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In many research labs, the use of asbestos gloves is required when operating the furnace because it can reach very high temperatures. The use of face masks is also recommended at higher temperatures to ensure the safety of researchers and junior lab members. It is also recommended that researchers performing the LOI procedure remove all jewelry and watches as they are excellent conductors of heat. When removing samples at high temperatures, these accessories can easily heat up and result in burns. | 3 | Analytical Chemistry |
Photopolymers can be used to generate printing plates, which are then pressed onto paper-like metal type. This is often used in modern fine printing to achieve the effect of embossing (or the more subtly three-dimensional effect of letterpress printing) from designs created on a computer without needing to engrave designs into metal or cast metal type. It is often used for business cards. | 5 | Photochemistry |
* Orbifold signature:
* Coxeter notation: [∞,2,∞] or [∞,2,∞]
* Lattice: rhombic
* Point group: D
* The group cm contains no rotations. It has reflection axes, all parallel. There is at least one glide reflection whose axis is not a reflection axis; it is halfway between two adjacent parallel reflection axes.
*This group applies for symmetrically staggered rows (i.e. there is a shift per row of half the translation distance inside the rows) of identical objects, which have a symmetry axis perpendicular to the rows.
;Examples of group cm | 3 | Analytical Chemistry |
Macromolecular crystallography was preceded by the older field of small-molecule x-ray crystallography (for structures with less than a few hundred atoms). Small-molecule diffraction data extends to much higher resolution than feasible for macromolecules, and has a very clean mathematical relationship between the data and the atomic model. The residual, or R-factor, measures the agreement between the experimental data and the values back-calculated from the atomic model. For a well-determined small-molecule structure the R-factor is nearly as small as the uncertainty in the experimental data (well under 5%). Therefore, that one test by itself provides most of the validation needed, but a number of additional consistency and methodology checks are done by automated software as a requirement for small-molecule crystal structure papers submitted to the International Union of Crystallography (IUCr) journals such as Acta Crystallographica section B or C. Atomic coordinates of these small-molecule structures are archived and accessed through the Cambridge Structural Database (CSD) or the Crystallography Open Database (COD).
The first macromolecular validation software was developed around 1990, for proteins. It included Rfree cross-validation for model-to-data match, bond length and angle parameters for covalent geometry, and sidechain and backbone conformational criteria. For macromolecular structures, the atomic models are deposited in the Protein Data Bank (PDB), still the single archive of this data. The PDB was established in the 1970s at Brookhaven National Laboratory, moved in 2000 to the [http://www.rcsb.org/pdb RCSB] (Research Collaboration for Structural Biology) centered at Rutgers, and expanded in 2003 to become the [http://www.wwpdb.org/ wwPDB] (worldwide Protein Data Bank), with access sites added in Europe ([http://pdbe.org|PDBe]) and Asia ([http://www.pdbj.org|PDBj]), and with NMR data handled at the [http://www.bmrb.wisc.edu BioMagResBank (BMRB)] in Wisconsin.
Validation rapidly became standard in the field, with further developments described below. *Obviously needs expansion*
A large boost was given to the applicability of comprehensive validation for both x-ray and NMR as of February 1, 2008, when the worldwide Protein Data Bank (wwPDB) made mandatory the deposition of experimental data along with atomic coordinates. Since 2012 strong forms of validation have been in the process of being adopted for [http://www.wwpdb.org/validation.html wwPDB deposition] from recommendations of the wwPDB Validation Task Force committees for x-ray crystallography, for NMR, for SAXS (small-angle x-ray scattering), and for cryoEM (cryo-Electron Microscopy). | 1 | Biochemistry |
mTOR inhibitors may be useful for treating/preventing several age-associated conditions, including neurodegenerative diseases such as Alzheimers disease and Parkinsons disease. After a short-term treatment with the mTOR inhibitors dactolisib and everolimus, in elderly (65 and older), treated subjects had a reduced number of infections over the course of a year.
Various natural compounds, including epigallocatechin gallate (EGCG), caffeine, curcumin, berberine, quercetin, resveratrol and pterostilbene, have been reported to inhibit mTOR when applied to isolated cells in culture. As yet no high quality evidence exists that these substances inhibit mTOR signaling or extend lifespan when taken as dietary supplements by humans, despite encouraging results in animals such as fruit flies and mice. Various trials are ongoing. | 1 | Biochemistry |
Prokaryotes use one type of RNA polymerase, transcribing mRNAs that code for more than one type of protein. Transcription, translation and mRNA degradation all happen simultaneously. Transcription termination is essential to define boundaries in transcriptional units, a function necessary to maintain the integrity of the strands and provide quality control. Termination in E. coli may be Rho dependent, utilizing Rho factor, or Rho independent, also known as intrinsic termination. Although most operons in DNA are Rho independent, Rho dependent termination is also essential to maintain correct transcription.
ρ factor
The Rho protein is an RNA translocase that recognizes a cytosine-rich region of the elongating mRNA, but the exact features of the recognized sequences and how the cleaving takes place remain unknown. Rho forms a ring-shaped hexamer and advances along the mRNA, hydrolyzing ATP toward RNA polymerase (5 to 3 with respect to the mRNA). When the Rho protein reaches the RNA polymerase complex, transcription is terminated by dissociation of the RNA polymerase from the DNA. The structure and activity of the Rho protein is similar to that of the F subunit of ATP synthase, supporting the theory that the two share an evolutionary link.
Rho factor is widely present in different bacterial sequences and is responsible for the genetic polarity in E. coli. It works as a sensor of translational status, inhibiting non-productive transcriptions, suppressing antisense transcriptions and resolving conflicts that happen between transcription and replication. The process of termination by Rho factor is regulated by attenuation and antitermination mechanisms, competing with elongation factors for overlapping utilization sites (ruts and nuts), and depends on how fast Rho can move during the transcription to catch up with the RNA polymerase and activate the termination process.
Inhibition of Rho dependent termination by bicyclomycin is used to treat bacterial infections. The use of this mechanism along with other classes of antibiotics is being studied as a way to address antibiotic resistance, by suppressing the protective factors in RNA transcription while working in synergy with other inhibitors of gene expression such as tetracycline or rifampicin. | 1 | Biochemistry |
The endocannabinoid system, broadly speaking, includes:
* The endogenous arachidonate-based lipids, anandamide (N-arachidonoylethanolamide) and 2-AG, besides other N-acylethanolamines (NAEs); these are known as "endocannabinoids" and are physiological ligands for the cannabinoid receptors. Endocannabinoids are all eicosanoids.
* The enzymes that synthesize and degrade the endocannabinoids, such as fatty acid amide hydrolase or monoacylglycerol lipase.
* The cannabinoid receptors CB and CB, two G protein-coupled receptors that are located in the central and peripheral nervous systems.
The neurons, neural pathways, and other cells where these molecules, enzymes, and one or both cannabinoid receptor types are all colocalized collectively comprise the endocannabinoid system.
The endocannabinoid system has been studied using genetic and pharmacological methods. These studies have revealed that cannabinoids act as neuromodulators for a variety of processes, including motor learning, appetite, and pain sensation, among other cognitive and physical processes. The localization of the CB1 receptor in the endocannabinoid system has a very large degree of overlap with the orexinergic projection system, which mediates many of the same functions, both physical and cognitive. Moreover, CB1 is colocalized on orexin projection neurons in the lateral hypothalamus and many output structures of the orexin system, where the CB1 and orexin receptor 1 (OX1) receptors physically and functionally join to form the CB1–OX1 receptor heterodimer. | 1 | Biochemistry |
NAD kinase (EC 2.7.1.23, NADK) is an enzyme that converts nicotinamide adenine dinucleotide (NAD) into NADP through phosphorylating the NAD coenzyme. NADP is an essential coenzyme that is reduced to NADPH primarily by the pentose phosphate pathway to provide reducing power in biosynthetic processes such as fatty acid biosynthesis and nucleotide synthesis. The structure of the NADK from the archaean Archaeoglobus fulgidus has been determined.
In humans, the genes NADK and MNADK encode NAD kinases localized in cytosol and mitochondria, respectively. Similarly, yeast have both cytosolic and mitochondrial isoforms, and the yeast mitochondrial isoform accepts both NAD and NADH as substrates for phosphorylation. | 1 | Biochemistry |
The reactive enodiolate species is also sensitive to oxygen (O), which results in the dual carboxylase / oxygenase activity of RuBisCO. This reaction is considered wasteful as it produces products (3-phosphoglycerate and 2-phosphoglycolate) that must be catabolized through photorespiration. This process requires energy and is a missed-opportunity for CO fixation, which results in the net loss of carbon fixation efficiency for the organism. The dual carboxylase / oxygenase activity of RuBisCO is exacerbated by the fact that O and CO are small, relatively indistinguishable molecules that can bind only weakly, if at all, in Michaelis-Menten complexes. There are four forms of RuBisCO (Form I, II, III, and IV), with Form I being the most abundantly used form. Form I is used extensively by higher plants, eukaryotic algae, cyanobacteria, and Pseudomonadota (formerly proteobacteria). Form II is also used but much less widespread, and can be found in some species of Pseudomonadota and in dinoflagellates. RuBisCOs from different photosynthetic organisms display varying abilities to distinguish between CO and O. This property can be quantified and is termed "specificity" (S). A higher value of S means that a RuBisCO's carboxylase activity is greater than its oxygenase activity. | 7 | Physical Chemistry |
The microarray—the dense, two-dimensional grid of biosensors—is the critical component of a biochip platform. Typically, the sensors are deposited on a flat substrate, which may either be passive (e.g. silicon or glass) or active, the latter
consisting of integrated electronics or micromechanical devices that perform or assist signal transduction. Surface chemistry is used to covalently bind the sensor molecules to the substrate medium. The fabrication of microarrays is non-trivial and is a major economic and technological hurdle that may ultimately decide the success of future biochip platforms. The primary manufacturing challenge is the process of placing each sensor at a specific position (typically on a Cartesian grid) on the substrate. Various means exist to achieve the placement, but typically robotic micro-pipetting or micro-printing systems are used to place tiny spots of sensor material on the chip surface. Because each sensor is unique, only a few spots can be placed at a time. The low-throughput nature of this
process results in high manufacturing costs.
Fodor and colleagues developed a unique fabrication process (later used by Affymetrix) in which a series of microlithography steps is used to combinatorially synthesize hundreds of thousands of unique, single-stranded DNA sensors on a substrate one nucleotide at a time. One lithography step is needed per base type; thus, a total of four steps is required per nucleotide level. Although this technique is very powerful in that many sensors can be created simultaneously, it is currently only feasible for creating short DNA strands (15–25 nucleotides). Reliability and cost factors limit the number of photolithography steps that can be done. Furthermore, light-directed combinatorial synthesis techniques are not currently possible for proteins or other sensing molecules.
As noted above, most microarrays consist of a Cartesian grid of sensors. This approach is used chiefly to map or "encode" the coordinate of each sensor to its function. Sensors in these arrays typically use a universal signalling technique (e.g. fluorescence), thus making coordinates their only identifying feature. These arrays must be made using a serial process (i.e. requiring multiple, sequential steps) to ensure that each sensor is placed at the correct position.
