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A trans-Neptunian object ( TNO ), also written transneptunian object , [ 1 ] is any minor planet in the Solar System that orbits the Sun at a greater average distance than Neptune , which has an orbital semi-major axis of 30.1 astronomical units (AU).
Typically, TNOs are further divided into the classical and resonant objects of the Kuiper belt , the scattered disc and detached objects with the sednoids being the most distant ones. [ nb 1 ] As of February 2025, the catalog of minor planets contains 1006 numbered and more than 4000 unnumbered TNOs . [ 3 ] [ 4 ] [ 5 ] [ 6 ] [ 7 ] However, nearly 5900 objects with semimajor axis over 30 AU are present in the MPC catalog, with 1009 being numbered.
The first trans-Neptunian object to be discovered was Pluto in 1930. It took until 1992 to discover a second trans-Neptunian object orbiting the Sun directly, 15760 Albion . The most massive TNO known is Eris , followed by Pluto , Haumea , Makemake , and Gonggong . More than 80 satellites have been discovered in orbit of trans-Neptunian objects. TNOs vary in color and are either grey-blue (BB) or very red (RR). They are thought to be composed of mixtures of rock, amorphous carbon and volatile ices such as water and methane , coated with tholins and other organic compounds.
Twelve minor planets with a semi-major axis greater than 150 AU and perihelion greater than 30 AU are known, which are called extreme trans-Neptunian objects (ETNOs). [ 8 ]
The orbit of each of the planets is slightly affected by the gravitational influences of the other planets. Discrepancies in the early 1900s between the observed and expected orbits of Uranus and Neptune suggested that there were one or more additional planets beyond Neptune . The search for these led to the discovery of Pluto in February 1930, which was progressively determined to be too small to explain the discrepancies. Revised estimates of Neptune's mass from the Voyager 2 flyby in 1989 showed that there is no real discrepancy: The problem was an error in the expectations for the orbits. [ 9 ] Pluto was easiest to find because it is the brightest of all known trans-Neptunian objects. It also has a lower inclination to the ecliptic than most other large TNOs, so its position in the sky is typically closer to the search zone in the disc of the Solar System.
After Pluto's discovery, American astronomer Clyde Tombaugh continued searching for some years for similar objects but found none. For a long time, no one searched for other TNOs as it was generally believed that Pluto, which up to August 2006 was classified as a planet, was the only major object beyond Neptune. Only after the 1992 discovery of a second TNO, 15760 Albion , did systematic searches for further such objects begin. A broad strip of the sky around the ecliptic was photographed and digitally evaluated for slowly moving objects. Hundreds of TNOs were found, with diameters in the range of 50 to 2,500 kilometers. Eris , the most massive TNO, was discovered in 2005, revisiting a long-running dispute within the scientific community over the classification of large TNOs, and whether objects like Pluto can be considered planets. Pluto and Eris were eventually classified as dwarf planets by the International Astronomical Union .
According to their distance from the Sun and their orbital parameters , TNOs are classified in two large groups: the Kuiper belt objects (KBOs) and the scattered disc objects (SDOs). [ nb 1 ] The diagram to the right illustrates the distribution of known trans-Neptunian objects (up to 70 au) in relation to the orbits of the planets and the centaurs for reference. Different classes are represented in different colours. Resonant objects (including Neptune trojans ) are plotted in red, classical Kuiper belt objects in blue. The scattered disc extends to the right, far beyond the diagram, with known objects at mean distances beyond 500 au ( Sedna ) and aphelia beyond 1,000 ( (87269) 2000 OO 67 ).
The Edgeworth– Kuiper belt contains objects with an average distance to the Sun of 30 to about 55 au, usually having close-to-circular orbits with a small inclination from the ecliptic . Edgeworth–Kuiper belt objects are further classified into the resonant trans-Neptunian object that are locked in an orbital resonance with Neptune , and the classical Kuiper belt objects , also called "cubewanos", that have no such resonance, moving on almost circular orbits, unperturbed by Neptune. There are a large number of resonant subgroups, the largest being the twotinos (1:2 resonance) and the plutinos (2:3 resonance), named after their most prominent member, Pluto . Members of the classical Edgeworth–Kuiper belt include 15760 Albion , Quaoar and Makemake .
Another subclass of Kuiper belt objects is the so-called scattering objects (SO). These are non-resonant objects that come near enough to Neptune to have their orbits changed from time to time (such as causing changes in semi-major axis of at least 1.5 AU in 10 million years) and are thus undergoing gravitational scattering . Scattering objects are easier to detect than other trans-Neptunian objects of the same size because they come nearer to Earth, some having perihelia around 20 AU. Several are known with g-band absolute magnitude below 9, meaning that the estimated diameter is more than 100 km. It is estimated that there are between 240,000 and 830,000 scattering objects bigger than r-band absolute magnitude 12, corresponding to diameters greater than about 18 km. Scattering objects are hypothesized to be the source of the so-called Jupiter-family comets (JFCs), which have periods of less than 20 years. [ 10 ] [ 11 ] [ 12 ]
The scattered disc contains objects farther from the Sun, with very eccentric and inclined orbits. These orbits are non-resonant and non-planetary-orbit-crossing. A typical example is the most-massive-known TNO, Eris . Based on the Tisserand parameter relative to Neptune (T N ), the objects in the scattered disc can be further divided into the "typical" scattered disc objects (SDOs, Scattered-near) with a T N of less than 3, and into the detached objects (ESDOs, Scattered-extended) with a T N greater than 3. In addition, detached objects have a time-averaged eccentricity greater than 0.2 [ 13 ] The Sednoids are a further extreme sub-grouping of the detached objects with perihelia so distant that it is confirmed that their orbits cannot be explained by perturbations from the giant planets , [ 14 ] nor by interaction with the galactic tides . [ 15 ] However, a passing star could have moved them on their orbit. [ 16 ]
Given the apparent magnitude (>20) of all but the biggest trans-Neptunian objects, the physical studies are limited to the following:
Studying colours and spectra provides insight into the objects' origin and a potential correlation with other classes of objects, namely centaurs and some satellites of giant planets ( Triton , Phoebe ), suspected to originate in the Kuiper belt . However, the interpretations are typically ambiguous as the spectra can fit more than one model of the surface composition and depend on the unknown particle size. More significantly, the optical surfaces of small bodies are subject to modification by intense radiation, solar wind and micrometeorites . Consequently, the thin optical surface layer could be quite different from the regolith underneath, and not representative of the bulk composition of the body.
Small TNOs are thought to be low-density mixtures of rock and ice with some organic ( carbon -containing) surface material such as tholins , detected in their spectra. On the other hand, the high density of Haumea , 2.6–3.3 g/cm 3 , suggests a very high non-ice content (compare with Pluto 's density: 1.86 g/cm 3 ). The composition of some small TNOs could be similar to that of comets . Indeed, some centaurs undergo seasonal changes when they approach the Sun, making the boundary blurred (see 2060 Chiron and 7968 Elst–Pizarro ) . However, population comparisons between centaurs and TNOs are still controversial. [ 17 ]
Colour indices are simple measures of the differences in the apparent magnitude of an object seen through blue (B), visible (V), i.e. green-yellow, and red (R) filters. The diagram illustrates known colour indices for all but the biggest objects (in slightly enhanced colour). [ 18 ] For reference, two moons, Triton and Phoebe , the centaur Pholus and the planet Mars are plotted (yellow labels, size not to scale) . Correlations between the colours and the orbital characteristics have been studied, to confirm theories of different origin of the different dynamic classes:
While the relatively dimmer bodies, as well as the population as the whole, are reddish (V−I = 0.3–0.6), the bigger objects are often more neutral in colour (infrared index V−I < 0.2). This distinction leads to suggestion that the surface of the largest bodies is covered with ices, hiding the redder, darker areas underneath. [ 21 ]
Among TNOs, as among centaurs , there is a wide range of colors from blue-grey (neutral) to very red, but unlike the centaurs, bimodally grouped into grey and red centaurs, the distribution for TNOs appears to be uniform. [ 17 ] The wide range of spectra differ in reflectivity in visible red and near infrared. Neutral objects present a flat spectrum, reflecting as much red and infrared as visible spectrum. [ 23 ] Very red objects present a steep slope, reflecting much more in red and infrared.
A recent attempt at classification (common with centaurs) uses the total of four classes from BB (blue, or neutral color, average B−V = 0.70, V−R = 0.39, e.g. Orcus ) to RR (very red, B−V = 1.08, V−R = 0.71, e.g. Sedna ) with BR and IR as intermediate classes. BR (intermediate blue-red) and IR (moderately red) differ mostly in the infrared bands I, J and H .
Typical models of the surface include water ice, amorphous carbon , silicates and organic macromolecules, named tholins , created by intense radiation. Four major tholins are used to fit the reddening slope:
As an illustration of the two extreme classes BB and RR, the following compositions have been suggested
Characteristically, big (bright) objects are typically on inclined orbits, whereas the invariable plane regroups mostly small and dim objects. [ 21 ]
It is difficult to estimate the diameter of TNOs. For very large objects, with very well known orbital elements (like Pluto), diameters can be precisely measured by occultation of stars. For other large TNOs, diameters can be estimated by thermal measurements. The intensity of light illuminating the object is known (from its distance to the Sun), and one assumes that most of its surface is in thermal equilibrium (usually not a bad assumption for an airless body). For a known albedo , it is possible to estimate the surface temperature, and correspondingly the intensity of heat radiation. Further, if the size of the object is known, it is possible to predict both the amount of visible light and emitted heat radiation reaching Earth. A simplifying factor is that the Sun emits almost all of its energy in visible light and at nearby frequencies, while at the cold temperatures of TNOs, the heat radiation is emitted at completely different wavelengths (the far infrared).
Thus there are two unknowns (albedo and size), which can be determined by two independent measurements (of the amount of reflected light and emitted infrared heat radiation). TNOs are so far from the Sun that they are very cold, hence producing black-body radiation around 60 micrometres in wavelength . This wavelength of light is impossible to observe from the Earth's surface, but can be observed from space using, e.g. the Spitzer Space Telescope . For ground-based observations, astronomers observe the tail of the black-body radiation in the far infrared. This far infrared radiation is so dim that the thermal method is only applicable to the largest KBOs. For the majority of (small) objects, the diameter is estimated by assuming an albedo. However, the albedos found range from 0.50 down to 0.05, resulting in a size range of 1,200–3,700 km for an object of magnitude of 1.0. [ 24 ]
The only mission to date that primarily targeted a trans-Neptunian object was NASA's New Horizons , which was launched in January 2006 and flew by the Pluto system in July 2015 [ 32 ] and 486958 Arrokoth in January 2019. [ 33 ]
In 2011, a design study explored a spacecraft survey of Quaoar, Sedna, Makemake, Haumea, and Eris. [ 34 ]
In 2019 one mission to TNOs included designs for orbital capture and multi-target scenarios. [ 35 ] [ 36 ]
Some TNOs that were studied in a design study paper were 2002 UX 25 , 1998 WW 31 , and Lempo . [ 36 ]
The existence of planets beyond Neptune , ranging from less than an Earth mass ( Sub-Earth ) up to a brown dwarf has been often postulated [ 37 ] [ 38 ] for different theoretical reasons to explain several observed or speculated features of the Kuiper belt and the Oort cloud . It was recently proposed to use ranging data from the New Horizons spacecraft to constrain the position of such a hypothesized body. [ 39 ]
NASA has been working towards a dedicated Interstellar Precursor in the 21st century, one intentionally designed to reach the interstellar medium, and as part of this the flyby of objects like Sedna are also considered. [ 40 ] Overall this type of spacecraft studies have proposed a launch in the 2020s, and would try to go a little faster than the Voyagers using existing technology. [ 40 ] One 2018 design study for an Interstellar Precursor, included a visit of minor planet 50000 Quaoar, in the 2030s. [ 41 ]
Among the extreme trans-Neptunian objects are three high-perihelion objects classified as sednoids : 90377 Sedna , 2012 VP 113 , and 541132 Leleākūhonua . They are distant detached objects with perihelia greater than 70 AU. Their high perihelia keep them at a sufficient distance to avoid significant gravitational perturbations from Neptune. Previous explanations for the high perihelion of Sedna include a close encounter with an unknown planet on a distant orbit and a distant encounter with a random star or a member of the Sun's birth cluster that passed near the Solar System. [ 42 ] [ 43 ] [ 44 ]
Solar System → Local Interstellar Cloud → Local Bubble → Gould Belt → Orion Arm → Milky Way → Milky Way subgroup → Local Group → Local Sheet → Virgo Supercluster → Laniakea Supercluster → Local Hole → Observable universe → Universe Each arrow ( → ) may be read as "within" or "part of". | https://en.wikipedia.org/wiki/Trans-Neptunian_object |
The Trans-Proteomic Pipeline ( TPP ) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group under the Seattle Proteome Center. The TPP includes PeptideProphet, [ 2 ] ProteinProphet, [ 3 ] ASAPRatio, XPRESS and Libra.
PeptideProphet performs statistical validation of peptide-spectra-matches (PSM) using the results of search engines by estimating a false discovery rate (FDR) on PSM level. [ 4 ] The initial PeptideProphet used a fit of a Gaussian distribution for the correct identifications and a fit of a gamma distribution for the incorrect identification. A later modification of the program allowed the usage of a target-decoy approach, using either a variable component mixture model or a semi-parametric mixture model. [ 5 ] In the PeptideProphet, specifying a decoy tag will use the variable component mixture model while selecting a non-parametric model will use the semi-parametric mixture model.
ProteinProphet identifies proteins based on the results of PeptideProphet. [ 6 ]
Mayu performs statistical validation of protein identification by estimating a false discovery rate (FDR) on protein level. [ 7 ]
The SpectraST tool is able to generate spectral libraries and search datasets using these libraries. [ 8 ] | https://en.wikipedia.org/wiki/Trans-Proteomic_Pipeline |
Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) is a transcriptomic technique that, like SAGE , allows for the digital detection of messenger RNA sequences. Unlike SAGE, detection and purification of transcripts from the 5’ end of the messenger RNA require the presence of a trans-spliced leader sequence.
Spliced leader sequences are short sequences of non coding RNA , not found within a gene itself, that are attached to the 5’ end of all, or a portion of, mRNAs transcribed in an organism. They have been found in several species to be responsible for separating polycistronic transcripts into single gene mRNAs , and in others to splice onto monocistronic transcripts. [ 1 ] The major role of trans-splicing on monocistronic transcripts is largely unknown. [ 2 ] It has been proposed that they may act as an independent promoter that aids in tissue specific expression of independent protein isoforms. [ 3 ] Spliced leaders have been seen in trypanosomatids, Euglena , flatworms, Caenorhabditis . [ 1 ] [ 4 ] Some species contain only one spliced leader sequence found on all mRNAs. In C. elegans two are seen and are labeled SL1 and SL2 . [ 5 ]
Total RNA is purified from the specimen of interest. Poly A messenger RNA is then purified from total RNA and subsequently translated into cDNA using a reverse transcription reaction. The cDNA produced from the mRNA is labeled using primers homologous to the spliced leader sequences of the organism. In a nine step PCR reaction the cDNAs are concurrently embedded with the BpmI restriction endonuclease site (though any class IIs restriction endonuclease may work) and a biotin label which are present in the primers. These tagged cDNAs are then cleaved 14 bp downstream from the recognition site using BpmI restriction endonuclease and blunt ended with T4 DNA polymerase. The fragments are further purified away from extraneous DNA material by using the biotin labels to bind them to a strepdavidin matrix. They are then ligated to adapter DNA, in six separate reactions, containing six different restriction endonuclease recognition sites. These tags are then amplified by PCR with primers containing a mismatch changing the Bpm1 site to a Xho1 site. The amplicons are concatenated and ligated into a plasmid vector . The clonal vectors are then sequenced and mapped to the genome. [ 6 ]
Concatenation of the tags, as developed in 2004, is different from that seen in SAGE. The cleavage of the tags with Xho1 and mixture of the different samples, followed by ligation, form the first concatenation step. The second step uses one of the restriction endonucleases with consensus to the adapter molecule attached to the 3’ end. They are again ligated, and PCR is performed to purify samples for the next joining. The concatenation is continued with the second restriction endonuclease, followed by the third and finally the fourth. This results in the concatamer formed by the six endonuclease ligations containing 32 tags, arranged 5’ to 5’ around the Xho1 site. [ 6 ] In SAGE, concatenation takes place after ditags are formed and amplified by PCR. The linkers on the outside of the ditags are cleaved with the enzyme that provided their binding and these sticky end ditags are concatenated randomly and placed into a cloning vector. [ 7 ]
The advantage of TEC-RED over SAGE is that no restriction endonuclease is needed for the initial linker binding. This prevents bias associated with restriction site sequences that will be missing from some genes, as is seen in SAGE. The ability to have a snapshot of specific RNA isoforms allows the deduction of differential regulation of isoforms through alternative selection of promoters. [ 8 ] This may also aid in the discernment of expression patterns unique to the SL1 or SL2 sequence. TEC-RED also allows characterization of the 5’ ends of RNA produced and therefore of isoforms that differ by the amino terminal splicing. The technology permits the determination and verification of all known and unknown genes that may be predicted as well as the 5’ splice isoforms or 5’ RNA ends that may be produced. Using TEC-RED in conjunction with SAGE or a modified protocol will allow discernment of the 5’ and 3’ ends of transcripts, respectively. The identification of alternative splice variants, and possibly the relative quantities, containing a trans-spliced leader sequence is therefore possible.
Two alternate techniques have been described that allow for 5’ tag analysis in organisms that do not have trans-spliced leader sequences. The techniques presented by Toshiyuki et al. and Shin-ichi et al. are called CAGE and 5’ SAGE respectively. CAGE utilizes biotinylated cap-trapper technology to maintain mRNA signal long enough to create and select full length cDNAs , which have adapter sequences ligated on the 5‘ end. 5’ SAGE utilizes oligo-capping technology. [ 9 ] Both use their adapter sequence to prime from after the cDNA is created. Both of these methods have disadvantages though. CAGE has shown tags with addition of a guanine on the first position and oligo-capping may lead to sequence bias due to the use of RNA ligase. [ 10 ] | https://en.wikipedia.org/wiki/Trans-Spliced_Exon_Coupled_RNA_End_Determination |
In the field of molecular biology , trans -acting ( trans -regulatory, trans -regulation), in general, means "acting from a different molecule" ( i.e. , intermolecular ). It may be considered the opposite of cis -acting ( cis -regulatory, cis -regulation), which, in general, means "acting from the same molecule" ( i.e. , intramolecular ).
In the context of transcription regulation, a trans -acting factor is usually a regulatory protein that binds to DNA . [ 1 ] The binding of a trans -acting factor to a cis -regulatory element in DNA can cause changes in transcriptional expression levels. microRNAs or other diffusible molecules are also examples of trans -acting factors that can regulate target sequences. [ 2 ] The trans -acting gene may be on a different chromosome to the target gene, but the activity is via the intermediary protein or RNA that it encodes. Cis -acting elements, on the other hand, do not code for protein or RNA. Both the trans -acting gene and the protein/RNA that it encodes are said to "act in trans " on the target gene.
Transcription factors are categorized as trans-acting factors.
This biochemistry article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Trans-acting |
Trans-endocytosis is the biological process where material created in one cell undergoes endocytosis (enters) into another cell. If the material is large enough, this can be observed using an electron microscope . [ 1 ] Trans-endocytosis from neurons to glia has been observed using time-lapse microscopy . [ 2 ]
Trans-endocytosis also applies to molecules . For example, this process is involved when a part of the protein Notch is cleaved off and undergoes endocytosis into its neighboring cell. [ 3 ] [ 4 ] Without Notch trans-endocytosis, there would be too many neurons in a developing embryo . [ 5 ] Trans-endocytosis is also involved in cell movement when the protein ephrin is bound by its receptor from a neighboring cell. [ 6 ]
This cell biology article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Trans-endocytosis |
Trans-regulatory elements (TRE) are DNA sequences encoding upstream regulators (ie. trans-acting factors ), which may modify or regulate the expression of distant genes. [ 1 ] Trans-acting factors interact with cis-regulatory elements to regulate gene expression. [ 2 ] TRE mediates expression profiles of a large number of genes via trans-acting factors. [ 3 ] While TRE mutations affect gene expression, it is also one of the main driving factors for evolutionary divergence in gene expression. [ 3 ]
Trans-regulatory elements work through an intermolecular interaction between two different molecules and so are said to be " acting in trans ". For example (1) a transcribed and translated transcription factor protein derived from the trans-regulatory element; and a (2) DNA regulatory element that is adjacent to the regulated gene. This is in contrast to cis-regulatory elements that work through an intramolecular interaction between different parts of the same molecule: (1) a gene; and (2) an adjacent regulatory element for that gene in the same DNA molecule. Additionally, each trans-regulatory element affects a large number of genes on both alleles, [ 2 ] while cis-regulatory element is allele specific [ 1 ] [ 2 ] and only controls genes nearby.
Exonic and promoter sequences of the genes are significantly more conserved than the genes in cis- and trans- regulatory elements. [ 3 ] Hence, they have higher resistance to genetic divergence, yet retains its susceptibility to mutations in upstream regulators. [ 3 ] This accentuates the significance of genetic divergence within species due to cis- and trans-regulatory variants.
Trans- and cis-regulatory elements co-evolved rapidly in large-scale to maintain gene expression. [ 2 ] [ 3 ] [ 4 ] They often act in opposite directions, one up-regulates while another down-regulates, to compensate for their effects on the exonic and promoter sequences they act on. [ 2 ] [ 3 ] Other evolutionary models, such as the independent evolution of trans- or cis-regulatory elements, were deemed incompatible in regulatory systems. [ 3 ] [ 5 ] Co-evolution of the two regulatory elements was suggested to arise from the same lineage. [ 3 ] [ 4 ]
TRE is more evolutionary constraint than cis-regulatory element, suggesting a hypothesis that TRE mutations are corrected by CRE mutations [ 3 ] to maintain stability in gene expression. This makes biological sense, due to TRE's effect on a broad range of genes and CRE's compensatory effect on specific genes. [ 1 ] [ 2 ] Following a TRE mutation, accumulation of CRE mutations act to fine-tune the mutative effect. [ 3 ]
Trans-acting factors can be categorized by their interactions with the regulated genes, cis-acting elements of the genes, or the gene products.
DNA binding trans-acting factors regulate gene expression by interfering with the gene itself or cis-acting elements of the gene, which lead to changes in transcription activities. This can be direct initiation of transcription, [ 6 ] promotion, or repression of transcriptional protein activities. [ 7 ]
Specific examples include:
DNA editing proteins edit and permanently change gene sequence, and subsequently the gene expression of the cell. [ 8 ] [ 9 ] All progenies of the cell will inherit the edited gene sequence. [ 10 ] DNA editing proteins often take part in the immune response system of both prokaryotes and eukaryotes, providing high variance in gene expression in adaptation to various pathogens. [ 11 ]
Specific examples include:
mRNA processing acts as a form of post-transcriptional regulation, which mostly happens in eukaryotes. 3′ cleavage/polyadenylation and 5’ capping increase overall RNA stability, and the presence of 5’ cap allows ribosome binding for translation. RNA splicing allows the expression of various protein variants from the same gene. [ 12 ]
Specific examples include:
mRNA binding allows repression of protein translation through direct blocking, degradation or cleavage of mRNA. [ 13 ] [ 14 ] Certain mRNA binding mechanisms have high specificity, which can act as a form of the intrinsic immune response during certain viral infections. [ 15 ] Certain segmented RNA viruses can also regulate viral gene expression through RNA binding of another genome segment, however, the details of this mechanism are still unclear. [ 16 ]
Specific examples include:
This genetics article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Trans-regulatory_element |
Trans-spanning ligands are bidentate ligands that can span opposite sites of a complex with square-planar geometry. A wide variety of ligands that chelate in the cis fashion already exist, but very few can link opposite vertices on a coordination polyhedron. Early attempts to generate trans-spanning bidentate ligands relied on long hydrocarbon chains to link the donor functionalities, but such ligands often lead to coordination polymers .
A diphosphane linked with pentamethylene was claimed to span across a square planar complex . This early attempt was followed by ligands with more rigid backbones. "TRANSPHOS" was the first trans-spanning diphosphane ligand that usually coordinates to palladium(II) and platinum(II) in a trans manner. TRANSPHOS features benzo[c]phenanthrene substituted by diphenylphosphinomethyl (Ph 2 PCH 2 ) groups at the 1 and 11 positions. [ 1 ] [ 2 ] The polycyclic framework suffers sterically clashing hydrogen centers.
TRANSDIP, based on a α- cyclodextrin , is the first ligand to give exclusively trans-spanned complexes, even with d 8 metal ion halides. [ 4 ] Xantphos is sometimes classified as a trans-spanning ligand, with less steric bulk compared to TRANSPHOS. SPANphos is comparable to XANTPHOS but more reliably trans-spanning. | https://en.wikipedia.org/wiki/Trans-spanning_ligand |
In inorganic chemistry , the trans effect is the increased lability of ligands that are trans to certain other ligands, which can thus be regarded as trans-directing ligands. It is attributed to electronic effects and it is most notable in square planar complexes , although it can also be observed for octahedral complexes. [ 1 ] The analogous cis effect is most often observed in octahedral transition metal complexes.
In addition to this kinetic trans effect , trans ligands also have an influence on the ground state of the molecule, the most notable ones being bond lengths and stability. Some authors prefer the term trans influence to distinguish it from the kinetic effect, [ 2 ] while others use more specific terms such as structural trans effect or thermodynamic trans effect . [ 1 ]
The discovery of the trans effect is attributed to Ilya Ilich Chernyaev , [ 3 ] who recognized it and gave it a name in 1926. [ 4 ]
The intensity of the trans effect (as measured by the increase in rate of substitution of the trans ligand) follows this sequence:
One classic example of the trans effect is the synthesis of cisplatin and its trans isomer . [ 5 ] The complex PtCl 4 2− reacts with ammonia to give [PtCl 3 NH 3 ] − . A second substitution by ammonia gives cis-[PtCl 2 (NH 3 ) 2 ], showing that Cl- has a greater trans effect than NH 3 . The procedure is however complicated by the production of Magnus's green salt . [ 6 ] As a result, cisplatin is produced commercially via [PtI 4 ] 2− as first reported by Dhara in 1970. [ 7 ]
If, on the other hand, one starts from Pt(NH 3 ) 4 2+ , the trans product is obtained instead:
The trans effect in square complexes can be explained in terms of an addition/elimination mechanism that goes through a trigonal bipyramidal intermediate. Ligands with a high trans effect are in general those with high π acidity (as in the case of phosphines) or low-ligand lone-pair–d π repulsions (as in the case of hydride), which prefer the more π-basic equatorial sites in the intermediate. The second equatorial position is occupied by the incoming ligand; due to the principle of microscopic reversibility , the departing ligand must also leave from an equatorial position. The third and final equatorial site is occupied by the trans ligand, so the net result is that the kinetically favored product is the one in which the ligand trans to the one with the largest trans effect is eliminated. [ 2 ]
The structural trans effect can be measured experimentally using X-ray crystallography , and is observed as a stretching of the bonds between the metal and the ligand trans to a trans-influencing ligand. Stretching by as much as 0.2 Å occurs with strong trans-influencing ligands such as hydride. A cis influence can also be observed, but is smaller than the trans influence. The relative importance of the cis and trans influences depends on the formal electron configuration of the metal center, and explanations have been proposed based on the involvement of the atomic orbitals. [ 8 ] | https://en.wikipedia.org/wiki/Trans_effect |
Trans fat is a type of unsaturated fat that occurs in foods. [ 1 ] [ 2 ] Small amounts of trans fats occur naturally, but large amounts are found in some processed foods made with partially hydrogenated oils. [ 1 ] [ 2 ] Because consumption of trans fats is associated with increased risk for cardiovascular diseases , artificial trans fats are highly regulated or banned in many countries. [ 3 ] [ 4 ] [ 5 ] [ 6 ] [ 7 ] However, they are still widely consumed in developing nations where they are associated with increased risk of diabetes , cardiovascular diseases, and death. [ 8 ]
In 2015, the US Food and Drug Administration (FDA) stated that artificial trans fats from partially hydrogenated oils were not generally recognized as safe (GRAS), and the use of such oils and trans fats should be limited or eliminated from manufactured foods. [ 2 ] Numerous governing bodies, including the European Union , Canada, and Australia/New Zealand, followed with restrictions or bans on the use of partially hydrogenated oils and trans fats in food manufacturing. [ 1 ] [ 9 ] The World Health Organization (WHO) had set a goal to make the world free from industrially produced trans fat by the end of 2023. [ 10 ] The goal was not met, and the WHO announced another goal in 2024 "for accelerated action until 2025 to complete this effort". [ 7 ]
Trans fatty acids (also called trans-unsaturated fatty acids ) are derived from trans fats, which are triglycerides ( esters of glycerin). Trans fats are converted to trans fatty acids in the digestive tract prior to absorption.
Trans fats occur naturally in the fats of products made from ruminant animals, such as cheese or butter. Some trans fats are the result of food processing, especially when applied to cooking oils and margarine .
Trans fats occur in meat and dairy products from ruminants. For example, butter contains about 3% trans fat by weight. [ 11 ] These naturally occurring trans fats include conjugated linoleic acid (CLA) and vaccenic acid . They arise from the action of bacteria in the rumen. Polyunsaturated fats are toxic to the rumen-based bacteria, which detoxify the fats by changing some cis-double bonds to trans-double bonds. In contrast to industrially produced trans fats, this bacterial process produces only a few specific isomers. As industrial sources of trans fats are eliminated, increased attention focuses on ruminant derived trans fats. [ 12 ]
Small amounts of trans fats occur in meat and milk fat . [ 13 ]
Trans fat can be an unintentional byproduct of the industrial processing of oils. Unlike naturally derived trans fats, the trans fats that result from hydrogenation consist of many isomers. In food production, liquid cis-unsaturated fats such as vegetable oils are hydrogenated to produce more saturated fats, which have desirable properties:
However, an isomerization side reaction during fat hydrogenation can convert remaining unsaturated fats to the thermodynamically-favored trans isomer.
A number of old and new ingredients are available to replace partially-hydrogenated oil containing significant levels of trans fat. These include partially-hydrogenated oil made with improved processes, plant oils rich in monounsaturated fats and saturated fats , and a mix of fats combined with interesterification . [ 14 ] The technology has improved such that a 2021 review indicates that trans fat from hydrogenated fats is no longer a problem in modern countries. [ 12 ]
When heated (cooked), some unsaturated fats change from their normal geometry to trans. The rate of isomerization is accelerated by free radicals. [ 15 ] [ 16 ] [ 17 ]
There were suggestions in the scientific literature as early as 1956 that trans fats could cause an increase in coronary artery disease . [ 18 ] Studies in the early 1990s brought renewed scrutiny and confirmation of the negative health impact of trans fats. In 1994, it was estimated that trans fats caused at least 20,000 deaths annually in the U.S. from heart disease. [ 19 ] In the 1990s, activists such as the Center for Science in the Public Interest (CSPI) that had promoted trans fat safety began arguing that trans fats should be disclosed on product labels and menus. [ 21 ] Several lawsuits were launched against high-visibility restaurants and food manufacturers with the objective of supporting a broader phase-out of trans fats. [ 22 ] [ 23 ]
Mandatory food labeling was introduced in several countries [ 24 ] and Denmark was first to mandate limits on industrially-produced trans fats in 2004. [ 25 ] In January 2007, faced with the prospect of an outright ban on the sale of their product, Crisco was reformulated to meet the U.S. Food and Drug Administration (FDA) definition of "zero grams trans fats per serving" (that is less than one gram per tablespoon, or up to 7% by weight; or less than 0.5 grams per serving size) [ 26 ] [ 27 ] [ 28 ] [ 29 ] by boosting the saturation and then diluting the resulting solid fat with unsaturated vegetable oils. Noting that elimination of industrially produced trans fat is feasible and achievable, the World Health Organization (WHO) has set a goal to make the world free from industrially produced trans fat by the end of 2023. By the end of 2021, the WHO announced that 40 countries had implemented industrial trans fat elimination policies that "are protecting 1.4 billion people from this deadly food compound" but that 10 of the 15 countries suffering the highest health impacts from trans fats had not yet adopted a policy. [ 10 ]
A fatty acid is characterized as either saturated or unsaturated based on the respective absence or presence of C=C double bonds in its backbone. If the molecule contains no double C=C bonds, it is said to be saturated; otherwise, it is unsaturated to some degree. [ 30 ] [ 31 ]
The C=C double bond is rotationally rigid. If the hydrogen bonded to each of the carbons in this double bond are on the same side, this is called cis , and leads to a bent molecular chain. If the two hydrogens are on opposite sides, this is called trans , and leads to a straight chain.
Because trans fats are more linear, they crystallize more easily, allowing them to be solid (rather than liquid) at room temperatures. This has several processing and storage advantages.
In nature, unsaturated fatty acids generally have cis configurations as opposed to trans configurations. [ 34 ] Saturated fatty acids (those without any carbon-carbon double bonds ) are abundant (see tallow ), but they also can be generated from unsaturated fats by the process of fat hydrogenation . In the course of hydrogenation, some cis double bonds convert into trans double bonds. Chemists call this conversion an isomerization reaction . [ 16 ] [ 17 ] [ 35 ]
Any molecule with a C=C double bond can be either a trans or a cis fatty acid depending on the configuration of the double bond. For example, oleic acid and elaidic acid are both unsaturated fatty acids with the chemical formula C 9 H 17 C 9 H 17 O 2 . [ 36 ] They both have a double bond located midway along the carbon chain. It is the geometry of this bond that sets oleic and elaidic acids apart. They have distinct physical-chemical properties of the molecule. For example, the melting point of elaidic acid is 45 °C higher than that of oleic acid. [ 36 ] This notably means that it is a solid at human body temperatures.
The hydrogenation process was widely adopted by the food industry in the early 1900s; first for the production of margarine , a replacement for butter and shortening, [ 37 ] and eventually for various other fats used in snack food, packaged baked goods, and deep fried products. [ 17 ]
Full hydrogenation of a fat or oil produces a fully saturated fat. For food purposes, hydrogenation generally is not allowed to go to completion. The main target is a specific melting point and hardness, and this fine-tuning requires that some unsaturation (C=C bonds) remain. This partial hydrogenation turns some of the cis double bonds into trans bonds by an isomerization reaction . [ 17 ] [ 38 ] This side reaction accounts for most of the trans fatty acids consumed today, by far. [ 39 ] [ 40 ]
The standard 140 kPa (20 psi) process of hydrogenation produces a product of about 40% trans fatty acid by weight, compared to about 17% using higher pressures of hydrogen. Blended with unhydrogenated liquid soybean oil, the high-pressure-processed oil produced margarine containing 5 to 6% trans fat. Based on current U.S. labeling requirements (see below), the manufacturer could claim the product was free of trans fat. [ 41 ] The level of trans fat may also be altered by modification of the temperature and the length of time during hydrogenation.
