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Porous polymers are a class of porous media materials in which monomers form 2D and 3D polymers containing angstrom- to nanometer-scale pores formed by the arrangement of the monomers. They may be either crystalline or amorphous. Subclasses include covalent organic frameworks (COFs), hydrogen-bonded organic frameworks (HOFs), metal-organic frameworks (MOFs), and porous organic polymers (POPs). The subfield of chemistry specializing in porous polymers is called reticular chemistry. | 6 | Supramolecular Chemistry |
The main criticism is directed to the formal presentation of the theory (heavy mathematical jargon), number of listed parameters, the symbol heavy notation, and the fact that modeled (state) variables and parameters are abstract quantities which cannot be directly measured, all making it less likely to reach its intended audience (ecologists) and be an "efficient" theory.
However, more recent publications aim to present the DEB theory in an "easier to digest" content to "bridge the ecology-mathematics gap". List of parameters is a direct result of list of processes which are of interest—if only growth under constant food and temperature is of interest, the standard DEB model can be simplified to the von Bertalanffy growth curve. Adding more processes into focus (such as reproduction and/or maturation), and forcing the model with fluctuating (dynamic) environmental conditions, needless to say, will result in more parameters.
The general methodology of estimation of DEB parameters from data is described in [http://www.bio.vu.nl/thb/research/bib/Meer2006.html van der Meer 2006]; [http://www.bio.vu.nl/thb/research/bib/KooySous2008.html Kooijman et al 2008] shows which particular compound parameters can be estimated from a few simple observations at a single food density and how an increasing number of parameters can be estimated if more quantities are observed at several food densities. A natural sequence exists in which parameters can be known in principle. In addition, routines for data entry and scripts for parameter estimation are available as a free and documented software package [http://www.bio.vu.nl/thb/deb/deblab/debtool/DEBtool_M/manual/index.html DEBtool] , aiming to provide a ready-to-use tool for users with less mathematical and programing background. Number of parameters, also pointed as relatively sparse for a bioenergetic model, vary depending on the main application and, because the whole life cycle of an organism is defined, the overall number of parameters per data-set ratio is relatively low. Linking the DEB (abstract) and measured properties is done by simple mathematical operations which include auxiliary parameters (also defined by the DEB theory and included in the [http://www.bio.vu.nl/thb/deb/deblab/debtool/DEBtool_M/manual/index.html DEBtool] routines), and include also switching between energy-time and mass-time contexts. [https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/index.html Add my pet (AmP)] project explores parameter pattern values across taxa. The DEB notation is a result of combining the symbols from the main fields of science (biology, chemistry, physics, mathematics) used in the theory, while trying to keep the symbols consistent. As the symbols themselves contain a fair bit of information (see [http://www.bio.vu.nl/thb/research/bib/Kooy2010_n.pdf DEB notation] document), they are kept in most of the DEB literature. | 1 | Biochemistry |
Funded by the European Commission- Horizon 2020 and European Green Deal
Duration: 4 years (October 2021-September 2025)
Objective: The main scope of the project is to support the EU farm to fork sustainable strategy by providing technical, financial, and political tools and solutions to reduce GHG emissions (by 2030) and achieve carbon neutrality (by 2050) in the food industry. | 7 | Physical Chemistry |
AR-TP009 is expressed by Halorubrum sp. TP009. Its ability to act as a neural silencer has been investigated in mouse cortical pyramidal neurons. | 5 | Photochemistry |
Developed by Julius Schäffer to help with the identification of Agaricus species. A positive reaction of Schaeffers test, which uses the reaction of aniline and nitric acid on the surface of the mushroom, is indicated by an orange to red color; it is characteristic of species in the section Flavescentes'. The compounds responsible for the reaction were named schaefferal A and B to honor Schäffer.
Two intersecting lines are drawn on the surface of the cap, the first with aniline or aniline water, the second with an aqueous solution of 65% nitric acid. The test is considered positive when a bright orange color forms where the lines cross.
Agaricus placomyces and Agaricus xanthodermus produce false negative reactions.
Sometimes referred to as "Schaeffers reaction", "Schaeffers cross reaction" or "Schaeffer's test". | 3 | Analytical Chemistry |
The Köhler curve is the visual representation of the Köhler equation. It shows the supersaturation at which the cloud drop is in equilibrium with the environment over a range of droplet diameters. The exact shape of the curve is dependent upon the amount and composition of the solutes present in the atmosphere. The Köhler curves where the solute is sodium chloride are different from when the solute is sodium nitrate or ammonium sulfate.
The figure above shows three Köhler curves of sodium chloride. Consider (for droplets containing solute with diameter equal to 0.05 micrometers) a point on the graph where the wet diameter is 0.1 micrometers and the supersaturation is 0.35%. Since the relative humidity is above 100%, the droplet will grow until it is in thermodynamic equilibrium. As the droplet grows, it never encounters equilibrium, and thus grows without bound. However, if the supersaturation is only 0.3%, the drop will only grow until about 0.5 micrometers. The supersaturation at which the drop will grow without bound is called the critical supersaturation. The diameter at which the curve peaks is called the critical diameter. | 7 | Physical Chemistry |
The YenR and YenI proteins produced by the gammaproteobacterium Yersinia enterocolitica are similar to Aliivibrio fischeri LuxR and LuxI. YenR activates the expression of a small non-coding RNA, YenS. YenS inhibits YenI expression and acylhomoserine lactone production. YenR/YenI/YenS are involved in the control of swimming and swarming motility. | 1 | Biochemistry |
Different classifications of stoma types exist. One that is widely used is based on the types that Julien Joseph Vesque introduced in 1889, was further developed by Metcalfe and Chalk, and later complemented by other authors. It is based on the size, shape and arrangement of the subsidiary cells that surround the two guard cells.
They distinguish for dicots:
* (meaning star-celled) stomata have guard cells that are surrounded by at least five radiating cells forming a star-like circle. This is a rare type that can for instance be found in the family Ebenaceae.
* (meaning unequal celled) stomata have guard cells between two larger subsidiary cells and one distinctly smaller one. This type of stomata can be found in more than thirty dicot families, including Brassicaceae, Solanaceae, and Crassulaceae. It is sometimes called cruciferous type.
* (meaning irregular celled) stomata have guard cells that are surrounded by cells that have the same size, shape and arrangement as the rest of the epidermis cells. This type of stomata can be found in more than hundred dicot families such as Apocynaceae, Boraginaceae, Chenopodiaceae, and Cucurbitaceae. It is sometimes called ranunculaceous type.
* (meaning cross-celled) stomata have guard cells surrounded by two subsidiary cells, that each encircle one end of the opening and contact each other opposite to the middle of the opening. This type of stomata can be found in more than ten dicot families such as Caryophyllaceae and Acanthaceae. It is sometimes called caryophyllaceous type.
* stomata are bordered by just one subsidiary cell that differs from the surrounding epidermis cells, its length parallel to the stoma opening. This type occurs for instance in the Molluginaceae and Aizoaceae.
* (meaning parallel celled) stomata have one or more subsidiary cells parallel to the opening between the guard cells. These subsidiary cells may reach beyond the guard cells or not. This type of stomata can be found in more than hundred dicot families such as Rubiaceae, Convolvulaceae and Fabaceae. It is sometimes called rubiaceous type.
In monocots, several different types of stomata occur such as:
* gramineous or graminoid (meaning grass-like) stomata have two guard cells surrounded by two lens-shaped subsidiary cells. The guard cells are narrower in the middle and bulbous on each end. This middle section is strongly thickened. The axis of the subsidiary cells are parallel stoma opening. This type can be found in monocot families including Poaceae and Cyperaceae.
* (meaning six-celled) stomata have six subsidiary cells around both guard cells, one at either end of the opening of the stoma, one adjoining each guard cell, and one between that last subsidiary cell and the standard epidermis cells. This type can be found in some monocot families.
* (meaning four-celled) stomata have four subsidiary cells, one on either end of the opening, and one next to each guard cell. This type occurs in many monocot families, but also can be found in some dicots, such as Tilia and several Asclepiadaceae.
In ferns, four different types are distinguished:
* stomata have two guard cells in one layer with only ordinary epidermis cells, but with two subsidiary cells on the outer surface of the epidermis, arranged parallel to the guard cells, with a pore between them, overlying the stoma opening.
* stomata have two guard cells that are entirely encircled by one continuous subsidiary cell (like a donut).
* stomata have two guard cells that are entirely encircled by one subsidiary cell that has not merged its ends (like a sausage).
* stomata have two guard cells that are largely encircled by one subsidiary cell, but also contact ordinary epidermis cells (like a U or horseshoe). | 5 | Photochemistry |
The demand for vanilla flavoring has long exceeded the supply of vanilla beans. , the annual demand for vanillin was 12,000 tons, but only 1,800 tons of natural vanillin were produced. The remainder was produced by chemical synthesis. Vanillin was first synthesized from eugenol (found in oil of clove) in 1874–75, less than 20 years after it was first identified and isolated. Vanillin was commercially produced from eugenol until the 1920s. Later it was synthesized from lignin-containing "brown liquor", a byproduct of the sulfite process for making wood pulp. Counterintuitively, though it uses waste materials, the lignin process is no longer popular because of environmental concerns, and today most vanillin is produced from the petrochemical raw material guaiacol. Several routes exist for synthesizing vanillin from guaiacol.
At present, the most significant of these is the two-step process practiced by Rhodia since the 1970s, in which guaiacol (1) reacts with glyoxylic acid by electrophilic aromatic substitution. The resulting vanillylmandelic acid (2) is then converted by 4-Hydroxy-3-methoxyphenylglyoxylic acid (3) to vanillin (4) by oxidative decarboxylation. | 0 | Organic Chemistry |
In these macromolecules, bonding between parts of the same macromolecule cause it to fold into a specific shape, which helps determine the molecule's physiological or biochemical role. For example, the double helical structure of DNA is due largely to hydrogen bonding between its base pairs (as well as pi stacking interactions), which link one complementary strand to the other and enable replication. | 6 | Supramolecular Chemistry |
In aqueous solution, bromocresol green will ionize to give the monoanionic form (yellow), that further deprotonates at higher pH to give the dianionic form (blue), which is stabilized by resonance:
The acid dissociation constant (pK) of this reaction is 4.8. Tap water is sufficiently basic to give a solution of bromocresol green its characteristic blue-green color.
The acid and basic forms of this dye have an isosbestic point in their UV-Visible spectrum, around 515 nm, indicate that the two forms interconvert directly without forming any other substance.
