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The data stored in SABIO-RK in a comprehensive manner is mainly extracted manually from literature. This includes reactions, their participants (substrates, products), modifiers (inhibitors, activators, cofactors), catalyst details (e.g. EC enzyme classification, protein complex composition, wild type / mutant information), kinetic parameters together with corresponding rate equation, biological sources (organism, tissue, cellular location), environmental conditions (pH, temperature, buffer) and reference details. Data are adapted, normalized and annotated to controlled vocabularies, ontologies and external data sources including KEGG, UniProt, ChEBI, PubChem, NCBI, Reactome, BRENDA, MetaCyc, BioModels, and PubMed.<br/> As of October 2021 SABIO-RK contains about 71.000 curated single entries extracted from more than 7.300 publications. <br/> Several tools, databases and workflows in Systems Biology make use of SABIO-RK biochemical reaction data by integration into their framework including SYCAMORE, MeMo-RK, CellDesigner, PeroxisomeDB, Taverna workflows or tools like KineticsWizard software for data capture and analysis. Additionally, SABIO-RK is part of MIRIAM registry, a set of guidelines for the annotation and curation of computational models

Biochemistry

DOC is conceptually divided into labile DOC, which is rapidly taken up by heterotrophic microbes, and the recalcitrant DOC reservoir, which has accumulated in the ocean (following a definition by Hansell). As a consequence of its recalcitrance, the accumulated DOC reaches average radiocarbon ages between 1,000 and 4,000 years in surface waters, and between 3,000 and 6,000 years in the deep ocean, indicating that it persists through several deep ocean mixing cycles between 300 and 1,400 years each. Behind these average radiocarbon ages, a large spectrum of ages is hidden. Follett et al. showed DOC comprises a fraction of modern radiocarbon age, as well as DOC reaching radiocarbon ages of up to 12,000 years.

Environmental Chemistry

A potentiometric selectivity coefficient defines the ability of an ion-selective electrode to distinguish one particular ion from others. The selectivity coefficient, K is evaluated by means of the emf response of the ion-selective electrode in mixed solutions of the primary ion, B, and interfering ion, C (fixed interference method) or less desirably, in separate solutions of B and C (separate solution method). For example, a potassium ion-selective membrane electrode utilizes the naturally occurring macrocyclic antibiotic valinomycin. In this case the cavity in the macrocyclic ring is just the right size to encapsulate the potassium ion, but too large to bind the sodium ion, the most likely interference, strongly. Chemical sensors, are being developed for specific target molecules and ions in which the target (guest) form a complex with a sensor (host). The sensor is designed to be an excellent match in terms of the size and shape of the target in order to provide for the maximum binding selectivity. An indicator is associated with the sensor which undergoes a change when the target forms a complex with the sensor . The indicator change is usually a colour change (gray to yellow in the illustration) seen in absorbance or, with greater sensitivity, luminescence. The indicator may be attached to the sensor via a spacer, in the ISR arrangement, or it may be displaced from the sensor, IDA arrangement.

Physical Chemistry

In condensed matter physics, a time crystal is a quantum system of particles whose lowest-energy state is one in which the particles are in repetitive motion. The system cannot lose energy to the environment and come to rest because it is already in its quantum ground state. Time crystals were first proposed theoretically by Frank Wilczek in 2012 as a time-based analogue to common crystals – whereas the atoms in crystals are arranged periodically in space, the atoms in a time crystal are arranged periodically in both space and time. Several different groups have demonstrated matter with stable periodic evolution in systems that are periodically driven. In terms of practical use, time crystals may one day be used as quantum computer memory. The existence of crystals in nature is a manifestation of spontaneous symmetry breaking, which occurs when the lowest-energy state of a system is less symmetrical than the equations governing the system. In the crystal ground state, the continuous translational symmetry in space is broken and replaced by the lower discrete symmetry of the periodic crystal. As the laws of physics are symmetrical under continuous translations in time as well as space, the question arose in 2012 as to whether it is possible to break symmetry temporally, and thus create a "time crystal" that is resistant to entropy. If a discrete time-translation symmetry is broken (which may be realized in periodically driven systems), then the system is referred to as a discrete time crystal. A discrete time crystal never reaches thermal equilibrium, as it is a type (or phase) of non-equilibrium matter. Breaking of time symmetry can only occur in non-equilibrium systems. Discrete time crystals have in fact been observed in physics laboratories as early as 2016 (published in 2017). One example of a time crystal, which demonstrates non-equilibrium, broken time symmetry is a constantly rotating ring of charged ions in an otherwise lowest-energy state.

Analytical Chemistry

Complexes of polymers with DNA are called polyplexes. Most polyplexes consist of cationic polymers and their fabrication is based on self-assembly by ionic interactions. One important difference between the methods of action of polyplexes and lipoplexes is that polyplexes cannot directly release their DNA load into the cytoplasm. As a result, co-transfection with endosome-lytic agents such as inactivated adenovirus was required to facilitate nanoparticle escape from the endocytic vesicle made during particle uptake. However, a better understanding of the mechanisms by which DNA can escape from endolysosomal pathway, i.e. proton sponge effect, has triggered new polymer synthesis strategies such as incorporation of protonable residues in polymer backbone and has revitalized research on polycation-based systems. Due to their low toxicity, high loading capacity, and ease of fabrication, polycationic nanocarriers demonstrate great promise compared to their rivals such as viral vectors which show high immunogenicity and potential carcinogenicity, and lipid-based vectors which cause dose dependence toxicity. Polyethyleneimine and chitosan are among the polymeric carriers that have been extensively studied for development of gene delivery therapeutics. Other polycationic carriers such as poly(beta-amino esters) and polyphosphoramidate are being added to the library of potential gene carriers. In addition to the variety of polymers and copolymers, the ease of controlling the size, shape, surface chemistry of these polymeric nano-carriers gives them an edge in targeting capability and taking advantage of enhanced permeability and retention effect.

Biochemistry

An adatom is an atom that lies on a crystal surface, and can be thought of as the opposite of a surface vacancy. This term is used in surface chemistry and epitaxy, when describing single atoms lying on surfaces and surface roughness. The word is a portmanteau of "adsorbed atom". A single atom, a cluster of atoms, or a molecule or cluster of molecules may all be referred to by the general term "adparticle". This is often a thermodynamically unfavorable state. However, cases such as graphene may provide counter-examples.

Physical Chemistry

In 2010, the FDA approved the combination drug dextromethorphan/quinidine under the brand name Nuedexta for the treatment of pseudobulbar affect (uncontrollable laughing/crying). Dextromethorphan is the actual therapeutic agent in the combination; quinidine merely serves to inhibit the enzymatic degradation of dextromethorphan and thereby increase its circulating concentrations via inhibition of CYP2D6.

Stereochemistry

The most established and well-known homoaromatic species are cationic homoaromatic compounds. As stated earlier, the homotropenylium cation is one of the most studied homoaromatic compounds. Many homoaromatic cationic compounds use as a basis a cyclopropenyl cation, a tropylium cation, or a cyclobutadiene dication as these compounds exhibit strong aromatic character. In addition to the homotropylium cation, another well established cationic homoaromatic compound is the norbornen-7-yl cation, which has been shown to be strongly homoaromatic, proven both theoretically and experimentally. An intriguing case of σ-bishomoaromaticity can be found in the dications of pagodanes. In these 4-center-2-electron systems the delocalization happens in the plane that is defined by the four carbon atoms (prototype for the phenomenon of σ-aromaticity is cyclopropane which gains about 11.3 kcal mol stability from the effect). The dications are accessible either via oxidation of pagodane or via oxidation of the corresponding bis-seco-dodecahedradiene: Reduction of the corresponding six electrons dianions was not possible so far.

Physical Chemistry

In Earth science, a geochemical cycle is the pathway that chemical elements take in the surface and crust of the Earth. The term "geochemical" tells us that geological and chemical factors are all included. The migration of heated and compressed chemical elements and compounds such as silicon, aluminium, and general alkali metals through the means of subduction and volcanism is known in the geological world as geochemical cycles. The geochemical cycle encompasses the natural separation and concentration of elements and heat-assisted recombination processes. Changes may not be apparent over a short term, such as with biogeochemical cycles, but over a long term changes of great magnitude occur, including the evolution of continents and oceans.

Geochemistry

Magnetic trapping is created by adding a spatially varying magnetic quadrupole field to the red detuned optical field needed for laser cooling. This causes a Zeeman shift in the magnetic-sensitive m levels, which increases with the radial distance from the center of the trap. Because of this, as an atom moves away from the center of the trap, the atomic resonance is shifted closer to the frequency of the laser light, and the atom becomes more likely to get a photon kick towards the center of the trap. The direction of the kick is given by the polarization of the light, which is either left or right handed circular, giving different interactions with the different m levels. The correct polarizations are used so that photons moving towards the center of the trap will be on resonance with the correct shifted atomic energy level, always driving the atom towards the center.

Physical Chemistry

Continuous quantum engines are the quantum analogues of turbines. The work output mechanism is coupling to an external periodic field, typically the electromagnetic field. Thus the heat engine is a model for a laser. The models differ by the choice of their working substance and heat source and sink. Externally driven two-level, three level four-level and coupled harmonic oscillators have been studied. The periodic driving splits the energy level structure of the working medium. This splitting allows the two level engine to couple selectively to the hot and cold baths and produce power. On the other hand, ignoring this splitting in the derivation of the equation of motion will violate the second law of thermodynamics. Non thermal fuels have been considered for quantum heat engines. The idea is to increase the energy content of the hot bath without increasing its entropy. This can be achieved by employing coherence or a squeezed thermal bath. These devices do not violate the second law of thermodynamics.

