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TCF7L2 is downstream of the WNT/β-catenin pathways. The activation of the WNT/β-catenin pathways have been associated demyelination in multiple sclerosis. TCF7L2 is unregulated during early remyelination, leading scientists to believe that it is involved in remyelination. TCF7L2 could act in dependence or independent of the WNT/β-catenin pathways. | 1 | Biochemistry |
While traditional nucleic acid synthesis only uses 4 base pairs - adenine, thymine, guanine and cytosine, oligonucleotide synthesis in the future could incorporate the use of unnatural base pairs, which are artificially designed and synthesized nucleobases that do not occur in nature.
In 2012, a group of American scientists led by Floyd Romesberg, a chemical biologist at the Scripps Research Institute in San Diego, California, published that his team designed an unnatural base pair (UBP). The two new artificial nucleotides or Unnatural Base Pair (UBP) were named d5SICS and dNaM. More technically, these artificial nucleotides bearing hydrophobic nucleobases, feature two fused aromatic rings that form a (d5SICS–dNaM) complex or base pair in DNA. In 2014 the same team from the Scripps Research Institute reported that they synthesized a stretch of circular DNA known as a plasmid containing natural T-A and C-G base pairs along with the best-performing UBP Romesbergs laboratory had designed, and inserted it into cells of the common bacterium E. coli that successfully replicated the unnatural base pairs through multiple generations. This is the first known example of a living organism passing along an expanded genetic code to subsequent generations. This was in part achieved by the addition of a supportive algal gene that expresses a nucleotide triphosphate transporter which efficiently imports the triphosphates of both d5SICSTP and dNaMTP into E. coli' bacteria. Then, the natural bacterial replication pathways use them to accurately replicate the plasmid containing d5SICS–dNaM.
The successful incorporation of a third base pair is a significant breakthrough toward the goal of greatly expanding the number of amino acids which can be encoded by DNA, from the existing 20 amino acids to a theoretically possible 172, thereby expanding the potential for living organisms to produce novel proteins. In the future, these unnatural base pairs could be synthesised and incorporated into oligonucleotides via DNA printing methods. | 1 | Biochemistry |
In chemistry, Vapochromism strongly overlaps with solvatochromism since vapochromic systems are ones in which dyes change colour in response to the vapour of an organic compound or gas. Vapochromic devices are the optical branch of electronic noses. The main applications are in sensors for detecting volatile organic compounds (VOCs) in a variety of environments, including industrial, domestic and medical areas.
An example of such a device is an array consisting of a metalloporphyrin (Lewis acid), a pH indicator dye and a solvatochromic dye. The array is scanned with a flat-bed recorder, and the result are compared with a library of known VOCs. Vaporchromic materials are sometimes Pt or Au complexes, which undergo distinct color changes when exposed to VOCs. | 7 | Physical Chemistry |
Several techniques are currently employed to assess average telomere length in eukaryotic cells. One method is the Terminal Restriction Fragment (TRF) southern blot. There is a Web-based Analyser of the Length of Telomeres ([https://www.ceitec.eu/chromatin-molecular-complexes/rg51/tab?tabId=125 WALTER]), software processing the TRF pictures. A Real-Time PCR assay for telomere length involves determining the Telomere-to-Single Copy Gene (T/S) ratio, which is demonstrated to be proportional to the average telomere length in a cell.
Tools have also been developed to estimate the length of telomere from whole genome sequencing (WGS) experiments. Amongst these are TelSeq, Telomerecat and telomereHunter. Length estimation from WGS typically works by differentiating telomere sequencing reads and then inferring the length of telomere that produced that number of reads. These methods have been shown to correlate with preexisting methods of estimation such as PCR and TRF. Flow-FISH is used to quantify the length of telomeres in human white blood cells. A semi-automated method for measuring the average length of telomeres with Flow FISH was published in Nature Protocols in 2006.
While multiple companies offer telomere length measurement services, the utility of these measurements for widespread clinical or personal use has been questioned. Nobel Prize winner Elizabeth Blackburn, who was co-founder of one company, promoted the clinical utility of telomere length measures. | 1 | Biochemistry |
As with all gene therapies, a number of safety and toxicity issues need to be evaluated during the development of DDRNAI therapeutics.
Oncogene activation by viral insertion: Some gene therapy vectors integrate into the host genome, thereby acting as insertional mutagens. This was a particular issue with early retroviral vectors where insertions adjacent to oncogenes resulted in the development of lymphoid tumors. AAV vectors are considered low-risk for host-genome integration, as adeno-associated virus infection has not been associated with the induction of cancers in humans despite widespread prevalence across the general population. Moreover, extensive clinical use of AAV vectors has provided no evidence of carcinogenicity. While lentiviral vectors do integrate into the genome they do not appear to show a propensity to activate oncogene expression.
Immune response to gene therapy vectors: An immunological response to an adenoviral vector resulted in the death of a patient in an early human trial. Careful monitoring of potential toxicities in preclinical testing and analyses of pre-existing antibodies to gene therapy vectors in patients minimizes such risks.
Innate immune response: siRNAs have been shown to activate immune responses through interaction with Toll-like receptors leading to interferon responses. These receptors reside on the cell's surface and so DDRNAIconstructs – delivered directly into intracellular space – are not expected to induce this response.
Toxic effects due to over-expression of shRNAs: High-level expression of shRNAs has been shown to be toxic. Strategies to minimize levels of shRNA expression or promote precise processing of shRNAs can overcome this problem.
Off-target effects: Unintended silencing of genes that share sequence homology with expressed shRNAs can theoretically occur. Careful selection of shRNA sequences and thorough preclinical testing of constructs can circumvent this issue. | 1 | Biochemistry |
Smart hydrogels are sensitive to stimuli such as changes in temperature or pH. Changes in the environment alter the swelling properties of the hydrogels and can cause them to increase or decrease the release of the drug impregnated into the fibers. An example of this would be hydrogels that release insulin in the presence of high glucose levels in the bloodstream. These glucose sensitive hydrogels are modified with the enzyme glucose oxidase. In the presence of glucose, the glucose oxidase will catalyze a reaction that ends in increased levels of H. These H ions raise the pH of the surrounding environment and could therefore cause a change in a smart hydrogel that would initiate the release of insulin. | 7 | Physical Chemistry |
Pauling first proposed the concept of electronegativity in 1932 to explain why the covalent bond between two different atoms (A–B) is stronger than the average of the A–A and the B–B bonds. According to valence bond theory, of which Pauling was a notable proponent, this "additional stabilization" of the heteronuclear bond is due to the contribution of ionic canonical forms to the bonding.
The difference in electronegativity between atoms A and B is given by:
where the dissociation energies, E, of the A–B, A–A and B–B bonds are expressed in electronvolts, the factor (eV) being included to ensure a dimensionless result. Hence, the difference in Pauling electronegativity between hydrogen and bromine is 0.73 (dissociation energies: H–Br, 3.79 eV; H–H, 4.52 eV; Br–Br 2.00 eV)
As only differences in electronegativity are defined, it is necessary to choose an arbitrary reference point in order to construct a scale. Hydrogen was chosen as the reference, as it forms covalent bonds with a large variety of elements: its electronegativity was fixed first at 2.1, later revised to 2.20. It is also necessary to decide which of the two elements is the more electronegative (equivalent to choosing one of the two possible signs for the square root). This is usually done using "chemical intuition": in the above example, hydrogen bromide dissolves in water to form H and Br ions, so it may be assumed that bromine is more electronegative than hydrogen. However, in principle, since the same electronegativities should be obtained for any two bonding compounds, the data are in fact overdetermined, and the signs are unique once a reference point has been fixed (usually, for H or F).
To calculate Pauling electronegativity for an element, it is necessary to have data on the dissociation energies of at least two types of covalent bonds formed by that element. A. L. Allred updated Pauling's original values in 1961 to take account of the greater availability of thermodynamic data, and it is these "revised Pauling" values of the electronegativity that are most often used.
The essential point of Pauling electronegativity is that there is an underlying, quite accurate, semi-empirical formula for dissociation energies, namely:
or sometimes, a more accurate fit
These are approximate equations but they hold with good accuracy. Pauling obtained the first equation by noting that a bond can be approximately represented as a quantum mechanical superposition of a covalent bond and two ionic bond-states. The covalent energy of a bond is approximate, by quantum mechanical calculations, the geometric mean of the two energies of covalent bonds of the same molecules, and there is additional energy that comes from ionic factors, i.e. polar character of the bond.
The geometric mean is approximately equal to the arithmetic mean—which is applied in the first formula above—when the energies are of a similar value, e.g., except for the highly electropositive elements, where there is a larger difference of two dissociation energies; the geometric mean is more accurate and almost always gives positive excess energy, due to ionic bonding. The square root of this excess energy, Pauling notes, is approximately additive, and hence one can introduce the electronegativity. Thus, it is these semi-empirical formulas for bond energy that underlie the concept of Pauling electronegativity.
The formulas are approximate, but this rough approximation is in fact relatively good and gives the right intuition, with the notion of the polarity of the bond and some theoretical grounding in quantum mechanics. The electronegativities are then determined to best fit the data.
In more complex compounds, there is an additional error since electronegativity depends on the molecular environment of an atom. Also, the energy estimate can be only used for single, not for multiple bonds. The enthalpy of formation of a molecule containing only single bonds can subsequently be estimated based on an electronegativity table, and it depends on the constituents and the sum of squares of differences of electronegativities of all pairs of bonded atoms. Such a formula for estimating energy typically has a relative error on the order of 10% but can be used to get a rough qualitative idea and understanding of a molecule. | 3 | Analytical Chemistry |
Organoperoxides can be reduced to alcohols with lithium aluminium hydride, as described in this idealized equation:
The phosphite esters and tertiary phosphines also effect reduction:
Cleavage to ketones and alcohols occurs in the base-catalyzed Kornblum–DeLaMare rearrangement, which involves the breaking of bonds within peroxides to form these products.
Some peroxides are drugs, whose action is based on the formation of radicals at desired locations in the organism. For example, artemisinin and its derivatives, such as artesunate, possess the most rapid action of all current drugs against falciparum malaria. Artesunate is also efficient in reducing egg production in Schistosoma haematobium infection. | 0 | Organic Chemistry |
The amino acid is not genetically coded, but it arises by post-translational methylation of cysteine. One pathway involves methyl transfer from alkylated DNA by zinc-cysteinate-containing repair enzymes.
Beyond its biological context, it has been examined as a chelating agent. | 1 | Biochemistry |
MITF is phosphorylated on several serine and tyrosine residues. Serine phosphorylation is regulated by several signaling pathways including MAPK/BRAF/ERK, receptor tyrosine kinase KIT, GSK-3 and mTOR. In addition, several kinases including PI3K, AKT, SRC and P38 are also critical activators of MITF phosphorylation. In contrast, tyrosine phosphorylation is induced by the presence of the KIT oncogenic mutation D816V. This KIT pathway is dependent on SRC protein family activation signaling. The induction of serine phosphorylation by the frequently altered MAPK/BRAF pathway and the GSK-3 pathway in melanoma regulates MITF nuclear export and thereby decreasing MITF activity in the nucleus. Similarly, tyrosine phosphorylation mediated by the presence of the KIT oncogenic mutation D816V also increases the presence of MITF in the cytoplasm. | 1 | Biochemistry |
Alpha-aminoadipic and alpha-ketoadipic aciduria is an autosomal recessive metabolic disorder characterized by an increased urinary excretion of alpha-ketoadipic acid and alpha-aminoadipic acid. It is caused by mutations in DHTKD1, which encodes the E1 subunit of the oxoglutarate dehydrogenase complex (alpha-ketoglutarate dehydrogenase complex). | 1 | Biochemistry |
Dextromethorphan was once thought to cause Olney's lesions when administered intravenously; however, this was later proven inconclusive, due to lack of research on humans. Tests were performed on rats, giving them 50 mg or more every day for as long as a month. Neurotoxic changes, including vacuolation, have been observed in posterior cingulate and retrosplenial cortices of rats administered other NMDA receptor antagonists such as PCP, but not with dextromethorphan. | 4 | Stereochemistry |
In 2001, Nakai et al. reported the development of GCaMP1 as a Ca probe with improved signal-to-noise ratio compared to previously developed fluorescent Ca probes. The first transgenic mouse expressing GCaMP1 was reported in 2004. However, at 37 ˚C (physiological temperature in mammals), GCaMP1 did not fold stably or fluoresce, limiting its potential use as a calcium indicator in vivo.
In 2006, Tallini et al. subsequently reported the improvement of GCaMP1 to GCaMP2, which exhibited brighter fluorescence than GCaMP1 and greater stability at mammalian body temperatures. Tallini et al. expressed GCaMP2 in cardiomyocytes in mouse embryos to perform the first in vivo GCaMP imaging of Ca in mammals.
Further modifications of GCaMP, including GCaMP3, GCaMP5, GCaMP6, and jGCaMP7, have been developed to progressively improve the signal, sensitivity, and dynamic range of Ca detection, with recent versions exhibiting fluorescence similar to native GFP. | 1 | Biochemistry |
The following is a list of consumer medicines that either contain pseudoephedrine or have switched to a less-regulated alternative such as phenylephrine.
