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For its medical uses, 1,1,1,2-tetrafluoroethane has the generic name norflurane. It is used as propellant for some metered dose inhalers. It is considered safe for this use. In combination with pentafluoropropane, it is used as a topical vapocoolant spray for numbing boils before curettage. It has also been studied as a potential inhalational anesthetic, but it is nonanaesthetic at doses used in inhalers. | 2 | Environmental Chemistry |
Following the lead of Dachlauer and Jackel, contemporary routes to episulfides utilize a two-step method, converting an olefin to an epoxide followed by thiation using thiocyanate or thiourea.
Episulfides can also be prepared from cyclic carbonates, hydroxy mercaptans, hydroxyalkyl halides, dihaloalkanes, and halo mercaptans. The reaction of ethylene carbonate and KSCN gives ethylene sulfide:
The metal-catalyzed reaction of sulfur with alkenes has been demonstrated. | 0 | Organic Chemistry |
The first PAFP, Kaede (protein), was isolated from Trachyphyllia geoffroyi in a cDNA library screen designed to identify new fluorescent proteins. A fluorescent green protein derived from this screen was serendipitously discovered to have sensitivity to ultraviolet light-- | 1 | Biochemistry |
C/EBPβ has been found to have a role in the development of osteoporosis. The full-length isoform of the C/EBPβ protein (LAP) activates the MafB gene, whereas the short isoform (LIP) suppresses it. MafB gene activation suppresses the formation of osteoclasts. Thus, upregulation of LAP diminishes the number of osteoclasts, and this weakens the osteoporotic process, whereas upregulation of LIP does the opposite, increasing loss of bone mass.
The LAP/LIP balance is determined by the mTOR protein. Inhibition of the expression of mTOR can stop osteoclast activity. | 1 | Biochemistry |
In general terms, the free energy change (ΔG) of a reaction determines whether a chemical change will take place, but kinetics describes how fast the reaction is. A reaction can be very exothermic and have a very positive entropy change but will not happen in practice if the reaction is too slow. If a reactant can produce two products, the thermodynamically most stable one will form in general, except in special circumstances when the reaction is said to be under kinetic reaction control. The Curtin–Hammett principle applies when determining the product ratio for two reactants interconverting rapidly, each going to a distinct product. It is possible to make predictions about reaction rate constants for a reaction from free-energy relationships.
The kinetic isotope effect is the difference in the rate of a chemical reaction when an atom in one of the reactants is replaced by one of its isotopes.
Chemical kinetics provides information on residence time and heat transfer in a chemical reactor in chemical engineering and the molar mass distribution in polymer chemistry. It is also provides information in corrosion engineering. | 7 | Physical Chemistry |
If Z is a state function then the balance of Z remains unchanged during a cyclic process:
Entropy is a state function and is defined in an absolute sense through the Third Law of Thermodynamics as
where a reversible path is chosen from absolute zero to the final state, so that for an isothermal reversible process
In general, for any cyclic process the state points can be connected by reversible paths, so that
meaning that the net entropy change of the working fluid over a cycle is zero. | 7 | Physical Chemistry |
In addition to lipid rafts, cholesterol can also interact with proteins that possess lipid-binding domains, such as certain types of sterol-sensing domains or cholesterol recognition/interaction amino acid consensus (CRAC) motifs. These interactions can affect protein conformation, stability, and function, thereby influencing various cellular processes like signal transduction, membrane trafficking, and enzyme activity. As a signaling lipid, cholesterol may act as a ligand. | 1 | Biochemistry |
Proteinase K is commonly used in molecular biology to digest protein and remove contamination from preparations of nucleic acid. Addition of Proteinase K to nucleic acid preparations rapidly inactivates nucleases that might otherwise degrade the DNA or RNA during purification. It is highly suited to this application since the enzyme is active in the presence of chemicals that denature proteins, such as SDS and urea, chelating agents such as EDTA, sulfhydryl reagents, as well as trypsin or chymotrypsin inhibitors.
Proteinase K is used for the destruction of proteins in cell lysates (tissue, cell culture cells) and for the release of nucleic acids, since it very effectively inactivates DNases and RNases. Some examples for applications:
Proteinase K is very useful in the isolation of highly native, undamaged DNAs or RNAs, since most microbial or mammalian DNases and RNases are rapidly inactivated by the enzyme, particularly in the presence of 0.5–1% SDS.
The enzyme's activity towards native proteins is stimulated by denaturants such as SDS. In contrast, when measured using peptide substrates, denaturants inhibit the enzyme. The reason for this result is that the denaturing agents unfold the protein substrates and make them more accessible to the protease. | 1 | Biochemistry |
A variety of nanoparticle materials have been demonstrated to promote various electrochemical reactions, although none have been commercialized. These catalysts can be tuned with respect to their size and shape, as well as the surface strain.
Also, higher reaction rates can be achieved by precisely controlling the arrangement of surface atoms: indeed, in nanometric systems, the number of available reaction sites is a better parameter than the exposed surface area in order to estimate electrocatalytic activity. Sites are the positions where the reaction could take place; the likelihood of a reaction to occur in a certain site depends on the electronic structure of the catalyst, which determines the adsorption energy of the reactants together with many other variables not yet fully clarified.
According to the TSK model, the catalyst surface atoms can be classified as terrace, step or kink atoms according to their position, each characterized by a different coordination number. In principle, atoms with lower coordination number (kinks and defects) tend to be more reactive and therefore adsorb the reactants more easily: this may promote kinetics but could also depress it if the adsorbing species isn't the reactant, thus inactivating the catalyst. Advances in nanotechnology make it possible to surface engineer the catalyst so that just some desired crystal planes are exposed to reactants, maximizing the number of effective reaction sites for the desired reaction.
To date, a generalized surface dependence mechanism cannot be formulated since every surface effect is strongly reaction-specific. A few classifications of reactions based on their surface dependence have been proposed but there are still many exceptions that do not fall into them. | 7 | Physical Chemistry |
Transduction was discovered in Salmonella by Norton Zinder and Joshua Lederberg at the University of Wisconsin–Madison in 1952. | 1 | Biochemistry |
Best polymerization conditions for acrylamide gels are obtained at 25–30 °C and polymerization seems terminated after 20–30 min of reaction although residual monomers (10–30%) are detected after this time. The co-polymerization of acrylamide (AA) monomer/N,N'-Methylenebisacrylamide (Bis-AA) cross-linker initiated by ammonium persulfate (APS)/tetramethylethylenediamine (TEMED) reactions, is most efficient at alkaline pH of the acrylamide solution. Thereby, acrylamide chains are created and cross-linked at a time. Due to the properties of the electrophoresis buffer, the gel polymerization is conducted at pH 10.00 making sure an efficient use of TEMED and APS as catalysts of the polymerization reaction, and concurrently, suppressing a competitive hydrolysis of the produced acrylamide polymer network. Polymer networks are three-dimensionally linked polymer chains. Otherwise, proteins could be modified by reaction with unpolymerized monomers of acrylamide, forming covalent acrylamide adduction products that may result in multiple bands.
Additionally, the time of polymerization of a gel may directly affect the peak-elution times of separated metalloproteins in the electropherogram due to the compression and dilatation of the gels and their pores if the incubation times for the reaction mixture (gel solution) used to prepare a gel are not optimized (cf. fig. Electropherogram, see sect. Reproducibility and recovery). In order to ensure maximum reproducibility in gel pore size and to obtain a fully polymerized and non-restrictive large pore gel for a PAGE run, the polyacrylamide gel is polymerized for a time period of 69 hr at room temperature (RT) in a gel column located on the casting stand. The exothermic heat generated by the polymerization processes is dissipated constantly while the temperature may rise rapidly to over 75 °C in the first minutes, after which it falls slowly. After 69 hr, the gel has reached room temperature and is in its lowest energy state, as the basic chemical reactions and gelation are complete. Gelation means that the
solvent (water) gets immobilized within the polymer network by means of hydrogen bonds and also van der Waals forces. As a result, the prepared gel is homogeneous (in terms of homogeneous distribution of cross-links throughout the gel sample), inherently stable and free of monomers or radicals. Fresh polyacrylamide gels are further hydrophilic, electrically neutral and do not bind proteins. Sieving effects due to gravity-induced compression of the gel can be excluded for the same reasons. Thus, in a medium without molecular sieving properties a high-resolution can be expected.
Before an electrophoretic run is started the prepared 4% T (total polymer content (T)), 2.67% C (cross-linker concentration (C)) gel is pre-run to equilibrate it. It is essentially non-sieving and optimal for electrophoresis of proteins greater than or equal to 200 ku. Proteins migrate in it more or less on the basis of their free mobility. For these reasons interactions of the gel with the biomolecules are negligibly low, and thus, the proteins separate cleanly and predictably at a polymerization time of 69 hr (cf. fig. Electropherogram). The separated metalloproteins including biomolecules ranging from approximately < 1 ku to greater than 30 ku (e.g., metal chaperones, prions, metal transport proteins, amyloids, metalloenzymes, metallopeptides, metallothionein, phytochelatins) are not dissociated into apoproteins and metal cofactors. | 3 | Analytical Chemistry |
Protein was studied using a protein nanoprobe (that enables cross-linking) that introduced photo-methionine within the protein (during the recombinant expression) which lead to the protein keeping its reserved structure while having the ability to be mapped out for its interactions. The model was used as a region of contact surface that is involved in a well-known interaction (homodimerization) between two molecules of 14-3-3ζ protein. Once the photo-methionine is introduced and has become activated using UV-light, it can cross-link with no specificity (meaning no group) and the links have zero-length. High resolution mass spectrometry or MS can (even MS/MS) be used then to determine the cross-linked residues and the reaction radius; allowing the researchers to characterize and research the homodimerization of the protein. The usage of the high-resolution MS with photo-methionine has its advantages as it again allows the protein to be in its native state, there are reasonable time scales while using small quantities of the protein. There are also fewer limitations on the reaction specificity and restrictions using a photo-active cross-linker (photo-methionine) compared to chemical cross-linking. This method of combined photo-initiated cross-linking from the protein nanoprobe in tandem with MS could be useful to characterize not only homodimer formation but also oligomers and in theory; heteromers (such as the composition of the protein-protein mixture and its functionality). | 5 | Photochemistry |
Tertiary alcohols react with strong acids to generate carbocations. The reaction is related to their dehydration, e.g. isobutylene from tert-butyl alcohol. A special kind of dehydration reaction involves triphenylmethanol and especially its amine-substituted derivatives. When treated with acid, these alcohols lose water to give stable carbocations, which are commercial dyes. | 0 | Organic Chemistry |
Precession electron diffraction (PED) is a specialized method to collect electron diffraction patterns in a transmission electron microscope (TEM). By rotating (precessing) a tilted incident electron beam around the central axis of the microscope, a PED pattern is formed by integration over a collection of diffraction conditions. This produces a quasi-kinematical diffraction pattern that is more suitable as input into direct methods algorithms to determine the crystal structure of the sample. | 3 | Analytical Chemistry |
The surface energy of a liquid may be measured by stretching a liquid membrane (which increases the surface area and hence the surface energy). In that case, in order to increase the surface area of a mass of liquid by an amount, , a quantity of work, , is needed (where is the surface energy density of the liquid). However, such a method cannot be used to measure the surface energy of a solid because stretching of a solid membrane induces elastic energy in the bulk in addition to increasing the surface energy.