Physical Chemistry

*Anoigmaichnus is a bioclaustration. It occurs in the Ordovician bryozoans. Apertures of Anoigmaichnus are elevated above their hosts' growth surfaces, forming short chimney-like structures. * Arachnostega is the name given to the irregular, branching burrows in the sediment fill of shells. They are visible on the surface of steinkerns. Their traces are known from the Cambrian period onwards. * Asteriacites is the name given to the five-rayed fossils found in rocks and they record the resting place of starfish on the sea floor. Asteriacites are found in European and American rocks, from the Ordovician period onwards, and are numerous in rocks from the Jurassic period of Germany. * Burrinjuckia is a bioclaustration. Burrinjuckia includes outgrowths of the brachiopod's secondary shell with a hollow interior in the mantle cavity of a brachiopod. * Chondrites (not to be confused with stony meteorites of the same name) are small branching burrows of the same diameter, which superficially resemble the roots of a plant. The most likely candidate for having constructed these burrows is a nematode (roundworm). Chondrites are found in marine sediments from the Cambrian period of the Paleozoic onwards. They are especially common in sediments which were deposited in reduced-oxygen environments. * Climactichnites is the name given to surface trails and burrows that consist of a series of chevron-shaped raised cross bars that are usually flanked on either side by a parallel ridge. They somewhat resemble tire tracks, and are larger (typically about wide) than most of the other trace fossils made by invertebrates. The trails were produced on sandy tidal flats during Cambrian time. While the identity of the animal is still conjectural, it may have been a large slug-like animal – its trails produced as it crawled over and processed the wet sand to obtain food. * Cruziana are excavation trace marks made on the sea floor which have a two-lobed structure with a central groove. The lobes are covered with scratch marks made by the legs of the excavating organism, usually a trilobite or allied arthropod. Cruziana are most common in marine sediments formed during the Paleozoic era, particularly in rocks from the Cambrian and Ordovician periods. Over 30 ichnospecies of Cruziana have been identified. See also Isopodichnus. * Entobia is a boring produced by endolithic clionaid sponges consisting of galleries excavated in a carbonate substrate; often has swollen chambers with connecting canals. * Gastrochaenolites are clavate (club-shaped) borings also produced in calcareous hard substrates, usually by bivalves. * Oikobesalon is an unbranched, elongate burrow with single-entrance and circular cross-section produced by terebellid polychaetes. They are covered with thin lining which has a transverse ornamentation in the form of fusiform annulation. * Petroxestes is a shallow groove boring produced by mytilacean bivalves in carbonate hard substrates. * Planolites is a small, 1-5mm (0.039–0.197 in), unlined and rarely branched, elongate burrow with fill that differs from the host rock, and is found throughout the Ediacaran and the Phanerozoic. * Protichnites consists of two rows of tracks and a linear depression between the two rows. The tracks are believed to have been made by the walking appendages of arthropods. The linear depression is thought to be the result of a dragging tail. The structures bearing this name were typically made on the tidal flats of Paleozoic seas, but similar ones extend into the Cenozoic. * Rhizocorallium is a type of burrow, the inclination of which is typically within 10° of the bedding planes of the sediment. These burrows can be very large, over a meter long in sediments that show good preservation, e.g. Jurassic rocks of the Yorkshire Coast (eastern United Kingdom), but the width is usually only up to , restricted by the size of the organisms producing it. It is thought that they represent fodinichnia as the animal (probably a nematode) scoured the sediment for food. * Rogerella is a small pouch-shaped boring with a slit-like aperture currently produced by acrothoracican barnacles. * Rusophycus are bilobed "resting traces" associated with trilobites and other arthropods such as horseshoe crabs. * Skolithos: One well-known occurrence of Cambrian trace fossils from this period is the famous Pipe Rock of northwest Scotland. The pipes that give the rock its name are closely packed straight tubes- which were presumably made by some kind of worm-like organism. The name given to this type of tube or burrow is Skolithos, which may be in length and between in diameter. Such traces are known worldwide from sands and sandstones deposited in shallow water environments, from the Cambrian period (542&ndash;488 Ma) onwards. * Thalassinoides are burrows which occur parallel to the bedding plane of the rock and are extremely abundant in rocks, worldwide, from the Jurassic period onwards. They are repeatedly branched, with a slight swelling present at the junctions of the tubes. The burrows are cylindrical and vary from in diameter. Thalassinoides sometimes contain scratch marks, droppings or the bodily remains of the crustaceans which made them. * Teichichnus has a distinctive form produced by the stacking of thin tongues of sediment, atop one another. They are again believed to be fodinichnia, with the organism adopting the habit of retracing the same route through varying heights of the sediment, which would allow it to avoid going over the same area. These tongues are often quite sinuous, reflecting perhaps a more nutrient-poor environment in which the feeding animals had to cover a greater area of sediment, in order to acquire sufficient nourishment. * Tremichnus is an embedment structure (i.e. bioclaustration) formed by an organism that inhibited growth of the crinoid host stereom. * Trypanites are elongated cylindrical borings in calcareous substrates such as shells, carbonate hardgrounds, and limestones. Usually produced by worms of various types and sipunculids.

Environmental Chemistry

Sulfur can replace oxygen, either in the carbonyl group or in the bridge. In the former case, the name of the acyl group is enclosed in parentheses to avoid ambiguity in the name, e.g., (thioacetic) anhydride (CHC(S)OC(S)CH). When two acyl groups are attached to the same sulfur atom, the resulting compound is called a thioanhydride, e.g., acetic thioanhydride ((CHC(O))S).

Organic Chemistry

F is a water insoluble protein with eight subunits and a transmembrane ring. The ring has a tetrameric shape with a helix-loop-helix protein that goes through conformational changes when protonated and deprotonated, pushing neighboring subunits to rotate, causing the spinning of F which then also affects conformation of F, resulting in switching of states of alpha and beta subunits. The F region of ATP synthase is a proton pore that is embedded in the mitochondrial membrane. It consists of three main subunits, a, b, and c. Six c subunits make up the rotor ring, and subunit b makes up a stalk connecting to F OSCP that prevents the αβ hexamer from rotating. Subunit a connects b to the c ring. Humans have six additional subunits, d, e, f, g, F6, and 8 (or A6L). This part of the enzyme is located in the mitochondrial inner membrane and couples proton translocation to the rotation that causes ATP synthesis in the F region. In eukaryotes, mitochondrial F forms membrane-bending dimers. These dimers self-arrange into long rows at the end of the cristae, possibly the first step of cristae formation. An atomic model for the dimeric yeast F region was determined by cryo-EM at an overall resolution of 3.6 Å.

Photochemistry

Alkyllithium reagents form deeply colored derivatives with phenanthroline. The alkyllithium content of solutions can be determined by treatment of such reagents with small amounts of phenanthroline (ca. 1 mg) followed by titration with alcohols to a colourless endpoint. Grignard reagents may be similarly titrated.

Analytical Chemistry

Nucleotides are initially made with ribose as the sugar component, which is a feature of RNA. DNA, however, requires deoxyribose, which is missing the 2'-hydroxyl (-OH group) on the ribose. The reaction to remove this -OH is catalyzed by ribonucleotide reductase. This enzyme converts NDPs (ucleoside-ihosphate) to dNDPs (eoxyucleoside-ihosphate). The nucleotides must be in the diphosphate form for the reaction to occur. In order to synthesize thymidine, a component of DNA which only exists in the deoxy form, uridine is converted to deoxyuridine (by ribonucleotide reductase), and then is methylated by thymidylate synthase to create thymidine.

Biochemistry

Ryōji Noyori was born in Kobe, Japan. Early in his school days Ryoji was interested in physics. His interest was kindled by the famous physicist Hideki Yukawa (1949 Nobel Prize in Physics winner), a close friend of his father. Later, he became fascinated with chemistry, after hearing a presentation on nylon at an industrial exposition. He saw the power of chemistry as being the ability to "produce high value from almost nothing". He was a student at the School of Engineering (Department of Industrial Chemistry) of the Kyoto University, where he graduated in 1961. He subsequently obtained a Master's degree in Industrial Chemistry from the Graduate School of Engineering of the Kyoto University. Between 1963 and 1967, he was a research associate at the School of Engineering of the Kyoto University, and an instructor in the research group of Hitoshi Nozaki. Noyori obtained a Doctor of Engineering degree (DEng) from the Kyoto University in 1967. He became an associate professor at the same university in 1968. After postdoctoral work with Elias J. Corey at Harvard he returned to Nagoya, becoming a full professor in 1972. He is still based at Nagoya, and served as president of RIKEN, a multi-site national research initiative with an annual budget of $800 million, from 2003 to 2015.

Stereochemistry

Nitrile ylides also known as nitrilium ylides or nitrilium methylides, are generally reactive intermediates formally consisting of a carbanion of an alkyl or similar group bonded to the nitrogen atom of a cyanide unit. With a few exceptions, they cannot be isolated. However, a structure has been determined on a particularly stable nitrile ylide by X-ray crystallography. Another nitrile ylide has been captured under cryogenic conditions. As ylides, they possess a negative charge and a positive charge on adjacent atoms. However, they also have resonance, including 1,3-dipole contributing structures: The most appropriate resonance structure is dependent upon the substituent pattern (the identity of the R and R′ groups). The 3-dimensional structure of the nitrilium ylide itself may also provide a clue as to the most appropriate resonance structure, with a linear R–C≡N–C unit supportive of the charge distribution indicated for resonance structures 1a & 1b and also consistent with the nomenclature nitrilium ylide. As resonance structures 1c and 1d become more important the nitrilium ylide distorts its geometry from linear in favor of a different valence tautomer 2 that is distinctly bent: Nitrile ylides are isoelectronic with nitrile oxides:

Organic Chemistry

Quality of measurements made in chemistry and other areas is an important issue in today's world as measurements influence quality of life, cross-border trade and commerce. In this respect, EN ISO 17025 is the main standard used by testing and calibration laboratories as to appropriately tackle quality management related issues. While chapter four of the standard deals with management requirements, chapter five describes requirements for technical competence. Management related issues can be found in other standards as well e.g. ISO 9000, however the technical requirements are specific for calibration and testing laboratories.

Analytical Chemistry

The nature of bonding in the 2-norbornyl cation was the center of a vigorous, well-known debate in the chemistry community through the middle of the twentieth century. While the majority of chemists believed that a three-center two-electron bond best depicted its ground state electronic structure, others argued that all data concerning the 2-norbornyl cation could be explained by depicting it as a rapidly equilibrating pair of cations. At the height of the debate, all chemists agreed that the delocalized picture of electron bonding could be applied to the 2-norbornyl cation. But this did not answer the fundamental question on which the debate hinged. Researchers continued to search for novel ways to determine whether the three-centered delocalized picture described a low-energy transition state (saddle point on the multidimensional potential energy surface) or a potential energy minimum in its own right. Proponents of the "classical" picture believed that the system was best described by a double-well potential with a very low barrier, while those in the "non-classical" camp envisioned the delocalized electronic state to describe a single potential energy well.

Physical Chemistry

Alexander Killen Macbeth CMG, DSc, FAA was born in Ireland on 11 August 1889 at Drumbuoy, Strabane, second son of William, a butcher, and Sarah Anna. He was educated at Queen’s University Belfast, and at University College London, where he was an 1851 Exhibition Scholar. He returned to Belfast and then, in 1919, to the University of St Andrews as a Senior Lecturer in Chemistry. From 1924 to 1928 he held the position of Reader in Chemistry at Durham University. On 13 January 1928, Macbeth with is wife and two daughters sailed on the RMS Mooltan from London to Adelaide. There he took up his appointment as the Angas Chair of Chemistry in the University of Adelaide, which he held until his retirement in 1954, when he was created Professor Emeritus. He held the degrees of M.A. and D.Sc. of the Queen’s University Belfast, and was elected to the Fellowship of the Australian Academy of Science in 1955. In 1946 he was awarded the CMG for his services to the University of Adelaide and to industry during the war. Macbeth’s tenure of the Adelaide Chair coincided with the depression and then with the Second World War. Nevertheless, he developed a thriving department, “starting initially with one Liebig condenser and a few flasks”. This perseverance finally resulted in a new chemistry school, which opened in 1933.

Organic Chemistry

The Free Thyroxine Index (FTI or T7) is obtained by multiplying the total T with T uptake. FTI is considered to be a more reliable indicator of thyroid status in the presence of abnormalities in plasma protein binding. This test is rarely used now that reliable free thyroxine and free triiodothyronine assays are routinely available. FTI is elevated in hyperthyroidism and decreased in hypothyroidism.

Biochemistry

Hyperfine interactions, the internal magnetic fields of local magnetic isotopes, play a significant role as well in the spin dynamics of radical-pairs.

Physical Chemistry

Generally, in progression to cancer, hundreds of genes are silenced or activated. Although silencing of some genes in cancers occurs by mutation, a large proportion of carcinogenic gene silencing is a result of altered DNA methylation (see DNA methylation in cancer). DNA methylation causing silencing in cancer typically occurs at multiple CpG sites in the CpG islands that are present in the promoters of protein coding genes. Altered expressions of microRNAs also silence or activate many genes in progression to cancer (see microRNAs in cancer). Altered microRNA expression occurs through hyper/hypo-methylation of CpG sites in CpG islands in promoters controlling transcription of the microRNAs. Silencing of DNA repair genes through methylation of CpG islands in their promoters appears to be especially important in progression to cancer (see methylation of DNA repair genes in cancer).

