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common method to get to imine precursors. Amine alkylation by direct SN2 reaction is only occasionally useful in producing starting materials due to the high propensity of amines to overalkylate. Reductive amination is a more common and effective alkylating procedure, typified in the first aza-Cope rearrangement. The most useful and standard method of amine alkylation is to have the amine form an amide bond, and subsequently reduce it, often with lithium aluminium hydride. ==== Oxazolidine use ==== Ketones and sterically hindered aldehydes are not suitable for the basic aza-Cope/Mannich reaction, as the amine cannot form an iminium ion with them. Dehydrative oxazoline formation followed by heating in the presence of a full equivalent of acid present a way to get around this issue. Overman has reported the use of oxizolidines to generate the iminium ion requisite for the reaction. Upon formation, Overman showed that cyclohexanones can be used for the carbonyl component in pyrrolidine synthesis. This reaction proceeded with various forms of cyclohexanones. When an acyclic ketone was substituted, the reaction proceeded with low yield, highlighting the thermodynamic favorability of releasing cyclohexanone from the double bonded carbonyl, as it creates unfavorable bond strain in the chair conformation. This represents one of the most convenient constructions of the 1-azaspiro[4,5]decane ring system, a useful natural product. === Installation of the vinyl substituent === ==== Vinylation of ketones ==== Vinylation can offer additional synthetic advantages, allowing for expanded functionality of the reaction. Organolithium reagents are typically used. Often, a substituent or protecting group will be added to the nitrogen, although this isn't always necessary. The addition of lithium to the reaction has a major effect on starting material stereochemistry, as the nitrogen coordinates to it. Starting materials affected by this coordination generally result in anti aza-Cope precursors, while those that aren't, such as
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those containing highly substituted, sterically hindered amines, result in syn precursors. Thus the nature of the nitrogen substituent is of high importance. ==== Cyanomethyl group use ==== Cyanomethyl groups represent an easy way to protect an iminium ion during allylic vinylation of the ketone. Cyanamide groups and analogs have been often used in the generation iminium ions. They are typically installed by nucleophilic addition onto an iminium ion, generally produced by amine alkylation with formaldehyde. The iminium ion is thus masked. It follows that usage of a cyanomethyl group provides an efficient way to control the aza-Cope/Mannich reaction. The cyanomethyl group protects the nitrogen at the 2-position during formation of the other allylic analog by logic similar to cyanide-type umpolung. It then later provides a good leaving group for formation of the iminium ion, in accordance with its usage in iminium ion generation. Iminium ion generation from cyanomethyl groups is normally promoted by addition of silver nitrate, although other silver and copper compounds have been used. This added step allows for more precise control of iminium ion generation. Importantly, these preparatory reactions must be carried out at -78 °C to prevent cyanomethyl/vinyllithium interaction. This method also allows for many different possible N-substituents, and can be used to simplify the synthesis of octahydroindoles and pyrroles. == The 1- and 3-aza-Cope rearrangements == The 1- and 3-aza-Cope rearrangements are obscure in comparison to the cationic 2-aza-Cope rearrangement due to their activation energies, which are comparatively much higher than that of the cationic 2-aza-Cope rearrangement. The 1- and 3-aza-Cope have a bias towards imine formation as opposed to enamine formation, as carbon-nitrogen π-bonding is stronger than carbon-nitrogen σ-bonding, meaning the 3-aza-Cope rearrangement is thermodynamically favored, while the 1-aza-Cope rearrangement is not: the imine is nearly 10kcal/mol less in energy. Thus the 3-aza Cope's
|
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large activation barriers are kinetically based. Research on both the 1 and 3-aza-Cope rearrangements has focused on finding good driving forces to lowering the activation barriers. Several versions of these rearrangements have been optimized for synthetic utility. The 1-aza-Cope rearrangement is normally paired with thermodynamic driving forces. The 3-aza-Cope rearrangements are generally performed cationically to lower the kinetic barrier to its thermodynamically favorable product. These rearrangements follow much of the mechanistic logic of the cationic 2-Aza-Cope rearrangement. The 1- and 3-aza-Cope rearrangements both occur preferentially via chair transition states (and retain stereochemistry, similarly to the cationic 2-aza-Cope rearrangement), and are sped up with the introduction of a positive charge, as this gives the transition state more diradical/dipolar character. The 3-aza-Cope rearrangement (and thus also the 1-aza-Cope rearrangement, which goes through the same transition state) is expected to show even less aromatic character in its transition state in comparison to the Cope rearrangement and cationic-2-aza-Cope rearrangement, contributing to the higher temperatures required (close to the temperatures required for the Cope rearrangement, at times even higher, from 170 to 300 degrees) to overcome the kinetic activation barriers for these arrangements. === The 3-aza-Cope rearrangement === The 3-aza-Cope reaction was discovered soon after the 2-aza-Cope rearrangement was identified, due to its analogous relationship to the Claisen rearrangement. Indeed, in early papers, this version of the aza-Cope rearrangement is often referred to as the amino-Claisen rearrangement, a misrepresentation of the rearrangement, as this would imply that both a nitrogen and oxygen are in the molecule. This rearrangement can be used to form heterocyclic rings involving carbon, most commonly piperidine. One of the first examples of this arrangement was identified by Burpitt, who recognized the rearrangement occurring in ammonium salts, which, due to their charged nature, proceeded exothermically without addition of heat—importantly, without a tetrasubstituted
|
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nitrogen, the rearrangement did not proceed. Following this logic, much of the research on the 3-aza-Cope rearrangement has focused on charged zwitterionic versions of this reaction, as the charge distribution helps lower the activation barrier: in certain cases, the rearrangement can occur at temperatures as low as -20 °C. Hill and Gilman first reported a general uncharged 3-aza-Cope rearrangement in 1967. Upon creation of appropriately substituted enamines, intense heating afforded an almost complete rearrangement to the imine product. However, this rearrangement pathway has limited utility. === The 1-aza-Cope rearrangement === The first discovered 1-aza-Cope reaction was a simple analog to the generic Cope reaction and required intense heat to overcome its large thermodynamic activation barrier; most subsequent work on the 1-aza-Cope rearrangement has thus focused on pairing the arrangement with a driving thermodynamic force to avoid these harsh reaction conditions. It has been hypothesized that the 1-aza-Cope rearrangement rate-determining transition state has partial diradical and dipolar transition state character due to the presence of the heteroatom. Fowler and coworkers have come up with a scheme that mobilizes the 1-aza-Cope rearrangement as a synthetically useful route. Fowler and coworkers recognized that because the barrier for the reaction lies in the nitrogen's thermodynamic preference to stay as an imine, stabilizing the nitrogen could have a thermodynamically beneficial effect. To that end, Fowler and coworkers installed a carbonyl group on the nitrogen, hypothesizing that the lone pair of the nitrogen would be stabilized by participation in an amide bond, and that the electronegativity of this amide group would lower the LUMO of the imine group, making the transition state more favorable. Using this strategy, Fowler and coworkers were able to use the 1-aza-Cope rearrangement to create piperidine and pyridine derivatives. This strategy was shown to be relatively robust, allowing for the formation of
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products even when forced through a boat transition state, when perturbed with substituent effects, or put in competition with alternative rearrangements. Also significant is the relative ease of production of the reactants, which uses a Diels-Alder reaction paired with relatively simple workup steps, allowing for syntheses using complex cycling. Other methods of overcoming this thermodynamic barrier include pairing it with cyclopropane ring strain release, which allows the reaction to proceed at much lower temperatures. == References == == Further reading == Overman, L. E.; Humphreys, P. G.; Welmaker, G. S. (2011). "The Aza-Cope/Mannich Reaction". Organic Reactions. Vol. 75. pp. 747–820. doi:10.1002/0471264180.or075.04. ISBN 978-0471264187. Overman, L. E. (2009). "Molecular rearrangements in the construction of complex molecules". Tetrahedron. 65 (33): 6432–6446. doi:10.1016/j.tet.2009.05.067. PMC 2902795. PMID 20640042. Siegfried Blechert (1989). "The Hetero-Cope Rearrangement in Organic Synthesis". Synthesis. 1989 (2): 71–82. doi:10.1055/s-1989-27158.
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Overeating occurs when an individual consumes more calories than the energy that is expended via physical activity or expelled via excretion, or when they consume food past the point of satiation, often leading to weight gain and often obesity. Overeating is the defining characteristic of binge eating disorder, and it can be a symptom of bulimia nervosa. In a broader sense, hyperalimentation includes excessive food administration through other means than eating, e.g. through parenteral nutrition. == Treatment == Cognitive behavioural therapy, individual therapy, and group therapy are often beneficial in helping people keep track of their eating habits and changing the way they cope with difficult situations. Often overeating and the related binge eating are related to dieting, body image issues, as well as social pressures. There are several 12-step programs that helps overeaters, such as Overeaters Anonymous or Food Addicts in Recovery Anonymous and others. It is quite clear through research, and various studies that overeating causes addictive behaviors. In some instances, overeating has been linked to the use of medications known as dopamine agonists, such as pramipexole. == See also == == References == == Further reading == Kessler, David A. The End of Overeating: Taking Control of the Insatiable American Appetite (2009) ISBN 1-60529-785-2 == External links == Media related to Overeating at Wikimedia Commons
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"page_id": 461462,
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"title": "Overeating"
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Statistical Physics of Particles and Statistical Physics of Fields are a two-volume series of textbooks by Mehran Kardar. Each book is based on a semester-long course taught by Kardar at the Massachusetts Institute of Technology. They cover statistical physics and thermodynamics at the graduate level. == Editions == Kardar, Mehran (2007). Statistical Physics of Particles. Cambridge University Press. ISBN 978-0-521-87342-0. OCLC 860391091. Kardar, Mehran (2007). Statistical Physics of Fields. Cambridge University Press. ISBN 978-0-521-87341-3. OCLC 920137477. == External links == Statistical Mechanics I at MIT OpenCourseWare Statistical Mechanics II at MIT OpenCourseWare Publisher's website for Particles Publisher's website for Fields == References ==
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"page_id": 63703703,
"source": null,
"title": "Statistical Physics of Particles"
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Einstein synchronisation (or Poincaré–Einstein synchronisation) is a convention for synchronising clocks at different places by means of signal exchanges. This synchronisation method was used by telegraphers in the middle 19th century, but was popularized by Henri Poincaré and Albert Einstein, who applied it to light signals and recognized its fundamental role in relativity theory. Its principal value is for clocks within a single inertial frame. == Einstein == According to Albert Einstein's prescription from 1905, a light signal is sent at time τ 1 {\displaystyle \tau _{1}} from clock 1 to clock 2 and immediately back, e.g. by means of a mirror. Its arrival time back at clock 1 is τ 2 {\displaystyle \tau _{2}} . This synchronisation convention sets clock 2 so that the time τ 3 {\displaystyle \tau _{3}} of signal reflection is defined to be τ 3 = τ 1 + 1 2 ( τ 2 − τ 1 ) = 1 2 ( τ 1 + τ 2 ) . {\displaystyle \tau _{3}=\tau _{1}+{\tfrac {1}{2}}(\tau _{2}-\tau _{1})={\tfrac {1}{2}}(\tau _{1}+\tau _{2}).} The same synchronisation is achieved by transporting a third clock from clock 1 to clock 2 "slowly" (that is, considering the limit as the transport velocity goes to zero). The literature discusses many other thought experiments for clock synchronisation giving the same result. The problem is whether this synchronisation does really succeed in assigning a time label to any event in a consistent way. To that end one should find conditions under which: If point (a) holds then it makes sense to say that clocks are synchronised. Given (a), if (b1)–(b3) hold then the synchronisation allows us to build a global time function t. The slices t = const. are called "simultaneity slices". Einstein (1905) did not recognize the possibility of reducing (a) and (b1)–(b3) to
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easily verifiable physical properties of light propagation (see below). Instead he just wrote "We assume that this definition of synchronism is free from contradictions, and possible for any number of points; and that the following (that is b2–b3) relations are universally valid." Max von Laue was the first to study the problem of the consistency of Einstein's synchronisation. Ludwik Silberstein presented a similar study although he left most of his claims as an exercise for the readers of his textbook on relativity. Max von Laue's arguments were taken up again by Hans Reichenbach, and found a final shape in a work by Alan Macdonald. The solution is that the Einstein synchronisation satisfies the previous requirements if and only if the following two conditions hold: No redshift: If from point A two flashes are emitted separated by a time interval Δt as recorded by a clock at A, then they reach B separated by the same time interval Δt as recorded by a clock at B. Reichenbach's round-trip condition: If a light beam is sent over the triangle ABC, starting from A and reflected by mirrors at B and C, then its arrival time back to A is independent of the direction followed (ABCA or ACBA). Once clocks are synchronised one can measure the one-way speed of light. However, the previous conditions that guarantee the applicability of Einstein's synchronisation do not imply that the one-way light speed turns out to be the same all over the frame. Consider Laue–Weyl's round-trip condition: The time needed by a light beam to traverse a closed path of length L is L/c, where L is the length of the path and c is a constant independent of the path. A theorem (whose origin can be traced back to von Laue and Hermann Weyl) states that
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Laue–Weyl's round trip condition holds if and only if the Einstein synchronisation can be applied consistently (i.e. (a) and (b1)–(b3) hold) and the one-way speed of light with respect to the so synchronised clocks is a constant all over the frame. The importance of Laue–Weyl's condition stands on the fact that the time there mentioned can be measured with only one clock; thus this condition does not rely on synchronisation conventions and can be experimentally checked. Indeed, it has been experimentally verified that the Laue–Weyl round-trip condition holds throughout an inertial frame. Since it is meaningless to measure a one-way velocity prior to the synchronisation of distant clocks, experiments claiming a measure of the one-way speed of light can often be reinterpreted as verifying the Laue–Weyl's round-trip condition. The Einstein synchronisation looks this natural only in inertial frames. One can easily forget that it is only a convention. In rotating frames, even in special relativity, the non-transitivity of Einstein synchronisation diminishes its usefulness. If clock 1 and clock 2 are not synchronised directly, but by using a chain of intermediate clocks, the synchronisation depends on the path chosen. Synchronisation around the circumference of a rotating disk gives a non-vanishing time difference that depends on the direction used. This is important in the Sagnac effect and the Ehrenfest paradox. The Global Positioning System accounts for this effect. A substantive discussion of Einstein synchronisation's conventionalism is due to Hans Reichenbach. Most attempts to negate the conventionality of this synchronisation are considered refuted, with the notable exception of David Malament's argument, that it can be derived from demanding a symmetrical relation of causal connectability. Whether this settles the issue is disputed. == History: Poincaré == Some features of the conventionality of synchronization were discussed by Henri Poincaré. In 1898 (in a philosophical paper)
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he argued that the assumption of light's uniform speed in all directions is useful to formulate physical laws in a simple way. He also showed that the definition of simultaneity of events at different places is only a convention. Based on those conventions, but within the framework of the now superseded aether theory, Poincaré in 1900 proposed the following convention for defining clock synchronisation: 2 observers A and B, which are moving in the aether, synchronise their clocks by means of optical signals. Because of the relativity principle they believe themselves to be at rest in the aether and assume that the speed of light is constant in all directions. Therefore, they have to consider only the transmission time of the signals and then crossing their observations to examine whether their clocks are synchronous. Let us suppose that there are some observers placed at various points, and they synchronize their clocks using light signals. They attempt to adjust the measured transmission time of the signals, but they are not aware of their common motion, and consequently believe that the signals travel equally fast in both directions. They perform observations of crossing signals, one traveling from A to B, followed by another traveling from B to A. The local time t ′ {\displaystyle t'} is the time indicated by the clocks which are so adjusted. If V = 1 K 0 {\displaystyle V={\tfrac {1}{\sqrt {K_{0}}}}} is the speed of light, and v {\displaystyle v} is the speed of the Earth which we suppose is parallel to the x {\displaystyle x} axis, and in the positive direction, then we have: t ′ = t − v x V 2 {\displaystyle t'=t-{\tfrac {vx}{V^{2}}}} . In 1904 Poincaré illustrated the same procedure in the following way: Imagine two observers who wish to adjust their
|
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timepieces by optical signals; they exchange signals, but as they know that the transmission of light is not instantaneous, they are careful to cross them. When station B perceives the signal from station A, its clock should not mark the same hour as that of station A at the moment of sending the signal, but this hour augmented by a constant representing the duration of the transmission. Suppose, for example, that station A sends its signal when its clock marks the hour 0, and that station B perceives it when its clock marks the hour t {\displaystyle t} . The clocks are adjusted if the slowness equal to t represents the duration of the transmission, and to verify it, station B sends in its turn a signal when its clock marks 0; then station A should perceive it when its clock marks t {\displaystyle t} . The timepieces are then adjusted. And in fact they mark the same hour at the same physical instant, but on the one condition, that the two stations are fixed. Otherwise the duration of the transmission will not be the same in the two senses, since the station A, for example, moves forward to meet the optical perturbation emanating from B, whereas the station B flees before the perturbation emanating from A. The watches adjusted in that way will not mark, therefore, the true time; they will mark what may be called the local time, so that one of them will be slow of the other. == See also == Relativity of simultaneity One-way speed of light == References == == Literature == Darrigol, Olivier (2005), "The Genesis of the theory of relativity" (PDF), Séminaire Poincaré, 1: 1–22, Bibcode:2006eins.book....1D, doi:10.1007/3-7643-7436-5_1, ISBN 978-3-7643-7435-8 D. Dieks, Becoming, relativity and locality, in The Ontology of Spacetime, online D.
