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Spongin, a modified type of collagen protein, forms the fibrous skeleton of most organisms among the phylum Porifera, the sponges. It is secreted by sponge cells known as spongocytes.
Spongin gives a sponge its flexibility. True spongin is found only in members of the class Demospongiae. | 1 | Biochemistry |
Small redox proteins such as cytochromes and ferredoxins can be investigated on condition that their electroactive coverage (the amount of protein undergoing direct electron transfer) is large enough (in practice, greater than a fraction of pmol/cm).
Electrochemical data obtained with small proteins can be used to measure the redox potentials of the protein's redox sites, the rate of electron transfer between the protein and the electrode, or the rates of chemical reactions (such as protonations) that are coupled to electron transfer. | 7 | Physical Chemistry |
Hydrothermal liquefaction (HTL) is a thermal depolymerization process used to convert wet biomass, and other macromolecules, into crude-like oil under moderate temperature and high pressure. The crude-like oil has high energy density with a lower heating value of 33.8-36.9 MJ/kg and 5-20 wt% oxygen and renewable chemicals. The process has also been called hydrous pyrolysis.
The reaction usually involves homogeneous and/or heterogeneous catalysts to improve the quality of products and yields. Carbon and hydrogen of an organic material, such as biomass, peat or low-ranked coals (lignite) are thermo-chemically converted into hydrophobic compounds with low viscosity and high solubility. Depending on the processing conditions, the fuel can be used as produced for heavy engines, including marine and rail or upgraded to transportation fuels, such as diesel, gasoline or jet-fuels.
The process may be significant in the creation of fossil fuels. Simple heating without water, anhydrous pyrolysis has long been considered to take place naturally during the catagenesis of kerogens to fossil fuels. In recent decades it has been found that water under pressure causes more efficient breakdown of kerogens at lower temperatures than without it. The carbon isotope ratio of natural gas also suggests that hydrogen from water has been added during creation of the gas. | 0 | Organic Chemistry |
While iron oxide used to make nanoparticles is biodegradable, the toxicity of magnetic nanoparticles is still under investigation. Some research has found no signs of damage to cells, while others claim that small (< 2 nm) nanoparticles can diffuse across cell membranes and disrupt organelles.
In addition, very high concentrations of iron oxide can disrupt homeostasis and lead to iron overload, which can damage or alter DNA, affect cellular responses, and kill cells. Lysosymes can also digest the nanoparticles and release free iron which can react with hydrogen peroxide to form free radicals, leading to cytotoxic, mutagenic, and carcinogenic effects. | 1 | Biochemistry |
Bacteria biooxidation is an oxidation process caused by microbes where the valuable metal remains (but becomes enriched) in the solid phase. In this process, the metal remains in the solid phase and the liquid can be discarded.
Bacterial oxidation is a biohydrometallurgical process developed for pre-cyanidation treatment of refractory gold ores or concentrates. The bacterial culture is a mixed culture of Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and Leptospirillum ferrooxidans. The bacterial oxidation process comprises contacting refractory sulfide ROM ore or concentrate with a strain of the bacterial culture for a suitable treatment period under an optimum operating environment. The bacteria oxidise the sulfide minerals, thus liberating the occluded gold for subsequent recovery via cyanidation.
The BIOX® process is a proprietary technology owned by Biomin South Africa and used under licence by a number of operating mines. The BIOX® process involves bacterial oxidation in agitated tanks for pre-treatment of refractory ores and concentrates ahead of conventional cyanide leach for gold recovery.
Under controlled continuous plant conditions, the number of bacterial cells and their activity is optimised to attain the highest rate of sulfide oxidation. The bacteria require a very acidic environment (pH 1.0 to 4.0), a temperature of between 30 and 45 °C, and a steady supply of oxygen and carbon dioxide for optimum growth and activity. The unusual operating conditions for the bacteria are not favourable for the growth of most other microbes, thus eliminating the need for sterility during the bacterial oxidation process. Because organic substances are toxic to the bacteria, they are non-pathogenic and incapable of causing disease. The bacteria employed in the process do not, therefore, pose a health risk to humans or any animals.
The bacterial oxidation of iron sulfide minerals produces iron(III) sulfate and sulfuric acid, and in the case of arsenopyrite, arsenic acid is also produced. The arsenic is removed from the liquor by coprecipitation with the iron and sulfate in a two-stage neutralisation process. This produces a solid neutralisation precipitate containing largely calcium sulfate, basic iron(III) arsenate and iron(III) hydroxide. The iron(III) arsenate is sufficiently insoluble and stable to allow the neutralisation product to be safely disposed of on a slimes dam. The neutralisation liquor, purified to contain an acceptable level of arsenic, can be re-used in the milling, flotation or bacterial oxidation circuits. | 9 | Geochemistry |
# Accessibility: Run over 200 regularly updated analysis and visualization tools (that support data preprocessing, gene expression analysis, proteomics, Single nucleotide polymorphism (SNP) analysis, flow cytometry, and next-generation sequencing) and create analytic workflows without any programming through a point and click user interface.
# Reproducibility: Automated history and provenance tracking with versioning so that any user can share, repeat and understand a complete computational analysis
# Extensibility: Computational users can import their methods and code for sharing using tools that support easy creation and integration
# Multiple interfaces: Web browser, application, and programmatic interfaces make analysis modules and pipelines available to a broad range of users; public hosted server | 1 | Biochemistry |
Gamma rays detected in a spectroscopic system produce peaks in the spectrum. These peaks can also be called lines by analogy to optical spectroscopy. The width of the peaks is determined by the resolution of the detector, a very important characteristic of gamma spectroscopic detectors, and high resolution enables the spectroscopist to separate two gamma lines that are close to each other. Gamma spectroscopy systems are designed and adjusted to produce symmetrical peaks of the best possible resolution. The peak shape is usually a Gaussian distribution. In most spectra the horizontal position of the peak is determined by the gamma ray's energy, and the area of the peak is determined by the intensity of the gamma ray and the efficiency of the detector.
The most common figure used to express detector resolution is full width at half maximum (FWHM). This is the width of the gamma ray peak at half of the highest point on the peak distribution. Resolution figures are given with reference to specified gamma ray energies. Resolution can be expressed in absolute (i.e., eV or MeV) or relative terms. For example, a sodium iodide (NaI) detector may have a FWHM of 9.15 keV at 122 keV, and 82.75 keV at 662 keV. These resolution values are expressed in absolute terms. To express the resolution in relative terms, the FWHM in eV or MeV is divided by the energy of the gamma ray and usually shown as percentage. Using the preceding example, the resolution of the detector is 7.5% at 122 keV, and 12.5% at 662 keV. A germanium detector may give resolution of 560 eV at 122 keV, yielding a relative resolution of 0.46%. | 7 | Physical Chemistry |
In addition to RNA, proteins can undergo splicing. Although the biomolecular mechanisms are different, the principle is the same: parts of the protein, called inteins instead of introns, are removed. The remaining parts, called exteins instead of exons, are fused together.
Protein splicing has been observed in a wide range of organisms, including bacteria, archaea, plants, yeast and humans. | 1 | Biochemistry |
FRET efficiency can also be determined from the change in the fluorescence lifetime of the donor. The lifetime of the donor will decrease in the presence of the acceptor. Lifetime measurements of the FRET-donor are used in fluorescence-lifetime imaging microscopy (FLIM). | 1 | Biochemistry |
Some animals, including birds, reptiles, and insects such as bees, can see near-ultraviolet wavelengths. Many fruits, flowers, and seeds stand out more strongly from the background in ultraviolet wavelengths as compared to human color vision. Scorpions glow or take on a yellow to green color under UV illumination, thus assisting in the control of these arachnids. Many birds have patterns in their plumage that are invisible at usual wavelengths but observable in ultraviolet, and the urine and other secretions of some animals, including dogs, cats, and human beings, are much easier to spot with ultraviolet. Urine trails of rodents can be detected by pest control technicians for proper treatment of infested dwellings.
Butterflies use ultraviolet as a communication system for sex recognition and mating behavior. For example, in the Colias eurytheme butterfly, males rely on visual cues to locate and identify females. Instead of using chemical stimuli to find mates, males are attracted to the ultraviolet-reflecting color of female hind wings. In Pieris napi butterflies it was shown that females in northern Finland with less UV-radiation present in the environment possessed stronger UV signals to attract their males than those occurring further south. This suggested that it was evolutionarily more difficult to increase the UV-sensitivity of the eyes of the males than to increase the UV-signals emitted by the females.
Many insects use the ultraviolet wavelength emissions from celestial objects as references for flight navigation. A local ultraviolet emitter will normally disrupt the navigation process and will eventually attract the flying insect.
The green fluorescent protein (GFP) is often used in genetics as a marker. Many substances, such as proteins, have significant light absorption bands in the ultraviolet that are of interest in biochemistry and related fields. UV-capable spectrophotometers are common in such laboratories.
Ultraviolet traps called bug zappers are used to eliminate various small flying insects. They are attracted to the UV and are killed using an electric shock, or trapped once they come into contact with the device. Different designs of ultraviolet radiation traps are also used by entomologists for collecting nocturnal insects during faunistic survey studies. | 5 | Photochemistry |
Japan was the first country that allowed the use of sucrose esters as food additives. The Japanese Ministry of Health and Welfare approved sucrose esters in 1959. Then, in 1969, FAO/WHO approved the use of sucrose esters.
Sucrose esters were approved and registered by European Food Safety Authority or EFSA under the E number of E 473.
In the US, sucrose esters were approved by the FDA (Food and Drug Administration). | 0 | Organic Chemistry |
Studies on evaluating antioxidant capacity can use electrochemical methods.
Detection can be made by recombinant luminescent bacterial sensors. | 0 | Organic Chemistry |
Trimethyl orthoformate is a useful building block for creating methoxymethylene groups and heterocyclic ring systems. It introduces a formyl group to a nucleophilic substrate, e.g. RNH to form R-NH-CHO, which can undergo further reactions. It is used in the production of the fungicides, azoxystrobin, and picoxystrobin, as well as for some members of the floxacin family of antibacterial drugs.
A number of pharmaceutical intermediates are also made from trimethyl orthoformate.
Trimethyl orthoformate is also an effective reagent for converting compatible carboxylic acids to their corresponding methyl esters. Alternatively, acid-catalyzed esterifications with methanol can be driven closer to completion by employing trimethyl orthoformate to convert water byproduct to methanol and methyl formate. | 0 | Organic Chemistry |
* National Museum of Australia
* Australian Museum
* National Museum of Natural History, Smithsonian Institution
* Art Gallery of New South Wales
* South Australian Museum
* State Herbarium of South Australia
* Art Gallery of South Australia
* State Library of South Australia (literary collections)
* Tasmanian Museum and Art Gallery
* Art Gallery of Western Australia
* Queensland Art Gallery
* National Gallery of Victoria | 1 | Biochemistry |
Surface science is the study of physical and chemical phenomena that occur at the interface of two phases, including solid–liquid interfaces, solid–gas interfaces, solid–vacuum interfaces, and liquid–gas interfaces. It includes the fields of surface chemistry and surface physics. Some related practical applications are classed as surface engineering. The science encompasses concepts such as heterogeneous catalysis, semiconductor device fabrication, fuel cells, self-assembled monolayers, and adhesives. Surface science is closely related to interface and colloid science. Interfacial chemistry and physics are common subjects for both. The methods are different. In addition, interface and colloid science studies macroscopic phenomena that occur in heterogeneous systems due to peculiarities of interfaces. | 7 | Physical Chemistry |
Lepidodinium viride and its close relatives are dinophytes (see below) that lost their original peridinin chloroplast and replaced it with a green algal derived chloroplast (more specifically, a prasinophyte). Lepidodinium is the only dinophyte that has a chloroplast that's not from the rhodoplast lineage. The chloroplast is surrounded by two membranes and has no nucleomorph—all the nucleomorph genes have been transferred to the dinophyte nucleus. The endosymbiotic event that led to this chloroplast was serial secondary endosymbiosis rather than tertiary endosymbiosis—the endosymbiont was a green alga containing a primary chloroplast (making a secondary chloroplast). | 5 | Photochemistry |
The Danishefsky Taxol total synthesis in organic chemistry is an important third Taxol synthesis published by the group of Samuel Danishefsky in 1996 two years after the first two efforts described in the Holton Taxol total synthesis and the Nicolaou Taxol total synthesis. Combined they provide a good insight in the application of organic chemistry in total synthesis.
