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The internal heating within stars is so great that (after an initial phase of gravitational contraction) they ignite and sustain thermonuclear reaction of hydrogen (with itself) to form helium, and can make heavier elements (see Stellar nucleosynthesis). The Sun for example has a core temperature of 13,600,000 K. The more massive and older the stars are, the more internal heating they have. During the end of its lifecycle, the internal heating of a star increases dramatically, caused by the change of composition of the core as successive fuels for fusion are consumed, and the resulting contraction (accompanied by faster consumption of the remaining fuel). Depending upon the mass of the star, the core may become hot enough to fuse helium (forming carbon and oxygen and traces of heavier elements), and for sufficiently massive stars even large quantities of heavier elements. Fusion to produce elements heavier than iron and nickel no longer produces energy, and since stellar cores massive enough to attain the temperatures required to produce these elements are too massive to form stable white dwarf stars, a core collapse supernova results, producing a neutron star or a black hole, depending upon the mass. Heat generated by the collapse is trapped within a neutron star and only escapes slowly, due to the small surface area; heat cannot be conducted out of a black hole at all (however, see Hawking radiation). | 7 | Physical Chemistry |
TERRA in biology is an abbreviation for "TElomeric Repeat-containing RNA". TERRA is RNA that is transcribed from telomeres — the repeating 6-nucleotide sequences that cap the ends of chromosomes. TERRA functions with shelterin to inhibit telomere lengthening by enzyme telomerase. However, other studies have shown that under certain conditions TERRA can recruit telomerase to telomeres.
TERRAs are essential for telomere length and maintenance. At least four factors contribute to telomere maintenance: telomerase, shelterin, TERRA and the CST Complex.
TERRA can also regulate telomere length by increasing euchromatin formation. On the other hand, nonsense-mediated decay factor enrichment at telomeres may exist to prevent TERRA inhibition of telomerase. TERRA levels vary during the cell cycle, decreasing during S phase, and increasing in the transition from G2 phase to G1 phase. | 1 | Biochemistry |
The question of how long a tunneling particle spends inside the barrier region has remained unresolved since the early days of quantum mechanics. It is sometimes suggested that the tunneling time is instantaneous because both the Keldysh and the closely related Buttiker-Landauer times are imaginary (corresponding to the decay of the wavefunction under the barrier). In a recent publication the main competing theories of tunneling time are compared against experimental measurements using the attoclock in strong laser field ionization of helium atoms. Refined attoclock measurements reveal a real and not instantaneous tunneling delay time over a large intensity regime. It is found that the experimental results are compatible with the probability distribution of tunneling times constructed using a Feynman path integral (FPI) formulation. However, later work in atomic hydrogen has demonstrated that most of the tunneling time measured in the experiment is purely from the long-range Coulomb force exerted by the ion core on the outgoing electron. | 7 | Physical Chemistry |
This hypothesis originated in a 1964 paper by Paul Ehrlich and Peter Raven, "Butterflies and plants: a study in coevolution". While this paper outlined the concept, the actual term "escape and radiate" was not actually coined until 1989 by John N. Thompson. The theory has been highly influential in chemical ecology and plant evolutionary ecology, but remains controversial due to the difficulty of collecting decisive evidence as well as uncertainty about the mechanisms linking ecological escape with evolutionary diversification. | 1 | Biochemistry |
As with all flavonoids, anthoxanthins have antioxidant properties and are important for nutrition. They are sometimes used as food additives to add color or flavor to foods. One of the most well-known anthoxanthins is quercetin, which is found in many fruits and vegetables, including capers, red onions, and kale.
In addition to their use as food additives, anthoxanthins are also used in the production of dyes and pigments. Anthoxanthins can also be used to create yellow, orange, or red dyes for use in textiles, cosmetics, and other products. | 2 | Environmental Chemistry |
A semiochemical, from the Greek σημεῖον (semeion), meaning "signal", is a chemical substance or mixture released by an organism that affects the behaviors of other individuals. Semiochemical communication can be divided into two broad classes: communication between individuals of the same species (intraspecific) or communication between different species (interspecific).
It is usually used in the field of chemical ecology to encompass pheromones, allomones, kairomones, attractants and repellents.
Many insects, including parasitic insects, use semiochemicals. Pheromones are intraspecific signals that aid in finding mates, food and habitat resources, warning of enemies, and avoiding competition. Interspecific signals known as allomones and kairomones have similar functions. | 1 | Biochemistry |
Hot filtration can be used to separate "compound A" from both "impurity B" and some "insoluble matter C". This technique normally uses a single-solvent system as described above. When both "compound A" and "impurity B" are dissolved in the minimum amount of hot solvent, the solution is filtered to remove "insoluble matter C". This matter may be anything from a third impurity compound to fragments of broken glass. For a successful procedure, one must ensure that the filtration apparatus is hot in order to stop the dissolved compounds from crystallizing from the solution during filtration, thus forming crystals on the filter paper or funnel.
One way to achieve this is to heat a conical flask containing a small amount of clean solvent on a hot plate. A filter funnel is rested on the mouth, and hot solvent vapors keep the stem warm. Jacketed filter funnels may also be used. The filter paper is preferably fluted, rather than folded into a quarter; this allows quicker filtration, thus less opportunity for the desired compound to cool and crystallize from the solution.
Often it is simpler to do the filtration and recrystallization as two independent and separate steps. That is dissolve "compound A" and "impurity B" in a suitable solvent at room temperature, filter (to remove insoluble compound/glass), remove the solvent and then recrystallize using any of the methods listed above. | 3 | Analytical Chemistry |
The economic importance of ultrapotassic rocks is wide and varied. Because kimberlites, lamproites and lamprophyres are all produced at depths of 120 km or greater, they are known to be a major source of diamond deposits and thus can bring diamonds to the surface as xenocrysts. Additionally, ultrapotassic granites are a known host for granite-hosted gold mineralization and well as significant porphyry-style mineralization. Ultrapotassic A-type intracontinental granites may also be associated with fluorite and columbite – tantalite mineralization. | 9 | Geochemistry |
RecA recombinase appears to be universally present in bacteria. RecA has multiple functions, all related to DNA repair. RecA has a central role in the repair of replication forks stalled by DNA damage and in the bacterial sexual process of natural genetic transformation. | 1 | Biochemistry |
Bottromycin is produced naturally as a series of products differing in methylation patterns. All products contain valine and phenylalanine methylation. Bottromycin A2 is singly methylated on proline, bottromycin B lacks methylation on proline, and bottromycin C contains a doubly methylated proline.
A partial structure of bottromycin was reported shortly after the initial discovery of bottromycin. The first structural studies relied on traditional methods of analysis. Its peptide-like structure, including the presence of glycine and valine, was first suggested by a combination of acidic hydrolysis, acetylation, ninhydrin staining, and paper chromatography, among other experiments. The presence of a thiazole ring, along with an adjacent β-methylated phenylalanine, was established by ninhydrin staining, potassium permanganate oxidation, and comparison to synthetic standards. A methyl ester substituent was reported in 1958. The same study also reported that the Kunz hydrolysis product lacking a methyl ester was biologically inactive. Nakamura and colleagues later reported that bottromycin contained tert-leucine and cis-3-methylproline. They also proposed a linear iminohexapeptide structure.
These early structural studies were not followed up until recent years with the renewed interest in bottromycin. The structure was confirmed in the 1980s and 1990s to be a cyclic iminopeptide based on NMR studies, with a linear side chain connected to the macrocycle via an amidine linkage.
Its absolute stereochemistry, however, was not characterized until 2009. Stereochemistry at carbon 18 and 25 was proposed by comparing predicted conformers obtained using molecular dynamics to experimental constraints obtained through NMR experiments. Stereochemistry at carbon 43 was confirmed by comparing H NMR of authentic hydrolysis product to a chemically synthesized sample of the same fragment. Finally, optical rotation, H NMR, and HRMS experiments of chemically synthesized bottromycin matched that of biologically produced bottromycin.
The three-dimensional solution structure of bottromycin A2 was solved by NMR in 2012. The overall structure was obtained with good resolution (RMSD 0.74±0.59 Å), with a RMSD of 0.09±0.06 Å for the macrocycle. In this study, it was proposed that the methylated proline residue contributed to the restricted conformation of the macrocycle. The methylated proline and β-OMe alanine residues were found to be on the same face of bottroymycin A2 and it was suggested that this characteristic contributed to binding of bottromycin to the ribosomal A site. | 0 | Organic Chemistry |
Preferential amplification is over-amplification of one of the alleles in comparison to the other. Most studies on MDA have reported this issue. The amplification bias is currently observed to be random. It might affect the analysis of small stretches of genomic DNA in identifying Short Tandem Repeats (STR) alleles. | 1 | Biochemistry |
UV-sensitive syndrome is a cutaneous condition inherited in an autosomal recessive fashion, characterized by photosensitivity and solar lentigines. Recent research identified that mutations of the KIAA1530 (UVSSA) gene as cause for the development of UV-sensitive syndrome. Furthermore, this protein was identified as a new player in the Transcription-coupled repair (TC-NER). | 5 | Photochemistry |
Ellipsometry is an indirect method, i.e. in general the measured and cannot be converted directly into the optical constants of the sample. Normally, a model analysis must be performed, for example the Forouhi Bloomer model. This is one weakness of ellipsometry. Models can be physically based on energy transitions or simply free parameters used to fit the data.
Direct inversion of and is only possible in very simple cases of isotropic, homogeneous and infinitely thick films. In all other cases a layer model must be established, which considers the optical constants (refractive index or dielectric function tensor) and thickness parameters of all individual layers of the sample including the correct layer sequence. Using an iterative procedure (least-squares minimization) unknown optical constants and/or thickness parameters are varied, and and values are calculated using the Fresnel equations. The calculated and values which match the experimental data best provide the optical constants and thickness parameters of the sample. | 7 | Physical Chemistry |
The SCODA DNA force results in the DNA sample concentrating in the center of the SCODA gel. To extract the DNA an extraction well can be pre-formed in the gel and filled with buffer. As the DNA does not experience non-linear mobility in buffer it accumulates in the extraction well. At the end of the concentration and purification stage the sample can then be pipetted out from this well. | 1 | Biochemistry |
*A helper strain, carrying a conjugative plasmid (such as the F-plasmid) that codes for genes required for conjugation and DNA transfer.
*A donor strain, carrying a mobilizable plasmid that can utilize the transfer functions of the conjugative plasmid.
*A recipient strain, you wish to introduce the mobilizable plasmid into.
Five to seven days are required to determine if the
plasmid was successfully introduced into the new bacterial
strain and confirm that there is no carryover of the helper or
donor strain.
In contrast, electroporation does not require a helper or
donor strain. This helps
avoid possible contamination with other strains. The introduction
of the plasmid can be verified in the recipient
strain in two days, making electroporation a faster and
more efficient method of transformation. Electroporation however does not work with all bacteria and is mostly limited to well-characterized model organisms. | 1 | Biochemistry |
;Grahams law: This law states that the rate at which gas molecules diffuse is inversely proportional to the square root of the gas density at a constant temperature. Combined with Avogadros law (i.e. since equal volumes have an equal number of molecules) this is the same as being inversely proportional to the root of the molecular weight.