The surface energy of a solid is usually measured at high temperatures. At such temperatures the solid creeps and even though the surface area changes, the volume remains approximately constant. If is the surface energy density of a cylindrical rod of radius and length at high temperature and a constant uniaxial tension , then at equilibrium, the variation of the total Helmholtz free energy vanishes and we have
where is the Helmholtz free energy and is the surface area of the rod:
Also, since the volume () of the rod remains constant, the variation () of the volume is zero, that is,
Therefore, the surface energy density can be expressed as
The surface energy density of the solid can be computed by measuring , , and at equilibrium.
This method is valid only if the solid is isotropic, meaning the surface energy is the same for all crystallographic orientations. While this is only strictly true for amorphous solids (glass) and liquids, isotropy is a good approximation for many other materials. In particular, if the sample is polygranular (most metals) or made by powder sintering (most ceramics) this is a good approximation.
In the case of single-crystal materials, such as natural gemstones, anisotropy in the surface energy leads to faceting. The shape of the crystal (assuming equilibrium growth conditions) is related to the surface energy by the Wulff construction. The surface energy of the facets can thus be found to within a scaling constant by measuring the relative sizes of the facets. | 7 | Physical Chemistry |
The excess volume is another important property in the characterization of grain boundaries. Excess volume was first proposed by Bishop in a private communication to Aaron and Bolling in 1972. It describes how much expansion is induced by the presence of a GB and is thought that the degree and susceptibility of segregation is directly proportional to this. Despite the name the excess volume is actually a change in length, this is because of the 2D nature of GBs the length of interest is the expansion normal to the GB plane. The excess volume () is defined in the following way,
at constant temperature , pressure and number of atoms . Although a rough linear relationship between GB energy and excess volume exists the orientations where this relationship is violated can behave significantly differently affecting mechanical and electrical properties.
Experimental techniques have been developed which directly probe the excess volume and have been used to explore the properties of nanocrystalline copper and nickel. Theoretical methods have also been developed and are in good agreement. A key observation is that there is an inverse relationship with the bulk modulus meaning that the larger the bulk modulus (the ability to compress a material) the smaller the excess volume will be, there is also direct relationship with the lattice constant, this provides methodology to find materials with a desirable excess volume for a specific application. | 8 | Metallurgy |
One of the most exciting and most studied uses of photocatalysis is the photo-oxidation of organics as it applies to environmental decontamination.
In contrast to gas phase interactions with the solid surface, the vast number of variables associated with the liquid solid interface (i.e. solution pH, photocatalyst concentration, solvent effects, diffusion rate, etc.) calls for greater care to be taken to control these variables to produce consistent experimental results. A greater variety of reactions also become possible due to the ability of solutions to stabilize charged species, making it possible to add an electron from the metal to a neutral species producing an anion that can go on to further react, or a hole to remove an electron, producing a cation that goes on to further react in solution. | 7 | Physical Chemistry |
The termination of transcription of pre-rRNA genes by polymerase Pol I is performed by a system that needs a specific transcription termination factor. The mechanism used bears some resemblance to the rho-dependent termination in prokaryotes. Eukaryotic cells contain hundreds of ribosomal DNA repeats, sometimes distributed over multiple chromosomes. Termination of transcription occurs in the ribosomal intergenic spacer region that contains several transcription termination sites upstream of a Pol I pausing site. Through a yet unknown mechanism, the 3’-end of the transcript is cleaved, generating a large primary rRNA molecule that is further processed into the mature 18S, 5.8S and 28S rRNAs.
As Pol II reaches the end of a gene, two protein complexes carried by the CTD, CPSF (cleavage and polyadenylation specificity factor) and CSTF (cleavage stimulation factor), recognize the poly-A signal in the transcribed RNA. Poly-A-bound CPSF and CSTF recruit other proteins to carry out RNA cleavage and then polyadenylation. Poly-A polymerase adds approximately 200 adenines to the cleaved 3’ end of the RNA without a template. The long poly-A tail is unique to transcripts made by Pol II.
In the process of terminating transcription by Pol I and Pol II, the elongation complex does not dissolve immediately after the RNA is cleaved. The polymerase continues to move along the template, generating a second RNA molecule associated with the elongation complex. Two models have been proposed to explain how termination is achieved at last. The allosteric model states that when transcription proceeds through the termination sequence, it causes disassembly of elongation factors and/or an assembly of termination factors that cause conformational changes of the elongation complex. The torpedo model suggests that a 5 to 3 exonuclease degrades the second RNA as it emerges from the elongation complex. Polymerase is released as the highly processive exonuclease overtakes it. It is proposed that an emerging view will express a merge of these two models. | 1 | Biochemistry |
The Debye length has become increasingly significant in the modeling of solid state devices as improvements in lithographic technologies have enabled smaller geometries.
The Debye length of semiconductors is given:
where
* ε is the dielectric constant,
* k is the Boltzmann constant,
* T is the absolute temperature in kelvins,
* q is the elementary charge, and
* N is the net density of dopants (either donors or acceptors).
When doping profiles exceed the Debye length, majority carriers no longer behave according to the distribution of the dopants. Instead, a measure of the profile of the doping gradients provides an "effective" profile that better matches the profile of the majority carrier density.
In the context of solids, Thomas–Fermi screening length may be required instead of Debye length. | 7 | Physical Chemistry |
N6,2'-O-dimethyladenosine, abundant in polyA+ mRNAs, occurs at the first nucleotide after the 5’ cap, when an additional methyl group is added to a 2ʹ-O-methyladenosine residue at the ‘capped’ 5ʹ end of mRNA.
Since m6Am can be recognized by anti-m6A antibodies at transcription start sites, the methods used for m6A profiling can be and were adapted for m6Am profiling, namely m6A-seq, and miCLIP (see m6A-seq and miCLIP descriptions above). | 1 | Biochemistry |
Trifluoromethanesulfonyl chloride (or triflyl chloride, CF3SO2Cl) can be used in a highly efficient method to introduce a trifluoromethyl group to aromatic and heteroaromatic systems, including known pharmaceuticals such as Lipitor. The chemistry is general and mild, and uses a photoredox catalyst and a light source at room temperature. | 0 | Organic Chemistry |
Following a major forgery of Australias newly introduced $10 notes in 1967, Solomon was invited to a meeting about how to make more secure bank notes. Given his background in polymer science Solomons idea was to print the notes on a plastic substrate rather than the traditional paper, and incorporate optically variable devices – defined as a device that changes its appearance when something external is done to the note.
Solomon went on to lead the research team and was the principal inventor of the worlds first polymer banknote, with the first note issued into circulation in 1988: the Australian bicentennial $10. He has chronicled the history of the development of polymer banknotes in The Plastic Banknote: From Concept to Reality', co-authored with Tom Spurling (published in 2014). | 7 | Physical Chemistry |
DNA fragmentation is the separation or breaking of DNA strands into pieces. It can be done intentionally by laboratory personnel or by cells, or can occur spontaneously. Spontaneous or accidental DNA fragmentation is fragmentation that gradually accumulates in a cell. It can be measured by e.g. the Comet assay or by the TUNEL assay.
Its main units of measurement is the DNA Fragmentation Index (DFI). A DFI of 20% or more significantly reduces the success rates after ICSI.
DNA fragmentation was first documented by Williamson in 1970 when he observed discrete oligomeric fragments occurring during cell death in primary neonatal liver cultures. He described the cytoplasmic DNA isolated from mouse liver cells after culture as characterized by DNA fragments with a molecular weight consisting of multiples of 135 kDa. This finding was consistent with the hypothesis that these DNA fragments were a specific degradation product of nuclear DNA. | 1 | Biochemistry |
Diverted total synthesis in chemistry is a strategy in drug discovery aiming at organic synthesis of natural product analogues rather than the natural product itself. The target can be the modification of a natural product or the modification of an intermediate. In this sense it differs from other strategies such as total synthesis and semisynthesis. The purpose can be gaining a scientific understanding of the biological activity of the original natural product or the discovery of new drugs with the same biological activity but simpler to produce. The concept was introduced by Samuel J. Danishefsky in 2006. Notable examples of this strategy are the potential drug ixabepilone which is an analogue of the natural product epothilone B and carfilzomib which is derived from epoxomicin and eravacycline derived from tetracycline. Cabergoline is derived from a number of ergot alkaloids one of which is lysergic acid and Simvastatin is based on Lovastatin.
Diverted total synthesis is a topic in academic research. | 0 | Organic Chemistry |
During application, the building is enclosed and filled with the gas for a period of time, usually at least 16–18 hours, sometimes as long as 72 hours. The building must then be ventilated, generally for at least 6 hours, before occupants can return. California regulations are such that the tent will be on for three to five days, which includes ventilation. In the US, sulfuryl fluoride must be transported in a vehicle marked with "Inhalation Hazard 2" placards. Most states require a license or certification for the individual applying the fumigant.
The concentration is continuously monitored and maintained at the specified level using electronic equipment. Possible leakages are also checked by low range electronic detectors. Reentry to the home is allowed when the concentration level is at or below 5 ppm. Sulfuryl fluoride is colorless and odorless, however, during the fumigation process, a warning agent called chloropicrin is first released into the building to ensure that no occupants remain. Tent fumigation is the most effective treatment for the extermination of known and unknown infestations of wood-destroying insects. Heat is the only other approved method for whole structure treatment for termites in California. Sulfuryl fluoride provides no protection from future infestations, although heavy re-infestation can take several years since drywood termites have slower growing colonies than ground termites. | 2 | Environmental Chemistry |
In his work at the University of Giessen, Kröhnke observed condensation of α-pyridinium methyl ketone salts 1 with α,β-unsaturated carbonyl compounds 2 via a Michael reaction when treated with ammonium acetate to give 2,4,6-trisubstituted pyridines in high yields under mild reaction conditions. The proposed intermediates, 1, 5-dicarbonyl compound 3, have not been isolated. Since its discovery, the Kröhnke synthesis has enjoyed broad applicability to the preparation of di-,tri- and tetrapyridine derivatives, demonstrating a number of advantages over related reactions such as the Hantzsch pyridine synthesis. | 0 | Organic Chemistry |
Nuclease Prime Editor uses Cas9 nuclease instead of Cas9(H840A) nickase. Unlike prime editor 3 (PE3) that requires dual-nick at both DNA strands to induce efficient prime editing, Nuclease Prime Editor requires only a single pegRNA since the single-gRNA already creates double-strand break instead of single-strand nick. | 1 | Biochemistry |
The IIR has over 200 publications available on refrigeration technologies and applications: reference documents, guides, technical books, conference and congress papers and proceedings, tables and diagrams comprising the thermophysical properties of refrigerants.
