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A splicing factor is a protein involved in the removal of introns from strings of messenger RNA, so that the exons can bind together; the process takes place in particles known as spliceosomes. Genes are progressively switched off as people age, and splicing factors can reverse this trend. Splicing factors regulate the binding of the snRNPs U1 and U2 to the 3 and 5 ends of the intron during splicing and can either be splicing promoters or splicing repressors.
In a research paper, splicing factors were found to be produced upon application of resveratrol analogues, which induced senescent cells to rejuvenate. | 1 | Biochemistry |
End sequence profiling (ESP) can be used to detect structural variations such as insertions, deletions, and chromosomal rearrangement. Compare to other methods that look at chromosomal abnormalities, ESP is particularly useful to identify copy neutral abnormalities such as inversions and translocations that would not be apparent when looking at copy number variation. From the BAC library, both ends of the inserted fragments are sequenced using a sequencing platform. Detection of variations is then achieved by mapping the sequenced reads onto a reference genome. | 1 | Biochemistry |
Since the 1960s, marine organisms with robust chemical defense systems have been targeted for “molecular mining,” a method of drug discovery that probes organisms of interest for useful compounds. Chemical agents involved in the defense systems of these organisms often exhibit antibacterial, anti-inflammatory, and chemotherapeutic properties. Capnellene derivatives and their terrestrial counterparts, hirsutanes, demonstrate antibacterial and antitumor properties with pharmacological potential. | 0 | Organic Chemistry |
Ionophores are chemical compounds that reversibly bind and transport ions through biological membranes in the absence of a protein pore. This can disrupt the membrane potential, and thus these substances could exhibit cytotoxic properties. Ionophores modify the permeability of biological membranes toward certain ions to which they show affinity and selectivity. Many ionophores are lipid-soluble and transport ions across hydrophobic membranes, such as lipid bilayers found in the living cells or synthetic vesicles (liposomes), or liquid polymeric membranes (carrier-based ion selective electrodes). Structurally, an ionophore contains a hydrophilic center and a hydrophobic portion that interacts with the membrane. Ions are bound to the hydrophilic center and form an ionophore-ion complex. The structure of the ionophore-ion complex has been verified by X-ray crystallography. | 7 | Physical Chemistry |
Alternative organophosphorus compounds include trioctylphosphine oxide and bis(2,4,4-trimethyl pentyl)phosphinic acid. Secondary, tertiary, and quaternary amines have also been used for some uranium extractions. Compared to phosphate extractants, amines are more selective for uranium, extract the uranium faster, and are easily stripped with a wider variety of reagents. However, the phosphates are more tolerant of solids in the feed solution and show faster phase separation. | 3 | Analytical Chemistry |
HIV protease inhibitors are used to treat patients having AIDS virus by preventing its DNA replication. HIV protease is used by the virus to cleave Gag-Pol polyprotein into 3 smaller proteins that are responsible for virion assembly, package and maturation. This enzyme targets the specific phenylalanine-proline cleave site within the target protein. If HIV protease is switched off the virion particle will lose function and cannot infect patients. Since it is essential in viral replication and is absent in healthy human, it is an ideal target for drug development.
HIV protease belongs to aspartic protease family and has a similar mechanism. Firstly the aspartate residue activates a water molecule and turns it into a nucleophile. Then it attacks the carbonyl group within the peptide bond (NH-CO) to form a tetrahedral intermediate. The nitrogen atom within the intermediate receives a proton, forming an amide group and subsequent rearrangement leads to the breakdown of the bond between it and the intermediate and forms two products.
Inhibitors usually contain a nonhydrolyzable hydroxyethylene or hydroxyethylamine groups that mimic the tetrahedral intermediate. Since they share a similar structure and electrostatic arrangement to the transition state of substrates they can still fit into the active site but cannot be broken down, so hydrolysis cannot occur. | 1 | Biochemistry |
As discussed previously, biomaterials are used in medical devices to treat, assist, or replace a function within the human body. The application of a specific biomaterial must combine the necessary composition, material properties, structure, and desired in vivo reaction in order to perform the desired function. Categorizations of different desired properties are defined in order to maximize functional results. | 1 | Biochemistry |
The word fugacity is derived from the Latin fugere, to flee. In the sense of an "escaping tendency", it was introduced to thermodynamics in 1901 by the American chemist Gilbert N. Lewis and popularized in an influential textbook by Lewis and Merle Randall, Thermodynamics and the Free Energy of Chemical Substances, in 1923. The "escaping tendency" referred to the flow of matter between phases and played a similar role to that of temperature in heat flow. | 7 | Physical Chemistry |
Isocyanates are common intermediates in the synthesis of primary amines via hydrolysis:
* Hofmann rearrangement, a reaction in which a primary amide is treated with a strong oxidizer such as sodium hypobromite or lead tetraacetate to form an isocyanate intermediate. | 0 | Organic Chemistry |
With the advent of high resolution imaging, researchers have started to obtain experimental data which have led them to question the assumptions of the Cassie–Baxter equation when calculating the apparent contact angle. These groups believe the apparent contact angle is largely dependent on the triple line. The triple line, which is in contact with the heterogeneous surface, cannot rest on the heterogeneous surface like the rest of the drop. In theory, it should follow the surface imperfection. This bending in the triple line is unfavorable and is not seen in real-world situations. A theory that preserves the Cassie–Baxter equation while at the same time explaining the presence of the minimized energy state of the triple line hinges on the idea of a precursor film. This film of submicrometer thickness advances ahead of the motion of the droplet and is found around the triple line. Furthermore, this precursor film allows the triple line to bend and take different conformations that were originally considered unfavorable. This precursor fluid has been observed using environmental scanning electron microscopy (ESEM) in surfaces with pores formed in the bulk. With the introduction of the precursor film concept, the triple line can follow energetically feasible conformations, thereby correctly explaining the Cassie–Baxter model. | 7 | Physical Chemistry |
DSIF (DRB Sensitivity Inducing Factor) is a protein complex that can either negatively or positively affect transcription by RNA polymerase II (Pol II). It can interact with the negative elongation factor (NELF) to promote the stalling of Pol II at some genes, which is called promoter proximal pausing. The pause occurs soon after initiation, once 20-60 nucleotides have been transcribed. This stalling is relieved by positive transcription elongation factor b (P-TEFb) and Pol II enters productive elongation to resume synthesis till finish. In humans, DSIF is composed of hSPT4 and hSPT5. hSPT5 has a direct role in mRNA capping which occurs while the elongation is paused.
SPT5 is preserved in humans to bacteria. SPT4 and SPT5 in yeast are the homologs of hSPT4 and hSPT5. In bacteria, the homologous complex only contains NusG, a Spt5 homolog. Archaea have both proteins.
The complex locks the RNA polymerase (RNAP) clamp into a closed state to prevent the elongation complex (EC) from dissociating. The Spt5 NGN domain helps anneal the two strands of DNA upstream. The single KOW domain in bacteria and archaea anchors a ribosome to the RNAP. | 1 | Biochemistry |
As well as the faecally derived stanol, two other isomers can be identified in the environment; 5α-cholestanol | 2 | Environmental Chemistry |
Silicon carbide is an important material in TRISO-coated fuel particles, the type of nuclear fuel found in high temperature gas cooled reactors such as the Pebble Bed Reactor. A layer of silicon carbide gives coated fuel particles structural support and is the main diffusion barrier to the release of fission products.
Silicon carbide composite material has been investigated for use as a replacement for Zircaloy cladding in light water reactors. One of the reasons for this investigation is that, Zircaloy experiences hydrogen embrittlement as a consequence of the corrosion reaction with water. This produces a reduction in fracture toughness with increasing volumetric fraction of radial hydrides. This phenomenon increases drastically with increasing temperature to the detriment of the material. Silicon carbide cladding does not experience this same mechanical degradation, but instead retains strength properties with increasing temperature. The composite consists of SiC fibers wrapped around a SiC inner layer and surrounded by an SiC outer layer. Problems have been reported with the ability to join the pieces of the SiC composite. | 8 | Metallurgy |
Lukinavičius completed his bachelors degree and masters degree in biochemistry at the Vilnius University in 2000 and 2002 respectively. During this period he worked as a research assistant in Saulius Klimašauskas group and investigating conformational movements of the catalytic loop of DNA methyltransferase.
Later he became interested in S-Adenosyl methionine analogues which can be cofactors for methyltransferases. He collaborated with Elmar Weinhold from RWTH Aachen University and learned chemical synthesis and received his PhD in biochemistry at Vilnius University, Lithuania in September 2007. This led to the development of a new DNA labeling method, the Methyltransferase-Directed Transfer of Activated Groups (mTAG). This method was applied for optical DNA mapping and for a profiling epigenetic modifications by several research groups.
After obtaining his PhD, he moved to École polytechnique fédérale de Lausanne for postdoctoral research where he continued on working with protein labeling methods in group of Kai Johnsson. He improved SNAP-tag protein labelling technology by developing a new biocompatible fluorophore, silicon-rhodamine (SiR). During this period, he began a collaboration with Stefan Hell to perform one of the first super-resolution microscopy experiments of living cells.
In 2016, Stefan Hell invited Lukinavičius to the Department of NanoBiophotonics of the Max Planck Institute for Biophysical Chemistry in Göttingen. He has continued working on fluorescence labeling of biomolecules and started a Chromatin Labeling and Imaging group in 2018. | 1 | Biochemistry |
General function of TFH:
# Initiation transcription of protein- coding gene.
# DNA nucleotide repairing.
(NER)TFH is a general transcription factor that acts to recruit RNA Pol II to the promoters of genes. It functions as a helicase that unwinds DNA. It also unwinds DNA after a DNA lesion has been recognized by either the global genome repair (GGR) pathway or the transcription-coupled repair (TCR) pathway of NER. Purified TFH has role in stopping further RNA synthesis by activating the cyclic peptide α-amanitin. | 1 | Biochemistry |
The collected experimental data reflects not only the binding thermodynamics of the interaction of interest, but any contributing competing equilibria associated to it. A post-hoc analysis can be performed to determine the buffer or solvent-independent enthalpy from the experimental thermodynamics, by simply going through the process of Hess’ law. Below example shows a simple interaction between a metal ion (M) and a ligand (L). B represents the buffer used for this interaction and represents protons.