The trans fat levels can be quantified using various forms of chromatography . [ 15 ]
Trans fatty acids (TFAs) occur in small amounts in meat and milk of ruminants (such as cattle and sheep), [ 13 ] [ 45 ] typically 2–5% of total fat. [ 46 ] Natural TFAs, which include conjugated linoleic acid (CLA) and vaccenic acid, originate in the rumen of these animals. CLA has two double bonds, one in the cis configuration and one in trans , which makes it simultaneously a cis - and a trans -fatty acid. [ 47 ] A type of trans fat occurs naturally in the milk and body fat of ruminants (such as cattle and sheep) at a level of 2–5% of total fat. [ 44 ]
The US National Dairy Council has asserted that the trans fats present in foods of animal origin are of a different type than those in partially hydrogenated oils, and do not appear to exhibit the same negative effects. [ 48 ] A scientific review agrees with the conclusion (stating that "the sum of the current evidence suggests that the Public health implications of consuming trans fats from ruminant products are relatively limited") but cautions that this may be due to the low consumption of trans fats from animal sources compared to artificial ones. [ 43 ]
Despite this concern, the NAS dietary recommendations have not included eliminating trans fat from the diet. This is because trans fat is naturally present in many animal foods in trace quantities, and thus its removal from ordinary diets might introduce undesirable side effects and nutritional imbalances if proper nutritional planning is not undertaken. The NAS has, thus, "recommended that trans fatty acid consumption be as low as possible while consuming a nutritionally adequate diet". [ 49 ] Like the NAS, the World Health Organization has tried to balance public health goals with a practical level of trans fat consumption, recommending in 2003 that trans fats be limited to less than 1% of overall energy intake. [ 44 ]
A meta-analysis showed that all trans fats, regardless of natural or artificial origin equally raise LDL and lower HDL levels. [ 6 ] Other studies though have shown different results when it comes to animal based trans fats like conjugated linoleic acid (CLA). Although CLA is known for its anticancer properties, researchers have also found that the cis-9, trans-11 form of CLA can reduce the risk for cardiovascular disease and help fight inflammation. [ 50 ] [ 51 ]
Some trans fatty acids occur in natural fats and traditionally processed foods. Vaccenic acid occurs in breast milk, and some isomers of conjugated linoleic acid (CLA) are found in meat and dairy products from ruminants. Butter, for example, contains about 3% trans fat. [ 52 ]
Partially hydrogenated vegetable oils were an increasingly significant part of the human diet for about 100 years, especially after 1950 as processed food rose in popularity. [ 40 ]
Animal-based fats were once the only trans fats consumed, but by far the largest amount of trans fat consumed today is created by the processed food industry as a side effect of partially hydrogenating unsaturated plant fats (generally vegetable oils). These partially hydrogenated fats have displaced natural solid fats and liquid oils in many areas, the most notable ones being in the fast food, snack food , fried food, and baked goods industries. [ 53 ]
Up to 45% of the total fat in those foods containing human-made trans fats formed by partially hydrogenating plant fats may be trans fat. [ 44 ] [ 46 ] An analysis of some industrialized foods in 2006 found up to 30% "trans fats" in artificial shortening, 10% in breads and cake products, 8% in cookies and crackers, 4% in salty snacks, 7% in cake frostings and sweets, and 26% in margarine and other processed spreads. [ 42 ] Another 2010 analysis however found only 0.2% of trans fats in margarine and other processed spreads. [ 54 ]
Foods containing higher amounts of trans fat is associated with fast food restaurants. [ 40 ] They are consumed in greater quantities by people who lack access to a diet consisting of fewer partially-hydrogenated fats, or who often consume fast food. A diet high in trans fats can contribute to obesity, high blood pressure, and higher risk for heart disease. Trans fat is also implicated in Type 2 diabetes. [ 55 ]
Shortenings, because they are widely used, are of particular concern. Baking shortenings, unless reformulated, contain around 30% trans fats compared to their total fats. High-fat dairy products such as butter contain about 4%. Margarines not reformulated to reduce trans fats may contain up to 15% trans fat by weight, [ 56 ] but some reformulated ones are less than 1% trans fat. Shortenings for deep-frying in restaurants can be used for longer than most conventional oils before becoming rancid. In the early 21st century, non-hydrogenated vegetable oils that have lifespans exceeding that of the frying shortenings became available. [ 57 ] In fast-food chains, trans fat levels in fast food can vary with location. For example, an analysis of samples of McDonald's French fries collected in 2004 and 2005 found that fries served in New York City contained twice as much trans fat as in Hungary , and 28 times as much as in Denmark , where trans fats are restricted. At KFC , the pattern was reversed, with Hungary's product containing twice the trans fat of the New York product. Even within the U.S. there was variation, with fries in New York containing 30% more trans fat than those from Atlanta . [ 58 ]
High levels of TFAs have been recorded in popular "fast food" meals. [ 40 ] An analysis of samples of McDonald's French fries collected in 2004 and 2005 found that fries served in New York City contained twice as much trans fat as in Hungary , and 28 times as much as in Denmark , where trans fats are restricted. For Kentucky Fried Chicken products, the pattern was reversed: the Hungarian product containing twice the trans fat of the New York product. Even within the United States, there was variation, with fries in New York containing 30% more trans fat than those from Atlanta . [ 59 ]
It has been established that trans fats in human breast milk fluctuate with maternal consumption of trans fat, and that the amount of trans fats in the bloodstream of breastfed infants fluctuates with the amounts found in their milk. In 1999, reported percentages of trans fats (compared to total fats) in human milk ranged from 1% in Spain, 2% in France, 4% in Germany, and 7% in Canada and the U.S. [ 60 ]
In the last few decades, there has been substantial amount of regulation in many countries, limiting trans fat contents of industrialized and commercial food products.
In light of recognized evidence and scientific agreement, nutritional authorities consider all trans fats equally harmful for health and recommend that their consumption be reduced to trace amounts. [ 1 ] [ 2 ] [ 4 ] [ 5 ] [ 9 ] In 2003, the WHO recommended that trans fats make up no more than 0.9% of a person's diet [ 46 ] and, in 2018, introduced a 6-step guide to eliminate industrially-produced trans-fatty acids from the global food supply. [ 61 ]
The National Academy of Sciences (NAS) advises the U.S. and Canadian governments on nutritional science for use in public policy and product labeling programs. Their 2002 Dietary Reference Intakes for Energy, Carbohydrate, Fiber, Fat, Fatty Acids, Cholesterol, Protein, and Amino Acids [ 62 ] contains their findings and recommendations regarding consumption of trans fat. [ 63 ]
Their recommendations are based on two key facts. First, "trans fatty acids are not essential and provide no known benefit to human health", [ 64 ] whether of animal or plant origin. [ 65 ] Second, given their documented effects on the LDL/HDL ratio, [ 66 ] the NAS concluded "that dietary trans fatty acids are more deleterious with respect to coronary artery disease than saturated fatty acids". A 2006 review stated "from a nutritional standpoint, the consumption of trans fatty acids results in considerable potential harm but no apparent benefit." [ 43 ]
Because of these facts and concerns, the NAS has concluded there is no safe level of trans fat consumption. There is no adequate level, recommended daily amount or tolerable upper limit for trans fats. This is because any incremental increase in trans fat intake increases the risk of coronary artery disease. [ 66 ]
Despite this concern, the NAS dietary recommendations have not included eliminating trans fat from the diet. This is because trans fat is naturally present in many animal foods in trace quantities, and thus its removal from ordinary diets might introduce undesirable side effects and nutritional imbalances. The NAS has, thus, "recommended that trans fatty acid consumption be as low as possible while consuming a nutritionally adequate diet". [ 67 ] Like the NAS, the WHO has tried to balance public health goals with a practical level of trans fat consumption, recommending in 2003 that trans fats be limited to less than 1% of overall energy intake. [ 46 ]
While trans fatty acids (popularly called "trans fats") are edible, they have been implicated in many health problems. [ 68 ]
The primary health risk identified for trans fat consumption is an elevated risk of coronary artery disease (CAD). [ 43 ] [ 69 ] [ 70 ] [ 71 ] A 1994 study estimated that over 30,000 cardiac deaths per year in the United States are attributable to the consumption of trans fats. [ 19 ] By 2006 upper estimates of 100,000 deaths were suggested. [ 72 ]
Major evidence for the effect of trans fat on CAD comes from the Nurses' Health Study – a cohort study that has been following 120,000 female nurses since its inception in 1976. In this study, Hu and colleagues analyzed data from 900 coronary events from the study's population during 14 years of followup. He determined that a nurse's CAD risk roughly doubled ( relative risk of 1.93, CI : 1.43 to 2.61) for each 2% increase in trans fat calories consumed (instead of carbohydrate calories). By contrast, for each 5% increase in saturated fat calories (instead of carbohydrate calories) there was a 17% increase in risk ( relative risk of 1.17, CI : 0.97 to 1.41). "The replacement of saturated fat or trans unsaturated fat by cis (unhydrogenated) unsaturated fats was associated with larger reductions in risk than an isocaloric replacement by carbohydrates." [ 73 ] Hu also reports on the benefits of reducing trans fat consumption. Replacing 2% of food energy from trans fat with non-trans unsaturated fats more than halves the risk of CAD (53%). By comparison, replacing a larger 5% of food energy from saturated fat with non-trans unsaturated fats reduces the risk of CAD by 43%. [ 73 ]
Another study considered deaths due to CAD, with consumption of trans fats being linked to an increase in mortality, and consumption of polyunsaturated fats being linked to a decrease in mortality. [ 71 ] [ 74 ]
Consuming trans fats has been shown to increase the risk of coronary artery disease in part by raising levels of low-density lipoprotein (LDL, often termed "bad cholesterol"), lowering levels of high-density lipoprotein (HDL, often termed "good cholesterol"), increasing triglycerides in the bloodstream and promoting systemic inflammation. [ 64 ] [ 66 ]
Trans fat has been found to act like saturated in raising the blood level of LDL ("bad cholesterol"); but, unlike saturated fat, it also decreases levels of HDL ("good cholesterol"). The net increase in LDL/HDL ratio with trans fat, a widely accepted indicator of risk for coronary artery disease, is approximately double that due to saturated fat. [ 75 ] [ 76 ] [ 77 ] One randomized crossover study published in 2003 comparing the effect of eating a meal on blood lipids of (relatively) cis and trans-fat-rich meals showed that cholesteryl ester transfer (CET) was 28% higher after the trans meal than after the cis meal and that lipoprotein concentrations were enriched in apolipoprotein (a) after the trans meals. [ 78 ]
The citokyne test is a potentially more reliable indicator of CAD risk, although is still being studied. [ 71 ] A study of over 700 nurses showed that those in the highest quartile of trans fat consumption had blood levels of C-reactive protein (CRP) that were 73% higher than those in the lowest quartile. [ 79 ]
Intake of dietary trans fat perturbs the body's ability to metabolize essential fatty acids (EFAs, including omega-3 ) leading to changes in the phospholipid fatty acid composition of the arterial walls, thereby raising risk of coronary artery disease. [ 80 ]
There are two accepted tests that measure an individual's risk for coronary artery disease, both blood tests . The first considers ratios of two types of cholesterol , the other the amount of a cell-signalling cytokine called C-reactive protein . The effect of trans fat consumption has been documented on each as follows:
The mechanisms through which trans fatty acids contribute to coronary artery disease are fairly well understood. The mechanism for their effects on diabetes is still under investigation. They may impair the metabolism of long-chain polyunsaturated fatty acids (LCPUFAs). [ 82 ] However, maternal pregnancy trans fatty acid intake has been inversely associated with LCPUFAs levels in infants at birth thought to underlie the positive association between breastfeeding and intelligence. [ 83 ]
Trans fats are processed by the liver differently than other fats. They may cause liver dysfunction by interfering with delta 6 desaturase , an enzyme involved in converting essential fatty acids to arachidonic acid and prostaglandins , both of which are important to the functioning of cells. [ 84 ]
Intake of dietary trans fat disrupts the body's ability to metabolize essential fatty acids (EFAs, including Omega-3 ) leading to changes in the phospholipid fatty acid composition of the arterial walls, thereby raising risk of coronary artery disease. [ 80 ]
The major evidence for the effect of trans fat on CAD comes from the Nurses' Health Study – a cohort study that has been following 120,000 female nurses since its inception in 1976. In this study, Hu and colleagues analyzed data from 900 coronary events from the study's population during 14 years of followup. He determined that a nurse's CAD risk roughly doubled ( relative risk of 1.93, CI : 1.43 to 2.61) for each 2% increase in trans fat calories consumed (instead of carbohydrate calories). By contrast, for each 5% increase in saturated fat calories (instead of carbohydrate calories) there was a 17% increase in risk ( relative risk of 1.17, CI : 0.97 to 1.41). "The replacement of saturated fat or trans unsaturated fat by cis (unhydrogenated) unsaturated fats was associated with larger reductions in risk than an isocaloric replacement by carbohydrates." [ 73 ] Hu also reports on the benefits of reducing trans fat consumption. Replacing 2% of food energy from trans fat with non-trans unsaturated fats more than halves the risk of CAD (53%). By comparison, replacing a larger 5% of food energy from saturated fat with non-trans unsaturated fats reduces the risk of CAD by 43%. [ 73 ]
Another study considered deaths due to CAD, with consumption of trans fats being linked to an increase in mortality, and consumption of polyunsaturated fats being linked to a decrease in mortality. [ 74 ]
Scientific studies have examined other negative effects of industrial trans fat beyond cardiovascular disease, with the next most studied area being type-2 diabetes.
Palm oil , a natural oil extracted from the fruit of oil palm trees that is semi-solid at room temperature (15–25 degrees Celsius), can potentially serve as a substitute for partially hydrogenated fats in baking and processed food applications, although there is disagreement about whether replacing partially hydrogenated fats with palm oil confers any health benefits. A 2006 study supported by the National Institutes of Health and the USDA Agricultural Research Service concluded that palm oil is not a safe substitute for partially hydrogenated fats (trans fats) in the food industry, because palm oil results in adverse changes in the blood concentrations of LDL and apolipoprotein B just as trans fat does. [ 106 ] [ 107 ]
In May 2003, BanTransFats.com Inc., a U.S. non-profit corporation, filed a lawsuit against the food manufacturer Kraft Foods in an attempt to force Kraft to remove trans fats from the Oreo cookie. The lawsuit was withdrawn when Kraft agreed to work on ways to find a substitute for the trans fat in the Oreo.
The J.M. Smucker Company , then the American manufacturer of Crisco (the original partially hydrogenated vegetable shortening), in 2004 released a new formulation made from solid saturated palm oil cut with soybean oil and sunflower oil . This blend yielded an equivalent shortening much like the prior partially hydrogenated Crisco, and was labelled zero grams of trans fat per 1 tablespoon serving (as compared with 1.5 grams per tablespoon of original Crisco). [ 108 ] As of 24 January 2007, Smucker said that all Crisco shortening products in the US had been reformulated to contain less than one gram of trans fat per serving while keeping saturated fat content less than butter. [ 109 ] The separately marketed trans fat free version introduced in 2004 was discontinued.
On 22 May 2004, Unilever , the corporate descendant of Joseph Crosfield & Sons (the original producer of Wilhelm Normann 's hydrogenation hardened oils) announced that they had eliminated trans fats from all their margarine products in Canada, including their flagship Becel brand. [ 110 ]
Agribusiness giant Bunge Limited , through their Bunge Oils division, produce an NT product line of non-hydrogenated oils, margarines and shortenings, made from corn, canola , and soy oils. [ 111 ]
Beginning around 2000, as the scientific evidence and public concern about trans fat increased, major American users of trans fat began to switch to safer alternatives. The process received a large boost in 2003 when the FDA announced it would require trans fat labeling on packaged food starting in 2006. Packaged food companies then faced the choice of either eliminating trans fat from their products, or having to declare the trans fat on their nutrition label. Lawsuits in the U.S. against trans fat users also encouraged its removal.
Major American fast food chains including McDonald's , Burger King , KFC and Wendy's reduced and then removed partially hydrogenated oils (containing artificial trans fats) by 2009. This was a major step toward trans fat removal, as french fries were one of the largest sources of trans fat in the American diet, with a large serving of fries typically having about 6 grams of trans fat until around 2007. [ 112 ] [ 113 ] [ 114 ] [ 115 ] [ 116 ] [ 117 ] [ 118 ] [ 119 ]
Two other events were important in the removal of trans fat. First, in 2013 the FDA announced it planned to completely ban artificial trans fat in the form of partially hydrogenated oil. Second, soon after this, Walmart informed its suppliers they needed to remove trans fat by 2015 if they wanted to continue to sell their products at its stores. As Walmart is the largest brick-and-mortar retailer in the U.S., mainstream food brands had little choice but to comply. [ 120 ]
These reformulations can be partly attributed to 2006 Center for Science in the Public Interest class action complaints, and to New York's restaurant trans fat ban, a massive effort led by Minal Amlani under the guidance of Michael Bloomberg , with companies such as McDonald's stating they would not be selling a unique product just for New York customers but would implement a nationwide or worldwide change. [ 121 ] [ 122 ] [ 123 ] | https://en.wikipedia.org/wiki/Trans_fat |
Transaction Processing Management System ( TPMS ) is an online transaction processing superstructure software from ICL (now Fujitsu Services ) that runs on their VME mainframe computers. The first versions were released in the mid-1970s and were sold worldwide.
The service runs in at least two Virtual Machines (VMs)
This computing article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transaction_Processing_Management_System |
In the field of databases in computer science , a transaction log (also transaction journal , database log , binary log or audit trail ) is a history of actions executed by a database management system used to guarantee ACID properties over crashes or hardware failures. Physically, a log is a file listing changes to the database, stored in a stable storage format.
If, after a start, the database is found in an inconsistent state or not been shut down properly, the database management system reviews the database logs for uncommitted transactions and rolls back the changes made by these transactions . Additionally, all transactions that are already committed but whose changes were not yet materialized in the database are re-applied. Both are done to ensure atomicity and durability of transactions.
This term is not to be confused with other, human-readable logs that a database management system usually provides.
In database management systems , a journal is the record of data altered by a given process. [ 1 ] [ 2 ] [ 3 ] [ 4 ]
A database log record is made up of:
All log records include the general log attributes above, and also other attributes depending on their type (which is recorded in the Type attribute, as above). | https://en.wikipedia.org/wiki/Transaction_log |
A transaction processing system ( TPS ) is a software system, or software/ hardware combination, that supports transaction processing .
The first transaction processing system was SABRE , made by IBM for American Airlines , which became operational in 1964. [ 1 ] Designed to process up to 83,000 transactions a day, the system ran on two IBM 7090 computers. SABRE was migrated to IBM System/360 computers in 1972, and became an IBM product first as Airline control Program (ACP) and later as Transaction Processing Facility (TPF) . In addition to airlines, TPF is used by large banks, credit card companies, and hotel chains.
The Hewlett Packard Enterprise NonStop system (formerly Tandem NonStop) is a hardware and software system designed for Online Transaction Processing (OLTP) introduced in 1976. [ 2 ] The system provides an extreme level of availability and data integrity.
Transaction processing is distinct from and can be contrasted with other computer processing models, such as batch processing , time-sharing , and real-time processing . [ 10 ]
Batch processing is execution of a series of programs ( jobs ) on a computer without manual intervention. Several transactions, called a batch are collected and processed at the same time. The results of each transaction are not immediately available when the transaction is being entered; [1] there is a time delay.
"Real time systems attempt to guarantee an appropriate response to a stimulus or request quickly enough to affect the conditions that caused the stimulus." [ 10 ] Each transaction in realtime processing is unique; it is not part of a group of transactions.
A Transaction Processing System (TPS) is an information system that collects, stores, modifies, and retrieves the data transactions of an enterprise. Transaction processing systems also attempt to provide predictable response times to requests, although this is not as critical as real-time systems. Rather than allowing the user to run arbitrary programs as time-sharing, transaction processing allows only predefined, structured transactions. Each transaction is usually short, and each transaction's processing activity is programmed in advance. It is an MIS model.
The following features are considered important in evaluating transaction processing systems. [ 10 ]
Fast performance with a rapid response time is critical. Transaction processing systems are usually measured by the number of transactions they can process in a given period of time.
The system must be available during the time period when the users are entering transactions. Many organizations rely heavily on their TPS; a breakdown will disrupt operations or even stop the business.
The system must be able to handle hardware or software problems without corrupting data. Multiple users must be protected from attempting to change the same piece of data at the same time, for example two operators cannot sell the same seat on an airplane.
Often users of transaction processing systems are casual users. The system should be simple for them to understand, protect them from data-entry errors as much as possible, and allow them to easily correct their errors.
The system should be capable of growth at incremental costs, rather than requiring a complete replacement. It should be possible to add, replace, or update hardware and software components without shutting down the system.
Transactions may be collected and processed as in batch processing. Transactions will be collected and later updated as a batch when it is convenient or economical to process them. Historically, this was the most common method as the information technology did not yet exist to allow real-time processing.
This is the immediate processing of data. It provides instant confirmation of a transaction. It may involve a large number of users who are simultaneously performing transactions which change data. Because of advances in technology (such as the increase in the speed of data transmission and larger systems and networking bandwidth ), real-time updating is possible.
A database is an organized collection of data. Databases offer fast retrieval times for non-structured requests as in a typical transaction processing application.
Databases for transaction processing may be constructed using hierarchical, network, or relational structures.
The following features are desirable in a database system used in transaction processing systems:
Since business organizations have become very dependent on transaction processing, a breakdown may disrupt the business' regular routine and stop its operation for a certain amount of time. In order to prevent data loss and minimize disruptions well-designed backup and recovery procedures must exist and be adhered to. The recovery process can rebuild the system when it goes down.
There are two main types of back-up procedures: grandfather-father-son and partial backups :
This procedure involves taking complete backups of all data at regular intervals – daily, weekly, monthly, or whatever is appropriate. Multiple generations of backup are retained, often three which gives rise to the name. The most recent backup is the son, the previous the father, and the oldest backup is the grandfather. This method is commonly used for a batch transaction processing system with a magnetic tape drive. If the system fails during a batch run, the master file is recreated by restoring the son backup and then restarting the batch. However, if the son backup fails, is corrupted or destroyed, then the previous generation of backup (the father) is used. Likewise, if that fails, then the generation of backup previous to the father (i.e. the grandfather) is required. Of course the older the generation, the more the data may be out of date.
Partial backups
Partial backups generally contain only records that have changed. For example, a full backup could be performed weekly, and then partial backups taken nightly. Recovery using this scheme involves restoring the last full backup and then restoring all partial backups in order to produce an up-to-date database. This process is quicker than taking only complete backups, at the expense of longer recovery time. | https://en.wikipedia.org/wiki/Transaction_processing_system |
The transactional interpretation of quantum mechanics ( TIQM ) takes the wave function of the standard quantum formalism , and its complex conjugate, to be retarded (forward in time) and advanced (backward in time) waves that form a quantum interaction as a Wheeler–Feynman handshake or transaction. It was first proposed in 1986 by John G. Cramer , who argues that it helps in developing intuition for quantum processes. He also suggests that it avoids the philosophical problems with the Copenhagen interpretation and the role of the observer, and also resolves various quantum paradoxes . [ 1 ] [ 2 ] [ 3 ] TIQM formed a minor plot point in his science fiction novel Einstein's Bridge .
More recently, he has also argued TIQM to be consistent with the Afshar experiment , while claiming that the Copenhagen interpretation and the many-worlds interpretation are not. [ 4 ]
The existence of both advanced and retarded waves as admissible solutions to Maxwell's equations was explored in the Wheeler–Feynman absorber theory. Cramer revived their idea of two waves for his transactional interpretation of quantum theory. While the ordinary Schrödinger equation does not admit advanced solutions, its relativistic version does, and these advanced solutions are the ones used by TIQM.
In TIQM, the source emits a usual (retarded) wave forward in time, but it also emits an advanced wave backward in time; furthermore, the receiver, who is later in time, also emits an advanced wave backward in time and a retarded wave forward in time. A quantum event occurs when a "handshake" exchange of advanced and retarded waves triggers the formation of a transaction in which energy, momentum, angular momentum, etc. are transferred. The quantum mechanism behind transaction formation has been demonstrated explicitly for the case of a photon transfer between atoms in Sect. 5.4 of Carver Mead 's book Collective Electrodynamics . In this interpretation, the collapse of the wavefunction does not happen at any specific point in time, but is "atemporal" and occurs along the whole transaction, and the emission/absorption process is time-symmetric. The waves are seen as physically real, rather than a mere mathematical device to record the observer's knowledge as in some other interpretations of quantum mechanics . [ citation needed ] Philosopher and writer Ruth Kastner argues that the waves exist as possibilities outside of physical spacetime and that therefore it is necessary to accept such possibilities as part of reality. [ 5 ]
Cramer has used TIQM in teaching quantum mechanics at the University of Washington in Seattle .
TIQM is explicitly non-local and, as a consequence, logically consistent with counterfactual definiteness (CFD), the minimum realist assumption. [ 2 ] As such it incorporates the non-locality demonstrated by the Bell test experiments and eliminates the observer-dependent reality that has been criticized as part of the Copenhagen interpretation . Cramer states that the key advances over Everett's Relative State Interpretation [ 6 ] are that the transactional interpretation has a physical collapse and is time-symmetric. [ 2 ] Cramer also states that the TI is consistent with but not dependent upon the notion of an Einsteinian block universe . [ 7 ] Kastner claims that by considering the product of the advanced and retarded wavefunctions, the Born rule can be explained ontologically. [ 8 ]
The transactional interpretation is superficially similar to the two-state vector formalism (TSVF) [ 9 ] which has its origin in work by Yakir Aharonov , Peter Bergmann and Joel Lebowitz of 1964. [ 10 ] [ 11 ] However, it has important differences—the TSVF is lacking the confirmation and therefore cannot provide a physical referent for the Born Rule (as TI does). Kastner has criticized some other time-symmetric interpretations, including TSVF, as making ontologically inconsistent claims. [ 12 ]
Kastner has developed a new Relativistic Transactional Interpretation (RTI) also called Possibilist Transactional Interpretation (PTI) in which space-time itself emerges by a way of transactions. It has been argued that this relativistic transactional interpretation can provide the quantum dynamics for the causal sets program. [ 13 ]
In 1996, Tim Maudlin proposed a thought experiment involving Wheeler's delayed choice experiment that is generally taken as a refutation of TIQM. [ 14 ] However Kastner showed Maudlin's argument is not fatal for TIQM. [ 15 ] [ 16 ]
In his book, The Quantum Handshake , Cramer has added a hierarchy to the description of pseudo-time to deal with Maudlin's objection and has pointed out that some of Maudlin's arguments are based on the inappropriate application of Heisenberg's knowledge interpretation to the transactional description. [ 7 ]
Transactional Interpretation faces criticisms. The following is partial list and some replies:
Maudlin's probability criticism confused the transactional interpretation with Heisenberg's knowledge interpretation. However, he raised a valid point concerning causally connected possible outcomes, which led Cramer to add hierarchy to the pseudo-time description of transaction formation. [ 19 ] [ 15 ] [ 20 ] [ 21 ] [ 22 ] Kastner has extended TI to the relativistic domain, and in light of this expansion of the interpretation, it can be shown that the Maudlin Challenge cannot even be mounted, and is therefore nullified; there is no need for the 'hierarchy' proposal of Cramer. [ 23 ] | https://en.wikipedia.org/wiki/Transactional_interpretation |
In a very generic sense, the term transactions per second (TPS) refers to the number of atomic actions performed by certain entity per second. In a more restricted view, the term is usually used by the DBMS vendor and user community to refer to the number of database transactions performed per second. Transactions per minute may be used when the transactions are more complex.
Recently, the term has also been used to describe the transaction rate of a cryptocurrency , [ 1 ] such as the distributed network running the Bitcoin blockchain . The development of transaction rates capable of scaling to real-world volumes is an important area of research for cryptocurrency technology.
This computing article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transactions_per_second |
In the context of gene regulation: transactivation is the increased rate of gene expression triggered either by biological processes or by artificial means, through the expression of an intermediate transactivator protein.
In the context of receptor signaling, transactivation occurs when one or more receptors activate yet another; [ 1 ] [ 2 ] receptor transactivation may result from the crosstalk of signaling cascades or the activation of G protein–coupled receptor hetero-oligomer subunits, among other mechanisms. [ 1 ]
Transactivation can be triggered either by endogenous cellular or viral proteins, also called transactivators . These protein factors act in trans ( i.e. , intermolecularly ). HIV and HTLV are just two of the many viruses that encode transactivators to enhance viral gene expression. These transactivators can also be linked to cancer if they start interacting with, and increasing expression of, a cellular proto-oncogene . HTLV, for instance, has been associated with causing leukemia primarily through this process. Its transactivator, Tax , can interact with p40 , inducing overexpression of interleukin 2 , interleukin receptors , GM-CSF and the transcription factor c-Fos . HTLV infects T-cells and via the increased expression of these stimulatory cytokines and transcription factors , leads to uncontrolled proliferation of T-cells and hence lymphoma .
Artificial transactivation of a gene is achieved by inserting it into the genome at the appropriate area as transactivator gene adjoined to special promoter regions of DNA . The transactivator gene expresses a transcription factor that binds to specific promoter region of DNA. By binding to the promoter region of a gene, the transcription factor causes that gene to be expressed. The expression of one transactivator gene can activate multiple genes, as long as they have the same, specific promoter region attached. Because the expression of the transactivator gene can be controlled, transactivation can be used to turn genes on and off. If this specific promoter region is also attached to a reporter gene , we can measure when the transactivator is being expressed. | https://en.wikipedia.org/wiki/Transactivation |
Transamidation is a chemical reaction in which an amide reacts with an amine to generate a new amide:
The reaction is typically very slow, but it can be accelerated with Lewis acid [ 1 ] and organometallic catalysts . [ 2 ] Primary amides (RC(O)NH 2 ) are more amenable to this reaction.
In contrast to the reluctance of amides as substrates, urea is more susceptible to this exchange process. Transamidation is practiced, sometimes even on an industrial scale, to prepare a variety of N-substituted ureas : [ 3 ]
Methylurea, precursor to theobromine , is produced from methylamine and urea. Phenylurea is produced similarly but from anilinium chloride: [ 4 ]
Hydrazine derivatives of urea are often produced by transamidation-like reactions. These products include carbohydrazide , semicarbazide , and biurea . | https://en.wikipedia.org/wiki/Transamidation |
In organic chemistry , transamidification is the process of exchanging the subunits of a peptide , amide or ester compound with another amine or fatty acid to produce a new amide or peptide. The process has been used for the production of emulsifiers and dispersing agents [ 1 ] and oil drilling fluids. [ 2 ]
This organic chemistry article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transamidification |
Transamination is a chemical reaction that transfers an amino group to a ketoacid to form new amino acids.This pathway is responsible for the deamination of most amino acids. This is one of the major degradation pathways which convert essential amino acids to non-essential amino acids (amino acids that can be synthesized de novo by the organism).
Transamination in biochemistry is accomplished by enzymes called transaminases or aminotransferases. α-ketoglutarate acts as the predominant amino-group acceptor and produces glutamate as the new amino acid.
Glutamate's amino group, in turn, is transferred to oxaloacetate in a second transamination reaction yielding aspartate.
Transamination catalyzed by aminotransferase occurs in two stages. In the first step, the α amino group of an amino acid is transferred to the enzyme, producing the corresponding α-keto acid and the aminated enzyme. During the second stage, the amino group is transferred to the keto acid acceptor, forming the amino acid product while regenerating the enzyme. The chirality of an amino acid is determined during transamination. For the reaction to complete, aminotransferases require participation of aldehyde containing coenzyme, pyridoxal-5'-phosphate (PLP) , a derivative of Pyridoxine ( Vitamin B 6 ). The amino group is accommodated by conversion of this coenzyme to pyridoxamine-5'-phosphate (PMP). PLP is covalently attached to the enzyme via a Schiff Base linkage formed by the condensation of its aldehyde group with the ε-amino group of an enzymatic Lys residue. The Schiff base, which is conjugated to the enzyme's pyridinium ring, is the focus of the coenzyme activity.
Transamination is mediated by several types of aminotransferase enzymes. An aminotransferase may be specific for an individual amino acid, or it may be able to process any member of a group of similar ones, for example the branched-chain amino acids, which comprises valine, isoleucine, and leucine. The two common types of aminotransferases are alanine aminotransferase (ALT) and aspartate aminotransferase (AST) .
• Smith, M. B. and March, J. Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, 5th ed. Wiley, 2001, p. 503. ISBN 0-471-58589-0 • Gerald Booth "Naphthalene Derivatives" in Ullmann's Encyclopedia of Industrial Chemistry, 2005, Wiley-VCH, Weinheim. doi:10.1002/14356007.a17_009
Voet & Voet. "Biochemistry" Fourth edition | https://en.wikipedia.org/wiki/Transamination |
The Transcaspian Canal ( Russian : Транскаспийский канал ) was a proposed canal to divert the Amu Darya River from the Aral Sea and into the Caspian Sea . It was first proposed by Tsarist engineers and later considered by Soviet officials. Proponents argued that the project would return the Amu Darya into its supposed old bed.
Several other similar proposals were made in the early 20th century, including a Kazakh-Turkestan Canal to connect Kazakhstan with the Black Sea . [ 1 ] The projects were not seriously considered after the late-1920s, when a campaign was launched to ridicule "fantastic" hydraulic projects. [ 2 ] In 1928, over a dozen hydraulic engineers operating in Central Asia were tried for mismanaging the irrigation system and "devising intentionally fantastic projects". [ 3 ]
Following the Russian conquest of Central Asia , multiple suggestions were put forward for the construction of a transcaspian canal. Those who supported the project had Orientalist views and believed it would return "the [Khivan] oasis to cultured life". [ 4 ]
Among the initial proposals was one presented by Aleksandr Glukhovskoi in 1868. [ 5 ] He argued that such a canal would allow ships sailing down the Volga to reach Tashkent via Bukhara . His proposal was backed by the Ministry of Transport of the Russian empire. [ 6 ]
Many of Glukhovskoi's original reports and proposals were lost during the Russian Civil War and a 1924 flood. [ 1 ] In June 1925, the Water Section of the State Planning Committee discussed the project. Among the plans considered was one made by Gluvoskoi in 1893. [ 1 ]
After the October Revolution , Georgii Rizenkampf ( German : Georgi Riesenkampff ) proposed to build a 1,600-km (1,500- verst ) canal stretching from the upper reaches of the Amu Darya in Afghanistan through the Karakum Desert in Turkmenistan all the way to the Caspian sea. [ 7 ] In his 1921 book entitled "Trans-Kaspiiskii kanal (Problema orosheniia Zakaspiia)" ( Russian : Транс-Каспийский канал (Проблема орошения Закаспия) ), Rizenkampf argued that the canal would support the growing of cotton in the region. He predicted cotton would become the "fulcrum of life in Transcaspia". [ 1 ]
By the late 1920s, a media campaign was launched to ridicule large water diversion projects in Central Asia. In February and March 1928, 23 hydraulic engineers and water managers working in Central Asia, including those who had proposed a transcaspian canal, were tried in Tashkent. At the time the London Times reported that "Until recently the authorities in Moscow boasted of these 'fantastic projects,' but now apparently they need scapegoats to mollify the native population." [ 3 ] Historian Maya K. Peterson similarly argued that the trial was aimed to "distract from Soviet failings and find scapegoats". [ 8 ] | https://en.wikipedia.org/wiki/Transcaspian_Canal |
In cell biology , extracellular fluid ( ECF ) denotes all body fluid outside the cells of any multicellular organism . Total body water in healthy adults is about 50–60% (range 45 to 75%) of total body weight; [ 1 ] women and the obese typically have a lower percentage than lean men. [ 2 ] Extracellular fluid makes up about one-third of body fluid, the remaining two-thirds is intracellular fluid within cells. [ 3 ] The main component of the extracellular fluid is the interstitial fluid that surrounds cells.
Extracellular fluid is the internal environment of all multicellular animals , and in those animals with a blood circulatory system , a proportion of this fluid is blood plasma . [ 4 ] Plasma and interstitial fluid are the two components that make up at least 97% of the ECF. Lymph makes up a small percentage of the interstitial fluid. [ 5 ] The remaining small portion of the ECF includes the transcellular fluid (about 2.5%). The ECF can also be seen as having two components – plasma and lymph as a delivery system, and interstitial fluid for water and solute exchange with the cells. [ 6 ]
The extracellular fluid, in particular the interstitial fluid, constitutes the body's internal environment that bathes all of the cells in the body. The ECF composition is therefore crucial for their normal functions, and is maintained by a number of homeostatic mechanisms involving negative feedback . Homeostasis regulates, among others, the pH , sodium , potassium , and calcium concentrations in the ECF. The volume of body fluid, blood glucose , oxygen , and carbon dioxide levels are also tightly homeostatically maintained.
The volume of extracellular fluid in a young adult male of 70 kg (154 lbs) is 20% of body weight – about fourteen liters. Eleven liters are interstitial fluid and the remaining three liters are plasma. [ 7 ]
The main component of the extracellular fluid (ECF) is the interstitial fluid, or tissue fluid, which surrounds the cells in the body. The other major component of the ECF is the intravascular fluid of the circulatory system called blood plasma . The remaining small percentage of ECF includes the transcellular fluid. These constituents are often called " fluid compartments ". The volume of extracellular fluid in a young adult male of 70 kg, is 20% of body weight – about fourteen liters.
Interstitial fluid is essentially comparable to plasma . The interstitial fluid and plasma make up about 97% of the ECF, and a small percentage of this is lymph .
Interstitial fluid is the body fluid between blood vessels and cells, [ 8 ] containing nutrients from capillaries by diffusion and holding waste products discharged by cells due to metabolism . [ 9 ] [ 10 ] 11 liters of the ECF are interstitial fluid and the remaining three liters are plasma. [ 7 ] Plasma and interstitial fluid are very similar because water, ions, and small solutes are continuously exchanged between them across the walls of capillaries, through pores and capillary clefts .
Interstitial fluid consists of a water solvent containing sugars, salts, fatty acids, amino acids, coenzymes, hormones, neurotransmitters, white blood cells and cell waste-products. This solution accounts for 26% of the water in the human body. The composition of interstitial fluid depends upon the exchanges between the cells in the biological tissue and the blood. [ 11 ] This means that tissue fluid has a different composition in different tissues and in different areas of the body.
The plasma that filters through the blood capillaries into the interstitial fluid does not contain red blood cells or platelets as they are too large to pass through but can contain some white blood cells to help the immune system.
Once the extracellular fluid collects into small vessels ( lymph capillaries ) it is considered to be lymph, and the vessels that carry it back to the blood are called the lymphatic vessels. The lymphatic system returns protein and excess interstitial fluid to the circulation.
The ionic composition of the interstitial fluid and blood plasma vary due to the Gibbs–Donnan effect . This causes a slight difference in the concentration of cations and anions between the two fluid compartments.
Transcellular fluid is formed from the transport activities of cells , and is the smallest component of extracellular fluid. These fluids are contained within epithelial lined spaces. Examples of this fluid are cerebrospinal fluid , aqueous humor in the eye, serous fluid in the serous membranes lining body cavities , perilymph and endolymph in the inner ear, and joint fluid . [ 2 ] [ 12 ] Due to the varying locations of transcellular fluid, the composition changes dramatically. Some of the electrolytes present in the transcellular fluid are sodium ions, chloride ions , and bicarbonate ions.
Extracellular fluid provides the medium for the exchange of substances between the ECF and the cells, and this can take place through dissolving, mixing and transporting in the fluid medium. [ 13 ] Substances in the ECF include dissolved gases, nutrients, and electrolytes , all needed to maintain life. [ 14 ] ECF also contains materials secreted from cells in soluble form, but which quickly coalesce into fibers (e.g. collagen , reticular , and elastic fibres ) or precipitates out into a solid or semisolid form (e.g. proteoglycans which form the bulk of cartilage , and the components of bone ). These and many other substances occur, especially in association with various proteoglycans, to form the extracellular matrix , or the "filler" substance, between the cells throughout the body. [ 15 ] These substances occur in the extracellular space, and are therefore all bathed or soaked in ECF, without being part of it.