Danishefsky's route to Taxol has many similarities with that of Nicolaou. Both are examples of convergent synthesis with a coupling of the A and the C ring from two precursors. The main characteristic of the Danishefsky variant is the completion of the oxetane D ring onto the cyclohexanol C ring prior to the construction of the 8-membered B ring. The most prominent starting material is the (+) enantiomer of the Wieland-Miescher ketone. This compound is commercially available as a single enantiomer and the single chiral group present in this molecule is able to drive the entire sequence of organic reactions to a single optically active Taxol endproduct. The final step, the tail addition is identical to that of Nicolaou and is based on Ojima chemistry.
In terms of raw material shopping, this taxol molecule consists of the aforementioned Wieland-Miescher ketone, 2-methyl-3-pentanone, lithium aluminium hydride, osmium tetroxide, phenyllithium, pyridinium chlorochromate, the Corey-Chaykovsky reagent and acryloyl chloride. Key chemical transformations are the Johnson-Corey-Chaykovsky reaction and the Heck reaction. | 0 | Organic Chemistry |
Striations or string-like structures, also known as Birkeland currents, are seen in many plasmas, like the plasma ball, the aurora, lightning, electric arcs, solar flares, and supernova remnants. They are sometimes associated with larger current densities, and the interaction with the magnetic field can form a magnetic rope structure. (See also Plasma pinch)
Filamentation also refers to the self-focusing of a high power laser pulse. At high powers, the nonlinear part of the index of refraction becomes important and causes a higher index of refraction in the center of the laser beam, where the laser is brighter than at the edges, causing a feedback that focuses the laser even more. The tighter focused laser has a higher peak brightness (irradiance) that forms a plasma. The plasma has an index of refraction lower than one, and causes a defocusing of the laser beam. The interplay of the focusing index of refraction, and the defocusing plasma makes the formation of a long filament of plasma that can be micrometers to kilometers in length. One interesting aspect of the filamentation generated plasma is the relatively low ion density due to defocusing effects of the ionized electrons. (See also Filament propagation) | 7 | Physical Chemistry |
Acid rain can damage buildings, historic monuments, and statues, especially those made of rocks, such as limestone and marble, that contain large amounts of calcium carbonate. Acids in the rain react with the calcium compounds in the stones to create gypsum, which then flakes off.
:CaCO (s) + HSO (aq) CaSO (s) + CO (g) + HO (l)
The effects of this are commonly seen on old gravestones, where acid rain can cause the inscriptions to become completely illegible. Acid rain also increases the corrosion rate of metals, in particular iron, steel, copper and bronze. | 2 | Environmental Chemistry |
Ridaforolimus (AP23573, MK-8669), or deforolimus, is another rapamycin analogue that is not a prodrug for sirolimus. Like temsirolimus it can be administered intravenously, and oral formulation is being estimated for treatment of sarcoma. | 1 | Biochemistry |
The emerging understanding of the role of eNSCs in the adult mammalian brain suggested the relevance of these cells to disease. To address this issue, experiments were performed where the activation of eNSCs was induced in models of disease. This allowed the study of the consequences of activating eNSCs in the diseased brain. Several lines of evidence implicate the STAT3-Ser/Hes3 signaling axis in various diseases:
:* Activation of the signaling pathway by Delta4 in combination with basic fibroblast growth factor (bFGF) induces motor and sensory skill improvements in adult rat models of ischemic stroke (PMCAO model).
:* This signaling pathway may mediate pro-survival functions of macrophage migration inhibitory factor on neural stem cells.
:* Activation of the signaling pathway by Delta4, Angiopoietin 2, insulin, or a combination of the three and a JAK inhibitor induces motor skill improvements in adult rat models of Parkinson's disease (6-hydroxydopamine model).
:* RNA interference (“knockdown”) of Hes3 in cultures of cells with cancer stem cell properties from patients with glioblastoma multiforme reduces cell number.
:* Mice lacking Hes3 exhibit increased sensitivity to particular paradigms of pancreatic islet damage, suggesting roles in diabetes. | 1 | Biochemistry |
A diketopiperazine (DKP), also known as a dioxopiperazine or piperazinedione, is a class of organic compounds related to piperazine but containing two amide linkages. DKP's are the smallest known class of cyclic peptide. Despite their name, they are not ketones, but amides. Three regioisomers are possible, differing in the locations of the carbonyl groups.
* One isomer is an oxamide obtained from ethylenediamine.
* 2,5-Diketopiperazines are cyclodipeptides often obtainable via condensation of two α-amino acids.
* 2,6-Diketopiperazines may be viewed as cyclized imide derivatives derived from iminodiacetic acids.
Of these three isomeric diketopiperazines, the 2,5-derivatives have attracted the greatest interest. Due to their appearance in biologically active natural products, medicinal chemists have been inspired to use DKPs to circumvent the poor physical and metabolic properties of peptides in the course of drug discovery. | 0 | Organic Chemistry |
mA is not only found on mRNAs, various non-coding RNAs also contain this mark. For instance, XIST, the lncRNA that initiates X-inactivation, is enriched in mA. These mA are recognized and bound by the YTH domain protein YTHDC1. XIST mediated silencing of the X chromosome is negatively affected when XIST is not modified with mA.
RNA molecules containing mA are involved in UV-induced DNA damage repair mechanisms. When DNA is damaged, poly(A)+ transcripts containing numerous mA residues accumulate in the region. This facilitates the accessibility of DNA-repairing proteins, such as DNA polymerase K, so that they can fulfil their function. | 1 | Biochemistry |
The first named alkyl radical was ethyl, named so by Liebig in 1833 from the German word "Äther" (which in turn had been derived from the Greek word "aither" meaning "air", for the substance now known as diethyl ether) and the Greek word ύλη (hyle), meaning "matter". This was followed by methyl (Dumas and Peligot in 1834, meaning "spirit of wood") and amyl (Auguste Cahours in 1840). The word alkyl was introduced by Johannes Wislicenus in or before 1882, based on the German word "Alkoholradikale" and then-common suffix -yl. | 0 | Organic Chemistry |
The adsorption of water at surfaces is of broad importance in chemical engineering, materials science and catalysis. Also termed surface hydration, the presence of physically or chemically adsorbed water at the surfaces of solids plays an important role in governing interface properties, chemical reaction pathways and catalytic performance in a wide range of systems. In the case of physically adsorbed water, surface hydration can be eliminated simply through drying at conditions of temperature and pressure allowing full vaporization of water. For chemically adsorbed water, hydration may be in the form of either dissociative adsorption, where HO molecules are dissociated into surface adsorbed -H and -OH, or molecular adsorption (associative adsorption) where individual water molecules remain intact | 7 | Physical Chemistry |
The ability of geckos – which can hang on a glass surface using only one toe – to climb on sheer surfaces has been for many years mainly attributed to the van der Waals forces between these surfaces and the spatulae, or microscopic projections, which cover the hair-like setae found on their footpads.
There were efforts in 2008 to create a dry glue that exploits the effect, and success was achieved in 2011 to create an adhesive tape on similar grounds (i.e. based on van der Waals forces). In 2011, a paper was published relating the effect to both velcro-like hairs and the presence of lipids in gecko footprints.
A later study suggested that capillary adhesion might play a role, but that hypothesis has been rejected by more recent studies.
A 2014 study has shown that gecko adhesion to smooth Teflon and polydimethylsiloxane surfaces is mainly determined by electrostatic interaction (caused by contact electrification), not van der Waals or capillary forces.
Among the arthropods, some spiders have similar setae on their scopulae or scopula pads, enabling them to climb or hang upside-down from extremely smooth surfaces such as glass or porcelain. | 6 | Supramolecular Chemistry |
Robert and John Garton made a commercial start as R. & J. Garton. They launched their first variety, Abundance oat, in 1892.
Generous publicity followed in the press, together with the publication of articles by botanists in the Journal of the Royal Agricultural Society of England, and in the Transactions of the Royal Highland and Agricultural Society of Scotland in 1894 and 1898. Professor Robert Wallace (1853–1939) of the University of Edinburgh said Under the system originated by Mr John Garton an infinite number of new and distinct breeds of oats, barleys, wheats, clovers and grasses have been produced.
In 1898 a public company was launched, Gartons Limited. It was based in Warrington. Many of the 600 or so subscribers for £50,000 cumulative preference shares of 6% rising to 10% were farmers.
George Peddie Miln joined the company as Managing Director, together with Robert Garton, Thomas R. Garton, Thomas Baxter and Arthur Smith as directors. Robert and John Garton agreed to continue to work for the Company for five years for £500 and to receive the entire ordinary share capital of the new company of £50,000.
It rapidly became the United Kingdom's best known plant breeding and seed company, and also exported seeds widely. | 1 | Biochemistry |
Nitrogenous compounds have a variety of sources including washout of oxides of nitrogen from the atmosphere, some geological inputs and some from macrophyte and algal nitrogen fixation. However, for many rivers in the proximity of humans, the largest input is from sewage whether treated or untreated. The nitrogen derives from breakdown products of proteins found in urine and faeces. These products, being very soluble, often pass through sewage treatment process and are discharged into rivers as a component of sewage treatment effluent. Nitrogen may be in the form of nitrate, nitrite, ammonia or ammonium salts or what is termed albuminoid nitrogen or nitrogen still within an organic proteinoid molecule.
The differing forms of nitrogen are relatively stable in most river systems with nitrite slowly transforming into nitrate in well oxygenated rivers and ammonia transforming into nitrite/ nitrate. However, the process are slow in cool rivers and reduction in concentration may more often be attributed to simple dilution. All forms of nitrogen are taken up by macrophytes and algae and elevated levels of nitrogen are often associated with overgrowths of plants or eutrophication. These can have the effect of blocking channels and inhibiting navigation. However, ecologically, the more significant effect is on dissolved oxygen concentrations which may become super-saturated during daylight due to plant photosynthesis but then drop to very low levels during darkness as plant respiration uses up the dissolved oxygen. Coupled with the release of oxygen in photosynthesis is the creation of bi-carbonate ions which cause a steep rise in pH and this is matched in darkness as carbon dioxide is released through respiration which substantially lowers the pH. Thus high levels of nitrogenous compounds tends to lead to eutrophication with extreme variations in parameters which in turn can substantially degrade the ecological worth of the watercourse.
