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In the context of zeolites, the term heteroatom refers to partial isomorphous substitution of the typical framework atoms (silicon, aluminium, and phosphorus) by other elements such as beryllium, vanadium, and chromium. The goal is usually to adjust properties of the material (e.g., Lewis acidity) to optimize the material for a certain application (e.g., catalysis). | 0 | Organic Chemistry |
Nuclear DNA is normally tightly wrapped around histones rendering the DNA inaccessible to the general transcription machinery and hence this tight association prevents transcription of DNA. At physiological pH, the phosphate component of the DNA backbone is deprotonated which gives DNA a net negative charge. Histones are rich in lysine residues which at physiological pH are protonated and therefore positively charged. The electrostatic attraction between these opposite charges is largely responsible for the tight binding of DNA to histones.
Many coactivator proteins have intrinsic histone acetyltransferase (HAT) catalytic activity or recruit other proteins with this activity to promoters. These HAT proteins are able to acetylate the amine group in the sidechain of histone lysine residues which makes lysine much less basic, not protonated at physiological pH, and therefore neutralizes the positive charges in the histone proteins. This charge neutralization weakens the binding of DNA to histones causing the DNA to unwind from the histone proteins and thereby significantly increases the rate of transcription of this DNA.
Many corepressors can recruit histone deacetylase (HDAC) enzymes to promoters. These enzymes catalyze the hydrolysis of acetylated lysine residues restoring the positive charge to histone proteins and hence the tie between histone and DNA. PELP-1 can act as a transcriptional corepressor for transcription factors in the nuclear receptor family such as glucocorticoid receptors. | 1 | Biochemistry |
An emulsion is a mixture of two or more liquids that are normally immiscible (unmixable or unblendable) owing to liquid-liquid phase separation. Emulsions are part of a more general class of two-phase systems of matter called colloids. Although the terms colloid and emulsion are sometimes used interchangeably, emulsion should be used when both phases, dispersed and continuous, are liquids. In an emulsion, one liquid (the dispersed phase) is dispersed in the other (the continuous phase). Examples of emulsions include vinaigrettes, homogenized milk, liquid biomolecular condensates, and some cutting fluids for metal working.
Two liquids can form different types of emulsions. As an example, oil and water can form, first, an oil-in-water emulsion, in which the oil is the dispersed phase, and water is the continuous phase. Second, they can form a water-in-oil emulsion, in which water is the dispersed phase and oil is the continuous phase. Multiple emulsions are also possible, including a "water-in-oil-in-water" emulsion and an "oil-in-water-in-oil" emulsion.
Emulsions, being liquids, do not exhibit a static internal structure. The droplets dispersed in the continuous phase (sometimes referred to as the "dispersion medium") are usually assumed to be statistically distributed to produce roughly spherical droplets.
The term "emulsion" is also used to refer to the photo-sensitive side of photographic film. Such a photographic emulsion consists of silver halide colloidal particles dispersed in a gelatin matrix. Nuclear emulsions are similar to photographic emulsions, except that they are used in particle physics to detect high-energy elementary particles. | 7 | Physical Chemistry |
The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The term transcriptome is a portmanteau of the words transcript and genome; it is associated with the process of transcript production during the biological process of transcription.
The early stages of transcriptome annotations began with cDNA libraries published in the 1980s. Subsequently, the advent of high-throughput technology led to faster and more efficient ways of obtaining data about the transcriptome. Two biological techniques are used to study the transcriptome, namely DNA microarray, a hybridization-based technique and RNA-seq, a sequence-based approach. RNA-seq is the preferred method and has been the dominant transcriptomics technique since the 2010s. Single-cell transcriptomics allows tracking of transcript changes over time within individual cells.
Data obtained from the transcriptome is used in research to gain insight into processes such as cellular differentiation, carcinogenesis, transcription regulation and biomarker discovery among others. Transcriptome-obtained data also finds applications in establishing phylogenetic relationships during the process of evolution and in in vitro fertilization. The transcriptome is closely related to other -ome based biological fields of study; it is complementary to the proteome and the metabolome and encompasses the translatome, exome, meiome and thanatotranscriptome which can be seen as ome fields studying specific types of RNA transcripts. There are quantifiable and conserved relationships between the Transcriptome and other -omes, and Transcriptomics data can be used effectively to predict other molecular species, such as metabolites. There are numerous publicly available transcriptome databases. | 1 | Biochemistry |
By analyzing the chemical composition of a cows rumen, researchers can determine the effects of different feeds and processes on bovine digestion. Many of the earliest documented reports of cannulated cows were made by researchers working to understand how feed is processed through cows. For instance, a 1939 study discovered via cannulated cows that the pH of rumen varies throughout the day, becoming most alkaline just prior to feeding. A 1956 study used cannulated cows to determine that a hay-only diet does not change the proportion of fatty acids in a cows rumen, but every other type of feed measured does. | 1 | Biochemistry |
Neural stem cells (NSCs) in the brain must find a balance between maintaining their multipotency by self renewing and proliferating as opposed to differentiating and becoming quiescent. The PI3K/AKT pathway is crucial in this decision making process. NSCs are able to sense and respond to changes in the brain or throughout the organism. When blood glucose levels are elevated acutely, insulin is released from the pancreas. Activation of insulin receptors activates the PI3K/AKT pathway, which promotes proliferation. In this way, when there is high glucose and abundant energy in the organism, the PI3K/AKT pathway is activated and NSCs tend to proliferate. When there are low amounts of available energy, the PI3K/AKT pathway is less active and cells adopt a quiescent state.
This occurs, in part, when AKT phosphorylates FOXO, keeping FOXO in the cytoplasm. FOXO, when dephosphorylated, can enter the nucleus and work as a transcription factor to promote the expression of various tumor suppressors such as p27 and p21. These tumor suppressors push the NSC to enter quiescence. FOXO knockouts lose the ability for cells to enter a quiescent state as well as cells losing their neural stem cell character, possibly entering a cancer like state. | 1 | Biochemistry |
Carbon monoxide for FT catalysis is derived from hydrocarbons. In gas to liquids (GTL) technology, the hydrocarbons are low molecular weight materials that often would be discarded or flared. Stranded gas provides relatively cheap gas. For GTL to be commercially viable, gas must remain relatively cheaper than oil.
Several reactions are required to obtain the gaseous reactants required for FT catalysis. First, reactant gases entering a reactor must be desulfurized. Otherwise, sulfur-containing impurities deactivate ("poison") the catalysts required for FT reactions.
Several reactions are employed to adjust the H:CO ratio. Most important is the water-gas shift reaction, which provides a source of hydrogen at the expense of carbon monoxide:
For FT plants that use methane as the feedstock, another important reaction is dry reforming, which converts the methane into CO and H: | 0 | Organic Chemistry |
The formation of new blood capillaries is an important component of pathological tissue repair in response to ischemia. The angiogenic process is complex and involves endothelial cell (EC) movement and proliferation.
SFRP1 has been shown to have a role in new vascularization after an ischemic event and as a potent angiogenic factor. In vitro SFRP1 modulated the EC angiogenic response (migration, differentiation) and in vivo SFRP1 stimulated neovascularization in plug or tumor models. The directed movements of EC during de novo vessel formation are coordinated through cellular adhesion mechanisms, cytoskeletal reorganization and by association with elevated expression of angiogenic factors such as, the key factor, vascular endothelial growth factor. The regulation of the EC cytoskeleton is critical to EC spreading and motility. SFRP1 was found to have a major role in mediating EC spreading by regulating reorganization of the actin network and focal contact formations.
In vivo data supports a critical role for SFRP1 in ischemia-induced angiogenesis in adults. Using adenovirus-expressing SFRP1, impaired the canonical Wnt/Fzd pathway in the early phase of ischemia and as a result reduced vascular cell proliferation and delayed vessel formation. When SFRP1 was induced specifically in ECs along the kinetics of ischemia repair, a biphasic response was seen: a delay in capillary formation until day 15 and then an increase in vascular formation at day 25. This indicates that SFRP1 can fine tune the outcome of Wnt/Fzd signaling at different steps in the course of neovessel formation. | 1 | Biochemistry |
Pyruvate kinase catalyzes the last step within the glycolytic sequence, the dephosphorylation of phosphoenolpyruvate to pyruvate and is responsible for net energy production within the glycolytic pathway. Depending upon the different metabolic functions of the tissues, different isoenzymes of pyruvate kinase are expressed.
M2-PK (PKM2) is the predominant pyruvate kinase isoform in proliferating cells, such as fibroblasts, embryonic cells and adult stem cells and most human tissue, including lung, bladder, kidney and thymus; M2-PK is upgregulated in many human tumors.
M2-PK can occur in two different forms in proliferating cells:
* a tetrameric form, which consists of four subunits
* a dimeric form, consisting of two subunits.
The tetrameric form of M2-PK has a high affinity to its substrate, phosphoenolpyruvate (PEP), and is highly active at physiological PEP concentrations. Furthermore, the tetrameric form of M2-PK is associated with several other glycolytic enzymes within the so-called glycolytic enzyme complex. Due to the close proximity of the enzymes, the association within the glycolytic enzyme complex leads to a highly effective conversion of glucose to lactate.
When M2-PK is mainly in the highly active tetrameric form, which is the case in most normal cells, glucose is mostly converted to lactate, with the attendant production of energy.
In contrast, the dimeric form of M2-PK has a low affinity for phosphoenolpyruvate, being nearly inactive at physiological PEP concentrations. When M2-PK is mainly in the dimeric form, which is the case in tumor cells, all phosphometabolites above pyruvate kinase accumulate and are channelled into synthetic processes which branch off from glycolytic intermediates, such as nucleic acids, phospholipids and amino acids, important cell building blocks for highly proliferating cells such as tumor cells.
As a consequence of the key position of pyruvate kinase within glycolysis, the tetramer : dimer ratio of M2-PK determines whether glucose carbons are converted to pyruvate and lactate, along with the production of energy (tetrameric form), or channelled into synthetic processes (dimeric form). In tumor cells M2-PK is mainly in the dimeric form. Therefore, the dimeric form of M2-PK has been termed Tumor M2-PK.
The dimerization of M2-PK in tumor cells is induced by the direct interaction of M2-PK with different oncoproteins.
However, the tetramer : dimer ratio of M2-PK is not constant.
Oxygen starvation or highly accumulated glycolytic intermediates, such as fructose 1,6-bisphosphate (fructose 1,6-P2) or the amino acid serine, induce the reassociation of the dimeric form of M2-PK to the tetrameric form. Consequently, due to the activation of M2-PK, glucose is converted to pyruvate and lactate under the production of energy until the fructose 1,6-P2 levels drop below a certain threshold value, which allows the dissociation of the tetrameric form of M2-PK to the dimeric form. Thereafter, the cycle of oscillation starts again when the fructose 1,6-P2 levels reach a certain upper threshold value which induces the tetramerization of M2-PK.