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Dieks (ed.), The Ontology of Spacetime, Elsevier 2006, ISBN 0-444-52768-0 D. Malament, 1977. "Causal Theories of Time and the Conventionality of Simultaniety," Noûs 11, 293–300. Galison, P. (2003), Einstein's Clocks, Poincaré's Maps: Empires of Time, New York: W.W. Norton, ISBN 0-393-32604-7 A. Grünbaum. David Malament and the Conventionality of Simultaneity: A Reply, online S. Sarkar, J. Stachel, Did Malament Prove the Non-Conventionality of Simultaneity in the Special Theory of Relativity?, Philosophy of Science, Vol. 66, No. 2 H. Reichenbach, Axiomatization of the theory of relativity, Berkeley University Press, 1969 H. Reichenbach, The philosophy of space & time, Dover, New York, 1958 H. P. Robertson, Postulate versus Observation in the Special Theory of Relativity, Reviews of Modern Physics, 1949 R. Rynasiewicz, Definition, Convention, and Simultaneity: Malament's Result and Its Alleged Refutation by Sarkar and Stachel, Philosophy of Science, Vol. 68, No. 3, Supplement, online Hanoch Ben-Yami, Causality and Temporal Order in Special Relativity, British Jnl. for the Philosophy of Sci., Volume 57, Number 3, pp. 459–479, abstract online == External links == Stanford Encyclopedia of Philosophy, Conventionality of Simultaneity [1] (contains extensive bibliography) Neil Ashby, Relativity in the Global Positioning System, Living Rev. Relativ. 6, (2003), [2] How to Calibrate a Perfect Clock from John de Pillis: An interactive Flash animation showing how a clock with uniform ticking rate can precisely define a one-second time interval. Synchronizing Five Clocks from John de Pillis. An interactive Flash animation showing how five clocks are synchronised within a single inertial frame.
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Dissimilatory metal-reducing microorganisms are a group of microorganisms (both bacteria and archaea) that can perform anaerobic respiration utilizing a metal as terminal electron acceptor rather than molecular oxygen (O2), which is the terminal electron acceptor reduced to water (H2O) in aerobic respiration. The most common metals used for this end are iron [Fe(III)] and manganese [Mn(IV)], which are reduced to Fe(II) and Mn(II) respectively, and most microorganisms that reduce Fe(III) can reduce Mn(IV) as well. But other metals and metalloids are also used as terminal electron acceptors, such as vanadium [V(V)], chromium [Cr(VI)], molybdenum [Mo(VI)], cobalt [Co(III)], palladium [Pd(II)], gold [Au(III)], and mercury [Hg(II)]. == Conditions and mechanisms for dissimilatory metal reduction == Dissimilatory metal reducers are a diverse group of microorganisms, which is reflected in the factors that affect the different forms of metal reduction. The process of dissimilatory metal reduction occurs in the absence of oxygen (O2), but dissimilatory metal reducers include both obligate (strict) anaerobes, such as the family Geobacteraceae, and facultative anaerobes, such as Shewanella spp. As well, across the dissimilatory metal reducers species, various electron donors are used in the oxidative reaction that is coupled to metal reduction. For instance, some species are limited to small organic acids and hydrogen (H2), whereas others may oxidize aromatic compounds. In certain instances, such as Cr(VI) reduction, the use of small organic compounds can optimize the rate of metal reduction. Another factor that influences metal respiration is environmental acidity. Although acidophilic and alkaliphilic dissimilatory metal reducers exist, the neutrophilic metal reducers group contains the most well-characterized genera. In soil and sediment environments, where the pH is often neutral, metals like iron are found in their solid oxidized forms, and exhibit variable reduction potential, which can affect their use by microorganisms. Due to the impermeability of the cell wall
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to minerals and the insolubility of metal oxides, dissimilatory metal reducers have developed ways to reduce metals extracellularly via electron transfer. Cytochromes c, which are transmembrane proteins, play an important role in transporting electrons from the cytosol to enzymes attached to the outside of the cell. The electrons are then further transported to the terminal electron acceptor via direct interaction between the enzymes and the metal oxide. In addition to establishing direct contact, dissimilatory metal reducers also display the ability to perform ranged metal reduction. For instance, some species of dissimilatory metal reducers produce compounds that can dissolve insoluble minerals or act as electron shuttles, enabling them to perform metal reduction from a distance. Other organic compounds frequently found in soils and sediments, such as humic acids, may also act as electron shuttles. In biofilms, nanowires and multistep electron hopping (in which electrons jump from cell to cell towards the mineral) have also been suggested as methods for reducing metals without requiring direct cell contact. It has been proposed that cytochromes c are involved in both of these mechanisms. In nanowires, for instance, cytochromes c function as the final component that transfers electrons to the metal oxide. == Terminal electron acceptors == A wide range of Fe(III)-bearing minerals have been observed to function as terminal electron acceptors, including magnetite, hematite, goethite, lepidocrocite, ferrihydrite, hydrous ferric oxide, smectite, illite, jarosite, among others. == Secondary mineral formation == In natural systems, secondary minerals may form as a byproduct of bacterial metal reduction. Commonly observed secondary minerals produced during experimental bio-reduction by dissimilatory metal reducers include magnetite, siderite, green rust, vivianite, and hydrous Fe(II)-carbonate. == Genera that include dissimilatory metal reducers == Albidiferax (Betaproteobacteria) Shewanella (Gammaproteobacteria) Geobacter (Deltaproteobacteria) Geothrix fermentans (Acidobacteria) Deferribacter (Deferribacteres) Thermoanaerobacter (Firmicutes) == References ==
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Microbial DNA barcoding is the use of DNA metabarcoding to characterize a mixture of microorganisms. DNA metabarcoding is a method of DNA barcoding that uses universal genetic markers to identify DNA of a mixture of organisms. == History == Using metabarcoding to assess microbial communities has a long history. Back in 1972, Carl Woese, Mitchell Sogin and Stephen Sogin first tried to detect several families within bacteria using the 5S rRNA gene. Only a few years later, a new tree of life with three domains was proposed by again Woese and colleagues, who were the first to use the small subunit of the ribosomal RNA (SSU rRNA) gene to distinguish between bacteria, archaea and eukaryotes. Out of this approach, the SSU rRNA gene made its way to be the most frequently used genetic marker for both prokaryotes (16S rRNA) and eukaryotes (18S rRNA). The tedious process of cloning those DNA fragments for sequencing got fastened up by the steady improvement of sequencing technologies. With the development of HTS (High-Throughput-Sequencing) in the early 2000s and the ability to deal with this massive data using modern bioinformatics and cluster algorithms, investigating microbial life got much easier. == Genetic markers == Genetic diversity is varying from species to species. Therefore, it is possible to identify distinct species by the recovery of a short DNA sequence from a standard part of the genome. This short sequence is defined as barcode sequence. Requirements for a specific part of the genome to serve as barcode should be a high variation between two different species, but not much differences in the gene between two individuals of the same species to make differentiating individual species easier. For both bacteria and archaea the 16S rRNA/rDNA gene is used. It is a common housekeeping gene in all prokaryotic organisms and
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{
"page_id": 60361376,
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therefore is used as a standard barcode to assess prokaryotic diversity. For protists, the corresponding 18S rRNA/rDNA gene is used. To distinguish different species of fungi, the ITS (Internal Transcribed Spacer) region of the ribosomal cistron is used. == Advantages == The existing diversity of the microbial world is not unraveled completely yet, although we know that it is mainly composed by bacteria, fungi and unicellular eukaryotes. Taxonomic identification of microbial eukaryotes requires exceedingly skillful expertise and is often difficult due to small sizes of the organisms, fragmented individuals, hidden diversity and cryptic species. Further, prokaryotes can simply not be taxonomically assigned using traditional methods like microscopy, because they are too small and morphologically indistinguishable. Therefore, via the use of DNA metabarcoding, it is possible to identify organisms without taxonomic expertise by matching short High Throughput Sequences (HTS)-derived gene fragments to a reference sequence database, e.g. NCBI. These mentioned qualities make DNA barcoding a cost-effective, reliable and less time-consuming method, compared to the traditional ones, to meet the increasing need for large-scale environmental assessments. == Applications == A lot of studies followed the first usage of Woese et al., and are now covering a variety of applications. Not only in biological or ecological research metabarcoding is used. Also in medicine and human biology bacterial barcodes are used, e.g. to investigate the microbiome and bacterial colonization of the human gut in normal and obese twins or comparison studies of newborn, child and adult gut bacteria composition. Additionally, barcoding plays a major role in biomonitoring of e.g. rivers and streams and grassland restoration. Conservation parasitology, environmental parasitology and paleoparasitology rely on barcoding as a useful tool in disease investigating and management, too. === Cyanobacteria === Cyanobacteria are a group of photosynthetic prokaryotes. Similar as in other prokaryotes, taxonomy of cyanobacteria using DNA
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sequences is mostly based on similarity within the 16S ribosomal gene. Thus, the most common barcode used for identification of cyanobacteria is 16S rDNA marker. While it is difficult to define species within prokaryotic organisms, 16S marker can be used for determining individual operational taxonomic units (OTUs). In some cases, these OTUs can also be linked to traditionally defined species and can therefore be considered a reliable representation of the evolutionary relationships. However, when analyzing a taxonomic structure or biodiversity of a whole cyanobacterial community (see DNA metabarcoding), it is more informative to use markers specific for cyanobacteria. Universal 16S bacterial primers have been used successfully to isolate cyanobacterial rDNA from environmental samples, but they also recover many bacterial sequences. The use of cyanobacteria-specific or phyto-specific 16S markers is commonly used for focusing on cyanobacteria only. A few sets of such primers have been tested for barcoding or metabarcoding of environmental samples and gave good results, screening out majority of non-photosynthetic or non-cyanobacterial organisms. Number of sequenced cyanobacterial genomes available in databases is increasing. Besides 16S marker, phylogenetic studies could therefore include also more variable sequences, such as sequences of protein-coding genes (gyrB, rpoC, rpoD, rbcL, hetR, psbA, rnpB, nifH, nifD), internal transcribed spacer of ribosomal RNA genes (16S-23S rRNA-ITS) or phycocyanin intergenic spacer (PC-IGS). However, nifD and nifH can only be used for identification of nitrogen-fixing cyanobacterial strains. DNA barcoding of cyanobacteria can be applied in various ecological, evolutionary and taxonomical studies. Some examples include assessment of cyanobacterial diversity and community structure, identification of harmful cyanobacteria in ecologically and economically important waterbodies and assessment of cyanobacterial symbionts in marine invertebrates. It has a potential to serve as a part of routine monitoring programs for occurrence of cyanobacteria, as well as early detection of potentially toxic species in waterbodies. This
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|
might help us detect harmful species before they start to form blooms and thus improve our water management strategies. Species identification based on environmental DNA could be particularly useful for cyanobacteria, as traditional identification using microscopy is challenging. Their morphological characteristics which are the basis for species delimitation vary in different growth conditions. Identification under microscope is also time-consuming and therefore relatively costly. Molecular methods can detect much lower concentration of cyanobacterial cells in the sample than traditional identification methods. == Reference databases == The reference database is a collection of DNA sequences, which are assigned to either a species or a function. It can be used to link molecular obtained sequences of an organism to pre-existing taxonomy. General databases like the NCBI platform include all kind of sequences, either whole genomes or specific marker genes of all organisms. There are also different platforms where only sequences from a distinct group of organisms are stored, e.g. UNITE database exclusively for fungi sequences or the PR2 database solely for protist ribosomal sequences. Some databases are curated, which allows a taxonomic assignment with higher accuracy than using uncurated databases as a reference. == See also == Consortium for the Barcode of Life Algae DNA barcoding DNA Barcoding DNA barcoding in diet assessment Fish DNA barcoding == References ==
|
{
"page_id": 60361376,
"source": null,
"title": "Microbial DNA barcoding"
}
|
The EU's Chemicals Strategy for Sustainability Towards a Toxic-Free Environment is a strategy published in 2020 that is part of the EU's zero pollution ambition, a key commitment of the European Green Deal. innovation for the green transition of the chemical industry and its value chains must be stepped up and the existing EU chemicals policy must evolve and respond more rapidly and effectively to the challenges posed by hazardous chemicals. == See also == Registration, Evaluation, Authorisation and Restriction of Chemicals == References == == External links == https://ec.europa.eu/environment/strategy/chemicals-strategy_en
|
{
"page_id": 69470879,
"source": null,
"title": "EU Chemicals Strategy for Sustainability Towards a Toxic-Free Environment"
}
|
The Middle East Treaty Organization (METO) is a non-governmental organization founded in 2017 by a coalition of civil-society activists and disarmament practitioners, with the aim to rid the Middle East of all weapons of mass destruction (WMD). This proposal is in line with the 1970s proposal for a Middle East nuclear weapon free zone, albeit with broader scope following the 1990 Mubarak Initiative to include chemical and biological as well as nuclear weapons. Working toward the broader vision of regional security and peace, METO defines its purpose as the establishment of a zone free of weapons of mass destruction (WMDFZ) in the Middle East. To achieve that end, the organization embraces a traditional treaty-based approach relying on diplomatic mechanisms and civil society campaigns. This strategy is supported through programming and events centered around policy debates, advocacy and education. Three strategic pillars underlie METO's treaty-based approach for achieving the Middle East WMDFZ: A WMDFZ Treaty, based on a text negotiated, agreed and adopted by regional governments and relevant stakeholders through an inclusive, multilateral track I and track II diplomatic process facilitated by METO and partner organizations (including formal United Nations negotiations). A regional organization, which must be established to oversee and carry out functions necessary to the treaty’s eventual implementation, verification and compliance. Engagement with civil society, in particular to foster a civil society movement that can formulate demands to regional and international governments to advance the goals of the proposed treaty. METO is an international partner of International Campaign to Abolish Nuclear Weapons, International Physicians for the Prevention of Nuclear War, Geneva Centre for Security Policy, British American Security Information Council, Abolition 2000, and Geneva Disarmament Platform. == Draft Treaty and Annual UN Conferences == METO began facilitating the creation of a draft treaty text that would form the basis
|
{
"page_id": 67504802,
"source": null,
"title": "Middle East Treaty Organization"
}
|
for discussion on a WMDFZ Treaty in 2017 through track 1.5-2 diplomacy. Roundtable negotiations to discuss the treaty were organized among senior diplomatic and former diplomatic figures from regional governments and representatives from international organizations, as well as subject experts. The draft treaty text facilitated by METO's process was brought to the United Nations General Assembly by Egypt on 22 December 2018, alongside a proposal to launch an annual conference to discuss the zone. The UN General Assembly resolved to convene an annual meeting on the establishment of a Middle East WMDFZ. The first annual conference was held from 18 November to 22 November 2019 at UN Headquarters in New York, presided over by the UN Permanent Representative from Jordan. Almost all states of the region attended the conference, including the 22 members of the Arab League and Iran, as well as four nuclear-armed states China, France, Russia, and the United Kingdom, alongside other observer states and international organizations. The only regional country that did not participate was Israel. The conference adopted a Final Report and Political Declaration articulating the participating member states' commitment to pursue the elaboration of a consensus-based, legally binding treaty to establish a WMDFZ in the Middle East through an open and inclusive process involving all states in the region. They agreed to meet again from 16 to 20 November 2020. That meeting was postponed until 29 November 2021 - 03 December 2021 because of COVID. The third conference was held 14–18 November 2022. The fourth was held 13 to 17 November 2023, with the fifth scheduled for 18 to 22 November 2024. A description of all conferences held to date and planned is available from the website of the United Nations Office for Disarmament Affairs (UNODA). == METO in Publications and Media == As part
|
{
"page_id": 67504802,
"source": null,
"title": "Middle East Treaty Organization"
}
|
of the organization's education and advocacy programs, METO staff frequently contribute articles to academic publications and mainstream media outlets, as well as through film, radio and podcast productions. === Articles === Emad Kiyaei, Tony Robinson, Sharon Dolev, “Non-proliferation and Regional Cooperation in the Middle East,” Brown Journal of World Affairs, January 2021. Tariq Rauf, "Achieving the Possible: “Weapons of Mass Destruction Free Zone in the Middle East”", Inter Press Service, November 2019. Sharon Dolev, Emad Kiyaei, and Dina Saadallah, "Achieving the Possible: a WMD-free zone in the Middle East", Reaching Critical Will, November 2019. Paul Ingram and Emad Kiyaei, "Middle East WMD-Free Zone: Thinking the Possible", The Cairo Review of Global Affairs, Fall 2019. UN Office for Disarmament Affairs, "A Draft Treaty for a WMD Free Zone in the Middle East: Time to Envisage the Practical", UNODA, October 2017. === Reports === METO and GCSP, Round Table report on the Abraham Accords and WMDFZ, January 2021. Sharon Dolev, “Israel”, in Assuring destruction forever: 2020 edition, Reaching Critical Will, June 2020. === Book === Emad Kiyaei and Seyed Hossein Mousavian, A Middle East Free of Weapons of Mass Destruction, Routledge, April 2020. === Documentary film === Tony Robinson and Álvaro Orús, documentary film: "The Beginning of the End of Nuclear Weapons", Pressenza IPA, May 2019. === Podcast === The organization produces a fortnightly podcast series, In The Zone, which explores constructive approaches to improve the chances of achieving a WMDFZ in the Middle East. In the series, Paul Ingram and Anahita Parsa conduct interviews with WMD disarmament experts on technical and political solutions to overcome obstacles, how to build trust between countries and more broadly how to improve peace and security for people in the region. The podcast series is published on Pressenza and available on Soundcloud. == References ==
|
{
"page_id": 67504802,