</blockquote>
Therefore,</blockquote>which can be further processed to calculate the enthalpy of metal-ligand interaction. Although this example is between a metal and a ligand, it is applicable to any ITC experiment, regarding binding interactions.
As a part of the analysis, a number of protons are required to calculate the solvent-independent thermodynamics. This can be easily done by plotting a graph such as shown below.
The linear equation of this plot is the rearranged version of the equation above from the post-hoc analysis in a form of y = mx + b:</blockquote> | 7 | Physical Chemistry |
DNA‐templated organic synthesis (DTS) is a way to control the reactivity of synthetic molecules by using nature's molarity‐based approach. Historically, DTS was used as a model of prebiotic nucleic acid replication. Now however, it is capable of translating DNA sequences into complex small‐molecule and polymer products of multistep organic synthesis. | 1 | Biochemistry |
Fatty acids must be activated before they can be carried into the mitochondria, where fatty acid oxidation occurs. This process occurs in two steps catalyzed by the enzyme fatty acyl-CoA synthetase. | 1 | Biochemistry |
According to the Web of Science, the journal's two most cited papers () are:
* (cited 766 times)
* (cited 722 times) | 9 | Geochemistry |
In 2009, Ted Ellis produced an exhibit focusing on the theme of African-American history in light of slavery and emancipation. The exhibit, American Slavery: The Reason Why Were Here, tied into the Juneteenth commemoration of slaverys abolition in the State of Texas. It was located at and included tours of the historic residence of horticulturist Henry Stringfellow, an innovator in organic gardening who was enlightened in how he employed of freedmen. Ellis began the series of works at a 2006 exhibition at the same house.
The exhibit's more than 20 paintings were painted with brush and fingers, and Ellis sometimes added a collage of documents. The exhibit included images of the transportation of slaves, the industry of slavery in crop production, and the abolition of slavery.
The painting Free At Last includes depictions of Buffalo soldiers, Harriet Tubman, the year "1865", a mighty oak, and in the background, their heads bowed in prayer, the figures of the current owner and restorer of the house, Sam Collins III, and his wife and children. The exhibit also displayed Ellis famous depiction of Barack Obama, Obama, the 44th President'.
Ellis art was featured at a 2011 exhibition at the Rosa Parks Library and Museum. The Museum, at Troy University in Montgomery, Alabama, hosted the exhibit, called Our History, Heritage, and Culture: An American Story, the Art of Ted Ellis', as part of its celebration of Black History Month.
T. Ellis has been pictorially documenting African-American lifestyle, history and culture for thirty years. Ellis paintings are in the permanent collection of the DuSable museum, Charles Wright museum, the McKenna museum, Free People of Color Museum, and the Amistad Research Center. The City of Selma, Alabama, commissioned T. Ellis as the official artist for the 50th anniversary for the civil rights march, known as "Bloody Sunday". The City and County of Galveston, Texas, recognized T. Ellis for the 150th anniversary of Juneteenth. The Juneteenth Freedom Project was exhibited at the State Capitol in Washington, DC at the U.S. Senate Rotunda and House of Representatives Rayburn Building. President Barack Obama and the First Lady, Michelle Obama of the White House has thanked T. Ellis for his art and giving.
T.Ellis painting of the Tuskegee airmen, "The Lonely Angels" was signed by all the Tuskegge Airmen who were in attendance to receive their Congressional Medal of Honor from the President. President George W. Bush and Speaker of the House of Representatives Nancy Pelosi stand amidst 300 Tuskegee Airmen during a photo opportunity Thursday, March 29, 2007, in Statuary Hall at the U.S. Capitol. White House. | 3 | Analytical Chemistry |
The purpose function of intrinsic termination is to signal for the dissociation of the ternary elongation complex (TEC), ending the transcript. Intrinsic termination independent of the protein Rho, as opposed to Rho-dependent termination, where the bacterial Rho protein comes in and acts on the RNA polymerase, causing it to dissociate. Here, there is no extra protein and the transcript forms its own loop structure. Intrinsic termination thus regulates the level of transcription as well, determining how many Polymerase can transcribe a gene over a given period of time, and can help prevent interactions with neighboring chromosomes. | 1 | Biochemistry |
In some cases, an additional rate enhancement is seen for the lighter isotope, possibly due to quantum mechanical tunnelling. This is typically only observed for reactions involving bonds to hydrogen atoms.
Tunneling occurs when a molecule penetrates through a potential energy barrier rather than over it. Although not allowed by the laws of classical mechanics, particles can pass through classically forbidden regions of space in quantum mechanics based on wave–particle duality.
Analysis of tunneling can be made using Bell's modification of the Arrhenius equation, which includes the addition of a tunneling factor, Q:
where A is the Arrhenius parameter, E is the barrier height and
where and
Examination of the β term shows exponential dependency on the mass of the particle. As a result, tunneling is much more likely for a lighter particle such as hydrogen. Simply doubling the mass of a tunneling proton by replacing it with its deuterium isotope drastically reduces the rate of such reactions. As a result, very large kinetic isotope effects are observed that can not be accounted for by differences in zero point energies.
In addition, the β term depends linearly with barrier width, 2a. As with mass, tunneling is greatest for small barrier widths. Optimal tunneling distances of protons between donor and acceptor atom is 0.4 Å. | 7 | Physical Chemistry |
Molecular catalysts have been explored for the preparation of a variety of potential applications. the manufacturing of high-strength materials, the preparation of cancer-targeting nanoparticles, and the conversion of renewable plant-based feedstocks into hair and skin care products. | 0 | Organic Chemistry |
In second order reactions, the rate of reaction is proportional to the square of the concentration. By integrating this rate, it can be shown that the concentration of the reactant decreases following this formula:
We replace for in order to calculate the half-life of the reactant and isolate the time of the half-life ():This shows that the half-life of second order reactions depends on the initial concentration and rate constant. | 7 | Physical Chemistry |
While the standard addition method is effective in reducing the interference of most matrix effects on the analyte signal, it cannot correct for the translational matrix effects. These effects are caused by other substances present in the unknown sample that are often independent of the analyte concentration. They are commonly referred to as background and can impact the intercept of the regression line without affecting the slope. This results in bias towards the unknown concentration. In other words, standard addition will not correct for these backgrounds or other spectral interferences.
Analysts also needs to evaluate the precision of the determined unknown concentration by calculating for the standard deviation, . Lower indicates greater precision of the measurements. The value of is given by
where the calculation involves the following variables:
* standard deviation of the residuals,
* absolute value of the slope of the least-squares line,
* y-intercept of the linear curve,
* number of standards,
* average measurement of the standards,
* concentrations of the standards,
* average concentration of the standards, | 3 | Analytical Chemistry |
In a 2022 observational study aimed to identify preoperative serum metabolites that could predict postoperative opioid consumption, the role of imidazole-4-acetaldehyde was identified as one of the metabolites that showed different trends between gastric cancer patients with high postoperative opioid consumption and those with low opioid consumption group. The results suggest that imidazole-4-acetaldehyde, along with other metabolites, was significantly different between the two groups, so that that imidazole-4-acetaldehyde may serve as a potential biomarker for predicting postoperative opioid consumption in gastric cancer patients, still, the results of this study is inconclusive. | 1 | Biochemistry |
Nickel allergy is any of several allergic conditions provoked by exposure to the chemical element nickel. Nickel allergy often takes the form of nickel allergic contact dermatitis (Ni-ACD), a form of allergic contact dermatitis (ACD). Ni-ACD typically causes a rash that is red and itchy and that may be bumpy or scaly. The main treatment for it is avoiding contact with nickel-releasing metals, such as inexpensive jewelry. Another form of nickel allergy is a systemic form: systemic nickel allergy syndrome (SNAS) can mimic some of the symptoms of irritable bowel syndrome (IBS) and also has a dermatologic component. | 1 | Biochemistry |
In chemical kinetics, the overall rate of a reaction is often approximately determined by the slowest step, known as the rate-determining step (RDS or RD-step or r/d step) or rate-limiting step. For a given reaction mechanism, the prediction of the corresponding rate equation (for comparison with the experimental rate law) is often simplified by using this approximation of the rate-determining step.
In principle, the time evolution of the reactant and product concentrations can be determined from the set of simultaneous rate equations for the individual steps of the mechanism, one for each step. However, the analytical solution of these differential equations is not always easy, and in some cases numerical integration may even be required. The hypothesis of a single rate-determining step can greatly simplify the mathematics. In the simplest case the initial step is the slowest, and the overall rate is just the rate of the first step.
Also, the rate equations for mechanisms with a single rate-determining step are usually in a simple mathematical form, whose relation to the mechanism and choice of rate-determining step is clear. The correct rate-determining step can be identified by predicting the rate law for each possible choice and comparing the different predictions with the experimental law, as for the example of and CO below.
The concept of the rate-determining step is very important to the optimization and understanding of many chemical processes such as catalysis and combustion. | 7 | Physical Chemistry |
A phase diagram in physical chemistry, engineering, mineralogy, and materials science is a type of chart used to show conditions (pressure, temperature, volume, etc.) at which thermodynamically distinct phases (such as solid, liquid or gaseous states) occur and coexist at equilibrium. | 7 | Physical Chemistry |
For the stoichiometric reactions involving alkali metal or alkaline earth acetylides, work-up for the reaction requires liberation of the alcohol. To achieve this hydrolysis, aqueous acids are often employed.
Common solvents for the reaction include ethers, acetals, dimethylformamide, and dimethyl sulfoxide. | 0 | Organic Chemistry |
In working skeletal muscles and the brain, Phosphocreatine is stored as a readily available high-energy phosphate supply, and the enzyme creatine phosphokinase transfers a phosphate from phosphocreatine to ADP to produce ATP. Then the ATP releases giving chemical energy. This is sometimes erroneously considered to be substrate-level phosphorylation, although it is a transphosphorylation. | 1 | Biochemistry |
STAT2 has been shown to interact with:
* CREB-binding protein,
* IFNAR1
* IFNAR2,
* IRF9,
* MED14,
* SMARCA4, and
* STAT1. | 1 | Biochemistry |
McIlvaine buffer is a buffer solution composed of citric acid and disodium hydrogen phosphate, also known as citrate-phosphate buffer. It was introduced in 1921 by the United States agronomist Theodore Clinton McIlvaine (1875–1959) from West Virginia University, and it can be prepared in pH 2.2 to 8 by mixing two stock solutions. | 1 | Biochemistry |
Ballast tanks do not corrode uniformly throughout the tank. Each region behaves distinctively, according to it electrochemical loading. The differences can especially be seen in empty ballast tanks. The upper sections usually corrode but the lower sections will blister.