When M2-PK is mainly in the less active dimeric form, energy is produced by the degradation of the amino acid glutamine to aspartate, pyruvate and lactate, which is termed glutaminolysis.
In tumor cells the increased rate of lactate production in the presence of oxygen is termed the Warburg effect. | 1 | Biochemistry |
Briefly, SAGE experiments proceed as follows:
# The mRNA of an input sample (e.g. a tumour) is isolated and a reverse transcriptase and biotinylated primers are used to synthesize cDNA from mRNA.
# The cDNA is bound to Streptavidin beads via interaction with the biotin attached to the primers, and is then cleaved using a restriction endonuclease called an anchoring enzyme (AE). The location of the cleavage site and thus the length of the remaining cDNA bound to the bead will vary for each individual cDNA (mRNA).
# The cleaved cDNA downstream from the cleavage site is then discarded, and the remaining immobile cDNA fragments upstream from cleavage sites are divided in half and exposed to one of two adaptor oligonucleotides (A or B) containing several components in the following order upstream from the attachment site: 1) Sticky ends with the AE cut site to allow for attachment to cleaved cDNA; 2) A recognition site for a restriction endonuclease known as the tagging enzyme (TE), which cuts about 15 nucleotides downstream of its recognition site (within the original cDNA/mRNA sequence); 3) A short primer sequence unique to either adaptor A or B, which will later be used for further amplification via PCR.
# After adaptor ligation, cDNA are cleaved using TE to remove them from the beads, leaving only a short "tag" of about 11 nucleotides of original cDNA (15 nucleotides minus the 4 corresponding to the AE recognition site).
# The cleaved cDNA tags are then repaired with DNA polymerase to produce blunt end cDNA fragments.
# These cDNA tag fragments (with adaptor primers and AE and TE recognition sites attached) are ligated, sandwiching the two tag sequences together, and flanking adaptors A and B at either end. These new constructs, called ditags, are then PCR amplified using anchor A and B specific primers.
# The ditags are then cleaved using the original AE, and allowed to link together with other ditags, which will be ligated to create a cDNA concatemer with each ditag being separated by the AE recognition site.
# These concatemers are then transformed into bacteria for amplification through bacterial replication.
# The cDNA concatemers can then be isolated and sequenced using modern high-throughput DNA sequencers, and these sequences can be analysed with computer programs which quantify the recurrence of individual tags. | 1 | Biochemistry |
These have been no reports of serious adverse effects with overdose of drospirenone. Symptoms that may occur in the event of an overdose may include nausea, vomiting, and vaginal bleeding. There is no antidote for overdose of drospirenone and treatment of overdose should be based on symptoms. Since drospirenone has antimineralocorticoid activity, levels of potassium and sodium should be measured and signs of metabolic acidosis should be monitored. | 4 | Stereochemistry |
p53 - package - palindromic sequence - palmitoyl acyltransferase - Parkinson's disease - pBR322 - PCR - pedigree - peptide - peptide-transporting ATPase - peptide bond - phage - phagemid - phenotype - phenylacetaldoxime dehydratase - PhIP-Seq - phosphatase, alkaline - phosphatidylcholine 12-monooxygenase - phosphatidylcholine desaturase - phosphatidylinositol a-mannosyltransferase - phosphodiester bond - phospholipid acyltransferase - phosphonate-transporting ATPase - phosphorylation - physical map - plant calmodulin-binding domain - plasmid - plastoquinol/plastocyanin reductase - point mutation - poly-A track - polyA tail - polyacrylamide gel - polyclonal antibodies - polydactyly - polymerase - polymerase chain reaction - polymorphism - polynucleotide kinase - polypeptide - polyvinyl-alcohol dehydrogenase (acceptor) - positional cloning - positional sequencing - post-transcriptional regulation - post-translational modification - post-translational processing - post-translational regulation - PRE - precursor mRNA - primary immunodeficiency - primary transcript - primer - primer extension - probe - processivity - progesterone 5alpha-reductase - promoter - pronucleus - prostate cancer - protease - proteasome - proteasome ATPase - protein - Protein translocation - proto-oncogene - pseudobaptigenin synthase - pseudogene - pseudoknot - pseudorevertant - pulse sequence database - pulsed field gel electrophoresis - purine - PyrC leader - PyrD leader - pyrimidine | 1 | Biochemistry |
"Molecular assemblers" have been confused with self-replicating machines. To produce a practical quantity of a desired product, the nanoscale size of a typical science fiction universal molecular assembler requires an extremely large number of such devices. However, a single such theoretical molecular assembler might be programmed to self-replicate, constructing many copies of itself. This would allow an exponential rate of production. Then, after sufficient quantities of the molecular assemblers were available, they would then be re-programmed for production of the desired product. However, if self-replication of molecular assemblers were not restrained then it might lead to competition with naturally occurring organisms. This has been called ecophagy or the grey goo problem.
One method of building molecular assemblers is to mimic evolutionary processes employed by biological systems. Biological evolution proceeds by random variation combined with culling of the less-successful variants and reproduction of the more-successful variants. Production of complex molecular assemblers might be evolved from simpler systems since "A complex system that works is invariably found to have evolved from a simple system that worked. . . . A complex system designed from scratch never works and can not be patched up to make it work. You have to start over, beginning with a system that works." However, most published safety guidelines include "recommendations against developing ... replicator designs which permit surviving mutation or undergoing evolution".
Most assembler designs keep the "source code" external to the physical assembler. At each step of a manufacturing process, that step is read from an ordinary computer file and "broadcast" to all the assemblers. If any assembler gets out of range of that computer, or when the link between that computer and the assemblers is broken, or when that computer is unplugged, the assemblers stop replicating. Such a "broadcast architecture" is one of the safety features recommended by the "Foresight Guidelines on Molecular Nanotechnology", and a map of the 137-dimensional replicator design space recently published by Freitas and Merkle provides numerous practical methods by which replicators can be safely controlled by good design. | 6 | Supramolecular Chemistry |
In organosulfur chemistry, sulfinamide is a functional group with the structure (where R = alkyl or aryl). This functionality is composed of a sulfur-carbon () and sulfur-nitrogen () single bonds, as well as a sulfur-oxygen double bond (), resulting in a tetravalent sulfur centre (in resonance with its zwitterionic form). As a non-bonding electron pair is also present on the sulfur, these compounds are also chiral. They are sometimes referred to as S-chiral sulfinamides. Sulfinamides are amides of sulfinic acid (). | 0 | Organic Chemistry |
The stability of many (or most) organic radicals is not indicated by their isolability but is manifested in their ability to function as donors of H. This property reflects a weakened bond to hydrogen, usually O−H but sometimes N−H or C−H. This behavior is important because these H donors serve as antioxidants in biology and in commerce. Illustrative is α-tocopherol (vitamin E). The tocopherol radical itself is insufficiently stable for isolation, but the parent molecule is a highly effective hydrogen-atom donor. The C−H bond is weakened in triphenylmethyl (trityl) derivatives. | 2 | Environmental Chemistry |
A deformation mechanism map is a way of representing the dominant deformation mechanism in a material loaded under a given set of conditions. The technique is applicable to all crystalline materials, metallurgical as well as geological. Additionally, work has been conducted regarding the use of deformation maps to nanostructured or very fine grain materials. Deformation mechanism maps usually consist of some kind of stress plotted against some kind of temperature axis, typically stress normalized using the shear modulus versus homologous temperature with contours of strain rate. The normalized shear stress is plotted on a log scale. While plots of normalized shear stress vs. homologous temperature are most common, other forms of deformation mechanism maps include shear strain rate vs. normalized shear stress and shear strain rate vs. homologous temperature. Thus deformation maps can be constructed using any two of stress (normalized), temperature (normalized), and strain rate, with contours of the third variable. A stress/strain rate plot is useful because power-law mechanisms then have contours of temperature which are straight lines.
For a given set of operating conditions, calculations are conducted and experiments performed to determine the predominant mechanism operative for a given material. Constitutive equations for the type of mechanism have been developed for each deformation mechanism and are used in the construction of the maps. The theoretical shear strength of the material is independent of temperature and located along the top of the map, with the regimes of plastic deformation mechanisms below it. Constant strain rate contours can be constructed on the maps using the constitutive equations of the deformation mechanisms which makes the maps extremely useful. | 8 | Metallurgy |
Methylene blue is a dye behaving as a redox indicator that is commonly used in the food industry to test the freshness of milk and dairy products. A few drops of methylene blue solution added to a sample of milk should remain blue (oxidized form in the presence of enough dissolved ), otherwise (discoloration caused by the reduction of methylene blue into its colorless reduced form) the dissolved concentration in the milk sample is low indicating that the milk is not fresh (already abiotically oxidized by whose concentration in solution decreases) or could be contaminated by bacteria also consuming the atmospheric dissolved in the milk. In other words, aerobic conditions should prevail in fresh milk and methylene blue is simply used as an indicator of the dissolved oxygen remaining in the milk. | 3 | Analytical Chemistry |
The carbon atom at which the initial deprotonation takes place is a stereocenter. If, for example, D-glucose (an Aldose) rearranges to D-fructose, the ketose, the stereochemical configuration is lost in the enol form. In the chemical reaction the enol can be protonated from two faces, resulting in the backformation of glucose or the formation of the epimer D-mannose. The final product is a mix of D-glucose, D-fructose and D-mannose. | 0 | Organic Chemistry |
Pancuronium remains one of the few muscle relaxants logically and rationally designed from structure-action / effects relationship data. A steroid skeleton was chosen because of its appropriate size and rigidness. Acetylcholine moieties were inserted to increase receptor affinity. Although having many unwanted side-effects, a slow onset of action and recovery rate it was a big success and at the time the most potent neuromuscular drug available. Pancuronium and some other neuromuscular blocking agents block M2-receptors and therefore affect the vagus nerve, leading to hypotension and tachycardia. This muscarinic blocking effect is related to the acetylcholine moiety on the A ring on pancuronium. Making the N atom on the A ring tertiary, the ring loses its acetylcholine moiety, and the resulting compound, vecuronium, has nearly 100 times less affinity to muscarin receptors while maintaining its nicotinic affinity and a similar duration of action. Vecuronium is, therefore, free from cardiovascular effects. The D ring shows excellent properties validating Beers and Reich's rule with great precision. As a result, vecuronium has the greatest potency and specificity of all mono-quaternary compounds. | 1 | Biochemistry |
Microbial dark matter comprises the vast majority of microbial organisms (usually bacteria and archaea) that microbiologists are unable to culture in the laboratory, due to lack of knowledge or ability to supply the required growth conditions. Microbial dark matter is unrelated to the dark matter of physics and cosmology, but is so-called for the difficulty in effectively studying it as a result of its inability to be cultured by current methods. It is difficult to estimate its relative magnitude, but the accepted gross estimate is that as little as one percent of microbial species in a given ecological niche are culturable. In recent years, more effort has been directed towards deciphering microbial dark matter by means of recovering genome DNA sequences from environmental samples via culture independent methods such as single cell genomics and metagenomics. These studies have enabled insights into the evolutionary history and the metabolism of the sequenced genomes, providing valuable knowledge required for the cultivation of microbial dark matter lineages. | 1 | Biochemistry |
Several photons of energy below the ionization threshold may actually combine their energies to ionize an atom. This probability decreases rapidly with the number of photons required, but the development of very intense, pulsed lasers still makes it possible. In the perturbative regime (below about 10 W/cm at optical frequencies), the probability of absorbing N photons depends on the laser-light intensity I as I.