An ethanol solution (0.04 wt%) of bromocresol green has been proposed for TLC staining and is suitable for visualisation of the compounds with functional groups whose pK is below 5.0 (carboxylic acids, sulfonic acids, etc.). These appear as yellow spots on a light or dark blue background; no heating is necessary. Bromophenol blue solution can be used for the same purpose.
The compound is synthesized by bromination of cresol purple (m-cresolsulfonphthalein). | 3 | Analytical Chemistry |
Crystal structures for the E. coli SCS provide evidence that the coenzyme A binds within each α-subunit (within a Rossmann fold) in close proximity to a histidine residue (His246α). This histidine residue becomes phosphorylated during the succinate forming step in the reaction mechanism. The exact binding location of succinate is not well-defined. The formation of the nucleotide triphosphate occurs in an ATP grasp domain, which is located near the N-terminus of the each β subunit. However, this grasp domain is located about 35 Å away from the phosphorylated histidine residue. This leads researchers to believe that the enzyme must undergo a major change in conformation to bring the histidine to the grasp domain and facilitate the formation of the nucleoside triphosphate. Mutagenesis experiments have determined that two glutamate residues (one near the catalytic histidine, Glu208α and one near the ATP grasp domain, Glu197β) play a role in the phosphorylation and dephosphorylation of the histidine, but the exact mechanism by which the enzyme changes conformation is not fully understood. | 1 | Biochemistry |
GPC is often used to determine the relative molecular weight of polymer samples as well as the distribution of molecular weights. What GPC truly measures is the molecular volume and shape function as defined by the intrinsic viscosity. If comparable standards are used, this relative data can be used to determine molecular weights within ± 5% accuracy. Polystyrene standards with dispersities of less than 1.2 are typically used to calibrate the GPC. Unfortunately, polystyrene tends to be a very linear polymer and therefore as a standard it is only useful to compare it to other polymers that are known to be linear and of relatively the same size. | 3 | Analytical Chemistry |
Organic Rankine cycles are innovative power cycles which allow good performances for low enthalpy thermal sources and ensure condensation above the atmospheric pressure, thus avoiding deaerators and large cross sectional area in the heat rejection units. Moreover, with respect to steam Rankine cycles, ORC have a higher flexibility in handling low power sizes, allowing significant compactness.
Typical applications of ORC cover: waste heat recovery plants, geothermal plants, biomass plants and waste to energy power plants.
Organic Rankine cycles use organic fluids (such as hydrocarbons, perfluorocarbons, chlorofluorocarbon, and many others) as working fluids. Most of them have a critical temperature in the range of 100-200°C, for this reason perfectly adaptable to transcritical cycles in low temperature applications.
Considering organic fluids, having a maximum pressure above the critical one can more than double the temperature difference across the turbine, with respect to the subcritical counterpart, and significantly increase both the cycle specific work and cycle efficiency. | 7 | Physical Chemistry |
Transfer RNA (tRNA) helps decode a messenger RNA sequence into a protein. They function at specific sites within the ribosome during translation (the process going from code to protein). Within the mRNA molecule we have three nucleotides in length codons. These codons all have a unique universal code which represents a particular amino acid. tRNAs can be classified as an adaptor molecule, being typically 76 to 90 nucleotides in length. | 1 | Biochemistry |
In the wave theory of physics and engineering, a mode in a dynamical system is a standing wave state of excitation, in which all the components of the system will be affected sinusoidally at a fixed frequency associated with that mode.
Because no real system can perfectly fit under the standing wave framework, the mode concept is taken as a general characterization of specific states of oscillation, thus treating the dynamic system in a linear fashion, in which linear superposition of states can be performed.
Classical examples include
* In a mechanical dynamical system, a vibrating rope is the most clear example of a mode, in which the rope is the medium, the stress on the rope is the excitation, and the displacement of the rope with respect to its static state is the modal variable.
* In an acoustic dynamical system, a single sound pitch is a mode, in which the air is the medium, the sound pressure in the air is the excitation, and the displacement of the air molecules is the modal variable.
* In a structural dynamical system, a high tall building oscillating under its most flexural axis is a mode, in which all the material of the building -under the proper numerical simplifications- is the medium, the seismic/wind/environmental solicitations are the excitations and the displacements are the modal variable.
* In an electrical dynamical system, a resonant cavity made of thin metal walls, enclosing a hollow space, for a particle accelerator is a pure standing wave system, and thus an example of a mode, in which the hollow space of the cavity is the medium, the RF source (a Klystron or another RF source) is the excitation and the electromagnetic field is the modal variable.
* When relating to music, normal modes of vibrating instruments (strings, air pipes, drums, etc.) are called "overtones".
The concept of normal modes also finds application in other dynamical systems, such as optics, quantum mechanics, atmospheric dynamics and molecular dynamics.
Most dynamical systems can be excited in several modes, possibly simultaneously. Each mode is characterized by one or several frequencies, according to the modal variable field. For example, a vibrating rope in 2D space is defined by a single-frequency (1D axial displacement), but a vibrating rope in 3D space is defined by two frequencies (2D axial displacement).
For a given amplitude on the modal variable, each mode will store a specific amount of energy because of the sinusoidal excitation.
The normal or dominant mode of a system with multiple modes will be the mode storing the minimum amount of energy for a given amplitude of the modal variable, or, equivalently, for a given stored amount of energy, the dominant mode will be the mode imposing the maximum amplitude of the modal variable. | 7 | Physical Chemistry |
October 23, denoted 10/23 in the US, is recognized by some as Mole Day. It is an informal holiday in honor of the unit among chemists. The date is derived from the Avogadro number, which is approximately . It starts at 6:02 a.m. and ends at 6:02 p.m. Alternatively, some chemists celebrate June 2 (), June 22 (), or 6 February (), a reference to the 6.02 or 6.022 part of the constant. | 3 | Analytical Chemistry |
Monopolin is a protein complex that in budding yeast is composed of the four proteins CSM1, HRR25, LRS4, and MAM1. Monopolin is required for the segregation of homologous centromeres to opposite poles of a dividing cell during anaphase I of meiosis. This occurs by bridging DSN1 kinetochore proteins to sister kinetochores within the centromere to physically fuse them and allow for the microtubules to pull each homolog toward opposite mitotic spindles. | 1 | Biochemistry |
Industrial fermentation is the intentional use of fermentation in manufacturing processes. In addition to the mass production of fermented foods and drinks, industrial fermentation has widespread applications in chemical industry. Commodity chemicals, such as acetic acid, citric acid, and ethanol are made by fermentation. Moreover, nearly all commercially produced industrial enzymes, such as lipase, invertase and rennet, are made by fermentation with genetically modified microbes. In some cases, production of biomass itself is the objective, as is the case for single-cell proteins, baker's yeast, and starter cultures for lactic acid bacteria used in cheesemaking.
In general, fermentations can be divided into four types:
* Production of biomass (viable cellular material)
* Production of extracellular metabolites (chemical compounds)
* Production of intracellular components (enzymes and other proteins)
* Transformation of substrate (in which the transformed substrate is itself the product)
These types are not necessarily disjoined from each other, but provide a framework for understanding the differences in approach. The organisms used are typically microorganisms, particularly bacteria, algae, and fungi, such as yeasts and molds, but industrial fermentation may also involve cell cultures from plants and animals, such as CHO cells and insect cells. Special considerations are required for the specific organisms used in the fermentation, such as the dissolved oxygen level, nutrient levels, and temperature. The rate of fermentation depends on the concentration of microorganisms, cells, cellular components, and enzymes as well as temperature, pH and level of oxygen for aerobic fermentation. Product recovery frequently involves the concentration of the dilute solution. | 1 | Biochemistry |
Very commonly when the supersaturation (or degree of supercooling) is high, and sometimes even when it is not high, growth kinetics may be diffusion-controlled. Under such conditions, the polyhedral crystal form will be unstable, it will sprout protrusions at its corners and edges where the degree of supersaturation is at its highest level. The tips of these protrusions will clearly be the points of highest supersaturation. It is generally believed that the protrusion will become longer (and thinner at the tip) until the effect of interfacial free energy in raising the chemical potential slows the tip growth and maintains a constant value for the tip thickness.
In the subsequent tip-thickening process, there should be a corresponding instability of shape. Minor bumps or "bulges" should be exaggerated—and develop into rapidly growing side branches. In such an unstable (or metastable) situation, minor degrees of anisotropy should be sufficient to determine directions of significant branching and growth. The most appealing aspect of this argument, of course, is that it yields the primary morphological features of dendritic growth. | 3 | Analytical Chemistry |
Transition metal acyl complexes describes organometallic complexes containing one or more acyl (RCO) ligands. Such compounds occur as transient intermediates in many industrially useful reactions, especially carbonylations. | 0 | Organic Chemistry |
Genes interact in the sense that they affect each others function. For instance, a mutation may be harmless, but when it is combined with another mutation, the combination may turn out to be lethal. Such genes are said to "interact genetically". Genes that are connected in such a way form genetic interaction networks. Some of the goals of these networks are: develop a functional map of a cells processes, drug target identification using chemoproteomics, and to predict the function of uncharacterized genes.
In 2010, the most "complete" gene interactome produced to date was compiled from about 5.4 million two-gene comparisons to describe "the interaction profiles for ~75% of all genes in the budding yeast", with ~170,000 gene interactions. The genes were grouped based on similar function so as to build a functional map of the cells processes. Using this method the study was able to predict known gene functions better than any other genome-scale data set as well as adding functional information for genes that hadnt been previously described. From this model genetic interactions can be observed at multiple scales which will assist in the study of concepts such as gene conservation. Some of the observations made from this study are that there were twice as many negative as positive interactions, negative interactions were more informative than positive interactions, and genes with more connections were more likely to result in lethality when disrupted. | 1 | Biochemistry |
In the 1920s, the Russian embryologist Alexander Gurwitsch reported "ultraweak" photon emissions from living tissues in the UV-range of the spectrum. He named them "mitogenetic rays" because his experiments convinced him that they had a stimulating effect on cell division.
In the 1970s Fritz-Albert Popp and his research group at the University of Marburg (Germany) showed that the spectral distribution of the emission fell over a wide range of wavelengths, from 200 to 750 nm. Popps work on the biophoton emissions statistical properties, namely the claims on its coherence, was criticised for lack of scientific rigour.
One biophoton mechanism focuses on injured cells that are under higher levels of oxidative stress, which is one source of light, and can be deemed to constitute a "distress signal" or background chemical process, but this mechanism is yet to be demonstrated. The difficulty of teasing out the effects of any supposed biophotons amid the other numerous chemical interactions between cells makes it difficult to devise a testable hypothesis. A 2010 review article discusses various published theories on this kind of signaling.