"source": null,
"title": "Middle East Treaty Organization"
}
|
The Medicines Discovery Catapult (MDC) is the United Kingdom's catapult centre for medicine research and innovation, headquartered at Alderley Park in Cheshire. == History == The intention to form the company was announced by the Chancellor on 13 July 2015 with funding of £5m, on a visit to Cheshire. It would be part of the Northern Powerhouse initiative. The Medicines Technologies Catapult was established in December 2015, funded by a £10m grant from Innovate UK and based at the Alderley Park science park in Cheshire. On 1 March 2016 its name changed to the Medicines Discovery Catapult. Further funding of approximately £10m per year was secured from Innovate UK for the years 2018 to 2023. === Precision Medicine Catapult === The PMC was based in Cambridge and had regional centres of excellence at Belfast, Glasgow, Cardiff, Oxford, Leeds and Manchester. It worked with precision medicine. It started from April 2015, and worked with regional parts of the Diagnostic Evidence Cooperative and Academic Health Science Networks (AHSN). On 26 June 2017 it was announced that the PMC would close, with most of its functions transferred to the MDC. The Leeds site is now the Leeds Centre for Personalised Medicine and Health. == Activities == A not-for-profit company, the MDC works with a range of UK innovators to advance projects and products towards clinical impact. In 2019, the company stated that it worked in four sectors: Predictive biological models of human disease, for new drug testing Predictive computational techniques for drug discovery Collaboration between health service providers and government bodies Collaboration on drug discovery between research charities and industry. In the same year, the number of staff increased from 40 to 75, and the company reported that its income comprised £8.5m from Innovate UK and £152,000 from collaborative research and development. After
|
{
"page_id": 64555681,
"source": null,
"title": "Medicines Discovery Catapult"
}
|
charging £7.1m to administrative expenses, the company reported a loss for the year of £16,000. In 2020, the company was given the task of setting up one of the first PCR analysis centres for COVID-19 tests – known as Lighthouse labs – elsewhere at the Alderley Park site. By 2021, this centre employed over 700 staff and had a stated capacity of 80,000 test samples per day. == Key people == Dr Robin Brown has been the company's chairman since July 2018; he has a PhD in molecular biology and has worked in venture capital at Advent Healthcare. The company has no shareholders. Previously, Professor Graham Boulnois was chairman from January 2016; he was head of research from 1992 to 2000 at Zeneca Pharmaceuticals in Cheshire, and Professor of Microbiology from 1984 to 1992 at the University of Leicester. == See also == Innovative Medicines Initiative, OpenPHACTS and European Lead Factory == References == == External links == Official website
|
{
"page_id": 64555681,
"source": null,
"title": "Medicines Discovery Catapult"
}
|
Solid State Physics, better known by its colloquial name Ashcroft and Mermin, is an introductory condensed matter physics textbook written by Neil Ashcroft and N. David Mermin. Published in 1976 by Saunders College Publishing and designed by Scott Olelius, the book has been translated into over half a dozen languages and it and its competitor, Introduction to Solid State Physics (often shortened to Kittel), are considered the standard introductory textbooks of condensed matter physics. == Reception == The book has been reviewed several times and has been recommended in many other works. In a review of another work by the MRS Bulletin in 2011, the book was said to be "the indispensable work on electronic systems for experimental condensed matter physicists", due largely to the book's "lucidity and panache". The book is also recommended in other textbooks on condensed matter physics, including The Solid State by Harold Max Rosenberg in 1979, where it is called a "detailed, higher-level, modern treatment." The textbook Solid-State Physics for Electronics by Andre Moliton states in the foreword that the book aims to prepare students to "use by him- or herself the classic works of taught solid state physics, for example, those of Kittel and Ashcroft and Mermin." Along with Kittel, the textbook Introduction to Solid State Physics and Crystalline Nanostructures by Giuseppe Iadonisi, Giovanni Cantele, and Maria Luisa Chiofalo included the book in the "Acknowledgements" section as "special mentions". It is also called one of the standard textbooks of solid state physics in the textbook Polarized Electrons In Surface Physics. In a 2003 article detailing Mermin's contributions to solid state physics, the book was said to be "an extraordinarily readable textbook of the subject, which introduced a whole generation of solid state specialists to a subtle and elegant way of doing theoretical physics." The
|
{
"page_id": 65997474,
"source": null,
"title": "Ashcroft and Mermin"
}
|
book, along with Kittel is also used as a benchmark for other books on solid-state physics; the publisher's description for the book Advanced Solid State Physics by Philip Phillips that was supplied to the Library of Congress for its bibliography entry states: "This is a modern book in solid state physics that should be accessible to anyone who has a working level of solid state physics at the Kittel or Ashcroft/Mermin level." === Reviews === The book received several reviews, including published articles in Science, Physics Today, and Physics Bulletin in 1977. It was also reviewed in German. === Impressionism, Realism, and the aging of Ashcroft and Mermin === In July 2013, José Menéndez, a physics professor at the Arizona State University Tempe campus published an article titled "Impressionism, Realism, and the aging of Ashcroft and Mermin" in Physics Today that stated: "It is undoubtedly one of the best physics books ever written, but it is not aging well". Both Ashcroft and Mermin wrote separate responses that were published in the same issue, addressing Menéndez's concerns. In his reply, Ashcroft wrote: "Over the years many readers have remarked that the initial edition of our book should 'not be touched'; it is just right in its treatments of the fundamentals." He then went on to say that writing a sequel "encompassing the many advances in condensed-matter physics that have occurred over the past 38 years" could be an option, but pointed to the fact that the book was translated into French, German, and Portuguese in the previous ten years as evidence that others agree it should be left as is. == Release details == Ashcroft, Neil W.; Mermin, N. David (1976). Solid state physics. New York: Saunders College Publishing. ISBN 0-03-083993-9. OCLC 934604. Ashcroft, Neil W.; Mermin, N. David (1979). Fizika
|
{
"page_id": 65997474,
"source": null,
"title": "Ashcroft and Mermin"
}
|
tverdogo tela (in Russian). Vol. 1. Translated by Mihajlov, Aleksandr S; Kaganov, Moisej Isaakovič; Kugel', Kliment Il'ič. Moskva: Izdatel'stvo "Mir". OCLC 313609844. Ashcroft, Neil W.; Mermin, N. David (1979). Fizika tverdogo tela (in Russian). Vol. 2. Translated by Mihajlov, Aleksandr S; Kaganov, Moisej Isaakovič; Kugel', Kliment Il'ič. Moskva: Izdatel'stvo "Mir". OCLC 934758977. Ashcroft, Neil W.; Mermin, N.David (1982). 固体の物性各論 / Kotai no bussei kakuron (in Japanese). Translated by Matsubara, Takeo; Machida, Kazushige. Kyōto: Yoshioka Shoten. ISBN 978-4-8427-0205-6. OCLC 47518375. Ashcroft, Neil W.; Mermin, N. David (1986). Fizyka ciała stałego (in Polish). Translated by Kowalski, Jacek Maria. Warszawa: Państ. Wydaw. Naukowe. ISBN 978-83-01-05360-4. OCLC 1150493985. Ashcroft, Neil W.; Mermin, N. David (2002). Physique des solides (in French). Translated by Biet, Franck; Kachkachi, Hamid. Les Ulis: EDP sciences. ISBN 978-2-86883-577-2. OCLC 470239249. Ashcroft, Neil W.; Mermin, N. David (2012). Physikē stereas katastasēs (in Greek). Translated by Kamaratos, Matthaios K. Athēna: Ekdosē A.G. Pneumatikos. ISBN 978-960-7258-77-9. OCLC 880484572. Ashcroft, Neil W.; Mermin, N. David (2011). Física do estado sólido (in Portuguese). Translated by De Oliveira, Maria Lucia Godinho. São Paulo: Cengage Learning. ISBN 978-85-221-0902-9. OCLC 817233944. Ashcroft, Neil W.; Mermin, N. David (2013). 固态物理学 (in Chinese). Beijing: 世界图书出版公司. ISBN 978-7-5062-6631-4. OCLC 951624419. Ashcroft, Neil W.; Mermin, N. David (2013). Festkörperphysik (in German). Translated by Gress, Jochen. Munich: München Oldenbourg. ISBN 978-3-486-71301-5. OCLC 829307060. == References == == External links == "Solid State Physics, 1st Edition - 9780030839931". Cengage Learning. Retrieved 3 December 2020. Bethe, Hans A.; Mermin, N. David (12 January 2007). "A Conversation About Solid-State Physics". Physics Today. 57 (6): 53. doi:10.1063/1.1784274. ISSN 0031-9228. "Solid State Physics". Library of Congress. Retrieved 3 December 2020.
|
{
"page_id": 65997474,
"source": null,
"title": "Ashcroft and Mermin"
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The Wittig reaction or Wittig olefination is a chemical reaction of an aldehyde or ketone with a triphenyl phosphonium ylide called a Wittig reagent. Wittig reactions are most commonly used to convert aldehydes and ketones to alkenes. Most often, the Wittig reaction is used to introduce a methylene group using methylenetriphenylphosphorane (Ph3P=CH2). Using this reagent, even a sterically hindered ketone such as camphor can be converted to its methylene derivative. == Reaction mechanism == Mechanistic studies have focused on unstabilized ylides, because the intermediates can be followed by NMR spectroscopy. The existence and interconversion of the betaine (3a and 3b) is subject of ongoing research. For lithium-free Wittig reactions, studies support a concerted formation of the oxaphosphetane without intervention of a betaine. In particular, phosphonium ylides 1 react with carbonyl compounds 2 via a [2+2] cycloaddition that is sometimes described as having [π2s+π2a] topology to directly form the oxaphosphetanes 4a and 4b. Under lithium-free conditions, the stereochemistry of the product 5 is due to the kinetically controlled addition of the ylide 1 to the carbonyl 2. When lithium is present, there may be equilibration of the intermediates, possibly via betaine species 3a and 3b. Bruce E. Maryanoff and A. B. Reitz identified the issue about equilibration of Wittig intermediates and termed the process "stereochemical drift". For many years, the stereochemistry of the Wittig reaction, in terms of carbon-carbon bond formation, had been assumed to correspond directly with the Z/E stereochemistry of the alkene products. However, certain reactants do not follow this simple pattern. Lithium salts can also exert a profound effect on the stereochemical outcome. Mechanisms differ for aliphatic and aromatic aldehydes and for aromatic and aliphatic phosphonium ylides. Evidence suggests that the Wittig reaction of unbranched aldehydes under lithium-salt-free conditions do not equilibrate and are therefore under kinetic reaction
|
{
"page_id": 1837735,
"source": null,
"title": "Wittig reaction"
}
|
control. E. Vedejs has put forth a theory to explain the stereoselectivity of stabilized and unstabilized Wittig reactions. Strong evidence indicated that under Li-free conditions, Wittig reactions involving unstabilized (R1= alkyl, H), semistabilized (R1 = aryl), and stabilized (R1 = EWG) Wittig reagents all proceed via a [2+2]/retro-[2+2] mechanism under kinetic control, with oxaphosphetane as the one and only intermediate. == Scope and limitations == === Functional group tolerance === The Wittig reagents generally tolerate carbonyl compounds containing several kinds of functional groups such as OH, OR, nitroarenes, epoxides, and sometimes esters and amides. Even ketone, aldehyde, and nitrile groups can be present if conjugated with the ylide — these are the stabilised ylides mentioned above. Bis-ylides (containing two P=C bonds) have also been made and used successfully. There can be a problem with sterically hindered ketones, where the reaction may be slow and give poor yields, particularly with stabilized ylides, and in such cases the Horner–Wadsworth–Emmons (HWE) reaction (using phosphonate esters) is preferred. Another reported limitation is the often labile nature of aldehydes, which can oxidize, polymerize or decompose. In a so-called tandem oxidation-Wittig process the aldehyde is formed in situ by oxidation of the corresponding alcohol. === Stereochemistry === For the reaction with aldehydes, the double bond geometry is readily predicted based on the nature of the ylide. With unstabilised ylides (R3 = alkyl) this results in (Z)-alkene product with moderate to high selectivity. If the reaction is performed in dimethylformamide in the presence of lithium iodide or sodium iodide, the product is almost exclusively the Z-isomer. With stabilized ylides (R3 = ester or ketone), the (E)-alkene is formed with high selectivity. The (E)/(Z) selectivity is often poor with semistabilized ylides (R3 = aryl). To obtain the (E)-alkene for unstabilized ylides, the Schlosser modification of the Wittig reaction
|
{
"page_id": 1837735,
"source": null,
"title": "Wittig reaction"
}
|
can be used. Alternatively, the Julia olefination and its variants also provide the (E)-alkene selectively. Ordinarily, the Horner–Wadsworth–Emmons reaction provides the (E)-enoate (α,β-unsaturated ester), just as the Wittig reaction does. To obtain the (Z)-enolate, the Still-Gennari modification of the Horner-Wadsworth-Emmons reaction can be used. === Schlosser modification === The main limitation of the traditional Wittig reaction is that the reaction proceeds mainly via the erythro betaine intermediate, which leads to the Z-alkene. The erythro betaine can be converted to the threo betaine using phenyllithium at low temperature. This modification affords the E-alkene. Allylic alcohols can be prepared by reaction of the betaine ylide with a second aldehyde. For example: == Example == An example of its use is in the synthesis of leukotriene A methyl ester. The first step uses a stabilised ylide, where the carbonyl group is conjugated with the ylide preventing self condensation, although unexpectedly this gives mainly the cis product. The second Wittig reaction uses a non-stabilised Wittig reagent, and as expected this gives mainly the cis product. == History == The Wittig reaction was reported in 1954 by Georg Wittig and his coworker Ulrich Schöllkopf. In part for this contribution, Wittig was awarded the Nobel Prize in Chemistry in 1979. == See also == Corey–Chaykovsky reagent Horner–Wadsworth–Emmons reaction Julia olefination Peterson olefination Tebbe's reagent Organophosphorus chemistry Homologation reaction Kauffmann olefination Titanium–zinc methylenation == References == == External links == Wittig reaction in Organic Syntheses, Coll. Vol. 10, p. 703 (2004); Vol. 75, p. 153 (1998). (Article) Wittig reaction in Organic Syntheses, Coll. Vol. 5, p. 361 (1973); Vol. 45, p. 33 (1965). (Article)
|
{
"page_id": 1837735,
"source": null,
"title": "Wittig reaction"
}
|
Igor Jurisica is a Professor in the departments of Computer Science and Medical Biophysics at the University of Toronto. He is a Tier I Canada Research Chair in Integrative Cancer Informatics, and an associate editor for BMC Bioinformatics, Proteomes, Cancer Informatics, International Journal of Knowledge Discovery in Bioinformatics, and Interdisciplinary Sciences: Computational Life Sciences. In 2014, 2015 and 2016, he is an ISI Highly Cited Researcher. == See also == Computational biology == External links == About Jurisica's publications == References ==
|
{
"page_id": 50137769,
"source": null,
"title": "Igor Jurisica"
}
|
The Census of Antarctic Marine Life (CAML) is a field project of the Census of Marine Life that researches the marine biodiversity of Antarctica, how it is affected by climate change, and how this change is altering the ecosystem of the Southern Ocean. The program started in 2005 as a 5-year initiative with the scientific goal being to study the evolution of life in Antarctic waters, to determine how this has influenced the diversity of the present biota, and use these observations to predict how it might respond to future change. However, due to modern and extravagant changes within technology, we are able to witness and influence biodiversity reproduction and development. This enables us to gain further insight toward characteristics that allow such biodiversity to flourish within this barren desert referred to as the Arctic and Antarctic. CAML has collected its data from 18 Antarctic research vessels during the International Polar Year, which is freely accessible at Scientific Committee on Antarctic Research Marine Biodiversity Information Network (SCAR-MarBIN). The Register of Antarctic Marine Species has 9,350 verified species (16,500 taxa) in 17 phyla, from microbes to whales. For 1500 species the DNA barcode is available. The information from CAML is a robust baseline against which future change may be measured. == References == == External links == Official website Australian Antarctic Division media release Archived 2013-09-30 at the Wayback Machine SCAR-MarBIN Register of Antarctic Marine Species Archived 2015-11-18 at the Wayback Machine Scientific Committee on Antarctic Research
|
{
"page_id": 21957291,
"source": null,
"title": "Census of Antarctic Marine Life"
}
|
Pseudo-panspermia (sometimes called soft panspermia, molecular panspermia or quasi-panspermia) is a well-supported hypothesis for a stage in the origin of life. The theory first asserts that many of the small organic molecules used for life originated in space (for example, being incorporated in the solar nebula, from which the planets condensed). It continues that these organic molecules were distributed to planetary surfaces, where life then emerged on Earth and perhaps on other planets. Pseudo-panspermia differs from the fringe theory of panspermia, which asserts that life arrived on Earth from distant planets. == Background == Theories of the origin of life have been recorded since the 5th century BC, when the Greek philosopher Anaxagoras proposed an initial version of panspermia: life arrived on earth from the heavens. In modern times, full panspermia has little support amongst mainstream scientists. Pseudo-panspermia, in which molecules are formed and transported through space is, however, well-supported. == Extraterrestrial creation of organic molecules == Interstellar molecules are formed by chemical reactions within very sparse interstellar or circumstellar clouds of dust and gas. Usually this occurs when a molecule becomes ionised, often as the result of an interaction with cosmic rays. This positively charged molecule then draws in a nearby reactant by electrostatic attraction of the neutral molecule's electrons. Molecules can also be generated by reactions between neutral atoms and molecules, although this process is generally slower. The dust plays a critical role of shielding the molecules from the ionizing effect of ultraviolet radiation emitted by stars. The Murchison meteorite contains the organic molecules uracil and xanthine, which must therefore already have been present in the early Solar System, where they could have played a role in the origin of life. Nitriles, key molecular precursors of the RNA World scenario, are among the most abundant chemical families in
|
{
"page_id": 59837099,
"source": null,
"title": "Pseudo-panspermia"
}
|
the universe and have been found in molecular clouds in the center of the Milky Way, protostars of different masses, meteorites and comets, and also in the atmosphere of Titan, the largest moon of Saturn. Evidence for the extraterrestrial creation of organic molecules includes both their discovery in various contexts in space, and their laboratory synthesis under extraterrestrial conditions: == Planetary distribution of organic molecules == Organic molecules can then be distributed to planets including Earth both when the planets formed and later. If the materials from which planets formed contained organic molecules, and were not destroyed by heat or other processes, then these would be available for abiogenesis on those planets. Later distribution is by means of bodies such as comets and asteroids. These may fall to the planetary surface as meteorites, releasing any molecules they are carrying as they vaporise on impact or later as they erode. Studies of rock and dust from asteroid Bennu delivered to Earth by NASA’s OSIRIS-REx have revealed molecules that, on Earth, are key to life, as well as a history of saltwater. Findings of organic molecules in meteorites include: == References ==
|
{
"page_id": 59837099,
"source": null,
"title": "Pseudo-panspermia"
}
|