Above threshold ionization (ATI) is an extension of multi-photon ionization where even more photons are absorbed than actually would be necessary to ionize the atom. The excess energy gives the released electron higher kinetic energy than the usual case of just-above threshold ionization. More precisely, the system will have multiple peaks in its photoelectron spectrum which are separated by the photon energies, this indicates that the emitted electron has more kinetic energy than in the normal (lowest possible number of photons) ionization case. The electrons released from the target will have approximately an integer number of photon-energies more kinetic energy. In intensity regions between 10 W/cm and 10 W/cm, each of MPI, ATI, and barrier suppression ionization can occur simultaneously, each contributing to the overall ionization of the atoms involved. | 7 | Physical Chemistry |
Demethylation often refers to cleavage of ethers, especially aryl ethers.
Historically, aryl methyl ethers, including natural products such as codeine (O-methylmorphine), have been demethylated by heating the substance in molten pyridine hydrochloride (melting point ) at , sometimes with excess hydrogen chloride, in a process known as the Zeisel–Prey ether cleavage. Quantitative analysis for aromatic methyl ethers can be performed by argentometric determination of the N-methylpyridinium chloride formed. The mechanism of this reaction starts with proton transfer from pyridinium ion to the aryl methyl ether, a highly unfavorable step (K ) that accounts for the harsh conditions required, given the much weaker acidity of pyridinium (pK = 5.2) compared to the protonated aryl methyl ether (an arylmethyloxonium ion, pK = –6.7 for aryl = Ph). This is followed by S2 attack of the arylmethyloxonium ion at the methyl group by either pyridine or chloride ion (depending on the substrate) to give the free phenol and, ultimately, N-methylpyridinium chloride, either directly or by subsequent methyl transfer from methyl chloride to pyridine.
Another classical (but, again, harsh) method for the removal of the methyl group of an aryl methyl ether is to heat the ether in a solution of hydrogen bromide or hydrogen iodide sometimes also with acetic acid. The cleavage of ethers by hydrobromic or hydroiodic acid proceeds by protonation of the ether, followed by displacement by bromide or iodide. A slightly milder set of conditions uses cyclohexyl iodide (CyI, 10.0 equiv) in N,N-dimethylformamide to generate a small amount of hydrogen iodide in situ.
Boron tribromide, which can be used at room temperature or below, is a more specialized reagent for the demethylation of aryl methyl ethers. The mechanism of ether dealkylation proceeds via the initial reversible formation of a Lewis acid-base adduct between the strongly Lewis acidic BBr and the Lewis basic ether. This Lewis adduct can reversibly dissociate to give a dibromoboryl oxonium cation and Br. Rupture of the ether linkage occurs through the subsequent nucleophilic attack on the oxonium species by Br to yield an aryloxydibromoborane and methyl bromide. Upon completion of the reaction, the phenol is liberated along with boric acid (HBO) and hydrobromic acid (aq. HBr) upon hydrolysis of the dibromoborane derivative during aqueous workup.
Stronger nucleophiles such as diorganophosphides (LiPPh) also cleave aryl ethers, sometimes under mild conditions. Other strong nucleophiles that have been employed include thiolate salts like EtSNa.
Aromatic methyl ethers, particularly those with an adjacent carbonyl group, can be regioselectively demethylated using magnesium iodide etherate. An example of this being used is in the synthesis of the natural product Calphostin A, as seen below.
Methyl esters also are susceptible to demethylation, which is usually achieved by saponification. Highly specialized demethylations are abundant, such as the Krapcho decarboxylation:
A mixture of anethole, KOH, and alcohol was heated in an autoclave. Although the product of this reaction was the expected anol, a highly reactive dimerization product in the mother liquors called dianol was also discovered by Charles Dodds. | 0 | Organic Chemistry |
Metabolic control analysis (MCA) is a mathematical framework for describing
metabolic, signaling, and genetic pathways. MCA quantifies how variables, such as fluxes and species concentrations, depend on network parameters.
In particular, it is able to describe how network-dependent properties,
called control coefficients, depend on local properties called elasticities or Elasticity Coefficients.
MCA was originally developed to describe the control in metabolic pathways
but was subsequently extended to describe signaling and genetic networks. MCA has sometimes also been referred to as Metabolic Control Theory, but this terminology was rather strongly opposed by Henrik Kacser, one of the founders.
More recent work has shown that MCA can be mapped directly on to classical control theory and are as such equivalent.
Biochemical systems theory (BST) is a similar formalism, though with rather different objectives. Both are evolutions of an earlier theoretical analysis by Joseph Higgins.
Chemical reaction network theory is another theoretical framework that has overlap with both MCA and BST but is considerably more mathematically formal in its approach. It's emphasis is primarily on dynamic stability criteria and related theorems associated with mass-action networks. In more recent years the field has also developed a sensitivity analysis which is similar if not identical to MCA and BST. | 1 | Biochemistry |
In physics, the cross section is a measure of the probability that a specific process will take place in a collision of two particles. For example, the Rutherford cross-section is a measure of probability that an alpha particle will be deflected by a given angle during an interaction with an atomic nucleus. Cross section is typically denoted (sigma) and is expressed in units of area, more specifically in barns. In a way, it can be thought of as the size of the object that the excitation must hit in order for the process to occur, but more exactly, it is a parameter of a stochastic process.
When two discrete particles interact in classical physics, their mutual cross section is the area transverse to their relative motion within which they must meet in order to scatter from each other. If the particles are hard inelastic spheres that interact only upon contact, their scattering cross section is related to their geometric size. If the particles interact through some action-at-a-distance force, such as electromagnetism or gravity, their scattering cross section is generally larger than their geometric size.
When a cross section is specified as the differential limit of a function of some final-state variable, such as particle angle or energy, it is called a differential cross section (see detailed discussion below). When a cross section is integrated over all scattering angles (and possibly other variables), it is called a total cross section or integrated total cross section. For example, in Rayleigh scattering, the intensity scattered at the forward and backward angles is greater than the intensity scattered sideways, so the forward differential scattering cross section is greater than the perpendicular differential cross section, and by adding all of the infinitesimal cross sections over the whole range of angles with integral calculus, we can find the total cross section.
Scattering cross sections may be defined in nuclear, atomic, and particle physics for collisions of accelerated beams of one type of particle with targets (either stationary or moving) of a second type of particle. The probability for any given reaction to occur is in proportion to its cross section. Thus, specifying the cross section for a given reaction is a proxy for stating the probability that a given scattering process will occur.
The measured reaction rate of a given process depends strongly on experimental variables such as the density of the target material, the intensity of the beam, the detection efficiency of the apparatus, or the angle setting of the detection apparatus. However, these quantities can be factored away, allowing measurement of the underlying two-particle collisional cross section.
Differential and total scattering cross sections are among the most important measurable quantities in nuclear, atomic, and particle physics.
With light scattering off of a particle, the cross section specifies the amount of optical power scattered from light of a given irradiance (power per area). It is important to note that although the cross section has the same units as area, the cross section may not necessarily correspond to the actual physical size of the target given by other forms of measurement. It is not uncommon for the actual cross-sectional area of a scattering object to be much larger or smaller than the cross section relative to some physical process. For example, plasmonic nanoparticles can have light scattering cross sections for particular frequencies that are much larger than their actual cross-sectional areas. | 7 | Physical Chemistry |
Sulfidic (or euxinic) conditions, which exist today in many water bodies from ponds to various land-surrounded mediterranean seas such as the Black Sea, were particularly prevalent in the Cretaceous Atlantic but also characterised other parts of the world ocean. In an ice-free sea of these supposed super-greenhouse worlds, oceanic waters were as much as higher, in some eras. During the timespans in question, the continental plates are believed to have been well separated, and the mountains as they are known today were (mostly) future tectonic events—meaning the overall landscapes were generally much lower— and even the half super-greenhouse climates would have been eras of highly expedited water erosion carrying massive amounts of nutrients into the world oceans fuelling an overall explosive population of microorganisms and their predator species in the oxygenated upper layers.
Detailed stratigraphic studies of Cretaceous black shales from many parts of the world have indicated that two oceanic anoxic events (OAEs) were particularly significant in terms of their impact on the chemistry of the oceans, one in the early Aptian (~120 Ma), sometimes called the Selli Event (or OAE 1a) after the Italian geologist Raimondo Selli (1916–1983), and another at the Cenomanian–Turonian boundary (~93 Ma), also called the Bonarelli Event (or OAE2) after the Italian geologist Guido Bonarelli (1871–1951). OAE1a lasted for ~1.0 to 1.3 Myr. The duration of OAE2 is estimated to be ~820 kyr based on a high-resolution study of the significantly expanded OAE2 interval in southern Tibet, China.
* Insofar as the Cretaceous OAEs can be represented by type localities, it is the striking outcrops of laminated black shales within the vari-coloured claystones and pink and white limestones near the town of Gubbio in the Italian Apennines that are the best candidates.
* The 1-metre thick black shale at the Cenomanian–Turonian boundary that crops out near Gubbio is termed the Livello Bonarelli after the scientist who first described it in 1891.
More minor oceanic anoxic events have been proposed for other intervals in the Cretaceous (in the Valanginian, Hauterivian, Albian and Coniacian–Santonian stages), but their sedimentary record, as represented by organic-rich black shales, appears more parochial, being dominantly represented in the Atlantic and neighbouring areas, and some researchers relate them to particular local conditions rather than being forced by global change. | 9 | Geochemistry |
Exposure to UV radiation is associated with skin aging, wrinkle production, liver spots, loss of skin elasticity, erythema (reddening of the skin), sunburn, photokeratitis (snow blindness), ocular melanoma (eye cancer), and infections. Tanning beds can contain many microbes, some of which are pathogens that can cause skin infections and gastric distress. In one study in New York in 2009, the most common pathogens found on tanning beds were Pseudomonas spp. (aeruginosa and putida), Bacillus spp., Klebsiella pneumoniae, Enterococcus species, Staphylococcus aureus, and Enterobacter cloacae. Several prescription and over-the-counter drugs, including antidepressants, antibiotics, antifungals and anti-diabetic medication, can cause photosensitivity, which makes burning the skin while tanning more likely. This risk is increased by a lack of staff training in tanning facilities. | 5 | Photochemistry |
Several hormones can affect insulin secretion. Estrogen is correlated with an increase of insulin secretion by depolarizing the β-cells membrane and enhancing the entry of Ca+2. In contrast, growth hormone is known to lower the serum level of insulin by promoting the production of insulin-like growth factor-I (IGF-I). IGF-I, in turn, suppresses the insulin secretion. | 1 | Biochemistry |
Another Henry's law solubility constant is:
Here is the molar mixing ratio in the aqueous phase. For a dilute aqueous solution the conversion between and is:
where is the density of water and is the molar mass of water. Thus
The SI unit for is Pa, although atm is still frequently used. | 7 | Physical Chemistry |
In interferometric microscopy, the image of a micro-object is synthesized numerically as a coherent combination
of partial images with registered amplitude and phase.