The hypothesis of cellular communication by biophotons was highly criticised for failing to explain how could cells detect photonic signals several orders of magnitude weaker than the natural background illumination. | 1 | Biochemistry |
The three most important roles that PEP carboxylase plays in plants and bacteria metabolism are in the cycle, the CAM cycle, and the citric acid cycle biosynthesis flux.
The primary mechanism of carbon dioxide assimilation in plants is through the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (also known as RuBisCO), that adds CO to ribulose-1,5-bisphosphate (a 5 carbon sugar), to form two molecules of 3-phosphoglycerate (2x3 carbon sugars). However, at higher temperatures and lower CO concentrations, RuBisCO adds oxygen instead of carbon dioxide, to form the unusable product glycolate in a process called photorespiration. To prevent this wasteful process, plants increase the local CO concentration in a process called the cycle. PEP carboxylase plays the key role of binding CO in the form of bicarbonate with PEP to create oxaloacetate in the mesophyll tissue. This is then converted back to pyruvate (through a malate intermediate), to release the CO in the deeper layer of bundle sheath cells for carbon fixation by RuBisCO and the Calvin cycle. Pyruvate is converted back to PEP in the mesophyll cells, and the cycle begins again, thus actively pumping CO.
The second important and very similar biological significance of PEP carboxylase is in the CAM cycle. This cycle is common in organisms living in arid habitats. Plants cannot afford to open stomata during the day to take in CO, as they would lose too much water by transpiration. Instead, stomata open at night, when water evaporation is minimal, and take in CO by fixing with PEP to form oxaloacetate though PEP carboxylase. Oxaloacetate is converted to malate by malate dehydrogenase, and stored for use during the day when the light dependent reaction generates energy (mainly in the form of ATP) and reducing equivalents such as NADPH to run the Calvin cycle.
Third, PEP carboxylase is significant in non-photosynthetic metabolic pathways. Figure 3 shows this metabolic flow (and its regulation). Similar to pyruvate carboxylase, PEP carboxylase replenishes oxaloacetate in the citric acid cycle. At the end of glycolysis, PEP is converted to pyruvate, which is converted to acetyl-coenzyme-A (acetyl-CoA), which enters the citric acid cycle by reacting with oxaloacetate to form citrate. To increase flux through the cycle, some of the PEP is converted to oxaloacetate by PEP carboxylase. Since the citric acid cycle intermediates provide a hub for metabolism, increasing flux is important for the biosynthesis of many molecules, such as for example amino acids. | 5 | Photochemistry |
Processive enzymes are proteins that catalyze consecutive reactions without releasing its substrate. An example of processive enzymes is RNA polymerase which binds to a DNA strand and repeatedly catalyzes nucleotide transfers, effectively synthesizing a corresponding RNA strand.
Nolte and coworkers developed an artificial processive enzyme in a form of manganese porphyrin rotaxane that treads along a long polymer of alkene and catalyze multiple rounds of alkene epoxidation. Manganese (III) ion in the porphyrin is the molecule's catalytic center, capable of epoxidation in the presence of an oxygen donor and an activating ligand. With a small ligand such pyridine that binds manganese from inside the cavity of the rotaxane, epoxidation happens outside the catalyst. With a large bulky ligand such as tert-butyl pyridine that does not fit inside the cavity however, epoxidation happens on the inside of the catalyst. | 6 | Supramolecular Chemistry |
The thickness of the ozone layer varies worldwide and is generally thinner near the equator and thicker near the poles. Thickness refers to how much ozone is in a column over a given area and varies from season to season. The reasons for these variations are due to atmospheric circulation patterns and solar intensity.
The majority of ozone is produced over the tropics and is transported towards the poles by stratospheric wind patterns. In the northern hemisphere these patterns, known as the Brewer–Dobson circulation, make the ozone layer thickest in the spring and thinnest in the fall. When ozone is produced by solar UV radiation in the tropics, it is done so by circulation lifting ozone-poor air out of the troposphere and into the stratosphere where the sun photolyzes oxygen molecules and turns them into ozone. Then, the ozone-rich air is carried to higher latitudes and drops into lower layers of the atmosphere.
Research has found that the ozone levels in the United States are highest in the spring months of April and May and lowest in October. While the total amount of ozone increases moving from the tropics to higher latitudes, the concentrations are greater in high northern latitudes than in high southern latitudes, with spring ozone columns in high northern latitudes occasionally exceeding 600 DU and averaging 450 DU whereas 400 DU constituted a usual maximum in the Antarctic before anthropogenic ozone depletion. This difference occurred naturally because of the weaker polar vortex and stronger Brewer–Dobson circulation in the northern hemisphere owing to that hemisphere’s large mountain ranges and greater contrasts between land and ocean temperatures. The difference between high northern and southern latitudes has increased since the 1970s due to the ozone hole phenomenon. The highest amounts of ozone are found over the Arctic during the spring months of March and April, but the Antarctic has the lowest amounts of ozone during the summer months of September and October, | 5 | Photochemistry |
Sulfuric acid at high concentrations is frequently the major ingredient in domestic acidic drain cleaners which are used to remove grease, hair, tissue paper, etc. Similar to their alkaline versions, such drain openers can dissolve fats and proteins via hydrolysis. Moreover, as concentrated sulfuric acid has a strong dehydrating property, it can remove tissue paper via dehydrating process as well. Since the acid may react with water vigorously, such acidic drain openers should be added slowly into the pipe to be cleaned. | 7 | Physical Chemistry |
In order to confirm the effectiveness and quality of the qPCR process that was performed, there are several actions and subsequent data that must be presented. This includes explaining the specific method of checking that the process functioned, such as using a gel, direct sequencing of the genetic material, showing a melt profile, or from digestion by restriction enzyme. If SYBR Green I was used, then the Cq of the control group with no template DNA must be given. Further essential data includes the calibration of the machine curves with the slope and y intercept noted, the efficiency of the PCR process as determined from the aforementioned slope, the correlation coefficients (r squared) for the calibration curves, the dynamic range of the linear curves, the Cq found at the lowest concentration where 95% of the results were still positive (LOD) along with the evidence for the LOD itself, and lastly if a multiplex is used, then the efficiency and LOD must be given for each assay done.
The extra desired information includes evidence given that qPCR optimization occurred by the use of gradients, the confidence intervals to show efficiency of the qPCR, and the confidence intervals for the entire range tested. | 1 | Biochemistry |
AGEs are responsible for many things. These molecules play an important role especially in nutrition, they are responsible for the brownish color and the aromas and flavors of some foods. It is demonstrated that cooking at high temperature results in various food products having high levels of AGEs.
Having elevated levels of AGEs in the body has a direct impact on the development of many diseases. It has a direct implication in diabetes mellitus type 2 that can lead to many complications such as: cataracts, renal failure, heart damage... And, if they are present at a decreased level, skin elasticity is reduced which is an important symptom of aging.
They are also the precursors of many hormones and regulate and modify their receptor mechanisms at the DNA level. | 0 | Organic Chemistry |
Given the genetic makeup of an organism, the complete set of possible reactions constitutes its reactome. Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human biological processes/pathway data. The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways The Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, and signal transduction, and high-level processes, such as the cell cycle. Reactome provides a qualitative framework, on which quantitative data can be superimposed. Tools have been developed to facilitate custom data entry and annotation by expert biologists, and to allow visualization and exploration of the finished dataset as an interactive process map. Although the primary curational domain is pathways from Homo sapiens, electronic projections of human pathways onto other organisms are regularly created via putative orthologs, thus making Reactome relevant to model organism research communities. The database is publicly available under open source terms, which allows both its content and its software infrastructure to be freely used and redistributed. Studying whole transcriptional profiles and cataloging protein–protein interactions has yielded much valuable biological information, from the genome or proteome to the physiology of an organism, an organ, a tissue or even a single cell. The Reactome database containing a framework of possible reactions which, when combined with expression and enzyme kinetic data, provides the infrastructure for quantitative models, therefore, an integrated view of biological processes, which links such gene products and can be systematically mined by using bioinformatics applications. Reactome data available in a variety of standard formats, including BioPAX, SBML and PSI-MI, and also enable data exchange with other pathway databases, such as the Cycs, KEGG and amaze, and molecular interaction databases, such as BIND and HPRD. The next data release will cover apoptosis, including the death receptor signaling pathways, and the Bcl2 pathways, as well as pathways involved in hemostasis. Other topics currently under development include several signaling pathways, mitosis, visual phototransduction and hematopoeisis. In summary, Reactome provides high-quality curated summaries of fundamental biological processes in humans in a form of biologist-friendly visualization of pathways data, and is an open-source project. | 7 | Physical Chemistry |
Carboxypeptidase E is found in brain and throughout the neuroendocrine system, including the endocrine pancreas, pituitary, and adrenal gland chromaffin cells. Within cells, carboxypeptidase E is present in the secretory granules along with its peptide substrates and products. Carboxypeptidase E is a glycoprotein that exists in both membrane-associated and soluble forms. The membrane-binding is due to an amphiphilic α-helix within the C-terminal region of the protein. | 1 | Biochemistry |
PEX genes encode the protein machinery (peroxins) required for proper peroxisome assembly. Peroxisomal membrane proteins are imported through at least two routes, one of which depends on interaction between peroxin 19 and peroxin 3, while the other is required for import of peroxin 3, either of which may occur without the import of matrix (lumen) enzymes, which possess the peroxisomal targeting signal PTS1 or PTS2 as previously discussed. Elongation of the peroxisome membrane and the final fission of the organelle are regulated by Pex11p.
Genes that encode peroxin proteins include: PEX1, PEX2 (PXMP3), PEX3, PEX5, PEX6, PEX7, PEX9, PEX10, PEX11A, PEX11B, PEX11G, PEX12, PEX13, PEX14, PEX16, PEX19, PEX26, PEX28, PEX30, and PEX31. Between organisms, PEX numbering and function can differ. | 1 | Biochemistry |
Electrowinning, also called electroextraction, is the electrodeposition of metals from their ores that have been put in solution via a process commonly referred to as leaching. Electrorefining uses a similar process to remove impurities from a metal. Both processes use electroplating on a large scale and are important techniques for the economical and straightforward purification of non-ferrous metals. The resulting metals are said to be electrowon.