;Daltons law of partial pressures: This law states that the pressure of a mixture of gases simply is the sum of the partial pressures of the individual components. Daltons law is as follows:
:and all component gases and the mixture are at the same temperature and volume
:where P is the total pressure of the gas mixture
:P is the partial pressure or pressure of the component gas at the given volume and temperature.
;Amagats law of partial volumes: This law states that the volume of a mixture of gases (or the volume of the container) simply is the sum of the partial volumes of the individual components. Amagats law is as follows:
:and all component gases and the mixture are at the same temperature and pressure
:where V is the total volume of the gas mixture or the volume of the container,
:V is the partial volume, or volume of the component gas at the given pressure and temperature.
;Henry's law: This states that at constant temperature, the amount of a given gas dissolved in a given type and volume of liquid is directly proportional to the partial pressure of that gas in equilibrium with that liquid. The equation is as follows:
;Real gas law: This was formulated by Johannes Diderik van der Waals in 1873. | 7 | Physical Chemistry |
Emulsion stability refers to the ability of an emulsion to resist change in its properties over time. There are four types of instability in emulsions: flocculation, coalescence, creaming/sedimentation, and Ostwald ripening. Flocculation occurs when there is an attractive force between the droplets, so they form flocs, like bunches of grapes. This process can be desired, if controlled in its extent, to tune physical properties of emulsions such as their flow behaviour. Coalescence occurs when droplets bump into each other and combine to form a larger droplet, so the average droplet size increases over time. Emulsions can also undergo creaming, where the droplets rise to the top of the emulsion under the influence of buoyancy, or under the influence of the centripetal force induced when a centrifuge is used. Creaming is a common phenomenon in dairy and non-dairy beverages (i.e. milk, coffee milk, almond milk, soy milk) and usually does not change the droplet size. Sedimentation is the opposite phenomenon of creaming and normally observed in water-in-oil emulsions. Sedimentation happens when the dispersed phase is denser than the continuous phase and the gravitational forces pull the denser globules towards the bottom of the emulsion. Similar to creaming, sedimentation follows Stokes' law.
An appropriate surface active agent (or surfactant) can increase the kinetic stability of an emulsion so that the size of the droplets does not change significantly with time. The stability of an emulsion, like a suspension, can be studied in terms of zeta potential, which indicates the repulsion between droplets or particles. If the size and dispersion of droplets does not change over time, it is said to be stable. For example, oil-in-water emulsions containing mono- and diglycerides and milk protein as surfactant showed that stable oil droplet size over 28 days storage at 25 °C. | 7 | Physical Chemistry |
In chemistry, the law of mass action is the proposition that the rate of a chemical reaction is directly proportional to the product of the activities or concentrations of the reactants. It explains and predicts behaviors of solutions in dynamic equilibrium. Specifically, it implies that for a chemical reaction mixture that is in equilibrium, the ratio between the concentration of reactants and products is constant.
Two aspects are involved in the initial formulation of the law: 1) the equilibrium aspect, concerning the composition of a reaction mixture at equilibrium and 2) the kinetic aspect concerning the rate equations for elementary reactions. Both aspects stem from the research performed by Cato M. Guldberg and Peter Waage between 1864 and 1879 in which equilibrium constants were derived by using kinetic data and the rate equation which they had proposed. Guldberg and Waage also recognized that chemical equilibrium is a dynamic process in which rates of reaction for the forward and backward reactions must be equal at chemical equilibrium. In order to derive the expression of the equilibrium constant appealing to kinetics, the expression of the rate equation must be used. The expression of the rate equations was rediscovered independently by Jacobus Henricus van 't Hoff.
The law is a statement about equilibrium and gives an expression for the equilibrium constant, a quantity characterizing chemical equilibrium. In modern chemistry this is derived using equilibrium thermodynamics. It can also be derived with the concept of chemical potential. | 7 | Physical Chemistry |
A phosphorane (IUPAC name: λ-phosphane) is a functional group in organophosphorus chemistry with pentavalent phosphorus. Phosphoranes have the general formula PR.
Phosphoranes of the type PX adopt a trigonal bipyramidal molecular geometry with the two apical bonds longer than the three equatorial bonds. Hypervalent bonding is described by inclusion of non-bonding MOs, as also invoked for the closely related molecule phosphorus pentafluoride. | 0 | Organic Chemistry |
The glycerol phosphate shuttle was first characterized as a major route of mitochondrial hydride transport in the flight muscles of blow flies. It was initially believed that the system would be inactive in mammals due to the predominance of lactate dehydrogenase activity over Glycerol-3-phosphate dehydrogenase 1 (GPD1) until high GPD1 and GPD2 activity were demonstrated in mammalian brown adipose tissue and pancreatic ß-islets. | 1 | Biochemistry |
Natural isotopic variations amongst the noble gases result from both radiogenic and nucleogenic production processes. Because of their unique properties, it is useful to distinguish them from the conventional radiogenic isotope systems described above. | 9 | Geochemistry |
The thermodynamic limit is essentially a consequence of the central limit theorem of probability theory. The internal energy of a gas of N molecules is the sum of order N contributions, each of which is approximately independent, and so the central limit theorem predicts that the ratio of the size of the fluctuations to the mean is of order 1/N. Thus for a macroscopic volume with perhaps the Avogadro number of molecules, fluctuations are negligible, and so thermodynamics works. In general, almost all macroscopic volumes of gases, liquids and solids can be treated as being in the thermodynamic limit.
For small microscopic systems, different statistical ensembles (microcanonical, canonical, grand canonical) permit different behaviours. For example, in the canonical ensemble the number of particles inside the system is held fixed, whereas particle number can fluctuate in the grand canonical ensemble. In the thermodynamic limit, these global fluctuations cease to be important.
It is at the thermodynamic limit that the additivity property of macroscopic extensive variables is obeyed. That is, the entropy of two systems or objects taken together (in addition to their energy and volume) is the sum of the two separate values. In some models of statistical mechanics, the thermodynamic limit exists, but depends on boundary conditions. For example, this happens in six vertex model: the bulk free energy is different for periodic boundary conditions and for domain wall boundary conditions. | 7 | Physical Chemistry |
Allele-specific oligonucleotide (ASO) is a technique that allows detection of single base mutations without the need for PCR or gel electrophoresis. Short (20–25 nucleotides in length), labeled probes are exposed to the non-fragmented target DNA, hybridization occurs with high specificity due to the short length of the probes and even a single base change will hinder hybridization. The target DNA is then washed and the labeled probes that did not hybridize are removed. The target DNA is then analyzed for the presence of the probe via radioactivity or fluorescence. In this experiment, as in most molecular biology techniques, a control must be used to ensure successful experimentation.
In molecular biology, procedures and technologies are continually being developed and older technologies abandoned. For example, before the advent of DNA gel electrophoresis (agarose or polyacrylamide), the size of DNA molecules was typically determined by rate sedimentation in sucrose gradients, a slow and labor-intensive technique requiring expensive instrumentation; prior to sucrose gradients, viscometry was used. Aside from their historical interest, it is often worth knowing about older technology, as it is occasionally useful to solve another new problem for which the newer technique is inappropriate. | 1 | Biochemistry |
In 1975, Kono and Ito reported that Wilkinsons catalyst (Rh(PPh)Cl) can undergo oxidative addition with catecholborane (HBcat) or 4,4,6-trimethyl-1,3,2-dioxaborinane. These two borane compounds are otherwise slow to participate in hydroboration. In 1985, Männig and Nöth demonstrated for the first time that Wilkinsons catalyst indeed catalyzes hydroboration of alkenes with HBcat.
Whereas uncatalyzed hydroboration using HBcat leads to reduction of the carbonyl group, the catalyzed version is selective for the alkene.
As indicated by subsequent research, transition metal-catalyzed hydroboration proceeds with attractive functional group-, regio-, stereo-, and chemo- selectivity. | 0 | Organic Chemistry |
It was excavated between 1968 and 1974 under the direction of German archaeologist Harald Hauptmann as part of the salvage project to document archaeological sites that would be flooded by the construction of the Keban Dam. Excavation of the site focused on three areas: the western slope, the so-called "acropolis" area, and the south terrace. | 8 | Metallurgy |
Wrackmeyer-type 1,1 carboboration is proposed to go through a zwitterionic intermediate, and this intermediate has been isolated and characterized in some cases. However, the mechanism can be highly substrate and reagent dependent.
In a borane, the compound typically adopts a trigonal planar molecular geometry, making the boron atom an electrophilic center. The substituents can affect the strength of the borane as a Lewis acid. Boranes which are stronger Lewis acids are better electrophiles and therefore better able to facilitate carboboration. Boranes can be optimized to work on less activated substrates. Tris(pentafluorophenyl)borane [B(CF)] is a strongly Lewis acidic borane which functions well in 1,1 carboborations with both activated and unactivated substrates, and it allows for the reaction to be facilitated with more mild conditions. An activated substrate such as an alkene or alkyne has an electron-withdrawing group directly attached to a carbon within the double or triple bond. Transition metal catalysts have been utilized to develop enantioselective 1,1 carboborations on unactivated alkenes. These reactions go through a catalytic cycle which may or may not go through a zwitterionic intermediate. | 0 | Organic Chemistry |
Another simple case of diffusion is the Brownian motion of one particle. The particle's Mean squared displacement from its original position is:
where is the dimension of the particle's Brownian motion. For example, the diffusion of a molecule across a cell membrane 8 nm thick is 1-D diffusion because of the spherical symmetry; However, the diffusion of a molecule from the membrane to the center of a eukaryotic cell is a 3-D diffusion. For a cylindrical cactus, the diffusion from photosynthetic cells on its surface to its center (the axis of its cylindrical symmetry) is a 2-D diffusion.
The square root of MSD, , is often used as a characterization of how far has the particle moved after time has elapsed. The MSD is symmetrically distributed over the 1D, 2D, and 3D space. Thus, the probability distribution of the magnitude of MSD in 1D is Gaussian and 3D is a Maxwell-Boltzmann distribution. | 7 | Physical Chemistry |
Levomethamphetamine can register on urine drug screens as either methamphetamine, amphetamine, or both, depending on the subject's metabolism and dosage. L-methamphetamine metabolizes completely into L-amphetamine after a period of time. | 4 | Stereochemistry |
In organic chemistry, carboboration describes an addition of both a carbon and a boron moiety to certain carbon-containing double and triple bonds, such as alkenes, alkynes, and allenes.
In the synthesis of organic compounds, this chemical reaction is used to install a new carbon-carbon bond and carbon-boron bond. The product of carboboration reactions are organoborane compounds which prove to be useful in organic synthesis, containing both a new carbon group and a boron handle for further functionalization. This carbon-boron bond allows for organoboron chemistry, which facilitates a wide variety of chemical transformations such as oxidation and the Suzuki Reaction. The carbon-boron bond can be transformed into a variety of functional groups and moieties, making it highly useful in pharmaceutical chemistry and organic synthesis.