For registration of partial images, a conventional holographic set-up is used with a reference wave, as is usual in optical holography. Capturing multiple exposures allows the numerical emulation of a large numerical aperture objective from images obtained with an objective lens with smaller-value numerical aperture.
Similar techniques allows scanning and precise detection of small particles.
As the combined image keeps both amplitude and phase information, the interferometric microscopy can be especially efficient for the phase objects, allowing detection of light variations of index of refraction, which cause the phase shift or the light passing through for a small fraction of a radian. | 7 | Physical Chemistry |
Most proteins that are translated from mRNA undergo modifications before becoming functional in cells. These modifications are collectively known as post-translational modifications. The nascent or folded proteins, which are stable under physiological conditions, are then subjected to a battery of specific enzyme-catalyzed modifications on the side chains or backbones.
Post-translational modification of proteins can include acetylation, acylation (myristoylation, palmitoylation), alkylation, arginylation, ADP-ribosylation, biotinylation, formylation, geranylgeranylation, glutamylation, glycosylation, glycylation, hydroxylation, isoprenylation, lipoylation, methylation, nitroalkylation, phosphopantetheinylation, phosphorylation, prenylation, selenation, S-nitrosylation, succinylation, sulfation, transglutamination, sulfinylation, sulfonylation and ubiquitination (sumoylation, neddylation).
Post-translational modifications occurring at the N-terminus of the amino acid chain play an important role in translocation across biological membranes. These include secretory proteins in prokaryotes and eukaryotes and also proteins that are intended to be incorporated in various cellular and organelle membranes such as lysosomes, chloroplast, mitochondria and plasma membrane. Expression of posttranslated proteins is important in several diseases. | 0 | Organic Chemistry |
Yuan Tseh Lee (; born 19 November 1936) is a Taiwanese chemist. He is a Professor Emeritus at the University of California, Berkeley. He was the first Taiwanese Nobel Prize laureate who, along with the Hungarian-Canadian John C. Polanyi and American Dudley R. Herschbach, won the Nobel Prize in Chemistry in 1986 "for their contributions to the dynamics of chemical elementary processes".
Lee's particular physical chemistry work was related to the use of advanced chemical kinetics techniques to investigate and manipulate the behavior of chemical reactions using crossed molecular beams. From 15 January 1994 to 19 October 2006, Lee served as the President of the Academia Sinica of Taiwan. In 2011, he was elected head of the International Council for Science. | 7 | Physical Chemistry |
Lead(II) fluoride is used in low melting glasses, in glass coatings to reflect infrared rays, in phosphors for television-tube screens, and as a catalyst for the manufacture of picoline. The Muon g−2 experiment uses scintillators in conjunction with silicon photomultipliers. | 0 | Organic Chemistry |
Substances that have the ability to reduce other substances (cause them to gain electrons) are said to be reductive or reducing and are known as reducing agents, reductants, or reducers. The reductant transfers electrons to another substance and is thus itself oxidized. Because it donates electrons, the reducing agent is also called an electron donor. Electron donors can also form charge transfer complexes with electron acceptors. The word reduction originally referred to the loss in weight upon heating a metallic ore such as a metal oxide to extract the metal. In other words, ore was "reduced" to metal. Antoine Lavoisier demonstrated that this loss of weight was due to the loss of oxygen as a gas. Later, scientists realized that the metal atom gains electrons in this process. The meaning of reduction then became generalized to include all processes involving a gain of electrons. Reducing equivalent refers to chemical species which transfer the equivalent of one electron in redox reactions. The term is common in biochemistry. A reducing equivalent can be an electron or a hydrogen atom as a hydride ion.
Reductants in chemistry are very diverse. Electropositive elemental metals, such as lithium, sodium, magnesium, iron, zinc, and aluminium, are good reducing agents. These metals donate electrons relatively readily.
Hydride transfer reagents, such as NaBH and LiAlH, reduce by atom transfer: they transfer the equivalent of hydride or H. These reagents are widely used in the reduction of carbonyl compounds to alcohols. A related method of reduction involves the use of hydrogen gas (H) as sources of H atoms. | 9 | Geochemistry |
Enone–alkene cycloadditions can produce two isomers, depending on the orientation of substituents on the alkene and the enone carbonyl group. When the enone carbonyl and substituent of highest priority are proximal, the isomer is termed "head-to-head." When the enone carbonyl and substituent are distal, the isomer is called "head-to-tail." Selectivity for one of these isomers depends on both steric and electronic factors (see below).
The regiochemistry of the reaction is controlled primarily by two factors: steric interactions and electrostatic interactions between the excited enone and alkene. In their excited state, the polarity of enones is reversed so that the β carbon possesses a partial negative charge. In the transition state for the first bond formation, the alkene tends to align itself so that the negative end of its dipole points away from the β carbon of the enone.
Steric interactions encourage the placement of large substituents on opposite sides of the new
cyclobutane ring.
If the enone and alkene are contained in rings of five atoms or fewer, double-bond configuration
is preserved. However, when larger rings are used, double bond isomerization during the reaction becomes a
possibility. This energy-wasting process competes with cycloaddition and is evident in reactions that yield mixtures of cis- and trans-fused products.
Diastereofacial selectivity is highly predictable in most cases. The less hindered faces of the enone
and alkene react.
Intramolecular enone–alkene cycloaddition may give either "bent" or "straight" products depending on the reaction
regioselectivity. When the tether between the enone and alkene is two atoms long, bent products predominate
due to the rapid formation of five-membered rings. Longer tethers tend to give straight products.
The tether can also be attached at the 2 position of the enone. When the alkene is tethered here, bulky substituents at the 4 position of the enone enforce moderate diastereoselectivity.
Enone–alkene cycloaddition has been applied to the synthesis of a cubane. The Favorskii rearrangement established the carbon skeleton of cubane, and further synthetic manipulations provided the desired unfunctionalized target. | 5 | Photochemistry |
PKA has always been considered important in formation of a memory. In the fruit fly, reductions in expression activity of DCO (PKA catalytic subunit encoding gene) can cause severe learning disabilities, middle term memory and short term memory. Long term memory is dependent on the CREB transcription factor, regulated by PKA. A study done on drosophila reported that an increase in PKA activity can affect short term memory. However, a decrease in PKA activity by 24% inhibited learning abilities and a decrease by 16% affected both learning ability and memory retention. Formation of a normal memory is highly sensitive to PKA levels. | 1 | Biochemistry |
LTR retrotransposons came about later than non-LTR retrotransposons, possibly from an ancestral non-LTR retrotransposon acquiring an integrase from a DNA transposon. Retroviruses gained additional properties to their virus envelopes by taking the relevant genes from other viruses using the power of LTR retrotransposon.
Due to their retrotransposition mechanism, retrotransposons amplify in number quickly, composing 40% of the human genome. The insertion rates for LINE1, Alu and SVA elements are 1/200 – 1/20, 1/20 and 1/900 respectively. The LINE1 insertion rates have varied a lot over the past 35 million years, so they indicate points in genome evolution.
Notably a large number of 100 kilobases in the maize genome show variety due to the presence or absence of retrotransposons. However since maize is unusual genetically as compared to other plants it cannot be used to predict retrotransposition in other plants.
Mutations caused by retrotransposons include:
* Gene inactivation
* Changing gene regulation
* Changing gene products
* Acting as DNA repair sites | 1 | Biochemistry |
Initially in the process of degradation, fatty acids are stored in adipocytes. The breakdown of this fat is known as lipolysis. The products of lipolysis, free fatty acids, are released into the bloodstream and circulate throughout the body. During the breakdown of triacylglycerols into fatty acids, more than 75% of the fatty acids are converted back into triacylglycerol, a natural mechanism to conserve energy, even in cases of starvation and exercise. | 1 | Biochemistry |
In atmospheric radiation, Chandrasekhars X- and Y-function appears as the solutions of problems involving diffusive reflection and transmission, introduced by the Indian American astrophysicist Subrahmanyan Chandrasekhar. The Chandrasekhars X- and Y-function
where the characteristic function is an even polynomial in generally satisfying the condition
and is the optical thickness of the atmosphere. If the equality is satisfied in the above condition, it is called conservative case, otherwise non-conservative. These functions are related to Chandrasekhar's H-function as
and also | 7 | Physical Chemistry |
A hyperaccumulator is a plant capable of growing in soil or water with high concentrations of metals, absorbing these metals through their roots, and concentrating extremely high levels of metals in their tissues. The metals are concentrated at levels that are toxic to closely related species not adapted to growing on the metalliferous soils. Compared to non-hyperaccumulating species, hyperaccumulator roots extract the metal from the soil at a higher rate, transfer it more quickly to their shoots, and store large amounts in leaves and roots. The ability to hyperaccumulate toxic metals compared to related species has been shown to be due to differential gene expression and regulation of the same genes in both plants.
Hyperaccumulating plants are of interest for their ability to extract metals from the soils of contaminated sites (phytoremediation) to return the ecosystem to a less toxic state. The plants also hold potential to be used to mine metals from soils with very high concentrations (phytomining) by growing the plants, then harvesting them for the metals in their tissues.
The genetic advantage of hyperaccumulation of metals may be that the toxic levels of heavy metals in leaves deter herbivores or increase the toxicity of other anti-herbivory metabolites. | 2 | Environmental Chemistry |
A transcription bubble is a molecular structure formed during DNA transcription when a limited portion of the DNA double helix is unwound. The size of a transcription bubble ranges from 12 to 14 base pairs. A transcription bubble is formed when the RNA polymerase enzyme binds to a promoter and causes two DNA strands to detach. It presents a region of unpaired DNA, where a short stretch of nucleotides are exposed on each strand of the double helix. | 1 | Biochemistry |
Rouging is a form of corrosion found in stainless steel. It can be due to iron contamination of the stainless steel surface due to welding of non-stainless steel for support columns, or other temporary means, which when welded off leaves a low chromium area.
There are three classes of rouging: Class I, Class II, and Class III.
Class I – stainless steel surface and the Cr/Fe ratio of the metal surface beneath such deposits usually remain unaltered.