*Actifed (made by GlaxoSmithKline) — contains 60 mg pseudoephedrine and 2.5 mg triprolidine in certain countries.
*Advil Cold & Sinus (made by Pfizer Canada Inc.) — contains 30 mg pseudoephedrine hydrochloride and 200 mg ibuprofen.
*Aleve-D Sinus & Cold (made by Bayer Healthcare) — contains 120 mg pseudoephedrine hydrochloride (also 220 mg naproxen).
*Allegra-D (made by Sanofi Aventis) — contains 120 mg of pseudoephedrine hydrochloride (also 60 mg of fexofenadine).
*Allerclear-D (made by Kirkland Signature) — contains 240 mg of pseudoephedrine sulfate (also 10 mg of loratadine).
*Benadryl Allergy Relief Plus Decongestant (made by McNeil Consumer Healthcare, a Johnson & Johnson company) — contains 60 mg pseudoephedrine hydrochloride (also 8 mg acrivastine)
*Cirrus (made by UCB) — contains 120 mg pseudoephedrine hydrochloride (also 5 mg cetirizine).
*Claritin-D (made by Bayer Healthcare) — contains 120 mg of pseudoephedrine sulfate (also 5 mg of loratadine).
*Claritin-D 24 Hour (made by Bayer Healthcare) — contains 240 mg of pseudoephedrine sulfate (also 10 mg of loratadine).
*Codral (made by Asia-Pacific subsidiary of Johnson & Johnson) — Codral Original contains pseudoephedrine, Codral New Formula substitutes phenylephrine for pseudoephedrine.
*Congestal (made by SIGMA Pharmaceutical Industries) — contains 60 mg pseudoephedrine hydrochloride (also 650 mg paracetamol and 4 mg chlorpheniramine).
*Contac (made by GlaxoSmithKline) — previously contained pseudoephedrine, now contains phenylephrine. As at Nov 2014 UK version still contains 30 mg pseudoephedrine hydrochloride per tablet.
*Demazin (made by Bayer Healthcare) — contains pseudoephedrine sulfate and chlorpheniramine maleate
*Eltor (made by Sanofi Aventis) — contains pseudoephedrine hydrochloride.
*Mucinex D (made by Reckitt Benckiser) — contains 60 mg pseudoephedrine hydrochloride (also 1200 mg guaifenesin).
*Nexafed (made by Acura Pharmaceuticals) — contains 30 mg pseudoephedrine per tablet, formulated with Impede Meth-Deterrent technology.
*Nurofen Cold & Flu (made by Reckitt Benckiser) — contains 30 mg pseudoephedrine hydrochloride (also 200 mg ibuprofen).
*Respidina – contains 120 mg of pseudoephedrine in the form of extended release tablets.
*Rhinex Flash (made by Pharma Product Manufacturing, Cambodia) — contains pseudoephedrine combined with paracetamol and triprolidine.
*Rhinos SR (made by Dexa Medica) — contains 120 mg of pseudoephedrine hydrochloride
* Sinutab (made by McNeil Consumer Healthcare, a Johnson & Johnson company) — contains 500 mg paracetamol and 30 mg pseudoephedrine hydrochloride.
* Sudafed Decongestant (made by McNeil Consumer Healthcare, a Johnson & Johnson company) — contains 60 mg of pseudoephedrine hydrochloride. Not to be confused with Sudafed PE, which contains phenylephrine.
* Theraflu (made by Novartis) — previously contained pseudoephedrine, now contains phenylephrine
* Trima — contains 60 mg pseudoephedrine hydrochloride
* Tylol Hot (made by NOBEL İLAÇ SANAYİİ VE TİCARET A.Ş., Turkey) — a packet of 20 g contains 60 mg pseudoephedrine hydrochloride, 500 mg paracetamol and 4 mg chlorpheniramine maleate
* Unifed (made by United Pharmaceutical Manufacturer, Jordan) — contains pseudoephedrine hydrochloride (also triprolidine and guaifenesin).
*Zyrtec-D 12 Hour (made by McNeil Consumer Healthcare, a Johnson & Johnson company) — contains 120 mg pseudoephedrine hydrochloride (also 5 mg of cetirizine).
*Zephrex-D (made by Westport Pharmaceuticals) – a special meth-resistant form of pseudoephedrine that becomes gooey when heated. | 4 | Stereochemistry |
The second rule holds that both Α% ≈ Τ% and G% ≈ C% are valid for each of the two DNA strands. This describes only a global feature of the base composition in a single DNA strand. | 1 | Biochemistry |
Metabolites produced by marine algae have been found to have many antimicrobial properties. This is because they are produced by the marine organisms as chemical deterrents and as such contain bioactive compounds. The principal classes of marine algae that produce these types of secondary metabolites are Cyanophyceae, Chlorophyceae and Rhodophyceae. Observed biogenic products include polyketides, amides, alkaloids, fatty acids, indoles and lipopeptides. For example, over 10% of compounds isolated from Lyngbya majuscula, which is one of the most abundant cyanobacteria, have antifungal and antimicrobial properties. Additionally, a study by Ren et al. (2002) tested halogenated furanones produced by Delisea pulchra from the Rhodophyceae class against the growth of Bacillus subtilis. When applied at a 40 µg/mL concentration, the furanone inhibited the formation of a biofilm by the bacteria and reduced the biofilm's thickness by 25% and the number of live cells by 63%.
These characteristics then have the potential to be utilised in man-made materials, such as making anti-fouling paints without the environment-damaging chemicals. Environmentally safe alternatives are needed to TBT (tin-based antifouling agent) which releases toxic compounds into water and the environment and has been banned in several countries. A class of biogenic compounds that has had a sizeable effect against the bacteria and microalgae that cause fouling are acetylene sesquiterpenoid esters produced by Caulerpa prolifera (from the Chlorophyceae class), which Smyrniotopoulos et al. (2003) observed inhibiting bacterial growth with up to 83% of the efficacy of TBT oxide.
Current research also aims to produce these biogenic substances on a commercial level using metabolic engineering techniques. By pairing these techniques with biochemical engineering design, algae and their biogenic substances can be produced on a large scale using photobioreactors. Different system types can be used to yield different biogenic products. | 0 | Organic Chemistry |
Three out of 10 advanced colorectal tumors had mutations leading to premature termination of the SFRP1 translation product. The mutations were two single-base deletions (26delG and 67delG) and a single-base change (G450A), which generates an in-frame stop codon. These three mutations were found within the first exon, which was shown previously to be sufficient for Wnt antagonist activity by itself [26, 32]. Of the 10 tumors analyzed, no truncating mutations were found in the second or third exons of SFRP1.
An additional 51 tumors were analyzed via direct sequence analysis, yielding 49 clearly interpretable results. Only the first exon was sequenced for stop codon mutations, but none were found. This indicates that point mutation is not a frequent method of inactivation of the SFRP1 gene in colorectal cancer. | 1 | Biochemistry |
Inosine monophosphate is synthesized on a pre-existing ribose-phosphate through a complex pathway (as shown in the figure on the right). The source of the carbon and nitrogen atoms of the purine ring, 5 and 4 respectively, come from multiple sources. The amino acid glycine contributes all its carbon (2) and nitrogen (1) atoms, with additional nitrogen atoms from glutamine (2) and aspartic acid (1), and additional carbon atoms from formyl groups (2), which are transferred from the coenzyme tetrahydrofolate as 10-formyltetrahydrofolate, and a carbon atom from bicarbonate (1). Formyl groups build carbon-2 and carbon-8 in the purine ring system, which are the ones acting as bridges between two nitrogen atoms.
A key regulatory step is the production of 5-phospho-α--ribosyl 1-pyrophosphate (PRPP) by ribose phosphate pyrophosphokinase, which is activated by inorganic phosphate and inactivated by purine ribonucleotides. It is not the committed step to purine synthesis because PRPP is also used in pyrimidine synthesis and salvage pathways.
The first committed step is the reaction of PRPP, glutamine and water to 5'-phosphoribosylamine (PRA), glutamate, and pyrophosphate - catalyzed by amidophosphoribosyltransferase, which is activated by PRPP and inhibited by AMP, GMP and IMP.
:PRPP + L-Glutamine + HO → PRA + L-Glutamate + PPi
In the second step react PRA, glycine and ATP to create GAR, ADP, and pyrophosphate - catalyzed by phosphoribosylamine—glycine ligase (GAR synthetase). Due to the chemical lability of PRA, which has a half-life of 38 seconds at PH 7.5 and 37 °C, researchers have suggested that the compound is channeled from amidophosphoribosyltransferase to GAR synthetase in vivo.
:PRA + Glycine + ATP → GAR + ADP + Pi
The third is catalyzed by phosphoribosylglycinamide formyltransferase.
:GAR + fTHF → fGAR + THF
The fourth is catalyzed by phosphoribosylformylglycinamidine synthase.
:fGAR + L-Glutamine + ATP → fGAM + L-Glutamate + ADP + Pi
The fifth is catalyzed by AIR synthetase (FGAM cyclase).
:fGAM + ATP → AIR + ADP + Pi + HO
The sixth is catalyzed by phosphoribosylaminoimidazole carboxylase.
:AIR + CO → CAIR + 2H+
The seventh is catalyzed by phosphoribosylaminoimidazolesuccinocarboxamide synthase.
:CAIR + L-Aspartate + ATP → SAICAR + ADP + Pi
The eight is catalyzed by adenylosuccinate lyase.
:SAICAR → AICAR + Fumarate
The products AICAR and fumarate move on to two different pathways. AICAR serves as the reactant for the ninth step, while fumarate is transported to the citric acid cycle which can then skip the carbon dioxide evolution steps to produce malate. The conversion of fumarate to malate is catalyzed by fumarase. In this way, fumarate connects purine synthesis to the citric acid cycle.
The ninth is catalyzed by phosphoribosylaminoimidazolecarboxamide formyltransferase.
:AICAR + fTHF → FAICAR + THF
The last step is catalyzed by Inosine monophosphate synthase.
:FAICAR → IMP + HO
In eukaryotes the second, third, and fifth step are catalyzed by trifunctional purine biosynthetic protein adenosine-3, which is encoded by the GART gene.
Both ninth and tenth step are accomplished by a single protein named Bifunctional purine biosynthesis protein PURH, encoded by the ATIC gene. | 1 | Biochemistry |
In rare cases, carbido ligands are terminal. One example is with a Ru-C distance of 163 pm, typical for a triple bond. The complex can be obtained by metathesis of vinyl acetate to give results in a metastable complex, which eliminates acetic acid.
Such transition metal, one coordinate-carbon bonded complexes are comparable to carbon monoxide, cyanide, and isonitrile analogues. These carbides can be used as synthons to access a wide range of carbyne complexes, the most notable being Fischer carbynes. American chemist Christopher C. Cummins is one of the pioneers of this area. | 0 | Organic Chemistry |
Natural products chemist Udo Gräfe collected a sample of P. rudis HKI 0254 from a dead log in Siberia from which hexacyclinol was isolated. His group's 2002 paper showed that the compound behaved as an antiproliferative drug against cancer cell lines and proposed a structure (2) for the compound.
An initial total synthesis was published by James J. La Clair in 2006, purporting a synthesis of Gräfe's proposed structure based on H nuclear magnetic resonance (NMR) spectra.
Natural products chemist Scott D. Rychnovsky simulated the C nuclear magnetic resonance spectrum of the structure proposed by Gräfe and found that it did not correspond to the spectrum of the structure allegedly synthesized by La Clair. Rychnovsky proposed a different structure (1) based on panepophenanthrin, another molecule isolated from a different strain of P. rudis. The scientific community then began criticizing La Clairs work, claiming that his work was sloppy or that he fabricated data. La Clairs publication of his purported synthesis was retracted in 2012, citing a lack of validation of its claims.
In 2006, a group led by John Porco, Jr. synthesized Rychnovskys proposed structure. They showed that the H- and C-NMR spectra matched that of the compound isolated by Gräfe, confirming Rychnovskys structure. La Clair claimed that since the two structures were isomers, it is possible that they would have similar H-NMR spectra. However, a later paper by Saielli and Bagno claims that there would be significant differences in the H- and C-NMR spectra of compounds (1) and (2).
The controversy was covered extensively by a number of science blogs.
In response to the controversy, Nobel Prize-winning synthetic chemist E.J. Corey remarked, "Occasionally, blatantly wrong science is published, and to the credit of synthetic chemistry, the corrections usually come quickly and cleanly." | 0 | Organic Chemistry |
Iodolactonization (or, more generally, halolactonization) is an organic reaction that forms a ring (the lactone) by the addition of an oxygen and iodine across a carbon-carbon double bond. It is an intramolecular variant of the halohydrin synthesis reaction. The reaction was first reported by M. J. Bougalt in 1904 and has since become one of the most effective ways to synthesize lactones. Strengths of the reaction include the mild conditions and incorporation of the versatile iodine atom into the product.