One of the main roles of extracellular fluid is to facilitate the exchange of molecular oxygen from blood to tissue cells and for carbon dioxide, CO 2 , produced in cell mitochondria, back to the blood. Since carbon dioxide is about 20 times more soluble in water than oxygen, it can relatively easily diffuse in the aqueous fluid between cells and blood. [ 16 ]
However, hydrophobic molecular oxygen has very poor water solubility and prefers hydrophobic lipid crystalline structures. [ 17 ] [ 18 ] As a result of this, plasma lipoproteins can carry significantly more O 2 than in the surrounding aqueous medium. [ 19 ] [ 20 ]
If hemoglobin in erythrocytes is the main transporter of oxygen in the blood , plasma lipoproteins may be its only carrier in the ECF.
The oxygen-carrying capacity of lipoproteins, reduces in ageing and inflammation . This results in changes of ECF functions, reduction of tissue O 2 supply and contributes to development of tissue hypoxia . These changes in lipoproteins are caused by oxidative or inflammatory damage. [ 21 ]
The internal environment is stabilised in the process of homeostasis . Complex homeostatic mechanisms operate to regulate and keep the composition of the ECF stable. Individual cells can also regulate their internal composition by various mechanisms. [ 22 ]
There is a significant difference between the concentrations of sodium and potassium ions inside and outside the cell. The concentration of sodium ions is considerably higher in the extracellular fluid than in the intracellular fluid. [ 23 ] The converse is true of the potassium ion concentrations inside and outside the cell. These differences cause all cell membranes to be electrically charged, with the positive charge on the outside of the cells and the negative charge on the inside. In a resting neuron (not conducting an impulse) the membrane potential is known as the resting potential , and between the two sides of the membrane is about −70 mV. [ 24 ]
This potential is created by sodium–potassium pumps in the cell membrane, which pump sodium ions out of the cell, into the ECF, in return for potassium ions which enter the cell from the ECF. The maintenance of this difference in the concentration of ions between the inside of the cell and the outside, is critical to keep normal cell volumes stable, and also to enable some cells to generate action potentials . [ 25 ]
In several cell types voltage-gated ion channels in the cell membrane can be temporarily opened under specific circumstances for a few microseconds at a time. This allows a brief inflow of sodium ions into the cell (driven in by the sodium ion concentration gradient that exists between the outside and inside of the cell). This causes the cell membrane to temporarily depolarize (lose its electrical charge) forming the basis of action potentials.
The sodium ions in the ECF also play an important role in the movement of water from one body compartment to the other. When tears are secreted, or saliva is formed, sodium ions are pumped from the ECF into the ducts in which these fluids are formed and collected. The water content of these solutions results from the fact that water follows the sodium ions (and accompanying anions ) osmotically. [ 26 ] [ 27 ] The same principle applies to the formation of many other body fluids .
Calcium ions have a great propensity to bind to proteins . [ 28 ] This changes the distribution of electrical charges on the protein, with the consequence that the 3D (or tertiary) structure of the protein is altered. [ 29 ] [ 30 ] The normal shape, and therefore function of very many of the extracellular proteins, as well as the extracellular portions of the cell membrane proteins, is dependent on a very precise ionized calcium concentration in the ECF. The proteins that are particularly sensitive to changes in the ECF ionized calcium concentration are several of the clotting factors in the blood plasma, which are functionless in the absence of calcium ions, but become fully functional on the addition of the correct concentration of calcium salts. [ 23 ] [ 28 ] The voltage gated sodium ion channels in the cell membranes of nerves and muscle have an even greater sensitivity to changes in the ECF ionized calcium concentration. [ 31 ] Relatively small decreases in the plasma ionized calcium levels ( hypocalcemia ) cause these channels to leak sodium into the nerve cells or axons, making them hyper-excitable, thus causing spontaneous muscle spasms ( tetany ) and paraesthesia (the sensation of "pins and needles") of the extremities and round the mouth. [ 29 ] [ 31 ] [ 32 ] When the plasma ionized calcium rises above normal ( hypercalcemia ) more calcium is bound to these sodium channels having the opposite effect, causing lethargy, muscle weakness, anorexia, constipation and labile emotions. [ 32 ] [ 33 ]
The tertiary structure of proteins is also affected by the pH of the bathing solution. In addition, the pH of the ECF affects the proportion of the total amount of calcium in the plasma which occurs in the free, or ionized form, as opposed to the fraction that is bound to protein and phosphate ions. A change in the pH of the ECF therefore alters the ionized calcium concentration of the ECF. Since the pH of the ECF is directly dependent on the partial pressure of carbon dioxide in the ECF, hyperventilation , which lowers the partial pressure of carbon dioxide in the ECF, produces symptoms that are almost indistinguishable from low plasma ionized calcium concentrations. [ 29 ]
The extracellular fluid is constantly "stirred" by the circulatory system , which ensures that the watery environment which bathes the body's cells is virtually identical throughout the body. This means that nutrients can be secreted into the ECF in one place (e.g. the gut, liver, or fat cells) and will, within about a minute, be evenly distributed throughout the body. Hormones are similarly rapidly and evenly spread to every cell in the body, regardless of where they are secreted into the blood. Oxygen taken up by the lungs from the alveolar air is also evenly distributed at the correct partial pressure to all the cells of the body. Waste products are also uniformly spread to the whole of the ECF, and are removed from this general circulation at specific points (or organs), once again ensuring that there is generally no localized accumulation of unwanted compounds or excesses of otherwise essential substances (e.g. sodium ions, or any of the other constituents of the ECF). The only significant exception to this general principle is the plasma in the veins , where the concentrations of dissolved substances in individual veins differ, to varying degrees, from those in the rest of the ECF. However, this plasma is confined within the waterproof walls of the venous tubes, and therefore does not affect the interstitial fluid in which the body's cells live. When the blood from all the veins in the body mixes in the heart and lungs, the differing compositions cancel out (e.g. acidic blood from active muscles is neutralized by the alkaline blood homeostatically produced by the kidneys). From the left atrium onward, to every organ in the body, the normal, homeostatically regulated values of all of the ECF's components are therefore restored.
The arterial blood plasma, interstitial fluid and lymph interact at the level of the blood capillaries . The capillaries are permeable and water can move freely in and out. At the arteriolar end of the capillary the blood pressure is greater than the hydrostatic pressure in the tissues. [ 34 ] [ 23 ] Water will therefore seep out of the capillary into the interstitial fluid. The pores through which this water moves are large enough to allow all the smaller molecules (up to the size of small proteins such as insulin ) to move freely through the capillary wall as well. This means that their concentrations across the capillary wall equalize, and therefore have no osmotic effect (because the osmotic pressure caused by these small molecules and ions – called the crystalloid osmotic pressure to distinguish it from the osmotic effect of the larger molecules that cannot move across the capillary membrane – is the same on both sides of capillary wall). [ 34 ] [ 23 ]
The movement of water out of the capillary at the arteriolar end causes the concentration of the substances that cannot cross the capillary wall to increase as the blood moves to the venular end of the capillary. The most important substances that are confined to the capillary tube are plasma albumin , the plasma globulins and fibrinogen . They, and particularly the plasma albumin, because of its molecular abundance in the plasma, are responsible for the so-called "oncotic" or "colloid" osmotic pressure which draws water back into the capillary, especially at the venular end. [ 34 ]
The net effect of all of these processes is that water moves out of and back into the capillary, while the crystalloid substances in the capillary and interstitial fluids equilibrate. Since the capillary fluid is constantly and rapidly renewed by the flow of the blood, its composition dominates the equilibrium concentration that is achieved in the capillary bed. This ensures that the watery environment of the body's cells is always close to their ideal environment (set by the body's homeostats ).
A small proportion of the solution that leaks out of the capillaries is not drawn back into the capillary by the colloid osmotic forces. This amounts to between 2–4 liters per day for the body as a whole. This water is collected by the lymphatic system and is ultimately discharged into the left subclavian vein , where it mixes with the venous blood coming from the left arm, on its way to the heart. [ 23 ] The lymph flows through lymph capillaries to lymph nodes where bacteria and tissue debris are removed from the lymph, while various types of white blood cells (mainly lymphocytes ) are added to the fluid. In addition the lymph which drains the small intestine contains fat droplets called chylomicrons after the ingestion of a fatty meal. [ 28 ] This lymph is called chyle which has a milky appearance, and imparts the name lacteals (referring to the milky appearance of their contents) to the lymph vessels of the small intestine. [ 35 ]
Extracellular fluid may be mechanically guided in this circulation by the vesicles between other structures. Collectively this forms the interstitium , which may be considered a newly identified biological structure in the body. [ 36 ] However, there is some debate over whether the interstitium is an organ. [ 37 ]
Main cations : [ 38 ]
Main anions : [ 38 ]
[ 39 ] | https://en.wikipedia.org/wiki/Transcellular_fluid |
Transcellular transport involves the transportation of solutes by a cell through a cell. [ 1 ] Transcellular transport can occur in three different ways active transport, passive transport, and transcytosis.
Active transport is the process of moving molecules from an area of low concentrations to an area of high concentration. There are two types of active transport, primary active transport and secondary active transport . [ citation needed ] Primary active transport uses adenosine triphosphate (ATP) to move specific molecules and solutes against its concentration gradient. Examples of molecules that follow this process are potassium K + , sodium Na + , and calcium Ca 2+ . A place in the human body where this occurs is in the intestines with the uptake of glucose . Secondary active transport is when one solute moves down the electrochemical gradient to produce enough energy to force the transport of another solute from low concentration to high concentration. [ citation needed ] An example of where this occurs is in the movement of glucose within the proximal convoluted tubule (PCT).
Passive transport is the process of moving molecules from an area of high concentration to an area of low concentration without expelling any energy. There are two types of passive transport, passive diffusion and facilitated diffusion . Passive diffusion is the unassisted movement of molecules from high concentration to low concentration across a permeable membrane . [ 2 ] One example of passive diffusion is the gas exchange that occurs between the oxygen in the blood and the carbon dioxide present in the lungs. [ 3 ] Facilitated diffusion is the movement of polar molecules down the concentration gradient with the assistance of membrane proteins . Since the molecules associated with facilitated diffusion are polar, they are repelled by the hydrophobic sections of permeable membrane, therefore they need to be assisted by the membrane proteins. Both types of passive transport will continue until the system reaches equilibrium . [ 4 ] One example of facilitated diffusion is the movement glucose from small intestine epithelial cells into the extracellular matrix of the blood capillaries. [ 5 ]
Transcytosis is the movement of large molecules across the interior of a cell. This process occurs by engulfing the molecule as it moves across the interior of the cell and then releasing the molecule on the other side. There are two types of transcytosis are receptor-mediated transcytosis (RMT) and adsorptive-mediated transcytosis (AMT). An example where both types of transcytosis occur is the movement of macromolecules across the blood-brain barrier (BBB) into the central nervous system (CNS). [ citation needed ]
In contrast, paracellular transport is the transfer of substances across an epithelium by passing through an intercellular space between the cells.
This cell biology article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transcellular_transport |
Transcendental anatomy , also known as philosophical anatomy , was a form of comparative anatomy that sought to find ideal patterns and structures common to all organisms in nature. [ 1 ] The term originated from naturalist philosophy in the German provinces, and culminated in Britain especially by scholars Robert Knox and Richard Owen , who drew from Goethe and Lorenz Oken . [ 1 ] From the 1820s to 1859, it persisted as the medical expression of natural philosophy before the Darwinian revolution . [ 2 ]
Amongst its various definitions, transcendental anatomy has four main tenets:
Johann Wolfgang Goethe was one of many naturalists and anatomists in the nineteenth century who was in search of an Ideal Plan in nature. In Germany, this was known as Urpflanze for the plant kingdom and Urtier for animals. He popularized the term " morphology " for this search. Transcendental anatomy first derived from the naturalist philosophy known as Naturphilosophie . [ 4 ]
In the 1820s, French anatomist Etienne Reynaud Augustin Serres (1786–1868) popularized the term transcendental anatomy to refer to the collective morphology of animal development. [ 3 ] Synonymous expressions such as philosophical anatomy, higher anatomy, and transcendental morphology also arose at this time.
Some advocates regarded transcendental anatomy as the ultimate explanation for biological structures, while others saw it as one of several necessary explanatory devices. [ 3 ]
Transcendental anatomists theorized that the bones of the skull were "cranial vertebra", or modified bones from the vertebrae. [ 1 ] Owen ardently supported the theory as major evidence for his theory of homology . [ 5 ]
The theory has since been discredited. | https://en.wikipedia.org/wiki/Transcendental_anatomy |
A transcendental argument is a kind of deductive argument that appeals to the necessary conditions that make experience and knowledge possible . [ 1 ] [ 2 ] Transcendental arguments may have additional standards of justification which are more demanding than those of traditional deductive arguments. [ 3 ] The philosopher Immanuel Kant gave transcendental arguments both their name and their notoriety.
Typically, a transcendental argument starts from some proposition , and then makes the case that its truth or falsehood contradicts the necessary conditions for it to be possible to know, think or argue about it.
So-called progressive transcendental arguments begin with an apparently indubitable and universally accepted statement about people's experiences of the world. They use this to make substantive knowledge-claims about the world, e.g., that it is causally and spatiotemporally related. They start with what is left at the end of the skeptic's process of doubting.
Progressive transcendental arguments take the form of modus ponens with modal operators :
Regressive transcendental arguments, on the other hand, begin at the same point as the skeptic, e.g., the fact that we have experience of a causal and spatiotemporal world, and show that certain notions are implicit in our conceptions of such experience. Regressive transcendental arguments are more conservative in that they do not purport to make substantive ontological claims about the world.
Regressive transcendental arguments take the form of modus tollens with modal operators :
Transcendental arguments are often used to refute skepticism . [ 1 ] For example:
Kant uses an example in his refutation of idealism . Idealists believe that objects have no existence independent of the mind . Briefly, Kant shows that:
He has not established that outer objects exist, but only that the concept of them is legitimate, contrary to idealism. [ 4 ] [ 5 ]
Robert Lockie makes a transcendental argument for libertarian free will : [ 6 ]
However, not all use of transcendental arguments is intended to counter skepticism. The Dutch philosopher Herman Dooyeweerd used transcendental critique to establish the conditions that make a theoretical (or scientific) attitude of thought (not just the process of thinking, as in Kant) possible. [ 7 ] In particular, he showed that theoretical thought is not independent (or neutral) of pre-commitments and relationships but are rather grounded in commitments, attitudes, and presuppositions that are "religious" in nature.
C.S. Lewis made transcendental arguments to prove the existence of God and refute naturalism .
It was Immanuel Kant who gave transcendental arguments their name and notoriety. It is open to controversy, though, whether his own transcendental arguments should be classified as progressive or regressive. [ 8 ]
In the Critique of Pure Reason (1781) Kant developed one of philosophy's most famous transcendental arguments in 'The Deduction of the Pure Concepts of the Understanding'. [ 9 ] In the 'Transcendental Aesthetic', Kant used transcendental arguments to show that sensory experiences would not be possible if we did not impose their spatial and temporal forms on them, making space and time "conditions of the possibility of experience".
One of the main uses of transcendental arguments is to appeal to something that cannot be consistently denied to counter skeptics' arguments that we cannot know something about the nature of the world. One need not be a skeptic about those matters, however, to find transcendental arguments unpersuasive. There are a number of ways that one might deny that a given transcendental argument gives us knowledge of the world. The following responses may suit some versions and not others. | https://en.wikipedia.org/wiki/Transcendental_argument |
In applied mathematics , a transcendental equation is an equation over the real (or complex ) numbers that is not algebraic , that is, if at least one of its sides describes a transcendental function . [ 1 ] Examples include:
A transcendental equation need not be an equation between elementary functions , although most published examples are.
In some cases, a transcendental equation can be solved by transforming it into an equivalent algebraic equation.
Some such transformations are sketched below ; computer algebra systems may provide more elaborated transformations. [ a ]
In general, however, only approximate solutions can be found. [ 2 ]
Ad hoc methods exist for some classes of transcendental equations in one variable to transform them into algebraic equations which then might be solved.
If the unknown, say x , occurs only in exponents:
If the unknown x occurs only in arguments of a logarithm function:
If the unknown x occurs only as argument of trigonometric functions :
If the unknown x occurs only in linear expressions inside arguments of hyperbolic functions ,
Approximate numerical solutions to transcendental equations can be found using numerical , analytical approximations, or graphical methods.
These equations can be solved by direct iteration by reordering the equation into the form x = f ( x ) {\displaystyle x=f(x)} and
making an initial guess x 0 {\displaystyle x_{0}} , computing f ( x ) {\displaystyle f(x)} which becomes x 1 {\displaystyle x_{1}} and substituting it back into f ( x ) {\displaystyle f(x)} , etc. Convergence may be very slow. Some reorderings may diverge, so some other reordering that converges must be found. f ( x ) {\displaystyle f(x)} must be continuous and "sufficiently smooth" or the method may fail.
Numerical methods for solving arbitrary equations are called root-finding algorithms . By rearranging the equation into the form f ( x ) = 0 {\displaystyle f(x)=0} , if f ( x ) {\displaystyle f(x)} is continuous and differentiable, Newton's method involving taking the derivative of f ( x ) {\displaystyle f(x)} , is a common iterative method of approximating a root; an initial guess x 0 {\displaystyle x_{0}} must be "sufficiently close" to the root of interest to converge to it.
In some cases, the equation can be well approximated using Taylor series near the zero. For example, for k ≈ 1 {\displaystyle k\approx 1} , the solutions of sin x = k x {\displaystyle \sin x=kx} are approximately those of ( 1 − k ) x − x 3 / 6 = 0 {\displaystyle (1-k)x-x^{3}/6=0} , namely x = 0 {\displaystyle x=0} and x = ± 6 1 − k {\displaystyle x=\pm {\sqrt {6}}{\sqrt {1-k}}} .
For a graphical solution, one method is to set each side of a single-variable transcendental equation equal to a dependent variable and plot the two graphs , using their intersecting points to find solutions (see picture). | https://en.wikipedia.org/wiki/Transcendental_equation |
In mathematics, the transcendental law of homogeneity ( TLH ) is a heuristic principle enunciated by Gottfried Wilhelm Leibniz most clearly in a 1710 text entitled Symbolismus memorabilis calculi algebraici et infinitesimalis in comparatione potentiarum et differentiarum, et de lege homogeneorum transcendentali . [ 1 ] Henk J. M. Bos describes it as the principle to the effect that in a sum involving infinitesimals of different orders, only the lowest-order term must be retained, and the remainder discarded. [ 2 ] Thus, if a {\displaystyle a} is finite and d x {\displaystyle dx} is infinitesimal, then one sets
Similarly,
where the higher-order term du dv is discarded in accordance with the TLH. A 2012 study argues that Leibniz's TLH was a precursor of the standard part function over the hyperreals . [ 3 ]
This article about the history of mathematics is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transcendental_law_of_homogeneity |
In mathematics , a transcendental number is a real or complex number that is not algebraic : that is, not the root of a non-zero polynomial with integer (or, equivalently, rational ) coefficients . The best-known transcendental numbers are π and e . [ 1 ] [ 2 ] The quality of a number being transcendental is called transcendence .
Though only a few classes of transcendental numbers are known, partly because it can be extremely difficult to show that a given number is transcendental, transcendental numbers are not rare: indeed, almost all real and complex numbers are transcendental, since the algebraic numbers form a countable set , while the set of real numbers R {\displaystyle \mathbb {R} } and the set of complex numbers C {\displaystyle \mathbb {C} } are both uncountable sets , and therefore larger than any countable set.
All transcendental real numbers (also known as real transcendental numbers or transcendental irrational numbers ) are irrational numbers , since all rational numbers are algebraic. [ 3 ] [ 4 ] [ 5 ] [ 6 ] The converse is not true: Not all irrational numbers are transcendental. Hence, the set of real numbers consists of non-overlapping sets of rational, algebraic irrational , and transcendental real numbers. [ 3 ] For example, the square root of 2 is an irrational number, but it is not a transcendental number as it is a root of the polynomial equation x 2 − 2 = 0 . The golden ratio (denoted φ {\displaystyle \varphi } or ϕ {\displaystyle \phi } ) is another irrational number that is not transcendental, as it is a root of the polynomial equation x 2 − x − 1 = 0 .
The name "transcendental" comes from Latin trānscendere ' to climb over or beyond, surmount ' , [ 7 ] and was first used for the mathematical concept in Leibniz's 1682 paper in which he proved that sin x is not an algebraic function of x . [ 8 ] Euler , in the eighteenth century, was probably the first person to define transcendental numbers in the modern sense. [ 9 ]
Johann Heinrich Lambert conjectured that e and π were both transcendental numbers in his 1768 paper proving the number π is irrational , and proposed a tentative sketch proof that π is transcendental. [ 10 ]
Joseph Liouville first proved the existence of transcendental numbers in 1844, [ 11 ] and in 1851 gave the first decimal examples such as the Liouville constant
L b = ∑ n = 1 ∞ 10 − n ! = 10 − 1 + 10 − 2 + 10 − 6 + 10 − 24 + 10 − 120 + 10 − 720 + 10 − 5040 + 10 − 40320 + … = 0. 1 1 000 1 00000000000000000 1 00000000000000000000000000000000000000000000000000000 … {\displaystyle {\begin{aligned}L_{b}&=\sum _{n=1}^{\infty }10^{-n!}\\[2pt]&=10^{-1}+10^{-2}+10^{-6}+10^{-24}+10^{-120}+10^{-720}+10^{-5040}+10^{-40320}+\ldots \\[4pt]&=0.{\textbf {1}}{\textbf {1}}000{\textbf {1}}00000000000000000{\textbf {1}}00000000000000000000000000000000000000000000000000000\ \ldots \end{aligned}}}
in which the n th digit after the decimal point is 1 if n = k ! ( k factorial ) for some k and 0 otherwise. [ 12 ] In other words, the n th digit of this number is 1 only if n is one of 1! = 1, 2! = 2, 3! = 6, 4! = 24 , etc. Liouville showed that this number belongs to a class of transcendental numbers that can be more closely approximated by rational numbers than can any irrational algebraic number, and this class of numbers is called the Liouville numbers . Liouville showed that all Liouville numbers are transcendental. [ 13 ]
The first number to be proven transcendental without having been specifically constructed for the purpose of proving transcendental numbers' existence was e , by Charles Hermite in 1873.
In 1874 Georg Cantor proved that the algebraic numbers are countable and the real numbers are uncountable. He also gave a new method for constructing transcendental numbers . [ 14 ] Although this was already implied by his proof of the countability of the algebraic numbers, Cantor also published a construction that proves there are as many transcendental numbers as there are real numbers. [ a ] Cantor's work established the ubiquity of transcendental numbers.
In 1882 Ferdinand von Lindemann published the first complete proof that π is transcendental. He first proved that e a is transcendental if a is a non-zero algebraic number. Then, since e iπ = −1 is algebraic (see Euler's identity ), iπ must be transcendental. But since i is algebraic, π must therefore be transcendental. This approach was generalized by Karl Weierstrass to what is now known as the Lindemann–Weierstrass theorem . The transcendence of π implies that geometric constructions involving compass and straightedge only cannot produce certain results, for example squaring the circle .
In 1900 David Hilbert posed a question about transcendental numbers, Hilbert's seventh problem : If a is an algebraic number that is not 0 or 1, and b is an irrational algebraic number, is a b necessarily transcendental? The affirmative answer was provided in 1934 by the Gelfond–Schneider theorem . This work was extended by Alan Baker in the 1960s in his work on lower bounds for linear forms in any number of logarithms (of algebraic numbers). [ 16 ]
A transcendental number is a (possibly complex) number that is not the root of any integer polynomial. Every real transcendental number must also be irrational , since every rational number is the root of some integer polynomial of degree one. [ 17 ] The set of transcendental numbers is uncountably infinite . Since the polynomials with rational coefficients are countable , and since each such polynomial has a finite number of zeroes , the algebraic numbers must also be countable. However, Cantor's diagonal argument proves that the real numbers (and therefore also the complex numbers ) are uncountable. Since the real numbers are the union of algebraic and transcendental numbers, it is impossible for both subsets to be countable. This makes the transcendental numbers uncountable.
No rational number is transcendental and all real transcendental numbers are irrational. The irrational numbers contain all the real transcendental numbers and a subset of the algebraic numbers, including the quadratic irrationals and other forms of algebraic irrationals.
Applying any non-constant single-variable algebraic function to a transcendental argument yields a transcendental value. For example, from knowing that π is transcendental, it can be immediately deduced that numbers such as 5 π {\displaystyle 5\pi } , π − 3 2 {\displaystyle {\tfrac {\pi -3}{\sqrt {2}}}} , ( π − 3 ) 8 {\displaystyle ({\sqrt {\pi }}-{\sqrt {3}})^{8}} , and π 5 + 7 4 {\displaystyle {\sqrt[{4}]{\pi ^{5}+7}}} are transcendental as well.
However, an algebraic function of several variables may yield an algebraic number when applied to transcendental numbers if these numbers are not algebraically independent . For example, π and (1 − π ) are both transcendental, but π + (1 − π ) = 1 is obviously not. It is unknown whether e + π , for example, is transcendental, though at least one of e + π and eπ must be transcendental. More generally, for any two transcendental numbers a and b , at least one of a + b and ab must be transcendental. To see this, consider the polynomial ( x − a )( x − b ) = x 2 − ( a + b ) x + a b . If ( a + b ) and a b were both algebraic, then this would be a polynomial with algebraic coefficients. Because algebraic numbers form an algebraically closed field , this would imply that the roots of the polynomial, a and b , must be algebraic. But this is a contradiction, and thus it must be the case that at least one of the coefficients is transcendental.
The non-computable numbers are a strict subset of the transcendental numbers.
All Liouville numbers are transcendental, but not vice versa. Any Liouville number must have unbounded partial quotients in its simple continued fraction expansion. Using a counting argument one can show that there exist transcendental numbers which have bounded partial quotients and hence are not Liouville numbers.
Using the explicit continued fraction expansion of e , one can show that e is not a Liouville number (although the partial quotients in its continued fraction expansion are unbounded). Kurt Mahler showed in 1953 that π is also not a Liouville number. It is conjectured that all infinite continued fractions with bounded terms, that have a "simple" structure, and that are not eventually periodic are transcendental [ 18 ] (in other words, algebraic irrational roots of at least third degree polynomials do not have apparent pattern in their continued fraction expansions, since eventually periodic continued fractions correspond to quadratic irrationals, see Hermite's problem ).
Numbers proven to be transcendental:
Numbers which have yet to be proven to be either transcendental or algebraic:
The first proof that the base of the natural logarithms, e , is transcendental dates from 1873. We will now follow the strategy of David Hilbert (1862–1943) who gave a simplification of the original proof of Charles Hermite . The idea is the following:
Assume, for purpose of finding a contradiction , that e is algebraic. Then there exists a finite set of integer coefficients c 0 , c 1 , ..., c n satisfying the equation: c 0 + c 1 e + c 2 e 2 + ⋯ + c n e n = 0 , c 0 , c n ≠ 0 . {\displaystyle c_{0}+c_{1}e+c_{2}e^{2}+\cdots +c_{n}e^{n}=0,\qquad c_{0},c_{n}\neq 0~.} It is difficult to make use of the integer status of these coefficients when multiplied by a power of the irrational e , but we can absorb those powers into an integral which “mostly” will assume integer values. For a positive integer k , define the polynomial f k ( x ) = x k [ ( x − 1 ) ⋯ ( x − n ) ] k + 1 , {\displaystyle f_{k}(x)=x^{k}\left[(x-1)\cdots (x-n)\right]^{k+1},} and multiply both sides of the above equation by ∫ 0 ∞ f k ( x ) e − x d x , {\displaystyle \int _{0}^{\infty }f_{k}(x)\,e^{-x}\,\mathrm {d} x\ ,} to arrive at the equation: c 0 ( ∫ 0 ∞ f k ( x ) e − x d x ) + c 1 e ( ∫ 0 ∞ f k ( x ) e − x d x ) + ⋯ + c n e n ( ∫ 0 ∞ f k ( x ) e − x d x ) = 0 . {\displaystyle c_{0}\left(\int _{0}^{\infty }f_{k}(x)e^{-x}\,\mathrm {d} x\right)+c_{1}e\left(\int _{0}^{\infty }f_{k}(x)e^{-x}\,\mathrm {d} x\right)+\cdots +c_{n}e^{n}\left(\int _{0}^{\infty }f_{k}(x)e^{-x}\,\mathrm {d} x\right)=0~.}
By splitting respective domains of integration, this equation can be written in the form P + Q = 0 {\displaystyle P+Q=0} where P = c 0 ( ∫ 0 ∞ f k ( x ) e − x d x ) + c 1 e ( ∫ 1 ∞ f k ( x ) e − x d x ) + c 2 e 2 ( ∫ 2 ∞ f k ( x ) e − x d x ) + ⋯ + c n e n ( ∫ n ∞ f k ( x ) e − x d x ) Q = c 1 e ( ∫ 0 1 f k ( x ) e − x d x ) + c 2 e 2 ( ∫ 0 2 f k ( x ) e − x d x ) + ⋯ + c n e n ( ∫ 0 n f k ( x ) e − x d x ) {\displaystyle {\begin{aligned}P&=c_{0}\left(\int _{0}^{\infty }f_{k}(x)e^{-x}\,\mathrm {d} x\right)+c_{1}e\left(\int _{1}^{\infty }f_{k}(x)e^{-x}\,\mathrm {d} x\right)+c_{2}e^{2}\left(\int _{2}^{\infty }f_{k}(x)e^{-x}\,\mathrm {d} x\right)+\cdots +c_{n}e^{n}\left(\int _{n}^{\infty }f_{k}(x)e^{-x}\,\mathrm {d} x\right)\\Q&=c_{1}e\left(\int _{0}^{1}f_{k}(x)e^{-x}\,\mathrm {d} x\right)+c_{2}e^{2}\left(\int _{0}^{2}f_{k}(x)e^{-x}\,\mathrm {d} x\right)+\cdots +c_{n}e^{n}\left(\int _{0}^{n}f_{k}(x)e^{-x}\,\mathrm {d} x\right)\end{aligned}}} Here P will turn out to be an integer, but more importantly it grows quickly with k .
There are arbitrarily large k such that P k ! {\displaystyle \ {\tfrac {P}{k!}}\ } is a non-zero integer.
Proof. Recall the standard integral (case of the Gamma function ) ∫ 0 ∞ t j e − t d t = j ! {\displaystyle \int _{0}^{\infty }t^{j}e^{-t}\,\mathrm {d} t=j!} valid for any natural number j {\displaystyle j} . More generally,
This would allow us to compute P {\displaystyle P} exactly, because any term of P {\displaystyle P} can be rewritten as c a e a ∫ a ∞ f k ( x ) e − x d x = c a ∫ a ∞ f k ( x ) e − ( x − a ) d x = { t = x − a x = t + a d x = d t } = c a ∫ 0 ∞ f k ( t + a ) e − t d t {\displaystyle c_{a}e^{a}\int _{a}^{\infty }f_{k}(x)e^{-x}\,\mathrm {d} x=c_{a}\int _{a}^{\infty }f_{k}(x)e^{-(x-a)}\,\mathrm {d} x=\left\{{\begin{aligned}t&=x-a\\x&=t+a\\\mathrm {d} x&=\mathrm {d} t\end{aligned}}\right\}=c_{a}\int _{0}^{\infty }f_{k}(t+a)e^{-t}\,\mathrm {d} t} through a change of variables . Hence P = ∑ a = 0 n c a ∫ 0 ∞ f k ( t + a ) e − t d t = ∫ 0 ∞ ( ∑ a = 0 n c a f k ( t + a ) ) e − t d t {\displaystyle P=\sum _{a=0}^{n}c_{a}\int _{0}^{\infty }f_{k}(t+a)e^{-t}\,\mathrm {d} t=\int _{0}^{\infty }{\biggl (}\sum _{a=0}^{n}c_{a}f_{k}(t+a){\biggr )}e^{-t}\,\mathrm {d} t} That latter sum is a polynomial in t {\displaystyle t} with integer coefficients, i.e., it is a linear combination of powers t j {\displaystyle t^{j}} with integer coefficients. Hence the number P {\displaystyle P} is a linear combination (with those same integer coefficients) of factorials j ! {\displaystyle j!} ; in particular P {\displaystyle P} is an integer.
Smaller factorials divide larger factorials, so the smallest j ! {\displaystyle j!} occurring in that linear combination will also divide the whole of P {\displaystyle P} . We get that j ! {\displaystyle j!} from the lowest power t j {\displaystyle t^{j}} term appearing with a nonzero coefficient in ∑ a = 0 n c a f k ( t + a ) {\displaystyle \textstyle \sum _{a=0}^{n}c_{a}f_{k}(t+a)} , but this smallest exponent j {\displaystyle j} is also the multiplicity of t = 0 {\displaystyle t=0} as a root of this polynomial. f k ( x ) {\displaystyle f_{k}(x)} is chosen to have multiplicity k {\displaystyle k} of the root x = 0 {\displaystyle x=0} and multiplicity k + 1 {\displaystyle k+1} of the roots x = a {\displaystyle x=a} for a = 1 , … , n {\displaystyle a=1,\dots ,n} , so that smallest exponent is t k {\displaystyle t^{k}} for f k ( t ) {\displaystyle f_{k}(t)} and t k + 1 {\displaystyle t^{k+1}} for f k ( t + a ) {\displaystyle f_{k}(t+a)} with a > 0 {\displaystyle a>0} . Therefore k ! {\displaystyle k!} divides P {\displaystyle P} .
To establish the last claim in the lemma, that P {\displaystyle P} is nonzero, it is sufficient to prove that k + 1 {\displaystyle k+1} does not divide P {\displaystyle P} . To that end, let k + 1 {\displaystyle k+1} be any prime larger than n {\displaystyle n} and | c 0 | {\displaystyle |c_{0}|} . We know from the above that ( k + 1 ) ! {\displaystyle (k+1)!} divides each of c a ∫ 0 ∞ f k ( t + a ) e − t d t {\displaystyle \textstyle c_{a}\int _{0}^{\infty }f_{k}(t+a)e^{-t}\,\mathrm {d} t} for 1 ⩽ a ⩽ n {\displaystyle 1\leqslant a\leqslant n} , so in particular all of those are divisible by k + 1 {\displaystyle k+1} . It comes down to the first term c 0 ∫ 0 ∞ f k ( t ) e − t d t {\displaystyle \textstyle c_{0}\int _{0}^{\infty }f_{k}(t)e^{-t}\,\mathrm {d} t} . We have (see falling and rising factorials ) f k ( t ) = t k [ ( t − 1 ) ⋯ ( t − n ) ] k + 1 = [ ( − 1 ) n ( n ! ) ] k + 1 t k + higher degree terms {\displaystyle f_{k}(t)=t^{k}{\bigl [}(t-1)\cdots (t-n){\bigr ]}^{k+1}={\bigl [}(-1)^{n}(n!){\bigr ]}^{k+1}t^{k}+{\text{higher degree terms}}} and those higher degree terms all give rise to factorials ( k + 1 ) ! {\displaystyle (k+1)!} or larger. Hence P ≡ c 0 ∫ 0 ∞ f k ( t ) e − t d t ≡ c 0 [ ( − 1 ) n ( n ! ) ] k + 1 k ! ( mod ( k + 1 ) ) {\displaystyle P\equiv c_{0}\int _{0}^{\infty }f_{k}(t)e^{-t}\,\mathrm {d} t\equiv c_{0}{\bigl [}(-1)^{n}(n!){\bigr ]}^{k+1}k!{\pmod {(k+1)}}} That right hand side is a product of nonzero integer factors less than the prime k + 1 {\displaystyle k+1} , therefore that product is not divisible by k + 1 {\displaystyle k+1} , and the same holds for P {\displaystyle P} ; in particular P {\displaystyle P} cannot be zero.
For sufficiently large k , | Q k ! | < 1 {\displaystyle \left|{\tfrac {Q}{k!}}\right|<1} .
Proof. Note that
f k e − x = x k [ ( x − 1 ) ( x − 2 ) ⋯ ( x − n ) ] k + 1 e − x = ( x ( x − 1 ) ⋯ ( x − n ) ) k ⋅ ( ( x − 1 ) ⋯ ( x − n ) e − x ) = u ( x ) k ⋅ v ( x ) {\displaystyle {\begin{aligned}f_{k}e^{-x}&=x^{k}\left[(x-1)(x-2)\cdots (x-n)\right]^{k+1}e^{-x}\\&=\left(x(x-1)\cdots (x-n)\right)^{k}\cdot \left((x-1)\cdots (x-n)e^{-x}\right)\\&=u(x)^{k}\cdot v(x)\end{aligned}}}
where u ( x ), v ( x ) are continuous functions of x for all x , so are bounded on the interval [0, n ] . That is, there are constants G , H > 0 such that
| f k e − x | ≤ | u ( x ) | k ⋅ | v ( x ) | < G k H for 0 ≤ x ≤ n . {\displaystyle \ \left|f_{k}e^{-x}\right|\leq |u(x)|^{k}\cdot |v(x)|<G^{k}H\quad {\text{ for }}0\leq x\leq n~.}
So each of those integrals composing Q is bounded, the worst case being
| ∫ 0 n f k e − x d x | ≤ ∫ 0 n | f k e − x | d x ≤ ∫ 0 n G k H d x = n G k H . {\displaystyle \left|\int _{0}^{n}f_{k}e^{-x}\ \mathrm {d} \ x\right|\leq \int _{0}^{n}\left|f_{k}e^{-x}\right|\ \mathrm {d} \ x\leq \int _{0}^{n}G^{k}H\ \mathrm {d} \ x=nG^{k}H~.}
It is now possible to bound the sum Q as well:
| Q | < G k ⋅ n H ( | c 1 | e + | c 2 | e 2 + ⋯ + | c n | e n ) = G k ⋅ M , {\displaystyle |Q|<G^{k}\cdot nH\left(|c_{1}|e+|c_{2}|e^{2}+\cdots +|c_{n}|e^{n}\right)=G^{k}\cdot M\ ,}
where M is a constant not depending on k . It follows that
| Q k ! | < M ⋅ G k k ! → 0 as k → ∞ , {\displaystyle \ \left|{\frac {Q}{k!}}\right|<M\cdot {\frac {G^{k}}{k!}}\to 0\quad {\text{ as }}k\to \infty \ ,}
finishing the proof of this lemma.