<br />Class II – Iron particles originating in-situ on unpassivated or improperly passivated stainless steel surfaces. By their formation the Cr/Fe ratio of the metal surface is altered.
<br />Class III – Iron oxide (or scale) which forms on surfaces in high temperature steam systems. The Cr/Fe ratio of the protective film is usually altered. | 8 | Metallurgy |
Coal tar was formerly one of the products of gasworks. Tar made from coal or petroleum is considered toxic and carcinogenic because of its high benzene content, though coal tar in low concentrations is used as a topical medicine for conditions such as psoriasis. Coal and petroleum tar has a pungent odor.
Coal tar is listed at number 1999 in the United Nations list of dangerous goods. | 7 | Physical Chemistry |
Sawdust (or wood dust) is a by-product or waste product of woodworking operations such as sawing, sanding, milling and routing. It is composed of very small chips of wood. These operations can be performed by woodworking machinery, portable power tools or by use of hand tools. In some manufacturing industries it can be a significant fire hazard and source of occupational dust exposure.
Sawdust, as particulates, is the main component of particleboard. Research on health hazards comes from the field of occupational safety and health, and study of ventilation happens in indoor air quality engineering. Sawdust is an IARC group 1 Carcinogen. | 2 | Environmental Chemistry |
Deuterium is often represented by the chemical symbol D. Since it is an isotope of hydrogen with mass number 2, it is also represented by H. IUPAC allows both D and H, though H is preferred. A distinct chemical symbol is used for convenience because of the isotopes common use in various scientific processes. Also, its large mass difference with protium (H) confers non-negligible chemical differences with protium compounds. Deuterium has a mass of , about twice the mean hydrogen atomic weight of , or twice protiums mass of . The isotope weight ratios within other chemical elements are largely insignificant in this regard. | 9 | Geochemistry |
The single-cell eukaryote Paramecium tetraurelia can undergo both asexual and sexual reproduction. Asexual or clonal reproduction occurs by binary fission. Binary fission involves mitosis-like behavior of the chromosomes similar to that of cells in higher organisms. The sexual forms of reproduction are autogamy, a kind of self-fertilization, and conjugation, a kind of sexual interation between different cells. Clonal asexual reproduction can be initiated after completion of autogamy or conjugation. P. tetraurelia is able to replicate asexually for many generations but the dividing cells gradually age and after about 200 cell divisions, if the cells fail to undergo another autogamy or conjugation, they lose vitality and expire. This process is referred to as clonal aging. Experiments by Smith-Sonneborn, Holmes and Holmes and Gilley and Blackburn showed that accumulation of DNA damage is the likely cause of clonal aging in P. tetraurelia. This aging process has similarities to the aging process in multicellular eukaryotes (See DNA damage theory of aging). | 1 | Biochemistry |
Chemical and geological evidence indicate that photosynthetic cyanobacteria existed about 2.6 billion years ago and anoxygenic photosynthesis had been taking place since a billion years before that. Oxygenic photosynthesis was the primary source of free oxygen and led to the Great Oxidation Event roughly 2.4 to 2.1 billion years ago during the Neoarchean-Paleoproterozoic boundary. Although the end of the Great Oxidation Event was marked by a significant decrease in gross primary productivity that eclipsed extinction events, the development of aerobic respiration enabled more energetic metabolism of organic molecules, leading to symbiogenesis and the evolution of eukaryotes, and allowing the diversification of complex life on Earth. | 5 | Photochemistry |
A similar analysis, done by J. M. Harris, has been applied to the competing S1 and S2 nucleophilic aliphatic substitution pathways. The effects of increasing the nucleophilicity of the nucleophile are shown as an example in Figure 3. An agreement with Hammet ρ-values is also apparent in this application. | 7 | Physical Chemistry |
Protein Data Bank in Europe – Knowledge Base (PDBe-KB) is a community-driven, open-access, integrated resource whose mission is to place macromolecular structure data in their biological context and to make them accessible to the scientific community in order to support fundamental and translational research and education. It is part of the European Bioinformatics Institute (EMBL-EBI), based at the Wellcome Genome Campus, Hinxton, Cambridgeshire, England. | 1 | Biochemistry |
Retinal is bound to opsins, which are G protein-coupled receptors (GPCRs). Opsins, like other GPCRs, have seven transmembrane alpha-helices connected by six loops. They are found in the photoreceptor cells in the retina of eye. The opsin in the vertebrate rod cells is rhodopsin. The rods form disks, which contain the rhodopsin molecules in their membranes and which are entirely inside of the cell. The N-terminus head of the molecule extends into the interior of the disk, and the C-terminus tail extends into the cytoplasm of the cell. The opsins in the cone cells are OPN1SW, OPN1MW, and OPN1LW. The cones form incomplete disks that are part of the plasma membrane, so that the N-terminus head extends outside of the cell. In opsins, retinal binds covalently to a lysine in the seventh transmembrane helix through a Schiff base. Forming the Schiff base linkage involves removing the oxygen atom from retinal and two hydrogen atoms from the free amino group of lysine, giving HO. Retinylidene is the divalent group formed by removing the oxygen atom from retinal, and so opsins have been called retinylidene proteins.
Opsins are prototypical G protein-coupled receptors (GPCRs). Cattle rhodopsin, the opsin of the rod cells, was the first GPCR to have its amino acid sequence and 3D-structure (via X-ray crystallography) determined. Cattle rhodopsin contains 348 amino acid residues. Retinal binds as chromophore at Lys. This lysine is conserved in almost all opsins, only a few opsins have lost it during evolution. Opsins without the retinal binding lysine are not light sensitive. Such opsins may have other functions.
Although mammals use retinal exclusively as the opsin chromophore, other groups of animals additionally use four chromophores closely related to retinal: 3,4-didehydroretinal (vitamin A), (3R)-3-hydroxyretinal, (3S)-3-hydroxyretinal (both vitamin A), and (4R)-4-hydroxyretinal (vitamin A). Many fish and amphibians use 3,4-didehydroretinal, also called dehydroretinal. With the exception of the dipteran suborder Cyclorrhapha (the so-called higher flies), all insects examined use the (R)-enantiomer of 3-hydroxyretinal. The (R)-enantiomer is to be expected if 3-hydroxyretinal is produced directly from xanthophyll carotenoids. Cyclorrhaphans, including Drosophila, use (3S)-3-hydroxyretinal. Firefly squid have been found to use (4R)-4-hydroxyretinal. | 1 | Biochemistry |
Christopher J. Chetsanga (born 1935 in Murehwa, Rhodesia) is a prominent Zimbabwean scientist who is a member of the African Academy of Sciences and The World Academy of Sciences. He discovered two enzymes involved in DNA repair. He has also held various academic administrative posts like Vice-Chancellor, Director and Dean. | 1 | Biochemistry |
Its activities are focused on both fundamental objectives in analytical sciences and interactions with the socio-economic environment at local, national and international levels. The Institute has partnerships with international research centers (e.g. MIT, the École Polytechnique Fédérale de Lausanne, International Agency for Research on Cancer) and national academic partners (e.g. LabexIMUST, , ...) and industrial partners (BioMérieux, , Sanofi, Solvay, Total) and manufacturers (Agilent, Bruker, Waters ...).
The institute is involved in competitiveness clusters (Axelera, , Techtera, Plastipolis) and regional cluster (). Some scientists are experts in standardization committees at national and European levels. In addition, the Institute of Analytical Sciences plays a «Business incubator» role and hosts start-ups: ANAQUANT, metabolomics technical platform, etc. | 3 | Analytical Chemistry |
The established performance criteria, definitions, and nomenclature for electrochemical engineering can be found in Kreysa et al. and an IUPAC report. | 7 | Physical Chemistry |
Compared to concentration dependent bactericidal antibiotics like aminoglycosides and fluoroquinolones, the antibacterial activity of β-lactam antibiotics are generally more time dependent. Unlike the former, when piperacillin-tazobactam concentrations exceed minimum inhibitory concentrations (MIC) of a pathogen by five folds, the exponential relationship between concentration and activity begins to level off. Otherwise, piperacillin-tazobactam bactericidal efficacy is shown to consist of a strong association with the duration of time the concentration exceeds minimum inhibitory concentrations (T). When the T in the serum equates to 60–70% of the frequency for drug administration (dosing interval), maximal activity is achieved against Gram-negative bacteria, while for Gram-positive bacteria it occurs at around 40–50%.
Within a 24-hour period in one clinical study, a T surpassing 60% was found for piperacillin-susceptible bacteria including Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus in two dosing regimes (4.5 g every 8 hours and 3.375 g every 8 hours).
The evidence for this was obtained through Monte Carlo experiments procured by a special program (OPTAMA), where for several different scenarios (e.g. hospital acquired infections, secondary peritonitis, skin or soft tissue infections), the probability of attaining those figures were in the ranges of 85–95% and 90–89% respectively for the two regimes. In addition, two similar dosing regimes (3.375 g and 4.5 g every 6 hours) both had lower chances of reaching the 90% T threshold compared to the 50% threshold against hospital acquired pneumonia pathogens.
The optimization of piperacillin-tazobactam drug efficiency has been covered by various studies, limiting the focus down to two types of infusions; continuous and intermittent. A comparison using the two administration methods under the same dosage regime of 13.5 g per day highlighted no major differences when treating complex intra-abdominal infections. Furthermore, a follow-up analysis of this trial deduced that both methods of administration lead to higher concentrations compared to the MIC of the pathogens that were used. Similar results are found in a study where a select number of β-lactam susceptible pathogens consisting of Enterococcus faecalis, Klebsiella pneumoniae and Citrobacter freundii were used to test a ~10 g every 24 hour dosing interval for continuous infusion.