Biochemistry

Neurotransmitter release can be measured by determining the amplitude of the postsynaptic potential after triggering an action potential in the presynaptic neuron. Measuring neurotransmitter release this way can be problematic because the effect of the postsynaptic neuron to the same amount of released neurotransmitter can change over time. Another way is to measure vesicle fusion with the presynaptic membrane directly using a patch pipette. A cell membrane can be thought of as a capacitor in that positive and negative ions are stored on both sides of the membrane. The larger the area of membrane the more ions that are necessary to hold the membrane at a certain potential. In electrophysiology this means that a current injection into the terminal will take less time to charge a membrane to a given potential before vesicle fusion than it will after vesicle fusion. The time course to charge the membrane to a potential and the resistance of the membrane is measured and with these values the capacitance of the membrane can be calculated by the equation Tau/Resistance=Capacitance. With this technique researchers can measure synaptic vesicle release directly by measuring increases in the membrane capacitance of the presynaptic terminal.

Biochemistry

Methanation is an important step in the creation of synthetic or substitute natural gas (SNG). Coal or wood undergo gasification which creates a producer gas that must undergo methanation in order to produce a usable gas that just needs to undergo a final purification step. The first commercial synthetic gas plant opened in 1984 and is the Great Plains Synfuel plant in Beulah, North Dakota. It is still operational and produces 1500 MW worth of SNG using coal as the carbon source. In the years since its opening, other commercial facilities have been opened using other carbon sources such as wood chips. In France, the AFUL Chantrerie, located in Nantes, started in November 2017 the demonstrator MINERVE. This methanation unit of 14 Nm3/day was carried out by Top Industrie, with the support of Leaf. This installation is used to feed a CNG station and to inject methane into the natural gas boiler.

Organic Chemistry

Cryosurgery is a minimally invasive procedure, and is often preferred to other types of surgery because of its safety, ease of use, minimal pain and scarring as well as low cost; however, as with any medical treatment, there are risks involved, primarily that of damage to nearby healthy tissue. Damage to nerve tissue is of particular concern but is rare. Cryosurgery cannot be used on lesions that would subsequently require biopsy as the technique destroys tissue and precludes the use of histopathology. More common complications of cryosurgery include blistering and edema which are transient. Cryosurgery may cause complications due to damage of underlying structures. Destruction of the basement membrane may cause scarring and destruction of hair follicles can cause alopecia or hair loss. Occasionally, hypopigmentation may occur in the area of skin treated with cryosurgery, however, this complication is usually transient and often resolves as melanocytes migrate and repigment the area over several months. Bleeding can also occur, which can be delayed or immediate, due to damage of underlying arteries and arterioles. Tendon rupture and cartillage necrosis can occur, particularly if cryosurgery is done over bony prominences. These complications can be avoided or minimized if freeze times of less than 30 seconds are used during cryosurgery. Patients undergoing cryosurgery usually experience redness and minor-to-moderate localized pain, which most of the time can be alleviated sufficiently by oral administration of mild analgesics such as ibuprofen, codeine or acetaminophen (paracetamol). Blisters may form as a result of cryosurgery, but these usually scab over and peel away within a few days.

Biochemistry

In many insect species of interest to agriculture, such as those in the order Lepidoptera, females emit an airborne trail of a specific chemical blend constituting that species' sex pheromone. This aerial trail is referred to as a pheromone plume. Males of that species use the information contained in the pheromone plume to locate the emitting female (known as a “calling” female). Mating disruption exploits the male insects' natural response to follow the plume by introducing a synthetic pheromone into the insects’ habitat. The synthetic pheromone is a volatile organic chemical designed to mimic the species-specific sex pheromone produced by the female insect. The general effect of mating disruption is to confuse the male insects by masking the natural pheromone plumes, causing the males to follow “false pheromone trails” at the expense of finding mates, and affecting the males’ ability to respond to “calling" females. Consequently, the male population experiences a reduced probability of successfully locating and mating with females, which leads to the eventual cessation of breeding and collapse of the insect infestation. The California Department of Pesticide Regulation, the California Department of Food and Agriculture, and the United States Environmental Protection Agency consider mating disruption to be among the most environmentally friendly treatments used to eradicate pest infestations. Mating disruption works best if large areas are treated with pheromones. Ten acres is a good minimum size for a successful MD program, but larger areas are preferable

Biochemistry

Ilya Iosifovich Moiseev (; 15 March 1929 – 10 October 2020) was a Soviet and Russian chemist. An expert in both kinetics and the coordination chemistry of transition metals, he made significant advances in metal-complex catalysis.

Physical Chemistry

Surface-enhanced Raman spectroscopy or surface-enhanced Raman scattering (SERS) is a surface-sensitive technique that enhances Raman scattering by molecules adsorbed on rough metal surfaces or by nanostructures such as plasmonic-magnetic silica nanotubes. The enhancement factor can be as much as 10 to 10, which means the technique may detect single molecules.

Physical Chemistry

Some tetrabutylammonium salts of simple anions include: *tetrabutylammonium fluoride, a desilylation reagent. *tetrabutylammonium bromide, a precursor to other tetrabutylammonium salts via salt metathesis reactions. *tetrabutylammonium iodide, a low cost catalyst. *tetrabutylammonium triiodide, a common carrier of the triiodide anion used in chemical synthesis. *tetrabutylammonium hydroxide, a precursor to other tetrabutylammonium salts via acid-base reactions. *tetrabutylammonium hexafluorophosphate, an electrolyte for nonaqueous electrochemistry. Some tetrabutylammonium salts of more complex examples include: *polyoxometalates. *NS. *metal carbonyl anions. *Synthetic iron-sulfur clusters such as *Octachlorodirhenate ().

Organic Chemistry

In concert with the primary surface forces described above, there are several circumstantial effects in play. While the forces themselves each contribute to the magnitude of the adhesion between the surfaces, the following play a crucial role in the overall strength and reliability of an adhesive device.

Supramolecular Chemistry

Susceptibility to photo-oxidation varies depending on the chemical structure of the polymer. Some materials have excellent stability, such as fluoropolymers, polyimides, silicones and certain acrylate polymers. However, global polymer production is dominated by a range of commodity plastics which account for the majority of plastic waste. Of these polyethylene terephthalate (PET) has only moderate UV resistance and the others, which include polystyrene, polyvinyl chloride (PVC) and polyolefins like polypropylene (PP) and polyethylene (PE) are all highly susceptible. Photo-oxidation is a form of photodegradation and begins with formation of free radicals on the polymer chain, which then react with oxygen in chain reactions. For many polymers the general autoxidation mechanism is a reasonable approximation of the underlying chemistry. The process is autocatalytic, generating increasing numbers of radicals and reactive oxygen species. These reactions result in changes to the molecular weight (and molecular weight distribution) of the polymer and as a consequence the material becomes more brittle. The process can be divided into four stages: :Initiation the process of generating the initial free radical. :Propagation the conversion of one active species to another :Chain branching steps which end with more than one active species being produced. The photolysis of hydroperoxides is the main example. :Termination steps in which active species are removed, for instance by radical disproportionation Photo-oxidation can occur simultaneously with other processes like thermal degradation, and each of these can accelerate the other.

Photochemistry

The Monsanto process is an industrial method for the manufacture of acetic acid by catalytic carbonylation of methanol. The Monsanto process has largely been supplanted by the Cativa process, a similar iridium-based process developed by BP Chemicals Ltd which is more economical and environmentally friendly. This process operates at a pressure of 30–60 atm and a temperature of 150–200 °C and gives a selectivity greater than 99%. It was developed in 1960 by the German chemical company, BASF, and improved by the Monsanto Company in 1966, which introduced a new catalyst system.

Organic Chemistry

Around the world, household drinking water purification systems, including a RO step, are commonly used for improving water for drinking and cooking. Such systems typically include these steps: * a sediment filter to trap particles, including rust and calcium carbonate * a second sediment filter with smaller pores * an activated carbon filter to trap organic chemicals and chlorine, which degrades certain types of thin-film composite membrane * an RO thin-film composite membrane * an ultraviolet lamp for sterilizing any microbes that survive RO * a second carbon filter to capture chemicals that survive RO In some systems, the carbon prefilter is replaced by a cellulose triacetate (CTA) membrane. CTA is a paper by-product membrane bonded to a synthetic layer that allows contact with chlorine in the water. These require a small amount of chlorine in the water source to prevent bacteria from forming on it. The typical rejection rate for CTA membranes is 85–95%. The cellulose triacetate membrane rots unless protected by chlorinated water, while the thin-film composite membrane breaks down in the presence of chlorine. The thin-film composite (TFC) membrane is made of synthetic material, and requires the chlorine to be removed before the water enters the membrane. To protect the TFC membrane elements from chlorine damage, carbon filters are used as pre-treatment. TFC membranes have a higher rejection rate of 95–98% and a longer life than CTA membranes. Portable RO water processors are sold for personal water available. To work effectively, the water feeding to these units should be under pressure (typically 280 kPa (40 psi) or greater). These processors can be used in areas lacking clean water. US mineral water production uses RO. In Europe such processing of natural mineral water (as defined by a European directive) is not allowed. In practice, a fraction of the living bacteria pass through RO through membrane imperfections or bypass the membrane entirely through leaks in seals. For household purification absent the need to remove dissolved minerals (soften the water), the alternative to RO is an activated carbon filter with a microfiltration membrane.

Analytical Chemistry

Assay offices are institutions set up to assay (test the purity of) precious metals. This is often done to protect consumers from buying fake items. Upon successful completion of an assay (i.e. if the metallurgical content is found be equal or better than that claimed by the maker and it otherwise conforms to the prevailing law) the assay offices typically stamp a hallmark on the item to certify its metallurgical content. Hallmarking first appeared in France, with the Goldsmiths' Statute of 1260 promulgated under Étienne Boileau, Provost of Paris, for King Louis IX.

Analytical Chemistry

The initial adsorption of the molecule adhesive will also depend on the wetting between the adhesive and membrane. This can be described using Young's equation: where is the interfacial tension between the membrane and gas or bodily environment, is the interfacial tension between the bioadhesive and membrane, is the interfacial tension between the bioadhesive and bodily environment, and is the contact angle of the bioadhesive on the membrane. The ideal contact angle is 0° meaning the bioadhesive perfectly wets the membrane and good contact is achieved. The interfacial tensions can be measured using common experimental techniques such as a Wilhelmy plate or the Du Noüy ring method to predict if the adhesive will make good contact with the membrane.

Biochemistry

Biopolymers can be sustainable, carbon neutral and are always renewable, because they are made from plant or animal materials which can be grown indefinitely. Since these materials come from agricultural crops, their use could create a sustainable industry. In contrast, the feedstocks for polymers derived from petrochemicals will eventually deplete. In addition, biopolymers have the potential to cut carbon emissions and reduce CO quantities in the atmosphere: this is because the CO released when they degrade can be reabsorbed by crops grown to replace them: this makes them close to carbon neutral. Almost all biopolymers are biodegradable in the natural environment: they are broken down into CO and water by microorganisms. These biodegradable biopolymers are also compostable: they can be put into an industrial composting process and will break down by 90% within six months. Biopolymers that do this can be marked with a compostable symbol, under European Standard EN 13432 (2000). Packaging marked with this symbol can be put into industrial composting processes and will break down within six months or less. An example of a compostable polymer is PLA film under 20μm thick: films which are thicker than that do not qualify as compostable, even though they are "biodegradable". In Europe there is a home composting standard and associated logo that enables consumers to identify and dispose of packaging in their compost heap.