Carboboration was developed soon after the advent and widespread use of hydroboration. Carboboration is often facilitated via catalysis, often employing transition metals, and usually involves an activated alkene or alkyne. The two most well-documented categories of carboboration are 1,1 and 1,2 carboboration, which differ in the regioselectivity of the incoming carbon group. | 0 | Organic Chemistry |
The malate is oxidized by NAD (the oxidizing agent) to oxaloacetate again, releasing NADH. The replenishment of oxaloacetate can be achieved. The oxaloacetate can react with the acetyl-CoA in the first step, completing a cycle. | 1 | Biochemistry |
Extrapolating site or depth specific measurements to the entire lake can be problematic as there can be significant metabolic variability both vertically and horizontally within a lake (see variability section). For example, many lake metabolism studies only have a single epilimnetic estimate of metabolism, however, this may overestimate metabolic characteristics about the lake such as NEP depending on the mixed layer depth to light extinction depth ratio. Averaging daily metabolism estimates over longer time periods may help overcome some of these single site extrapolation issues, but one must carefully consider the implications of the metabolic estimates and not over extrapolate measurements. | 1 | Biochemistry |
Fulmer Research Institute was founded in 1945 by Col W C (Dev) Devereux and incorporated in 1946. He had been a pioneer in the use of light metal alloys in aero engines and, in the Second World War, he had an important role in the UK Ministry of Aircraft Production, organizing the assembly in Britain of American aircraft and reorganizing the repair of aircraft and aero-engines.
After the war, in 1945, he set up a company called Almin Ltd (Associated Light Metal Industries) which brought together a group of companies mostly concerned with the production and processing of aluminium and magnesium alloys. He wanted Almin to have research facilities but he recognised that Almin's R&D needs alone were not sufficient to justify the investment in staff and capital equipment required for properly equipped laboratories. His answer was to establish a contract research organization
along the lines of Battelle Memorial Institute and The Mellon Institute of Industrial Research in the USA.
Thus he founded Fulmer Research Institute as one of the first contract research companies in Britain. Initially it was in temporary accommodation but he soon found a permanent base by purchasing a large Edwardian country house with ten acres of grounds, in the Buckinghamshire village of Stoke Poges. The name Fulmer was the name of the local telephone exchange and that of a nearby village. | 8 | Metallurgy |
Lynda Soderholm is a physical chemist at the U.S. Department of Energys (DOE) Argonne National Laboratory with a specialty in f-block elements. She is a senior scientist and the lead of the Actinide, Geochemistry & Separation Sciences Theme within Argonnes Chemical Sciences and Engineering Division. Her specific role is the Separation Science group leader within Heavy Element Chemistry and Separation Science (HESS), directing basic research focused on low-energy methods for isolating lanthanide and actinide elements from complex mixtures. She has made fundamental contributions to understanding f-block chemistry and characterizing f-block elements.
Soderholm became a Fellow of the American Association for the Advancement of Science (AAAS) in 2013, and is also an Argonne Distinguished Fellow. | 7 | Physical Chemistry |
The two-step conversion of ammonia to nitrate observed in ammonia-oxidizing bacteria, ammonia-oxidizing archaea and nitrite-oxidizing bacteria (such as Nitrobacter) is puzzling to researchers. Complete nitrification, the conversion of ammonia to nitrate in a single step known as comammox, has an energy yield (∆G°′) of −349 kJ mol NH, while the energy yields for the ammonia-oxidation and nitrite-oxidation steps of the observed two-step reaction are −275 kJ mol NH, and −74 kJ mol NO, respectively. These values indicate that it would be energetically favourable for an organism to carry out complete nitrification from ammonia to nitrate (comammox), rather than conduct only one of the two steps. The evolutionary motivation for a decoupled, two-step nitrification reaction is an area of ongoing research. In 2015, it was discovered that the species Nitrospira inopinata possesses all the enzymes required for carrying out complete nitrification in one step, suggesting that this reaction does occur. | 1 | Biochemistry |
1 - Enzymatic hydrolysis - a single source of feedstock, switchgrass for example, is mixed with strong enzymes which convert a portion of cellulosic material into sugars which can then be fermented into ethanol. Genencor and Novozymes are two companies that have received United States government Department of Energy funding for research into reducing the cost of cellulase, a key enzyme in the production cellulosic ethanol by this process.
2 - Synthesis gas fermentation - a blend of feedstock, not exceeding 30% water, is gasified in a closed environment into a syngas containing mostly carbon monoxide and hydrogen. The cooled syngas is then converted into usable products through exposure to bacteria or other catalysts. BRI Energy, LLC is a company whose pilot plant in Fayetteville, Arkansas is currently using synthesis gas fermentation to convert a variety of waste into ethanol. After gasification, anaerobic bacteria (Clostridium ljungdahlii) are used to convert the syngas (CO, CO, and H) into ethanol. The heat generated by gasification is also used to co-generate excess electricity.
3 - C.O.R.S. and Grub Composting are sustainable technologies that employ organisms that feed on organic matter to reduce and convert organic waste in to high quality feedstuff and oil rich material for the biodiesel industry.
Organizations pioneering this novel approach to waste management are EAWAG, ESR International, Prota Culture and BIOCONVERSION that created the e-CORS® system to meet large scale organic waste management needs and environmental sustainability in both urban and livestock farming reality. This type of engineered system introduces a substantial innovation represented by the automatic modulation of the treatment, able to adapt conditions of the system to the biology of the scavenger used, improving their performances and the power of this technology. | 2 | Environmental Chemistry |
Functional selectivity has been proposed to broaden conventional definitions of pharmacology.
Traditional pharmacology posits that a ligand can be either classified as an agonist (full or partial), antagonist or more recently an inverse agonist through a specific receptor subtype, and that this characteristic will be consistent with all effector (second messenger) systems coupled to that receptor. While this dogma has been the backbone of ligand-receptor interactions for decades now, more recent data indicates that this classic definition of ligand-protein associations does not hold true for a number of compounds; such compounds may be termed as mixed agonist-antagonists.
Functional selectivity posits that a ligand may inherently produce a mix of the classic characteristics through a single receptor isoform depending on the effector pathway coupled to that receptor. For instance, a ligand can not easily be classified as an agonist or antagonist, because it can be a little of both, depending on its preferred signal transduction pathways. Thus, such ligands must instead be classified on the basis of their individual effects in the cell, instead of being either an agonist or antagonist to a receptor.
It is also important to note that these observations were made in a number of different expression systems and therefore functional selectivity is not just an epiphenomenon of one particular expression system. | 1 | Biochemistry |
Dioxane has an of 5170 mg/kg in rats. It is irritating to the eyes and respiratory tract. Exposure may cause damage to the central nervous system, liver and kidneys. In a 1978 mortality study conducted on workers exposed to 1,4-dioxane, the observed number of deaths from cancer was not significantly different from the expected number. Dioxane is classified by the National Toxicology Program as "reasonably anticipated to be a human carcinogen". It is also classified by the IARC as a Group 2B carcinogen: possibly carcinogenic to humans because it is a known carcinogen in other animals. The United States Environmental Protection Agency classifies dioxane as a probable human carcinogen (having observed an increased incidence of cancer in controlled animal studies, but not in epidemiological studies of workers using the compound), and a known irritant (with a no-observed-adverse-effects level of 400 milligrams per cubic meter) at concentrations significantly higher than those found in commercial products. Under California Proposition 65, dioxane is classified in the U.S. State of California to cause cancer. Animal studies in rats suggest that the greatest health risk is associated with inhalation of vapors in the pure form. The State of New York has adopted a first-in-the-nation drinking water standard for 1,4-Dioxane and set the maximum contaminant level of 1 part per billion.
It tends to concentrate in the water and has little affinity for soil. It is resistant to abiotic degradation in the environment, and was formerly thought to also resist biodegradation. However, more recent studies since the 2000s have found that it can be biodegraded through a number of pathways, suggesting that bioremediation can be used to treat 1,4-dioxane contaminated water. | 6 | Supramolecular Chemistry |
A conductometric titration method can also be used for the determination of the base number of petroleum products. A conductivity sensor is used to measure the conductivity of the analyte which allows the endpoint to be detected. It is suitable for both new and used products having base numbers from 1 mg to 40 mg KOH/g. A sample is dissolved in a solvent mixture of Toluene/ Propan-2-ol with 0.5% deionised water. A conductivity cell is placed in the titration vessel. The sample solution is titrated with alcoholic hydrochloric acid. | 3 | Analytical Chemistry |
The spectral resolution of a spectrograph, or, more generally, of a frequency spectrum, is a measure of its ability to resolve features in the electromagnetic spectrum. It is usually denoted by , and is closely related to the resolving power of the spectrograph, defined as
where is the smallest difference in wavelengths that can be distinguished at a wavelength of . For example, the Space Telescope Imaging Spectrograph (STIS) can distinguish features 0.17 nm apart at a wavelength of 1000 nm, giving it a resolution of 0.17 nm and a resolving power of about 5,900. An example of a high resolution spectrograph is the Cryogenic High-Resolution IR Echelle Spectrograph (CRIRES+) installed at ESO's Very Large Telescope, which has a spectral resolving power of up to 100,000. | 7 | Physical Chemistry |
One consequence of this difference is that the color charge is too large for perturbative computations which are the mainstay of QED. As a result, the main theoretical tools to explore the theory of the QGP is lattice gauge theory. The transition temperature (approximately ) was first predicted by lattice gauge theory. Since then lattice gauge theory has been used to predict many other properties of this kind of matter. The AdS/CFT correspondence conjecture may provide insights in QGP, moreover the ultimate goal of the fluid/gravity correspondence is to understand QGP. The QGP is believed to be a phase of QCD which is completely locally thermalized and thus suitable for an effective fluid dynamic description. | 7 | Physical Chemistry |
A related intensive system parameter is the particle number density, a quantity of kind volumetric number density obtained by dividing the particle number of a system by its volume. This parameter is often denoted by the lower-case letter n. | 7 | Physical Chemistry |
Dodecahedrane is a chemical compound, a hydrocarbon with formula , whose carbon atoms are arranged as the vertices (corners) of a regular dodecahedron. Each carbon is bound to three neighbouring carbon atoms and to a hydrogen atom. This compound is one of the three possible Platonic hydrocarbons, the other two being cubane and tetrahedrane.
Dodecahedrane does not occur in nature and has no significant uses. It was synthesized by Leo Paquette in 1982, primarily for the "aesthetically pleasing symmetry of the dodecahedral framework".
For many years, dodecahedrane was the simplest real carbon-based molecule with full icosahedral symmetry. Buckminsterfullerene (), discovered in 1985, also has the same symmetry, but has three times as many carbons and 50% more atoms overall. The synthesis of the C fullerene in 2000, from brominated dodecahedrane, may have demoted to second place. | 0 | Organic Chemistry |
4-Toluenesulfonyl chloride (p-toluenesulfonyl chloride, toluene-p-sulfonyl chloride) is an organic compound with the formula CHCHSOCl. This white, malodorous solid is a reagent widely used in organic synthesis. Abbreviated TsCl or TosCl, it is a derivative of toluene and contains a sulfonyl chloride (−SOCl) functional group. | 0 | Organic Chemistry |
In the 1960s, a light driven proton pump was discovered in Halobacterium salinarum, and called Bacteriorhodopsin. Over the following years, there were various studies of the membrane of H. salinarum to determine the mechanism of these light-driven proton pumps.