Iodolactonization has been used in the synthesis of many natural products including those with medicinal applications such as vernolepin and vernomenin, two compounds used in tumor growth inhibition, and vibralactone, a pancreatic lipase inhibitor. Iodolactonization has also been used by Elias James Corey to synthesize numerous prostaglandins. | 0 | Organic Chemistry |
There are three types of glycosylation disorders sorted by the type of alterations that are made to the glycosylation process: congenital alterations, acquired alterations and non-enzymatic acquired alterations.
* Congenital alterations: Over 40 congenital disorders of glycosylation (CGDs) have been reported in humans. These can be divided into four groups: disorders of protein N-glycosylation, disorders of protein O-glycosylation, disorders of lipid glycosylation and disorders of other glycosylation pathways and of multiple glycosylation pathways. No effective treatment is known for any of these disorders. 80% of these affect the nervous system.
* Acquired alterations: In this second group the main disorders are infectious diseases, autoimmune illnesses or cancer. In these cases, the changes in glycosylation are the cause of certain biological events. For example, in Rheumatoid Arthritis (RA), the body of the patient produces antibodies against the enzyme lymphocytes galactosyltransferase which inhibits the glycosylation of IgG. Therefore, the changes in the N-glycosylation produce the immunodeficiency involved in this illness. In this second group we can also find disorders caused by mutations on the enzymes that control the glycosylation of Notch proteins, such as Alagille syndrome.
* Non-enzymatic acquired alterations: Non-enzymatic disorders, are also acquired, but they are due to the lack of enzymes that attach oligosaccharides to the protein. In this group the illnesses that stand out are Alzheimer's disease and diabetes.
All these diseases are difficult to diagnose because they do not only affect one organ, they affect many of them and in different ways. As a consequence, they are also hard to treat. However, thanks to the many advances that have been made in next-generation sequencing, scientists can now understand better these disorders and have discovered new CDGs. | 0 | Organic Chemistry |
Similar mechanism of action for enhancer-blocking insulators; chromatin loop domains are formed in the nucleus that separates the enhancer and the promoter of a target gene. Loop domains are formed through the interaction between enhancer-blocking elements interacting with each other or securing chromatin fibre to structural elements within the nucleus. The action of these insulators is dependent on being positioned between the promoter of the target gene and the upstream or down stream enhancer. The specific way in which insulators block enhancers is dependent on the enhancers mode of action. Enhancers can directly interact with their target promoters through looping (direct-contact model), in which case an insulator prevents this interaction through the formation of a loop domain that separates the enhancer and promoter sites and prevents the promoter-enhancer loop from forming. An enhancer can also act on a promoter through a signal (tracking model of enhancer action). This signal may be blocked by an insulator through the targeting of a nucleoprotein complex at the base of the loop formation. | 1 | Biochemistry |
The lone pair of electrons on the nitrogen atom is delocalized into the carbonyl group, thus forming a partial double bond between nitrogen and carbon. In fact the O, C and N atoms have molecular orbitals occupied by delocalized electrons, forming a conjugated system. Consequently, the three bonds of the nitrogen in amides is not pyramidal (as in the amines) but planar. This planar restriction prevents rotations about the N linkage and thus has important consequences for the mechanical properties of bulk material of such molecules, and also for the configurational properties of macromolecules built by such bonds. The inability to rotate distinguishes amide groups from ester groups which allow rotation and thus create more flexible bulk material.
The C-C(O)NR core of amides is planar. The C=O distance is shorter than the C-N distance by almost 10%. The structure of an amide can be described also as a resonance between two alternative structures: neutral (A) and zwitterionic (B).
It is estimated that for acetamide, structure A makes a 62% contribution to the structure, while structure B makes a 28% contribution (these figures do not sum to 100% because there are additional less-important resonance forms that are not depicted above). There is also a hydrogen bond present between the hydrogen and nitrogen atoms in the active groups. Resonance is largely prevented in the very strained quinuclidone.
In their IR spectra, amides exhibit a moderately intense ν band near 1650 cm. The energy of this band is about 60 cm lower than for the ν of esters and ketones. This difference reflects the contribution of the zwitterionic resonance structure. | 0 | Organic Chemistry |
Other examples of non-Kekulé molecules are the biradicaloid quinodimethanes, that have a six-membered ring with methylene substituents.
Non-Kekulé polynuclear aromatic hydrocarbons are composed of several fused six-membered rings. The simplest member of this class is triangulene. After unsuccessful attempts by Erich Clar in 1953, trioxytriangulene was synthesized by Richard J. Bushby in 1995, and kinetically stabilized triangulene by Kazuhiro Nakasuji in 2001. However, in 2017 a project led by David Fox and Anish Mistry from the University of Warwick in collaboration with IBM synthesized and imaged triangulene. In 2019, larger homologues of triangulene, consisting of ten ([4]triangulene) and fifteen fused six-membered rings ([5]triangulene) were synthesized in 2019. In 2021, synthesis of the hitherto largest triangulene homologue, consisting of twenty-eight fused six-membered rings ([7]triangulene) was achieved. Scanning tunneling microscopy experiments on triangulene spin chains have revealed the clearest proof yet of the existence of Haldane gap and fractional edge states predicted for spin-1 Heisenberg chain. A related class of biradicals are para-benzynes.
Other studied biradicals are those based on pleiadene, extended viologens, corannulenes, nitronyl-nitroxide, bis(phenalenyl)s and teranthenes.
Pleiadene has been synthesised from acenaphthylene and anthranilic acid / amyl nitrite: | 0 | Organic Chemistry |
Although ribozymes are quite rare in most cells, their roles are sometimes essential to life. For example, the functional part of the ribosome, the biological machine that translates RNA into proteins, is fundamentally a ribozyme, composed of RNA tertiary structural motifs that are often coordinated to metal ions such as Mg as cofactors. In a model system, there is no requirement for divalent cations in a five-nucleotide RNA catalyzing trans-phenylalanation of a four-nucleotide substrate with 3 base pairs complementary with the catalyst, where the catalyst/substrate were devised by truncation of the C3 ribozyme.
The best-studied ribozymes are probably those that cut themselves or other RNAs, as in the original discovery by Cech and Altman. However, ribozymes can be designed to catalyze a range of reactions, many of which may occur in life but have not been discovered in cells.
RNA may catalyze folding of the pathological protein conformation of a prion in a manner similar to that of a chaperonin. | 7 | Physical Chemistry |
Rubisco also catalyzes RuBP with oxygen () in an interaction called photorespiration, a process that is more prevalent at high temperatures. During photorespiration RuBP combines with to become 3-PGA and . Like the Calvin-Benson Cycle, the photorespiratory pathway has been noted for its enzymatic inefficiency although this characterization of the enzymatic kinetics of rubisco have been contested. Due to enhanced RuBP carboxylation and decreased rubisco oxygenation stemming from the increased concentration of in the bundle sheath, rates of photorespiration are decreased in plants. Similarly, photorespiration is limited in CAM photosynthesis due to kinetic delays in enzyme activation, again stemming from the ratio of carbon dioxide to oxygen. | 5 | Photochemistry |
Phosphonates are also used as concrete retarder. They delay the cement setting time, allowing a longer time to place the concrete or to spread the cement hydration heat on a longer period of time to avoid too high temperature and resulting cracks. They also have favourable dispersing properties and so are investigated as a possible new class of superplasticizers. However, presently, phosphonates are not commercially available as superplasticizers. Superplasticizers are concrete admixtures designed to increase the concrete fluidity and workability of concrete or to decrease its water-to-cement (w/c) ratio. By reducing the water content in concrete, it decreases its porosity, improving so the mechanical properties (compressive and tensile strength) and the durability of concrete (lower water, gas and solutes transport properties). | 0 | Organic Chemistry |
1,2-Indandione is an organic compound with the molecular formula CH(CO)CH. A yellow solid, it is classified as a vicinal diketone on an indane framework.
1,2-Indandione is used in the first stage of forensic identification of latent fingerprints. It is particularly useful for paper, and for items printed with thermal inks such as receipts. Amino acids left behind by the human hand may be developed into fingerprints by the use of it; the results, photographed with a special filter under a strong yellow-green fluorescent or green laser. It is usually the first method employed in a sequential analysis aimed at the production of evidence of a grade suitable for use in the courtroom.
1,2-Indanedione is prepared by oxidation of 1-indanone with selenium dioxide. | 0 | Organic Chemistry |
The electronic properties of ordered, crystalline solids are determined by the distribution of the electronic states with respect to energy and momentum—the electronic band structure of the solid. Theoretical models of photoemission from solids show that this distribution is, for the most part, preserved in the photoelectric effect. The phenomenological three-step model for ultraviolet and soft X-ray excitation decomposes the effect into these steps:
# Inner photoelectric effect in the bulk of the material that is a direct optical transition between an occupied and an unoccupied electronic state. This effect is subject to quantum-mechanical selection rules for dipole transitions. The hole left behind the electron can give rise to secondary electron emission, or the so-called Auger effect, which may be visible even when the primary photoelectron does not leave the material. In molecular solids phonons are excited in this step and may be visible as satellite lines in the final electron energy.
# Electron propagation to the surface in which some electrons may be scattered because of interactions with other constituents of the solid. Electrons that originate deeper in the solid are much more likely to suffer collisions and emerge with altered energy and momentum. Their mean-free path is a universal curve dependent on electron's energy.
# Electron escape through the surface barrier into free-electron-like states of the vacuum. In this step the electron loses energy in the amount of the work function of the surface, and suffers from the momentum loss in the direction perpendicular to the surface. Because the binding energy of electrons in solids is conveniently expressed with respect to the highest occupied state at the Fermi energy , and the difference to the free-space (vacuum) energy is the work function of the surface, the kinetic energy of the electrons emitted from solids is usually written as .
There are cases where the three-step model fails to explain peculiarities of the photoelectron intensity distributions. The more elaborate one-step model treats the effect as a coherent process of photoexcitation into the final state of a finite crystal for which the wave function is free-electron-like outside of the crystal, but has a decaying envelope inside. | 7 | Physical Chemistry |
Some cryoprotectants function by lowering the glass transition temperature of a solution or of a material. In this way, the cryoprotectant prevents actual freezing, and the solution maintains some flexibility in a glassy phase. Many cryoprotectants also function by forming hydrogen bonds with biological molecules as water molecules are displaced. Hydrogen bonding in aqueous solutions is important for proper protein and DNA function. Thus, as the cryoprotectant replaces the water molecules, the biological material retains its native physiological structure and function, although they are no longer immersed in an aqueous environment. This preservation strategy is most often utilized in anhydrobiosis. | 1 | Biochemistry |
Satyam et al. from National University of Ireland, Galway (NUI Galway) proposed macromolecular crowding as means to create ECM-rich tissue equivalents. The principle of macromolecular crowding is derived from the notion that in vivo cells reside in a highly crowded/dense extracellular space and therefore the conversion of the de novo synthesised procollagen to collagen I is rapid. However, in the even substantially more dilute than body fluids (e.g., urine: 36–50 g/L; blood: 80 g/L) culture conditions (e.g., HAM F10 nutrient medium: 16.55 g/L; DMEM/ F12 medium: 16.78 g/L; DMEM high glucose and L-glutamine medium: 17.22 g/L), the rate limiting conversion of procollagen to collagen I is very slow. It was confirmed that the addition of inert polydispersed macromolecules (presented as spherical objects of variable diameter) in the culture media will facilitate amplified production of ECM-rich living substitutes. Macromolecular crowding, by imitating native tissue localised density, can be utilised to effectively modulate in vitro microenvironments and ultimately produce ECM-rich cell substitutes, within hours rather than days or months in culture, without compromising fundamental cellular functions. A recent study by researchers from the University of Twente has shown that emulating physiological molecular crowding may enhance chondrogenic properties of damaged chondrocytes. | 7 | Physical Chemistry |
Recalescence is an increase in temperature that occurs while cooling metal when a change in structure with an increase in entropy occurs. The heat responsible for the change in temperature is due to the change in entropy. When a structure transformation occurs the Gibbs free energy of both structures are more or less the same. Therefore, the process will be exothermic. The heat provided is the latent heat.
Recalescence also occurs after supercooling, when the supercooled liquid suddenly crystallizes, forming a solid but releasing heat in the process. | 8 | Metallurgy |
Glucuronidation consists of transfer of the glucuronic acid component of uridine diphosphate glucuronic acid to a substrate by any of several types of UDP-glucuronosyltransferase.
UDP-glucuronic acid (glucuronic acid linked via a glycosidic bond to uridine diphosphate) is an intermediate in the process and is formed in the liver. One example is the N-glucuronidation of an aromatic amine, 4-aminobiphenyl, by UGT1A4 or UGT1A9 from human, rat, or mouse liver.
The substances resulting from glucuronidation are known as glucuronides (or glucuronosides) and are typically much more water-soluble than the non-glucuronic acid-containing substances from which they were originally synthesised. The human body uses glucuronidation to make a large variety of substances more water-soluble, and, in this way, allow for their subsequent elimination from the body through urine or feces (via bile from the liver). Hormones are glucuronidated to allow for easier transport around the body. Pharmacologists have linked drugs to glucuronic acid to allow for more effective delivery of a broad range of potential therapeutics. Sometimes toxic substances are also less toxic after glucuronidation.