Organisms with a piperacillin-tazobactam MIC values equal to 32 or less than 16 μg/mL lead to 50% T when extended-interval intermittent administrations under two different dosing intervals (8.1 g and 6.75 g every 12 hours) were used against them. The pharmacodynamic target attainments corresponding to pathogens with MIC values of 16 μg/mL are found to reach 92% when a more traditional 4 hour dosing regime is utilized to administer at irregular intervals. One study using the Monte Carlo simulation produced contradicting results to the previous studies, deducing that inadequate pharmacodynamic targets were achieved (T > 50%) for similar ESBL-producing bacteria, applying to both continuous and high dosage intermittent infusion. | 4 | Stereochemistry |
Synthetic accessibility is a simple approach to network simulation whose goal is to predict which metabolic gene knockouts are lethal. The synthetic accessibility approach uses the topology of the metabolic network to calculate the sum of the minimum number of steps needed to traverse the metabolic network graph from the inputs, those metabolites available to the organism from the environment, to the outputs, metabolites needed by the organism to survive. To simulate a gene knockout, the reactions enabled by the gene are removed from the network and the synthetic accessibility metric is recalculated. An increase in the total number of steps is predicted to cause lethality. Wunderlich and Mirny showed this simple, parameter-free approach predicted knockout lethality in E. coli and S. cerevisiae as well as elementary mode analysis and flux balance analysis in a variety of media. | 1 | Biochemistry |
Histidine methyl ester (HME) is an irreversible histidine decarboxylase inhibitor. It is the methyl ester of histidine. | 1 | Biochemistry |
* Furaneol (strawberry)
* 1-Hexanol (herbaceous, woody)
* cis-3-Hexen-1-ol (fresh cut grass)
* Menthol (peppermint) | 0 | Organic Chemistry |
The tetrazole-alkene "photoclick" reaction is another dipolar addition that Huisgen first introduced in the late 1960s ChemBioChem 2007, 8, 1504. (68) Clovis, J. S.; Eckell, A.; Huisgen, R.; Sustmann, R. Chem. Ber. 1967, 100, 60.) Tetrazoles with amino or styryl groups that can be activated by UV light at 365 nm (365 does not damage cells) react quickly (so that the UV light does not have to be on for a long time, usually around 1–4 minutes) to make fluorogenic pyrazoline products. This reaction scheme is well suited for the purpose of labeling in live cells, because UV light at 365 nm damages cells minimally. Moreover, the reaction proceeds quickly, so that the UV light can be administered for short durations. Quantum yields for short wavelength UV light can be higher than 0.5. This allows tetrazoles to be used wavelength selectively in combination with another photoligation reaction, where at the short wavelength the tetrazole ligation reaction proceeds nearly exclusively and at longer wavelength another reaction (ligation via o-quinodimethanes) proceeds exclusively. Finally, the non-fluorogenic reactants give rise to a fluorogenic product, equipping the reaction with a built-in spectrometry handle.
Both tetrazoles and the alkene groups have been incorporated as protein handles as unnatural amino acids, but this benefit is not unique. Instead, the photoinducibility of the reaction makes it a prime candidate for spatiotemporal specificity in living systems. Challenges include the presence of endogenous alkenes, though usually cis (as in fatty acids) they can still react with the activated tetrazole. | 0 | Organic Chemistry |
The molar gas constant (also known as the gas constant, universal gas constant, or ideal gas constant) is denoted by the symbol or . It is the molar equivalent to the Boltzmann constant, expressed in units of energy per temperature increment per amount of substance, rather than energy per temperature increment per particle. The constant is also a combination of the constants from Boyles law, Charless law, Avogadros law, and Gay-Lussacs law. It is a physical constant that is featured in many fundamental equations in the physical sciences, such as the ideal gas law, the Arrhenius equation, and the Nernst equation.
The gas constant is the constant of proportionality that relates the energy scale in physics to the temperature scale and the scale used for amount of substance. Thus, the value of the gas constant ultimately derives from historical decisions and accidents in the setting of units of energy, temperature and amount of substance. The Boltzmann constant and the Avogadro constant were similarly determined, which separately relate energy to temperature and particle count to amount of substance.
The gas constant R is defined as the Avogadro constant N multiplied by the Boltzmann constant k (or k):
Since the 2019 redefinition of SI base units, both N and k are defined with exact numerical values when expressed in SI units. As a consequence, the SI value of the molar gas constant is exactly .
Some have suggested that it might be appropriate to name the symbol R the Regnault constant in honour of the French chemist Henri Victor Regnault, whose accurate experimental data were used to calculate the early value of the constant. However, the origin of the letter R to represent the constant is elusive. The universal gas constant was apparently introduced independently by Clausius' student, A.F. Horstmann (1873) and Dmitri Mendeleev who reported it first on Sep. 12, 1874. Using his extensive measurements of the properties of gases,
Mendeleev also calculated it with high precision, within 0.3% of its modern value.
The gas constant occurs in the ideal gas law:
where P is the absolute pressure, V is the volume of gas, n is the amount of substance, m is the mass, and T is the thermodynamic temperature. R is the mass-specific gas constant. The gas constant is expressed in the same unit as are molar entropy and molar heat. | 7 | Physical Chemistry |
RNA-targeting small molecule drug discovery has greatly benefitted from the available cellular models for disease. The use of cell culture in early development has become a requirement for assessing the basic efficacy of a drug candidate. Thus, more research groups have implemented these techniques in their programs. In a leading example, Al-Hashimi and coworkers identified six small molecules with high affinity for TAR of HIV-1 through a computational approach. They docked a library of small molecules onto RNA dynamic structures generated by NMR and Molecular Dynamics (MD) simulations. The hit molecules inhibited the Tat—TAR interaction in vitro. They arrived at lead molecule, netilmicin, that had the best selectivity for HIV-1 TAR and inhibited HIV-1 replication in cells with a low IC50. The Disney group has studied aminoglycoside derivatives in 2009 for their ability to inhibit interactions between repeat RNA and proteins. Using their prediction database INFORNA, they discovered that a compound could bind to 1 x 1 UU internal loops on an N-methyl peptide backbone. They confirmed that like other compounds that target DM1 r(CUG), they could inhibit the complex between r(CUG)-MBNL1, disrupt nuclear foci, and increase nucleocytoplasmic transport of the gene in patient-derived DM1 fibroblasts. In that study the Disney group also described several approaches to validate the RNA targets of small molecules. In the first approach termed chemical cross-linking and isolation by pull down (Chem-CLIP) and chemical cross-linking and isolation by pull down to map binding sites (Chem-CLIP-Map).
These studies showed in cells that small molecules can direct target disease-causing r(CUG) repeats in DM1 and that impressively the compound can discriminate against other RNAs with shorter repeats and also between the mutant and wild type allele of the DMPK mRNA that contains r(CUG) disease-causing repeats. In an additional approach, dubbed small–molecule nucleic acid profiling by cleavage applied to RNA (Ribo-SNAP) showed that small molecules can be used to cleave RNA targets in cells and also importantly demonstrated that designer small molecules target precisely disease causing RNA repeats and discriminate against RNAs that are not disease causing but have short repeats of r(CUG). Thus, targeting RNA structure with small molecules can have important selectively discrimination implications in cells.
In 2014, Chenowith and colleagues reported a cationic triptycene scaffold that targets RNA and DNA three-way junctions. Subsequent studies showed that these molecules exhibited favorable cellular uptake and cytotoxicity in human ovarian cancer cell lines. In 2017, the Xodo group reported anthrafurandione and anthrathiophenedione small molecules with aminoethyl side chains could bind to RNA G-quadraplexes at the 5’-UTR of certain mRNAs. Further, these compounds were shown to suppress the KRAS oncogene in pancreatic cancer cells and induce apoptosis by reducing the metabolic activity of the cells. | 1 | Biochemistry |
A biosignature must be able to last for long enough so that a probe, telescope, or human can be able to detect it. A consequence of a biological organism's use of metabolic reactions for energy is the production of metabolic waste. In addition, the structure of an organism can be preserved as a fossil and we know that some fossils on Earth are as old as 3.5 billion years. These byproducts can make excellent biosignatures since they provide direct evidence for life. However, in order to be a viable biosignature, a byproduct must subsequently remain intact so that scientists may discover it. | 2 | Environmental Chemistry |
As an example camphor tosylhydrazone is synthesised from camphor and tosylhydrazine in ethanol with hydrochloric acid catalysis. | 0 | Organic Chemistry |
Live cell imaging and proteomic studies have allowed researchers at the centre to gain fresh understanding of protein function and cell behaviour.
The centre is studying many aspects of the cell cycle, including the way in which chromosomes replicate and separate during cell division and how DNA damage is detected. Failure of these events can lead to major faults within a genome, potentially leading to the rise of cancerous cells. The centre is also investigating how DNA is tightly wound and compacted so that it can fit into the nuclei of eukaryotic cells, as well as the protein-DNA complexes that are involved in this packaging. The controlled unravelling of DNA is an important step in the regulation of gene function. | 1 | Biochemistry |
Van der Waals strain, or steric strain, occurs when atoms are forced to get closer than their Van der Waals radii allow. Specifically, Van der Waals strain is considered a form of strain where the interacting atoms are at least four bonds away from each other. The amount on steric strain in similar molecules is dependent on the size of the interacting groups; bulky tert-butyl groups take up much more space than methyl groups and often experience greater steric interactions.
The effects of steric strain in the reaction of trialkylamines and trimethylboron were studied by Nobel laureate Herbert C. Brown et al. They found that as the size of the alkyl groups on the amine were increased, the equilibrium constant decreased as well. The shift in equilibrium was attributed to steric strain between the alkyl groups of the amine and the methyl groups on boron. | 4 | Stereochemistry |
While lipolysis is triglyceride hydrolysis (the process by which triglycerides are broken down), esterification is the process by which triglycerides are formed. Esterification and lipolysis are, in essence, reversals of one another. | 1 | Biochemistry |
In 1902, The Electrochemical Society (ECS) was founded.
In 1909, Robert Andrews Millikan began a series of experiments (see oil drop experiment) to determine the electric charge carried by a single electron.
In 1911, Harvey Fletcher, working with Millikan, was successful in measuring the charge on the electron, by replacing the water droplets used by Millikan, which quickly evaporated, with oil droplets. Within one day Fletcher measured the charge of an electron within several decimal places.
In 1923, Johannes Nicolaus Brønsted and Martin Lowry published essentially the same theory about how acids and bases behave, using an electrochemical basis.
In 1937, Arne Tiselius developed the first sophisticated electrophoretic apparatus. Some years later, he was awarded the 1948 Nobel Prize for his work in protein electrophoresis.
A year later, in 1949, the International Society of Electrochemistry (ISE) was founded.
By the 1960s–1970s quantum electrochemistry was developed by Revaz Dogonadze and his students. | 7 | Physical Chemistry |
Another form of amylase, β-amylase () (alternative names: 1,4-α--glucan maltohydrolase; glycogenase; saccharogen amylase) is also synthesized by bacteria, fungi, and plants. Working from the non-reducing end, β-amylase catalyzes the hydrolysis of the second α-1,4 glycosidic bond, cleaving off two glucose units (maltose) at a time. During the ripening of fruit, β-amylase breaks starch into maltose, resulting in the sweet flavor of ripe fruit. They belong to glycoside hydrolase family 14.
Both α-amylase and β-amylase are present in seeds; β-amylase is present in an inactive form prior to germination, whereas α-amylase and proteases appear once germination has begun. Many microbes also produce amylase to degrade extracellular starches. Animal tissues do not contain β-amylase, although it may be present in microorganisms contained within the digestive tract. The optimum pH for β-amylase is 4.0–5.0. | 1 | Biochemistry |
Petroleum, also known as crude oil or simply oil, is a naturally occurring yellowish-black liquid mixture of mainly hydrocarbons, and is found in geological formations. The name petroleum covers both naturally occurring unprocessed crude oil and petroleum products that consist of refined crude oil.
Petroleum is primarily recovered by oil drilling. Drilling is carried out after studies of structural geology, sedimentary basin analysis, and reservoir characterisation. Unconventional reserves such as oil sands and oil shale exist.