Books in the refrigeration field published by other publishers are also available for purchase. | 7 | Physical Chemistry |
In thermodynamics, an adiabatic wall between two thermodynamic systems does not allow heat or chemical substances to pass across it, in other words there is no heat transfer or mass transfer.
In theoretical investigations, it is sometimes assumed that one of the two systems is the surroundings of the other. Then it is assumed that the work transferred is reversible within the surroundings, but in thermodynamics it is not assumed that the work transferred is reversible within the system. The assumption of reversibility in the surroundings has the consequence that the quantity of work transferred is well defined by macroscopic variables in the surroundings. Accordingly, the surroundings are sometimes said to have a reversible work reservoir.
Along with the idea of an adiabatic wall is that of an adiabatic enclosure. It is easily possible that a system has some boundary walls that are adiabatic and others that are not. When some are not adiabatic, then the system is not adiabatically enclosed, though adiabatic transfer of energy as work can occur across the adiabatic walls.
The adiabatic enclosure is important because, according to one widely cited author, Herbert Callen, "An essential prerequisite for the measurability of energy is the existence of walls that do not permit the transfer of energy in the form of heat." In thermodynamics, it is customary to assume a priori the physical existence of adiabatic enclosures, though it is not customary to label this assumption separately as an axiom or numbered law. | 7 | Physical Chemistry |
UDP-Galactose is especially relevant in glycolysis. It is derived from galactose an epimer of glucose, and via the Leloir Pathway, it is used be used as a precursor for the metabolism of glucose into pyruvate. When lactose is hydrolyzed, D-Galactose enters the liver via the bloodstream. There, galactokinase phosphorylates it to galactose-1-phosphate using ATP. This compound then engages in a "ping-pong" reaction with UDP-Glucose, catalyzed by uridylyltransferase, yielding glucose-1-phosphate and UDP-Galactose. This glucose-1-phosphate feeds into glycolysis, while UDP-Galactose undergoes epimerization to regenerate UDP-Glucose. | 1 | Biochemistry |
3-phosphoglycerate can be separated and measured using paper chromatography as well as with column chromatography and other chromatographic separation methods. It can be identified using both gas-chromatography and liquid-chromatography mass spectrometry and has been optimized for evaluation using tandem MS techniques. | 5 | Photochemistry |
The D-PUFAs are currently undergoing clinical trials in several human indications.
In general, reinforced by deuterium polyunsaturated fatty acids (D-PUFA) drugs:
* are deuterated forms of natural, essential PUFAs, identical to natural PUFAs bar one key property: D-PUFAs are significantly more resistant to lipid peroxidation;
* are chemically modified (novel chemical entity), but transported, processed and incorporated into membranes “naturally” by the body. Deuterium is naturally present in all humans, so H in place of H is recognized by the body as a “normal” hydrogen subtype;
* stop the chain reaction through a novel non-antioxidant mechanism at low, easily attainable levels, with no overt toxicity-related side effects.
* are delivered orally. PUFAs are essential nutrients, so the body avidly takes up dosed D-PUFA drugs, building up a therapeutic level in a matter of weeks;
* Favorably modulate important pathways such as ferroptosis, by inhibiting lipid peroxidation. | 7 | Physical Chemistry |
Polyprotic acids are acids that can lose more than one proton. The constant for dissociation of the first proton may be denoted as K, and the constants for dissociation of successive protons as K, etc. Citric acid is an example of a polyprotic acid HA, as it can lose three protons.
When the difference between successive pK values is less than about 3, there is overlap between the pH range of existence of the species in equilibrium. The smaller the difference, the more the overlap. In the case of citric acid, the overlap is extensive and solutions of citric acid are buffered over the whole range of pH 2.5 to 7.5.
Calculation of the pH with a polyprotic acid requires a speciation calculation to be performed. In the case of citric acid, this entails the solution of the two equations of mass balance:
C is the analytical concentration of the acid, C is the analytical concentration of added hydrogen ions, β are the cumulative association constants. K is the constant for self-ionization of water. There are two non-linear simultaneous equations in two unknown quantities [A] and [H]. Many computer programs are available to do this calculation. The speciation diagram for citric acid was produced with the program HySS.
N.B. The numbering of cumulative, overall constants is the reverse of the numbering of the stepwise, dissociation constants.
Cumulative association constants are used in general-purpose computer programs such as the one used to obtain the speciation diagram above. | 7 | Physical Chemistry |
Another use for FRET is in the study of metabolic or signaling pathways. For example, FRET and BRET have been used in various experiments to characterize G-protein coupled receptor activation and consequent signaling mechanisms. Other examples include the use of FRET to analyze such diverse processes as bacterial chemotaxis and caspase activity in apoptosis. | 1 | Biochemistry |
Ionic Atmosphere is a concept employed in Debye–Hückel theory which explains the electrolytic conductivity behaviour of solutions. It can be generally defined as the area at which a charged entity is capable of attracting an entity of the opposite charge. | 7 | Physical Chemistry |
Although all water that enters pit workings originates from atmospheric precipitation, the miner distinguishes between surface water and groundwater. Surface water enters the pit through openings in the mine at the surface of the ground, such as tunnel portals or shaft entrances. During heavy rain, water seeps into the earth and forms ground water when it meets layers of impervious rock. Pit water is mainly interstitial water and groundwater that seeps into the mine workings. | 9 | Geochemistry |
The ATP test is a process of rapidly measuring actively growing microorganisms through detection of adenosine triphosphate, or ATP. | 2 | Environmental Chemistry |
Several other minerals, such as the gemstone topaz, contain fluoride. Fluoride is not significant in seawater or brines, unlike the other halides, because the alkaline earth fluorides precipitate out of water. Commercially insignificant quantities of organofluorines have been observed in volcanic eruptions and in geothermal springs. Their ultimate origin (from biological sources or geological formation) is unclear.
The possibility of small amounts of gaseous fluorine within crystals has been debated for many years. One form of fluorite, antozonite, has a smell suggestive of fluorine when crushed. The mineral also has a dark black color, perhaps from free calcium (not bonded to fluoride). In 2012, a study reported detection of trace quantities (0.04% by weight) of diatomic fluorine in antozonite. It was suggested that radiation from small amounts of uranium within the crystals had caused the free fluorine defects. | 9 | Geochemistry |
Ampicillin is contraindicated in those with a hypersensitivity to penicillins, as they can cause fatal anaphylactic reactions. Hypersensitivity reactions can include frequent skin rashes and hives, exfoliative dermatitis, erythema multiforme, and a temporary decrease in both red and white blood cells.
Ampicillin is not recommended in people with concurrent mononucleosis, as over 40% of patients develop a skin rash. | 4 | Stereochemistry |
Activating Protein 2 (AP-2) is a family of closely related transcription factors which plays a critical role in regulating gene expression during early development. | 1 | Biochemistry |
Combined with the energy needed to produce hydrogen and purified atmospheric nitrogen, ammonia production is energy-intensive, accounting for 1% to 2% of global energy consumption, 3% of global carbon emissions, and 3% to 5% of natural gas consumption. Hydrogen required for ammonia synthesis is most often produced through gasification of carbon-containing material, mostly natural gas, but other potential carbon sources include coal, petroleum, peat, biomass, or waste. As of 2012, the global production of ammonia produced from natural gas using the steam reforming process was 72%. Hydrogen can also be produced from water and electricity using electrolysis: at one time, most of Europe's ammonia was produced from the Hydro plant at Vemork. Other possibilities include biological hydrogen production or photolysis, but at present, steam reforming of natural gas is the most economical means of mass-producing hydrogen.
The choice of catalyst is important for synthesizing ammonia. In 2012, Hideo Hosonos group found that Ru-loaded calcium-aluminum oxide C12A7: electride works well as a catalyst and pursued more efficient formation. This method is implemented in a small plant for ammonia synthesis in Japan. In 2019, Hosonos group found another catalyst, a novel perovskite oxynitride-hydride , that works at lower temperature and without costly ruthenium. | 7 | Physical Chemistry |
The PV diagram, then called an indicator diagram, was developed in 1796 by James Watt and his employee John Southern. Volume was traced by a plate moving with the piston, while pressure was traced by a pressure gauge whose indicator moved at right angles to the piston. A pencil was used to draw the diagram. Watt used the diagram to make radical improvements to steam engine performance. | 7 | Physical Chemistry |
An active metabolite, or pharmacologically active metabolite is a biologically active metabolite of a xenobiotic substance, such as a drug or environmental chemical. Active metabolites may produce therapeutic effects, as well as harmful effects. | 1 | Biochemistry |
Chromatofocusing is a protein-separation technique that allows resolution of single proteins and other ampholytes from a complex mixture according to differences in their isoelectric point. Chromatofocusing uses ion exchange resins and is typically performed on fast protein liquid chromatography (FPLC) or similar equipment capable of producing continuous buffer gradients, though this is not a requirement.
In contrast to typical ion exchange chromatography, where bound molecules are eluted from the resin by increasing the ionic strength of the buffer environment, chromatofocusing elutes bound species by altering the pH of the buffer. This changes the net surface charge of bound molecules, altering their avidity for the resin. As the changing pH of the buffer system traverses the pI of a given molecule, that molecule will elute from the resin as it will no longer possess a net surface charge (a requisite for molecular binding to ion exchange resins).
Chromatofocusing is a powerful purification technique with respect to proteins as it can resolve very similar species differing by less than 0.05 pH units that may not separate well, or at all, using traditional ion exchange strategies.
A major drawback to this technique is that some proteins will aggregate when they are present at relatively high concentrations and carry no net surface charge. This can cause blockage of the resin, which is highly problematic when using sealed columns of ion exchange resin on FPLC equipment, resulting in pressure buildup and possible equipment failure. Apparent aggregation issues can sometimes be overcome by limiting the sample concentration and use of buffer additives that deter aggregate formation. | 3 | Analytical Chemistry |
Crystal violet is one of the components of methyl violet, a dye first synthesized by Charles Lauth in 1861. From 1866, methyl violet was manufactured by the Saint-Denis-based firm of Poirrier et Chappat and marketed under the name "Violet de Paris". It was a mixture of the tetra-, penta- and hexamethylated pararosanilines.