The conjugation of xenobiotic molecules with hydrophilic molecular species such as glucuronic acid is known as phase II metabolism. | 0 | Organic Chemistry |
Ortho-, pyro-, and tripolyphosphate compounds have been commonly used in detergents (i. e. cleaners) formulations. For example, see Sodium tripolyphosphate. Sometimes pyrophosphate, tripolyphosphate, tetrapolyphosphate, etc. are called diphosphate, triphosphate, tetraphosphate, etc., especially when they are part of phosphate esters in biochemistry. They are also used for scale and corrosion control by potable water providers. As a corrosion inhibitor, polyphosphates work by forming a protective film on the interior surface of pipes. | 0 | Organic Chemistry |
An ideal chain (or freely-jointed chain) is the simplest model in polymer chemistry to describe polymers, such as nucleic acids and proteins. It assumes that the monomers in a polymer are located at the steps of a hypothetical random walker that does not remember its previous steps. By neglecting interactions among monomers, this model assumes that two (or more) monomers can occupy the same location. Although it is simple, its generality gives insight about the physics of polymers.
In this model, monomers are rigid rods of a fixed length , and their orientation is completely independent of the orientations and positions of neighbouring monomers. In some cases, the monomer has a physical interpretation, such as an amino acid in a polypeptide. In other cases, a monomer is simply a segment of the polymer that can be modeled as behaving as a discrete, freely jointed unit. If so, is the Kuhn length. For example, chromatin is modeled as a polymer in which each monomer is a segment approximately 14-46 kbp in length. | 7 | Physical Chemistry |
Advantages cited for the IsaKidd technology include:
* long life – the operational life of the permanent cathodes without repair is said to be over seven years under correct operating conditions for electrowinning applications and over 15 years for electrorefining applications
* reduced labour costs – due to the elimination of the starter-sheet production process and the automation of cathode stripping. The average labour requirement for refineries based on the IsaKidd technology is 0.9 man-hours per tonne of cathode, compared to 2.4 man-hours/t for tank houses using starter sheets. Atlantic Copper personnel reported a figure of 0.43 man-hours/t for the Huelva refinery in Spain in 1998
* no suspension loops – the suspension loops of starter sheets can corrode and thus cause cutting of the electrolytic cell liners. The lack of suspension loops also makes crane handling easier
* improved cathode quality – due to the straight cathode plates, which eliminates short-circuiting, and the lack of bends and other surface irregularities reduces the capture of contaminants such as floating arsenic, antimony and bismuth and other slimes compounds. The elimination of the starter-sheet suspension loops also improved cathode quality. In SX–EW operations, the use of stainless-steel cathode plates eliminates lead flakes and other debris from the cathode copper.
* improved current efficiency – this arises both from eliminating short circuits caused by bent and irregular electrodes and from the shorter cathode cycles possible with the use of the reusable cathode plates. Current efficiencies of over 98% are claimed
* increased refining intensity – this reduces the number of electrolytic cells needed in a refinery and its capital cost because the gap between the anodes and the cathodes can be narrower due to the lower risk of short circuits and because the current density can be increased, making the refining process faster. Refineries operating with the IsaKidd technology can achieve current densities of 330 amperes per square meter (“A/m”) of cathode area, whereas a refinery using starter sheets can only operate at around 240 A/m
* shorter cathode cycles – shorter cathode cycles are possible using the IsaKidd technology, which reduces the metal inventory and means that the refinery or SX–EW operator is paid more quickly
* shorter anode cycles – the higher intensity of the refining also results in about a 12% reduction in anode cycle time, also reducing the metal inventory
* uniform cathode copper sheets for ease of transport – the control over the dimensions of the copper sheets made possible by the IsaKidd technology, provides uniform cathode bundles that can be securely strapped and easily transported (see Figure 7)
* improved safety – elimination of much of the manual handling leads to improved safety conditions in the workplace.
Staff of the Cyprus Miami copper refinery wrote after their installation of the Isa Process technology that: “It is now well proven that tankhouses applying stainless steel cathode technology can consistently produce high quality cathodes while operating at higher cathode current density and at a lower cathode spacing than those used in conventional tankhouses.” | 8 | Metallurgy |
Green algae have been taken up by the euglenids, chlorarachniophytes, a lineage of dinoflagellates, and possibly the ancestor of the CASH lineage (cryptomonads, alveolates, stramenopiles and haptophytes) in three or four separate engulfments. Many green algal derived chloroplasts contain pyrenoids, but unlike chloroplasts in their green algal ancestors, storage product collects in granules outside the chloroplast. | 5 | Photochemistry |
Similar to mineralization processes that take place within rocks, mineralization can also occur under the sea. The rate of dissolution of carbon dioxide from atmosphere to oceanic regions is determined by the circulation period of the ocean and buffering ability of subducting surface water. Researchers have demonstrated that the carbon dioxide marine storage at several kilometers depth could be viable for up to 500 years, but is dependent on injection site and conditions. Several studies have shown that although it may fix carbon dioxide effectively, carbon dioxide may be released back to the atmosphere over time. However, this is unlikely for at least a few more centuries. The neutralization of CaCO, or balancing the concentration of CaCO on the seafloor, land and in the ocean, can be measured on a timescale of thousands of years. More specifically, the predicted time is 1700 years for ocean and approximately 5000 to 6000 years for land. Further, the dissolution time for CaCO can be improved by injecting near or downstream of the storage site.
In addition to carbon mineralization, another proposal is deep sea sediment injection. It injects liquid carbon dioxide at least 3000 m below the surface directly into ocean sediments to generate carbon dioxide hydrate. Two regions are defined for exploration: 1) the negative buoyancy zone (NBZ), which is the region between liquid carbon dioxide denser than surrounding water and where liquid carbon dioxide has neutral buoyancy, and 2) the hydrate formation zone (HFZ), which typically has low temperatures and high pressures. Several research models have shown that the optimal depth of injection requires consideration of intrinsic permeability and any changes in liquid carbon dioxide permeability for optimal storage. The formation of hydrates decreases liquid carbon dioxide permeability, and injection below HFZ is more energetically favored than within the HFZ. If the NBZ is a greater column of water than the HFZ, the injection should happen below the HFZ and directly to the NBZ. In this case, liquid carbon dioxide will sink to the NBZ and be stored below the buoyancy and hydrate cap. Carbon dioxide leakage can occur if there is dissolution into pore fluid or via molecular diffusion. However, this occurs over thousands of years. | 5 | Photochemistry |
Rare-earth borides REBCN, REBCN and REBC are homologous, i.e. have a similar crystal structure, to BC. The latter has a structure typical of icosahedron-based borides, as shown in figure 11a. There, B icosahedra form a rhombohedral lattice unit (space group: Rm (No. 166), lattice constants: a = 0.56 nm and c = 1.212 nm) surrounding a C-B-C chain that resides at the center of the lattice unit, and both C atoms bridge the neighboring three icosahedra. This structure is layered: as shown in figure 11b, B icosahedra and bridging carbons form a network plane that spreads parallel to the c-plane and stacks along the c-axis.
These homologous compounds have two basic structure units – the B icosahedron and the B octahedron. The network plane of BC structure can be periodically replaced by a B octahedron layer so that replacement of
every third, fourth and fifth layer would correspond to REBCN, REBCN and REBC, respectively. The B octahedron is smaller than the B icosahedron; therefore, rare-earth elements can reside in the space created by the replacement. The stacking sequences of BC, REBCN, REBCN and REBC are shown in figures 12a, b, c and d, respectively. High-resolution transmission electron microscopy (HRTEM) lattice images of the latter three compounds, added to Fig. 12, do confirm the stacking sequence of each compound. The symbols 3T, 12R and 15R in brackets indicate the number of layers necessary to complete the stacking sequence, and T and R refer to trigonal and rhombohedral. Thus, REBCN and REBC have rather large c-lattice constants.
Because of the small size of the B octahedra, they cannot interconnect. Instead, they bond to the B icosahedra in the neighboring layer, and this decreases bonding strength in the c-plane. Nitrogen atoms strengthen the bonding in the c-plane by bridging three icosahedra, like C atoms in the C-B-C chain. Figure 13 depicts the c-plane network revealing the alternate bridging of the boron icosahedra by N and C atoms. Decreasing the number of the B octahedra diminishes the role of nitrogen because the C-B-C chains start bridging the icosahedra. On the other hand, in MgBN the B octahedron layer and the B icosahedron layer stack alternatively and there is no C-B-C chains; thus only N atoms bridge the B icosahedra. However, REBN compounds have not been identified yet.
Sc, Y, Ho, Er, Tm and Lu are confirmed to form REBCN-type compounds. Single-crystal structure analysis yielded trigonal symmetry for ScBCN (space group Pm1 (No.164) with a = 0.5568(2) and c = 1.0756(2) nm), and the deduced atomic coordinates are summarized in table IVa.
REBCN was synthesized for Y, Ho, Er, Tm and Lu. The crystal structure, solved for a representative compound YBCN, belongs to the trigonal with space group Rm (No.166); it has six formula units in the unit cell and lattice constants a = b = 0.5623(0) nm and c = 4.4785(3) nm. Atomic coordinates of YBCN are summarized in table IVb.
Y, Ho, Er, Tm and Lu also form REBC which has a trigonal crystal structure with space group Rm
(No. 166). Lattice constants of the representative compound YBC are a = b = 0.56457(9) nm and c = 5.68873(13) nm and there are six formula units in the unit cell. Structure data of YBC are
summarized in table IVc. | 3 | Analytical Chemistry |
The law of combining volumes states that when gases chemically react together, they do so in amounts by volume which bear small whole-number ratios (the volumes calculated at the same temperature and pressure).
The ratio between the volumes of the reactant gases and the gaseous products can be expressed in simple whole numbers.
For example, Gay-Lussac found that two volumes of hydrogen react with one volume of oxygen to form two volumes of gaseous water. Expressed concretely, 100 mL of hydrogen combine with 50 mL of oxygen to give 100 mL of water vapor: Hydrogen(100 mL) + Oxygen(50 mL) = Water(100 mL). Thus, the volumes of hydrogen and oxygen which combine (i.e., 100mL and 50mL) bear a simple ratio of 2:1, as also is the case for the ratio of product water vapor to reactant oxygen.
Based on Gay-Lussacs results, Amedeo Avogadro hypothesized in 1811 that, at the same temperature and pressure, equal volumes of gases (of whatever kind) contain equal numbers of molecules (Avogadros law). He pointed out that if this hypothesis is true, then the previously stated result
:2 volumes of hydrogen + 1 volume of oxygen = 2 volume of gaseous water
could also be expressed as
:2 molecules of hydrogen + 1 molecule of oxygen = 2 molecule of water.
The law of combining volumes of gases was announced publicly by Joseph Louis Gay-Lussac on the last day of 1808, and published in 1809. Since there was no direct evidence for Avogadros molecular theory, very few chemists adopted Avogadros hypothesis as generally valid until the Italian chemist Stanislao Cannizzaro argued convincingly for it during the First International Chemical Congress in 1860. | 7 | Physical Chemistry |
The types of hydrogen-bond donors used in catalysis vary widely from reaction to reaction, even among similar catalytic strategies. While specific systems are often studied and optimized extensively, a general understanding of the optimal donor for a reaction or the relationship between catalyst structure and reactivity is greatly lacking. It is not yet practical to rationally design structures to promote a desired reaction with the desired selectivity. However, contemporary hydrogen-bond catalysis is primarily focused on a few types of systems that experimentally seem to be effective in a variety of situations. These are termed "privileged structures". However, it is worth noting that other structural scaffolds and motifs have also shown promising results, such as metal-coordinated hydrogen-bond donors.
*Ureas and thioureas are by far the most common structures and can stabilize a variety of negatively charged intermediates, as well as engage in anion-binding catalysis. Bifunctional urea and thiourea catalysis are abundant in the literature. Thioureas are often found to be stronger hydrogen-bond donors (i.e., more acidic) than ureas because their amino groups are more positively charged. Quantum chemical analyses revealed that this counterintuitive phenomenon, which is not explainable by the relative electronegativities of O and S, results from the effective steric size of the chalcogen atoms.
*Guanidinium and amidinium ions are structural relatives of ureas and thioureas and can catalyze similar reactions but, by virtue of their positive charge, are stronger donors and much more acidic. The mechanism of guanidinium and amidinium catalysis is thought to often involve partial protonation of substrate.
*Diol catalysts are thought to engage substrate with a single hydrogen bond, with the other hydroxyl participating in an internal hydrogen bond. These are some of the earliest hydrogen-bond catalysts investigated. They are most commonly used in stabilizing partial anionic charge in transition states, for example coordinating to aldehyde dienophiles in hetero-Diels-Alder reactions.