Pesticide residue refers to the pesticides that may remain on or in food, after they are applied to food crops. The maximum allowable levels of these residues in foods are stipulated by regulatory bodies in many countries. Regulations such as pre-harvest intervals also prevent harvest of crop or livestock products if recently treated in order to allow residue concentrations to decrease over time to safe levels before harvest. == Definition == A pesticide is a substance or a mixture of substances used for killing pests: organisms dangerous to cultivated plants or to animals. The term applies to various pesticides such as insecticides, fungicides, herbicides and nematocides. The definition of residue of pesticide according to the World Health Organization (WHO) is: Any specified substances in or on food, agricultural commodities or animal feed resulting from the use of a pesticide. The term includes any derivatives of a pesticide, such as conversion products, metabolites, reaction products and impurities considered to be of toxicological significance. The term “pesticide residue” includes residues from unknown or unavoidable sources (e.g. environmental) as well as known uses of the chemical. The definition of a residue for compliance with maximum residue limits (MRLs) is that combination of the pesticide and its metabolites, derivatives and related compounds to which the MRL applies. == Background == Prior to 1940, pesticides consisted of inorganic compounds (copper, arsenic, mercury, and lead) and plant derived products. Most of these were abandoned because they were highly toxic and ineffective. Since World War II pesticides composed of synthetic organic compounds were the most important form of pest control. The growth in these pesticides accelerated in late 1940s after Paul Müller discovered DDT in 1939. The effects of pesticides such as aldrin, dieldrin, endrin, chlordane, parathion, captan and 2,4-D were also found at this time. Those
|
{
"page_id": 3148461,
"source": null,
"title": "Pesticide residue"
}
|
pesticides were widely used due to their effective pest control. Problems with environmental issues of DDT became increasingly apparent, since it is persistent and bioaccumulates in the body and the food chain. In the 1960s, Rachel Carson wrote Silent Spring to illustrate a risk of DDT and how it threatened biodiversity. DDT was banned for agricultural use in 1972 and the others in 2001. Persistent pesticides are no longer used for agriculture, and will not be approved by the authorities. Because the half life in soil is long (for DDT 2–15 years) residues can still be detected in humans at levels 5 to 10 times lower than found in the 1970s. == Regulations == Each country adopts their own agricultural policies and Maximum Residue Limits (MRL) and Acceptable Daily Intake (ADI). The level of food additive usage varies by country because forms of agriculture are different in regions according to their geographical or climatical factors. Pre-harvest intervals are also set to require a crop or livestock product not be harvested before a certain period after application in order to allow the pesticide residue to decrease below maximum residue limits or other tolerance levels. Likewise, restricted entry intervals are the amount of time to allow residue concentrations to decrease before a worker can reenter without protective equipment an area where pesticides have been applied. === International === Some countries use the International Maximum Residue Limits -Codex Alimentarius to define the residue limits; this was established by Food and Agriculture Organization of the United Nations (FAO) and World Health Organization (WHO) in 1963 to develop international food standards, guidelines codes of practices, and recommendation for food safety. Currently the CODEX has 185 Member Countries and 1 member organization (EU). The following is the list of maximum residue limits (MRLs) for spices adopted
|
{
"page_id": 3148461,
"source": null,
"title": "Pesticide residue"
}
|
by the commission. === European Union === The European Union has a searchable database with the Maximum Residue Limits (MRLs) for 716 pesticides. Under the previous system, revised in 2008, certain pesticide residues were regulated by the commission; others were regulated by Member States, and others were not regulated at all. === New Zealand === Food Standards Australia New Zealand develops the standards for levels of pesticide residues in foods through a consultation process. The New Zealand Food Safety Authority publishes the maximum limits of pesticide residues for foods produced in New Zealand. === United Kingdom === Monitoring of pesticide residues in the UK began in the 1950s. From 1977 to 2000 the work was carried out by the Working Party on Pesticide Residues (WPPR), until in 2000 the work was taken over by the Pesticide Residue Committee (PRC). The PRC advise the government through the Pesticides Safety Directorate and the Food Standards Agency (FSA). === United States === In the US, tolerances for the amount of pesticide residue that may remain on food are set by the EPA, and measures are taken to keep pesticide residues below the tolerances. The US EPA has a web page for the allowable tolerances. In order to assess the risks associated with pesticides on human health, the EPA analyzed individual pesticide active ingredients as well as the common toxic effect that groups of pesticides have, called the cumulative risk assessment. Limits that the EPA sets on pesticides before approving them includes a determination of how often the pesticide should be used and how it should be used, in order to protect the public and the environment. In the US, the Food and Drug Administration (FDA) and USDA also routinely check food for the actual levels of pesticide residues. A US organic food advocacy
|
{
"page_id": 3148461,
"source": null,
"title": "Pesticide residue"
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group, the Environmental Working Group, is known for creating a list of fruits and vegetables referred to as the Dirty Dozen; it lists produce with the highest number of distinct pesticide residues or most samples with residue detected in USDA data. This list is generally considered misleading and lacks scientific credibility because it lists detections without accounting for the risk of the usually small amount of each residue with respect to consumer health. In 2016, over 99% of samples of US produce had no pesticide residue or had residue levels well below the EPA tolerance levels for each pesticide. === Japan === In Japan, pesticide residues are regulated by the Food Safety Act. Pesticide tolerances are set by the Ministry of Health, Labour and Welfare through the Drug and Food Safety Committee. Unlisted residue amounts are restricted to 0.01ppm. === China === In China, the Ministry of Health and the Ministry of Agriculture have jointly established mechanisms and working procedures relating to maximum residue limit standards, while updating them continuously, according to the food safety law and regulations issued by the State Council. From GB25193-2010 to GB28260-2011, from Maximum Residue Limits for 12 Pesticides to 85 pesticides, they have improved the standards in response to Chinese national needs. == Health impacts == The maximum residue limits of pesticides in food are low, and are carefully set by the authorities to ensure, to their best judgement, no health impacts. According to the American Cancer Society there is no evidence that pesticide residues in food increase the risk of people getting cancer. The ACA advises washing fruit and vegetables before eating to remove both pesticide residue and other undesirable contaminants. A 2009 study estimated that lifetime exposure to pesticide residues from eating fruits and vegetables results in only 4.2 and 3.2 minutes
|
{
"page_id": 3148461,
"source": null,
"title": "Pesticide residue"
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|
of lost life per person in Switzerland and the United States, respectively. There are many studies on the health differences between consumers of organic foods vs consumers of organically grown foods. When the American Academy of Pediatrics reviewed the literature on organic foods in 2012, they found that "current evidence does not support any meaningful nutritional benefits or deficits from eating organic compared with conventionally grown foods, and there are no well-powered human studies that directly demonstrate health benefits or disease protection as a result of consuming an organic diet." === Chinese incidents === In China, a number of incidents have occurred where state limits were exceeded by large amounts or where the wrong pesticide was used. In August 1994, a serious incident of pesticide poisoning of sweet potato crops occurred in Shandong province, China. Because local farmers were not fully educated in the use of insecticides, they used the highly-toxic pesticide named parathion instead of trichlorphon. It resulted in over 300 cases of poisoning and 3 deaths. Also, there was a case where a large number of students were poisoned and 23 of them were hospitalized because of vegetables that contained excessive pesticide residues. === Child neurodevelopment === Many pesticides achieve their intended use of killing pests by disrupting the nervous system. Due to similarities in brain biochemistry among many different organisms, there is much speculation that these chemicals can have a negative impact on humans as well. Children are especially vulnerable to exposure to pesticides, especially at critical windows of development. Infants and children consume higher amounts of food relative to their body-weight, and have a more permeable blood–brain barrier, all of which can contribute to increased risks from exposure to pesticide residues. However, in 2008 the OECD report that the existing guideline represents the best available science
|
{
"page_id": 3148461,
"source": null,
"title": "Pesticide residue"
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|
for assessing the potential for developmental neurotoxicity in human health risk assessment. == See also == Child development Dose–response relationship Environmental effects of pesticides Environmental issues with agriculture Food safety List of environmental issues Pesticide poisoning QuEChERS - method for testing pesticide residues == References == == External links == WHO fact sheet on pesticide residues in food The European Pesticide Residue Workshop Pesticide residue in Europe International Maximum Residue Level Database US EPA Pesticide Chemical Search CODEX Alimentarius International Food Standards Pesticides and Food:What the Pesticide Residue Limits are on Food
|
{
"page_id": 3148461,
"source": null,
"title": "Pesticide residue"
}
|
Sex as a biological variable (SABV) is a research policy recognizing sex as an important variable to consider when designing studies and assessing results. Research including SABV has strengthened the rigor and reproducibility of findings. Public research institutions including the European Commission, Canadian Institutes of Health Research, and the U.S. National Institutes of Health have instituted SABV policies. Editorial policies were established by various scientific journals recognizing the importance and requiring research to consider SABV. == Background == === Public research institutions === In 1999, the Institute Of Medicine established a committee on understanding the biology of sex and gender differences. In 2001, they presented a report that sex is an important variable in designing studies and assessing results. The quality and generalizability of biomedical research depends on the consideration of key biological variables, such as sex. To improve the rigor and reproducibility of research findings, the European Commission, Canadian Institutes of Health Research, and the U.S. National Institutes of Health (NIH) established policies on sex as a biological variable (SABV). Enrolling both men and women in clinical trials can impact the application of results and permit the identification of factors that affect the course of disease and the outcome of treatment. In 2003, the European Commission (EC) began influencing investigators to include sex and gender in their research methodologies. The Canadian Institutes of Health Research (CIHR) requires four approaches: sex and gender integration in research proposals, sex and gender expertise among research teams, sex and gender platform in large consortiums, and starting in September 2015, the completion of sex and gender online training programs. In May 2014, the NIH announced the formation of SABV policy. The policy came into effect in 2015 which specified that "SABV is frequently ignored in animal study designs and analyses, leading to an incomplete
|
{
"page_id": 66914990,
"source": null,
"title": "Sex as a biological variable"
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|
understanding of potential sex-based differences in basic biological function, disease processes, and treatment response. NIH expects that sex as a biological variable will be factored into research designs, analyses, and reporting in vertebrate animal and human studies. Strong justification from the scientific literature, preliminary data or other relevant considerations must be provided for applications proposing to study only one sex." The review criteria should assess the extent to which the sex of participants has been incorporated into the research plan. === Scientific journals === In 2010, the National Centre for the Replacement, Refinement and Reduction of Animals in Research published the ARRIVE guidelines which promotes incorporating SABV in animal studies. In 2012, the American Physiological Society (APS) journals began requiring sex and gender to be reported in studies involving cells, tissues, animals, and humans. This APS editorial policy was not widely accepted by reviewers and researchers. The European Association of Science Editors established the gender policy committee (GPC) in 2012. The GPC published Sex and Gender Equity in Research (SAGER) guidelines in 2016. In January 2017, the Journal of Neuroscience Research began requiring the consideration of SABV. The December 2017 ICMJE recommendations encouraged the use of SABV by researchers. == Impact == Research incorporating sex as a biological variable increases the rigor and reproducibility of results. After publishing the NIH published SABV policy, there were increases in the percentage of scientists understanding and recognizing its importance. Some investigators were critical of the NIH SABV policy, saying it would increase cost and labor requirements. Including SABV in basic research and preclinical studies can reduce costs and time requirements to test sex differences in clinical trials. Historically, there were concerns among researchers of the female reproductive system impacting findings in animal studies. Other studies using mice models found that despite the estrous
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{
"page_id": 66914990,
"source": null,
"title": "Sex as a biological variable"
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cycle, variability was the same among sexes. Studies following SABV policies can identify potential hormonal variability in earlier phases of biomedical research. In 2020, the NIH Office on Women's Health and the Food and Drug Administration Office of Women's Health created an educational tool, Bench-to-Bedside: Integrating Sex and Gender to Improve Human Health. == References ==
|
{
"page_id": 66914990,
"source": null,
"title": "Sex as a biological variable"
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|
Korilophyton is a genus of branching Cambrian acritarchs of presumed algal affinity. == References ==
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{
"page_id": 45025965,
"source": null,
"title": "Korilophyton"
}
|
The molecular formula C22H24Br2N10O2 (molar mass: 620.310 g/mol) may refer to: Ageliferin Sceptrin
|
{
"page_id": 61147824,
"source": null,
"title": "C22H24Br2N10O2"
}
|
In materials science, a polymer blend, or polymer mixture, is a member of a class of materials analogous to metal alloys, in which at least two polymers are blended together to create a new material with different physical properties. == History == During the 1940s, '50s and '60s, the commercial development of new monomers for production of new polymers seemed endless. In this period, it was discovered that the development of the new techniques for the modification of the already existing polymers, would be economically viable. The first technique of modification developed was the polymerization, in other words, the joint polymerization of more than one kind of polymer. A new polymers modification process, based on a simple mechanical mixture of two polymers first appeared when Thomas Hancock created a mixture of natural rubber with gutta-percha. This process generated a new polymer class called "polymer blends." == Basic concepts == Polymer blends can be broadly divided into three categories: immiscible polymer blends (heterogeneous polymer blends): This is by far the most populous group. If the blend is made of two polymers, two glass transition temperatures will be observed. compatible polymer blends: Immiscible polymer blends that exhibit macroscopically uniform physical properties. The macroscopically uniform properties are usually caused by sufficiently strong interactions between the component polymers. miscible polymer blends (homogeneous polymer blends): Polymer blend that is a single-phase structure. In this case, one glass transition temperature will be observed. The use of the term polymer alloy for a polymer blend is discouraged, as the former term includes multiphase copolymers but excludes incompatible polymer blends. Examples of miscible polymer blends: homopolymer–homopolymer: polyphenylene oxide (PPO) – polystyrene (PS): noryl developed by General Electric Plastics in 1966 (now owned by SABIC). The miscibility of the two polymers in noryl is caused by the presence of
|
{
"page_id": 11471537,
"source": null,
"title": "Polymer blend"
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|
an aromatic ring in the repeat units of both chains. polyethylene terephthalate (PET) – polybutylene terephthalate (PBT) poly(methyl methacrylate) (PMMA) – polyvinylidene fluoride (PVDF) homopolymer–copolymer: polypropylene (PP) – EPDM polycarbonate (PC) – acrylonitrile butadiene styrene (ABS): Bayblend, Pulse, Anjablend A Polymer blends can be used as thermoplastic elastomers. == See also == Flory–Huggins solution theory Emulsion dispersion == References == == External links == Miscible polymer blends: http://pslc.ws/macrog/blend.htm Immiscible polymer blends: http://pslc.ws/macrog/iblend.htm
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{
"page_id": 11471537,
"source": null,
"title": "Polymer blend"
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|
Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology is an anthology published in 2003 edited by Gerd B. Müller and Stuart A. Newman. The book is the outcome of the 4th Altenberg Workshop in Theoretical Biology on "Origins of Organismal Form: Beyond the Gene Paradigm", hosted in 1999 at the Konrad Lorenz Institute for Evolution and Cognition Research. It has been cited over 200 times and has a major influence on extended evolutionary synthesis research. == Description of the book == The book explores the multiple factors that may have been responsible for the origination of biological form in multicellular life. These biological forms include limbs, segmented structures, and different body symmetries. It explores why the basic body plans of nearly all multicellular life arose in the relatively short time span of the Cambrian Explosion. The authors focus on physical factors (structuralism) other than changes in an organism's genome that may have caused multicellular life to form new structures. These physical factors include differential adhesion of cells and feedback oscillations between cells. The book also presents recent experimental results that examine how the same embryonic tissues or tumor cells can be coaxed into forming dramatically different structures under different environmental conditions. One of the goals of the book is to stimulate research that may lead to a more comprehensive theory of evolution. It is frequently cited as foundational to the development of the extended evolutionary synthesis. == List of contributions == Origination of Organismal Form: The Forgotten Cause in Evolutionary Theory, Gerd B. Müller and Stuart A. Newman The Cambrian "Explosion" of Metazoans, Simon Conway Morris Convergence and Homoplasy in the Evolution of Organismal Form, Pat Willmer Homology:The Evolution of Morphological Organization, Gerd B. Müller Only Details Determine, Roy J. Britten The Reactive Genome, Scott F.