Choosing a value of k that satisfies both lemmas leads to a non-zero integer ( P k ! ) {\displaystyle \left({\tfrac {P}{k!}}\right)} added to a vanishingly small quantity ( Q k ! ) {\displaystyle \left({\tfrac {Q}{k!}}\right)} being equal to zero: an impossibility. It follows that the original assumption, that e can satisfy a polynomial equation with integer coefficients, is also impossible; that is, e is transcendental.
A similar strategy, different from Lindemann 's original approach, can be used to show that the number π is transcendental. Besides the gamma-function and some estimates as in the proof for e , facts about symmetric polynomials play a vital role in the proof.
For detailed information concerning the proofs of the transcendence of π and e , see the references and external links. | https://en.wikipedia.org/wiki/Transcendental_number |
In a telecommunication network Transcoder free operation , or TrFO, also known as Out of band transcoder control is the concept of removing transcoding function in a call path. In legacy GSM networks a call between two mobile stations involved two transcoding functions, one at each BSC . This transcoding functionality was generally implemented in a separate Transcoder and Rate Adaptation Unit, or TRAU. TRAU was connected to BSC and MSC through TDM E1 or STM-1 .
With the introduction of NGN and 3G networks the Radio Network Controller was connected to MGW through ATM or IP instead of TDM . Therefore, this external transcoder was removed and transcoding function was moved up to the MGW. NGN also introduced Nb interface over IP such that it became possible to carry compressed voice codecs such as AMR in the Nb interface. In a call scenario such as this the transcoding functionality in the MGW could be eliminated such that voice quality can be improved and resources in MGW also could be saved. Concept of TrFO became applicable for 2G networks also with the "A interface over IP" implementation.
This article related to telecommunications is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transcoder_free_operation |
Transcripts of unknown function (TUFs) is the name that has been suggested for known RNA transcripts of DNA whose function is unclear. Most are probably ncRNAs , such as RNAi or snoRNAs , but could also represent a whole new class of ncRNA. [ 1 ] Their DNA sequences reside in the intergenic or intronic regions of the genome , which is often called junk DNA .
Broadly speaking, TUFs can be classified into three categories: [ 1 ] | https://en.wikipedia.org/wiki/Transcript_of_unknown_function |
Transcription-mediated amplification ( TMA ) is an isothermal (performed at constant temperature), single-tube nucleic acid amplification system utilizing two enzymes , RNA polymerase and reverse transcriptase .
"Amplification" means creating many more copies of a strand of nucleic acid than was present at first, in order to readily detect it or test it. Rapidly amplifying the target RNA/DNA allows a lab to simultaneously detect multiple pathogenic organisms in a single tube. TMA technology allows a clinical laboratory to perform nucleic acid test (NAT) assays for blood screening with fewer steps, less processing time, and faster results.
It is used in molecular biology , forensics , and medicine for the rapid identification and diagnosis of pathogenic organisms.
In contrast to similar techniques such as polymerase chain reaction and ligase chain reaction , this method involves RNA transcription (via RNA polymerase ) and DNA synthesis (via reverse transcriptase ) to produce an RNA amplicon (the source or product of amplification) from a target nucleic acid. This technique can be used to target both RNA and DNA.
Transcription-mediated amplification has several advantages compared to other amplification methods including:
From: http://www.gen-probe.com
This biochemistry article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transcription-mediated_amplification |
Transcription-translation coupling is a mechanism of gene expression regulation in which synthesis of an mRNA ( transcription ) is affected by its concurrent decoding ( translation ). In prokaryotes , mRNAs are translated while they are transcribed. This allows communication between RNA polymerase , the multisubunit enzyme that catalyzes transcription, and the ribosome , which catalyzes translation. Coupling involves both direct physical interactions between RNA polymerase and the ribosome ("expressome" complexes), as well as ribosome-induced changes to the structure and accessibility of the intervening mRNA that affect transcription ("attenuation" and "polarity"). [ 1 ] [ 2 ] [ 3 ]
Bacteria depend on transcription-translation coupling for genome integrity , termination of transcription and control of mRNA stability . Consequently, artificial disruption of transcription-translation coupling impairs the fitness of bacteria. Without coupling, genome integrity is compromised as stalled transcription complexes interfere with DNA replication and induce DNA breaks. [ 4 ] Lack of coupling produces premature transcription termination, likely due to increased binding of termination factor Rho . [ 5 ] Degradation of prokaryotic mRNAs is accelerated by loss of coupled translation due to increased availability of target sites of RNase E . [ 6 ] It has also been suggested that coupling of transcription with translation is an important mechanism of preventing formation of deleterious R-loops . [ 7 ] While transcription-translation coupling is likely prevalent across prokaryotic organisms, not all species are dependent on it. Unlike Escherichia coli , in Bacillus subtilis transcription significantly outpaces translation, and coupling consequently does not occur. [ 8 ]
Translation promotes transcription elongation and regulates transcription termination. Functional coupling between transcription and translation is caused by direct physical interactions between the ribosome and RNA polymerase ("expressome complex"), ribosome-dependent changes to nascent mRNA secondary structure which affect RNA polymerase activity (e.g. "attenuation"), and ribosome-dependent changes to nascent mRNA availability to transcription termination factor Rho ("polarity").
The expressome is a supramolecular complex consisting of RNA polymerase and a trailing ribosome linked by a shared mRNA transcript. It is supported by the transcription factors NusG and NusA, which interact with both RNA polymerase and the ribosome to couple the complexes together. [ 9 ] [ 10 ] [ 11 ] When coupled by transcription factor NusG, the ribosome binds newly synthesized mRNA and prevents formation of secondary structures that inhibit transcription. [ 9 ] Formation of an expressome complex also aids transcription elongation by the trailing ribosome opposing back-tracking of RNA polymerase. [ 12 ] [ 13 ] Three-dimensional models of ribosome-RNA polymerase expressome complexes have been determined by cryo-electron microscopy. [ 14 ] [ 10 ] [ 11 ] [ 9 ]
Ribosome-mediated attenuation is a gene expression mechanism in which a transcriptional termination signal is regulated by translation. [ 15 ] [ 16 ] [ 17 ] Attenuation occurs at the start of some prokaryotic operons at sequences called "attenuators", which have been identified in operons encoding amino acid biosynthesis enzymes, pyrimidine biosynthesis enzymes and antibiotic resistance factors. The attenuator functions via a set of mRNA sequence elements that coordinate the status of translation to a transcription termination signal:
Once the start of the leader open reading frame has been transcribed, RNA polymerase pauses due to folding of the nascent mRNA. This programmed arrest of transcription gives time for translation of the leader peptide to commence, and transcription to resume once coupled to translation. The downstream "control region" then modulates the elongation rate of either the ribosome or RNA polymerase. The factor determining this depends on the function of the downstream genes (e.g. the operon encoding enzymes involved in the synthesis of histidine contains a series of histidine codons is the control region). The role of the control region is to modulate whether transcription remains coupled to translation depending on the cellular state (e.g. a low availability of histidine slows translation leading to uncoupling, while high availability of histidine permits efficient translation and maintains coupling). Finally, the transcription terminator sequence is transcribed. Whether transcription is coupled to translation determines whether this stops transcription. The terminator requires folding of the mRNA, and by unwinding mRNA structures the ribosome elects the formation of either of two alternative structures: the terminator, or a competing fold termed the "antiterminator".
For amino acid biosynthesis operons, these allow the gene expression machinery to sense the abundance of the amino acid produced by the encoded enzymes, and adjust the level of downstream gene expression accordingly: transcription occurring only if the amino acid abundance is low and the demand for the enzymes is therefore high. Examples include the histidine ( his ) [ 18 ] [ 19 ] and tryptophan ( trp ) [ 20 ] biosynthetic operons.
The term "attenuation" was introduced to describe the his operon. [ 18 ] While it is typically used to describe biosynthesis operons of amino acids and other metabolites, programmed transcription termination that does not occur at the end of a gene was first identified in λ phage . [ 21 ] The discovery of attenuation was significant as it represented a regulatory mechanism distinct from repression . [ 22 ] [ 23 ] The trp operon is regulated by both attenuation and repression, and was the first evidence that gene expression regulation mechanisms can be overlapping or redundant. [ 17 ]
"Polarity" is a gene expression mechanism in which transcription terminates prematurely due to a loss of coupling between transcription and translation. Transcription outpaces translation when the ribosome pauses [ citation needed ] or encounters a premature stop codon . [ 24 ] This allows the transcription termination factor Rho to bind the mRNA and terminate mRNA synthesis. Consequently, genes that are downstream in the operon are not transcribed, and therefore not expressed. Polarity serves as mRNA quality control, allowing unused transcripts to be terminated prematurely, rather than synthesized and degraded. [ 25 ]
The term "polarity" was introduced to describe the observation that the order of genes within an operon is important: a nonsense mutation within an upstream gene effects the transcription of downstream genes. [ 24 ] Furthermore, the position of the nonsense mutation within the upstream gene modulates the "degree of polarity", with nonsense mutations at the start of the upstream genes exerting stronger polarity (more reduced transcription) on downstream genes.
Unlike the mechanism of attenuation, which involves intrinsic termination of transcription at well-defined programmed sites, polarity is Rho -dependent and termination occurs at variable position.
The potential for transcription and translation to regulate each other was recognized by the team of Marshall Nirenberg, who discovered that the processes are physically connected through the formation of a DNA-ribosome complex. [ 26 ] [ 27 ] As part of the efforts of Nirenberg's group to determine the genetic code that underlies protein synthesis, they pioneered the use of cell-free in vitro protein synthesis reactions. Analysis of these reactions revealed that protein synthesis is mRNA-dependent, and that the sequence of the mRNA strictly defines the sequence of the protein product. For this work in breaking in the genetic code, Nirenberg was jointly awarded the Nobel Prize in Physiology or Medicine in 1968. Having established that transcription and translation are linked biochemically (translation depends on the product of transcription), an outstanding question remained whether they were linked physically - whether the newly synthesized mRNA released from the DNA before it is translated, or if can translation occur concurrently with transcription. Electron micrographs of stained cell-free protein synthesis reactions revealed branched assemblies in which strings of ribosomes are linked to a central DNA fibre. [ 27 ] DNA isolated from bacterial cells co-sediment with ribosomes, further supporting the conclusion that transcription and translation occur together. [ 26 ] Direct contact between ribosomes and RNA polymerase are observable within these early micrographs. [ 3 ] The potential for simultaneous regulation of transcription and translation at this junction was noted in Nirenberg's work as early as 1964. [ 26 ] | https://en.wikipedia.org/wiki/Transcription-translation_coupling |
Transcription is the process of copying a segment of DNA into RNA for the purpose of gene expression . Some segments of DNA are transcribed into RNA molecules that can encode proteins , called messenger RNA (mRNA). Other segments of DNA are transcribed into RNA molecules called non-coding RNAs (ncRNAs).
Both DNA and RNA are nucleic acids , which use base pairs of nucleotides as a complementary language. During transcription, a DNA sequence is read by an RNA polymerase , which produces a complementary, antiparallel RNA strand called a primary transcript .
In virology , the term transcription is used when referring to mRNA synthesis from a viral RNA molecule. The genome of many RNA viruses [ a ] is composed of negative-sense RNA which acts as a template for positive sense viral messenger RNA - a necessary step in the synthesis of viral proteins needed for viral replication . This process is catalyzed by a viral RNA dependent RNA polymerase . [ 1 ]
A DNA transcription unit encoding for a protein may contain both a coding sequence , which will be translated into the protein, and regulatory sequences , which direct and regulate the synthesis of that protein. The regulatory sequence before ( upstream from) the coding sequence is called the five prime untranslated regions (5'UTR); the sequence after ( downstream from) the coding sequence is called the three prime untranslated regions (3'UTR). [ 2 ]
As opposed to DNA replication , transcription results in an RNA complement that includes the nucleotide uracil (U) in all instances where thymine (T) would have occurred in a DNA complement. [ 3 ]
Only one of the two DNA strands serves as a template for transcription. The antisense strand of DNA is read by RNA polymerase from the 3' end to the 5' end during transcription (3' → 5'). The complementary RNA is created in the opposite direction, in the 5' → 3' direction, matching the sequence of the sense strand except switching uracil for thymine. This directionality is because RNA polymerase can only add nucleotides to the 3' end of the growing mRNA chain. This use of only the 3' → 5' DNA strand eliminates the need for the Okazaki fragments that are seen in DNA replication. [ 2 ] This also removes the need for an RNA primer to initiate RNA synthesis, as is the case in DNA replication.
The non -template (sense) strand of DNA is called the coding strand , because its sequence is the same as the newly created RNA transcript (except for the substitution of uracil for thymine). This is the strand that is used by convention when presenting a DNA sequence. [ 4 ]
Transcription has some proofreading mechanisms, but they are fewer and less effective than the controls for copying DNA. As a result, transcription has a lower copying fidelity than DNA replication. [ 5 ]
Transcription is divided into initiation , promoter escape , elongation, and termination . [ 6 ]
Setting up for transcription in mammals is regulated by many cis-regulatory elements , including core promoter and promoter-proximal elements that are located near the transcription start sites of genes. Core promoters combined with general transcription factors are sufficient to direct transcription initiation, but generally have low basal activity. [ 7 ] Other important cis-regulatory modules are localized in DNA regions that are distant from the transcription start sites. These include enhancers , silencers , insulators and tethering elements. [ 8 ] Among this constellation of elements, enhancers and their associated transcription factors have a leading role in the initiation of gene transcription. [ 9 ] An enhancer localized in a DNA region distant from the promoter of a gene can have a very large effect on gene transcription, with some genes undergoing up to 100-fold increased transcription due to an activated enhancer. [ 10 ]
Enhancers are regions of the genome that are major gene-regulatory elements. Enhancers control cell-type-specific gene transcription programs, most often by looping through long distances to come in physical proximity with the promoters of their target genes. [ 11 ] While there are hundreds of thousands of enhancer DNA regions, [ 12 ] for a particular type of tissue only specific enhancers are brought into proximity with the promoters that they regulate. In a study of brain cortical neurons, 24,937 loops were found, bringing enhancers to their target promoters. [ 10 ] Multiple enhancers, each often at tens or hundred of thousands of nucleotides distant from their target genes, loop to their target gene promoters and can coordinate with each other to control transcription of their common target gene. [ 11 ]
The schematic illustration in this section shows an enhancer looping around to come into close physical proximity with the promoter of a target gene. The loop is stabilized by a dimer of a connector protein (e.g. dimer of CTCF or YY1 ), with one member of the dimer anchored to its binding motif on the enhancer and the other member anchored to its binding motif on the promoter (represented by the red zigzags in the illustration). [ 13 ] Several cell function specific transcription factors (there are about 1,600 transcription factors in a human cell [ 14 ] ) generally bind to specific motifs on an enhancer [ 15 ] and a small combination of these enhancer-bound transcription factors, when brought close to a promoter by a DNA loop, govern level of transcription of the target gene. Mediator (a complex usually consisting of about 26 proteins in an interacting structure) communicates regulatory signals from enhancer DNA-bound transcription factors directly to the RNA polymerase II (pol II) enzyme bound to the promoter. [ 16 ]
Enhancers, when active, are generally transcribed from both strands of DNA with RNA polymerases acting in two different directions, producing two enhancer RNAs (eRNAs) as illustrated in the Figure. [ 17 ] An inactive enhancer may be bound by an inactive transcription factor. Phosphorylation of the transcription factor may activate it and that activated transcription factor may then activate the enhancer to which it is bound (see small red star representing phosphorylation of transcription factor bound to enhancer in the illustration). [ 18 ] An activated enhancer begins transcription of its RNA before activating transcription of messenger RNA from its target gene. [ 19 ]
Transcription regulation at about 60% of promoters is also controlled by methylation of cytosines within CpG dinucleotides (where 5' cytosine is followed by 3' guanine or CpG sites ). 5-methylcytosine (5-mC) is a methylated form of the DNA base cytosine (see Figure). 5-mC is an epigenetic marker found predominantly within CpG sites. About 28 million CpG dinucleotides occur in the human genome. [ 20 ] In most tissues of mammals, on average, 70% to 80% of CpG cytosines are methylated (forming 5-methylCpG or 5-mCpG). [ 21 ] However, unmethylated cytosines within 5'cytosine-guanine 3' sequences often occur in groups, called CpG islands , at active promoters. About 60% of promoter sequences have a CpG island while only about 6% of enhancer sequences have a CpG island. [ 22 ] CpG islands constitute regulatory sequences, since if CpG islands are methylated in the promoter of a gene this can reduce or silence gene transcription. [ 23 ]
DNA methylation regulates gene transcription through interaction with methyl binding domain (MBD) proteins, such as MeCP2, MBD1 and MBD2. These MBD proteins bind most strongly to highly methylated CpG islands . [ 24 ] These MBD proteins have both a methyl-CpG-binding domain as well as a transcription repression domain. [ 24 ] They bind to methylated DNA and guide or direct protein complexes with chromatin remodeling and/or histone modifying activity to methylated CpG islands. MBD proteins generally repress local chromatin such as by catalyzing the introduction of repressive histone marks, or creating an overall repressive chromatin environment through nucleosome remodeling and chromatin reorganization. [ 24 ]
As noted in the previous section, transcription factors are proteins that bind to specific DNA sequences in order to regulate the expression of a gene. The binding sequence for a transcription factor in DNA is usually about 10 or 11 nucleotides long. As summarized in 2009, Vaquerizas et al. indicated there are approximately 1,400 different transcription factors encoded in the human genome by genes that constitute about 6% of all human protein encoding genes. [ 25 ] About 94% of transcription factor binding sites (TFBSs) that are associated with signal-responsive genes occur in enhancers while only about 6% of such TFBSs occur in promoters. [ 15 ]
EGR1 protein is a particular transcription factor that is important for regulation of methylation of CpG islands. An EGR1 transcription factor binding site is frequently located in enhancer or promoter sequences. [ 26 ] There are about 12,000 binding sites for EGR1 in the mammalian genome and about half of EGR1 binding sites are located in promoters and half in enhancers. [ 26 ] The binding of EGR1 to its target DNA binding site is insensitive to cytosine methylation in the DNA. [ 26 ]
While only small amounts of EGR1 transcription factor protein are detectable in cells that are un-stimulated, translation of the EGR1 gene into protein at one hour after stimulation is drastically elevated. [ 27 ] Production of EGR1 transcription factor proteins, in various types of cells, can be stimulated by growth factors, neurotransmitters, hormones, stress and injury. [ 27 ] In the brain, when neurons are activated, EGR1 proteins are up-regulated and they bind to (recruit) the pre-existing TET1 enzymes that are produced in high amounts in neurons. TET enzymes can catalyse demethylation of 5-methylcytosine. When EGR1 transcription factors bring TET1 enzymes to EGR1 binding sites in promoters, the TET enzymes can demethylate the methylated CpG islands at those promoters. Upon demethylation, these promoters can then initiate transcription of their target genes. Hundreds of genes in neurons are differentially expressed after neuron activation through EGR1 recruitment of TET1 to methylated regulatory sequences in their promoters. [ 26 ]
The methylation of promoters is also altered in response to signals. The three mammalian DNA methyltransferasess (DNMT1, DNMT3A, and DNMT3B) catalyze the addition of methyl groups to cytosines in DNA. While DNMT1 is a maintenance methyltransferase, DNMT3A and DNMT3B can carry out new methylations. There are also two splice protein isoforms produced from the DNMT3A gene: DNA methyltransferase proteins DNMT3A1 and DNMT3A2. [ 28 ]
The splice isoform DNMT3A2 behaves like the product of a classical immediate-early gene and, for instance, it is robustly and transiently produced after neuronal activation. [ 29 ] Where the DNA methyltransferase isoform DNMT3A2 binds and adds methyl groups to cytosines appears to be determined by histone post translational modifications. [ 30 ] [ 31 ] [ 32 ]
On the other hand, neural activation causes degradation of DNMT3A1 accompanied by reduced methylation of at least one evaluated targeted promoter. [ 33 ]
Transcription begins with the RNA polymerase and one or more general transcription factors binding to a DNA promoter sequence to form an RNA polymerase-promoter closed complex. In the closed complex, the promoter DNA is still fully double-stranded. [ 6 ]
RNA polymerase, assisted by one or more general transcription factors, then unwinds approximately 14 base pairs of DNA to form an RNA polymerase-promoter open complex. In the open complex, the promoter DNA is partly unwound and single-stranded. The exposed, single-stranded DNA is referred to as the " transcription bubble ". [ 6 ]
RNA polymerase, assisted by one or more general transcription factors, then selects a transcription start site in the transcription bubble, binds to an initiating NTP and an extending NTP (or a short RNA primer and an extending NTP) complementary to the transcription start site sequence, and catalyzes bond formation to yield an initial RNA product. [ 6 ]
In bacteria , RNA polymerase holoenzyme consists of five subunits: 2 α subunits, 1 β subunit, 1 β' subunit, and 1 ω subunit. In bacteria, there is one general RNA transcription factor known as a sigma factor . RNA polymerase core enzyme binds to the bacterial general transcription (sigma) factor to form RNA polymerase holoenzyme and then binds to a promoter. [ 6 ] (RNA polymerase is called a holoenzyme when sigma subunit is attached to the core enzyme which is consist of 2 α subunits, 1 β subunit, 1 β' subunit only). Unlike eukaryotes, the initiating nucleotide of nascent bacterial mRNA is not capped with a modified guanine nucleotide. The initiating nucleotide of bacterial transcripts bears a 5′ triphosphate (5′-PPP), which can be used for genome-wide mapping of transcription initiation sites. [ 35 ]
In archaea and eukaryotes , RNA polymerase contains subunits homologous to each of the five RNA polymerase subunits in bacteria and also contains additional subunits. In archaea and eukaryotes, the functions of the bacterial general transcription factor sigma are performed by multiple general transcription factors that work together. [ 6 ] In archaea, there are three general transcription factors: TBP , TFB , and TFE . In eukaryotes, in RNA polymerase II -dependent transcription, there are six general transcription factors: TFIIA , TFIIB (an ortholog of archaeal TFB), TFIID (a multisubunit factor in which the key subunit, TBP , is an ortholog of archaeal TBP), TFIIE (an ortholog of archaeal TFE), TFIIF , and TFIIH . The TFIID is the first component to bind to DNA due to binding of TBP, while TFIIH is the last component to be recruited. In archaea and eukaryotes, the RNA polymerase-promoter closed complex is usually referred to as the " preinitiation complex ". [ 36 ]
Transcription initiation is regulated by additional proteins, known as activators and repressors , and, in some cases, associated coactivators or corepressors , which modulate formation and function of the transcription initiation complex. [ 6 ]
After the first bond is synthesized, the RNA polymerase must escape the promoter. During this time there is a tendency to release the RNA transcript and produce truncated transcripts. This is called abortive initiation , and is common for both eukaryotes and prokaryotes. [ 37 ] Abortive initiation continues to occur until an RNA product of a threshold length of approximately 10 nucleotides is synthesized, at which point promoter escape occurs and a transcription elongation complex is formed. [ citation needed ]
Mechanistically, promoter escape occurs through DNA scrunching , providing the energy needed to break interactions between RNA polymerase holoenzyme and the promoter. [ 38 ]
In bacteria, it was historically thought that the sigma factor is definitely released after promoter clearance occurs. This theory had been known as the obligate release model. However, later data showed that upon and following promoter clearance, the sigma factor is released according to a stochastic model known as the stochastic release model . [ 39 ]
In eukaryotes, at an RNA polymerase II-dependent promoter, upon promoter clearance, TFIIH phosphorylates serine 5 on the carboxy terminal domain of RNA polymerase II, leading to the recruitment of capping enzyme (CE). [ 40 ] [ 41 ] The exact mechanism of how CE induces promoter clearance in eukaryotes is not yet known.
One strand of the DNA, the template strand (or noncoding strand), is used as a template for RNA synthesis. As transcription proceeds, RNA polymerase traverses the template strand and uses base pairing complementarity with the DNA template to create an RNA copy (which elongates during the traversal). Although RNA polymerase traverses the template strand from 3' → 5', the coding (non-template) strand and newly formed RNA can also be used as reference points, so transcription can be described as occurring 5' → 3'. This produces an RNA molecule from 5' → 3', an exact copy of the coding strand (except that thymines are replaced with uracils , and the nucleotides are composed of a ribose (5-carbon) sugar whereas DNA has deoxyribose (one fewer oxygen atom) in its sugar-phosphate backbone). [ 3 ]
mRNA transcription can involve multiple RNA polymerases on a single DNA template and multiple rounds of transcription (amplification of particular mRNA), so many mRNA molecules can be rapidly produced from a single copy of a gene. [ citation needed ] The characteristic elongation rates in prokaryotes and eukaryotes are about 10–100 nts/sec. [ 42 ] In eukaryotes, however, nucleosomes act as major barriers to transcribing polymerases during transcription elongation. [ 43 ] [ 44 ] In these organisms, the pausing induced by nucleosomes can be regulated by transcription elongation factors such as TFIIS. [ 44 ]
Elongation also involves a proofreading mechanism that can replace incorrectly incorporated bases. In eukaryotes, this may correspond with short pauses during transcription that allow appropriate RNA editing factors to bind. These pauses may be intrinsic to the RNA polymerase or due to chromatin structure. [ citation needed ]
Double-strand breaks in actively transcribed regions of DNA are repaired by homologous recombination during the S and G2 phases of the cell cycle . [ 45 ] [ 46 ] Since transcription enhances the accessibility of DNA to exogenous chemicals and internal metabolites that can cause recombinogenic lesions, homologous recombination of a particular DNA sequence may be strongly stimulated by transcription. [ 47 ]
Bacteria use two different strategies for transcription termination – Rho-independent termination and Rho-dependent termination. In Rho-independent transcription termination , RNA transcription stops when the newly synthesized RNA molecule forms a G-C-rich hairpin loop followed by a run of Us. When the hairpin forms, the mechanical stress breaks the weak rU-dA bonds, now filling the DNA–RNA hybrid. This pulls the poly-U transcript out of the active site of the RNA polymerase, terminating transcription. In Rho-dependent termination, Rho , a protein factor, destabilizes the interaction between the template and the mRNA, thus releasing the newly synthesized mRNA from the elongation complex. [ 48 ]
Transcription termination in eukaryotes is less well understood than in bacteria, but involves cleavage of the new transcript followed by template-independent addition of adenines at its new 3' end, in a process called polyadenylation . [ 49 ]
Beyond termination by a terminator sequences (which is a part of a gene ), transcription may also need to be terminated when it encounters conditions such as DNA damage or an active replication fork . In bacteria, the Mfd ATPase can remove a RNA polymerase stalled at a lesion by prying open its clamp. It also recruits nucleotide excision repair machinery to repair the lesion. Mfd is proposed to also resolve conflicts between DNA replication and transcription. [ 50 ] In eukayrotes, ATPase TTF2 helps to suppress the action of RNAP I and II during mitosis , preventing errors in chromosomal segregation. [ 51 ] In archaea, the Eta ATPase is proposed to play a similar role. [ 52 ]
Genome damage occurs with a high frequency, estimated to range between tens and hundreds of thousands of DNA damages arising in each cell every day. [ 53 ] The process of transcription is a major source of DNA damage, due to the formation of single-strand DNA intermediates that are vulnerable to damage. [ 53 ] The regulation of transcription by processes using base excision repair and/or topoisomerases to cut and remodel the genome also increases the vulnerability of DNA to damage. [ 53 ]
RNA polymerase plays a very crucial role in all steps including post-transcriptional changes in RNA.
As shown in the image in the right it is evident that the CTD (C Terminal Domain) is a tail that changes its shape; this tail will be used as a carrier of splicing, capping and polyadenylation , as shown in the image on the left. [ 54 ]
Transcription inhibitors can be used as antibiotics against, for example, pathogenic bacteria ( antibacterials ) and fungi ( antifungals ). An example of such an antibacterial is rifampicin , which inhibits bacterial transcription of DNA into mRNA by inhibiting DNA-dependent RNA polymerase by binding its beta-subunit, while 8-hydroxyquinoline is an antifungal transcription inhibitor. [ 55 ] The effects of histone methylation may also work to inhibit the action of transcription. Potent, bioactive natural products like triptolide that inhibit mammalian transcription via inhibition of the XPB subunit of the general transcription factor TFIIH has been recently reported as a glucose conjugate for targeting hypoxic cancer cells with increased glucose transporter production. [ 56 ]
In vertebrates, the majority of gene promoters contain a CpG island with numerous CpG sites . [ 57 ] When many of a gene's promoter CpG sites are methylated the gene becomes inhibited (silenced). [ 58 ] Colorectal cancers typically have 3 to 6 driver mutations and 33 to 66 hitchhiker or passenger mutations. [ 59 ] However, transcriptional inhibition (silencing) may be of more importance than mutation in causing progression to cancer. For example, in colorectal cancers about 600 to 800 genes are transcriptionally inhibited by CpG island methylation (see regulation of transcription in cancer ). Transcriptional repression in cancer can also occur by other epigenetic mechanisms, such as altered production of microRNAs . [ 60 ] In breast cancer, transcriptional repression of BRCA1 may occur more frequently by over-produced microRNA-182 than by hypermethylation of the BRCA1 promoter (see Low expression of BRCA1 in breast and ovarian cancers ). [ citation needed ]
Active transcription units are clustered in the nucleus, in discrete sites called transcription factories or euchromatin . Such sites can be visualized by allowing engaged polymerases to extend their transcripts in tagged precursors (Br-UTP or Br-U) and immuno-labeling the tagged nascent RNA. Transcription factories can also be localized using fluorescence in situ hybridization or marked by antibodies directed against polymerases. There are ≈10,000 factories in the nucleoplasm of a HeLa cell , among which are ≈8,000 polymerase II factories and ≈2,000 polymerase III factories. Each polymerase II factory contains ≈8 polymerases. As most active transcription units are associated with only one polymerase, each factory usually contains ≈8 different transcription units. These units might be associated through promoters and/or enhancers, with loops forming a "cloud" around the factor. [ 61 ]
A molecule that allows the genetic material to be realized as a protein was first hypothesized by François Jacob and Jacques Monod . Severo Ochoa won a Nobel Prize in Physiology or Medicine in 1959 for developing a process for synthesizing RNA in vitro with polynucleotide phosphorylase , which was useful for cracking the genetic code . RNA synthesis by RNA polymerase was established in vitro by several laboratories by 1965; however, the RNA synthesized by these enzymes had properties that suggested the existence of an additional factor needed to terminate transcription correctly. [ citation needed ]
Roger D. Kornberg won the 2006 Nobel Prize in Chemistry "for his studies of the molecular basis of eukaryotic transcription ". [ 62 ]
Transcription can be measured and detected in a variety of ways: [ citation needed ]
Some viruses (such as HIV , the cause of AIDS ), have the ability to transcribe RNA into DNA. HIV has an RNA genome that is reverse transcribed into DNA. The resulting DNA can be merged with the DNA genome of the host cell. The main enzyme responsible for synthesis of DNA from an RNA template is called reverse transcriptase . [ 65 ]
In the case of HIV, reverse transcriptase is responsible for synthesizing a complementary DNA strand (cDNA) to the viral RNA genome. The enzyme ribonuclease H then digests the RNA strand, and reverse transcriptase synthesises a complementary strand of DNA to form a double helix DNA structure (cDNA). The cDNA is integrated into the host cell's genome by the enzyme integrase , which causes the host cell to generate viral proteins that reassemble into new viral particles. In HIV, subsequent to this, the host cell undergoes programmed cell death, or apoptosis , of T cells . [ 66 ] However, in other retroviruses, the host cell remains intact as the virus buds out of the cell. [ citation needed ]
Some eukaryotic cells contain an enzyme with reverse transcription activity called telomerase . Telomerase carries an RNA template from which it synthesizes a telomere , a repeating sequence of DNA, to the end of linear chromosomes. It is important because every time a linear chromosome is duplicated, it is shortened. With the telomere at the ends of chromosomes, the shortening eliminates some of the non-essential, repeated sequence, rather than the protein-encoding DNA sequence farther away from the chromosome end.
Telomerase is often activated in cancer cells to enable cancer cells to duplicate their genomes indefinitely without losing important protein-coding DNA sequence. Activation of telomerase could be part of the process that allows cancer cells to become immortal. The immortalizing factor of cancer via telomere lengthening due to telomerase has been proven to occur in 90% of all carcinogenic tumors in vivo with the remaining 10% using an alternative telomere maintenance route called ALT or Alternative Lengthening of Telomeres. [ 67 ] | https://en.wikipedia.org/wiki/Transcription_(biology) |
TAL ( transcription activator-like ) effectors (often referred to as TALEs , but not to be confused with the t hree a mino acid l oop e xtension homeobox class of proteins) are proteins secreted by some β- and γ-proteobacteria . [ 1 ] Most of these are Xanthomonads . Plant pathogenic Xanthomonas bacteria are especially known for TALEs, produced via their type III secretion system . These proteins can bind promoter sequences in the host plant and activate the expression of plant genes that aid bacterial infection. The TALE domain responsible for binding to DNA is known to have 1.5 to 33.5 short sequences that are repeated multiple times (tandem repeats). [ 2 ] Each of these repeats was found to be specific for a certain base pair of the DNA. [ 2 ] These repeats also have repeat variable residues (RVD) that can detect specific DNA base pairs. [ 2 ] They recognize plant DNA sequences through a central repeat domain consisting of a variable number of ~34 amino acid repeats. There appears to be a one-to-one correspondence between the identity of two critical amino acids in each repeat and each DNA base in the target sequence. These proteins are interesting to researchers both for their role in disease of important crop species and the relative ease of retargeting them to bind new DNA sequences. Similar proteins can be found in the pathogenic bacterium Ralstonia solanacearum [ 3 ] [ 4 ] [ 1 ] and Burkholderia rhizoxinica , [ 5 ] [ 1 ] as well as yet unidentified marine microorganisms. [ 6 ] The term TALE-likes is used to refer to the putative protein family encompassing the TALEs and these related proteins.
Xanthomonas are Gram-negative bacteria that can infect a wide variety of plant species including pepper/capsicum, rice, citrus, cotton, tomato, and soybeans. [ 7 ] Some types of Xanthomonas cause localized leaf spot or leaf streak while others spread systemically and cause black rot or leaf blight disease. They inject a number of effector proteins, including TAL effectors, into the plant via their type III secretion system . TAL effectors have several motifs normally associated with eukaryotes including multiple nuclear localization signals and an acidic activation domain. When injected into plants, these proteins can enter the nucleus of the plant cell, bind plant promoter sequences, and activate transcription of plant genes that aid in bacterial infection. [ 7 ] Plants have developed a defense mechanism against type III effectors that includes R (resistance) genes triggered by these effectors. Some of these R genes appear to have evolved to contain TAL-effector binding sites similar to site in the intended target gene. This competition between pathogenic bacteria and the host plant has been hypothesized to account for the apparently malleable nature of the TAL effector DNA binding domain. [ 8 ]
R. solanacearum , B. rhizoxinica , and banana blood disease (a bacterium not yet definitively identified, in the R. solanacearum species group). [ 1 ]
The most distinctive characteristic of TAL effectors is a central repeat domain containing between 1.5 and 33.5 repeats that are usually 34 residues in length (the C-terminal repeat is generally shorter and referred to as a “half repeat”). [ 7 ] A typical repeat sequence is LTPEQVVAIAS HD GGKQALETVQRLLPVLCQAHG , but the residues at the 12th and 13th positions are hypervariable (these two amino acids are also known as the repeat variable diresidue or RVD). There is a simple relationship between the identity of these two residues in sequential repeats and sequential DNA bases in the TAL effector's target site. [ 8 ] The crystal structure of a TAL effector bound to DNA indicates that each repeat comprises two alpha helices and a short RVD-containing loop where the second residue of the RVD makes sequence-specific DNA contacts while the first residue of the RVD stabilizes the RVD-containing loop. [ 10 ] [ 11 ] Target sites of TAL effectors also tend to include a thymine flanking the 5’ base targeted by the first repeat; this appears to be due to a contact between this T and a conserved tryptophan in the region N-terminal of the central repeat domain. [ 10 ] However, this "zero" position does not always contain a thymine, as some scaffolds are more permissive. [ 12 ]
The TAL-DNA code was broken by two separate groups in 2010. [ 8 ] The first group, headed by Adam Bogdanove , broke this code computationally by searching for patterns in protein sequence alignments and DNA sequences of target promoters derived from a database of genes upregulated by TALEs. [ 13 ] The second group (Boch) deduced the code through molecular analysis of the TAL effector AvrBs3 and its target DNA sequence in the promoter of a pepper gene activated by AvrBs3. [ 14 ] The experimentally validated code between RVD sequence and target DNA base can be expressed as follows:
TAL effectors can induce susceptibility genes that are members of the NODULIN3 (N3) gene family. These genes are essential for the development of the disease. In rice two genes, Os-8N3 and Os-11N3, are induced by TAL effectors. Os-8N3 is induced by PthXo1 and Os-11N3 is induced by PthXo3 and AvrXa7.