Ammonium ions also have a toxic effect, especially on fish. The toxicity of ammonia is dependent on both pH and temperature and an added complexity is the buffering effect of the blood/water interface across the gill membrane which masks any additional toxicity over about pH 8.0. The management of river chemistry to avoid ecological damage is particularly difficult in the case of ammonia as a wide range of potential scenarios of concentration, pH and temperature have to be considered and the diurnal pH fluctuation caused by photosynthesis considered. On warm summer days with high-bi-carbonate concentrations unexpectedly toxic conditions can be created. | 2 | Environmental Chemistry |
In this part of the experiment, Tamm et al. transfected 293 cells with survivin and lysed them to obtain cell lysate. The lysates were incubated with different caspase forms and survivin was immunopercipitated with anti-survivin antibody. The idea behind this is that, if survivin binds physically with the caspase it is incubated with, it will be co-precipitated along with the survivin while everything else in the lysate is washed away. The immunoprecipitates were then run on SDS-PAGE and then immunoblotted for detection of the desired caspase. If the caspase of interest was detected, it meant that it was bound to survivin in the immunoprecipitation step implicating that survivin and the particular caspase had bound beforehand. Active caspase-3 and -7 coimmunoprecipitated with survivin. The inactive proforms of caspase-3 and -7 did not bind survivin. Survivin also does not bind to active caspase-8. Caspase-3 and -7 are effector proteases whereas caspase-8 is an initiator caspase that sits more upstream in the apoptotic pathway. These results demonstrate survivins capability to bind with particular caspases in vitro, but may not necessarily translate over to actual physiological conditions. Later, a 2001 study confirmed that human survivin tightly binds caspase-3 and -7 when expressed in E. coli'.
Further evidence to support the idea that survivin blocks apoptosis by directly inhibiting caspases was given by Tamm et al. 293 cells were transfected with either overexposed caspase-3 or -7 encoding plasmid and with survivin. They showed that survivin inhibited processing of these two caspases into their active forms. While survivin has been shown as mentioned above to bind to only the active forms of these caspases, it is likely here that survivin inhibits the active forms of the caspases resulting from cleaving and activating more of its own proforms. Thus, survivin acts possibly by preventing such a cascade of cleavage and activation amplification from happening resulting in decreased apoptosis.
In similar manner, looking at the mitochondrial pathway of apoptosis, cytochrome c was transiently expressed in 293 cells to look at the inhibitory effects survivin had on this pathway. Although the details are not here, survivin was shown to also inhibit cytochrome c and caspase-8-induced activation of caspases. | 1 | Biochemistry |
BEDT-TTF is the short form of bisethylenedithio-tetrathiafulvalene commonly abbreviated with ET. These molecules form planes which are separated by anions. The pattern of the molecules in the planes is not unique but there are several different phases growing, depending on the anion and the growth conditions. Important phases concerning superconductivity are the α- and θ- phase with the molecules ordering in a fishbone structure and the β- and especially κ-phase which order in a checkerboard structure with molecules being dimerized in the κ-phase. This dimerization makes the κ-phases special as they are not quarter- but half-filled systems, driving them into superconductivity at higher temperatures compared to the other phases.
The amount of possible anions separating two sheets of ET-molecules is nearly infinite. There are simple anions such as triiodide (), polymeric ones such as the very famous Cu[N(CN)]Br and anions containing solvents for example Ag(CF)·112DCBE. The electronic properties of the ET-based crystals are determined by its growing phase, its anion and by the external pressure applied. The external pressure needed to drive an ET-salt with insulating ground state to a superconducting one is much less than those needed for Bechgaard salts. For example, κ-(ET)Cu[N(CN)]Cl needs only a pressure of about 300 bar to become superconducting, which can be achieved by placing a crystal in grease frozen below and then providing sufficient stress to induce the superconducting transition. The crystals are very sensitive, which can be observed impressively in α-(ET)I lying several hours in the sun (or more controlled in an oven at ). After this treatment one gets α-(ET)I which is superconducting.
In contrast to the Fabre or Bechgaard salts universal phase diagrams for all the ET-based salts have only been proposed yet. Such a phase diagram would depend not only on temperature and pressure (i.e. bandwidth), but also on electronic correlations. In addition to the superconducting ground state these materials show charge-order, antiferromagnetism or remain metallic down to lowest temperatures. One compound is even predicted to be a spin liquid.
The highest transition temperatures at ambient pressure and with external pressure are both found in κ-phases with very similar anions. κ-(ET)Cu[N(CN)]Br becomes superconducting at T = 11.8 K at ambient pressure, and a pressure of 300 bar drives deuterated κ-(ET)Cu[N(CN)]Cl from an antiferromagnetic to a superconducting ground state with a transition temperature of T = 13.1 K. The following table shows only a few exemplary superconductors of this class. For more superconductors, see Lebed (2008) in the references.
Even more superconductors can be found by changing the ET-molecules slightly either by replacing the sulfur atoms by selenium (BEDT-TSF, BETS) or by oxygen (BEDO-TTF, BEDO).
Some two-dimensional organic superconductors of the κ-(ET)X and λ(BETS)X families are candidates for the Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) phase when superconductivity is suppressed by an external magnetic field. | 0 | Organic Chemistry |
Highly charged ions interact strongly with water, breaking hydrogen bonds and inducing electrostatic structuring of nearby water, and are thus called "structure-makers" or "kosmotropes". Conversely, weak ions can disrupt the structure of water, and are thus called "structure-breakers" or
"chaotropes". The order of the tendency of ions to make or break water structure is the basis of the Hofmeister series.
Hofmeister discovered a series of salts that have consistent effects on the solubility of proteins and (it was discovered later) on the stability of their secondary and tertiary structure. Anions appear to have a larger effect than cations, and are usually ordered
(kosmotropic) : (chaotropic)
(This is a partial listing; many more salts have been studied.)
The order of cations is usually given as
(chaotropic) : (kosmotropic)
When oppositely charged kosmotropic cations and anions are in solution together, they are attracted to each other, rather than to water, and the same can be said for chaotropic cations and anions. Thus, the preferential associations of oppositely charged ions can be ordered as:
kosmotrope-kosmotrope > kosmotrope-water > water-water > chaotrope-water > chaotrope-chaotrope
Combining kosmotropic anions with kosmotropic cations reduces the kosmotropic effect of these ions because they are pairing to each other too strongly to be structuring water. Kosmotropic anions do not readily pair with chaotropic cations. The combination of kosmotropic anions with chaotropic cations is the best ion combination to stabilize proteins. | 7 | Physical Chemistry |
* Since the technique involves the use of SDS-PAGE which utilizes the effect that sodium-dodecyl sulfate has on proteins which is to denature them, there is the possibility of dissociating protein factors that possess multiple subunits through the process. This could end up affecting how well the protein factor binds to DNA in later steps of the technique.
* Not all proteins renature during the transfer process to the nitrocellulose membranes after separation via SDS-PAGE. This area of protein renaturation is still being experimented with.
* Also being experimented with is reusability of southwestern blots to test proteins with a variety of DNA probes before disposal. However, the main challenge is putting together a scheme that outlines conditions that can remove previously used probes from the blot without the expense of denaturing the proteins or extracting them. | 1 | Biochemistry |
Many alkyl amines are produced industrially by the amination of alcohols using ammonia in the presence of solid acid catalysts. Illustrative is the production of tert-butylamine:
:NH + CH=C(CH) → HNC(CH)
The Ritter reaction of isobutene with hydrogen cyanide is not useful in this case because it produces too much waste. | 0 | Organic Chemistry |
Sublimation is the transition of a substance directly from the solid to the gas state, without passing through the liquid state. The verb form of sublimation is sublime, or less preferably, sublimate. Sublimate also refers to the product obtained by sublimation. The point at which sublimation occurs rapidly (for further details, see below) is called critical sublimation point, or simply sublimation point. Notable examples include sublimation of dry ice at room temperature and atmospheric pressure, and that of solid iodine with heating.
The reverse process of sublimation is deposition (also called desublimation), in which a substance passes directly from a gas to a solid phase, without passing through the liquid state.
All solids sublime, though most sublime at extremely low rates that are hardly detectable. At normal pressures, most chemical compounds and elements possess three different states at different temperatures. In these cases, the transition from the solid to the gas state requires an intermediate liquid state. The pressure referred to is the partial pressure of the substance, not the total (e.g. atmospheric) pressure of the entire system. Thus, any solid can sublime if its vapour pressure is higher than the surrounding partial pressure of the same substance, and in some cases, sublimes at an appreciable rate (e.g. water ice just below 0 °C).
For some substances, such as carbon and arsenic, sublimation from solid state is much more achievable than evaporation from liquid state and it is difficult to obtain them as liquids. This is because the pressure of their triple point in its phase diagram (which corresponds to the lowest pressure at which the substance can exist as a liquid) is very high.
Sublimation is caused by the absorption of heat which provides enough energy for some molecules to overcome the attractive forces of their neighbors and escape into the vapor phase. Since the process requires additional energy, sublimation is an endothermic change. The enthalpy of sublimation (also called heat of sublimation) can be calculated by adding the enthalpy of fusion and the enthalpy of vaporization. | 3 | Analytical Chemistry |
Researchers have investigated the role of surface plasmon resonances present on gold nanorods in the performance of dye-sensitized solar cells. They found that with an increase nanorod concentration, the light absorption grew linearly; however, charge extraction was also dependent on the concentration. With an optimized concentration, they found that the overall power conversion efficiency improved from 5.31 to 8.86% for Y123 dye-sensitized solar cells.
The synthesis of one-dimensional TiO nanostructures directly on fluorine-doped tin oxide glass substrates was successful demonstrated via a two-stop solvothermal reaction. Additionally, through a TiO sol treatment, the performance of the dual TiO nanowire cells was enhanced, reaching a power conversion efficiency of 7.65%.
Stainless steel based counter-electrodes for DSSCs have been reported which further reduce cost compared to conventional platinum based counter electrode and are suitable for outdoor application.
Researchers from EPFL have advanced the DSSCs based on copper complexes redox electrolytes, which have achieved 13.1% efficiency under standard AM1.5G, 100 mW/cm conditions and record 32% efficiency under 1000 lux of indoor light.
Researchers from Uppsala University have used n-type semiconductors instead of redox electrolyte to fabricate solid state p-type dye sensitized solar cells. | 5 | Photochemistry |
The cladiellin family of marine natural products possesses interesting molecular architecture, generally containing a 9-membered medium-sized ring. The synthesis of (−)-cladiella-6,11-dien-3-ol allowed access to a variety of other members of the cladiellin family. Notably, the conversion to cladiell-11-ene-3,6,7-triol makes use of macrocyclic stereocontrol in the dihydroxylation of a trisubstituted olefin. Below is shown the synthetic step controlled by the ground state conformation of the macrocycle, allowing stereoselective dihydroxylation without the usage of an asymmetric reagent. This example of substrate controlled addition is an example of the peripheral attack model in which two centers on the molecule are added two at once in a concerted fashion. | 0 | Organic Chemistry |
The Berry mechanism, or Berry pseudorotation mechanism, is a type of vibration causing molecules of certain geometries to isomerize by exchanging the two axial ligands (see Figure at right) for two of the equatorial ones. It is the most widely accepted mechanism for pseudorotation and most commonly occurs in trigonal bipyramidal molecules such as PF, though it can also occur in molecules with a square pyramidal geometry. The Berry mechanism is named after R. Stephen Berry, who first described this mechanism in 1960. | 4 | Stereochemistry |
Consider a variable to be some function , that is . If increases from to then the change in the value of will be given by . The proportional change, however, is given by:
The rate of proportional change at the point is given by the above expression divided by the step change in the value, namely :
Rate of proportional change
Using calculus, we know that
therefore the rate of proportional change equals:
This quantity serves as a measure of the rate of proportional change of the function . Just as measures the gradient of the curve plotted on a linear scale, measures the slope of the curve when plotted on a semi-logarithmic scale, that is the rate of proportional change. For example, a value of means that the curve increases at per unit .
