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The pressure dependence of the equilibrium constant is usually weak in the range of pressures normally encountered in industry, and therefore, it is usually neglected in practice. This is true for condensed reactant/products (i.e., when reactants and products are solids or liquid) as well as gaseous ones.
For a gaseous-reaction example, one may consider the well-studied reaction of hydrogen with nitrogen to produce ammonia:
:N + 3 H 2 NH
If the pressure is increased by the addition of an inert gas, then neither the composition at equilibrium nor the equilibrium constant are appreciably affected (because the partial pressures remain constant, assuming an ideal-gas behaviour of all gases involved). However, the composition at equilibrium will depend appreciably on pressure when:
* the pressure is changed by compression or expansion of the gaseous reacting system, and
* the reaction results in the change of the number of moles of gas in the system.
In the example reaction above, the number of moles changes from 4 to 2, and an increase of pressure by system compression will result in appreciably more ammonia in the equilibrium mixture. In the general case of a gaseous reaction:
:α A + β B σ S + τ T
the change of mixture composition with pressure can be quantified using:
where p denote the partial pressures and X the mole fractions of the components, P is the total system pressure, K is the equilibrium constant expressed in terms of partial pressures and K is the equilibrium constant expressed in terms of mole fractions.
The above change in composition is in accordance with Le Chateliers principle and does not involve any change of the equilibrium constant with the total system pressure. Indeed, for ideal-gas reactions K' is independent of pressure.
In a condensed phase, the pressure dependence of the equilibrium constant is associated with the reaction volume. For reaction:
:α A + β B σ S + τ T
the reaction volume is:
where V̄ denotes a partial molar volume of a reactant or a product.
For the above reaction, one can expect the change of the reaction equilibrium constant (based either on mole-fraction or molal-concentration scale) with pressure at constant temperature to be:
The matter is complicated as partial molar volume is itself dependent on pressure. | 7 | Physical Chemistry |
Cloning, or more precisely, the reconstruction of functional DNA from extinct species has, for decades, been a dream. Possible implications of this were dramatized in the 1984 novel Carnosaur and the 1990 novel Jurassic Park. The best current cloning techniques have an average success rate of 9.4 percent (and as high as 25 percent) when working with familiar species such as mice, while cloning wild animals is usually less than 1 percent successful. | 1 | Biochemistry |
Samy El-Shall (Mohamed Samy El-Shall) is an Egyptian-American physical chemist and a researcher in nanoscience, heterogeneous catalysis, molecular clusters and cluster ions, nucleation and ion mobility. He is the Mary Eugenia Kapp Endowed Chair in Chemistry and Commonwealth Professor at Virginia Commonwealth University (VCU). | 7 | Physical Chemistry |
The glass transition of a liquid to a solid-like state may occur with either cooling or compression. The transition comprises a smooth increase in the viscosity of a material by as much as 17 orders of magnitude within a temperature range of 500 K without any pronounced change in material structure. This transition is in contrast to the freezing or crystallization transition, which is a first-order phase transition in the Ehrenfest classification and involves discontinuities in thermodynamic and dynamic properties such as volume, energy, and viscosity. In many materials that normally undergo a freezing transition, rapid cooling will avoid this phase transition and instead result in a glass transition at some lower temperature. Other materials, such as many polymers, lack a well defined crystalline state and easily form glasses, even upon very slow cooling or compression. The tendency for a material to form a glass while quenched is called glass forming ability. This ability depends on the composition of the material and can be predicted by the rigidity theory.
Below the transition temperature range, the glassy structure does not relax in accordance with the cooling rate used. The expansion coefficient for the glassy state is roughly equivalent to that of the crystalline solid. If slower cooling rates are used, the increased time for structural relaxation (or intermolecular rearrangement) to occur may result in a higher density glass product. Similarly, by annealing (and thus allowing for slow structural relaxation) the glass structure in time approaches an equilibrium density corresponding to the supercooled liquid at this same temperature. T is located at the intersection between the cooling curve (volume versus temperature) for the glassy state and the supercooled liquid.
The configuration of the glass in this temperature range changes slowly with time towards the equilibrium structure. The principle of the minimization of the Gibbs free energy provides the thermodynamic driving force necessary for the eventual change. At somewhat higher temperatures than T, the structure corresponding to equilibrium at any temperature is achieved quite rapidly. In contrast, at considerably lower temperatures, the configuration of the glass remains sensibly stable over increasingly extended periods of time.
Thus, the liquid-glass transition is not a transition between states of thermodynamic equilibrium. It is widely believed that the true equilibrium state is always crystalline. Glass is believed to exist in a kinetically locked state, and its entropy, density, and so on, depend on the thermal history. Therefore, the glass transition is primarily a dynamic phenomenon. Time and temperature are interchangeable quantities (to some extent) when dealing with glasses, a fact often expressed in the time–temperature superposition principle. On cooling a liquid, internal degrees of freedom successively fall out of equilibrium. However, there is a longstanding debate whether there is an underlying second-order phase transition in the hypothetical limit of infinitely long relaxation times.
In a more recent model of glass transition, the glass transition temperature corresponds to the temperature at which the largest openings between the vibrating elements in the liquid matrix become smaller than the smallest cross-sections of the elements or parts of them when the temperature is decreasing. As a result of the fluctuating input of thermal energy into the liquid matrix, the harmonics of the oscillations are constantly disturbed and temporary cavities ("free volume") are created between the elements, the number and size of which depend on the temperature. The glass transition temperature T defined in this way is a fixed material constant of the disordered (non-crystalline) state that is dependent only on the pressure. As a result of the increasing inertia of the molecular matrix when approaching T, the setting of the thermal equilibrium is successively delayed, so that the usual measuring methods for determining the glass transition temperature in principle deliver T values that are too high. In principle, the slower the temperature change rate is set during the measurement, the closer the measured T value T approaches. Techniques such as dynamic mechanical analysis can be used to measure the glass transition temperature. | 7 | Physical Chemistry |
Lanthanide probes' ligands must meet several chemical requirements for the probes to work properly. These qualities are: water solubility, large thermodynamic stability at physiological pHs, kinetic inertness and absorption above 330 nm to minimize destruction of live biological materials.
The chelates which have been studied and utilized to date can be classified into the following groups:
# Tris chelates (three ligands)
# Tetrakis chelates (four ligands)
# Mixed ligand complexes
# Complexes with neutral donors
# Others such as: phthalate, picrate, and salicylate complexes.
The efficiency of the energy transfer from the ligand to the ion is determined ligand-metal bond. The energy transfer is more efficient when bonded covalently than through ionic bonding. Substituents in the ligand which are of electron-donating such as hydroxy, methoxy and methyl groups increase the fluorescence. The opposite effect is seen when an electron-withdrawing group (such as nitro) is attached. Furthermore, the fluorescence intensity is increased by fluorine substitution to the ligand. The energy transfer to the metal ion increases as the electronegativity of the fluorinated group makes the europium-oxygen bond of a more covalent nature. Increased conjugation by aromatic substituents by replacing phenyl by naphtyl groups is shown to enhance fluorescence. | 1 | Biochemistry |
Cycloalkylamines are chemical compounds featuring a cycloalkyl group and an amine. Some examples include propylhexedrine, cyclopentamine, cypenamine, and tranylcypromine. Some chemicals act as stimulants. | 0 | Organic Chemistry |
As shown in Scheme 1, the first steps in the synthesis created the bicyclo[5.3.1]undecane AB ring system of Taxol. Reaction of epoxide 1 with tert-butyllithium removed the acidic α-epoxide proton, leading to an elimination reaction and simultaneous ring-opening of the epoxide to give allylic alcohol 2. The allylic alcohol was epoxidized to epoxyalcohol 3 using tert-butyl hydroperoxide and titanium(IV)tetraisopropoxide. In the subsequent reaction, the Lewis acid boron trifluoride catalyzed the ring opening of the epoxide followed by skeletal rearrangement and an elimination reaction to give unsaturated diol 4. The newly created hydroxyl group was protected as the triethylsilyl ether (5). A tandem epoxidation with meta-chloroperbenzoic acid and Lewis acid-catalyzed Grob fragmentation gave ketone 6, which was then protected as the tert-butyldimethylsilyl ether 7 in 94% yield over three steps. | 0 | Organic Chemistry |
A few COFs possess the stability and conductivity necessary to perform well in energy storage applications like lithium-ion batteries, and various different metal-ion batteries and cathodes. | 6 | Supramolecular Chemistry |
CKIδ activity is implicated in mitosis and in response to DNA damage. During interphase, CKIδ associates with the Golgi Apparatus and appears to regulate the budding of clathrin coated vesicles from the TGN; it also appears to associate with tubulin. While undamaged mitotic cells shows no CKIδ association with tubulin, the kinase was recruited during mitosis in cells with DNA damage, indicative of a role for CKIδ in arranging the microtubule network during mitosis. The mechanisms for these biochemical interactions remain unknown. | 1 | Biochemistry |
Type I photooxygenation reactions are frequently used in the process of forming and trapping diradical species. Mirbach et al. reported on one such reaction in which an azo compound is lysed via photolysis to form the diradical hydrocarbon and then trapped in a stepwise fashion by molecular oxygen: | 5 | Photochemistry |
Imines are typically prepared by the condensation of primary amines and aldehydes. Ketones undergo similar reactions, but less commonly than aldehydes. In terms of mechanism, such reactions proceed via the nucleophilic addition giving a hemiaminal -C(OH)(NHR)- intermediate, followed by an elimination of water to yield the imine (see alkylimino-de-oxo-bisubstitution for a detailed mechanism). The equilibrium in this reaction usually favors the carbonyl compound and amine, so that azeotropic distillation or use of a dehydrating agent, such as molecular sieves or magnesium sulfate, is required to favor of imine formation. In recent years, several reagents such as Tris(2,2,2-trifluoroethyl)borate [B(OCHCF)], pyrrolidine or titanium ethoxide [Ti(OEt)] have been shown to catalyse imine formation.
Rarer than primary amines is the use of ammonia to give a primary imine. In the case of hexafluoroacetone, the hemiaminal intermediate can be isolated. | 0 | Organic Chemistry |
To be defined as ferroelectric, a material must have a spontaneous electric polarization that is switchable by an applied electric field. Usually such an electric polarization arises via an inversion-symmetry-breaking structural distortion from a parent centrosymmetric phase. For example, in the prototypical ferroelectric barium titanate, BaTiO, the parent phase is the ideal cubic ABO perovskite structure, with the B-site Ti ion at the center of its oxygen coordination octahedron and no electric polarisation. In the ferroelectric phase the Ti ion is shifted away from the center of the octahedron causing a polarization. Such a displacement only tends to be favourable when the B-site cation has an electron configuration with an empty d shell (a so-called d configuration), which favours energy-lowering covalent bond formation between the B-site cation and the neighbouring oxygen anions.
This "d0-ness" requirement is a clear obstacle for the formation of multiferroics, since the magnetism in most transition-metal oxides arises from the presence of partially filled transition metal d shells. As a result, in most multiferroics, the ferroelectricity has a different origin. The following describes the mechanisms that are known to circumvent this contraindication between ferromagnetism and ferroelectricity. | 7 | Physical Chemistry |
The applications of fluorescence resonance energy transfer (FRET) have expanded tremendously in the last 25 years, and the technique has become a staple in many biological and biophysical fields. FRET can be used as a spectroscopic ruler to measure distance and detect molecular interactions in a number of systems and has applications in biology and biochemistry. | 1 | Biochemistry |
Brine rejection plays a crucial role in ocean circulation. In coastal polynyas, it is the key to the ventilation of multiple water masses across both the Arctic and Antarctic. A coastal polynya is an area of open water surrounded by ice. The reason that coastal polynyas are the most active areas of brine rejection is that these waters often see offshore winds which give the water direct contact with cold air. This leads to heat loss and ice production. One area that is commonly studied to look at these impacts is the coastal polynyas of the Okhotsk Sea. The Okhotsk Sea has wide, shallow shelves, severe wintertime conditions, high background salinity, and easy summertime access, making it an ideal study location. There have been many studies done that look at the influence of brine rejection in the Okhotsk Sea.
