissue of interest. The microdialysis probe is designed to mimic a blood capillary and consists of a shaft with a semipermeable hollow fiber membrane at its tip, which is connected to inlet and outlet tubing. The probe is continuously perfused with an aqueous solution (perfusate) that closely resembles the (ionic) composition of the surrounding tissue fluid at a low flow rate of approximately 0.1-5μL/min. Once inserted into the tissue or (body)fluid of interest, small solutes can cross the semipermeable membrane by passive diffusion. The direction of the analyte flow is determined by the respective concentration gradient and allows the usage of microdialysis probes as sampling as well as delivery tools. The solution leaving the probe (dialysate) is collected at certain time intervals for analysis. | 1 | Biochemistry |
The first models which tried to explain the clustering of genes were, of course, focused on operons because they were discovered before eukaryote gene clusters were. In 1999 Lawrence proposed a model for the origin operons. This selfish operon model suggests that individual genes were grouped together by vertical en horizontal transfer and were preserved as a single unit because that was beneficial for the genes, not per se for the organism. This model predicts that the gene clusters must have conserved between species. This is not the case for many operons and gene clusters seen in eukaryotes.
According to Eichler and Sankoff the two mean processes in eukaryotic chromosome evolution are 1) rearrangements of chromosomal segments and 2) localized duplication of genes. Clustering could be explained by reasoning that all genes in a cluster are originated from tandem duplicates of a common ancestor. If all co-expressed genes in a cluster were evolved from a common ancestral gene it would have been expected that theyre co-expressed because they all have comparable promoters. However, gene clustering is a very common tread in genomes and it isnt clear how this duplication model could explain all of the clustering. Furthermore, many genes that are present in clusters are not homologous.
How did evolutionary non-related genes come in close proximity in the first place? Either there is a force that brings functionally related genes near to each other, or the genes came near by change. Singer et al. proposed that genes came in close proximity by random recombination of genome segments. When functionally related genes came in close proximity to each other, this proximity was conserved. They determined all possible recombination sites between genes of human and mouse. After that, they compared the clustering of the mouse and human genome and looked if recombination had occurred at the potentially recombination sites. It turned out that recombination between genes of the same cluster was very rare. So, as soon as a functional cluster is formed recombination is suppressed by the cell. On sex chromosomes, the amount of clusters is very low in both human and mouse. The authors reasoned this was due to the low rate of chromosomal rearrangements of sex chromosomes.
Open chromatin regions are active regions. It is more likely that genes will be transferred to these regions. Genes from organelle and virus genome are inserted more often in these regions. In this way non-homologous genes can be pressed together in a small domain.
It is possible that some regions in the genome are better suited for important genes. It is important for the cell that genes that are responsible for basal functions are protected from recombination. It has been observed in yeast and worms that essential genes tend to cluster in regions with a small replication rate.
It is possible that genes came in close proximity by change. Other models have been proposed but none of them can explain all observed phenomena. It's clear that as soon as clusters are formed they are conserved by natural selection. However, a precise model of how genes came in close proximity is still lacking.
The bulk of the present clusters must have formed relatively recent because only seven clusters of functionally related genes are conserved between phyla. Some of these differences can be explained by the fact that gene expression is very differently regulated by different phyla. For example, in vertebrates and plants DNA methylation is used, whereas it is absent in yeast and flies. | 1 | Biochemistry |
Masahiro Ishiura, Takao Kondo, Susan S. Golden, Carl H. Johnson, and their colleagues discovered the gene cluster in 1998 and named the gene cluster kaiABC, as "kai" means “cycle” in Japanese. They generated 19 different clock mutants that were mapped to kaiA, kaiB, and kaiC genes, and successfully cloned the gene cluster in the cyanobacteria Synechococcus elongatus. Using a bacterial luciferase reporter to monitor the expression of clock-controlled gene psbAI in Synechococcus, they investigated and reported on the rescue to normal rhythmicity of long-period clock mutant C44a (with a period of 44 hours) by kaiABC. They inserted wild-type DNA through a pNIBB7942 plasmid vector into the C44a mutant, and generated clones that restored normal period (a period of 25 hours). They were eventually able to localize the gene region causing this rescue, and observed circadian rhythmicity in upstream promotor activity of kaiA and kaiB, as well as in the expression of kaiA and kaiBC messenger RNA. They determined abolishing any of the three kai genes would cause arrhythmicity in the circadian clock and reduce kaiBC promoter activity. KaiC was later found to have both autokinase and autophosphatase activity. These findings suggested that circadian rhythm was controlled by a TTFL mechanism, which is consistent with other known biological clocks.
In 2000, S. elongatus was observed in constant dark (DD) and constant light (LL). In DD, transcription and translation halted due to the absence of light but the circadian mechanism showed no significant phase shift after transitioning to constant light. In 2005, after closer examination of the KaiABC protein interactions, the phosphorylation of KaiC proved to oscillate with daily rhythms in the absence of light. In addition to the TTFL model, the PTO model was hypothesized for the KaiABC phosphorylation cycle.
Also in 2005, Nakajima et al. lysed S. elongatus and isolated KaiABC proteins. In test tubes containing only KaiABC proteins and ATP, in vitro phosphorylation of KaiC oscillated with a near 24 hour period with a slightly smaller amplitude than in vivo oscillation, proving that the KaiABC proteins are sufficient for circadian rhythm solely in the presence of ATP. Combined with the TTFL model, KaiABC as a circadian PTO was shown to be the fundamental clock regulator in S. elongatus | 1 | Biochemistry |
A bioeffector is a viable microorganism or active natural compound which directly or indirectly affects plant performance (biofertilizer), and thus has the potential to reduce fertilizer and pesticide use in crop production. | 1 | Biochemistry |
Solar cells share some of the same processing and manufacturing techniques as other semiconductor devices. However, the strict requirements for cleanliness and quality control of semiconductor fabrication are more relaxed for solar cells, lowering costs.
Polycrystalline silicon wafers are made by wire-sawing block-cast silicon ingots into 180 to 350 micrometer wafers. The wafers are usually lightly p-type-doped. A surface diffusion of n-type dopants is performed on the front side of the wafer. This forms a p–n junction a few hundred nanometers below the surface.
Anti-reflection coatings are then typically applied to increase the amount of light coupled into the solar cell. Silicon nitride has gradually replaced titanium dioxide as the preferred material, because of its excellent surface passivation qualities. It prevents carrier recombination at the cell surface. A layer several hundred nanometers thick is applied using plasma-enhanced chemical vapor deposition. Some solar cells have textured front surfaces that, like anti-reflection coatings, increase the amount of light reaching the wafer. Such surfaces were first applied to single-crystal silicon, followed by multicrystalline silicon somewhat later.