In electrowinning, an electrical current is passed from an inert anode through a leach solution containing the dissolved metal ions so that the metal is recovered as it is reduced and deposited in an electroplating process onto the cathode. In electrorefining, the anode consists of the impure metal (e.g., copper) to be refined. The impure metallic anode is oxidized and the metal dissolves into solution. The metal ions migrate through the electrolyte towards the cathode where the pure metal is deposited. Insoluble solid impurities sedimenting below the anode often contain valuable rare elements such as gold, silver and selenium. | 8 | Metallurgy |
The primary structure of RiAFP (the sequence may be found [https://www.ncbi.nlm.nih.gov/protein/313766639 here]) determined by Mass Spectroscopy, Edman degradation and by constructing a partial cDNA sequence and PCR have shown that a TxTxTxT internal repeat exists. Sequence logos constructed from the RiAFP internal repeats, have been particularly helpful in the determination of the consensus sequence of these repeats. The TxTxTxT domains are irregularly spaced within the protein and have been shown to be conserved from the TxT binding motif of other AFPs. The hydroxyl moiety of the T residues fits well, when spaced as they are in the internal repeats, with the hydroxyl moieties of externally facing water molecules in the forming ice lattice. This mimics the formation of the growth cone at a nucleation site in the absence of AFPs. Thus, the binding of RiAFP inhibits the growth of the crystal in the basal and prism planes of the ice. | 1 | Biochemistry |
Phototherapy may cause lipid peroxidation leading to rupture of red blood cell cell membranes in this way.
In addition, end-products of lipid peroxidation may be mutagenic and carcinogenic. For instance, the end-product MDA reacts with deoxyadenosine and deoxyguanosine in DNA, forming DNA adducts to them, primarily MG.
Reactive aldehydes can also form Michael adducts or Schiff bases with thiol or amine groups in amino acid side chains. Thus, they are able to inactivate sensitive proteins through electrophilic stress.
The toxicity of lipid hydroperoxides to animals is best illustrated by the lethal phenotype of glutathione peroxidase 4 (GPX4) knockout mice. These animals do not survive past embryonic day 8, indicating that the removal of lipid hydroperoxides is essential for mammalian life.
On the other hand, it's unclear whether dietary lipid peroxides are bioavailable and play a role in disease, as a healthy human body has protective mechanisms in place against such hazards. | 1 | Biochemistry |
The above cations except for methanium are not, strictly speaking, organic, since they do not contain carbon. However, many organic cations are obtained by substituting another element or some functional group for a hydrogen.
The name of each substitution is prefixed to the hydride cation name. If many substitutions by the same functional group occur, then the number is indicated by prefixing with "di-", "tri-" as with halogenation. is trimethyloxonium. is trifluoromethylammonium. | 0 | Organic Chemistry |
In general, a sample is a limited quantity of something which is intended to be similar to and represent a larger amount of that thing(s). The things could be countable objects such as individual items available as units for sale, or an uncountable material. Even though the word "sample" implies a smaller quantity taken from a larger amount, sometimes full biological or mineralogical specimens are called samples if they are taken for analysis, testing, or investigation like other samples. They are also considered samples in the sense that even whole specimens are "samples" of the full population of many individual organisms. The act of obtaining a sample is called "sampling" and can be performed manually by a person or by automatic process. Samples of material can be taken or provided for testing, analysis, investigation, quality control, demonstration, or trial use. Sometimes, sampling may be performed continuously. | 3 | Analytical Chemistry |
The ionic activity coefficient is connected to the ionic diameter by the formula obtained from Debye–Hückel theory of electrolytes:
where A and B are constants, z is the valence number of the ion, and I is ionic strength. | 7 | Physical Chemistry |
Methanandamide (AM-356) is a synthetically created stable chiral analog of anandamide. Its effects have been observed to act on the cannabinoid receptors (specifically on CB receptors, which are part of the central nervous system) found in different organisms such as mammals, fish, and certain invertebrates (e.g. Hydra). | 1 | Biochemistry |
* Insertional mutagenesis uses the features of a TE to insert a sequence. In most cases, this is used to remove a DNA sequence or cause a frameshift mutation.
** In some cases the insertion of a TE into a gene can disrupt that gene's function in a reversible manner where transposase-mediated excision of the DNA transposon restores gene function.
** This produces plants in which neighboring cells have different genotypes.
** This feature allows researchers to distinguish between genes that must be present inside of a cell in order to function (cell-autonomous) and genes that produce observable effects in cells other than those where the gene is expressed. | 1 | Biochemistry |
One of the earliest ideas for the use of π-conjugated molecules in molecular computation was proposed by Ari Aviram from IBM in 1988. The motivation for this work was to develop theoretical models for mixed-valence type-σ-π-σ-bonded molecules and explore their stereochemical properties for potential applications in molecular devices. The system comprised two π-conjugated systems, 1 and 2, made of oligothiophenes joined by a spiro linkage, and connected to gold electrodes by thiol linkers. π-system 1 is non-conducting in its neutral state, whereas system 2 is electrically conducting in its radical cation form. The twisted structure of the system courtesy of the spiro linkage provides hindrance to the transport of electrons between the two π-systems. However, through electrodes directed toward the linkage, a strong electric field could facilitate electron transfer from system 1 to system 2, with the radical cation going the opposite way.
The first practical realization of molecular logic was courtesy of de Silva and coworkers in their seminal work, in which they constructed a molecular photoionic AND gate with a fluorescent output. While a YES molecular logic gate, as described previously, can convert signals from their ionic to photonic forms (hence the term “photoionic”), they are singular-input-singular-output systems. To build more complex molecular logic architectures, two-input gates, namely AND and OR gates, are needed. Some early works made some progress in this direction, but could not realize a complete truth table as their ionic forms (protonated) could not bind to the substrate in all cases. De Silva and co. constructed an anthracene-based AND gate made up of tertiary amine and benzo-18-crown-6 units, both of which were known to show photoinduced electron transfer (PET) processes. In the system shown, they both acted as receptors, connected to the anthracene-based fluorophore by alkyl spacers. The PET is quenched upon coordination with protons and sodium ions, respectively, for the two receptors, and would lead the anthracene unit to fluoresce. The truth table for an AND gate was completely realized as the system would exhibit a fluorescence output only in the presence of both protons and sodium ions in the system. | 6 | Supramolecular Chemistry |
Approximately 64% of the maize genome is made up of TEs, as is 44% of the human genome, and almost half of murine genomes.
New discoveries of transposable elements have shown the exact distribution of TEs with respect to their transcription start sites (TSSs) and enhancers. A recent study found that a promoter contains 25% of regions that harbor TEs. It is known that older TEs are not found in TSS locations because TEs frequency starts as a function once there is a distance from the TSS. A possible theory for this is that TEs might interfere with the transcription pausing or the first-intro splicing. Also as mentioned before, the presence of TEs closed by the TSS locations is correlated to their evolutionary age (number of different mutations that TEs can develop during the time). | 1 | Biochemistry |
A plasmid preparation is a method of DNA extraction and purification for plasmid DNA, it is an important step in many molecular biology experiments and is essential for the successful use of plasmids in research and biotechnology. Many methods have been developed to purify plasmid DNA from bacteria. During the purification procedure, the plasmid DNA is often separated from contaminating proteins and genomic DNA.
These methods invariably involve three steps: growth of the bacterial culture, harvesting and lysis of the bacteria, and purification of the plasmid DNA. Purification of plasmids is central to molecular cloning. A purified plasmid can be used for many standard applications, such as sequencing and transfections into cells. | 1 | Biochemistry |
Ionic compounds normally dissociate into their constituent ions when they dissolve in water. For example, for silver chloride:
The expression for the equilibrium constant for this reaction is:
where is the thermodynamic equilibrium constant and braces indicate activity. The activity of a pure solid is, by definition, equal to one.
When the solubility of the salt is very low the activity coefficients of the ions in solution are nearly equal to one. By setting them to be actually equal to one this expression reduces to the solubility product expression:
For 2:2 and 3:3 salts, such as CaSO and FePO, the general expression for the solubility product is the same as for a 1:1 electrolyte
: (electrical charges are omitted in general expressions, for simplicity of notation)
With an unsymmetrical salt like Ca(OH) the solubility expression is given by
Since the concentration of hydroxide ions is twice the concentration of calcium ions this reduces to
In general, with the chemical equilibrium
and the following table, showing the relationship between the solubility of a compound and the value of its solubility product, can be derived.
Solubility products are often expressed in logarithmic form. Thus, for calcium sulfate, with , . The smaller the value of K, or the more negative the log value, the lower the solubility.
Some salts are not fully dissociated in solution. Examples include MgSO, famously discovered by Manfred Eigen to be present in seawater as both an inner sphere complex and an outer sphere complex. The solubility of such salts is calculated by the method outlined in dissolution with reaction. | 7 | Physical Chemistry |
RoXaN is capable of interacting with NSP3 in vivo and during rotavirus infection. Domains of interaction correspond to the dimerization domain of NSP3 (amino acids 163 to 237) and the LD domain of RoXaN (amino acids 244 to 341). The interaction between NSP3 and RoXaN does not impair the interaction between NSP3 and eIF4G I, and a ternary complex made of NSP3, RoXaN, and eIF4G I can be detected in rotavirus-infected cells, implicating RoXaN in translation regulation.
Expression of RoXaN was found to be correlated with a higher tumor grad in GIST (gastrointestinal stromal tumors). | 1 | Biochemistry |
In biochemistry, fermentation theory refers to the historical study of models of natural fermentation processes, especially alcoholic and lactic acid fermentation. Notable contributors to the theory include Justus Von Liebig and Louis Pasteur, the latter of whom developed a purely microbial basis for the fermentation process based on his experiments. Pasteurs work on fermentation later led to his development of the germ theory of disease, which put the concept of spontaneous generation to rest. Although the fermentation process had been used extensively throughout history prior to the origin of Pasteurs prevailing theories, the underlying biological and chemical processes were not fully understood. In the contemporary, fermentation is used in the production of various alcoholic beverages, foodstuffs, and medications. | 1 | Biochemistry |
Diols react as alcohols, by esterification and ether formation.
Diols such as ethylene glycol are used as co-monomers in polymerization reactions forming polymers including some polyesters and polyurethanes. A different monomer with two identical functional groups, such as a dioyl dichloride or dioic acid is required to continue the process of polymerization through repeated esterification processes.
A diol can be converted to cyclic ether by using an acid catalyst, this is diol cyclization. Firstly, it involves protonation of the hydroxyl group. Then, followed by intramolecular nucleophilic substitution, the second hydroxyl group attacks the electron deficient carbon. Provided that there are enough carbon atoms that the angle strain is not too much, a cyclic ether can be formed.
1,2-diols and 1,3-diols can be protected using a protecting group. Protecting groups are used so that the functional group does not react to future reactions. Benzylidene groups are used to protect 1,3-diols. There are extremely useful in biochemistry as shown below of a carbohydrate derivative being protected.