In 1988, another Manabu Yoshidas group at Osaka University reported a novel light-sensitive proton pump from a strain of Halobacterium' which they termed Archaerhodopsin. A year later, the same group reported isolating the gene that encodes Archaerhodopsin. | 5 | Photochemistry |
Some chiral three-dimensional objects, such as the helix, can be assigned a right or left handedness, according to the right-hand rule.
Many other familiar objects exhibit the same chiral symmetry of the human body, such as gloves and shoes. Right shoes differ from left shoes only by being mirror images of each other. In contrast thin gloves may not be considered chiral if you can wear them inside-out.
The J-, L-, S- and Z-shaped tetrominoes of the popular video game Tetris also exhibit chirality, but only in a two-dimensional space. Individually they contain no mirror symmetry in the plane. | 4 | Stereochemistry |
INT (iodonitrotetrazolium or 2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl-2H-tetrazolium) is a commonly used tetrazolium salt (usually prepared with chloride ions), similar to tetrazolium chloride that on reduction produces a red formazan dye that can be used for quantitative redox assays. It is also toxic to prokaryotes.
INT is an artificial electron acceptor that can be utilized in a colorimetric assay to determine the concentration of protein in a solution. It can be reduced by succinate dehydrogenase to furazan, the formation of which can be measured by absorbance at 490 nm. The activity of succinate dehydrogenase is readily observed by the naked eye as the solution turns from colorless to rusty red. | 7 | Physical Chemistry |
The silicon-vacancy center (Si-V) is an optically active defect in diamond (referred to as a color center) that is receiving an increasing amount of interest in the diamond research community. This interest is driven primarily by the coherent optical properties of the Si-V, especially compared to the well-known and extensively-studied nitrogen-vacancy center (N-V). | 7 | Physical Chemistry |
Photosynthetic oxygen evolution is the fundamental process by which oxygen is generated in the earth's biosphere. The reaction is part of the light-dependent reactions of photosynthesis in cyanobacteria and the chloroplasts of green algae and plants. It utilizes the energy of light to split a water molecule into its protons and electrons for photosynthesis. Free oxygen, generated as a by-product of this reaction, is released into the atmosphere.
Water oxidation is catalyzed by a manganese-containing cofactor contained in photosystem II, known as the oxygen-evolving complex (OEC) or the water-splitting complex. Manganese is an important cofactor, and calcium and chloride are also required for the reaction to occur. The stoichiometry of this reaction is as follows:
: 2HO ⟶ 4e + 4H + O
The protons are released into the thylakoid lumen, thus contributing to the generation of a proton gradient across the thylakoid membrane. This proton gradient is the driving force for adenosine triphosphate (ATP) synthesis via photophosphorylation and the coupling of the absorption of light energy and the oxidation of water for the creation of chemical energy during photosynthesis. | 5 | Photochemistry |
Selective deprotection of silyl groups is possible in many instances. For example, in the synthesis of taxol:
Silyl ethers are mainly differentiated on the basis of sterics or electronics. In general, acidic deprotections deprotect less hindered silyl groups faster, with the steric bulk on silicon being more significant than the steric bulk on oxygen. Fluoride-based deprotections deprotect electron-poor silyl groups faster than electron-rich silyl groups. There is some evidence that some silyl deprotections proceed via hypervalent silicon species.
The selective deprotection of silyl ethers has been extensively reviewed. Although selective deprotections have been achieved under many different conditions, some procedures, outlined below, are more reliable. A selective deprotection will likely be successful if there is a substantial difference in sterics (e.g., primary TBS vs. secondary TBS or primary TES vs primary TBS) or electronics (e.g. primary TBDPS vs. primary TBS). Unfortunately, some optimization is inevitably required and it is often necessary to run deprotections partway and recycle material.
;Some common acidic conditions:
* 100 mol% 10-CSA (camphorsulfonic acid) in MeOH, room temperature; a "blast" of acid, deprotects primary TBS groups within ten minutes.
* 10 mol% 10-CSA, 1:1 MeOH:DCM, −20 or 0 °C; deprotects a primary TBS group within two hours at 0; if CSA is replaced by PPTS, the rate is approximately ten times slower; with p-TsOH, approximately ten times faster; solvent mixture is crucial.
* 4:1:1 v/v/v AcOH:THF:water, room temp.; this is very slow, but can be very selective.
;Some common basic conditions:
* HF-pyridine, 10:1 THF:pyridine, 0 °C; an excellent deprotection; removes primary TBS groups within eight hours; reactions using HF must be run in plastic containers.
* TBAF, THF or 1:1 TBAF/AcOH, THF; TBDPS and TBS groups can be deprotected in the presence of one another under different conditions. | 0 | Organic Chemistry |
For many years, gene mapping was limited to identifying organisms by traditional phenotypes markers. This included genes that encoded easily observable characteristics such as blood types or seed shapes. The insufficient number of these types of characteristics in several organisms limited the mapping efforts that could be done. This prompted the development of gene markers which could identify genetic characteristics that are not readily observable in organisms (such as protein variation). | 1 | Biochemistry |
It was originally used against microsporidian parasites Nosema apis infections in honey bees.
Some studies found it to be effective against some myxozoan parasites, including Myxobolus cerebralis, an important parasite of fish; however, in the more rigorous tests required for U.S. Food and Drug Administration approval, it was ineffective.
There are reports that fumagillin controls Nosema ceranae, which has recently been hypothesized as a possible cause of colony collapse disorder.
The latest report, however, has shown it to be ineffective against N. ceranae.
Fumagillin is also investigated as an inhibitor of malaria parasite growth. | 0 | Organic Chemistry |
The octadecanoid pathway is a biosynthetic pathway for the production of the phytohormone jasmonic acid (JA), an important hormone for induction of defense genes. JA is synthesized from alpha-linolenic acid, which can be released from the plasma membrane by certain lipase enzymes. For example, in the wound defense response, phospholipase C will cause the release of alpha-linolenic acid for JA synthesis.
In the first step, alpha-linolenic acid is oxidized by the enzyme lipoxygenase. This forms 13-hydroperoxylinolenic acid, which is then modified by a dehydrase and undergoes cyclization by allene oxide cyclase to form 12-oxo-phytodienoic acid. This undergoes reduction and three rounds of beta oxidation to form jasmonic acid. | 1 | Biochemistry |
An aquatic system lacking dissolved oxygen (0% saturation) is termed anaerobic, reducing, or anoxic.
In water, oxygen levels are approximately 7 ppm or 0.0007% in good quality water, but fluctuate.
Many organisms require hypoxic conditions. Oxygen is poisonous to anaerobic bacteria for example.
Oxygen depletion is typically expressed as a percentage of the oxygen that would dissolve in the water at the prevailing temperature and salinity. A system with low concentration—in the range between 1 and 30% saturation—is called hypoxic or dysoxic. Most fish cannot live below 30% saturation since they rely on oxygen to derive energy from their nutrients. Hypoxia leads to impaired reproduction of remaining fish via endocrine disruption. A "healthy" aquatic environment should seldom experience less than 80% saturation. The exaerobic zone is found at the boundary of anoxic and hypoxic zones.
Hypoxia can occur throughout the water column and also at high altitudes as well as near sediments on the bottom. It usually extends throughout 20-50% of the water column, but depends on the water depth and location of pycnoclines (rapid changes in water density with depth). It can occur in 10-80% of the water column. For example, in a 10-meter water column, it can reach up to 2 meters below the surface. In a 20-meter water column, it can extend up to 8 meters below the surface. | 9 | Geochemistry |
Tetrakis(pyridine)silver(II) peroxydisulfate is a chemical compound which contains silver in the rare oxidation state of +2. | 0 | Organic Chemistry |
RIN for a sample is computed using several characteristics of an RNA electropherogram trace, with the first two listed below being most significant. RIN assigns an electropherogram a value of 1 to 10, with 10 being the least degraded. All the following descriptions apply to mammalian RNA because RNAs in other species have different rRNA sizes:
The total RNA ratio is calculated by taking the ratio of the area under the 18S and 28S rRNA peaks to the total area under the graph, a large number here is desired, indicating much of the rRNA is still at these sizes and thus little to no degradation has occurred. An ideal ratio can be seen in figure 1, where almost all of the RNA is in the 18S and 28S RNA peaks.
For the height of 28S peak, a large value is desired. 28S, the most prominent rRNA species, is used in RIN calculation as it is typically degraded more quickly than 18S rRNA, and so measuring its peak height allows for detection of the early stages of degradation. Again, this is seen in figure 1, where the 28S peak is the largest, and so this is good.
The fast region is the area between the 18S and 5S rRNA peaks on an electropherogram. Initially, as the fast area ratio value increases, it indicates degradation of the 18S and 28S rRNA to an intermediate size, though the ratio subsequently decreases as RNA degrades further, to even smaller sizes. Thus, a low value doesn't necessarily indicate either good or bad RNA integrity.
A small marker height is desired, indicating only small amounts of RNA have been degraded and proceeded to the smallest lengths, indicated by the short marker. If a large number is found here, that indicates that large amounts of the rRNAs have been degraded to small pieces that would be found closer to this marker. This situation can be seen in the poor quality RNA electropherogram found in figure 2, where the height of the peak over the marker (far left) is very large, so the RNA has been greatly degraded.
In prokaryotic samples, the algorithm is somewhat different, but the Agilent 2100 Bioanalyzer Expert software is able to calculate RIN for prokaryotic samples now as well. The difference likely arises from the fact that, while mammalian samples have 28S and 18S ribosomal RNAs as their predominant species, prokaryotic RNAs have the sizes shifted slightly smaller, to 23S and 16S, so the algorithm must be shifted to accommodate that. Another crucial fact about calculating prokaryotic RNA integrity numbers is that RIN has not been validated to the extent that it has for eukaryotic RNA. It has been shown that higher RIN values correlate with better downstream results in eukaryotes, but this hasn't been done as extensively for prokaryotes, so it may mean less in prokaryotes.
These electropherograms for calculating RIN are done using the Agilent Bioanalyzer machine, which is capable of performing electrophoresis and generating the electropherograms. The Agilent 2100 software is uniquely able to perform the RIN software, as the exact algorithm is proprietary, so there are additional important RNA electropherogram features that are used in its calculation that are not publicly available. | 1 | Biochemistry |
Level 2 vectors have two inverted BpiI sites from the insertion of level 1 modules. The upstream fusion site is compatible to a gene cloned in level 1 vector while the downstream fusion site has a universal sequence. Each cloning allows 2-6 genes to be inserted in the same vector.
Adding more genes in one cloning step is not recommended, for this would result in incorrect constructs. On one hand, this can induce more restriction sites in the construct, where this open construct allows additional genes be added. On the other hand, this can also eliminate restriction sites, where this close construct stop the further addition of genes.