A full area metal contact is made on the back surface, and a grid-like metal contact made up of fine "fingers" and larger "bus bars" are screen-printed onto the front surface using a silver paste. This is an evolution of the so-called "wet" process for applying electrodes, first described in a US patent filed in 1981 by Bayer AG. The rear contact is formed by screen-printing a metal paste, typically aluminium. Usually this contact covers the entire rear, though some designs employ a grid pattern. The paste is then fired at several hundred degrees Celsius to form metal electrodes in ohmic contact with the silicon. Some companies use an additional electroplating step to increase efficiency. After the metal contacts are made, the solar cells are interconnected by flat wires or metal ribbons, and assembled into modules or "solar panels". Solar panels have a sheet of tempered glass on the front, and a polymer encapsulation on the back.
Different types of manufacturing and recycling partly determine how effective it is in decreasing emissions and having a positive environmental effect. Such differences and effectiveness could be quantified for production of the most optimal types of products for different purposes in different regions across time. | 7 | Physical Chemistry |
The Journal of Photochemistry was established in 1972 under founding editor-in-chief Richard P. Wayne. Originally published quarterly, by 1987 frequency had increased to monthly.
In 1986, the 38th Council of the American Society for Photobiology (ASP) established a committee to investigate the proposal that the European Society for Photobiology (ESP) share the operation of the ASP official journal, Photochemistry and Photobiology. In 1987, financial and contractual problems prevented agreement and, instead, ESP contracted with Elsevier, leading to the restructuring of the Journal of Photochemistry into two separate journals: the Journal of Photochemistry and Photobiology A: Chemistry, continuing under Richard P. Wayne and covering photochemistry and the Journal of Photochemistry and Photobiology B: Biology under founding editor Giulio Jori, covering photobiology.
The Journal of Photochemistry and Photobiology C: Photochemistry Reviews was first published in 2000 with Akira Fujishima as founding editor-in-chief. When the journal was first established, it aimed to increase from two issues a year to four, an objective achieved and maintained since 2003. | 5 | Photochemistry |
A finery forge is a forge used to produce wrought iron from pig iron by decarburization in a process called "fining" which involved liquifying cast iron in a fining hearth and removing carbon from the molten cast iron through oxidation. Finery forges were used as early as the 3rd century BC in China. The finery forge process was replaced by the puddling process and the roller mill, both developed by Henry Cort in 1783–4, but not becoming widespread until after 1800. | 8 | Metallurgy |
The sialic acid family includes many derivatives of the nine-carbon sugar neuraminic acid, but these acids rarely appear free in nature. Normally they can be found as components of oligosaccharide chains of mucins, glycoproteins and glycolipids occupying terminal, nonreducing positions of complex carbohydrates on both external and internal membrane areas where they are very exposed and develop important functions.
The numbering of the carbon atoms starts at the carboxylate carbon and continues along the chain. The configuration that places the carboxylate in the axial position is the alpha-anomer.
The alpha-anomer is the form that is found when sialic acid is bound to glycans. However, in solution, it is mainly (over 90%) in the beta-anomeric form. A bacterial enzyme with sialic acid mutarotase activity, NanM, that is able to rapidly equilibrate solutions of sialic acid to the resting equilibrium position of around 90% beta/10% alpha has been discovered.
In contrast to other animals, humans are genetically unable to produce the sialic acid variant N-glycolylneuraminic acid (Neu5Gc). Small amounts of Neu5Gc detected in human tissue however may be incorporated from exogenous (nutrient) sources. | 0 | Organic Chemistry |
In the detection sub-process location and property vectors are recorded to allow particle localization for ejection and material classification for discrimination purposes. All detection technologies applied have in common to be cheap, contactless and fast. The technologies are subdivided in transmitting and reflecting groups, the first measuring the inner content of a particle while the later only uses the surface reflection for discrimination. Surface, or reflection technologies have the disadvantage that the surfaces need to be representing the content, thus need to be clean from clay and dust adhesions. But by default surface reflection technologies violate the Fundamental Sampling Principle because not all components of a particle have the same probability of being detected.
The main transmitting technologies are EM (Electromagnetics) and XRT (X-ray-Transmission). EM detection is based on the conductivity of the material passing an alternating electromagnetic field. The principle of XRT is widely known through the application in medical diagnostics and airport luggage scanners. The main surface or reflection technologies are traditionally X-ray luminescence detectors capturing the fluorescence of diamonds under the excitation of X-ray radiation and color cameras detecting brightness and colour difference. Spectroscopic methods such as near-infrared spectroscopy known from remote sensing in exploration in mining for decades, have found their way into industrial scale sensor-based sorters. Advantage of the application of near-infrared spectroscopy is that the evidence can be measured on the presence of specific molecular bonds, thus minerals composition of the near-infrared active minerals. There is more detection technologies available on industrial scale sensor-based ore sorters. Readers that want to go into detail can find more in the literature. | 3 | Analytical Chemistry |
Biophotons may be detected with photomultipliers or by means of an ultra low noise CCD camera to produce an image, using an exposure time of typically 15 minutes for plant materials. Photomultiplier tubes have been used to measure biophoton emissions from fish eggs, and some applications have measured biophotons from animals and humans. Electron Multiplying CCD (EM-CCD) optimized for the detection of ultraweak light have also been used to detect the bioluminescence produced by yeast cells at the onset of their growth.
The typical observed radiant emittance of biological tissues in the visible and ultraviolet frequencies ranges from 10 to 10 W/cm with a photon count from a few to nearly 1000 photons per cm in the range of 200 nm to 800 nm. | 1 | Biochemistry |
Geometric dynamic recrystallization occurs in grains with local serrations. Upon deformation, grains undergoing GDRX elongate until the thickness of the grain falls below a threshold (below which the serration boundaries intersect and small grains pinch off into equiaxed grains). The serrations may predate stresses being exerted on the material, or may result from the material’s deformation.
Geometric Dynamic Recrystallization has 6 main characteristics:
* It generally occurs with deformation at elevated temperatures, in materials with high stacking fault energy
* Stress increases and then declines to a steady state
* Subgrain formation requires a critical deformation
* Subgrain misorientation peaks at 2˚
* There is little texture change
* Pinning of grain boundaries causes an increase in the required strain
While GDRX is primarily affected by the initial grain size and strain (geometry-dependent), other factors that occur during the hot working process complicate the development of predictive modeling (which tend to oversimplify the process) and can lead to incomplete recrystallization. The equiaxed grain formation does not occur immediately and uniformly along the entire grain once the threshold stress is reached, as individual regions are subjected to different strains/stresses. In practice, a generally sinusoidal edge (as predicted by Martorano et al.) gradually forms as the grains begin to pinch off as they each reach the threshold. More sophisticated models consider complex initial grain geometries, local pressures along grain boundaries, and hot working temperature, but the models are unable to make accurate predictions throughout the entire stress regime and the evolution of the overall microstructure. Additionally, grain boundaries may migrate during GDRX at high temperatures and GB curvatures, dragging along subgrain boundaries and resulting in unwanted growth of the original grain. This new, larger grain will require far more deformation for GDRX to occur, and the local area will be weaker rather than strengthened. Lastly, recrystallization can be accelerated as grains are shifted and stretched, causing subgrain boundaries to become grain boundaries (angle increases). The affected grains are thinner and longer, and thus more easily undergo deformation. | 8 | Metallurgy |
For liquid solutions, the osmotic coefficient is often used to calculate the salt activity coefficient from the solvent activity, or vice versa. For example, freezing point depression measurements, or measurements of deviations from ideality for other colligative properties, allows calculation of the salt activity coefficient through the osmotic coefficient. | 7 | Physical Chemistry |
The compatibility of two different metals may be predicted by consideration of their anodic index. This parameter is a measure of the electrochemical voltage that will be developed between the metal and gold. To find the relative voltage of a pair of metals it is only required to subtract their anodic indices.