"Random" fabrication, in which the sensors are placed at arbitrary positions on the chip, is an alternative to the serial method. The tedious and expensive positioning process is
not required, enabling the use of parallelized self-assembly techniques. In this approach, large batches of identical sensors can be produced; sensors from each batch are then combined and assembled into an array. A non-coordinate based encoding scheme must be used to identify each sensor. As the figure shows, such a design was first demonstrated (and later commercialized by Illumina) using functionalized beads placed randomly in the wells of an etched fiber optic cable. Each bead was uniquely encoded with a fluorescent signature. However, this encoding scheme is limited in the number of unique dye combinations that can be used and successfully differentiated. | 1 | Biochemistry |
An alternative method used to create ATP is through oxidative phosphorylation, which takes place during cellular respiration. This process utilizes the oxidation of NADH to NAD, yielding 3 ATP, and of FADH to FAD, yielding 2 ATP. The potential energy stored as an electrochemical gradient of protons (H) across the inner mitochondrial membrane is required to generate ATP from ADP and P (inorganic phosphate molecule), a key difference from substrate-level phosphorylation. This gradient is exploited by ATP synthase acting as a pore, allowing H from the mitochondrial intermembrane space to move down its electrochemical gradient into the matrix and coupling the release of free energy to ATP synthesis. Conversely, electron transfer provides the energy required to actively pump H out of the matrix. | 1 | Biochemistry |
A historic example of L1-conferred disease is Haemophilia A, which is caused by insertional mutagenesis. There are nearly 100 examples of known diseases caused by retroelement insertions, including some types of cancer and neurological disorders. Correlation between L1 mobilization and oncogenesis has been reported for epithelial cell cancer (carcinoma). Hypomethylation of LINES is associated with chromosomal instability and altered gene expression and is found in various cancer cell types in various tissues types. Hypomethylation of a specific L1 located in the MET onco gene is associated with bladder cancer tumorogenesis, Shift work sleep disorder is associated with increased cancer risk because light exposure at night reduces melatonin, a hormone that has been shown to reduce L1-induced genome instability. | 1 | Biochemistry |
Quantum dots (QDs) are nano-scale semiconductor particles on the order of 2–10 nm in diameter. They possess electrical properties between those of bulk semi-conductors and individual molecules, as well as optical characteristics that make them suitable for applications where fluorescence is desirable, such as medical imaging. Most QDs synthesized for medical imaging are in the form of CdSe(ZnS) core(shell) particles. CdSe QDs have been shown to possess optical properties superior to organic dyes. The ZnS shell has a two-fold effect:
# to interact with dangling bonds that would otherwise result in particle aggregation, loss of visual resolution, and impedance of quantum confinement effects
# to further increase the fluorescence of the particles themselves. | 7 | Physical Chemistry |
Since the neutron is not charged it does not interact via the Coulomb force and therefore does not ionize the scintillation material. It must first transfer some or all of its energy via the strong force to a charged atomic nucleus. The positively charged nucleus then produces ionization. Fast neutrons (generally >0.5 MeV ) primarily rely on the recoil proton in (n,p) reactions; materials rich in hydrogen, e.g. plastic scintillators, are therefore best suited for their detection. Slow neutrons rely on nuclear reactions such as the (n,γ) or (n,α) reactions, to produce ionization. Their mean free path is therefore quite large unless the scintillator material contains nuclides having a high cross section for these nuclear reactions such as Li or B. Materials such as LiI(Eu) or glass silicates are therefore particularly well-suited for the detection of slow (thermal) neutrons. | 5 | Photochemistry |
Two discoveries led to the development of glycosynthase enzymes. The first was that a change of the active site nucleophile of a glycosidase from a carboxylate to another amino acid resulted in a properly folded protein that had no hydrolase activity.
The second discovery was that some glycosidase enzymes were able to catalyze the hydrolysis of glycosyl fluorides that had the incorrect anomeric configuration. The enzymes underwent a transglycosidation reaction to form a disaccharide, which was then a substrate for hydrolase activity.
The first reported glycosynthase was a mutant of the sp. β-glucosidase / galactosidase in which the nucleophile glutamate 358 was mutated to an alanine by site directed mutagenesis. When incubated with α-glycosyl fluorides and an acceptor sugar it was found to catalyze the transglycosidation reaction without any hydrolysis. This glycosynthase was used to synthesize a series of di- and trisaccharide products with yields between 64% and 92%. | 0 | Organic Chemistry |
Metabolites can be divided into two groups: those produced during the growth phase of the organism, called primary metabolites and those produced during the stationary phase, called secondary metabolites. Some examples of primary metabolites are ethanol, citric acid, glutamic acid, lysine, vitamins and polysaccharides. Some examples of secondary metabolites are penicillin, cyclosporin A, gibberellin, and lovastatin. | 1 | Biochemistry |
During his time at the University of Wisconsin, Stork kept a steak on his windowsill in the winter in order to keep it refrigerated. The steak began to degrade and to dispose of it Stork put it in a hot acid bath used to clean glassware which contained nitric and sulphuric acids. He was then concerned he would produce nitroglycerine due to the glycerine in the steak and the presence of nitric and sulphuric acids. However, due to the high temperature of the bath, the oxidation of glycerol was much faster than the nitration of glycerin thus preventing the formation of explosives. | 0 | Organic Chemistry |
Different polymer surfaces have different side chains on their monomers that can become charged due to the adsorption or dissociation of adsorbates. For example, polystyrene sulfonate has monomers containing negatively charged side chains which can adsorb positively charged adsorbates. Polystyrene sulfonate will adsorb more positively charged adsorbate than negatively charged. Conversely, for a polymer that contains positively charged side chains, such as poly(diallyldimethylammonium chloride), negatively charged adsorbates will be strongly attracted. | 7 | Physical Chemistry |
The function of the HNMT enzyme is histamine metabolism by ways of N-methylation using S-adenosyl--methionine (SAM-e) as the methyl donor, producing N-methylhistamine, which, unless excreted, can be further processed by monoamine oxidase B (MAOB) or by diamine oxidase (DAO). Methylated histamine metabolites are excreted with urine.
In mammals, there are two main ways to inactivate histamine by metabolism: one is through a process called oxidative deamination, which involves the enzyme diamine oxidase (DAO) produced by the AOC1 gene, and the other is through a process called N-methylation, which involves the enzyme N-methyltransferase. In the context of biochemistry, inactivation by metabolism refers to the process where a substance, such as a hormone, is converted into a form that is no longer active or effective (inactivation), via a process where the substance is chemically altered (metabolism).
HNMT and DAO are two enzymes that play distinct roles in histamine metabolism. DAO is primarily responsible for metabolizing histamine in extracellular (outside cells) fluids, which include interstitial fluid (fluid surrounding cells) and blood plasma. Such histamine can be exogenous (from food or intestinal flora) or endogenous (released from granules of mast cells and basophils, such as during allergic reactions). DAO is predominantly expressed in the cells of the intestinal epithelium and placenta but not in the central nervous system (CNS). In contrast, HNMT is expressed in CNS and involved in the metabolism of intracellular (inside cells) histamine, which is primarily endogenous and persistently present. HNMT operates in the cytosol, which is the fluid inside cells. Histamine is required to be carried into the cytosol through transporters such as plasma membrane monoamine transporter (SLC29A4) or organic cation transporter 3 (SLC22A3). HNMT enzyme is found in cells of diverse tissues: neurons and glia, brain, kidneys, liver, bronchi, large intestine, ovary, prostate, spinal cord, spleen, and trachea, etc. While DAO is primarily found in the intestinal epithelium, HNMT is present in a wider range of tissues throughout the body. This difference in location also requires different transport mechanisms for histamine to reach each enzyme, reflecting the distinct roles of these enzymes in histamine metabolism. Another distinction between HNMT and DAO lies in their substrate specificity. While HNMT has a strong preference for histamine, DAO can metabolize other biogenic amines—substances, produced by a life form (like a bacteria or an animal) that has an amine functional group (−NH). The examples of biogenic amines besides histamine that DAO can metabolize are putrescine and cadaverine; still, DAO has a preference for histamine. Both DAO and HNMT exhibit comparable affinities toward histamine.
In the brain of mammals, histamine takes part in histaminergic neurotransmission, that is a process where histamine acts as a messenger molecule between the neurons—the nerve cells. Histamine neurotransmitter activity is controlled by HNMT, since DAO is not present in the CNS. Consequently, the deactivation of histamine via HNMT represents the sole mechanism for ending neurotransmission within the mammalian CNS. This highlights the key role of HNMT for the histamine system of the brain and the brain function in general. | 1 | Biochemistry |
The calcium cycle is a transfer of calcium between dissolved and solid phases. There is a continuous supply of calcium ions into waterways from rocks, organisms, and soils. Calcium ions are consumed and removed from aqueous environments as they react to form insoluble structures such as calcium carbonate and calcium silicate, which can deposit to form sediments or the exoskeletons of organisms. Calcium ions can also be utilized biologically, as calcium is essential to biological functions such as the production of bones and teeth or cellular function. The calcium cycle is a common thread between terrestrial, marine, geological, and biological processes. Calcium moves through these different media as it cycles throughout the Earth. The marine calcium cycle is affected by changing atmospheric carbon dioxide due to ocean acidification.
Biogenic calcium carbonate is formed when marine organisms, such as coccolithophores, corals, pteropods, and other mollusks transform calcium ions and bicarbonate into shells and exoskeletons of calcite or aragonite, both forms of calcium carbonate. This is the dominant sink for dissolved calcium in the ocean. Dead organisms sink to the bottom of the ocean, depositing layers of shell which over time cement to form limestone. This is the origin of both marine and terrestrial limestone.
Calcium precipitates into calcium carbonate according to the following equation:
Ca + 2HCO → CO+ HO + CaCO
The relationship between dissolved calcium and calcium carbonate is affected greatly by the levels of carbon dioxide (CO) in the atmosphere.
Increased carbon dioxide leads to more bicarbonate in the ocean according to the following equation:
CO + CO + HO → 2HCO
With its close relation to the carbon cycle and the effects of greenhouse gasses, both calcium and carbon cycles are predicted to change in the coming years. Tracking calcium isotopes enables the prediction of environmental changes, with many sources suggesting increasing temperatures in both the atmosphere and marine environment. As a result, this will drastically alter the breakdown of rock, the pH of oceans and waterways and thus calcium sedimentation, hosting an array of implications on the calcium cycle.
Due to the complex interactions of calcium with many facets of life, the effects of altered environmental conditions are unlikely to be known until they occur. Predictions can however be tentatively made, based upon evidence-based research. Increasing carbon dioxide levels and decreasing ocean pH will alter calcium solubility, preventing corals and shelled organisms from developing their calcium-based exoskeletons, thus making them vulnerable or unable to survive.
Most biological production of biogenic silica in the ocean is driven by diatoms, with further contributions from radiolarians. These microorganisms extract dissolved silicic acid from surface waters during growth, and return this by recycling throughout the water column after they die. Inputs of silicon to the ocean from above arrive via rivers and aeolian dust, while those from below include seafloor sediment recycling, weathering, and hydrothermal activity. | 9 | Geochemistry |
In chemistry, dissociative substitution describes a reaction pathway by which compounds interchange ligands. The term is typically applied to coordination and organometallic complexes, but resembles the S1 mechanism in organic chemistry. This pathway can be well described by the cis effect, or the labilization of CO ligands in the cis position. The opposite pathway is associative substitution, being analogous to S2 pathway. Pathways that are intermediate between the pure dissociative and pure associative pathways are called interchange mechanisms.
Complexes that undergo dissociative substitution are often coordinatively saturated and often have octahedral molecular geometry. The entropy of activation is characteristically positive for these reactions, which indicates that the disorder of the reacting system increases in the rate-determining step. | 0 | Organic Chemistry |
Syntrophy, in the context of microbial metabolism, refers to the pairing of multiple species to achieve a chemical reaction that, on its own, would be energetically unfavorable. The best studied example of this process is the oxidation of fermentative end products (such as acetate, ethanol and butyrate) by organisms such as Syntrophomonas. Alone, the oxidation of butyrate to acetate and hydrogen gas is energetically unfavorable. However, when a hydrogenotrophic (hydrogen-using) methanogen is present the use of the hydrogen gas will significantly lower the concentration of hydrogen (down to 10 atm) and thereby shift the equilibrium of the butyrate oxidation reaction under standard conditions (ΔGº’) to non-standard conditions (ΔG’). Because the concentration of one product is lowered, the reaction is "pulled" towards the products and shifted towards net energetically favorable conditions (for butyrate oxidation: ΔGº’= +48.2 kJ/mol, but ΔG = -8.9 kJ/mol at 10 atm hydrogen and even lower if also the initially produced acetate is further metabolized by methanogens). Conversely, the available free energy from methanogenesis is lowered from ΔGº’= -131 kJ/mol under standard conditions to ΔG = -17 kJ/mol at 10 atm hydrogen. This is an example of intraspecies hydrogen transfer. In this way, low energy-yielding carbon sources can be used by a consortium of organisms to achieve further degradation and eventual mineralization of these compounds. These reactions help prevent the excess sequestration of carbon over geologic time scales, releasing it back to the biosphere in usable forms such as methane and . | 1 | Biochemistry |
Thermodynamic equilibrium is characterized by the free energy for the whole (closed) system being a minimum. For systems at constant temperature and pressure the Gibbs free energy is minimum. The slope of the reaction free energy with respect to the extent of reaction, ξ, is zero when the free energy is at its minimum value.