|
{
"page_id": 3082931,
"source": null,
"title": "Origination of Organismal Form"
}
|
Gilbert Tissue Specificity: Structural Cues Allow Diverse Phenotypes from a Constant Genotype, Mina J. Bissell, I. Saira Mian, Derek Radisky and Eva Turley Genes, Cell Behavior, and the Evolution of Form, Ellen Larsen Cell Adhesive Interactions and Tissue Self-Organization, Malcolm Steinberg Gradients, Diffusion, and Genes in Pattern Formation, H. Frederik Nijhout A Biochemical Oscillator Linked to Vertebrate Segmentation, Olivier Pourquié Organization through Intra-Inter Dynamics, Kunihiko Kaneko From Physics to Development: The Evolution of Morphogenetic Mechanisms, Stuart A. Newman Phenotypic Plasticity and Evolution by Genetic Assimilation, Vidyanand Nanjundiah Genetic and Epigenetic Factors in the Origin of the Tetrapod Limb, Günter P. Wagner and Chi-hua Chiu Epigenesis and Evolution of Brains: From Embryonic Divisions to Functional Systems, Georg F. Striedter Boundary Constraints for the Emergence of Form, Diego Rasskin-Gutman == References ==
|
{
"page_id": 3082931,
"source": null,
"title": "Origination of Organismal Form"
}
|
Temperature gradient gel electrophoresis (TGGE) and denaturing gradient gel electrophoresis (DGGE) are forms of electrophoresis which use either a temperature or chemical gradient to denature the sample as it moves across an acrylamide gel. TGGE and DGGE can be applied to nucleic acids such as DNA and RNA, and (less commonly) proteins. TGGE relies on temperature dependent changes in structure to separate nucleic acids. DGGE separates genes of the same size based on their different denaturing ability which is determined by their base pair sequence. DGGE was the original technique, and TGGE a refinement of it. == History == DGGE was invented by Leonard Lerman, while he was a professor at SUNY Albany. The same equipment can be used for analysis of protein, which was first done by Thomas E. Creighton of the MRC Laboratory of Molecular Biology, Cambridge, England. Similar looking patterns are produced by proteins and nucleic acids, but the fundamental principles are quite different. TGGE was first described by Thatcher and Hodson and by Roger Wartell of Georgia Tech. Extensive work was done by the group of Riesner in Germany. Commercial equipment for DGGE is available from Bio-Rad, INGENY and CBS Scientific; a system for TGGE is available from Biometra. == Temperature gradient gel electrophoresis == DNA has a negative charge and so will move to the positive electrode in an electric field. A gel is a molecular mesh, with holes roughly the same size as the diameter of the DNA string. When an electric field is applied, the DNA will begin to move through the gel, at a speed roughly inversely proportional to the length of the DNA molecule (shorter lengths of DNA travel faster) — this is the basis for size dependent separation in standard electrophoresis. In TGGE there is also a temperature gradient across
|
{
"page_id": 1641139,
"source": null,
"title": "Temperature gradient gel electrophoresis"
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|
the gel. At room temperature, the DNA will exist stably in a double-stranded form. As the temperature is increased, the strands begin to separate (melting), and the speed at which they move through the gel decreases drastically. Critically, the temperature at which melting occurs depends on the sequence (GC basepairs are more stable than AT due to stacking interactions, not due to the difference in hydrogen bonds (there are three hydrogen bonds between a cytosine and guanine base pair, but only two between adenine and thymine), so TGGE provides a "sequence dependent, size independent method" for separating DNA molecules. TGGE separates molecules and gives additional information about melting behavior and stability (Biometra, 2000). == Denaturing gradient gel electrophoresis == Denaturing gradient gel electrophoresis (DGGE) works by applying a small sample of DNA (or RNA) to an electrophoresis gel that contains a denaturing agent. Researchers have found that certain denaturing gels are capable of inducing DNA to melt at various stages. As a result of this melting, the DNA spreads through the gel and can be analyzed for single components, even those as small as 200-700 base pairs. What is unique about the DGGE technique is that as the DNA is subjected to increasingly extreme denaturing conditions, the melted strands fragment completely into single strands. The process of denaturation on a denaturing gel is very sharp: "Rather than partially melting in a continuous zipper-like manner, most fragments melt in a step-wise process. Discrete portions or domains of the fragment suddenly become single-stranded within a very narrow range of denaturing conditions" (Helms, 1990). This makes it possible to discern differences in DNA sequences or mutations of various genes: sequence differences in fragments of the same length often cause them to partially melt at different positions in the gradient and therefore "stop" at
|
{
"page_id": 1641139,
"source": null,
"title": "Temperature gradient gel electrophoresis"
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|
different positions in the gel. By comparing the melting behavior of the polymorphic DNA fragments side by side on denaturing gradient gels, it is possible to detect fragments that have mutations in the first melting domain (Helms, 1990). Placing two samples side by side on the gel and allowing them to denature together, researchers can easily see even the smallest differences in two samples or fragments of DNA. There are a number of disadvantages to this technique: "Chemical gradients such as those used in DGGE are not as reproducible, are difficult to establish and often do not completely resolve heteroduplexes" (Westburg, 2001). These problems are addressed by TGGE, which uses a temperature, rather than chemical, gradient to denature the sample. == Method == To separate nucleic acids by TGGE, the following steps must be performed: preparing and pouring the gels, electrophoresis, staining, and elution of DNA. Because a buffered system must be chosen, it is important that the system remain stable within the context of increasing temperature. Thus, urea is typically utilized for gel preparation; however, researchers need to be aware that the amount of urea used will affect the overall temperature required to separate the DNA. The gel is loaded, the sample is placed on the gel according to the type of gel that is being run—i.e. parallel or perpendicular—the voltage is adjusted and the sample can be left to run. Depending on which type of TGGE is to be run, either perpendicular or parallel, varying amounts of sample need to be prepared and loaded. A larger amount of one sample is used with perpendicular, while a smaller amount of many samples are used with parallel TGGE. Once the gel has been run, the gel must be stained to visualize the results. While there are a number of stains
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{
"page_id": 1641139,
"source": null,
"title": "Temperature gradient gel electrophoresis"
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|
that can be used for this purpose, silver staining has proven to be the most effective tool. The DNA can be eluted from the silver stain for further analysis through PCR amplification. == Applications == TGGE and DGGE are broadly useful in biomedical and ecological research; selected applications are described below. === Mutations in mtDNA === According to a recent investigation by Wong, Liang, Kwon, Bai, Alper and Gropman, TGGE can be utilized to examine the mitochondrial DNA of an individual. According to these authors, TGGE was utilized to determine two novel mutations in the mitochondrial genome: "A 21-year-old woman who has been suspected of mitochondrial cytopathy, but negative for common mitochondrial DNA (mtDNA) point mutations and deletions, was screened for unknown mutations in the entire mitochondrial genome by temperature gradient gel electrophoresis". === p53 mutation in pancreatic secretions === Lohr and coworkers (2001) report that in a comprehensive study of pancreatic secretions of individuals without pancreatic carcinoma, p53 mutations could be found in the pancreatic juices of a small percentage of participants. Because mutations of p53 has been extensively found in pancreatic carcinomas, the researchers for this investigation were attempting to determine if the mutation itself can be linked to the development of pancreatic cancer. While Lohr was able to find p53 mutations via TGGE in a few subjects, none subsequently developed pancreatic carcinoma. Thus, the researchers conclude by noting that the p53 mutation may not be the sole indicator of pancreatic carcinoma oncogenesis. === Microbial ecology === DGGE of small ribosomal subunit coding genes was first described by Gerard Muyzer, while he was Post-doc at Leiden University, and has become a widely used technique in microbial ecology. PCR amplification of DNA extracted from mixed microbial communities with PCR primers specific for 16S rRNA gene fragments of bacteria and
|
{
"page_id": 1641139,
"source": null,
"title": "Temperature gradient gel electrophoresis"
}
|
archaea, and 18S rRNA gene fragments of eukaryotes results in mixtures of PCR products. Because these amplicons all have the same length, they cannot be separated from each other by agarose gel electrophoresis. However, sequence variations (i.e. differences in GC content and distribution) between different microbial rRNAs result in different denaturation properties of these DNA molecules. Hence, DGGE banding patterns can be used to visualize variations in microbial genetic diversity and provide a rough estimate of the richness of abundance of predominant microbial community members. This method is often referred to as community fingerprinting. Recently, several studies have shown that DGGE of functional genes (e.g. genes involved in sulfur reduction, nitrogen fixation, and ammonium oxidation) can provide information about microbial function and phylogeny simultaneously. For instance, Tabatabaei et al. (2009) applied DGGE and managed to reveal the microbial pattern during the anaerobic fermentation of palm oil mill effluent (POME) for the first time. == References == Charles J. Sailey, M.D., M.S. Parts taken from a summary paper entitled "TGGE." 2003. The University of the Sciences in Philadelphia.
|
{
"page_id": 1641139,
"source": null,
"title": "Temperature gradient gel electrophoresis"
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|
Thermodynamic diagrams are diagrams used to represent the thermodynamic states of a material (typically fluid) and the consequences of manipulating this material. For instance, a temperature–entropy diagram (T–s diagram) may be used to demonstrate the behavior of a fluid as it is changed by a compressor. == Overview == Especially in meteorology, they are used to analyze the actual state of the atmosphere derived from the measurements of radiosondes, usually obtained with weather balloons. In such diagrams, temperature and humidity values (represented by the dew point) are displayed with respect to pressure. Thus the diagram gives at a first glance the actual atmospheric stratification and vertical water vapor distribution. Further analysis gives the actual base and top height of convective clouds or possible instabilities in the stratification. By assuming the energy amount due to solar radiation it is possible to predict the 2 m (6.6 ft) temperature, humidity, and wind during the day, the development of the boundary layer of the atmosphere, the occurrence and development of clouds and the conditions for soaring flight during the day. The main feature of thermodynamic diagrams is the equivalence between the area in the diagram and energy. When air changes pressure and temperature during a process and prescribes a closed curve within the diagram the area enclosed by this curve is proportional to the energy which has been gained or released by the air. == Types of thermodynamic diagrams == General purpose diagrams include: PV diagram T–s diagram h–s (Mollier) diagram Psychrometric chart Cooling curve Indicator diagram Saturation vapor curve Thermodynamic surface Specific to weather services, there are mainly three different types of thermodynamic diagrams used: Skew-T log-P diagram Tephigram Emagram Stüve diagram All four diagrams are derived from the physical P–alpha diagram which combines pressure (P) and specific volume (alpha) as its
|
{
"page_id": 4262587,
"source": null,
"title": "Thermodynamic diagrams"
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|
basic coordinates. The P–alpha diagram shows a strong deformation of the grid for atmospheric conditions and is therefore not useful in atmospheric sciences. The three diagrams are constructed from the P–alpha diagram by using appropriate coordinate transformations. Not a thermodynamic diagram in a strict sense, since it does not display the energy–area equivalence, is the Stüve diagram But due to its simpler construction it is preferred in education. Another widely-used diagram that does not display the energy–area equivalence is the θ-z diagram (Theta-height diagram), extensively used boundary layer meteorology. == Characteristics == Thermodynamic diagrams usually show a net of five different lines: isobars = lines of constant pressure isotherms = lines of constant temperature dry adiabats = lines of constant potential temperature representing the temperature of a rising parcel of dry air saturated adiabats or pseudoadiabats = lines representing the temperature of a rising parcel saturated with water vapor mixing ratio = lines representing the dewpoint of a rising parcel The lapse rate, dry adiabatic lapse rate (DALR) and moist adiabatic lapse rate (MALR), are obtained. With the help of these lines, parameters such as cloud condensation level, level of free convection, onset of cloud formation. etc. can be derived from the soundings. == Example == The path or series of states through which a system passes from an initial equilibrium state to a final equilibrium state and can be viewed graphically on a pressure-volume (P-V), pressure-temperature (P-T), and temperature-entropy (T-s) diagrams. There are an infinite number of possible paths from an initial point to an end point in a process. In many cases the path matters, however, changes in the thermodynamic properties depend only on the initial and final states and not upon the path. Consider a gas in cylinder with a free floating piston resting on top of
|
{
"page_id": 4262587,
"source": null,
"title": "Thermodynamic diagrams"
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|
a volume of gas V1 at a temperature T1. If the gas is heated so that the temperature of the gas goes up to T2 while the piston is allowed to rise to V2 as in Figure 1, then the pressure is kept the same in this process due to the free floating piston being allowed to rise making the process an isobaric process or constant pressure process. This Process Path is a straight horizontal line from state one to state two on a P-V diagram. It is often valuable to calculate the work done in a process. The work done in a process is the area beneath the process path on a P-V diagram. Figure 2 If the process is isobaric, then the work done on the piston is easily calculated. For example, if the gas expands slowly against the piston, the work done by the gas to raise the piston is the force F times the distance d. But the force is just the pressure P of the gas times the area A of the piston, F = PA. Thus W = Fd W = PAd W = P(V2 − V1) Now let’s say that the piston was not able to move smoothly within the cylinder due to static friction with the walls of the cylinder. Assuming that the temperature was increased slowly, you would find that the process path is not straight and no longer isobaric, but would instead undergo an isometric process till the force exceeded that of the frictional force and then would undergo an isothermal process back to an equilibrium state. This process would be repeated till the end state is reached. See figure 3. The work done on the piston in this case would be different due to the additional work required for
|
{
"page_id": 4262587,
"source": null,
"title": "Thermodynamic diagrams"
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|
the resistance of the friction. The work done due to friction would be the difference between the work done on these two process paths. Many engineers neglect friction at first in order to generate a simplified model. For more accurate information, the height of the highest point, or the max pressure, to surpass the static friction would be proportional to the frictional coefficient and the slope going back down to the normal pressure would be the same as an isothermal process if the temperature was increased at a slow enough rate. Another path in this process is an isometric process. This is a process where volume is held constant which shows as a vertical line on a P-V diagram. Figure 3 Since the piston is not moving during this process, there is not any work being done. == See also == Thermodynamics Timeline of thermodynamics == References == The Physics of Atmospheres by John Houghton, Cambridge University Press 2002. Especially chapter 3.3. deals solely with the tephigram. German version of Handbook of meteorological soaring flight from the Organisation Scientifique et Technique Internationale du Vol à Voile (OSTIV) (chapter 2.3) == Further reading == Handbook of meteorological forecasting for soaring flight WMO Technical Note No. 158. ISBN 92-63-10495-6 especially chapter 2.3. == External links == www.met.tamu.edu/../aws-tr79-006.pdf A very large technical manual (164 pages) how to use the diagrams. www.comet.ucar.edu/../sld010.htm A course on how to use diagrams at Comet, the 'Cooperative Program for Operational Meteorology, Education and Training'.
|
{
"page_id": 4262587,
"source": null,
"title": "Thermodynamic diagrams"
}
|
In nuclear physics and nuclear chemistry, the fission barrier is the activation energy required for a nucleus of an atom to undergo fission. This barrier may also be defined as the minimum amount of energy required to deform the nucleus to the point where it is irretrievably committed to the fission process. The energy to overcome this barrier can come from either neutron bombardment of the nucleus, where the additional energy from the neutron brings the nucleus to an excited state and undergoes deformation, or through spontaneous fission, where the nucleus is already in an excited and deformed state. Efforts to understand fission processes are ongoing and have been a very difficult problem since fission was first discovered by Lise Meitner, Otto Hahn, and Fritz Strassmann in 1938. While nuclear physicists understand many aspects of the fission process, there is currently no encompassing theoretical framework that gives a satisfactory account of the basic observations. == Scission == The fission process can be understood when a nucleus with some equilibrium deformation absorbs energy (through neutron capture, for example), becomes excited and deforms to a configuration known as the "transition state" or "saddle point" configuration. As the nucleus deforms, the nuclear Coulomb energy decreases while the nuclear surface energy increases. At the saddle point, the rate of change of the Coulomb energy is equal to the rate of change of the nuclear surface energy. The formation and eventual decay of this transition state nucleus is the rate-determining step in the fission process and corresponds to the passage over an activation energy barrier to the fission reaction. When this occurs, the neck between the nascent fragments disappears and the nucleus divides into two fragments. The point at which this occurs is called the "scission point". == Liquid drop model == From the description
|
{
"page_id": 56036030,
"source": null,
"title": "Fission barrier"
}
|
of the beginning of the fission process to the "scission point," it is apparent that the change of the shape of the nucleus is associated with a change of energy of some kind. In fact, it is the change of two types of energies: (1) the macroscopic energy related to the nuclear bulk properties as given by the liquid drop model and (2) the quantum mechanical energy associated with filling the shell model orbitals. For the nuclear bulk properties with small distortions, the surface, E s {\displaystyle E_{s}} , and Coulomb, E c {\displaystyle E_{c}} , energies are given by: E s = E s 0 ( 1 + 2 5 α 2 2 ) {\displaystyle E_{s}=E_{s}^{0}\left(1+{\frac {2}{5}}\alpha _{2}^{2}\right)} E c = E c 0 ( 1 − 1 5 α 2 2 ) {\displaystyle E_{c}=E_{c}^{0}\left(1-{\frac {1}{5}}\alpha _{2}^{2}\right)} where E s 0 {\displaystyle E_{s}^{0}} and E c 0 {\displaystyle E_{c}^{0}} are the surface and Coulomb energies of the undistorted spherical drops, respectively, and α 2 {\displaystyle \alpha _{2}} is the quadrupole distortion parameter. When the changes in the Coulomb and surface energies ( Δ E c = E c 0 − E c {\displaystyle \Delta E_{c}=E_{c}^{0}-E_{c}} , Δ E s = E s 0 − E s {\displaystyle \Delta E_{s}=E_{s}^{0}-E_{s}} ) are equal, the nucleus becomes unstable with respect to fission. At that point, the relationship between the undistorted surface and Coulomb energies becomes: x = E c 0 2 E s 0 {\displaystyle x={\frac {E_{c}^{0}}{2E_{s}^{0}}}} where x {\displaystyle x} is called the fissionability parameter. If x > 1 {\displaystyle x>1} , the liquid drop energy decreases with increasing α 2 {\displaystyle \alpha _{2}} , which leads to fission. If x < 1 {\displaystyle x<1} , then the liquid drop energy decreases with decreasing α 2 {\displaystyle \alpha _{2}} ,
|
{
"page_id": 56036030,
"source": null,
"title": "Fission barrier"
}
|
