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It is an A-5 size consciousness-raising mind opener, free of technical jargon, on Accessibility for All to built environments to convince decision makers that it is a low cost investment and a Win – Win game of indispensable National importance for everyone. | 3 | Analytical Chemistry |
Low-angle laser light scattering or LALLS is an application of light scattering that is particularly useful in conjunction with the technique of Size exclusion chromatography, one of the most powerful and widely used techniques to study the molecular mass distribution of a polymer.
Typically the eluent of the SEC column is allowed to pass through both a refractive index detector (that gives measures for the concentration in the solution as a function time) and through a laser scattering cell. The scattered intensity is measured as a function of time under a small angle with respect to the laser beam. The low-angle light scattering data can be analyzed if one assumes that the low-angle data is the same as the scattering at zero angle. For the relevant equations, see the article on static light scattering. Under these conditions the laser signal together with the concentration data can be translated into a curve that yields both the M and the M, the molar mass weighted by number and by weight respectively. The combination of those two data gives information on the linearity of the polymer.
The technique is sometimes complemented or combined with viscometry and polystyrene standards are available for validation of the results. | 7 | Physical Chemistry |
Selenium has a protective effect towards mercury toxicity. Mercury binds to selenium with high affinity, so this metal can inhibit selenium-dependent enzymes. However, increased selenium intake can preserve the enzyme activities, reducing the adverse effects caused by mercury exposure. | 1 | Biochemistry |
The Wilfley Table was conceived by Arthur Wilfley, a mining engineer based in Kokomo, Colorado in the United States. As a silver mine operator, Wilfley spent many years refining his separation table design in order to make the extraction of silver more economic. Rather than using heating processes (smelting) to concentrate the ore, Wilfley had been experimenting on mineral separation by use mineral density contrasts.
Wilfley was able to perfect a mechanical solution for the recovery of gold and silver from low-grade ores by means of the Wilfley table. The first Wilfley table was built on a preliminary scale in May 1895. The first full-sized table was used in Wilfley's own mill in Kokomo, in May 1896, while the first table sold for installation was placed in the Puzzle Mill, Breckinridge, Colorado, in August 1896. Patented in 1897, the Wilfley table made mining lower-grade ores profitable. Pulverised ore, suspended in a water solution, was washed across a sloping riffled vibrating table so that metals separated as they drained off.
The Wilfley Table was said to have revolutionised ore dressing worldwide and more than 25,000 were in service by the 1930s. | 8 | Metallurgy |
A 2012 report from the U.S. National Research Council calls for a new focus on glycoscience, a field that explores the structures and functions of glycans and promises great advances in areas as diverse as medicine, energy generation, and materials science. Until now, glycans have received little attention from the research community due to a lack of tools to probe their often complex structures and properties. The report presents a roadmap for transforming glycoscience from a field dominated by specialists to a widely studied and integrated discipline. | 0 | Organic Chemistry |
A third group of genes in which mutations lead to a significant susceptibility to cancer is the class of landscaper genes. Products encoded by landscaper genes do not directly affect cellular growth, but when mutated, contribute to the neoplastic growth of cells by fostering stromal environments conducive to unregulated cell proliferation.
Landscaper genes encode gene products that control the microenvironment in which cells grow. Growth of cells depends both on cell-to-cell interactions and cell-to-extracellular matrix (ECM) interactions. Mechanisms of control via regulation of extracellular matrix proteins, cellular surface markers, cellular adhesion molecules, and growth factors have been proposed.
Cells communicate with each other via the ECM through both direct contact and through signaling molecules. Stromal cell abnormalities arising from gene products coded by faulty landscaper genes could induce abnormal cell growth on the epithelium, leading to cancer of that tissue.
Biochemical cascades consisting of signaling proteins occur in the ECM and play an important role to the regulation of many aspects of cell life. Landscaper genes encode products that determine the composition of the membranes in which cells live. For example, large molecular weight glycoproteins and proteoglycans have been found to in association with signaling and structural roles. There exist proteolytic molecules in the ECM that are essential for clearing unwanted molecules, such as growth factors, cell adhesion molecules, and others from the space surrounding cells. It is proposed that landscaper genes control the mechanisms by which these factors are properly cleared. Different characteristics of these membranes lead to different cellular effects, such as differing rates of cell proliferation or differentiation. If, for example, the ECM is disrupted, incoming cells, such as those of the immune system, can overload the area and release chemical signals that induce abnormal cell proliferation. These conditions lead to an environment conducive to tumor growth and the cancerous phenotype. | 1 | Biochemistry |
In organic chemistry, an acyl cyanide is a functional group with the formula and structure . It consists of an acyl group () attached to cyanide (). Examples include acetyl cyanide, formyl cyanide, and oxalyl dicyanide. Acyl cyanides are reagents in organic synthesis. | 0 | Organic Chemistry |
In coupling reactions between aromatic compounds and metal-trifluoromethyl complexes the metal is usually copper, Pd and Ni are less prominent. The reactions are stoichiometric or catalytic. In the McLoughlin-Thrower reaction (1962) iodobenzene reacts with trifluoroiodomethane (CFI) and copper powder in dimethylformamide at 150 °C to trifluoromethylbenzene. The intermediate in this reaction type is a perfluoromethyl-metal complex.
A palladium acetate catalysed reaction described in 1982 used zinc powder with the main intermediate believed to be CFZnI with Pd(0) is the active catalyst. The first copper catalysed coupling was reported in 2009 and based on an iodoarene, a trifluoromethylsilane, copper iodide and 1,10-phenanthroline. Variations include another CF donor potassium (trifluoromethyl)trimethoxyborate, the use of aryl boronic acids or the use of a trifluoromethyl sulfonium salt or the use of a trifluoromethylcopper(I) phenanthroline complex. A catalytic palladium catalysed reaction was reported in 2010 using aryl halides, (trifluoromethyl)triethylsilane and allylpalladium chloride dimer | 0 | Organic Chemistry |
The largest number of lichenized fungi occur in the Ascomycota, with about 40% of species forming such an association. Some of these lichenized fungi occur in orders with nonlichenized fungi that live as saprotrophs or plant parasites (for example, the Leotiales, Dothideales, and Pezizales). Other lichen fungi occur in only five orders in which all members are engaged in this habit (Orders Graphidales, Gyalectales, Peltigerales, Pertusariales, and Teloschistales). Overall, about 98% of lichens have an ascomycetous mycobiont. Next to the Ascomycota, the largest number of lichenized fungi occur in the unassigned fungi imperfecti, a catch-all category for fungi whose sexual form of reproduction has never been observed. Comparatively few basidiomycetes are lichenized, but these include agarics, such as species of Lichenomphalia, clavarioid fungi, such as species of Multiclavula, and corticioid fungi, such as species of Dictyonema. | 2 | Environmental Chemistry |
A chemical reaction may undergo different reaction mechanisms at different temperatures.
In this case, a Van t Hoff plot with two or more linear fits may be exploited. Each linear fit has a different slope and intercept, which indicates different changes in enthalpy and entropy for each distinct mechanisms. The Van t Hoff plot can be used to find the enthalpy and entropy change for each mechanism and the favored mechanism under different temperatures.
In the example figure, the reaction undergoes mechanism 1 at high temperature and mechanism 2 at low temperature. | 7 | Physical Chemistry |
The Bayer process is the principal industrial means of refining bauxite to produce alumina (aluminium oxide) and was developed by Carl Josef Bayer. Bauxite, the most important ore of aluminium, contains only 30–60% aluminium oxide (AlO), the rest being a mixture of silica, various iron oxides, and titanium dioxide. The aluminium oxide must be further purified before it can be refined into aluminium.
The Bayer process is also the main source of gallium as a byproduct despite low extraction yields. | 8 | Metallurgy |
Nitriles () are named by adding the suffix "-nitrile" to the longest hydrocarbon chain (including the carbon of the cyano group). It can also be named by replacing the "-oic acid" of their corresponding carboxylic acids with "-carbonitrile." The prefix form is "cyano-." Functional class IUPAC nomenclature may also be used in the form of alkyl cyanides. For example, is called pentanenitrile or butyl cyanide. | 0 | Organic Chemistry |
Before MMC was considered as a chromatographic approach, secondary interactions were generally believed to be the main cause of peak tailing.
However, it was discovered afterwards that secondary interactions can be applied for improving separation power. In 1986, Regnier’s group synthesized a stationary phase that had characteristics of anion exchange chromatography (AEX) and hydrophobic interaction chromatography (HIC) on protein separation.
In 1998, a new form of MMC, hydrophobic charge induction chromatography (HCIC), was proposed by Burton and Harding.
In the same year, conjoint liquid chromatography (CLC), which combines different types of monolithic convective interaction media (CIM) disks in the same housing, was introduced by Štrancar et al.
In 1999, Yates’ group [11] loaded strong-cation exchange (SCX) and reversed phase liquid chromatography (RPLC) stationary phases sequentially into a capillary column coupled with tandem mass spectrometry (MS/MS) in the analysis of peptides, which became one of the most efficient technique in proteomics afterwards.
In 2009, Geng’s group first achieved online two-dimensional (2D) separation of intact proteins using a single column possessing separation features of weak-cation exchange chromatography (WCX) and HIC (termed as two-dimensional liquid chromatography using a single column, (2D-LC-1C). | 3 | Analytical Chemistry |
Traditional and presently most widespread categorisation of pure working fluids was first used by H. Tabor et al. and O. Badr et al. dating back to the 60s. This three-class classification system sorts pure working fluids into three categories. The base of the classification is the shape of the saturation vapour curve of the fluid in temperature-entropy plane. If the slope of the saturation vapour curve in all states is negative (ds/dT<0), which means that with decreasing saturation temperature the value of entropy increases, the fluid is called wet. If the slope of the saturation vapour curve of the fluid is mainly positive (regardless of a short negative slope somewhat below the critical point), which means that with decreasing saturation temperature the value of entropy also decreases (dT/ds>0), the fluid is dry. The third category is called isentropic, which means constant entropy and refers to those fluids that have a vertical saturation vapour curve (regardless of a short negative slope somewhat below the critical point) in temperature-entropy diagram. According to mathematical approach, it means a (negative) infinite slope (ds/dT=0). The terms of wet, dry and isentropic refer to the quality of vapour after the working fluid undergoes an isentropic (reversible adiabatic) expansion process from saturated vapour state. During an isentropic expansion process the working fluid always ends in the two-phase (also called wet) zone, if it is a wet-type fluid. If the fluid is of dry-type, the isentropic expansion necessarily ends in the superheated (also called dry) steam zone. If the working fluid is of isentropic-type, after an isentropic expansion process the fluid stays in saturated vapour state. The quality of vapour is a key factor in choosing steam turbine or expander for heat engines. See figure for better understanding. | 7 | Physical Chemistry |
The limit of quantification (LoQ, or LOQ) is the lowest value of a signal (or concentration, activity, response...) that can be quantified with acceptable precision and accuracy.