Once extracted, oil is refined and separated, most easily by distillation, into innumerable products for direct use or use in manufacturing. Products include fuels such as petrol (gasoline), diesel, kerosene and jet fuel; asphalt and lubricants; chemical reagents used to make plastics; solvents, textiles, refrigerants, paint, synthetic rubber, fertilizers, pesticides, pharmaceuticals, and thousands of others. Petroleum is used in manufacturing a vast variety of materials essential for modern life, and it is estimated that the world consumes about each day. Petroleum production can be extremely profitable and was critical to global economic development in the 20th century, with some countries, so-called "oil states", gaining significant economic and international power because of their control of oil production.
Petroleum exploitation can be damaging to the environment and human health. Extraction, refining and burning of petroleum fuels all release large quantities of greenhouse gases, so petroleum is one of the major contributors to climate change. Other negative environmental effects include direct releases, such as oil spills, and as well as air and water pollution at almost all stages of use. These environmental effects have direct and indirect health consequences for humans. Oil has also been a source of internal and inter-state conflict, leading to both state-led wars and other resource conflicts. Production of petroleum is estimated to reach peak oil before 2035 as global economies lower dependencies on petroleum as part of climate change mitigation and a transition towards renewable energy and electrification. Oil has played a key role in industrialization and economic development. | 7 | Physical Chemistry |
A meta-analysis of observational studies showed that children with ADHD have lower vitamin D levels, and that there was a small association between low vitamin D levels at the time of birth and later development of ADHD. Several small, randomized controlled trials of vitamin D supplementation indicated improved ADHD symptoms such as impulsivity and hyperactivity. | 1 | Biochemistry |
Single nucleotide variant can also affect the cis-acting regulatory elements in mRNA’s to inhibit/promote the translation initiation. Change in the synonymous codons region due to mutation may affect the translation efficiency because of codon usage biases. The translation elongation can also be retarded by mutations along the ramp of ribosomal movement. In the post-translational level, genetic variants can contribute to proteostasis and amino acid modifications. However, mechanisms of variant effect in this field are complicated and there are only a few tools available to predict variant’s effect on translation related modifications. | 1 | Biochemistry |
Many contaminated brownfield sites sit unused for decades because the cost of cleaning them to safe standards is more than the land would be worth after redevelopment, in the process becoming involuntary parks as they grow over. However, redevelopment has become more common in the first decade of the 21st century, as developable land has become less available in highly populated areas, and brownfields contribute to environmental stigma which can delay redevelopment. Also, the methods of studying contaminated land have become more sophisticated and costly.
Some states and localities have spent considerable money assessing the contamination on local brownfield sites, to quantify the cleanup costs in an effort to move the redevelopment process forward. Therefore, federal and state programs have been developed to help developers interested in cleaning up brownfield sites and restoring them to practical uses.
In the process of cleaning contaminated brownfield sites, previously unknown underground storage tanks, buried drums or buried railroad tank cars containing wastes are sometimes encountered. Unexpected circumstances increase the cost for study and clean-up. As a result, the cleanup work may be delayed or stopped entirely. To avoid unexpected contamination and increased costs, many developers insist that a site be thoroughly investigated (via a Phase II Site Investigation or Remedial Investigation) prior to commencing remedial cleanup activities. | 2 | Environmental Chemistry |
Imine formation is an important reaction. Primary amines react with ketones and aldehydes to form imines. In the case of formaldehyde (R' H), these products typically exist as cyclic trimers.
Reduction of these imines gives secondary amines:
Similarly, secondary amines react with ketones and aldehydes to form enamines: | 0 | Organic Chemistry |
For the simplest embodiment of linearly-polarized microwave scattering in the absence of magnetic depolarization, three regimes may arise due to the correlation between scatterers. The Thomson regime refers to free plasma electrons oscillating in-phase with the incident microwave field. The total scattering cross-section of an independent electron then coincides with the classical Thomson cross section and is independent of the microwave wavelength λ. Second, Shneider-Miles scattering (SM, often referred to as collisional scattering) refers to collision-dominated electron motion with displacement oscillations shifted 90 degrees with respect to the irradiating field. The total scattering cross-section correspondingly exhibits a ω dependency - a unique regime made possible through interparticle interactions. Finally, the Rayleigh scattering regime can be observed which is associated with restoring-force-dominated electron motion and shares a ω dependence with its volumetric polarizability optical counterpart. In this case the "scattering particle" refers to the entire plasma object. As such, plasma expansion may cause a transition towards Mie scattering. Note that the Rayleigh regime refers to small particle ω scattering here, rather than an even broader small-dipole approximation of the radiation. | 7 | Physical Chemistry |
It is prepared in the laboratory by disproportionation of phosphorous acid:
Alternative methods are the hydrolysis of tris(trimethylsilyl)phosphine, or of metal phosphides such as aluminium phosphide, or calcium phosphide:
Pure samples of phosphine, free from , may be prepared using the action of potassium hydroxide on phosphonium iodide: | 0 | Organic Chemistry |
There is no conclusive evidence that thalidomide or lenalidomide is useful to bring about or maintain remission in Crohn's disease.
Thalidomide was studied in a Phase II trial for Kaposis sarcoma, a rare soft-tissue cancer most commonly seen in the immunocompromised, that is caused by the Kaposis sarcoma-associated herpesvirus (KSHV).
* AIDS wasting syndrome, associated diarrhea
* Renal cell carcinoma (RCC)
* Glioblastoma multiforme
* Prostate cancer
* Melanoma
* Colorectal cancer
* Crohn's disease
* Rheumatoid arthritis
* Behcet's syndrome
* Breast cancer
* Head and neck cancer
* Ovarian cancer
* Chronic heart failure
* Graft-versus-host disease
* Tuberculous meningitis | 4 | Stereochemistry |
Clark has an undergraduate degree in geological sciences completed at The State University of New York at Geneseo in 2013, a master's degree in geological sciences from The University of Alabama completed in 2015, and a PhD in geological and earth sciences completed at The University of Houston in 2021. | 9 | Geochemistry |
Extracellular binding of cytokines or growth factors induce activation of receptor-associated Janus kinases, which phosphorylate a specific tyrosine residue within the STAT protein promoting dimerization via their SH2 domains. The phosphorylated dimer is then actively transported to the nucleus via an importin α/β ternary complex. Originally, STAT proteins were described as latent cytoplasmic transcription factors as phosphorylation was thought to be required for nuclear retention. However, unphosphorylated STAT proteins also shuttle between the cytosol and nucleus, and play a role in gene expression. Once STAT reaches the nucleus, it binds to a consensus DNA-recognition motif called gamma-activated sites (GAS) in the promoter region of cytokine-inducible genes and activates transcription. The STAT protein can be dephosphorylated by nuclear phosphatases, which leads to inactivation of STAT and subsequent transport out of the nucleus by an exportin-RanGTP complex. | 1 | Biochemistry |
The gram per cubic centimetre is a unit of density in the CGS system, and is commonly used in chemistry. It is defined by dividing the CGS unit of mass, the gram, by the CGS unit of volume, the cubic centimetre. The official SI symbols are g/cm, g·cm, or g cm. It is equivalent to the units gram per millilitre (g/mL) and kilogram per litre (kg/L). The density of water is about 1 g/cm, since the gram was originally defined as the mass of one cubic centimetre of water at its maximum density at . | 3 | Analytical Chemistry |
Bisulfite sequencing relies on the conversion of every single unmethylated cytosine residue to uracil. If conversion is incomplete, the subsequent analysis will incorrectly interpret the unconverted unmethylated cytosines as methylated cytosines, resulting in false positive results for methylation. Only cytosines in single-stranded DNA are susceptible to attack by bisulfite, therefore denaturation of the DNA undergoing analysis is critical. It is important to ensure that reaction parameters such as temperature and salt concentration are suitable to maintain the DNA in a single-stranded conformation and allow for complete conversion. Embedding the DNA in agarose gel has been reported to improve the rate of conversion by keeping strands of DNA physically separate. Incomplete conversion rates can be estimated and adjusted-for after sequencing by including an internal control in the sequencing library, such as lambda phage DNA (which is known to be unmethylated) or by aligning bisulfite sequencing reads to a known unmethylated region in the organism, such as the chloroplast genome. | 1 | Biochemistry |
Hidden stops are non-stop codons that would be read as stop codons if they were frameshifted +1 or −1. These prematurely terminate translation if the corresponding frame-shift (such as due to a ribosomal RNA slip) occurs before the hidden stop. It is hypothesised that this decreases resource wastage on nonfunctional proteins and the production of potential cytotoxins. Researchers at Louisiana State University propose the ambush hypothesis, that hidden stops are selected for. Codons that can form hidden stops are used in genomes more frequently compared to synonymous codons that would otherwise code for the same amino acid. Unstable rRNA in an organism correlates with a higher frequency of hidden stops.
However, this hypothesis could not be validated with a larger data set.
Stop-codons and hidden stops together are collectively referred as stop-signals. Researchers at University of Memphis found that the ratios of the stop-signals on the three reading frames of a genome (referred to as translation stop-signals ratio or TSSR) of genetically related bacteria, despite their great differences in gene contents, are much alike. This nearly identical genomic-TSSR value of genetically related bacteria may suggest that bacterial genome expansion is limited by their unique stop-signals bias of that bacterial species. | 1 | Biochemistry |
The development of an analytical instrument that utilizes the reduction-oxidation (redox) chemistry of oxygen in the presence of dissimilar metal electrodes was introduced during the 1950s. This redox electrode utilized an oxygen-permeable membrane to allow the diffusion of the gas into an electrochemical cell and its concentration determined by polarographic or galvanic electrodes. This analytical method is sensitive and accurate down to levels of ± 0.1 mg/L dissolved oxygen. Calibration of the redox electrode of this membrane electrode still requires the use of the Henry's law table or the Winkler test for dissolved oxygen. | 3 | Analytical Chemistry |
Hyrax midden structures and accumulation rates can vary considerably based on the relative proportion of their two primary components, pellets and hyraceum, which is determined by the architecture of the site itself. Depending on the shape and irregularities of the floor of the site in question, pellets are likely to either accumulate (in concave structures) or roll away (in convex or inclined structures). Whereas hyrax urine will deposit only a very thin film of hyraceum after evaporation, pellets are usually 0.5-1 cm in diameter, and thereby accumulate much more quickly., with deep piles accumulating perhaps within just a few years, or even months. Compared to this, we have observed that middens composed primarily of hyraceum accumulate much more slowly; generally between ~5 and >1000 years/mm. The rate of hyraceum accumulation depends on the morphology of the midden, the architecture of the site, as well as presumably the size of the hyrax colony, and as such net rates can be highly variable | 9 | Geochemistry |
The Patterson function is used to solve the phase problem in X-ray crystallography. It was introduced in 1935 by Arthur Lindo Patterson while he was a visiting researcher in the laboratory of Bertram Eugene Warren at MIT.