which leads to spherical shapes of the nucleus. The Coulomb and surface energies of a uniformly charged sphere can be approximated by the following expressions: E c 0 = 3 5 Z 2 e 2 R 0 A 1 / 3 = a c Z 2 A 1 / 3 {\displaystyle E_{c}^{0}={\frac {3}{5}}{\frac {Z^{2}e^{2}}{R_{0}A^{1/3}}}=a_{c}{\frac {Z^{2}}{A^{1/3}}}} E s 0 = 4 π R 0 2 S A 2 / 3 = a s A 2 / 3 {\displaystyle E_{s}^{0}=4\pi R_{0}^{2}SA^{2/3}=a_{s}A^{2/3}} where Z {\displaystyle Z} is the atomic number of the nucleus, A {\displaystyle A} is the mass number of the nucleus, e {\displaystyle e} is the charge of an electron, R 0 {\displaystyle R_{0}} is the radius of the undistorted spherical nucleus, S {\displaystyle S} is the surface tension per unit area of the nucleus, a c = 3 e 2 / 5 R 0 {\displaystyle a_{c}=3e^{2}/5R_{0}} and a s = 4 π R 0 2 S {\displaystyle a_{s}=4\pi R_{0}^{2}S} . The equation for the fissionability parameter then becomes: x = ( a c 2 a s ) ( Z 2 A ) = ( Z 2 A ) / ( Z 2 A ) c r i t i c a l {\displaystyle x=\left({\frac {a_{c}}{2a_{s}}}\right)\left({\frac {Z^{2}}{A}}\right)=\left({\frac {Z^{2}}{A}}\right)/\left({\frac {Z^{2}}{A}}\right)_{critical}} where the ratio of the constant ( a c / 2 a s ) − 1 {\displaystyle \left(a_{c}/2a_{s}\right)^{-1}} is referred to as ( Z 2 / A ) c r i t i c a l {\displaystyle \left(Z^{2}/A\right)_{critical}} . The fissionability of a given nucleus can then be categorized relative to ( Z 2 / A ) {\displaystyle \left(Z^{2}/A\right)} . As an example, plutonium-239 has a ( Z 2 / A ) {\displaystyle \left(Z^{2}/A\right)} value of 36.97, while less fissionable nuclei like bismuth-209 have a ( Z 2 / A ) {\displaystyle
|
{
"page_id": 56036030,
"source": null,
"title": "Fission barrier"
}
|
\left(Z^{2}/A\right)} value of 32.96. For all stable nuclei, x {\displaystyle x} must be less than 1. In that case, the total deformation energy of nuclei undergoing fission will increase by an amount ( 1 / 5 ) α 2 2 ( 2 E s 0 − E c 0 ) {\displaystyle (1/5)\alpha _{2}^{2}(2E_{s}^{0}-E_{c}^{0})} , as the nucleus deforms towards fission. This increase in potential energy can be thought of as the activation energy barrier for the fission reaction. However, modern calculations of the potential energy of deformation for the liquid drop model involve many deformation coordinates aside from α 2 {\displaystyle \alpha _{2}} and represent major computational tasks. == Shell corrections == In order to get more reasonable values for the nuclear masses in the liquid drop model, it is necessary to include shell effects. Soviet physicist Vilen Strutinsky proposed such a method using "shell correction" and corrections for nuclear pairing to the liquid drop model. In this method, the total energy of the nucleus is taken as the sum of the liquid drop model energy, E L D M {\displaystyle E_{LDM}} , the shell, δ S {\displaystyle \delta S} , and pairing, δ P {\displaystyle \delta P} , corrections to this energy as: E = E L D M + ∑ p , n ( δ S + δ P ) {\displaystyle E=E_{LDM}+\sum _{p,n}(\delta S+\delta P)} The shell corrections, just like the liquid drop energy, are functions of the nuclear deformation. The shell corrections tend to lower the ground state masses of spherical nuclei with magic or near-magic numbers of neutrons and protons. They also tend to lower the ground state mass of mid shell nuclei at some finite deformation thus accounting for the deformed nature of the actinides. Without these shell effects, the heaviest nuclei could not be
|
{
"page_id": 56036030,
"source": null,
"title": "Fission barrier"
}
|
observed, as they would decay by spontaneous fission on a time scale much shorter than we can observe. This combination of macroscopic liquid drop and microscopic shell effects predicts that for nuclei in the U-Pu region, a double-humped fission barrier with equal barrier heights and a deep secondary minimum will occur. For heavier nuclei, like californium, the first barrier is predicted to be much larger than the second barrier and passage over the first barrier is rate determining. In general, there is ample experimental and theoretical evidence that the lowest energy path in the fission process corresponds to having the nucleus, initially in an axially symmetric and mass (reflection) symmetric shape pass over the first maximum in the fission barrier with an axially asymmetric but mass symmetric shape and then to pass over the second maximum in the barrier with an axially symmetric but mass (reflection) asymmetric shape. Because of the complicated multidimensional character of the fission process, there are no simple formulas for the fission barrier heights. However, there are extensive tabulations of experimental characterizations of the fission barrier heights for various nuclei. == See also == Cold fission Nuclear fusion == References ==
|
{
"page_id": 56036030,
"source": null,
"title": "Fission barrier"
}
|
The Density Functional Based Tight Binding method is an approximation to density functional theory, which reduces the Kohn-Sham equations to a form of tight binding related to the Harris functional. The original approximation limits interactions to a non-self-consistent two center hamiltonian between confined atomic states. In the late 1990s a second-order expansion of the Kohn-Sham energy enabled a charge self-consistent treatment of systems where Mulliken charges of the atoms are solved self-consistently. This expansion has been continued to the 3rd order in charge fluctuations and with respect to spin fluctuations. Unlike empirical tight binding the (single particle) wavefunction of the resulting system is available, since the integrals used to produce the matrix elements are calculated using a set of atomic basis functions. == References ==
|
{
"page_id": 63900356,
"source": null,
"title": "DFTB"
}
|
Until the late 1950s, the Precambrian was not believed to have hosted multicellular organisms. However, with radiometric dating techniques, it has been found that fossils initially found in the Ediacara Hills in Southern Australia date back to the late Precambrian. These fossils are body impressions of organisms shaped like disks, fronds and some with ribbon patterns that were most likely tentacles. These are the earliest multicellular organisms in Earth's history, despite the fact that unicellularity had been around for a long time before that. The requirements for multicellularity were embedded in the genes of some of these cells, specifically choanoflagellates. These are thought to be the precursors for all animals. They are highly related to sponges (Porifera), which are the simplest multicellular animals. In order to understand the transition to multicellularity during the Precambrian, it is important to look at the requirements for multicellularity—both biological and environmental. == Precambrian == The Precambrian dates from the beginning of Earth's formation (4.6 billion years ago) to the beginning of the Cambrian Period, 539 million years ago. The Precambrian consists of the Hadean, Archaean and Proterozoic eons. Specifically, this article examines the Ediacaran, when the first multicellular bodies are believed to have arisen, as well as what caused the rise of multicellularity. This time period arose after the Snowball Earth of the mid Neoproterozoic. The "Snowball Earth" was a period of worldwide glaciation, which is believed to have served as a population bottleneck for the subsequent evolution of multicellular organisms. === Precambrian bodies === The Earth formed around 4.6 billion years ago, with unicellular life emerging somewhat later after the cessation of the Late Heavy Bombardment, a period of intense asteroid impacts possibly caused by migration of the gas giant planets to their current orbits, however multicellularity and bodies are a relatively recent
|
{
"page_id": 46336709,
"source": null,
"title": "Precambrian body plans"
}
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event in Earth's history. Bodies first started appearing towards the end of the Precambrian Era, during the Ediacaran period. The fossils of the Ediacaran period were first found in Southern Australia in the Ediacara Hills, hence the name. However these fossils were initially thought to be part of the Cambrian and it wasn't until the late 1950s when Martin Glaessner identified the fossils as actually being from the Precambrian era. The fossils that were found date to about 600 million years ago and are found in a variety of morphologies. == Fossils of the Ediacaran == For more information, see Ediacaran biota. The fossils found that date back to the Precambrian lack distinct structures since there were no skeletal forms during this period. Skeletons did not arise until the Cambrian Period when oxygen levels increased. This is because skeletons require collagen, which uses Vitamin C as a cofactor, which requires oxygen. For more information on the rise of oxygen see the section on oxygen. The majority of fossils from this Era come from either Mistaken Point on the East Coast of Canada or the Ediacara Hills in Southern Australia. Most of the fossils are found as impressions of soft-bodied organisms in the shape of disks, ribbons or fronds. There are also trace fossils that provide evidence that some of these Precambrian organisms were most-likely worm-like creatures that were locomotive. Most of these fossils lack any recognizable heads, mouths or digestive organs, and are thought to have fed via absorptive mechanisms and symbiotic relationships with chemoautotrophs (Chemotroph), photoautotrophs (Phototroph) or osmoautotrophs. The ribbon-like fossils resemble tentacled organisms, and are thought to have fed by capturing prey. The frondose fossils resemble sea pens and other cnidarians. The trace fossils suggest that there were annelid type creatures, and the disk fossils resemble sponges.
|
{
"page_id": 46336709,
"source": null,
"title": "Precambrian body plans"
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|
Despite these similarities, much of the identification is speculation since the fossils do not show very distinct structures. Other fossils do not resemble any known lineages. Many of the organisms, such as Charnia, found in Mistaken Point, were not like any organisms seen today. They had distinct bodies, however were lacking a head and digestive regions. Rather their body was organized in a very simple, fractal-like branching pattern. Every element of the body was finely branched and grew by repetitive branching. This allowed the organism to have a large surface area and maximize nutrient absorption without needing a mouth and digestive system. However, there was minimal genetic information and therefore did not have the requirements that would have allowed them to evolve more efficient feeding techniques. This means they were probably outcompeted by other organisms, and thus became extinct. The organisms found in the Ediacaran Hills in Southern Australia displayed either radially symmetric body plans or, one organism, Spriggina, displayed the first bilateral symmetry. The Ediacaran Hills are thought to have once had a shallow reef where more light could penetrate the bottom of the ocean floor. This allowed for more diversity of organisms. The organisms found here resemble relatives of the cnidarians, mollusks or annelids. === Charnia === Charnia fossils were originally found in the Charnwood Forest in England, hence named Charnia. These fossils are from marine organisms that lived on the bottom of the ocean floor. The fossils have a fractal body plan and were frond shaped, meaning they resembled broad-leafed plants such as ferns. However they could not have been plants since they resided in the dark depths of the ocean floor. In Charnwood Forest, Charnia was found as an isolated species, however there were many more fossils found on the East Coast of Canada in Mistaken
|
{
"page_id": 46336709,
"source": null,
"title": "Precambrian body plans"
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|
Point in Newfoundland. Charnia was attached to the bottom of the ocean floor, and was strongly current aligned. This is seen because there are disk-like shapes at the bottom of the Charnia fossil, which show where Charnia was tethered, and all the nearby fossils are facing the same direction. These fossils at Mistaken Point were preserved well under volcanic ash and layers of soft mud. It has been determined via radiometric dating of the fossils that Charnia must have lived around 565 million years ago. === Dickinsonia === Dickinsonia fossils are another notable fossil from the Ediacaran period, found in Southern Australia and Russia. It remains unknown what type of organism Dickinsonia was; however, it has been considered a polychaete, turbellarian/annelid worm, jellyfish, polyp, protist, lichen or mushroom. They were preserved in quartz sandstones, and date back to around 550 million years ago. Dickinsonia were soft-bodied organisms, that show some evidence of very slow movement. There are faint, circular imprints in the rock which follow a path, and then following the same path there is a more definite circular imprint of the same size. This indicates that the organism probably moved slowly from one feeding area to the next and absorbed nutrients. It is speculated that the organism probably had very small appendages that allowed it to move much like starfish do today. === Spriggina === Spriggina fossils represent the first known organisms with a bilaterally symmetric body plan. They had a head, tail and almost identical halves. They probably had sensory organs in the head and digestive organs in the tail which would have allowed them to find food more efficiently. They were capable of locomotion, which gave them an advantage over other organisms from that era that were either tethered to the bottom of the ocean floor or
|
{
"page_id": 46336709,
"source": null,
"title": "Precambrian body plans"
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moved very slowly. Spriggina was soft bodied, which leave the fossils as faint imprints. It is most likely related to annelids, however there is some speculation that it could be related to arthropods since it somewhat resembles trilobite fossils. === Trace fossils === The Ediacaran fossils of Southern Australia contain trace fossils, which indicate that there were motile benthic organisms. The organisms that produced the traces in the sediments were all worm-like sediment feeders or detritus feeders (Detritivore). There are a few trace fossils, which resemble arthropod trails. Evidence suggests that arthropod-like organisms existed during the Precambrian. This evidence is in the type of trails left behind; specifically one specimen that shows six pairs of symmetrically placed impressions, which resemble trilobite walking trails. == Transition from unicellularity to multicellularity == For the majority of Earth’s history life has been unicellular. However, unicellular organisms had the ingredients in them for multicellularity to arise. Despite having the ingredients for multicellularity, organisms were restricted due to the lack of hospitable environmental conditions. The rise of oxygen (The Great Oxygenation Event) led organisms to be able to develop more complex body plans. In order for multicellularity to have occurred, organisms must have been capable of cellular communication, aggregation, and specialized functions. The transition to multicellularity that began the evolution of animals from protozoa is one of the most poorly understood of history’s life events. Understanding choanoflagellates and their relation to sponges is important when positing theories on the origins of multicellularity === Choanoflagellates === Choanoflagellates, also called "collar-flagellates" are unicellular protists that exist in both freshwaters and oceans. Choanoflagellates have a spherical (or ovoid) cell body and a flagellum that is surrounded by a collar composed of actin microvilli. The flagellum is used to facilitate movement and food intake. As the flagellum beats, it
|
{
"page_id": 46336709,
"source": null,
"title": "Precambrian body plans"
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|
takes in water through the microvilli attached to the collar, which helps filter out unwanted bacteria and other tiny food particles. Choanoflagellates are composed of approximately 150 species and reproduce by simple division. ==== Choanoflagellate Salpingoeca rosetta ==== (also known as Choanoflagellate Proterospongia) The choanoflagellate Salpingoeca rosetta is a rare freshwater eukaryote consisting of a number of cells embedded in a jelly-like matrix. This organism demonstrates a very primitive level of cell differentiation and specialization. This is seen with flagellated cells and their collar structures that move the cell colony through the water, while the amoeboid cells on the inside serve to divide into new cells to assist in colony growth. Similar low level cellular differentiation and specification can also be seen in sponges. They also have collar cells (also called choanocytes due to their similarities to choanoflaggellates) and amoeboid cells arranged in a gelatinous matrix. Unlike choanoflagellate Salpingoeca rosetta, sponges also have other cell-types that can perform different functions (see sponges). Also, the collar cells of sponges beat within canals in the sponge body, whereas Salpingoeca rosetta’s collar cells reside on the inside and it lacks internal canals. Despite these minor differences, there is strong evidence that Proterospongia and Metazoa are highly related. ==== Choanoflagellate Perplexa ==== These choanoflagellates are able to attach to one another via the pairing of collar microvilli. ==== Choanoflagellate Codosiga Botrytis and Desmerella ==== These choanoflagellates are capable of forming colonies via fine intercellular bridges that allow the individual cells to attach. These bridges resemble ring canals that link developing spermatogonia or oogonia in animals. === Sponges (Porifera) === Sponges are some of Earth’s oldest and most ubiquitous animals. The appearance of sponge spicule fossils date back to the Precambrian Era around 580 million years ago. An assemblage of these fossils were found in
|
{
"page_id": 46336709,
"source": null,
"title": "Precambrian body plans"
}
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the Doushanto formation in Southern China. Some circular impressions from the Ediacaran Hills in Southern Australia are also reported to be sponges. They are one of the only lineages of metazoans from this era that continue to survive, and remain relatively unchanged. Sponges are such successful organisms due to their simple, yet effective morphology. They do not possess mouths or any digestive, nervous or circulatory systems. Instead they are filter feeders, which means that they obtain food through nutrients in the water. They have pores, called ostia, that water travels through to a chamber called the spongocoel, and exits through a chamber called the osculum. Through this water filtration system, they obtain nutrients that are needed for their survival. Specifically, they intracellularly digest bacteria, micro-algae or colloids. Sponge skeletons consist of either spongin or calcareous and siliceous spicules with some collagen molecules interspersed. The collagen holds the sponge cells together. Different lineages of sponges are distinguished based on the composition of their skeletons. The three main classes of sponges are Demospongiae, Hexactinellid, and Calcareous. Demonsponges are the most well-known type of sponge since they are used by humans. They are distinguished by a siliceous skeleton of two and four rayed spicules and contain the protein spongin. Hexactinellid are also called glass sponges, and are distinguished by a six-rayed glass skeleton. These sponges are also capable of carrying out action potentials. Calcareous sponges are characterized by a calcium carbonate skeleton and comprise less than 5% of sponges. ==== Cells ==== Sponges have around 6 different types of cells that can perform different functions. Sponges are a good model for studying the origin of multicellularity because the cells are capable of communicating with one another and re-aggregating. In an experiment conducted by Henry Van Peters Wilson in 1910, it was found that
|
{
"page_id": 46336709,
"source": null,
"title": "Precambrian body plans"
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cells from dissociated sponges could send out signals and recognize each other to form a new individual. This suggests that the cells that compose sponges are capable of independent living, however once multicellularity was possible then aggregating together to form one organism was a more efficient way of living. The most notable cell types of sponges are the goblet-shaped cells called choanocytes, so named for their similarity to choanoflagellates. The similarities between these two cells types makes scientists believe that choanoflagellates are the sister taxa to metazoa. The flagella of these cells are what drive the water movement through the sponge body. The cell body of choanocytes is what is responsible for nutrient absorption. In some species these cells can develop into gametes. The Pinacocytes are the cells on the exterior of the sponge that line the cell body. They are tightly packed together and very thin. The mesenchyme lines the region between the pinacocytes and the choanocytes. They contain a matrix composed of proteins and spicules. Archaeocytes are special types of cells, in that they can transform into all of the other cell types. They will do what is needed in the sponge body, such as ingest and digest food, transport nutrients to other cells in the sponge body. These cells are also capable of developing into gametes in some sponge species. The sclerocytes are responsible for the secretion of spicules. In species of sponges that use spongin instead of calcaerous and silicaceous spicules, the sclerocytes are replaced by spongocytes, which secrete spongin skeletal fibres. The myocytes and porocytes are responsible for contraction of the sponge. These contractions are analogous to muscle contractions in other organisms, since sponges do not have muscles. They are responsible for regulating the water flow through the sponge. == The formation of multicellularity ==
|
{
"page_id": 46336709,
"source": null,
"title": "Precambrian body plans"