In a paper done by Shcherbina et al. (2003), they analyze the influence of brine rejection well. Within the Okhotsk Sea, circulation is driven by the brine rejection that occurs in the winter months. As is typical for the rejection of brine, sea ice develops that is 70-90% fresher than seawater. The water underneath becomes saltier and colder, leading to an increase in density. This parcel of water in the Okhotsk Sea is referred to as dense shelf water (DSW). The saltier and colder a water parcel is, the denser it becomes, causing it to sink below other parcels of water. For this reason, the DSW will begin to sink within the water column. The parcel then moves southward along the coast of Sakhalin. From here, the water moves over into the Pacific and ventilates the North Pacific Intermediate Water (NPIW). The NPIW is known to be the densest water in the North Pacific, and it is a key water mass in ocean circulation.
Brine rejection has been shown to ventilate the North Pacific Ocean to a depth of 300-1,000 meters. Some studies have even shown it reaching mixing depths of 2,000 meters. The mixing and ventilation of the water column is key in helping to replenish the oxygen within intermediate waters. It can also lead to an upwelling of nutrients, which can influence productivity. An increase in primary production can lead to an increase in other organisms from krill to whales. | 9 | Geochemistry |
Copper metallurgy in Africa encompasses the study of copper production across the continent and an understanding of how it influenced aspects of African archaeology. | 8 | Metallurgy |
The high strength of silicon–halogen bonds can be leveraged toward the synthesis of phosphaalkynes. Heating bis-trimethylsilylated methyldichlorophosphines ((SiMe)CRPCl) under vacuum results in the expulsion of two equivalents of chlorotrimethylsilane and the ultimate formation of a new phosphaalkyne. This synthetic strategy has been applied in the synthesis of 2-phenylphosphaacetylene and 2-trimethylsilylphosphaacetylene. As in the case of synthetic routes reliant upon the elimination of a hydrogen halide, this route is suspected to involve an intermediate phosphaethylene species containing a C=P double bond, though such a species has not yet been observed. | 0 | Organic Chemistry |
A key choice that must be made is how many atoms to explicitly include in ones calculation. In Big-O notation, calculations general scale as O(N3) where N is the number of combined ions and valence electrons. For structure calculations, it is generally desirable to choose the smallest number of ions that can represent the structure. For example, NaCl is a bcc cubic structure. At a first guess, one might construct a cell of two interlocked cubes – 8 Na and 8 Cl – as ones unit cell. This will give the correct answer but is computationally wasteful. By choosing appropriate coordinates, one might simulate it with just two atoms: 1 Na and 1 Cl.
Crystal structure calculations rely on periodic boundary conditions. That is, the assumption is that the cell you have chosen is in the midst of an infinite lattice of identical cells. By taking our 1 Na 1 Cl cell and copying it many times along each of the crystal axes, we will have simulated the same superstructure as our 8 Na 8 Cl cell but with much reduced computational cost. | 3 | Analytical Chemistry |
The equilibrium constant of a chemical reaction is the value of its reaction quotient at chemical equilibrium, a state approached by a dynamic chemical system after sufficient time has elapsed at which its composition has no measurable tendency towards further change. For a given set of reaction conditions, the equilibrium constant is independent of the initial analytical concentrations of the reactant and product species in the mixture. Thus, given the initial composition of a system, known equilibrium constant values can be used to determine the composition of the system at equilibrium. However, reaction parameters like temperature, solvent, and ionic strength may all influence the value of the equilibrium constant.
A knowledge of equilibrium constants is essential for the understanding of many chemical systems, as well as biochemical processes such as oxygen transport by hemoglobin in blood and acid–base homeostasis in the human body.
Stability constants, formation constants, binding constants, association constants and dissociation constants are all types of equilibrium constants. | 7 | Physical Chemistry |
The first reverberatory furnaces were perhaps in the medieval period, and were used for melting bronze for casting bells. They were first applied to smelting metals in the late 17th century. Sir Clement Clerke and his son Talbot built cupolas or reverberatory furnaces in the Avon Gorge below Bristol in about 1678. In 1687, while obstructed from smelting lead (by litigation), they moved on to copper. In the following decades, reverberatory furnaces were widely adopted for smelting these metals and also tin. They had the advantage over older methods that the fuel was mineral coal, not charcoal or white coal (chopped dried wood).
In the 1690s, they (or associates) applied the reverberatory furnace (in this case known as an air furnace) to melting pig iron for foundry purposes. This was used at Coalbrookdale and various other places, but became obsolete at the end of the 18th century with the introduction of the foundry cupola furnace, which was a kind of small blast furnace, and a quite different species from the reverberatory furnace.
The puddling furnace, introduced by Henry Cort in the 1780s to replace the older finery process, was also a variety of reverberatory furnace. | 8 | Metallurgy |
Humans, like all animals, produce heat as a result of metabolism. In warm conditions, this heat exceeds a level required for homeostasis in warm-blooded animals, and is disposed of by various thermoregulation methods such as sweating and panting. Fiala et al. modelled human thermoregulation. | 7 | Physical Chemistry |
Traditionally Grignard reagents are prepared by treating an organic halide (normally organobromine) with magnesium metal. Ethers are required to stabilize the organomagnesium compound. Water and air, which rapidly destroy the reagent by protonolysis or oxidation, are excluded. Although the reagents still need to be dry, ultrasound can allow Grignard reagents to form in wet solvents by activating the magnesium such that it consumes the water.
As is common for reactions involving solids and solution, the formation of Grignard reagents is often subject to an induction period. During this stage, the passivating oxide on the magnesium is removed. After this induction period, the reactions can be highly exothermic. This exothermicity must be considered when a reaction is scaled-up from laboratory to production plant.
Most organohalides will work, but carbon-fluorine bonds are generally unreactive, except with specially activated magnesium (through Rieke metals). | 0 | Organic Chemistry |
It is surprising to note that In 1980, there was no single chiral stationary phase available in the market for performing chiral chromatography. However, In late 1980s the subject of enantioselective chromatography attracted growing interest, particularly under the drive of the institution of Okamoto in Japan, the teams of Pirkle, and Armstrong in the US, Schurig and König in Germany, Lindner in Austria, and Francotte in Switzerland . The Polysaccharides, amylose and cellulose, form the most abundant chiral polymers on earth. These naturally occurring polysaccharides form basis for an important class of chiral selectors. | 4 | Stereochemistry |
Fusing angular rings around a benzene moiety leads to an increase in stability. The Clar structure of anthracene, for instance, has only one π-sextet, but moving one ring into the angular position phenanthrene is obtained, the Clar structure of which carries two circles instead of one – notice that this molecule can be thought of as a benzene moiety with two fused rings; a third ring can be fused to obtain triphenylene, with three aromatic π-sextets in its Clar structure. The chemical stability of these molecules is greatly influenced by the degree of aromaticity of their Clar structures. As a result, while anthracene reacts with maleic acid, phenanthrene does not, and triphenylene is the most stable species of these three. | 7 | Physical Chemistry |
# The saturation pressure at the maximum temperature of the cycle should not be excessive. Very high pressures lead to mechanical stress problems, and therefore, unnecessarily expensive components may be required.
# The saturation pressure at the minimum temperature of the cycle (i.e. the condensing pressure) should not be so low as to lead to problems of sealing against infiltration of the atmospheric air into the system.
# The triple point should lie below the expected minimum ambient temperature. This ensures that the fluid does not solidify at any point during the cycle nor whilst being handled outside the system.
# The working fluid should possess a low value of the liquid viscosity, a high latent heat of vaporisation, a high liquid thermal conductivity and a good wetting capability. These ensure that the working fluid pressure drops in passing through the heat exchangers and the auxiliary piping are low and that the heat transfer rates in the exchangers are high.
# The working fluid should have low vapour and liquid specific volumes. These properties affect the rates of heat transfer in the heat exchangers. The vapour specific volume relates directly to the size and cost of the cycle components. Moreover, a high vapour specific volume leads to larger volumetric flows requiring a multiplicity of exhaust ends of the expander at heat engines or compressor in refrigeration cycles and resulting in significant pressure losses. The specific volume of the liquid at the condenser pressure should be as small as possible in order to minimise the required feedwater pump work.
# Non-corrosivity and compatibility with common system materials are important selection criteria.
# The fluid should be chemically stable over the whole temperature and pressure range employed. The thermal decomposition resistance of the working fluid in the presence of lubricants and container materials is a highly important criterion. In addition to making the replacement of the working fluid necessary, chemical decomposition of the fluid can produce non-condensable gases which lower the heat transfer rate in the heat exchangers, as well as compounds, which have corrosive effects on the materials of the system.
# Non-toxicity, non-flammability, non-explosiveness, non-radioactiveness and current industrial acceptability are also desirable attributes.
# The fluid should meet the criteria of environmental protection requirements such as a low grade ozone depletion potential (ODP) and global warming potential (GWP).
# The fluid should possess good lubrication properties to reduce friction between surfaces in mutual contact, which reduces the heat generated when the surfaces move and ultimately increases cycle performance.
# The substance should be of low cost and readily available in large quantities.
# Long-term (operational) experience with the working fluid and possible fluid recycling is also beneficial. | 7 | Physical Chemistry |
In order to perform a dynamic simulation with such a network it is necessary to construct an ordinary differential equation
system that describes the rates of change in each metabolite's concentration or amount. To this end, a rate law, i.e., a kinetic equation that determines the rate of reaction based on the concentrations of all reactants is required for each reaction. Software packages that include numerical integrators, such as COPASI or [http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsimulator SBMLsimulator], are then able to simulate the system dynamics given an initial condition. Often these rate laws contain kinetic parameters with uncertain values. In many cases it is desired to estimate these parameter values with respect to given time-series data of metabolite concentrations. The system is then supposed to reproduce the given data. For this purpose the distance between the given data set and the result of the simulation, i.e., the numerically or in few cases analytically obtained solution of the differential equation system is computed. The values of the parameters are then estimated to minimize this distance. One step further, it may be desired to estimate the mathematical structure of the differential equation system because the real rate laws are not known for the reactions within the system under study. To this end, the program [http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsqueezer SBMLsqueezer] allows automatic creation of appropriate rate laws for all reactions with the network. | 1 | Biochemistry |
A glow-discharge device (GD) serves as a versatile source, as it can simultaneously introduce and atomize the sample. The glow discharge occurs in a low-pressure argon gas atmosphere between 1 and 10 torr. In this atmosphere lies a pair of electrodes applying a DC voltage of 250 to 1000 V to break down the argon gas into positively charged ions and electrons. These ions, under the influence of the electric field, are accelerated into the cathode surface containing the sample, bombarding the sample and causing neutral sample atom ejection through the process known as sputtering. The atomic vapor produced by this discharge is composed of ions, ground state atoms, and fraction of excited atoms. When the excited atoms relax back into their ground state, a low-intensity glow is emitted, giving the technique its name.