The free energy change, dG, can be expressed as a weighted sum of change in amount times the chemical potential, the partial molar free energy of the species. The chemical potential, μ, of the ith species in a chemical reaction is the partial derivative of the free energy with respect to the number of moles of that species, N
A general chemical equilibrium can be written as
where n are the stoichiometric coefficients of the reactants in the equilibrium equation, and m are the coefficients of the products. At equilibrium
The chemical potential, μ, of the ith species can be calculated in terms of its activity, a.
μ is the standard chemical potential of the species, R is the gas constant and T is the temperature. Setting the sum for the reactants j to be equal to the sum for the products, k, so that δG(Eq) = 0
Rearranging the terms,
This relates the standard Gibbs free energy change, ΔG</sup> to an equilibrium constant, K, the reaction quotient of activity values at equilibrium. | 7 | Physical Chemistry |
Olson remained at the Flory group for a post doc research, after which she became a Damon Runyon Cancer Research Foundation Postdoctoral Fellow with geneticist Charles R. Cantor at Columbia University.
In 1972, Olson became an assistant professor at Rutgers University and full professor in 1979.
During her time at Rutgers, she was a visiting professor at the University of Basel in Switzerland (1979–1980) and at the Polymer Chemistry Department of the Jilin University in Changchun, China (1981).
Wilma Olson was involved in setting up the nucleic acid database, in collaboration with Helen M. Berman. | 1 | Biochemistry |
In this case, both electrons and H ions are involved and the electrode potential is a function of pH. The reaction equation may be written:
Using the expressions for the free energy in terms of potentials, the energy balance is given by a Nernst equation:
For the iron and water example, considering the boundary line between the ferrous ion Fe and hematite FeO, the reaction equation is:
: with .
The equation of the boundary line, expressed in base-10 logarithms is:
As, the activities, or the concentrations, of the solid phases and water are always taken equal to unity by convention in the definition of the equilibrium constant : [FeO] = [HO] = 1.
The Nernst equation thus limited to the dissolved species and is written as:
For, [Fe] = 10 M, this yields:
Note the negative slope (-0.1775) of this line in a E–pH diagram. | 7 | Physical Chemistry |
# Using ATP as energy, citrate is broken down into the acetyl group and oxaloacetate.
# The acetyl group joins the coenzyme in the cytosol, forming acetyl-CoA. | 1 | Biochemistry |
One of the zilches has been rediscovered. This is the zilch known as "optical chirality". This name was given by Tang and Cohen since this zilch determines the degree of chiral asymmetry in the rate of excitation of a small chiral molecule by an incident electromagnetic field.
A further physical insight of optical chirality was offered in 2012; optical chirality is to the curl or time derivative of the electromagnetic field what helicity, spin and related quantities are to the electromagnetic field itself.
The physical interpretation of all zilches for topologically non-trivial electromagnetic fields was investigated in 2018.
Since the discovery of the ten zilches in 1964, there is an important open mathematical question concerning their relation with symmetries. (Recently, the full answer to this question seems to have been found ). The question is:
What are the symmetries of the standard Maxwell action functional :
(with ,
where is the dynamical field variable) that give rise to the conservation of all zilches using Noether's theorem? Until recently, the answer to this question had been given only for the case of optical chirality by Philbin in 2013.
This open question was also emphasized by Aghapour, Andersson and Rosquist in 2020,
while these authors found the symmetries of the duality-symmetric Maxwell action underlying the conservation of all zilches. (Aghapour, Andersson and Rosquist did not find the symmetries of the standard Maxwell action, but they speculated that such symmetries should exist ).
There are also earlier works studying the conservation of zilch in the context of duality-symmetric electromagnetism, but the variational character of the corresponding symmetries was not established.
The full answer to the aforementioned question seems to have been given for the first time in 2022, where the symmetries of the standard Maxwell action underlying the conservation of all zilches were found. According to this work, there is a hidden invariance algebra of free Maxwell equations in potential form that is related to the conservation of all zilches. | 4 | Stereochemistry |
During the Dark Ages of the transition from bronze to iron, the decorative arts stood almost still but industrial metalwork was freely produced. There are a few remains of Geometric bronze vessels, but as in the case of the Early Minoan material, metal forms are recorded in their pottery derivatives. Some vase-shapes are clearly survivals from the Mycenaean repertory, but a greater number are new, and these are elementary and somewhat clumsy, spherical or biconical bodies, huge cylindrical necks with long band-handles and no spouts. Ceramic painted ornament also reflects originals of metal, and some scraps of thin bronze plate embossed with rows of knobs and lightly engraved in hatched or zig-zag outline doubtless represent the art which the newcomers brought with them to Greek lands. This kind of decorative work is better seen in bronzes of the closely related Villanova culture of north and central Italy. A novel feature is the application of small figures in the round, particularly birds and heads of oxen, as ornaments of handles, lids and rims. The Italian Geometric style developed towards complication, in crowded narrow bands of conventional patterns and serried rows of ducks; but contemporary Greek work was a refinement of the same crude elements.
Engraving appears at its best on the large catch-plates of fibulae, some of which bear the earliest known pictures of Hellenic mythology. Small statuettes of animals were made for votive use and also served as seals, the devices being cast underneath their bases. There is a large series of such figures, mostly horses, standing on engraved or perforated plates, which were evidently derived from seals; among the later examples are groups of men and centaurs. Pieces of tripod-cauldrons from Olympia have animals lying or standing on their upright ring-handles, which are steadied by human figures on the rims. Handles and legs are cast, and are enriched with graceful geometric mouldings. The bowls are wrought, and their shape and technique are pre-Hellenic. Here are two of the elements of classical Greek art in full course of development: the forms and processes of earlier times invigorated by a new aesthetic sense. | 8 | Metallurgy |
Off-targeting is another challenge to the use of siRNAs as a gene knockdown tool. Here, genes with incomplete complementarity are inadvertently downregulated by the siRNA (in effect, the siRNA acts as a miRNA), leading to problems in data interpretation and potential toxicity. This, however, can be partly addressed by designing appropriate control experiments, and siRNA design algorithms are currently being developed to produce siRNAs free from off-targeting. Genome-wide expression analysis, e.g., by microarray technology, can then be used to verify this and further refine the algorithms. A 2006 paper from the laboratory of Dr. Khvorova implicates 6- or 7-basepair-long stretches from position 2 onward in the siRNA matching with 3'UTR regions in off-targeted genes. The tool of siRNA off-target predition is available at http://crdd.osdd.net/servers/aspsirna/asptar.php and published as ASPsiRNA resource. | 1 | Biochemistry |
* For burner fuel, Concarbon provides an approximation of the tendency of the fuel to form deposits in vaporizing pot-type and sleeve-type burners.
* For diesel fuel, Concarbon correlates approximately with combustion chamber deposits, provided that alkyl nitrates are absent, or if present, that the test is performed on the base fuel without additive.
*For motor oil, Concarbon was once regarded as indicative of the amount of carbonaceous deposits the oil would form in the combustion chamber of an engine. This is now considered to be of doubtful significance due to the presence of additives in many oils.
* For gas oil, Concarbon provides a useful correlation in the manufacture of gas there from.
* For delayed cokers, the Concarbon of the feed correlates positively to the amount of coke that will be produced.
* For fluid catalytic cracking units, the Concarbon of the feed can be used to estimate the feed's coke-forming tendency. | 9 | Geochemistry |
Selecting an oocyte for in vitro fertilization involves assessing the quality of the oocyte which is usually done by accessing the morphological features of the oocyte. The major parts of the oocyte that are accessed for quality in terms of morphological characteristics are the cumulus cells, zona pellucida, polar body, perivitelline space, and cytoplasm; These are the main parts of the oocyte and are usually assessed by conventional microscopy. The size of an oocyte is another factor of the quality of the oocyte; Larger oocyte are usually more quality than smaller ones. Chromosomal evaluation may be performed. Embryos from rescued in vitro-matured metaphase II (IVM-MII) oocytes show significantly higher fertilization rates and more blastomeres per embryo compared with those from arrested metaphase I (MI) oocytes (58.5% vs. 43.9% and 5.7 vs. 5.0, respectively).
Also, morphological features of the oocyte that can be obtained by standard light or polarized light microscopy. However, there is no clear tendency in recent publications to a general increase in predictive value of morphological features. Suggested techniques include zona pellucida imaging, which can detect differences in birefringence between eggs, which is a predictor of compaction, blastulation and pregnancy.
Potentially, polar body biopsy may be used for molecular analysis, and can be used for preimplantation genetic screening. | 1 | Biochemistry |
In the highly versatile and widely used Evans’ Aldol Reaction, allylic strain played a major role in the development of the reaction. The Z enolate was created to avoid the allylic strain with oxazolidinone. The formation of a specific enolate enforces the development of relative stereochemistry throughout the reaction, making the aldol reaction a very predictive and useful methodology out there to synthesize chiral molecules. The absolute stereochemistry is then determined by the chirality of the oxazolidinone.
There is another aspect of aldol reaction that is influenced by the allylic strain. On the second aldol reaction, the product which is a 1,3 dicarbonyl is formed in high diastereoselectivity. This is because the acidity of the proton is significantly reduced because for the deprotonation to occur, it will have to go through a developing allylic strain in the unfavored conformation. In the favored conformation, the proton is not aligned properly for deprotonation to occur. | 4 | Stereochemistry |
The measured full SPR curves (x-axis: angle, y-axis: reflected light intensity) can be transcribed into sensograms (x-axis: time, y-axis: selected parameter such as peak minimum, light intensity, peak width). The sensograms can be fitted using binding models to obtain kinetic parameters including on- and off-rates and affinity. The full SPR curves are used to fit Fresnel equations to obtain thickness and refractive index of the layers. Also due to the ability of scanning the whole SPR curve, MP-SPR is able to separate bulk effect and analyte binding from each other using parameters of the curve.
While QCM-D measures wet mass, MP-SPR and other optical methods measure dry mass, which enables analysis of water content of nanocellulose films. | 7 | Physical Chemistry |
The history of ferrous metallurgy in the Indian subcontinent began in the 2nd millennium BC. Archaeological sites in Gangetic plains have yielded iron implements dated between 1800 and 1200 BC. By the early 13th century BC, iron smelting was practiced on a large scale in India. In Southern India (present day Mysore) iron was in use 12th to 11th centuries BC. The technology of iron metallurgy advanced in the politically stable Maurya period and during a period of peaceful settlements in the 1st millennium BC.
Iron artifacts such as spikes, knives, daggers, arrow-heads, bowls, spoons, saucepans, axes, chisels, tongs, door fittings, etc., dated from 600 to 200 BC, have been discovered at several archaeological sites of India. The Greek historian Herodotus wrote the first western account of the use of iron in India. The Indian mythological texts, the Upanishads, have mentions of weaving, pottery and metallurgy, as well. The Romans had high regard for the excellence of steel from India in the time of the Gupta Empire.
Perhaps as early as 500 BC, although certainly by 200 AD, high-quality steel was produced in southern India by the crucible technique. In this system, high-purity wrought iron, charcoal, and glass were mixed in a crucible and heated until the iron melted and absorbed the carbon. Iron chain was used in Indian suspension bridges as early as the 4th century.