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The formation of multicellularity was a pivotal point in the evolution of life on Earth. Shortly after multicellularity arose, there was an immense increase in the diversity of living organisms at the beginning of the Cambrian Era, called the Cambrian Explosion. Multicellularity is believed to have evolved multiple times on Earth because it was a beneficial life strategy for organisms. For multicellularity to occur, cells need to be capable of self-replication, cell-cell adhesion and cell-cell communication. There also must have been available oxygen and selective pressures in the environment. === Theory of cellular division: S. Rosetta === Work by Fairclough, Dayel and King suggests that S. Rosetta can exist in either single-cellular form or in colonies of 4-50 cells, which arrange themselves in tight knit packs of spheres. This was established by performing an experiment involving the introduction of prey bacterium Algoriphagus species to a sample of uni-celled S. Rosetta organism and monitored the activity for 12 hours. Results of this study demonstrated that cell colonies were formed through cell-division of the initial solitary S. Rosetta cell rather than by cell aggregation. Further studies to support the theory of cell-proliferation were done by introducing then removing the drug aphidicolin which serves to block cell-division. When the drug was introduced, cell division stopped and colony formation resulted through cell-cell aggregation. When the drug was removed, cell-division dominated once again. === Building blocks for cell-adhesion === By looking at the genome of the Choanoflagellate, "Monosiga brevicollis", scientists have inferred that choanoflagellates play a key role in the development of multicellularity. Nicole King has done work looking at the genome of Monisiga brevicollis, and has found key protein domains that are shared between metazoans and choanoflagellates. These domains play a role in cell signalling and adhesion processes in metazoans. The finding that choanoflagellates
|
{
"page_id": 46336709,
"source": null,
"title": "Precambrian body plans"
}
|
also have these genes is an incredible discovery because it was previously thought that only metazoans had genes responsible for cell-cell communication and aggregation. This suggests that these domains play a key role in the origins of multicellularity since it ties a unicellular organism (choanoflagellates) to multicellular organisms (metazoans). It shows that the components required for multicellularity were present in the common ancestor between metazoans and choanoflagellates. === Cell signaling and cell communication === Neither sponges nor the placozoan Trichoplax adhaerens appear to be equipped with neuron synapses, however they both possess several factors related to the same synaptic function. Therefore, it is likely that central features involved in synaptic transmission arose early in metazoan evolution, most likely around the time that much of the life on Earth was transitioning to multicellularity. It was found that the Munc18/syntaxin 1 complex could be an important component for the production of the SNARE protein. The secretion of SNARE protein from synaptic vesicles is believed to be critical for neuronal communication. The Munc18/syntaxin 1 complex found in M. brevicollis is both structurally and functionally similar to the metazoan complex. This suggests that it constitutes an important step in the reaction pathway toward SNARE assembly. It is believed that the common ancestor of choanoflagellates and metazoans used this primordial secretion machinery as a precursor to synaptic communication. This mechanism would eventually be used for cell-cell communication in animals. === Reasons for the development of multicellularity === Despite the fact that prokaryotic cells contained the building blocks required for multicellularity to arise, this transition did not occur for around 1500 million years after the origins of the first eukaryotic cell. Scientists have proposed two major theories for the reason that multicellularity arose so late after the appearance of life on Earth. ==== Predation theory for
|
{
"page_id": 46336709,
"source": null,
"title": "Precambrian body plans"
}
|
multicellularity ==== This theory postulates that multicellularity arose as a means for prey to escape predation. Larger prey are less likely to be preyed upon, and larger predators are more likely to catch prey. Therefore it is likely that multicellularity arose when the first predators evolved. By assembling as a larger, multicelled organism, prey could escape the attempts of a predator. Therefore multicellularity was selectively favoured over unicellularity. This can be seen in a simple experiment conducted by Boraas et al. (1998). When a predatory protist, Ochromonas valencia, was introduced to a prey population of Chlorella vulgaris, it was seen that within less than 100 generations of the prey species a multicellular growth form of the alga became dominant. This is interesting because before the predator was introduced, the population of Chlorella vulgaris retained its unicellular growth form for thousands of generations. It is likely that it would have remained unicellular indefinitely if the selective pressure that was induced by the predators had not been introduced. After multiple generations with the predator, the algal species retained a growth form of 8-10 cells, which was large enough to avoid the predator, but small enough that each cell still had access to nutrients. This predator-prey relationship provides a likely reason for why it was beneficial for organisms to be multicellular. ==== Rise in oxygen levels theory for multicellularity ==== Despite the fact that organisms had the potential to become multicellular it is likely that it was not actually possible until the late Neoproterozoic. This is because multicellularity requires oxygen, and before the late Neoproterozoic there was very limited oxygen availability. After the melting of the “Snowball Earth” during the mid Neoproterozoic, nutrients that were trapped in the ice flooded the oceans. Surviving bacteria flourished due to the increased nutrient levels. Among these
|
{
"page_id": 46336709,
"source": null,
"title": "Precambrian body plans"
}
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microbes were cyanobacteria and other oxygen producing bacteria, which led to the massive rise in oxygen levels. The increased oxygen availability allowed it to be used by cells in order to manufacture collagen. Collagen is the key component for cell aggregation, It is a rope-like molecule that “ties” cells together. Oxygen is required for collagen synthesis because ascorbic acid (Vitamin C) is essential for this process to occur. A key component in the ascorbic acid molecule is oxygen (chemical formula C6H8O6). Therefore, it is evident that the rise in oxygen is a crucial step to the rise of multicellularity since it is essential for the synthesis of collagen. == Building blocks found in both sponges and humans == === Collagen === Collagen is the most abundant protein in mammals and is an essential molecule in the formation of bones, skin and other connective tissue. Different types of collagen have been found in all multicellular organisms, including sponges. It has been found that sponges do have a gene sequence coding for collagen type IV which is a diagnostic feature of the basal lamina. It has also been found that 29 types of collagen have been found to exist in humans. This vast group can further be divided into several families according to their primary structures and supramolecular organization. Among the many types of collagens, only the fibrillar and the basement membrane (type IV) collagens have been found in the sponges and cnidarians, which are the two earliest branching metazoan lineages. Studies have focused on the origin of fibrillar collagen molecules. In Sponges, there exist three clades of fibrillar molecules, A, B and C. It is proposed that only the B clade fibrillar collagens preserved their characteristic modular structure from sponge to human. In mammals, the fibrillar collagens involved in the formation
|
{
"page_id": 46336709,
"source": null,
"title": "Precambrian body plans"
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|
of cross-striated fibrils are types I–III, V, and XI. Type II and type XI collagens compose the fibrils present in cartilage. These can be distinguished from collagens located in non-cartilaginous tissues, which include type I, III, and V collagens. === Protein === Additional research on sponge proteins found that of 42 sponge proteins that were analysed, all of them had homologous proteins that are found in humans. An identity score of 53% was given to the similarity among sponge and human proteins, compared to a score of 42% when the same sequence was compared to that of C. elegans. == References ==
|
{
"page_id": 46336709,
"source": null,
"title": "Precambrian body plans"
}
|
Coulomb excitation is a technique in experimental nuclear physics to probe the electromagnetic aspect of nuclear structure. In Coulomb excitation, a nucleus is excited by an inelastic collision with another nucleus through the electromagnetic interaction. In order to ensure that the interaction is electromagnetic in nature — and not nuclear — the distance of closest approach of the colliding nuclei has to be sufficiently large. In particular, in low-energy Coulomb excitation (taking place at beam energies of a few megaelectronvolts per nucleon) the commonly adopted empirical criterion is that if the surfaces of the colliding nuclei are separated by at least 5 femtometers, the contribution of the short-range nuclear interaction to the excitation process can be neglected. From the measured excitation cross sections, electromagnetic transition probabilities between the nuclear energy levels can be extracted. This method is particularly useful for investigating collectivity in nuclei, as collective excitations are often connected by strong electric quadrupole transitions. Moreover, it is the only experimental method in nuclear physics that is sensitive to electric quadrupole moments of excited nuclear states with lifetimes shorter than nanoseconds. == References ==
|
{
"page_id": 28117700,
"source": null,
"title": "Coulomb excitation"
}
|
In particle physics, the acronym WISP refers to a largely hypothetical weakly interacting sub-eV particle, or weakly interacting slender particle, or weakly interacting slim particle – low-mass particles which rarely interact with conventional particles. The term is used to generally categorize a type of dark matter candidate, and is essentially synonymous with axion-like particle (ALP). WISPs are generally hypothetical particles. WISPs are the low-mass counterpart of weakly interacting massive particles (WIMPs). == Discussion == Except for conventional, active neutrinos, all WISPs are candidate dark matter constituents, and many proposed experiments to detect WISPs might possibly be able to detect several different kinds. "WISP" is most often used to refer to a low-mass hypothetical particles which are viable dark matter candidates. Examples include: Axion – long-standing hypothetical strong force related light particle Sterile neutrino – never-observed particles explicitly excluded (if they exist) from the weak, strong and electromagnetic interactions Supersymmetric particles, particularly the lightest supersymmetric particle which might be a Neutralino – supersymmetric fermions that are electrically neutral composites of superpartners to bosons == Excluded active neutrinos == Although ordinary "active" neutrinos (left-chiral neutrinos and right-chiral antineutrinos) are particles known to exist, and though active neutrinos do indeed technically satisfy the description of the term, they are often excluded from lists of "WISP" particles. The reason that active neutrinos are often not included among WISPs is that they are no longer viable dark matter candidates: current estimated limits on their number density and mass indicate that their cumulative mass-density could not be high enough to account for the amount of dark matter inferred from its observed effects, although they certainly do make some small contribution to dark matter density. == Sources == The various sources of WISPs could possibly include hot astrophysical plasma and energy transport in stars. Note however, that
|
{
"page_id": 67046091,
"source": null,
"title": "WISP (particle physics)"
}
|
since they remain hypothetical (except for active neutrinos), the means of creation of WISPs depends on the theoretical framework used to propose them. == See also == Axion Feebly interacting particle (FIP) Hot dark matter Light dark matter Lightest supersymmetric particle (LSP) Sterile neutrino Weakly interacting massive particle (WIMP) == References ==
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{
"page_id": 67046091,
"source": null,
"title": "WISP (particle physics)"
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|
In genetics, dominance is the phenomenon of one variant (allele) of a gene on a chromosome masking or overriding the effect of a different variant of the same gene on the other copy of the chromosome. The first variant is termed dominant and the second is called recessive. This state of having two different variants of the same gene on each chromosome is originally caused by a mutation in one of the genes, either new (de novo) or inherited. The terms autosomal dominant or autosomal recessive are used to describe gene variants on non-sex chromosomes (autosomes) and their associated traits, while those on sex chromosomes (allosomes) are termed X-linked dominant, X-linked recessive or Y-linked; these have an inheritance and presentation pattern that depends on the sex of both the parent and the child (see Sex linkage). Since there is only one Y chromosome, Y-linked traits cannot be dominant or recessive. Additionally, there are other forms of dominance, such as incomplete dominance, in which a gene variant has a partial effect compared to when it is present on both chromosomes, and co-dominance, in which different variants on each chromosome both show their associated traits. Dominance is a key concept in Mendelian inheritance and classical genetics. Letters and Punnett squares are used to demonstrate the principles of dominance in teaching, and the upper-case letters are used to denote dominant alleles and lower-case letters are used for recessive alleles. An often quoted example of dominance is the inheritance of seed shape in peas. Peas may be round, associated with allele R, or wrinkled, associated with allele r. In this case, three combinations of alleles (genotypes) are possible: RR, Rr, and rr. The RR (homozygous) individuals have round peas, and the rr (homozygous) individuals have wrinkled peas. In Rr (heterozygous) individuals, the R allele
|
{
"page_id": 68300,
"source": null,
"title": "Dominance (genetics)"
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|
masks the presence of the r allele, so these individuals also have round peas. Thus, allele R is dominant over allele r, and allele r is recessive to allele R. Dominance is not inherent to an allele or its traits (phenotype). It is a strictly relative effect between two alleles of a given gene of any function; one allele can be dominant over a second allele of the same gene, recessive to a third, and co-dominant with a fourth. Additionally, one allele may be dominant for one trait but not others. Dominance differs from epistasis, the phenomenon of an allele of one gene masking the effect of alleles of a different gene. == Background == Gregor Johann Mendel, "The Father of Genetics", promulgated the idea of dominance in the 1860s. However, it was not widely known until the early twentieth century. Mendel observed that, for a variety of traits of garden peas having to do with the appearance of seeds, seed pods, and plants, there were two discrete phenotypes, such as round versus wrinkled seeds, yellow versus green seeds, red versus white flowers or tall versus short plants. When bred separately, the plants always produced the same phenotypes, generation after generation. However, when lines with different phenotypes were crossed (interbred), one and only one of the parental phenotypes showed up in the offspring (green, round, red, or tall). However, when these hybrid plants were crossed, the offspring plants showed the two original phenotypes, in a characteristic 3:1 ratio, the more common phenotype being that of the parental hybrid plants. Mendel reasoned that each parent in the first cross was a homozygote for different alleles (one parent AA and the other parent aa), that each contributed one allele to the offspring, with the result that all of these hybrids were heterozygotes
|
{
"page_id": 68300,
"source": null,
"title": "Dominance (genetics)"
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|
(Aa), and that one of the two alleles in the hybrid cross dominated expression of the other: A masked a. The final cross between two heterozygotes (Aa X Aa) would produce AA, Aa, and aa offspring in a 1:2:1 genotype ratio with the first two classes showing the (A) phenotype, and the last showing the (a) phenotype, thereby producing the 3:1 phenotype ratio. Mendel did not use the terms gene, allele, phenotype, genotype, homozygote, and heterozygote, all of which were introduced later. He did introduce the notation of capital and lowercase letters for dominant and recessive alleles, respectively, still in use today. In 1928, British population geneticist Ronald Fisher proposed that dominance acted based on natural selection through the contribution of modifier genes. In 1929, American geneticist Sewall Wright responded by stating that dominance is simply a physiological consequence of metabolic pathways and the relative necessity of the gene involved. == Types of dominance == === Complete dominance (Mendelian) === In complete dominance, the effect of one allele in a heterozygous genotype completely masks the effect of the other. The allele that masks are considered dominant to the other allele, and the masked allele is considered recessive. When we only look at one trait determined by one pair of genes, we call it monohybrid inheritance. If the crossing is done between parents (P-generation, F0-generation) who are homozygote dominant and homozygote recessive, the offspring (F1-generation) will always have the heterozygote genotype and always present the phenotype associated with the dominant gene. However, if the F1-generation is further crossed with the F1-generation (heterozygote crossed with heterozygote) the offspring (F2-generation) will present the phenotype associated with the dominant gene ¾ times. Although heterozygote monohybrid crossing can result in two phenotype variants, it can result in three genotype variants - homozygote dominant, heterozygote and
|
{
"page_id": 68300,
"source": null,
"title": "Dominance (genetics)"
}
|
homozygote recessive, respectively.In dihybrid inheritance we look at the inheritance of two pairs of genes simultaneous. Assuming here that the two pairs of genes are located at non-homologous chromosomes, such that they are not coupled genes (see genetic linkage) but instead inherited independently. Consider now the cross between parents (P-generation) of genotypes homozygote dominant and recessive, respectively. The offspring (F1-generation) will always heterozygous and present the phenotype associated with the dominant allele variant. However, when crossing the F1-generation there are four possible phenotypic possibilities and the phenotypical ratio for the F2-generation will always be 9:3:3:1. === Incomplete dominance (non-Mendelian) === Incomplete dominance (also called partial dominance, semi-dominance, intermediate inheritance, or occasionally incorrectly co-dominance in reptile genetics) occurs when the phenotype of the heterozygous genotype is distinct from and often intermediate to the phenotypes of the homozygous genotypes. The phenotypic result often appears as a blended form of characteristics in the heterozygous state. For example, the snapdragon flower color is homozygous for either red or white. When the red homozygous flower is paired with the white homozygous flower, the result yields a pink snapdragon flower. The pink snapdragon is the result of incomplete dominance. A similar type of incomplete dominance is found in the four o'clock plant wherein pink color is produced when true-bred parents of white and red flowers are crossed. In quantitative genetics, where phenotypes are measured and treated numerically, if a heterozygote's phenotype is exactly between (numerically) that of the two homozygotes, the phenotype is said to exhibit no dominance at all, i.e. dominance exists only when the heterozygote's phenotype measure lies closer to one homozygote than the other. When plants of the F1 generation are self-pollinated, the phenotypic and genotypic ratio of the F2 generation will be 1:2:1 (Red:Pink:White). === Co-dominance (non-Mendelian) === Co-dominance occurs when the
|
{
"page_id": 68300,
"source": null,
"title": "Dominance (genetics)"
}
|
contributions of both alleles are visible in the phenotype and neither allele masks another. For example, in the ABO blood group system, chemical modifications to a glycoprotein (the H antigen) on the surfaces of blood cells are controlled by three alleles, two of which are co-dominant to each other (IA, IB) and dominant over the recessive i at the ABO locus. The IA and IB alleles produce different modifications. The enzyme coded for by IA adds an N-acetylgalactosamine to a membrane-bound H antigen. The IB enzyme adds a galactose. The i allele produces no modification. Thus the IA and IB alleles are each dominant to i (IAIA and IAi individuals both have type A blood, and IBIB and IBi individuals both have type B blood), but IAIB individuals have both modifications on their blood cells and thus have type AB blood, so the IA and IB alleles are said to be co-dominant. Another example occurs at the locus for the beta-globin component of hemoglobin, where the three molecular phenotypes of HbA/HbA, HbA/HbS, and HbS/HbS are all distinguishable by protein electrophoresis. (The medical condition produced by the heterozygous genotype is called sickle-cell trait and is a milder condition distinguishable from sickle-cell anemia, thus the alleles show incomplete dominance concerning anemia, see above). For most gene loci at the molecular level, both alleles are expressed co-dominantly, because both are transcribed into RNA. Co-dominance, where allelic products co-exist in the phenotype, is different from incomplete dominance, where the quantitative interaction of allele products produces an intermediate phenotype. For example, in co-dominance, a red homozygous flower and a white homozygous flower will produce offspring that have red and white spots. When plants of the F1 generation are self-pollinated, the phenotypic and genotypic ratio of the F2 generation will be 1:2:1 (Red:Spotted:White). These ratios are