The LoQ is the limit at which the difference between two distinct signals / values can be discerned with a reasonable certainty, i.e., when the signal is statistically different from the background. The LoQ may be drastically different between laboratories, so another detection limit is commonly used that is referred to as the Practical Quantification Limit (PQL). | 3 | Analytical Chemistry |
Cremer graduated from University of Wisconsin-Madison with a BA in 1990, completed his PhD at University of California, Berkeley in 1996, and completed postdoctoral work at Stanford University (1996-1998).
Cremer joined the faculty in the chemistry department, Texas A&M University in 1998.
He is known for his work in Hofmeister series and supported lipid bilayers. He is also interested in nanofabrication, sum-frequency generation and biosensing.
Cremer joined the faculty in the chemistry department, Penn State University, in 2013. He continues his research in the lipid bilayer and protein folding. | 3 | Analytical Chemistry |
Ct analysis, a technique based on the principles of DNA reassociation kinetics, is a biochemical technique that measures how much repetitive DNA is in a DNA sample such as a genome. It is used to study genome structure and organization and has also been used to simplify the sequencing of genomes that contain large amounts of repetitive sequence. | 1 | Biochemistry |
Alternatively, it can be made as a carbonated soft drink by two methods.
When served before the fermentation process is complete. Kilju made this way is high in sugar and carbon dioxide (CO) content, and has little to no alcohol, being similar to a sweet lemon soda. It is a family tradition to many. The simple production process also makes it accessible to underage drinkers. Cf. sima, commonly seasoned with lemon and unpurified cane sugar, leading to a small beer or a light mead.
To make homemade alcopop (typically to 3–7%) water is added to kilju after the fermentation process is complete to dilute the ABV accordingly. The solution is then carbonated with a soda machine, and soft drink syrup (which will lower the ABV approximately 10%) is added. Alternatively, it can be made as a carbonated soft drink when served before the fermentation process is complete. Fermented water made this way is high in sugar and carbon dioxide (CO) content, and do not need to be diluted with water because it has little to no alcohol depending on how many days it has been fermented, being similar to a sweet lemon soda. | 1 | Biochemistry |
The elements of a eukaryotic and prokaryotic 5′ UTR differ greatly. The prokaryotic 5′ UTR contains a ribosome binding site (RBS), also known as the Shine–Dalgarno sequence (AGGAGGU), which is usually 3–10 base pairs upstream from the initiation codon. In contrast, the eukaryotic 5′ UTR contains the Kozak consensus sequence (ACCAUGG), which contains the initiation codon. The eukaryotic 5′ UTR also contains cis-acting regulatory elements called upstream open reading frames (uORFs) and upstream AUGs (uAUGs) and termination codons, which have a great impact on the regulation of translation (see below). Unlike prokaryotes, 5′ UTRs can harbor introns in eukaryotes. In humans, ~35% of all genes harbor introns within the 5′ UTR. | 1 | Biochemistry |
In bacteria, such as E. coli, genes, are regulated by sequence elements in promoters and related binding sites). RegulonDB provides a database of such regulatory elements, their binding sites and the transcription factors that bind to these sites in E. coli. RegulonDB 9.0 includes 184 experimentally determined transcription factors (TFs) as well as 120 computationally predicted TFs, that is, a total of 304.
The complete repertoire of 189 genetic sensory-response units (GENSOR units) are reported, integrating their signal, regulatory interactions, and metabolic pathways. A total of 78 GENSOR units have their four components highlighted; 119 include the genetic switch and the response, and 2 contain only the genetic switch.
A total of 103 TFs have a known effector in RegulonDB, including 25 two-component systems. There were enough sites to build a motif for 93 TFs to infer 16,207 predicted TF binding sites. This set of predicted binding sites corresponds to 12,574 TF → gene regulatory interactions; this represents a recovery of 52% of the 1592 annotated regulatory interactions in the database for the 93 TFs for which RegulonDB has a position-weight matrix (PWM). If only TFs with a good-quality PWM are taken into account, the total number of predicted TF → gene interactions is 8,714, recovering 672 (57%) of annotated interactions for this TF subset. Semi-automatic curation produced a total of 3,195 regulatory interactions for 199 TFs. | 1 | Biochemistry |
Nayar et al. published reference data for the surface tension of seawater over the salinity range of and a temperature range of at atmospheric pressure. The range of temperature and salinity encompasses both the oceanographic range and the range of conditions encountered in thermal desalination technologies. The uncertainty of the measurements varied from 0.18 to 0.37 mN/m with the average uncertainty being 0.22 mN/m.
Nayar et al. correlated the data with the following equation
where is the surface tension of seawater in mN/m, is the surface tension of water in mN/m, is the reference salinity in g/kg, and is temperature in degrees Celsius. The average absolute percentage deviation between measurements and the correlation was 0.19% while the maximum deviation is 0.60%.
The International Association for the Properties of Water and Steam (IAPWS) has adopted this correlation as an international standard guideline. | 6 | Supramolecular Chemistry |
2,3-butanediol has a variety of industrial applications and products it can produce. The levo isomer of butanediol has a low freezing point of -60 °C, which allows it to work as an antifreeze agent. Through catalytic dehydrogenation, butanediol can form diacetyl. Diacetyl is a food additive that can be used to add flavor. 0.1% butanediol will kill most pathogenic bacteria due to its antiseptic properties. Through esterification, forms of precursors of polyurethane foams are produced. These can be used in various applications, including in pharmaceuticals, cosmetics, lotions, ointments, and antiperspirants. Butanediol itself even has applications in the pharmaceutical industry as a drug carrier. | 1 | Biochemistry |
For a given stress profile and temperature, the point lies in a particular "deformation field". If the values place the point near the center of a field, it is likely that the primary mechanism by which the material will fail, i.e.: the type and rate of failure expected, grain boundary diffusion, plasticity, Nabarro–Herring creep, etc. If however, the stress and temperature conditions place the point near the boundary between two deformation mechanism regions then the dominating mechanism is less clear. Near the boundary of the regimes there can be a combination of mechanisms of deformation occurring simultaneously. Deformation mechanism maps are only as accurate as the number of experiments and calculations undertaken in their creation.
For a given stress and temperature, the strain rate and deformation mechanism of a material is given by a point on the map. By comparing maps of various materials, crystal structures, bonds, grain sizes, etc., studies of these materials properties on plastic flow can be conducted and a more complete understanding of deformation in materials is obtained. | 8 | Metallurgy |
Electronic biosensing offers significant advantages over optical, biochemical and biophysical methods, in terms of high sensitivity and new sensing mechanisms, high spatial resolution for localized detection, facile integration with standard wafer-scale semiconductor processing and label-free, real-time detection in a nondestructive manner [6].
Devices based on field-effect transistors (FETs) have attracted great attention because they can directly translate the interactions between target biological molecules and the FET surface into readable electrical signals. In a FET, current flows along the channel which is connected to the source and the drain. The channel conductance between the source and the drain is switched on and off by gate electrode that is capacitively coupled through a thin dielectric layer [6].
In FET-based biosensors, the channel is in direct contact with the environment, and this gives better control over the surface charge. This improves the sensitivity of surface FET-based biosensors as biological events occurring at the channel surface could result in the surface potential variation of the semiconductor channel and then modulate the channel conductance. In addition to ease of on-chip integration of device arrays and the cost-effective device fabrication, the surface ultrasensitivity of FET-based biosensors makes it an attractive alternative to existing biosensor technologies[6]. | 1 | Biochemistry |
One universal distinction between polymerization types is development of molecular weight by the different modes of propagation. Addition polymers form high molecular weight chains rapidly, with much monomer remaining. Since addition polymerization has rapidly growing chains and free monomer as its reactants, and condensation polymerization occurs in step-wise fashion between monomers, dimers, and other smaller growing chains, the effect of a polymer molecule's current size on a continuing reaction is profoundly different in these two cases. This has important effects on the distribution of molecular weights, or polydispersity, in the finished polymer. | 7 | Physical Chemistry |
Wiggins realised that water can exist in two different states, and that the existence of these states explains the way that living cells work, and has implications for DNA and protein structure. | 7 | Physical Chemistry |
Among these four moisture condition of aggregates, saturated surface dry is the condition that has the most applications in laboratory experiments, researches and studies, especially these related to water absorption, composition ratio or shrinkage test in materials like concrete. For many related experiments, a saturated surface dry condition is a premise that must be realize before the experiment. In saturated surface dry condition, the aggregate's water content is in a relatively stable and static situation where it would not be affected by its environment. Therefore, in experiments and tests where aggregates are in saturated surface dry condition, there would be fewer disrupting factors than in other three conditions. | 7 | Physical Chemistry |
The development process is modeled as the development of gene expression states. The gene expression pattern at time is defined as the initial expression state. The interactions among genes change the expression states during the development process. This process is modeled by the following differential equations
where τ) represents the expression state of at time . It is determined by a filter function σ. represents the weighted sum of regulatory effects () of all genes on gene at time . In the original Wagner model, the filter function is a step function
In other variants, the filter function is implemented as a sigmoidal function
In this way, the expression states will acquire a continuous distribution. The gene expression will reach the final state if it reaches a stable pattern. | 1 | Biochemistry |
For the present purposes, the light from a star, and for some particular purposes, the light of the sun, can be treated as a practically collimated beam, but apart from this, a collimated beam is rarely if ever found in nature, though artificially produced beams can be very nearly collimated. The spectral radiance (or specific intensity) is suitable for the description of an uncollimated radiative field. The integrals of spectral radiance (or specific intensity) with respect to solid angle, used above, are singular for exactly collimated beams, or may be viewed as Dirac delta functions. Therefore, the specific radiative intensity is unsuitable for the description of a collimated beam, while spectral flux density is suitable for that purpose. At a point within a collimated beam, the spectral flux density vector has a value equal to the Poynting vector, a quantity defined in the classical Maxwell theory of electromagnetic radiation. | 7 | Physical Chemistry |
In 1975, Peter V. Wright, a polymer chemist from Sheffield (UK), produced the first polymer electrolyte, which contained sodium and potassium salts in a polyethylene oxide (PEO) matrix. Later another type of polymer electrolytes, polyelectrolyte, was put forward, where ions moved through an electrically charged, rather than neutral, polymer matrix. Polymer electrolytes showed lower conductivities than glasses, but they were cheaper, much more flexible and could be easier machined and shaped into various forms. While ionic glasses are typically operated below, polymer conductors are typically heated above their glass transition temperatures. Consequently, both the electric field and mechanical deformation decay on a similar time scale in polymers, but not in glasses.