Wootz steel was produced in India and Sri Lanka from around 300 BC. Wootz steel is famous from Classical Antiquity for its durability and ability to hold an edge. When asked by King Porus to select a gift, Alexander is said to have chosen, over gold or silver, thirty pounds of steel. Wootz steel was originally a complex alloy with iron as its main component together with various trace elements. Recent studies have suggested that its qualities may have been due to the formation of carbon nanotubes in the metal. According to Will Durant, the technology passed to the Persians and from them to Arabs who spread it through the Middle East. In the 16th century, the Dutch carried the technology from South India to Europe, where it was mass-produced.
Steel was produced in Sri Lanka from 300 BC by furnaces blown by the monsoon winds. The furnaces were dug into the crests of hills, and the wind was diverted into the air vents by long trenches. This arrangement created a zone of high pressure at the entrance, and a zone of low pressure at the top of the furnace. The flow is believed to have allowed higher temperatures than bellows-driven furnaces could produce, resulting in better-quality iron. Steel made in Sri Lanka was traded extensively within the region and in the Islamic world.
One of the world's foremost metallurgical curiosities is an iron pillar located in the Qutb complex in Delhi. The pillar is made of wrought iron (98% Fe), is almost seven meters high and weighs more than six tonnes. The pillar was erected by Chandragupta II Vikramaditya and has withstood 1,600 years of exposure to heavy rains with relatively little corrosion. | 8 | Metallurgy |
Multiplex ligation-dependent probe amplification was invented by Jan Schouten, a Dutch scientist. The method was first described in 2002 in the scientific journal Nucleic Acid Research. The first applications included the detection of exon deletions in the human genes BRCA1, MSH2 and MLH1, which are linked to hereditary breast and colon cancer. Now MLPA is used to detect hundreds of hereditary disorders, as well as for tumour profiling. | 1 | Biochemistry |
The matte, which is produced in the smelter, contains 30–70% copper (depending on the process used and the operating philosophy of the smelter), primarily as copper sulfide, as well as iron sulfide. The sulfur is removed at a high temperature as sulfur dioxide by blowing air through molten matte:
:2 CuS + 3 O → 2 CuO + 2 SO
:CuS + O → Cu + SO
In a parallel reaction the iron sulfide is converted to slag:
:2 FeS + 3 O → 2 FeO + 2 SO
:2 FeO + SiO → FeSiO
The purity of this product is 98%, it is known as blister because of the broken surface created by the escape of sulfur dioxide gas as blister copper pigs or ingots are cooled. By-products generated in the process are sulfur dioxide and slag. The sulfur dioxide is captured and converted to sulfuric acid and either sold on the open market or used in copper leaching processes. | 8 | Metallurgy |
A well studied pioneer factor family is the Groucho-related (Gro/TLE/Grg) transcription factors that often have a negative effect on transcription. These chromatin binding domains can span up to 3-4 nucleosomes. These large domains are scaffolds for further protein interactions and also modify the chromatin for other pioneer factors such as FoxA1 which has been shown to bind to Grg3. Transcription factors with zinc finger DNA binding domains, such as the GATA family and glucocorticoid receptor. The zinc finger domains do not appear to bind nucleosomes well and can be displaced by FOX factors.
In the skin epidermis, SOX family transcription factor, SOX9, also behaves as a pioneer factor that governs hair follicle cell fate and can reprogram epidermal stem cells to a hair follicle fate. | 1 | Biochemistry |
The history of metallurgy in the Urals stands out to historians and economists as a separate stage in the history of Russian industry and covers the period from the 4th millennium BC to the present day. The emergence of the mining district is connected with the history of Ural metallurgy. The geography of the Ural metallurgy covers the territories of modern Perm Krai, Sverdlovsk Oblast, Udmurtia, Bashkortostan, Chelyabinsk Oblast and Orenburg Oblast.
In the 18th century, periods of formation and development of industrial metallurgical centers stand out in Urals metallurgy, for example, the rapid construction and economic growth of more than two hundred metallurgy factories during the 18th to the first half of the 19th centuries until the abolition of serfdom on February 19, 1861 in the Russian Empire, which led to reductions in the labor force. There was also a sharp drop in production rates in the early 1900s but that was followed by recovery and growth by 1913. In the 20th century, after recovering from the decline caused by the Russian Revolution(s): 1905, February 1917, and October 1917 and the Russian Civil War (November 1917 - June 1923), Ural metallurgy had a strategic impact on ensuring the defense of the USSR on the Eastern Front of World War II which is known in Russia as the Great Patriotic War. In the 21st century, the development of metallurgical enterprises in the Urals is associated with the formation of vertically integrated full cycle companies.
The main milestones in the development of metal production technologies in the Urals include the transition from bloomery or the old iron production method to the Kontuazsky forge (for remelting heavy scrap) and the puddling method in the second half of the 19th century. Later, there was the development of hot blast at the end of the 19th century. Further, there was a transition to coke fuel and the introduction of steam engines. Finally, there was the development of open-hearth and Bessemer methods of steel production at the beginning of the 20th century. | 8 | Metallurgy |
Professor David Knowles FREng FIMMM (born 6 January 1967) is Professor of Nuclear Engineering at the University of Bristol and Chief Executive of the UK's Henry Royce Institute for advanced materials research. From 2016 to 2019, he was the co-director of the South West Nuclear Hub, and Atkins Fellow. His work focusses primarily on understanding and modelling the degradation mechanisms in metallic materials and their interrelation with the structural integrity of rotating and static equipment in the energy sector. | 8 | Metallurgy |
It is very rare for activity coefficient values to have been determined experimentally for a system at equilibrium. There are three options for dealing with the situation where activity coefficient values are not known from experimental measurements.
#Use calculated activity coefficients, together with concentrations of reactants. For equilibria in solution estimates of the activity coefficients of charged species can be obtained using Debye–Hückel theory, an extended version, or SIT theory. For uncharged species, the activity coefficient γ mostly follows a "salting-out" model: log γ = bI where I stands for ionic strength.
#Assume that the activity coefficients are all equal to 1. This is acceptable when all concentrations are very low.
#For equilibria in solution use a medium of high ionic strength. In effect this redefines the standard state as referring to the medium. Activity coefficients in the standard state are, by definition, equal to 1. The value of an equilibrium constant determined in this manner is dependent on the ionic strength. When published constants refer to an ionic strength other than the one required for a particular application, they may be adjusted by means of specific ion theory (SIT) and other theories. | 7 | Physical Chemistry |
Lithium enolates, one of the precursors to silyl enol ethers, can also be generated from silyl enol ethers using methyllithium. The reaction occurs via nucleophilic substitution at the silicon of the silyl enol ether, producing the lithium enolate and tetramethylsilane. | 0 | Organic Chemistry |
In thermodynamics, the excess chemical potential is defined as the difference between the chemical potential of a given species and that of an ideal gas under the same conditions (in particular, at the same pressure, temperature, and composition).
The chemical potential of a particle species is therefore given by an ideal part and an excess part.
Chemical potential of a pure fluid can be estimated by the Widom insertion method. | 7 | Physical Chemistry |
The Ycf4 protein domain found on the thylakoid membrane is vital to photosystem I. This thylakoid transmembrane protein helps assemble the components of photosystem I. Without it, photosynthesis would be inefficient. | 5 | Photochemistry |
RNA silencing describes several mechanistically related pathways which are involved in controlling and regulating gene expression. RNA silencing pathways are associated with the regulatory activity of small non-coding RNAs (approximately 20–30 nucleotides in length) that function as factors involved in inactivating homologous sequences, promoting endonuclease activity, translational arrest, and/or chromatic or DNA modification. In the context in which the phenomenon was first studied, small RNA was found to play an important role in defending plants against viruses. For example, these studies demonstrated that enzymes detect double-stranded RNA (dsRNA) not normally found in cells and digest it into small pieces that are not able to cause disease.
While some functions of RNA silencing and its machinery are understood, many are not. For example, RNA silencing has been shown to be important in the regulation of development and in the control of transposition events. RNA silencing has been shown to play a role in antiviral protection in plants as well as insects. Also in yeast, RNA silencing has been shown to maintain heterochromatin structure. However, the varied and nuanced role of RNA silencing in the regulation of gene expression remains an ongoing scientific inquiry. A range of diverse functions have been proposed for a growing number of characterized small RNA sequences—e.g., regulation of developmental, neuronal cell fate, cell death, proliferation, fat storage, haematopoietic cell fate, insulin secretion.
RNA silencing functions by repressing translation or by cleaving messenger RNA (mRNA), depending on the amount of complementarity of base-pairing. RNA has been largely investigated within its role as an intermediary in the translation of genes into proteins. More active regulatory functions, however, only began to be addressed by researchers beginning in the late-1990s. The landmark study providing an understanding of the first identified mechanism was published in 1998 by Fire et al., demonstrating that double-stranded RNA could act as a trigger for gene silencing. Since then, various other classes of RNA silencing have been identified and characterized. Presently, the therapeutic potential of these discoveries is being explored, for example, in the context of targeted gene therapy.
While RNA silencing is an evolving class of mechanisms, a common theme is the fundamental relationship between small RNAs and gene expression. It has also been observed that the major RNA silencing pathways currently identified have mechanisms of action which may involve both post-transcriptional gene silencing (PTGS) as well as chromatin-dependent gene silencing (CDGS) pathways. CDGS involves the assembly of small RNA complexes on nascent transcripts and is regarded as encompassing mechanisms of action which implicate transcriptional gene silencing (TGS) and co-transcriptional gene silencing (CTGS) events. This is significant at least because the evidence suggests that small RNAs play a role in the modulation of chromatin structure and TGS.
Despite early focus in the literature on RNA interference (RNAi) as a core mechanism which occurs at the level of messenger RNA translation, others have since been identified in the broader family of conserved RNA silencing pathways acting at the DNA and chromatin level. RNA silencing refers to the silencing activity of a range of small RNAs and is generally regarded as a broader category than RNAi. While the terms have sometimes been used interchangeably in the literature, RNAi is generally regarded as a branch of RNA silencing. To the extent it is useful to craft a distinction between these related concepts, RNA silencing may be thought of as referring to the broader scheme of small RNA related controls involved in gene expression and the protection of the genome against mobile repetitive DNA sequences, retroelements, and transposons to the extent that these can induce mutations. The molecular mechanisms for RNA silencing were initially studied in plants but have since broadened to cover a variety of subjects, from fungi to mammals, providing strong evidence that these pathways are highly conserved.
At least three primary classes of small RNA have currently been identified, namely: small interfering RNA (siRNA), microRNA (miRNA), and piwi-interacting RNA (piRNA). | 1 | Biochemistry |
The cycle's importance is based on preventing lactic acidosis during anaerobic conditions in the muscle. However, normally, before this happens, the lactic acid is moved out of the muscles and into the liver.
Additionally, this cycle is important in ATP production, an energy source, during muscle exertion. The end of muscle exertion allows the Cori cycle to function more effectively. This repays the oxygen debt so both the electron transport chain and citric acid cycle can produce energy at optimum effectiveness.
The Cori cycle is a much more important source of substrate for gluconeogenesis than food. The contribution of Cori cycle lactate to overall glucose production increases with fasting duration before plateauing. Specifically, after 12, 20, and 40 hours of fasting by human volunteers, gluconeogenesis accounts for 41%, 71%, and 92% of glucose production, but the contribution of Cori cycle lactate to gluconeogenesis is 18%, 35%, and 36%, respectively. The remaining glucose production comes from protein breakdown, muscle glycogen, and glycerol from lipolysis.
The drug metformin can cause lactic acidosis in patients with kidney failure because metformin inhibits the hepatic gluconeogenesis of the Cori cycle, particularly the mitochondrial respiratory chain complex 1. The buildup of lactate and its substrates for lactate production, pyruvate and alanine, lead to excess lactate. Normally, the excess acid that is the result of the inhibition of the mitochondrial chain complex would be cleared by the kidneys, but in patients with kidney failure, the kidneys cannot handle the excess acid.