Two hypotheses exist about possible functions for N3 proteins:
This simple correspondence between amino acids in TAL effectors and DNA bases in their target sites makes them useful for protein engineering applications. Numerous groups have designed artificial TAL effectors capable of recognizing new DNA sequences in a variety of experimental systems. [ 14 ] [ 16 ] [ 17 ] [ 18 ] [ 19 ] [ 20 ] Such engineered TAL effectors have been used to create artificial transcription factors that can be used to target and activate or repress endogenous genes in tomato , [ 16 ] Arabidopsis thaliana , [ 16 ] and human cells. [ 17 ] [ 19 ] [ 9 ] [ 21 ]
Genetic constructs to encode TAL effector-based proteins can be made using either conventional gene synthesis or modular assembly. [ 19 ] [ 21 ] [ 22 ] [ 23 ] [ 24 ] [ 25 ] [ 26 ] [ 27 ] A plasmid kit for assembling custom TALEN and other TAL effector constructs is available through the public, not-for-profit repository Addgene . Webpages providing access to public software, protocols, and other resources for TAL effector-DNA targeting applications include the TAL Effector-Nucleotide Targeter and taleffectors.com .
Engineered TAL effectors can also be fused to the cleavage domain of FokI to create TAL effector nucleases (TALEN) or to meganucleases (nucleases with longer recognition sites) to create "megaTALs." [ 28 ] Such fusions share some properties with zinc finger nucleases and may be useful for genetic engineering and gene therapy applications. [ 29 ]
TALEN-based approaches are used in the emerging fields of gene editing and genome engineering . TALEN fusions show activity in a yeast-based assay, [ 18 ] [ 30 ] at endogenous yeast genes, [ 22 ] in a plant reporter assay, [ 20 ] at an endogenous plant gene, [ 23 ] at endogenous zebrafish genes, [ 31 ] [ 32 ] at an endogenous rat gene, [ 33 ] and at endogenous human genes. [ 17 ] [ 23 ] [ 34 ] The human HPRT1 gene has been targeted at detectable, but unquantified levels. [ 23 ] In addition, TALEN constructs containing the FokI cleavage domain fused to a smaller portion of the TAL effector still containing the DNA binding domain have been used to target the endogenous NTF3 and CCR5 genes in human cells with efficiencies of up to 25%. [ 17 ] TAL effector nucleases have also been used to engineer human embryonic stem cells and induced pluripotent stem cells (IPSCs) [ 34 ] and to knock out the endogenous ben-1 gene in C. elegans . [ 35 ]
TALE-induced non-homologous end joining modification has been used to produce novel disease resistance in rice. [ 1 ] | https://en.wikipedia.org/wiki/Transcription_activator-like_effector |
Transcription activator-like effector nucleases ( TALEN ) are restriction enzymes that can be engineered to cut specific sequences of DNA. They are made by fusing a TAL effector DNA-binding domain to a DNA cleavage domain (a nuclease which cuts DNA strands). Transcription activator-like effectors (TALEs) can be engineered to bind to practically any desired DNA sequence, so when combined with a nuclease, DNA can be cut at specific locations. [ 1 ] The restriction enzymes can be introduced into cells, for use in gene editing or for genome editing in situ , a technique known as genome editing with engineered nucleases . Alongside zinc finger nucleases and CRISPR/Cas9 , TALEN is a prominent tool in the field of genome editing .
TAL effectors are proteins that are secreted by Xanthomonas bacteria via their type III secretion system when they infect plants . [ 2 ] The DNA binding domain contains a repeated highly conserved 33–34 amino acid sequence with divergent 12th and 13th amino acids. These two positions, referred to as the Repeat Variable Diresidue (RVD), are highly variable and show a strong correlation with specific nucleotide recognition. [ 3 ] [ 4 ] This straightforward relationship between amino acid sequence and DNA recognition has allowed for the engineering of specific DNA-binding domains by selecting a combination of repeat segments containing the appropriate RVDs. [ 1 ] Notably, slight changes in the RVD and the incorporation of "nonconventional" RVD sequences can improve targeting specificity. [ 5 ]
The non-specific DNA cleavage domain from the end of the FokI endonuclease can be used to construct hybrid nucleases that are active in a yeast assay. [ 6 ] [ 7 ] These reagents are also active in plant cells [ 8 ] [ 9 ] and in animal cells. [ 9 ] [ 10 ] [ 11 ] [ 12 ] Initial TALEN studies used the wild-type FokI cleavage domain, but some subsequent TALEN studies [ 11 ] [ 13 ] [ 14 ] also used FokI cleavage domain variants with mutations designed to improve cleavage specificity [ 15 ] [ 16 ] and cleavage activity. [ 17 ] The FokI domain functions as a dimer, requiring two constructs with unique DNA binding domains for sites in the target genome with proper orientation and spacing. Both the number of amino acid residues between the TALE DNA binding domain and the FokI cleavage domain and the number of bases between the two individual TALEN binding sites appear to be important parameters for achieving high levels of activity. [ 10 ] [ 18 ]
The simple relationship between amino acid sequence and DNA recognition of the TALE binding domain allows for the efficient engineering of proteins. In this case, artificial gene synthesis is problematic because of improper annealing of the repetitive sequence found in the TALE binding domain. [ 19 ] One solution to this is to use a publicly available software program (DNAWorks [ 20 ] ) to calculate oligonucleotides suitable for assembly in a two step PCR oligonucleotide assembly followed by whole gene amplification. A number of modular assembly schemes for generating engineered TALE constructs have also been reported. [ 9 ] [ 19 ] [ 21 ] [ 22 ] [ 23 ] [ 24 ] Both methods offer a systematic approach to engineering DNA binding domains that is conceptually similar to the modular assembly method for generating zinc finger DNA recognition domains.
Once the TALEN constructs have been assembled, they are inserted into plasmids ; the target cells are then transfected with the plasmids, and the gene products are expressed and enter the nucleus to access the genome. Alternatively, TALEN constructs can be delivered to the cells as mRNAs, which removes the possibility of genomic integration of the TALEN-expressing protein. Using an mRNA vector can also dramatically increase the level of homology directed repair (HDR) and the success of introgression during gene editing.
TALEN can be used to edit genomes by inducing double-strand breaks (DSB), which cells respond to with repair mechanisms.
Non-homologous end joining (NHEJ) directly ligates DNA from either side of a double-strand break where there is very little or no sequence overlap for annealing. This repair mechanism induces errors in the genome via indels (insertion or deletion), or chromosomal rearrangement; any such errors may render the gene products coded at that location non-functional. [ 10 ] Because this activity can vary depending on the species, cell type, target gene, and nuclease used, it should be monitored when designing new systems. A simple heteroduplex cleavage assay can be run which detects any difference between two alleles amplified by PCR. Cleavage products can be visualized on simple agarose gels or slab gel systems.
Alternatively, DNA can be introduced into a genome through NHEJ in the presence of exogenous double-stranded DNA fragments. [ 10 ]
Homology directed repair can also introduce foreign DNA at the DSB as the transfected double-stranded sequences are used as templates for the repair enzymes. [ 10 ]
TALEN has been used to efficiently modify plant genomes, [ 25 ] creating economically important food crops with favorable nutritional qualities. [ 26 ] They have also been harnessed to develop tools for the production of biofuels . [ 27 ] In addition, it has been used to engineer stably modified human embryonic stem cell and induced pluripotent stem cell (IPSCs) clones and human erythroid cell lines, [ 11 ] [ 28 ] to generate knockout C. elegans , [ 12 ] knockout rats , [ 13 ] knockout mice, [ 29 ] and knockout zebrafish . [ 14 ] [ 30 ] Moreover, the method can be used to generate knockin organisms. Wu et al.obtained a Sp110 knockin cattle using Talen nickases to induce increased resistance of tuberculosis. [ 31 ] This approach has also been used to generate knockin rats by TALEN mRNA microinjection in one-cell embryos. [ 32 ]
TALEN has also been utilized experimentally to correct the genetic errors that underlie disease. [ 33 ] For example, it has been used in vitro to correct the genetic defects that cause disorders such as sickle cell disease , [ 28 ] [ 34 ] xeroderma pigmentosum , [ 35 ] and epidermolysis bullosa . [ 36 ] Recently, it was shown that TALEN can be used as tools to harness the immune system to fight cancers; TALEN-mediated targeting can generate T cells that are resistant to chemotherapeutic drugs and show anti-tumor activity. [ 37 ] [ 38 ]
In theory, the genome-wide specificity of engineered TALEN fusions allows for correction of errors at individual genetic loci via homology-directed repair from a correct exogenous template. [ 33 ] In reality, however, the in situ application of TALEN is currently limited by the lack of an efficient delivery mechanism, unknown immunogenic factors, and uncertainty in the specificity of TALEN binding. [ 33 ]
Another emerging application of TALEN is its ability to combine with other genome engineering tools, such as meganucleases . The DNA binding region of a TAL effector can be combined with the cleavage domain of a meganuclease to create a hybrid architecture combining the ease of engineering and highly specific DNA binding activity of a TAL effector with the low site frequency and specificity of a meganuclease. [ 39 ]
In comparison to other genome editing techniques, TALEN falls in the middle in terms of difficulty and cost. Unlike ZFNs , TALEN recognizes single nucleotides. It's far more straightforward to engineer interactions between TALEN DNA binding domains and their target nucleotides than it is to create interactions with ZFNs and their target nucleotide triplets. [ 40 ] On the other hand, CRISPR relies on ribonucleotide complex formation instead of protein/DNA recognition. gRNAs [ definition needed ] have occasionally limitations regarding feasibility due to lack of PAM sites [ definition needed ] in the target sequence and even though they can be cheaply produced, the current development lead to a remarkable decrease of cost for TALENs, so that they are in a similar price and time range like CRISPR based genome editing [ clarification needed ] .
The off-target activity of an active nuclease may lead to unwanted double-strand breaks and may consequently yield chromosomal rearrangements and/or cell death. Studies have been carried out to compare the relative nuclease-associated toxicity of available technologies. Based on these studies [ 18 ] and the maximal theoretical distance between DNA binding and nuclease activity, TALEN constructs are believed to have the greatest precision of the currently available technologies. [ 41 ] | https://en.wikipedia.org/wiki/Transcription_activator-like_effector_nuclease |
A transcription bubble is a molecular structure formed during the initialization of DNA transcription , when a limited portion of the DNA double helix is unwound, providing enough space for RNA polymerase (RNAP) to bind to the template strand and begin RNA synthesis. The transcription bubble size is usually 12 to 14 base pairs, which allows the incorporation of complementary RNA nucleotides by the enzyme with ease. [ 1 ] The dynamics and structure of the transcription bubble are variable, and play a role in the regulation of gene expression at the transcriptional level. [ 2 ] The formation of bubbles depends on the structure of chromatin, the DNA sequence, and transcription factor , including H3K27ac histone acetylation marks, SWI/SNF nucleosome remodeling, and TFIIH and sigma (σ) factors . [ 3 ] [ 4 ] While the evolutionary history cannot be completely confirmed, scientists have provided various models to explain the most likely progression of bubble evolution, tying it directly to the divergence of archaea , eukaryotes , prokaryotes , and bacteria from the last universal common ancestor (LUCA). [ 5 ] [ 6 ] Many drugs, including chemotherapeutic and antibiotic compounds, target elements of the transcription bubble to regulate gene transcription. [ 7 ]
The formation of a transcriptional bubble precedes RNA synthesis and is initialized by the binding of the RNA polymerase (RNAP) to a promoter site, followed by the unwinding of the DNA double helix. This exposes a portion of single-stranded DNA, allowing RNA to be synthesized using it as a template. [ 8 ] As such, the formation of the transcription bubble depends heavily on promoter quality and RNAP search mechanisms.
In prokaryotes, three mechanisms of RNAP's promoter search have been observed to various extents: 1D sliding, intersegment transfer (1D diffusion mechanisms), and hopping (3D diffusion mechanism). [ 8 ] While the extent that each mechanism contributes is uncertain, mechanism which depends on 3D diffusion seem to outweigh 1D diffusion in vitro . However, due to the abundance of macromolecules found in living cells, 3D diffusion may be hindered, leading to a larger contribution of 1D diffusion than in vitro studies observe. [ 8 ]
Various sigma (σ) factors mediate the association and stability of RNAP binding at a promoter site. RNAP binding of the σ factor creates RNA polymerase holoenzyme, the "active" form of bacterial RNAP. [ 9 ] Binding of RNAP forms the closed promoter complex (RPc) which must then isomerize into the open promoter complex (RPo), driving the formation of the transcription bubble. [ 9 ] Two broad classes of σ factors exist: σ 54 and σ 70 . [ 10 ] σ 54 binds to consensus sequences at -12 and -24 from the transcription start site (TSS; +1), and recruits RNAP to form a stable RPc which rarely isomerizes into an RPo. Meanwhile, σ 70 class factors recruit RNAP at -10 and -35, forming the RPo spontaneously. The recruitment of σ 70 is mediated by various activators which can promote the formation of the RPc. [ 10 ] After the formation of the transcription bubble, the σ factors dissociate from holoenzyme complex, allowing RNAP to proceed along the DNA template strand to complete RNA synthesis alone. [ 11 ] The progression of RNAP occurs simultaneously with the rewinding of single stranded DNA upstream from the enzyme and the unwinding of double stranded DNA downstream from the enzyme, resulting in the "movement" of the transcription bubble with the RNAP. [ 12 ]
In eukaryotes, the search for loci to open transcription bubbles occur through the recruitment of general transcription factors to a promoter region and formation of the preinitiation complex (PIC). [ 13 ] Once the PIC forms, the DNA duplex is melted, forming the transcription bubble. Of the enzymes involved, the TATA-binding protein (TBP) binds to the TATA box and causes DNA bending that leads to melting of the promoter region. [ 14 ] The ATP-dependent helicase activity of XPB, a subunit of TFIIH, is required for DNA duplex unwinding and the formation of the transcription bubble after the PIC forms . [ 15 ] [ 16 ]
After about 25 base pairs of the DNA double strand are unwound, RNA synthesis takes place within the transcription bubble region. [ 17 ] DNA regions in front of RNA polymerase II unwinds to accommodate the movement of the enzyme while DNA regions behind it simultaneously rewind to reform the double helix in a manner similar to that of prokaryotes. [ 11 ]
RNAP carries out the majority of the steps during the transcription cycle, especially in maintaining the transcription bubble open for the complementary base pairing . [ 18 ] Some steps of the transcription cycle that require more proteins, such as the Rpb4/7 complex and the elongation factor Transcription Factor IIS (TFIIS). [ 17 ]
After initiation, RNAP moves downstream along the template strand. The net effect of each RNA extension step is that RNAP takes one nucleotide triphosphate , elongates the nascent RNA by one nucleotide, and generates a single pyrophosphate ion (PPi). This is an energetically favorable reaction with a free energy change of approximately −5.6 kcal/mol, allowing RNAP to go forward along its target template which by association moves the bubble forward as well. [ 12 ]
In Escherichia coli , the process of transcription termination via dissociation of the RNA polymerase have been found to depend on 3 possible mechanisms: an interaction between the polymerase and an intrinsic terminator sequence found on the hairpin loops of completed RNA, the presence of the RNA-dependent termination factor Rho , and the ATP-dependent DNA translocase Mfd. [ 19 ]
Studies have found that the disruption of the RNAP-DNA transcription complex by termination factor Rho is inhibited for as long as the upstream DNA in the transcription bubble remain unpaired. Thus, the detachment of bacterial RNAP from DNA in a rho-dependent process is preceded by and depends on the re-annealing of DNA within the transcription bubble. [ 20 ]
During rho-independent termination, the transcription of a hairpin loop on completed RNA, which serves as the intrinsic termination sequence, contributes to the collapse of the transcription bubble. This is followed by the detachment of RNAP from the template DNA and the re-annealing of DNA strands. [ 21 ] This method of termination does not require the presence of the transcription bubble, as E.coli RNAP have been observed in vitro to release the completed RNA transcript while using single-stranded DNA templates. [ 22 ]
The third process of termination, involving DNA translocase Mfd, affects primarily transcription bubbles which have stalled in the presence of DNA damage. The presence of Mfd in the transcription bubble forces the downstream movement of RNAP without the addition of nucleoside triphosphates, inducing the re-annealing of the DNA in the transcription bubble and the detachment of both the RNAP and the nascent RNA. [ 23 ]
Transcription bubble termination in E. coli is regulated by a variety of transcription factors. One such factor is NusG, a ribosomal protein that enhances the efficiency of Rho-dependent termination by aiding Rho recognition of termination sequences. NusG action is mandatory in situations where RNA release has to be performed in a small window of time. [ 24 ]
Transcription termination by eukaryotic RNA polymerase I (Pol I) requires transcription termination factors similar to rho-dependent termination in prokaryotes. [ 25 ] In mice, repeated terminators encoded on DNA are exposed as single-stranded binding sites for protein TTF-I once they are reached by the transcription bubble. The complex produced by the terminator and TTF-I binding then induces the release of the transcript. [ 26 ] RNA Polymerase II is terminated through direct binding of the 3′-end cleavage and polyadenylation (CPA) complex to the enzyme, which then releases the transcribed RNA. The recruitment of the CPA complex to the transcription bubble is induced by the transcription of a Poly-A signal on the nascent RNA. [ 27 ] [ 28 ]
In both cases, RNA cleavage and release occurs before the dissociation of the polymerase from the transcription bubble. Thus, the integrity of the transcription bubble is temporarily preserved after the initiation of termination. [ 29 ] [ 27 ] Two models have been proposed to explain the process of polymerase dissociation after RNA release for both polymerases. The first is the torpedo model , in which the polymerase continues to synthesize RNA after the release of the nascent RNA. Exonuclease activity then degrades the new RNA strand, destabilizing RNA polymerase and achieving its dissociation from the transcription bubble. [ 30 ] The second mechanism, the allosteric model , proposes that transcription of the poly A sequence near the end of nascent RNAs causes gradual dissociation of other transcription factors from the transcription bubble, causing a chain effect that eventually collapses the transcription bubble thorough destabilization. [ 27 ]
Molecular dynamic simulations have found that the lifetime of the transcription bubble is sequence-dependent, and longer bubble lifetimes are associated with A-T rich core promoter sequences. [ 31 ] The weaker A-T base interactions enable transcription bubbles to form due to the less energy needed for A-T pairs to separate. [ 32 ] The supercoiling condition of DNA strongly affects how transcription processes regulate. Negative supercoiling that occurs before the transcription start site creates DNA strand separation which leads to transcription initiation. [ 33 ] Positive supercoiling in front of RNA polymerase creates a barrier that leads to transcription stalling during elongation. [ 33 ] The management of supercoiling stress depends on enzymes including DNA gyrase and topoisomerase. DNA gyrase creates negative supercoils while relaxing positive supercoils to establish the required superhelical tension for effective transcription. [ 34 ] Topoisomerase I relax negative supercoils which keeps the DNA structure suitable for transcriptional activities. [ 34 ]
The general transcription factors (GTFs) TFIIH function as key elements for transcription initiation in eukaryotic cells. The XPB and XPD helicase subunits of TFIIH enable DNA unwinding through DNA duplex translocation which produces single-stranded regions needed for RNA polymerase II to start transcription. σ factors in bacteria serve as essential components to guide RNA polymerase toward particular promoter sequences which leads to the creation of the transcription bubble and the start of transcription . The protein p53 binds near promoter regions to affect the stability of the transcription bubble while showing different effects on transcription initiation at various target promoters . [ 35 ]
A variety of transcription factors also affect the stability of transcription bubble initiation. DksA is crucial for rRNA transcription regulation. It has been found to decrease RNAP complex half-life , thereby inhibiting transcription from rRNA promoters and causing the destabilization of transcription bubble. Similarly, GreA and GreB are homologous factors that have effects similar to DksA, both are also known to reduce RNAP complex half-life. However, it has been discovered that the deletion of GreA and GreB has only minuscule effects on rRNA promoter activity and transcription bubble stability. [ 36 ]
Epigenetic modifications significantly influence chromatin structure and transcriptional activity. The acetylation of lysine 27 on histone 3 (H3K27ac) creates a less stable nucleosome structure, which leads to the formation of essential transcription bubbles that initiate transcription. [ 37 ] The acetylation mark is predominantly found at active promoters together with enhancer regions where it leads to elevated transcriptional activity. [ 38 ] The transcriptional impact of promoter region methylation varies based on the specific context and associated proteins present. The SWI/SNF complex functions as a chromatin remodeler to modify nucleosome positions through ATP-dependent mechanisms that remove or reposition nucleosomes to control RNA polymerase access and regulate transcription rates. [ 39 ]
The formation and maintenance of the transcription bubble is likely also temperature-dependent: temperature analyses on E.coli DNA suggest that the complex is formed at 37°C and collapses at lower temperatures. These temperatures may vary depending on species. [ 40 ] In conjunction with temperature, the presence of magnesium ions (Mg 2+ ) alongside an increase in temperature causes the unwinding of transcription bubbles further downstream up to a base position of +2, which correlates with the start of RNA synthesis. [ 41 ] Extended melting at higher temperatures also enhances bubble stability during early transcription stages. [ 10 ]
In both eukaryotes and prokaryotes, multiple transcription start sites have been observed within the same promoter, and transcription bubble dynamics—such as expansion ("scrunching") and contraction ("unscrunching")—have been shown to play a role in the positioning of these variable transcription start sites to the RNA polymerase active site . [ 2 ] [ 42 ] As such, the structure of the transcription bubble plays a role in regulating gene expression through mediating the creation of different transcripts.
Scrunching of the transcription bubble is essential to RNAP promoter escape–an obligatory step that releases the RNAP from the promoter to begin elongation of the transcript. [ 2 ] Prior to escape, RNAP conducts abortive initiation , where it synthesizes short ~2-9 nt RNA fragments without moving from where it is bound to the promoter. Scrunching of the transcription bubble is essential for this process, to keep the template DNA bases at the RNAP active site without RNAP translocation. The extent of bubble scrunching increases with the size of RNA. Thus, transcription elongation can only occur after sufficient bubble scrunching allows the formation of a large enough RNA product (~10 nt) to trigger promoter escape. [ 43 ] The DNA bulges that form the transcription bubble occur at different locations on each strand. [ 44 ]
The transcription bubble also generates DNA supercoiling upon RPo formation—a process known to be important to gene regulation. [ 45 ] Transcription and bubble movement generates positive supercoiling (overwound helix) ahead of RNAP and negative supercoiling (underwound helix) behind it. The supercoiled structure of the DNA around the transcription bubble has been shown to inhibit elongation when stress is too high. [ 46 ] Thus supercoiling due to bubble processes must be managed by topoisomerases . [ 45 ]
The first DNA replication origins were hypothesized to be promoters for the 2-double-Ψ-β-barrel (2-DPBB) domains of RNAP. Replication was initiated using 2-DPBB type RNAPs followed by DNA synthesis with reverse transcriptase , providing the earliest known instances of transcription bubbles. [ 5 ] 2-DPBB type RNAPs can either be RNA or DNA-template dependent, suggesting that these enzymes, and by extension transcription bubbles, evolved in an RNA world where DNA genomes gradually rose to prominence. Additionally, both DNA and RNA-dependent RNAPs possess a trigger loop and bridge helix, implying that these transcription bubble mechanisms are of ancient origins. [ 6 ]
2-DPBB type RNAPs were most likely the primary machinery for transcription and replication of LUCA genome, which suggests that the divergence of bacteria and archaea stems from co-evolution with 2-DPBB type RNAPs, RNAP promoters, and RNAP general transcription factors (GTF). [ 5 ] Bacterial promoters were noted to be strong promoters that have contacts with RNAP σA subunits but lack TATA-binding protein (TBP) and Transcription Factor E (TFE). This shows that transcription bubble machinery has been lost during bacterial divergence. [ 6 ]
The similar consensus sequences between the Pribnow and TATA boxes found in archaea and eukaryotes respectively caused speculation that both had a common promoter structure in LUCA which diverged at some point in time. Divergence of promoters possibly influenced co-evolution with interacting transcription factors, implying that transcription bubble mechanisms most likely had shared origins stemming from LUCA. [ 5 ]
Due to the importance of the transcription bubble to the initiation, propagation and termination of transcription, enzymes involved in transcription bubble upkeep are viable targets for drugs that function through gene expression regulation. [ 8 ]
Dactinomycin is a potent intercalating agent and chemotherapeutic drug that works by inhibiting RNA synthesis. It binds directly to single-stranded DNA in the transcription bubble, the region of DNA where transcription is actively occurring. [ 47 ] First isolated in 1940 by chemists Selman A. Waksman and H. Boyd Woodruff from Streptomyces , it has since become widely known for its use in cancer chemotherapy due to its ability to preferentially target and kill tumor cells. [ 48 ] [ 49 ]
Dactinomycin has wide applicability and is cytotoxic to a wide range of organisms. It is an effective bactericide, capable of inhibiting growth of both Gram positive and Gram negative bacteria, with higher dilutions required to achieve the same antibiotic effects. In eukaryotes, Dactinomycin is preferentially toxic to tumor cells, which makes it an effective chemotherapy drug. [ 50 ] [ 51 ] Dactinomycin can insert itself between the base pairs of double-stranded or single-stranded DNA, disrupting its normal structure. The drug binds primarily to guanine and cytosine residues found on newly separated single stranded DNA in transcription bubbles. [ 47 ] The drug interferes with RNA synthesis machinery upon binding, physically preventing RNA polymerase from moving downstream and effectively inhibiting RNA elongation. This results in the lack of RNA synthesis in the affected cell, resulting in premature cell death . [ 51 ]
Aside from its usage in medicine, the ability of Dactinomycin to inhibit RNA production makes it an effective experimental tool for RNA quantification and analysis. [ 52 ]
Rifampicin is a widely used antibiotic that targets bacterial RNA polymerase, inhibiting its ability to synthesize RNA. It is particularly effective against Mycobacterium tuberculosis , the bacterium responsible for tuberculosis , and has been commonly used in combination therapy for tuberculosis and other bacterial infections since 1965. [ 53 ] [ 54 ] Rifampicin directly binds to the bacterial RNA polymerase subunit β within the transcription bubble immediately after transcription initiation, physically preventing the elongation of the RNA strand past the first few nucleotides. [ 55 ] The ongoing evolution of rifampicin-resistant strains of M. tuberculosis continue to present significant challenges to the usage of this drug in tuberculosis treatment. All recorded resistance-conferring mutations are isolated to the sequence of the bacterial RNA polymerase subunit β, the location where Rifampicin physically binds. [ 56 ] [ 57 ] | https://en.wikipedia.org/wiki/Transcription_bubble |
In molecular biology and genetics , transcription coregulators are proteins that interact with transcription factors to either activate or repress the transcription of specific genes. [ 1 ] Transcription coregulators that activate gene transcription are referred to as coactivators while those that repress are known as corepressors . The mechanism of action of transcription coregulators is to modify chromatin structure and thereby make the associated DNA more or less accessible to transcription. In humans several dozen to several hundred coregulators are known, depending on the level of confidence with which the characterisation of a protein as a coregulator can be made. [ 2 ] One class of transcription coregulators modifies chromatin structure through covalent modification of histones . A second ATP dependent class modifies the conformation of chromatin. [ 3 ]
Nuclear DNA is normally tightly wrapped around histones rendering the DNA inaccessible to the general transcription machinery and hence this tight association prevents transcription of DNA. At physiological pH, the phosphate component of the DNA backbone is deprotonated which gives DNA a net negative charge. Histones are rich in lysine residues which at physiological pH are protonated and therefore positively charged. The electrostatic attraction between these opposite charges is largely responsible for the tight binding of DNA to histones.
Many coactivator proteins have intrinsic histone acetyltransferase (HAT) catalytic activity or recruit other proteins with this activity to promoters . These HAT proteins are able to acetylate the amine group in the sidechain of histone lysine residues which makes lysine much less basic, not protonated at physiological pH, and therefore neutralizes the positive charges in the histone proteins. This charge neutralization weakens the binding of DNA to histones causing the DNA to unwind from the histone proteins and thereby significantly increases the rate of transcription of this DNA.
Many corepressors can recruit histone deacetylase (HDAC) enzymes to promoters. These enzymes catalyze the hydrolysis of acetylated lysine residues restoring the positive charge to histone proteins and hence the tie between histone and DNA. PELP-1 can act as a transcriptional corepressor for transcription factors in the nuclear receptor family such as glucocorticoid receptors . [ 4 ]
Nuclear receptors bind to coactivators in a ligand-dependent manner. A common feature of nuclear receptor coactivators is that they contain one or more LXXLL binding motifs (a contiguous sequence of 5 amino acids where L = leucine and X = any amino acid) referred to as NR (nuclear receptor) boxes. The LXXLL binding motifs have been shown by X-ray crystallography to bind to a groove on the surface of ligand binding domain of nuclear receptors. [ 5 ] Examples include:
Corepressor proteins also bind to the surface of the ligand binding domain of nuclear receptors, but through a LXXXIXXX(I/L) motif of amino acids (where L = leucine, I = isoleucine and X = any amino acid). [ 7 ] In addition, compressors bind preferentially to the apo (ligand free) form of the nuclear receptor (or possibly antagonist bound receptor). | https://en.wikipedia.org/wiki/Transcription_coregulator |
In molecular biology , a transcription factor ( TF ) (or sequence-specific DNA-binding factor ) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA , by binding to a specific DNA sequence . [ 1 ] [ 2 ] The function of TFs is to regulate—turn on and off—genes in order to make sure that they are expressed in the desired cells at the right time and in the right amount throughout the life of the cell and the organism. Groups of TFs function in a coordinated fashion to direct cell division , cell growth , and cell death throughout life; cell migration and organization ( body plan ) during embryonic development; and intermittently in response to signals from outside the cell, such as a hormone . There are approximately 1600 TFs in the human genome . [ 3 ] [ 4 ] [ 5 ] Transcription factors are members of the proteome as well as regulome .
TFs work alone or with other proteins in a complex, by promoting (as an activator ), or blocking (as a repressor ) the recruitment of RNA polymerase (the enzyme that performs the transcription of genetic information from DNA to RNA) to specific genes. [ 6 ] [ 7 ] [ 8 ]
A defining feature of TFs is that they contain at least one DNA-binding domain (DBD), which attaches to a specific sequence of DNA adjacent to the genes that they regulate. [ 9 ] [ 10 ] TFs are grouped into classes based on their DBDs. [ 11 ] [ 12 ] Other proteins such as coactivators , chromatin remodelers , histone acetyltransferases , histone deacetylases , kinases , and methylases are also essential to gene regulation, but lack DNA-binding domains, and therefore are not TFs. [ 13 ]
TFs are of interest in medicine because TF mutations can cause specific diseases, and medications can be potentially targeted toward them.
Transcription factors are essential for the regulation of gene expression and are, as a consequence, found in all living organisms. The number of transcription factors found within an organism increases with genome size, and larger genomes tend to have more transcription factors per gene. [ 14 ]
There are approximately 2800 proteins in the human genome that contain DNA-binding domains, and 1600 of these are presumed to function as transcription factors, [ 3 ] though other studies indicate it to be a smaller number. [ 15 ] Therefore, approximately 10% of genes in the genome code for transcription factors, which makes this family the single largest family of human proteins. Furthermore, genes are often flanked by several binding sites for distinct transcription factors, and efficient expression of each of these genes requires the cooperative action of several different transcription factors (see, for example, hepatocyte nuclear factors ). Hence, the combinatorial use of a subset of the approximately 2000 human transcription factors easily accounts for the unique regulation of each gene in the human genome during development . [ 13 ]
Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the genes that they regulate based on recognizing specific DNA motifs. Depending on the transcription factor, the transcription of the adjacent gene is either up- or down-regulated . Transcription factors use a variety of mechanisms for the regulation of gene expression. [ 16 ] These mechanisms include:
Transcription factors are one of the groups of proteins that read and interpret the genetic "blueprint" in the DNA. They bind to the DNA and help initiate a program of increased or decreased gene transcription. As such, they are vital for many important cellular processes. Below are some of the important functions and biological roles transcription factors are involved in:
In eukaryotes , an important class of transcription factors called general transcription factors (GTFs) are necessary for transcription to occur. [ 19 ] [ 20 ] [ 21 ] Many of these GTFs do not actually bind DNA, but rather are part of the large transcription preinitiation complex that interacts with RNA polymerase directly. The most common GTFs are TFIIA , TFIIB , TFIID (see also TATA binding protein ), TFIIE , TFIIF , and TFIIH . [ 22 ] The preinitiation complex binds to promoter regions of DNA upstream to the gene that they regulate.
Other transcription factors differentially regulate the expression of various genes by binding to enhancer regions of DNA adjacent to regulated genes. These transcription factors are critical to making sure that genes are expressed in the right cell at the right time and in the right amount, depending on the changing requirements of the organism. [ citation needed ]
Many transcription factors in multicellular organisms are involved in development. [ 23 ] Responding to stimuli, these transcription factors turn on/off the transcription of the appropriate genes, which, in turn, allows for changes in cell morphology or activities needed for cell fate determination and cellular differentiation . The Hox transcription factor family, for example, is important for proper body pattern formation in organisms as diverse as fruit flies to humans. [ 24 ] [ 25 ] Another example is the transcription factor encoded by the sex-determining region Y (SRY) gene, which plays a major role in determining sex in humans. [ 26 ]
Cells can communicate with each other by releasing molecules that produce signaling cascades within another receptive cell. If the signal requires upregulation or downregulation of genes in the recipient cell, often transcription factors will be downstream in the signaling cascade. [ 27 ] Estrogen signaling is an example of a fairly short signaling cascade that involves the estrogen receptor transcription factor: Estrogen is secreted by tissues such as the ovaries and placenta , crosses the cell membrane of the recipient cell, and is bound by the estrogen receptor in the cell's cytoplasm . The estrogen receptor then goes to the cell's nucleus and binds to its DNA-binding sites , changing the transcriptional regulation of the associated genes. [ 28 ]
Not only do transcription factors act downstream of signaling cascades related to biological stimuli but they can also be downstream of signaling cascades involved in environmental stimuli. Examples include heat shock factor (HSF), which upregulates genes necessary for survival at higher temperatures, [ 29 ] hypoxia inducible factor (HIF), which upregulates genes necessary for cell survival in low-oxygen environments, [ 30 ] and sterol regulatory element binding protein (SREBP), which helps maintain proper lipid levels in the cell. [ 31 ]
Many transcription factors, especially some that are proto-oncogenes or tumor suppressors , help regulate the cell cycle and as such determine how large a cell will get and when it can divide into two daughter cells. [ 32 ] [ 33 ] One example is the Myc oncogene, which has important roles in cell growth and apoptosis . [ 34 ]
Transcription factors can also be used to alter gene expression in a host cell to promote pathogenesis. A well studied example of this are the transcription-activator like effectors ( TAL effectors ) secreted by Xanthomonas bacteria. When injected into plants, these proteins can enter the nucleus of the plant cell, bind plant promoter sequences, and activate transcription of plant genes that aid in bacterial infection. [ 35 ] TAL effectors contain a central repeat region in which there is a simple relationship between the identity of two critical residues in sequential repeats and sequential DNA bases in the TAL effector's target site. [ 36 ] [ 37 ] This property likely makes it easier for these proteins to evolve in order to better compete with the defense mechanisms of the host cell. [ 38 ]
It is common in biology for important processes to have multiple layers of regulation and control. This is also true with transcription factors: Not only do transcription factors control the rates of transcription to regulate the amounts of gene products (RNA and protein) available to the cell but transcription factors themselves are regulated (often by other transcription factors). Below is a brief synopsis of some of the ways that the activity of transcription factors can be regulated:
Transcription factors (like all proteins) are transcribed from a gene on a chromosome into RNA, and then the RNA is translated into protein. Any of these steps can be regulated to affect the production (and thus activity) of a transcription factor. An implication of this is that transcription factors can regulate themselves. For example, in a negative feedback loop, the transcription factor acts as its own repressor: If the transcription factor protein binds the DNA of its own gene, it down-regulates the production of more of itself. This is one mechanism to maintain low levels of a transcription factor in a cell. [ 39 ]
In eukaryotes , transcription factors (like most proteins) are transcribed in the nucleus but are then translated in the cell's cytoplasm . Many proteins that are active in the nucleus contain nuclear localization signals that direct them to the nucleus. But, for many transcription factors, this is a key point in their regulation. [ 40 ] Important classes of transcription factors such as some nuclear receptors must first bind a ligand while in the cytoplasm before they can relocate to the nucleus. [ 40 ]
Transcription factors may be activated (or deactivated) through their signal-sensing domain by a number of mechanisms including:
In eukaryotes, DNA is organized with the help of histones into compact particles called nucleosomes , where sequences of about 147 DNA base pairs make ~1.65 turns around histone protein octamers. DNA within nucleosomes is inaccessible to many transcription factors. Some transcription factors, so-called pioneer factors are still able to bind their DNA binding sites on the nucleosomal DNA. For most other transcription factors, the nucleosome should be actively unwound by molecular motors such as chromatin remodelers . [ 43 ] Alternatively, the nucleosome can be partially unwrapped by thermal fluctuations, allowing temporary access to the transcription factor binding site. In many cases, a transcription factor needs to compete for binding to its DNA binding site with other transcription factors and histones or non-histone chromatin proteins. [ 44 ] Pairs of transcription factors and other proteins can play antagonistic roles (activator versus repressor) in the regulation of the same gene . [ citation needed ]
Most transcription factors do not work alone. Many large TF families form complex homotypic or heterotypic interactions through dimerization. [ 45 ] For gene transcription to occur, a number of transcription factors must bind to DNA regulatory sequences. This collection of transcription factors, in turn, recruit intermediary proteins such as cofactors that allow efficient recruitment of the preinitiation complex and RNA polymerase . Thus, for a single transcription factor to initiate transcription, all of these other proteins must also be present, and the transcription factor must be in a state where it can bind to them if necessary.