The same argument can be applied to the case when we plot a function on both and logarithmic scales. In such a case, the following result is true: | 7 | Physical Chemistry |
RNA polymerase III appears to be essential for homologous recombinational repair of DNA double-strand breaks. RNA polymerase III catalyzes the formation of a transient RNA-DNA hybrid at double strand breaks, an essential intermediate step in homologous recombination mediated double-strand break repair. This step protects the 3’ overhanging DNA strand from degradation. After the transient RNA-DNA hybrid intermediate is formed, the RNA strand is replaced by the RAD51 protein, which then catalyzes the ssDNA invasion step of homologous recombination. | 1 | Biochemistry |
Positive material identification (PMI) is the analysis of a material, this can be any material but is generally used for the analysis of metallic alloy to establish composition by reading the quantities by percentage of its constituent elements. Typical methods for PMI include X-ray fluorescence (XRF) and optical emission spectrometry (OES).
PMI is a portable method of analysis and can be used in the field on components.
X-ray fluorescence (XRF) PMI can not detect small elements such as carbon. This means that when undertaking analysis of stainless steels such as grades 304 and 316 the low carbon L variant can not be determined. This however can be analysed with optical emission spectrometry (OES) | 3 | Analytical Chemistry |
E. coli has seven main sigma factors, five of which have a specific anti-sigma factor. The anti-sigma factor binding to its sigma factors depends upon environmental cues. This mechanism blocks the transcription of genes that are unnecessary in new conditions. The table below shows five sigma factors, what process it affects, and its corresponding anti-sigma factor. In E. coli, sigma factors transcribe their anti-sigma factors; this creates a negative feedback loop. The sigma factor can be regulated when the anti-sigma factor is transcribed and the anti-sigma factor when the sigmas gene is transcribed. Sigma factors 70 and 54 don't have specific anti-sigma factors; they have other negative feedback loop mechanisms. | 1 | Biochemistry |
The skeletal muscle accounts for more than 80 percent of the postprandial whole body glucose uptake and therefore plays an important role in glucose homeostasis. Skeletal muscle lipid levels – intramyocellular lipids (IMCL) – correlate negatively with insulin sensitivity in a sedentary population and hence were considered predictive for insulin resistance and causative in obesity-associated insulin resistance. However, endurance athletes also have high IMCL levels despite being highly insulin sensitive, which indicates that not the level of IMCL accumulation per se, but rather the characteristics of this intramyocellular fat determine whether it negatively affects insulin signaling. Intramyocellular lipids are mainly stored in lipid droplets, the organelles for fat storage. Recent research indicates that creating intramyocellular neutral lipid storage capacity for example by increasing the abundance of lipid droplet coat proteins protects against obesity-associated insulin resistance in skeletal muscle. | 1 | Biochemistry |
Archaeometallurgical experimentation typically takes place in controlled laboratories or tries to remain as authentic as possible by being conducted using only the materials and facilities that were available to the subjects whose technology is trying to be reconstructed. Regardless of location though, the experimentation is always conducted under a different mindset outside the context of what was originally intended. A constant problem in any type of experimental archaeology is the cultural distance between the archaeologist and the individual who originally was involved with the metallurgy. This difference in mindset may lead to misunderstandings in the processes behind the metallurgy. Second to this, not all experiments are successful and it is hard to determine if this is the fault of the techniques used or the individual conducting the experiment. | 8 | Metallurgy |
Corrosion inhibitors, such as gas-phase or volatile inhibitors, can be used to prevent corrosion inside sealed systems. They are not effective when air circulation disperses them, and brings in fresh oxygen and moisture. | 8 | Metallurgy |
Due to the energy range typically used in ion scattering experiments (> 500 eV), effects of thermal vibrations, phonon oscillations, and interatomic binding are ignored since they are far below this range (~a few eV), and the interaction of particle and surface may be thought of as a classical two-body elastic collision problem. Measuring the energy of ions scattered in this type of interaction can be used to determine the elemental composition of a surface, as is shown in the following:
Two-body elastic collisions are governed by the concepts of energy and momentum conservation. Consider a particle with mass m, velocity v, and energy given as impacting another particle at rest with mass m. The energies of the particles after collision are and where and thus . Additionally, we know . Using trigonometry we are able to determine
Similarly, we know
In a well-controlled experiment the energy and mass of the primary ions (E and m, respectively) and the scattering or recoiling geometries are all known, so determination of surface elemental composition is given by the correlation between E or E and m. Higher energy scattering peaks correspond to heavier atoms and lower energy peaks correspond to lighter atoms. | 7 | Physical Chemistry |
A genomic library is a collection of overlapping DNA fragments that together make up the total genomic DNA of a single organism. The DNA is stored in a population of identical vectors, each containing a different insert of DNA. In order to construct a genomic library, the organism's DNA is extracted from cells and then digested with a restriction enzyme to cut the DNA into fragments of a specific size. The fragments are then inserted into the vector using DNA ligase. Next, the vector DNA can be taken up by a host organism - commonly a population of Escherichia coli or yeast - with each cell containing only one vector molecule. Using a host cell to carry the vector allows for easy amplification and retrieval of specific clones from the library for analysis.
There are several kinds of vectors available with various insert capacities. Generally, libraries made from organisms with larger genomes require vectors featuring larger inserts, thereby fewer vector molecules are needed to make the library. Researchers can choose a vector also considering the ideal insert size to find the desired number of clones necessary for full genome coverage.
Genomic libraries are commonly used for sequencing applications. They have played an important role in the whole genome sequencing of several organisms, including the human genome and several model organisms. | 1 | Biochemistry |
The p-toluene-sulfinyl imines have been used for the highly diastereoselective asymmetric synthesis of α-amino acids, β-amino acids, syn- and anti-2,3-diamino esters, α-amino aldehydes and ketones, β-amino ketones, α-amino phosphonates, aziridine 2-carboxylates, and aziridine 2-phosphonates. Many of these same transformations can be carried out with tert-butylsulfinyl imines. For the asymmetric synthesis of amines, tert-butylsulfinyl imines are required as lithium and Grignard reagents react at the sulfinyl sulfur in p-toluene-sulfinyl imines. Mild acid treatment readily removes the N-sulfinyl group in the sulfinamide products affording the free amine derivatives. An advantage of tert-butylsulfinyl imines is that acid treatment of the corresponding sulfinamides leads to easily removal by-products | 0 | Organic Chemistry |
When a plant or animal dies or an animal expels waste, the initial form of nitrogen is organic. Bacteria or fungi convert the organic nitrogen within the remains back into ammonium (), a process called ammonification or mineralization. Enzymes involved are:
* GS: Gln Synthetase (cytosolic & plastic)
* GOGAT: Glu 2-oxoglutarate aminotransferase (Ferredoxin & NADH-dependent)
* GDH: Glu Dehydrogenase:
** Minor role in ammonium assimilation.
** Important in amino acid catabolism. | 1 | Biochemistry |
Photoexcitation is the mechanism of electron excitation by photon absorption, when the energy of the photon is too low to cause photoionization. The absorption of the photon takes place in accordance with Planck's quantum theory.
Photoexcitation plays role in photoisomerization. Photoexcitation is exploited in dye-sensitized solar cells, photochemistry, luminescence, optically pumped lasers, and in some photochromic applications. | 7 | Physical Chemistry |
Thaumasite is a calcium silicate mineral, containing Si atoms in unusual octahedral configuration, with chemical formula CaSi(OH)(CO)(SO)·12HO, also sometimes more simply written as CaSiO·CaCO·CaSO·15HO.
Thaumasite is formed under special conditions in the presence of sulfate ions in concrete containing, or exposed to, a source of carbonate anions such as limestone aggregates, or finely milled limestone filler (). Bicarbonate anions () dissolved in groundwater may also contribute to the reaction. The detrimental reaction proceeds at the expense of calcium silicate hydrates (C-S-H, with dashes denoting here their non-stoichiometry) present in the hardened cement paste (HCP). The thaumasite form of sulfate attack (TSA) is a particular type of very destructive sulfate attack. C-S-H are the "glue" in the hardened cement paste filling the interstices between the concrete aggregates. As the TSA reaction consumes the silicates of the "cement glue", it can lead to a harmful decohesion and a softening of concrete. Expansion and cracking are more rarely observed. Unlike the common sulfate attack, in which the calcium hydroxide (portlandite) and calcium aluminate hydrates react with sulfates to respectively form gypsum and ettringite (an expansive phase), in the case of TSA the C-S-H ensuring the cohesion of HCP and aggregates are destroyed. As a consequence, even concrete containing low- sulfate-resisting Portland cement may be affected.
TSA is sometimes easily recognizable on the field when examining the altered concrete. TSA-affected concrete becomes powdery and can be dug with a scoop, or even scrapped with the fingers. Concrete decohesion is very characteristic of TSA.
TSA was first identified during the years 1990 in England in the United Kingdom in the foundation piles of bridges of the motorway M5 located in the Kimmeridgian marls. These marls are a mixture of clay and limestone sedimented under anoxic conditions and are rich in pyrite (, a disulfide). Once these marls were excavated, pyrite was exposed to atmospheric oxygen or oxygen-rich infiltration water and rapidly oxidized. Pyrite oxidation produces sulfuric acid. In its turn, reacts with portlandite (present in the hardened cement paste, HCP) and calcite ( (present in limestone aggregates or in carbonated HCP). The strong acidification of the medium caused by pyrite oxidation releases bicarbonate ions () or carbon dioxide () along with calcium () and sulfate ions ().
Full pyrite oxidation can be schematized as:
The sulfuric acid released by pyrite oxidation then reacts with portlandite ()) present in the hardened cement paste to give gypsum:
When concrete also contains limestone aggregates or a filler addition, reacts with calcite () and water to also form gypsum while releasing :
Gypsum is relatively soluble in water , so there is plenty of calcium and sulfates ions available for TSA.
Simultaneously, carbonic acid () dissolves calcite to form soluble calcium bicarbonate:
So, when all the chemical ingredients necessary to react with C-S-H from the hardened cement paste in concrete are present together the TSA reaction can occur. When grounds rich in pyrite, such as many clays or marls, are excavated for civil engineering works, the strong acidification produced by pyrite oxidation is the powerful driving force triggering TSA because it frees up and mobilizes all the ions needed to attack C-S-H and to form thaumasite ().
TSA is favored by a low temperature, although it can be encountered at higher temperature in warm areas. The reason is to be found in the retrograde solubility of most of the ingredients needed for the TSA reaction. Indeed, the solubility of dissolved carbon dioxide (), portlandite (), calcite (), and gypsum (·2), increases when the temperature is lowered. This is because the dissolution reactions of these mineral species are exothermic and release heat. A lower temperature facilitates the heat release and therefore favors the exothermic reaction. Only the solubility of silica (from C-S-H) increases with temperature because silica dissolution is an endothermic process which requires heat to proceed. | 8 | Metallurgy |
The early work performed by Katz and Schmitt demonstrated that ephaptic coupling between the two adjacent nerves was insufficient to stimulate an action potential in the resting nerve. Under ideal conditions the maximum depolarization observed was approximately 20% of the threshold stimulus. However, conditions can be manipulated in such a way that the action potential from one neuron can be spread to a neighboring neuron. This was accomplished in one study in two experimental conditions: increased calcium concentrations, which lowered the threshold potential, or by submerging the axons in mineral oil, which increased resistance. While these manipulations do not reflect normal conditions, they do highlight the mechanisms behind ephaptic excitation.