Diols can also be used to protect carbonyl groups. They are commonly used and are quite efficient at synthesizing cyclic acetals. These protect the carbonyl groups from reacting from any further synthesis until it is necessary to remove them. The reaction below depicts a diol being used to protect a carbonyl using zirconium tetrachloride.
Diols can also be converted to lactones employing the Fétizon oxidation reaction. | 0 | Organic Chemistry |
The main advantage of FbFPs over GFP is their independence of molecular oxygen. Since all GFP derivatives and homologues require molecular oxygen for the maturation of their chromophore, these fluorescent proteins are of limited use under anaerobic or hypoxic conditions.
Since FbFPs bind FMN as chromophore, which is synthesized independently of molecular oxygen, their fluorescence signal does not differ between aerobic and anaerobic conditions.<br />
Another advantage is the small size of FbFPs, which is typically between 100 and 150 amino acids. This is about half the size of GFP (238 amino acids). It could for example be shown that this renders them superior tags for monitoring tobacco mosaic virus infections in tobacco leaves.<br />
Due to their extraordinary long average fluorescence lifetime of up to 5.7 ns they are also very well suited for the use as donor domains in FRET systems in conjunction with e.g. YFP (see photophysical properties). A fusion of EcFbFP and YFP was e.g. used to develop the first genetically encoded fluorescence biosensor for oxygen (FluBO)
The main disadvantage compared to GFP variants is their lower brightness (the product of ε and Φ). The commonly used EGFP (ε = 55,000 Mcm; Φ = 0.60 ) for example is approximately five times as bright as EcFbFP.<br />
Another disadvantage of the FbFPs is the lack of color variants to tag and distinguish multiple proteins in a single cell or tissue. The largest spectral shift reported for FbFPs so far is 10 nm. Although this variant (Pp2FbFP Q116V) can be visually distinguished from the others with the human eye, the spectral differences are too small for fluorescence microscopy filters. | 1 | Biochemistry |
To date there are more than 300 known coregulators. Some examples of these coactivators include:
* ARA54 targets androgen receptors
* ATXN7L3 targets several members of the nuclear receptor superfamily
* BCL3 targets 9-cis retinoic acid receptor (RXR)
* CBP targets many transcription factors
* CDC25B targets steroid receptors
* COPS5 targets several nuclear receptors
* DDC targets androgen receptors
* EP300 targets many transcription factors
* KAT5 targets many nuclear receptors
* KDM1A targets androgen receptors
* Steroid receptor coactivator (SRC) family
** NCOA1 targets several members of the nuclear receptor superfamily
** NCOA2 targets several members of the nuclear receptor superfamily
** NCOA3 targets several nuclear receptors and transcription factors
* YAP targets transcription factors
* WWTR1 targets transcription factors | 1 | Biochemistry |
Cyclic Corrosion Testing (CCT) has evolved in recent years, largely within the automotive industry, as a way of accelerating real-world corrosion failures, under laboratory controlled conditions.
As the name implies, the test comprises different climates which are cycled automatically so the samples under test undergo the same sort of changing environment that would be encountered in the natural world. The intention being to bring about the type of failure that might occur naturally, but more quickly i.e. accelerated. By doing this manufacturers and suppliers can predict, more accurately, the service life expectancy of their products.
Until the development of Cyclic Corrosion Testing, the traditional Salt spray test was virtually all that manufacturers could use for this purpose. However, this test was never intended for this purpose. Because the test conditions specified for salt spray testing are not typical of a naturally occurring environment, this type of test cannot be used as a reliable means of predicting the ‘real world’ service life expectancy for the samples under test. The sole purpose of the salt spray test is to compare and contrast results with previous experience to perform a quality audit. So, for example, a spray test can be used to ‘police’ a production process and forewarn of potential manufacturing problems or defects, which might affect corrosion resistance.
To recreate these different environments within an environmental chamber requires much more flexible testing procedures than are available in a standard salt spray chamber.
The lack of correlation between results obtained from traditional salt spray testing and the ‘real world’ atmospheric corrosion of vehicles, left the automotive industry without a reliable test method for predicting the service life expectancy of their products. This was and remains of particular concern in an industry where anti-corrosion warranties have been gradually increasing and now run to several years for new vehicles.
With ever increasing consumer pressure for improved vehicle corrosion resistance and a few ‘high profile’ corrosion failures amongst some vehicle manufactures – with disastrous commercial consequences, the automotive industry recognized the need for a different type of corrosion test.
Such a test would need to simulate the types of conditions a vehicle might encounter naturally, but recreate and accelerate these conditions, with good repeatability, within the convenience of the laboratory.
CCT is effective for evaluating a variety of corrosion types, including galvanic corrosion and crevice corrosion. One of the earliest introduced cyclic testing machines was the Prohesion cabinet. | 8 | Metallurgy |
A typical XPS spectrum is a plot of the number of electrons detected at a specific binding energy. Each element produces a set of characteristic XPS peaks. These peaks correspond to the electron configuration of the electrons within the atoms, e.g., 1s, 2s, 2p, 3s, etc. The number of detected electrons in each peak is directly related to the amount of element within the XPS sampling volume. To generate atomic percentage values, each raw XPS signal is corrected by dividing the intensity by a relative sensitivity factor (RSF), and normalized over all of the elements detected. Since hydrogen is not detected, these atomic percentages exclude hydrogen. | 7 | Physical Chemistry |
Ultrasonic impact treatment (UIT) is a metallurgical processing technique, similar to work hardening, in which ultrasonic energy is applied to a metal object. This technique is part of the High Frequency Mechanical Impact (HFMI) processes. Other acronyms are also equivalent: Ultrasonic Needle Peening (UNP), Ultrasonic Peening (UP). Ultrasonic impact treatment can result in controlled residual compressive stress, grain refinement and grain size reduction. Low and high cycle fatigue are enhanced and have been documented to provide increases up to ten times greater than non-UIT specimens. | 8 | Metallurgy |
Suspended solids (or SS), is the mass of dry solids retained by a filter of a given porosity related to the volume of the water sample. This includes particles 10 μm and greater.
Colloids are particles of a size between 1 nm (0.001 µm) and 1 µm depending on the method of quantification. Because of Brownian motion and electrostatic forces balancing the gravity, they are not likely to settle naturally.
The limit sedimentation velocity of a particle is its theoretical descending speed in clear and still water. In settling process theory, a particle will settle only if:
# In a vertical ascending flow, the ascending water velocity is lower than the limit sedimentation velocity.
# In a longitudinal flow, the ratio of the length of the tank to the height of the tank is higher than the ratio of the water velocity to the limit sedimentation velocity.
Removal of suspended particles by sedimentation depends upon the size, zeta potential and specific gravity of those particles. Suspended solids retained on a filter may remain in suspension if their specific gravity is similar to water while very dense particles passing through the filter may settle. Settleable solids are measured as the visible volume accumulated at the bottom of an Imhoff cone after water has settled for one hour.
Gravitational theory is employed, alongside the derivation from Newton's second law and the Navier–Stokes equations.
Stokes' law explains the relationship between the settling rate and the particle diameter. Under specific conditions, the particle settling rate is directly proportional to the square of particle diameter and inversely proportional to liquid viscosity.
The settling velocity, defined as the residence time taken for the particles to settle in the tank, enables the calculation of tank volume. Precise design and operation of a sedimentation tank is of high importance in order to keep the amount of sediment entering the diversion system to a minimum threshold by maintaining the transport system and stream stability to remove the sediment diverted from the system. This is achieved by reducing stream velocity as low as possible for the longest period of time possible. This is feasible by widening the approach channel and lowering its floor to reduce flow velocity thus allowing sediment to settle out of suspension due to gravity. The settling behavior of heavier particulates is also affected by the turbulence. | 3 | Analytical Chemistry |
MG-RAST, an open-source web application server, facilitates automatic phylogenetic and functional analysis of metagenomes. It stands as one of the largest repositories for metagenomic data, employing the acronym for Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST). This platform utilizes a pipeline that automatically assigns functions to metagenomic sequences, conducting sequence comparisons at both nucleotide and amino acid levels. Users benefit from phylogenetic and functional insights into the analyzed metagenomes, along with tools for comparing different datasets. MG-RAST also offers a RESTful API for programmatic access.
Argonne National Laboratory from the University of Chicago created and maintains this server. As of December 29, 2016, MG-RAST had analyzed a substantial 60 terabase-pairs of data from over 150,000 datasets. Notably, more than 23,000 of these datasets are publicly available. Computational resources are currently sourced from the DOE Magellan cloud at Argonne National Laboratory, Amazon EC2 Web services, and various traditional clusters. | 1 | Biochemistry |
On Curtius rearrangement, acyl azides yield isocyanates.
Acyl azides are also formed in Darapsky degradation, | 0 | Organic Chemistry |
Space-based measurements of carbon dioxide are also a recent addition to atmospheric X measurements. SCIAMACHY aboard ESAs ENVISAT made global column X measurements from 2002 to 2012. AIRS aboard NASAs Aqua satellite makes global X measurements and was launched shortly after ENVISAT in 2012. More recent satellites have significantly improved the data density and precision of global measurements. Newer missions have higher spectral and spatial resolutions. JAXAs GOSAT was the first dedicated GHG monitoring satellite to successfully achieve orbit in 2009. NASAs OCO-2 launched in 2014 was the second. Various other satellites missions to measure atmospheric X are planned. | 2 | Environmental Chemistry |
AGEs affect nearly every type of cell and molecule in the body and are thought to be one factor in aging and some age-related chronic diseases. They are also believed to play a causative role in the vascular complications of diabetes mellitus.
AGEs arise under certain pathologic conditions, such as oxidative stress due to hyperglycemia in patients with diabetes. AGEs play a role as proinflammatory mediators in gestational diabetes as well.
In the context of cardiovascular disease, AGEs can induce crosslinking of collagen, which can cause vascular stiffening and entrapment of low-density lipoprotein particles (LDL) in the artery walls. AGEs can also cause glycation of LDL which can promote its oxidation. Oxidized LDL is one of the major factors in the development of atherosclerosis. Finally, AGEs can bind to RAGE (receptor for advanced glycation end products) and cause oxidative stress as well as activation of inflammatory pathways in vascular endothelial cells. | 1 | Biochemistry |
Ketoacidosis is a pathological state of uncontrolled production of ketones that results in a metabolic acidosis, with serum ketone levels typically in excess of 3 mM. Ketoacidosis is most commonly caused by a deficiency of insulin in type 1 diabetes or late stage type 2 diabetes but can also be the result of chronic heavy alcohol use, salicylate poisoning, or isopropyl alcohol ingestion. Ketoacidosis causes significant metabolic derangements and is a life-threatening medical emergency. Ketoacidosis is distinct from physiological ketosis as it requires failure of the normal regulation of ketone body production. | 1 | Biochemistry |
* L.P. Hammett, 1970, Physical Organic Chemistry, 2nd Edn., New York, NY, US: McGraw-Hill.