*Phosphoric acid catalysts are the most common strong acid catalysts and work by formation of chiral ion pairs with basic substrates such as imines. | 0 | Organic Chemistry |
Due to bonds breaking and forming during various processes (changes in state, chemical reactions), there is usually a change in energy. If the energy of the forming bonds is greater than the energy of the breaking bonds, then energy is released. This is known as an exothermic reaction. However, if more energy is needed to break the bonds than the energy being released, energy is taken up. Therefore, it is an endothermic reaction. | 7 | Physical Chemistry |
Lichens have been shown to deteriorate polyester resins, as can be seen in archaeological sites in the Roman city of Baelo Claudia Spain. | 7 | Physical Chemistry |
A plasma arc furnace (PAF) uses plasma torches instead of graphite electrodes. Each of these torches has a casing with a nozzle and axial tubing for feeding a plasma-forming gas (either nitrogen or argon) and a burnable cylindrical graphite electrode within the tubing. Such furnaces can be called plasma arc melt (PAM) furnaces; they are used extensively in the titanium-melting industry and similar specialty metal industries. | 8 | Metallurgy |
When polymers are oxidized, unstable alkyl radicals are formed which react further with oxygen to form peroxy bonds. The excitation and stabilization of the peroxy radical causes chemiluminescence. The light produced by this reaction is typically low wavelength infrared light. The amount of light emitted is used to determine the oxidation rate of an adhesive.
Chemiluminescence (CL) light intensity can be measured at various isothermal oxidation cycles; however, the temperature need not be raised to high levels. Correlation of light intensity is made to oxidation process parameters such as Oxidation Induction Temperature (OIT). By obtaining measurements at different temperatures, an accelerated oxidation progression correlation can be established. The prediction of oxidation during service life can then be carried out. | 3 | Analytical Chemistry |
The first issue with using concretes in perfumery is that their extracts can become rancid after several months, especially if the containers are exposed to strong light.
The second issue is regarding residual pesticides in concretes. Cultivation of natural raw materials for producing concretes is often done by using monoculture techniques that use pesticides. The international regulation of pesticides in use for natural raw materials is not consistent yet. In Europe, the Regulation no. 396/2005/CE and Regulation n° 1107/2009 of the European Parliament and the European Council set target maximum pesticide residue limit as 0.01 mg kg. However, currently, there is no universal method for analyzing the amount of residual pesticides in concretes that could show if the amount of residual pesticide in a concrete sample is safe. Previous analyses that used gas chromatography were heavily affected by the different components of the complex mixture of concrete samples. Therefore, it is likely that their analyses of the amount of pesticide in concrete was inaccurate. This is a concern, as a level of pesticide in concrete that is above the safe limit could lead to health risks. | 7 | Physical Chemistry |
Dexrazoxane hydrochloride (Zinecard, Cardioxane) is a cardioprotective agent. It was discovered by Eugene Herman in 1972. The IV administration of dexrazoxane is in acidic condition with HCl adjusting the pH. | 4 | Stereochemistry |
Since these drugs may cause paralysis of the diaphragm, mechanical ventilation should be at hand to provide respiration.
In addition, these drugs may exhibit cardiovascular effects, since they are not fully selective for the nicotinic receptor and hence may have effects on muscarinic receptors. If nicotinic receptors of the autonomic ganglia or adrenal medulla are blocked, these drugs may cause autonomic symptoms. Also, neuromuscular blockers may facilitate histamine release, which causes hypotension, flushing, and tachycardia.
Succinylcholine may also trigger malignant hyperthermia in rare cases in patients who may be susceptible.
In depolarizing the musculature, suxamethonium may trigger a transient release of large amounts of potassium from muscle fibers. This puts the patient at risk for life-threatening complications, such as hyperkalemia and cardiac arrhythmias. Other effects include myalgia, increased intragastric pressure, increased intraocular pressure, increased intracranial pressure, cardiac dysrhythmias (bradycardia is the most common type) and allergic reactions. As a result, it is contraindicated for patients with susceptibility to malignant hyperthermia, denervating conditions, major burns after 48 hours, and severe hyperkalemia.
For nondepolarizing NMBAs except vecuronium, pipecuronium, doxacurium, cisatracurium, rocuronium and rapacuronium, they produce certain extent of cardiovascular effect. Moreover, Tubocurarine can produce hypotension effect while Pancuronium can lead to moderate increase in heart rate and small increase in cardiac output with little or no increase in systemic vascular resistance, which is unique in nondeploarizing NMBAs.
Certain drugs such as aminoglycoside antibiotics and polymyxin and some fluoroquinolones also have neuromuscular blocking action as their side-effect. | 1 | Biochemistry |
The typical current density at which electromigration occurs in Cu or Al interconnects is 10 to 10 A/cm. For solder joints (SnPb or SnAgCu lead-free) used in IC chips, however, electromigration occurs at much lower current densities, e.g. 10 A/cm.
It causes a net atom transport along the direction of electron flow. The atoms accumulate at the anode, while voids are generated at the cathode and back stress is induced during electromigration. The typical failure of a solder joint due to electromigration will occur at the cathode side. Due to the current crowding effect, voids form first at the corners of the solder joint. Then the voids extend and join to cause a failure. Electromigration also influences formation of intermetallic compounds, as the migration rates are a function of atomic mass. | 7 | Physical Chemistry |
Normal phase elution is achieved by pumping the non-aqueous or phase of a biphasic solvent system through the column as the mobile phase, with a more polar stationary phase being retained in the column. The cause of original nomenclature of is relevant. As original stationary phases of paper chromatography were superseded by more efficient materials such as diatomaceous earths (natural micro-porous silica) and followed by modern silica gel, the thin-layer chromatography stationary phase was polar (hydroxy groups attached to silica) and maximum retention was achieved with non-polar solvents such as n-hexane. Progressively more polar eluents were then used to move polar compounds up the plate. Various alkane bonded phases were tried with C18 becoming the most popular. Alkane chains were chemically bonded to the silica, and a reversal of the elution trend occurred. Thus a polar stationary became "normal" phase chromatography, and the non-polar stationary phase chromatography became "reversed" phase chromatography. | 3 | Analytical Chemistry |
In inorganic chemistry, it is common to consider a single value of electronegativity to be valid for most "normal" situations. While this approach has the advantage of simplicity, it is clear that the electronegativity of an element is not an invariable atomic property and, in particular, increases with the oxidation state of the element.
Allred used the Pauling method to calculate separate electronegativities for different oxidation states of the handful of elements (including tin and lead) for which sufficient data were available. However, for most elements, there are not enough different covalent compounds for which bond dissociation energies are known to make this approach feasible. This is particularly true of the transition elements, where quoted electronegativity values are usually, of necessity, averages over several different oxidation states and where trends in electronegativity are harder to see as a result.
The chemical effects of this increase in electronegativity can be seen both in the structures of oxides and halides and in the acidity of oxides and oxoacids. Hence CrO and MnO are acidic oxides with low melting points, while CrO is amphoteric and MnO is a completely basic oxide.
The effect can also be clearly seen in the dissociation constants pK of the oxoacids of chlorine. The effect is much larger than could be explained by the negative charge being shared among a larger number of oxygen atoms, which would lead to a difference in pK of log() = –0.6 between hypochlorous acid and perchloric acid. As the oxidation state of the central chlorine atom increases, more electron density is drawn from the oxygen atoms onto the chlorine, diminishing the partial negative charge of individual oxygen atoms. At the same time, the positive partial charge on the hydrogen increases with a higher oxidation state. This explains the observed increased acidity with an increasing oxidation state in the oxoacids of chlorine. | 3 | Analytical Chemistry |
The color reaction between borates and curcumin is used for the spectrophotometric determination and quantification of boron present in food or materials. Curcumin is a yellow coloring natural pigment found in the root stocks of some Curcuma species, especially Curcuma longa (turmeric), in concentrations up to 3%. In the so-called curcumin method for boron quantification it serves as reaction partner for boric acid. The reaction is very sensitive and so the smallest quantities of boron can be detected. The maximum absorbance at 540 nm for rosocyanine is used in this colorimetric method. The formation of rosocyanine depends on the reaction conditions. The reaction is carried out preferentially in acidic solutions containing hydrochloric or sulfuric acid. The color reaction also takes place under different conditions; however, in alkaline solution, gradual decomposition is observed. The reaction might be disturbed at higher pH values, interfering with other compounds.
Rosocyanine is formed as a 2:1 complex from curcumin and boric acid in acidic solutions. The boron complexes formed with rosocyanine are dioxaborines (here a 1,3,2-dioxaborine). Curcumin possesses a 1,3-diketone structure and can therefore be considered as a chelating agent. Unlike the simpler 1,3-diketone–containing compound acetylacetone (which forms acetylacetonate complexes with metals), the entire skeleton of curcumin is in resonance with the 1,3-dicarbonyl section, making the backbone an extended conjugated system. Investigations of the structure have shown that the positive charge is distributed throughout the molecule. In rosocyanine, the two curcumin moieties are not coplanar but rather perpendicular relative to one another (as seen in the 3D model), as a result of the tetrahedral geometry of tetracoordinate boron. The same applies to rubrocurcumin.
In order to exclude the presence of other materials during the boron quantification using the curcumin method, a variant of the process was developed. In this process, 2,2-dimethyl-1,3-hexanediol or 2-ethyl-1,3-hexanediol are added, in addition to curcumin, to a neutral solution of the boron-containing solution. The complex formed between boron and the 1,3-hexanediol derivative is removed from the aqueous solution by extraction in an organic solvent. Acidification of the organic phase yields rubrocyanine, which can be detected by colorimetric methods. The reaction of curcumin with borates in presence of oxalic acid produces the coloring compound rubrocurcumin. | 3 | Analytical Chemistry |
Adverse effects of captopril include cough due to increase in the plasma levels of bradykinin, angioedema, agranulocytosis, proteinuria, hyperkalemia, taste alteration, teratogenicity, postural hypotension, acute renal failure, and leukopenia.
Except for postural hypotension, which occurs due to the short and fast mode of action of captopril, most of the side effects mentioned are common for all ACE inhibitors. Among these, cough is the most common adverse effect. Hyperkalemia can occur, especially if used with other drugs which elevate potassium level in blood, such as potassium-sparing diuretics. Other side effects are:
* Itching
* Headache
* Tachycardia
* Chest pain
* Palpitations
* Dysgeusia
* Weakness
The adverse drug reaction (ADR) profile of captopril is similar to other ACE inhibitors, with cough being the most common ADR. However, captopril is also commonly associated with rash and taste disturbances (metallic or loss of taste), which are attributed to the unique thiol moiety. | 4 | Stereochemistry |
In one variation the mechanism is thought to be as follows:
The dichromate oxidizes the mercury, forming a layer of mercury oxide. In the process the dichromate is reduced to the chromium(III) ion. The oxidized layer on the mercury reduces the surface tension of the blob and the blob flattens out coming in contact with the iron nail. Then the mercury sulfate oxidizes the iron to the iron(II) ion, and in the process is reduced back to metallic mercury. Once there is no oxide coating left on the mercury blob, the surface tension increases and the blob rounds up and loses contact with the nail, ready to start the process over again.
The net reaction is that the dichromate oxidizes the iron. This favorable reaction drives the mercury oxidations/reductions and the oscillations in shape. When the dichromate is fully reduced, the reaction stops.
There may be other mechanisms involved, however. Lin et al. appear to report that the oscillations occur without the presence of the oxidizing agent, though the mercury does not appear to get an oxidizing layer on it and the oscillations are much weaker.
An electrical double layer forms between the surface of the mercury droplet and the electrolyte solution. At rest this layer is uniform. When the iron tip is introduced, a redox reaction starts in which iron is oxidized to the ferric ion and the oxidizing reagent is spent (e.g. when hydrogen peroxide together with hydronium ions is reduced to water). Because the oxidation only takes place in the vicinity of the tip, and the reduction process covers the whole droplet surface, the surface tension is no longer homogeneous; this results in the observed oscillations.
Although this reaction is mediated by changes in surface tension, it is very similar in mechanism to other chemical oscillators such as the Belousov–Zhabotinsky reaction, which has several intermediate redox reactions driven by the oxidation of malate by bromine. | 7 | Physical Chemistry |
*[http://www.isallaboutmath.com/proof.aspx Proof about Stereographic Projection taking circles in the sphere to circles in the plane] | 3 | Analytical Chemistry |
Gene guns have also been used to deliver DNA vaccines.
The delivery of plasmids into rat neurons through the use of a gene gun, specifically DRG neurons, is also used as a pharmacological precursor in studying the effects of neurodegenerative diseases such as Alzheimer's disease.
The gene gun has become a common tool for labeling subsets of cells in cultured tissue. In addition to being able to transfect cells with DNA plasmids coding for fluorescent proteins, the gene gun can be adapted to deliver a wide variety of vital dyes to cells.
Gene gun bombardment has also been used to transform Caenorhabditis elegans, as an alternative to microinjection. | 1 | Biochemistry |
Thomson scattering is a model for the effect of electromagnetic fields on electrons when the field energy is much less than the rest mass of the electron . In the model the electric field of the incident wave accelerates the charged particle, causing it, in turn, to emit radiation at the same frequency as the incident wave, and thus the wave is scattered. Thomson scattering is an important phenomenon in plasma physics and was first explained by the physicist J. J. Thomson. As long as the motion of the particle is non-relativistic (i.e. its speed is much less than the speed of light), the main cause of the acceleration of the particle will be due to the electric field component of the incident wave. In a first approximation, the influence of the magnetic field can be neglected. The particle will move in the direction of the oscillating electric field, resulting in electromagnetic dipole radiation. The moving particle radiates most strongly in a direction perpendicular to its acceleration and that radiation will be polarized along the direction of its motion. Therefore, depending on where an observer is located, the light scattered from a small volume element may appear to be more or less polarized.