Therefore, constructs of more than six genes need successive cloning steps, which requires end-linkers containing BsaI or BsmBI internal restriction sites and blue or purple markers. Each cloning step needs to alternate the restriction site and the marker. Furthermore, two restriction enzymes are needed, where BpiI is used for releasing level 1 modules from level 1 constructs and BsaI/BsmBI is for digesting and opening the recipient level 2-n plasmid. When screening, the correct colonies should alternate from blue to purple every cloning step, but if a "closed" end-linker is used, the colonies will be white. | 1 | Biochemistry |
During exercise when the ATP reservoir is low (ADP>ATP), the purine nucleotide cycle produces ammonia (NH) when it converts AMP into IMP. (With the exception of AMP deaminase deficiency, where ammonia is produced during exercise when adenosine, from AMP, is converted into inosine). During rest (ADP<ATP), ammonia is produced from the conversion of adenosine into inosine by adenosine deaminase.
:AMP + HO + H → IMP + NH (catalyzed by AMP deaminase in skeletal muscle)
:Adenosine + HO → Inosine + NH (catalyzed by adenosine deaminase in skeletal muscle, blood, liver)
Ammonia is toxic, disrupts cell function, and permeates cell membranes. Ammonia becomes ammonium (NH) depending on the pH of the cell or plasma. Ammonium is relatively non-toxic and does not readily permeate cell membranes. + H ⇌ NH) diffuses into the blood, circulating to the liver to be neutralized by the urea cycle. (N.b. urea is not the same as uric acid, though both are end products of the purine nucleotide cycle, from ammonia and nucleotides respectively.) When the skeletal muscles are at rest (ADP) combines with glutamate to produce glutamine, which is an energy-consuming step, and the glutamine enters the blood. + ATP → Glutamine + ADP + P (catalyzed by glutamine synthetase in resting skeletal muscle) molecules neutralise the organic acids (lactic acid and ketone bodies) produced in the muscles.O → Glutamate + NH (catalyzed by glutaminase in the kidneys)</blockquote> | 1 | Biochemistry |
Dielectric constants are not the only measure of polarity. Because solvents are used by chemists to carry out chemical reactions or observe chemical and biological phenomena, more specific measures of polarity are required. Most of these measures are sensitive to chemical structure.
The Grunwald–Winstein mY scale measures polarity in terms of solvent influence on buildup of positive charge of a solute during a chemical reaction.
Kosowers Z scale' measures polarity in terms of the influence of the solvent on UV-absorption maxima of a salt, usually pyridinium iodide or the pyridinium zwitterion.
Donor number and donor acceptor scale measures polarity in terms of how a solvent interacts with specific substances, like a strong Lewis acid or a strong Lewis base.
The Hildebrand parameter is the square root of cohesive energy density. It can be used with nonpolar compounds, but cannot accommodate complex chemistry.
Reichardts dye, a solvatochromic dye that changes color in response to polarity, gives a scale of E(30) values. E is the transition energy between the ground state and the lowest excited state in kcal/mol, and (30) identifies the dye. Another, roughly correlated scale (E'(33)) can be defined with Nile red.
The polarity, dipole moment, polarizability and hydrogen bonding of a solvent determines what type of compounds it is able to dissolve and with what other solvents or liquid compounds it is miscible. Generally, polar solvents dissolve polar compounds best and non-polar solvents dissolve non-polar compounds best; hence "like dissolves like". Strongly polar compounds like sugars (e.g. sucrose) or ionic compounds, like inorganic salts (e.g. table salt) dissolve only in very polar solvents like water, while strongly non-polar compounds like oils or waxes dissolve only in very non-polar organic solvents like hexane. Similarly, water and hexane (or vinegar and vegetable oil) are not miscible with each other and will quickly separate into two layers even after being shaken well.
Polarity can be separated to different contributions. For example, the Kamlet-Taft parameters are dipolarity/polarizability (π*), hydrogen-bonding acidity (α) and hydrogen-bonding basicity (β). These can be calculated from the wavelength shifts of 3–6 different solvatochromic dyes in the solvent, usually including Reichardt's dye, nitroaniline and diethylnitroaniline. Another option, Hansen solubility parameters, separates the cohesive energy density into dispersion, polar, and hydrogen bonding contributions. | 2 | Environmental Chemistry |
SaltMod is computer program for the prediction of the salinity of soil moisture, groundwater and drainage water, the depth of the watertable, and the drain discharge (hydrology) in irrigated agricultural lands, using different (geo)hydrologic conditions, varying water management options, including the use of ground water for irrigation, and several cropping rotation schedules.
The water management options include irrigation, drainage, and the use of subsurface drainage water from pipe drains, ditches or wells for irrigation. | 9 | Geochemistry |
Centrifugal partition chromatography is a special chromatographic technique where both stationary and mobile phase are liquid, and the stationary phase is immobilized by a strong centrifugal force. Centrifugal partition chromatography consists of a series-connected network of extraction cells, which operates as elemental extractors, and the efficiency is guaranteed by the cascade. | 3 | Analytical Chemistry |
RNA polymerase binding in bacteria involves the sigma factor recognizing the core promoter region containing the −35 and −10 elements (located before the beginning of sequence to be transcribed) and also, at some promoters, the α subunit C-terminal domain recognizing promoter upstream elements. There are multiple interchangeable sigma factors, each of which recognizes a distinct set of promoters. For example, in E. coli, σ is expressed under normal conditions and recognizes promoters for genes required under normal conditions ("housekeeping genes"), while σ recognizes promoters for genes required at high temperatures ("heat-shock genes"). In archaea and eukaryotes, the functions of the bacterial general transcription factor sigma are performed by multiple general transcription factors that work together. The RNA polymerase-promoter closed complex is usually referred to as the "transcription preinitiation complex."
After binding to the DNA, the RNA polymerase switches from a closed complex to an open complex. This change involves the separation of the DNA strands to form an unwound section of DNA of approximately 13 bp, referred to as the "transcription bubble". Supercoiling plays an important part in polymerase activity because of the unwinding and rewinding of DNA. Because regions of DNA in front of RNAP are unwound, there are compensatory positive supercoils. Regions behind RNAP are rewound and negative supercoils are present. | 1 | Biochemistry |
Liquid chromatography as we know it today really got its start in 1969, when the first modern HPLC was designed and marketed as a nucleic acid analyzer. Columns throughout the 1970s were unreliable, pump flow rates were inconsistent, and many biologically active compounds escaped detection by UV and fluorescence detectors. Focus on purification methods in the 70s morphed into faster analyses in the 1980s, when computerized controls were integrated into HPLC equipment. Higher degrees of computerization then led to emphasis on more precise, faster, automated equipment in the 1990s. Atypical of many technologies of the 60s and '70s, the emphasis in improvements was not on “bigger and better,” but on “smaller and better”. At the same time the HPLC user-interface was improving, it was critical to be able to isolate hundreds of peptides or biomarkers from ever decreasing sample sizes.
Laboratory analytical instrumentation has only been recognized as a separate and distinct industry by NAICS and SIC since 1987. This market segmentation includes not only gas and liquid chromatography, but also mass spectrometry and spectrophotometric instruments. Since first recognized as a separate market, sales of analytical laboratory equipment increased from about $3.5 billion in 1987 to more than $26 billion in 2004. Revenues in the world liquid chromatography market, specifically, are expected to grow from $3.4 billion in 2007 to $4.7 billion in 2013, with a slight decrease in spending expected in 2008 and 2009 from the worldwide economic slump and decreased or stagnant spending. The pharmaceutical industry alone accounts for 35% of all the HPLC instruments in use. The main source of growth in LC stems from biosciences and pharmaceutical companies. | 3 | Analytical Chemistry |
To demonstrate its capability in rapidly depolymerizing in presence of UV-light, DiLauro et al. synthesized a PPA polymer with two UV-sensitive endcaps, 2-nitro-4,5-dimethoxybenzyl alcohol and 1-[[(chlorocarbonyl)oxy]methyl]-4,5-dimethoxy-2 nitrobenzene, and were able to achieve complete depolymerization in a few minutes. In a practical application in organic electronics, cyclic PPA in the presence of 2-(4-methoxystyryl)-4,6-bis(trichloromethyl)-1,3,5-triazine (MBTT used as PAG) undergoes depolymerization upon exposure to UV-light, which in turn deactivates the transient electronics. Another similar application in transient electronics was reported where an organic light-emitting diode (OLED) was integrated on the PPA substrate and can cause depolymerization in the presence of a PAG. | 7 | Physical Chemistry |
Carbonyl hydrido tris(triphenylphosphine)rhodium(I) [Carbonyl(hydrido)tris(triphenylphosphane)rhodium(I)] is an organorhodium compound with the formula [RhH(CO)(PPh)] (Ph = CH). It is a yellow, benzene-soluble solid, which is used industrially for hydroformylation. | 0 | Organic Chemistry |
When acidic solution of ephedrine or pseudoephedrine is mixed with copper sulfate and sodium hydroxide solutions, a violet color is formed. Upon shaking with ether, the organic phase turns red/purple and the aqueous phase turns blue. The staining is based on the formation of a coordination complex of two ephedrine molecules and a copper ion Cu
This works, because, in an alkaline solution, the hydroxyl and amine groups are de-protonated, leaving a negative charge on the central atoms. They can then form a coordination complex with the positively-charged cupric ions from the copper sulfate. Phenethylamines (and their derivatives) that have a β-ketone group will also react, but less predictably and dramatically (the carbonyl oxygen is less nucleophilic than the deprotonated hydroxyl group). They usually form a deeper blue color, and often a grey-ish precipitate. This includes the cathinones and presumably βK-2C-x compounds. | 3 | Analytical Chemistry |
One limitation of classic yeast two-hybrid screens is that they are limited to soluble proteins. It is therefore impossible to use them to study the protein–protein interactions between insoluble integral membrane proteins. The split-ubiquitin system provides a method for overcoming this limitation. In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety ("Cub", residues 35–76) and an N-terminal ubiquitin moiety ("Nub", residues 1–34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait–prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the transcription factor, allowing it to induce the transcription of reporter genes. | 1 | Biochemistry |
Biosynthesis of msDNA is purported to follow a unique pathway found nowhere else in DNA/RNA biochemistry. Because of the similarity of the 2-5 branch junction to the branch junctions found in RNA splicing intermediates, it might at first have been expected that branch formation would be via spliceosome- or ribozyme-mediated ligation. Surprisingly, however, experiments in cell-free systems using purified retron reverse transcriptase indicate that cDNA synthesis is directly primed from the 2-OH group of the specific internal G residue of the primer RNA. The RT recognizes specific stem-loop structures in the precursor RNA, rendering synthesis of msDNA by the RT highly specific to its own retron. The priming of msDNA synthesis offers a fascinating challenge to our understanding of DNA synthesis. DNA polymerases (which include RT) share highly conserved structural features, which means that their active catalytic sites vary little from species to species, or even between DNA polymerases using DNA as a template, versus DNA polymerases using RNA as a template. The catalytic region of eukaryotic reverse transcriptase comprises three domains termed the "fingers", "palm", and "thumb" which hold the double-stranded primer-template in a right-hand grip with the 3-OH of the primer buried in the active site of the polymerase, a cluster of highly conserved acidic and polar residues situated on the palm between what would be the index and middle fingers. In eukaryotic RTs, the RNase H domain lies on the wrist below the base of the thumb, but retron RTs lack RNase H activity. The nucleic acid binding cleft, extending from the polymerase active site to the RNase H active site, is about 60 Å in length in eukaryotic RTs, corresponding to nearly two helical turns. When eukaryotic RT extends a conventional primer, the growing DNA/RNA double helix spirals along the cleft, and as the double helix passes the RNase H domain, the template RNA is digested to release the nascent strand of cDNA. In the case of msDNA primer extension, however, a long strand of RNA remains attached to the 3-OH of the priming G. Although it is possible to model an RT-primer template complex which would make the 2-OH accessible for the priming reaction, further extension of the DNA strand presents a problem: as DNA synthesis progresses, the bulky RNA strand extending from the 3'-OH needs somehow to spiral down the binding cleft without being blocked by steric hindrance. To overcome this issue, the msDNA reverse transcriptase clearly would require special features not shared by other RTs. | 1 | Biochemistry |
Genomes can be analyzed systematically to identify regulatory regions. Conserved non-coding sequences often contain regulatory regions, and so they are often the subject of these analyses.