To reduce galvanic corrosion for metals stored in normal environments such as storage in warehouses or non-temperature and humidity controlled environments, there should not be more than 0.25V difference in the anodic index of the two metals in contact. For controlled environments in which temperature and humidity are controlled, 0.50V can be tolerated. For harsh environments such as outdoors, high humidity, and salty environments, there should be not more than 0.15V difference in the anodic index. For example: gold and silver have a difference of 0.15V, therefore the two metals will not experience significant corrosion even in a harsh environment.
When design considerations require that dissimilar metals come in contact, the difference in anodic index is often managed by finishes and plating. The finishing and plating selected allow the dissimilar materials to be in contact, while protecting the more base materials from corrosion by the more noble. It will always be the metal with the most negative anodic index which will ultimately suffer from corrosion when galvanic incompatibility is in play. This is why sterling silver and stainless steel tableware should never be placed together in a dishwasher at the same time, as the steel items will likely experience corrosion by the end of the cycle (soap and water having served as the chemical electrolyte, and heat having accelerated the process). | 8 | Metallurgy |
In the hard sphere model, the particles are described as impenetrable spheres with radius ; thus, their center-to-center distance and they experience no interaction beyond this distance. Their interaction potential can be written as:
This model has an analytical solution in the Percus–Yevick approximation. Although highly simplified, it provides a good description for systems ranging from liquid metals to colloidal suspensions. In an illustration, the structure factor for a hard-sphere fluid is shown in the Figure, for volume fractions from 1% to 40%. | 3 | Analytical Chemistry |
DNA concentration and purification has been achieved directly from tar sands samples resuspended in buffer using the SCODA technique. DNA sequencing was subsequently performed and tentatively over 200 distinct bacterial genomes have been identified. SCODA has also been used for purification of DNA from many other environmental sources. | 1 | Biochemistry |
Lithium has a diffuse series with diffuse lines averaged around 6103.53, 4603.0, 4132.3, 3915.0 and 3794.7 Å. | 7 | Physical Chemistry |
Restriction fragment length polymorphism (RFLP) is considered to be the simplest and earliest method to detect SNPs. SNP-RFLP makes use of the many different restriction endonucleases and their high affinity to unique and specific restriction sites. By performing a digestion on a genomic sample and determining fragment lengths through a gel assay it is possible to ascertain whether or not the enzymes cut the expected restriction sites. A failure to cut the genomic sample results in an identifiably larger than expected fragment implying that there is a mutation at the point of the restriction site which is rendering it protection from nuclease activity.
The combined factors of the high complexity of most eukaryotic genomes, the requirement for specific endonucleases, the fact that the exact mutation cannot necessarily be resolved in a single experiment, and the slow nature of gel assays make RFLP a poor choice for high throughput analysis. | 1 | Biochemistry |
One route to thioesters involves the reaction of an acid chloride with an alkali metal salt of a thiol:
Another common route entails the displacement of halides by the alkali metal salt of a thiocarboxylic acid. For example, thioacetate esters are commonly prepared by alkylation of potassium thioacetate:
The analogous alkylation of an acetate salt is rarely practiced. The alkylation can be conducted using Mannich bases and the thiocarboxylic acid:
Thioesters can be prepared by condensation of thiols and carboxylic acids in the presence of dehydrating agents:
A typical dehydration agent is DCC. Efforts to improve the sustainability of thioester synthesis have also been reported utilising safer coupling reagent T3P and greener solvent cyclopentanone. Acid anhydrides and some lactones also give thioesters upon treatment with thiols in the presence of a base.
Thioesters can be conveniently prepared from alcohols by the Mitsunobu reaction, using thioacetic acid.
They also arise via carbonylation of alkynes and alkenes in the presence of thiols. | 0 | Organic Chemistry |
In genetics, an isochore is a large region of genomic DNA (greater than 300 kilobases) with a high degree of uniformity in GC content; that is, guanine (G) and cytosine (C) bases. The distribution of bases within a genome is non-random: different regions of the genome have different amounts of G-C base pairs, such that regions can be classified and identified by the proportion of G-C base pairs they contain.
Bernardi and colleagues first noticed the compositional non-uniformity of vertebrate genomes using thermal melting and density gradient centrifugation.
The DNA fragments extracted by the gradient centrifugation were later termed "isochores", which was subsequently defined as "very long (much greater than 200 KB) DNA segments" that "are fairly homogeneous in base composition and belong to a small number of major classes distinguished by differences in guanine-cytosine (GC) content". Subsequently, the isochores "grew" and were claimed to be ">300 kb in size."
The theory proposed that the isochore composition of genomes varies markedly between "warm-blooded" (homeotherm) vertebrates and "cold-blooded" (poikilotherm) vertebrates and later became known as the isochore theory. | 1 | Biochemistry |
One of the major goals of chemistry is the study of material transformations where chemical kinetics plays an important role. Scientists during the 19th century stated macroscopic chemical processes consist of many elementary chemical reactions that are themselves simply a series of encounters between atomic or molecular species. In order to understand the time dependence of chemical reactions, chemical kineticists have traditionally focused on sorting out all of the elementary chemical reactions involved in a macroscopic chemical process and determining their respective rates.
Swedish chemist Svante Arrhenius studied this phenomenon during the late 1880s, and stated the relations between reactive molecular encounters and rates of reactions (formulated in terms of activation energies).
Other scientists at the time also stated a chemical reaction is fundamentally a mechanical event, involving the rearrangement of atoms and molecules
during a collision. Although these initial theoretical studies were only qualitative, they heralded a new era in the field of chemical kinetics; allowing the prediction of the dynamical course of a chemical reaction.
In the 1950s, 1960s and 1970s, with the development of many sophisticated experimental techniques, it became possible to study the dynamics of elementary chemical reactions in the laboratory. Such as the analysis of the threshold operating conditions of a chemical laser or the spectra obtained using various linear or non-linear laser spectroscopic techniques.