The Patterson function is defined as
It is essentially the Fourier transform of the intensities rather than the structure factors. The Patterson function is also equivalent to the electron density convolved with its inverse:
Furthermore, a Patterson map of N points will have peaks, excluding the central (origin) peak and any overlap.
The peaks' positions in the Patterson function are the interatomic distance vectors and the peak heights are proportional to the product of the number of electrons in the atoms concerned.
Because for each vector between atoms i and j there is an oppositely oriented vector of the same length (between atoms j and i), the Patterson function always has centrosymmetry. | 3 | Analytical Chemistry |
In organometallic chemistry, acetylide refers to chemical compounds with the chemical formulas and , where M is a metal. The term is used loosely and can refer to substituted acetylides having the general structure (where R is an organic side chain). Acetylides are reagents in organic synthesis. The calcium acetylide commonly called calcium carbide is a major compound of commerce. | 0 | Organic Chemistry |
As mentioned above, the CCE separates cells based on their sedimentation property but not specific features (e.g. surface protein, cell shape). It cannot separate different types of cells which have similar sedimentation properties. This means that previous purification needs to be done for mixed cell type sample. The CCE is also limited to cells which are able to be individually suspended in the buffer solution. Cells which always attach to something cannot be separated by the CCE. | 3 | Analytical Chemistry |
Candidate gene association study is commonly used in genetic study before the invention of high throughput genotyping or sequencing technologies. Candidate gene association study is to investigate limited number of pre-specified SNPs for association with diseases or clinical phenotypes or traits. So this is a hypothesis driven approach. Since only a limited number of SNPs are tested, a relatively small sample size is sufficient to detect the association. Candidate gene association approach is also commonly used to confirm findings from GWAS in independent samples. | 1 | Biochemistry |
When the mean free path of an atom is much smaller than the wavelength of the radiative transition, the atom changes velocity and direction many times during the emission or absorption of a photon. This causes an averaging over different Doppler states and results in an atomic linewidth that is narrower than the Doppler width. | 7 | Physical Chemistry |
The first clear advantage of chain shuttling is that one can design copolymers with more desirable traits. A polymer that is normally semi crystalline and rigid can be altered so that it has a lower glass transition temperature. An amorphous, elastic polymer membrane can be altered to have a higher melting point. The technique opens the door for tailor-made polymers to be widely accessible and simple to make inexpensively. | 7 | Physical Chemistry |
From the 7th to 3rd Century BC, the Scythian people of the Pontic–Caspian steppe engaged in the widespread practice of metallurgy. Though Scythian society was heavily based around a nomadic, mobile lifestyle, the culture was capable of practicing metallurgy and of producing metal objects. Many works of Scythian metalworking have subsequently been found throughout the range of the people. | 8 | Metallurgy |
The electrochemist John Bockris proposed the words electronation and deelectronation to describe reduction and oxidation processes, respectively, when they occur at electrodes. These words are analogous to protonation and deprotonation. They have not been widely adopted by chemists worldwide, although IUPAC has recognized the terms electronation and de-electronation. | 9 | Geochemistry |
*Estimation of the size of DNA molecules following restriction enzyme digestion, e.g. in restriction mapping of cloned DNA.
*Analysis of PCR products, e.g. in molecular genetic diagnosis or genetic fingerprinting
*Separation of restricted genomic DNA prior to Southern transfer, or of RNA prior to Northern transfer.
Gel electrophoresis is used in forensics, molecular biology, genetics, microbiology and biochemistry. The results can be analyzed quantitatively by visualizing the gel with UV light and a gel imaging device. The image is recorded with a computer-operated camera, and the intensity of the band or spot of interest is measured and compared against standard or markers loaded on the same gel. The measurement and analysis are mostly done with specialized software.
Depending on the type of analysis being performed, other techniques are often implemented in conjunction with the results of gel electrophoresis, providing a wide range of field-specific applications. | 1 | Biochemistry |
The TOC complex, or translocon on the outer chloroplast membrane, is a collection of proteins that imports preproteins across the outer chloroplast envelope. Five subunits of the TOC complex have been identified—two GTP-binding proteins Toc34 and Toc159, the protein import tunnel Toc75, plus the proteins Toc64 and Toc12.
The first three proteins form a core complex that consists of one Toc159, four to five Toc34s, and four Toc75s that form four holes in a disk 13 nanometers across. The whole core complex weighs about 500 kilodaltons. The other two proteins, Toc64 and Toc12, are associated with the core complex but are not part of it. | 5 | Photochemistry |
According to some scholars, lost-wax casting was used in China already during the Spring and Autumn period (770 – 476 BCE), although this is often disputed.
The lost-wax method is used in most parts of the world. As the name suggests, the lost-wax method is to use wax as a mold, and heat it to melt the wax mold and lose it, thereby casting bronze ware, making the model (the outer layer of the wax model is coated with mud), lost-wax (heating to make the wax flow out), pouring copper liquid to fill the cavity left by the wax model, etc.
The development and spread of the lost-wax method in the West has never stopped, but the main bronze casting method in the Bronze Age in China is the section mold process. When the lost-wax method was introduced into China is also a topic of academic discussion. But there is no doubt that the lost-wax method already existed in China during the Spring and Autumn Period. In 1978, the Bronze Zun-Pan unearthed from the tomb of Marquis Yi of Zeng in Leigudun, Suixian County, Hubei Province, used a mixed process of section mold method and lost-wax method. | 8 | Metallurgy |
Senapathy addressed the origin of the spliceosomal machinery that edits out the introns from RNA transcripts. If the split genes had originated from random DNA, then the introns would have become an unnecessary but integral part of eukaryotic genes along with the splice junctions. The spliceosomal machinery would be required to remove them and to enable the short exons to be linearly spliced together as a contiguously coding mRNA that can be translated into a complete protein. Thus, the split gene theory argues that spliceosomal machinery exists to remove the unnecessary introns.
Blake states, “Work by Senapathy, when applied to RNA, comprehensively explains the origin of the segregated form of RNA into coding and noncoding regions. It also suggests why a splicing mechanism was developed at the start of primordial evolution.” | 1 | Biochemistry |
There are at least three other possible resolutions to the Kauzmann paradox. It could be that the heat capacity of the supercooled liquid near the Kauzmann temperature smoothly decreases to a smaller value. It could also be that a first order phase transition to another liquid state occurs before the Kauzmann temperature with the heat capacity of this new state being less than that obtained by extrapolation from higher temperature. Finally, Kauzmann himself resolved the entropy paradox by postulating that all supercooled liquids must crystallize before the Kauzmann temperature is reached. | 7 | Physical Chemistry |
Acetalisation is the organic reaction that involves the formation of an acetal (or ketals). One way of acetal formation is the nucleophilic addition of an alcohol to a ketone or an aldehyde. Acetalisation is often used in organic synthesis to create a protecting group because it is a reversible reaction.
Acetalisation is acid catalysed with elimination of water; acetals do not form under basic conditions. The reaction can be driven to the acetal when water is removed from the reaction system either by azeotropic distillation or trapping water with molecular sieves or aluminium oxide.
The carbonyl group in 1 takes a proton from hydronium. The protonated carbonyl group 2 is activated for nucleophilic addition of the alcohol. The structures 2a and 2b are mesomers. After deprotonation of 3 by water the hemiacetal or hemiketal 4 is formed. The hydroxyl group in 4 is protonated leading to the oxonium ion 6 which accepts a second alcohol group to 7 with a final deprotonation to the acetal 8. The reverse reaction takes place by adding water in the same acidic medium. Acetals are stable towards basic media. In a transacetalisation or crossacetalisation a diol reacts with an acetal or two different acetals react with each other. Again this is possible because all the reaction steps are equilibria. | 0 | Organic Chemistry |
Spectroscopy measures the interaction of the molecules with electromagnetic radiation. Spectroscopy consists of many different applications such as atomic absorption spectroscopy, atomic emission spectroscopy, ultraviolet-visible spectroscopy, X-ray fluorescence spectroscopy, infrared spectroscopy, Raman spectroscopy, nuclear magnetic resonance spectroscopy, photoemission spectroscopy, Mössbauer spectroscopy, and circular dichroism spectroscopy. | 3 | Analytical Chemistry |
Spectrum analyzer types are distinguished by the methods used to obtain the spectrum of a signal. There are swept-tuned and fast Fourier transform (FFT) based spectrum analyzers:
*A swept-tuned analyzer uses a superheterodyne receiver to down-convert a portion of the input signal spectrum to the center frequency of a narrow band-pass filter, whose instantaneous output power is recorded or displayed as a function of time. By sweeping the receiver's center-frequency (using a voltage-controlled oscillator) through a range of frequencies, the output is also a function of frequency. But while the sweep centers on any particular frequency, it may be missing short-duration events at other frequencies.
*An FFT analyzer computes a time-sequence of periodograms. FFT refers to a particular mathematical algorithm used in the process. This is commonly used in conjunction with a receiver and analog-to-digital converter. As above, the receiver reduces the center-frequency of a portion of the input signal spectrum, but the portion is not swept. The purpose of the receiver is to reduce the sampling rate that the analyzer must contend with. With a sufficiently low sample-rate, FFT analyzers can process all the samples (100% duty-cycle), and are therefore able to avoid missing short-duration events. | 7 | Physical Chemistry |
This detector usually consists of a heated thin filament or ribbon of a metal with a high work function (typically tungsten or rhenium). Neutral atoms or molecules that strike the filament can boil off as positive ions in a process known as surface ionization, and these may be either measured as a current or detected, individually, using an electron multiplier and particle counting electronics. | 3 | Analytical Chemistry |
In protein structures determined by X-ray crystallography, poor peptide-plane geometry has been described as a common problem; many structures need correction by peptide-plane flips or peptide bond flips. | 1 | Biochemistry |
Because of its ability to cause chemical reactions and excite fluorescence in materials, ultraviolet radiation has a number of applications. The following table gives some uses of specific wavelength bands in the UV spectrum.
* 13.5 nm: Extreme ultraviolet lithography
* 30–200 nm: Photoionization, ultraviolet photoelectron spectroscopy, standard integrated circuit manufacture by photolithography
* 230–365 nm: UV-ID, label tracking, barcodes
* 230–400 nm: Optical sensors, various instrumentation
* 240–280 nm: Disinfection, decontamination of surfaces and water (DNA absorption has a peak at 260 nm), germicidal lamps
* 200–400 nm: Forensic analysis, drug detection
* 270–360 nm: Protein analysis, DNA sequencing, drug discovery
* 280–400 nm: Medical imaging of cells
* 300–320 nm: Light therapy in medicine
* 300–365 nm: Curing of polymers and printer inks
* 350–370 nm: Bug zappers (flies are most attracted to light at 365 nm) | 5 | Photochemistry |
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