The requirement for samples of glow discharge atomizers is that they are electrical conductors. Consequently, atomizers are most commonly used in the analysis of metals and other conducting samples. However, with proper modifications, it can be utilized to analyze liquid samples as well as nonconducting materials by mixing them with a conductor (e.g. graphite). | 3 | Analytical Chemistry |
Ex situ conservation (literally "off-site conservation") is the process of protecting an endangered species, variety or breed, of plant or animal outside its natural habitat. For example, by removing part of the population from a threatened habitat and placing it in a new location, an artificial environment which is similar to the natural habitat of the respective animal and within the care of humans, such as a zoological park or wildlife sanctuary. The degree to which humans control or modify the natural dynamics of the managed population varies widely, and this may include alteration of living environments, reproductive patterns, access to resources, and protection from predation and mortality.
Ex situ management can occur within or outside a species natural geographic range. Individuals maintained ex situ exist outside an ecological niche. This means that they are not under the same selection pressures as wild populations, and they may undergo artificial selection if maintained ex situ' for multiple generations.
Agricultural biodiversity is also conserved in ex situ collections. This is primarily in the form of gene banks where samples are stored in order to conserve the genetic resources of major crop plants and their wild relatives. | 1 | Biochemistry |
In molecular biology and genetics, the sense of a nucleic acid molecule, particularly of a strand of DNA or RNA, refers to the nature of the roles of the strand and its complement in specifying a sequence of amino acids. Depending on the context, sense may have slightly different meanings. For example, the negative-sense strand of DNA is equivalent to the template strand, whereas the positive-sense strand is the non-template strand whose nucleotide sequence is equivalent to the sequence of the mRNA transcript. | 1 | Biochemistry |
The DNA double helix was discovered in 1953 (with further details in 1954) based on X-ray diffraction images of DNA (most notably photo 51, taken by Raymond Gosling and Rosalind Franklin) as well as base-pairing chemical and biochemical information. Prior to this, X-ray data being gathered in the 1950s indicated that DNA formed some sort of helix, but it had not yet been discovered what the exact structure of that helix was. There were therefore several proposed structures that were later overturned by the data supporting a DNA duplex. The most famous of these early models was by Linus Pauling and Robert Corey in 1953 in which they proposed a triple helix with the phosphate backbone on the inside, and the nucleotide bases pointing outwards. A broadly similar, but detailed structure was also proposed by Bruce Fraser that same year. However, Watson and Crick soon identified several problems with these models:
* Negatively charged phosphates near the axis repel each other, leaving the question of how the three-chain structure stays together.
* In a triple-helix model (specifically Pauling and Corey's model), some of the van der Waals distances appear to be too small.
The initial double helix model discovered, now termed B-form DNA is by far the most common conformation in cells. Two additional rarer helical conformations that also naturally occur were identified in the 1970s: A-form DNA, and Z-form DNA. | 1 | Biochemistry |
Triple bonds between sulfur and carbon in sulfaalkynes are rare and can be found in carbon monosulfide (CS) and have been suggested for the compounds FCCSF and FSCSF. The compound HCSOH is also represented as having a formal triple bond. | 9 | Geochemistry |
The Portlethen Moss is a recognised nature preserve by the Scottish Wildlife Trust (with designation PLM076) and the Aberdeenshire Council. While peat cutting was conducted in prehistoric and Middle Ages times, there has been no harvesting of peat in the modern era. There is some ongoing loss of moss habitat from cattle grazing, but the most significant threat is from ongoing land development pressure; in fact, half of the Portlethen Moss has been lost to urban (low density) land development by the town of Portlethen during the period 1985 to 2005. Trampling is considered an insignificant threat due to the small animal or human presence in the existing nature reserve area; furthermore, cattle grazing, while ongoing, is deemed a much lesser current threat than population expansion pressure. Enrichment (addition of grazing animal manure) is not a major issue due to the low density of animals. As a net result damage to the primordial moss is considered extensive and widespread by the Scottish Wildlife Trust. The raised bog habitat of the Portlethen Moss is also protected by the United Kingdom Biodiversity Action Plan. | 2 | Environmental Chemistry |
If a gamma spectrometer is used for identifying samples of unknown composition, its energy scale must be calibrated first. Calibration is performed by using the peaks of a known source, such as caesium-137 or cobalt-60. Because the channel number is proportional to energy, the channel scale can then be converted to an energy scale. If the size of the detector crystal is known, one can also perform an intensity calibration, so that not only the energies but also the intensities of an unknown source—or the amount of a certain isotope in the source—can be determined.
Because some radioactivity is present everywhere (i.e., background radiation), the spectrum should be analyzed when no source is present. The background radiation must then be subtracted from the actual measurement. Lead absorbers can be placed around the measurement apparatus to reduce background radiation. | 7 | Physical Chemistry |
Macro-creatine kinase (macro-CK) is a macroenzyme, an enzyme of high molecular weight and prolonged half-life found in human serum. It is one of the most common macroenzymes. Macro-CK type 1 is a complex formed by one of the creatine kinase isoenzyme types, typically CK-BB, and antibodies; typically IgG, sometimes IgA, rarely IgM. Macro-CK type 2 is formed from mitochondrial CK polymer.
Macro-CK type 1 has been associated with autoimmune and other chronic conditions. Macro-CK type 2 has been associated with malignancy.
Macro-CK has been implicated as a source of interference in interpretation of medical labs. | 1 | Biochemistry |
In the chemistry of electrolyte solutions, an ideal solution is a solution whose colligative properties are proportional to the concentration of the solute. Real solutions may show departures from this kind of ideality. In order to accommodate these effects in the thermodynamics of solutions, the concept of activity was introduced: the properties are then proportional to the activities of the ions. Activity, a, is proportional to concentration, c. The proportionality constant is known as an activity coefficient, .
In an ideal electrolyte solution the activity coefficients for all the ions are equal to one. Ideality of an electrolyte solution can be achieved only in very dilute solutions. Non-ideality of more concentrated solutions arises principally (but not exclusively) because ions of opposite charge attract each other due to electrostatic forces, while ions of the same charge repel each other. In consequence ions are not randomly distributed throughout the solution, as they would be in an ideal solution.
Activity coefficients of single ions cannot be measured experimentally because an electrolyte solution must contain both positively charged ions and negatively charged ions. Instead, a mean activity coefficient, is defined. For example, with the electrolyte NaCl
In general, the mean activity coefficient of a fully dissociated electrolyte of formula AB is given by
Activity coefficients are themselves functions of concentration as the amount of inter-ionic interaction increases as the concentration of the electrolyte increases. Debye and Hückel developed a theory with which single ion activity coefficients could be calculated. By calculating the mean activity coefficients from them the theory could be tested against experimental data. It was found to give excellent agreement for "dilute" solutions. | 7 | Physical Chemistry |
The expression for the magnetooptical absorption of a polaron is:
Here, is the cyclotron frequency for a rigid-band electron. The magnetooptical absorption Γ(Ω) at the frequency Ω takes the form Σ(Ω) is the so-called "memory function", which describes the dynamics of the polaron. Σ(Ω) depends also on α, β and .
In the absence of an external magnetic field () the optical absorption spectrum (3) of the polaron at weak coupling is determined by the absorption of radiation energy, which is reemitted in the form of LO phonons. At larger coupling, , the polaron can undergo transitions toward a relatively stable internal excited state called the "relaxed excited state" (RES) (see Fig. 2). The RES peak in the spectrum also has a phonon sideband, which is related to a Franck–Condon-type transition.
A comparison of the DSG results with the optical conductivity spectra given by approximation-free numerical and approximate analytical approaches is given in ref.
Calculations of the optical conductivity for the Fröhlich polaron performed within the Diagrammatic Quantum Monte Carlo method, see Fig. 3, fully confirm the results of the path-integral variational approach at In the intermediate coupling regime the low-energy behavior and the position of the maximum of the optical conductivity spectrum of ref. follow well the prediction of Devreese. There are the following qualitative differences between the two approaches in the intermediate and strong coupling regime: in ref., the dominant peak broadens and the second peak does not develop, giving instead rise to a flat shoulder in the optical conductivity spectrum at . This behavior can be attributed to the optical processes with participation of two or more phonons. The nature of the excited states of a polaron needs further study.
The application of a sufficiently strong external magnetic field allows one to satisfy the resonance condition , which {(for )} determines the polaron cyclotron resonance frequency. From this condition also the polaron cyclotron mass can be derived. Using the most accurate theoretical polaron models to evaluate , the experimental cyclotron data can be well accounted for.
Evidence for the polaron character of charge carriers in AgBr and AgCl was obtained through high-precision cyclotron resonance experiments in external magnetic fields up to 16 T. The all-coupling magneto-absorption calculated in ref., leads to the best quantitative agreement between theory and experiment for AgBr and AgCl. This quantitative interpretation of the cyclotron resonance experiment in AgBr and
AgCl by the theory of Peeters provided one of the most convincing and clearest demonstrations of Fröhlich polaron features in solids.
Experimental data on the magnetopolaron effect, obtained using far-infrared photoconductivity techniques, have been applied to study the energy spectrum of shallow donors in polar semiconductor layers of CdTe.
The polaron effect well above the LO phonon energy was studied through cyclotron resonance measurements, e. g., in II–VI semiconductors, observed in ultra-high magnetic fields. The resonant polaron effect manifests itself when the cyclotron frequency approaches the LO phonon energy in sufficiently high magnetic fields.
In the lattice models the optical conductivity is given by the formula:
Here is the activation energy of polaron, which is of the order of polaron binding energy . This formula was derived and extensively discussed in and was tested experimentally for example in photodoped parent compounds of high temperature superconductors. | 7 | Physical Chemistry |
Resolution of structural variation detection by ESP has been increased to the similar level as PCR, and can be further improved by selection of more evenly sized DNA fragments. ESP can be applied for either with or without constructed artificial chromosome. With BAC, precious samples can be immortalized and conserved, which is particularly important for small quantity of smalls which are planned for extensive analyses. Furthermore, BACs carrying rearranged DNA fragments can be directly transfected in vitro or in vivo to analyze the function of these arrangements. However, BAC construction is still expensive and labor-intensive. Researchers should be really careful to choose which strategy they need for particular project. Because ESP only looks at short paired-end sequences, it has the advantage of providing useful information genome-wide without the need for large-scale sequencing. Approximately 100-200 tumors can be sequenced at a resolution greater than 150kb when compared to sequencing an entire genome. | 1 | Biochemistry |
One of the most commonly used fiber production methods is the crosslinking of sodium alginate by CaCl, where the formed calcium alginate will act as the crosslinking point to link the alginate chains together to form the network and solidified the polymer. Afterward, this alginate hydrogel fiber can be used as a template for the polymerization of secondary networks. Additionally, by controlling the fluid dynamics inside the microfluid device, the diameter and the shape of the resulting fiber can be tuned without doing modification to the devices.