Crystal violet itself was first synthesized in 1883 by Alfred Kern (1850–1893) working in Basel at the firm of Bindschedler and Busch. To optimize the difficult synthesis which used the highly toxic phosgene, Kern entered into a collaboration with the German chemist Heinrich Caro at BASF. Kern also found that by starting with diethylaniline rather than dimethylaniline, he could synthesize the closely related violet dye now known as C.I. 42600 or C.I. Basic violet 4. | 3 | Analytical Chemistry |
The HILIC mode of separation is used extensively for separation of some biomolecules, organic and some inorganic molecules by differences in polarity. Its utility has increased due to the simplified sample preparation for biological samples, when analyzing for metabolites, since the metabolic process generally results in the addition of polar groups to enhance elimination from the cellular tissue. This separation technique is also particularly suitable for glycosylation analysis and quality assurance of glycoproteins and glycoforms in biologic medical products. For the detection of polar compounds with the use of electrospray-ionization mass spectrometry as a chromatographic detector, HILIC can offer a ten fold increase in sensitivity over reversed-phase chromatography because the organic solvent is much more volatile. | 1 | Biochemistry |
Advantages:
* Process controllability - Unlike a traditional electric or gas furnace the induction system requires no pre-heat cycle or controlled shutdown. The heat is available on demand. In addition to the benefits of rapid availability in the event of a downstream interruption to production, the power can be switched off thus saving energy.
* Energy efficiency - Due to the heat being generated within the component energy transfer is extremely efficient. The induction heater heats only the part not the atmosphere around it.
* Process consistency - The induction heating process produces extremely uniform consistent heat this often allows less heat to be used for a given process.
* No naked flame - This allows induction heating to be used in a wide variety of applications in volatile environments in particular in petrochemical applications.
The main disadvantage of this process is that, in general, it is limited to components which have a cylindrical shape. | 8 | Metallurgy |
plants have a competitive advantage over plants possessing the more common carbon fixation pathway under conditions of drought, high temperatures, and nitrogen or limitation. When grown in the same environment, at 30 °C, grasses lose approximately 833 molecules of water per molecule that is fixed, whereas grasses lose only 277. This increased water use efficiency of grasses means that soil moisture is conserved, allowing them to grow for longer in arid environments.
carbon fixation has evolved in at least 62 independent occasions in 19 different families of plants, making it a prime example of convergent evolution. This convergence may have been facilitated by the fact that many potential evolutionary pathways to a phenotype exist, many of which involve initial evolutionary steps not directly related to photosynthesis. plants arose around during the Oligocene (precisely when is difficult to determine) and were becoming ecologically significant in the early Miocene around . metabolism in grasses originated when their habitat migrated from the shady forest undercanopy to more open environments, where the high sunlight gave it an advantage over the pathway. Drought was not necessary for its innovation; rather, the increased parsimony in water use was a byproduct of the pathway and allowed plants to more readily colonize arid environments.
Today, plants represent about 5% of Earth's plant biomass and 3% of its known plant species. Despite this scarcity, they account for about 23% of terrestrial carbon fixation. Increasing the proportion of plants on earth could assist biosequestration of and represent an important climate change avoidance strategy. Present-day plants are concentrated in the tropics and subtropics (below latitudes of 45 degrees) where the high air temperature increases rates of photorespiration in plants. | 5 | Photochemistry |
Unimolecular ion decomposition is the fragmentation of a gas phase ion in a reaction with a molecularity of one. Ions with sufficient internal energy may fragment in a mass spectrometer, which in some cases may degrade the mass spectrometer performance, but in other cases, such as tandem mass spectrometry, the fragmentation can reveal information about the structure of the ion. | 7 | Physical Chemistry |
Gas phase species absorb and display unique spectra between 120 – 240 nm where high energy σ→σ*, n→σ*, π→π*, n → π* electronic transitions can be excited and probed. VUV spectra reflect the absorbance cross section of compounds and are specific to their electronic structure and functional group arrangement. The ability of VUV detectors to produce spectra for most compounds results in universal and highly selective compound identification. VUV spectroscopy data is highly characteristic while also providing quantitative information. Many commonly used GC detectors such as the electron capture detector (ECD), flame ionization detector (FID), and thermal conductivity detector (TCD) produce quantitative but not qualitative detail. Gas chromatography–mass spectrometry (GC-MS) generates qualitative and quantitative data but has difficulty characterizing labile and low mass compounds, as well as differentiating between isomers. GC-VUV complements MS by overcoming its limitations and providing a secondary method of confirmation. It also offers a single instrument alternative to the use of multiple detectors for qualitative and quantitative analysis.
Naphthols, xylenes, and cis- and trans- fatty acids are compounds that are prohibitively difficult to distinguish according to their electron ionization mass spectral profiles. Xylenes present the additional challenge of natural co-elution that makes separating their isoforms problematic. Figure 2 shows the distinct VUV spectra of m-, p-, and o-xylene. These compounds can be differentiated despite their only difference being the position of two methyl groups around a benzene ring. The spectral differences of these isomers enable their co-elution to be resolved through spectral deconvolution.
Fatty acid screening and profiling is an application that commonly requires the use of multiple detectors to achieve quantitative and qualitative results. FID is a quantitative detector that is suitable for routine screening when guided by retention index information. GC-MS has traditionally been used for qualitative compound profiling, but falls short where isobaric analytes are prevalent. It especially struggles with differentiating cis and trans fatty acid isomers. Electron impact ionization can also cause double bond migration and lead to ambiguous fatty acid structural data.
Determining cis and trans fatty acid distribution in oils and fats is important in assessing their potential health impacts. VUV spectra of trans-containing fatty acid methyl ester (FAME) isomers typically found in butter and vegetable oils are shown in Figure 3. These trans-containing isomers separate chromatographically from cis-containing isomers and have the tendency to co-elute with each other and, in some cases, with select C20:1 isomers. GC-VUV is not only able to differentiate the C18:3 FAME variants, but is also capable of telling cis isomers apart from trans isomers. Degrees of unsaturation such as C20:1 vs. C18:3 can additionally be distinguished. Previous work has demonstrated how distinct VUV spectra enable straightforward deconvolution and accurate quantitation of cis and trans FAME isomers. | 7 | Physical Chemistry |
For experimental setups of chemisorption, the amount of adsorption of a particular system is quantified by a sticking probability value.
However, chemisorption is very difficult to theorize. A multidimensional potential energy surface (PES) derived from effective medium theory is used to describe the effect of the surface on absorption, but only certain parts of it are used depending on what is to be studied. A simple example of a PES, which takes the total of the energy as a function of location:
where is the energy eigenvalue of the Schrödinger equation for the electronic degrees of freedom and is the ion interactions. This expression is without translational energy, rotational energy, vibrational excitations, and other such considerations.
There exist several models to describe surface reactions: the Langmuir–Hinshelwood mechanism in which both reacting species are adsorbed, and the Eley–Rideal mechanism in which one is adsorbed and the other reacts with it.
Real systems have many irregularities, making theoretical calculations more difficult:
* Solid surfaces are not necessarily at equilibrium.
* They may be perturbed and irregular, defects and such.
* Distribution of adsorption energies and odd adsorption sites.
* Bonds formed between the adsorbates.
Compared to physisorption where adsorbates are simply sitting on the surface, the adsorbates can change the surface, along with its structure. The structure can go through relaxation, where the first few layers change interplanar distances without changing the surface structure, or reconstruction where the surface structure is changed. A direct transition from physisorption to chemisorption has been observed by attaching a CO molecule to the tip of an atomic force microscope and measuring its interaction with a single iron atom.
For example, oxygen can form very strong bonds (~4 eV) with metals, such as Cu(110). This comes with the breaking apart of surface bonds in forming surface-adsorbate bonds. A large restructuring occurs by missing row. | 7 | Physical Chemistry |
In an ideal plug flow reactor (PFR) the fluid particles leave in the same order they arrived, not mixing with those in front and behind. Therefore, the particles entering at time t will exit at time t + T, all spending a time T inside the reactor. The residence time distribution will be then a Dirac delta function delayed by T:
The mean is T and the variance is zero.
The RTD of a real reactor deviates from that of an ideal reactor, depending on the hydrodynamics within the vessel. A non-zero variance indicates that there is some dispersion along the path of the fluid, which may be attributed to turbulence, a non-uniform velocity profile, or diffusion. If the mean of the distribution is earlier than the expected time T it indicates that there is stagnant fluid within the vessel. If the RTD curve shows more than one main peak it may indicate channeling, parallel paths to the exit, or strong internal circulation.
In PFRs, reactants enter the reactor at one end and react as they move down the reactor. Consequently, the reaction rate is dependent on the concentrations which vary along the reactor requiring the inverse of the reaction rate to be integrated over the fractional conversion. | 9 | Geochemistry |
This approach is based on first-principles physics alone and is not limited to vortex tubes only, but applies to moving gas in general. It shows that temperature separation in a moving gas is due only to enthalpy conservation in a moving frame of reference.
The thermal process in the vortex tube can be estimated in the following way:
The main physical phenomenon of the vortex tube is the temperature separation between the cold vortex core and the warm vortex periphery. The "vortex tube effect" is fully explained with the work equation of Euler, also known as Euler's turbine equation, which can be written in its most general vectorial form as:
where is the total, or stagnation temperature of the rotating gas at radial position , the absolute gas velocity as observed from the stationary frame of reference is denoted with ; the angular velocity of the system is and is the isobaric heat capacity of the gas. This equation was published in 2012; it explains the fundamental operating principle of vortex tubes (Here's a video with animated demonstration of how this works). The search for this explanation began in 1933 when the vortex tube was discovered and continued for more than 80 years.
The above equation is valid for an adiabatic turbine passage; it clearly shows that while gas moving towards the center is getting colder, the peripheral gas in the passage is "getting faster". Therefore, vortex cooling is due to angular propulsion. The more the gas cools by reaching the center, the more rotational energy it delivers to the vortex and thus the vortex rotates even faster. This explanation stems directly from the law of energy conservation. Compressed gas at room temperature is expanded in order to gain speed through a nozzle; it then climbs the centrifugal barrier of rotation during which energy is also lost. The lost energy is delivered to the vortex, which speeds its rotation. In a vortex tube, the cylindrical surrounding wall confines the flow at periphery and thus forces conversion of kinetic into internal energy, which produces hot air at the hot exit.
Therefore, the vortex tube is a rotorless turboexpander. It consists of a rotorless radial inflow turbine (cold end, center) and a rotorless centrifugal compressor (hot end, periphery). The work output of the turbine is converted into heat by the compressor at the hot end. | 7 | Physical Chemistry |
Oximes are commonly used as ligands and sequestering agents for metal ions. Dimethylglyoxime (dmgH) is a reagent for the analysis of nickel and a popular ligand in its own right. In the typical reaction, a metal reacts with two equivalents of dmgH concomitant with ionization of one proton. Salicylaldoxime is a chelator in hydrometallurgy.
Amidoximes such as polyacrylamidoxime can be used to capture trace amounts of uranium from sea water. In 2017 researchers announced a configuration that absorbed up to nine times as much uranyl as previous fibers without saturating. | 0 | Organic Chemistry |
Over-the-counter preparations containing dextromethorphan have been used in manners inconsistent with their labeling, often as a recreational drug. At doses much higher than medically recommended, dextromethorphan and its major metabolite, dextrorphan, acts as an NMDA receptor antagonist, which produces dissociative hallucinogenic states somewhat similar to ketamine and phencyclidine.