A ballast tank has three distinct sections: 1) upper, 2) mid or "boottop" area and, 3) the "double bottom" or lower wing sections. The upper regions are constantly affected by weather. This area experiences a high degree of thermal cycling and mechanical damage through vibration. This area tends to undergo anodic oxidation more rapidly than other sections and will weaken more rapidly. This ullage or headspace area contains more oxygen and thus speeds atmospheric corrosion, as evidenced by the appearance of rust scales.
In the midsection corrodes more slowly than upper or the bottom sections of the tank.
Double bottoms are prone to cathodic blistering. Temperatures in this area are much lower due to the cooling of the sea. If this extremely cathodic region is placed close to an anodic source (e.g. a corroding ballast pipe), cathodic blistering may occur especially where the epoxy coating is relatively new. Mud retained in ballast water can lead to microbial corrosion. | 8 | Metallurgy |
The worlds first oil well was drilled in 1859 by Edwin Drake at what is now called the Drake Well in Cherrytree Township, Pennsylvania. Drakes well is considered the first because it was drilled, not dug, and used a steam engine. There also was a company associated with it, and it sparked a major oil drilling boom.
Prior to the first well drilled by Drake, there was activity in various parts of the world in the mid-19th century. A group directed by Major Alexeyev of the Bakinskii Corps of Mining Engineers hand-drilled a well in the Baku region of Bibi-Heybat in 1846. There were engine-drilled wells in West Virginia in the same year as Drakes well. An early commercial well was hand dug in Poland in 1853, and another in nearby Romania in 1857. At around the same time the worlds first, small, oil refinery was opened at Jasło in Poland, with a larger one opened at Ploiești in Romania shortly after. Romania is the first country in the world to have had its annual crude oil output officially recorded in international statistics: 275 tonnes for 1857.
In 1858, Georg Christian Konrad Hunäus found a significant amount of petroleum while drilling for lignite in Wietze, Germany. Wietze later provided about 80% of German consumption in the Wilhelminian Era. The production stopped in 1963, but Wietze has hosted a Petroleum Museum since 1970.
Oil sands have been mined since the 18th century. In Wietze in lower Saxony, natural asphalt/bitumen has been explored since the 18th century. Both in Pechelbronn as in Wietze, the coal industry dominated the petroleum technologies.
Chemist James Young in 1847 noticed a natural petroleum seepage in the coal mine at riddings Alfreton, Derbyshire from which he distilled a light thin oil suitable for use as lamp oil, at the same time obtaining a more viscous oil suitable for lubricating machinery. In 1848, Young set up a small business refining crude oil.
Young eventually succeeded, by distilling cannel coal at low heat, in creating a fluid resembling petroleum, which when treated in the same way as the seep oil gave similar products. Young found that by slow distillation he could obtain several useful liquids from it, one of which he named "paraffine oil" because at low temperatures it congealed into a substance resembling paraffin wax.
The production of these oils and solid paraffin wax from coal formed the subject of his patent dated October 17, 1850. In 1850, Young & Meldrum and Edward William Binney entered into partnership under the title of E.W. Binney & Co. at Bathgate in West Lothian and E. Meldrum & Co. at Glasgow; their works at Bathgate were completed in 1851 and became the first truly commercial oil-works in the world with the first modern oil refinery.
The worlds first oil refinery was built in 1856 by Ignacy Łukasiewicz. His achievements also included the discovery of how to distill kerosene from seep oil, the invention of the modern kerosene lamp (1853), the introduction of the first modern street lamp in Europe (1853), and the construction of the worlds first modern oil "mine" (1854). at Bóbrka, near Krosno (still operational as of 2020).
The demand for petroleum as a fuel for lighting in North America and around the world quickly grew.
The first commercial oil well in Canada became operational in 1858 at Oil Springs, Ontario (then Canada West). Businessman James Miller Williams dug several wells between 1855 and 1858 before discovering a rich reserve of oil four metres below ground. Williams extracted 1.5 million litres of crude oil by 1860, refining much of it into kerosene lamp oil. Williamss well became commercially viable a year before Drakes Pennsylvania operation and could be argued to be the first commercial oil well in North America. The discovery at Oil Springs touched off an oil boom which brought hundreds of speculators and workers to the area. Advances in drilling continued into 1862 when local driller Shaw reached a depth of 62 metres using the spring-pole drilling method. On January 16, 1862, after an explosion of natural gas, Canada's first oil gusher came into production, shooting into the air at a recorded rate of per day. By the end of the 19th century the Russian Empire, particularly the Branobel company in Azerbaijan, had taken the lead in production. | 7 | Physical Chemistry |
The synthesis of an mRNA display library starts from the synthesis of a DNA library. A DNA library for any protein or small peptide of interest can be synthesized by solid-phase synthesis followed by PCR amplification. Usually, each member of this DNA library has a T7 RNA polymerase transcription site and a ribosomal binding site at the 5’ end. The T7 promoter region allows large-scale in vitro T7 transcription to transcribe the DNA library into an mRNA library, which provides templates for the in vitro translation reaction later. The ribosomal binding site in the 5’-untranslated region (5’ UTR) is designed according to the in vitro translation system to be used. There are two popular commercially available in vitro translation systems. One is E. coli S30 Extract System (Promega) that requires a Shine-Dalgarno sequence in the 5’ UTR as a ribosomal binding site; the other one is Red Nova Lysate (Novagen), which needs a ΔTMV ribosomal binding site.
Once the mRNA library is generated, it will be Urea-PAGE purified and ligated using T4 DNA ligase to the DNA spacer linker containing puromycin at the 3’ end. In this ligation step, a piece of mRNA is ligated with a single stranded DNA with the help from T4 DNA ligase. This is not a standard T4 DNA ligase ligation reaction, where two pieces of double stranded DNA are ligated together. To increase the yield of this special ligation, a single stranded DNA splint may be used to aid the ligation reaction. The 5’ terminus of the splint is designed to be complementary to the 3’ end of the mRNA, and the 3’ terminus of the splint is designed to be complementary to the 5’ end of the DNA spacer linker, which usually consists of poly dA nucleotides (Figure 2).
The ligated mRNA-DNA-puromycin library is translated in Red Nova Lysate (Novagen) or E. coli S30 Extract System (Promega), resulting in polypeptides covalently linked in cis to the encoding mRNA. The in vitro translation can also be done in a PURE (protein synthesis using recombinant elements) system. PURE system is an E. coli cell-free translation system in which only essential translation components are present. Some components, such as amino acids and aminoacyl-tRNA synthases (AARSs) can be omitted from the system. Instead, chemically acylated tRNA can be added into the PURE system. It has been shown that some unnatural amino acids, such as N-methyl-amino acid accylated tRNA can be incorporated into peptides or mRNA-polypeptide fusions in a PURE system.
After translation, the single-stranded mRNA portions of the fusions will be converted to heteroduplex of RNA/DNA by reverse transcriptase to eliminate any unwanted RNA secondary structures, and render the nucleic acid portion of the fusion more stable. This step is a standard reverse transcription reaction. For instance, it can be done by using Superscript II (GIBCO-BRL) following the manufacturer’s protocol.
The mRNA/DNA-polypeptide fusions can be selected over immobilized selection targets for several rounds (Figure 3). There might be a relatively high background for the first few rounds of selection, and this can be minimized by increasing selection stringency, such as adjusting salt concentration, amount of detergent, and/or temperature during the target/fusion binding period. Following binding selection, those library members that stay bound to the immobilized target are PCR amplified. The PCR amplification step will enrich the population from the mRNA-display library that has higher affinity for the immobilized target. Error-prone PCR can also be done in between each round of selection to further increase the diversity of the mRNA-display library and reduce background in selection.
A less time-consuming protocol for mRNA display was recently published. | 1 | Biochemistry |
A system is said to present annealed disorder when some parameters entering its definition are random variables, but whose evolution is related to that of the degrees of freedom defining the system. It is defined in opposition to quenched disorder, where the random variables may not change their values.
Systems with annealed disorder are usually considered to be easier to deal with mathematically, since the average on the disorder and the thermal average may be treated on the same footing. | 3 | Analytical Chemistry |
The theorem also holds for adiabatic processes. That is, for closed systems, which are not in thermal contact with any heat reservoirs.
Similarly to the non-adiabatic case, the lost work is measured relative to some reference reservoir . Even though the process itself is adiabatic, the corresponding reversible process may not be, and might require heat exchange with the reference reservoir. Thus, this can be thought of as a special case of the above statement of the theorem - an adiabatic process is one for which the heat interactions with all reservoirs are zero, and in the reversible process, only the heat interaction with the reference thermal reservoir may be different.
The adiabatic case of the theorem holds also for the other formulation of the theorem, presented below. | 7 | Physical Chemistry |
There are three main categories for triggering the release of sigmas factors from anti-sigma factors: partner switching, direct signaling, and a mechanism regulated by proteolysis.
The partner-switching mechanism is commonly found in Gram-positive bacteria. It consists of four key players: a sigma factor, an anti-sigma factor, an anti-anti-sigma factor, and an input phosphatase complex. A cell that is not under stress has an anti-sigma factor that is bound to the sigma factor on the gene and keeps it inactive. In times of stress, a phosphatase complex dephosphorylates the anti-sigma factor, allowing the anti-sigma factor to switch partners and bind to the anti-anti-sigma factor. This frees the sigma factors to activate the gene. Environmental stressors, such as heat, often activate this mechanism.
The direct signaling mechanism is as it sounds: the anti-sigma factor binds to a signal, which causes conformation changes in the structure of the anti-sigma factors, resulting in the release of the sigma factors.