Between 1983 and 2001 it was believed that the amorphous fraction is responsible for ionic conductivity, i.e., that (nearly) complete structural disorder is essential for the fast ionic transport in polymers. However, a number of crystalline polymers have been described in 2001 and later with ionic conductivity as high as 0.01 S/cm 30 °C and activation energy of only 0.24 eV. | 7 | Physical Chemistry |
Bacterial conjugation is the transfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells. This takes place through a pilus. It is a parasexual mode of reproduction in bacteria.
It is a mechanism of horizontal gene transfer as are transformation and transduction although these two other mechanisms do not involve cell-to-cell contact.
Classical E. coli bacterial conjugation is often regarded as the bacterial equivalent of sexual reproduction or mating since it involves the exchange of genetic material. However, it is not sexual reproduction, since no exchange of gamete occurs, and indeed no generation of a new organism: instead an existing organism is transformed. During classical E. coli conjugation the donor cell provides a conjugative or mobilizable genetic element that is most often a plasmid or transposon. Most conjugative plasmids have systems ensuring that the recipient cell does not already contain a similar element.
The genetic information transferred is often beneficial to the recipient. Benefits may include antibiotic resistance, xenobiotic tolerance or the ability to use new metabolites. Other elements can be detrimental and may be viewed as bacterial parasites.
Conjugation in Escherichia coli by spontaneous zygogenesis and in Mycobacterium smegmatis by distributive conjugal transfer differ from the better studied classical E. coli conjugation in that these cases involve substantial blending of the parental genomes. | 1 | Biochemistry |
Compounds with the formula [PR]X comprise the phosphonium salts. These species are tetrahedral phosphorus(V) compounds. From the commercial perspective, the most important member is tetrakis(hydroxymethyl)phosphonium chloride, [P(CHOH)]Cl, which is used as a fire retardant in textiles. Approximately 2M kg are produced annually of the chloride and the related sulfate. They are generated by the reaction of phosphine with formaldehyde in the presence of the mineral acid:
:PH + HX + 4 CHO → [P(CHOH)]X
A variety of phosphonium salts can be prepared by alkylation and arylation of organophosphines:
:PR + RX → [PRR]X
The methylation of triphenylphosphine is the first step in the preparation of the Wittig reagent.
The parent phosphorane (σλ) is PH, which is unknown. Related compounds containing both halide and organic substituents on phosphorus are fairly common. Those with five organic substituents are rare, although P(CH) is known, being derived from P(CH) by reaction with phenyllithium.
Phosphorus ylides are unsaturated phosphoranes, known as Wittig reagents, e.g. CHP(CH). These compounds feature tetrahedral phosphorus(V) and are considered relatives of phosphine oxides. They also are derived from phosphonium salts, but by deprotonation not alkylation. | 0 | Organic Chemistry |
Activated protein C–protein C inhibitor (APC-PCI) is a complex of activated protein C (APC) and protein C inhibitor (PCI). It has been measured in coagulation testing to evaluate coagulation, thrombosis, and other cardiovascular complications. It is a marker of thrombin generation and indicates hypercoagulability. The half-life of APC-PCI is either 40 minutes or 140minutes.
Ethinylestradiol-containing birth control pills have been found to increase levels of APC-PCI to a similar degree as thrombin–antithrombin complex (TAT) and to a greater extent than D-dimer. However, only APC-PCI was able to differentiate between a second- and third-generation birth control pill.
Another complex related to APC-PCI is the activated protein C–α-antitrypsin (APCAT) complex. | 1 | Biochemistry |
Apart from the end replication problem, in vitro studies have shown that telomeres accumulate damage due to oxidative stress and that oxidative stress-mediated DNA damage has a major influence on telomere shortening in vivo. There is a multitude of ways in which oxidative stress, mediated by reactive oxygen species (ROS), can lead to DNA damage; however, it is yet unclear whether the elevated rate in telomeres is brought about by their inherent susceptibility or a diminished activity of DNA repair systems in these regions. Despite widespread agreement of the findings, widespread flaws regarding measurement and sampling have been pointed out; for example, a suspected species and tissue dependency of oxidative damage to telomeres is said to be insufficiently accounted for. Population-based studies have indicated an interaction between anti-oxidant intake and telomere length. In the Long Island Breast Cancer Study Project (LIBCSP), authors found a moderate increase in breast cancer risk among women with the shortest telomeres and lower dietary intake of beta carotene, vitamin C or E. These results suggest that cancer risk due to telomere shortening may interact with other mechanisms of DNA damage, specifically oxidative stress. | 1 | Biochemistry |
Jerry March, Ph.D. (August 1, 1929 – December 25, 1997) was an American organic chemist and a professor of chemistry at Adelphi University.
March authored the Marchs Advanced Organic Chemistry' text, which is considered to be a pillar of graduate-level organic chemistry texts. The book was prepared in its fifth edition at the time of his death. | 0 | Organic Chemistry |
The following are examples of cyclic compounds exhibiting more complex ring systems and stereochemical features: | 4 | Stereochemistry |
α,β-unsaturated carbonyl compounds undergo hydrocyanation in the absence of metal catalysts. One manifestation is a special case of the Michael reaction, leading to β-cyanoketones. Another manifestation leads to vinyl cyanohydrins. β-cyano-cyanohydrins are also observed. Reaction conditions allows access to any of these products.
Generally acidic conditions favor 1,2-adducts, while basic conditions favor 1,4-adducts. Additions of alkali metal cyanides, for instance, lead exclusively to 1,4-addition. In contrast to alkali metal cyanides and cyanoaluminates, Lewis acidic cyanides, such as TMSCN, favor 1,2-addition. Acetylenic substrates undergo the reaction; however the scope of this reaction is limited and yields are often low.
1,4-Addition to imines has been observed in a few cases, although imines are often base labile.
Esters, nitriles and other carbonyl derivatives also undergo conjugative hydrocyanation.
When alkali metal cyanides are used, at least partial neutralization of the reaction medium is usually necessary. Neutralization can be accomplished through an acidic group on the substate itself (internal neutralization). or through the addition of an external acid (external neutralization). Acetic acid is commonly used for this purpose, in a procedure pioneered by Lapworth.
Conjugative hydrocyanation was used to prepare the steroidal D ring. Diastereoselectivity is generally high in these addition reactions, and the resulting β-cyano carbonyl compounds can be converted to a number of steroidal products. | 0 | Organic Chemistry |
The pressure transmitting medium is the compressible fluid that fills the sample chamber and transmits the applied force to the sample. Hydrostatic pressure is preferred for high-pressure experiments because variation in strain throughout the sample can lead to distorted observations of different behaviors. In some experiments stress and strain relationships are investigated and the effects of non-hydrostatic forces are desired. A good pressure medium will remain a soft, compressible fluid to high pressure.
The full range of techniques that are available has been summarized in a tree diagram by William Bassett. The ability to utilize any and all of these techniques hinges on being able to look through the diamonds which was first demonstrated by visual observations. | 7 | Physical Chemistry |
The dihydrolipoate, covalently bound to a lysine residue of the complex, is then transfered to the dihydrolipoyl dehydrogenase (E3) active site, where it undergoes a flavin-mediated oxidation, similar in chemistry to e.g. thioredoxin reductase. First, FAD oxidizes dihydrolipoate back to its lipoate (disulfide) resting state, producing FADH. Then, the substrate NAD oxidizes FADH back to its FAD resting state, producing NADH and H. | 1 | Biochemistry |
N-tert-Butylbenzenesulfinimidoyl chloride is a useful oxidant for organic synthesis reactions. It is a good electrophile, and the sulfimide S=N bond can be attacked by nucleophiles, such as alkoxides, enolates, and amide ions. The nitrogen atom in the resulting intermediate is basic, and can abstract an α-hydrogen to create a new double bond. | 0 | Organic Chemistry |
To identify diverse post-transcriptional modifications of RNA molecules and determine the transcriptome-wide landscape of RNA modifications by means of next generation RNA sequencing, recently many studies have developed conventional or specialised sequencing methods. Examples of specialised methods are MeRIP-seq, m6A-seq, PA-mC-seq , methylation-iCLIP, m6A-CLIP, Pseudo-seq, Ψ-seq, CeU-seq, Aza-IP and RiboMeth-seq). Many of these methods are based on specific capture of the RNA species containing the specific modification, for example through antibody binding coupled with sequencing of the captured reads. After the sequencing these reads are mapped against the whole transcriptome to see where they originate from. Generally with this kind of approach it is possible to see the location of the modifications together with possible identification of some consensus sequences that might help identification and mapping further on. One example of the specialize methods is PA-mC-seq. This method was further developed from PA-mA-seq method to identify mC modifications on mRNA instead of the original target N6-methyladenosine. The easy switch between different modifications as target is made possible with a simple change of the capturing antibody form m6A specific to mC specific. Application of these methods have identified various modifications (e.g. pseudouridine, mA, m5C, 2′-O-Me) within coding genes and non-coding genes (e.g. tRNA, lncRNAs, microRNAs) at single nucleotide or very high resolution. | 1 | Biochemistry |
Transcription of the msl-2 transcript is regulated by multiple binding sites for fly Sxl at the 5′ UTR. In particular, these poly-uracil sites are located close to a small intron that is spliced in males, but kept in females through splicing inhibition. This splicing inhibition is maintained by Sxl. When present, Sxl will repress the translation of msl2 by increasing translation of a start codon located in a uORF in the 5′ UTR (see above for more information on uORFs). Also, Sxl outcompetes TIA-1 to a poly(U) region and prevents snRNP (a step in alternative splicing) recruitment to the 5′ splice site. | 1 | Biochemistry |
Siddiqui migrated to Pakistan in 1951, four years after the emergence of Pakistan in 1947, after being offered and appointed as "science advisor" to the government by Prime minister Liaquat Ali Khan. He was appointed as Director of the Pakistan Department of Research that was reformulated in 1953 as Pakistan Council of Scientific and Industrial Research (PCSIR). The aim of PCSIR was to support the industrial infrastructure through research and development. The regional laboratories of the institution were located in Dhaka, Rajshahi and Chittagong (East Pakistan), and in Lahore and Peshawar (West Pakistan). In 1953, he founded the Pakistan Academy of Sciences as a non-political think tank of distinguished scientists in the country. In 1956, when Government of Pakistan established Pakistan Atomic Energy Commission (PAEC) as an atomic research agency, Siddiqui was designated as its technical member.