Ephaptic coupling has also been found to play an important role in inhibition of neighboring neurons. Depending on the location and identity of the neurons, various mechanisms have been found to underlie ephaptic inhibition. In one study, newly excited neighboring neurons interfered with already sustained currents, thus lowering the extracellular potential and depolarizing the neuron in relation to its surrounding environment, effectively inhibiting the action potential's propagation. | 1 | Biochemistry |
Because it contains free iodine, Lugol's solution at 2% or 5% concentration without dilution is irritating and destructive to mucosa, such as the lining of the esophagus and stomach. Doses of 10 mL of undiluted 5% solution have been reported to cause gastric lesions when used in endoscopy. The LD50 for 5% Iodine is 14,000 mg/kg (14 g/kg) in rats, and 22,000 mg/kg (22 g/kg) in mice.
The World Health Organization classifies substances taken orally with an LD50 of 5–50 mg/kg as the second highest toxicity class, Class Ib (Highly Hazardous). The Global Harmonized System of Classification and Labeling of Chemicals categorizes this as Category 2 with a hazard statement "Fatal if swallowed". Potassium iodide is not considered hazardous. | 3 | Analytical Chemistry |
2-Methoxy-1,3-butadiene and ethyl-2-butynoate undergo a Diels-Alder reaction to generate a precursor which is hydrolyzed to obtain Hagemanns ester. By varying the substituents on the butynoate starting material, this approach allows for different C2 alkylated Hagemanns ester derivatives to be synthesized. | 0 | Organic Chemistry |
Four chemical processes contribute to industrial benzene production: catalytic reforming, toluene hydrodealkylation, toluene disproportionation, and steam cracking etc. According to the ATSDR Toxicological Profile for benzene, between 1978 and 1981, catalytic reformates accounted for approximately 44–50% of the total U.S. benzene production. | 2 | Environmental Chemistry |
The KhAB-250 is the provisional naming of an aerial bomb developed by the Soviet Air Force to deliver the chemical weapon sarin.
The KhAB-250 operational weight has been reported as and . 24 could be carried by the Tupolev Tu-22.
The bomb uses a burst charge to detonate on impact with the ground. It contains a payload of of sarin.
The KhAB-250 was displayed at Shikani Test and Proving Grounds in 1986 as a component of the then-current Soviet chemical arsenal. Contemporary analysts noted that it appeared relatively unsophisticated compared to Soviet conventional munitions of the same time frame.
The bomb was removed from service as a result of the Chemical Weapons Convention in the early 1990s. | 1 | Biochemistry |
In any study, some of the protein domains, those under investigation, will be varied according to the goals of the study whereas other domains, those that are not themselves being investigated, will be kept constant. For example, in a two-hybrid study to select DNA-binding domains, the DNA-binding domain, BD, will be varied while the two interacting proteins, the bait and prey, must be kept constant to maintain a strong binding between the BD and AD. There are a number of domains from which to choose the BD, bait and prey and AD, if these are to remain constant. In protein–protein interaction investigations, the BD may be chosen from any of many strong DNA-binding domains such as Zif268. A frequent choice of bait and prey domains are residues 263–352 of yeast Gal11P with a N342V mutation and residues 58–97 of yeast Gal4, respectively. These domains can be used in both yeast- and bacterial-based selection techniques and are known to bind together strongly.
The AD chosen must be able to activate transcription of the reporter gene, using the cells own transcription machinery. Thus, the variety of ADs available for use in yeast-based techniques may not be suited to use in their bacterial-based analogues. The herpes simplex virus-derived AD, VP16 and yeast Gal4 AD have been used with success in yeast whilst a portion of the α-subunit of E. coli RNA polymerase has been utilised in E. coli'-based methods.
Whilst powerfully activating domains may allow greater sensitivity towards weaker interactions, conversely, a weaker AD may provide greater stringency. | 1 | Biochemistry |
A superalloy, or high-performance alloy, is an alloy with the ability to operate at a high fraction of its melting point. Key characteristics of a superalloy include mechanical strength, thermal creep deformation resistance, surface stability, and corrosion and oxidation resistance.
The crystal structure is typically face-centered cubic (FCC) austenitic. Examples of such alloys are Hastelloy, Inconel, Waspaloy, Rene alloys, Incoloy, MP98T, TMS alloys, and CMSX single crystal alloys.
Superalloy development relies on chemical and process innovations. Superalloys develop high temperature strength through solid solution strengthening and precipitation strengthening from secondary phase precipitates such as gamma prime and carbides. Oxidation or corrosion resistance is provided by elements such as aluminium and chromium. Superalloys are often cast as a single crystal in order to eliminate grain boundaries, which decrease creep resistance (even though they may provide strength at low temperatures).
The primary application for such alloys is in aerospace and marine turbine engines. Creep is typically the lifetime-limiting factor in gas turbine blades.
Superalloys have made much of very-high-temperature engineering technology possible. | 8 | Metallurgy |
Capillary action (sometimes called capillarity, capillary motion, capillary rise, capillary effect, or wicking) is the process of a liquid flowing in a narrow space in opposition to or at least without the assistance of any external forces like gravity.
The effect can be seen in the drawing up of liquids between the hairs of a paint-brush, in a thin tube such as a straw, in porous materials such as paper and plaster, in some non-porous materials such as sand and liquefied carbon fiber, or in a biological cell.
It occurs because of intermolecular forces between the liquid and surrounding solid surfaces. If the diameter of the tube is sufficiently small, then the combination of surface tension (which is caused by cohesion within the liquid) and adhesive forces between the liquid and container wall act to propel the liquid. | 7 | Physical Chemistry |
Lasers have been used to indirectly generate non-coherent extreme UV (E‑UV) radiation at 13.5 nm for extreme ultraviolet lithography. The E‑UV is not emitted by the laser, but rather by electron transitions in an extremely hot tin or xenon plasma, which is excited by an excimer laser. This technique does not require a synchrotron, yet can produce UV at the edge of the X‑ray spectrum. Synchrotron light sources can also produce all wavelengths of UV, including those at the boundary of the UV and X‑ray spectra at 10 nm. | 5 | Photochemistry |
Gene therapy uses genetically modified viruses to deliver genes which can cure disease in humans. Although gene therapy is still relatively new, it has had some successes. It has been used to treat genetic disorders such as severe combined immunodeficiency, and Lebers congenital amaurosis. Treatments are also being developed for a range of other currently incurable diseases, such as cystic fibrosis, sickle cell anemia, Parkinsons disease, cancer, diabetes, heart disease and muscular dystrophy. These treatments only effect somatic cells, meaning any changes would not be inheritable. Germline gene therapy results in any change being inheritable, which has raised concerns within the scientific community.
In 2015, CRISPR was used to edit the DNA of non-viable human embryos. In November 2018, He Jiankui announced that he had edited the genomes of two human embryos, in an attempt to disable the CCR5 gene, which codes for a receptor that HIV uses to enter cells. He said that twin girls, Lulu and Nana, had been born a few weeks earlier and that they carried functional copies of CCR5 along with disabled CCR5 (mosaicism) and were still vulnerable to HIV. The work was widely condemned as unethical, dangerous, and premature. | 1 | Biochemistry |
Hypolimnetic oxygen depletion can lead to both summer and winter "kills". During summer stratification, inputs or organic matter and sedimentation of primary producers can increase rates of respiration in the hypolimnion. If oxygen depletion becomes extreme, aerobic organisms, like fish, may die, resulting in what is known as a "summer kill". The same phenomena can occur in the winter, but for different reasons. During winter, ice and snow cover can attenuate light, and therefore reduce rates of photosynthesis. The freezing over of a lake also prevents air-water interactions that allow the exchange of oxygen. This creates a lack of oxygen while respiration continues. When the oxygen becomes badly depleted, anaerobic organisms can die, resulting in a "winter kill". | 9 | Geochemistry |
The 5 melanocortin receptors are seven-transmembrane G-protein coupled receptors with differing ligand affinities, tissue and cell type expression, and downstream functions (Figure 2). MC1R is expressed on melanocytes, macrophages, epithelial cells, endothelial cells, fibroblasts, monocytes and numerous other immune cells, but is also present in brain, testis, and intestine. Its main functions are in melanogenesis and anti-inflammatory signaling. MC2R is expressed in the adrenal cortex and adipocytes and promotes steroidogenesis. MC3R and MC4R are primarily expressed in the brain and regulate energy homeostasis. MC3R is additionally involved in immunomodulation while MC4R has a role in sexual function. MC5R is highly expressed in skin and adrenal glands and has a role in exocrine function. MC2R is activated exclusively by ACTH, whereas the other 4 receptors can be activated by ACTH, a-MSH, b-MSH, and g-MSH, although the binding affinities differ. For all the melanocortin receptors, binding of an agonistic ligand activates the receptor, leading to dissociation of the G protein and activation of the enzyme adenyl cyclase. Adenyl cyclase then cleaves ATP to generate the second messenger cyclic AMP (cAMP), which in turn activates multiple downstream pathways.
There are two known accessory proteins belonging to the melanocortin system which modulate function of the receptors. These are melanocortin-2-receptor accessory protein (MRAP) and MRAP2. | 1 | Biochemistry |
Across from each single strand of DNA, we typically see adenine pair with thymine, and cytosine pair with guanine to form a parallel complementary strand as described below. Two nucleotide sequences which correspond to each other in this manner are referred to as complementary:
A frayed end refers to a region of a double stranded (or other multi-stranded) DNA molecule near the end with a significant proportion of non-complementary sequences; that is, a sequence where nucleotides on the adjacent strands do not match up correctly:
The term "frayed" is used because the incorrectly matched nucleotides tend to avoid bonding, thus appearing similar to the strands in a fraying piece of rope.
Although non-complementary sequences are also possible in the middle of double stranded DNA, mismatched regions away from the ends are not referred to as "frayed". | 1 | Biochemistry |
FAM227B is located at 15q21.2 and contains 24 exons. The current size determined for FAM227B is 293,961 base pairs (NCBI). Neighbors of FAM227B on chromosome fifteen include: “ribosomal protein L15 pseudogene”, “galactokinase 2”, “RNA, 7SL, cytoplasmic 307, pseudogene”, “signal peptide peptidase like 2A pseudogene”, “fibroblast growth factor 7”, “uncharacterized LOC105370811”, “DTW domain containing 1”, and “ring finger protein, LIM domain interacting pseudogene 3”. | 1 | Biochemistry |
The structure of a gel network can be conceptualised as a random graph. This analogy is exploited to calculate the gel point and gel fraction for monomer precursors with arbitrary types of functional groups. Random graphs can be used to derive analytical expressions for simple polymerisation mechanisms, such as step-growth polymerisation, or alternatively, they can be combined with a system of rate equations that are integrated numerically. | 7 | Physical Chemistry |
Compared with single-phase heat transfer, heat transfer with a phase change is an effective way of heat transfer. It generally has high value of heat transfer coefficient due to the large value of latent heat of phase change followed by induced mixing of the flow. Boiling and condensation heat transfers are concerned with wide range of phenomena. | 7 | Physical Chemistry |
Aqueous solutions of transition metals cations react with sulfide sources (HS, NaHS, NaS) to precipitate solid sulfides. Such inorganic sulfides typically have very low solubility in water, and many are related to minerals with the same composition (see below). One famous example is the bright yellow species CdS or "cadmium yellow". The black tarnish formed on sterling silver is AgS. Such species are sometimes referred to as salts. In fact, the bonding in transition metal sulfides is highly covalent, which gives rise to their semiconductor properties, which in turn is related to the deep colors. Several have practical applications as pigments, in solar cells, and as catalysts. The fungus Aspergillus niger plays a role in the solubilization of heavy metal sulfides. | 0 | Organic Chemistry |
Vanadium is present in petroleum, especially from Canada, western United States, Venezuela and the Caribbean region, often bound to porphyrine in organometallic complexes. These complexes get concentrated on the higher-boiling fractions, which are then form the base of heavy residual fuel oils. Residues of sodium, primarily from sodium chloride and spent oil treatment chemicals, are also present in this petroleum fraction. Combusting any amount more than 100 ppm of sodium and vanadium will yield ash capable of causing fuel ash corrosion.