The regulated intramembrane proteolysis (RIP) mechanism allows signal transduction across membranes. This mechanism is often used to regulate ECF sigma factors. The mechanism involves two sequential cleavages, the first being an external cleavage of membrane-traversing anti-sigma factor and the second cleavage of the anti-sigma factors in the membrane's plane, resulting in a free cytoplasmic domain. | 1 | Biochemistry |
Electrofreezing is the tendency of a material to solidify upon being exposed to an external electric field. Electrofreezing was initially introduced by Dufour in 1892. Examples are the electrofreezing of liquid ammonia supposed to be naturally occurring during electrical storms in Jupiter-like planets, and ice χ supposedly being a form of high pressure ice.
Depending on the material, freezing occur only at certain field intensities, above which electric fields are strong enough to induce chemical reactions. | 7 | Physical Chemistry |
Neurturin has been shown to upregulate B1 (bradykinin) receptors in neurons of mice, indicating a possible influence on pain and inflammation pathways. In addition knockout mice have shown that in the absence of neurturin an increased acetylcholine response is observed. The exact role and function of neurturin in multiple signaling pathways is widely unknown. | 1 | Biochemistry |
Symbols for chemical elements shall be written in roman (upright) type. The symbol is not followed by a full-stop.
Examples:
: H He C Ca
Attached subscripts or superscripts specifying a nucleotide or molecule have the following meanings and positions:
* The nucleon number (mass number) is shown in the left superscript position (e.g., N)
* The number of atoms of a nucleotide is shown in the right subscript position (e.g., N)
* The proton number (atomic number) may be indicated in the left subscript position (e.g., Gd)
* If necessary, a state of ionization or an excited state may be indicated in the right superscript position (e.g., state of ionization Na) | 7 | Physical Chemistry |
The Krische allylation involves the enantioselective iridium-catalyzed addition of an allyl group to an aldehyde or an alcohol, resulting in the formation of a secondary homoallylic alcohol. The mechanism of the Krische allylation involves primary alcohol dehydrogenation or, when using aldehyde reactants, hydrogen transfer from 2-propanol. Unlike other allylation methods, the Krische allylation avoids the use of preformed allyl metal reagents and enables the direct conversion of primary alcohols to secondary homoallylic alcohols (precluding alcohol to aldehyde oxidation). | 0 | Organic Chemistry |
The isoelectric point (pI, pH(I), IEP), is the pH at which a molecule carries no net electrical charge or is electrically neutral in the statistical mean. The standard nomenclature to represent the isoelectric point is pH(I). However, pI is also used. For brevity, this article uses pI. The net charge on the molecule is affected by pH of its surrounding environment and can become more positively or negatively charged due to the gain or loss, respectively, of protons (H).
Surfaces naturally charge to form a double layer. In the common case when the surface charge-determining ions are H/HO, the net surface charge is affected by the pH of the liquid in which the solid is submerged.
The pI value can affect the solubility of a molecule at a given pH. Such molecules have minimum solubility in water or salt solutions at the pH that corresponds to their pI and often precipitate out of solution. Biological amphoteric molecules such as proteins contain both acidic and basic functional groups. Amino acids that make up proteins may be positive, negative, neutral, or polar in nature, and together give a protein its overall charge. At a pH below their pI, proteins carry a net positive charge; above their pI they carry a net negative charge. Proteins can, thus, be separated by net charge in a polyacrylamide gel using either preparative native PAGE, which uses a constant pH to separate proteins, or isoelectric focusing, which uses a pH gradient to separate proteins. Isoelectric focusing is also the first step in 2-D gel polyacrylamide gel electrophoresis.
In biomolecules, proteins can be separated by ion exchange chromatography. Biological proteins are made up of zwitterionic amino acid compounds; the net charge of these proteins can be positive or negative depending on the pH of the environment. The specific pI of the target protein can be used to model the process around and the compound can then be purified from the rest of the mixture. Buffers of various pH can be used for this purification process to change the pH of the environment. When a mixture containing a target protein is loaded into an ion exchanger, the stationary matrix can be either positively-charged (for mobile anions) or negatively-charged (for mobile cations). At low pH values, the net charge of most proteins in the mixture is positive – in cation exchangers, these positively-charged proteins bind to the negatively-charged matrix. At high pH values, the net charge of most proteins is negative, where they bind to the positively-charged matrix in anion exchangers. When the environment is at a pH value equal to the protein's pI, the net charge is zero, and the protein is not bound to any exchanger, and therefore, can be eluted out. | 7 | Physical Chemistry |
Devardas alloy (Copper/Aluminium/Zinc) is a reducing agent. When reacted with nitrate in sodium hydroxide solution, ammonia is liberated. The ammonia formed may be detected by its characteristic odor, and by damp red litmus papers turning blue, signalling that it is an alkali — very few gases other than ammonia evolved from wet chemistry are alkaline.
:3 + 8 Al + 5 + 18 → 3 + 8
Aluminium is the reducing agent in this reaction that will occur. | 3 | Analytical Chemistry |
When a water droplet is on a surface that is not flat and the surface topographical features lead to a surface area that is larger than that of a perfectly flat version of the same surface, the Wenzel model is a more accurate predictor of the wettability of this surface. Wenzel's model is described by the following equation:
= Contact angle of water predicted by Wenzel's model
= Ratio of surface area of rough surface to the surface area of a flat projection of the same surface | 7 | Physical Chemistry |
LIBS is one of several analytical techniques that can be deployed in the field as opposed to pure laboratory techniques e.g. spark OES. , recent research on LIBS focuses on compact and (man-)portable systems. Some industrial applications of LIBS include the detection of material mix-ups, analysis of inclusions in steel, analysis of slags in secondary metallurgy, analysis of combustion processes, and high-speed identification of scrap pieces for material-specific recycling tasks. Armed with data analysis techniques, this technique is being extended to pharmaceutical samples. | 7 | Physical Chemistry |
Phosphine is an attractive fumigant because it is lethal to insects and rodents, but degrades to phosphoric acid, which is non-toxic. As sources of phosphine, for farm use, pellets of aluminium phosphide (AlP), calcium phosphide (), or zinc phosphide () are used. These phosphides release phosphine upon contact with atmospheric water or rodents' stomach acid. These pellets also contain reagents to reduce the potential for ignition or explosion of the released phosphine.
An alternative is the use of phosphine gas itself which requires dilution with either or or even air to bring it below the flammability point. Use of the gas avoids the issues related with the solid residues left by metal phosphide and results in faster, more efficient control of the target pests.
One problem with phosphine fumigants is the increased resistance by insects. | 0 | Organic Chemistry |
In an ideal continuous stirred-tank reactor (CSTR), the flow at the inlet is completely and instantly mixed into the bulk of the reactor. The reactor and the outlet fluid have identical, homogeneous compositions at all times. The residence time distribution is exponential:
Where; the mean is T and the variance is 1. A notable difference from the plug flow reactor is that material introduced into the system will never completely leave it.
In reality, it is impossible to obtain such rapid mixing, as there is necessarily a delay between any molecule passing through the inlet and making its way to the outlet, and hence the RTD of a real reactor will deviate from the ideal exponential decay, especially in the case of large reactors. For example, there will be some finite delay before E reaches its maximum value and the length of the delay will reflect the rate of mass transfer within the reactor. Just as was noted for a plug-flow reactor, an early mean will indicate some stagnant fluid within the vessel, while the presence of multiple peaks could indicate channeling, parallel paths to the exit, or strong internal circulation. Short-circuiting fluid within the reactor would appear in an RTD curve as a small pulse of concentrated tracer that reaches the outlet shortly after injection.
Reactants continuously enter and leave a tank where they are mixed. Consequently, the reaction proceeds at a rate dependent on the outlet concentration: | 9 | Geochemistry |
Fretting resistance is not an intrinsic property of a material, or even of a material couple. There are several factors affecting fretting behavior of a contact:
* Contact load
* Sliding amplitude
* Number of cycles
* Temperature
* Relative humidity
* Inertness of materials
* Corrosion and resulting motion-triggered contact insufficiency | 8 | Metallurgy |
A pyrometer, or radiation thermometer, is a type of remote sensing thermometer used to measure the temperature of distant objects. Various forms of pyrometers have historically existed. In the modern usage, it is a device that from a distance determines the temperature of a surface from the amount of the thermal radiation it emits, a process known as pyrometry, a type of radiometry.
The word pyrometer comes from the Greek word for fire, "πῦρ" (pyr), and meter, meaning to measure. The word pyrometer was originally coined to denote a device capable of measuring the temperature of an object by its incandescence, visible light emitted by a body which is at least red-hot. Infrared thermometers, can also measure the temperature of cooler objects, down to room temperature, by detecting their infrared radiation flux. Modern pyrometers are available for a wide range of wavelengths and are generally called radiation thermometers. | 8 | Metallurgy |
Reductive stress (RS) is defined as an abnormal accumulation of reducing equivalents despite being in the presence of intact oxidation and reduction systems. A redox reaction involves the transfer of electrons from reducing agents (reductants) to oxidizing agents (oxidants) and redox couples are accountable for the majority of the cellular electron flow. RS is a state where there are more reducing equivalents compared to reductive oxygen species (ROS) in the form of known biological redox couples such as GSH/GSSG, NADP+/NADPH, and NAD+/NADH. Reductive stress is the counterpart to oxidative stress, where electron acceptors are expected to be mostly reduced. Reductive stress is likely derived from intrinsic signals that allow for the cellular defense against pro-oxidative conditions. There is a feedback regulation balance between reductive and oxidative stress where chronic RS induce oxidative species (OS), resulting in an increase in production of RS, again. | 1 | Biochemistry |
6-Phosphogluconic acid (6-phosphogluconate) is an intermediate in the pentose phosphate pathway and the Entner–Doudoroff pathway.