A common misconception posits that lactate is the agent responsible for the acidosis, but lactate is a conjugate base, being mostly ionised at physiologic pH, and serves as a marker of associated acid production rather than being its cause. | 1 | Biochemistry |
Synaptic transmission can be changed by previous activity. These changes are called synaptic plasticity and may result in either a decrease in the efficacy of the synapse, called depression, or an increase in efficacy, called potentiation. These changes can either be long-term or short-term. Forms of short-term plasticity include synaptic fatigue or depression and synaptic augmentation. Forms of long-term plasticity include long-term depression and long-term potentiation. Synaptic plasticity can be either homosynaptic (occurring at a single synapse) or heterosynaptic (occurring at multiple synapses). | 1 | Biochemistry |
Serotonylation is the process by which serotonin effects the exocytosis of alpha-granules from platelets (also known as thrombocytes). This involves the serotonylation of small GTPases such as Rab4 and RhoA. It has been suggested that "further understanding of the specific hormonal role of 5-HT in hemostasis and thrombosis is important to possibly prevent and treat deleterious hemorrhagic and cardiovascular disorders." Serotonylation has recently identified as playing a critical role in pulmonary hypertension.
Serotonylation also through small GTPases is involved in the process by which serotonin controls the release of insulin from beta cells in the pancreas and so the regulation of blood glucose levels. This role helps explain why defects in transglutaminase can lead to glucose intolerance. Though small GTPases are involved, the existence of a large amount of protein-bound serotonin suggests the presence of yet unidentified other serotonylation interactions.
Serotonylation of proteins other than small GTPases underlies the regulation of vascular smooth muscle "tone" in blood vessels including the aorta. This may occur through serotonylation modifying proteins integral to the contractility and the cytoskeleton such as alpha-actin, beta-actin, gamma-actin, myosin heavy chain and filamin A | 1 | Biochemistry |
TALEN can be used to edit genomes by inducing double-strand breaks (DSB), which cells respond to with repair mechanisms.
Non-homologous end joining (NHEJ) directly ligates DNA from either side of a double-strand break where there is very little or no sequence overlap for annealing. This repair mechanism induces errors in the genome via indels (insertion or deletion), or chromosomal rearrangement; any such errors may render the gene products coded at that location non-functional. Because this activity can vary depending on the species, cell type, target gene, and nuclease used, it should be monitored when designing new systems. A simple heteroduplex cleavage assay can be run which detects any difference between two alleles amplified by PCR. Cleavage products can be visualized on simple agarose gels or slab gel systems.
Alternatively, DNA can be introduced into a genome through NHEJ in the presence of exogenous double-stranded DNA fragments.
Homology directed repair can also introduce foreign DNA at the DSB as the transfected double-stranded sequences are used as templates for the repair enzymes. | 1 | Biochemistry |
For clarification, a distinction between the two corresponding cases is needed. With reference to a phase diagram, the sublimation that occurs left of the solid-gas boundary, the triple point or the solid-liquid boundary (corresponding to evaporation in vaporization) may be called gradual sublimation; and the substance sublimes gradually, regardless of rate. The sublimation that occurs at the solid-gas boundary (critical sublimation point) (corresponding to boiling in vaporization) may be called rapid sublimation, and the substance sublimes rapidly. The words "gradual" and "rapid" have acquired special meanings in this context and no longer describe the rate of sublimation. | 3 | Analytical Chemistry |
Much of the early understanding of transcription came from bacteria, although the extent and complexity of transcriptional regulation is greater in eukaryotes. Bacterial transcription is governed by three main sequence elements:
* Promoters are elements of DNA that may bind RNA polymerase and other proteins for the successful initiation of transcription directly upstream of the gene.
* Operators recognize repressor proteins that bind to a stretch of DNA and inhibit the transcription of the gene.
* Positive control elements that bind to DNA and incite higher levels of transcription.
While these means of transcriptional regulation also exist in eukaryotes, the transcriptional landscape is significantly more complicated both by the number of proteins involved as well as by the presence of introns and the packaging of DNA into histones.
The transcription of a basic bacterial gene is dependent on the strength of its promoter and the presence of activators or repressors. In the absence of other regulatory elements, a promoter's sequence-based affinity for RNA polymerases varies, which results in the production of different amounts of transcript. The variable affinity of RNA polymerase for different promoter sequences is related to regions of consensus sequence upstream of the transcription start site. The more nucleotides of a promoter that agree with the consensus sequence, the stronger the affinity of the promoter for RNA Polymerase likely is.
In the absence of other regulatory elements, the default state of a bacterial transcript is to be in the “on” configuration, resulting in the production of some amount of transcript. This means that transcriptional regulation in the form of protein repressors and positive control elements can either increase or decrease transcription. Repressors often physically occupy the promoter location, occluding RNA polymerase from binding. Alternatively a repressor and polymerase may bind to the DNA at the same time with a physical interaction between the repressor preventing the opening of the DNA for access to the minus strand for transcription. This strategy of control is distinct from eukaryotic transcription, whose basal state is to be off and where co-factors required for transcription initiation are highly gene dependent.
Sigma factors are specialized bacterial proteins that bind to RNA polymerases and orchestrate transcription initiation. Sigma factors act as mediators of sequence-specific transcription, such that a single sigma factor can be used for transcription of all housekeeping genes or a suite of genes the cell wishes to express in response to some external stimuli such as stress.
In addition to processes that regulate transcription at the stage of initiation, mRNA synthesis is also controlled by the rate of transcription elongation. RNA polymerase pauses occur frequently and are regulated by transcription factors, such as NusG and NusA, transcription-translation coupling, and mRNA secondary structure. | 1 | Biochemistry |
Often, modification of the structure will take place around the glycosidic linkage. Replacement of one or other of the glycosidic oxygen atoms by carbon, sulfur, nitrogen etc. will alter the properties of the glycosidic bond. The molecules produced in this way would be called carbasugars or C-glycosides, thiosugars or thioglycosides, or iminosugars or glycosylamines.
When nitrogen is introduced, the glycomimetic may become positively charged at physiological pH, meaning that it may act as an enzyme inhibitor, either by Coulombic interaction with carboxylate amino acid side-chains in the enzyme active site, or by mimicking positive-charge build-up at the transition state of the reaction, or both. Iminosugars (sometimes referred to erroneously as azasugars) are classic examples of molecules with this behaviour. Glycosylamines typically have a lower stability, being easily hydrolysed, which means that to exploit an exocyclic nitrogen substituent at C-1, further modification is necessary. An example of this would be the additional substitution of the ring-oxygen for carbon as is seen in valienamine.
Altering the structure of a carbohydrate will normally result in several changes to the properties of the molecule. As well as changing the stability of the glycosidic bond, the ring-conformation may be affected. Also the conformation of the glycosidic bond may be affected. As well as obvious changes in the immediate vicinity of the substitution, e.g. that replacement of an acetal oxygen by methylene (CH2) would result in loss of a hydrogen-bond participatory atom, such a substitution is expected to have more subtle effects resulting from a change in the dipole of the molecule, such as slight changes in hydrogen bonding or pKa values of the unchanged hydroxyl groups. Substitution by CF2 rather than methylene has been explored in efforts to address this and come up with better mimetics while still retaining the hydrolytic stability gained by the modification. | 1 | Biochemistry |
Monoaminergic cell groups refers to collections of neurons in the central nervous system that have been demonstrated by histochemical fluorescence to contain one of the neurotransmitters serotonin, dopamine, norepinephrine or epinephrine. Thus, it represents the combination of catecholaminergic cell groups and serotonergic cell groups. | 1 | Biochemistry |
An inert gas (or noble gas), such as helium, is one that does not react with other elements or compounds. Adding an inert gas into a gas-phase equilibrium at constant volume does not result in a shift. This is because the addition of a non-reactive gas does not change the equilibrium equation, as the inert gas appears on both sides of the chemical reaction equation. For example, if A and B react to form C and D, but X does not participate in the reaction: . While it is true that the total pressure of the system increases, the total pressure does not have any effect on the equilibrium constant; rather, it is a change in partial pressures that will cause a shift in the equilibrium. If, however, the volume is allowed to increase in the process, the partial pressures of all gases would be decreased resulting in a shift towards the side with the greater number of moles of gas. The shift will never occur on the side with fewer moles of gas. It is also known as Le Chatelier's postulate. | 7 | Physical Chemistry |
Crystal optics is the branch of optics that describes the behaviour of light in anisotropic media, that is, media (such as crystals) in which light behaves differently depending on which direction the light is propagating. The index of refraction depends on both composition and crystal structure and can be calculated using the Gladstone–Dale relation. Crystals are often naturally anisotropic, and in some media (such as liquid crystals) it is possible to induce anisotropy by applying an external electric field. | 3 | Analytical Chemistry |
Particulate inorganic carbon (PIC) usually takes the form of calcium carbonate (CaCO), and plays a key part in the ocean carbon cycle. This biologically fixed carbon is used as a protective coating for many planktonic species (coccolithophores, foraminifera) as well as larger marine organisms (mollusk shells). Calcium carbonate is also excreted at high rates during osmoregulation by fish, and can form in whiting events. While this form of carbon is not directly taken from the atmospheric budget, it is formed from dissolved forms of carbonate which are in equilibrium with CO and then responsible for removing this carbon via sequestration.
CO + HO → HCO → H + HCO
Ca + 2HCO → CaCO + CO + HO
While this process does manage to fix a large amount of carbon, two units of alkalinity are sequestered for every unit of sequestered carbon. The formation and sinking of CaCO therefore drives a surface to deep alkalinity gradient which serves to raise the pH of surface waters, shifting the speciation of dissolved carbon to raise the partial pressure of dissolved CO in surface waters, which actually raises atmospheric levels. In addition, the burial of CaCO in sediments serves to lower overall oceanic alkalinity, tending to raise pH and thereby atmospheric CO levels if not counterbalanced by the new input of alkalinity from weathering. The portion of carbon that is permanently buried at the sea floor becomes part of the geologic record. Calcium carbonate often forms remarkable deposits that can then be raised onto land through tectonic motion as in the case with the White Cliffs of Dover in Southern England. These cliffs are made almost entirely of the plates of buried coccolithophores. | 9 | Geochemistry |
Beryllium halides are formed by a combination of halogen with a beryllium atom. Beryllium halides are mostly covalent in nature except for the fluoride which is more ionic. They can be used as Lewis acid catalysts. Preparation for these compounds varies by the halogen. Beryllium halides are among the most common starting points to form complexes with other types of ligand. Halides can donate 2 electrons into the beryllium center with a charge of −1. | 0 | Organic Chemistry |
A total synthesis of progesterone was reported in 1971 by W.S. Johnson. The synthesis begins with reacting the phosphonium salt with phenyl lithium to produce the phosphonium ylide . The ylide is reacted with an aldehyde to produce the alkene . The ketal protecting groups of are hydrolyzed to produce the diketone , which in turn is cyclized to form the cyclopentenone . The ketone of is reacted with methyl lithium to yield the tertiary alcohol , which in turn is treated with acid to produce the tertiary cation . The key step of the synthesis is the π-cation cyclization of in which the B-, C-, and D-rings of the steroid are simultaneously formed to produce . This step resembles the cationic cyclization reaction used in the biosynthesis of steroids and hence is referred to as biomimetic. In the next step the enol orthoester is hydrolyzed to produce the ketone . The cyclopentene A-ring is then opened by oxidizing with ozone to produce . Finally, the diketone undergoes an intramolecular aldol condensation by treating with aqueous potassium hydroxide to produce progesterone. | 0 | Organic Chemistry |
Metal-organic frameworks are crystalline porous polymers assembled from organic monomers connected by coordination to metal atom centers. | 6 | Supramolecular Chemistry |
Despite having only four choices for each monomer unit (nucleotides), compared to 20 amino acid side chains found in proteins, ribozymes have diverse structures and mechanisms. In many cases they are able to mimic the mechanism used by their protein counterparts. For example, in self cleaving ribozyme RNAs, an in-line SN2 reaction is carried out using the 2’ hydroxyl group as a nucleophile attacking the bridging phosphate and causing 5’ oxygen of the N+1 base to act as a leaving group. In comparison, RNase A, a protein that catalyzes the same reaction, uses a coordinating histidine and lysine to act as a base to attack the phosphate backbone.