* John Shorter, 1982, Correlation Analysis of Organic Reactivity, Chichester 1982.
* Otto Exner, 1988, Correlation Analysis of Chemical Data, New York, NY, US: Plenum. | 7 | Physical Chemistry |
The sum of molar concentrations gives the total molar concentration, namely the density of the mixture divided by the molar mass of the mixture or by another name the reciprocal of the molar volume of the mixture. In an ionic solution, ionic strength is proportional to the sum of the molar concentration of salts. | 3 | Analytical Chemistry |
Physical systems found in nature are practically always dynamic and complex, but in many cases, macroscopic physical systems are amenable to description based on proximity to ideal conditions. One such ideal condition is that of a stable equilibrium state. Such a state is a primitive object of classical or equilibrium thermodynamics, in which it is called a thermodynamic state. Based on many observations, thermodynamics postulates that all systems that are isolated from the external environment will evolve so as to approach unique stable equilibrium states. There are a number of different types of equilibrium, corresponding to different physical variables, and a system reaches thermodynamic equilibrium when the conditions of all the relevant types of equilibrium are simultaneously satisfied. A few different types of equilibrium are listed below.
*Thermal equilibrium: When the temperature throughout a system is uniform, the system is in thermal equilibrium.
*Mechanical equilibrium: If at every point within a given system there is no change in pressure with time, and there is no movement of material, the system is in mechanical equilibrium.
*Phase equilibrium: This occurs when the mass for each individual phase reaches a value that does not change with time.
*Chemical equilibrium: In chemical equilibrium, the chemical composition of a system has settled and does not change with time. | 7 | Physical Chemistry |
There is one assay office in Praha.
Assay Office was established by the Czech National Council Law No. 19/1993 Coll., concerning
the Administration Authorities of the Czech Republic in the Field of Hallmarking and Precious Metal Testing, from which the Assay Office competences and duties are resulting. The provision of the financing is included in the Law about Hallmarking and Precious Metal Testing (Hallmarking Act), No. 539/1992 Coll., and in the procedural Decree of the Federal Ministry of Economy (FME), No. 540/1992 Coll., according to which the Hallmarking Act is implemented. | 3 | Analytical Chemistry |
Historically, two conventions for sign for the electrode potential have formed:
# convention "Nernst–Lewis–Latimer" (sometimes referred to as "American"),
# convention "Gibbs–Ostwald–Stockholm" (sometimes referred to as "European").
In 1953 in Stockholm IUPAC recognized that either of the conventions is permissible; however, it unanimously recommended that only the magnitude expressed according to the convention (2) be called "the electrode potential". To avoid possible ambiguities, the electrode potential thus defined can also be referred to as Gibbs–Stockholm electrode potential. In both conventions, the standard hydrogen electrode is defined to have a potential of 0 V. Both conventions also agree on the sign of for a half-cell reaction when it is written as a reduction.
The main difference between the two conventions is that upon reversing the direction of a half-cell reaction as written, according to the convention (1) the sign of also switches, whereas in the convention (2) it does not. The logic behind switching the sign of is to maintain the correct sign relationship with the Gibbs free energy change, given by where is the number of electrons involved and is the Faraday constant. It is assumed that the half-reaction is balanced by the appropriate SHE half-reaction. Since switches sign when a reaction is written in reverse, so too, proponents of the convention (1) argue, should the sign of . Proponents of the convention (2) argue that all reported electrode potentials should be consistent with the electrostatic sign of the relative potential difference. | 7 | Physical Chemistry |
The IL-10 family is one of the important types of cytokines, that can stop the inflammation. In general. these cytokines have a helical structure of homodimers. The difference that the members of IL-10 family have between each other is that they have various receptor-binding residues, which help with interaction with specific cytokine receptors. The features of the IL-10 family consists of their genomic structure being similar, their primary and secondary protein structures being similar, their a clustering of encoding genes, and their utilization the similar receptor complexes. | 1 | Biochemistry |
Polymersomes that contain active enzymes and that provide a way to selectively transport substrates for conversion by those enzymes have been described as nanoreactors.
Polymersomes have been used to create controlled release drug delivery systems. Similar to coating liposomes with polyethylene glycol, polymersomes can be made invisible to the immune system if the hydrophilic block consists of polyethylene glycol. Thus, polymersomes are useful carriers for targeted medication.
For in vivo applications, polymersomes are de facto limited to the use of FDA-approved polymers, as most pharmaceutical firms are unlikely to develop novel polymers due to cost issues. Fortunately, there are a number of such polymers available, with varying properties, including:
Hydrophilic blocks
* Poly(ethylene glycol) (PEG/PEO)
* Poly(2-methyloxazoline)
Hydrophobic blocks
* Polydimethylsiloxane (PDMS)
* Poly(caprolactone (PCL)
* Poly(lactide) (PLA)
* Poly(methyl methacrylate) (PMMA)
If enough of the block copolymer molecules that make up a polymersome are cross-linked, the polymersome can be made into a transportable powder.
Polymersomes can be used to make an artificial cell if hemoglobin and other components are added. The first artificial cell was made by Thomas Chang. | 1 | Biochemistry |
Many polymer chemists are concerned with limiting the rate of disproportionation during polymerization. Although disproportionation results in formation of one new double bond which may react with the polymer chain, a saturated hydrocarbon is also formed, and thus the chain reaction does not readily proceed. During living free radical polymerization, termination pathways for a growing polymer chain are removed. This can be achieved through several methods, one of which is reversible termination with stable radicals. Nitroxide radicals and other stable radicals reduce recombination and disproportionation rates and control the concentration of polymeric radicals. | 0 | Organic Chemistry |
Crystalline sponges are series of organometallic networks developed by Japanese chemist Makoto Fujita. The organic small molecules are absorbed into the void space of the crystalline sponges. Since the organometallic network of crystalline sponges can interact with the small molecule substrates via non-covalent interactions, the absorption can be selective. That is, the crystalline sponge can enrich certain molecules from a mixture.
As the crystal sponges are highly organized frameworks, the structure of the whole host-guest complex can be characterized by X-ray diffraction. Because the absorbate is encapsulated in a pre-organized environment, no single crystal of the substrate is needed in the X-ray diffraction. Besides, the X-ray crystallography of liquid samples can also be conducted. | 0 | Organic Chemistry |
The parent phosphonium is as found in the iodide salt, phosphonium iodide. Salts of the parent are rarely encountered, but this ion is an intermediate in the preparation of the industrially useful tetrakis(hydroxymethyl)phosphonium chloride:
:PH + HCl + 4 CHO →
Many organophosphonium salts are produced by protonation of primary, secondary, and tertiary phosphines:
:PR + H →
The basicity of phosphines follows the usual trends, with R = alkyl being more basic than R = aryl. | 0 | Organic Chemistry |
Section A on Cryogenics and Liquefied Gases focuses on refrigeration science and technology at low temperatures: the cryogenic domain spans the lower part of the temperature scale, from absolute zero to 120 K, thus encompassing the normal boiling points of air gases as well as of liquid natural gas (LNG).
Section A comprises two Commissions, A1 Cryophysics and Cryoengineering, and A2 Liquefaction and Separation of Gases. Commission A1 deals with research, development and industrial activities at the lowest temperatures, including low-temperature physics, applications of superconductivity and helium cryogenics. Commission A2 essentially covers the liquefied gas industry, including air separation and LNG technology, two mature domains with high economic stakes and ongoing developments addressing important societal issues such as energy efficiency and carbon sequestration.
Section A also maintains and develops relations with other Sections of the IIR, mainly Commission B1 Thermodynamics and Transfer Processes in the field of thermodynamics and transfer processes, essential tools of the cryogenic engineer, and Commission C1 Cryobiology, Cryomedicine and Health Products for the cooling of biological specimens and living tissues for preservation or treatment which require implementing cryogenic processes. Section A consists of a panel of multidisciplinary professionals and experts in sciences and technologies such as thermodynamics, condensed matter physics, materials science, heat transfer, fluid dynamics, vacuum and leak-tightness, instrumentation and process control, applied to the low-temperature domain.
* Commission A1: Cryophysics and Cryoengineering
Commission A1 on Cryophysics and Cryoengineering deals with research, development and industrial activities at the lowest temperatures, including low-temperature physics, applications of superconductivity and helium cryogenics.
* Commission A2: Liquefaction and Separation of Gases
The work of Commission A2 Liquefaction and Separation of Gases reflects world-wide activities in the domain of separation of gases and liquefaction. Apart from the personal involvement of Commission members in various projects, the commission is present at conferences, workshops and seminars: LNG International Exhibition and Conference, GASTECH, Cryogenics, Cryogen Expos, European Cryogenic Course and others.
The commission is close to academia, industry and end users of separated and liquefied gases.
Commission members work closely with Commission A1 Cryophysics, Cryoengineering and Commission C1 Cryobiology, Cryomedicine and Health Products. | 7 | Physical Chemistry |
A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone proteins and resembles thread wrapped around a spool. The nucleosome is the fundamental subunit of chromatin. Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones, which are known as a histone octamer. Each histone octamer is composed of two copies each of the histone proteins H2A, H2B, H3, and H4.
DNA must be compacted into nucleosomes to fit within the cell nucleus. In addition to nucleosome wrapping, eukaryotic chromatin is further compacted by being folded into a series of more complex structures, eventually forming a chromosome. Each human cell contains about 30 million nucleosomes.
Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones. Nucleosome positions in the genome are not random, and it is important to know where each nucleosome is located because this determines the accessibility of the DNA to regulatory proteins.
Nucleosomes were first observed as particles in the electron microscope by Don and Ada Olins in 1974, and their existence and structure (as histone octamers surrounded by approximately 200 base pairs of DNA) were proposed by Roger Kornberg. The role of the nucleosome as a regulator of transcription was demonstrated by Lorch et al. in vitro in 1987 and by Han and Grunstein and Clark-Adams et al. in vivo in 1988.
The nucleosome core particle consists of approximately 146 base pairs (bp) of DNA wrapped in 1.67 left-handed superhelical turns around a histone octamer, consisting of 2 copies each of the core histones H2A, H2B, H3, and H4. Core particles are connected by stretches of linker DNA, which can be up to about 80 bp long. Technically, a nucleosome is defined as the core particle plus one of these linker regions; however the word is often synonymous with the core particle. Genome-wide nucleosome positioning maps are now available for many model organisms and human cells.