It is formed by 6-phosphogluconolactonase from 6 phosphogluconolactone, and acted upon by phosphogluconate dehydrogenase to produce ribulose 5-phosphate.These two steps are the part of Pentose Phosphate Pathway. It may also be acted upon by 6-phosphogluconate dehydratase to produce 2-keto-3-deoxy-6-phosphogluconate. | 1 | Biochemistry |
Asteroid mining has also been seriously considered. A NASA design study evaluated a 10,000-ton mining vehicle (to be assembled in orbit) that would return a 500,000-ton asteroid fragment to geostationary orbit. Only about 3,000 tons of the mining ship would be traditional aerospace-grade payload. The rest would be reaction mass for the mass-driver engine, which could be arranged to be the spent rocket stages used to launch the payload. Assuming that 100% of the returned asteroid was useful, and that the asteroid miner itself couldn't be reused, that represents nearly a 95% reduction in launch costs. However, the true merits of such a method would depend on a thorough mineral survey of the candidate asteroids; thus far, we have only estimates of their composition. One proposal is to capture the asteroid Apophis into Earth orbit and convert it into 150 solar power satellites of 5 GW each or the larger asteroid 1999 AN10, which is 50 times the size of Apophis and large enough to build 7,500 5-gigawatt solar power satellites | 7 | Physical Chemistry |
PSII is a transmembrane structure found in all chloroplasts. It splits water into electrons, protons and molecular oxygen. The electrons are transferred to plastoquinol, which carries them to a proton pump. The oxygen is released into the atmosphere.
The emergence of such an incredibly complex structure, a macromolecule that converts the energy of sunlight into chemical energy and thus potentially useful work with efficiencies that are impossible in ordinary experience, seems almost magical at first glance. Thus, it is of considerable interest that, in essence, the same structure is found in purple bacteria. | 5 | Photochemistry |
It is also possible to synthesise heterocyclic compounds via the Elbs reaction. In 1956 an Elbs reaction of a thiophene derivative was published. The expected linear product was not obtained due to a change in reaction mechanism after formation of the first intermediate which caused multiple free radical reaction steps. | 0 | Organic Chemistry |
There is recent evidence that suggests that the Aztec civilization was a distinct locus of metallurgy, though gold objects from this area had previously been attributed to the Mixtec. | 8 | Metallurgy |
Adherents to the MaxEnt viewpoint take a clear position on some of the conceptual/philosophical questions in thermodynamics. This position is sketched below. | 7 | Physical Chemistry |
In prokaryotes, structural genes of related function are typically adjacent to one another on a single strand of DNA, forming an operon. This permits simpler regulation of gene expression, as a single regulatory factor can affect transcription of all associated genes. This is best illustrated by the well-studied lac operon, in which three structural genes (lacZ, lacY, and lacA) are all regulated by a single promoter and a single operator. Prokaryotic structural genes are transcribed into a polycistronic mRNA and subsequently translated.
In eukaryotes, structural genes are not sequentially placed. Each gene is instead composed of coding exons and interspersed non-coding introns. Regulatory sequences are typically found in non-coding regions upstream and downstream from the gene. Structural gene mRNAs must be spliced prior to translation to remove intronic sequences. This in turn lends itself to the eukaryotic phenomenon of alternative splicing, in which a single mRNA from a single structural gene can produce several different proteins based on which exons are included. Despite the complexity of this process, it is estimated that up to 94% of human genes are spliced in some way. Furthermore, different splicing patterns occur in different tissue types.
An exception to this layout in eukaryotes are genes for histone proteins, which lack introns entirely. Also distinct are the rDNA clusters of structural genes, in which 28S, 5.8S, and 18S sequences are adjacent, separated by short internally transcribed spacers, and likewise the 45S rDNA occurs five distinct places on the genome, but is clustered into adjacent repeats. In eubacteria these genes are organized into operons. However, in archaebacteria these genes are non-adjacent and exhibit no linkage. | 1 | Biochemistry |
On May 9, 2006, a New Drug Application was submitted to the United States Food and Drug Administration (FDA) by Pharmacyclics, Inc.
In December 2007, the FDA issued a not approvable letter for motexafin gadolinium. | 1 | Biochemistry |
The Zeeman effect is utilized in many laser cooling applications such as a magneto-optical trap and the Zeeman slower. | 7 | Physical Chemistry |
While flame and electrothermal vaporizers are the most common atomization techniques, several other atomization methods are utilized for specialized use. | 3 | Analytical Chemistry |
The recrystallization temperature is temperature at which recrystallization can occur for a given material and processing conditions. This is not a set temperature and is dependent upon factors including the following:
* Increasing annealing time decreases recrystallization temperature
* Alloys have higher recrystallization temperatures than pure metals
* Increasing amount of cold work decreases recrystallization temperature
* Smaller cold-worked grain sizes decrease the recrystallization temperature | 8 | Metallurgy |
Isotopomers or isotopic isomers are isomers with isotopic atoms, having the same number of each isotope of each element but differing in their positions in the molecule. The result is that the molecules are either constitutional isomers or stereoisomers solely based on isotopic location. The term isotopomer was first proposed by Seeman and Paine in 1992 to distinguish isotopic isomers from isotopologues (isotopic homologues). | 4 | Stereochemistry |
A symmetry of a pattern is, loosely speaking, a way of transforming the pattern so that it looks exactly the same after the transformation. For example, translational symmetry is present when the pattern can be translated (in other words, shifted) some finite distance and appear unchanged. Think of shifting a set of vertical stripes horizontally by one stripe. The pattern is unchanged. Strictly speaking, a true symmetry only exists in patterns that repeat exactly and continue indefinitely. A set of only, say, five stripes does not have translational symmetry—when shifted, the stripe on one end "disappears" and a new stripe is "added" at the other end. In practice, however, classification is applied to finite patterns, and small imperfections may be ignored.
The types of transformations that are relevant here are called Euclidean plane isometries. For example:
* If one shifts example B one unit to the right, so that each square covers the square that was originally adjacent to it, then the resulting pattern is exactly the same as the starting pattern. This type of symmetry is called a translation. Examples A and C are similar, except that the smallest possible shifts are in diagonal directions.
* If one turns example B clockwise by 90°, around the centre of one of the squares, again one obtains exactly the same pattern. This is called a rotation. Examples A and C also have 90° rotations, although it requires a little more ingenuity to find the correct centre of rotation for C.
* One can also flip example B across a horizontal axis that runs across the middle of the image. This is called a reflection. Example B also has reflections across a vertical axis, and across two diagonal axes. The same can be said for A.
However, example C is different. It only has reflections in horizontal and vertical directions, not across diagonal axes. If one flips across a diagonal line, one does not get the same pattern back, but the original pattern shifted across by a certain distance. This is part of the reason that the wallpaper group of A and B is different from the wallpaper group of C.
Another transformation is "Glide", a combination of reflection and translation parallel to the line of reflection. | 3 | Analytical Chemistry |
N-glycan processing is carried out in endoplasmic reticulum and the Golgi body. Initial trimming of the precursor molecule occurs in the ER and the subsequent processing occurs in the Golgi.
Upon transferring the completed glycan onto the nascent polypeptide, two glucose residues are removed from the structure. Enzymes known as glycosidases remove some sugar residues. These enzymes can break glycosidic linkages by using a water molecule. These enzymes are exoglycosidases as they only work on monosaccharide residues located at the non-reducing end of the glycan. This initial trimming step is thought to act as a quality control step in the ER to monitor protein folding.
Once the protein is folded correctly, two glucose residues are removed by glucosidase I and II. The removal of the final third glucose residue signals that the glycoprotein is ready for transit from the ER to the cis-Golgi. ER mannosidase catalyses the removal of this final glucose. However, if the protein is not folded properly, the glucose residues are not removed and thus the glycoprotein can't leave the endoplasmic reticulum. A chaperone protein (calnexin/calreticulin) binds to the unfolded or partially folded protein to assist protein folding.
The next step involves further addition and removal of sugar residues in the cis-Golgi. These modifications are catalyzed by glycosyltransferases and glycosidases respectively. In the cis-Golgi, a series of mannosidases remove some or all of the four mannose residues in α-1,2 linkages. Whereas in the medial portion of the Golgi, glycosyltransferases add sugar residues to the core glycan structure, giving rise to the three main types of glycans: high mannose, hybrid and complex glycans.
*High-mannose is, in essence, just two N-acetylglucosamines with many mannose residues, often almost as many as are seen in the precursor oligosaccharides before it is attached to the protein.
*Complex oligosaccharides are so named because they can contain almost any number of the other types of saccharides, including more than the original two N-acetylglucosamines.
*Hybrid oligosaccharides contain a mannose residues on one side of the branch, while on the other side a N-acetylglucosamine initiates a complex branch.
The order of addition of sugars to the growing glycan chains is determined by the substrate specificities of the enzymes and their access to the substrate as they move through secretory pathway. Thus, the organization of this machinery within a cell plays an important role in determining which glycans are made. | 0 | Organic Chemistry |
A mixture of racemic acid and meso-tartaric acid is formed when dextro-Tartaric acid is heated in water at 165 °C for about 2 days. meso-Tartaric acid can also be prepared from dibromosuccinic acid using silver hydroxide:
:HOCCHBrCHBrCOH + 2 AgOH → HOCCH(OH)CH(OH)COH + 2 AgBr
meso-Tartaric acid can be separated from residual racemic acid by crystallization, the racemate being less soluble. | 4 | Stereochemistry |
1,3-Bisphosphoglyceric acid (1,3-Bisphosphoglycerate or 1,3BPG) is a 3-carbon organic molecule present in most, if not all, living organisms. It primarily exists as a metabolic intermediate in both glycolysis during respiration and the Calvin cycle during photosynthesis. 1,3BPG is a transitional stage between glycerate 3-phosphate and glyceraldehyde 3-phosphate during the fixation/reduction of CO. 1,3BPG is also a precursor to 2,3-bisphosphoglycerate which in turn is a reaction intermediate in the glycolytic pathway. | 5 | Photochemistry |
Proteins are usually glycated through their lysine residues. In humans, histones in the cell nucleus are richest in lysine, and therefore form the glycated protein N(6)-Carboxymethyllysine (CML).