Professors Lees research focused on the possibility to control the energies of the reagents, and to understand the dependence of chemical reactivity on molecular orientation, among other studies related to the nature of reaction intermediates, decay dynamics, and identifying complex reaction mechanisms. To do so, Professor Lee used a breakthrough laboratory technique at the time, called the "crossed molecular beams technique", where the information derived from the measurements of angular and velocity distributions allowed him and his team to understand the dynamics of elementary chemical reactions. | 7 | Physical Chemistry |
In animal communication, an alarm signal is an antipredator adaptation in the form of signals emitted by social animals in response to danger. Many primates and birds have elaborate alarm calls for warning conspecifics of approaching predators. For example, the alarm call of the blackbird is a familiar sound in many gardens. Other animals, like fish and insects, may use non-auditory signals, such as chemical messages. Visual signs such as the white tail flashes of many deer have been suggested as alarm signals; they are less likely to be received by conspecifics, so have tended to be treated as a signal to the predator instead.
Different calls may be used for predators on the ground or from the air. Often, the animals can tell which member of the group is making the call, so that they can disregard those of little reliability.
Evidently, alarm signals promote survival by allowing the receivers of the alarm to escape from the source of peril; this can evolve by kin selection, assuming the receivers are related to the signaller. However, alarm calls can increase individual fitness, for example by informing the predator it has been detected.
Alarm calls are often high-frequency sounds because these sounds are harder to localize. | 1 | Biochemistry |
In chemistry, axial chirality is a special case of chirality in which a molecule contains two pairs of chemical groups in a non-planar arrangement about an axis of chirality so that the molecule is not superposable on its mirror image. The axis of chirality (or chiral axis) is usually determined by a chemical bond that is constrained against free rotation either by steric hindrance of the groups, as in substituted biaryl compounds such as BINAP, or by torsional stiffness of the bonds, as in the C=C double bonds in allenes such as glutinic acid. Axial chirality is most commonly observed in substituted biaryl compounds wherein the rotation about the aryl–aryl bond is restricted so it results in chiral atropisomers, as in various ortho-substituted biphenyls, and in binaphthyls such as BINAP.
Axial chirality differs from central chirality (point chirality) in that axial chirality does not require a chiral center such as an asymmetric carbon atom, the most common form of chirality in organic compounds. Bonding to asymmetric carbon has the form Cabcd where a, b, c, and d must be distinct groups. Allenes have the form and the groups need not all be distinct as long as groups in each pair are distinct: abC=C=Cab is sufficient for the compound to be chiral, as in penta-2,3-dienedioic acid. Similarly, chiral atropisomers of the form may have some identical groups (), as in BINAP. | 4 | Stereochemistry |
In electrochemistry, protein film voltammetry (or protein film electrochemistry, or direct electrochemistry of proteins) is a technique for examining the behavior of proteins immobilized (either adsorbed or covalently attached) on an electrode. The technique is applicable to proteins and enzymes that engage in electron transfer reactions and it is part of the methods available to study enzyme kinetics.
Provided that it makes suitable contact with the electrode surface (electron transfer between the electrode and the protein is direct) and provided that it is not denatured, the protein can be fruitfully interrogated by monitoring current as a function of electrode potential and other experimental parameters.
Various electrode materials can be used. Special electrode designs are required to address membrane-bound proteins. | 7 | Physical Chemistry |
Energy expenditure is mainly a sum of internal heat produced and external work. The internal heat produced is, in turn, mainly a sum of basal metabolic rate (BMR) and the thermic effect of food. External work may be estimated by measuring the physical activity level (PAL). | 1 | Biochemistry |
Caustic embrittlement is the phenomenon in which the material of a boiler becomes brittle due to the accumulation of caustic substances. | 8 | Metallurgy |
Temperature plays a major role in the conversion of biomass to bio-oil. The temperature of the reaction determines the depolymerization of the biomass to bio-oil, as well as the repolymerization into char. While the ideal reaction temperature is dependent on the feedstock used, temperatures above ideal lead to an increase in char formation and eventually increased gas formation, while lower than ideal temperatures reduce depolymerization and overall product yields.
Similarly to temperature, the rate of heating plays a critical role in the production of the different phase streams, due to the prevalence of secondary reactions at non-optimum heating rates. Secondary reactions become dominant in heating rates that are too low, leading to the formation of char. While high heating rates are required to form liquid bio-oil, there is a threshold heating rate and temperature where liquid production is inhibited and gas production is favored in secondary reactions. | 0 | Organic Chemistry |
For superconductors the bosons involved are the so-called Cooper pairs which are quasiparticles formed by two electrons. Hence m = 2m and q = −2e where m and e are the mass of an electron and the elementary charge. It follows from Eq. () that
Integrating Eq. () over a closed loop gives
As in the case of helium we define the vortex strength
and use the general relation
where Φ is the magnetic flux enclosed by the loop. The so-called fluxoid is defined by
In general the values of κ and Φ depend on the choice of the loop. Due to the single-valued nature of the wave function and Eq. () the fluxoid is quantized
The unit of quantization is called the flux quantum
The flux quantum plays a very important role in superconductivity. The earth magnetic field is very small (about 50 μT), but it generates one flux quantum in an area of 6 μm by 6 μm. So, the flux quantum is very small. Yet it was measured to an accuracy of 9 digits as shown in Eq. (). Nowadays the value given by Eq. () is exact by definition.
In Fig. 3 two situations are depicted of superconducting rings in an external magnetic field. One case is a thick-walled ring and in the other case the ring is also thick-walled, but is interrupted by a weak link. In the latter case we will meet the famous Josephson relations. In both cases we consider a loop inside the material. In general a superconducting circulation current will flow in the material. The total magnetic flux in the loop is the sum of the applied flux Φ and the self-induced flux Φ induced by the circulation current | 7 | Physical Chemistry |
*Agricola, Georgius, 1556, Translation Hoover, Herbert, 1912, De re metallica, [http://farlang.com/books/agricola-hoover-de-re-metallica Farlang, full streaming version + scientific introduction]
*Craddock, P. T., 1989. Metalworking Techniques. In: Youngs, S. (ed), Work of Angels: Masterpieces of Celtic Metalwork, 6th-9th centuries AD, 170–213.
*Forbes, R. J., 1957. Metallurgy. In: Singer, C., Holmyard, E. J., Hall, A. R. & Williams, T. I. (eds), A History of Technology, vol. 2: The Mediterranean Civilizations and the Middle Ages c. 700 BC to AD 1500. Oxford: Clarendon Press, 41–80.
*Martinon-Torres, M. & Rehren, Th., in press (a). Metallurgy, Europe. In: Encyclopedia of Society and Culture in the Medieval World. Dallas: Schlager.
*Martinon-Torres, M. & Rehren, Th., in press (b). Mining, Europe. In: Encyclopedia of Society and Culture in the Medieval World. Dallas: Schlager.