In recognition of his scientific leadership, Frankfurt University granted him the degree of D.Med. Honoris causa in 1958. Also in 1958, the Government of Pakistan awarded him with Tamgha-e-Pakistan. In 1960, he became the President of Pan-Indian Ocean Science Association. The same year, he was elected Fellow of the Royal Society. In 1962, he was awarded the Sitara-e-Imtiaz for distinguished merit in the fields of science and medicine. Siddiqui remained the director and chairman of PCSIR until the time of his retirement in 1966. In that year, the President of Pakistan awarded him the Pride of Performance Medal for the respectable completion of his service.
In 1967, Siddiqui was invited by University of Karachi to set up a Postgraduate Institute of Chemistry in affiliation with the Department of Chemistry. He was designated as the institute's Founder Director, whereas the additional research staff was provided by PCSIR.
In 1976, the institute was offered a generous donation from Hussain Jamal Foundation. In appreciation of this donation, the institute was renamed as Hussain Ebrahim Jamal Research Institute of Chemistry. In due time, Siddiqui transformed the institute into a distinguished centre of international excellence in the field of chemistry and natural products. In March 1975, he headed the National Commission for Indigenous Medicines His tireless efforts for the promotion of science and technology earned him Hilal-e-Imtiaz by the Government of Pakistan in 1980. In 1983, he played a major role in the establishment of the Third World Academy of Sciences and became its Founding Fellow. He remained the director of the Hussain Ebrahim Jamal Research Institute of Chemistry until 1990. Later on, he continued research in his personal laboratory. He published over 400 research papers and was granted 50 patents. | 0 | Organic Chemistry |
Solvent–solute interactions are the same as solute–solute and solvent–solvent interactions, on average. Consequently, the enthalpy of mixing (solution) is zero and the change in Gibbs free energy on mixing is determined solely by the entropy of mixing. Hence the molar Gibbs free energy of mixing is
or for a two-component ideal solution
where m denotes molar, i.e., change in Gibbs free energy per mole of solution, and is the mole fraction of component . Note that this free energy of mixing is always negative (since each , each or its limit for must be negative (infinite)), i.e., ideal solutions are miscible at any composition and no phase separation will occur.
The equation above can be expressed in terms of chemical potentials of the individual components
where is the change in chemical potential of on mixing. If the chemical potential of pure liquid is denoted , then the chemical potential of in an ideal solution is
Any component of an ideal solution obeys Raoult's Law over the entire composition range:
where is the equilibrium vapor pressure of pure component and is the mole fraction of component in solution. | 7 | Physical Chemistry |
Coelenterazine is found in radiolarians, ctenophores, cnidarians, squid, brittle stars, copepods, chaetognaths, fish, and shrimp. It is the prosthetic group in the protein aequorin responsible for the blue light emission. | 1 | Biochemistry |
The technique of this method is based on the monitoring of acoustic waves that are generated with a pulsed laser. Localized heating of a material will create a localized temperature increase, which induces thermal stress. This stress build in a localized region causes an acoustic strain pulse. At an interface, the pulse will be subjected to a transmittance/reflectance state, and the characteristics of the interface may be monitored with the reflected waves. A probe laser will detect the effects of the reflecting acoustic waves by sensing the piezo-optic effect.
The amount of strain is related to the optical laser pulse as follows. Take the localized temperature increase due to the laser,
where R is the sample reflectivity, Q is the optical pulse energy, C is the specific heat (per unit volume), A is the optical spot area, ζ is the optical absorption length, and z is the distance into the sample (Ref A). This temperature increase results in a strain that can be estimated by multiplying it with the linear coefficient of thermal expansion of the film. Usually, a typical magnitude value of the acoustic pulse will be small, and for long propagation nonlinear effects could become important. But propagation of such short duration pulses will suffer acoustic attenuation if the temperature is not very low (Ref B). Thus, this method is most efficient with the utilization of surface acoustic waves, and studies on investigation of this method toward lateral structures are being conducted.
To sense the piezo-optic effect of the reflected waves, fast monitoring is required due to the travel time of the acoustic wave and heat flow. Acoustic waves travel a few nanometers in a picosecond, where heat flows about a hundred nanometers in a second. Thus, lasers such as titanium sapphire (Ti:Al2O3) laser, with pulse width of ~200 fs, are used to monitor the characteristics of the interface. Other type of lasers include Yb:fiber, Yb:tungstate, Er:fiber, Nd:glass. Second-harmonic generation may be utilized to achieve frequency of double or higher.
The output of the laser is split into pump and probe beams by a half-wave plate followed by a polarizing beam splitter leading to a cross-polarized pump and probe. The pump beam is modulated on the order of a few megahertz by an acousto-optic or electro-optic modulator and focused onto the sample with a lens. The probe is directed into an optical delay line. The probe beam is then focused with a lens onto the same spot on the sample as the pulse. Both pump and probe have a spot size on the order of 10–50 μm. The reflected probe light is input to a high bandwidth photodetector. The output is fed into a lock-in amplifier whose reference signal has the same frequency used to modulate the pump. The voltage output from the lock-in will be proportional to ΔR. Recording this signal as the optical delay line is changed provides a measurement of ΔR as a function of optical probe-pulse time delay. | 7 | Physical Chemistry |
This library construction process is similar to that of the short-jump library except that the condition is optimized for longer fragments (5 kb). | 1 | Biochemistry |
Of all light emitters in the ocean, bio-luminescent bacteria is the most abundant and diverse. However, the distribution of bio-luminescent bacteria is uneven, which suggests evolutionary adaptations. The bacterial species in terrestrial genera such as Photorhabdus are bio-luminescent. On the other hand, marine genera with bio-luminescent species such as Vibrio and Shewanella oneidensis have different closely related species that are not light emitters. Nevertheless, all bio-luminescent bacteria share a common gene sequence: the enzymatic oxidation of Aldehyde and reduced Flavin mononucleotide by luciferase which are contained in the lux operon. Bacteria from distinct ecological niches contain this gene sequence; therefore, the identical gene sequence evidently suggests that bio-luminescence bacteria result from evolutionary adaptations. | 1 | Biochemistry |
Photons hitting a thin film of alkali metal or semiconductor material such as gallium arsenide in an image intensifier tube cause the ejection of photoelectrons due to the photoelectric effect. These are accelerated by an electrostatic field where they strike a phosphor coated screen, converting the electrons back into photons. Intensification of the signal is achieved either through acceleration of the electrons or by increasing the number of electrons through secondary emissions, such as with a micro-channel plate. Sometimes a combination of both methods is used. Additional kinetic energy is required to move an electron out of the conduction band and into the vacuum level. This is known as the electron affinity of the photocathode and is another barrier to photoemission other than the forbidden band, explained by the band gap model. Some materials such as gallium arsenide have an effective electron affinity that is below the level of the conduction band. In these materials, electrons that move to the conduction band all have sufficient energy to be emitted from the material, so the film that absorbs photons can be quite thick. These materials are known as negative electron affinity materials. | 7 | Physical Chemistry |
In clinical pharmacology, a potentiator is a drug, herb, or chemical that intensifies the effects of a given drug. For example, hydroxyzine or dextromethorphan is used to get more pain relief and anxiolysis out of an equal dose of an opioid medication. The potentiation can take place at any part of the liberation, absorption, distribution, metabolism and elimination of the drug. | 0 | Organic Chemistry |
A host–guest complex, also known as a donor–acceptor complex, may be formed from a Lewis base, B, and a Lewis acid, A. The host may be either a donor or an acceptor. In biochemistry host–guest complexes are known as receptor-ligand complexes; they are formed primarily by non-covalent bonding. Many host–guest complexes has 1:1 stoichiometry, but many others have more complex structures. The general equilibrium can be written as
:p A + q B AB
The study of these complexes is important for supramolecular chemistry and molecular recognition. The objective of these studies is often to find systems with a high binding selectivity of a host (receptor) for a particular target molecule or ion, the guest or ligand. An application is the development of chemical sensors. Finding a drug which either blocks a receptor, an antagonist which forms a strong complex the receptor, or activate it, an agonist, is an important pathway to drug discovery. | 7 | Physical Chemistry |
Stemming from the National Pollutant Discharge Elimination System (NPDES) EPA permitting guidelines, point and nonpoint discharges may adversely affect sediment quality. As per state regulatory criteria, information on point and nonpoint source contamination, and its effects on sediment quality may be required for assessment of compliance. For example, Washington State Sediment Management Standards, Part IV, mandates sediment control standards which allow for establishment of discharge sediment monitoring requirements, and criteria for creation and maintenance of sediment impact zones (WADOE 2013). In this instance, the SQT could be particularly useful encompassing multiple relevant analyses simultaneously. | 2 | Environmental Chemistry |
Analytical band centrifugation (ABC) (also known as analytical band ultracentrifugation, or band sedimentation-velocity), is a specialized ultracentrifugation procedure, where unlike the typical use of (boundary) sedimentation velocity analytical ultracentrifugation (SV-AUC) wherein a homogenous bulk solution is centrifuged, in ABC a thin (~15 µL, ~500 µm) sample is layered on top of a bulk solvent and then centrifuged. The method is distinguished from zone-sedimentation in that a stabilizing density gradient is self-generated during centrifugation, through the use of a higher density (than the sample) bulk "binary solvent", containing both a solvent (i.e. HO), and a second component (small molecules, i.e. CsCl) that will sediment to form a stabilizing density gradient for the sample.
ABC also requires specially designed analytical ultracentrifuge cells, as the sample is not manually applied by pipette but instead automatically delivered via capillary under low g-forces at the beginning of a run from a reservoir within the cell. It was first demonstrated in 1963, and was not commonly used for many decades, but recently has become more widely used due to its applicability to quality control measurements on therapeutic viruses such as adeno-associated viruses (AAVs). The profiles resulting from ABC analyses are similar in their interpretation to the profiles from electrophoretic separations ("electropherograms"), and thus have been dubbed "centrifugrams". | 1 | Biochemistry |
In chemical kinetics, the elementary reactions are represented by the stoichiometric equations
where are the components and are the stoichiometric coefficients. Here, the reverse reactions with positive constants are included in the list separately. We need this separation of direct and reverse reactions to apply later the general formalism to the systems with some irreversible reactions. The system of stoichiometric equations of elementary reactions is the reaction mechanism.