* CAAT box
* CCAAT box
* Operator (biology)
* Pribnow box
* TATA box
* SECIS element, mRNA
* Polyadenylation signal, mRNA
* A-box
* Z-box
* C-box
* E-box
* G-box | 1 | Biochemistry |
In polymer chemistry, compatibilization is the addition of a substance to an immiscible blend of polymers that will increase their stability. Polymer blends are typically described by coarse, unstable phase morphologies; this results in poor mechanical properties. Compatibilizing the system will make a more stable and better blended phase morphology by creating interactions between the two previously immiscible polymers. Not only does this enhance the mechanical properties of the blend, but it often yields properties that are generally not attainable in either single pure component. | 7 | Physical Chemistry |
1. van Kretschmar, J. B., Bailey W. D., Arellano, C., Thompson, G. D., Sutula, C. L., Roe, R. M., Feeding disruption tests for monitoring the frequency of larval lepidopteran resistance to Cry1Ac, Cry1F, and Cry1Ab, Crop Prot. 30(7), 863-870 (2011)
2. Roe, R. M., W. D. Bailey, W. D., Gould, F., Sorenson, C. E., Kennedy, G. G., Bacheler, J. S., Rose, R. Hodgson, L. E., Sutula, C. L., Detection of resistant insects and IPM, Emerging technologies for integrated pest management concepts, research and implementation. Proceedings of a Conference, Raleigh, North Carolina, US, 8–10 March 1999. 2000 pp. 67–84. [Book ]
3. Zeng, F., Ramaswamy, S. B., Luttrell, R. G., Reed, J., Parker, C. D., Stewart, S., Harris, A., Knighten, K., Robbins, J., Xia, J. Q., Sutula, C. L., Comparison of monoclonal antibody and laboratory rearing techniques to identify Heliothentinaen (Lepidoptera: Noctuidae) eggs from Mississippi cotton fields, Environmental Entomology 28 (2): 275-281 (1999)
4. Yuen, G. Y., Xia, J. Q., Sutula, C. L., A Sensitive ELISA for Pythium ultimum Using Polyclonal and Species-Specific Monoclonal Antibodies, Plant Dis. 82(9), 1029-1032 (1998)
5. Xia, J. Q., Sutula, C. L., Marti, D., Development of a greenhouse test for tomato spotted wilt virus and impatiens necrotic spot virus, Acta Horticulturae 431:193-198 (1995)
6. Sutula, C. L., Gillett, J. M., Morrissey, S. M., Ramsdell, D. C., Interpreting ELISA data and establishing the positive-negative threshold, Plant Dis. 70(8s), 722 (1986)
7. Wershaw, R. L., Burcar, J. P., Sutula, C. L., Wiginton, B. L., Sodium humate solution studied with small-angle x-ray scattering, Science 157(3795), 1429-31 (1967)
8. Sutula, C. L., Wilson, J. E., Solid-like films at a moving interface, Society of Petroleum Engineers Journal 7(1), (1967)
9. Bartell, L. S., Sutula, C. L., Mechanically induced molecular reorientation in multimolecular films, The Journal of Physical Chemistry 67(11), 2413-2416 (1963)
10. Sutula, C. L., Bartell, L. S., Structure and molecular orientation in multimolecular films of long-chain n-hydrocarbon derivatives, The Journal of Physical Chemistry 66(6), 1010-1014 (1962) | 3 | Analytical Chemistry |
The Dische test, or Dische reaction, is used to distinguish DNA from RNA. It was invented by Zacharias Dische. | 3 | Analytical Chemistry |
In the Gallagher–Hollander degradation (1946) pyruvic acid is removed from a linear aliphatic carboxylic acid yielding a new acid with two carbon atoms fewer. The original publication concerns the conversion of bile acid in a series of reactions: acid chloride (2) formation with thionyl chloride, diazoketone formation (3) with diazomethane, chloromethyl ketone formation (4) with hydrochloric acid, organic reduction of chlorine to methylketone (5), ketone halogenation to 6, elimination reaction with pyridine to enone 7 and finally oxidation with chromium trioxide to bisnorcholanic acid 8. | 0 | Organic Chemistry |
Because it is biologically inert and chemically stable, perfluorohexane has attracted attention in medicine. Like other fluorocarbons, perfluorohexane dissolves gases, including oxygen from the air, to a higher concentration than ordinary organic solvents. This effect is attributed to the weak intermolecular forces between perfluorohexane molecules, which allows "space" for gas molecules to partition into the liquid. Animals can be submerged in a bath of oxygenated perfluorohexane without drowning, as there is sufficient oxygen available in the solvent to allow respiration to continue. This effect has led to the experimental use of perfluorohexane in treating burn victims, as their lungs can be filled with either perfluorohexane vapor or in extreme cases liquid perfluorohexane, allowing breathing to continue without the problems normally seen with pulmonary edema that sometimes occur when the inside of the lungs have been burnt e.g. by inhalation of hot smoke. Research was particularly active on the topic of partial liquid ventilation (PLV) in the 1990s and early 2000s, however, perfluorohexane and other perfluorocarbons showed no significant improvement of patient outcomes in clinical trials. | 2 | Environmental Chemistry |
Vancomycin was first isolated in 1953, by Edmund Kornfeld (working at Eli Lilly) from a bacteria in a soil sample collected from the interior jungles of Borneo by a missionary, William M. Bouw (1918–2006). The organism that produced it was eventually named Amycolatopsis orientalis. The original indication for vancomycin was for the treatment of penicillin-resistant Staphylococcus aureus.
The compound was initially called compound 05865, but was eventually given the generic name vancomycin, derived from the term "vanquish". One advantage that was quickly apparent was that staphylococci did not develop significant resistance, despite serial passage in culture media containing vancomycin. The rapid development of penicillin resistance by staphylococci led to its being fast-tracked for approval by the Food and Drug Administration. In 1958, Eli Lilly first marketed vancomycin hydrochloride under the trade name Vancocin.
Vancomycin never became the first-line treatment for S. aureus for several reasons:
# It possesses poor oral bioavailability, so must be given intravenously for most infections.
# β-Lactamase-resistant semisynthetic penicillins such as methicillin (and its successors, nafcillin and cloxacillin) were subsequently developed, which have better activity against non-MRSA staphylococci.
# Early trials used early, impure forms of the drug ("Mississippi mud"), which were found to be toxic to the inner ear and to the kidneys; these findings led to vancomycin's being relegated to the position of a drug of last resort.
In 2004, Eli Lilly licensed Vancocin to ViroPharma in the U.S., Flynn Pharma in the UK, and Aspen Pharmacare in Australia. The patent had expired in the early 1980s, and the FDA authorized the sale of several generic versions in the US, including from manufacturers Bioniche Pharma, Baxter Healthcare, Sandoz, Akorn-Strides, and Hospira. | 0 | Organic Chemistry |
Two solutions are prepared separately:
* Solution A: 0.02 g of thymol blue, 0.01 g cresol red and 2 mL of ethanol
* Solution B: 0.8 g of sodium bicarbonate, 7.48 g of potassium chloride and 90 mL of water
* Mix Solution A and B and mix 9 mL of the mixed solution to 1000 mL of distilled water.
* This method to determinate the concentration of bicarbonates and carbonates is also called "Magni's method." | 3 | Analytical Chemistry |
A selectable marker is carried by the vector to allow the selection of positively transformed cells. Antibiotic resistance is often used as marker, an example being the beta-lactamase gene, which confers resistance to the penicillin group of beta-lactam antibiotics like ampicillin. Some vectors contain two selectable markers, for example the plasmid pACYC177 has both ampicillin and kanamycin resistance gene. Shuttle vector which is designed to be maintained in two different organisms may also require two selectable markers, although some selectable markers such as resistance to zeocin and hygromycin B are effective in different cell types. Auxotrophic selection markers that allow an auxotrophic organism to grow in minimal growth medium may also be used; examples of these are LEU2 and URA3 which are used with their corresponding auxotrophic strains of yeast.
Another kind of selectable marker allows for the positive selection of plasmid with cloned gene. This may involve the use of a gene lethal to the host cells, such as barnase, Ccda, and the parD/parE toxins. This typically works by disrupting or removing the lethal gene during the cloning process, and unsuccessful clones where the lethal gene still remains intact would kill the host cells, therefore only successful clones are selected. | 1 | Biochemistry |
Electron acceptors participate in electron-transfer reactions. In this context, the oxidizing agent is called an electron acceptor and the reducing agent is called an electron donor. A classic oxidizing agent is the ferrocenium ion , which accepts an electron to form Fe(CH). One of the strongest acceptors commercially available is "Magic blue", the radical cation derived from N(CH-4-Br).
Extensive tabulations of ranking the electron accepting properties of various reagents (redox potentials) are available, see Standard electrode potential (data page). | 7 | Physical Chemistry |
An electrical synapse is an electrically conductive link between two abutting neurons that is formed at a narrow gap between the pre- and postsynaptic cells, known as a gap junction. At gap junctions, cells approach within about 3.5 nm of each other, rather than the 20 to 40 nm distance that separates cells at chemical synapses. As opposed to chemical synapses, the postsynaptic potential in electrical synapses is not caused by the opening of ion channels by chemical transmitters, but rather by direct electrical coupling between both neurons. Electrical synapses are faster than chemical synapses. Electrical synapses are found throughout the nervous system, including in the retina, the reticular nucleus of the thalamus, the neocortex, and in the hippocampus. While chemical synapses are found between both excitatory and inhibitory neurons, electrical synapses are most commonly found between smaller local inhibitory neurons. Electrical synapses can exist between two axons, two dendrites, or between an axon and a dendrite. In some fish and amphibians, electrical synapses can be found within the same terminal of a chemical synapse, as in Mauthner cells. | 1 | Biochemistry |
Metabolic networks can be used to detect comorbidity patterns in diseased patients. Certain diseases, such as obesity and diabetes, can be present in the same individual concurrently, sometimes one disease being a significant risk factor for the other disease. The disease phenotypes themselves are normally the consequence of the cell's inability to breakdown or produce an essential substrate. However, an enzyme defect at one reaction may affect the fluxes of other subsequent reactions. These cascading effects couple the metabolic diseases associated with subsequent reactions resulting in comorbidity effects. Thus, metabolic disease networks can be used to determine if two disorders are connected due to their correlated reactions. | 1 | Biochemistry |
Governmental regulatory agencies stipulate for the food and dietary supplement industries certain health claims as allowable as statements on packaging.