A receptor nicknamed RAGE, from receptor for advanced glycation end products, is found on many cells, including endothelial cells, smooth muscle, cells of the immune system from tissue such as lung, liver, and kidney. This receptor, when binding AGEs, contributes to age- and diabetes-related chronic inflammatory diseases such as atherosclerosis, asthma, arthritis, myocardial infarction, nephropathy, retinopathy, periodontitis and neuropathy. The pathogenesis of this process hypothesized to activation of the nuclear factor kappa B (NF-κB) following AGE binding. NF-κB controls several genes which are involved in inflammation. AGEs can be detected and quantified using bioanalytical and immunological methods. | 1 | Biochemistry |
Black oxide for copper, sometimes known by the trade name Ebonol C, converts the copper surface to cupric oxide. For the process to work the surface has to have at least 65% copper; for copper surfaces that have less than 90% copper it must first be pretreated with an activating treatment. The finished coating is chemically stable and very adherent. It is stable up to ; above this temperature the coating degrades due to oxidation of the base copper. To increase corrosion resistance, the surface may be oiled, lacquered, or waxed. It is also used as a pre-treatment for painting or enamelling. The surface finish is usually satin, but it can be turned glossy by coating in a clear high-gloss enamel.
On a microscopic scale dendrites form on the surface finish, which trap light and increase absorptivity. Because of this property the coating is used in aerospace, microscopy and other optical applications to minimise light reflection.
In printed circuit boards (PCBs), the use of black oxide provides better adhesion for the fiberglass laminate layers. The PCB is dipped in a bath containing hydroxide, hypochlorite, and cuprate, which becomes depleted in all three components. This indicates that the black copper oxide comes partially from the cuprate and partially from the PCB copper circuitry. Under microscopic examination, there is no copper(I) oxide layer.
An applicable U.S. military specification is MIL-F-495E. | 7 | Physical Chemistry |
The bond length in peroxides is about 1.45 Å, and the angles (R = H, C) are about 110° (water-like). Characteristically, the dihedral angles are about 120°. The bond is relatively weak, with a bond dissociation energy of , less than half the strengths of , , and bonds.
Hydroperoxides are typically more volatile than the corresponding alcohols:
* tert-BuOOH (b.p. 36°C) vs tert-BuOH (b.p. 82-83°C)
* Methyl hydroperoxide| (b.p. 46°C) vs Methanol| (b.p. 65°C)
* cumene hydroperoxide (b.p. 153°C) vs cumyl alcohol (b.p. 202°C) | 0 | Organic Chemistry |
Exome sequencing, also known as whole exome sequencing (WES), is a genomic technique for sequencing all of the protein-coding regions of genes in a genome (known as the exome). It consists of two steps: the first step is to select only the subset of DNA that encodes proteins. These regions are known as exons—humans have about 180,000 exons, constituting about 1% of the human genome, or approximately 30 million base pairs. The second step is to sequence the exonic DNA using any high-throughput DNA sequencing technology.
The goal of this approach is to identify genetic variants that alter protein sequences, and to do this at a much lower cost than whole-genome sequencing. Since these variants can be responsible for both Mendelian and common polygenic diseases, such as Alzheimer's disease, whole exome sequencing has been applied both in academic research and as a clinical diagnostic. | 1 | Biochemistry |
As in any power cycle, the most important indicator of its performance is the thermal efficiency. The thermal efficiency of a transcritical cycle is computed as:
where is the thermal input of the cycle, provided by either combustion or with a heat exchanger, and is the power produced by the cycle.
The power produced is considered comprehensive of the produced power during the expansion process of the working fluid and the one consumed during the compression step.
The typical conceptual configuration of a transcritical cycle employs a single heater, thanks to the absence of drastic phase change from one state to another, being the pressure above the critical one. In subcritical cycles, instead, the heating process of the working fluid occurs in three different heat exchangers: in economizers the working fluid is heated (while remaining in the liquid phase) up to a condition approaching the saturated liquid conditions. Evaporators accomplish fluid evaporation process (typically up to the saturated vapour conditions) and in superheaters the working fluid is heated form the saturated vapour conditions to a superheated vapor. Moreover, using Rankine cycles as bottoming cycles in the context of combined gas-steam cycles keeps the configuration of the former ones as always subcritical. Therefore, there will be multiple pressure levels and hence multiple evaporators, economizers and superheaters, which introduces a significant complication to the heat injection process in the cycle. | 7 | Physical Chemistry |
Along with dissolved organic matter, POM drives the lower aquatic food web by providing energy in the form of carbohydrates, sugars, and other polymers that can be degraded. POM in water bodies is derived from terrestrial inputs (e.g. soil organic matter, leaf litterfall), submerged or floating aquatic vegetation, or autochthonous production of algae (living or detrital). Each source of POM has its own chemical composition that affects its lability, or accessibility to the food web. Algal-derived POM is thought to be most labile, but there is growing evidence that terrestrially-derived POM can supplement the diets of micro-organisms such as zooplankton when primary productivity is limited. | 9 | Geochemistry |
Commonly silylation of alcohols requires a silyl chloride and an amine base. One reliable and rapid procedure is the Corey protocol in which the alcohol is reacted with a silyl chloride and imidazole at high concentration in DMF. If DMF is replaced by dichloromethane, the reaction is somewhat slower, but the purification of the compound is simplified. A common hindered base for use with silyl triflates is 2,6-lutidine. Primary alcohols can be protected in less than one hour while some hindered alcohols may require days of reaction time.
When using a silyl chloride, no special precautions are usually required, except for the exclusion of large amounts of water. An excess of silyl chloride can be employed but is not necessary. If excess reagent is used, the product will require flash chromatography to remove excess silanol and siloxane.
Sometimes silyl triflate and a hindered amine base are used. Silyl triflates are more reactive than their corresponding chlorides, so they can be used to install silyl groups onto hindered positions. Silyl triflate is more reactive and also converts ketones to silyl enol ethers. Silyl triflates are water sensitive and must be run under inert atmosphere conditions. Purification involves the addition of an aqueous acid such as saturated ammonium chloride solution. Water quenches remaining silyl reagent and protonates amine bases prior to their removal from the reaction mixture. Following extraction, the product can be purified by flash chromatography.
Ketones react with hydrosilanes in the presence of metal catalysts. | 0 | Organic Chemistry |
A knot is called achiral if it can be continuously deformed into its mirror image, otherwise it is called a chiral knot. For example, the unknot and the figure-eight knot are achiral, whereas the trefoil knot is chiral. | 4 | Stereochemistry |
In electrochemistry differential capacitance is a parameter introduced for characterizing electrical double layers:
where σ is surface charge and ψ is electric surface potential.
Capacitance is usually defined as the stored charge between two conducting surfaces separated by a dielectric divided by the voltage between the surfaces. Another definition is the rate of change of the stored charge or surface charge (σ) divided by the rate of change of the voltage between the surfaces or the electric surface potential (ψ). The latter is called the "differential capacitance," but usually the stored charge is directly proportional to the voltage, making the capacitances given by the two definitions equal.
This type of differential capacitance may be called "parallel plate capacitance," after the usual form of the capacitor. However, the term is meaningful when applied to any two conducting bodies such as spheres, and not necessarily ones of the same size, for example, the elevated terminals of a Tesla wireless system and the earth. These are widely spaced insulated conducting bodies positioned over a spherically conducting ground plane.
Another form of differential capacitance refers to single isolated conducting bodies. It is usually discussed in books under the topic of "electrostatics." This capacitance is best defined as the rate of change of charge stored in the body divided by the rate of change of the potential of the body. The definition of the absolute potential of the body depends on what is selected as a reference. This is sometimes referred to as the "self-capacitance" of a body. If the body is a conducting sphere, the self-capacitance is proportional to its radius, and is roughly 1pF per centimetre of radius. | 7 | Physical Chemistry |
In organic chemistry, an aryl is any functional group or substituent derived from an aromatic ring, usually an aromatic hydrocarbon, such as phenyl and naphthyl. "Aryl" is used for the sake of abbreviation or generalization, and "Ar" is used as a placeholder for the aryl group in chemical structure diagrams, analogous to “R” used for any organic substituent. “Ar” is not to be confused with the elemental symbol for argon.
A simple aryl group is phenyl (), a group derived from benzene. Examples of other aryl groups consist of:
* The tolyl group () which is derived from toluene (methylbenzene)
* The xylyl group (), which is derived from xylene (dimethylbenzene)
* The naphthyl group (), which is derived from naphthalene
Arylation is the process in which an aryl group is attached to a substituent. It is typically achieved by cross-coupling reactions. | 0 | Organic Chemistry |
Neurodegeneration is classified as a massive death of neurons, and encompasses diseases such as Alzheimers, Parkinsons, and Huntingtons. Although many cells die due to necrosis, many cells in neurodegenerative disorders are killed via the apoptotic pathway. Excitotoxicity, which involves overstimulation of a cell via its glutamate receptors, is one of the major processes which can initiate cell death. Other inducers include mitochondrial dysfunction, oxidative stress, and abnormal protein aggregation. Surprisingly, both necrotic and apoptotic processes utilize a similar intracellular signaling cascade which uses caspase proteins to induce cell death. Abnormal protein accumulation causes Alzheimers, Parkinsons, and Huntingtons diseases. | 1 | Biochemistry |
Hammond's postulate can be used to examine the structure of the transition states of a SN1 reaction. In particular, the dissociation of the leaving group is the first transition state in a S1 reaction. The stabilities of the carbocations formed by this dissociation are known to follow the trend tertiary > secondary > primary > methyl.
Therefore, since the tertiary carbocation is relatively stable and therefore close in energy to the R-X reactant, then the tertiary transition state will have a structure that is fairly similar to the R-X reactant. In terms of the graph of reaction coordinate versus energy, this is shown by the fact that the tertiary transition state is further to the left than the other transition states. In contrast, the energy of a methyl carbocation is very high, and therefore the structure of the transition state is more similar to the intermediate carbocation than to the R-X reactant. Accordingly, the methyl transition state is very far to the right. | 7 | Physical Chemistry |
# Leave out the Bravais type
# Convert all symmetry elements with translational components into their respective symmetry elements without translation symmetry (Glide planes are converted into simple mirror planes; Screw axes are converted into simple axes of rotation)
# Axes of rotation, rotoinversion axes and mirror planes remain unchanged. | 4 | Stereochemistry |
This information can then be used to measure velocity or path length, or as a way to learn about the particle or medium's properties (such as composition or flow rate). The traveling object may be detected directly (direct time of flight, dToF, e.g., via an ion detector in mass spectrometry) or indirectly (indirect time of flight, iToF, e.g., by light scattered from an object in laser doppler velocimetry). Time of flight technology has found valuable applications in the monitoring and characterization of material and biomaterials, hydrogels included. | 7 | Physical Chemistry |
Examples of the application of ICP-AES include the determination of metals in wine, arsenic in food, and trace elements bound to proteins. ICP-AES methods are used to test for metals contamination in drinking water and wastewater.