Like many protein enzymes, metal binding is also critical to the function of many ribozymes. Often these interactions use both the phosphate backbone and the base of the nucleotide, causing drastic conformational changes. There are two mechanism classes for the cleavage of a phosphodiester backbone in the presence of metal. In the first mechanism, the internal 2’- OH group attacks the phosphorus center in a SN mechanism. Metal ions promote this reaction by first coordinating the phosphate oxygen and later stabling the oxyanion. The second mechanism also follows a SN displacement, but the nucleophile comes from water or exogenous hydroxyl groups rather than RNA itself. The smallest ribozyme is UUU, which can promote the cleavage between G and A of the GAAA tetranucleotide via the first mechanism in the presence of Mn. The reason why this trinucleotide (rather than the complementary tetramer) catalyzes this reaction may be because the UUU-AAA pairing is the weakest and most flexible trinucleotide among the 64 conformations, which provides the binding site for Mn.
Phosphoryl transfer can also be catalyzed without metal ions. For example, pancreatic ribonuclease A and hepatitis delta virus (HDV) ribozymes can catalyze the cleavage of RNA backbone through acid-base catalysis without metal ions. Hairpin ribozyme can also catalyze the self-cleavage of RNA without metal ions, but the mechanism for this is still unclear.
Ribozyme can also catalyze the formation of peptide bond between adjacent amino acids by lowering the activation entropy. | 7 | Physical Chemistry |
The corrosive effects of nitric acid are exploited for some specialty applications, such as etching in printmaking, pickling stainless steel or cleaning silicon wafers in electronics.
A solution of nitric acid, water and alcohol, nital, is used for etching metals to reveal the microstructure. ISO 14104 is one of the standards detailing this well known procedure.
Nitric acid is used either in combination with hydrochloric acid or alone to clean glass cover slips and glass slides for high-end microscopy applications. It is also used to clean glass before silvering when making silver mirrors.
Commercially available aqueous blends of 5–30% nitric acid and 15–40% phosphoric acid are commonly used for cleaning food and dairy equipment primarily to remove precipitated calcium and magnesium compounds (either deposited from the process stream or resulting from the use of hard water during production and cleaning). The phosphoric acid content helps to passivate ferrous alloys against corrosion by the dilute nitric acid.
Nitric acid can be used as a spot test for alkaloids like LSD, giving a variety of colours depending on the alkaloid. | 3 | Analytical Chemistry |
An arrastra (or arastra) is a primitive mill for grinding and pulverizing (typically) gold or silver ore. Its simplest form is two or more flat-bottomed drag stones placed in a circular pit paved with flat stones, and connected to a center post by a long arm. With a horse, mule or human providing power at the other end of the arm, the stones were dragged slowly around in a circle, crushing the ore. Some arrastras were powered by a water wheel; a few were powered by steam or gasoline engines, and even electricity.
Arrastras were widely used throughout the Mediterranean region since Phoenician times. The Spanish introduced the arrastra to the New World in the 16th century. The word "arrastra" comes from the Spanish language arrastrar, meaning to drag along the ground. Arrastras were suitable for use in small or remote mines, since they could be built from local materials and required little investment capital.
For gold ore, the gold was typically recovered by amalgamation with quicksilver. The miner would add clean mercury to the ground ore, continue grinding, rinse out the fines, then add more ore and repeat the process. At cleanup, the gold amalgam was carefully recovered from the low places and crevices in the arrastra floor. The amalgam was then heated in a distillation retort to recover the gold, and the mercury was saved for reuse.
For silver ore, the patio process, invented in Mexico in 1554, was generally used to recover the silver from ore ground in the arrastra. | 8 | Metallurgy |
The E. coli strain W3110 was genetically engineered to generate 2 moles of acetate for every 1 mole of glucose that undergoes fermentation. This is known as a homoacetate pathway. | 1 | Biochemistry |
Systemic agmatine can potentiate opioid analgesia and prevent tolerance to chronic morphine in laboratory rodents. Since then, cumulative evidence amply shows that agmatine inhibits opioid dependence and relapse in several animal species. | 1 | Biochemistry |
The type II receptors phosphorylate the type I receptors; the type I receptors are then enabled to phosphorylate cytoplasmic R-Smads, which then act as transcriptional regulators. Signaling is initiated by the binding of TGF-β to its serine/threonine receptors. The serene/threonine receptors are the type II and type I receptors on the cell membrane. Binding of a TGF-β members induces assembly of a heterotetrameric complex of two type I and two type II receptors at the plasma membrane. Individual members of the TGF-β family bind to a certain set of characteristic combination of these type I and type II receptors. The type I receptors can be divided into two groups, which depends on the cytoplasmic R-Smads that they bind and phosphorylate. The first group of type I receptors (Alk1/2/3/6) bind and activate the R-Smads, Smad1/5/8. The second group of type I reactors (Alk4/5/7) act on the R-Smads, Smad2/3. The phosphorylated R-Smads then form complexes and the signals are funneled through two regulatory Smad (R-Smad) channels (Smad1/5/8 or Smad2/3). After the ligand-receptor complexes phosphorylate the cytoplasmic R-Smads, the signal is then sent through Smad 1/5/8 or Smad 2/3. This leads to the downstream signal cascade and cellular gene targeting. | 1 | Biochemistry |
Most domains have a very broad substrate specificity and usually only the A-domain determines which amino acid is incorporated in a module. Ten amino acids that control substrate specificity and can be considered the codons of nonribosomal peptide synthesis have been identified, and rational protein design has yielded methodologies to computationally switch the specificities of A-domains. The condensation C-domain is also believed to have substrate specificity, especially if located behind an epimerase E-domain-containing module where it functions as a filter for the epimerized isomer. Computational methods, such as SANDPUMA and NRPSpredictor2, have been developed to predict substrate specificity from DNA or protein sequence data. | 1 | Biochemistry |
Silica gel is a chemically inert, non-toxic, polar and dimensionally stable (. It is prepared by the reaction between sodium silicate and acetic acid, which is followed by a series of after-treatment processes such as aging, pickling, etc. These after-treatment methods results in various pore size distributions.
Silica is used for drying of process air (e.g. oxygen, natural gas) and adsorption of heavy (polar) hydrocarbons from natural gas. | 7 | Physical Chemistry |
Sodium trifluoromethanesulfinate (CFSONa) as a trifluoromethylation reagent was introduced by Langlois in 1991. The reaction requires t-butyl hydroperoxide and generally a metal and proceeds through a radical mechanism. The reagent has been applied with heterocyclic substrates | 0 | Organic Chemistry |
In 1814, Jean-Jacques Colin discovered (to his surprise) that a mixture of dry gaseous ammonia and iodine formed a shiny, metallic-appearing liquid. Frederick Guthrie established the precise composition of the resulting I···NH complex fifty years later, but the physical processes underlying the molecular interaction remained mysterious until the development of Robert S. Mullikens theory of inner-sphere and outer-sphere interactions. In Mullikens categorization, the intermolecular interactions associated with small partial charges affect only the "inner sphere" of an atom's electron distribution; the electron redistribution associated with Lewis adducts affects the "outer sphere" instead.
Then, in 1954, Odd Hassel fruitfully applied the distinction to rationalize the X-ray diffraction patterns associated with a mixture of 1,4-dioxane and bromine. The patterns suggested that only 2.71 Å separated the dioxane oxygen atoms and bromine atoms, much closer than the sum (3.35 Å) of the atoms' van der Waals radii; and that the angle between the O−Br and Br−Br bond was about 180°. From these facts, Hassel concluded that halogen atoms are directly linked to electron pair donors in a direction with a bond direction that coincides with the axes of the orbitals of the lone pairs in the electron pair donor molecule. For this work, Hassel was awarded the 1969 Nobel Prize in Chemistry.
Dumas and coworkers first coined the term "halogen bond" in 1978, during their investigations into complexes of CCl, CBr, SiCl, and SiBr with tetrahydrofuran, tetrahydropyran, pyridine, anisole, and di-n-butyl ether in organic solvents.
However, it was not until the mid-1990s, that the nature and applications of the halogen bond began to be intensively studied. Through systematic and extensive microwave spectroscopy of gas-phase halogen bond adducts, Legon and coworkers drew attention to the similarities between halogen-bonding and better-known hydrogen-bonding interactions.
In 2007, computational calculations by Politzer and Murray showed that an anisotropic electron density distribution around the halogen nucleus — the "σ-hole" — underlay the high directionality of the halogen bond. This hole was then experimentally observed using Kelvin probe force microscopy.
In 2020, Kellett et al. showed that halogen bonds also have a π-covalent character similar to metal coordination bonds. In August 2023 the "π-hole" was too experimentally observed | 6 | Supramolecular Chemistry |
*Kefir
**In Kefir, the lactose in milk is fermented by lactic acid bacteria to produce lactic acid, further breakdown to propionic acid is done by propionibacteria. Yeast in Kefir ferment to produce ethanol, which is consumed by other bacteria to make acids and aldehydes that contribute to flavor.
* Sake
** In the making of Sake, Koji molds are used to ferment rice producing free sugars that are then fermented by lactic acid bacteria and yeast, providing ethanol and flavor active compounds.
* Lambic Beer
** Wheat is fermented by yeast and LAB.
* Shochu
** Rice, wheat, and batata are fermented by mold, yeast, and LAB.
* Vinegar
** Rice is fermented by mold, yeast, LAB, and acetic acid bacteria.
* Soy Sauce
** Soy bean and wheat are fermented by mold, yeast, and LAB.
* Whiskey
** Barely, corn, and rye are fermented by yeast and LAB.
* Wine
** Grapes are fermented by yeast and LAB.
* Kombucha
** Tea and sucrose are fermented by yeast and acetic acid bacteria from a SCOBY. | 1 | Biochemistry |
The site was opened in 1931 by the Lindsay Light and Chemical Company. It processed ores like monazite to produce elements, including thorium and uranium. It also made gaslight mantles, and during World War II, hydrofluoric acid.
In 1958, it became owned by American Potash and Chemical Company (AMPOT), which at one point had a Lindsay Chemical Division.
In 1967, AMPOT, and thus the facility, were bought by Kerr-McGee. The Rare Earths Facility were closed by Kerr-McGee in 1973.