Linker histones such as H1 and its isoforms are involved in chromatin compaction and sit at the base of the nucleosome near the DNA entry and exit binding to the linker region of the DNA. Non-condensed nucleosomes without the linker histone resemble "beads on a string of DNA" under an electron microscope.
In contrast to most eukaryotic cells, mature sperm cells largely use protamines to package their genomic DNA, most likely to achieve an even higher packaging ratio. Histone equivalents and a simplified chromatin structure have also been found in Archaea, suggesting that eukaryotes are not the only organisms that use nucleosomes. | 1 | Biochemistry |
According to Liouville's theorem for Hamiltonian dynamics, the hyper-volume of a cloud of points in phase space remains constant as the system evolves. Therefore, the information entropy must also remain constant, if we condition on the original information, and then follow each of those microstates forward in time:
However, as time evolves, that initial information we had becomes less directly accessible. Instead of being easily summarizable in the macroscopic description of the system, it increasingly relates to very subtle correlations between the positions and momenta of individual molecules. (Compare to Boltzmann's H-theorem.) Equivalently, it means that the probability distribution for the whole system, in 6N-dimensional phase space, becomes increasingly irregular, spreading out into long thin fingers rather than the initial tightly defined volume of possibilities.
Classical thermodynamics is built on the assumption that entropy is a state function of the macroscopic variables—i.e., that none of the history of the system matters, so that it can all be ignored.
The extended, wispy, evolved probability distribution, which still has the initial Shannon entropy S, should reproduce the expectation values of the observed macroscopic variables at time t. However it will no longer necessarily be a maximum entropy distribution for that new macroscopic description. On the other hand, the new thermodynamic entropy S assuredly will measure the maximum entropy distribution, by construction. Therefore, we expect:
At an abstract level, this result implies that some of the information we originally had about the system has become "no longer useful" at a macroscopic level. At the level of the 6N-dimensional probability distribution, this result represents coarse graining—i.e., information loss by smoothing out very fine-scale detail. | 7 | Physical Chemistry |
Ankaramite is volcanic rock type of mafic composition. It is a dark porphyritic variety of basanite containing abundant pyroxene and olivine phenocrysts. It contains minor amounts of plagioclase and accessory biotite, apatite, and iron oxides.
Its type locality is Ankaramy in Madagascar. It was first described in 1916. It is also found in the Sierra de Guanajuato of Central Mexico, the South Pacific on islands such as Tahiti, Rarotonga, Samoa and in the Zealandia, Alexandra Volcanic Group. | 9 | Geochemistry |
This test uses a saturated solution of calcium hypochlorite (bleaching powder), or alternatively a dilute solution (5.25% is typically used) of sodium hypochlorite, or undiluted household bleach. These solutions are typically replaced daily since they break down within 24–48 hours; they break down even more rapidly when exposed to sunlight (less than an hour) and so are recommended to keep in a dark-coloured bottle. Other factors that accelerate the decomposition of these solutions are heat, humidity, and carbon dioxide.
Colours typically observed with the C test are red and orange-rose. Chemicals causing a red reaction include anziaic acid, erythrin, and lecanoric acid, while those resulting in orange-red include gyrophoric acid. Rarely, an emerald-green colour is produced, caused by reaction with dihydroxy dibenzofurans, such as the chemical strepsilin. Another rare colour produced by this test is yellow, which is observed with Cladonia portentosa as a result of the dibenzofuran usnic acid.
Some common and widely distributed lichens that have lichen products with a positive reaction to C include Lecanora expallens, which is C+ (orange) because of the xanthone thiophanic acid, and Diploschistes muscorum, which is C+ (red) because of the didepside diploschistesic acid. | 3 | Analytical Chemistry |
The ropB protein binding location lies adjacent to speB promoter 1 that is also located within the highly repetitive intergenic region, however the ropB gene and the speB gene are transcribed in opposite directions. The -10 and -35 regions of speB promoter 1 have poor consensus; in order to ameliorate this, the ropB aids the RNA polymerase bondage with the help of a polyU polypyrimidine tract inside the palindromic inverted repeat region in a fashion uncannily similar to intrinsic termination in E.coli. | 1 | Biochemistry |
The Wilfley Table was built to solve a problem common in the recovery of heavy ore minerals; approximately 90% of gold grains, platinum group minerals, sulphides, arsenides/antimonides and tellurides, in source rocks are silt-sized (<). Concentration of these minerals requires preconcentration techniques that include recovery of this fraction. Preconcentration may involve any number of methods including jigs, spirals, shaking tables, Knelson concentration, dense media separation, panning and hydroseparation. The Wilfley Table exploits preconcentration on the basis of density to separate minerals. It can recover silt to coarse sand-sized heavy minerals for a broad spectrum of commodities including diamonds, precious and base metals, and uranium. | 8 | Metallurgy |
After a year in Birmingham doing chemical research, he was appointed head of the chemistry at Blackburn Technical School in Blackburn, Lancashire and was principal from 1908-1920. While at Blackburn was involved in publication of 35 papers in the Journal of the Chemical Society. He did original work on chemical structure and optical isomerism and as a result became a Fellow of the Royal Society (FRS) in 1917. Pickard was Principal of Battersea Polytechnic (which later became the University of Surrey) from 1920 to 1927.
He was also consulted by the cotton industry and later became director of the British Cotton Industry Research Association (then the Shirley Institute) in Manchester from 1927-1943 and expanded the technical facilities extensively in 1936.
He had considerable organisational skills and was active in several scientific organisations including the Royal Society (council); Society of Chemical Industry (president 1932-33); the Royal Institute of Chemistry (now the Royal Society of Chemistry) (president 1936-1939); the Chemical Society (vice-president); the now defunct [http://www.charitycommission.gov.uk/Showcharity/RegisterOfCharities/RemovedCharityMain.aspx?RegisteredCharityNumber=214247&SubsidiaryNumber=0 Chemical Council] (chairman) and various positions over a long period with the University of London including Vice-Chancellor, 1937-1939. | 4 | Stereochemistry |
A wide variety of algorithms have been developed to facilitate detection of promoters in genomic sequence, and promoter prediction is a common element of many gene prediction methods. A promoter region is located before the -35 and -10 Consensus sequences. The closer the promoter region is to the consensus sequences the more often transcription of that gene will take place. There is not a set pattern for promoter regions as there are for consensus sequences. | 1 | Biochemistry |
In swine, ractopamine is correlated with adverse effects, especially hyperactivity, trembling, and broken limbs, leading to censure by animal rights groups.
In a conversation with Boulder Weekly newspaper, Colorado State University Professor of Animal Science Temple Grandin, an expert on animal welfare, described harmful effects of ractopamine on feedlot animals, such as cattle with stiff, sore, and lame limbs, and increased heat stress. In the same column, she also opines that meat from ractopamine-treated animals may be tougher.
Ractopamine use is a factor in the incidence of downer pigs, animals that are unable to move or stand. | 4 | Stereochemistry |
tert-Butanesulfinamide has been used as an auxiliary in an asymmetric synthesis of cetirizine (more potent than the racemic mixture of the drug) starting from p-chlorobenzaldehyde and phenylmagnesium bromide. | 0 | Organic Chemistry |
In this variant the OAA produced by aspartate aminotransferase in the bundle sheath is decarboxylated to PEP by PEPCK. The fate of PEP is still debated. The simplest explanation is that PEP would diffuse back to the mesophyll to serve as a substrate for PEPC. Because PEPCK uses only one ATP molecule, the regeneration of PEP through PEPCK would theoretically increase photosynthetic efficiency of this subtype, however this has never been measured. An increase in relative expression of PEPCK has been observed under low light, and it has been proposed to play a role in facilitating balancing energy requirements between mesophyll and bundle sheath. | 5 | Photochemistry |
Some simple systems are amenable to spreadsheet calculations.
A large number of general-purpose computer programs for equilibrium constant calculation have been published. See for a bibliography. The most frequently used programs are:
* Potentiometric data: [http://www.hyperquad.co.uk/hq2000.htm Hyperquad], BEST PSEQUAD, [http://jplusconsulting.com/products/reactlab-ph/ ReactLab pH PRO]
* Spectrophotometric data:[http://www.hyperquad.co.uk/HypSpec.htm HypSpec], SQUAD, Specfit, [http://jplusconsulting.com/products/reactlab-equilibria/ ReactLab EQUILIBRIA]
* NMR data [http://www.hyperquad.co.uk/hypnmr.htm HypNMR], [http://www.nuigalway.ie/chem/Mike/wineqnmr.htm EQNMR ]
*Calorimetric data [http://www.hyperquad.co.uk/hypdeltah.htm HypΔH]. [https://www.affinimeter.com/site/itc/ Affinimeter] <br>Commercial Isothermal titration calorimeters are usually supplied with software with which an equilibrium constant and standard formation enthalpy for the formation of a 1:1 adduct can be obtained. Some software for handling more complex equilibria may also be supplied. | 7 | Physical Chemistry |
Alcohols can also undergo ammonolysis when in the presence of ammonia. An example is the conversion of phenol to aniline, catalyzed by stannic chloride. | 1 | Biochemistry |
The microdialysis principle was first employed in the early 1960s, when push-pull canulas and dialysis sacs were implanted into animal tissues, especially into rodent brains, to directly study the tissues biochemistry. While these techniques had a number of experimental drawbacks, such as the number of samples per animal or no/limited time resolution, the invention of continuously perfused dialytrodes in 1972 helped to overcome some of these limitations. Further improvement of the dialytrode concept resulted in the invention of the "hollow fiber", a tubular semipermeable membrane with a diameter of ~200-300μm, in 1974. Todays most prevalent shape, the needle probe, consists of a shaft with a hollow fiber at its tip and can be inserted by means of a guide cannula into the brain and other tissues. An alternative method, open flow micro-perfusion (OFM), replaces the membrane with macroscopic openings which facilitates sampling of lipophilic and hydrophilic compounds, protein bound and unbound drugs, neurotransmitters, peptides and proteins, antibodies, nanoparticles and nanocarriers, enzymes and vesicles. | 1 | Biochemistry |
The thermometric titrimetric analysis of sodium aluminate liquor ("Bayer liquor") in the production of alumina from bauxite is accomplished in an automated two titration sequence. This is an adaptation of a classic thermometric titration application (VanDalen and Ward, 1973). In the first titration, tartrate solution is added to an aliquot of liquor to complex aluminate, releasing one mole of hydroxyl for each mole of aluminate present. This is titrated acidimetrically along with "free" hydroxyl present and the carbonate content (as a second endpoint). The second titration is preceded by the automatic addition of fluoride solution. The alumina-tartrate complex is broken in favour of the formation of an aluminium fluoride complex and the concomitant release of three moles of hydroxyl for each mole of aluminium present, which are then titrated acidimetrically. The whole determination can be completed in less than 5 minutes. | 3 | Analytical Chemistry |
Thermochemistry rests on two generalizations. Stated in modern terms, they are as follows:
#Lavoisier and Laplace's law (1780): The energy change accompanying any transformation is equal and opposite to energy change accompanying the reverse process.