Most fuels contain small traces of vanadium. The vanadium is oxidized to different vanadates. Molten vanadates present as deposits on metal can flux oxide scales and passivation layers. Furthermore, the presence of vanadium accelerates the diffusion of oxygen through the fused salt layer to the metal substrate. Vanadates can be present in semiconducting or ionic form, where the semiconducting form has significantly higher corrosivity as the oxygen is transported via oxygen vacancies. The ionic form, in contrast, transports oxygen by diffusion of the entire vanadate, which is significantly slower. The semiconducting form is rich in vanadium pentoxide.
At high temperatures or when there is a lower availability of oxygen, refractory oxidesvanadium dioxide and vanadium trioxideform. These more reduced forms of vanadium do not promote corrosion. However, at conditions most common for burning, vanadium pentoxide gets formed. Together with sodium oxide, vanadates of various composition ratios are formed. Vanadates of composition approximating NaO.6 VO have the highest corrosion rates at the temperatures between 593 °C and 816 °C; at lower temperatures, the vanadate is in solid state, and at higher temperatures, vanadates with higher proportion of vanadium contribute the most to higher corrosion rates.
The solubility of the passivation layer oxides in the molten vanadates depends on the composition of the oxide layer. Iron(III) oxide is readily soluble in vanadates between NaO.6 VO and 6 NaO.VO, at temperatures below 705 °C in amounts up to equal to the mass of the vanadate. This composition range is common for ashes, which aggravates the problem. Chromium(III) oxide, nickel(II) oxide, and cobalt(II) oxide are less soluble in vanadates; they convert the vanadates to the less corrosive ionic form and their vanadates are tightly adherent, refractory, and act as oxygen barriers.
The rate of corrosion caused by vanadates can be lowered by reducing the amount of excess air available for combustion to preferentially form the refractory oxides, using refractory coatings on the exposed surfaces, or using high-chromium alloys, such as 50% Ni/50% Cr or 40% Ni/60% Cr.
The presence of sodium in a ratio of 1:3 gives the lowest melting point and must be avoided. This melting point of 535 °C can cause problems on the hot spots of the engine like piston crowns, valve seats, and turbochargers. | 8 | Metallurgy |
A biofilm is a community of microorganisms adsorbed to a surface. Microorganisms in biofilms are enclosed in a polymeric matrix consisting of exopolysaccharides, extracellular DNA and proteins. Seconds after a surface (usually metal) is placed in a solution, inorganic and organic molecules adsorb onto the surface. These molecules are attracted mainly by Coulombic forces (see above section), and can adhere very strongly to the surface. This first layer is called the conditioning layer, and is necessary for the microorganisms to bind to the surface. These microorganisms then attach reversibly by Van der Waals forces, followed by irreversible adhesion through self-produced attachment structures such as pili or flagella. Biofilms form on solid substrates such as stainless steel. A biofilm's enclosing polymeric matrix offers protection to its microbes, increasing their resistance to detergents and cleaning agents. Biofilms on food processing surfaces can be a biological hazard to food safety. Increased chemical resistance in biofilms can lead to a persistent contamination condition. | 1 | Biochemistry |
Carbon tetrachloride was discovered along with chloromethane and chloroform in oceans, marine algae and volcanoes. The natural emissions of carbon tetrachloride are too little compared to those from anthropogenic sources; for example, the Momotombo Volcano in Nicaragua emits carbon tetrachloride at a flux of 82 grams per year while the global industrial emissions were at 2 × 10 grams per year.
Carbon tetrachloride was found in Red algae Asparagopsis taxiformis and Asparagopsis armata. It was detected in Southern California ecosystems, salt lakes of Kalmykian Steppe and a common liverwort in Czechia. | 2 | Environmental Chemistry |
In this class it is worthwhile to highlight the small non-peptide molecules LM22A-24 and LM11A-31 developed by Longo and Massa. Through the modulation of p75NTR activity, these compounds downregulate degenerative and upregulate trophic signaling. In particular, LM11A-31 was found to inhibit several pathophysiological mechanisms involved in AD and related to p75NTR. Oral administration in AD mice models reduces degeneration of cholinergic neurites. Furthermore, by a direct activation of p75NTR signaling and inhibition of apoptotic pathway, it improves motor function in a spinal cord injury (SCI) mice model and leads to an antiapoptotic effect in mice after traumatic brain injury (TBI). In February 2017, a phase 2 clinical trial started focusing on the evaluation of the safety of LM11A-31 in mild to moderate AD (NCT03069014). This study was completed in June 2020, but the results have not been published yet.
Another drug belonging to the class of p75NTR antagonists is THX-B, which inhibits NGF-p75NTR binding and prevents the death of RGCs in axotomy and glaucoma. In addition, in combination with LM22A-24, THX-B delays the loss of retinal structure, prevents RGC degeneration and preserves ganglion cell layer-inner plexiform layer thickness with a better efficacy compared to LM22A-24. Finally, a p75NTR antagonist, EVT901, was able to improve functional outcomes in two models of traumatic brain injury. Furthermore it was found to reduce inflammation in vivo in the TGFAD344 rat model of AD. | 1 | Biochemistry |
In the first step, manganese(II) sulphate (at 48% of the total volume) is added to an environmental water sample. Next, potassium iodide (15% in potassium hydroxide 70%) is added to create a pinkish-brown precipitate. In the alkaline solution, dissolved oxygen will oxidize manganese(II) ions to the tetravalent state.
: 2 Mn + O + 2 HO → 2 MnO(OH)
Mn has been oxidised to 4+, and MnO(OH) appears as a brown precipitate. There is some uncertainty about whether the oxidised manganese is tetravalent or trivalent. Some sources claim that Mn(OH) is the brown precipitate, but hydrated MnO may also give the brown colour.
: 4 Mn(OH) + O + 2 HO → 4 Mn(OH)
The second part of the Winkler test reduces (acidifies) the solution. The precipitate will dissolve back into solution as the H reacts with the O and OH to form water.
: MnO(OH) + 4 H → Mn + 3 HO
The acid facilitates the conversion by the brown, Manganese-containing precipitate of the Iodide ion into elemental Iodine.
The Mn(SO) formed by the acid converts the iodide ions into iodine, itself being reduced back to manganese(II) ions in an acidic medium.
: Mn(SO) + 2 I → Mn + I + 2
Thiosulfate is used, with a starch indicator, to titrate the iodine.
: 2 + I → + 2 I | 3 | Analytical Chemistry |
The Betts electrolytic process is an industrial process for purification of lead from bullion. Lead obtained from its ores is impure because lead is a good solvent for many metals. Often these impurities are tolerated, but the Betts electrolytic process is used when high purity lead is required, especially for bismuth-free lead. | 8 | Metallurgy |
The manufacturing process is similar to that of ordinary coins, except that two blanks (the inner and the outer) are struck at the same time, deforming the separate blanks sufficiently to hold them together. | 8 | Metallurgy |
Surface tension is dependent on temperature. For that reason, when a value is given for the surface tension of an interface, temperature must be explicitly stated. The general trend is that surface tension decreases with the increase of temperature, reaching a value of 0 at the critical temperature. For further details see Eötvös rule. There are only empirical equations to relate surface tension and temperature:
* Eötvös: Here is the molar volume of a substance, is the critical temperature and is a constant valid for almost all substances. A typical value is = . For water one can further use = 18 ml/mol and = 647 K (374 °C). A variant on Eötvös is described by Ramay and Shields: where the temperature offset of 6 K provides the formula with a better fit to reality at lower temperatures.
* Guggenheim–Katayama: is a constant for each liquid and is an empirical factor, whose value is for organic liquids. This equation was also proposed by van der Waals, who further proposed that could be given by the expression where is a universal constant for all liquids, and is the critical pressure of the liquid (although later experiments found to vary to some degree from one liquid to another).
Both Guggenheim–Katayama and Eötvös take into account the fact that surface tension reaches 0 at the critical temperature, whereas Ramay and Shields fails to match reality at this endpoint. | 6 | Supramolecular Chemistry |
Chloroeremomycin is composed of seven amino acids (three non-proteinogenic, and four proteinogenic) and three saccharide units. From N-terminus to C-terminus, the order is: Me--Leu, -Tyr, -Asn, -4-hydroxyphenylglycine (HPG), -HPG, -Tyr, and -3,5-dihydroxyphenylglycine (DHPG). When referring to specific amino acids, this article will reference the amino acid in the order it appears within the heptapeptide. Chloroeremomycin is glycosylated at aa4 with a Glc-(2→α1)-epivancosamine disaccharide and at aa6 with a -BHT-(→α1)-epivancosamine saccharide.
Some amino acids are modified prior to the completion of the heptapeptide (in cis) and some are modified after the heptapeptide is formed (in trans). During the synthesis of the heptapeptide, the stereocenters of aa3, aa4, aa6, and aa7 are changed from L to D. Both Tyr residues are hydroxylated and chlorinated after the amino acids have been incorporated to the growing polypeptide to form 4-chloro-β-hydroxytyrosine (BHT). The now-BHT residues are then crosslinked to the aa4 HPG through aryl-ether linkages. An aryl-aryl bond is formed between aa5 and aa7 at the aa5-C3 and aa7-C2 positions on the aromatic rings. Finally, the N-terminus Leu is methylated.
In addition to the presence of -amino acids, the molecule has atropisomer chemistry. The orientations of the chloro-substituted phenyl rings add another aspect of stereochemistry to the molecule. | 0 | Organic Chemistry |
Chemisorption is a kind of adsorption which involves a chemical reaction between the surface and the adsorbate. New chemical bonds are generated at the adsorbent surface. Examples include macroscopic phenomena that can be very obvious, like corrosion, and subtler effects associated with heterogeneous catalysis, where the catalyst and reactants are in different phases. The strong interaction between the adsorbate and the substrate surface creates new types of electronic bonds.
In contrast with chemisorption is physisorption, which leaves the chemical species of the adsorbate and surface intact. It is conventionally accepted that the energetic threshold separating the binding energy of "physisorption" from that of "chemisorption" is about 0.5 eV per adsorbed species.
Due to specificity, the nature of chemisorption can greatly differ, depending on the chemical identity and the surface structural properties.
The bond between the adsorbate and adsorbent in chemisorption is either ionic or covalent. | 7 | Physical Chemistry |
Photaki was selected in 1962 by the US Department of Health, Education and Welfare among an international pool of candidates to conduct research by the side of Nobel laureate Vincent du Vigneaud at Cornell University. While in New York, she also delivered a short series of lectures both in Cornell and at the National Institutes of Health (NIH).
Back in the University of Athens after Cornell, Photaki continued her research and was soon habilitated in 1965 following a thesis on oxytocin, building on the work she started under du Vigneaud. Despite her internationally distinguished research and sizeable recent grants from the NHRF and the United States NIH, she was not allowed to teach by the Greek military junta until 1969 and was intensively interrogated by the Cities Police Security Directorate on account of her anti-dictatorial political beliefs.
Photaki's teaching career was purposefully hindered by the Ministry of Education until the restoration of democracy in 1974; indeed, in 1975 she was promoted to extraordinary professor, a decade after receiving her habilitation. Shortly afterwards, in 1977, she was promoted to full professor (as Professor of Organic Chemistry) and Head of the Organic Chemistry Laboratory, both positions once held by her mentor Zervas. Photaki died in 1983 at the age of 62.