In 2005, KMCC was spun off from Kerr-McGee as Tronox, shortly before Kerr-McGee was acquired by Anadarko Petroleum. Tronox inherited responsibility for the Rare Earths Facility and other sites. Tronox went bankrupt in 2009 and shareholders sued Anadarko Petroleum, partly for having misled investors in Tronox about its environmental debts. | 8 | Metallurgy |
Saturation conditions can be viewed as a special case of pre-equilibrium conditions. At the concentration of substrate examined, formation of the catalyst-substrate complex is rapid and essentially irreversible. The catalyst resting state consists entirely of the bound complex, and [A] is no longer present in the rate law; changing [A] will have no effect on reaction rate because the catalyst is already completely bound and reacting as rapidly as k allows. The simplest case of saturation kinetics is the well-studied Michaelis-Menten model for enzyme kinetics. | 7 | Physical Chemistry |
Binding of a number of hormones and steroids, including testosterone, progesterone, and cholesterol, has been found to occur with sigma-2 receptors, though in some cases with lower affinity than to the sigma-1 receptor. Signaling caused by this binding is thought to occur via a calcium secondary messenger and calcium-dependent phosphorylation, and in association with sphingolipids following endoplasmic reticulum release of calcium. Known effects include decrease of expression of effectors in the mTOR pathway, and suppression of cyclin D1 and PARP-1. | 1 | Biochemistry |
As for aldehydes, the hydrogen atoms on the carbon adjacent ("α to") the carboxyl group in esters are sufficiently acidic to undergo deprotonation, which in turn leads to a variety of useful reactions. Deprotonation requires relatively strong bases, such as alkoxides. Deprotonation gives a nucleophilic enolate, which can further react, e.g., the Claisen condensation and its intramolecular equivalent, the Dieckmann condensation. This conversion is exploited in the malonic ester synthesis, wherein the diester of malonic acid reacts with an electrophile (e.g., alkyl halide), and is subsequently decarboxylated. Another variation is the Fráter–Seebach alkylation. | 0 | Organic Chemistry |
Fusion of a cyclooctyne to two aryl rings increases the reaction rate, and the cyclooctyne reagents of the Bertozzi group proceeded through a series of fusions that sought to increase the ring strain even further. DIBO (dibenzo cyclooctyne) was developed as a precursor to BARAC (biarylazacyclooctynone), although calculations had predicted that a single fused aryl ring would be optimal. Attempts to make a difluoro benzo cyclooctyne (DIFBO) were unsuccessful due to the instability of the compound.
The reason for the instability of DIFBO is that it is so reactive that it spontaneously trimerizes to form two asymmetric products that can be characterized by X-ray crystallography. To stabilize the DIFBO, it is trapped by forming a stable inclusion complex with β-cyclodextrin in aqueous media. This complex, formed with the β-cyclodextrin, can then be stored as a lyophilized powder. To obtain the free DIFBO, the lyophilized powder is dissociated with organic solvents to produce the free DIFBO for in situ kinetic and spectroscopic analysis.
Problems with DIFO with in vivo mouse studies illustrate the difficulty of producing bioorthogonal reactions. | 0 | Organic Chemistry |
The Flory–Stockmayer Theory predicts the gel point for the system consisting of three types of monomer units
:linear units with two A-groups (concentration ),
:linear units with two B groups (concentration ),
:branched A units (concentration ).
The following definitions are used to formally define the system
The theory states that the gelation occurs only if , where
is the critical value for cross-linking and is presented as a function of ,
or, alternatively, as a function of ,
One may now substitute expressions for into definition of and obtain
the critical values of that admit gelation. Thus gelation occurs if
alternatively, the same condition for reads,
The both inequalities are equivalent and one may use the one that is more convenient. For instance, depending on which conversion or is resolved analytically. | 7 | Physical Chemistry |
Perhaps the single most important reaction of enolate ions is their alkylation by treatment with an alkyl halide or tosylate, thereby forming a new C-C bond and joining two smaller pieces into one larger molecule. Alkylation occurs when the nucleophilic enolate ion reacts with the electrophilic alkyl halide in an SN reaction and displaces the leaving group by backside attack.
Alkylation reactions are subject to the same constraints that affect all SN reactions. Thus, the leaving group X in the alkylating agent R-X can be chloride, bromide, iodide, or tosylate . Tile alkyl group R should be primary or methyl, and preferably should be allylic or benzylic. Secondary halides react poorly, and tertiary halides don't react at all because a competing E2 elimination of HX occurs instead. Vinylic and aryl halides are also unreactive because backside approach is sterically prevented. | 0 | Organic Chemistry |
Propionyl chloride (also propanoyl chloride) is the organic compound with the formula CHCHC(O)Cl. It is the acyl chloride derivative of propionic acid. It undergoes the characteristic reactions of acyl chlorides. It is a colorless, corrosive, volatile liquid.
It is used as a reagent for organic synthesis. In derived chiral amides and esters, the methylene protons are diastereotopic.
There have been efforts to schedule Propionyl chloride as a DEA List 1 Chemical as it can be used to synthesize fentanyl. | 0 | Organic Chemistry |
A study of four distinct hydrolases (human serum paraoxonase (PON1), pseudomonad phosphotriesterase (PTE), Protein tyrosine phospatase(PTP) and human carbonic anhydrase II (CAII)) has shown the main activity is "robust" towards change, whereas the promiscuous activities are weak and more "plastic". Specifically, selecting for an activity that is not the main activity (via directed evolution), does not initially diminish the main activity (hence its robustness), but greatly affects the non-selected activities (hence their plasticity).
The phosphotriesterase (PTE) from Pseudomonas diminuta was evolved to become an arylesterase (P–O to C–O hydrolase) in eighteen rounds gaining a 10 shift in specificity (ratio of K), however most of the change occurred in the initial rounds, where the unselected vestigial PTE activity was retained and the evolved arylesterase activity grew, while in the latter rounds there was a little trade-off for the loss of the vestigial PTE activity in favour of the arylesterase activity.
This means firstly that a specialist enzyme (monofunctional) when evolved goes through a generalist stage (multifunctional), before becoming a specialist again—presumably after gene duplication according to the IAD model—and secondly that promiscuous activities are more plastic than the main activity. | 1 | Biochemistry |
A suitable setup for automated thermometric titrimetry comprises the following:
* Precision fluid dispensing devices – "burettes" – for adding titrants and dosing of other reagents
* Thermistor-based thermometric sensor
* Titration vessel
* Stirring device, capable of highly efficient stirring of vessel contents without splashing
* Computer with thermometric titration operating system
* Thermometric titration interface module – this regulates the data flow between the burettes, sensors and the computer
Figure 6 illustrates a modern automated thermometric titration system based on the Metrohm 859 Titrotherm interface module with Thermoprobe sensor, Metrohm 800 Dosino dispensing devices and a computer running the operational software.
Figure 7 is a schematic of the relationship between components in automated thermometric titration system.
A = dosing device <br>
B = thermometric sensor <br>
C = stirring device <br>
D = thermometric titration interface module <br>
E = computer | 3 | Analytical Chemistry |
The Brinkman number (Br) is a dimensionless number related to heat conduction from a wall to a flowing viscous fluid, commonly used in polymer processing. It is named after the Dutch mathematician and physicist Henri Brinkman. There are several definitions; one is
where
* μ is the dynamic viscosity;
* u is the flow velocity;
* κ is the thermal conductivity;
* T is the bulk fluid temperature;
* T is the wall temperature;
* Pr is the Prandtl number
* Ec is the Eckert number
It is the ratio between heat produced by viscous dissipation and heat transported by molecular conduction. i.e., the ratio of viscous heat generation to external heating. The higher its value, the slower the conduction of heat produced by viscous dissipation and hence the larger the temperature rise.
In, for example, a screw extruder, the energy supplied to the polymer melt comes primarily from two sources:
* viscous heat generated by shear between elements of the flowing liquid moving at different velocities;
* direct heat conduction from the wall of the extruder.
The former is supplied by the motor turning the screw, the latter by heaters. The Brinkman number is a measure of the ratio of the two. | 7 | Physical Chemistry |
The Gill Mantle ("Txampaysye" in Navi) is a large jellyfish like creature native to Pandoras reefs. The Navi can bond with them in the water, which can supply them with oxygen through the water allowing Navi to remain underwater much longer. They are primarily used by Kiri throughout Avatar: The Way of Water. | 1 | Biochemistry |
Iodosobenzene has no commercial uses, but in the laboratory it is employed as an "oxo-transfer reagent." It epoxidizes certain alkenes and converts some metal complexes into the corresponding oxo derivatives. Although it is an oxidant, it is also mildly nucleophilic. These oxo-transfer reactions operate by the intermediacy of adducts PhI=O→M, which release PhI.
A mixture of iodosobenzene and sodium azide in acetic acid converts alkenes to vicinal diazides:. | 0 | Organic Chemistry |
Catalysts based on synthetic metalloporphyrins have been extensively investigated, although few or no applications exist. Due to their distinctive redox properties, Co(II)–porphyrin-based systems are radical initiators. Some complexes emulate the action of various heme enzymes such as cytochrome P450, lignin peroxidase. Metalloporphyrins are also studied as catalysts for water splitting, with the purpose of generating molecular hydrogen and oxygen for fuel cells.
In addition, porous organic polymers based on porphyrins, along with metal oxide nanoparticles, | 1 | Biochemistry |
In the tables of quantities and their units, the ISO 31-8 standard shows symbols for substances as subscripts (e.g., c, w, p). It also notes that it is generally advisable to put symbols for substances and their states in parentheses on the same line, as in c(HSO). | 7 | Physical Chemistry |
An amphibolic pathway is one that can be either catabolic or anabolic based on the availability of or the need for energy. The currency of energy in a biological cell is adenosine triphosphate (ATP), which stores its energy in the phosphoanhydride bonds. The energy is utilized to conduct biosynthesis, facilitate movement, and regulate active transport inside of the cell. Examples of amphibolic pathways are the citric acid cycle and the glyoxylate cycle. These sets of chemical reactions contain both energy producing and utilizing pathways. To the right is an illustration of the amphibolic properties of the TCA cycle.
The glyoxylate shunt pathway is an alternative to the tricarboxylic acid (TCA) cycle, for it redirects the pathway of TCA to prevent full oxidation of carbon compounds, and to preserve high energy carbon sources as future energy sources. This pathway occurs only in plants and bacteria and transpires in the absence of glucose molecules. | 1 | Biochemistry |
* 1912: Nobel Prize in Chemistry for his discovery of the Grignard reagent (shared the award with fellow Frenchman Paul Sabatier).
* 1912: Lavoisier Medal, Société Chimique de France
* 1933: Légion d'Honneur, Commander | 0 | Organic Chemistry |
is a dense, colourless liquid, although crude samples may be yellow or even red-brown. It is one of the rare transition metal halides that is a liquid at room temperature, vanadium tetrachloride| being another example. This property reflects the fact that molecules of weakly self-associate. Most metal chlorides are polymers, wherein the chloride atoms bridge between the metals. Its melting point is similar to that of Carbon tetrachloride|.
has a "closed" electronic shell, with the same number of electrons as the noble gas argon. The tetrahedral structure for is consistent with its description as a d metal center () surrounded by four identical ligands. This configuration leads to highly symmetrical structures, hence the tetrahedral shape of the molecule. adopts similar structures to Titanium tetrabromide| and Titanium tetraiodide|; the three compounds share many similarities. and react to give mixed halides , where x = 0, 1, 2, 3, 4. Magnetic resonance measurements also indicate that halide exchange is also rapid between and .
is soluble in toluene and chlorocarbons. Certain arenes form complexes of the type . reacts exothermically with donor solvents such as THF to give hexacoordinated adducts. Bulkier ligands (L) give pentacoordinated adducts . | 0 | Organic Chemistry |
The iron–sulfur world hypothesis is a set of proposals for the origin of life and the early evolution of life advanced in a series of articles between 1988 and 1992 by Günter Wächtershäuser, a Munich patent lawyer with a degree in chemistry, who had been encouraged and supported by philosopher Karl R. Popper to publish his ideas. The hypothesis proposes that early life may have formed on the surface of iron sulfide minerals, hence the name. It was developed by retrodiction (making a "prediction" about the past) from extant biochemistry (non-extinct, surviving biochemistry) in conjunction with chemical experiments. | 1 | Biochemistry |
In 1978 the United States banned the use of CFCs such as Freon in aerosol cans, the beginning of a long series of regulatory actions against their use. The critical DuPont manufacturing patent for Freon ("Process for Fluorinating Halohydrocarbons", U.S. Patent #3258500) was set to expire in 1979. In conjunction with other industrial peers DuPont formed a lobbying group, the "Alliance for Responsible CFC Policy", to combat regulations of ozone-depleting compounds. In 1986 DuPont, with new patents in hand, reversed its previous stance and publicly condemned CFCs. DuPont representatives appeared before the Montreal Protocol urging that CFCs be banned worldwide and stated that their new HCFCs would meet the worldwide demand for refrigerants. | 2 | Environmental Chemistry |
The introduction of atom into a crystal of atom creates a pinning point for multiple reasons. An alloying atom is by nature a point defect, thus it must create a stress field when placed into a foreign crystallographic position, which could block the passage of a dislocation. However, it is possible that the alloying material is approximately the same size as the atom that is replaced, and thus its presence would not stress the lattice (as occurs in cobalt alloyed nickel). The different atom would, though, have a different elastic modulus, which would create a different terrain for the moving dislocation. A higher modulus would look like an energy barrier, and a lower like an energy trough – both of which would stop its movement. | 8 | Metallurgy |
In mass spectroscopy based proteomics there are three major steps needed for peptide identification: sample preparation, separation of peptides, and identification of peptides. Several groups have focused on oocytes or very early cleavage-stage cells since these cells are unusually large and provide enough material for analysis. Another approach, single cell proteomics by mass spectrometry (SCoPE-MS) has quantified thousands of proteins in mammalian cells with typical cell sizes (diameter of 10-15 μm) by combining carrier-cells and single-cell barcoding. The second generation, SCoPE2, increased the throughput by automated and miniaturized sample preparation; It also improved quantitative reliability and proteome coverage by data-driven optimization of LC-MS/MS and peptide identification. The sensitivity and consistency of these methods have been further improved by prioritization, and massively parallel sample preparation in nanoliter size droplets. Another direction for single-cell protein analysis is based on a scalable framework of multiplexed data-independent acquisition (plexDIA) enables time saving by parallel analysis of both peptide ions and protein samples, thereby realizing multiplicative gains in throughput.