A practice would be the production of alginate solution reported by Yang et al. They used the sodium alginate as core fluid and CaCl as shealth fluid, the crosslinked network (hydrogel fiber) formed once this two fluid met, the laminar flow kept its tubular shape during the reaction. | 7 | Physical Chemistry |
In the presence of air and various cofactors and enzymes, fatty acids are converted to acetyl-CoA. The pathway is called beta-oxidation. Each cycle of beta-oxidation shortens the fatty acid chain by two carbon atoms and produces one equivalent each of acetyl-CoA, NADH, and FADH. The acetyl-CoA is metabolized by the citric acid cycle to generate ATP, while the NADH and FADH are used by oxidative phosphorylation to generate ATP. Dozens of ATP equivalents are generated by the beta-oxidation of a single long acyl chain. | 1 | Biochemistry |
* Acetals
** Hemiacetals
** Thioacetals
** Ketals
* Alcohols and alkyl halides, diols, thiols
* Alkanes and cycloalkanes
* Alkenes
* Alkynes
* Amines
* Amino acids, peptides, proteins
* Aromatics
** Acetophenones
** Anilines
** Anisoles
** Benzene
** Benzenesulfonic acids
**Benzophenones
** Nitrobenzenes
** Phenols
* Aromatic hydrocarbons
**Toluene
**Xylenes
***m-Xylenes
***o-Xylenes
***p-Xylenes
* Aryl halides
* Carbohydrates
** Sugar
* Carbonyl compounds
**Acid anhydride
** Acyl halides
*** Acyl chlorides
** Aldehydes
** Amides
*** Lactams
** Carboxylic acids
**Dicarbonyl
**Enones
**Esters
*** Lactones
**Imides
**Ketones
* Enols
** Enolate anions
** Enamines
* Ethers
** Epoxides
** Sulfides
* Imines
** Schiff bases
* Ketenes
* Lipids
* Nitriles
* Nucleic acids
* Organometallic compounds
* Oximes | 0 | Organic Chemistry |
Because push-pull technology was developed mainly outside of Sub-saharan Africa—where international agencies today aim to grow its impact the most—a lack of trust was initially faced. This distrust was fueled by local suspicions that external agents had hidden self-interested agendas. In relationships where resources to implement new technologies are also externally provided, farmers often feel that they must simply passively follow the instructions they are given; however, efforts have been made in Ethiopia to encourage farmer engagement with the development of push-pull technology and to thus make the process more collaborative and bridge this gap. Additionally, as mentioned above, push-pull technology is very similar to traditional intercropping methods which has helped it gain community acceptance
Push-pull technology has also been more widely seen as culturally acceptable and congruent because of the way it provides traditional roles for men and women in the agriculture work. Because push-pull technology can fit within existing family frameworks, the practice does not demand an overhaul of existing dynamics. In order to further make the implementation of push-pull technology, farmers played a participatory and influential role in deciding how the technology would be carried out to best suit their needs and align with traditional practices. For example, local farmers preferred to drill the lines in which seeds would be sown using an ox-drawn plough. In general, by promoting the participatory leadership of local farmers, the prospects of sustainability of such projects are anticipated to be strengthened. | 1 | Biochemistry |
Ion beams produced by ion and plasma thrusters on board a spacecraft can be used to transmit a force to a nearby object (e.g. another spacecraft, an asteroid, etc.) that is irradiated by the beam. This innovative propulsion technique named Ion Beam Shepherd has been shown to be effective in the area of active space debris removal as well as asteroid deflection. | 7 | Physical Chemistry |
In geology, igneous differentiation, or magmatic differentiation, is an umbrella term for the various processes by which magmas undergo bulk chemical change during the partial melting process, cooling, emplacement, or eruption. The sequence of (usually increasingly silicic) magmas produced by igneous differentiation is known as a magma series. | 9 | Geochemistry |
Cooling catheters are inserted into a femoral vein. Cooled saline solution is circulated through either a metal coated tube or a balloon in the catheter. The saline cools the persons whole body by lowering the temperature of a persons blood. Catheters reduce temperature at rates ranging from per hour. Through the use of the control unit, catheters can bring body temperature to within of the target level. Furthermore, catheters can raise temperature at a steady rate, which helps to avoid harmful rises in intracranial pressure. A number of studies have demonstrated that targeted temperature management via catheter is safe and effective.
Adverse events associated with this invasive technique include bleeding, infection, vascular puncture, and deep vein thrombosis (DVT). Infection caused by cooling catheters is particularly harmful, as resuscitated people are highly vulnerable to the complications associated with infections. Bleeding represents a significant danger, due to a decreased clotting threshold caused by hypothermia. The risk of deep vein thrombosis may be the most pressing medical complication.
Deep vein thrombosis can be characterized as a medical event whereby a blood clot forms in a deep vein, usually the femoral vein. This condition may become potentially fatal if the clot travels to the lungs and causes a pulmonary embolism. Another potential problem with cooling catheters is the potential to block access to the femoral vein, which is a site normally used for a variety of other medical procedures, including angiography of the venous system and the right side of the heart. However, most cooling catheters are triple lumen catheters, and the majority of people post-arrest will require central venous access. Unlike non-invasive methods which can be administered by nurses, the insertion of cooling catheters must be performed by a physician fully trained and familiar with the procedure. The time delay between identifying a person who might benefit from the procedure and the arrival of an interventional radiologist or other physician to perform the insertion may minimize some of the benefit of invasive methods' more rapid cooling. | 1 | Biochemistry |
In vertebrates, ferritin is usually found within cells, although it is also present in smaller quantities in the plasma. | 1 | Biochemistry |
S-Nitroso compounds (S-nitrosothiols) are typically prepared by condensation of a thiol and nitrous acid:
:RSH + HONO → RSNO + HO | 0 | Organic Chemistry |
* [http://www.thebiogrid.org/ BioGRID] database
* [http://mentha.uniroma2.it mentha] the interactome browser
* [http://www.ebi.ac.uk/intact IntAct: The Molecular Interaction Database]
* [http://interactome.org Interactome.org] — a dedicated interactome web site. | 1 | Biochemistry |
Sodium borohydride and lithium aluminium hydride are commonly used for the reduction of organic compounds. These two reagents are on the extremes of reactivity—whereas lithium aluminium hydride reacts with nearly all reducible functional groups, sodium borohydride reacts with a much more limited range of functional groups. Diminished or enhanced reactivity may be realized by the replacement of one or more of the hydrogens in these reagents with alkoxy groups.
Additionally, substitution of hydrogen for chiral alkoxy groups in these reagents enables asymmetric reductions. Although methods involving stoichiometric amounts of chiral metal hydrides have been supplanted in modern times by enantioselective catalytic reductions, they are of historical interest as early examples of stereoselective reactions.
The table below summarizes the reductions that may be carried out with a variety of metal aluminium hydrides and borohydrides. The symbol "+" indicates that reduction does occur, "-" indicates that reduction does not occur, "±" indicates that reduction depends on the structure of the substrate, and "0" indicates a lack of literature information. | 0 | Organic Chemistry |
The Ski complex is a multi-protein complex involved in the 3' end degradation of messenger RNAs in yeast. | 1 | Biochemistry |
Decantation is frequently used to purify a liquid by separating it from a suspension of insoluble particles (e.g. in red wine, where the wine is decanted from the potassium bitartrate crystals to avoid unsavory taste). This makes the wine more tonic and astringent.
Cream accelerates to the top of milk, allowing the separation of milk and cream. This is used in the cheese industry. Fat is determined in butter by decantation.
To obtain a sample of clear water from muddy water, muddy water is poured into another container, which separates the water from the mud.
In the sugar industry, the processing of sugar beets into granular sugar involves many liquid–solid separations; e.g. separation of syrups from crystals.
Decantation is also present in nanotechnology. In the synthesis of high quality silver nanowire (AgNW) solutions and fabrication process of high performance electrodes, decantation is also being applied which greatly simplifies the purification process.
After using a desiccant to absorb water from an organic liquid, the organic liquid can often be decanted away from the desiccant.
The process of deriving vinegar also requires decantation to remove fats and biomolecular antioxidants from the raw substance.
Plasma can be separated from blood through decantation by using a centrifuge.
Mercury is disposed of in water bodies during mining, turning the water unfit and toxic. The mercury can be removed through decantation. | 3 | Analytical Chemistry |
The wires that make up the thermocouple must be insulated from each other everywhere, except at the sensing junction. Any additional electrical contact between the wires, or contact of a wire to other conductive objects, can modify the voltage and give a false reading of temperature.
Plastics are suitable insulators for low temperatures parts of a thermocouple, whereas ceramic insulation can be used up to around 1000 °C. Other concerns (abrasion and chemical resistance) also affect the suitability of materials.
When wire insulation disintegrates, it can result in an unintended electrical contact at a different location from the desired sensing point. If such a damaged thermocouple is used in the closed loop control of a thermostat or other temperature controller, this can lead to a runaway overheating event and possibly severe damage, as the false temperature reading will typically be lower than the sensing junction temperature. Failed insulation will also typically outgas, which can lead to process contamination. For parts of thermocouples used at very high temperatures or in contamination-sensitive applications, the only suitable insulation may be vacuum or inert gas; the mechanical rigidity of the thermocouple wires is used to keep them separated. | 8 | Metallurgy |
The dual ligation hybridization assay (DLA) extends the specificity of the hybridization-ligation assay to a specific method for the parent compound. Despite hybridization-ligation assays robustness, sensitivity and added specificity for the 3-end of the oligonculeotide analyte, the hybridization-ligation assay is not specific for the 5' end of the analyte.
The DLA is intended to quantify the full-length, parent oligonucleotide compound only, with both intact 5 and 3 ends. DLA probes are ligated at the 5 and 3 ends of the analyte by the joint action of T4 DNA ligase and T4 polynucleotide kinase. The kinase phosphorylates the 5-end of the analyte and the ligase will join the capture probe to the analyte to the detection probe. The capture and detection probes in the DLA can thus be termed ligation probes. As for the hybridization-ligation assay, the DLA is specific for the parent compound because the efficiency of ligation over a bulge loop is low, and thus the DLA detects the full-length analyte with both intact 5 and 3'-ends. The DLA can also be used for the determination of individual metabolites in biological matrices.
The limitations with the hybridization-ligation assay also apply to the dual ligation assay, with the 5-end in addition to the 3-end requiring to have a free hydroxyl (or a phosphate group). Further, T4 DNA ligases are incompatible with ligation of RNA molecules as a donor (i.e. RNA at the 5 end of the ligation). Therefore, second generation antisense that comprise 2-O-methyl RNA, 2'-O-methoxyethyl or locked nucleic acids may not be compatible with the dual ligation assay. | 1 | Biochemistry |
The Lattice Boltzmann methods for solids (LBMS) are a set of methods for solving partial differential equations (PDE) in solid mechanics. The methods use a discretization of the Boltzmann equation(BM), and their use is known as the lattice Boltzmann methods for solids.
LBMS methods are categorized by their reliance on:
* Vectorial distributions
* Wave solvers
* Force tuning
The LBMS subset remains highly challenging from a computational aspect as much as from a theoretical point of view. Solving solid equations within the LBM framework is still a very active area of research. If solids are solved, this shows that the Boltzmann equation is capable of describing solid motions as well as fluids and gases: thus unlocking complex physics to be solved such as fluid-structure interaction (FSI) in biomechanics. | 7 | Physical Chemistry |
The microcystin-producing Microcystis is a genus of freshwater cyanobacteria and thrives in warm water conditions, especially in stagnant waters. The EPA predicted in 2013 that climate change and changing environmental conditions may lead to harmful algae growth and may negatively impact human health. Algal growth is also encouraged through the process of eutrophication (oversupply of nutrients). In particular, dissolved reactive phosphorus promotes algal growth.
Microcystins may have evolved as a way to deal with low iron supply in cyanobacteria: the molecule binds iron, and non-producing strains are significantly worse at coping with low iron levels. Low iron supply up-regulates McyD, one of the microcystin synthetic operons. Sufficient iron supply, however, can still boost microcystin production by making the bacterium better at photosynthesis, therefore producing sufficient ATP for MC biosynthesis.
Microcystin production is also positively correlated with temperature. Bright light and red light increases transcription of McyD, but blue light reduces it. A wide range of other factors such as pH may also affect MC production, but comparison is complicated due to a lack of standard testing conditions. | 2 | Environmental Chemistry |
To analyze the behavior of the crystals in this type of polymers, the WAXS and DSC techniques are used; these techniques help to determine what percentage of the polymer are crystals and how they are organized. This is due to the fact that the crystallinity decreases as the crosslinking increases, since the chains lose the ability to arrange themselves and order is essential to achieve crystallinity.