Cofactors are proteins that modulate the effects of transcription factors. Cofactors are interchangeable between specific gene promoters; the protein complex that occupies the promoter DNA and the amino acid sequence of the cofactor determine its spatial conformation. For example, certain steroid receptors can exchange cofactors with NF-κB , which is a switch between inflammation and cellular differentiation; thereby steroids can affect the inflammatory response and function of certain tissues. [ 46 ]
Transcription factors and methylated cytosines in DNA both have major roles in regulating gene expression. (Methylation of cytosine in DNA primarily occurs where cytosine is followed by guanine in the 5' to 3' DNA sequence, a CpG site .) Methylation of CpG sites in a promoter region of a gene usually represses gene transcription, [ 47 ] while methylation of CpGs in the body of a gene increases expression. [ 48 ] TET enzymes play a central role in demethylation of methylated cytosines. Demethylation of CpGs in a gene promoter by TET enzyme activity increases transcription of the gene. [ 49 ]
The DNA binding sites of 519 transcription factors were evaluated. [ 50 ] Of these, 169 transcription factors (33%) did not have CpG dinucleotides in their binding sites, and 33 transcription factors (6%) could bind to a CpG-containing motif but did not display a preference for a binding site with either a methylated or unmethylated CpG. There were 117 transcription factors (23%) that were inhibited from binding to their binding sequence if it contained a methylated CpG site, 175 transcription factors (34%) that had enhanced binding if their binding sequence had a methylated CpG site, and 25 transcription factors (5%) were either inhibited or had enhanced binding depending on where in the binding sequence the methylated CpG was located. [ citation needed ]
TET enzymes do not specifically bind to methylcytosine except when recruited (see DNA demethylation ). Multiple transcription factors important in cell differentiation and lineage specification, including NANOG , SALL4 A, WT1 , EBF1 , PU.1 , and E2A , have been shown to recruit TET enzymes to specific genomic loci (primarily enhancers) to act on methylcytosine (mC) and convert it to hydroxymethylcytosine hmC (and in most cases marking them for subsequent complete demethylation to cytosine). [ 51 ] TET-mediated conversion of mC to hmC appears to disrupt the binding of 5mC-binding proteins including MECP2 and MBD ( Methyl-CpG-binding domain ) proteins, facilitating nucleosome remodeling and the binding of transcription factors, thereby activating transcription of those genes. EGR1 is an important transcription factor in memory formation. It has an essential role in brain neuron epigenetic reprogramming. The transcription factor EGR1 recruits the TET1 protein that initiates a pathway of DNA demethylation . [ 52 ] EGR1, together with TET1, is employed in programming the distribution of methylation sites on brain DNA during brain development and in learning (see Epigenetics in learning and memory ).
Transcription factors are modular in structure and contain the following domains : [ 1 ]
The portion ( domain ) of the transcription factor that binds DNA is called its DNA-binding domain. Below is a partial list of some of the major families of DNA-binding domains/transcription factors:
The DNA sequence that a transcription factor binds to is called a transcription factor-binding site or response element . [ 62 ]
Transcription factors interact with their binding sites using a combination of electrostatic (of which hydrogen bonds are a special case) and Van der Waals forces . Due to the nature of these chemical interactions, most transcription factors bind DNA in a sequence specific manner. However, not all bases in the transcription factor-binding site may actually interact with the transcription factor. In addition, some of these interactions may be weaker than others. Thus, transcription factors do not bind just one sequence but are capable of binding a subset of closely related sequences, each with a different strength of interaction. [ citation needed ]
For example, although the consensus binding site for the TATA-binding protein (TBP) is TATAAAA, the TBP transcription factor can also bind similar sequences such as TATATAT or TATATAA. [ citation needed ]
Because transcription factors can bind a set of related sequences and these sequences tend to be short, potential transcription factor binding sites can occur by chance if the DNA sequence is long enough. It is unlikely, however, that a transcription factor will bind all compatible sequences in the genome of the cell . Other constraints, such as DNA accessibility in the cell or availability of cofactors may also help dictate where a transcription factor will actually bind. Thus, given the genome sequence, it is still difficult to predict where a transcription factor will actually bind in a living cell.
Additional recognition specificity, however, may be obtained through the use of more than one DNA-binding domain (for example tandem DBDs in the same transcription factor or through dimerization of two transcription factors) that bind to two or more adjacent sequences of DNA.
Transcription factors are of clinical significance for at least two reasons: (1) mutations can be associated with specific diseases, and (2) they can be targets of medications.
Due to their important roles in development, intercellular signaling, and cell cycle, some human diseases have been associated with mutations in transcription factors. [ 63 ]
Many transcription factors are either tumor suppressors or oncogenes , and, thus, mutations or aberrant regulation of them is associated with cancer. Three groups of transcription factors are known to be important in human cancer: (1) the NF-kappaB and AP-1 families, (2) the STAT family and (3) the steroid receptors . [ 64 ]
Below are a few of the better-studied examples:
Approximately 10% of currently prescribed drugs directly target the nuclear receptor class of transcription factors. [ 75 ] Examples include tamoxifen and bicalutamide for the treatment of breast and prostate cancer , respectively, and various types of anti-inflammatory and anabolic steroids . [ 76 ] In addition, transcription factors are often indirectly modulated by drugs through signaling cascades . It might be possible to directly target other less-explored transcription factors such as NF-κB with drugs. [ 77 ] [ 78 ] [ 79 ] [ 80 ] Transcription factors outside the nuclear receptor family are thought to be more difficult to target with small molecule therapeutics since it is not clear that they are "drugable" but progress has been made on Pax2 [ 81 ] [ 82 ] and the notch pathway. [ 83 ]
Gene duplications have played a crucial role in the evolution of species. This applies particularly to transcription factors. Once they occur as duplicates, accumulated mutations encoding for one copy can take place without negatively affecting the regulation of downstream targets. However, changes of the DNA binding specificities of the single-copy Leafy transcription factor, which occurs in most land plants, have recently been elucidated. In that respect, a single-copy transcription factor can undergo a change of specificity through a promiscuous intermediate without losing function. Similar mechanisms have been proposed in the context of all alternative phylogenetic hypotheses, and the role of transcription factors in the evolution of all species. [ 84 ] [ 85 ]
The transcription factors have a role in resistance activity which is important for successful biocontrol activity. The resistant to oxidative stress and alkaline pH sensing were contributed from the transcription factor Yap1 and Rim101 of the Papiliotrema terrestris LS28 as molecular tools revealed an understanding of the genetic mechanisms underlying the biocontrol activity which supports disease management programs based on biological and integrated control. [ 86 ]
There are different technologies available to analyze transcription factors. On the genomic level, DNA- sequencing and database research are commonly used. [ 87 ] The protein version of the transcription factor is detectable by using specific antibodies . The sample is detected on a western blot . By using electrophoretic mobility shift assay (EMSA), [ 88 ] the activation profile of transcription factors can be detected. A multiplex approach for activation profiling is a TF chip system where several different transcription factors can be detected in parallel. [ citation needed ]
The most commonly used method for identifying transcription factor binding sites is chromatin immunoprecipitation (ChIP). [ 89 ] This technique relies on chemical fixation of chromatin with formaldehyde , followed by co-precipitation of DNA and the transcription factor of interest using an antibody that specifically targets that protein. The DNA sequences can then be identified by microarray or high-throughput sequencing ( ChIP-seq ) to determine transcription factor binding sites. If no antibody is available for the protein of interest, DamID may be a convenient alternative. [ 90 ]
As described in more detail below, transcription factors may be classified by their (1) mechanism of action, (2) regulatory function, or (3) sequence homology (and hence structural similarity) in their DNA-binding domains. They are also classified by 3D structure of their DBD and the way it contacts DNA. [ 91 ] [ 92 ]
There are two mechanistic classes of transcription factors:
Transcription factors have been classified according to their regulatory function: [ 13 ]
Transcription factors are often classified based on the sequence similarity and hence the tertiary structure of their DNA-binding domains. [ 95 ] [ 12 ] [ 96 ] [ 11 ] The following classification is based of the 3D structure of their DBD and the way it contacts DNA. It was first developed for Human TF and later extended to rodents [ 91 ] and also to plants. [ 92 ]
There are numerous databases cataloging information about transcription factors, but their scope and utility vary dramatically. Some may contain only information about the actual proteins, some about their binding sites, or about their target genes. Examples include the following: | https://en.wikipedia.org/wiki/Transcription_factor |
Transcription factor TF II A is a nuclear protein involved in the RNA polymerase II -dependent transcription of DNA . [ 1 ] TF II A is one of several general (basal) transcription factors ( GTFs ) that are required for all transcription events that use RNA polymerase II. Other GTFs include TF II D , a complex composed of the TATA binding protein TBP and TBP-associated factors (TAFs), as well as the factors TF II B , TF II E , TF II F , and TF II H . Together, these factors are responsible for promoter recognition and the formation of a transcription preinitiation complex (PIC) capable of initiating RNA synthesis from a DNA template.
TF II A interacts with the TBP subunit of TF II D and aids in the binding of TBP to TATA-box containing promoter DNA. [ 2 ] [ 3 ] Interaction of TF II A with TBP facilitates formation of and stabilizes the preinitiation complex . Interaction of TF II A with TBP also results in the exclusion of negative (repressive) factors that might otherwise bind to TBP and interfere with PIC formation. TF II A also acts as a coactivator for some transcriptional activators , assisting with their ability to increase, or activate, transcription. The requirement for TF II A in vitro transcription systems has been variable, and it can be considered either as a GTF and/or a loosely associated TAF-like coactivator. Genetic analysis in yeast has shown that TF II A is essential for viability.
TF II A is a heterodimer with two subunits : one large unprocessed (subunit 1, or alpha/beta; gene name GTF2A1 ) and one small (subunit 2, or gamma; gene name GTF2A2 ). [ 4 ] [ 5 ] It was originally believed to be a heterotrimer of an alpha (p35), a beta (p19) and a gamma subunit (p12). In humans, the sizes of the encoded proteins are approximately 55 kD and 12 kD. Both genes are present in species ranging from humans to yeast, and their protein products interact to form a complex composed of a beta barrel domain and an alpha helical bundle domain. It is the N-terminal and C-terminal regions of the large subunit that participate in interactions with the small subunit. These regions are separated by another domain whose sequence is always present in large subunits from various species but whose size varies and whose sequence is poorly conserved . A second gene encoding a large TF II A subunit has been found in some higher eukaryotes . This gene, ALF/TFIIAtau (gene name GTF2A1LF ) is expressed only in oocytes and spermatocytes , suggesting it has a TF II A-like regulatory role for gene expression only in germ cells . | https://en.wikipedia.org/wiki/Transcription_factor_II_A |
1C9B , 1DL6 , 1RLY , 1RO4 , 1TFB , 1VOL , 2PHG , 5IY7 , 5IYA , 5IY6 , 5IY9 , 5IYB , 5IYD , 5IY8 , 5IYC
2959
229906
ENSG00000137947
ENSMUSG00000028271
Q00403
P62915
NM_001514
NM_145546
NP_001505
NP_663521
Transcription factor II B ( TFIIB ) is a general transcription factor that is involved in the formation of the RNA polymerase II preinitiation complex (PIC) [ 5 ] and aids in stimulating transcription initiation. TFIIB is localised to the nucleus and provides a platform for PIC formation by binding and stabilising the DNA-TBP ( TATA-binding protein ) complex and by recruiting RNA polymerase II and other transcription factors. It is encoded by the TFIIB gene, [ 6 ] [ 7 ] and is homologous to archaeal transcription factor B and analogous to bacterial sigma factors . [ 8 ]
TFIIB is a single 33kDa polypeptide consisting of 316 amino acids . [ 9 ] TFIIB is made up of four functional regions: the C-terminal core domain; the B linker; the B reader and the amino terminal zinc ribbon.
TFIIB makes protein-protein interactions with the TATA-binding protein (TBP) subunit of transcription factor IID , [ 10 ] [ 11 ] and the RPB1 subunit of RNA polymerase II . [ 11 ]
TFIIB makes sequence-specific protein-DNA interactions with the B recognition element (BRE), a promoter element flanking the TATA element . [ 12 ] [ 13 ]
There are six steps in the mechanism of TFIIB action in the formation of the PIC and transcription initiation: [ 14 ]
Each of the functional regions of TFIIB interacts with different parts of RNA polymerase II. The amino terminal B ribbon is located on dock domain of RNA polymerase II and extends in to the cleft towards the active site. Extending the B ribbon is the B reader that extends via the RNA exit tunnel to the binding site of the DNA-RNA hybrid and towards the active site . The B linker is the region between the B reader and the B core that is found in the cleft of RNA polymerase II and continues by the rudder and the clamp coiled-coil until it reaches the C terminal B core that is found above the wall of RNA polymerase II. [ 14 ] [ 15 ] The B reader and the B linker consist of highly conserved residues that are positioned through the RNA polymerase II tunnel towards the active site and ensure tight binding, without these key residues dissociation would occur. These two domains are also thought to adjust the position of some of the more flexible areas of RNA polymerase II to allow for the precise positioning of the DNA and allowing the addition of the new NTPs onto the nascent RNA chain. [ 16 ] Upon binding RNA polymerase II, the B reader and B linker cause slight repositioning of the protrusion domain of RNA polymerase II which allows an essential second magnesium ion to bind in the active site. [ 17 ] It forms a beta sheet and an ordered loop that helps with the stability of the structure when transcription is initiated. [ 15 ]
The open and closed conformations refer to the state of the DNA and whether the template strand has been separated from the non-template strand within the PIC. The place at which the DNA opens to form the bubble lies above a tunnel that is lined by the B-core, B-linker and B-reader as well as parts of RNA polymerase II. The B linker is found directly aligned with the point at which the DNA opens [ 18 ] and in the open complex it is found between the two DNA strands, suggesting that it has a role in promoter melting, but it does not have a role in the catalytic RNA synthesis. Although TFIIB keeps a similar structure in both conformations some of the intramolecular interactions between the core and the B reader are disrupted upon DNA opening.
After DNA melting the transcription initiator (Inr) must be located on the DNA so the TSS can be identified by the RNA polymerase II and transcription can begin. This is done by passing the DNA through the 'template tunnel' and the DNA is scanned, looking for the Inr and placing it in a position that ensures the transcription start site is located in the correct place by the RNA polymerase active site. The B reader of TFIIB is found in the template tunnel and is important in locating the Inr, mutations in the B reader cause the TSS to change and therefore incorrect transcription to occur [ 19 ] (although PIC formation and DNA melting still take place). Yeast are a particularly good example of this alignment as the yeast Inr motif has a strictly conserved A residue at position 28 and in the open complex model a complementary T residue can be found in the B reader helix. When this T residue is mutated, transcription was significantly less effective emphasizing the role of the B reader. [ 14 ]
The B reader loop is further thought to stabilise NTPs in the active site and, due to its flexibility, allow the nucleic acids to remain in contact during the early synthesis of the RNA molecule (i.e. stabilises the growing RNA-DNA hybrid)
When the RNA transcript reaches 7 nucleotides long, transcription enters the elongation phase, the beginning of which is characterised by the collapsing of the DNA bubble and the ejection of TFIIB. [ 14 ] This is thought to be because the nascent RNA clashes with the B linker helix when it is 6 bases long and upon further elongation to 12-13 bases it will clash with the B-reader and B-ribbon leading to dissociation. [ 17 ] The DNA duplex also clashes with the B linker above the rudder (caused by rewinding of the DNA into a double helix).
TFIIB is phosphorylated at serine 65 which is found in the B reader domain. Without this phosphorylation, transcription initiation does not occur. It has been suggested that the general transcription factor TFIIH could act as the kinase for this phosphorylation although more evidence is needed to support this. Although TFIIB does not travel with the RNA polymerase II complex along the DNA during elongation, it has been recently suggested that it has a role in gene looping which links the promoter to the terminator of the gene. [ 20 ] however, recent research has shown that a depletion in TFIIB is not lethal to cells and transcription levels are not significantly affected. [ 21 ] This is because over 90% of mammalian promoters do not contain a BRE (B recognition element) or TATA box sequence which are required for TFIIB to bind. In addition to this, TFIIB levels have been shown to fluctuate in different types of cell, and at different points in the cell cycle , supporting the evidence that it is not required for all RNA polymerase II transcription. Gene looping is reliant on the interaction between phosphorylated serine residues found on the C terminal domain of RNA polymerase II and polyadenylation factors. TFIIB is needed for the interaction of promoters with these polyadenylation factors, such as SSu72 and CstF-64 . It has also been suggested that both gene loop formation and the collapse of the DNA bubble are a result of TFIIB phosphorylation; however, it is unclear whether this gene loop formation is a cause or consequence of transcription initiation.
RNA polymerase III uses a very similar factor to TFIIB called Brf (TFIIB-related factor) which also contains a conserved zinc ribbon and C terminal core. However, the structure diverges in the more flexible linker region although Brf still contains highly conserved sequences in the same positions that the B reader and B linker are found. These conserved regions probably carry out similar functions as the domains in TFIIB. RNA polymerase I does not use a factor that is similar to TFIIB; however, it is thought that another unknown factor fulfils the same function. [ 22 ] There is no direct homologue for TFIIB in bacterial systems but there are proteins that bind the bacterial polymerase in a similar manner with no sequence similarity. In particular the bacterial protein σ70 [ 14 ] contains domains that bind the polymerase at the same points as the B-linker, B-ribbon and B-core. This is especially apparent in the σ 3 region and the region 4 linker which might stabilise the DNA in the polymerase active site. [ 23 ]
Recent studies have shown that decreased TFIIB levels do not affect transcription levels within cells, this is thought to be partially because over 90% of mammalian promoters do not contain a BRE or TATA box. However, it has been shown that TFIIB is vital to the in vitro transcription and regulation of the herpes simplex virus . This is thought to be due to similarity TFIIB has to cyclin A . In order to undergo replication , viruses often stop host cell progression through the cell cycle , using cyclins and other proteins. As TFIIB has a similar structure to cyclin A it has been suggested that depleted levels of TFIIB could have antiviral effects. [ 21 ]
Studies have shown that the binding of TFIIB to TBP is affected by the length of the polyglutamine tract in TBP. Extended polyglutamine tracts such as those found in neurodegenerative diseases cause increased interaction with TFIIB. [ 24 ] This is thought to affect transcription in these diseases as it reduces the availability of TFIIB to other promoters in the brain as the TFIIB is instead interacting with the expanded polyglutamine tracts. | https://en.wikipedia.org/wiki/Transcription_factor_II_B |
Transcription factor II D ( TF II D ) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex . RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein -coding genes in living cells. It consists of RNA polymerase II , a subset of general transcription factors , and regulatory proteins known as SRB proteins. Before the start of transcription , the transcription Factor II D (TF II D) complex binds to the core promoter DNA of the gene through specific recognition of promoter sequence motifs, including the TATA box , Initiator , Downstream Promoter , Motif Ten, or Downstream Regulatory elements. [ 1 ]
TF II D is itself composed of TBP and several subunits called TATA-binding protein Associated Factors ( TBP-associated factors , or TAFs ). In a test tube, only TBP is necessary for transcription at promoters that contain a TATA box . [ 2 ] TAFs, however, add promoter selectivity, especially if there is no TATA box sequence for TBP to bind to. [ 1 ] TAFs are included in two distinct complexes, TF II D [ 3 ] and B-TF II D. [ 4 ] The TF II D complex is composed of TBP and more than eight TAFs. But, the majority of TBP is present in the B-TF II D complex, which is composed of TBP and TAFII170 ( BTAF1 ) in a 1:1 ratio. [ 5 ] TF II D and B-TF II D are not equivalent, since transcription reactions utilizing TF II D are responsive to gene specific transcription factors such as SP1, while reactions reconstituted with B-TF II D are not. [ 5 ]
Subunits in the TF II D complex include: [ 2 ]
This genetics article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transcription_factor_II_D |
Transcription factor II E ( TF II E ) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex . [ 1 ] It is a tetramer of two alpha and two beta chains and interacts with TAF6/TAFII80, ATF7IP, and varicella-zoster virus IE63 protein. [ 2 ]
TF II E recruits TF II H to the initiation complex and stimulates the RNA polymerase II C-terminal domain kinase and DNA-dependent ATPase activities of TF II H. Both TF II H and TF II E are required for promoter clearance by RNA polymerase. [ 2 ] Transcription factor II E is encoded by the GTF2E1 and GTF2E2 genes. [ 3 ] [ 4 ] [ 5 ] [ 6 ] TF II E is thought to be involved in DNA melting at the promoter : it contains a zinc ribbon motif that can bind single stranded DNA. [ 7 ]
This gene article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transcription_factor_II_E |
Transcription factor II F ( TF II F ) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex . [ 1 ] [ 2 ] [ 3 ]
TF II F is encoded by the GTF2F1 , GTF2F2 , and GTF2F2L genes. [ 4 ] [ 5 ] [ 6 ]
TF II F binds to RNA polymerase II when the enzyme is already unbound to any other transcription factor, thus preventing it from contacting DNA outside the promoter . Furthermore, TF II F stabilizes the RNA polymerase II while it's contacting TBP and TF II B .
This genetics article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transcription_factor_II_F |
Transcription factor II H ( TF II H ) is an important protein complex , having roles in transcription of various protein-coding genes and DNA nucleotide excision repair (NER) pathways. TF II H first came to light in 1989 when general transcription factor-δ or basic transcription factor 2 was characterized as an indispensable transcription factor in vitro. This factor was also isolated from yeast and finally named TF II H in 1992. [ 1 ] [ 2 ]
TF II H consists of ten subunits, 7 of which ( ERCC2 /XPD, ERCC3 /XPB, GTF2H1 /p62, GTF2H4 /p52, GTF2H2 /p44, GTF2H3 /p34 and GTF2H5 /TTDA) form the core complex. The cyclin-activating kinase-subcomplex ( CDK7 , MAT1, and cyclin H) is linked to the core via the XPD protein. [ 3 ] Two of the subunits, ERCC2 /XPD and ERCC3/ XPB , have helicase and ATPase activities and help create the transcription bubble . In a test tube, these subunits are only required for transcription if the DNA template is not already denatured or if it is supercoiled .
Two other TF II H subunits, CDK7 and cyclin H , phosphorylate serine amino acids on the RNA polymerase II C-terminal domain and possibly other proteins involved in the cell cycle . Next to a vital function in transcription initiation, TF II H is also involved in nucleotide excision repair .
Before TF II H identified it, it had several names. It was isolated in 1989 isolated from rat liver, known by factor transcription delta. When identified from cancer cells it was known that time as Basic transcription factor 2. Also, when isolated from yeast it was termed transcription factor B. Finally, in 1992 known as TF II H. [ 4 ]
TF II H is a ten‐subunit complex; seven of these subunits comprise the “core” whereas three comprise the dissociable “CAK” (CDK Activating Kinase) module. [ 5 ] The core consists of subunits XPB, XPD, p62 , p52 , p44, p34 and p8 while CAK is composed of CDK7 , cyclin H , and MAT1 . [ 5 ]
General function of TF II H:
(NER)TF II H is a general transcription factor that acts to recruit RNA Pol II to the promoters of genes. It functions as a DNA translocase, tracking along the DNA, reeling DNA into the Pol II cleft, and creating torsional strain leading to DNA unwinding [ 7 ] . It also unwinds DNA after a DNA lesion has been recognized by either the global genome repair (GGR) pathway or the transcription-coupled repair (TCR) pathway of NER. [ 8 ] [ 9 ] Purified TF II H has role in stopping further RNA synthesis by activating the cyclic peptide α-amanitin.
Mutation in genes ERCC3 ( XPB ), ERCC2 ( XPD ) or GTF2H5 ( TTDA ) cause trichothiodystrophy , a condition characterized by photosensitivity , ichthyosis , brittle hair and nails, intellectual impairment, decreased fertility and/or short stature. [ 10 ]
Genetic polymorphisms of genes that encode subunits of TF II H are known to be associated with increased cancer susceptibility in many tissues, e.g.; skin tissue, breast tissue and lung tissue. Mutations in the subunits (such as XPD and XPB) can lead to a variety of diseases, including xeroderma pigmentosum (XP) or XP combined with Cockayne syndrome . [ 11 ] In addition to genetic variations, virus-encoded proteins also target TF II H. [ 12 ]
TF II H participates in nucleotide excision repair (NER) by opening the DNA double helix after damage is initially recognized. NER is a multi-step pathway that removes a wide range of different damages that distort normal base pairing, including bulky chemical damages and UV-induced damages. Individuals with mutational defects in genes specifying protein components that catalyze the NER pathway, including the TF II H components, often display features of premature aging [ 10 ] [ 13 ] (see DNA damage theory of aging ).
Potent, bioactive natural products like triptolide that inhibit mammalian transcription via inhibition of the XPB subunit of the general transcription factor TF II H has been recently reported as a glucose conjugate for targeting hypoxic cancer cells with increased glucose transporter expression. [ 14 ]
This biochemistry article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transcription_factor_II_H |
Transcription factors are proteins that bind genomic regulatory sites. Identification of genomic regulatory elements is essential for understanding the dynamics of developmental, physiological and pathological processes. Recent advances in chromatin immunoprecipitation followed by sequencing ( ChIP-seq ) have provided powerful ways to identify genome-wide profiling of DNA-binding proteins and histone modifications. [ 1 ] [ 2 ] The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.
Comprehensive List of transcription factor binding sites (TFBSs) databases based on ChIP-seq data as follows: | https://en.wikipedia.org/wiki/Transcription_factor_binding_site_databases |
Transcription factories , in genetics describe the discrete sites where transcription occurs in the cell nucleus , and are an example of a biomolecular condensate . They were first discovered in 1993 and have been found to have structures analogous to replication factories, sites where replication also occurs in discrete sites. The factories contain an RNA polymerase (active or inactive) and the necessary transcription factors ( activators and repressors ) for transcription. [ 1 ] Transcription factories containing RNA polymerase II are the most studied but factories can exist for RNA polymerase I and III ; the nucleolus being seen as the prototype for transcription factories. It is possible to view them under both light and electron microscopy . [ 2 ] The discovery of transcription factories has challenged the original view of how RNA polymerase interacts with the DNA polymer and it is thought that the presence of factories has important effects on gene regulation and nuclear structure .
The first use of the term ‘transcription factory’ was used in 1993 by Jackson and his colleagues who noticed that transcription occurred at discrete sites in the nucleus. [ 3 ] This contradicted the original view that transcription occurred at an even distribution throughout the nucleus.
The structure of a transcription factory appears to be determined by cell type , transcriptional activity of the cell and also the method of technique used to visualise the structure. The generalised view of a transcription factory would feature between 4 – 30 RNA polymerase molecules [ 1 ] and it is thought that the more transcriptionally active a cell is, the more polymerases that will be present in a factory in order to meet the demands of transcription. The core of the factory is porous and protein rich, with the hyperphosphorylated, elongating form polymerases on the perimeter. The type of proteins present include: ribonucleoproteins , co-activators , transcription factors , RNA helicase and splicing and processing enzymes. [ 4 ] A factory only contains one type of RNA polymerase and the diameter of the factory varies depending on the RNA polymerase featured; RNA polymerase I factories are roughly 500 nm in width whereas RNA polymerase II and III factories a magnitude smaller at 50 nm. [ 5 ] It has been experimentally shown that the transcription factory is immobilised to a structure and it is postulated that this immobilisation is because of a tethering to the nuclear matrix ; this is because it has been shown it is tied to a structure that is unaffected by restriction enzymes . Proteins that have been thought to be involved in the tethering includes spectrin , actin and lamins . [ 4 ]
The structure of a transcriptional factory directly relates to its function. Transcription is made more efficient because of the clustered nature of the transcription factory. All the necessary proteins: RNA polymerase, transcription factors and other co-regulators are present in the transcription factory that allows for faster RNA polymerisation when the DNA template reaches the factory, it also allows for a number of genes to be transcribed at the same time. [ 6 ]
The amount of transcription factories found per nucleus appears to be determined by cell type, species and the type of measurement. Cultured mouse embryonic fibroblasts have been found to have roughly 1500 factories through immunofluorescence detection of RNAP II however cells taken from different tissues of the same mouse group had between 100 and 300 factories. [ 7 ] Measurements of the number of transcription factories in HeLa cells give a varied result. For example, using the traditional fluorescence microscopy approach 300 – 500 factories were found but using both confocal and electron microscopy roughly 2100 were detected. [ 1 ]
In addition to the specialisation factories have for the type of RNA polymerase they contain, there is a further level of specialisation present. There are some factories that only transcribe a certain set of related genes, this further strengthens the concept that the main function of a transcription factory is for transcriptional efficiency. [ 7 ]
There is much debate to whether transcription factories assemble because of the transcriptional demands of the genome or if they are stable structures that are conserved over time. Experimentally, it appears that they remain fixed over a short period of time; newly made mRNA were pulse labelled over 15 minutes and it showed no new transcription factories appearing. [ 1 ] This is also supported by inhibition experiments. In these studies heat shock was used to turn off transcription which resulted in no change in the number of polymerases detected. [ 8 ] Upon further analysis of western blot data it was suggested that there was in fact a slight decrease over time of transcription factories. Therefore, it could be claimed that polymerase molecules are released gently over time from the factory when there is a lack of transcription which would eventually lead to the complete loss of the transcription factory. [ 9 ]
There is also several pieces of evidence that promotes the idea of transcription factories assembling de novo due to transcriptional demands. GFP polymerase fluorescence experiments have shown that the inducement of transcription in Drosophila polytene nuclei leads to the formation of a factory which contradicts the notion of a stable and secure structure. [ 10 ]
It was previously thought that it was the relatively small RNA polymerase that moves along the comparatively larger DNA template during transcription. However, increasing evidence supports the notion that due to the tethering of a transcription factory to the nuclear matrix , it is in fact the large DNA template that is moved to accommodate RNA polymerisation. In vitro studies for example have shown that RNA polymerases attached to a surface are capable of both rotating the DNA template and threading it through the polymerase to start transcription; which indicates the capabilities of RNA polymerase to be a molecular motor. [ 6 ] Chromosome Conformation Capture (3C) also supports the idea of the DNA template diffusing towards a stationary RNA polymerase. [ 11 ]
There remains a doubt to this mechanism of transcription. Firstly, it is unknown how a stationary polymerase is capable of transcribing genes on the (+)-strand and (-)-strand at the same genomic locus at the same time. This is in addition to a lack of conclusive evidence on how the polymerase remains immobilised (how it is tethered) and what structure it is tethered to. [ 12 ]
There are several consequences the formation of a transcription factory has on nuclear and genomic structures. It has been proposed that the factories are responsible for nuclear organisation; they have been suggested to promote chromatin loop formation by two potential mechanisms:
The first mechanism suggests that loops form because 2 genes on the same chromosome require the same transcription machinery that would be found in a specific transcription factory. This requirement will attract the gene loci to the factory thus creating a loop. [ 13 ]
Transcription factories are also suggested to be responsible for gene clustering , this is because related genes would require the same transcriptional machinery and if a factory satisfies these needs the genes would be attracted to the factory [ 14 ] . While the clustering of genes can be beneficial for transcriptional efficiency, there could be negative consequences to this. Gene translocation events occur when genes are in close proximity to one another; which will occur more often when a transcriptional factory is present. Gene translocation events, like point mutations , generally are detrimental to the organism and so therefore could lead to the possibility of disease . However, on the other hand recent research has suggested that there is no correlation between inter-gene interactions and translocation frequencies. [ 15 ] | https://en.wikipedia.org/wiki/Transcription_factory |
The preinitiation complex (abbreviated PIC ) is a complex of approximately 100 proteins that is necessary for the transcription of protein-coding genes in eukaryotes and archaea . The preinitiation complex positions RNA polymerase II (Pol II) at gene transcription start sites , denatures the DNA , and positions the DNA in the RNA polymerase II active site for transcription. [ 1 ] [ 2 ] [ 3 ] [ 4 ]
The minimal PIC includes RNA polymerase II and six general transcription factors : TF II A , TF II B , TF II D , TF II E , TF II F , and TF II H . Additional regulatory complexes (such as the mediator coactivator [ 5 ] and chromatin remodeling complexes) may also be components of the PIC.
Preinitiation complexes are also formed during RNA Polymerase I and RNA Polymerase III transcription.
A classical view of PIC formation at the promoter involves the following steps:
An alternative hypothesis of PIC assembly postulates the recruitment of a pre-assembled " RNA polymerase II holoenzyme " directly to the promoter (composed of all, or nearly all GTFs and RNA polymerase II and regulatory complexes), in a manner similar to the bacterial RNA polymerase (RNAP).
Archaea have a preinitiation complex resembling that of a minimized Pol II PIC, with a TBP and an Archaeal transcription factor B (TFB, a TFIIB homolog). The assembly follows a similar sequence, starting with TBP binding to the promoter. An interesting aspect is that the entire complex is bound in an inverse orientation compared to those found in eukaryotic PIC. [ 8 ] They also use TFE, a TFIIE homolog, which assists in transcription initiation but is not required. [ 9 ] [ 10 ]
Formation of the Pol I preinitiation complex requires the binding of selective factor 1 (SL1 or TIF-IB) to the core element of the rDNA promoter. [ 11 ] SL1 is a complex composed of TBP and at least three TBP-associated factors (TAFs). For basal levels of transcription, only SL1 and the initiation-competent form of Pol I (Pol Iβ), characterized by RRN3 binding, are required. [ 12 ] [ 13 ]
For activated transcription levels, UBTF (UBF) is also required. UBTF binds as a dimer to both the upstream control element (UCE) and core element of the rDNA promoter, bending the DNA to form an enhanceosome . [ 13 ] [ 12 ] SL1 has been found to stabilize the binding of UBTF to the rDNA promoter. [ 11 ]
The subunits of the Pol I PIC differ between organisms. [ 14 ]
Pol III has three classes of initiation, which start with different factors recognizing different control elements but all converging on TFIIIB (similar to TFIIB-TBP; consists of TBP/TRF, a TFIIB-related factor , and a B″ unit ) recruiting the Pol III preinitiation complex. The overall architecture resembles that of Pol II. Only TFIIIB needs to remain attached during elongation. [ 15 ] | https://en.wikipedia.org/wiki/Transcription_preinitiation_complex |
Transcription-translation feedback loop ( TTFL ) is a cellular model for explaining circadian rhythms in behavior and physiology . Widely conserved across species, the TTFL is auto-regulatory, in which transcription of clock genes is regulated by their own protein products.