The electric fields of the incoming and observed wave (i.e. the outgoing wave) can be divided up into those components lying in the plane of observation (formed by the incoming and observed waves) and those components perpendicular to that plane. Those components lying in the plane are referred to as "radial" and those perpendicular to the plane are "tangential". (It is difficult to make these terms seem natural, but it is standard terminology.)
The diagram on the right depicts the plane of observation. It shows the radial component of the incident electric field, which causes the charged particles at the scattering point to exhibit a radial component of acceleration (i.e., a component tangent to the plane of observation). It can be shown that the amplitude of the observed wave will be proportional to the cosine of χ, the angle between the incident and observed waves. The intensity, which is the square of the amplitude, will then be diminished by a factor of cos(χ). It can be seen that the tangential components (perpendicular to the plane of the diagram) will not be affected in this way.
The scattering is best described by an emission coefficient which is defined as ε where ε dt dV dΩ dλ is the energy scattered by a volume element in time dt into solid angle dΩ between wavelengths λ and λ+dλ. From the point of view of an observer, there are two emission coefficients, ε corresponding to radially polarized light and ε corresponding to tangentially polarized light. For unpolarized incident light, these are given by:
where is the density of charged particles at the scattering point, is incident flux (i.e. energy/time/area/wavelength), is the angle between the incident and scattered photons (see figure above) and is the Thomson cross section for the charged particle, defined below. The total energy radiated by a volume element in time dt between wavelengths λ and λ+dλ is found by integrating the sum of the emission coefficients over all directions (solid angle):
The Thomson differential cross section, related to the sum of the emissivity coefficients, is given by
expressed in SI units; q is the charge per particle, m the mass of particle, and a constant, the permittivity of free space. (To obtain an expression in cgs units, drop the factor of 4ε.) Integrating over the solid angle, we obtain the Thomson cross section
in SI units.
The important feature is that the cross section is independent of light frequency. The cross section is proportional by a simple numerical factor to the square of the classical radius of a point particle of mass m and charge q, namely
Alternatively, this can be expressed in terms of , the Compton wavelength, and the fine structure constant:
For an electron, the Thomson cross-section is numerically given by: | 7 | Physical Chemistry |
Strictly speaking, this reaction results in the formation of a rhodium carbonyl complex rather than free carbon monoxide.
The catalytic cycle is assumed to involve oxidative addition of the aldehyde (or acid chloride) to gives a 16e acyl Rh(III)-hydride intermediate, which undergoes migratory extrusion of CO proceed to form an 18-electron d6 Rh(III) carbonyl complex. Reductive elimination produces the decarbonylated product. In the catalytic variant of the Tsuji–Wilkinson decarbonylation, RhCl(CO)(PPh) evolves CO above 200 °C, thereby regenerating RhCl(PPh). Otherwise, the reaction mechanism halts by formation of this thermodynamically stable carbonyl complex. | 0 | Organic Chemistry |
Many marine-derived polyketides that are often found in sponges cannot be cultured out of their natural environment. Finding the genes responsible for the biosynthesis of a sponge derived polyketides is a difficult task to accomplish because of the sponges’ colonial nature Scientists are not yet able to culture the sponges; therefore, the genes for the biosynthesis of (+)-discodermolide have not yet been discovered. | 0 | Organic Chemistry |
Sumner is the author of a widely used anti-harassment statement that she made public so that other universities and institutes could use it as a model. A leader in helping institutions develop anti-harassment plans, Sumner presented to a workshop at the 2016 American Geophysical Union on “Addressing harassment and improving workplace climate.” She was also an invited presenter for Association of Polar Early Career Scientists webinar on sexual harassment during fieldwork. Sumner is presently chair of advisory board for The Feminist Research Institute at the UC, Davis In June 2020 she became the leader of the Anti-Racism Action Committee in her department (Earth and Planetary Science) at UC Davis. Sumner also wrote four letters concerning racism and its effects on the science community between late May and early June 2020 | 9 | Geochemistry |
The glyoxylate cycle is a variant of the citric acid cycle. It is an anabolic pathway occurring in plants and bacteria utilizing the enzymes isocitrate lyase and malate synthase. Some intermediate steps of the cycle are slightly different from the citric acid cycle; nevertheless oxaloacetate has the same function in both processes. This means that oxaloacetate in this cycle also acts as the primary reactant and final product. In fact the oxaloacetate is a net product of the glyoxylate cycle because its loop of the cycle incorporates two molecules of acetyl-CoA. | 1 | Biochemistry |
The general mechanism is shown below. The resonating arrow (1) shows a resonance contributor of the diazo compound with a lone pair of electrons on the carbon adjacent to the nitrogen. The diazo compound then does a nucleophilic attack on the carbonyl-containing compound (nucleophilic addition), producing a tetrahedral intermediate (2). This intermediate decomposes by the evolution of nitrogen gas forming the tertiary carbocation intermediate (3).
The reaction is then completed either by the reformation of the carbonyl through an 1,2-rearrangement or by the formation of the epoxide. There are two possible carbonyl products: one formed by migration of R (4) and the other by migration of R (5). The relative yield of each possible carbonyl is determined by the migratory preferences of the R-groups.
The epoxide product is formed by an intramolecular addition reaction in which a lone pair from the oxygen attacks the carbocation (6).
This reaction is exothermic due to the stability of nitrogen gas and the carbonyl containing compounds. This specific mechanism is supported by several observations. First, kinetic studies of reactions between diazomethane and various ketones have shown that the overall reaction follows second order kinetics. Additionally, the reactivity of two series of ketones are in the orders ClCCOCH > CHCOCH > CHCOCH and cyclohexanone > cyclopentanone > cycloheptanone > cyclooctanone. These orders of reactivity are the same as those observed for reactions that are well established as proceeding through nucleophilic attack on a carbonyl group. | 0 | Organic Chemistry |
SIR proteins have been identified in many screens, and have historically been known as SIR (silent information regulator), MAR (mating-type regulator), STE (sterile), CMT (change of mating type) or SSP (sterile suppressor) according to which screen led to their identification. Ultimately, the name SIR had the most staying power, because it most accurately describes the function of the encoded proteins.
One of the early yeast screens to identify SIR genes was performed by Anita Hopper and Benjamin Hall, who screened with mutagenesis for alleles that allow sporulation in a normally sporulation-deficient heterothallic α/α (ho/ho MATα/MATα). Their screen identified a mutation in a novel gene that was not linked to HO that allowed the α/α diploid to sporulate, as if it were an α/a diploid, and inferred that the mutation affected a change in mating type by an HO-independent mechanism. Later, it was discovered at the CMT allele identified by Hopper & Hall did not cause a mating type conversion at the MAT locus, but rather allowed the expression of cryptic mating type genes that are silenced in wild-type yeast. In their paper clarifying the mechanism of the CMT mutation, Haber and acknowledge the contribution of Amar Klar, who presented his MAR mutant strains that had similar properties as the CMT mutants at the Cold Spring Harbor Laboratory yeast genetics meeting, which led Haber and to consider the hypothesis that the cmt mutants may act by de-repressing silent information.
In the same year that Haber & demonstrated that the cmt mutant restores sporulation by de-repressing hidden mating type loci, two other groups published screens for genes involved in the regulation of silent mating type cassettes. The first study, performed by Amar Klar, Seymour Fogel and Kathy Macleod, identified a mutation in a spontaneous a/a diploid that caused the products of sporulation to be haploids with an apparent diploid phenotype, as assayed by ability to mate. The authors reasoned that the mutation caused the de-repression of then-recently appreciated silent mating type loci HMa and HMα, which would allow an a/a diploid to sporulate and would cause haploid segregants inheriting the mutant allele to behave as a/α diploids despite being haploid. The authors named the mutation MAR for its apparent role in mating type regulation, and were able to map the mutation to chromosome IV, and determined that it was located 27.3 cM from a commonly used trp1 marker.
A few months later, Jasper Rine and Ira Herskowitz published a different screen for genes that affect the ability of yeast to mate, and ultimate discovered the gene family that they called SIR, a name that remains in the modern parlance. Unlike the Klar et al. screen that identified a mutant by its inability to mate, Rine & Herskowitz took a more directed approach towards discovering factors responsible for mating type silencing. Specifically, Rine & Herskowitz reasoned that a haploid yeast cell with a recessive mutation in matα1 could be complemented if the silent copy of MATα were de-repressed. Starting in a ho matα1 haploid strain, Rine & Herskowitz screened mutants arising from mutagenesis and identified five mutants that restored a MATα phenotype in matα cells, but were not linked to the MAT locus and did not cause a gene conversion between the HMα locus and matα. These mutants, they reasoned, were specifically defective in silencing the cryptic mating type genes.
Eventually, all of the mutants resulting from the original Hopper & Hall screen as well as the later Rine & Herskowitz screen and the Klar et al. screen were characterized and mapped, and it was shown that the causative genes were the same. In fact, the genes that are now referred to as SIR1-4 have at one time been referred to as MAR, CMT or STE according to the screen that identified the mutants.
Although Klar, Hartwell and Hopper identified mutations in SIR genes and applied other names to the genes before Rine performed his screen, the SIR name was eventually adopted because Rine eventually identified the most complete set of functionally related genes (SIR1-4), and because the work by Rine and Herskowitz most accurately described the function of the SIR family genes. Later it would be shown that in yeast and in higher organisms, SIR proteins are important for transcriptional regulation of many chromatin domains. | 1 | Biochemistry |
In the mid 2010s several techniques combined with Next Generation Sequencing were developed that employ the "tag" principle for "digital gene expression profiling" but without the use of the tagging enzyme. The "MACE" approach, (=Massive Analysis of cDNA Ends) generates tags somewhere in the last 1500 bps of a transcript. The technique does not depend on restriction enzymes anymore and thereby circumvents bias that is related to the absence or location of the restriction site within the cDNA. Instead, the cDNA is randomly fragmented and the 3ends are sequenced from the 5 end of the cDNA molecule that carries the poly-A tail. The sequencing length of the tag can be freely chosen. Because of this, the tags can be assembled into contigs and the annotation of the tags can be drastically improved. Therefore, MACE is also use for the analyses of non-model organisms. In addition, the longer contigs can be screened for polymorphisms. As UTRs show a large number of polymorphisms between individuals, the MACE approach can be applied for allele determination, allele specific gene expression profiling and the search for molecular markers for breeding. In addition, the approach allows determining alternative polyadenylation of the transcripts. Because MACE does only require 3’ ends of transcripts, even partly degraded RNA can be analyzed with less degradation dependent bias. The MACE approach uses unique molecular identifiers to allow for identification of PCR bias. | 1 | Biochemistry |
Thiosemicarbazides are precursors to thiosemicarbazones. They are precursors to heterocycles. Formylation of thiosemicarbazide provides access to triazole. | 0 | Organic Chemistry |
Drug checking has been shown to be an effective way to reduce the harm from drug use through informing safer use, limiting use, and helping users avoid the most dangerous substances. The services also provide monitoring and detection of new psychoactive substances to inform public health interventions. The Loop have stated that 20% of samples are handed in for disposal and 40% of service users reduce intake. KnowYourStuffNZ have found that, when substances are not as expected, half of service users state they will not take that substance and a quarter say they will take a smaller quantity. Drug checking services also reach drug users who are not reached by existing services. Evidence from research conducted by Austrian pill testing service CheckIt! found 58% of people who use the service would not otherwise seek out harm reduction information, and about 75% are more likely to access harm reduction services if pill testing is included.
Academic research from the UK has found that one in five substances were not what they were expected to be and two-thirds of misrepresented samples were disposed of. Such on-site testing accesses otherwise hard-to-reach user groups to reduce the harms associated with drug use.
Research that followed-up people who had used drug checking services in the UK revealed that those people acted upon the harm reduction advice that they received from the service. Those people disposed of unwanted substances, reduced their dosage of wanted substances, and reduced their risk of overdose. People also followed those risk management practices after attending festivals, alterted friends to the risks of drug use, and continued to follow that advice.
In a peer-reviewed study published in Journal of Psychopharmacology, researchers at Johns Hopkins found that people were about half as likely (relative risk = 0.56) to report intent to use a product if testing did not identify the substance as MDMA, and this was a statistically significant reduction. | 3 | Analytical Chemistry |
Mono(ADP-ribosyl)transferases commonly catalyze the addition of ADP-ribose to arginine side chains using a highly conserved R-S-EXE motif of the enzyme. The reaction proceeds by breaking the bond between nicotinamide and ribose to form an oxonium ion. Next, the arginine side chain of the target protein then acts a nucleophile, attacking the electrophilic carbon adjacent to the oxonium ion. In order for this step to occur, the arginine nucleophile is deprotonated by a glutamate residue on the catalyzing enzyme. Another conserved glutamate residue forms a hydrogen bond with one of the hydroxyl groups on the ribose chain to further facilitate this nucleophilic attack. As a result of the cleavage reaction, nicotinamide is released. The modification can be reversed by (ADP-ribosyl)hydrolases, which cleave the N-glycosidic bond between arginine and ribose to release ADP-ribose and unmodified protein; NAD is not restored by the reverse reaction. | 1 | Biochemistry |
Photoconductive atomic force microscopy (PC-AFM) is a variant of atomic force microscopy that measures photoconductivity in addition to surface forces. | 6 | Supramolecular Chemistry |
One way to identify the expression pattern of a particular gene is to place a reporter gene downstream of its promoter. In this configuration, the promoter gene will cause the reporter gene to be expressed only where and when the gene of interest is expressed. The expression distribution of the reporter gene can be determined by visualizing it. For example, the reporter gene green fluorescent protein can be visualized by stimulating it with blue light and then using a digital camera to record green fluorescent emission.