A second problem present when crosslinking molecules is melting, since an excess of crosslinking modifies the molecule in such a way that it stops melting (similar to a thermoset) and therefore the temporary shape cannot be obtained.
The control of curing either by electromagnetic waves or with peroxides is very important since it increases the T and decreases the crystallinity, determining factors in the shape-shape-memory effect.
In the case of biocompatible semicrystalline systems such as poly(ε-caprolactone) and poly(n-butyl acrylate), crosslinked by photopolymerization it has been reported that the crystallization behavior is affected by the cooling rate, as in any other semicrystalline polymer, but the heat of crystallization remains independent of the cooling rate.
The influence of the crosslinking of the molecules, the cooling rate and the crystallization behavior are specific to each system and impossible to enumerate since the synthesis possibilities are almost infinite.
Crystallizable polymers such as oligo(ε-caprolactone) can have amorphous segments such as poly(n-butyl acrylate) and the molecular mass ratio of each determine the behavior of the system in programming temporary form and recovery to permanent form. | 7 | Physical Chemistry |
Overexposure to UV‑B radiation not only can cause sunburn but also some forms of skin cancer. However, the degree of redness and eye irritation (which are largely not caused by UV‑A) do not predict the long-term effects of UV, although they do mirror the direct damage of DNA by ultraviolet.
All bands of UV radiation damage collagen fibers and accelerate aging of the skin. Both UV‑A and UV‑B destroy vitamin A in skin, which may cause further damage.
UVB radiation can cause direct DNA damage. This cancer connection is one reason for concern about ozone depletion and the ozone hole.
The most deadly form of skin cancer, malignant melanoma, is mostly caused by DNA damage independent from UV‑A radiation. This can be seen from the absence of a direct UV signature mutation in 92% of all melanoma. Occasional overexposure and sunburn are probably greater risk factors for melanoma than long-term moderate exposure. UV‑C is the highest-energy, most-dangerous type of ultraviolet radiation, and causes adverse effects that can variously be mutagenic or carcinogenic.
In the past, UV‑A was considered not harmful or less harmful than UV‑B, but today it is known to contribute to skin cancer via indirect DNA damage (free radicals such as reactive oxygen species). UV‑A can generate highly reactive chemical intermediates, such as hydroxyl and oxygen radicals, which in turn can damage DNA. The DNA damage caused indirectly to skin by UV‑A consists mostly of single-strand breaks in DNA, while the damage caused by UV‑B includes direct formation of thymine dimers or cytosine dimers and double-strand DNA breakage. UV‑A is immunosuppressive for the entire body (accounting for a large part of the immunosuppressive effects of sunlight exposure), and is mutagenic for basal cell keratinocytes in skin.
UVB photons can cause direct DNA damage. UV‑B radiation excites DNA molecules in skin cells, causing aberrant covalent bonds to form between adjacent pyrimidine bases, producing a dimer. Most UV-induced pyrimidine dimers in DNA are removed by the process known as nucleotide excision repair that employs about 30 different proteins. Those pyrimidine dimers that escape this repair process can induce a form of programmed cell death (apoptosis) or can cause DNA replication errors leading to mutation.
As a defense against UV radiation, the amount of the brown pigment melanin in the skin increases when exposed to moderate (depending on skin type) levels of radiation; this is commonly known as a sun tan. The purpose of melanin is to absorb UV radiation and dissipate the energy as harmless heat, protecting the skin against both direct and indirect DNA damage from the UV. UV‑A gives a quick tan that lasts for days by oxidizing melanin that was already present and triggers the release of the melanin from melanocytes. UV‑B yields a tan that takes roughly 2 days to develop because it stimulates the body to produce more melanin. | 5 | Photochemistry |
Camphorsultam, also known as bornanesultam, is a crystalline solid primarily used as a chiral auxiliary in the synthesis of other chemicals with a specific desired stereoselectivity. Camphorsultam is commercially available in both enantiomers of its exo forms: (1R)-(+)-2,10-camphorsultam and (1S)-(−)-2,10-camphorsultam. | 0 | Organic Chemistry |
Blue MX-R or Reactive Blue 4 has a formula of CHClNOS and a molecular weight of 637.4 g/mol. It contains dichlorotriazine ring to the chromophore unlike Cibacron Blue F3GA. For a large scale protein purification, Blue MX-R can be used to purify protein such as lactate dehydrogenase (LDH). In fast-protein liquid chromatography (FPLC) using Blue MX-R immobilized on poly(glycidyl methacrylate-co-ethylene dimethacrylate) beads, it was seen to separate lysozyme and bovine serum albumin (BSA), purified lysozyme from chicken albumin. | 3 | Analytical Chemistry |
Organostannane addition reactions comprise the nucleophilic addition of an allyl-, allenyl-, or propargylstannane to an aldehyde, imine, or, in rare cases, a ketone. The reaction is widely used for carbonyl allylation.
Organostannane addition to carbonyl groups constitutes one of the most common and efficient methods for the construction of contiguous, oxygen-containing stereocenters in organic molecules. As many molecules containing this motif—polypropionates and polyacetates, for instance—are desired by natural products chemists, the title reaction has become important synthetically and has been heavily studied over the years. Substituted allylstannanes may create one or two new stereocenters, often with a very high degree of stereocontrol.
Organostannanes are known for their stability, ease of handling, and selective reactivity. Chiral allylstannanes often react with good stereoselectivity to give single diastereomers. Models explaining the sense of selectivity are reliable. In terms of disadvantages, stoichiometric amounts of metal-containing byproducts are generated. Additions to sterically encumbered pi bonds, such as those of ketones, are uncommon. | 0 | Organic Chemistry |
Effective 18 August 2014, tramadol has been placed into Schedule IV of the federal Controlled Substances Act in the United States. Before that, some US states had already classified tramadol as a Schedule IV controlled substance under their respective state laws.
Tramadol is classified in Schedule 4 (prescription only) in Australia, rather than as a Schedule 8 Controlled Drug (Possession without authority illegal) like most other opioids.
Effective May 2008, Sweden classified tramadol as a controlled substance in the same category as codeine and dextropropoxyphene, but allows a normal prescription to be used.
On 10 June 2014, the United Kingdom's Home Office classified tramadol as a Class C, Schedule 3 controlled drug, but exempted it from the safe custody requirement.
On 1 October 2023, New Zealand's Medsafe reclassified tramadol as a Class C2 Controlled Drug (in addition to its existing status as a prescription only medication). | 4 | Stereochemistry |
Gold cyanidation (also known as the cyanide process or the MacArthur–Forrest process) is a hydrometallurgical technique for extracting gold from low-grade ore by converting the gold to a water-soluble coordination complex. It is the most commonly used leaching process for gold extraction. Cyanidation is also widely used in the extraction of silver, usually after froth flotation.
Production of reagents for mineral processing to recover gold represents more than 70% of cyanide consumption globally. Other metals are recovered from the process include copper, zinc, and silver, but gold is the main driver of this technology. Due to the highly poisonous nature of cyanide, the process is controversial and its use is even banned in some parts of the world. Cyanide can be safely used in the gold mining industry. A key feature for safe use of cyanide is to ensure adequate pH control at an alkaline pH level above 10.5. At industrial scale, pH control is mainly achieved using lime, as an important enabling reagent in gold processing. | 8 | Metallurgy |
The mechanism of action of bottromycin was confirmed nearly 20 years following the discovery of bottromycin. Bottromycin functions as an antibiotic through inhibition of protein synthesis. It blocks aminoacyl tRNA binding to the ribosome by binding to the A site of the 50s subunit. This results in release of aminoacyl tRNA from the ribosome and premature termination of protein synthesis. A comparison of other antibiotics known to bind to the A site of the ribosome, including micrococcin, tetracycline, streptomycin, and chloramphenicol, suggested that only bottromycin and chloramphenicol caused release of aminoacyl tRNA from the ribosome. Of those antibiotics, only micrococcin is also a macrocyclic peptide. | 0 | Organic Chemistry |
PDE3 inhibitors:
*antagonize platelet aggregation
*block oocyte maturation
*increase contractility of the heart
*enhance vascular smooth muscle relaxation
*enhance airway smooth muscle relaxation
It has been demonstrated that PDE3A inhibition prevents oocyte maturation in vitro and in vivo. For example, when mice are made completely deficient of PDE3A, they become infertile.
Aggregation of platelets is highly regulated by cyclic nucleotides. PDE3A is a regulator of this process, and PDE3 inhibitors effectively prevent aggregation of platelets. Cilostazol is approved for treatment of intermittent claudication and is thought to involve inhibition of platelet aggregation and also inhibition of smooth muscle proliferation and vasodilation.
The most studied roles of PDE3B have been in the areas of insulin, IGF1, and leptin signaling. When PDE3B is overexpressed in β-cells in mice, it causes impaired insulin secretion and glucose intolerance. | 1 | Biochemistry |
Almost two decades later, René Just Haüy introduced wooden crystal models to illustrate the two-dimensional drawings in the atlas volume of his "Traité de Minéralogie" (1801). For the production of crystal models, wood appeared to be much more convenient than clay. Especially pear wood permitted getting smooth faces, sharp edges and accurate dihedral angles required for the production of these three-dimensional objects. In general, the angular accuracy was very high and some models, especially those illustrating crystal twins and Haüy's figures of decrement, still appear as masterpieces of fine woodwork and carving. Skilful craftsmen such as Pleuvin, Beloeuf and Lambotin (to name only a few) became specialists in this field and the models they offered were highly esteemed.
Between 1802 and 1804, Martin van Marum bought 597 of these pear wood models, 550 of these are still present in the collection of Teylers Museum. Each model is labeled, mentioning a number and the name of the crystal form. This set is the most complete collection of Haüy crystal models that still survives. That Van Marum was able to acquire such a unique collection was due to his networking. Van Marum allowed Haüy as a member of the Hollandsche Maatschappij, a nomination to which Haüy attached great value. Haüy mentioned this membership in all of his publications.
After their introduction by Romé de l'Isle and Haüy, crystal models were increasingly demanded both by scholars for teaching purposes as well as by mineral collectors. The quality of the models improved due to the technical progress in their production. Several mineralogists and crystallographers started designing their own series of models. Although pear wood kept a prominent place, models were also manufactured using materials like plaster, cast iron, lead, brass, glass, porcelain, cardboard, etc. | 3 | Analytical Chemistry |
In addition to BLOSUM matrices, a previously developed scoring matrix can be used. This is known as a PAM. The two result in the same scoring outcome, but use differing methodologies. BLOSUM looks directly at mutations in motifs of related sequences while PAM's extrapolate evolutionary information based on closely related sequences.
Since both PAM and BLOSUM are different methods for showing the same scoring information, the two can be compared but due to the very different method of obtaining this score, a PAM100 does not equal a BLOSUM100. | 1 | Biochemistry |
Aqueous biphasic systems (ABS) or aqueous two-phase systems (ATPS) are clean alternatives for traditional organic-water solvent extraction systems.