It may produce distortions of the visual field – feelings of dissociation, distorted bodily perception, excitement, and a loss of sense of time. Some users report stimulant-like euphoria, particularly in response to music. Dextromethorphan usually provides its recreational effects in a non-linear fashion, so that they are experienced in significantly varied stages. These stages are commonly referred to as "plateaus". These plateaus are numbered from one to four, with the first having the mildest effects to fourth being the most intense. Each plateau is said to come with different related effects and experiences.
The first plateau is said to induce music euphoria and mild stimulation, likened to that of MDMA. The second plateau is likened to a state of being on moderate amounts of alcohol and cannabis at the same time, featuring euphoria, sedation and minor hallucinations. The third plateau induces a significant dissociative state which can often cause anxiety in users. Reaching the fourth plateau is said to cause extreme sedation and a significant hallucinatory state as well as complete dissociation from reality. Teenagers tend to have a higher likelihood to use dextromethorphan-related drugs as they are easier to access, and an easier way to cope with psychiatric disorders. | 4 | Stereochemistry |
CeCoIn ("Cerium-Cobalt-Indium 5") is a heavy-fermion superconductor with a layered crystal structure, with somewhat two-dimensional electronic transport properties. The critical temperature of 2.3 K is the highest among all of the Ce-based heavy-fermion superconductors. | 8 | Metallurgy |
Neurotransmitters are tiny signal molecules stored in membrane-enclosed synaptic vesicles and released via exocytosis. Indeed, a change in electrical potential in the presynaptic cell triggers the release of these molecules. By attaching to transmitter-gated ion channels, the neurotransmitter causes an electrical alteration in the postsynaptic cell and rapidly diffuses across the synaptic cleft. Once released, the neurotransmitter is swiftly eliminated, either by being absorbed by the nerve terminal that produced it, taken up by nearby glial cells, or broken down by specific enzymes in the synaptic cleft. Numerous Na+-dependent neurotransmitter carrier proteins recycle the neurotransmitters and enable the cells to maintain rapid rates of release.
At chemical synapses, transmitter-gated ion channels play a vital role in rapidly converting extracellular chemical impulses into electrical signals. These channels are located in the postsynaptic cells plasma membrane at the synapse region, and they temporarily open in response to neurotransmitter molecule binding, causing a momentary alteration in the membranes permeability. Additionally, transmitter-gated channels are comparatively less sensitive to the membrane potential than voltage-gated channels, which is why they are unable to generate self-amplifying excitement on their own. However, they result in graded variations in membrane potential due to local permeability, influenced by the amount and duration of neurotransmitter released at the synapse.
Recently, mechanical tension, a phenomenon never thought relevant to synapse function has been found to be required for those on hippocampal neurons to fire. | 1 | Biochemistry |
;Magnesium–halogen exchange
Grignard reagents can be prepared by treating a preformed Grignard reagent with an organic halide. This method offers the advantage that the Mg transfer tolerates many functional groups. A typical reaction involves isopropylmagnesium chloride and aryl bromide or iodides:
: i-PrMgCl + ArCl → i-PrCl + ArMgCl
Magnesium ate complexes metalate aryl halides:
: ArBr + Li[MgBu] → ArMgBu + BuBr
;Zinc–halogen exchange
Zinc–halogen exchange:
: LiBuZn + R−I → Li[R−ZnBu] + BuI | 0 | Organic Chemistry |
The simplest DNA end of a double stranded molecule is called a blunt end. Blunt ends are also known as non-cohesive ends. In a blunt-ended molecule, both strands terminate in a base pair. Blunt ends are not always desired in biotechnology since when using a DNA ligase to join two molecules into one, the yield is significantly lower with blunt ends. When performing subcloning, it also has the disadvantage of potentially inserting the insert DNA in the opposite orientation desired. On the other hand, blunt ends are always compatible with each other. Here is an example of a small piece of blunt-ended DNA: | 1 | Biochemistry |
The Association for Clinical Biochemistry and Laboratory Medicine is a United Kingdom-based learned society dedicated to the practice and promotion of clinical biochemistry. It was founded in 1953 and its official journal is the Annals of Clinical Biochemistry. The association is a full, national society member of the International Federation of Clinical Chemistry and Laboratory Medicine IFCC as well as a full member of the regional European Federation of Clinical Chemistry and Laboratory Medicine. | 1 | Biochemistry |
The genes that encode both the dihydroxy acid dehydrase used in the creation of α-ketoisovalerate and Transaminase E, as well as other enzymes are encoded on the ilvEDA operon. This operon is bound and inactivated by valine, leucine, and isoleucine. (Isoleucine is not a direct derivative of pyruvate, but is produced by the use of many of the same enzymes used to produce valine and, indirectly, leucine.) When one of these amino acids is limited, the gene furthest from the amino-acid binding site of this operon can be transcribed. When a second of these amino acids is limited, the next-closest gene to the binding site can be transcribed, and so forth. | 1 | Biochemistry |
In the migratory insertion, a ligand that is viewed as an anion (X) ligand in and a ligand that is viewed as neutral couple, generating a new anionic ligand. The anion and neutral ligands that react are adjacent. If the precursor complex is coordinatively saturated, migratory insertion often result in a coordinatively unsaturated product. A new (neutral) ligand can then react with the metal leading to a further insertion. The process can occur many times on a single metal, as in olefin polymerization.
The anionic ligand can be: H (hydride), R (alkyl), acyl, Ar (aryl), or OR (alkoxide). The ability of these groups to migrate is called their migratory aptitude. The neutral ligand can be CO, alkene, alkyne, or in some cases, even carbene.
Diverse reactions apply to the migratory insertion. One mechanism involves the attack of the anionic ligand on the electrophilic part of the neutral ligand (the anionic ligand migrates to the neutral ligand). The other mechanism involves the neutral ligand inserts itself between the metal and the anionic ligand. | 0 | Organic Chemistry |
For certain purposes in an item of electrical equipment or a portion of it, definite type and size of materials with proper rating for voltage, current and temperature, are used. The circuit resistance never kept too low. Sometimes some parts placed inside the board and box, maintaining a proper distance from each other, to avoid heat damage and short-circuit damage. To prevent short circuit, appropriate types of electrical connectors and mechanical fasteners are used. | 7 | Physical Chemistry |
The 62-ton Ivy Mike device built by the United States and exploded on 1 November 1952, was the first fully successful "hydrogen bomb" (thermonuclear bomb). In this context, it was the first bomb in which most of the energy released came from nuclear reaction stages that followed the primary nuclear fission stage of the atomic bomb. The Ivy Mike bomb was a factory-like building, rather than a deliverable weapon. At its center, a very large cylindrical, insulated vacuum flask or cryostat, held cryogenic liquid deuterium in a volume of about 1000 liters (160 kilograms in mass, if this volume had been completely filled). Then, a conventional atomic bomb (the "primary") at one end of the bomb was used to create the conditions of extreme temperature and pressure that were needed to set off the thermonuclear reaction.
Within a few years, so-called "dry" hydrogen bombs were developed that did not need cryogenic hydrogen. Released information suggests that all thermonuclear weapons built since then contain chemical compounds of deuterium and lithium in their secondary stages. The material that contains the deuterium is mostly lithium deuteride, with the lithium consisting of the isotope lithium-6. When the lithium-6 is bombarded with fast neutrons from the atomic bomb, tritium (hydrogen-3) is produced, and then the deuterium and the tritium quickly engage in thermonuclear fusion, releasing abundant energy, helium-4, and even more free neutrons. "Pure" fusion weapons such as the Tsar Bomba are believed to be obsolete. In most modern ("boosted") thermonuclear weapons, fusion directly provides only a small fraction of the total energy. Fission of a natural uranium U-238 tamper by fast neutrons produced from D-T fusion accounts for a much larger (i.e. boosted) energy release than the fusion reaction itself. | 9 | Geochemistry |
Once a nucleic acid sequence has been obtained from an organism, it is stored in silico in digital format. Digital genetic sequences may be stored in sequence databases, be analyzed (see Sequence analysis below), be digitally altered and be used as templates for creating new actual DNA using artificial gene synthesis. | 1 | Biochemistry |
A 3–10% solution of potassium hydroxide (KOH) gives a color change in some species of mushrooms:
* In Agaricus, some species such as A. xanthodermus turn yellow with KOH, many have no reaction, and A. subrutilescens turns green.
* Distinctive change occurs for some species of Cortinarius and Boletes | 3 | Analytical Chemistry |
The Warburg diffusion element is an equivalent electrical circuit component that models the diffusion process in dielectric spectroscopy. That element is named after German physicist Emil Warburg.
A Warburg impedance element can be difficult to recognize because it is nearly always associated with a charge-transfer resistance (see charge transfer complex) and a double-layer capacitance, but is common in many systems. The presence of the Warburg element can be recognised if a linear relationship on the log of a Bode plot ( vs. ) exists with a slope of value –1/2. | 7 | Physical Chemistry |
As mentioned above, a diathermal wall may pass energy as heat by thermal conduction, but not the matter. A diathermal wall can move and thus be a part of a transfer of energy as work. Amongst walls that are impermeable to matter, diathermal and adiabatic walls are contraries.
For radiation, some further comments may be useful.
In classical thermodynamics, one-way radiation, from one system to another, is not considered. Two-way radiation between two systems is one of the two mechanisms of transfer of energy as heat. It may occur across a vacuum, with the two systems separated from the intervening vacuum by walls that are permeable only to radiation; such an arrangement fits the definition of a diathermal wall. The balance of radiative transfer is transfer of heat.
In thermodynamics, it is not necessary that the radiative transfer of heat be of pure black-body radiation, nor of incoherent radiation. Of course black-body radiation is incoherent. Thus laser radiation counts in thermodynamics as a one-way component of two-way radiation that is heat transfer. Also, by the [Helmholtz reciprocity] principle, the target system radiates into the laser source system, though of course relatively weakly compared with the laser light. According to Planck, an incoherent monochromatic beam of light transfers entropy and has a temperature. For a transfer to qualify as work, it must be reversible in the surroundings, for example in the concept of a reversible work reservoir. Laser light is not reversible in the surroundings and is therefore a component of transfer of energy as heat, not work.
In radiative transfer theory, one-way radiation is considered. For investigation of Kirchhoff's law of thermal radiation the notions of absorptivity and emissivity are necessary, and they rest on the idea of one-way radiation. These things are important for the study of the Einstein coefficients, which relies partly on the notion of thermodynamic equilibrium.
For the thermodynamic stream of thinking, the notion of empirical temperature is coordinately presupposed in the notion of heat transfer for the definition of an adiabatic wall.
For the mechanical stream of thinking, the exact way in which the walls are defined is important.