*Smith, C.S. & Hawthorne, J.H., 1974. Mappae Clavicula, A little key to the world of medieval techniques. Transactions of American Philosophical Society 64 (4), 1–128.
*Theophilus, On Divers Arts: The foremost medieval treatise on Painting, Glassmaking and Metalwork. Hawthorne, J.G. & Smith, C.S. (trans), 1979. New York: Dover Publications. | 8 | Metallurgy |
As part of the Synthetic Yeast 2.0 project, various research groups around the world have participated in a project to synthesise synthetic yeast genomes, and through this process, optimise the genome of the model organism Saccharomyces cerevisiae. The Yeast 2.0 project applied various DNA assembly methods that have been discussed above, and in March 2014, Jef Boeke of the Langone Medical Centre at New York University, revealed that his team had synthesized chromosome III of S. cerevisiae. The procedure involved replacing the genes in the original chromosome with synthetic versions and the finished synthetic chromosome was then integrated into a yeast cell. It required designing and creating 273,871 base pairs of DNA – fewer than the 316,667 pairs in the original chromosome. In March 2017, the synthesis of 6 of the 16 chromosomes had been completed, with synthesis of the others still ongoing. | 1 | Biochemistry |
Generally, oral CoQ supplementation is well tolerated. The most common side effects are gastrointestinal symptoms (nausea, vomiting, appetite suppression, and abdominal pain), rashes, and headaches. Some adverse effects, largely gastrointestinal, are reported with intakes. Doses of 100-300 mg per day may induce insomnia or elevate liver enzymes. The observed safe level risk assessment method indicated that the evidence of safety is acceptable at intakes up to 1200 mg per day.
Use of CoQ supplementation is not recommended in people with liver or kidney disease, during pregnancy or breastfeeding, or in the elderly. | 1 | Biochemistry |
For the C. finmarchicus species specifically, the start of reproduction is linked to the start of the spring bloom. Thus, changes in the timing of the spring bloom would directly influence the reproductive capabilities of C. finmarchicus and alter the food chain from the bottom-up. However, the food chain could also be altered from the top-down through habitat disturbance and the removal of marine mammals and fish. Large-scale commercial fisheries exert top-down effects by lowering the abundance of larger species and increasing the amount of lipid-rich copepods and even paving way for other species to consume them. Under warming ocean conditions, prey switching is to be expected. Egg production and hatching success may also be affected with increasing sea surface temperatures and ocean acidification. | 9 | Geochemistry |
The clustered regularly interspaced short palindrome repeats (CRISPR)/Cas9 system is a gene-editing technology that can introduce double-strand breaks (DSBs) at a target genomic locus. By using a single guide RNA (sgRNA), the endonuclease Cas9 can be delivered to a specific DNA sequence where it cleaves the nucleotide chain. The specificity of the sgRNA is determined by a 20-nt sequence, homologous to the genomic locus of interest, and the binding to Cas9 is mediated by a constant scaffold region of the sgRNA. The desired target site must be immediately followed (5’ to 3’) by a conserved 3 nucleotide protospacer adjacent motif (PAM). In order to repair the DSBs, the cell may use the highly error prone non-homologous end joining, or homologous recombination. By designing suitable sgRNAs, planned insertions or deletions can be introduced into the genome. In the context of genome-wide LOF screens, the aim is to cause gene disruption and knockout. | 1 | Biochemistry |
When current varies, as it does in AC circuits,
where t is time and P is the instantaneous active power being converted from electrical energy to heat. Far more often, the average power is of more interest than the instantaneous power:
where "avg" denotes average (mean) over one or more cycles, and "rms" denotes root mean square.
These formulas are valid for an ideal resistor, with zero reactance. If the reactance is nonzero, the formulas are modified:
where is phase difference between current and voltage, means real part, Z is the complex impedance, and Y* is the complex conjugate of the admittance (equal to 1/Z*).
For more details in the reactive case, see AC power. | 7 | Physical Chemistry |
Sigma-2 receptors have been associated with pancreatic cancer, lung cancer, breast cancer, melanoma, prostate cancer, and ovarian cancer. Tumor cells are shown to over-express sigma-2 receptors, allowing for potential cancer therapies as many sigma-2 receptor mediated cell responses happen only in tumor cells. Tumor cell responses are modulated via ligand binding. Sigma receptor ligands can act as agonists or antagonists, generating different cellular responses. Agonists inhibit tumor cell proliferation and induce apoptosis, which is thought to be triggered by caspase-3 activity. Antagonists promote tumor cell proliferation, but this mechanism is less understood. Sigma receptor ligands have been conjugated to nanoparticles and peptides to deliver cancer treatment to tumor cells without targeting other tissues. The success with these methods have been limited to in vitro trials. Additionally, using sigma-2 receptors to target tumor cells allows for synergizing anti-cancer drug therapies. Some studies have shown that certain sigma receptor inhibitors increase cancer cells' susceptibility to chemotherapy. Other types of binding to sigma-2 receptors increases cytotoxicity of doxorubicin, antinomyocin, and other cancer cell killing drugs. | 1 | Biochemistry |
Emerin is a 29.0 kDa (34 kDa observed MW) protein composed of 254 amino acids. Emerin is a serine-rich protein with an N-terminal 20-amino acid hydrophobic region that is flanked by charged residues; the hydrophobic region may be important for anchoring the protein to the membrane, with the charged terminal tails being cytosolic. In cardiac, skeletal, and smooth muscle, emerin localizes to the inner nuclear membrane; expression of emerin is highest in skeletal and cardiac muscle. In cardiac muscle specifically, emerin also resides at adherens junctions within intercalated discs. | 1 | Biochemistry |
In organic chemistry, tolyl groups are functional groups related to toluene. They have the general formula , the change of the relative position of the methyl and the R substituent on the aromatic ring can generate three possible structural isomers 1,2 (ortho), 1,3 (meta), and 1,4 (para). Tolyl groups are aryl groups which are commonly found in the structure of diverse chemical compounds. They are considered nonpolar and hydrophobic groups.
The functionalization to include tolyl groups into compounds is often done by Williamson etherification, using tolyl alcohols as reagents, or by C-C coupling reactions. Tolyl sulfonates are excellent leaving groups in nucleophilic substitutions, for this reason, they are commonly generated as intermediaries to activate alcohols. To this end, 4-toluenesulfonyl chloride is reacted in the presence of a base with the corresponding alcohol. | 0 | Organic Chemistry |
1,3-diaxial strain is another form of strain similar to syn-pentane. In this case, the strain occurs due to steric interactions between a substituent of a cyclohexane ring (α) and gauche interactions between the alpha substituent and both methylene carbons two bonds away from the substituent in question (hence, 1,3-diaxial interactions). When the substituent is axial, it is brought near to an axial gamma hydrogen. The amount of strain is largely dependent on the size of the substituent and can be relieved by forming into the major chair conformation placing the substituent in an equatorial position. The difference in energy between conformations is called the A value and is well known for many different substituents. The A value is a thermodynamic parameter and was originally measured along with other methods using the Gibbs free energy equation and, for example, the Meerwein–Ponndorf–Verley reduction/Oppenauer oxidation equilibrium for the measurement of axial versus equatorial values of cyclohexanone/cyclohexanol (0.7 kcal mol). | 4 | Stereochemistry |
Many template reactions are only stoichiometric, and the decomplexation of the "templating ion" can be difficult. The alkali metal-templated syntheses of crown ether syntheses are notable exceptions. Metal Phthalocyanines are generated by metal-templated condensations of phthalonitriles, but the liberation of metal-free phthalocyanine is difficult.