ABS are formed when either two polymers, one polymer and one kosmotropic salt, or two salts (one chaotropic salt and the other a kosmotropic salt) are mixed at appropriate concentrations or at a particular temperature. The two phases are mostly composed of water and non volatile components, thus eliminating volatile organic compounds. They have been used for many years in biotechnological applications as non-denaturing and benign separation media. Recently, it has been found that ATPS can be used for separations of metal ions like mercury and cobalt, carbon nanotubes, environmental remediation, metallurgical applications and as a reaction media. | 3 | Analytical Chemistry |
RNAPII can exist in two forms: RNAPII0, with a highly phosphorylated CTD, and RNAPIIA, with a nonphosphorylated CTD. Phosphorylation occurs principally on Ser2 and Ser5 of the repeats, although these positions are not equivalent. The phosphorylation state changes as RNAPII progresses through the transcription cycle: The initiating RNAPII is form IIA, and the elongating enzyme is form II0. While RNAPII0 does consist of RNAPs with hyperphosphorylated CTDs, the pattern of phosphorylation on individual CTDs can vary due to differential phosphorylation of Ser2 versus Ser5 residues and/or to differential phosphorylation of repeats along the length of the CTD. The PCTD (phosphoCTD of an RNAPII0) physically links pre-mRNA processing to transcription by tethering processing factors to elongating RNAPII, e.g., 5′-end capping, 3′-end cleavage, and polyadenylation.
Ser5 phosphorylation (Ser5PO) near the 5′ ends of genes depends principally on the kinase activity of TFIIH (Kin28 in yeast; CDK7 in metazoans). The transcription factor TFIIH is a kinase and will hyperphosphorylate the CTD of RNAP, and in doing so, causes the RNAP complex to move away from the initiation site. Subsequent to the action of TFIIH kinase, Ser2 residues are phosphorylated by CTDK-I in yeast (CDK9 kinase in metazoans). Ctk1 (CDK9) acts in complement to phosphorylation of serine 5 and is, thus, seen in middle to late elongation.
CDK8 and cyclin C (CCNC) are components of the RNA polymerase II holoenzyme that phosphorylate the carboxy-terminal domain (CTD). CDK8 regulates transcription by targeting the CDK7/cyclin H subunits of the general transcription initiation factor IIH (TFIIH), thereby providing a link between the mediator and the basal transcription machinery.
The gene CTDP1 encodes a phosphatase that interacts with the carboxy-terminus of transcription initiation factor TFIIF, a transcription factor that regulates elongation as well as initiation by RNA polymerase II.
Also involved in the phosphorylation and regulation of the RPB1 CTD is cyclin T1 (CCNT1). Cyclin T1 tightly associates and forms a complex with CDK9 kinase, both of which are involved in the phosphorylation and regulation.
: ATP + [DNA-directed RNA polymerase II] <=> ADP + [DNA-directed RNA polymerase II] phosphate : catalyzed by CDK9 EC 2.7.11.23.
TFIIF and FCP1 cooperate for RNAPII recycling. FCP1, the CTD phosphatase, interacts with RNA polymerase II. Transcription is regulated by the state of phosphorylation of a heptapeptide repeat. The nonphosphorylated form, RNAPIIA, is recruited to the initiation complex, whereas the elongating polymerase is found with RNAPII0. RNAPII cycles during transcription. CTD phosphatase activity is regulated by two GTFs (TFIIF and TFIIB). The large subunit of TFIIF (RAP74) stimulates the CTD phosphatase activity, whereas TFIIB inhibits TFIIF-mediated stimulation. Dephosphorylation of the CTD alters the migration of the largest subunit of RNAPII (RPB1). | 1 | Biochemistry |
The idea that there must be specific transport proteins associated with the uptake of monoamines and acetylcholine into vesicles developed due to the discovery of specific inhibitors which interfered with monoamine neurotransmission and also depleted monoamines in neuroendocrine tissues. VMAT1 and VMAT2 were first identified in rats upon cloning cDNAs for proteins which gave non-amine accumulating recipient cells the ability to sequester monoamines. Subsequently, human VMATs were cloned using human cDNA libraries with the rat homologs as probes, and heterologous-cell amine uptake assays were performed to verify transport properties. | 1 | Biochemistry |
It is branded as Dynorm, Inhibace, Vascace and many other names in various countries. None of these are available in the United States as of May 2010. | 4 | Stereochemistry |
Crystallographic data are primarily extracted from published scientific articles and supplementary material. Newer versions of crystallographic databases are built on the relational database model, which enables efficient cross-referencing of tables. Cross-referencing serves to derive additional data or enhance the search capacity of the database.
Data exchange among crystallographic databases, structure visualization software, and structure refinement programs has been facilitated by the emergence of the Crystallographic Information File (CIF) format. The CIF format is the standard file format for the exchange and archiving of crystallographic data.
It was adopted by the International Union of Crystallography (IUCr), who also provides full specifications of the format. It is supported by all major crystallographic databases.
The increasing automation of the crystal structure determination process has resulted in ever higher publishing rates of new crystal structures and, consequentially, new publishing models. Minimalistic articles contain only crystal structure tables, structure images, and, possibly, abstract-like structure description. They tend to be published in author-financed or subsidized open-access journals. Acta Crystallographica Section E and Zeitschrift für Kristallographie belong in this category. More elaborate contributions may go to traditional subscriber-financed journals. Hybrid journals, on the other hand, embed individual author-financed open-access articles among subscriber-financed ones. Publishers may also make scientific articles available online, as Portable Document Format (PDF) files.
Crystal structure data in CIF format are linked to scientific articles as supplementary material. CIFs may be accessible directly from the publisher's website, crystallographic databases, or both. In recent years, many publishers of crystallographic journals have come to interpret CIFs as formatted versions of open data, i.e. representing non-copyrightable facts, and therefore tend to make them freely available online, independent of the accessibility status of linked scientific articles. | 7 | Physical Chemistry |
Karat is a variant of carat. First attested in English in the mid-15th century, the word carat came from Middle French , in turn derived either from Italian or Medieval Latin . These were borrowed into Medieval Europe from the Arabic meaning "fruit of the carob tree", also "weight of 5 grains", () and was a unit of mass though it was probably not used to measure gold in classical times. The Arabic term ultimately originates from the Greek () meaning carob seed (literally "small horn") (diminutive of – , "horn").
In 309 CE, Roman Emperor Constantine I began to mint a new gold coin solidus that was of a libra (Roman pound) of gold equal to a mass of 24 siliquae, where each siliqua (or carat) was of a libra. This is believed to be the origin of the value of the karat. | 8 | Metallurgy |
Carboxylic acids, amides, esters, and carboxylate salts convert to the trifluoromethyl derivatives, although conditions vary widely:
For carboxlic acids, the first step gives the acyl fluorides, in keeping with the tendency of SF to fluorinate acidic hydroxyl groups:
Similarly SF converts sulfonic acids to sulfonyl fluorides:
Aldehydes and ketones convert to geminal difluorides:
Alcohols convert to alkyl fluorides, although this conversion works best with acidic alcohols, such as fluorinated alcohols: | 0 | Organic Chemistry |
IR near-field scanning optical microscopy (IR-NSOM) is a powerful spectroscopic tool because it allows subwavelength resolution in IR spectroscopy. Previously, IR-NSOM was realized by applying a solid immersion lens with a refractive index of n, which shortens wavelength (λ) to (λ/n), compared to FTIR-based IR microscopy. In 2004, an IR-SNOM achieved a spatial resolution ~λ/7 that is less than 1 μm. This resolution was further improved to about λ/60 that is 50–150 nm for a boron nitride thin film sample.
IR-NSOM uses an AFM to detect the absorption response of a material to the modulated infrared radiation from an FTIR spectrometer and therefore is also referred to as AFM/FTIR spectroscopy. Two approaches have been used to measure the response of polymer systems to infrared absorption. The first mode relies on the AFM contact mode, and the second mode of operation employs a scanning thermal microscopy probe (invented in 1986) to measure the polymer's temperature increase. In 2007, AFM was combined with infrared attenuated total reflection (IR-ATR) spectroscopy to study the dissolution process of urea in a cyclohexane/butanol solution with a high spatial resolution. | 7 | Physical Chemistry |
: The codon AUG both codes for methionine and serves as an initiation site: the first AUG in an mRNA's coding region is where translation into protein begins. | 1 | Biochemistry |
FS 49 C2 is believed to cause less damage to the environment. Its main component is the most widely used replacement gas for refrigeration systems, characterized by zero Ozone Depletion Potential (ODP) factor. FS 49 C2 is suitable to replace Halon 1301 as a "drop in" upgrade of existing Halon systems.
Filling a room 12% by FS 49 C2 is sufficient to suppress a flame-based fire.
Even though FS 49 C2 gas does not leave toxic gases behind, a self-contained breathing apparatus is recommended when in a fire site because in the process of extinguishing the fire, FS 49 C2 may release potentially harmful gases. | 2 | Environmental Chemistry |
In geochemistry, hydrology, paleoclimatology and paleoceanography, δN (pronounced "delta fifteen n") or delta-N-15 is a measure of the ratio of the two stable isotopes of nitrogen, N:N. | 9 | Geochemistry |
Ocean acidification has occurred previously in Earth's history. It happened during the Capitanian mass extinction, at the end-Permian extinction, during the end-Triassic extinction, and during the Cretaceous–Palaeogene extinction event.
Three of the big five mass extinction events in the geologic past were associated with a rapid increase in atmospheric carbon dioxide, probably due to volcanism and/or thermal dissociation of marine gas hydrates. Elevated CO levels impacted biodiversity. Decreased saturation due to seawater uptake of volcanogenic CO has been suggested as a possible kill mechanism during the marine mass extinction at the end of the Triassic. The end-Triassic biotic crisis is still the most well-established example of a marine mass extinction due to ocean acidification, because (a) carbon isotope records suggest enhanced volcanic activity that decreased the carbonate sedimentation which reduced the carbonate compensation depth and the carbonate saturation state, and a marine extinction coincided precisely in the stratigraphic record, and (b) there was pronounced selectivity of the extinction against organisms with thick aragonitic skeletons, which is predicted from experimental studies. Ocean acidification has also been suggested as a one cause of the end-Permian mass extinction and the end-Cretaceous crisis. Overall, multiple climatic stressors, including ocean acidification, was likely the cause of geologic extinction events.
The most notable example of ocean acidification is the Paleocene-Eocene Thermal Maximum (PETM), which occurred approximately 56 million years ago when massive amounts of carbon entered the ocean and atmosphere, and led to the dissolution of carbonate sediments across many ocean basins. Relatively new geochemical methods of testing for pH in the past indicate the pH dropped 0.3 units across the PETM. One study that solves the marine carbonate system for saturation state shows that it may not change much over the PETM, suggesting the rate of carbon release at our best geological analogy was much slower than human-induced carbon emissions. However, stronger proxy methods to test for saturation state are needed to assess how much this pH change may have affected calcifying organisms. | 9 | Geochemistry |
Jones became interested in science as a freshman at high school, where she took part in a national Science Technology Engineering Program. She earned a BS in biochemistry at Syracuse University in 1999. Jones completed her PhD at Georgia State University and specialized in structural biology.
Jones received postdoctoral training in structural virology at the University of Alabama at Birmingham. She was a Pfizer postdoctoral researcher at Washington University in St. Louis working with Michael Gross on MassSpec-based protein foot-printing. | 1 | Biochemistry |
It has been shown that ATM phosphorylates KAP1 upon the discovery of damaged or broken DNA. Phosphorylated KAP1, along with many other DNA damage proteins, rapidly migrate to the site of the DNA damage. Its exact involvement in this pathway is somewhat unclear, but it has been implicated in triggering cell arrest, allowing for the damaged DNA to be repaired. | 1 | Biochemistry |
The number of female scientists in the organic chemistry community, industry and academics, remains low (<20%). Advancement of women in the chemical sciences is a challenge due to the so-called “leaky pipeline,” wherein growing numbers of women enter academics and industry to study science opt out to pursue alternative careers, some of which are congruent with science while others are outside the discipline altogether. Inspired by the Grace Hopper Celebration of Women in Computing series of Conferences to encourage women to participate in computer science, gender diversity should be a goal across our community and we should actively be looking for opportunities to recognize, identify and retain women in the field of organic chemistry regardless of gender or any other protected characteristic.