Biochemistry

For a complete list of the 209 PCB congeners, see PCB congener list. Note that biphenyl, while not technically a PCB congener because of its lack of chlorine substituents, is still typically included in the literature.

Environmental Chemistry

At its simplest, the theory holds that when gravity becomes vanishingly weak—levels seen only at interstellar distances—it diverges from its classically understood nature and its strength begins to decay linearly with distance from a mass. Entropic gravity provides an underlying framework to explain Modified Newtonian Dynamics, or MOND, which holds that at a gravitational acceleration threshold of approximately , gravitational strength begins to vary inversely linearly with distance from a mass rather than the normal inverse-square law of the distance. This is an exceedingly low threshold, measuring only 12 trillionths gravitys strength at Earths surface; an object dropped from a height of one meter would fall for 36 hours were Earths gravity this weak. It is also 3,000 times less than the remnant of Earths gravitational field that exists at the point where crossed the solar system's heliopause and entered interstellar space. The theory claims to be consistent with both the macro-level observations of Newtonian gravity as well as Einstein's theory of general relativity and its gravitational distortion of spacetime. Importantly, the theory also explains (without invoking the existence of dark matter and tweaking of its new free parameters) why galactic rotation curves differ from the profile expected with visible matter. The theory of entropic gravity posits that what has been interpreted as unobserved dark matter is the product of quantum effects that can be regarded as a form of positive dark energy that lifts the vacuum energy of space from its ground state value. A central tenet of the theory is that the positive dark energy leads to a thermal-volume law contribution to entropy that overtakes the area law of anti-de Sitter space precisely at the cosmological horizon. Thus this theory provides an alternative explanation for what mainstream physics currently attributes to dark matter. Since dark matter is believed to compose the vast majority of the universe's mass, a theory in which it is absent has huge implications for cosmology. In addition to continuing theoretical work in various directions, there are many experiments planned or in progress to actually detect or better determine the properties of dark matter (beyond its gravitational attraction), all of which would be undermined by an alternative explanation for the gravitational effects currently attributed to this elusive entity.

Physical Chemistry

Burks became an assistant professor of chemistry at St. Edward's University in Austin, Texas, in 2016, where she taught and conducted research until 2020. She then moved to Washington, D.C., to join the faculty at American University as an associate professor of chemistry. Her current research centers on developing low-cost colorimetric sensors for detecting chemicals of forensic interest including explosives and illicit drugs. To maximize portability in the field, her group focuses on transforming smartphones into detection devices. Her research interests lie in the applied science domain, which she believes is well-suited to capturing and holding students' attention because they are working to solve real-world problems. She has spoken about her intersectional research approach to equipping students with the technical knowledge they need to work on these real-world challenges with the United States Department of Defense Science, Technology, and Innovation Exchange.

Analytical Chemistry

Current methods include liquid chromatography coupled to mass spectrometry (LC-MS), mouse bioassay, protein synthesis inhibition assay, and reverse-phase HPLC-PDA (Photo Diode Array) analysis. A cell free protein synthesis assay has been developed which appears to be comparable to HPLC-MS.

Organic Chemistry

Prepared samples are combusted from 1000 up to 1200 degrees C in an oxygen-rich atmosphere. All carbon present converts to carbon dioxide, flows through scrubber tubes to remove interferences such as chlorine gas, and water vapor, and the carbon dioxide is measured either by absorption into a strong base then weighed, or using an infrared detector. Most modern analyzers use non-dispersive infrared (NDIR) for detection of the carbon dioxide. Compared to the conventional high temperature catalytic oxidation, the great benefit of the combustion-method is the high oxidation power, so that oxidation-promoting catalysts are superfluous.

Analytical Chemistry

Levonorgestrel is the generic name of the drug and its , , , , , and , while lévonorgestrel is its . It is also known as d-norgestrel, d(–)-norgestrel, or -norgestrel, as well as by its developmental code names WY-5104 (Wyeth) and SH-90999 (Schering AG).

Stereochemistry

Zuclopenthixol (brand names Cisordinol, Clopixol and others), also known as zuclopentixol, is a medication used to treat schizophrenia and other psychoses. It is classed, pharmacologically, as a typical antipsychotic. Chemically it is a thioxanthene. It is the cis-isomer of clopenthixol (Sordinol, Ciatyl). Clopenthixol was introduced in 1961, while zuclopenthixol was introduced in 1978. Zuclopenthixol is a D and D antagonist, α-adrenergic and 5-HT antagonist. While it is approved for use in Australia, Canada, Ireland, India, New Zealand, Singapore, South Africa and the UK it is not approved for use in the United States.

Stereochemistry

Plant viruses are viruses that affect plants. Like all other viruses, plant viruses are obligate intracellular parasites that do not have the molecular machinery to replicate without a host. Plant viruses can be pathogenic to vascular plants ("higher plants"). Most plant viruses are rod-shaped, with protein discs forming a tube surrounding the viral genome; isometric particles are another common structure. They rarely have an envelope. The great majority have an RNA genome, which is usually small and single stranded (ss), but some viruses have double-stranded (ds) RNA, ssDNA or dsDNA genomes. Although plant viruses are not as well understood as their animal counterparts, one plant virus has become very recognizable: tobacco mosaic virus (TMV), the first virus to be discovered. This and other viruses cause an estimated US$60 billion loss in crop yields worldwide each year. Plant viruses are grouped into 73 genera and 49 families. However, these figures relate only to cultivated plants, which represent only a tiny fraction of the total number of plant species. Viruses in wild plants have not been well-studied, but the interactions between wild plants and their viruses often do not appear to cause disease in the host plants. To transmit from one plant to another and from one plant cell to another, plant viruses must use strategies that are usually different from animal viruses. Most plants do not move, and so plant-to-plant transmission usually involves vectors (such as insects). Plant cells are surrounded by solid cell walls, therefore transport through plasmodesmata is the preferred path for virions to move between plant cells. Plants have specialized mechanisms for transporting mRNAs through plasmodesmata, and these mechanisms are thought to be used by RNA viruses to spread from one cell to another. Plant defenses against viral infection include, among other measures, the use of siRNA in response to dsRNA. Most plant viruses encode a protein to suppress this response. Plants also reduce transport through plasmodesmata in response to injury.

Biochemistry

A Woods lamp is a diagnostic tool used in dermatology by which ultraviolet light is shone (at a wavelength of approximately 365 nanometers) onto the skin of the patient; a technician then observes any subsequent fluorescence. For example, porphyrins—associated with some skin diseases—will fluoresce pink. Though the technique for producing a source of ultraviolet light was devised by Robert Williams Wood in 1903 using "Woods glass", it was in 1925 that the technique was used in dermatology by Margarot and Deveze for the detection of fungal infection of hair. It has many uses, both in distinguishing fluorescent conditions from other conditions and in locating the precise boundaries of the condition.

Photochemistry

Krefts dichromaticity index (DI) is a measure for quantification of dichromatism. It is defined as the difference in hue angle (Δh) between the color of the sample at the dilution, where the chroma (color saturation) is maximal, and the color of four times more diluted (or thinner) and four times more concentrated (or thicker) sample. The two hue angle differences are called the dichromaticity index towards lighter (Krefts DI) and dichromaticity index towards darker (Krefts DI) respectively. Krefts dichromaticity indexes DI and DI for pumpkin seed oil, which is one of the most dichromatic substances, are −9 and −44, respectively. This means, that pumpkin seed oil changes its color from green-yellow to orange-red (for 44 degrees in Lab color space) when the thickness of the observed layer is increased from cca 0.5 mm to 2 mm; and it changes slightly towards green (for 9 degrees) if its thickness is reduced for four-fold. The color of pumpkin oil at increasing thickness or concentration presented in CIELAB colorspace diagram. Straight lines are vectors showing hue (angle) and chroma (length) of the color at maximal chroma (toward the square mark), and the colors of four-fold less or more diluted or thick pumpkin oil (DI and DI). Note that DI is −44.1 degrees and DI corresponds to −8.97 degrees. Dichromaticity (DI and DI) of selected substances, calculated from their VIS absorption spectra by the computer algorithm “Dichromaticity index calculator”: Maximal chroma: chroma at concentration (thickness) where the color of the substance has maximal chroma (saturation). Angle at maximal chroma: the hue, which is represented by the angle of the vector to the color with maximal chroma in the CIELAB colorspace diagram.

Physical Chemistry

As only particles that exhibit non-linear velocity experience the SCODA concentrating force, small charged particles that respond linearly to electrophoretic fields are not concentrated. These particles instead of spiraling towards the center of the SCODA gel orbit at a constant radius. If a weak DC field is superimposed on the SCODA rotating fields these particles will be "washed" off from the SCODA gel resulting in highly pure DNA remaining in the gel center.

Biochemistry

Ellipsometry has been used widely for measuring protein adsorption kinetics as well as the structure of the adsorbed protein layer. It is an optical technique that measures the change of the polarization of light after reflection from a surface. This technique requires planar, reflecting surfaces, preferably quartz, silicon or silica, and a strong change in refractive index upon protein adsorption.

Biochemistry

# The slope ds/dT of the saturated vapour line in T–s diagram (see Chapter Classification of pure (single-component) working fluids) should be nearly zero, but never positive in the applied pressure ratio of the compressor. This prevents significant moisture (liquid droplet) formation or excessive superheat occurring during the compression. Compressors are very sensitive to liquid droplets. # The saturation pressure at the temperature of evaporation should not be lower than atmospheric pressure. This mainly corresponds to open-type compressors. # The saturation pressure at the temperature of condensation should not be high. # The ratio of condensation and evaporation pressures should be low.

Physical Chemistry

Glutamate levels are observed to be elevated during mania. Lithium is thought to provide long-term mood stabilization and have anti-manic properties by modulating glutamate levels. It is proposed that lithium competes with magnesium for binding to NMDA glutamate receptor, increasing the availability of glutamate in post-synaptic neurons, leading to a homeostatic increase in glutamate re-uptake which reduces glutamatergic transmission. The NMDA receptor is also affected by other neurotransmitters such as serotonin and dopamine. Effects observed appear exclusive to lithium and have not been observed by other monovalent ions such as rubidium and caesium.

Biochemistry

Gels are used as stationary phase for GPC. The pore size of a gel must be carefully controlled in order to be able to apply the gel to a given separation. Other desirable properties of the gel forming agent are the absence of ionizing groups and, in a given solvent, low affinity for the substances to be separated. Commercial gels like PLgel & Styragel (cross-linked polystyrene-divinylbenzene), LH-20 (hydroxypropylated Sephadex), Bio-Gel (cross-linked polyacrylamide), HW-20 & HW-40 (hydroxylated methacrylic polymer), and agarose gel are often used based on different separation requirements.