In the presentation of Carathéodory, it is essential that the definition of the adiabatic wall should in no way depend upon the notions of heat or temperature. This is achieved by careful wording and reference to transfer of energy only as work. Buchdahl is careful in the same way. Nevertheless, Carathéodory explicitly postulates the existence of walls that are permeable only to heat, that is to say impermeable to work and to matter, but still permeable to energy in some unspecified way; they are called diathermal walls. One might be forgiven for inferring from this that heat is energy in transfer across walls permeable only to heat, and that such are admitted to exist unlabeled as postulated primitives.
The mechanical stream of thinking thus regards the adiabatic enclosure's property of not allowing the transfer of heat across itself as a deduction from the Carathéodory axioms of thermodynamics, and regards transfer as heat as a residual rather than a primary concept. | 7 | Physical Chemistry |
The atoms that are used to build the purine nucleotides come from a variety of sources:
The de novo synthesis of purine nucleotides by which these precursors are incorporated into the purine ring proceeds by a 10-step pathway to the branch-point intermediate IMP, the nucleotide of the base hypoxanthine. AMP and GMP are subsequently synthesized from this intermediate via separate, two-step pathways. Thus, purine moieties are initially formed as part of the ribonucleotides rather than as free bases.
Six enzymes take part in IMP synthesis. Three of them are multifunctional:
* GART (reactions 2, 3, and 5)
* PAICS (reactions 6, and 7)
* ATIC (reactions 9, and 10)
The pathway starts with the formation of PRPP. PRPS1 is the enzyme that activates R5P, which is formed primarily by the pentose phosphate pathway, to PRPP by reacting it with ATP. The reaction is unusual in that a pyrophosphoryl group is directly transferred from ATP to C of R5P and that the product has the α configuration about C1. This reaction is also shared with the pathways for the synthesis of Trp, His, and the pyrimidine nucleotides. Being on a major metabolic crossroad and requiring much energy, this reaction is highly regulated.
In the first reaction unique to purine nucleotide biosynthesis, PPAT catalyzes the displacement of PRPP's pyrophosphate group (PP) by an amide nitrogen donated from either glutamine (N), glycine (N&C), aspartate (N), folic acid (C), or CO. This is the committed step in purine synthesis. The reaction occurs with the inversion of configuration about ribose C, thereby forming β-5-phosphorybosylamine (5-PRA) and establishing the anomeric form of the future nucleotide.
Next, a glycine is incorporated fueled by ATP hydrolysis, and the carboxyl group forms an amine bond to the NH previously introduced. A one-carbon unit from folic acid coenzyme N-formyl-THF is then added to the amino group of the substituted glycine followed by the closure of the imidazole ring. Next, a second NH group is transferred from glutamine to the first carbon of the glycine unit. A carboxylation of the second carbon of the glycin unit is concomitantly added. This new carbon is modified by the addition of a third NH unit, this time transferred from an aspartate residue. Finally, a second one-carbon unit from formyl-THF is added to the nitrogen group and the ring is covalently closed to form the common purine precursor inosine monophosphate (IMP).
Inosine monophosphate is converted to adenosine monophosphate in two steps. First, GTP hydrolysis fuels the addition of aspartate to IMP by adenylosuccinate synthase, substituting the carbonyl oxygen for a nitrogen and forming the intermediate adenylosuccinate. Fumarate is then cleaved off forming adenosine monophosphate. This step is catalyzed by adenylosuccinate lyase.
Inosine monophosphate is converted to guanosine monophosphate by the oxidation of IMP forming xanthylate, followed by the insertion of an amino group at C. NAD is the electron acceptor in the oxidation reaction. The amide group transfer from glutamine is fueled by ATP hydrolysis. | 1 | Biochemistry |
Phytochemistry is the study of phytochemicals, which are chemicals derived from plants. Phytochemists strive to describe the structures of the large number of secondary metabolites found in plants, the functions of these compounds in human and plant biology, and the biosynthesis of these compounds. Plants synthesize phytochemicals for many reasons, including to protect themselves against insect attacks and plant diseases. The compounds found in plants are of many kinds, but most can be grouped into four major biosynthetic classes: alkaloids, phenylpropanoids, polyketides, and terpenoids.
Phytochemistry can be considered a subfield of botany or chemistry. Activities can be led in botanical gardens or in the wild with the aid of ethnobotany. Phytochemical studies directed toward human (i.e. drug discovery) use may fall under the discipline of pharmacognosy, whereas phytochemical studies focused on the ecological functions and evolution of phytochemicals likely fall under the discipline of chemical ecology. Phytochemistry also has relevance to the field of plant physiology. | 1 | Biochemistry |
Agents such as hydrogen peroxide, elemental chlorine, hypochlorous acid (chlorine water), bromine, bromine water, iodine, nitric and oxidising acids, and ozone react with sensitive moieties such as sulfide/thiol, activated aromatic rings (phenylalanine) in effect damage the protein and render it useless. | 1 | Biochemistry |
The most notable classes of biological macromolecules used in the fundamental processes of living organisms include:
* Proteins, which are the building blocks from which the structures of living organisms are constructed (this includes almost all enzymes, which catalyse organic chemical reactions).
* Amino acid, make up proteins, included the use in genetic code of life.
* Nucleic acids, which carry genetic information.
* Ribonucleic acid (RNA), production of proteins.
* Deoxyribonucleic acid (DNA), nucleic acid in genetic form.
* Peptide, building block of proteins.
* Lipids, which also store energy, but in a more concentrated form, and which may be stored for extended periods in the bodies of animals.
* Phospholipid used in cell membrane.
* Carbohydrates, which store energy in a form that can be used by living cells.
* Lectin, for binding proteins.
* Monosaccharide, simple sugars, including glucose and fructose.
* Disaccharides, sugar soluble in water, including lactose, maltose, and sucrose.
* Starch, made of amylose and amylopectin, plants energy storage.
* Glycogen, energy in animals.
* Cellulose, a biopolymer, found in the cell walls of plants.
* Fatty acid, two types, saturated fat and unsaturated fat (oil), are stored energy.
* Essential fatty acid, needed but not synthesized by the human body.
* Steroid, hormone, and used in cell membrane.
* Neurotransmitter, are signaling molecules.
* Cholesterol, used in the brain and spinal cord of animals.
* Wax, found in beeswax and lanolin. Plant wax used for protection. | 1 | Biochemistry |
Quinapril is indicated for the treatment of high blood pressure (hypertension) and as adjunctive therapy in the management of heart failure. It may be used for the treatment of hypertension by itself or in combination with thiazide diuretics, and with diuretics and digoxin for heart failure. | 4 | Stereochemistry |
Molecular biology sits at the intersection of biochemistry and genetics; as these scientific disciplines emerged and evolved in the 20th century, it became clear that they both sought to determine the molecular mechanisms which underlie vital cellular functions. Advances in molecular biology have been closely related to the development of new technologies and their optimization. Molecular biology has been elucidated by the work of many scientists, and thus the history of the field depends on an understanding of these scientists and their experiments.
The field of genetics arose as an attempt to understand the molecular mechanisms of genetic inheritance and the structure of a gene. Gregor Mendel pioneered this work in 1866, when he first wrote the laws of genetic inheritance based on his studies of mating crosses in pea plants. One such law of genetic inheritance is the law of segregation, which states that diploid individuals with two alleles for a particular gene will pass one of these alleles to their offspring. Because of his critical work, the study of genetic inheritance is commonly referred to as Mendelian genetics.
A major milestone in molecular biology was the discovery of the structure of DNA. This work began in 1869 by Friedrich Miescher, a Swiss biochemist who first proposed a structure called nuclein, which we now know to be (deoxyribonucleic acid), or DNA. He discovered this unique substance by studying the components of pus-filled bandages, and noting the unique properties of the "phosphorus-containing substances". Another notable contributor to the DNA model was Phoebus Levene, who proposed the "polynucleotide model" of DNA in 1919 as a result of his biochemical experiments on yeast. In 1950, Erwin Chargaff expanded on the work of Levene and elucidated a few critical properties of nucleic acids: first, the sequence of nucleic acids varies across species. Second, the total concentration of purines (adenine and guanine) is always equal to the total concentration of pyrimidines (cysteine and thymine). This is now known as Chargaff's rule. In 1953, James Watson and Francis Crick published the double helical structure of DNA, based on the X-ray crystallography work done by Rosalind Franklin which was conveyed to them by Maurice Wilkins and Max Perutz. Watson and Crick described the structure of DNA and conjectured about the implications of this unique structure for possible mechanisms of DNA replication. Watson and Crick were awarded the Nobel Prize in Physiology or Medicine in 1962, along with Wilkins, for proposing a model of the structure of DNA.
In 1961, it was demonstrated that when a gene encodes a protein, three sequential bases of a gene's DNA specify each successive amino acid of the protein. Thus the genetic code is a triplet code, where each triplet (called a codon) specifies a particular amino acid. Furthermore, it was shown that the codons do not overlap with each other in the DNA sequence encoding a protein, and that each sequence is read from a fixed starting point.
During 1962–1964, through the use of conditional lethal mutants of a bacterial virus, fundamental advances were made in our understanding of the functions and interactions of the proteins employed in the machinery of DNA replication, DNA repair, DNA recombination, and in the assembly of molecular structures. | 1 | Biochemistry |
Although all commercially available DBU is produced synthetically, it may also be isolated from the sea sponge Niphates digitalis. The biosynthesis of DBU has been proposed to begin with adipaldehyde and 1,3-diaminopropane. | 0 | Organic Chemistry |
Regulation of CYP7A1 occurs at several levels including synthesis. Bile acids, steroid hormones, inflammatory cytokines, insulin, and growth factors inhibit CYP7A1 transcription through the 5′-upstream region of the promoter. The average life of this enzyme is between two and three hours. Activity can be regulated by phosphorylation-dephosphorylation.
CYP7A1 is upregulated by the nuclear receptor LXR (liver X receptor) when cholesterol (to be specific, oxysterol) levels are high. The effect of this upregulation is to increase the production of bile acids and reduce the level of cholesterol in hepatocytes.
It is downregulated by sterol regulatory element-binding proteins (SREBP) when plasma cholesterol levels are low.
Bile acids provide feedback inhibition of CYP7A1 by at least two different pathways, both involving the farnesoid X receptor, FXR. In the liver, bile acids bound to FXR induce small heterodimer partner, SHP which binds to LRH-1 and so inhibits the transcription of the enzyme. In the intestine, bile acids/FXR stimulate production of FGF15/19 (depending on species), which then acts as a hormone in the liver via FGFR4. | 1 | Biochemistry |
Krige is originally a physical chemist by training, earning a PhD from the University of Pretoria in the subject. After earning a PhD in philosophy at the University of Sussex, in the United Kingdom in 1979, Krige's intellectual career has been in the history of science and technology, including notable efforts within the project to write the history of CERN and the European Space Agency in the 1980s and 1990s. His main focus is on the place of science and technology in the foreign policies of governments both intra-European and between the U.S. and Western Europe in the cold war.
In 2000, Krige became a professor at Georgia Institute of Technology's School of History and Sociology.