European Food Safety Authority
* normal function of the immune system
* normal inflammatory response
* normal muscle function
* reduced risk of falling in people over age 60
US Food and Drug Administration (FDA)
* "Adequate calcium and vitamin D, as part of a well balanced diet, along with physical activity, may reduce the risk of osteoporosis."
Health Canada
* "Adequate calcium and regular exercise may help to achieve strong bones in children and adolescents and may reduce the risk of osteoporosis in older adults. An adequate intake of vitamin D is also necessary."
Other possible agencies with claim guidance: Japan FOSHU and Australia-New Zealand. | 1 | Biochemistry |
When a molecule or atom in the ground state (S) absorbs light, one electron is excited to a higher orbital level. This electron maintains its spin according to the spin selection rule; other transitions would violate the law of conservation of angular momentum. The excitation to a higher singlet state can be from HOMO to LUMO or to a higher orbital, so that singlet excitation states S, S, S... at different energies are possible.
Kasha's rule stipulates that higher singlet states would quickly relax by radiationless decay or internal conversion (IC) to S. Thus, S is usually, but not always, the only relevant singlet excited state. This excited state S can further relax to S by IC, but also by an allowed radiative transition from S to S that emits a photon; this process is called fluorescence.
Alternatively, it is possible for the excited state S to undergo spin inversion and to generate a triplet excited state T having two unpaired electrons with the same spin. This violation of the spin selection rule is possible by intersystem crossing (ISC) of the vibrational and electronic levels of S and T. According to Hund's rule of maximum multiplicity, this T state would be somewhat more stable than S.
This triplet state can relax to the ground state S by radiationless IC or by a radiation pathway called phosphorescence. This process implies a change of electronic spin, which is forbidden by spin selection rules, making phosphorescence (from T to S) much slower than fluorescence (from S to S). Thus, triplet states generally have longer lifetimes than singlet states. These transitions are usually summarized in a state energy diagram or Jablonski diagram, the paradigm of molecular photochemistry.
These excited species, either S or T, have a half-empty low-energy orbital, and are consequently more oxidizing than the ground state. But at the same time, they have an electron in a high-energy orbital, and are thus more reducing. In general, excited species are prone to participate in electron transfer processes. | 5 | Photochemistry |
Mammalian FAS consists of a homodimer of two identical protein subunits, in which three catalytic domains in the N-terminal section (-ketoacyl synthase (KS), malonyl/acetyltransferase (MAT), and dehydrase (DH)), are separated by a core region (known as the interdomain) of 600 residues from four C-terminal domains (enoyl reductase (ER), -ketoacyl reductase (KR), acyl carrier protein (ACP) and thioesterase (TE)). The interdomain region allows the two monomeric domains to form a dimer.
The conventional model for organization of FAS (see the head-to-tail model on the right) is largely based on the observations that the bifunctional reagent 1,3-dibromopropanone (DBP) is able to crosslink the active site cysteine thiol of the KS domain in one FAS monomer with the phosphopantetheine prosthetic group of the ACP domain in the other monomer. Complementation analysis of FAS dimers carrying different mutations on each monomer has established that the KS and MAT domains can cooperate with the ACP of either monomer. and a reinvestigation of the DBP crosslinking experiments revealed that the KS active site Cys161 thiol could be crosslinked to the ACP 4'-phosphopantetheine thiol of either monomer. In addition, it has been recently reported that a heterodimeric FAS containing only one competent monomer is capable of palmitate synthesis.
The above observations seemed incompatible with the classical head-to-tail model for FAS organization, and an alternative model has been proposed, predicting that the KS and MAT domains of both monomers lie closer to the center of the FAS dimer, where they can access the ACP of either subunit (see figure on the top right).
A low resolution X-ray crystallography structure of both pig (homodimer) and yeast FAS (heterododecamer) along with a ~6 Å resolution electron cryo-microscopy (cryo-EM) yeast FAS structure have been solved. | 1 | Biochemistry |
Due to the binding capabilities of antipsychotic drugs and various neurotransmitters associated with mood, the sigma-2 receptor is a viable target for therapies related to neuropsychiatric disorders and modulation of emotional response. It is thought to be involved in the pathophysiology of schizophrenia, and sigma-2 receptors have been shown to be less abundant in schizophrenic patients. Additionally, PCP, which is an NMDA antagonist, can induce schizophrenia, while sigma-2 receptor activation has been shown to antagonize effects of PCP, implying antipsychotic capabilities. Sigma receptors are a potential target for treatment of dystonia, given high densities in affected regions of the brain. Anti-ischemics ifenprodil and eliprodil, the binding of which increases blood flow, have also shown affinity to sigma receptors.
In experimental trials in mice and rats, the sigma-2 receptor ligand siramesine caused reduced anxiety and displayed antidepressant capabilities, while other studies have shown inhibition of selective sigma receptor radioligands by antidepressants, in the mouse and rat brain. | 1 | Biochemistry |
A type of ion exchange chromatography, membrane exchange is a relatively new method of purification designed to overcome limitations of using columns packed with beads. Membrane Chromatographic devices are cheap to mass-produce and disposable unlike other chromatography devices that require maintenance and time to revalidate. There are three types of membrane absorbers that are typically used when separating substances. The three types are flat sheet, hollow fibre, and radial flow. The most common absorber and best suited for membrane chromatography is multiple flat sheets because it has more absorbent volume. It can be used to overcome mass transfer limitations and pressure drop, making it especially advantageous for isolating and purifying viruses, plasmid DNA, and other large macromolecules. The column is packed with microporous membranes with internal pores which contain adsorptive moieties that can bind the target protein. Adsorptive membranes are available in a variety of geometries and chemistry which allows them to be used for purification and also fractionation, concentration, and clarification in an efficiency that is 10 fold that of using beads. Membranes can be prepared through isolation of the membrane itself, where membranes are cut into squares and immobilized. A more recent method involved the use of live cells that are attached to a support membrane and are used for identification and clarification of signaling molecules. | 3 | Analytical Chemistry |
mA describes the methylation of the nitrogen at position 6 in the adenosine base within mRNA. Discovered in 1974, mA is the most abundant eukaryotic mRNA modification; most mRNAs contain approximately three mA residues. However, some mRNA transcripts do not contain any mA at all, while others may have 10 or more. The term "epitranscriptome" was coined following transcriptome-wide mappings of mA sites, but does not necessarily exclude other post-transcriptional mRNA modifications. How, and in response to what stimulus, the cell endogenously regulates the level of mA methylation remains unclear at present. However, it is known that the levels of this epitranscriptional mark are dynamically altered during embryonic development. Moreover, environmental stimuli such as stress can also alter the levels of mA.
The mA mRNA methylomes of different eukaryotic organisms have two common characteristics. First of all, the mark is usually found in the R[G > A]mAC[U>A>C>] or RRmACH sequence. Secondly, this mark is enriched in specific regions of the transcriptome; it is mostly found close to stop codons, in 3’-UTRs and in long internal exons. Nevertheless, mA levels vary between different RNAs within a cell and between different cell types of the same organism. The mechanisms controlling the addition of mA to some types of RNA have been described, but others remain unknown. | 1 | Biochemistry |
Artificially constructed plasmids may be used as vectors in genetic engineering. These plasmids serve as important tools in genetics and biotechnology labs, where they are commonly used to clone and amplify (make many copies of) or express particular genes. A wide variety of plasmids are commercially available for such uses. The gene to be replicated is normally inserted into a plasmid that typically contains a number of features for their use. These include a gene that confers resistance to particular antibiotics (ampicillin is most frequently used for bacterial strains), an origin of replication to allow the bacterial cells to replicate the plasmid DNA, and a suitable site for cloning (referred to as a multiple cloning site).
DNA structural instability can be defined as a series of spontaneous events that culminate in an unforeseen rearrangement, loss, or gain of genetic material. Such events are frequently triggered by the transposition of mobile elements or by the presence of unstable elements such as non-canonical (non-B) structures. Accessory regions pertaining to the bacterial backbone may engage in a wide range of structural instability phenomena. Well-known catalysts of genetic instability include direct, inverted, and tandem repeats, which are known to be conspicuous in a large number of commercially available cloning and expression vectors. Insertion sequences can also severely impact plasmid function and yield, by leading to deletions and rearrangements, activation, down-regulation or inactivation of neighboring gene expression. Therefore, the reduction or complete elimination of extraneous noncoding backbone sequences would pointedly reduce the propensity for such events to take place, and consequently, the overall recombinogenic potential of the plasmid. | 1 | Biochemistry |
FYVE, RhoGEF and PH domain containing (FGD) is a gene family consisting of:
* FGD1
* FGD2
* FGD3
* FGD4
Type 1 is associated with Aarskog-Scott syndrome. | 1 | Biochemistry |
Limited precision of chemical shift measurements also puts an upper limit of about 4 on . Limited to diamagnetic systems. H NMR cannot be used with solutions of compounds in HO. | 7 | Physical Chemistry |
The earliest records of bloomery-type furnaces in East Africa are discoveries of smelted iron and carbon in Nubia n ancient Sudan dated at least to the seventh to the sixth century BC. The ancient bloomeries that produced metal tools for the Nubians and Kushites produced a surplus for sale. All traditional sub-Saharan African iron-smelting processes are variants of the bloomery process. There is considerable discussion about the origins of iron metallurgy in Africa. Smelting in bloomery type furnaces in West Africa and forging of tools appeared in the Nok culture of central Nigeria by at least 550 BC and possibly several centuries earlier. Also, evidence indicates iron smelting with bloomery-style furnaces dated to 750 BC in Opi (Augustin Holl 2009) and Lejja dated to 2,000 BC (Pamela Eze-Uzomaka 2009), both sites in the Nsukka region of southeast Nigeria in what is now Igboland. The site of Gbabiri, in the Central African Republic, has also yielded evidence of iron metallurgy, from a reduction furnace and blacksmith workshop, with earliest dates of 896–773 and 907–796 BC, respectively. | 8 | Metallurgy |
Solarization refers to a phenomenon in physics where a material undergoes a temporary change in color after being subjected to high-energy electromagnetic radiation, such as ultraviolet light or X-rays. Clear glass and many plastics will turn amber, green or other colors when subjected to X-radiation, and glass may turn blue after long-term solar exposure in the desert. It is believed that solarization is caused by the formation of internal defects, called color centers, which selectively absorb portions of the visible light spectrum. In glass, color center absorption can often be reversed by heating the glass to high temperatures (a process called thermal bleaching) to restore the glass to its initial transparent state. Solarization may also permanently degrade a material's physical or mechanical properties, and is one of the mechanisms involved in the breakdown of plastics within the environment. | 7 | Physical Chemistry |
In comparison to Proton exchange membrane electrolysis, the advantages of alkaline water electrolysis are mainly:
# Cheaper catalysts with respect to the platinum metal group based catalysts used for PEM water electrolysis.
# Higher durability due to an exchangeable electrolyte and lower dissolution of anodic catalyst.
# Higher gas purity due to lower gas diffusivity in alkaline electrolytes. | 7 | Physical Chemistry |
In biochemistry, electron bifurcation (EB) refers to a system that enables an unfavorable (endergonic) transformation by coupling to a favorable (exergonic) transformation. Two electrons are involved: one flows to an acceptor with a "higher reduction potential and the other with a lower reduction potential" than the donor. The process is suspected of being common in bioenergetics.