The stoichiometric matrix is , (gain minus loss). This matrix need not be square. The stoichiometric vector is the rth row of with coordinates .
According to the generalized mass action law, the reaction rate for an elementary reaction is
where is the activity (the "effective concentration") of .
The reaction mechanism includes reactions with the reaction rate constants . For each r the following notations are used: ; ; is the reaction rate constant for the reverse reaction if it is in the reaction mechanism and 0 if it is not; is the reaction rate for the reverse reaction if it is in the reaction mechanism and 0 if it is not. For a reversible reaction, is the equilibrium constant.
The principle of detailed balance for the generalized mass action law is: For given values there exists a positive equilibrium that satisfies detailed balance, that is, . This means that the system of linear detailed balance equations
is solvable (). The following classical result gives the necessary and sufficient conditions for the existence of a positive equilibrium with detailed balance (see, for example, the textbook).
Two conditions are sufficient and necessary for solvability of the system of detailed balance equations:
# If then and, conversely, if then (reversibility);
# For any solution of the system
the Wegscheider's identity holds:
Remark. It is sufficient to use in the Wegscheider conditions a basis of solutions of the system .
In particular, for any cycle in the monomolecular (linear) reactions the product of the reaction rate constants in the clockwise direction is equal to the product of the reaction rate constants in the counterclockwise direction. The same condition is valid for the reversible Markov processes (it is equivalent to the "no net flow" condition).
A simple nonlinear example gives us a linear cycle supplemented by one nonlinear step:
There are two nontrivial independent Wegscheider's identities for this system:
and
They correspond to the following linear relations between the stoichiometric vectors:
and
The computational aspect of the Wegscheider conditions was studied by D. Colquhoun with co-authors.
The Wegscheider conditions demonstrate that whereas the principle of detailed balance states a local property of equilibrium, it implies the relations between the kinetic constants that are valid for all states far from equilibrium. This is possible because a kinetic law is known and relations between the rates of the elementary processes at equilibrium can be transformed into relations between kinetic constants which are used globally. For the Wegscheider conditions this kinetic law is the law of mass action (or the generalized law of mass action). | 7 | Physical Chemistry |
Homogeneous Schrock-type carbene complexes such as Tebbe's reagent can be used for the olefination of carbonyls, replacing the oxygen atom with a methylidene group. The nucleophilic carbon atom behaves similarly to the carbon atom of the phosphorus ylide in the Wittig reaction, attacking the electrophilic carbonyl atom of a ketone, followed by elimination of a metal oxide.
In the nucleophilic abstraction reaction, a methyl group can be abstracted from the donating group of a Fischer carbene, making it a strong nucleophile for further reaction.
Diazo compounds like methyl phenyldiazoacetate can be used for cyclopropanation or to insert into C-H bonds of organic substrates. These reactions are catalyzed by dirhodium tetraacetate or related chiral derivatives. Such catalysis is assumed to proceed via the intermediacy of carbene complexes. | 0 | Organic Chemistry |
Pyruvate is an important chemical compound in biochemistry. It is the output of the metabolism of glucose known as glycolysis. One molecule of glucose breaks down into two molecules of pyruvate, which are then used to provide further energy, in one of two ways. Pyruvate is converted into acetyl-coenzyme A, which is the main input for a series of reactions known as the Krebs cycle (also known as the citric acid cycle or tricarboxylic acid cycle). Pyruvate is also converted to oxaloacetate by an anaplerotic reaction, which replenishes Krebs cycle intermediates; also, the oxaloacetate is used for gluconeogenesis.
These reactions are named after Hans Adolf Krebs, the biochemist awarded the 1953 Nobel Prize for physiology, jointly with Fritz Lipmann, for research into metabolic processes. The cycle is also known as the citric acid cycle or tricarboxylic acid cycle, because citric acid is one of the intermediate compounds formed during the reactions.
If insufficient oxygen is available, the acid is broken down anaerobically, creating lactate in animals and ethanol in plants and microorganisms (and carp). Pyruvate from glycolysis is converted by fermentation to lactate using the enzyme lactate dehydrogenase and the coenzyme NADH in lactate fermentation, or to acetaldehyde (with the enzyme pyruvate decarboxylase) and then to ethanol in alcoholic fermentation.
Pyruvate is a key intersection in the network of metabolic pathways. Pyruvate can be converted into carbohydrates via gluconeogenesis, to fatty acids or energy through acetyl-CoA, to the amino acid alanine, and to ethanol. Therefore, it unites several key metabolic processes. | 1 | Biochemistry |
In chemistry, transition state theory (TST) explains the reaction rates of elementary chemical reactions. The theory assumes a special type of chemical equilibrium (quasi-equilibrium) between reactants and activated transition state complexes.
TST is used primarily to understand qualitatively how chemical reactions take place. TST has been less successful in its original goal of calculating absolute reaction rate constants because the calculation of absolute reaction rates requires precise knowledge of potential energy surfaces, but it has been successful in calculating the standard enthalpy of activation (ΔH, also written ΔH), the standard entropy of activation (ΔS or ΔS), and the standard Gibbs energy of activation (ΔG or ΔG) for a particular reaction if its rate constant has been experimentally determined. (The notation refers to the value of interest at the transition state; ΔH is the difference between the enthalpy of the transition state and that of the reactants.)
This theory was developed simultaneously in 1935 by Henry Eyring, then at Princeton University, and by Meredith Gwynne Evans and Michael Polanyi of the University of Manchester. TST is also referred to as "activated-complex theory", "absolute-rate theory", and "theory of absolute reaction rates".
Before the development of TST, the Arrhenius rate law was widely used to determine energies for the reaction barrier. The Arrhenius equation derives from empirical observations and ignores any mechanistic considerations, such as whether one or more reactive intermediates are involved in the conversion of a reactant to a product. Therefore, further development was necessary to understand the two parameters associated with this law, the pre-exponential factor (A) and the activation energy (E). TST, which led to the Eyring equation, successfully addresses these two issues; however, 46 years elapsed between the publication of the Arrhenius rate law, in 1889, and the Eyring equation derived from TST, in 1935. During that period, many scientists and researchers contributed significantly to the development of the theory. | 7 | Physical Chemistry |
Microbial production of Succinic acid can be performed with wild bacteria like Actinobacillus succinogenes, Mannheimia succiniciproducens and Anaerobiospirillum succiniciproducens or genetically modified Escherichia coli, Corynebacterium glutamicum and Saccharomyces cerevisiae. Understanding of the central carbon metabolism of these organisms is crucial in determining the maximum obtainable yield of succinic acid on the carbon source employed as substrate. | 1 | Biochemistry |
The HO radical is linked with the production of HO in molecular clouds. Studies of HO distribution in Taurus Molecular Cloud-1 (TMC-1) suggest that in dense gas, HO is mainly formed by dissociative recombination of HO. Dissociative recombination is the reaction in which a molecular ion recombines with an electron and dissociates into neutral fragments. Important formation mechanisms for HO are:
HO + e → HO + H (1a) Dissociative recombination
HO + e → HO + H + H (1b) Dissociative recombination
HCO + e → HO + CO (2a) Dissociative recombination
O + HCO → HO + CO (3a) Neutral-neutral
H + HO → HO + H + H (4a) Ion-molecular ion neutralization | 2 | Environmental Chemistry |
Thermodynamics is a branch of physics that deals with heat, work, and temperature, and their relation to energy, entropy, and the physical properties of matter and radiation. The behavior of these quantities is governed by the four laws of thermodynamics which convey a quantitative description using measurable macroscopic physical quantities, but may be explained in terms of microscopic constituents by statistical mechanics. Thermodynamics applies to a wide variety of topics in science and engineering, especially physical chemistry, biochemistry, chemical engineering and mechanical engineering, but also in other complex fields such as meteorology.
Historically, thermodynamics developed out of a desire to increase the efficiency of early steam engines, particularly through the work of French physicist Sadi Carnot (1824) who believed that engine efficiency was the key that could help France win the Napoleonic Wars. Scots-Irish physicist Lord Kelvin was the first to formulate a concise definition of thermodynamics in 1854 which stated, "Thermo-dynamics is the subject of the relation of heat to forces acting between contiguous parts of bodies, and the relation of heat to electrical agency." German physicist and mathematician Rudolf Clausius restated Carnot's principle known as the Carnot cycle and gave to the theory of heat a truer and sounder basis. His most important paper, "On the Moving Force of Heat", published in 1850, first stated the second law of thermodynamics. In 1865 he introduced the concept of entropy. In 1870 he introduced the virial theorem, which applied to heat.
The initial application of thermodynamics to mechanical heat engines was quickly extended to the study of chemical compounds and chemical reactions. Chemical thermodynamics studies the nature of the role of entropy in the process of chemical reactions and has provided the bulk of expansion and knowledge of the field. Other formulations of thermodynamics emerged. Statistical thermodynamics, or statistical mechanics, concerns itself with statistical predictions of the collective motion of particles from their microscopic behavior. In 1909, Constantin Carathéodory presented a purely mathematical approach in an axiomatic formulation, a description often referred to as geometrical thermodynamics. | 7 | Physical Chemistry |
A blank solution is a solution containing little to no analyte of interest, usually used to calibrate instruments such as a colorimeter. According to the EPA, the "primary purpose of blanks is to trace sources of artificially introduced contamination." Different types of blanks are used to identify the source of contamination in the sample. The types of blanks include equipment blank, field blank, trip blank, method blank, and instrument blank. | 3 | Analytical Chemistry |
According to the Carothers equation number-average degree of polymerization is given by
where is the extent of the reaction and is the average functionality of reaction mixture. For the gel can be considered to be infinite, thus the critical extent of the reaction at the gel point is found as
If is greater or equal to , gelation occurs. | 7 | Physical Chemistry |
The 65 "Sohncke" space groups, not containing any mirrors, inversion points, improper rotations or glide planes, yield chiral crystals, not identical to their mirror image; whereas space groups that do include at least one of those give achiral crystals. Achiral molecules sometimes form chiral crystals, but chiral molecules always form chiral crystals, in one of the space groups that permit this.