As a Francis Bacon Award recipient, Krige became a visiting professor at Caltech's Division of Humanities and Social Science. | 7 | Physical Chemistry |
Two-dimensional chromatography is a type of chromatographic technique in which the injected sample is separated by passing through two different separation stages. Two different chromatographic columns are connected in sequence, and the effluent from the first system is transferred onto the second column. Typically the second column has a different separation mechanism, so that bands that are poorly resolved from the first column may be completely separated in the second column. (For instance, a C18 reversed-phase chromatography column may be followed by a phenyl column.) Alternately, the two columns might run at different temperatures. During the second stage of separation the rate at which the separation occurs must be faster than the first stage, since there is still only a single detector. The plane surface is amenable to sequential development in two directions using two different solvents. | 3 | Analytical Chemistry |
The experimental procedure first requires a sample of purified plasmid DNA for each digest to be run. Digestion is then performed with each enzyme(s) chosen. The resulting samples are subsequently run on an electrophoresis gel, typically on agarose gel.
The first step following the completion of electrophoresis is to add up the sizes of the fragments in each lane. The sum of the individual fragments should equal the size of the original fragment, and each digest's fragments should also sum up to be the same size as each other. If fragment sizes do not properly add up, there are two likely problems. In one case, some of the smaller fragments may have run off the end of the gel. This frequently occurs if the gel is run too long. A second possible source of error is that the gel was not dense enough and therefore was unable to resolve fragments close in size. This leads to a lack of separation of fragments which were close in size. If all of the digests produce fragments that add up one may infer the position of the REN (restriction endonuclease) sites by placing them in spots on the original DNA fragment that would satisfy the fragment sizes produced by all three digests | 1 | Biochemistry |
VAR is used most frequently in high value applications. It is an additional processing step to improve the quality of metal. Because it is time consuming and expensive, a majority of commercial alloys do not employ the process. Nickel, titanium, and specialty steels are materials most often processed with this method. The conventional path for production of titanium alloys includes single, double or even triple VAR processing. Use of this technique over traditional methods presents several advantages:
*The solidification rate of molten material can be tightly controlled. This allows a high degree of control over the microstructure as well as the ability to minimize segregation
*The gases dissolved in liquid metal during melting metals in open furnaces, such as nitrogen, oxygen and hydrogen are considered to be detrimental to the majority of steels and alloys. Under vacuum conditions these gases escape from liquid metal.
*Elements with high vapor pressure such as carbon, sulfur, and magnesium (frequently contaminants) are lowered in concentration.
*Centerline porosity and segregation are eliminated.
*Certain metals and alloys, such as Ti, cannot be melted in open air furnaces | 8 | Metallurgy |
A polar molecule has a net dipole as a result of the opposing charges (i.e. having partial positive and partial negative charges) from polar bonds arranged asymmetrically. Water (HO) is an example of a polar molecule since it has a slight positive charge on one side and a slight negative charge on the other. The dipoles do not cancel out, resulting in a net dipole. The dipole moment of water depends on its state. In the gas phase the dipole moment is ≈ 1.86 debye (D), whereas liquid water (≈ 2.95 D) and ice (≈ 3.09 D) are higher due to differing hydrogen-bonded environments. Other examples include sugars (like sucrose), which have many polar oxygen–hydrogen (−OH) groups and are overall highly polar.
If the bond dipole moments of the molecule do not cancel, the molecule is polar. For example, the water molecule (HO) contains two polar O−H bonds in a bent (nonlinear) geometry. The bond dipole moments do not cancel, so that the molecule forms a molecular dipole with its negative pole at the oxygen and its positive pole midway between the two hydrogen atoms. In the figure each bond joins the central O atom with a negative charge (red) to an H atom with a positive charge (blue).
The hydrogen fluoride, HF, molecule is polar by virtue of polar covalent bondsin the covalent bond electrons are displaced toward the more electronegative fluorine atom.
Ammonia, NH, is a molecule whose three N−H bonds have only a slight polarity (toward the more electronegative nitrogen atom). The molecule has two lone electrons in an orbital that points towards the fourth apex of an approximately regular tetrahedron, as predicted by the VSEPR theory. This orbital is not participating in covalent bonding; it is electron-rich, which results in a powerful dipole across the whole ammonia molecule.
In ozone (O) molecules, the two O−O bonds are nonpolar (there is no electronegativity difference between atoms of the same element). However, the distribution of other electrons is unevensince the central atom has to share electrons with two other atoms, but each of the outer atoms has to share electrons with only one other atom, the central atom is more deprived of electrons than the others (the central atom has a formal charge of +1, while the outer atoms each have a formal charge of −). Since the molecule has a bent geometry, the result is a dipole across the whole ozone molecule. | 7 | Physical Chemistry |
cfDNA, cell death-related and chromatin fragmented DNA molecules contained in blood plasma, has been used to detect transplant tissue rejection, prenatal fetal aneuploidy testing, tumour profiling, and early cancer detection in previous research. Nevertheless, prevalent liquid biopsy methods for cfDNA profiling depend on detecting germline or somatic genetic variations, which may be absent even in high disease burden-bearing patients and cancers with high tumour mutation rates.
Historically, the usage of fragmentomic features of cfDNA samples was shown to be another method to approach the problems mentioned. They demonstrated the capability to inform about the originated tissue classification of cfDNA molecules, which can help segregate tumour-related somatic mutations. However, current methods that use fragmentomic features, such as shallow whole genome sequencing (WGS) on cfDNA, do not fully cover all the tissues' effects and provide low sequencing depth and breadth to infer low-level, for example, gene level, properties. Hence, these methods require a high tumour burden from the patients. | 1 | Biochemistry |
Gas chromatography (GC) coupled to mass spectrometry (MS) is one of the most widespread routine technologies applied to the large scale screening and discovery of novel biomarkers in metabolomics. However, the majority of MSTs currently measured in plant metabolomic profiling experiments remains unidentified due to the lack of authenticated pure reference substances and the expensive and time-consuming effort to maintain mass spectral RI libraries required for compound identification by GC-MS.
As the communication of analytical results and other approach-related details such as mass spectral and RI reference information within the scientific community is becoming increasingly popular, open access platforms for information exchange, such as the GMD, are obligatory.
Due to the lack of mandatory standards it remains difficult to compare individual mass spectrums.
While the different mass detector technologies, namely
quadrupole, ion trap and time of flight, can be deemed irrelevant, the chromatography settings such as temperature programming, type of capillary column and choice of column manufacturer heavily affect the empirically determined RI properties. Procedures for the transfer of RI properties between chromatography variants are, therefore, highly relevant for a shared library use. The GMD assesses the accuracy of RI transfer between chromatography variants and implements means to transfer empirically determined RI properties.
Aiming at the classification and identification of un-identified MSTs, the GMD accesses the information on available reference compounds. These compounds serve as training set of data to apply decision trees (DT) as a supervised machine learning approach. Structural feature extraction was applied to classify the metabolite space of the GMD prior to DT training. DT-based predictions of the most frequent substructures classify low resolution GC-MS mass spectra of the linked (potentially unknown) metabolite with respect to the presence or absence of the chemical moieties.
The web-based frontend supports conventional mass spectral and RI comparison by ranked hit lists as well as advanced DT supported substructure prediction. Batch processing is enabled via Simple Object Access Protocol (SOAP)-based web services while web-based data access services expose particular data base entities adapting Representational State Transfer (ReST) principles and mass spectral standards such as NIST-MSP and JCAMP-DX.
The GMD visualise quantitative metabolite pool size changes data. | 0 | Organic Chemistry |
The ambush hypothesis is a hypothesis in the field of molecular genetics that suggests that the prevalence of “hidden” or off-frame stop codons in DNA selectively deters off-frame translation of mRNA to save energy, molecular resources, and to reduce strain on biosynthetic machinery by truncating the production of non-functional, potentially cytotoxic protein products. Typical coding sequences of DNA lack in-frame internal stop codons to avoid the premature reduction of protein products when translation proceeds normally. The ambush hypothesis suggests that kinetic, cis-acting mechanisms are responsible for the productive frameshifting of translational units so that the degeneracy of the genetic code can be used to prevent deleterious translation. Ribosomal slippage is the most well described mechanism of translational frameshifting where the ribosome moves one codon position either forward (+1) or backward (-1) to translate the mRNA sequence in a different reading frame and thus produce different protein products.
In respect to codon usage, the ambush hypothesis theorizes that there is a positive correlation between the use of a codon and the amount a codon contributes to hidden stops. Phylogenetic analyses of both the nuclear and mitochondrial genomes of all major taxonomic kingdoms suggests ubiquitous off-frame stop codon existence and a positive correlation between the usage frequency of a codon and the number of ways a codon can contribute to hidden stop codons in different translational reading frames.
Combinatorics have been used across genetic codes to determine how each in-frame codon can potentially contribute to stop codons in off-frame contexts. The standard genetic code only contains 20 codons that cannot become stop codons in a frameshifted ribosomal environment (-1 frameshift: 42, +1 frameshift: 28) and 127 out of the 400 (31.75%) possible adjacent amino acid combinations in the vertebrate mitochondrial code creates an off-frame stop codon. This suggests that substitutions and synonymous codon usage are not neutral and that selective pressures might have readjusted codon assignments to increase the frequencies of those that can be used as hidden stops.
Observations that the number of off-frame stop codons is positively correlated with the expression level of a gene support the ambush hypothesis by increasing translational regulation (hidden stop frequency) to discourage off-frame reading in genes that are expressed at a high level. The positive correlation indicates that the off-frame translation of larger genes with higher expression levels likely costs a cell more energy, resources, and pathway efficiency than translating smaller, more rare genes in a shifted reading frame. Off-frame stop codon frequency is negatively correlated with gestation time in primates and though there are many factors that link molecular translational efficiency to the rate of morphogenesis, these findings suggests that not only individual cells but entire organisms may benefit from the development of hidden stop codons to effectively halt off-frame synthesis.
The ambush hypothesis is challenged by recent observations that off-frame stop codons are directly correlated with the GC content in the genome because stop codons are GC-poor. [http://www.biomedcentral.com/1471-2164/14/418 Morgens et al. 2013] argues that previous research concerning the ambush hypothesis has relied on codon usage data which is representative of the GC content of an organism and thus not appropriate to evaluate the selective effect of off-frame stop codons. | 1 | Biochemistry |
Bioavailability, or the amount of a substance that is physiochemically accessible to microorganisms is a key factor in the efficient biodegradation of pollutants. OLoughlin et al. (2000) showed that, with the exception of kaolinite clay, most soil clays and cation exchange resins attenuated biodegradation of 2-picoline by Arthrobacter' sp. strain R1, as a result of adsorption of the substrate to the clays. Chemotaxis, or the directed movement of motile organisms towards or away from chemicals in the environment is an important physiological response that may contribute to effective catabolism of molecules in the environment. In addition, mechanisms for the intracellular accumulation of aromatic molecules via various transport mechanisms are also important. | 2 | Environmental Chemistry |
In a cyclic voltammetry experiment carried out with an adsorbed redox protein, the oxidation and reduction of each redox site shows as a pair of positive and negative peaks. Since all the sample is oxidised or reduced during the potential sweep, the peak current and peak area should be proportional to scan rate (observing that the peak current is proportional to scan rate proves that the redox species that gives the peak is actually immobilised). The same is true for experiments performed with non-biological redox molecules adsorbed onto electrodes. The theory was mainly developed by the French electrochemist Etienne Laviron in the 1980s.