Analytical Chemistry

A thermocouple can be used as a vacuum gauge over the range of approximately 0.001 to 1 torr absolute pressure. In this pressure range, the mean free path of the gas is comparable to the dimensions of the vacuum chamber, and the flow regime is neither purely viscous nor purely molecular. In this configuration, the thermocouple junction is attached to the centre of a short heating wire, which is usually energised by a constant current of about 5 mA, and the heat is removed at a rate related to the thermal conductivity of the gas. The temperature detected at the thermocouple junction depends on the thermal conductivity of the surrounding gas, which depends on the pressure of the gas. The potential difference measured by a thermocouple is proportional to the square of pressure over the low- to medium-vacuum range. At higher (viscous flow) and lower (molecular flow) pressures, the thermal conductivity of air or any other gas is essentially independent of pressure. The thermocouple was first used as a vacuum gauge by Voege in 1906. The mathematical model for the thermocouple as a vacuum gauge is quite complicated, as explained in detail by Van Atta, but can be simplified to: where P is the gas pressure, B is a constant that depends on the thermocouple temperature, the gas composition and the vacuum-chamber geometry, V is the thermocouple voltage at zero pressure (absolute), and V is the voltage indicated by the thermocouple. The alternative is the Pirani gauge, which operates in a similar way, over approximately the same pressure range, but is only a 2-terminal device, sensing the change in resistance with temperature of a thin electrically heated wire, rather than using a thermocouple.

Metallurgy

Phenylalanine and tyrosine are the precursors used in the phenylpropanoids biosynthesis. The phenylpropanoids are then used to produce the flavonoids, coumarins, tannins and lignin. The first enzyme involved is phenylalanine ammonia-lyase (PAL) that converts -phenylalanine to trans-cinnamic acid and ammonia.

Biochemistry

To help mitigate inbreeding depression for two endangered species, the Black-footed ferret(Mustela nigripes), Revive & Restore facilitates on-going efforts to clone individuals from historic cell lines stored at the San Diego Zoo Wildlife Alliance Frozen Zoo. The program seeks to restore genetic variation lost from the living gene pool. On December 10, 2020, the world's first cloned black-footed ferret was born. This ferret, named Elizabeth Ann, marked the first time a U.S. endangered species was successfully cloned. The cells of two 1980s wild-caught black-footed ferrets that never bred in captivity were preserved in the San Diego Wildlife Alliance Frozen Zoo. One of them was cloned to increase genetic diversity in this species in December 2020. More clones of both are planned. They will initially be bred separately from the non-cloned population.

Biochemistry

Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA. A codon is a series of three nucleotides (a triplet) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation (stop codons). There are 64 different codons (61 codons encoding for amino acids and 3 stop codons) but only 20 different translated amino acids. The overabundance in the number of codons allows many amino acids to be encoded by more than one codon. Because of such redundancy it is said that the genetic code is degenerate. The genetic codes of different organisms are often biased towards using one of the several codons that encode the same amino acid over the others—that is, a greater frequency of one will be found than expected by chance. How such biases arise is a much debated area of molecular evolution. Codon usage tables detailing genomic codon usage bias for organisms in GenBank and RefSeq can be found in the [https://hive.biochemistry.gwu.edu/cuts/about HIVE-Codon Usage Tables (HIVE-CUTs) project], which contains two distinct databases, CoCoPUTs and TissueCoCoPUTs. Together, these two databases provide comprehensive, up-to-date codon, codon pair and dinucleotide usage statistics for all organisms with available sequence information and 52 human tissues, respectively. It is generally acknowledged that codon biases reflect the contributions of 3 main factors, GC-biased gene conversion that favors GC-ending codons in diploid organisms, arrival biases reflecting mutational preferences (typically favoring AT-ending codons), and natural selection for codons that are favorable in regard to translation. Optimal codons in fast-growing microorganisms, like Escherichia coli or Saccharomyces cerevisiae (bakers yeast), reflect the composition of their respective genomic transfer RNA (tRNA) pool. It is thought that optimal codons help to achieve faster translation rates and high accuracy. As a result of these factors, translational selection is expected to be stronger in highly expressed genes, as is indeed the case for the above-mentioned organisms. In other organisms that do not show high growing rates or that present small genomes, codon usage optimization is normally absent, and codon preferences are determined by the characteristic mutational biases seen in that particular genome. Examples of this are Homo sapiens (human) and Helicobacter pylori. Organisms that show an intermediate level of codon usage optimization include Drosophila melanogaster (fruit fly), Caenorhabditis elegans (nematode worm), Strongylocentrotus purpuratus (sea urchin), and Arabidopsis thaliana' (thale cress). Several viral families (herpesvirus, lentivirus, papillomavirus, polyomavirus, adenovirus, and parvovirus) are known to encode structural proteins that display heavily skewed codon usage compared to the host cell. The suggestion has been made that these codon biases play a role in the temporal regulation of their late proteins. The nature of the codon usage-tRNA optimization has been fiercely debated. It is not clear whether codon usage drives tRNA evolution or vice versa. At least one mathematical model has been developed where both codon usage and tRNA expression co-evolve in feedback fashion (i.e., codons already present in high frequencies drive up the expression of their corresponding tRNAs, and tRNAs normally expressed at high levels drive up the frequency of their corresponding codons). However, this model does not seem to yet have experimental confirmation. Another problem is that the evolution of tRNA genes has been a very inactive area of research.

Biochemistry

*Nuffield Commonwealth Fellow 1971–1972 (Cambridge) *Fulbright Senior Scholar (California Institute of Technology, 1977, and Harvard University, 1986) *H.G. Smith Memorial Medal 1981 (RACI) *Member of the Australian Academy of Science 1983 *Flintoff Medal and Prize (RSC) 1990 *Fellow of the Royal Society of London 1990 *Hon. Fellow of the Royal Society of New Zealand 1991 (FRSNZ Hon) *Made a Companion of the Order of Australia "for eminent service to science through pioneering contributions to organic chemistry in the field of plant growth hormones, to higher education as an academic, researcher and author, and to national and international scientific societies".

Organic Chemistry

Between 1840 and 1843, Joule carefully studied the heat produced by an electric current. From this study, he developed Joules laws of heating, the first of which is commonly referred to as the Joule effect. Joules first law expresses the relationship between heat generated in a conductor and current flow, resistance, and time.

Physical Chemistry

According to the US Energy Information Administration (EIA) estimate for 2017, the world consumes 98.8 million barrels of oil each day. This table orders the amount of petroleum consumed in 2011 in thousand barrels (1000 bbl) per day and in thousand cubic metres (1000 m) per day: Source: [http://www.eia.gov/cfapps/ipdbproject/IEDIndex3.cfm?tid=5&pid=5&aid=2 US Energy Information Administration] Population Data: peak production of oil already passed in this state</small> This country is not a major oil producer</small>

Physical Chemistry

Another widely cited characteristic of gene regulatory network is their abundance of certain repetitive sub-networks known as network motifs. Network motifs can be regarded as repetitive topological patterns when dividing a big network into small blocks. Previous analysis found several types of motifs that appeared more often in gene regulatory networks than in randomly generated networks. As an example, one such motif is called feed-forward loops, which consist three nodes. This motif is the most abundant among all possible motifs made up of three nodes, as is shown in the gene regulatory networks of fly, nematode, and human. The enriched motifs have been proposed to follow convergent evolution, suggesting they are "optimal designs" for certain regulatory purposes. For example, modeling shows that feed-forward loops are able to coordinate the change in node A (in terms of concentration and activity) and the expression dynamics of node C, creating different input-output behaviors. The galactose utilization system of E. coli contains a feed-forward loop which accelerates the activation of galactose utilization operon galETK, potentially facilitating the metabolic transition to galactose when glucose is depleted. The feed-forward loop in the arabinose utilization systems of E.coli delays the activation of arabinose catabolism operon and transporters, potentially avoiding unnecessary metabolic transition due to temporary fluctuations in upstream signaling pathways. Similarly in the Wnt signaling pathway of Xenopus, the feed-forward loop acts as a fold-change detector that responses to the fold change, rather than the absolute change, in the level of β-catenin, potentially increasing the resistance to fluctuations in β-catenin levels. Following the convergent evolution hypothesis, the enrichment of feed-forward loops would be an adaptation for fast response and noise resistance. A recent research found that yeast grown in an environment of constant glucose developed mutations in glucose signaling pathways and growth regulation pathway, suggesting regulatory components responding to environmental changes are dispensable under constant environment. On the other hand, some researchers hypothesize that the enrichment of network motifs is non-adaptive. In other words, gene regulatory networks can evolve to a similar structure without the specific selection on the proposed input-output behavior. Support for this hypothesis often comes from computational simulations. For example, fluctuations in the abundance of feed-forward loops in a model that simulates the evolution of gene regulatory networks by randomly rewiring nodes may suggest that the enrichment of feed-forward loops is a side-effect of evolution. In another model of gene regulator networks evolution, the ratio of the frequencies of gene duplication and gene deletion show great influence on network topology: certain ratios lead to the enrichment of feed-forward loops and create networks that show features of hierarchical scale free networks. De novo evolution of coherent type 1 feed-forward loops has been demonstrated computationally in response to selection for their hypothesized function of filtering out a short spurious signal, supporting adaptive evolution, but for non-idealized noise, a dynamics-based system of feed-forward regulation with different topology was instead favored.

Biochemistry

5-Methylcytosine and 5-hydroxymethylcytosine both read as a C in bisulfite sequencing. Oxidative bisulfite sequencing is a method to discriminate between 5-methylcytosine and 5-hydroxymethylcytosine at single base resolution. The method employs a specific (Tet-assisted) chemical oxidation of 5-hydroxymethylcytosine to 5-formylcytosine, which subsequently converts to uracil during bisulfite treatment. The only base that then reads as a C is 5‑methylcytosine, giving a map of the true methylation status in the DNA sample. Levels of 5‑hydroxymethylcytosine can also be quantified by measuring the difference between bisulfite and oxidative bisulfite sequencing.

Biochemistry

The 4th analytical group of cations includes ions that precipitate as sulfides at pH 9. The reagent used is ammonium sulfide or NaS 0.1 M added to the ammonia/ammonium chloride solution used to detect group 3 cations. It includes: Zn, Ni, Co, and Mn. Zinc will form a white precipitate, nickel and cobalt a black precipitate and manganese a brick/flesh colored precipitate. Dimethylglyoxime can be used to confirm nickel presence, while ammonium thiocyanate in ether will turn blue in the presence of cobalt. This group is sometimes denoted as IIIB since groups III and IV are tested for at the same time, with the addition of sulfide being the only difference.

Analytical Chemistry

No interaction studies have been conducted except with digoxin, which slightly decreases imidapril levels, possibly because it reduces its absorption from the gut. Other potential interactions are not well studied: Rifampicin reduces the activation of imidapril to its active metabolite imidaprilat. Like other ACE inhibitors, imidapril increases potassium levels in the blood and can therefore cause hyperkalaemia, especially when combined with potassium-sparing diuretics or potassium substitution. Other diuretics, vasodilators, tricyclic antidepressants and antipsychotics can add to the antihypertensive effect of imidapril. Lithium can reach toxic levels when combined with imidapril. The effect of antidiabetic drugs can be increased, potentially causing hypoglycaemia (low blood glucose levels).

Stereochemistry

In biochemistry there are many instances of acyl groups, in all major categories of biochemical molecules. Acyl-CoAs are acyl derivatives formed via fatty acid metabolism. Acetyl-CoA, the most common derivative, serves as an acyl donor in many biosynthetic transformations. Such acyl compounds are thioesters. Names of acyl groups of amino acids are formed by replacing the -ine suffix with -yl. For example, the acyl group of glycine is glycyl, and of lysine is lysyl. Names of acyl groups of ribonucleoside monophosphates such as AMP (5′-adenylic acid), GMP (5′-guanylic acid), CMP (5′-cytidylic acid), and UMP (5′-uridylic acid) are adenylyl, guanylyl, cytidylyl, and uridylyl respectively. In phospholipids, the acyl group of phosphatidic acid is called phosphatidyl-. Finally, many saccharides are acylated.