Among the 65 Sohncke groups are 22 that come in 11 enantiomorphic pairs. | 4 | Stereochemistry |
Adenylate Kinase 2 (AK2) deficiency in humans causes hematopoietic defects associated with sensorineural deafness. Reticular dysgenesis is an autosomal recessive form of human combined immunodeficiency. It is also characterized by an impaired lymphoid maturation and early differentiation arrest in the myeloid lineage. AK2 deficiency results in absent or a large decrease in the expression of proteins. AK2 is specifically expressed in the stria vascularis of the inner ear which indicates why individuals with an AK2 deficiency will have sensorineural deafness. | 1 | Biochemistry |
In nucleophilic aliphatic substitution, sodium nitrite (NaNO) replaces an alkyl halide. In the so-called Ter Meer reaction (1876) named after Edmund ter Meer, the reactant is a 1,1-halonitroalkane:
The reaction mechanism is proposed in which in the first slow step a proton is abstracted from nitroalkane 1 to a carbanion 2 followed by protonation to an aci-nitro 3 and finally nucleophilic displacement of chlorine based on an experimentally observed hydrogen kinetic isotope effect of 3.3. When the same reactant is reacted with potassium hydroxide the reaction product is the 1,2-dinitro dimer. | 0 | Organic Chemistry |
A fluid inclusion is a bubble of liquid and/or gas that is trapped within a crystal. As minerals often form from a liquid or aqueous medium, tiny bubbles of that liquid can become trapped within the crystal, or along healed crystal fractures. These inclusions usually range in size from 0.01 mm to 1 mm and are only visible in detail by microscopic study, however specimens of fenster or skeletal quartz may include thin sheet-like inclusions that are many millimetres in length and breadth within their lamellar voids.
These inclusions occur in a wide variety of environments. For example, they are found within cementing minerals of sedimentary rocks, in gangue minerals such as quartz or calcite in hydrothermal circulation deposits, in fossil amber, and in deep ice cores from the Greenland and Antarctic ice caps. The inclusions can provide information about the conditions existing during the formation of the enclosing mineral. Fourier transform infrared spectroscopy and Raman spectroscopy can be used to determine the composition of fluid inclusions. | 9 | Geochemistry |
Since refinement depends on finding the best fit between a calculated and experimental pattern, it is important to have a numerical figure of merit quantifying the quality of the fit. Below are the figures of merit generally used to characterize the quality of a refinement. They provide insight to how well the model fits the observed data.
Profile residual (reliability factor):
Weighted profile residual:
Bragg residual:
Expected profile residual:
Goodness of fit:
It is worth mentioning that all but one () figure of merit include a contribution from the background. There are some concerns about the reliability of these figures, as well there is no threshold or accepted value which dictates what represents a good fit. The most popular and conventional figure of merit used is the goodness of fit which should approach unity given a perfect fit, though this is rarely the case. In practice, the best way to assess quality is a visual analysis of the fit by plotting the difference between the observed and calculated data plotted on the same scale. | 3 | Analytical Chemistry |
Blood pH and concentrations of several chemicals are tested in a corpse to help determine the time of death of the victim, also known as the post-mortem interval. These chemicals include lactic acid, hypoxanthine, uric acid, ammonia, NADH and formic acid.
The decrease in the concentration of oxygen because of the lack of circulation causes a dramatic switch from aerobic to anaerobic metabolism
This type of analysis can be used to help diagnose various different types of deaths such as: drowning, anaphylactic shock, hypothermia or any deaths related to alcohol or diabetes. Although these types of diagnosis become very difficult because of the changes to the body and biochemical measurements vary after death. | 1 | Biochemistry |
Surfactants are usually composed of a hydrocarbon chain and a polar head group.
Increasing the length of the hydrocarbon chain increases the Krafft temperature because it improves Van der Waals forces.
Moreover, since Krafft point is related to solid-liquid transition, better-packed polar heads within surfactant crystals increase Krafft temperature. | 7 | Physical Chemistry |
Being a good solvent for many materials (such as grease and tar), carbon tetrachloride was widely used as a cleaning fluid for nearly 70 years. It is nonflammable and nonexplosive and did not leave any odour on the cleaned material, unlike gasoline, which was also used for cleaning at the time. It was used as a "safe" alternative to gasoline. It was first marketed as Katharin, in 1890 or 1892 and as Benzinoform later.
Carbon tetrachloride was the first chlorinated solvent to be used in dry-cleaning and was used until the 1950s. It had the downsides of being corrosive to the dry-cleaning equipment and causing illness among dry-cleaning operators, and was replaced by trichloroethylene, tetrachloroethylene and methyl chloroform (trichloroethane).
Carbon tetrachloride was also used as an alternative to petrol (gasoline) in dry shampoos, from the beginning of 1903 to the 1930s. Several women had fainted from its fumes during the hair wash in barber shops, the hairdressers often used electric fans to blow the fumes away. In 1909, a baronet's daughter, Helenora Elphinstone-Dalrymple (aged 29), died after having her hair shampooed with carbon tetrachloride.
It is assumed that carbon tetrachloride was still used as a dry cleaning solvent in North Korea as of 2006. | 2 | Environmental Chemistry |
Heating a lactone with a base (sodium hydroxide) will hydrolyse the lactone to its parent compound, the straight chained bifunctional compound. Like straight-chained esters, the hydrolysis-condensation reaction of lactones is a reversible reaction, with an equilibrium. However, the equilibrium constant of the hydrolysis reaction of the lactone is lower than that of the straight-chained ester i.e. the products (hydroxyacids) are less favored in the case of the lactones. This is because although the enthalpies of the hydrolysis of esters and lactones are about the same, the entropy of the hydrolysis of lactones is less than the entropy of straight-chained esters. Straight-chained esters give two products upon hydrolysis, making the entropy change more favorable than in the case of lactones which gives only a single product.
Lactones also react with amines to give the ring-opened alcohol and amide. | 0 | Organic Chemistry |
Oceanographers and engineers continue to find novel and more accurate methods of measuring carbon content in seawater. One method is to collect water samples and directly measure the DIC by using a TOC analyzer. Samples can be combined with stable isotope ratios C/C, alkalinity measurements, and estimation of physical processes, to create diagnostic techniques. Researchers at Scripps Institution of Oceanography developed a tool that uses flow injection analysis to measures microfluidic samples of seawater and continuously monitor dissolved inorganic carbon content. | 9 | Geochemistry |
Relative Surface Excess quantities are more useful than arbitrary surface excess quantities. The Relative surface excess relates the adsorption at the interface to a solvent in the bulk phase. An advantage of using the relative surface excess quantities is that they don't depend on the location of the dividing surface. The relative surface excess of species and solvent 1 is therefore: | 7 | Physical Chemistry |
In molecular biology, an interactome is the whole set of molecular interactions in a particular cell. The term specifically refers to physical interactions among molecules (such as those among proteins, also known as protein–protein interactions, PPIs; or between small molecules and proteins) but can also describe sets of indirect interactions among genes (genetic interactions).
The word "interactome" was originally coined in 1999 by a group of French scientists headed by Bernard Jacq. Mathematically, interactomes are generally displayed as graphs. Though interactomes may be described as biological networks, they should not be confused with other networks such as neural networks or food webs. | 1 | Biochemistry |
Polariton superfluid is predicted to be a state of the exciton-polaritons system that combines the characteristics of lasers with those of excellent electrical conductors. Researchers look for this state in a solid state optical microcavity coupled with quantum well excitons. The idea is to create an ensemble of particles known as exciton-polaritons and trap them.
Wave behavior in this state results in a light beam similar to that from a laser but possibly more energy efficient.
Unlike traditional superfluids that need temperatures of approximately ~4 K, the polariton superfluid could in principle be stable at much higher temperatures, and might soon be demonstrable at room temperature. Evidence for polariton superfluidity was reported in by Alberto Amo and coworkers, based on the suppressed scattering of the polaritons during their motion.
Although several other researchers are working in the same field, the terminology and conclusions are not completely shared by the different groups. In particular, important properties of superfluids, such as zero viscosity, and of lasers, such as perfect optical coherence, are a matter of debate. Although, there is clear indication of quantized vortices when the pump beam has orbital angular momentum.
Furthermore, clear evidence has been demonstrated also for superfluid motion of polaritons, in terms of the Landau criterion and the suppression of scattering from defects when the flow velocity is slower than the speed of sound in the fluid.
The same phenomena have been demonstrated in an organic exciton polariton fluid, representing the first achievement of room-temperature superfluidity of a hybrid fluid of photons and excitons. | 7 | Physical Chemistry |
Earths atmosphere and hydrosphere—Earths heat engine—are coupled processes that constantly even out solar heating imbalances through evaporation of surface water, convection, rainfall, winds and ocean circulation, when distributing heat around the globe.
A Hadley cell is an example of a heat engine. It involves the rising of warm and moist air in the earth's equatorial region and the descent of colder air in the subtropics creating a thermally driven direct circulation, with consequent net production of kinetic energy. | 7 | Physical Chemistry |
The modification required to biosynthesize mature chloroeremomycin include: oxidative cross-linking of aromatic rings, hydroxylation and chlorination of the two Tyr residues, methylation of Leu, and glycosylation at aa4 and aa6.
The oxidative crosslinks are catalyzed by enzymes OxyA-C. The glycosylations are catalyzed by enzymes GtfA-C (coded by Orf11-13 respectively). The chlorinations are performed by enzymes encoded by Orf10 and 18. | 0 | Organic Chemistry |
The first mitogen-activated protein kinase to be discovered was ERK1 (MAPK3) in mammals. Since ERK1 and its close relative ERK2 (MAPK1) are both involved in growth factor signaling, the family was termed "mitogen-activated". With the discovery of other members, even from distant organisms (e.g. plants), it has become increasingly clear that the name is a misnomer, since most MAPKs are actually involved in the response to potentially harmful, abiotic stress stimuli (hyperosmosis, oxidative stress, DNA damage, low osmolarity, infection, etc.). Because plants cannot "flee" from stress, terrestrial plants have the highest number of MAPK genes per organism ever found. Thus the role of mammalian ERK1/2 kinases as regulators of cell proliferation is not a generic, but a highly specialized function. | 1 | Biochemistry |
ITCH is regulated by MAPK8. MAPK8 regulates JUNB protein turnover by MAPK8-dependent phosphorylation of ITCH and a subsequent conformational change in ITCH. This mechanism is discrete from the direct activation of Jun family transcription factors by direct phosphorylation. ITCH serves as a paradigm for our understanding of the regulation of the ubiquitylation machinery by direct protein phosphorylation of its components. Importantly, this regulatory process controls the balance of Th2 cytokine secretion by negatively regulating JUNB levels and Interleukin 4 transcription. | 1 | Biochemistry |
The process of mating type switching is a gene conversion event initiated by the HO gene. The HO gene is a tightly regulated haploid-specific gene that is only activated in haploid cells during the G phase of the cell cycle. The protein encoded by the HO gene is a DNA endonuclease, which physically cleaves DNA, but only at the MAT locus (due to the DNA sequence specificity of the HO endonuclease).