Some so-called template reactions proceed similarly in the absence of the templating ion. One example being the condensation of acetone and ethylenediamine, which yields isomeric 14-membered tetraaza rings. Similarly, porphyrins, which feature 16-membered central rings, form in the absence of metal templates. | 7 | Physical Chemistry |
In 1932, it was reported that dinitrogen gas was generated via an unknown mechanism during fermentation in the sediments of Lake Mendota, Wisconsin, USA. In 1965, F. A. Richards noticed that most of the ammonium that should be produced during the anaerobic remineralization of organic matter was unaccounted for. As there was no known biological pathway for this transformation, biological anaerobic oxidation of ammonium received little further attention.
In 1977, Engelbert Broda predicted the existence of two chemolithoautotrophic microorganisms capable of oxidizing ammonium to dinitrogen gas on the basis of thermodynamic calculations. It was thought that anaerobic oxidation of ammonium would not be feasible, assuming that the predecessors had tried and failed to establish a biological basis for those reactions. By the 1990s, Arnold Mulders observations were just consistent with Richards suggestion. In their anoxic denitrifying pilot reactor, ammonium disappeared at the expense of nitrite with a clear nitrogen production. The reactor used the effluent from a methanogenic pilot reactor, which contained ammonium, sulphide and other compounds, and nitrate from a nitrifying plant as the influent. The process was named "anammox," and was realized to have great significance in the removal of unwanted ammonium.
The discovery of the anammox process was first publicly presented at the 5th European congress on biotechnology. By the mid-1990s, the discovery of anammox in the fluidized bed reactor was published. A maximum ammonium removal rate of 0.4 kg N/m/d was achieved. It was shown that for every mole of ammonium consumed, 0.6 mol of nitrate was required, resulting in the formation of 0.8 mol of gas.
In 1995, the biological nature of anammox was identified. Labeling experiments with in combination with showed that was the dominant product making up 98.2% of the total labeled . It was realized that, instead of nitrate, nitrite was assumed as the oxidizing agent of ammonium in anammox reaction. Based on a previous study, Strous et al. calculated the stoichiometry of anammox process by mass balancing, which is widely accepted by other groups. Later, anammox bacteria were identified as Planctomycetota, and the first identified anammox organism was named Candidatus "Brocadia anammoxidans."
Before 2002, anammox was assumed to be a minor player in the nitrogen cycle within natural ecosystems. In 2002 however, anammox was found to play an important part in the biological nitrogen cycle, accounting for 24–67% of the total production in the continental shelf sediments that were studied. The discovery of anammox process modified the concept of biological nitrogen cycle, as depicted in Figure 2. | 1 | Biochemistry |
In 1709, at Coalbrookdale in Shropshire, England, Abraham Darby began to fuel a blast furnace with coke instead of charcoal. Cokes initial advantage was its lower cost, mainly because making coke required much less labor than cutting trees and making charcoal, but using coke also overcame localized shortages of wood, especially in Britain and on the Continent. Metallurgical grade coke will bear heavier weight than charcoal, allowing larger furnaces. A disadvantage is that coke contains more impurities than charcoal, with sulfur being especially detrimental to the irons quality. Coke's impurities were more of a problem before hot blast reduced the amount of coke required and before furnace temperatures were hot enough to make slag from limestone free flowing. (Limestone ties up sulfur. Manganese may also be added to tie up sulfur.)
Coke iron was initially only used for foundry work, making pots and other cast iron goods. Foundry work was a minor branch of the industry, but Darbys son built a new furnace at nearby Horsehay, and began to supply the owners of finery forges with coke pig iron for the production of bar iron. Coke pig iron was by this time cheaper to produce than charcoal pig iron. The use of a coal-derived fuel in the iron industry was a key factor in the British Industrial Revolution. Darbys original blast furnace has been archaeologically excavated and can be seen in situ at Coalbrookdale, part of the Ironbridge Gorge Museums. Cast iron from the furnace was used to make girders for the world's first cast iron bridge in 1779. The Iron Bridge crosses the River Severn at Coalbrookdale and remains in use for pedestrians. | 8 | Metallurgy |
As RNA integrity has long been known to be a problem in molecular biology studies, there are a few methods that have been used historically to determine the integrity of RNA. The most popular has long been agarose gel electrophoresis with ethidium bromide staining, allowing one to visualize the bands from the rRNA peaks. The height of the 28S and 18S bands can be compared to each other, with a 2:1 ratio indicating non-degraded RNA. While this method is very cheap and easy, there are several issues with this method, primarily its subjectivity, leading to inconsistent, non-standardized RNA quality assessments, and the large amounts of RNA that are needed to visualize it on an agarose gel, which can be problematic if there is not much RNA to work with. There are also a number of different problems that can arise from agarose gel electrophoresis, such as poor loading, uneven running, and uneven staining that lead to increased variability in the accuracy of using agarose gel electrophoresis to determine RNA integrity.
The RNA Integrity Number was developed by Agilent Technologies in 2005. The algorithm was generated by taking hundreds of samples and having specialists manually assign them all a value of 1 to 10 based on their integrity, with 10 being the highest. Adaptive learning tools using a Bayesian learning technique were used to generate an algorithm that could predict the RIN, predominantly by using the features listed below under "Computation". This allows for all Agilent software to produce the same RIN for a given RNA sample, standardizing the measurement and making it much less subjective than earlier methods. | 1 | Biochemistry |
Sum frequency generation spectroscopy uses two laser beams mixed at an interface to generate an output beam with a frequency equal to the sum of the two input frequencies. Sum frequency generation spectroscopy is used to analyze surfaces and interfaces, carrying complementary information to infrared and Raman spectroscopy. | 7 | Physical Chemistry |
Rhee and Pugh introduce ChIP-exo by performing analyses on a small collection of transcription factors: Reb1, Gal4, Phd1, Rap1 in yeast and CTCF in human. Reb1 sites were often found in clusters and these clusters had ~10-fold higher occupancy than expected. Secondary sites in clusters were found ~40 bp from a primary binding site. Binding motifs of Gal4 showed a strong preference for three of the four nucleotides, suggesting a negative interaction between Gal4 and the excluded nucleotide. Phd1 recognizes three different motifs which explains previous reports of the ambiguity of Phd1's binding motif. Rap1 was found to recognize four motifs.