#Hess' law of constant heat summation (1840): The energy change accompanying any transformation is the same whether the process occurs in one step or many.
These statements preceded the first law of thermodynamics (1845) and helped in its formulation.
Thermochemistry also involves the measurement of the latent heat of phase transitions. Joseph Black had already introduced the concept of latent heat in 1761, based on the observation that heating ice at its melting point did not raise the temperature but instead caused some ice to melt.
Gustav Kirchhoff showed in 1858 that the variation of the heat of reaction is given by the difference in heat capacity between products and reactants: dΔH / dT = ΔC. Integration of this equation permits the evaluation of the heat of reaction at one temperature from measurements at another temperature. | 7 | Physical Chemistry |
A-values are numerical values used in the determination of the most stable orientation of atoms in a molecule (conformational analysis), as well as a general representation of steric bulk. A-values are derived from energy measurements of the different cyclohexane conformations of a monosubstituted cyclohexane chemical.
Substituents on a cyclohexane ring prefer to reside in the equatorial position to the axial. The difference in Gibbs free energy (ΔG) between the higher energy conformation (axial substitution) and the lower energy conformation (equatorial substitution) is the A-value for that particular substituent. | 4 | Stereochemistry |
* J.G. Nicholls, A.R. Martin, B.G. Wallace and P.A. Fuchs. "From Neuron to Brain". 4th ed. Sinauer Associates, Sunderland, MA. | 1 | Biochemistry |
Like many ACE inhibitors, this prodrug is converted to the active metabolite spiraprilat following oral administration. Unlike other members of the group, it is eliminated both by renal and hepatic routes, which may allow for greater use in patients with renal impairment.
However, data on its effect upon the renal function are conflicting. | 4 | Stereochemistry |
The entropy is given by the entropic equation of state:
Using as before, and integrating the second term using we obtain simply
This is the entropic equation of state for a perfect vdW fluid, or in reduced form | 7 | Physical Chemistry |
The mutation of Dally is a consequence of the P-element and the place where it is located. It is possible to differentiate between the mutants Dally-P1 and Dally-P2, depending on where the insertion of P-element is. It is known that Dally-P2 generates a bigger amount of defects. This mutated Dally disrupts the cell cycle progression, delaying the process during the G2-mitosis transition. As a matter of fact, mutations affecting Dally disrupt patterning of many tissues, for instance of the nervous system. Dally mutants display cell cycle progression defects in specific sets of dividing cells. Those mutations are pleiotropic and can affect viability and produce morphological defects in several adult tissues, such as the eye, antenna, wing and genitalia. | 1 | Biochemistry |
Accurate and consistent measurement of gases and deposition at every monitoring site is of the utmost importance to the NADP. This is accomplished, in part, by ensuring that all sites adhere to specific standard operating procedures. This provides consistent methodology at all sites within the networks. The SOPs can be viewed here:
* http://nadp.slh.wisc.edu/siteops/ | 2 | Environmental Chemistry |
The process is named for its inventor Anson Gardner Betts who filed several patents for this method starting in 1901. | 8 | Metallurgy |
Modulation of neurotransmitter release by G-protein-coupled receptors (GPCRs) is a prominent presynaptic mechanism for regulation of synaptic transmission. The activation of GPCRs located at the presynaptic terminal, can decrease the probability of neurotransmitter release. This presynaptic depression involves activation of Gi/o-type G-proteins that mediate different inhibitory mechanisms, including inhibition of voltage-gated calcium channels, activation of potassium channels, and direct inhibition of the vesicle fusion process. Endocannabinoids, synthesized in and released from postsynaptic neuronal elements, and their cognate receptors, including the (GPCR) CB1 receptor, located at the presynaptic terminal, are involved in this modulation by a retrograde signaling process, in which these compounds are synthesized in and released from postsynaptic neuronal elements, and travel back to the presynaptic terminal to act on the CB1 receptor for short-term or long-term synaptic depression, that cause a short or long lasting decrease in neurotransmitter release. | 1 | Biochemistry |
The term matrix-assisted laser desorption ionization (MALDI) was coined in 1985 by Franz Hillenkamp, Michael Karas and their colleagues. These researchers found that the amino acid alanine could be ionized more easily if it was mixed with the amino acid tryptophan and irradiated with a pulsed 266 nm laser. The tryptophan was absorbing the laser energy and helping to ionize the non-absorbing alanine. Peptides up to the 2843 Da peptide melittin could be ionized when mixed with this kind of "matrix". The breakthrough for large molecule laser desorption ionization came in 1987 when Koichi Tanaka of Shimadzu Corporation and his co-workers used what they called the "ultra fine metal plus liquid matrix method" that combined 30 nm cobalt particles in glycerol with a 337 nm nitrogen laser for ionization. Using this laser and matrix combination, Tanaka was able to ionize biomolecules as large as the 34,472 Da protein carboxypeptidase-A. Tanaka received one-quarter of the 2002 Nobel Prize in Chemistry for demonstrating that, with the proper combination of laser wavelength and matrix, a protein can be ionized. Karas and Hillenkamp were subsequently able to ionize the 67 kDa protein albumin using a nicotinic acid matrix and a 266 nm laser. Further improvements were realized through the use of a 355 nm laser and the cinnamic acid derivatives ferulic acid, caffeic acid and sinapinic acid as the matrix. The availability of small and relatively inexpensive nitrogen lasers operating at 337 nm wavelength and the first commercial instruments introduced in the early 1990s brought MALDI to an increasing number of researchers. Today, mostly organic matrices are used for MALDI mass spectrometry. | 1 | Biochemistry |
LDH is also regulated by the relative concentrations of its substrates. LDH becomes more active under periods of extreme muscular output due to an increase in substrates for the LDH reaction. When skeletal muscles are pushed to produce high levels of power, the demand for ATP in regards to aerobic ATP supply leads to an accumulation of free ADP, AMP, and Pi. The subsequent glycolytic flux, specifically production of pyruvate, exceeds the capacity for pyruvate dehydrogenase and other shuttle enzymes to metabolize pyruvate. The flux through LDH increases in response to increased levels of pyruvate and NADH to metabolize pyruvate into lactate. | 1 | Biochemistry |
Inductively coupled plasma mass spectrometry (ICP-MS) is a type of mass spectrometry that uses an inductively coupled plasma to ionize the sample. It atomizes the sample and creates atomic and small polyatomic ions, which are then detected. It is known and used for its ability to detect metals and several non-metals in liquid samples at very low concentrations. It can detect different isotopes of the same element, which makes it a versatile tool in isotopic labeling.
Compared to atomic absorption spectroscopy, ICP-MS has greater speed, precision, and sensitivity. However, compared with other types of mass spectrometry, such as thermal ionization mass spectrometry (TIMS) and glow discharge mass spectrometry (GD-MS), ICP-MS introduces many interfering species: argon from the plasma, component gases of air that leak through the cone orifices, and contamination from glassware and the cones. | 3 | Analytical Chemistry |
Coal comes in four main types or ranks: lignite or brown coal, bituminous coal or black coal, anthracite and graphite. Each type of coal has a certain set of physical parameters which are mostly controlled by moisture, volatile content (in terms of aliphatic or aromatic hydrocarbons) and carbon content. | 3 | Analytical Chemistry |
Wavy single bonds are the standard way to represent unknown or unspecified stereochemistry or a mixture of isomers (as with tetrahedral stereocenters). A crossed double-bond has been used sometimes; it is no longer considered an acceptable style for general use by IUPAC but may still be required by computer software. | 4 | Stereochemistry |
A potentially significant problem following bisulfite treatment is incomplete desulfonation of pyrimidine residues due to inadequate alkalization of the solution. This may inhibit some DNA polymerases, rendering subsequent PCR difficult. However, this situation can be avoided by monitoring the pH of the solution to ensure that desulfonation will be complete.
A final concern is that bisulfite treatment greatly reduces the level of complexity in the sample, which can be problematic if multiple PCR reactions are to be performed (2006). Primer design is more difficult, and inappropriate cross-hybridization is more frequent. | 1 | Biochemistry |
ATP hydrolysis is the catabolic reaction process by which chemical energy that has been stored in the high-energy phosphoanhydride bonds in adenosine triphosphate (ATP) is released after splitting these bonds, for example in muscles, by producing work in the form of mechanical energy. The product is adenosine diphosphate (ADP) and an inorganic phosphate (P). ADP can be further hydrolyzed to give energy, adenosine monophosphate (AMP), and another inorganic phosphate (P). ATP hydrolysis is the final link between the energy derived from food or sunlight and useful work such as muscle contraction, the establishment of electrochemical gradients across membranes, and biosynthetic processes necessary to maintain life.
Anhydridic bonds are often labelled as "high-energy bonds". P-O bonds are in fact fairly strong (~30 kJ/mol stronger than C-N bonds) and themselves not particularly easy to break. As noted below, energy is released by the hydrolysis of ATP. However, when the P-O bonds are broken, input of energy is required. It is the formation of new bonds and lower-energy inorganic phosphate with a release of a larger amount of energy that lowers the total energy of the system and makes it more stable.
Hydrolysis of the phosphate groups in ATP is especially exergonic, because the resulting inorganic phosphate molecular ion is greatly stabilized by multiple resonance structures, making the products (ADP and P) lower in energy than the reactant (ATP). The high negative charge density associated with the three adjacent phosphate units of ATP also destabilizes the molecule, making it higher in energy. Hydrolysis relieves some of these electrostatic repulsions, liberating useful energy in the process by causing conformational changes in enzyme structure.
In humans, approximately 60 percent of the energy released from the hydrolysis of ATP produces metabolic heat rather than fuel the actual reactions taking place.
Due to the acid-base properties of ATP, ADP, and inorganic phosphate, the hydrolysis of ATP has the effect of lowering the pH of the reaction medium. Under certain conditions, high levels of ATP hydrolysis can contribute to lactic acidosis. | 1 | Biochemistry |
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