The separation of differently sized proteins can be accomplished by using capillary electrophoresis (CE) or liquid chromatography (LC) (using liquid chromatography with mass spectroscopy is also known as LC-MS). This step gives order to the peptides before quantification using tandem mass-spectroscopy (MS/MS). The major difference between quantification methods is some use labels on the peptides such as tandem mass tags (TMT) or dimethyl labels which are used to identify which cell a certain protein came from (proteins coming from each cell have a different label) while others use not labels (quantify cells individually). The mass spectroscopy data is then analyzed by running data through databases that convert the information about peptides identified to quantification of protein levels. These methods are very similar to those used to quantify the proteome of bulk cells, with modifications to accommodate the very small sample volume. | 1 | Biochemistry |
Catalysts that promote chain walking were discovered in the 1980-1990s. Nickel(II) and palladium(II) complexes of α-diimine ligands were known to efficiently catalyze polymerization of alkenes. They are also referred as Brookhart's catalysts after being used for making of high molar mass polyolefins for the first time at University of North Carolina at Chapel Hill in 1995. Currently nickel and palladium complexes bearing α-diimine ligands, such as the two examples shown, are the most thoroughly described chain walking catalysts in scientific literature. Ligand design influences not only CW extent but also regio- and stereoselectivity and also the sensitivity of the catalyst to undergo chain-breaking reactions, mainly β-H elimination, influencing achievable molar mass and also the possibility to achieve living polymerization behaviour. Thus stereo block copolymers could be made by combination of living and stereospecific CW polymerization catalysts. Continuous research effort led to design of other ligands which provide CW polymerization catalysts upon complexation to late transition metals. Examples are β-diimine, α-keto-β-diimine, amine-imine and most recently diamine ligands. As the vast majority of CW polymerization catalysts is based on late-transition metal complexes, having generally lower oxophilicity, these complexes were demonstrated also to provide copolymerisation of olefins with polar monomers like acrylates, alkylvinylketones, ω-alken-1-ols, ω-alken-1-carboxylic acids etc., which was the main initial intention of development of this class of catalysts. These random copolymers could further be utilized in the construction of sophisticated amphiphilic grafted copolymers with hydrophobic polyolefin core and shell based on hydrophilic arms, in some cases made of stimuli-responsive polymers. | 7 | Physical Chemistry |
As series resistance increases, the voltage drop between the junction voltage and the terminal voltage becomes greater for the same current. The result is that the current-controlled portion of the I-V curve begins to sag toward the origin, producing a significant decrease in the terminal voltage V and a slight reduction in I, the short-circuit current. Very high values of R will also produce a significant reduction in I; in these regimes, series resistance dominates and the behavior of the solar cell resembles that of a resistor. These effects are shown for crystalline silicon solar cells in the I-V curves displayed in the figure to the right.
Losses caused by series resistance are in a first approximation given by P = VI = IR and increase quadratically with (photo-)current. Series resistance losses are therefore most important at high illumination intensities. | 7 | Physical Chemistry |
Nanocars are a new class of molecular machines that can roll across solid surfaces with structurally defined direction. They are molecules essentially composed of a few tens or hundreds of hydrogen and carbon atoms and are measuring one to three nanometers.
The nanocar is propelled step by step by electrical impulses and electron transfer from the tip of the STM. The resulting tunnel current flows through the nanocar between the tip of the microscope and the common metal track. There is no direct mechanical contact with the tip. The nanocar is therefore neither pushed nor deformed by the tip of the microscope during the race. Some of the electrons that pass through the nanocar release energy as small intramolecular vibrations that activate the nanocar's motor. | 6 | Supramolecular Chemistry |
In organic chemistry, anti-periplanar, or antiperiplanar, describes the bond angle in a molecule. In this conformer, the dihedral angle of the bond and the bond is greater than +150° or less than −150° (Figures 1 and ). Anti-periplanar is often used in textbooks to mean strictly anti-coplanar, with an dihedral angle of 180° (Figure 3). In a Newman projection, the molecule will be in a staggered arrangement with the anti-periplanar functional groups pointing up and down, 180° away from each other (see Figure 4). Figure 5 shows 2-chloro-2,3-dimethylbutane in a sawhorse projection with chlorine and a hydrogen anti-periplanar to each other.
Syn-periplanar or synperiplanar is similar to anti-periplanar. In the syn-periplanar conformer, the A and D are on the same side of the plane of the bond, with the dihedral angle of and between +30° and −30° (see Figure 2). | 0 | Organic Chemistry |
The essence of Brønsted–Lowry theory is that an acid is only such in relation to a base, and vice versa. Water is amphoteric as it can act as an acid or as a base. In the image shown at the right one molecule of acts as a base and gains to become while the other acts as an acid and loses to become .
Another example is illustrated by substances like aluminium hydroxide, . | 7 | Physical Chemistry |
In March 1865 Macadam sailed to New Zealand to give evidence at the trial of Captain W. A. Jarvey, accused of fatally poisoning his wife, but the jury did not reach a verdict. During the return voyage, Macadam fractured his ribs during a storm. He was advised, on medical grounds, not to return for the adjourned trial but did so and died on the ship on 2 September 1865. His medical-student assistant John Drummond Kirkland gave evidence at the trial in Macadam's place, and Jarvey was convicted.
The Australian News commented, "At the time of his death, Dr Macadam was but 38 years of age; there can be little doubt that the various and onerous duties he discharged for the public must be attributed in great measure the shortening of his days." The Australian Medical Journal stated, "For some time it had been evident to his friends that his general health was giving way: that a frame naturally robust and vigorous was gradually becoming undermined by the incessant and harassing duties of the multifarious offices he filled." The inquest verdict (he died at sea) stated, "His death was caused by excessive debility and general exhaustion." | 3 | Analytical Chemistry |
* The first TEs were discovered in maize (Zea mays) by Barbara McClintock in 1948, for which she was later awarded a Nobel Prize. She noticed chromosomal insertions, deletions, and translocations caused by these elements. These changes in the genome could, for example, lead to a change in the color of corn kernels. About 64% of the maize genome consists of TEs. The Ac/Ds system described by McClintock are Class II TEs. Transposition of Ac in tobacco has been demonstrated by B. Baker.
* In the pond microorganism, Oxytricha, TEs play such a critical role that when removed, the organism fails to develop.
* One family of TEs in the fruit fly Drosophila melanogaster are called P elements. They seem to have first appeared in the species only in the middle of the twentieth century; within the last 50 years, they spread through every population of the species. Gerald M. Rubin and Allan C. Spradling pioneered technology to use artificial P elements to insert genes into Drosophila by injecting the embryo.
* In bacteria, TEs usually carry an additional gene for functions other than transposition, often for antibiotic resistance. In bacteria, transposons can jump from chromosomal DNA to plasmid DNA and back, allowing for the transfer and permanent addition of genes such as those encoding antibiotic resistance (multi-antibiotic resistant bacterial strains can be generated in this way). Bacterial transposons of this type belong to the Tn family. When the transposable elements lack additional genes, they are known as insertion sequences.
* In humans, the most common TE is the Alu sequence. It is approximately 300 bases long and can be found between 300,000 and one million times in the human genome. Alu alone is estimated to make up 15–17% of the human genome.
* Mariner-like elements are another prominent class of transposons found in multiple species, including humans. The Mariner transposon was first discovered by Jacobson and Hartl in Drosophila. This Class II transposable element is known for its uncanny ability to be transmitted horizontally in many species. There are an estimated 14,000 copies of Mariner in the human genome comprising 2.6 million base pairs. The first mariner-element transposons outside of animals were found in Trichomonas vaginalis.
* Mu phage transposition is the best-known example of replicative transposition.
* In Yeast genomes (Saccharomyces cerevisiae) there are five distinct retrotransposon families: Ty1, Ty2, Ty3, Ty4 and Ty5.
* A helitron is a TE found in eukaryotes that is thought to replicate by a rolling-circle mechanism.
* In human embryos, two types of transposons combined to form noncoding RNA that catalyzes the development of stem cells. During the early stages of a fetuss growth, the embryos inner cell mass expands as these stem cells enumerate. The increase of this type of cells is crucial, since stem cells later change form and give rise to all the cells in the body.
* In peppered moths, a transposon in a gene called cortex caused the moths' wings to turn completely black. This change in coloration helped moths to blend in with ash and soot-covered areas during the Industrial Revolution.
* Aedes aegypti carries a large and diverse number of TEs. This analysis by Matthews et al. 2018 also suggests this is common to all mosquitoes. | 1 | Biochemistry |
The usual definition of a splash zone is the area just above and just below the average water level of a body of water. It also includes areas that may be subject to water spray and mist.
A significant amount of corrosion of fences is due to landscaper tools scratching fence coatings and irrigation sprinklers spraying these damaged fences. Recycled water typically has a higher salt content than potable drinking water, meaning that it is more corrosive than regular tap water. The same risk from damage and water spray exists for above ground piping and backflow preventers. Fiberglass covers, cages, and concrete footings have worked well to keep tools at an arms length. Even the location where a roof drain splashes down can matter. Drainage from a homes roof valley can fall directly down onto a gas meter causing its piping to corrode at an accelerated rate reaching 50% wall thickness within 4 years. It is the same effect as a splash zone in the ocean, or in a pool with lot of oxygen and agitation that removes material as it corrodes.
Tanks or structural tubing such as bench seat supports or amusement park rides can accumulate water and moisture if the structure does not allow for drainage. This humid environment can then lead to internal corrosion of the structure affecting the structural integrity. The same can happen in tropical environments leading to external corrosion. This would include Corrosion in ballast tanks on ships. | 8 | Metallurgy |
The second law of thermodynamics can be interpreted as quantifying state transformations which are statistically unlikely so that they become effectively forbidden. The second law typically applies to systems composed of many particles interacting; Quantum thermodynamics resource theory is a formulation of thermodynamics in the regime where it can be applied to a small number of particles interacting with a heat bath. For processes which are cyclic or very close to cyclic, the second law for microscopic systems takes on a very different form than it does at the macroscopic scale, imposing not just one constraint on what state transformations are possible, but an entire family of constraints. These second laws are not only relevant for small systems, but also apply to individual macroscopic systems interacting via long-range interactions, which only satisfy the ordinary second law on average. By making precise the definition of thermal operations, the laws of thermodynamics take on a form with the first law defining the class of thermal operations, the zeroth law emerging as a unique condition ensuring the theory is nontrivial, and the remaining laws being a monotonicity property of generalised free energies. | 7 | Physical Chemistry |
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