Organic Chemistry

The Robinson synthesis is an example of a so-called relay synthesis. As many of the chemical intermediates (all steroids) were already known and available from natural resources all that was needed for a formal synthesis was proof that these intermediates could be linked to each other via chemical synthesis. Starting point for the Robinson synthesis was 1,6-dihydroxynaphthalene 1 that was converted in about 20 steps into the then already known androsterone 4. Ruzicka had already demonstrated in 1938 that androsterone could be converted into androstenedione 5 and Robinson demonstrated its conversion to dehydroepiandrosterone 6 (note the epimerized hydroxyl group) also already a known compound. Conversion of 6 to pregnenolone 7 and then to allopregnanolone 8 allowed the addition of the tail group as the acetate in 9 and then conversion to cholestanol 10. The conversion of cholestanol to cholesterol was already demonstrated by oxidation of the ketone, bromination to the bromoketone and elimination to the enone. The conversion of cholestenone into cholesterol by the method of Dauben and Eastham (1950) consisted of reduction of the enol acetate (lithium aluminium hydride) and fractionation with digitonin for the isolation of the correct isomer.

Organic Chemistry

The phosphorus cycle is the biogeochemical cycle that involves the movement of phosphorus through the lithosphere, hydrosphere, and biosphere. Unlike many other biogeochemical cycles, the atmosphere does not play a significant role in the movement of phosphorus, because phosphorus and phosphorus-based materials do not enter the gaseous phase readily. The production of phosphine gas occurs in isolated and specific conditions. Therefore, the phosphorus cycle is primarily examined studying the movement of orthophosphate (PO), the form of phosphorus that is most commonly seen in the environment, through terrestrial and aquatic ecosystems. Living organisms require phosphorus, a vital component of DNA, RNA, ATP, etc., for their proper functioning. Plants assimilate phosphorus as phosphate and incorporate it into organic compounds. In animals, phosphorus is a key component of bones, teeth, etc. On the land, phosphorus gradually becomes less available to plants over thousands of years, since it is slowly lost in runoff. Low concentration of phosphorus in soils reduces plant growth and slows soil microbial growth, as shown in studies of soil microbial biomass. Soil microorganisms act as both sinks and sources of available phosphorus in the biogeochemical cycle. Furthermore, phosphorus tends to be a limiting nutrient in aquatic ecosystems. However, as phosphorus enters aquatic ecosystems, it has the possibility to lead to over-production in the form of eutrophication, which can happen in both freshwater and saltwater environments. Short-term transformation of phosphorus is chemical, biological, or microbiological. In the long-term global cycle, however, the major transfer is driven by tectonic movement over geologic time. Humans have caused major changes to the global phosphorus cycle primarily through the mining and subsequent shipping of phosphorus minerals for use in fertilizer and industrial products. Some phosphorus is also lost as effluent through the shipping process as well.

Geochemistry

Fatty acid metabolism consists of various metabolic processes involving or closely related to fatty acids, a family of molecules classified within the lipid macronutrient category. These processes can mainly be divided into (1) catabolic processes that generate energy and (2) anabolic processes where they serve as building blocks for other compounds. In catabolism, fatty acids are metabolized to produce energy, mainly in the form of adenosine triphosphate (ATP). When compared to other macronutrient classes (carbohydrates and protein), fatty acids yield the most ATP on an energy per gram basis, when they are completely oxidized to CO and water by beta oxidation and the citric acid cycle. Fatty acids (mainly in the form of triglycerides) are therefore the foremost storage form of fuel in most animals, and to a lesser extent in plants. In anabolism, intact fatty acids are important precursors to triglycerides, phospholipids, second messengers, hormones and ketone bodies. For example, phospholipids form the phospholipid bilayers out of which all the membranes of the cell are constructed from fatty acids. Phospholipids comprise the plasma membrane and other membranes that enclose all the organelles within the cells, such as the nucleus, the mitochondria, endoplasmic reticulum, and the Golgi apparatus. In another type of anabolism, fatty acids are modified to form other compounds such as second messengers and local hormones. The prostaglandins made from arachidonic acid stored in the cell membrane are probably the best-known of these local hormones.

Biochemistry

Dialkyl (E)-enones have been most commonly epoxidized using either lanthanide/BINOL systems or a magnesium tartrate catalyst. For alkyl aryl (E)-enones, both polypeptides and lanthanide/BINOL catalysts give good yields and enantioselectivities. The most common polypeptide employed is poly-L-leucine. Aryl alkyl (E)-enones have been epoxidized with high enantioselectivity using stoichiometric zinc peroxide systems. Polyleucine may be used with these substrates as well; when an existing stereocenter in the substrate biases the sense of selectivity of the epoxidation, polyleucine is able to overcome this bias. Phase-transfer catalysis has been applied successfully to epoxidations of diaryl (E)-enones (chalcones). Lanthanide/BINOL is effective for this class of substrates as well. (Z)-Enones are difficult to epoxidize without intermediate bond rotation to afford trans-epoxides. Lanthanide catalysts do effectively prevent bond rotation, however, and provide access to cis epoxide products. With the lone exception of methylidene tetralone substrates, no general methods are available for the asymmetric nucleophilic epoxidation of trisubstituted double bonds.

Organic Chemistry

Phosphinites are prepared by alcoholysis of organophosphinous chlorides. For example, treatment of chlorodiphenylphosphine with methanol and base gives methyl diphenylphosphinite: :ClPPh + CHOH → CHOPPh + HCl Although they are esters of phosphinous acids (RPOH), phosphinites are not made via such intermediates.

Organic Chemistry

A suitable pH indicator must be chosen in order to detect the end point of the titration. The colour change or other effect should occur close to the equivalence point of the reaction so that the experimenter can accurately determine when that point is reached. The pH of the equivalence point can be estimated using the following rules: * A strong acid will react with a strong base to form a neutral (pH = 7) solution. * A strong acid will react with a weak base to form an acidic (pH < 7) solution. * A weak acid will react with a strong base to form a basic (pH > 7) solution. These indicators are essential tools in chemistry and biology, aiding in the determination of a solution's acidity or alkalinity through the observation of colour transitions. The table below serves as a reference guide for these indicator choices, offering insights into the pH ranges and colour transformations associated with specific indicators: Phenolphthalein is widely recognized as one of the most commonly used acid-base indicators in chemistry. Its popularity is because of its effectiveness in a broad pH range and its distinct colour transitions. Its sharp and easily detectable colour changes makes phenolphthalein a valuable tool for determining the endpoint of acid-base titrations, as a precise pH change signifies the completion of the reaction. When a weak acid reacts with a weak base, the equivalence point solution will be basic if the base is stronger and acidic if the acid is stronger. If both are of equal strength, then the equivalence pH will be neutral. However, weak acids are not often titrated against weak bases because the colour change shown with the indicator is often quick, and therefore very difficult for the observer to see the change of colour. The point at which the indicator changes colour is called the endpoint. A suitable indicator should be chosen, preferably one that will experience a change in colour (an endpoint) close to the equivalence point of the reaction. In addition to the wide variety of indicator solutions, pH papers, crafted from paper or plastic infused with combinations of these indicators, serve as a practical alternative. The pH of a solution can be estimated by immersing a strip of pH paper into it and matching the observed colour to the reference standards provided on the container.

Analytical Chemistry

The Journal of Organic Chemistry, colloquially known as JOC, is a peer-reviewed scientific journal for original contributions of fundamental research in all branches of theory and practice in organic and bioorganic chemistry. It is published by the publishing arm of the American Chemical Society, with 24 issues per year. According to the Journal Citation Reports, the journal had a 2017 impact factor of 4.805 and it is the journal that received the most cites (100,091 in 2017) in the field of organic chemistry. According to Web of Knowledge (and as December 2012), eleven papers from the journal have received more than 1,000 citations, with the most cited paper having received 7,967 citations. The current editor-in-chief is Scott J. Miller from Yale University.

Organic Chemistry

To 6.25 g (50 mmol) of 4,4-dimethyl-2-cyclohexen-1-one and 0.5 g (5.6 mmol) of cuprous cyanide in 400 mL of diethyl ether at –23° under argon was added 100 mL (~0.75 M in diethyl ether) of 5-trimethylsilyl-4-pentynylmagnesium iodide during 4 hours. Methyl chloroformate (8 mL, 100 mmol) was added and stirring continued for 1 hour at –23° and 0.5 hour at room temperature. Hydrochloric acid (100 mL, 2.0 M) then was added and the organic phase separated and dried with magnesium sulfate. The solvent was removed and the residue chromatographed on silica gel using 5% diethyl ether–petroleum ether to give methyl 3,3-dimethyl-6-oxo-2-[5-(trimethylsilyl)-4-pentynyl]cyclohexanecarboxylate, 9.66 g (60%). IR 2000, 2140, 1755, 1715, 1660, 1615, 1440, 1280, 1250, 1225, 1205, and 845 cm–1; 1H NMR ( CDCl) δ 0.13 (s, 9H), 0.93 (s, 3H), 1.02 (s, 3H), 1.2–2.3 (m, 11H), 3.74 (s, 3H). Anal. Calc. for CHOSi: C, 67.05; H, 9.4. Found: C, 67.1; H, 9.65.

Organic Chemistry

Activated Ras then activates the protein kinase activity of a RAF kinase. The RAF kinase phosphorylates and activates a MAPK/ERK Kinase (MEK1 or MEK2). The MEK phosphorylates and activates a mitogen-activated protein kinase (MAPK). RAF and MAPK/ERK are both serine/threonine-specific protein kinases. MEK is a serine/tyrosine/threonine kinase. In a technical sense, RAF, MEK, and MAPK are all mitogen-activated kinases, as is MNK (see below). MAPKs were originally called "extracellular signal-regulated kinases" (ERKs) and "microtubule associated protein kinases" (MAPKs). One of the first proteins known to be phosphorylated by ERK was a microtubule-associated protein (MAP). As discussed below, many additional targets for phosphorylation by MAPK were later found, and the protein was renamed "mitogen-activated protein kinase" (MAPK). The series of kinases from RAF to MEK to MAPK is an example of a protein kinase cascade. Such series of kinases provide opportunities for feedback regulation and signal amplification.

Biochemistry

Several routes exist for the synthesis of Dextromethorphan. Even though many of the syntheses have been known since the middle of the 20th century, researchers are still working today to further develop the synthesis of Dextromethorphan and, for example, to make it more environmentally friendly. This includes the synthesis by means of ionic liquids.

Stereochemistry

The term surface enhanced Raman spectroscopy implies that it provides the same information that traditional Raman spectroscopy does, simply with a greatly enhanced signal. While the spectra of most SERS experiments are similar to the non-surface enhanced spectra, there are often differences in the number of modes present. Additional modes not found in the traditional Raman spectrum can be present in the SERS spectrum, while other modes can disappear. The modes observed in any spectroscopic experiment are dictated by the symmetry of the molecules and are usually summarized by Selection rules. When molecules are adsorbed to a surface, the symmetry of the system can change, slightly modifying the symmetry of the molecule, which can lead to differences in mode selection. One common way in which selection rules are modified arises from the fact that many molecules that have a center of symmetry lose that feature when adsorbed to a surface. The loss of a center of symmetry eliminates the requirements of the mutual exclusion rule, which dictates that modes can only be either Raman or infrared active. Thus modes that would normally appear only in the infrared spectrum of the free molecule can appear in the SERS spectrum. A molecule's symmetry can be changed in different ways depending on the orientation in which the molecule is attached to the surface. In some experiments, it is possible to determine the orientation of adsorption to the surface from the SERS spectrum, as different modes will be present depending on how the symmetry is modified.