Since both this faradaic current (which results from the oxidation/reduction of the adsorbed molecule) and the capacitive current (which results from electrode charging) increase in proportion to scan rate, the peaks should remain visible when the scan rate is increased. In contrast, when the redox analyte is in solution and diffuses to/from the electrode, the peak current is proportional to the square root of the scan rate (see: Randles–Sevcik equation). | 7 | Physical Chemistry |
Atmospheric hypoxia occurs naturally at high altitudes. Total atmospheric pressure decreases as altitude increases, causing a lower partial pressure of oxygen, which is defined as hypobaric hypoxia. Oxygen remains at 20.9% of the total gas mixture, differing from hypoxic hypoxia, where the percentage of oxygen in the air (or blood) is decreased. This is common in the sealed burrows of some subterranean animals, such as blesmols. Atmospheric hypoxia is also the basis of altitude training, which is a standard part of training for elite athletes. Several companies mimic hypoxia using normobaric artificial atmosphere. | 9 | Geochemistry |
Structural ambiguity in protein complexes covers a wide spectrum. In a polymorphic complex, the protein adopts two or more different conformations upon binding to the same partner, and these conformations can be resolved. Clamp, flanking and random complexes are dynamic, where ambiguous conformations interchange with each other and cannot be resolved. Interactions in fuzzy complexes are usually mediated by short motifs. Flanking regions are tolerant to sequence changes as long as the amino acid composition is maintained, for example in case of linker histone C-terminal domains and H4 histone N-terminal domains. | 4 | Stereochemistry |
Per the classification by Albert six-membered heterocycles can be described as π-deficient. Substitution by electronegative groups or additional nitrogen atoms in the ring significantly increase the π-deficiency. These effects also decrease the basicity.
Like pyridines, in pyrimidines the π-electron density is decreased to an even greater extent. Therefore, electrophilic aromatic substitution is more difficult while nucleophilic aromatic substitution is facilitated. An example of the last reaction type is the displacement of the amino group in 2-aminopyrimidine by chlorine and its reverse.
Electron lone pair availability (basicity) is decreased compared to pyridine. Compared to pyridine, N-alkylation and N-oxidation are more difficult. The pK value for protonated pyrimidine is 1.23 compared to 5.30 for pyridine. Protonation and other electrophilic additions will occur at only one nitrogen due to further deactivation by the second nitrogen. The 2-, 4-, and 6- positions on the pyrimidine ring are electron deficient analogous to those in pyridine and nitro- and dinitrobenzene. The 5-position is less electron deficient and substituents there are quite stable. However, electrophilic substitution is relatively facile at the 5-position, including nitration and halogenation.
Reduction in resonance stabilization of pyrimidines may lead to addition and ring cleavage reactions rather than substitutions. One such manifestation is observed in the Dimroth rearrangement.
Pyrimidine is also found in meteorites, but scientists still do not know its origin. Pyrimidine also photolytically decomposes into uracil under ultraviolet light. | 1 | Biochemistry |
Other techniques for writing data in three-dimensions have also been examined, including:
Persistent spectral hole burning (PSHB), which also allows the possibility of spectral multiplexing to increase data density. However, PSHB media currently requires extremely low temperatures to be maintained in order to avoid data loss.
Void formation, where microscopic bubbles are introduced into a media by high intensity laser irradiation.
Chromophore poling, where the laser-induced reorientation of chromophores in the media structure leads to readable changes. | 5 | Photochemistry |
The standard pressure, , is used to define the reference state for the Van 't Hoff equation, which is
where denotes the natural logarithm, is the thermodynamic equilibrium constant, and is the ideal gas constant. This equation is exact at any one temperature and all pressures, derived from the requirement that the Gibbs free energy of reaction be stationary in a state of chemical equilibrium.
In practice, the equation is often integrated between two temperatures under the assumption that the standard reaction enthalpy is constant (and furthermore, this is also often assumed to be equal to its value at standard temperature). Since in reality and the standard reaction entropy do vary with temperature for most processes, the integrated equation is only approximate. Approximations are also made in practice to the activity coefficients within the equilibrium constant.
A major use of the integrated equation is to estimate a new equilibrium constant at a new absolute temperature assuming a constant standard enthalpy change over the temperature range. To obtain the integrated equation, it is convenient to first rewrite the Van 't Hoff equation as
The definite integral between temperatures and is then
In this equation is the equilibrium constant at absolute temperature , and is the equilibrium constant at absolute temperature . | 7 | Physical Chemistry |
The term dispersion also refers to the physical property of the degree to which particles clump together into agglomerates or aggregates. While the two terms are often used interchangeably, according to ISO nanotechnology definitions, an agglomerate is a reversible collection of particles weakly bound, for example by van der Waals forces or physical entanglement, whereas an aggregate is composed of irreversibly bonded or fused particles, for example through covalent bonds. A full quantification of dispersion would involve the size, shape, and number of particles in each agglomerate or aggregate, the strength of the interparticle forces, their overall structure, and their distribution within the system. However, the complexity is usually reduced by comparing the measured size distribution of "primary" particles to that of the agglomerates or aggregates. When discussing suspensions of solid particles in liquid media, the zeta potential is most often used to quantify the degree of dispersion, with suspensions possessing a high absolute value of zeta potential being considered as well-dispersed. | 7 | Physical Chemistry |
EPA first listed MTBE in 1998 as a candidate for development of a national Maximum Contaminant Level (MCL) standard in drinking water. As of 2020 the agency has not announced whether it will develop an MCL. EPA uses toxicity data in developing MCLs for public water systems.
California established a state-level MCL for MTBE, 13 micrograms per liter, in 2000. | 2 | Environmental Chemistry |
The development of Hydrofluoroolefins (HFOs) as replacements for Hydrochlorofluorocarbons and Hydrofluorocarbons began after the Kigali amendment to the Montreal Protocol in 2016, which called for the phase out of high global warming potential (GWP) refrigerants and to replace them with other refrigerants with a lower GWP, closer to that of carbon dioxide. HFOs have an ozone depletion potential of 0.0, compared to the 1.0 of principal CFC-11, and a low GWP which make them environmentally safer alternatives to CFCs, HCFCs and HFCs.
Hydrofluoroolefins serve as functional replacements for applications where high GWP hydrofluorocarbons were once used. In April 2022, the EPA signed a pre-published final rule Listing of HFO-1234yf under the Significant New Alternatives Policy (SNAP) Program for Motor Vehicle Air Conditioning in Nonroad Vehicles and Servicing Fittings for Small Refrigerant Cans. This ruling allows HFO-1234yf to take over in applications where ozone depleting CFCs such as R-12, and high GWP HFCs such as R-134a were once used. The phaseout and replacement of CFCs and HFCs in the automotive industry will ultimately reduce the release of these gases to atmosphere and intern have a positive contribution to the mitigation of climate change. | 2 | Environmental Chemistry |
Phosphine oxides (designation σλ) have the general structure RP=O with formal oxidation state V. Phosphine oxides form hydrogen bonds and some are therefore soluble in water. The P=O bond is very polar with a dipole moment of 4.51 D for triphenylphosphine oxide.
Compounds related to phosphine oxides include phosphine imides (RPNR') and related chalcogenides (RPE, where E = S, Se, Te). These compounds are some of the most thermally stable organophosphorus compounds. | 0 | Organic Chemistry |
CA 242 is a tumor marker for sialylated Lewis carbohydrates associated with adenocarcinomas and e-selectin-mediated metastatic risk. It is commonly tested along with CEA, CA19-9, and CA242 for detecting pancreatic cancer. The specificity of CA 242 is higher than similar markers. Current research dictates that diagnostic efficiency is highest when various tumor markers are tested for at once.
CA 242 has been used clinically as a diagnostic biomarker for pancreatic, colorectal and other cancers. Since CA 242 is overexpressed in malignant tumors, it is within reason to assume that CA 242 could be a product of cancer cells. A study was conducted where CA 242 serum levels were acquired from 34, 680 patients with 27 clinically defined diseases. The data acquired shows that patients with pancreatic cancer, cervical cancer and lymphoma had the highest levels of the CA 242 serum, which was followed by esophageal, colon and ovarian cancer. CA 242 can be shown to detect other types of cancer as shown. | 1 | Biochemistry |
Chiral acyclic alkenes also show diastereoselectivity upon reactions such as epoxidation and enolate alkylation. The substituents around the alkene can favour the approach of the electrophile from one or the other face of the molecule. This is the basis of the Houks model, based on theoretical work by Kendall Houk, which predicts that the selectivity is stronger for cis than for trans' double bonds.
In the example shown, the cis alkene assumes the shown conformation to minimize steric clash between R and the methyl group. The approach of the electrophile preferentially occurs from the same side of the medium group (R) rather than the large group (R), mainly producing the shown diastereoisomer. Since for a trans alkene the steric hindrance between R and the H group is not as large as for the cis case, the selectivity is much lower. | 4 | Stereochemistry |
High levels of lactate dehydrogenase in cerebrospinal fluid are often associated with bacterial meningitis. In the case of viral meningitis, high LDH, in general, indicates the presence of encephalitis and poor prognosis. | 1 | Biochemistry |
CellViewer allows to visualize the sample material in four modes widely used in material research:
* 3D model of atomic structure (direct space),
* simulated diffraction pattern (reciprocal space),
* stereographic projection (projection of 3D space of crystallographic planes and directions to 2D),
* inverse pole figure (defined part of stereographic projection).
Graphical user interface provides user with two interactive views side by side. These views can display arbitrary combination of the four aforementioned visualization modes allowing to perceive their mutual relations. For instance, rotation of the atomic structure in direct space leads (if set so) to an instant update of the simulated diffraction pattern. If any diffraction spot is selected, corresponding crystallographic planes are shown in the unit cell etc. Such interconnections are implemented for each pair of the four available visualization modes. The electronic visualization allows to simplify understanding of widely used, yet less intuitive representations such as the inverse pole figure. For instance by drawing the coloured triangle of the inverse pole figure into the stereographic projection or to the more intuitive 3D atomic structure. | 3 | Analytical Chemistry |
DRAM-v is the standard for AMG annotation of metagenome assembled genomes (MAGs) identified as viruses. DRAM-v searches the following databases for AMGs that match the input MAGs: Pfam, KEGG, UniProt, CAZy, MEROPS, VOGDB, and NCBI Viral RefSeq. KEGG can then be referenced to classify annotated AMGs through VIBRANT. | 1 | Biochemistry |
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