To accomplish this goal a group of scientists (Lara Kallander, Donna Huryn, Ellie Cantor, Rebecca Ruck, Margaret Faul and Mary Watson) founded the non-profit Empowering Women in Organic Chemistry (EWOC) Conferences in 2019. The volunteer-run EWOC conferences allow women leaders to present their scientific research and also allows the participants to hear career stories of how eminent women in the field of organic chemistry have developed their careers and the challenges they have faced – and overcome – along the way. The meeting consists of both science and career topics to provide support and guidance for the next generation of women chemists, as well as provide opportunities for professionals to learn up-to-date science, network and share experiences.
Since 2021, various regional chapters of EWOC chapters have been launched, featuring virtual symposia and other events. | 0 | Organic Chemistry |
With an active surface area of 160 cm, the nasal cavity is another noteworthy route of mucoadhesive administration. Due to the sweeping motion of the cilia that lines the mucosa, nasal mucus has a quick turnover of 10 to 15 minutes. Because of this, the nasal cavity is most suitable for rapid, local medicinal dosages. Additionally, its close proximity to the blood–brain barrier makes it a convenient route for administering specialized drugs to the central nervous system. Gels, solutions, and aerosols are common dosage forms in the nasal cavity. However, recent research into particles and microspheres have shown increased bioavailability over non-solid forms of medicine largely due to the use of mucoadhesives. | 1 | Biochemistry |
In thermodynamics, superheating (sometimes referred to as boiling retardation, or boiling delay) is the phenomenon in which a liquid is heated to a temperature higher than its boiling point, without boiling. This is a so-called metastable state or metastate, where boiling might occur at any time, induced by external or internal effects. Superheating is achieved by heating a homogeneous substance in a clean container, free of nucleation sites, while taking care not to disturb the liquid.
This may occur by microwaving water in a very smooth container. Disturbing the water may cause an unsafe eruption of hot water and result in burns. | 7 | Physical Chemistry |
Price, Reed, and Papin, from the Palsson lab, use a method of singular value decomposition (SVD) of extreme pathways in order to understand regulation of a human red blood cell metabolism. Extreme pathways are convex basis vectors that consist of steady state functions of a metabolic network. For any particular metabolic network, there is always a unique set of extreme pathways available. Furthermore, Price, Reed, and Papin, define a constraint-based approach, where through the help of constraints like mass balance and maximum reaction rates, it is possible to develop a ‘solution space’ where all the feasible options fall within. Then, using a kinetic model approach, a single solution that falls within the extreme pathway solution space can be determined. Therefore, in their study, Price, Reed, and Papin, use both constraint and kinetic approaches to understand the human red blood cell metabolism. In conclusion, using extreme pathways, the regulatory mechanisms of a metabolic network can be studied in further detail. | 1 | Biochemistry |
The initial melting of the material to be smelted is usually referred to as the smelting or matte smelting stage. It can be undertaken in a variety of furnaces, including the largely obsolete blast furnaces and reverberatory furnaces, as well as flash furnaces, Isasmelt furnaces, etc. The product of this smelting stage is a mixture of copper, iron and sulfur that is enriched in copper, which is called matte or copper matte. The term matte grade is normally used to refer to the copper content of the matte.
The purpose of the matte smelting stage is to eliminate as much of the unwanted iron, sulfur and gangue minerals (such as silica, magnesia, alumina and limestone) as possible, while minimizing the loss of copper. This is achieved by reacting iron sulfides with oxygen (in air or oxygen enriched air) to produce iron oxides (mainly as FeO, but with some magnetite (FeO)) and sulfur dioxide.
Copper sulfide and iron oxide can mix, but when sufficient silica is added, a separate slag layer is formed. Adding silica also reduces the melting point (or, more properly, the liquidus temperature) of the slag, meaning that the smelting process can be operated at a lower temperature.
The slag forming reaction is:
:FeO + SiO → FeO.SiO
Slag is less dense than matte, so it forms a layer that floats on top of the matte.
Copper can be lost from the matte in three ways: as cuprous oxide (CuO) dissolved in the slag, as sulfide copper dissolved in the slag or as tiny droplets (or prills) of matte suspended in the slag.
The amount of copper lost as oxide copper increases as the oxygen potential of the slag increases. The oxygen potential generally increases as the copper content of the matte is increased. Thus, the loss of copper as oxide increases as the copper content of the matte increases.
On the other hand, the solubility of sulfidic copper in slag decreases as the copper content of the matte increases beyond about 40%. Nagamori calculated that more than half the copper dissolved in slags from mattes containing less than 50% copper is sulfidic copper. Above this figure, oxidic copper begins to dominate.
The loss of copper as prills suspended in the slag depends on the size of the prills, the viscosity of the slag and the settling time available. Rosenqvist suggested that about half the copper losses to slag were due to suspended prills.
The mass of slag generated in the smelting stage depends on the iron content of the material fed into the smelting furnace and the target matte grade. The greater the iron content of the feed, the more iron that will need to be rejected to the slag for a given matte grade. Similarly, increasing the target matte grade requires the rejection of more iron and an increase in the slag volume.
Thus, the two factors that most affect the loss of copper to slag in the smelting stage are:
* matte grade
* mass of slag.
This means that there is a practical limit on how high the matte grade can be if the loss of copper to slag is to be minimized. Therefore, further stages of processing (converting and fire refining) are required.
The following subsections briefly describe some of the processes used in matte smelting. | 8 | Metallurgy |
A structural feature common to all IAP family proteins is that they all contain at least one baculoviral IAP repeat (BIR) domain characterized by a conserved zinc-coordinating Cys/His motif at the N-terminal half of the protein.
Survivin is distinguished from other IAP family members in that it has only one BIR domain. The mice and human BIR domain of survivin are very similar structurally except for two differences that may affect function variability. The human survivin also contains an elongated C-terminal helix comprising 42 amino acids. Survivin is 16.5 kDa large and is the smallest member of the IAP family.
X-ray crystallography has shown two molecules of human survivin coming together to form a bowtie-shape dimer through a hydrophobic interface. This interface includes N-terminal residues 6-10 just before the BIR domain region and the 10 residue region connecting the BIR domain to the C-terminal helix. The structural integrity of the determined crystal structure of survivin is quite reliable, as physiological conditions were used to obtain the images. | 1 | Biochemistry |
The Burgess reagent (methyl N-(triethylammoniumsulfonyl)carbamate) is a mild and selective dehydrating reagent often used in organic chemistry. It was developed in the laboratory of Edward M. Burgess at Georgia Tech.
The Burgess reagent is used to convert secondary and tertiary alcohols with an adjacent proton into alkenes. Dehydration of primary alcohols does not work well. The reagent is soluble in common organic solvents and alcohol dehydration takes place with syn elimination through an intramolecular elimination reaction. The Burgess reagent is a carbamate and an inner salt. A general mechanism is shown below. | 0 | Organic Chemistry |
A common way to determine the coordination number of an atom is by X-ray crystallography. Related techniques include neutron or electron diffraction. The coordination number of an atom can be determined straightforwardly by counting nearest neighbors.
α-Aluminium has a regular cubic close packed structure, fcc, where each aluminium atom has 12 nearest neighbors, 6 in the same plane and 3 above and below and the coordination polyhedron is a cuboctahedron. α-Iron has a body centered cubic structure where each iron atom has 8 nearest neighbors situated at the corners of a cube.
The two most common allotropes of carbon have different coordination numbers. In diamond, each carbon atom is at the centre of a regular tetrahedron formed by four other carbon atoms, the coordination number is four, as for methane. Graphite is made of two-dimensional layers in which each carbon is covalently bonded to three other carbons; atoms in other layers are further away and are not nearest neighbours, giving a coordination number of 3.
For chemical compounds with regular lattices such as sodium chloride and caesium chloride, a count of the nearest neighbors gives a good picture of the environment of the ions. In sodium chloride each sodium ion has 6 chloride ions as nearest neighbours (at 276 pm) at the corners of an octahedron and each chloride ion has 6 sodium atoms (also at 276 pm) at the corners of an octahedron. In caesium chloride each caesium has 8 chloride ions (at 356 pm) situated at the corners of a cube and each chloride has eight caesium ions (also at 356 pm) at the corners of a cube. | 4 | Stereochemistry |
There is a substantial body of research showing that a combination of ocean acidification and elevated ocean temperature have a compounded effect on marine life and the ocean environment. This effect far exceeds the individual harmful impact of either. In addition, ocean warming, along with increased productivity of phytoplankton from higher CO levels exacerbates ocean deoxygenation. Deoxygenation of ocean waters is an additional stressor on marine organisms that increases ocean stratification therefore limiting nutrients over time and reducing biological gradients.
Meta analyses have quantified the direction and magnitude of the harmful effects of combined ocean acidification, warming and deoxygenation on the ocean. These meta-analyses have been further tested by mesocosm studies that simulated the interaction of these stressors and found a catastrophic effect on the marine food web: thermal stress more than negates any primary producer to herbivore increase in productivity from elevated . | 9 | Geochemistry |
An inelastic collision, in contrast to an elastic collision, is a collision in which kinetic energy is not conserved due to the action of internal friction.
In collisions of macroscopic bodies, some kinetic energy is turned into vibrational energy of the atoms, causing a heating effect, and the bodies are deformed.
The molecules of a gas or liquid rarely experience perfectly elastic collisions because kinetic energy is exchanged between the molecules translational motion and their internal degrees of freedom with each collision. At any one instant, half the collisions are – to a varying extent – inelastic (the pair possesses less kinetic energy after the collision than before), and half could be described as “super-elastic” (possessing more' kinetic energy after the collision than before). Averaged across an entire sample, molecular collisions are elastic.
Although inelastic collisions do not conserve kinetic energy, they do obey conservation of momentum. Simple ballistic pendulum problems obey the conservation of kinetic energy only when the block swings to its largest angle.
In nuclear physics, an inelastic collision is one in which the incoming particle causes the nucleus it strikes to become excited or to break up. Deep inelastic scattering is a method of probing the structure of subatomic particles in much the same way as Rutherford probed the inside of the atom (see Rutherford scattering). Such experiments were performed on protons in the late 1960s using high-energy electrons at the Stanford Linear Accelerator (SLAC). As in Rutherford scattering, deep inelastic scattering of electrons by proton targets revealed that most of the incident electrons interact very little and pass straight through, with only a small number bouncing back. This indicates that the charge in the proton is concentrated in small lumps, reminiscent of Rutherford's discovery that the positive charge in an atom is concentrated at the nucleus. However, in the case of the proton, the evidence suggested three distinct concentrations of charge (quarks) and not one. | 7 | Physical Chemistry |
E. J. Bowen was the eldest of four born to Edmund Riley Bowen and Lilias Bowen (née Kamester) in 1898 in Worcester, England. He attended the Royal Grammar School Worcester.