Physical Chemistry

The EN 13432 industrial standard must be met in order to claim that a plastic product is compostable in the European marketplace. In summary, it requires multiple tests and sets pass/fail criteria, including disintegration (physical and visual break down) of the finished item within 12 weeks, biodegradation (conversion of organic carbon into ) of polymeric ingredients within 180 days, plant toxicity and heavy metals. The ASTM 6400 standard is the regulatory framework for the United States and has similar requirements. Many starch-based plastics, PLA-based plastics and certain aliphatic-aromatic co-polyester compounds, such as succinates and adipates, have obtained these certificates. Additive-based bioplastics sold as photodegradable or Oxo Biodegradable do not comply with these standards in their current form.

Physical Chemistry

The Sakaguchi test is a chemical test used to detect presence of arginine in proteins. It is named after the Japanese food scientist and organic chemist, Shoyo Sakaguchi (1900&ndash;1995) who described the test in 1925. The Sakaguchi reagent used in the test consists of 1-Naphthol and a drop of sodium hypobromite. The guanidino (–C group in arginine reacts with the Sakaguchi reagent to form a red-coloured complex.

Analytical Chemistry

Dawn Yvonne Sumner is an American geologist, planetary scientist, and astrobiologist. She is a professor at the University of California, Davis. Sumner's research includes evaluating microbial communities in Antarctic lakes, exploration of Mars via the Curiosity rover, and characterization of microbial communities in the lab and from ancient geologic samples. She is an investigator on the NASA Mars Science Laboratory (MSL) and was Chair of the UC Davis Department of Earth & Planetary Sciences from 2014 to 2016. She is Fellow of the Geological Society of America.

Geochemistry

Surprisal analysis was formulated at the Hebrew University of Jerusalem as a joint effort between Raphael David Levine, Richard Barry Bernstein and Avinoam Ben-Shaul in 1972. Levine and colleagues had recognized a need to better understand the dynamics of non-equilibrium systems, particularly of small systems, that are not seemingly applicable to thermodynamic reasoning. Alhassid and Levine first applied surprisal analysis in nuclear physics, to characterize the distribution of products in heavy ion reactions. Since its formulation, surprisal analysis has become a critical tool for the analysis of reaction dynamics and is an official IUPAC term.*

Physical Chemistry

Myogenin has been shown to interact with: * MDFI, * POLR2C, * Serum response factor * Sp1 transcription factor, and * TCF3.

Biochemistry

The dissolved copper (Cu) ions are removed from the solution by ligand exchange solvent extraction, which leaves other ions in the solution. The copper is removed by bonding to a ligand, which is a large molecule consisting of a number of smaller groups, each possessing a lone electron pair. The ligand-copper complex is extracted from the solution using an organic solvent such as kerosene: :Cu + 2LH(organic) &rarr; CuL(organic) + 2H The ligand donates electrons to the copper, producing a complex - a central metal atom (copper) bonded to the ligand. Because this complex has no charge, it is no longer attracted to polar water molecules and dissolves in the kerosene, which is then easily separated from the solution. Because the initial reaction is reversible, it is determined by pH. Adding concentrated acid reverses the equation, and the copper ions go back into an aqueous solution. Then the copper is passed through an electro-winning process to increase its purity: An electric current is passed through the resulting solution of copper ions. Because copper ions have a 2+ charge, they are attracted to the negative cathodes and collect there. The copper can also be concentrated and separated by displacing the copper with Fe from scrap iron: :Cu + Fe &rarr; Cu + Fe The electrons lost by the iron are taken up by the copper. Copper is the oxidising agent (it accepts electrons), and iron is the reducing agent (it loses electrons). Traces of precious metals such as gold may be left in the original solution. Treating the mixture with sodium cyanide in the presence of free oxygen dissolves the gold. The gold is removed from the solution by adsorbing (taking it up on the surface) to charcoal.

Metallurgy

There are other LISICON type solid electrolytes which make use of other elements to achieve higher ionic conductivities.  One such material has the chemical formula of LiGeVO, where the value of x is between 0 and 1. There are two compositions, LiGeVO and LiGeVO, which had ionic conductivities of 4*10 S/cm and 10 S/cm, an order of magnitude of improvement upon the base LISICON structure.  These materials show good thermal stability and are stable in contact with CO and ambient atmosphere, dealing with some problems extant with the original structure. There are materials with the chemical structure of LiSiPO.  This is a solid solution between LiSiO and LiPO.  This solid solution can be formed over the whole composition range at room temperature.  The highest ionic conductivity are achieved at compositions of LiSiPO and LiSiP, with conductivity on the order of 10 S/cm.  This results from the substitution of some Si for P in the lattice, resulting in the addition of interstitial Li-ions which diffuse much more easily.  The ionic conductivity is further improved with the doping of Cl to replace O in the lattice.  The compositions LiSiPCl and LiGePCl achieved ionic conductivities of 1.03 * 10 S/cm and 3.7*10 S/cm respectively.  This is theorized to be the due to the widening of the “bottlenecks” between interstitial points due to the Cl ions smaller size, and the weakening of the ionic bonding Li ions experienced due to chlorine's lower electronegativity. The conductivities are almost 100 times higher in thio-LISICONs, where oxygen is replaced by sulfur, i.e. the corresponding thiosilicates. The bonding between S and Li is weaker than that between O and Li, allowing for the Li in the sulfide structure to be far more normal than its oxide counterparts.  Ceramic thio-LISCON materials based on the chemical formula LiGePS are promising electrolyte materials, with ionic conductivities on the order of 10 S/m or 10 S/m.

Physical Chemistry

Industrially, the main methods for producing nitriles are ammoxidation and hydrocyanation. Both routes are green in the sense that they do not generate stoichiometric amounts of salts.

Organic Chemistry

The molality of a solution is defined as the amount of a constituent (in moles) divided by the mass of the solvent (not the mass of the solution): The SI unit for molality is mol/kg.

Analytical Chemistry

In May, a new method using an altered version of HIV as a lentivirus vector was reported in the treatment of 50 children with ADA-SCID obtaining positive results in 48 of them, this method is expected to be safer than retroviruses vectors commonly used in previous studies of SCID where the development of leukemia was usually observed and had already been used in 2019, but in a smaller group with X-SCID. In June a clinical trial on six patients affected with transthyretin amyloidosis reported a reduction the concentration of missfolded transthretin (TTR) protein in serum through CRISPR-based inactivation of the TTR gene in liver cells observing mean reductions of 52% and 87% among the lower and higher dose groups.This was done in vivo without taking cells out of the patient to edit them and reinfuse them later. In July results of a small gene therapy phase I study was published reporting observation of dopamine restoration on seven patients between 4 and 9 years old affected by aromatic L-amino acid decarboxylase deficiency (AADC deficiency).

Biochemistry

The structure of trityl persulfide has been determined by X-ray crystallography. The S-S bond length is 204 picometers and the C-S-S-H dihedral angle is 82°. These parameters are unexceptional. (CH)CSSH behaves as a source of sulfur, illustrated by its reaction with triphenylphosphine to give triphenylphosphine sulfide and triphenylmethanethiol: :(CH)CSSH + P(CH) → (CH)CSH + SP(CH)

Organic Chemistry

One path to the reciprocal lattice of an arbitrary collection of atoms comes from the idea of scattered waves in the Fraunhofer (long-distance or lens back-focal-plane) limit as a Huygens-style sum of amplitudes from all points of scattering (in this case from each individual atom). This sum is denoted by the complex amplitude in the equation below, because it is also the Fourier transform (as a function of spatial frequency or reciprocal distance) of an effective scattering potential in direct space: Here g = q/(2) is the scattering vector q in crystallographer units, N is the number of atoms, f[g] is the atomic scattering factor for atom j and scattering vector g, while r is the vector position of atom j. The Fourier phase depends on one's choice of coordinate origin. For the special case of an infinite periodic crystal, the scattered amplitude F = M F from M unit cells (as in the cases above) turns out to be non-zero only for integer values of , where when there are j = 1,m atoms inside the unit cell whose fractional lattice indices are respectively {u, v, w}. To consider effects due to finite crystal size, of course, a shape convolution for each point or the equation above for a finite lattice must be used instead. Whether the array of atoms is finite or infinite, one can also imagine an "intensity reciprocal lattice" I[g], which relates to the amplitude lattice F via the usual relation I = FF where F is the complex conjugate of F. Since Fourier transformation is reversible, of course, this act of conversion to intensity tosses out "all except 2nd moment" (i.e. the phase) information. For the case of an arbitrary collection of atoms, the intensity reciprocal lattice is therefore: Here r is the vector separation between atom j and atom k. One can also use this to predict the effect of nano-crystallite shape, and subtle changes in beam orientation, on detected diffraction peaks even if in some directions the cluster is only one atom thick. On the down side, scattering calculations using the reciprocal lattice basically consider an incident plane wave. Thus after a first look at reciprocal lattice (kinematic scattering) effects, beam broadening and multiple scattering (i.e. dynamical) effects may be important to consider as well.

Analytical Chemistry

Paredes and Quiles concluded that chloroplasts under stress from water deficit rely on processes like the opening of stomata to disperse excess heat accumulated via metabolic processes within plant cells. These metabolic processes are responsible for chemical energy synthesis that can be achieved via chlororespiratory ETCs when a reduction in photosynthesis activity is evident.

Biochemistry

Chamber construction, testing procedure and testing parameters are standardized under national and international standards, such as ASTM B 117 and ISO 9227. These standards describe the necessary information to carry out this test; testing parameters such as temperature, air pressure of the sprayed solution, preparation of the spraying solution, concentration, pH, etc. Daily checking of testing parameters is necessary to show compliance with the standards, so records shall be maintained accordingly. ASTM B117 and ISO 9227 are widely used as reference standards. Testing cabinets are manufactured according to the specified requirements here. However, these testing standards neither provide information of testing periods for the coatings to be evaluated, nor the appearance of corrosion products in form of salts. Requirements are agreed between customer and manufacturer. In the automotive industry requirements are specified under material specifications. Different coatings have different behavior in salt spray test and consequently, test duration will differ from one type of coating to another. For example, a typical electroplated zinc and yellow passivated steel part lasts 96 hours in salt spray test without white rust. Electroplated zinc-nickel steel parts can last more than 720 hours in NSS test without red rust (or 48 hours in CASS test without red rust) Requirements are established in test duration (hours) and coatings shall comply with minimum testing periods. Artificial seawater which is sometimes used for Salt Spray Testing can be found at ASTM International. The standard for Artificial Seawater is ASTM D1141-98 which is the standard practice for the preparation of substitute ocean water.