Ribosomal protein genes bound by this protein had a tendency to use a particular motif with a stronger consensus sequence. Other genes often used clusters of weaker consensus motifs, possibly to achieve a similar occupancy. Binding motifs of CTCF employed four "modules". Half of the bound CTCF sites used modules 1 and 2, while the rest used some combination of the four. It is believed that CTCF uses its zinc fingers to recognize different combinations of these modules.
Rhee and Pugh analyzed pre-initiation complex (PIC) structure and organization in Saccharomyces genomes. Using ChIP-exo, they were able to, among other discoveries, precisely identify TATA-like features in promoters reported to be TATA-less. | 1 | Biochemistry |
The structure of eukaryotic genes includes features not found in prokaryotes. Most of these relate to post-transcriptional modification of pre-mRNAs to produce mature mRNA ready for translation into protein. Eukaryotic genes typically have more regulatory elements to control gene expression compared to prokaryotes. This is particularly true in multicellular eukaryotes, humans for example, where gene expression varies widely among different tissues.
A key feature of the structure of eukaryotic genes is that their transcripts are typically subdivided into exon and intron regions. Exon regions are retained in the final mature mRNA molecule, while intron regions are spliced out (excised) during post-transcriptional processing. Indeed, the intron regions of a gene can be considerably longer than the exon regions. Once spliced together, the exons form a single continuous protein-coding regions, and the splice boundaries are not detectable. Eukaryotic post-transcriptional processing also adds a 5' cap to the start of the mRNA and a poly-adenosine tail to the end of the mRNA. These additions stabilise the mRNA and direct its transport from the nucleus to the cytoplasm, although neither of these features are directly encoded in the structure of a gene. | 1 | Biochemistry |
Salbutamol has been studied in subtypes of congenital myasthenic syndrome associated with mutations in Dok-7.
It has also been tested in a trial aimed at treatment of spinal muscular atrophy; it is speculated to modulate the alternative splicing of the SMN2 gene, increasing the amount of the SMN protein, the deficiency of which is regarded as a cause of the disease.
Albuterol increases energy expenditure by 10-15 percent at a therapeutic dose for asthma and around 25 percent at a higher, oral dose. In several human studies, albuterol increased lean body mass, reduced fat mass, and caused lipolysis; it has been studied for use as an anti-obesity and anti-muscle wasting medication when taken orally. | 4 | Stereochemistry |
The Chemical Weapons Act 1996 was passed in the UK during the time of a Conservative government under John Major. It was adopted on the 03/04/1996 and came into force in 16/09/1996. This act was made so that the UK could be compliant with the 1993 Convention on the Prohibition of the Development, Production, Stockpiling and Use of Chemical Weapons and their Destruction. Not only that, but it also creates the criminal offence of producing, developing, handling or transferring chemical weapons. This act gives Britain extra territorial jurisdiction in regard to British nationals who are handling such material. This act also applies to Isle of Man, Guernsey and to Jersey. The department of trade and industry acts as a liaison between the UK and the Organisation for the Prohibition of Chemical Weapons.
The general interpretation of chemical weapons according to this act is as follows:
# "Toxic chemicals and their precursors"
# "Munitions and other devices designed to cause death or harm through the toxic properties of toxic chemicals released by them"
# And finally- "equipment designed for use in connection with munitions and devices falling within paragraph (b)"
Yet there are some exceptions to these rules. For example: the chemical weapons can be used for "peaceful purposes", "purposes related to protection against toxic chemicals", "legitimate military purposes" and "purposes of enforcing the law".
"Legitimate military purposes" are described as being military purposes, which do not cause harm to people, animals or otherwise harm them.
Section 33 of the Chemical Weapon's act requires The secretary of State to prepare a document on the operation of this act and present it to Parliament annually. | 1 | Biochemistry |
Dissolved organic matter is a heterogeneous pool of thousands, likely millions, of organic compounds. These compounds differ not only in composition and concentration (from pM to μM), but also originate from various organisms (phytoplankton, zooplankton, and bacteria) and environments (terrestrial vegetation and soils, coastal fringe ecosystems) and may have been produced recently or thousands of years ago. Moreover, even organic compounds deriving from the same source and of the same age may have been subjected to different processing histories prior to accumulating within the same pool of DOM.
Interior ocean DOM is a highly modified fraction that remains after years of exposure to sunlight, utilization by heterotrophs, flocculation and coagulation, and interaction with particles. Many of these processes within the DOM pool are compound- or class-specific. For example, condensed aromatic compounds are highly photosensitive, whereas proteins, carbohydrates, and their monomers are readily taken up by bacteria. Microbes and other consumers are selective in the type of DOM they utilize and typically prefer certain organic compounds over others. Consequently, DOM becomes less reactive as it is continually reworked. Said another way, the DOM pool becomes less labile and more refractory with degradation. As it is reworked, organic compounds are continually being added to the bulk DOM pool by physical mixing, exchange with particles, and/or production of organic molecules by the consumer community. As such, the compositional changes that occur during degradation are more complex than the simple removal of more labile components and resultant accumulation of remaining, less labile compounds.
Dissolved organic matter recalcitrance (i.e., its overall reactivity toward degradation and/or utilization) is therefore an emergent property. The perception of DOM recalcitrance changes during organic matter degradation and in conjunction with any other process that removes or adds organic compounds to the DOM pool under consideration.
The surprising resistance of high concentrations of DOC to microbial degradation has been addressed by several hypotheses. The prevalent notion is that the recalcitrant fraction of DOC has certain chemical properties, which prevent decomposition by microbes ("intrinsic stability hypothesis"). An alternative or additional explanation is given by the "dilution hypothesis", that all compounds are labile, but exist in concentrations individually too low to sustain microbial populations but collectively form a large pool. The dilution hypothesis has found support in recent experimental and theoretical studies. | 2 | Environmental Chemistry |
Values of Henrys law constants for aqueous solutions depend on the composition of the solution, i.e., on its ionic strength and on dissolved organics. In general, the solubility of a gas decreases with increasing salinity ("salting out"). However, a "salting in" effect has also been observed, for example for the effective Henrys law constant of glyoxal. The effect can be described with the Sechenov equation, named after the Russian physiologist Ivan Sechenov (sometimes the German transliteration "Setschenow" of the Cyrillic name Се́ченов is used). There are many alternative ways to define the Sechenov equation, depending on how the aqueous-phase composition is described (based on concentration, molality, or molar fraction) and which variant of the Henry's law constant is used. Describing the solution in terms of molality is preferred because molality is invariant to temperature and to the addition of dry salt to the solution. Thus, the Sechenov equation can be written as
where is the Henrys law constant in pure water, is the Henrys law constant in the salt solution, is the molality-based Sechenov constant, and is the molality of the salt. | 7 | Physical Chemistry |
The history of thermodynamics as a scientific discipline generally begins with Otto von Guericke who, in 1650, built and designed the worlds first vacuum pump and demonstrated a vacuum using his Magdeburg hemispheres. Guericke was driven to make a vacuum in order to disprove Aristotles long-held supposition that nature abhors a vacuum. Shortly after Guericke, the Anglo-Irish physicist and chemist Robert Boyle had learned of Guerickes designs and, in 1656, in coordination with English scientist Robert Hooke, built an air pump. Using this pump, Boyle and Hooke noticed a correlation between pressure, temperature, and volume. In time, Boyles Law was formulated, which states that pressure and volume are inversely proportional. Then, in 1679, based on these concepts, an associate of Boyle's named Denis Papin built a steam digester, which was a closed vessel with a tightly fitting lid that confined steam until a high pressure was generated.