ICP-AES is widely used in minerals processing to provide the data on grades of various streams, for the construction of mass balances.
In 2008, the technique was used at Liverpool University to demonstrate that a Chi Rho amulet found in Shepton Mallet and previously believed to be among the earliest evidence of Christianity in England, only dated to the nineteenth century.
ICP-AES is often used for analysis of trace elements in soil, and it is for that reason it is often used in forensics to ascertain the origin of soil samples found at crime scenes or on victims etc. Taking one sample from a control and determining the metal composition and taking the sample obtained from evidence and determine that metal composition allows a comparison to be made. While soil evidence may not stand alone in court it certainly strengthens other evidence.
It is also fast becoming the analytical method of choice for the determination of nutrient levels in agricultural soils. This information is then used to calculate the amount of fertiliser required to maximise crop yield and quality.
ICP-AES is used for motor oil analysis. Analyzing used motor oil reveals a great deal about how the engine is operating. Parts that wear in the engine will deposit traces in the oil which can be detected with ICP-AES. ICP-AES analysis can help to determine whether parts are failing. In addition, ICP-AES can determine what amount of certain oil additives remain and therefore indicate how much service life the oil has remaining. Oil analysis is often used by fleet manager or automotive enthusiasts who have an interest in finding out as much about their engine's operation as possible. ICP-AES is also used during the production of motor oils (and other lubricating oils) for quality control and compliance with production and industry specifications. | 3 | Analytical Chemistry |
Group I and group II introns are found in genes encoding proteins (messenger RNA), transfer RNA and ribosomal RNA in a very wide range of living organisms. Following transcription into RNA, group I and group II introns also make extensive internal interactions that allow them to fold into a specific, complex three-dimensional architecture. These complex architectures allow some group I and group II introns to be self-splicing, that is, the intron-containing RNA molecule can rearrange its own covalent structure so as to precisely remove the intron and link the exons together in the correct order. In some cases, particular intron-binding proteins are involved in splicing, acting in such a way that they assist the intron in folding into the three-dimensional structure that is necessary for self-splicing activity. Group I and group II introns are distinguished by different sets of internal conserved sequences and folded structures, and by the fact that splicing of RNA molecules containing group II introns generates branched introns (like those of spliceosomal RNAs), while group I introns use a non-encoded guanosine nucleotide (typically GTP) to initiate splicing, adding it on to the 5'-end of the excised intron. | 1 | Biochemistry |
In SKP the probe and sample are held parallel to each other and electrically connected to form a parallel plate capacitor. The probe is selected to be of a different material to the sample, therefore each component initially has a distinct Fermi level. When electrical connection is made between the probe and the sample electron flow can occur between the probe and the sample in the direction of the higher to the lower Fermi level. This electron flow causes the equilibration of the probe and sample Fermi levels. Furthermore, a surface charge develops on the probe and the sample, with a related potential difference known as the contact potential (V). In SKP the probe is vibrated along a perpendicular to the plane of the sample. This vibration causes a change in probe to sample distance, which in turn results in the flow of current, taking the form of an ac sine wave. The resulting ac sine wave is demodulated to a dc signal through the use of a lock-in amplifier. Typically the user must select the correct reference phase value used by the lock-in amplifier. Once the dc potential has been determined, an external potential, known as the backing potential (V) can be applied to null the charge between the probe and the sample. When the charge is nullified, the Fermi level of the sample returns to its original position. This means that V is equal to -V, which is the work function difference between the SKP probe and the sample measured.
The cantilever in the AFM is a reference electrode that forms a capacitor with the surface, over which it is scanned laterally at a constant separation. The cantilever is not piezoelectrically driven at its mechanical resonance frequency ω as in normal AFM although an alternating current (AC) voltage is applied at this frequency.
When there is a direct-current (DC) potential difference between the tip and the surface, the AC+DC voltage offset will cause the cantilever to vibrate. The origin of the force can be understood by considering that the energy of the capacitor formed by the cantilever and the surface is
plus terms at DC. Only the cross-term proportional to the V·V product is at the resonance frequency ω. The resulting vibration of the cantilever is detected using usual scanned-probe microscopy methods (typically involving a diode laser and a four-quadrant detector). A null circuit is used to drive the DC potential of the tip to a value which minimizes the vibration. A map of this nulling DC potential versus the lateral position coordinate therefore produces an image of the work function of the surface.
A related technique, electrostatic force microscopy (EFM), directly measures the force produced on a charged tip by the electric field emanating from the surface. EFM operates much like magnetic force microscopy in that the frequency shift or amplitude change of the cantilever oscillation is used to detect the electric field. However, EFM is much more sensitive to topographic artifacts than KPFM. Both EFM and KPFM require the use of conductive cantilevers, typically metal-coated silicon or silicon nitride. Another AFM-based technique for the imaging of electrostatic surface potentials, scanning quantum dot microscopy, quantifies surface potentials based on their ability to gate a tip-attached quantum dot. | 7 | Physical Chemistry |
Internal corrosion is occasioned by the combined effects and severity of four modes of material deterioration, namely: general corrosion, pitting corrosion, microbial corrosion, and fluid corrosivity. The same principals of external corrosion control can be applied to internal corrosion but due to accessibility, the approaches can be different. Thus special instruments for internal corrosion control and inspection are used that are not used in external corrosion control. Video scoping of pipes and high tech smart pigs are used for internal inspections. The smart pigs can be inserted into a pipe system at one point and "caught" far down the line. The use of corrosion inhibitors, material selection, and internal coatings are mainly used to control corrosion in piping while anodes along with coatings are used to control corrosion in tanks.
Internal corrosion challenges apply to the following amongst others: Water pipes; Gas pipes; Oil pipes and Water tank reservoirs. | 8 | Metallurgy |
A single antigen can be thought of as a sequence of multiple overlapping epitopes. Many unique B cell clones may be able to bind to the individual epitopes. This imparts even greater multiplicity to the overall response. All of these B cells can become activated and produce large colonies of plasma cell clones, each of which can secrete up to 1000 antibody molecules against each epitope per second. | 1 | Biochemistry |
A common sulfonyl hydrazide is p-toluenesulfonyl hydrazide, a white air-stable solid. They are also widely used as organic reagents.
Toluenesulfonyl hydrazide is used to generate toluenesulfonyl hydrazones. When derived from ketones, these hydrazones participate in the Shapiro reaction and the Eschenmoser–Tanabe fragmentation.
2,4,6-Triisopropylbenzenesulfonylhydrazide is a useful source of diimide. | 0 | Organic Chemistry |
Single-cell AMTECs with open voltages as high as 1.55 V and maximum power density as high as 0.50 W/cm of solid electrolyte area at a temperature of 1173 K (900 °C) have been obtained with long-term stable refractory metal electrodes.
Efficiency of AMTEC cells has reached 16% in the laboratory. High-voltage multi-tube modules are predicted to have 20–25% efficiency, and power densities up to 0.2 kW/L appear to be achievable in the near future. Calculations show that replacing sodium with a potassium working fluid increases the peak efficiency from 28% to 31% at 1100 K with a 1 mm thick BASE tube.
Most work on AMTECs has concerned sodium working fluid devices. Potassium AMTECs have been run with potassium beta″-alumina solid electrolyte ceramics and show improved power at lower operating temperatures compared to sodium AMTECs.
A detailed quantitative model of the mass transport and interfacial kinetics behavior of AMTEC electrodes has been developed and used to fit and analyze the performance of a wide variety of electrodes, and to make predictions of the performance of optimized electrodes. The interfacial electrochemical kinetics can be further described quantitatively with a tunneling, diffusion, and desorption model. A reversible thermodynamic cycle for AMTEC shows that it is, at best, slightly less efficient than a Carnot cycle.
A related technology, the Johnson thermoelectric energy converter, uses a similar concept of pumping positive ions through an ion-selective membrane, using hydrogen rather than an alkali metal as the working fluid. | 7 | Physical Chemistry |
Tramadol is marketed as a racemic mixture of both R- and S-stereoisomers, because the two isomers complement each other's analgesic activities. The (+)-isomer is predominantly active as an opiate with a higher affinity for the µ-opiate receptor (20 times higher affinity than the (-)-isomer). | 4 | Stereochemistry |
BOGS was formed in 1987. The founding members were Prof G.A. Wolff (University of Liverpool),
Dr G.D. Abbott (Newcastle University), Dr J. McEvoy (then at University of Bangor) and Prof S.J. Rowland (University of Plymouth). | 9 | Geochemistry |
In April of 2022, Pfizer voluntarily recalled five batches of the drug because of the presence of a nitrosamine, NNitroso-quinapril. Testing found that the amount of nitrosamines was above the acceptable daily intake level (all humans are exposed to nitrosamines up to a certain daily level by cured and grilled meats, water, dairy products, and vegetables) set by the U.S.'s Food and Drug Administration (FDA). Though long-term ingestion of NNitroso-quinapril potentially might cause cancer in some individuals, there is not believed to be an imminent risk of harm. | 4 | Stereochemistry |
In thermodynamic terms, all organic tissues are composed of chemical energy, which, when not maintained by the constant biochemical maintenance of the living organism, begin to chemically break down due to the reaction with water into amino acids, known as hydrolysis. The breakdown of the proteins of a decomposing body is a spontaneous process. Protein hydrolysis is accelerated as the anaerobic bacteria of the digestive tract consume, digest, and excrete the cellular proteins of the body.