She was reported to spend very long hours at the laboratory, occasionally from "8 in the morning till 10 in the evening". In her 20-year career as a member of the University of Athens faculty, she supervised (alone or jointly with other colleagues) more than 15 doctoral dissertations. | 0 | Organic Chemistry |
In humans, fatty acids are formed from carbohydrates predominantly in the liver and adipose tissue, as well as in the mammary glands during lactation. The pyruvate produced by glycolysis is an important intermediary in the conversion of carbohydrates into fatty acids and cholesterol. This occurs via the conversion of pyruvate into acetyl-CoA in the mitochondrion. However, this acetyl CoA needs to be transported into cytosol where the synthesis of fatty acids and cholesterol occurs. This cannot occur directly. To obtain cytosolic acetyl-CoA, citrate (produced by the condensation of acetyl CoA with oxaloacetate) is removed from the citric acid cycle and carried across the inner mitochondrial membrane into the cytosol. There it is cleaved by ATP citrate lyase into acetyl-CoA and oxaloacetate. The oxaloacetate is returned to mitochondrion as malate (and then converted back into oxaloacetate to transfer more acetyl-CoA out of the mitochondrion). The cytosolic acetyl-CoA is carboxylated by acetyl CoA carboxylase into malonyl CoA, the first committed step in the synthesis of fatty acids. | 1 | Biochemistry |
According to JAXA, the Ibuki satellite is equipped with a greenhouse gas observation sensor (TANSO-FTS) and a cloud/aerosol sensor (TANSO-CAI) that supplements TANSO-FTS. The greenhouse gas observation sensor of Ibuki observes a wide range of wavelengths (near-infrared region–thermal infrared region) within the infrared band to enhance observation accuracy. The satellite uses a spectrometer to measure different elements and compounds based on their response to certain types of light. This technology allows the satellite to measure "the concentration of greenhouse gases in the atmosphere at a super-high resolution." | 2 | Environmental Chemistry |
As early as the 1970s specific property purchasers in the United States undertook studies resembling current Phase I ESAs, to assess risks of ownership of commercial properties which had a high degree of risk from prior toxic chemical use or disposal. Many times these studies were preparatory to understanding the nature of cleanup costs if the property was being considered for redevelopment or change of land use.
In the United States of America demand increased dramatically for this type of study in the 1980s following judicial decisions related to liability of property owners to effect site cleanup. Interpreting the Comprehensive Environmental Response, Compensation and Liability Act of 1980 (CERCLA), the U.S. courts have held that a buyer, lessor, or lender may be held responsible for remediation of hazardous substance residues, even if a prior owner caused the contamination; performance of a Phase I Environmental Site Assessment, according to the courts reasoning, creates a safe harbor, known as the Innocent Landowner Defense'. The original standard under CERCLA for establishing an innocent landowner defense was based upon the requirement to perform a "all appropriate inquiry" prior to ownership transfer. At such time, engineering firms started performing professional engineering reports under a variety of monikers including, "Environmental Audits", "Property Transfer Screens", "Environmental Due-Diligence Reports" and "Environmental Site Assessments". In 1991, [https://impactenvironmental.com/history/ Impact Environmental] coined the industry term, “Environmental Site Assessment” to replace the commonly used "Environmental Audit” for property transfer studies. A 1990 Court decision, No. 89-8094 (11th Cir. May 23, 1990), United States v. Fleet Factors Corp. found that a secured creditor can be liable for property contamination under the strict, joint and several liability scheme outlined in CERCLA. As a result of this decision, banks elevated their demands for pre-transfer all appropriate inquiries to hedge against financial risk. Starting in the New York market among banks and regional environmental consulting engineers, the term-of-choice evolved to be the Phase I Environmental Site Assessment.
In 1998 the necessity of performing a Phase I ESA was underscored by congressional action in passing the Superfund Cleanup Acceleration Act of 1998. This act requires purchasers of commercial property to perform a Phase I study meeting the specific standard of ASTM E1527: Standard Practice for Environmental Site Assessments: Phase I Environmental Site Assessment Process.
The most recent standard is "Standards and Practices for All Appropriate Inquiries" 40 Code of Federal Regulations, Section 312 which drew heavily from ASTM E1527-13, which is the ASTM Standard for conducting All Appropriate Inquiry (AAI) for the environmental assessment of a real property. Previous guidances regarding the ASTM E1527 standard were ASTM E1527-97, ASTM E1527-00, and ASTM E1527-05.
Residential property purchasers are only required to conduct a site inspection and chain of title survey. | 2 | Environmental Chemistry |
Transcriptional initiation, termination and regulation are mediated by “DNA looping” which brings together promoters, enhancers, transcription factors and RNA processing factors to accurately regulate gene expression. Chromosome conformation capture (3C) and more recently Hi-C techniques provided evidence that active chromatin regions are “compacted” in nuclear domains or bodies where transcriptional regulation is enhanced. The configuration of the genome is essential for enhancer-promoter proximity. Cell-fate decisions are mediated upon highly dynamic genomic reorganizations at interphase to modularly switch on or off entire gene regulatory networks through short to long range chromatin rearrangements. Related studies demonstrate that metazoan genomes are partitioned in structural and functional units around a megabase long called Topological association domains (TADs) containing dozens of genes regulated by hundreds of enhancers distributed within large genomic regions containing only non-coding sequences. The function of TADs is to regroup enhancers and promoters interacting together within a single large functional domain instead of having them spread in different TADs. However, studies of mouse development point out that two adjacent TADs may regulate the same gene cluster. The most relevant study on limb evolution shows that the TAD at the 5’ of the HoxD gene cluster in tetrapod genomes drives its expression in the distal limb bud embryos, giving rise to the hand, while the one located at 3’ side does it in the proximal limb bud, giving rise to the arm. Still, it is not known whether TADs are an adaptive strategy to enhance regulatory interactions or an effect of the constrains on these same interactions.
TAD boundaries are often composed by housekeeping genes, tRNAs, other highly expressed sequences and Short Interspersed Elements (SINE). While these genes may take advantage of their border position to be ubiquitously expressed, they are not directly linked with TAD edge formation. The specific molecules identified at boundaries of TADs are called insulators or architectural proteins because they not only block enhancer leaky expression but also ensure an accurate compartmentalization of cis-regulatory inputs to the targeted promoter. These insulators are DNA-binding proteins like CTCF and TFIIIC that help recruiting structural partners such as cohesins and condensins. The localization and binding of architectural proteins to their corresponding binding sites is regulated by post-translational modifications. DNA binding motifs recognized by architectural proteins are either of high occupancy and at around a megabase of each other or of low occupancy and inside TADs. High occupancy sites are usually conserved and static while intra-TADs sites are dynamic according to the state of the cell therefore TADs themselves are compartmentalized in subdomains that can be called subTADs from few kb up to a TAD long (19). When architectural binding sites are at less than 100 kb from each other, Mediator proteins are the architectural proteins cooperate with cohesin. For subTADs larger than 100 kb and TAD boundaries, CTCF is the typical insulator found to interact with cohesion. | 1 | Biochemistry |
Level 0 modules are the base for MoClo system, where they contain genetic elements like a promoter, a 5' untranslated region (UTR), a coding sequence, and a terminator. For the purpose of Golden Gate Cloning, the internal sequences of level 0 modules should not contain type IIS restriction enzymes sites for BsaI, BpiI, and Esp3I while surrounded by two BsaI restriction sites in inverted orientation. Level 0 modules without type IIS restriction sites flanking can add the BsaI sites during the process of Golden Gate Cloning.
If the level 0 modules contains any unwanted restriction site, they can be mutated in silico by removing one nucleotide from the Type IIS restriction site. In this process, one needs to make sure that the introduced mutation will not affect the genetic function encoded by the sequence of interest. A silent mutation in the coding sequence is preferred, for it neither changes the protein sequence nor the function of the gene of interest. | 1 | Biochemistry |
Dmitri Petrovich Konovalov (22 March 1856 – 6 January 1929) was a Russian-Soviet physical chemist who worked on gas-liquid phases of solutions in equilibrium and came up with several rules that were also independently worked on by J. Willard Gibbs and the rules are often called Gibbs-Konovalov rules. They provide the basis for distillation and separation of components that form azeotropes. | 7 | Physical Chemistry |
The frequency of codons, also known as codon usage bias, can vary from species to species with functional implications for the control of translation. The codon varies by organism; for example, most common proline codon in E. coli is CCG, whereas in humans this is the least used proline codon. | 1 | Biochemistry |
GenGIS merges geographic, ecological and phylogenetic biodiversity data in a single interactive visualization and analysis environment. A key feature of GenGIS is the testing of geographic axes that can correspond to routes of migration or gradients that influence community similarity. Data can also be explored using graphical summaries of data on a site-by-site basis, as 3D geophylogenies, or custom visualizations developed using a plugin framework. Standard statistical test such as linear regression and Mantel are provided, and the R statistical language can be accessed directly within GenGIS. Since its release, GenGIS has been used to investigate the phylogeography of viruses and bacteriophages, bacteria, and eukaryotes. | 1 | Biochemistry |
Two transport mechanisms are fundamental for nanoelectrochemistry: electron transfer and mass transport. The formulation of theoretical models allows to understand the role of the different species involved in the electrochemical reactions.
The electron transfer between the reactant and the nanoelectrode can be explained by the combination of various theories based on the Marcus theory.
Mass transport, that is the diffusion of the reactant molecules from the electrolyte bulk to the nanoelectrode, is influenced by the formation of a double electric layer at the electrode/electrolyte interface. At the nanoscale it is necessary to theorize a dynamic double electric layer which takes into account an overlap of the Stern layer and the diffuse layer.
Knowledge of the mechanisms involved allows to build computational models that combine the density functional theory with electron transfer theories and the dynamic double electric layer.
In the field of molecular modelling, accurate models could predict the behaviour of the system as reactants, electrolyte or electrode change. | 7 | Physical Chemistry |
Bulat is a type of steel alloy known in Russia from medieval times; it was regularly mentioned in Russian legends as the material of choice for cold steel. The name булат is a Russian transliteration of the Persian word fulad, meaning steel. This type of steel was used by the armies of nomadic peoples. Bulat steel was the main type of steel used for swords in the armies of Genghis Khan. Bulat Steel is generally agreed to be a Russian name for wootz steel, the production method of which has been lost for centuries, and the bulat steel used today makes use of a more recently developed technique. | 8 | Metallurgy |
Crosslinking generally involves covalent bonds that join two polymer chains. The term curing refers to the crosslinking of thermosetting resins, such as unsaturated polyester and epoxy resin, and the term vulcanization is characteristically used for rubbers. When polymer chains are crosslinked, the material becomes more rigid. The mechanical properties of a polymer depend strongly on the cross-link density. Low cross-link densities increase the viscosities of polymer melts. Intermediate cross-link densities transform gummy polymers into materials that have elastomeric properties and potentially high strengths. Very high cross-link densities can cause materials to become very rigid or glassy, such as phenol-formaldehyde materials.
In one implementation, unpolymerized or partially polymerized resin is treated with a crosslinking reagent. In vulcanization, sulfur is the cross-linking agent. Its introduction changes rubber to a more rigid, durable material associated with car and bike tires. This process is often called sulfur curing. In most cases, cross-linking is irreversible, and the resulting thermosetting material will degrade or burn if heated, without melting. Chemical covalent cross-links are stable mechanically and thermally. Therefore, cross-linked products like car tires cannot be recycled easily. A class of polymers known as thermoplastic elastomers rely on physical cross-links in their microstructure to achieve stability, and are widely used in non-tire applications, such as snowmobile tracks, and catheters for medical use. They offer a much wider range of properties than conventional cross-linked elastomers because the domains that act as cross-links are reversible, so can be reformed by heat. The stabilizing domains may be non-crystalline (as in styrene-butadiene block copolymers) or crystalline as in thermoplastic copolyesters.