Two versions of EB are recognized. One involves redox of quinones and the other involves flavins. Quinones and flavins are cofactors that are capable of undergoing 2 – 2 proton redox.
A pervasive example of electron bifurcation is the Q cycle, which is part of the machinery that results in oxidative phosphorylation. In that case one electron from ubiquinol is directed to a Rieske cluster and the other electron is directed to a cytochrome b. | 7 | Physical Chemistry |
Molecular cloning is the laboratory process used to produce recombinant DNA. It is one of two most widely used methods, along with polymerase chain reaction (PCR), used to direct the replication of any specific DNA sequence chosen by the experimentalist. There are two fundamental differences between the methods. One is that molecular cloning involves replication of the DNA within a living cell, while PCR replicates DNA in the test tube, free of living cells. The other difference is that cloning involves cutting and pasting DNA sequences, while PCR amplifies by copying an existing sequence.
Formation of recombinant DNA requires a cloning vector, a DNA molecule that replicates within a living cell. Vectors are generally derived from plasmids or viruses, and represent relatively small segments of DNA that contain necessary genetic signals for replication, as well as additional elements for convenience in inserting foreign DNA, identifying cells that contain recombinant DNA, and, where appropriate, expressing the foreign DNA. The choice of vector for molecular cloning depends on the choice of host organism, the size of the DNA to be cloned, and whether and how the foreign DNA is to be expressed. The DNA segments can be combined by using a variety of methods, such as restriction enzyme/ligase cloning or Gibson assembly.
In standard cloning protocols, the cloning of any DNA fragment essentially involves seven steps: (1) Choice of host organism and cloning vector, (2) Preparation of vector DNA, (3) Preparation of DNA to be cloned, (4) Creation of recombinant DNA, (5) Introduction of recombinant DNA into the host organism, (6) Selection of organisms containing recombinant DNA, and (7) Screening for clones with desired DNA inserts and biological properties.
These steps are described in some detail in a related article (molecular cloning). | 1 | Biochemistry |
There are a number of non-invasive head cooling caps and helmets designed to target cooling at the brain. A hypothermia cap is typically made of a synthetic material such as neoprene, silicone, or polyurethane and filled with a cooling agent such as ice or gel which is either cooled to a very cold temperature, , before application or continuously cooled by an auxiliary control unit. Their most notable uses are in preventing or reducing alopecia in chemotherapy, and for preventing cerebral palsy in babies born with hypoxic ischemic encephalopathy. In the continuously cooled iteration, coolant is cooled with the aid of a compressor and pumped through the cooling cap. Circulation is regulated by means of valves and temperature sensors in the cap. If the temperature deviates or if other errors are detected, an alarm system is activated. The frozen iteration involves continuous application of caps filled with Crylon gel cooled to to the scalp before, during and after intravenous chemotherapy. As the caps warm on the head, multiple cooled caps must be kept on hand and applied every 20 to 30 minutes. | 1 | Biochemistry |
Much of the Bay is shallow. At the point where the Susquehanna River flows into the Bay, the average depth is , although this soon diminishes to an average of southeast of the city of Havre de Grace, Maryland, to about just north of Annapolis. On average, the depth of the Bay is , including tributaries; over 24 percent of the Bay is less than deep.
Because the Bay is an estuary, it has fresh water, salt water and brackish water. Brackish water has three salinity zones: oligohaline, mesohaline, and polyhaline. The freshwater zone runs from the mouth of the Susquehanna River to north Baltimore. The oligohaline zone has very little salt. Salinity varies from 0.5 ppt (parts per thousand) to 10 ppt, and freshwater species can survive there. The north end of the oligohaline zone is north Baltimore and the south end is the Chesapeake Bay Bridge. The mesohaline zone has a medium amount of salt and runs from the Bay Bridge to the mouth of the Rappahannock River. Salinity there ranges from 1.07% to 1.8%. The polyhaline zone is the saltiest zone, and some of the water can be as salty as sea water. It runs from the mouth of the Rappahannock River to the mouth of the Bay. The salinity ranges from 1.87% to 3.6%. (3.6% is as salty as the ocean.)
The climate of the area surrounding the Bay is primarily humid subtropical, with hot, very humid summers and cold to mild winters. Only the area around the mouth of the Susquehanna River is continental in nature, and the mouth of the Susquehanna River and the Susquehanna flats often freeze in winter. It is rare for the surface of the Bay to freeze in winter, something that happened most recently in the winter of 1976–77.
The Chesapeake Bay is the end point of over 150 rivers and streams. The largest rivers flowing directly into the Bay, in order of discharge, are:
* Susquehanna River
* Potomac River
* James River
* Rappahannock River
* York River
* Patuxent River
* Choptank River
For more information on Chesapeake Bay rivers, see the List of Chesapeake Bay rivers. | 2 | Environmental Chemistry |
As a separation technique, GPC has many advantages. First of all, it has a well-defined separation time due to the fact that there is a final elution volume for all unretained analytes. Additionally, GPC can provide narrow bands, although this aspect of GPC is more difficult for polymer samples that have broad ranges of molecular weights present. Finally, since the analytes do not interact chemically or physically with the column, there is a lower chance for analyte loss to occur. For investigating the properties of polymer samples in particular, GPC can be very advantageous. GPC provides a more convenient method of determining the molecular weights of polymers. In fact most samples can be thoroughly analyzed in an hour or less. Other methods used in the past were fractional extraction and fractional precipitation. As these processes were quite labor-intensive molecular weights and mass distributions typically were not analyzed. Therefore, GPC has allowed for the quick and relatively easy estimation of molecular weights and distribution for polymer samples | 3 | Analytical Chemistry |
Activation of β adrenergic receptors on airway smooth muscle leads to the activation of adenylate cyclase and to an increase in the intracellular concentration of 3,5-cyclic adenosine monophosphate (cyclic AMP). The increase in cyclic AMP is associated with the activation of protein kinase A, which in turn, inhibits the phosphorylation of myosin and lowers intracellular ionic calcium concentrations, resulting in muscle relaxation.
Levosalbutamol relaxes the smooth muscles of all airways, from the trachea to the terminal bronchioles. Increased cyclic AMP concentrations are also associated with the inhibition of the release of mediators from mast cells in the airways. Levosalbutamol acts as a functional agonist that relaxes the airway irrespective of the spasmogen involved, thereby protecting against all bronchoconstrictor challenges.
While it is recognized that β adrenergic receptors are the predominant receptors on bronchial smooth muscle, data indicate that there are beta receptors in the human heart, 10–50% of which are β adrenergic receptors. The precise function of these receptors has not been established. However, all β adrenergic agonist drugs can produce a significant cardiovascular effect in some patients, as measured by pulse rate, blood pressure, and restlessness symptoms, and/or electrocardiographic (ECG). | 4 | Stereochemistry |
Macroprolactin is the term used to describe complexed forms of the pituitary hormone prolactin which are found in blood. The most common complex found in blood consists of prolactin and immunoglobulin G (IgG). While the free prolactin hormone is active, prolactin in the macroprolactin complex does not have any biological activity in the body and is considered benign. However, macroprolactin is detected by all Laboratory tests that measure prolactin in blood. This leads to misdiagnosis of hyperprolactinaemia in many people, especially those with other symptoms, such as infertility or menstrual problems.
"Macroprolactin" is most commonly a complex of prolactin and IgG (typically IgG4), displaying a molecular weight of approximately 150 kDa (which is hence 6–7 fold higher that the native molecule). Polymeric aggregate of highly glycosylated prolactin monomers or prolactin-IgA complexes (i.e. non-IgG-type macroprolactin) act similarly and also count as "macroprolactin".
In patients with hyperprolactinemia, the serum pattern of prolactin isoforms usually encompasses 60%–90% monomeric prolactin, 15%–30% big-prolactin (40–60 kDa: usually prolactin dimers or big-big degradation products) and 0%–10% big-big prolactin (>100 kDa). The condition of macroprolactinaemia is hence defined as predominance (i.e. >30%–60%) of circulating prolactin isoforms with molecular weight >100 kDa.
There are certain chemicals, such as polyethylene glycol, that can be added to remove macroprolactin from a suspicious sample. The sample can then be re-analysed to see if the prolactin levels are still high. The gold standard test to diagnose macroprolactin is gel-filtration chromatography. | 1 | Biochemistry |
The liver is the second largest organ (after the skin) and is an accessory digestive gland which plays a role in the body's metabolism. The liver has many functions some of which are important to digestion. The liver can detoxify various metabolites; synthesise proteins and produce biochemicals needed for digestion. It regulates the storage of glycogen which it can form from glucose (glycogenesis). The liver can also synthesise glucose from certain amino acids. Its digestive functions are largely involved with the breaking down of carbohydrates. It also maintains protein metabolism in its synthesis and degradation. In lipid metabolism it synthesises cholesterol. Fats are also produced in the process of lipogenesis. The liver synthesises the bulk of lipoproteins. The liver is located in the upper right quadrant of the abdomen and below the diaphragm to which it is attached at one part, the bare area of the liver. This is to the right of the stomach and it overlies the gall bladder. The liver synthesises bile acids and lecithin to promote the digestion of fat. | 1 | Biochemistry |
The idea of microscopic reversibility was born together with physical kinetics. In 1872, Ludwig Boltzmann represented kinetics of gases as statistical ensemble of elementary collisions. Equations of mechanics are reversible in time, hence, the reverse collisions obey the same laws. This reversibility of collisions is the first example of microreversibility. According to Boltzmann, this microreversibility implies the principle of detailed balance for collisions: at the equilibrium ensemble each collision is equilibrated by its reverse collision. These ideas of Boltzmann were analyzed in detail and generalized by Richard C. Tolman.
In chemistry, J. H. van't Hoff (1884) came up with the idea that equilibrium has dynamical nature and is a result of the balance between the forward and backward reaction rates. He did not study reaction mechanisms with many elementary reactions and could not formulate the principle of detailed balance for complex reactions. In 1901, Rudolf Wegscheider introduced the principle of detailed balance for complex chemical reactions. He found that for a complex reaction the principle of detailed balance implies important and non-trivial relations between reaction rate constants for different reactions. In particular, he demonstrated that the irreversible cycles of reaction are impossible and for the reversible cycles the product of constants of the forward reactions (in the "clockwise" direction) is equal to the product of constants of the reverse reactions (in the "anticlockwise" direction). Lars Onsager (1931) used these relations in his well-known work, without direct citation but with the following remark:
The quantum theory of emission and absorption developed by Albert Einstein (1916, 1917) gives an example of application of the microreversibility and detailed balance to development of a new branch of kinetic theory.
Sometimes, the principle of detailed balance is formulated in the narrow sense, for chemical reactions only but in the history of physics it has the broader use: it was invented for collisions, used for emission and absorption of quanta, for transport processes and for many other phenomena.
In its modern form, the principle of microreversibility was published by Lewis (1925). In the classical textbooks full theory and many examples of applications are presented. | 7 | Physical Chemistry |
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