|
{
"page_id": 68300,
"source": null,
"title": "Dominance (genetics)"
}
|
the same as those for incomplete dominance. Again, this classical terminology is inappropriate – in reality, such cases should not be said to exhibit dominance at all. == Relationship to other genetic concepts == Dominance can be influenced by various genetic interactions and it is essential to evaluate them when determining phenotypic outcomes. Multiple alleles, epistasis, pleiotropic genes, and polygenic characteristics are some factors that might influence the phenotypic outcome. === Multiple alleles === Although any individual of a diploid organism has at most two different alleles at a given locus, most genes exist in a large number of allelic versions in the population as a whole. This is called polymorphism, and is caused by mutations. Polymorphism can have an effect on the dominance relationship and phenotype, which is observed in the ABO blood group system. The gene responsible for human blood type have three alleles; A, B, and O, and their interactions result in different blood types based on the level of dominance the alleles expresses towards each other. === Epistasis === Epistasis is interactions between multiple alleles at different loci. More specifically, epistasis is when one gene can mask the phenotype of a gene at a completely different locus. Therefore, several genes can influence the phenotype expressed. Epistasis is slightly different from dominance in the fact that dominance is an allele-to-allele interaction at one locus while epistasis is a gene-to-gene interaction at different loci. The dominance relationship between alleles involved in epistatic interactions can influence the observed phenotypic ratios in offspring. An example of epistasis can be seen in Labrador retriever coat colors. One gene at one locus codes for the color of hair but another gene at a different locus determines if the color is even deposited in the hair. Recessive epistasis is seen in this example
|
{
"page_id": 68300,
"source": null,
"title": "Dominance (genetics)"
}
|
due to recessive alleles for color desposition masking both the dominant black (B) allele and recessive brown (b) allele at the first locus to express a yellow coat in the Labrador retriever. The yellow color comes from no pigment being deposited in the hair shaft. Other examples of epistasis interactions are dominant epistasis and duplicate recessive epistasis. Each type of epistasis is a modification of the dihyrbid ratio of 9:3:3:1. === Pleiotropic genes === Pleiotropic genes are genes where one single gene affects two or more characteristics. An example of this concept is Marfan Syndrome which is a mutation of the FBN1 gene. The effects this causes are a person's appearance being tall and long limbed. They can also have Scoliosis, Ectopia Lentis, and larger than normal aortas. Pleiotropy shares a relationship with Epistasis. While pleiotropy represents one single gene, epistasis is multiple genes interacting with one another to cause different traits to arise. it is helpful to recognize how Epistasis could affect viewing pleiotropic genes if different traits arise or mask themselves to varying degrees. === Polygenic characteristics === Polygenic characteristics are those affected by multiple genes at different loci. These different genes interact in a way to produce a quantitative characteristic, which is a characteristic that presents a wide variety phenotypes, such as height in humans. The greater the number of genes that interact to influence this characteristic, the greater the number of different phenotypes possible due to more possible genotypes. Many more characteristics also appear to be affected by more than one gene located on different loci, including diabetes and some autoimmune diseases. == See also == Ambidirectional dominance List of Mendelian traits in humans Mitochondrial DNA Punnett square Penetrance Summation theorems (biochemistry) Chimerism == References == "On-line notes for Biology 2250 – Principles of Genetics". Memorial
|
{
"page_id": 68300,
"source": null,
"title": "Dominance (genetics)"
}
|
University of Newfoundland. Online Mendelian Inheritance in Man (OMIM): Hemoglobin—Beta Locus; HBB - 141900 — Sickle-Cell Anemia Online Mendelian Inheritance in Man (OMIM): ABO Glycosyltransferase - 110300 — ABO blood groups == External links == "Online Mendelian Inheritance in Man" (OMIM) "Autosomal dominance of Huntington's Disease". Huntington's Disease Outreach Project for Education at Stanford
|
{
"page_id": 68300,
"source": null,
"title": "Dominance (genetics)"
}
|
Rikku is a character in the Final Fantasy series, created by Tetsuya Nomura. Rikku first appears in Final Fantasy X as one of its protagonists, where she accompanies her cousin Yuna and others on a journey to defeat the monster Sin. Rikku again appears as a protagonist in the game's direct sequel, Final Fantasy X-2. In that game, she, Yuna, and new friend Paine journey to find missing FFX protagonist Tidus. Square originally planned to make Rikku the protagonist of her own game, but the developer cancelled the idea. In order to make a game revolving around a group of female heroes, Final Fantasy X-2's protagonists became Yuna, Paine, and Rikku. To reflect the changing social mores between game titles, Rikku wears much more casual and minimal clothing in X-2 than the games' predecessor. Rikku generally received a positive reception, with her X-2 design receiving praise for its attractiveness. Some critics have considered her attire to be fan service, and her character development thin. Most fans, however, have expressed positive views of her cheerful and bubbly personality. The character has appeared on many lists of fans' favorite Final Fantasy characters. == Concept and creation == Rikku first appeared in Final Fantasy X. Tetsuya Nomura designed her as a 15-year-old Al Bhed girl. She is Cid's daughter and Brother's younger sister. After the game's release, the video game press reported that she might get her own game, code-named "Rikku Version", but was later confirmed to not be in the works. Rikku, along with Yuna, were the leads of Final Fantasy X-2 and were the only characters from Final Fantasy X to appear. Developers chose her in order to create a game that centered on women. Tetsu Tsukamoto, the designer of Final Fantasy X-2's "alternate" costumes, explained that Rikku's outfit was the
|
{
"page_id": 20646605,
"source": null,
"title": "Rikku"
}
|
product of a cultural change in Spira, the world Rikku inhabits. The staff also wished to make that cast seem more physically active. Rikku is voiced by Tara Strong in English and by Marika Matsumoto in Japanese. Strong was offered an audition by Final Fantasy X casting director Jack Fletcher. Before her audition, the Fletcher gave Strong recordings of the Japanese version of Rikku and a description of the character. Many of Strong's lines ended with "you know" in order to match the English dub with the character's mouth movements, particularly to end the sentence with a vowel sound. They decided to make this a vocal tic for her. == Appearances == Rikku first appears in Final Fantasy X as one of its protagonists. She helps Tidus when he first arrives as a stranger in Spira, but then she disappears during an attack from the monster Sin. Upon meeting Tidus again at the Moonflow, she becomes the last character to join her cousin Yuna's entourage of guardians. Rikku's attitude is somewhat childish but is mostly quite cheerful and positive. She does occasionally suffer from instances of anxiety. This feeling originates from being attacked by a fiend on a beach when she was young; her brother then tried to destroy it with a Thunder spell, but he missed and electrocuted her instead. Cid's sister married Braska, which makes Braska Rikku's uncle. This relationship also makes Rikku Yuna's cousin. Rikku wishes to prevent Yuna from going through with her summoner pilgrimage as she will die in the process of defeating Sin. Rikku returns in Final Fantasy X-2 once again as a protagonist, now 17 years old. She is also the one who convinces Yuna to leave the land of Besaid and go on a journey along with their new friend Paine. Rikku
|
{
"page_id": 20646605,
"source": null,
"title": "Rikku"
}
|
convinces Yuna by showing her a mysterious sphere featuring a person resembling Yuna's lost love, Tidus. Rikku appears in the game Theatrhythm Final Fantasy: Curtain Call as a playable character. Her appearance resembles a chibi-esque version of her Final Fantasy X-2 character. She also appears alongside Yuna and Paine in Kingdom Hearts II as a miniature fairy version of herself wearing modified versions of her X-2 attire. The game Itadaki Street Special features a miniature Rikku also in her X-2 outfit, along with Yuna and Paine. Rikku also appears as a character in the game World of Final Fantasy. === Merchandise === Rikku, along with characters Paine and Yuna, received a series of singles performed by Marika Matsumoto in a collection called "Final Fantasy X-2 Vocal Collection - Rikku". The three characters also had figurines produced by Play Arts. They were the first figurines Play Arts produced in-house. == Reception == Rikku has received generally positive reception since appearing in Final Fantasy X and X-2. Final Fantasy fans voted her the 13th best female Final Fantasy character. Famitsu readers ranked her as one of the best video game characters. She has been identified as one of the most attractive female characters in and outside of the series by IGN, Play, UGO, and G4TV readers. Complex identified her outfit as the main reason to play Final Fantasy X-2. Houston Press expressed disappointment that the story of Final Fantasy X focused so much on Tidus, noting how much more interesting the relationship between Rikku and Yuna was. Game Informer identified her as a character they would like to be around due to an abundance of positive energy. Digitally Downloaded enjoyed her character as well, noting she was their ideal rogue and praised her for her uplifting attitude. They also found her a
|
{
"page_id": 20646605,
"source": null,
"title": "Rikku"
}
|
highlight of Final Fantasy X and hoped to see her in Dissidia Final Fantasy. Game Informer was critical of the sexualization of Rikku, noting her as being underage. Digitally Downloaded noted that her outfit in Final Fantasy X-2 was fan service. They also noted, however, that it was story-related as it demonstrated the liberation of her society from restrictive rules between games. Despite enjoying her "bubbly personality" in the face of hardships, they felt that there was not much depth to her character, and that people were too focused on her outfit. CNET felt Rikku was a highly underrated character, though noting that she was mostly known for her outfit and "being scared" than her engineering prowess. Tara Strong was awarded "Outstanding Achievement in Character Performance — Female" for her portrayal of Rikku by the Academy of Interactive Arts & Sciences. Game Informer identified Rikku as one of Strong's most notable roles. == References ==
|
{
"page_id": 20646605,
"source": null,
"title": "Rikku"
}
|
β-Carbon elimination (beta-carbon elimination) is a type of reaction in organometallic chemistry wherein an allyl ligand bonded to a metal center is broken into the corresponding metal-bonded alkyl (aryl) ligand and an alkene. It is a subgroup of elimination reactions. Though less common and less understood than β-hydride elimination, it is an important step involved in some olefin polymerization processes and transition-metal-catalyzed organic reactions. == Overview == Like β-hydride elimination, β-carbon elimination requires the metal to have an open coordination site cis to the alkyl group for this reaction to occur. β-carbon elimination is usually less favored than hydride elimination because the metal–hydride bond is stronger than the metal–carbon bond for most metals in catalytic reactions. The principles governing β-alkyl elimination are not well-established experimentally. One reason for this is that breaking C−C bonds in the presence of other reactive C−H bonds is a rare event, and systems designed to interrogate the reaction are more difficult to devise. == β-alkyl elimination == β-alkyl elimination is the most common and useful type among all β-carbon elimination reactions. === Classification/Driving force === ==== β-alkyl elimination with early transition metal complexes ==== In terms of thermodynamics, more electron-deficient metal centers increase the likelihood of β-alkyl elimination. For example, β-alkyl elimination is more favorable than β-hydride elimination when it is bonded to electron-deficient early transition metals (Hf, Ti, Zr, Nb, etc.) with d0 configuration. Computational studies show a thermodynamic preference for β-Me elimination over β-H elimination in these complexes due to additional stability for the metal–alkyl species. The origin of the additional bonding interaction comes from an orbital centered on the CH3 weakly π-donating to the LUMO of the d0 of the metal center which is analogous to the hyperconjugation effect (see figure on the right), thus increasing the stability of M−CH3 over M−H
|
{
"page_id": 60885710,
"source": null,
"title": "Β-Carbon elimination"
}
|
species. Their calculations predict that a more electrophilic metal ion enhances the −CH3 π-donation, which consequently increases the stability of M−CH3 over M−H species. Conversely, a more electron-rich metal ion will favor M−H formation (for example, using the more electron-donating Cp* ligand in Cp*2MX2). In terms of kinetics, steric effects of ligands could play a role in increasing the energy barrier of β-H elimination relative to β-alkyl elimination, specifically when the ligand is Cp*. A model was proposed to illustrate this effect: In both β-methyl elimination (A) and β-hydride elimination (B), the transferring group aligns perpendicular to the Cp*(centroid)−Zr−Cp*(centroid), allowing the σC−C or σC−H bond to overlap with the metal d-orbital. However, to achieve the prerequisite geometry for β-H elimination (B), the adjacent methyl group experiences a significant steric repulsion from the Cp* ligand, thereby elevating the barrier to hydride transfer. By contrast, transition state A for β-Me elimination experiences less steric interaction with the Cp* ligand. ==== β-alkyl elimination with middle and late transition metal complexes ==== In middle and late transition metal complexes, there is larger thermodynamic preference for β-H elimination over β-alkyl elimination, where the difference is usually >15 kcal/mol. Examples involved middle and late transition metal complexes are either absent of β-hydrogens or use ring strain relief and aromaticity as driving forces to favor β-alkyl elimination over β-hydride elimination. == Applications == === Ring-opening polymerization (ROP) === Ring-opening polymerization that involves β-alkyl elimination can be catalyzed by Ti, Zr, Pd-based catalyst, and some Lanthanide-based metallocene catalyst, where different polymerization patterns vary when catalysts are different. Examples of copolymerization with alkene or carbon monoxide were also reported. The key step of this kind of ROP is string-driven β-alkyl elimination, which provides linear polymer with unsaturation in the polymer chain. === Organic synthesis === There is enormous amount
|
{
"page_id": 60885710,
"source": null,
"title": "Β-Carbon elimination"
}
|
of catalytic processes involving β-alkyl elimination that are synthetically useful. β-alkyl elimination in this case, however, is often considered as an alternative way of C–C bond cleavage while oxidative addition is the direct way. One of the examples is β-alkyl elimination of tert-alcoholates which can generate from either addition of an organometallic reagent or ligand exchange. The consequent organometallic species can undergo various downstream reactivities (reductive elimination, carbonyl insertion, etc.) to generate useful building blocks. In addition to ring strain, aromaticity-driven β-Me elimination can be effectively employed to dealkylate steroid derivatives and some other cyclohexyl compounds. == β-aryl elimination == β-aryl elimination is much less common and understood than β-alkyl elimination. Examples are reported to occur from metal alkoxide and amido complexes. A theoretical study showed that these reactions are driven by consequent extensive conjugation system. A very recent example of catalytic β-aryl elimination which leads to enantioselective synthesis of biaryl atropisomers is driven by release of distorted ring string. == References ==
|
{
"page_id": 60885710,
"source": null,
"title": "Β-Carbon elimination"
}
|
Samarendra Nath Biswas (1 May 1926 – 4 January 2005) was an Indian theoretical physicist specialized in theoretical high energy physics, particle physics and mathematical physics and is known for his work in several diverse areas. == Life, education and career == Samarendra Nath Biswas (1 May 1926 – 4 January 2005) was born in the undivided Bengal now part of Bangladesh and had his education there till the graduate level graduating from Pabna Edward college. He obtained his DPhil degree (1951) from the University of Calcutta and PhD degree (under the supervision of Herbert S. Green) (1958) from the University of Adelaide, Australia. He worked in theoretical physics, specializing in elementary particle physics. He was a Fellow at the Tata Institute of Fundamental Research, Mumbai (1958–64). Professor of Physics, Centre for Advanced Study in Physics, Department of Physics and Astrophysics, University of Delhi (1969–91), during which he also headed the Department for a period of three years (1977-1979). He was Dean, School of Environmental Science, Jawahar Lal Nehru University, Delhi (1974–76). == Scientific research == Biswas worked in several diverse areas of theoretical high energy physics and particle physics, that includes his early work in collaboration with Herbert S. Green on the Bethe-Salpeter equation and its solution, several investigations in particle physics phenomenology, two-dimensional quantum electrodynamics, analysis of anharmonic oscillator in quantum mechanics, scattering theory, study of dispersion relations in collision processes of elementary particles based on unitarity and analyticity, geometric phases of wave function in quantum mechanics and quantum optics, equation of state of neutron stars, quark stars, weak interaction processes, weak decays involving neutral currents, processes involving stellar energy loss, supersymmetry in weak currents, chiral anomalies, super-propagator for a non-polynomial field, phase transitions in gauge theories, development of supersymmetric classical mechanics, supersymmetric quantum mechanics, stochastic quantization, quark
|
{
"page_id": 64096980,
"source": null,
"title": "Samarendra Nath Biswas"
}
|
stars, continued fraction theory, role of parastatistics in statistical mechanics, Biswas has written over 90 scientific articles, which have received a large number of citations. == Authored books == Classical Mechanics (ISBN 978-8187134183) Quantum Mechanics (ISBN 978-8187134176) == Awards and honors == Fellow, Tata Institute of Fundamental Research, Mumbai (1958–64) UGC National Lecturer (1974) Senior Associate Member of International Centre for Theoretical Physics, Trieste (1976–81) Fellow, Indian National Science Academy, New Delhi Fellow, Indian Academy of Sciences, Bangalore Fellow, National Academy of Sciences (India), Allahabad == References == == External links == Indian National Science Academy, New Delhi Profile Indian Academy of Sciences, Bengaluru, Fellow Profile Inspirehep Publications Profile Research Gate Publications Profile Former faculty, department of physics and astrophysics, University of Delhi
|
{
"page_id": 64096980,
"source": null,
"title": "Samarendra Nath Biswas"
}
|
The Sustained Spheromak Physics Experiment (SSPX) is a program at Lawrence Livermore National Laboratory in the United States established to investigate spheromak plasma. A spheromak device produces a plasma in magnetohydrodynamic equilibrium mainly through self-induced plasma currents, as opposed to a tokamak device which depends on large externally generated magnetic fields. The series of experiments examines the potential for a spheromak device to contain fusion fuel. According to a 1999 abstract, The Sustained Spheromak Physics Experiment, SSPX , will study spheromak physics with particular attention to energy confinement and magnetic fluctuations in a spheromak sustained by electrostatic helicity injection. == See also == Magnetohydrodynamics Magnetic helicity Magnetic reconnection Turbulence == References == == External links == Science@Livermore - Press release Fusion Energy Program publications The Sustained Spheromak Physics Experiment: A Short Overview at the Wayback Machine (archived September 17, 2006) Romero-Talamas, Investigations of Spheromak plasma dynamics, Ph.D. thesis Selected abstracts: Romero-Talamas, Spheromak formation and sustainment studies Wang, Large-amplitude electron density Hooper, Sustained Spheromak Physics Experiment
|
{
"page_id": 6818518,
"source": null,
"title": "Sustained Spheromak Physics Experiment"
}
|
The following is a list of parent-child pairs who were both notable for their contribution in physics. The list is in alphabetical order by the father's last name. Four parent-child pairs have been awarded the Nobel Prize in Physics: J. J. and George Paget Thomson (1906, 1937), William H. and Lawrence Bragg (1915), Niels and Aage Bohr (1922,1975), Manne and Kai Siegbahn (1924,1981). Marie and Pierre Curie won together the Nobel Prize in Physics in 1903, Marie also won the 1911 Nobel Prize in Chemistry and their daughter Irène and her husband Frédéric Joliot-Curie won together the Nobel Prize in Chemistry in 1935. == List == == See also == List of second-generation mathematicians Langevin family Curie family Bernoulli family == References ==
|
{
"page_id": 79629014,
"source": null,
"title": "List of second-generation physicists"
}
|
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