If the promoter of the gene of interest is unknown, there are several ways to identify its spatiotemporal distribution. Immunohistochemistry involves preparing an antibody with specific affinity for the protein associated with the gene of interest. This distribution of this antibody can then be visualized by a technique such as fluorescent labeling. Immunohistochemistry has the advantages of being methodologically feasible and relatively inexpensive. Its disadvantages include non-specificity of the antibody leading to false positive identification of expression. Poor penetrance of the antibody into the target tissue can lead to false negative results. Furthermore, since immunohistochemistry visualizes the protein generated by the gene, if the protein product diffuses between cells, or has a particularly short or long half-life relative to the mRNA that is used to translate the protein, this can lead to distorted interpretation of which cells are expressing the mRNA.
In situ hybridization is an alternate method in which a "probe," a synthetic nucleic acid with a sequence complementary to the mRNA of the gene, is added to the tissue. This probe is then chemically tagged so that it can be visualized later. This technique enables visualization specifically of mRNA-producing cells without any of the artifacts associated with immunohistochemistry. However, it is notoriously difficult, and requires knowledge of the sequence of DNA corresponding to the gene of interest.
A method called enhancer-trap screening reveals the diversity of spatiotemporal gene expression patterns possible in an organism. In this technique, DNA that encodes a reporter gene is randomly inserted into the genome. Depending on the gene promoters proximal to the insertion point, the reporter gene will be expressed in particular tissues at particular points in development. While enhancer-trap derived expression patterns do not necessarily reflect the actual patterns of expression of specific genes, they reveal the variety of spatiotemporal patterns that are accessible to evolution.
Reporter genes can be visualized in living organisms, but both immunohistochemistry and in situ hybridization must be performed in fixed tissues. Techniques that require fixation of tissue can only generate a single temporal time point per individual organism. However, using live animals instead of fixed tissue can be crucial in dynamically understanding expression patterns over an individual's lifespan. Either way, variation between individuals can confound the interpretation of temporal expression patterns. | 1 | Biochemistry |
A crystallographic database is a database specifically designed to store information about the structure of molecules and crystals. Crystals are solids having, in all three dimensions of space, a regularly repeating arrangement of atoms, ions, or molecules. They are characterized by symmetry, morphology, and directionally dependent physical properties. A crystal structure describes the arrangement of atoms, ions, or molecules in a crystal. (Molecules need to crystallize into solids so that their regularly repeating arrangements can be taken advantage of in X-ray, neutron, and electron diffraction based crystallography.)
Crystal structures of crystalline material are typically determined from X-ray or neutron single-crystal diffraction data and stored in crystal structure databases. They are routinely identified by comparing reflection intensities and lattice spacings from X-ray powder diffraction data with entries in powder-diffraction fingerprinting databases.
Crystal structures of nanometer sized crystalline samples can be determined via structure factor amplitude information from single-crystal electron diffraction data or structure factor amplitude and phase angle information from Fourier transforms of HRTEM images of crystallites. They are stored in crystal structure databases specializing in nanocrystals and can be identified by comparing zone axis subsets in lattice-fringe fingerprint plots with entries in a lattice-fringe fingerprinting database.
Crystallographic databases differ in access and usage rights and offer varying degrees of search and analysis capacity. Many provide structure visualization capabilities. They can be browser based or installed locally. Newer versions are built on the relational database model and support the Crystallographic Information File (CIF) as a universal data exchange format. | 7 | Physical Chemistry |
In organic chemistry, thioesters are organosulfur compounds with the molecular structure . They are analogous to carboxylate esters () with the sulfur in the thioester replacing oxygen in the carboxylate ester, as implied by the thio- prefix. They are the product of esterification of a carboxylic acid () with a thiol (). In biochemistry, the best-known thioesters are derivatives of coenzyme A, e.g., acetyl-CoA. The R and R' represent organyl groups, or H in the case of R. | 0 | Organic Chemistry |
Terahertz transitions in solids can be systematically approached by generalizing the semiconductor Bloch equations and the related many-body correlation dynamics. At this level, one realizes the THz field are directly absorbed by two-particle correlations that modify the quantum kinetics of electron and hole distributions. Therefore, a systematic THz analysis must include the quantum kinetics of many-body correlations, that can be treated systematically, e.g., with the cluster-expansion approach. At this level, one can explain and predict a wide range of effects with the same theory, ranging from Drude-like response of plasma to extreme nonlinear effects of excitons. | 7 | Physical Chemistry |
Restlessness, apprehension, and anxiety were reported effects after the use of various beta-agonists, particularly after oral or parenteral treatment. In pilot clinical trials with ractopamine, four patients showed little evidence for central nervous system stimulation. Whether long-term treatment with these drugs results in the development of tolerance to these adverse effects is unclear. | 4 | Stereochemistry |
In the laboratory, it is used to detect the presence of alkaline phosphatase activity by hydrolysis of PNPP. In basic conditions, presence of hydrolytic enzymes will turn reaction vessel yellow.
4-Nitrophenol is a product of the enzymatic cleavage of several synthetic substrates such as 4-nitrophenyl phosphate (used as a substrate for alkaline phosphatase), 4-nitrophenyl acetate (for carbonic anhydrase), 4-nitrophenyl-β--glucopyranoside and other sugar derivatives which are used to assay various glycosidase enzymes. Amounts of 4-nitrophenol produced by a particular enzyme in the presence of its corresponding substrate can be measured with a spectrophotometer at or around 405 nm and used as a proxy measurement for the amount of the enzyme activity in the sample.
Accurate measurement of enzyme activity requires that the 4-nitrophenol product is fully deprotonated, existing as 4-nitrophenolate, given the weak absorbance of 4-nitrophenol at 405 nm. Complete ionization of the alcohol functional group affects the conjugation of the pi bonds on the compound. A lone pair from the oxygen can be delocalized via conjugation to the benzene ring and nitro group. Since the length of conjugated systems affects the color of organic compounds, this ionization change causes the 4-nitrophenol to turn yellow when fully deprotonated and existing as 4-nitrophenolate.
A common mistake in measuring enzyme activity using these substrates is to perform the assays at neutral or acidic pH without considering that only part of the chromophoric product is ionized. The problem can be overcome by stopping the reaction with sodium hydroxide (NaOH) or other strong base, which converts all product into 4-nitrophenoxide; final pH must be > ca. 9.2 to ensure more than 99% of the product is ionised. Alternatively enzyme activity can be measured at 348 nm, the isosbestic point for 4-nitrophenol/4-nitrophenoxide. | 3 | Analytical Chemistry |
Silicon thin-film cells are mainly deposited by chemical vapor deposition (typically plasma-enhanced, PE-CVD) from silane gas and hydrogen gas. Depending on the deposition parameters, this can yield amorphous silicon (a-Si or a-Si:H), protocrystalline silicon or nanocrystalline silicon (nc-Si or nc-Si:H), also called microcrystalline silicon.
Amorphous silicon is the most well-developed thin film technology to-date. An amorphous silicon (a-Si) solar cell is made of non-crystalline or microcrystalline silicon. Amorphous silicon has a higher bandgap (1.7 eV) than crystalline silicon (c-Si) (1.1 eV), which means it absorbs the visible part of the solar spectrum more strongly than the higher power density infrared portion of the spectrum. The production of a-Si thin film solar cells uses glass as a substrate and deposits a very thin layer of silicon by plasma-enhanced chemical vapor deposition (PECVD).
Protocrystalline silicon with a low volume fraction of nanocrystalline silicon is optimal for high open-circuit voltage. Nc-Si has about the same bandgap as c-Si and nc-Si and a-Si can advantageously be combined in thin layers, creating a layered cell called a tandem cell. The top cell in a-Si absorbs the visible light and leaves the infrared part of the spectrum for the bottom cell in nc-Si. | 7 | Physical Chemistry |
Ninhydrin may cause allergic, IgE-mediated rhinitis and asthma. A case has been described in which a 41 year old forensic laboratory worker working with Ninhydrin developed rhinitis and respiratory difficulty. Her specific IgE levels were found almost doubled. | 0 | Organic Chemistry |
For some polyprotic acids, dissociation (or association) occurs at more than one nonequivalent site, and the observed macroscopic equilibrium constant, or macro-constant, is a combination of micro-constants involving distinct species. When one reactant forms two products in parallel, the macro-constant is a sum of two micro-constants, This is true for example for the deprotonation of the amino acid cysteine, which exists in solution as a neutral zwitterion . The two micro-constants represent deprotonation either at sulphur or at nitrogen, and the macro-constant sum here is the acid dissociation constant
Similarly, a base such as spermine has more than one site where protonation can occur. For example, mono-protonation can occur at a terminal group or at internal groups. The K values for dissociation of spermine protonated at one or other of the sites are examples of micro-constants. They cannot be determined directly by means of pH, absorbance, fluorescence or NMR measurements; a measured K value is the sum of the K values for the micro-reactions.
Nevertheless, the site of protonation is very important for biological function, so mathematical methods have been developed for the determination of micro-constants.
When two reactants form a single product in parallel, the macro-constant For example, the abovementioned equilibrium for spermine may be considered in terms of K values of two tautomeric conjugate acids, with macro-constant In this case This is equivalent to the preceding expression since is proportional to
When a reactant undergoes two reactions in series, the macro-constant for the combined reaction is the product of the micro-constant for the two steps. For example, the abovementioned cysteine zwitterion can lose two protons, one from sulphur and one from nitrogen, and the overall macro-constant for losing two protons is the product of two dissociation constants This can also be written in terms of logarithmic constants as | 7 | Physical Chemistry |
Semicarbazide is used in preparing pharmaceuticals including nitrofuran antibacterials (furazolidone, nitrofurazone, nitrofurantoin) and related compounds. It is also a product of degradations of the blowing agent azodicarbonamide (ADC). Semicarbazide forms in heat-treated flour containing ADC as well as breads made from ADC-treated flour.
Semicarbazide is used as a detection reagent in thin layer chromatography (TLC). Semicarbazide stains α-keto acids on the TLC plate, which can then be viewed under ultraviolet light. | 0 | Organic Chemistry |
For explanatory purposes consider an electrophoretic particle moving (driven) in an electric field. Let:
and
denote an electric field and the velocity of the particle in such a field. If is constant the time average of .
If is not constant as a function of time and if has a frequency component proportional to the time average of need not be zero.
Consider the following example:
Substituting (3) in (2) and computing the time average, , we obtain:
Thus, it is possible to have the particle experience a non-zero time average velocity, in other words, a net electrophoretic drift, even when the time average of the applied electric field is zero. | 1 | Biochemistry |
Photoactivatable fluorescent proteins (PAFPs) is a type of fluorescent protein that exhibit fluorescence that can be modified by a light-induced chemical reaction. | 1 | Biochemistry |
Alarm signalling varies depending on the receiver's knowledge of a certain threat. Chimpanzees are significantly more likely to produce an alarm call when conspecifics are unaware of a potential threat or were not nearby when a previous alarm call was emitted. When judging if conspecifics are unaware of potential dangers, chimpanzees do not solely look for behavioural cues, but also assess receiver mental states and use this information to target signalling and monitoring. In a recent experiment, caller chimpanzees were shown a fake snake as a predator and were played pre-recorded calls from receivers. Some receivers emitted calls that were snake-related, and therefore represented receivers with knowledge of the predator, while other receivers emitted calls that were not snake-related, and therefore represented receivers without knowledge of the predator. In response to the non-snake-related calls from receivers, the signallers increased their vocal and nonvocal signalling and coupled it with increased receiver monitoring. | 1 | Biochemistry |
In forensic science, hybridization probes are used, for example, for detection of short tandem repeats (microsatellite) regions and in restriction fragment length polymorphism (RFLP) methods, all of which are widely used as part of DNA profiling analysis. | 1 | Biochemistry |
The HTL process differs from pyrolysis as it can process wet biomass and produce a bio-oil that contains approximately twice the energy density of pyrolysis oil. Pyrolysis is a related process to HTL, but biomass must be processed and dried in order to increase the yield. The presence of water in pyrolysis drastically increases the heat of vaporization of the organic material, increasing the energy required to decompose the biomass. Typical pyrolysis processes require a water content of less than 40% to suitably convert the biomass to bio-oil. This requires considerable pretreatment of wet biomass such as tropical grasses, which contain a water content as high as 80-85%, and even further treatment for aquatic species, which can contain higher than 90% water content.