Circadian rhythms have been documented for centuries. For example, French astronomer Jean-Jacques d’Ortous de Mairan noted the periodic 24-hour movement of Mimosa plant leaves as early as 1729. However, science has only recently begun to uncover the cellular mechanisms responsible for driving observed circadian rhythms. The cellular basis of circadian rhythms is supported by the fact that rhythms have been observed in single-celled organisms [ 1 ]
Beginning in the 1970s, experiments conducted by Ron Konopka and colleagues, in which forward genetic methods were used to induce mutation, revealed that Drosophila melanogaster specimens with altered period ( Per ) genes also demonstrated altered periodicity. As genetic and molecular biology experimental tools improved, researchers further identified genes involved in sustaining normal rhythmic behavior, giving rise to the concept that internal rhythms are modified by a small subset of core clock genes. Hardin and colleagues (1990) were the first to propose that the mechanism driving these rhythms was a negative feedback loop. Subsequent major discoveries confirmed this model; notably experiments led by Thomas K. Darlington and Nicholas Gekakis in the late 1990s that identified clock proteins and characterized their methods in Drosophila and mice, respectively. These experiments gave rise to the transcription-translation feedback loop (TTFL) model that has now become the dominant paradigm for explaining circadian behavior in a wide array of species. [ 2 ]
The TTFL is a negative feedback loop , in which clock genes are regulated by their protein products. Generally, the TTFL involves two main arms: positive regulatory elements that promote transcription and protein products that suppress transcription. When a positive regulatory element binds to a clock gene promoter , transcription proceeds, resulting in the creation of an mRNA transcript, and then translation proceeds, resulting in a protein product. There are characteristic delays between mRNA transcript accumulation, protein accumulation, and gene suppression due to translation dynamics, post-translational protein modification , protein dimerization, and intracellular travel to the nucleus . [ 3 ] Across species, proteins involved in the TTFL contain common structural motifs such PAS domains , involved in protein-protein interactions, and bHLH domains , involved in DNA binding. [ 4 ]
Once enough modified protein products accumulate in the cytoplasm , they are transported into the nucleus where they inhibit the positive element from the promoter to stop transcription of clock genes. The clock gene is thus transcribed at low levels until its protein products are degraded, allowing for positive regulatory elements to bind to the promoter and restart transcription. The negative feedback loop of the TTFL has multiple properties important for the cellular circadian clock. First, it results in daily rhythms in both gene transcription and protein abundance and size, caused by the delay between translation and negative regulation of the gene. The cycle's period, or time required to complete one cycle, remains consistent in each individual and, barring mutation, is typically near 24 hours. This enables stable entrainment to the 24 hour light-dark cycle that Earth experiences. Additionally, the protein products of clock genes control downstream genes that are not part of the feedback loop, allowing clock genes to create daily rhythms in other processes, such as metabolism, within the organism. [ 3 ] Lastly, the TTFL is a limit cycle, meaning that it is a closed loop that will return to its fixed trajectory even if it is disturbed, maintaining the oscillatory path on its fixed 24-hour period. [ 5 ]
The presence of the TTFL is highly conserved across animal species; however, many of the players involved in the process have changed across evolutionary time within different species. There are differences in the genes and proteins involved in the TTFL when comparing plants, animals, fungi and other eukaryotes. This suggests that a clock that follows the TTFL model has evolved multiple times during the existence of life. [ 6 ]
The TTFL was first discovered in Drosophila , and the system shares several components with the mammalian TTFL. Transcription of the clock genes, Period (per) and Timeless (tim) , is initiated when positive elements Cycle (dCYC) and Clock (dCLK) form a heterodimer and bind E-box promoters , initiating transcription. During the day TIM is degraded; light exposure facilitates CRY binging to TIM, which leads to TIM's ubiquitination and eventual degradation. [ 7 ] During the night, TIM and PER are able to form heterodimers and accumulate slowly in the cytoplasm, where PER is phosphorylated by the kinase DOUBLETIME (DBT). The post-transcriptional modification of multiple phosphate groups both targets the complex for degradation and facilitates nuclear localization. In the nucleus, the PER-TIM dimer binds to the CYC-CLK dimer, which makes the CYC-CLK dimer release from the E-boxes and inhibits transcription. Once PER and TIM degrade, CYC-CLK dimers are able to bind the E-boxes again to initiate transcription, closing the negative feedback loop. [ 8 ]
Secondary feedback loops interact with this primary feedback loop. CLOCKWORK ORANGE (CWO) binds the E-boxes to act as a direct competitor of CYC-CLK, therefore inhibiting transcription. PAR-DOMAIN PROTEIN 1 ε (PDP1ε) is a feedback activator and VRILLE (VRI) is a feedback inhibitor of the Clk promoter, and their expression is activated by dCLK-dCYC. Ecdysone-induced protein 75 (E75) inhibits clk expression and tim -dependently activates pe r transcription. All of these secondary loops act to reinforce the primary TTFL. [ 8 ]
Cryptochrome in Drosophila is a blue-light photoreceptor that triggers degradation of TIM, indirectly leading to the clock phase being reset and the renewed promotion of per expression. [ 8 ]
The mammalian TTFL model contains many components that are homologs of the ones found in Drosophila . The way the mammalian system works is that BMAL1 forms a heterodimer with CLOCK to initiate transcription of mPer and cryptochrome ( cry ). There are three paralogs, or historically similar genes that now appear as a duplication, of the period gene in mammals listed as mPer1 , mPer2 , and mPer3 . There are also two paralogs of cryptochrome in mammals. PER and CRY proteins form a heterodimer, and PER's phosphorylation by CK1δ and CK1ε regulates the localization of the dimer to the nucleus. In the nucleus, PER-CRY negatively regulates the transcription of their cognate genes by binding BMAL1-CLOCK and causing their release from the E-box promoter. [ 8 ]
Although the mPer paralogs work together as a functional ortholog of dPer , they each have a distinguished function. mPer1 and mPer2 are necessary for clock function in the brain, while mPer3 only plays a discernible role in the circadian rhythms of peripheral tissues. Knocking out either mPer1 or mPer2 causes a change in period, with mPer1 knockouts free-running with a shorter period and mPer2 knockouts free running with a longer period compared to the original tau before eventually becoming arrhythmic. Similarly, mCry1 knockouts result in a shortened period and mCry2 knockouts result in a lengthened period, with a double mCry1 /m Cry2 knockouts result in arrhythmicity. [ 8 ]
There are also secondary loops in mammals, although they are more complex than those seen in Drosophila . Like CWO in Drosophila , Deleted in esophageal cancer1,2 (Dec1 Dec2) repress mPer expression by binding E-boxes which prevents CLOCK-BMAL1 from binding their targets. The receptors REV-ERB and retinoic acid-related orphan receptor (ROR) play a similar role to PDP1ε and VRI in Drosophila , except they regulate CLOCK's binding partner BMAL1 instead of directly regulating CLOCK. D site-binding protein (DBP) and E4-binding protein (E4BP4) bind to the D-Box promoter sequence to regulate mPer expression. [ 8 ]
The way these genes relate to Drosophila melanogaster is seen in the function of each of the genes and how they have evolutionarily changed. BMAL1 is an ortholog of CYCLE . This means that BMAL1 and CYCLE appear to have a common history, but are found in different species. Another example of the parallels between Drosophila melanogaster and mammals is also seen in cry and mPer since they are functional orthologs of per and tim . [ 8 ]
The gene frequency ( frq ) in Neurospora was identified as the second known clock gene in 1979 by JF Feldman and his colleagues. Frq was first cloned in 1989 by CR McClung and his colleagues. This gene was of particular interest because its expression is very complex compared to other known microbial genes. Two positive regulator proteins, White Collar-1 (WC-1) and White Collar-2 (WC-2) bind the frq promoter, which is called the Clock Box, during late subjective night to activate transcription. Light is also important for inducing FRQ expression; WC-1 is a photopigment, and light allows WC-1 and WC-2 to bind another promoter called the proximal light-response element (PLRE). FRQ protein negatively regulates the activity of WC-1 and WC-2. Several kinases (CK1, CK2, and PRD-4/checkpoint kinase 2) and phosphatases (PP1 and PP2A) regulate the ability of FRQ to translocate to the nucleus and FRQ, WC-1 and WC-2 stability. [ 9 ]
The first TTFL model was proposed for Arabidopsis thaliana in 2001 and included two MYB transcription factors, LATE ELONGATED HYPOCOTYL (LHY), CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), and TIMING OF CAB EXPRESSION 1 (TOC1). CCA1 and LHY are expressed in the morning, and interact together to repress the expression of TOC1. CCA1 and LHY expression decreases in the darkness, allowing for TOC1 to express and negatively regulate CCA1 and LHY expression. CCA1 and LHY can also bind to their own promoter to repress their own transcription. [ 10 ]
A second loop exists involving PRR9, PRR7, and PRR5, which are all homologs of TOC1 and repress CCA1 and LHY expression. These PRR genes are directly repressed by LHY and TOC1. These genes are also regulated by the “evening complex” (EC), which is formed by LUX ARRHYTHMO (LUX), EARLY FLOWERING 3 (ELF3) and EARLY FLOWERING 4 (ELF4). LUX is a transcription factor with a similar function to MYB, while ELF3 and ELF4 are nuclear proteins whose functions are unknown. The "evening complex" indirectly promotes the expression of LHY and CCA1, which repress transcription of its own components. Since this model consists of two inhibitions leading to an activation, it is also referred to as a repressilator. [ 10 ]
A recently discovered loop includes the reveille ( reveille ) family of genes, which are expressed in the morning and induce transcription of evening genes such as PRR5, TOC1, LUX, and ELF4. Once the resulting proteins are translated, PRR9, PRR7, and PRR5 repress RVE8. RVE8 also interacts with the NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED (LNK1, 2, 3, and 4) morning components, with LNKs either antagonizing or co-activating RVE8. [ 10 ]
Although GIGANTEA (GI) is not known as a core part of the Arabdopsis TTFL model, it is repressed by CCA1, LHY and TOC1. Additionally, GI activates CCA1 and LHY expression. [ 10 ]
Studies of the cyanobacteria clock led to the discovery of three essential clock genes: KaiA , KaiB , and KaiC . Initially, these proteins were thought to follow the TTFL model similar to that proposed for eukarya , as there was a daily pattern in mRNA and protein abundance and level of phosphorylation, negative feedback of proteins on their cognate genes, resetting of clock phase in response to KaiC over-expression, and modified Kai activity through interactions with one another. [ 11 ] Each of these results was consistent with understandings of the TTFL at the time. However, later studies have since concluded that post translational modifications such as phosphorylation are more important for clock control. When promoters for the Kai proteins were replaced with non-specific promoters, there was no interruption of the central feedback loop, as would be expected if inhibition occurred through the proteins’ feedback onto their specific promoters. As a consequence, the TTFL model has largely been determined to be inaccurate for cyanobacteria; transcriptional regulation is not the central process driving cyanobacteria rhythms. Though transcriptional and translational regulation are present, they were deemed to be effects of the clock rather than necessary for clock function. [ 12 ]
Post-translational feedback loops (PTFLs) involved in clock gene regulation have also been uncovered, often working in tandem with the TTFL model. In both mammals and plants, post-translational modifications such as phosphorylation and acetylation regulate the abundance and/or activity of clock genes and proteins. For example, levels of phosphorylation of TTFL components have been shown to vary rhythmically. These post-translational modifications can serve as degradation signals, binding regulators, and signals for the recruitment of additional factors. [ 13 ]
Notably, cyanobacteria demonstrate rhythmic 24-hour changes in phosphorylation in a feedback loop that is independent of transcription and translation: circadian rhythms in phosphorylation are observed when the feedback loop Kai proteins are placed in a test tube with ATP, independent of any other cellular machinery. This three-protein post-translational system is widely accepted to be the core oscillator, both necessary and sufficient to drive daily rhythms. [ 14 ] In addition to the Kai system in cyanobacteria, oxidation of peroxiredoxin proteins has been shown to occur independently of transcription and translation in both mammalian red blood cells and algae Ostreococcus tauri cells; this system has been seen to be conserved in many organisms. [ 15 ] It is not clear whether the peroxiredoxin system interacts with TTFL-based clocks or is itself a part of a new PTFL-based clock. However, both of these findings imply that in some organisms or cell types, PTFLs are sufficient to drive circadian rhythms. | https://en.wikipedia.org/wiki/Transcription_translation_feedback_loop |
Transcriptional adaptation is a recently described type of genetic compensation by which a mutation in one gene leads to the transcriptional modulation of related genes, termed adapting genes or modifiers. [ 1 ] [ 2 ] | https://en.wikipedia.org/wiki/Transcriptional_adaptation |
In genetics , transcriptional amplification is the process in which the total amount of messenger RNA (mRNA) molecules from expressed genes is increased during disease, development , or in response to stimuli.
In eukaryotic cells, the transcribing activity of RNA Polymerase II results in mRNA production. Transcriptional amplification is specifically defined as the increase in per-cell abundance of this set of expressed mRNAs. Transcriptional amplification is caused by changes in the amount or activity of transcription-regulating proteins.
Gene expression is regulated by numerous types of proteins that directly or indirectly influence transcription by RNA Polymerase II. As opposed to transcriptional activators or repressors that selectively activate or repress specific genes, amplifiers of transcription act globally on expressed genes.
Several known regulators of transcriptional amplification have been characterized including the oncogene Myc , [ 1 ] [ 2 ] the Rett syndrome protein MECP2 , [ 3 ] and the BET bromodomain protein BRD4 . [ 4 ] In particular, the Myc protein amplifies transcription by binding to promoters and enhancers of active genes where it directly recruits the transcription elongation factor P-TEFb . Furthermore, the BRD4 protein is a regulator of Myc activity.
Commonly used gene expression experiments interrogate the expression of one gene ( qPCR ) or many genes ( microarray , RNA-Seq ). These techniques generally measure relative mRNA levels and employ normalization methods that assume only a small number of genes show altered expression. [ 5 ] In contrast, single cell or cell-count normalized absolute measurements of mRNA abundance are required to reveal transcriptional amplification. [ 6 ] Additionally, global measurements of mRNA or total mRNA per cell can also uncover evidence for transcriptional amplification. [ 7 ] [ 8 ]
Cells in which transcription has been amplified have additional hallmarks suggesting that amplification has occurred. Cells with increased mRNA levels may be larger, consistent with an increased abundance of gene products. This increase in the amount of gene products may result in a decreased doubling time.
Transcriptional amplification has been implicated in cancer, [ 9 ] [ 10 ] Rett syndrome, [ 11 ] heart disease, [ 12 ] Down syndrome, [ 13 ] and cellular aging. [ 14 ] In cancer, Myc-driven transcriptional amplification is posited to help tumor cells overcome rate-limiting constraints in growth and proliferation. [ 15 ] Drugs that target the transcription or mRNA processing machinery are known to be particularly effective against Myc-driven tumor models, [ 16 ] [ 17 ] suggesting that dampening of transcriptional amplification can have anti-tumor effects. Similarly, small molecules targeting the BET bromodomain protein BRD4, which is up-regulated during heart failure, can block cardiac hypertrophy in mouse models. [ 18 ] [ 19 ] In Rett syndrome, which is caused by loss of function of the transcriptional regulator MeCP2, MeCP2 was shown to specifically amplify transcription in neurons and not neuronal precursors. [ 20 ] Restoration of MeCP2 reverses disease symptoms associated with Rett syndrome [ 21 ] [ 22 ] | https://en.wikipedia.org/wiki/Transcriptional_amplification |
Transcriptional bursting , also known as transcriptional pulsing , is a fundamental property of genes in which transcription from DNA to RNA can occur in "bursts" or "pulses", which has been observed in diverse organisms, from bacteria to mammals. [ 1 ] [ 2 ] [ 3 ] [ 4 ] [ 5 ]
This phenomenon came to light with the advent of technologies, such as MS2 tagging and single molecule RNA fluorescence in situ hybridisation , to detect RNA production in single cells, through precise measurements of RNA number or RNA appearance at the gene. Other, more widespread techniques, such as Northern blotting , microarrays , RT-PCR and RNA-Seq , measure bulk RNA levels from homogenous population extracts. These techniques lose dynamic information from individual cells and give the impression that transcription is a continuous smooth process. Observed at an individual cell level, transcription is irregular, with strong periods of activity interspersed by long periods of inactivity.
Bursting may result from the stochastic nature of biochemical events superimposed upon a two step fluctuation. In its simplest form, the gene is proposed to exist in two states, one where activity is negligible and one where there is a certain probability of activation. [ 6 ] Only in the second state does transcription readily occur. It seems likely that some rudimentary eukaryotes have genes which do not show bursting. The genes are always in the permissive state, with a simple probability describing the numbers of RNAs generated. [ 7 ]
More recent data indicate the two state model can be an oversimplification. Transcription of the c-Fos gene in response to serum stimulation can, for the most part, be summarised by two states, although at certain times after stimulation, a third state better explains the variance in the data. [ 8 ] Another model suggests a two state model can apply, but with each cell having a different transcription rate in the active state. [ 9 ] Other analyses indicate a spectrum or continuum of activity states. [ 10 ] [ 11 ] The nuclear and signaling landscapes of complex eukaryotic nuclei may favour more than two simple states- for example, there are over several dozen post-translational modifications of nucleosomes and perhaps a hundred different proteins involved in the average eukaryotic transcription reaction.
What do the repressive and permissive states represent? An attractive idea is that the repressed state is a closed chromatin conformation whilst the permissive states are more open. Another hypothesis is that the fluctuations between states reflect reversible transitions in the binding and dissociation of pre-initiation complexes. [ 12 ] Bursts may also result from bursty signalling, cell cycle effects or movement of chromatin to and from transcription factories . Bursting dynamics have been demonstrated to be influenced by cell size [ 13 ] and the frequency of extracellular signalling. [ 14 ] Recent data suggest different degrees of supercoiling distinguish the permissive and inactive states. [ 15 ]
The bursting phenomenon, as opposed to simple probabilistic models of transcription, can account for the high variability (see transcriptional noise ) in gene expression occurring between cells in isogenic populations. This variability in turn can have tremendous consequences on cell behaviour, and must be mitigated or integrated. Suggested mechanisms by which noise can be dampened include strong extracellular signalling, [ 16 ] diffusion of RNA and protein in cell syncitia, [ 17 ] promoter proximal pausing, [ 18 ] and nuclear retention of transcripts. [ 19 ] In certain contexts, such as the survival of microbes in rapidly changing stressful environments, the expression variability may be essential. [ 20 ] Variability also impacts upon the effectiveness of clinical treatment, with resistance of bacteria to antibiotics demonstrably caused by non-genetic differences. [ 21 ] [ 22 ] Similar phenomena may contribute to the resistance of sub-populations of cancer cells to chemotherapy. [ 23 ] Spontaneous variability in gene expression is also proposed to act as a source of cell fate diversity in self-organizing differentiation processes, [ 24 ] and may act as a barrier to effective cellular reprogramming strategies. [ 25 ] | https://en.wikipedia.org/wiki/Transcriptional_bursting |
Transcriptional memory is a biological phenomenon, initially discovered in yeast, [ 1 ] during which cells primed with a particular cue show increased rates of gene expression after re-stimulation at a later time. This event was shown to take place: in yeast during growth in galactose [ 1 ] [ 2 ] and inositol starvation; [ 3 ] plants during environmental stress; [ 4 ] [ 5 ] [ 6 ] in mammalian cells during LPS [ 7 ] and interferon [ 8 ] [ 9 ] [ 10 ] induction. Prior work has shown that certain characteristics of chromatin may contribute to the poised transcriptional state allowing faster re-induction. These include: activity of specific transcription factors, [ 11 ] [ 12 ] [ 13 ] retention of RNA polymerase II at the promoters of poised genes, [ 9 ] activity of chromatin remodeling complexes, [ 2 ] propagation of H3K4me2 [ 8 ] [ 13 ] and H3K36me3 [ 10 ] histone modifications , occupancy of the H3.3 histone variant , [ 10 ] as well as binding of nuclear pore components. [ 9 ] [ 14 ] Moreover, locally bound cohesin was shown to inhibit establishment of transcriptional memory in human cells during interferon gamma stimulation. [ 15 ]
This microbiology -related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transcriptional_memory |
Transcriptional noise is a primary cause of the variability ( noise ) in gene expression occurring between cells in isogenic populations (see also cellular noise ) . [ 1 ] A proposed source of transcriptional noise is transcriptional bursting [ 2 ] [ 3 ] [ 4 ] although other sources of heterogeneity, such as unequal separation of cell contents at mitosis are also likely to contribute considerably. [ 5 ] Bursting transcription, as opposed to simple probabilistic models of transcription, reflects multiple states of gene activity, with fluctuations between states separated by irregular intervals, generating uneven protein expression between cells. Noise in gene expression can have tremendous consequences on cell behaviour, and must be mitigated or integrated. In certain contexts, such as establishment of viral latency, the survival of microbes in rapidly changing stressful environments, or several types of scattered differentiation, the variability may be essential. [ 6 ] [ 7 ] Variability also impacts upon the effectiveness of clinical treatment, with resistance of bacteria and yeast to antibiotics demonstrably caused by non-genetic differences. [ 8 ] [ 9 ] Variability in gene expression may also contribute to resistance of sub-populations of cancer cells to chemotherapy [ 10 ] and appears to be a barrier to curing HIV. [ 11 ] | https://en.wikipedia.org/wiki/Transcriptional_noise |
In molecular biology and genetics , transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA ( transcription ), thereby orchestrating gene activity . A single gene can be regulated in a range of ways, from altering the number of copies of RNA that are transcribed, to the temporal control of when the gene is transcribed. This control allows the cell or organism to respond to a variety of intra- and extracellular signals and thus mount a response. Some examples of this include producing the mRNA that encode enzymes to adapt to a change in a food source, producing the gene products involved in cell cycle specific activities, and producing the gene products responsible for cellular differentiation in multicellular eukaryotes, as studied in evolutionary developmental biology .
The regulation of transcription is a vital process in all living organisms. It is orchestrated by transcription factors and other proteins working in concert to finely tune the amount of RNA being produced through a variety of mechanisms. Bacteria and eukaryotes have very different strategies of accomplishing control over transcription, but some important features remain conserved between the two. Most importantly is the idea of combinatorial control, which is that any given gene is likely controlled by a specific combination of factors to control transcription. In a hypothetical example, the factors A and B might regulate a distinct set of genes from the combination of factors A and C. This combinatorial nature extends to complexes of far more than two proteins, and allows a very small subset (less than 10%) of the genome to control the transcriptional program of the entire cell.
Much of the early understanding of transcription came from bacteria, [ 2 ] although the extent and complexity of transcriptional regulation is greater in eukaryotes. Bacterial transcription is governed by three main sequence elements:
While these means of transcriptional regulation also exist in eukaryotes, the transcriptional landscape is significantly more complicated both by the number of proteins involved as well as by the presence of introns and the packaging of DNA into histones .
The transcription of a basic bacterial gene is dependent on the strength of its promoter and the presence of activators or repressors. In the absence of other regulatory elements, a promoter's sequence-based affinity for RNA polymerases varies, which results in the production of different amounts of transcript. The variable affinity of RNA polymerase for different promoter sequences is related to regions of consensus sequence upstream of the transcription start site. The more nucleotides of a promoter that agree with the consensus sequence, the stronger the affinity of the promoter for RNA Polymerase likely is. [ 4 ]
In the absence of other regulatory elements, the default state of a bacterial transcript is to be in the “on” configuration, resulting in the production of some amount of transcript. This means that transcriptional regulation in the form of protein repressors and positive control elements can either increase or decrease transcription. Repressors often physically occupy the promoter location, occluding RNA polymerase from binding. Alternatively a repressor and polymerase may bind to the DNA at the same time with a physical interaction between the repressor preventing the opening of the DNA for access to the minus strand for transcription. This strategy of control is distinct from eukaryotic transcription, whose basal state is to be off and where co-factors required for transcription initiation are highly gene dependent. [ 8 ]
Sigma factors are specialized bacterial proteins that bind to RNA polymerases and orchestrate transcription initiation. Sigma factors act as mediators of sequence-specific transcription, such that a single sigma factor can be used for transcription of all housekeeping genes or a suite of genes the cell wishes to express in response to some external stimuli such as stress. [ 9 ]
In addition to processes that regulate transcription at the stage of initiation, mRNA synthesis is also controlled by the rate of transcription elongation. [ 10 ] RNA polymerase pauses occur frequently and are regulated by transcription factors, such as NusG and NusA, transcription-translation coupling , and mRNA secondary structure. [ 11 ] [ 12 ]
The added complexity of generating a eukaryotic cell carries with it an increase in the complexity of transcriptional regulation. Eukaryotes have three RNA polymerases, known as Pol I , Pol II , and Pol III . Each polymerase has specific targets and activities, and is regulated by independent mechanisms. There are a number of additional mechanisms through which polymerase activity can be controlled. These mechanisms can be generally grouped into three main areas:
All three of these systems work in concert to integrate signals from the cell and change the transcriptional program accordingly.
While in prokaryotic systems the basal transcription state can be thought of as nonrestrictive (that is, “on” in the absence of modifying factors), eukaryotes have a restrictive basal state which requires the recruitment of other factors in order to generate RNA transcripts. This difference is largely due to the compaction of the eukaryotic genome by winding DNA around histones to form higher order structures. This compaction makes the gene promoter inaccessible without the assistance of other factors in the nucleus, and thus chromatin structure is a common site of regulation. Similar to the sigma factors in prokaryotes, the general transcription factors (GTFs) are a set of factors in eukaryotes that are required for all transcription events. These factors are responsible for stabilizing binding interactions and opening the DNA helix to allow the RNA polymerase to access the template, but generally lack specificity for different promoter sites. [ 13 ] A large part of gene regulation occurs through transcription factors that either recruit or inhibit the binding of the general transcription machinery and/or the polymerase. This can be accomplished through close interactions with core promoter elements, or through the long distance enhancer elements.
Once a polymerase is successfully bound to a DNA template, it often requires the assistance of other proteins in order to leave the stable promoter complex and begin elongating the nascent RNA strand. This process is called promoter escape, and is another step at which regulatory elements can act to accelerate or slow the transcription process. Similarly, protein and nucleic acid factors can associate with the elongation complex and modulate the rate at which the polymerase moves along the DNA template.
In eukaryotes, genomic DNA is highly compacted in order to be able to fit it into the nucleus. This is accomplished by winding the DNA around protein octamers called histones , which has consequences for the physical accessibility of parts of the genome at any given time. Significant portions are silenced through histone modifications, and thus are inaccessible to the polymerases or their cofactors. The highest level of transcription regulation occurs through the rearrangement of histones in order to expose or sequester genes, because these processes have the ability to render entire regions of a chromosome inaccessible such as what occurs in imprinting.
Histone rearrangement is facilitated by post-translational modifications to the tails of the core histones. A wide variety of modifications can be made by enzymes such as the histone acetyltransferases (HATs) , histone methyltransferases (HMTs) , and histone deacetylases (HDACs) , among others. These enzymes can add or remove covalent modifications such as methyl groups, acetyl groups, phosphates, and ubiquitin. Histone modifications serve to recruit other proteins which can either increase the compaction of the chromatin and sequester promoter elements, or to increase the spacing between histones and allow the association of transcription factors or polymerase on open DNA. [ 14 ] For example, H3K27 trimethylation by the polycomb complex PRC2 causes chromosomal compaction and gene silencing. [ 15 ] These histone modifications may be created by the cell, or inherited in an epigenetic fashion from a parent.
Transcription regulation at about 60% of promoters is controlled by methylation of cytosines within CpG dinucleotides (where 5’ cytosine is followed by 3’ guanine or CpG sites ). 5-methylcytosine (5-mC) is a methylated form of the DNA base cytosine (see Figure). 5-mC is an epigenetic marker found predominantly within CpG sites. About 28 million CpG dinucleotides occur in the human genome. [ 16 ] In most tissues of mammals, on average, 70% to 80% of CpG cytosines are methylated (forming 5-methylCpG or 5-mCpG). [ 17 ] Methylated cytosines within 5’cytosine-guanine 3’ sequences often occur in groups, called CpG islands . About 60% of promoter sequences have a CpG island while only about 6% of enhancer sequences have a CpG island. [ 18 ] CpG islands constitute regulatory sequences, since if CpG islands are methylated in the promoter of a gene this can reduce or silence gene transcription. [ 19 ]
DNA methylation regulates gene transcription through interaction with methyl binding domain (MBD) proteins , such as MeCP2 , MBD1 and MBD2 . These MBD proteins bind most strongly to highly methylated CpG islands . [ 20 ] These MBD proteins have both a methyl-CpG-binding domain as well as a transcription repression domain. [ 20 ] They bind to methylated DNA and guide or direct protein complexes with chromatin remodeling and/or histone modifying activity to methylated CpG islands. MBD proteins generally repress local chromatin such as by catalyzing the introduction of repressive histone marks, or creating an overall repressive chromatin environment through nucleosome remodeling and chromatin reorganization. [ 20 ]
Transcription factors are proteins that bind to specific DNA sequences in order to regulate the expression of a gene. The binding sequence for a transcription factor in DNA is usually about 10 or 11 nucleotides long. As summarized in 2009, Vaquerizas et al. indicated there are approximately 1,400 different transcription factors encoded in the human genome by genes that constitute about 6% of all human protein encoding genes. [ 21 ] About 94% of transcription factor binding sites (TFBSs) that are associated with signal-responsive genes occur in enhancers while only about 6% of such TFBSs occur in promoters. [ 22 ]
EGR1 protein is a particular transcription factor that is important for regulation of methylation of CpG islands. An EGR1 transcription factor binding site is frequently located in enhancer or promoter sequences. [ 23 ] There are about 12,000 binding sites for EGR1 in the mammalian genome and about half of EGR1 binding sites are located in promoters and half in enhancers. [ 23 ] The binding of EGR1 to its target DNA binding site is insensitive to cytosine methylation in the DNA. [ 23 ]
While only small amounts of EGR1 transcription factor protein are detectable in cells that are un-stimulated, translation of the EGR1 gene into protein at one hour after stimulation is drastically elevated. [ 24 ] Expression of EGR1 transcription factor proteins, in various types of cells, can be stimulated by growth factors, neurotransmitters, hormones, stress and injury. [ 24 ] In the brain, when neurons are activated, EGR1 proteins are up-regulated and they bind to (recruit) the pre-existing TET1 enzymes which are highly expressed in neurons. TET enzymes can catalyse demethylation of 5-methylcytosine. When EGR1 transcription factors bring TET1 enzymes to EGR1 binding sites in promoters, the TET enzymes can demethylate the methylated CpG islands at those promoters. Upon demethylation, these promoters can then initiate transcription of their target genes. Hundreds of genes in neurons are differentially expressed after neuron activation through EGR1 recruitment of TET1 to methylated regulatory sequences in their promoters. [ 23 ]
The methylation of promoters is also altered in response to signals. The three mammalian DNA methyltransferasess (DNMT1, DNMT3A, and DNMT3B) catalyze the addition of methyl groups to cytosines in DNA. While DNMT1 is a “maintenance” methyltransferase, DNMT3A and DNMT3B can carry out new methylations. There are also two splice protein isoforms produced from the DNMT3A gene: DNA methyltransferase proteins DNMT3A1 and DNMT3A2. [ 25 ]
The splice isoform DNMT3A2 behaves like the product of a classical immediate-early gene and, for instance, it is robustly and transiently produced after neuronal activation. [ 26 ] Where the DNA methyltransferase isoform DNMT3A2 binds and adds methyl groups to cytosines appears to be determined by histone post translational modifications. [ 27 ] [ 28 ] [ 29 ]
On the other hand, neural activation causes degradation of DNMT3A1 accompanied by reduced methylation of at least one evaluated targeted promoter. [ 30 ]
Transcription factors are proteins that bind to specific DNA sequences in order to regulate the expression of a given gene. There are approximately 1,400 transcription factors in the human genome and they constitute about 6% of all human protein coding genes. [ 21 ] The power of transcription factors resides in their ability to activate and/or repress wide repertoires of downstream target genes. The fact that these transcription factors work in a combinatorial fashion means that only a small subset of an organism's genome encodes transcription factors.
Transcription factors function through a wide variety of mechanisms. In one mechanism, CpG methylation influences binding of most transcription factors to DNA—in some cases negatively and in others positively. [ 31 ] In addition, often they are at the end of a signal transduction pathway that functions to change something about the factor, like its subcellular localization or its activity. Post-translational modifications to transcription factors located in the cytosol can cause them to translocate to the nucleus where they can interact with their corresponding enhancers. Other transcription factors are already in the nucleus, and are modified to enable the interaction with partner transcription factors. Some post-translational modifications known to regulate the functional state of transcription factors are phosphorylation , acetylation , SUMOylation and ubiquitylation .
Transcription factors can be divided in two main categories: activators and repressors . While activators can interact directly or indirectly with the core machinery of transcription through enhancer binding, repressors predominantly recruit co-repressor complexes leading to transcriptional repression by chromatin condensation of enhancer regions. It may also happen that a repressor may function by allosteric competition against a determined activator to repress gene expression: overlapping DNA-binding motifs for both activators and repressors induce a physical competition to occupy the site of binding. If the repressor has a higher affinity for its motif than the activator, transcription would be effectively blocked in the presence of the repressor.
Tight regulatory control is achieved by the highly dynamic nature of transcription factors. Again, many different mechanisms exist to control whether a transcription factor is active. These mechanisms include control over protein localization or control over whether the protein can bind DNA. [ 32 ] An example of this is the protein HSF1 , which remains bound to Hsp70 in the cytosol and is only translocated into the nucleus upon cellular stress such as heat shock. Thus the genes under the control of this transcription factor will remain untranscribed unless the cell is subjected to stress. [ 33 ]
Enhancers or cis-regulatory modules/elements (CRM/CRE) are non-coding DNA sequences containing multiple activator and repressor binding sites. Enhancers range from 200 bp to 1 kb in length and can be either proximal, 5’ upstream to the promoter or within the first intron of the regulated gene, or distal, in introns of neighboring genes or intergenic regions far away from the locus. Through DNA looping, active enhancers contact the promoter dependently of the core DNA binding motif promoter specificity. [ 34 ] Promoter-enhancer dichotomy provides the basis for the functional interaction between transcription factors and transcriptional core machinery to trigger RNA Pol II escape from the promoter. Whereas one could think that there is a 1:1 enhancer-promoter ratio, studies of the human genome predict that an active promoter interacts with 4 to 5 enhancers. Similarly, enhancers can regulate more than one gene without linkage restriction and are said to “skip” neighboring genes to regulate more distant ones. Even though infrequent, transcriptional regulation can involve elements located in a chromosome different from one where the promoter resides. Proximal enhancers or promoters of neighboring genes can serve as platforms to recruit more distal elements. [ 35 ]
Up-regulated expression of genes in mammals can be initiated when signals are transmitted to the promoters associated with the genes. Cis-regulatory DNA sequences that are located in DNA regions distant from the promoters of genes can have very large effects on gene expression, with some genes undergoing up to 100-fold increased expression due to such a cis-regulatory sequence. [ 36 ] These cis-regulatory sequences include enhancers , silencers , insulators and tethering elements. [ 37 ] Among this constellation of sequences, enhancers and their associated transcription factor proteins have a leading role in the regulation of gene expression. [ 38 ]
Enhancers are sequences of the genome that are major gene-regulatory elements. Enhancers control cell-type-specific gene expression programs, most often by looping through long distances to come in physical proximity with the promoters of their target genes. [ 39 ] In a study of brain cortical neurons, 24,937 loops were found, bringing enhancers to promoters. [ 36 ] Multiple enhancers, each often at tens or hundred of thousands of nucleotides distant from their target genes, loop to their target gene promoters and coordinate with each other to control expression of their common target gene. [ 39 ]
The schematic illustration in this section shows an enhancer looping around to come into close physical proximity with the promoter of a target gene. The loop is stabilized by a dimer of a connector protein (e.g. dimer of CTCF or YY1 ), with one member of the dimer anchored to its binding motif on the enhancer and the other member anchored to its binding motif on the promoter (represented by the red zigzags in the illustration). [ 40 ] Several cell function specific transcription factor proteins (in 2018 Lambert et al. indicated there were about 1,600 transcription factors in a human cell [ 41 ] ) generally bind to specific motifs on an enhancer [ 22 ] and a small combination of these enhancer-bound transcription factors, when brought close to a promoter by a DNA loop, govern the level of transcription of the target gene. Mediator (coactivator) (a complex usually consisting of about 26 proteins in an interacting structure) communicates regulatory signals from enhancer DNA-bound transcription factors directly to the RNA polymerase II (RNAP II) enzyme bound to the promoter. [ 42 ]
Enhancers, when active, are generally transcribed from both strands of DNA with RNA polymerases acting in two different directions, producing two eRNAs as illustrated in the Figure. [ 43 ] An inactive enhancer may be bound by an inactive transcription factor. Phosphorylation of the transcription factor may activate it and that activated transcription factor may then activate the enhancer to which it is bound (see small red star representing phosphorylation of a transcription factor bound to an enhancer in the illustration). [ 44 ] An activated enhancer begins transcription of its RNA before activating a promoter to initiate transcription of messenger RNA from its target gene. [ 45 ]
Typical enhancers are often of the size 151–240 base pairs. [ 46 ]
While enhancers are needed for transcription of a gene above a low level, clusters of enhancers, known as super-enhancers , can cause transcription of a target gene at a very high level.
Super-enhancers are a group of typical enhancers, all located within a region of 10,000 to 60,000 nucleotides. [ 47 ] [ 48 ] The typical enhancers within a super-enhancer simultaneously loop over from a distance to strongly increase initiation and transcription of a gene. The illustration in this section shows a super-enhancer of about 12,000 base pairs in length with four typical enhancers within its length. The enhancers are each associated with the same gene, transmitting signals from the transcription factors on each enhancer through a mediator protein complex to the promoter of the gene. Each typical enhancer within the cluster interacts with its own mediator multi-protein complex. The protein BRD4 complexes with each typical enhancer and stabilizes the super-enhancer structure. [ 49 ] Thus, there are a large number of proteins present in close association on a super-enhancer, including BRD4 proteins, transcription factors, 26 mediator proteins for each enhancer, etc.). Most of these proteins have a structured domain as well as a tail with an intrinsically disordered region. [ 50 ] The intrinsically disordered regions of these proteins interact with each other and usually form a water-excluding gel (phase-separated condensate) around the super-enhancer. [ 50 ]
As examples, in the case of the mouse α-globin super-enhancer, the five typical enhancers within the super-enhancer, acting together, increase transcription of the α-globin gene by 450-fold. [ 51 ] In the case of the mouse Wap super-enhancer, the three typical enhancers, acting together, increase transcription of the Wap gene by 1000-fold. [ 52 ]
In many types of cells, there are usually thousands of active typical enhancers and a few hundred super-enhancers. Super-enhancers (SEs) usually drive 2% to 4% of the actively transcribed regions of the genome. For instance, immune-system non-stimulated B cells have 140 super-enhancers (SEs) and 4,290 typical enhancers (TEs) (3.2% SEs). [ 53 ] Similarly, in mouse embryonic stem cells, there are 231 SEs compared to 8,794 TEs (2.6% SEs). [ 54 ] In neural stem cells there are 445 SEs and 9,436 TEs (4.7% SEs). [ 55 ]
While super-enhancers are only active at 2-4% of actively transcribed sites in a cell, they strongly recruit transcription machinery. The super-enhancers in a cell generally utilize 12% to 36% of the RNA polymerases, mediator proteins, BRD4 proteins, and other transcription machinery of the cell. [ 56 ]
Transcriptional initiation, termination and regulation are mediated by “DNA looping” which brings together promoters, enhancers, transcription factors and RNA processing factors to accurately regulate gene expression. [ 57 ] Chromosome conformation capture (3C) and more recently Hi-C techniques provided evidence that active chromatin regions are “compacted” in nuclear domains or bodies where transcriptional regulation is enhanced. [ 58 ] The configuration of the genome is essential for enhancer-promoter proximity. Cell-fate decisions are mediated upon highly dynamic genomic reorganizations at interphase to modularly switch on or off entire gene regulatory networks through short to long range chromatin rearrangements. [ 59 ] Related studies demonstrate that metazoan genomes are partitioned in structural and functional units around a megabase long called Topological association domains (TADs) containing dozens of genes regulated by hundreds of enhancers distributed within large genomic regions containing only non-coding sequences. The function of TADs is to regroup enhancers and promoters interacting together within a single large functional domain instead of having them spread in different TADs. [ 60 ] However, studies of mouse development point out that two adjacent TADs may regulate the same gene cluster. The most relevant study on limb evolution shows that the TAD at the 5’ of the HoxD gene cluster in tetrapod genomes drives its expression in the distal limb bud embryos, giving rise to the hand, while the one located at 3’ side does it in the proximal limb bud, giving rise to the arm. [ 61 ] Still, it is not known whether TADs are an adaptive strategy to enhance regulatory interactions or an effect of the constrains on these same interactions.