Later designs implemented a steam release valve that kept the machine from exploding. By watching the valve rhythmically move up and down, Papin conceived of the idea of a piston and a cylinder engine. He did not, however, follow through with his design. Nevertheless, in 1697, based on Papin's designs, engineer Thomas Savery built the first engine, followed by Thomas Newcomen in 1712. Although these early engines were crude and inefficient, they attracted the attention of the leading scientists of the time.
The fundamental concepts of heat capacity and latent heat, which were necessary for the development of thermodynamics, were developed by Professor Joseph Black at the University of Glasgow, where James Watt was employed as an instrument maker. Black and Watt performed experiments together, but it was Watt who conceived the idea of the external condenser which resulted in a large increase in steam engine efficiency. Drawing on all the previous work led Sadi Carnot, the "father of thermodynamics", to publish Reflections on the Motive Power of Fire (1824), a discourse on heat, power, energy and engine efficiency. The book outlined the basic energetic relations between the Carnot engine, the Carnot cycle, and motive power. It marked the start of thermodynamics as a modern science.
The first thermodynamic textbook was written in 1859 by William Rankine, originally trained as a physicist and a civil and mechanical engineering professor at the University of Glasgow. The first and second laws of thermodynamics emerged simultaneously in the 1850s, primarily out of the works of William Rankine, Rudolf Clausius, and William Thomson (Lord Kelvin).
The foundations of statistical thermodynamics were set out by physicists such as James Clerk Maxwell, Ludwig Boltzmann, Max Planck, Rudolf Clausius and J. Willard Gibbs.
Clausius, who first stated the basic ideas of the second law in his paper "On the Moving Force of Heat", published in 1850, and is called "one of the founding fathers of thermodynamics", introduced the concept of entropy in 1865.
During the years 1873–76 the American mathematical physicist Josiah Willard Gibbs published a series of three papers, the most famous being On the Equilibrium of Heterogeneous Substances, in which he showed how thermodynamic processes, including chemical reactions, could be graphically analyzed, by studying the energy, entropy, volume, temperature and pressure of the thermodynamic system in such a manner, one can determine if a process would occur spontaneously. Also Pierre Duhem in the 19th century wrote about chemical thermodynamics. During the early 20th century, chemists such as Gilbert N. Lewis, Merle Randall, and E. A. Guggenheim applied the mathematical methods of Gibbs to the analysis of chemical processes. | 7 | Physical Chemistry |
Process analysis initially involved sampling the variety of process streams or webs and transporting samples to quality control or central analytical service laboratories. Time delays for analytical results due to sample transport and analytical preparation steps negated the value of many chemical analyses for purposes other than product release. Over time it was understood that real-time measurements provided timely information about a process, which was far more useful for high efficiency and quality. The development of real-time process analysis has provided information for process optimization during any manufacturing process. The journal Analytical Chemistry (journal) publishes a biennial review of the most recent developments in the field.
The first real-time measurements in a production environment were made with modified laboratory instrumentation; in recent times specialized process and handheld instrumentation has been developed for immediate analysis. | 7 | Physical Chemistry |
dPCR rose out of an approach first published in 1988 by Cetus Corporation when researchers showed that a single copy of the β-globin gene could be detected and amplified by PCR. This was achieved by diluting DNA samples from a normal human cell line with DNA from a mutant line having a homozygous deletion of the β-globin gene, until it was no longer present in the reaction. In 1989, Peter Simmonds, AJ Brown et al. used this concept to quantify a molecule for the first time. Alex Morley and Pamela Sykes formally established the method as a quantitative technique in 1992.
In 1999, Bert Vogelstein and Kenneth Kinzler coined the term “digital PCR” and showed that the technique could be used to find rare cancer mutations. However, dPCR was difficult to perform; it was labor intensive, required a lot of training to do properly, and was difficult to do in large quantities. In 2003, Kinzler and Vogelstein continued to refine dPCR and created an improved method that they called BEAMing technology, an acronym for “beads, emulsion, amplification and magnetics.” The new protocol used emulsion to compartmentalize amplification reactions in a single tube. This change made it possible for scientists to scale the method to thousands of reactions in a single run.
Companies developing commercial dPCR systems have integrated technologies like automated partitioning of samples, digital counting of nucleic acid targets, and increasing droplet count that can help the process be more efficient. In recent years, scientists have developed and commercialized dPCR-based diagnostics for several conditions, including non-small cell lung cancer and Down’s Syndrome. The first dPCR system for clinical use was CE-marked in 2017 and cleared by the US Food and Drug Administration in 2019, for diagnosing chronic myeloid leukemia. | 1 | Biochemistry |
Like methane itself, halomethanes are tetrahedral molecules. The halogen atoms differ greatly in size and charge from hydrogen and from each other. Consequently, most halomethanes deviate from the perfect tetrahedral symmetry of methane.
The physical properties of halomethanes depend on the number and identity of the halogen atoms in the compound. In general, halomethanes are volatile but less so than methane because of the polarizability of the halides. The polarizability of the halides and the polarity of the molecules makes them useful as solvents. The halomethanes are far less flammable than methane. Broadly speaking, reactivity of the compounds is greatest for the iodides and lowest for the fluorides. | 2 | Environmental Chemistry |
The northern blot is used to study the presence of specific RNA molecules as relative comparison among a set of different samples of RNA. It is essentially a combination of denaturing RNA gel electrophoresis, and a blot. In this process RNA is separated based on size and is then transferred to a membrane that is then probed with a labeled complement of a sequence of interest. The results may be visualized through a variety of ways depending on the label used; however, most result in the revelation of bands representing the sizes of the RNA detected in sample. The intensity of these bands is related to the amount of the target RNA in the samples analyzed. The procedure is commonly used to study when and how much gene expression is occurring by measuring how much of that RNA is present in different samples, assuming that no post-transcriptional regulation occurs and that the levels of mRNA reflect proportional levels of the corresponding protein being produced. It is one of the most basic tools for determining at what time, and under what conditions, certain genes are expressed in living tissues. | 1 | Biochemistry |
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