The HTL oil can contain up to 80% of the feedstock carbon content (single pass). HTL oil has good potential to yield bio-oil with "drop-in" properties that can be directly distributed in existing petroleum infrastructure.
The energy returned on energy invested (EROEI) of these processes is uncertain and/or has not been measured. Furthermore, products of hydrous pyrolysis might not meet current fuel standards. Further processing may be required to produce fuels. | 0 | Organic Chemistry |
The PDE nomenclature signifies the PDE family with an Arabic numeral, then a capital letter denotes the gene in that family, and a second and final Arabic numeral then indicates the splice variant derived from a single gene (e.g., PDE1C3: family 1, gene C, splicing variant 3).
The superfamily of PDE enzymes is classified into 11 families, namely PDE1-PDE11, in mammals. The classification is based on:
* amino acid sequences
* substrate specificities
* regulatory properties
* pharmacological properties
* tissue distribution
Different PDEs of the same family are functionally related despite the fact that their amino acid sequences can show considerable divergence. PDEs have different substrate specificities. Some are cAMP-selective hydrolases (PDE4, 7 and 8); others are cGMP-selective (PDE5, 6, and 9). Others can hydrolyse both cAMP and cGMP (PDE1, 2, 3, 10, and 11). PDE3 is sometimes referred to as cGMP-inhibited phosphodiesterase. Although PDE2 can hydrolyze both cyclic nucleotides, binding of cGMP to the regulatory GAF-B domain will increase cAMP affinity and hydrolysis to the detriment of cGMP. This mechanism, as well as others, allows for cross-regulation of the cAMP and cGMP pathways. PDE12 cleaves 2,5-phosphodiester bond linking adenosines of the 5'-triphosphorylated oligoadenylates. PDE12 is not a member of the cyclic nucleotide phosphodiesterase superfamily that contains PDE1 through PDE11. | 1 | Biochemistry |
The Journal of Photochemistry and Photobiology B: Biology is published monthly. The editors are Robert Carpentier and Dominic J. Robinson. Carpentier covers the fields of biophysics, biomolecular spectroscopy, photosynthesis, environmental photobiology, oxygen radicals, DNA repair, and UV-/VIS effects. Robinson covers photomedicine, photodynamic therapy, photosensitisers and dermatology. | 5 | Photochemistry |
EAB sensors possess the potential to significantly advance our comprehension of metabolism, endocrinology, pharmacokinetics, and neurochemistry as valuable research tools. Specifically, these sensors offer improved resolution and more quantitative measurements of phenomena such as drug delivery, clearance, and the maintenance of metabolic homeostasis. Due to their capability for feedback control, E-AB sensors also present unprecedented opportunities to elucidate the correlation between, for instance, plasma drug levels and subsequent clinical or behavioral responses. The simultaneous measurements performed by E-AB sensors in multiple body locations can enhance our understanding of drug and metabolite transport within and between bodily compartments. Beyond in-body measurements, E-AB sensors could be beneficial for real-time monitoring in cell culture applications, ranging from small-scale (e.g., "organ on a chip") to industrial scale (e.g., monitoring industrial bioreactors). They have already demonstrated utility in applications such as monitoring ATP release in astrocytes and detecting serotonin in cell culture using glass nanopipettes. | 7 | Physical Chemistry |
When a virus transforms a cell it often causes cancer by either altering the cells' existing genome or introducing additional genetic material which causes cells to uncontrollably replicate. It is rarely considered that what causes so much harm also has the capability of reversing the process and slowing the cancer growth or even leading to remission. Viruses transform host cells in order to survive and replicate; however, the immune responses of the host cell are typically compromised during transformation making transformed cells more susceptible to other viruses.
The idea of using viruses to treat cancers was first introduced in 1951 when a 4-year-old boy suddenly went into a temporary remission from leukemia while he had chickenpox. This led to research in the 1990s where scientists worked to create a strain of the herpes simplex virus strong enough to infect and transform tumor cells but weak enough to leave healthy cells unharmed. Treating patients with viral transformation has the possibility of treating patients more safely and more effectively than using traditional methods, such as chemotherapy. Viruses used in the treatment of cancer gain strength and increase their effectiveness as the multiply in the body while causing only minor side effects, such as nausea, fatigue, and aches. | 1 | Biochemistry |
LD uses linearly polarized light, which is light that has been polarized in one direction only. This produces a wave, the electric field vector, which oscillates in only one plane, giving rise to a classic sinusoidal wave shape as the light travels through space. By using light parallel and perpendicular to the orientation direction it is possible to measure how much more energy is absorbed in one dimension of the molecule relative to the other, providing information to the experimentalist.
As light interacts with the molecule being investigated, should the molecule start absorbing the light then electron density inside the molecule will be shifted as the electron becomes photoexcited. This movement of charge is known as an electronic transition, the direction of which is called the electric transition polarisation. It is this property for which LD is a measurement.
The LD of an oriented molecule can be calculated using the following equation:-
:LD = A- A
Where A is the absorbance parallel to the orientation axis and A is the absorbance perpendicular to the orientation axis.
Note that light of any wavelength can be used to generate an LD signal.
The LD signal generated therefore has two limits upon the signal that can be generated. For a chemical system whose electric transition is parallel to the orientation axis, the following equation can be written:
:LD = A- A = A > 0
For most chemical systems this represents an electric transition polarised across the length of the molecule (i.e. parallel to the orientation axis).
Alternatively, the electric transition polarisation can be found to be perfectly perpendicular to the orientation of the molecule, giving rise to the following equation:
:LD = A- A = - A < 0
This equation represents the LD signal recorded if the electric transition is polarised across the width of the molecule (i.e. perpendicular to the orientation axis), which in the case of LD is the smaller of the two investigable axes.
LD can therefore be used in two ways. If the orientation of the molecules in flow is known, then the experimentalist can look at the direction of polarisation in the molecule (which gives an insight into the chemical structure of a molecule), or if the polarisation direction is unknown it can be used as a means of working out how oriented in flow a molecule is. | 7 | Physical Chemistry |
Assemblies of solar cells are used to make solar modules that generate electrical power from sunlight, as distinguished from a "solar thermal module" or "solar hot water panel". A solar array generates solar power using solar energy. | 7 | Physical Chemistry |
The Sullivan reaction is a chemical test used for detecting the presence of cysteine or cystine in proteins. A red colour appears when a protein with cysteine or cystine is heated with sodium 1,2-naphthoquinone-4-sulfonate (Folin's reagent) and sodium dithionite under alkaline conditions. This was pioneered by the American organic and industrial chemist Eugene Cornelius Sullivan (1872–1962). | 3 | Analytical Chemistry |
CSI is prepared by treating cyanogen chloride with sulfur trioxide, the product being distilled directly from the reaction mixture.
::SO + ClCN → ClSONCO
In this transformation, both the carbon and the nitrogen termini of CN are functionalized.
The structure of CSI is represented as ClS(O)-N=C=O. It consists of two electron-withdrawing components, the chlorosulfonyl group (SOCl) and the isocyanate group (-N=C=O). Because of its resulting electrophilicity, the use of CSI in chemical synthesis requires relatively inert solvents such as chlorocarbons, acetonitrile, and ethers. | 0 | Organic Chemistry |
In addition to both surfaces' being practically conformal (in practice often completely flat), the surfaces must also be extremely clean and free from any small contamination that would prevent or weaken the bond—including grease films and specks of dust. For bonding to occur, the surfaces need only to be brought together; the intermolecular forces draw the bodies into the lowest energy conformation, and no pressure needs to be applied. | 6 | Supramolecular Chemistry |
Cyanobacteria (), also called Cyanobacteriota or Cyanophyta, are a phylum of autotrophic gram-negative bacteria that can obtain biological energy via photosynthesis. The name cyanobacteria refers to their color (), which similarly forms the basis of cyanobacteria's common name, blue-green algae, although they are not scientifically classified as algae. They appear to have originated in a freshwater or terrestrial environment.
Cyanobacteria are probably the most numerous taxon to have ever existed on Earth and the first organisms known to have produced oxygen. By producing and releasing oxygen as a byproduct of photosynthesis, cyanobacteria are thought to have converted the early oxygen-poor, reducing atmosphere into an oxidizing one, causing the Great Oxidation Event and the "rusting of the Earth", which dramatically changed the composition of life forms on Earth.
Cyanobacteria use photosynthetic pigments, such as various forms of chlorophyll, carotenoids, phycobilins to convert the energy in sunlight to chemical energy. Unlike heterotrophic prokaryotes, cyanobacteria have internal membranes. These are flattened sacs called thylakoids where photosynthesis is performed. Phototrophic eukaryotes such as green plants perform photosynthesis in plastids that are thought to have their ancestry in cyanobacteria, acquired long ago via a process called endosymbiosis. These endosymbiotic cyanobacteria in eukaryotes then evolved and differentiated into specialized organelles such as chloroplasts, chromoplasts, etioplasts, and leucoplasts, collectively known as plastids.
Sericytochromatia, the proposed name of the paraphyletic and most basal group, is the ancestor of both the non-photosynthetic group Melainabacteria and the photosynthetic cyanobacteria, also called Oxyphotobacteria.
The cyanobacteria Synechocystis and Cyanothece are important model organisms with potential applications in biotechnology for bioethanol production, food colorings, as a source of human and animal food, dietary supplements and raw materials. Cyanobacteria produce a range of toxins known as cyanotoxins that can cause harmful health effects in humans and animals. | 5 | Photochemistry |
After the explanation of van der Waals forces by Fritz London, several scientists soon realised that his definition could be extended from the interaction of two molecules with induced dipoles to macro-scale objects by summing all of the forces between the molecules in each of the bodies involved. The theory is named after H. C. Hamaker, who derived the interaction between two spheres, a sphere and a wall, and presented a general discussion in a heavily cited 1937 paper.
The interaction of two bodies is then treated as the pairwise interaction of a set of N molecules at positions: R {i:1,2,... ...,N}. The distance between the molecules i and j is then:
The interaction energy of the system is taken to be:
where is the interaction of molecules i and j in the absence of the influence of other molecules.
The theory is however only an approximation which assumes that the interactions can be treated independently, the theory must also be adjusted to take into account quantum perturbation theory. | 6 | Supramolecular Chemistry |
Photoresists are coatings, or oligomers, that are deposited on a surface and are designed to change properties upon irradiation of light. These changes either polymerize the liquid oligomers into insoluble cross-linked network polymers or decompose the already solid polymers into liquid products. Polymers that form networks during photopolymerization are referred to as negative resist. Conversely, polymers that decompose during photopolymerization are referred to as positive resists. Both positive and negative resists have found many applications including the design and production of micro-fabricated chips. The ability to pattern the resist using a focused light source has driven the field of photolithography. | 5 | Photochemistry |
Luciferase can function in two different pathways: a bioluminescence pathway and a CoA-ligase pathway. In both pathways, luciferase initially catalyzes an adenylation reaction with MgATP. However, in the CoA-ligase pathway, CoA can displace AMP to form luciferyl CoA.
Fatty acyl-CoA synthetase similarly activates fatty acids with ATP, followed by displacement of AMP with CoA. Because of their similar activities, luciferase is able to replace fatty acyl-CoA synthetase and convert long-chain fatty acids into fatty-acyl CoA for beta oxidation. | 1 | Biochemistry |
The development has been undertaken from a project on modern diffraction methods for the investigation of thermo-mechanical processeses, and started with cold deformation of a copper specimen at the ESRF in 2007, followed by hot deformation of zirconium alloy at APS in 2008. Soon afterwards, a series of other materials has been tested and experience with the timeline traces gained. While ESRF and APS played the major role in experimental facilities, the Japanese high-energy synchrotron in the round, SPring-8 followed in 2013 by performing feasibility studies of this kind. Meanwhile, the new PETRA III synchrotron at DESY built a dedicated beamline for this purpose, opening the Materials Oscilloscope investigations to a larger public. The name materials oscilloscope was introduced in 2013 and used onward upon conferences such as MRS and TMS. | 7 | Physical Chemistry |
Metallacrowns are most widely studied for their potential use as SMMs (single-molecule magnets). Notably, the first mixed manganese-lanthanide SMM was a metallacrown. Metallacrowns with gadolinium as the central metal are potential MRI contrast agents. A lot of attention is focused on metallacrown molecular recognition and host–guest chemistry. Chelation of heavy metals by 15-MC-5 complexes could be utilized in lanthanide separation or heavy metal sequestration. Metallacrown container molecules constructed from the 15-MC-5 structure type have been shown to selectively encapsulate carboxylate anions in hydrophobic cavities. A crystalline solid displaying second-harmonic generation was generated by including a nonlinear optical chromophore in a chiral metallacrown compartment. Metallacrowns have also been utilized in the construction of microporous. and mesoporous materials. In another potential application, some metallacrowns exhibit antibacterial activity. | 6 | Supramolecular Chemistry |
Anisomycin is used as a component of Martin Lewis agar, an in vitro diagnostic product which is used extensively in the United States for the selective isolation of Neisseria gonorrhoeae and Neisseria meningitidis. The antimicrobial can also be used in buffered charcoal yeast extract media for the selective isolation of Legionella species. | 1 | Biochemistry |
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