Once HO cuts the DNA at MAT, exonucleases are attracted to the cut DNA ends and begin to degrade the DNA on both sides of the cut site. This DNA degradation by exonucleases eliminates the DNA which encoded the MAT allele; however, the resulting gap in the DNA is repaired by copying in the genetic information present at either HML or HMR, filling in a new allele of either the MATa or MATα gene. Thus, the silenced alleles of MATa and MATα present at HML and HMR serve as a source of genetic information to repair the HO-induced DNA damage at the active MAT locus. | 1 | Biochemistry |
In the isometric system, the most common types of twins are the Spinel Law (twin plane, parallel to an octahedron) <111>, where the twin axis is perpendicular to an octahedral face, and the Iron Cross <001>, which is the interpenetration of two pyritohedrons, a subtype of dodecahedron.
In the hexagonal system, calcite shows the contact twin laws {0001} and {0112}. Quartz shows the Brazil Law {1120}, and Dauphiné Law <0001>, which are penetration twins caused by transformation, and Japan Law {1122}, which is often caused by accidents during growth.
In the tetragonal system, cyclical contact twins are the most commonly observed type of twin, such as in rutile titanium dioxide and cassiterite tin oxide.
In the orthorhombic system, crystals usually twin on planes parallel to the prism face, where the most common is a {110} twin, which produces cyclical twins, such as in aragonite, chrysoberyl, and cerussite.
In the monoclinic system, twins occur most often on the planes {100} and {001} by the Manebach Law {001}, Carlsbad Law [001], Baveno Law {021} in orthoclase, and the Swallow Tail Twins (Manebach law) {001} in gypsum.
In the triclinic system, the most commonly twinned crystals are the feldspar minerals plagioclase and microcline. These minerals show the Albite and Pericline Laws.
The most common twin operations by crystal system are tabulated below. This list is not exhaustive, particularly for the crystal systems of lowest symmetry, such as the triclinic system. | 3 | Analytical Chemistry |
How much gas is present could be specified by giving the mass instead of the chemical amount of gas. Therefore, an alternative form of the ideal gas law may be useful. The chemical amount, n (in moles), is equal to total mass of the gas (m) (in kilograms) divided by the molar mass, M (in kilograms per mole):
By replacing n with m/M and subsequently introducing density ρ = m/V, we get:
Defining the specific gas constant R as the ratio R/M,
This form of the ideal gas law is very useful because it links pressure, density, and temperature in a unique formula independent of the quantity of the considered gas. Alternatively, the law may be written in terms of the specific volume v, the reciprocal of density, as
It is common, especially in engineering and meteorological applications, to represent the specific gas constant by the symbol R. In such cases, the universal gas constant is usually given a different symbol such as or to distinguish it. In any case, the context and/or units of the gas constant should make it clear as to whether the universal or specific gas constant is being used. | 7 | Physical Chemistry |
The Tremolite Asbestos Registry contains people who lived in or worked in Libby, Montana, while vermiculite was mined there; these people were at risk for exposure to the tremolite asbestos that was naturally occurring in the vermiculite. ATSDR began addressing public health concerns in Libby in 1999 and created the registry in 2004. The purpose of the registry was to monitor the long-term health effects of people in Libby exposed to tremolite asbestos and to assist with communicating important health information to registrants. Researchers have used the registry to study how asbestos exposure affects human health. This research has yielded several important findings. Registry data was used to conduct the first study of the relationship between asbestos exposure and respiratory problems in children. Another study using registry data found a significant relationship between asbestos exposure and death from cardiovascular disease. | 1 | Biochemistry |
Sources can be adapted in many ways, but the lists below give the general uses of a number of sources. Of these, flames are the most common due to their low cost and their simplicity. Although significantly less common, inductively-coupled plasmas, especially when used with mass spectrometers, are recognized for their outstanding analytical performance and their versatility.
For all atomic spectroscopy, a sample must be vaporized and atomized. For atomic mass spectrometry, a sample must also be ionized. Vaporization, atomization, and ionization are often, but not always, accomplished with a single source. Alternatively, one source may be used to vaporize a sample while another is used to atomize (and possibly ionize). An example of this is laser ablation inductively-coupled plasma atomic emission spectrometry, where a laser is used to vaporize a solid sample and an inductively-coupled plasma is used to atomize the vapor.
With the exception of flames and graphite furnaces, which are most commonly used for atomic absorption spectroscopy, most sources are used for atomic emission spectroscopy.
Liquid-sampling sources include flames and sparks (atom source), inductively-coupled plasma (atom and ion source), graphite furnace (atom source), microwave plasma (atom and ion source), and direct-current plasma (atom and ion source). Solid-sampling sources include lasers (atom and vapor source), glow discharge (atom and ion source), arc (atom and ion source), spark (atom and ion source), and graphite furnace (atom and vapor source). Gas-sampling sources include flame (atom source), inductively-coupled plasma (atom and ion source), microwave plasma (atom and ion source), direct-current plasma (atom and ion source), and glow discharge (atom and ion source). | 7 | Physical Chemistry |
Consider the following acid–base reaction:
Acetic acid, , is an acid because it donates a proton to water () and becomes its conjugate base, the acetate ion (). is a base because it accepts a proton from and becomes its conjugate acid, the hydronium ion, ().
The reverse of an acid–base reaction is also an acid–base reaction, between the conjugate acid of the base in the first reaction and the conjugate base of the acid. In the above example, ethanoate is the base of the reverse reaction and hydronium ion is the acid.
One feature of the Brønsted–Lowry theory in contrast to Arrhenius theory is that it does not require an acid to dissociate. | 7 | Physical Chemistry |
If an unsymmetrical ketone is subjected to base, it has the potential to form two regioisomeric enolates (ignoring enolate geometry). For example:
The trisubstituted enolate is considered the kinetic enolate, while the tetrasubstituted enolate is considered the thermodynamic enolate. The alpha hydrogen deprotonated to form the kinetic enolate is less hindered, and therefore deprotonated more quickly. In general, tetrasubstituted olefins are more stable than trisubstituted olefins due to hyperconjugative stabilization. The ratio of enolate regioisomers is heavily influenced by the choice of base. For the above example, kinetic control may be established with LDA at −78 °C, giving 99:1 selectivity of kinetic: thermodynamic enolate, while thermodynamic control may be established with triphenylmethyllithium at room temperature, giving 10:90 selectivity.
In general, kinetic enolates are favored by cold temperatures, conditions that give relatively ionic metal–oxygen bonding, and rapid deprotonation using a slight excess of a strong, sterically hindered base. The large base only deprotonates the more accessible hydrogen, and the low temperatures and excess base help avoid equilibration to the more stable alternate enolate after initial enolate formation. Thermodynamic enolates are favored by longer equilibration times at higher temperatures, conditions that give relatively covalent metal–oxygen bonding, and use of a slight sub-stoichiometric amount of strong base. By using insufficient base to deprotonate all of the carbonyl molecules, the enolates and carbonyls can exchange protons with each other and equilibrate to their more stable isomer. Using various metals and solvents can provide control over the amount of ionic character in the metal–oxygen bond. | 0 | Organic Chemistry |
Inputs from the biosphere may begin with lichen and other microorganisms that secrete oxalic acid. These microorganisms, associated with the lichen community or independently inhabiting rocks, include blue-green algae, green algae, various fungi, and numerous bacteria. Lichen has long been viewed as the pioneers of soil development as the following 1997 Isozaki statement suggests:
However, lichens are not necessarily the only pioneering organisms nor the earliest form of soil formation as it has been documented that seed-bearing plants may occupy an area and colonize quicker than lichen. Also, eolian sedimentation (wind generated) can produce high rates of sediment accumulation. Nonetheless, lichen can certainly withstand harsher conditions than most vascular plants, and although they have slower colonization rates, they do form the dominant group in alpine regions.
Organic acids released from plant roots include acetic acid and citric acid. During the decay of organic matter phenolic acids are released from plant matter and humic acid and fulvic acid are released by soil microbes. These organic acids speed up chemical weathering by combining with some of the weathering products in a process known as chelation. In the soil profile, these organic acids are often concentrated at the top of the profile, while carbonic acid plays a larger role towards the bottom of the profile or below in the aquifer.
As the soil column develops further into thicker accumulations, larger animals come to inhabit the soil and continue to alter the chemical evolution of their respective niche. Earthworms aerate the soil and convert large amounts of organic matter into rich humus, improving soil fertility. Small burrowing mammals store food, grow young and may hibernate in the pedosphere altering the course of soil evolution. Large mammalian herbivores above ground transport nutrients in form of nitrogen-rich waste and phosphorus-rich antlers, while predators leave phosphorus-rich piles of bones on the soil surface, leading to localized enrichment of the soil. | 9 | Geochemistry |
Some authors suggest the Le Bail technique exploits prior information more efficiently than Pawley method. This was an important consideration at the time of development when computing power was limited. Le Bail is also easily integrated into Rietveld analysis software, and is a part of a number of programs. Both methods improve subsequent structural refinements. | 3 | Analytical Chemistry |
A chiral sp hybridized isomer contains four different substituents. All four substituents are assigned prorites based on its atomic numbers. After the substituents of a stereocenter have been assigned their priorities, the molecule is oriented in space so that the group with the lowest priority is pointed away from the observer. If the substituents are numbered from 1 (highest priority) to 4 (lowest priority), then the sense of rotation of a curve passing through 1, 2 and 3 distinguishes the stereoisomers. In a configurational isomer, the lowest priority group (most times hydrogen) is positioned behind the plane or the hatched bond going away from the reader. The highest priority group will have an arc drawn connecting to the rest of the groups, finishing at the group of third priority. An arc drawn clockwise, has the rectus (R) assignment. An arc drawn counterclockwise, has the sinister (S) assignment. The names are derived from the Latin for right and left, respectively. When naming an organic isomer, the abbreviation for either rectus or sinister assignment is placed in front of the name in parentheses. For example, 3-methyl-1-pentene with a rectus assignment is formatted as (R)-3-methyl-1-pentene.