The bacterial digestion of the cellular proteins weakens the tissues of the body. As the proteins are continuously broken down to smaller components, the bacteria excrete gases and organic compounds, such as the functional-group amines putrescine (from ornithine) and cadaverine (from lysine), which carry the noxious odor of rotten flesh. Initially, the gases of putrefaction are constrained within the body cavities, but eventually diffuse through the adjacent tissues, and then into the circulatory system. Once in the blood vessels, the putrid gases infiltrate and diffuse to other parts of the body and the limbs.
The visual result of gaseous tissue-infiltration is notable bloating of the torso and limbs. The increased internal pressure of the continually rising volume of gas further stresses, weakens, and separates the tissues constraining the gas. In the course of putrefaction, the skin tissues of the body eventually rupture and release the bacterial gas. As the anaerobic bacteria continue consuming, digesting, and excreting the tissue proteins, the body's decomposition progresses to the stage of skeletonization. This continued consumption also results in the production of ethanol by the bacteria, which can make it difficult to determine the blood alcohol content (BAC) in autopsies, particularly in bodies recovered from water.
Generally, the term decomposition encompasses the biochemical processes that occur from the physical death of the person (or animal) until the skeletonization of the body. Putrefaction is one of seven stages of decomposition; as such, the term putrescible identifies all organic matter (animal and human) that is biochemically subject to putrefaction. In the matter of death by poisoning, the putrefaction of the body is chemically delayed by poisons such as antimony, arsenic, carbolic acid (phenol), nux vomica (plant), strychnine (pesticide), and zinc chloride. | 1 | Biochemistry |
A variety of parameters are considered when designing and conducting RNA-Seq experiments:
* Tissue specificity: Gene expression varies within and between tissues, and RNA-Seq measures this mix of cell types. This may make it difficult to isolate the biological mechanism of interest. Single cell sequencing can be used to study each cell individually, mitigating this issue.
* Time dependence: Gene expression changes over time, and RNA-Seq only takes a snapshot. Time course experiments can be performed to observe changes in the transcriptome.
* Coverage (also known as depth): RNA harbors the same mutations observed in DNA, and detection requires deeper coverage. With high enough coverage, RNA-Seq can be used to estimate the expression of each allele. This may provide insight into phenomena such as imprinting or cis-regulatory effects. The depth of sequencing required for specific applications can be extrapolated from a pilot experiment.
* Data generation artifacts (also known as technical variance): The reagents (e.g., library preparation kit), personnel involved, and type of sequencer (e.g., Illumina, Pacific Biosciences) can result in technical artifacts that might be mis-interpreted as meaningful results. As with any scientific experiment, it is prudent to conduct RNA-Seq in a well controlled setting. If this is not possible or the study is a meta-analysis, another solution is to detect technical artifacts by inferring latent variables (typically principal component analysis or factor analysis) and subsequently correcting for these variables.
* Data management: A single RNA-Seq experiment in humans is usually 1-5 Gb (compressed), or more when including intermediate files. This large volume of data can pose storage issues. One solution is compressing the data using multi-purpose computational schemas (e.g., gzip) or genomics-specific schemas. The latter can be based on reference sequences or de novo. Another solution is to perform microarray experiments, which may be sufficient for hypothesis-driven work or replication studies (as opposed to exploratory research). | 1 | Biochemistry |
The ideality factor (also called the emissivity factor) is a fitting parameter that describes how closely the diode's behavior matches that predicted by theory, which assumes the p-n junction of the diode is an infinite plane and no recombination occurs within the space-charge region. A perfect match to theory is indicated when . When recombination in the space-charge region dominate other recombination, however, . The effect of changing ideality factor independently of all other parameters is shown for a crystalline silicon solar cell in the I-V curves displayed in the figure to the right.
Most solar cells, which are quite large compared to conventional diodes, well approximate an infinite plane and will usually exhibit near-ideal behavior under standard test conditions (). Under certain operating conditions, however, device operation may be dominated by recombination in the space-charge region. This is characterized by a significant increase in I as well as an increase in ideality factor to . The latter tends to increase solar cell output voltage while the former acts to erode it. The net effect, therefore, is a combination of the increase in voltage shown for increasing n in the figure to the right and the decrease in voltage shown for increasing I in the figure above. Typically, I is the more significant factor and the result is a reduction in voltage.
Sometimes, the ideality factor is observed to be greater than 2, which is generally attributed to the presence of Schottky diode or heterojunction in the solar cell. The presence of a heterojunction offset reduces the collection efficiency of the solar cell and may contribute to low fill-factor. | 7 | Physical Chemistry |
Depending on the organism, an archaeon may use a bacteria-like HU system or a eukaryote-like nucleosome system for packaging. | 1 | Biochemistry |
*1996 – A. R. Day Award (ACS Philadelphia Section award)
*1997 – Chemical Society of Japan Award
*1998 – Herbert N. McCoy Award
*1998 – American Chemical Society Award for Organometallic Chemistry
*1998–2000 – Alexander von Humboldt Senior Researcher Award
*2003 – Sigma Xi Award, Purdue University
*2007 – Yamada–Koga Prize
*2007 – Gold Medal of Charles University, Prague, Czech Republic
*2010 – Nobel Prize in Chemistry
*2010 – ACS Award for Creative Work in Synthetic Organic Chemistry
*2015 – Fray International Sustainability Award, SIPS 2015 | 0 | Organic Chemistry |
In the first paper on AFM-based infrared by Hammiche et al., the relevant well-established theoretical considerations were outlined that predict that high spatial resolution can be achieved using rapid modulation frequencies because of the consequent reduction in the thermal diffusion length. They estimated that spatial resolutions in the range of 20 nm-30 nm should be achievable. The most readily available sources that can achieve high modulation frequencies are pulsed lasers: even when the rapidity of the pulses is not high, the square wave form of a pulse contains very high modulation frequencies in Fourier space. In 2001, Hammiche et al. used a type of bench-top tuneable, pulsed infrared laser known as an optical parametric oscillator or OPO and obtained the first probe-based infrared spectrum with a pulsed laser, however, they did not report any images.
Nanoscale spatial resolution AFM-IR imaging using a pulsed laser was first demonstrated by Dazzi et al at the University of Paris-Sud, France. Dazzi and his colleagues used a wavelength-tuneable, free electron laser at the CLIO facility in Orsay, France to provide an infrared source with short pulses. Like earlier workers, they used a conventional AFM probe to measure thermal expansion but introduced a novel optical configuration: the sample was mounted on an IR-transparent prism so that it could be excited by an evanescent wave. Absorption of short infrared laser pulses by the sample caused rapid thermal expansion that created a force impulse at the tip of the AFM cantilever. The thermal expansion pulse induced transient resonant oscillations of the AFM cantilever probe. This has led to the technique being dubbed Photo-Thermal Induced Resonance (PTIR), by some workers in the field. Some prefer the terms PTIR or PTMS to AFM-IR as the technique is not necessarily restricted to infrared wavelengths. The amplitude of the cantilever oscillation is directly related to the amount of infrared radiation absorbed by the sample. By measuring the cantilever oscillation amplitude as a function of wavenumber, Dazzi's group was able to obtain absorption spectra from nanoscale regions of the sample. Compared to earlier work, this approach improved spatial resolution because the use of short laser pulses reduced the duration of the thermal expansion pulse to the point that the thermal diffusion lengths can be on the scale of nanometres rather than microns.
A key advantage of the use of a tuneable laser source, with a narrow wavelength range, is the ability to rapidly map the locations of specific chemical components on the sample surface. To achieve this, Dazzis group tuned their free electron laser source to a wavelength corresponding to the molecular vibration of the chemical of interest, then mapped the cantilever oscillation amplitude as function of position across the sample. They demonstrated the ability to map chemical composition in E. coli bacteria. They could also visualize polyhydroxybutyrate (PHB) vesicles inside Rhodobacter capsulatus' cells and monitor the efficiency of PHB production by the cells.
At the University of East Anglia in the UK, as part of an EPSRC-funded project led by M. Reading and S. Meech, Hill and his co-workers followed the earlier work of Reading et al. and Hammiche et al. and measured thermal expansion using an optical configuration that illuminated the sample from above in contrast to Dazzi et al. who excited the sample with an evanescent wave from below. Hill also made use of an optical parametric oscillator as the infrared source in the manner of Hammiche et al. This novel combination of topside illumination, OPO source and measuring thermal expansion proved capable of nanoscale spatial resolution for infrared imaging and spectroscopy (the figures show a schematic of the UEA apparatus and results obtained with it). The use by Hill and co-workers of illumination from above allowed a substantially wider range of samples to be studied than was possible using Dazzi's technique. By introducing the use of a bench top IR source and topdown illumination, the work of Hammiche, Hill and their coworkers made possible the first commercially viable SPM-based infrared instrument (see Commercialization). | 3 | Analytical Chemistry |
Photosensitization, i.e., photochemical sensitization. Exposing dyed cellulosic material, such as plant-based fibers, to sunlight allows dyes to remove hydrogen from the cellulose, resulting in photoreduction on the cellulosic substrate. Simultaneously, the colorant will undergo oxidation in the presence of the atmospheric oxygen, resulting in photo-oxidation of the colourant. These processes result in both fading of the colorant and strength loss of the substrate. | 5 | Photochemistry |
Transfection is the process of deliberately introducing naked or purified nucleic acids into eukaryotic cells. It may also refer to other methods and cell types, although other terms are often preferred: "transformation" is typically used to describe non-viral DNA transfer in bacteria and non-animal eukaryotic cells, including plant cells. In animal cells, transfection is the preferred term as transformation is also used to refer to progression to a cancerous state (carcinogenesis) in these cells. Transduction is often used to describe virus-mediated gene transfer into eukaryotic cells.
The word transfection is a portmanteau of trans- and infection. Genetic material (such as supercoiled plasmid DNA or siRNA constructs), may be transfected. Transfection of animal cells typically involves opening transient pores or "holes" in the cell membrane to allow the uptake of material. Transfection can be carried out using calcium phosphate (i.e. tricalcium phosphate), by electroporation, by cell squeezing, or by mixing a cationic lipid with the material to produce liposomes that fuse with the cell membrane and deposit their cargo inside.
Transfection can result in unexpected morphologies and abnormalities in target cells. | 1 | Biochemistry |
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