He won the Brackenbury Scholarship in 1915 to the University of Oxford where he studied chemistry. In 1916, after less than a year of his undergraduate course, he volunteered for training as a gunner officer and served as Second Lieutenant in the Royal Garrison Artillery during World War I. After being demobilised in 1919, he returned to Balliol College. | 5 | Photochemistry |
In addition to crystallographic space groups there are also magnetic space groups (also called two-color (black and white) crystallographic groups or Shubnikov groups). These symmetries contain an element known as time reversal. They treat time as an additional dimension, and the group elements can include time reversal as reflection in it. They are of importance in magnetic structures that contain ordered unpaired spins, i.e. ferro-, ferri- or antiferromagnetic structures as studied by neutron diffraction. The time reversal element flips a magnetic spin while leaving all other structure the same and it can be combined with a number of other symmetry elements. Including time reversal there are 1651 magnetic space groups in 3D . It has also been possible to construct magnetic versions for other overall and lattice dimensions ([https://web.archive.org/web/20111119065722/http://www.bk.psu.edu/faculty/litvin/Download.html Daniel Litvin's papers], , ). Frieze groups are magnetic 1D line groups and layer groups are magnetic wallpaper groups, and the axial 3D point groups are magnetic 2D point groups. Number of original and magnetic groups by (overall, lattice) dimension: | 4 | Stereochemistry |
Involved in the earliest step for the formation of the active cleavage complex, the CFIm complex is formed by three proteins of 25, 59 and 68 kDa, respectively:
*CFIm25 (or CPSF5/NUDT21)
*CFIm59 (or CPSF7)
*CFIm68 (or CPSF6)
CFIm25 and CFIm68 are sufficient for the activity of the complex, proving the expected redundancy of CFIm68 and CFIm59, which share great sequence similarity. | 1 | Biochemistry |
Hemoglobin consists of protein subunits (globin molecules), which are polypeptides, long folded chains of specific amino acids which determine the proteins chemical properties and function. The amino acid sequence of any polypeptide is translated from a segment of DNA, the corresponding gene. The amino acid sequence that determines the proteins chemical properties and function.
There is more than one hemoglobin gene. In humans, hemoglobin A (the main form of hemoglobin in adults) is coded by genes HBA1, HBA2, and HBB. Alpha 1 and alpha 2 subunits are respectively coded by genes HBA1 and HBA2 close together on chromosome 16, while the beta subunit is coded by gene HBB on chromosome 11. The amino acid sequences of the globin subunits usually differ between species, with the difference growing with evolutionary distance. For example, the most common hemoglobin sequences in humans, bonobos and chimpanzees are completely identical, with exactly the same alpha and beta globin protein chains. Human and gorilla hemoglobin differ in one amino acid in both alpha and beta chains, and these differences grow larger between less closely related species.
Mutations in the genes for hemoglobin can result in variants of hemoglobin within a single species, although one sequence is usually "most common" in each species. Many of these mutations cause no disease, but some cause a group of hereditary diseases called hemoglobinopathies. The best known hemoglobinopathy is sickle-cell disease, which was the first human disease whose mechanism was understood at the molecular level. A mostly separate set of diseases called thalassemias involves underproduction of normal and sometimes abnormal hemoglobins, through problems and mutations in globin gene regulation. All these diseases produce anemia.
Variations in hemoglobin sequences, as with other proteins, may be adaptive. For example, hemoglobin has been found to adapt in different ways to the thin air at high altitudes, where lower partial pressure of oxygen diminishes its binding to hemoglobin compared to the higher pressures at sea level. Recent studies of deer mice found mutations in four genes that can account for differences between high- and low-elevation populations. It was found that the genes of the two breeds are "virtually identical—except for those that govern the oxygen-carrying capacity of their hemoglobin. . . . The genetic difference enables highland mice to make more efficient use of their oxygen." Mammoth hemoglobin featured mutations that allowed for oxygen delivery at lower temperatures, thus enabling mammoths to migrate to higher latitudes during the Pleistocene. This was also found in hummingbirds that inhabit the Andes. Hummingbirds already expend a lot of energy and thus have high oxygen demands and yet Andean hummingbirds have been found to thrive in high altitudes. Non-synonymous mutations in the hemoglobin gene of multiple species living at high elevations (Oreotrochilus, A. castelnaudii, C. violifer, P. gigas, and A. viridicuada) have caused the protein to have less of an affinity for inositol hexaphosphate (IHP), a molecule found in birds that has a similar role as 2,3-BPG in humans; this results in the ability to bind oxygen in lower partial pressures.
Birds unique circulatory lungs also promote efficient use of oxygen at low partial pressures of O. These two adaptations reinforce each other and account for birds remarkable high-altitude performance.
Hemoglobin adaptation extends to humans, as well. There is a higher offspring survival rate among Tibetan women with high oxygen saturation genotypes residing at 4,000 m. Natural selection seems to be the main force working on this gene because the mortality rate of offspring is significantly lower for women with higher hemoglobin-oxygen affinity when compared to the mortality rate of offspring from women with low hemoglobin-oxygen affinity. While the exact genotype and mechanism by which this occurs is not yet clear, selection is acting on these women's ability to bind oxygen in low partial pressures, which overall allows them to better sustain crucial metabolic processes. | 7 | Physical Chemistry |
Benzene is classified as a carcinogen, which increases the risk of cancer and other illnesses, and is also a notorious cause of bone marrow failure. Substantial quantities of epidemiologic, clinical, and laboratory data link benzene to aplastic anemia, acute leukemia, bone marrow abnormalities and cardiovascular disease. The specific hematologic malignancies that benzene is associated with include: acute myeloid leukemia (AML), aplastic anemia, myelodysplastic syndrome (MDS), acute lymphoblastic leukemia (ALL), and chronic myeloid leukemia (CML).
The American Petroleum Institute (API) stated as early as 1948 that "it is generally considered that the only absolutely safe concentration for benzene is zero". There is no safe exposure level; even tiny amounts can cause harm. The US Department of Health and Human Services (DHHS) classifies benzene as a human carcinogen. Long-term exposure to excessive levels of benzene in the air causes leukemia, a potentially fatal cancer of the blood-forming organs. In particular, acute myeloid leukemia or acute nonlymphocytic leukemia (AML & ANLL) is caused by benzene. IARC rated benzene as "known to be carcinogenic to humans" (Group 1).
As benzene is ubiquitous in gasoline and hydrocarbon fuels that are in use everywhere, human exposure to benzene is a global health problem. Benzene targets the liver, kidney, lung, heart and brain and can cause DNA strand breaks and chromosomal damage, hence is teratogenic and mutagenic. Benzene causes cancer in animals including humans. Benzene has been shown to cause cancer in both sexes of multiple species of laboratory animals exposed via various routes. | 2 | Environmental Chemistry |
The periactive zone surrounds the active zone and is the site of endocytosis of the presynaptic terminal. In the periactive zone, scaffolding proteins such as intersectin 1 recruit proteins that mediate endocytosis such as dynamin, clathrin and endophilin. In Drosophila the intersectin homolog, Dap160, is located in the periactive zone of the neuromuscular junction and mutant Dap160 deplete synaptic vesicles during high frequency stimulation. | 1 | Biochemistry |
Trace fossils are generally difficult or impossible to assign to a specific maker. Only in very rare occasions are the makers found in association with their tracks. Further, entirely different organisms may produce identical tracks. Therefore, conventional taxonomy is not applicable, and a comprehensive form of taxonomy has been erected. At the highest level of the classification, five behavioral modes are recognized:
* Domichnia, dwelling structures reflecting the life position of the organism that created it.
* Fodinichnia, three-dimensional structures left by animals which eat their way through sediment, such as deposit feeders;
* Pascichnia, feeding traces left by grazers on the surface of a soft sediment or a mineral substrate;
* Cubichnia, resting traces, in the form of an impression left by an organism on a soft sediment;
* Repichnia, surface traces of creeping and crawling.
Fossils are further classified into form genera, a few of which are even subdivided to a "species" level. Classification is based on shape, form, and implied behavioural mode.
To keep body and trace fossils nomenclatorially separate, ichnospecies are erected for trace fossils. Ichnotaxa are classified somewhat differently in zoological nomenclature than taxa based on body fossils (see trace fossil classification for more information). Examples include:
*Late Cambrian trace fossils from intertidal settings include Protichnites and Climactichnites, amongst others
*Mesozoic dinosaur footprints including ichnogenera such as Grallator, Atreipus, and Anomoepus
*Triassic to Recent termite mounds, which can encompass several square kilometers of sediment | 2 | Environmental Chemistry |
Biogenic sulfide corrosion is a bacterially mediated process of forming hydrogen sulfide gas and the subsequent conversion to sulfuric acid that attacks concrete and steel within wastewater environments. The hydrogen sulfide gas is biochemically oxidized in the presence of moisture to form sulfuric acid. The effect of sulfuric acid on concrete and steel surfaces exposed to severe wastewater environments can be devastating. In the USA alone, corrosion is causing sewer asset losses estimated at $14 billion per year. This cost is expected to increase as the aging infrastructure continues to fail. | 8 | Metallurgy |
Neutron backscattering is one of several inelastic neutron scattering techniques. Backscattering from monochromator and analyzer crystals is used to achieve an energy resolution on the order of a microelectronvolt (μeV). Neutron backscattering experiments are performed to study atomic or molecular motion on a nanosecond time scale. | 7 | Physical Chemistry |
In organic chemistry, "sulfide" usually refers to the linkage C–S–C, although the term thioether is less ambiguous. For example, the thioether dimethyl sulfide is CH–S–CH. Polyphenylene sulfide (see below) has the empirical formula CHS. Occasionally, the term sulfide refers to molecules containing the –SH functional group. For example, methyl sulfide can mean CH–SH. The preferred descriptor for such SH-containing compounds is thiol or mercaptan, i.e. methanethiol, or methyl mercaptan. | 0 | Organic Chemistry |
Botanical gardens, zoos, and aquariums are the most conventional methods of ex situ conservation. Also in ex situ conservation, all of which house whole, protected specimens for breeding and reintroduction into the wild when necessary and possible. These facilities provide not only housing and care for specimens of endangered species, but also have an educational value. They inform the public of the threatened status of endangered species and of those factors which cause the threat, with the hope of creating public interest in stopping and reversing those factors which jeopardize a species survival in the first place. They are the most publicly visited ex situ' conservation sites, with the WZCS (World Zoo Conservation Strategy) estimating that the 1,100 organized zoos in the world receive more than 600 million visitors annually. Globally there is an estimated total of 2,107 aquaria and zoos in 125 countries. Additionally many private collectors or other not-for-profit groups hold animals and they engage in conservation or reintroduction efforts. Similarly there are approximately 2,000 botanical gardens in 148 counties cultivating or storing an estimated 80,000 taxa of plants. | 1 | Biochemistry |
Although the mechanism of codon bias selection remains controversial, possible explanations for this bias fall into two general categories. One explanation revolves around the selectionist theory, in which codon bias contributes to the efficiency and/or accuracy of protein expression and therefore undergoes positive selection. The selectionist model also explains why more frequent codons are recognized by more abundant tRNA molecules, as well as the correlation between preferred codons, tRNA levels, and gene copy numbers. Although it has been shown that the rate of amino acid incorporation at more frequent codons occurs at a much higher rate than that of rare codons, the speed of translation has not been shown to be directly affected and therefore the bias towards more frequent codons may not be directly advantageous. However, the increase in translation elongation speed may still be indirectly advantageous by increasing the cellular concentration of free ribosomes and potentially the rate of initiation for messenger RNAs (mRNAs).
The second explanation for codon usage can be explained by mutational bias, a theory which posits that codon bias exists because of nonrandomness in the mutational patterns. In other words, some codons can undergo more changes and therefore result in lower equilibrium frequencies, also known as “rare” codons. Different organisms also exhibit different mutational biases, and there is growing evidence that the level of genome-wide GC content is the most significant parameter in explaining codon bias differences between organisms. Additional studies have demonstrated that codon biases can be statistically predicted in prokaryotes using only intergenic sequences, arguing against the idea of selective forces on coding regions and further supporting the mutation bias model. However, this model alone cannot fully explain why preferred codons are recognized by more abundant tRNAs. | 1 | Biochemistry |
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