A practical method of determining whether an enantiomer is R or S is by using the right-hand rule: one wraps the molecule with the fingers in the direction . If the thumb points in the direction of the fourth substituent, the enantiomer is R; otherwise, it is S.
It is possible in rare cases that two substituents on an atom differ only in their absolute configuration (R or S). If the relative priorities of these substituents need to be established, R takes priority over S. When this happens, the descriptor of the stereocenter is a lowercase letter (r or s) instead of the uppercase letter normally used. | 4 | Stereochemistry |
Mice with mutant carboxypeptidase E, Cpe, display endocrine disorders like obesity and infertility. In some strains of mice, the fat mutation also causes hyperproinsulinemia in adult male mice, but this is not found in all strains of mice. The obesity and infertility in the Cpe mice develop with age; young mice ( mice is impaired, with a large accumulation of peptides with C-terminal lysine and/or arginine extensions. Levels of the mature forms of peptides are generally reduced in these mice, but not eliminated. It is thought that a related enzyme (carboxypeptidase D) also contributes to neuropeptide processing and gives rise to the mature peptides in the Cpe mice.
Mutations in the CPE gene are not common within the human population, but have been identified. One patient with extreme obesity (Body Mass Index >50) was found to have a mutation that deleted nearly the entire CPE gene. This patient had intellectual disability (inability to read or write) and had abnormal glucose homeostasis, similar to mice lacking CPE activity.
In obesity, high levels of circulating free fatty acids have been reported to cause a decrease in the amount of carboxypeptidase E protein in pancreatic beta-cells, leading to beta-cell dysfunction (hyperproinsulinemia) and increased beta-cell apoptosis (via an increase in ER stress). However, because CPE is not a rate-limiting enzyme for the production of most neuropeptides and peptide hormones, it is not clear how relatively modest decreases in CPE activity can cause physiological effects. | 1 | Biochemistry |
One of the most useful chemical properties of n-BuLi is its ability to deprotonate a wide range of weak Brønsted acids. t-Butyllithium and s-butyllithium are more basic. n-BuLi can deprotonate (that is, metalate) many types of C−H bonds, especially where the conjugate base is stabilized by electron delocalization or one or more heteroatoms (non-carbon atoms). Examples include acetylenes (H−CC−R), methyl sulfides (H−CHSR), thioacetals (H−CH(SR), e.g. dithiane), methylphosphines (H−CHPR), furans, thiophenes and ferrocene (Fe(H−CH)(CH)). In addition to these, it will also deprotonate all more acidic compounds such as alcohols, amines, enolizable carbonyl compounds, and any overtly acidic compounds, to produce alkoxides, amides, enolates and other salts of lithium, respectively. The stability and volatility of the butane resulting from such deprotonation reactions is convenient, but can also be a problem for large-scale reactions because of the volume of a flammable gas produced.
: LiCH + RH → CH + RLi
The kinetic basicity of n-BuLi is affected by the solvent or cosolvent. Ligands that complex Li such as tetrahydrofuran (THF), tetramethylethylenediamine (TMEDA), hexamethylphosphoramide (HMPA), and 1,4-diazabicyclo[2.2.2]octane (DABCO) further polarize the Li−C bond and accelerate the metalation. Such additives can also aid in the isolation of the lithiated product, a famous example of which is dilithioferrocene.
:Fe(CH) + 2 LiCH + 2 TMEDA → 2 CH + Fe(CHLi)(TMEDA)
Schlossers base is a superbase produced by treating butyllithium with potassium t-butoxide. It is kinetically more reactive than butyllithium and is often used to accomplish difficult metalations. While some n-butylpotassium is present and is a stronger base than n-BuLi, the reactivity of the mixture is not exactly the same as isolated n'-butylpotassium.
An example of the use of n-butyllithium as a base is the addition of an amine to methyl carbonate to form a methyl carbamate, where n-butyllithium serves to deprotonate the amine:
: n-BuLi + RNH + (MeO)CO → RNCOMe + LiOMe + BuH | 0 | Organic Chemistry |
For membrane proteins, the situation is more complicated because the system that is being crystallized is not the membrane protein itself but the micellar system in which the membrane protein is embedded.
The size of the protein-detergent mixed micelles are affected by both additives and detergents which will strongly influence the crystals obtained. In addition to varying the concentration of primary detergents, additives (lipids and alcohols) and secondary detergents can be used to modulate the size and shape of the detergent micelles. By reducing the size of the mixed micelles lattice forming protein-protein contacts are encouraged. Lipid cubic phases, spontaneous self-assembling liquid crystals or lipid mesophases have been used successfully in the crystallization of integral membrane proteins.
Temperature, salts, detergents, various additives are used in this system to tailor the cubic phase to suit the target protein. Typical detergents used are n-dodecyl-β-d-maltopyranoside, n-decyl-β-d-glucopyranoside, lauryldimethylamine oxide LDAO, n-hexyl-β-d-glucopyranoside, n-nonyl-β-d-glucopyranoside and n-octyl-β-d-glucopyranoside; the various lipids are dioleoyl phosphatidylcholine, dioleoyl phosphatidylethanolamine and monoolein. | 3 | Analytical Chemistry |
Diphosphene is inert to ground-state oxygen but can be oxidized by triplet oxygen to give a mixture of phosphine oxides and hydroxy benzophosphole oxide. Compared to oxygen involved oxidation, reaction of diphosphene with ozone is much more rapid and indicates a 2:1 (ozone:diphosphene) stoichiometry. Ozonolysis of bis[tris(trimethylsilyl)methyl]diphosphene (TsiP) gives a cyclic diperoxides. | 0 | Organic Chemistry |
The transcriptomes of stem cells and cancer cells are of particular interest to researchers who seek to understand the processes of cellular differentiation and carcinogenesis. A pipeline using RNA-seq or gene array data can be used to track genetic changes occurring in stem and precursor cells and requires at least three independent gene expression data from the former cell type and mature cells.
Analysis of the transcriptomes of human oocytes and embryos is used to understand the molecular mechanisms and signaling pathways controlling early embryonic development, and could theoretically be a powerful tool in making proper embryo selection in in vitro fertilisation. Analyses of the transcriptome content of the placenta in the first-trimester of pregnancy in in vitro fertilization and embryo transfer (IVT-ET) revealed differences in genetic expression which are associated with higher frequency of adverse perinatal outcomes. Such insight can be used to optimize the practice. Transcriptome analyses can also be used to optimize cryopreservation of oocytes, by lowering injuries associated with the process.
Transcriptomics is an emerging and continually growing field in biomarker discovery for use in assessing the safety of drugs or chemical risk assessment.
Transcriptomes may also be used to infer phylogenetic relationships among individuals or to detect evolutionary patterns of transcriptome conservation.
Transcriptome analyses were used to discover the incidence of antisense transcription, their role in gene expression through interaction with surrounding genes and their abundance in different chromosomes. RNA-seq was also used to show how RNA isoforms, transcripts stemming from the same gene but with different structures, can produce complex phenotypes from limited genomes. | 1 | Biochemistry |
The ribbon synapse is a special type of synapse found in sensory neurons such as photoreceptor cells, retinal bipolar cells, and hair cells. Ribbon synapses contain a dense protein structure that tethers an array of vesicles perpendicular to the presynaptic membrane. In an electron micrograph it appears as a ribbon like structure perpendicular to the membrane. Unlike the traditional synapse, ribbon synapses can maintain a graded release of vesicles. In other words, the more depolarized a neuron the higher the rate of vesicle fusion. The Ribbon synapse active zone is separated into two regions, the archiform density and the ribbon. The archiform density is the site of vesicle fusion and the ribbon stores the releasable pool of vesicles. The ribbon structure is composed primarily of the protein RIBEYE, about 64–69% of the ribbon volume, and is tethered to the archiform density by scaffolding proteins such as Bassoon. | 1 | Biochemistry |
Tris(2-phenylpyridine)iridium, abbreviated [Ir(ppy)] is the organoiridium complex with the formula Ir(CH-CHN). The complex, a yellow-green solid, is a derivative of Ir bound to three monoanionic 2-pyridinylphenyl ligands. It is electroluminescent, emitting green light. The complex is observed with the facial stereochemistry, which is chiral.
The complex is prepared by cyclometalation reactions of 2-phenylpyridine and iridium trichloride, as represented by this idealized equation:
:IrCl + 3CH-CHN → Ir(CH-CHN) + 3 HCl
The complex and many analogues have been investigated for application in photoredox catalysis. Its excited state has a reduction potential of −2.14 V, nearly 1 V more negative than the reduction potential of excited [[Ruthenium tris(bipyridine)|[Ru(bipy)]]]. | 5 | Photochemistry |
Molecular beacons, or molecular beacon probes, are oligonucleotide hybridization probes that can report the presence of specific nucleic acids in homogenous solutions. Molecular beacons are hairpin-shaped molecules with an internally quenched fluorophore whose fluorescence is restored when they bind to a target nucleic acid sequence. This is a novel non-radioactive method for detecting specific sequences of nucleic acids. They are useful in situations where it is either not possible or desirable to isolate the probe-target hybrids from an excess of the hybridization probes. | 1 | Biochemistry |
Neuroproteomics has the difficult task of defining on a molecular level the pathways of consciousness, senses, and self. Neurological disorders are unique in that they do not always exhibit outward symptoms. Defining the disorders becomes difficult and so neuroproteomics is a step in the right direction of identifying bio-markers that can be used to detect diseases. Not only does the field have to map out the different proteins possible from the genome, but there are many modifications that happen after transcription that affect function as well. Because neurons are such dynamic structures, changing with every action potential that travels through them, neuroproteomics offers the most potential for mapping out the molecular template of their function. Genomics offers a static roadmap of the cell, while proteomics can offer a glimpse into structures smaller than the cell because of its specific nature to each moment in time. | 1 | Biochemistry |
The main components of a gamma spectrometer are the energy-sensitive radiation detector and the electronic devices that analyse the detector output signals, such as a pulse sorter (i.e., multichannel analyzer). Additional components may include signal amplifiers, rate meters, peak position stabilizers, and data handling devices. | 7 | Physical Chemistry |
There are many signals that control catabolism. Most of the known signals are hormones and the molecules involved in metabolism itself. Endocrinologists have traditionally classified many of the hormones as anabolic or catabolic, depending on which part of metabolism they stimulate. The so-called classic catabolic hormones known since the early 20th century are cortisol, glucagon, and adrenaline (and other catecholamines). In recent decades, many more hormones with at least some catabolic effects have been discovered, including cytokines, orexin (known as hypocretin), and melatonin. | 1 | Biochemistry |
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