Metallurgy

Transcriptome analysis is the study of all the RNA transcripts that are produced by the genome of an organism. Linked-read sequencing has been used by researchers to assemble transcript isoforms and alternative splicing events. Information regarding alternative splicing events can provide insights into the regulation of gene expression in human transcriptome

Biochemistry

Oxidative stress is suspected to be important in neurodegenerative diseases including Lou Gehrigs disease (aka MND or ALS), Parkinsons disease, Alzheimers disease, Huntingtons disease, depression, and multiple sclerosis. It is also indicated in Neurodevelopmental conditions such as Autism Spectrum Disorder. Indirect evidence via monitoring biomarkers such as reactive oxygen species, and reactive nitrogen species production indicates oxidative damage may be involved in the pathogenesis of these diseases, while cumulative oxidative stress with disrupted mitochondrial respiration and mitochondrial damage are related to Alzheimers disease, Parkinsons disease, and other neurodegenerative diseases. Oxidative stress is thought to be linked to certain cardiovascular disease, since oxidation of LDL in the vascular endothelium is a precursor to plaque formation. Oxidative stress also plays a role in the ischemic cascade due to oxygen reperfusion injury following hypoxia. This cascade includes both strokes and heart attacks. Oxidative stress has also been implicated in chronic fatigue syndrome (ME/CFS). Oxidative stress also contributes to tissue injury following irradiation and hyperoxia, as well as in diabetes. In hematological cancers, such as leukemia, the impact of oxidative stress can be bilateral. Reactive oxygen species can disrupt the function of immune cells, promoting immune evasion of leukemic cells. On the other hand, high levels of oxidative stress can also be selectively toxic to cancer cells. Oxidative stress is likely to be involved in age-related development of cancer. The reactive species produced in oxidative stress can cause direct damage to the DNA and are therefore mutagenic, and it may also suppress apoptosis and promote proliferation, invasiveness and metastasis. Infection by Helicobacter pylori which increases the production of reactive oxygen and nitrogen species in human stomach is also thought to be important in the development of gastric cancer. Oxidative stress can cause DNA damage in neurons. In neuronal progenitor cells, DNA damage is associated with increased secretion of amyloid beta proteins Aβ40 and Aβ42. This association supports the existence of a causal relationship between oxidative DNA damage and Aβ accumulation and suggests that oxidative DNA damage may contribute to Alzheimer's disease (AD) pathology. AD is associated with an accumulation of DNA damage (double-strand breaks) in vulnerable neuronal and glial cell populations from early stages onward, and DNA double-strand breaks are increased in the hippocampus of AD brains compared to non-AD control brains.

Biochemistry

A diamond anvil cell (DAC) is a high-pressure device used in geology, engineering, and materials science experiments. It enables the compression of a small (sub-millimeter-sized) piece of material to extreme pressures, typically up to around 100–200 gigapascals, although it is possible to achieve pressures up to 770 gigapascals (7,700,000 bars or 7.7 million atmospheres). The device has been used to recreate the pressure existing deep inside planets to synthesize materials and phases not observed under normal ambient conditions. Notable examples include the non-molecular ice X, polymeric nitrogen and metallic phases of xenon, lonsdaleite, and potentially metallic hydrogen. A DAC consists of two opposing diamonds with a sample compressed between the polished culets (tips). Pressure may be monitored using a reference material whose behavior under pressure is known. Common pressure standards include ruby fluorescence, and various structurally simple metals, such as copper or platinum. The uniaxial pressure supplied by the DAC may be transformed into uniform hydrostatic pressure using a pressure-transmitting medium, such as argon, xenon, hydrogen, helium, paraffin oil or a mixture of methanol and ethanol. The pressure-transmitting medium is enclosed by a gasket and the two diamond anvils. The sample can be viewed through the diamonds and illuminated by X-rays and visible light. In this way, X-ray diffraction and fluorescence; optical absorption and photoluminescence; Mössbauer, Raman and Brillouin scattering; positron annihilation and other signals can be measured from materials under high pressure. Magnetic and microwave fields can be applied externally to the cell allowing nuclear magnetic resonance, electron paramagnetic resonance and other magnetic measurements. Attaching electrodes to the sample allows electrical and magnetoelectrical measurements as well as heating up the sample to a few thousand degrees. Much higher temperatures (up to 7000 K) can be achieved with laser-induced heating, and cooling down to millikelvins has been demonstrated.

Physical Chemistry

Methylene blue is a monoamine oxidase inhibitor (MAOI), and if infused intravenously at doses exceeding 5 mg/kg, may precipitate serious serotonin toxicity, serotonin syndrome, if combined with any selective serotonin reuptake inhibitors (SSRIs) or other serotonin reuptake inhibitor (e.g., duloxetine, sibutramine, venlafaxine, clomipramine, imipramine). It causes hemolytic anemia in carriers of the G6PD (favism) enzymatic deficiency.

Analytical Chemistry

In the first step, holo-retinol binding protein (holo-RBP; simply means RBP bound to retinol, i.e. the RBP-ROH complex) binds to the extracellular portion of STRA6. This facilitates the release of retinol through the transporter. ROH is then transferred to cellular retinol binding protein 1 (CRBP1), an intracellular acceptor of retinol that attaches to the CRBP Binding Loop (or CBL) on STRA6. This transport of ROH, in turn, activates JAK2, thereby phosphorylating STRA6 at the Y643 (tyrosine) residue. This phosphorylation enables the extension of the CBL further into the cell. Holo-CRBP-I, leaves the CBL and is replaced by apo-CRBP-I (unbound). Holo-CRBP-I will continue to the Endoplasmic Reticulum (ER) where lecithin retinol acyltransferase (LRAT) is bound. ROH is released to LRAT which will convert retinol into retinylesters. Following the release of holo-CRBP-I from intercellular STRA6, STAT5 is recruited to STRA6 phosphorylated Y643 region where it is then phosphorylated by JAK2. This phosphorylation activates STAT5 which then makes its way to the nucleus to induce expression of target genes including suppressor of cytokine signaling 3 (SOCS3), a strong inhibitor of insulin signaling.

Biochemistry

A rare-cutter enzyme is a restriction enzyme with a recognition sequence which occurs only rarely in a genome. An example is NotI, which cuts after the first GC of a 5-GCGGCCGC-3 sequence; restriction enzymes with seven and eight base pair recognition sequences are often also called rare-cutter enzymes (six bp recognition sequences are much more common). For example, rare-cutter enzymes with 7-nucleotide recognition sites cut once every 4 bp (16,384 bp), and those with 8-nucleotide recognition sites cut every 4 bp (65,536 bp) respectively. They are used in top-down mapping to cut a chromosome into chunks of these sizes on average.

Biochemistry

BUN is an indication of kidney health. The normal range is 2.1–7.1 mmol/L or 6–20 mg/dL. The main causes of an increase in BUN are: high-protein diet, decrease in glomerular filtration rate (GFR) (suggestive of kidney failure), decrease in blood volume (hypovolemia), congestive heart failure, gastrointestinal hemorrhage, fever, rapid cell destruction from infections, athletic activity, excessive muscle breakdown, and increased catabolism. Hypothyroidism can cause both decreased GFR and hypovolemia, but BUN-to-creatinine ratio has been found to be lowered in hypothyroidism and raised in hyperthyroidism. The main causes of a decrease in BUN are malnutrition (low-protein diet), severe liver disease, anabolic state, and syndrome of inappropriate antidiuretic hormone. Another rare cause of a decreased BUN is ornithine transcarbamylase deficiency, which is a genetic disorder inherited in an X-linked recessive pattern. OTC deficiency is also accompanied by hyperammonemia and high orotic acid levels.

Biochemistry

All bacterial luciferases are approximately 80 KDa heterodimers containing two subunits: α and β. The α subunit is responsible for light emission. The luxA and luxB genes encode for the α and β subunits, respectively. In most bioluminescent bacteria, the luxA and luxB genes are flanked upstream by luxC and luxD and downstream by luxE. The bioluminescent reaction is as follows: FMNH + O + R-CHO -> FMN + HO + R-COOH + Light (~ 495 nm) Molecular oxygen reacts with FMNH (reduced flavin mononucleotide) and a long-chain aldehyde to produce FMN (flavin mononucleotide), water and a corresponding fatty acid. The blue-green light emission of bioluminescence, such as that produced by Photobacterium phosphoreum and Vibro harveyi, results from this reaction. Because light emission involves expending six ATP molecules for each photon, it is an energetically expensive process. For this reason, light emission is not constitutively expressed in bioluminescent bacteria; it is expressed only when physiologically necessary.

Biochemistry

Organic azides engage in useful organic reactions. The terminal nitrogen is mildly nucleophilic. Generally, nucleophiles attack the azide at the terminal nitrogen N, while electrophiles react at the internal atom N. Azides easily extrude diatomic nitrogen, a tendency that is exploited in many reactions such as the Staudinger ligation or the Curtius rearrangement. Azides may be reduced to amines by hydrogenolysis or with a phosphine (e.g., triphenylphosphine) in the Staudinger reaction. This reaction allows azides to serve as protected -NH synthons, as illustrated by the synthesis of 1,1,1-tris(aminomethyl)ethane: In the azide alkyne Huisgen cycloaddition, organic azides react as 1,3-dipoles, reacting with alkynes to give substituted 1,2,3-triazoles. Some azide reactions are shown in the following scheme. Probably the most famous is the reaction with phosphines, which leads to iminophosphoranes 22; these can be hydrolysed into primary amines 23 (the Staudinger reaction), react with carbonyl compounds to give imines 24 (the aza-Wittig reaction), or undergo other transformations. Thermal decomposition of azides gives nitrenes, which participate in a variety of reactions; vinyl azides 19 decompose into 2H-azirines 20. Alkyl azides with low nitrogen-content ((nC + nO) / nN ≥ 3) are relatively stable and decompose only above ca. 175 °C. Direct photochemical decomposition of alkyl azides leads almost exclusively to imines (e.g. 25 and 26). It is proposed that the azide group is promoted to the singlet excited state and then undergoes concerted rearrangement without the intermediacy of nitrenes. The presence of triplet sensitisers, however, may change the reaction mechanism and result in the formation of triplet nitrenes. The latter were observed directly by ESR spectroscopy at −269 °C as well as inferred in some photolyses. Triplet methyl nitrene is 31 kJ/mol more stable than its singlet form, and thus is most likely the ground state. The (3+2)-cycloaddition of azides to double or triple bonds is one of the most utilised cycloadditions in organic chemistry and affords triazolines (e.g. 17) or triazoles, respectively. The uncatalysed reaction is a concerted pericyclic process, in which the configuration of the alkene component is transferred to the triazoline product. The Woodward–Hoffmann denomination is [π4s+π2s] and the reaction is symmetry-allowed. According to Sustmann, this is a Type II cycloaddition, which means the two HOMOs and the two LUMOs have comparable energies, and thus both electron-withdrawing and electron-donating substituents may lead to an increase in the reaction rate. The reaction is generally free from significant solvent effects because both the reactants and the transition state (TS) are non-polar. Another azide regular is tosyl azide here in reaction with norbornadiene in a nitrogen insertion reaction:

Organic Chemistry

In the Fajans method, named after Kazimierz Fajans, typically dichlorofluorescein is used as an indicator; the end-point is marked by the green suspension turning pink. Prior to the end-point of the titration, chloride ions remain in excess. They adsorb on the AgCl surface, imparting a negative charge to the particles. Past the equivalence point, excess silver(I) ions adsorb on the AgCl surface, imparting a positive charge. Anionic dyes such as dichlorofluorescein are attracted to the particles, and undergo a colour change upon adsorption, representing the end-point. Eosin (tetrabromofluorescein) is suitable for titrating against bromide, iodide, and thiocyanate anions, giving a sharper end-point than dichlorofluorescein. It is not suitable for titrating against chloride anions because it binds to AgCl more strongly than chloride does.

Analytical Chemistry