Alkyd enamels, the dominant type of commercial oil-based paint, cure by oxidative crosslinking after exposure to air. | 7 | Physical Chemistry |
Multiferroics are defined as materials that exhibit more than one of the primary ferroic properties in the same phase:
* ferromagnetism – a magnetisation that is switchable by an applied magnetic field
* ferroelectricity – an electric polarisation that is switchable by an applied electric field
* ferroelasticity – a deformation that is switchable by an applied stress
While ferroelectric ferroelastics and ferromagnetic ferroelastics are formally multiferroics, these days the term is usually used to describe the magnetoelectric multiferroics that are simultaneously ferromagnetic and ferroelectric. Sometimes the definition is expanded to include nonprimary order parameters, such as antiferromagnetism or ferrimagnetism. In addition, other types of primary order, such as ferroic arrangements of magnetoelectric multipoles of which ferrotoroidicity is an example, were proposed.
Besides scientific interest in their physical properties, multiferroics have potential for applications as actuators, switches, magnetic field sensors and new types of electronic memory devices. | 7 | Physical Chemistry |
Hans Max Jahn (4 July 1853 – 7 August 1906) was a German physical chemist who worked on thermochemistry and electrochemistry. As an experimental chemist he identified problems in the contemporary theory of electrolyte conductivity and examined the thermodynamic validity of the Gibbs-Helmholtz equation.
Jahn was born in Küstrin (now in Poland) and was educated at the Universities of Berlin and Heidelberg in chemistry and mathematics. His early influences included A. W. von Hofmann whom he assisted as a student, Robert Bunsen, G. Kirchhoff and the mathematician L. Kronecker. After receiving a doctorate in 1875 for work in organic chemistry he became an assistant to Anastassios Christomanos at Athens. In 1877 he moved to Vienna, working under Ernst Ludwig (1842–1915) and in 1884 he moved to Graz. From 1899 he taught at the agricultural school and university in Berlin. Jahn worked with Walther Nernst and one of his experimental result in 1900 was that there was an increased conductivity with increase in concentration of certain electrolytes. This went against the theory that Svante August Arrhenius has proposed and resulted in a major debate.
Jahn married Sophie von Sichrovsky in 1883. Jahn was a keen violinist but suffered from deteriorating hearing. He died in 1906 following complications after an appendictomy. | 7 | Physical Chemistry |
The secret of bulat manufacturing had been lost by the beginning of the 19th century. It is known that the process involved dipping the finished weapon into a vat containing a special liquid of which spiny restharrow extract was a part (the plants name in Russian, stalnik', reflects its historical role), then holding the sword aloft while galloping on a horse, allowing it to dry and harden against the wind.
Pavel Anosov eventually managed to duplicate the qualities of that metal in 1838, when he completed ten years of study into the nature of Damascus steel swords.
Anosov had entered the Saint Petersburg Mine Cadet School in 1810, where a Damascus steel sword was stored in a display case. He became enchanted with the sword, and was filled with stories of them slashing through their European counterparts. In November 1817, he was sent to the factories of Zlatoust mining region in the southern Urals, where he was soon promoted to the inspector of the "weapon decoration department".
Here he again came into contact with Damascus steel of European origin (which was in fact pattern welded steel, and not at all similar), but quickly found that this steel was quite inferior to the original forged in the Middle East from wootz steel from India. Anosov had been working with various quenching techniques, and decided to attempt to duplicate Damascus steel with quenching. He eventually developed a methodology that greatly increased the hardness of his steels.
Bulat became popular in cannon manufacturing, until the Bessemer process was able to make the same quality steels for far less money. | 8 | Metallurgy |
The APE(X)C series included the following machines:
* APE(X)C: Birkbeck College, London, first time operated in May 1952, ready for use at the end of 1953
* APE(N)C: Board of Mathematical Machines, Oslo (N likely stands for Norway), also known as NUSSE
* APE(H)C: British Tabulating Machine Company (It is unclear what H stands for - perhaps Hollerith as the company sold Hollerith Unit record equipment
* APE(R)C: British Rayon Research Association (R stands for Rayon), ready for use in June 1952
* UCC: University College, London (circa January 1956)
* MAC or MAGIC (Magnetic Automatic Calculator): "built by Wharf Engineering Laboratories" (February 1955)
* The HEC (Hollerith Electronic Computer), built by the British Tabulating Machine Company (later to become International Computers and Tabulators (ICT), then International Computers Limited (ICL)), a commercial machine sold in several models and later known as the ICT200 series. There were likely the derivatives HEC 1, HEC 2, HEC 2M - M for marketable denoting the machine's orientation toward commercial rather than scientific customers, and HEC 4 (before 1955)
Only one of each of these machines was built, with the exception of HEC (and possibly MAC) which were commercial machines produced in quite large numbers for the time, around 150. They were similar in design, with various small differences, mostly in I/O equipment. The APEHC was a punched card machine while the APEXC, APERC and APENC were teletypers (keyboard and printer, plus paper tape reader and puncher). Also, the UCC had 8k words of storage, instead of 1k word for other machines, and the MAC used germanium diodes in replacement of many valves. | 3 | Analytical Chemistry |
In mass spectrometry, liquid junction interface is an ion source or set-up that couples peripheric devices, such as capillary electrophoresis, to mass spectrometry.
See the IUPAC recommendation definition as a means of coupling capillary electrophoresis to mass spectrometry in which a liquid reservoir surrounds the separation capillary and transfer capillary to the mass spectrometer. The reservoir provides electrical contact for the capillary electrophoresis.
The term liquid junction interface has also been used by Henry M. Fales and coworkers for ion sources where the analyte is in direct contact with the high voltage supply. This includes in particular nanospray ion sources where a wire made of stainless steel, gold or other conducting material makes contact with the sample solution inside uncoated spray capillaries. The principle is also applied when a stainless steel union connects a chromatography outlet to a spray capillary. Its use has a number of advantages with respect to simplification of interface or source design, easy handling and cost. Electrolysis effects have to be controlled.
Liquid junction interfaces have been used for on-line desalting in conjunction with mass spectrometry. Thereby, chromatographic material such as C18 phase was directly placed in the flow path coming from a pump or an HPLC device. In a variation of the method, fine capillaries were densely packed with chromatographic phase to form separation columns and act as electrospray capillaries at the same time. This method is commonly employed in many proteomics laboratories.
It is of note that experimental designs where the direct application of high voltages to liquids to form aerosols and sprays has been described as early as 1917 in the context of not ionization, but atomization of liquids. | 7 | Physical Chemistry |
In 1524, Italian explorer Giovanni da Verrazzano, (1485–1528), in service of the French crown, (famous for sailing through and thereafter naming the entrance to New York Bay as the "Verrazzano Narrows", including now in the 20th century, a suspension bridge also named for him) sailed past the Chesapeake, but did not enter the Bay. Spanish explorer Lucas Vásquez de Ayllón sent an expedition out from Hispaniola in 1525 that reached the mouths of the Chesapeake and Delaware Bays. It may have been the first European expedition to explore parts of the Chesapeake Bay, which the Spaniards called "Bahía de Santa María" ("Bay of St. Mary") or "Bahía de Madre de Dios."("Bay of the Mother of God") De Ayllón established a short-lived Spanish mission settlement, San Miguel de Gualdape, in 1526 along the Atlantic coast. Many scholars doubt the assertion that it was as far north as the Chesapeake; most place it in present-day Georgia's Sapelo Island. In 1573, Pedro Menéndez de Márquez, the governor of Spanish Florida, conducted further exploration of the Chesapeake. In 1570, Spanish Jesuits established the short-lived Ajacan Mission on one of the Chesapeake tributaries in present-day Virginia.
The arrival of English colonists under Sir Walter Raleigh and Humphrey Gilbert in the late 16th century to found a colony, later settled at Roanoke Island (off the present-day coast of North Carolina) for the Virginia Company, marked the first time that the English approached the gates to the Chesapeake Bay between the capes of Cape Charles and Cape Henry. Three decades later, in 1607, Europeans again entered the Bay. Captain John Smith of England explored and mapped the Bay between 1607 and 1609, resulting in the publication in 1612 back in the British Isles of "A Map of Virginia". Smith wrote in his journal: "Heaven and earth have never agreed better to frame a place for mans habitation." The Captain John Smith Chesapeake National Historic Trail, the first designated "all-water" National Historic Trail in the US, was established in 2006 by the National Park Service. The trail follows the route of Smiths historic 17th-century voyage. Because of economic hardships and civil strife in the "Mother Land", there was a mass migration of southern English Cavaliers and their servants to the Chesapeake Bay region between 1640 and 1675, to both of the new colonies of the Province of Virginia and the Province of Maryland. | 2 | Environmental Chemistry |
This step is the enzymatic transfer of a phosphate group from 1,3-bisphosphoglycerate to ADP by phosphoglycerate kinase, forming ATP and 3-phosphoglycerate. | 1 | Biochemistry |
In chemical analysis, matrix refers to the components of a sample other than the analyte of interest. The matrix can have a considerable effect on the way the analysis is conducted and the quality of the results are obtained; such effects are called matrix effects. For example, the ionic strength of the solution can have an effect on the activity coefficients of the analytes. The most common approach for accounting for matrix effects is to build a calibration curve using standard samples with known analyte concentration and which try to approximate the matrix of the sample as much as possible. This is especially important for solid samples where there is a strong matrix influence. In cases with complex or unknown matrices, the standard addition method can be used. In this technique, the response of the sample is measured and recorded, for example, using an electrode selective for the analyte. Then, a small volume of standard solution is added and the response is measured again. Ideally, the standard addition should increase the analyte concentration by a factor of 1.5 to 3, and several additions should be averaged. The volume of standard solution should be small enough to disturb the matrix as little as possible. | 3 | Analytical Chemistry |
In four dimensions, there are a geometrically chiral finite polytopes. One example is Roli's cube, a skew polytope on the skeleton of the 4-cube. | 4 | Stereochemistry |
Wetting is a measure of the thermodynamic compatibility of two surfaces. If the surfaces are well-matched, the surfaces will "desire" to interact with each other, minimizing the surface energy of both phases, and the surfaces will come into close contact. Because the intermolecular attractions strongly correlate with distance, the closer the interacting molecules are together, the stronger the attraction. Thus, two materials that wet well and have a large amount of surface area in contact will have stronger intermolecular attractions and a larger adhesive strength due to the dispersive mechanism. | 6 | Supramolecular Chemistry |
Ring A (12) and ring C (19) reacted together to alcohol 20 in a Shapiro reaction (tBuLi, CeCl) in a similar way as in the Nicolaou Taxol total synthesis. Subsequent steps were epoxidation (VO(acac), tBuOH) to 21, reduction (LiAlH) to the diol and alcohol protection (aqueous KOH, BnBr, BuNHSO) to benzyl ether 22, alcohol protection (MeSiHCl, imidazole) and oxidation (DDQ) to DMS ether 23, tosylation (TsCl, DMAP) to 24, deprotection to diol (TBAF) and reprotection (TMSOTf, 2,6-lutidine, DIPEA) as TMS ether 25, Ley oxidation to aldehyde 26, cyanohydrin formation (TMSCN, 18-crown-6, KCN) and alcohol protection (ethyl vinyl ether, camphorsulfonic acid) to EE ether 27. | 0 | Organic Chemistry |
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