TAD boundaries are often composed by housekeeping genes, tRNAs, other highly expressed sequences and Short Interspersed Elements (SINE). While these genes may take advantage of their border position to be ubiquitously expressed, they are not directly linked with TAD edge formation. The specific molecules identified at boundaries of TADs are called insulators or architectural proteins because they not only block enhancer leaky expression but also ensure an accurate compartmentalization of cis-regulatory inputs to the targeted promoter. These insulators are DNA-binding proteins like CTCF and TFIIIC that help recruiting structural partners such as cohesins and condensins. The localization and binding of architectural proteins to their corresponding binding sites is regulated by post-translational modifications. [ 62 ] DNA binding motifs recognized by architectural proteins are either of high occupancy and at around a megabase of each other or of low occupancy and inside TADs. High occupancy sites are usually conserved and static while intra-TADs sites are dynamic according to the state of the cell therefore TADs themselves are compartmentalized in subdomains that can be called subTADs from few kb up to a TAD long (19). When architectural binding sites are at less than 100 kb from each other, Mediator proteins are the architectural proteins cooperate with cohesin. For subTADs larger than 100 kb and TAD boundaries, CTCF is the typical insulator found to interact with cohesion. [ 63 ]
In eukaryotes, ribosomal rRNA and the tRNAs involved in translation are controlled by RNA polymerase I (Pol I) and RNA polymerase III (Pol III) . RNA Polymerase II (Pol II) is responsible for the production of messenger RNA (mRNA) within the cell. Particularly for Pol II, much of the regulatory checkpoints in the transcription process occur in the assembly and escape of the pre-initiation complex . A gene-specific combination of transcription factors will recruit TFIID and/or TFIIA to the core promoter, followed by the association of TFIIB , creating a stable complex onto which the rest of the General Transcription Factors (GTFs) can assemble. [ 64 ] This complex is relatively stable, and can undergo multiple rounds of transcription initiation. [ 65 ] After the binding of TFIIB and TFIID, Pol II the rest of the GTFs can assemble. This assembly is marked by the post-translational modification (typically phosphorylation) of the C-terminal domain (CTD) of Pol II through a number of kinases. [ 66 ] The CTD is a large, unstructured domain extending from the RbpI subunit of Pol II, and consists of many repeats of the heptad sequence YSPTSPS. TFIIH , the helicase that remains associated with Pol II throughout transcription, also contains a subunit with kinase activity which will phosphorylate the serines 5 in the heptad sequence. Similarly, both CDK8 (a subunit of the massive multiprotein Mediator complex) and CDK9 (a subunit of the p-TEFb elongation factor), have kinase activity towards other residues on the CTD. [ 67 ] These phosphorylation events promote the transcription process and serve as sites of recruitment for mRNA processing machinery. All three of these kinases respond to upstream signals, and failure to phosphorylate the CTD can lead to a stalled polymerase at the promoter.
In vertebrates, the majority of gene promoters contain a CpG island with numerous CpG sites . [ 68 ] When many of a gene's promoter CpG sites are methylated the gene becomes silenced. [ 69 ] Colorectal cancers typically have 3 to 6 driver mutations and 33 to 66 hitchhiker or passenger mutations. [ 70 ] However, transcriptional silencing may be of more importance than mutation in causing progression to cancer. For example, in colorectal cancers about 600 to 800 genes are transcriptionally silenced by CpG island methylation (see regulation of transcription in cancer ). Transcriptional repression in cancer can also occur by other epigenetic mechanisms, such as altered expression of microRNAs . [ 71 ] In breast cancer, transcriptional repression of BRCA1 may occur more frequently by over-expressed microRNA-182 than by hypermethylation of the BRCA1 promoter (see Low expression of BRCA1 in breast and ovarian cancers ). | https://en.wikipedia.org/wiki/Transcriptional_regulation |
The transcriptome is the set of all RNA transcripts, including coding and non-coding , in an individual or a population of cells . The term can also sometimes be used to refer to all RNAs , or just mRNA , depending on the particular experiment. The term transcriptome is a portmanteau of the words transcript and genome ; it is associated with the process of transcript production during the biological process of transcription .
The early stages of transcriptome annotations began with cDNA libraries published in the 1980s. Subsequently, the advent of high-throughput technology led to faster and more efficient ways of obtaining data about the transcriptome. Two biological techniques are used to study the transcriptome, namely DNA microarray , a hybridization-based technique and RNA-seq , a sequence-based approach. [ 1 ] RNA-seq is the preferred method and has been the dominant transcriptomics technique since the 2010s. Single-cell transcriptomics allows tracking of transcript changes over time within individual cells.
Data obtained from the transcriptome is used in research to gain insight into processes such as cellular differentiation , carcinogenesis , transcription regulation and biomarker discovery among others. Transcriptome-obtained data also finds applications in establishing phylogenetic relationships during the process of evolution and in in vitro fertilization . The transcriptome is closely related to other -ome based biological fields of study; it is complementary to the proteome and the metabolome and encompasses the translatome , exome , meiome and thanatotranscriptome which can be seen as ome fields studying specific types of RNA transcripts. There are quantifiable and conserved relationships between the Transcriptome and other -omes, and Transcriptomics data can be used effectively to predict other molecular species, such as metabolites. [ 2 ] There are numerous publicly available transcriptome databases.
The word transcriptome is a portmanteau of the words transcript and genome . It appeared along with other neologisms formed using the suffixes -ome and -omics to denote all studies conducted on a genome-wide scale in the fields of life sciences and technology. As such, transcriptome and transcriptomics were one of the first words to emerge along with genome and proteome. [ 3 ] The first study to present a case of a collection of a cDNA library for silk moth mRNA was published in 1979. [ 4 ] The first seminal study to mention and investigate the transcriptome of an organism was published in 1997 and it described 60,633 transcripts expressed in S. cerevisiae using serial analysis of gene expression (SAGE). [ 5 ] With the rise of high-throughput technologies and bioinformatics and the subsequent increased computational power, it became increasingly efficient and easy to characterize and analyze enormous amount of data. [ 3 ] Attempts to characterize the transcriptome became more prominent with the advent of automated DNA sequencing during the 1980s. [ 6 ] During the 1990s, expressed sequence tag sequencing was used to identify genes and their fragments. [ 7 ] This was followed by techniques such as serial analysis of gene expression (SAGE), cap analysis of gene expression (CAGE), and massively parallel signature sequencing (MPSS).
The transcriptome encompasses all the ribonucleic acid (RNA) transcripts present in a given organism or experimental sample. [ 8 ] RNA is the main carrier of genetic information that is responsible for the process of converting DNA into an organism's phenotype. A gene can give rise to a single-stranded messenger RNA (mRNA) through a molecular process known as transcription ; this mRNA is complementary to the strand of DNA it originated from. [ 6 ] The enzyme RNA polymerase II attaches to the template DNA strand and catalyzes the addition of ribonucleotides to the 3' end of the growing sequence of the mRNA transcript. [ 9 ]
In order to initiate its function, RNA polymerase II needs to recognize a promoter sequence , located upstream (5') of the gene. In eukaryotes, this process is mediated by transcription factors , most notably Transcription factor II D (TFIID) which recognizes the TATA box and aids in the positioning of RNA polymerase at the appropriate start site. To finish the production of the RNA transcript, termination takes place usually several hundred nuclecotides away from the termination sequence and cleavage takes place. [ 9 ] This process occurs in the nucleus of a cell along with RNA processing by which mRNA molecules are capped , spliced and polyadenylated to increase their stability before being subsequently taken to the cytoplasm. The mRNA gives rise to proteins through the process of translation that takes place in ribosomes .
Almost all functional transcripts are derived from known genes. The only exceptions are a small number of transcripts that might play a direct role in regulating gene expression near the prompters of known genes. (See Enhancer RNA .)
Gene occupy most of prokaryotic genomes so most of their genomes are transcribed. Many eukaryotic genomes are very large and known genes may take up only a fraction of the genome. In mammals, for example, known genes only account for 40-50% of the genome. [ 10 ] Nevertheless, identified transcripts often map to a much larger fraction of the genome suggesting that the transcriptome contains spurious transcripts that do not come from genes. Some of these transcripts are known to be non-functional because they map to transcribed pseudogenes or degenerative transposons and viruses. Others map to unidentified regions of the genome that may be junk DNA.
Spurious transcription is very common in eukaryotes, especially those with large genomes that might contain a lot of junk DNA . [ 11 ] [ 12 ] [ 13 ] [ 14 ] Some scientists claim that if a transcript has not been assigned to a known gene then the default assumption must be that it is junk RNA until it has been shown to be functional. [ 11 ] [ 15 ] This would mean that much of the transcriptome in species with large genomes is probably junk RNA. (See Non-coding RNA )
The transcriptome includes the transcripts of protein-coding genes (mRNA plus introns) as well as the transcripts of non-coding genes (functional RNAs plus introns).
In the human genome, all genes get transcribed into RNA because that's how the molecular gene is defined. (See Gene .) The transcriptome consists of coding regions of mRNA plus non-coding UTRs, introns, non-coding RNAs, and spurious non-functional transcripts.
Several factors render the content of the transcriptome difficult to establish. These include alternative splicing , RNA editing and alternative transcription among others. [ 17 ] Additionally, transcriptome techniques are capable of capturing transcription occurring in a sample at a specific time point, although the content of the transcriptome can change during differentiation. [ 6 ] The main aims of transcriptomics are the following: "catalogue all species of transcript, including mRNAs, non-coding RNAs and small RNAs; to determine the transcriptional structure of genes, in terms of their start sites, 5′ and 3′ ends, splicing patterns and other post-transcriptional modifications; and to quantify the changing expression levels of each transcript during development and under different conditions". [ 1 ]
The term can be applied to the total set of transcripts in a given organism , or to the specific subset of transcripts present in a particular cell type. Unlike the genome , which is roughly fixed for a given cell line (excluding mutations ), the transcriptome can vary with external environmental conditions. Because it includes all mRNA transcripts in the cell, the transcriptome reflects the genes that are being actively expressed at any given time, with the exception of mRNA degradation phenomena such as transcriptional attenuation . The study of transcriptomics , (which includes expression profiling , splice variant analysis etc.), examines the expression level of RNAs in a given cell population, often focusing on mRNA, but sometimes including others such as tRNAs and sRNAs.
Transcriptomics is the quantitative science that encompasses the assignment of a list of strings ("reads") to the object ("transcripts" in the genome). To calculate the expression strength, the density of reads corresponding to each object is counted. [ 18 ] Initially, transcriptomes were analyzed and studied using expressed sequence tags libraries and serial and cap analysis of gene expression (SAGE).
Currently, the two main transcriptomics techniques include DNA microarrays and RNA-Seq . Both techniques require RNA isolation through RNA extraction techniques, followed by its separation from other cellular components and enrichment of mRNA. [ 19 ] [ 20 ]
There are two general methods of inferring transcriptome sequences. One approach maps sequence reads onto a reference genome, either of the organism itself (whose transcriptome is being studied) or of a closely related species. The other approach, de novo transcriptome assembly , uses software to infer transcripts directly from short sequence reads and is used in organisms with genomes that are not sequenced. [ 21 ]
The first transcriptome studies were based on microarray techniques (also known as DNA chips). Microarrays consist of thin glass layers with spots on which oligonucleotides , known as "probes" are arrayed; each spot contains a known DNA sequence. [ 22 ]
When performing microarray analyses, mRNA is collected from a control and an experimental sample, the latter usually representative of a disease. The RNA of interest is converted to cDNA to increase its stability and marked with fluorophores of two colors, usually green and red, for the two groups. The cDNA is spread onto the surface of the microarray where it hybridizes with oligonucleotides on the chip and a laser is used to scan. The fluorescence intensity on each spot of the microarray corresponds to the level of gene expression and based on the color of the fluorophores selected, it can be determined which of the samples exhibits higher levels of the mRNA of interest. [ 7 ]
One microarray usually contains enough oligonucleotides to represent all known genes; however, data obtained using microarrays does not provide information about unknown genes. During the 2010s, microarrays were almost completely replaced by next-generation techniques that are based on DNA sequencing.
RNA sequencing is a next-generation sequencing technology; as such it requires only a small amount of RNA and no previous knowledge of the genome. [ 3 ] It allows for both qualitative and quantitative analysis of RNA transcripts, the former allowing discovery of new transcripts and the latter a measure of relative quantities for transcripts in a sample. [ 16 ]
The three main steps of sequencing transcriptomes of any biological samples include RNA purification, the synthesis of an RNA or cDNA library and sequencing the library. [ 16 ] The RNA purification process is different for short and long RNAs. [ 16 ] This step is usually followed by an assessment of RNA quality, with the purpose of avoiding contaminants such as DNA or technical contaminants related to sample processing. RNA quality is measured using UV spectrometry with an absorbance peak of 260 nm. [ 23 ] RNA integrity can also be analyzed quantitatively comparing the ratio and intensity of 28S RNA to 18S RNA reported in the RNA Integrity Number (RIN) score. [ 23 ] Since mRNA is the species of interest and it represents only 3% of its total content, the RNA sample should be treated to remove rRNA and tRNA and tissue-specific RNA transcripts. [ 23 ]
The step of library preparation with the aim of producing short cDNA fragments, begins with RNA fragmentation to transcripts in length between 50 and 300 base pairs . Fragmentation can be enzymatic (RNA endonucleases ), chemical (trismagnesium salt buffer, chemical hydrolysis ) or mechanical ( sonication , nebulisation). [ 24 ] Reverse transcription is used to convert the RNA templates into cDNA and three priming methods can be used to achieve it, including oligo-DT, using random primers or ligating special adaptor oligos.
Transcription can also be studied at the level of individual cells by single-cell transcriptomics . Single-cell RNA sequencing (scRNA-seq) is a recently developed technique that allows the analysis of the transcriptome of single cells, including bacteria . [ 25 ] With single-cell transcriptomics, subpopulations of cell types that constitute the tissue of interest are also taken into consideration. [ 26 ] This approach allows to identify whether changes in experimental samples are due to phenotypic cellular changes as opposed to proliferation, with which a specific cell type might be overexpressed in the sample. [ 27 ] Additionally, when assessing cellular progression through differentiation , average expression profiles are only able to order cells by time rather than their stage of development and are consequently unable to show trends in gene expression levels specific to certain stages. [ 28 ] Single-cell trarnscriptomic techniques have been used to characterize rare cell populations such as circulating tumor cells , cancer stem cells in solid tumors, and embryonic stem cells (ESCs) in mammalian blastocysts . [ 29 ]
Although there are no standardized techniques for single-cell transcriptomics, several steps need to be undertaken. The first step includes cell isolation, which can be performed using low- and high-throughput techniques. This is followed by a qPCR step and then single-cell RNAseq where the RNA of interest is converted into cDNA. Newer developments in single-cell transcriptomics allow for tissue and sub-cellular localization preservation through cryo-sectioning thin slices of tissues and sequencing the transcriptome in each slice. Another technique allows the visualization of single transcripts under a microscope while preserving the spatial information of each individual cell where they are expressed. [ 29 ]
A number of organism-specific transcriptome databases have been constructed and annotated to aid in the identification of genes that are differentially expressed in distinct cell populations.
RNA-seq is emerging (2013) as the method of choice for measuring transcriptomes of organisms, though the older technique of DNA microarrays is still used. [ 1 ] RNA-seq measures the transcription of a specific gene by converting long RNAs into a library of cDNA fragments. The cDNA fragments are then sequenced using high-throughput sequencing technology and aligned to a reference genome or transcriptome which is then used to create an expression profile of the genes. [ 1 ]
The transcriptomes of stem cells and cancer cells are of particular interest to researchers who seek to understand the processes of cellular differentiation and carcinogenesis . A pipeline using RNA-seq or gene array data can be used to track genetic changes occurring in stem and precursor cells and requires at least three independent gene expression data from the former cell type and mature cells. [ 30 ]
Analysis of the transcriptomes of human oocytes and embryos is used to understand the molecular mechanisms and signaling pathways controlling early embryonic development, and could theoretically be a powerful tool in making proper embryo selection in in vitro fertilisation . [ citation needed ] Analyses of the transcriptome content of the placenta in the first-trimester of pregnancy in in vitro fertilization and embryo transfer (IVT-ET) revealed differences in genetic expression which are associated with higher frequency of adverse perinatal outcomes. Such insight can be used to optimize the practice. [ 31 ] Transcriptome analyses can also be used to optimize cryopreservation of oocytes, by lowering injuries associated with the process. [ 32 ]
Transcriptomics is an emerging and continually growing field in biomarker discovery for use in assessing the safety of drugs or chemical risk assessment . [ 33 ]
Transcriptomes may also be used to infer phylogenetic relationships among individuals or to detect evolutionary patterns of transcriptome conservation. [ 34 ]
Transcriptome analyses were used to discover the incidence of antisense transcription, their role in gene expression through interaction with surrounding genes and their abundance in different chromosomes. [ 35 ] RNA-seq was also used to show how RNA isoforms, transcripts stemming from the same gene but with different structures, can produce complex phenotypes from limited genomes. [ 21 ]
Transcriptome analysis have been used to study the evolution and diversification process of plant species. In 2014, the 1000 Plant Genomes Project was completed in which the transcriptomes of 1,124 plant species from the families viridiplantae , glaucophyta and rhodophyta were sequenced. The protein coding sequences were subsequently compared to infer phylogenetic relationships between plants and to characterize the time of their diversification in the process of evolution. [ 36 ] Transcriptome studies have been used to characterize and quantify gene expression in mature pollen . Genes involved in cell wall metabolism and cytoskeleton were found to be overexpressed. Transcriptome approaches also allowed to track changes in gene expression through different developmental stages of pollen, ranging from microspore to mature pollen grains; additionally such stages could be compared across species of different plants including Arabidopsis , rice and tobacco . [ 37 ]
Similar to other -ome based technologies, analysis of the transcriptome allows for an unbiased approach when validating hypotheses experimentally. This approach also allows for the discovery of novel mediators in signaling pathways. [ 18 ] As with other -omics based technologies, the transcriptome can be analyzed within the scope of a multiomics approach. It is complementary to metabolomics but contrary to proteomics, a direct association between a transcript and metabolite cannot be established.
There are several -ome fields that can be seen as subcategories of the transcriptome. The exome differs from the transcriptome in that it includes only those RNA molecules found in a specified cell population, and usually includes the amount or concentration of each RNA molecule in addition to the molecular identities. Additionally, the transcritpome also differs from the translatome , which is the set of RNAs undergoing translation.
The term meiome is used in functional genomics to describe the meiotic transcriptome or the set of RNA transcripts produced during the process of meiosis . [ 38 ] Meiosis is a key feature of sexually reproducing eukaryotes , and involves the pairing of homologous chromosome , synapse and recombination. Since meiosis in most organisms occurs in a short time period, meiotic transcript profiling is difficult due to the challenge of isolation (or enrichment) of meiotic cells ( meiocytes ). As with transcriptome analyses, the meiome can be studied at a whole-genome level using large-scale transcriptomic techniques. [ 39 ] The meiome has been well-characterized in mammal and yeast systems and somewhat less extensively characterized in plants. [ 40 ]
The thanatotranscriptome consists of all RNA transcripts that continue to be expressed or that start getting re-expressed in internal organs of a dead body 24–48 hours following death. Some genes include those that are inhibited after fetal development . If the thanatotranscriptome is related to the process of programmed cell death ( apoptosis ), it can be referred to as the apoptotic thanatotranscriptome. Analyses of the thanatotranscriptome are used in forensic medicine . [ 41 ]
eQTL mapping can be used to complement genomics with transcriptomics; genetic variants at DNA level and gene expression measures at RNA level. [ 42 ]
The transcriptome can be seen as a subset of the proteome , that is, the entire set of proteins expressed by a genome.
However, the analysis of relative mRNA expression levels can be complicated by the fact that relatively small changes in mRNA expression can produce large changes in the total amount of the corresponding protein present in the cell. One analysis method, known as gene set enrichment analysis , identifies coregulated gene networks rather than individual genes that are up- or down-regulated in different cell populations. [1]
Although microarray studies can reveal the relative amounts of different mRNAs in the cell, levels of mRNA are not directly proportional to the expression level of the proteins they code for. [ 43 ] The number of protein molecules synthesized using a given mRNA molecule as a template is highly dependent on translation-initiation features of the mRNA sequence; in particular, the ability of the translation initiation sequence is a key determinant in the recruiting of ribosomes for protein translation . | https://en.wikipedia.org/wiki/Transcriptome |
Transcriptome-wide association study (TWAS) is a genetic methodology that can be used to compare the genetic components of gene expression and the genetic components of a trait to determine if an association is present between the two components. [ 1 ] [ 2 ] TWAS are useful for the identification and prioritization of candidate causal genes in candidate gene analysis following genome-wide association studies. [ 3 ] TWAS looks at the RNA products of a specific tissue and gives researchers the abilities to look at the genes being expressed as well as gene expression levels, which varies by tissue type. TWAS are valuable and flexible bioinformatics tools that looks at the associations between the expressions of genes and complex traits and diseases. [ 4 ] By looking at the association between gene expression and the trait expressed, genetic regulatory mechanisms can be investigated for the role that they play in the development of specific traits and diseases.
A transcriptome is the sum of all RNA transcripts that are present in a given cell, tissue, or organ within an organism. Transcriptomes include both mRNA, which functions as an intermediate to the central dogma; as well as noncoding RNAs that may play other roles in protein synthesis. [ 5 ] In the central dogma, it describes how DNA is able to make proteins through transcription and translation. RNAs are present in a cell in varied concentrations, and play various roles outside of the central dogma and are able to be identified based on length and function. It is through functional elements that the transcriptional and translational activities of genes is able to be regulated. [ 4 ] Transcriptome analysis is beneficial for obtaining information about all RNAs present and can provide valuable insight into the genetic mechanisms that are tissue specific. [ 6 ] The transcriptome was first investigated in the 1990s in an experiment performed to identify a partial transcriptome of the human brain. Researchers were able to identify 609 mRNA sequences. [ 5 ] Since then, many advances in Next Generation Sequencing methods have been made. [ 6 ] Transcriptomes are now able to be routinely developed due to advances in these methods and new technologies such as microarrays and RNA-Seq. Both methods require computed imaging as well as high reads and statistical analysis. [ 5 ] By obtaining information about gene expression through mRNAs, many applications have been discovered. Transcriptome analysis has proven to be beneficial in identifying disease processes as well as regulatory elements in disease progressions, has aided drug development through identification of disease processes, offers insight into therapeutic strategies, and has improved identification of genes that are able to respond to both biotic and abiotic environmental factors as well as how environmental conditions play a role in gene expression. [ 5 ]
A genome-wide association study , or GWAS, is a genetic tool that uses single nucleotide polymorphisms, or SNPs, to identify if a trait or disease is linked to a specific genetic variant. By observing if frequencies of a specific variant are more commonly associated, or higher than expected, with the given trait; an association is developed between the trait and the variant. However, many of these associations can be developed throughout an individual due to linkage disequilibrium and the large size of the genome. Although GWAS provide valuable insight into identifying markers throughout the genome, a large portion of the SNPs are present in non-coding mRNA regions, and many have unknown functions that are difficult to determine through standard methods, as no product is manufactured by these regions of the genome. [ 4 ]
Transcription-wide association studies are able to take the information from GWAS results and are able to utilize these results as reference data, and can then help to identify and prioritize genes. [ 4 ] In order to perform this analysis, a reference panel for gene expression should be obtained, such as an expression quantitative trait loci (eQTL), which helps to show gene expression regulation. [ 4 ] Using the reference panel, a predictive model can be generated to impute the expression variation of genes. Imputation is the process by which you can predict the expression levels of genes in other organisms through the variation that exists in their genome based on a reference panel. By predicting the levels of gene expression within a tissue, other variables such as environment and epigenetic effects are eliminated as this prediction is solely based on the variant present and the expected level of gene expression. However, this can lead to inaccuracies with gene expression predictions as both the environment and epigenetic modifications are able to alter the level of gene expression. [ 7 ] Cis-genetic components are the primary focus of the eQTLs as these are elements that are within 1 Megabase of a gene. [ 2 ] The predictive model can then be applied to the GWAS samples to predict gene expression of the significant SNPs from that study. After expression levels are imputated, gene-trait association tests are performed by associating levels of predicted expression and genotypes with the phenotypes of the individual. [ 8 ] Essentially, a TWAS is able to take GWAS results and are able to predict the effects of each variant on expression levels of genes that are associated with the trait, and it is able to do this for every loci that is associated with the trait throughout the genome. [ 7 ]
Results are able to be interpreted on a Manhattan plot, similarly to GWAS results. Any loci that are considered to have statistically significant results will have a higher P value, and this indicates that the loci is likely associated with the trait or disease being investigated. Any statistically significant P-values have a higher log P-value and show above the Bonferroni correction line . The Manhattan plot is named as such as the statistically significant genes appear to show up as "skyscrapers" on the plot, and when there are many genes that are associated with the trait, the plot resembles the Manhattan skyline. Although the Manhattan plot image is for a GWAS study, TWAS results are shown the same way. Statistically significant loci are genes that have significantly associated SNPs whose expression correlates with the trait or disease of interest.
PrediXcan [ 1 ] and FUSION [ 2 ] are both TWAS software that have been utilized in genetic studies to investigate the gene-trait associations. PrediXcan is a well-developed TWAS software that has the ability to estimate genetically regulated expression and determine associations with the phenotype being investigated. It uses a penalized regression model to give weight to levels of observed gene expression and cis-SNPs derived from the reference dataset. [ 8 ] The software then uses individual genotype data to perform gene-trait association tests. FUSION is another TWAS software that utilizes a different statistical analysis to create the association tests. In this model, imputation methods from the predictive model are calculated based on a Bayesian sparse linear mixed model. [ 8 ] The advantage of this software is that it is able to perform association tests on individual genotype data, but this software can also take information from large scale data sets using imputation.
The advantages of this methodology are through the insight it gives researchers into the function of genes and the association between gene functions and gene expression. TWAS has the potential to take results from GWAS and extend the results to aid in the understanding of disease mechanisms. [ 4 ] Additionally, as this method uses loci that were previously identified by GWAS analysis, there is a lower testing burden associated with a TWAS as less sites are analyzed. By lowering the number of loci being analyzed, this allows more in-depth analysis of the sites analyzed and can give further insight to the functions and associations of the significant loci.
TWAS also have the advantage of reducing the effects of confounding factors. When building a predictive model, it only looks at genetic expression, not total expression. Total expression includes factors like the environment and epigenetic modifications to levels of expression, and are not accounted for in the predictive model. By not accounting for these factors, it can reduce the accuracy of predicted levels of gene expression; however, it also reduces the effects of confounding variables in the results. [ 2 ]
Another advantage of TWAS is that the results are tissue specific. The level of gene expression differs by the tissue that the genes are in, as each tissue has specific splicing patterns and patterns of regulation. By having tissue specific results, this furthers the information that can be derived through these studies as results have the ability to show how gene regulation differs by tissue types as well as how functions are regulated and if there are common regulatory mechanisms between tissues or if regulatory mechanisms have different functions in different tissues. TWAS cross tissue methods also have the possibility to identify potential causal genes for diseases and traits on a larger scale, however, single tissue methods have the ability to determine associations on a case specific basis. [ 8 ]
Many of the disadvantages of TWAS are implications of the prediction capabilities of the model used to predict gene expression levels based on genotypes. One disadvantage of TWAS is that it mainly looks at cis-genetic components for imputation and for in most studies, does not identify any trans-genetic component variants. This acts as a disadvantage for TWAS as trans-genetic component variants are any regulatory mechanisms that are outside of a 1 Megabase range of the gene, and even though they are a significant distance away from the gene of interest, many regulatory mechanisms have the potential to act long range and can still impact expression. By not taking these components into account, it lowers the accuracy of predicted genetic expression levels and can cause deviation between expected and observed expression levels. As mentioned above, another disadvantage of these studies are that environmental and epigenetic mechanisms for regulation of gene expression is not taken into account with the predictive model for gene expression, which also has the potential to lead to inaccuracies with the predicted gene expression levels and observed expression levels. Another challenge for TWAS is that it can be hard to predict accurate gene expression levels when genes have low heritability levels. eQTLs rely on a level of heritability, and when low heritability is observed, it can affect the observance of false positives and can negatively impact the prediction capabilities of the model used for TWAS. [ 4 ]
Additionally, another challenge for TWAS, very similar to GWAS results, is that these studies can only demonstrate associations from results. Even though a statistically significant association can be seen between the gene or loci of interest and the trait or disease, no causal relationship can be derived. In order to establish a causal relationship, further studies utilizing a reverse genetics approach for knock-outs of genes or site-directed mutagenesis would need to be performed to identify causal relationships.
Another issue with TWAS results are the implications of tissue bias and coregulation. Due to the specificity of genetic regulation mechanisms within each tissue, many experiments would need to be performed to determine the tissue specific nature of each loci association and how these associations differ between tissue types. [ 3 ] Co-regulation results from a regulatory mechanism controlling the expression of more than one loci at a time. By controlling more than one loci, associations may be drawn between the loci of interest along with other genes or loci that are solely controlled by the same mechanism and may not have any association with the trait or disease of interest, leading to false positive results. [ 3 ]
A TWAS study was performed following a GWAS investigating loci associated with schizophrenia. From the GWAS results, over 100 risk loci were located. A TWAS was then used to identify 157 significant loci using expression data, and 35 of the identified loci from the TWAS did not align with the GWAS loci. Results were then further narrowed using regulatory target investigations. 42 of these genes were found to have a statistically significant association with chromatin phenotypes, which is a regulatory mechanism that could further be investigated. MAPK3 was one association that was observed to have a large impact on neurodevelopmental phenotypes, and was further prioritized as a candidate causal gene. [ 9 ]
In 2018, a TWAS was used to identify candidate causal genes for breast cancer. Data was collected from The Cancer Genome Atlas to establish genetic models as well as 229,000 women of European ancestry. In this study, 8,597 genes were evaluated. Through GWAS studies, around 170 loci were associated with at least one variant of breast cancer. In this study, 179 genes were found to have an association with a variant of breast cancer. Of the 179 genes with associations, 48 were identified to be statistically significant using a Bonferroni-correction threshold (as seen on the Manhattan plot above). [ 10 ] 14 of these had never been reported to be associated with a risk of breast cancer previously. The other 34 genes at known risk loci had 23 that do not have any associated risk SNPs. [ 10 ] Using gene knock-downs, 13 genes with high predicted levels of expression were found to be associated with an increased risk. When knocked-down, studies showed that 11 of the genes investigated had an effect in a cell line of breast cancer, especially in 184A1 normal breast cells. [ 10 ] These genes include the following: PIDD1, NRBF2, and ABHD8 . [ 10 ] All of the genes identified in the study, both up- and down-regulated had relatively high cis -heritability.
A TWAS study was completed in 2021 that utilized the most recent Parkinson's Disease (PD) GWAS that utilized 480.000 individuals. From those results, 18 genes were found to have a statistically significant association with PD. The most significant of these was LRRC37A2, which was found to be associated in all 13 brain tissues. [ 11 ]
TWAS Atlas is a site that has been curated to integrate the findings of many TWAS studies. This atlas exists virtually and is accessible to the public. Results and findings that are published in the TWAS Atlas are able to be integrated and combined to aid future studies and the understanding of genetic regulation mechanisms. Results are presented in a visual manner to improve the integration of results. Currently, 401,226 TWAS associations have been published from 200 publications, spanning 257 traits and 22,247 genes as of April 25, 2022. [ 12 ] | https://en.wikipedia.org/wiki/Transcriptome-wide_association_study |
A transcriptome in vivo analysis tag ( TIVA tag ) is a multifunctional, photoactivatable mRNA -capture molecule designed for isolating mRNA from a single cell in complex tissues .
A transcript is an RNA molecule that is copied or transcribed from a DNA template. A transcript can be further processed by alternative splicing , which is the retention of different combinations of exons . These unique combinations of exons are termed RNA transcript isoforms . The transcriptome is a set of all RNA, including rRNA , mRNA , tRNA , and non-coding RNA . Specifically mRNA transcripts can be used to investigate differences in gene expression patterns. Transcriptome profiling is determining the composition of transcripts and their relative expression levels in a given reference set of cells. This analysis involves characterization of all functional genomic elements, coding and non-coding. [ 1 ]
The current RNA capture methods involve sorting cells in suspension from acutely dissociated tissue, and thus can lose information about cell morphology and microenvironment . [ 2 ] Transcript abundance and isoforms are significantly different across tissues and are continually changing throughout an individual’s life. Gene expression is highly tissue specific, therefore with traditional RNA capture methods one must be cautious in the interpretation of gene expression patterns, as they often reflect expression of a heterogeneous mix of cell populations. [ 1 ] Even in the same cell type, tissue measurements, where a population of cells is obtained, mask both low-level mRNA expression in single cells and variation in expression between cells. [ 3 ] The photoactivatable TIVA tag is engineered to capture the mRNA of a single cell in complex tissues. [ 2 ]
TIVA tags are created initially via solid-phase synthesis with the cell-penetrating peptide conjugated afterwards. [ 2 ] The functional components of the tag can be summarized as following:
Tissue fixation is performed by chemical fixation using formalin . This prevents the postmortem degeneration of the tissue and hardens soft tissue. The tissue is dehydrated using ethanol and the alcohol is cleared using an organic solvent such as xylene . The tissue is embedded in paraffin which infiltrates the microscopic spaces present throughout the tissue. The embedded tissue is sliced using a microtome and subsequently stained to produce contrast needed to visualize the tissue. [ 2 ]
A cell saline buffer containing the TIVA tag is added to the coverslip and incubated. During the incubation period, the TIVA tag penetrates the cell membrane via the CPP that is bound to it. Subsequently, the cytosolic environment cleaves the CPP and the TIVA tag is trapped inside the cell. After incubation, the coverslip is rinsed twice with cell saline buffer and then transferred to an imaging chamber. Using a confocal microscope , loading of the tag is confirmed by detecting the Cy5 signal at a wavelength of 561 nm. [ 2 ]
Photolysis is performed resulting in photoactivation of the TIVA tag in the target cell or cells. Specifically, uncaging of the TIVA tag is accomplished using a 405-nm laser while measuring FRET excited by 514 nm. During this process, the mRNA-capturing moiety is released and subsequently anneals to the poly(A) tail of cellular mRNA. To confirm that the cell is not damaged during photolysis, the cell is imaged with the confocal microscope . [ 2 ]
Using a glass pipette, the photolysed cell is isolated by aspiration. Cells are lysed and affinity purification is performed using streptavidin -coated beads that bind, immobilize and purify the biotinylated TIVA tag. [ 2 ]
RNA-seq uses reverse transcriptase to convert the mRNA template to cDNA . During library preparation, the cDNA is fragmented into small pieces, which then serve as the template for sequencing. After sequencing RNA-seq analysis can then be performed. [ 1 ] | https://en.wikipedia.org/wiki/Transcriptome_in_vivo_analysis_tag |
Transcriptome instability is a genome -wide, pre-mRNA splicing -related characteristic of certain cancers . In general, pre-mRNA splicing is dysregulated in a high proportion of cancerous cells . [ 1 ] [ 2 ] [ 3 ] For certain types of cancer, like in colorectal and prostate , the number of splicing errors per cancer has been shown to vary greatly between individual cancers, a phenomenon referred to as transcriptome instability . [ 4 ] [ 5 ] Transcriptome instability correlates significantly with reduced expression level of splicing factor genes. Mutation of DNMT3A contributes to development of hematologic malignancies , and DNMT3A -mutated cell lines exhibit transcriptome instability as compared to their isogenic wildtype counterparts. [ 6 ] | https://en.wikipedia.org/wiki/Transcriptome_instability |
A transcriptor is a transistor -like device composed of DNA and RNA rather than a semiconducting material such as silicon . Prior to its invention in 2013, the transcriptor was considered an important component to build biological computers . [ 1 ]
To function, a modern computer needs three different capabilities: It must be able to store information , transmit information between components, and possess a basic system of logic . [ 2 ] Prior to March 2013, scientists had successfully demonstrated the ability to store and transmit data using biological components made of proteins and DNA . [ 2 ] Simple two-terminal logic gates had been demonstrated, but required multiple layers of inputs and thus were impractical due to scaling difficulties. [ 3 ]
On March 28, 2013, a team of bioengineers from Stanford University led by Drew Endy announced that they had created the biological equivalent of a transistor, which they named a "transcriptor". That is, they created a three-terminal device with a logic system that can control other components. [ 2 ] [ 3 ] The transcriptor regulates the flow of RNA polymerase across a strand of DNA using special combinations of enzymes to control movement. [ 1 ] According to project member Jerome Bonnet, "The choice of enzymes is important. We have been careful to select enzymes that function in bacteria, fungi, plants and animals, so that bio-computers can be engineered within a variety of organisms." [ 1 ]
Transcriptors can replicate traditional AND , OR , NOR , NAND , XOR , and XNOR gates with equivalents, which Endy dubbed "Boolean Integrase Logic (BIL) gates", in a single-layer process (i.e., without requiring multiple instances of the simpler gates to build up more complex ones). [ 2 ] [ 3 ] Like a traditional transistor, a transcriptor can amplify an input signal. [ 1 ] A group of transcriptors can do almost any type of computing, including counting and comparison. [ 2 ] [ 4 ]
Stanford dedicated the BIL gate's design to the public domain , which may speed its adoption. [ 1 ] According to Endy, other researchers were already using the gates to reprogram metabolism when the Stanford team published its research. [ 4 ]
Computing by transcriptor is still very slow; it can take a few hours between receiving an input signal and generating an output. [ 5 ] Endy doubted that biocomputers would ever be as fast as traditional computers, but added that is not the goal of his research. "We're building computers that will operate in a place where your cellphone isn't going to work", he said. [ 2 ] Medical devices with built-in biological computers could monitor, or even alter, cell behavior from inside a patient's body. [ 1 ] ExtremeTech writes:
Moving forward, though, the potential for real biological computers is immense. We are essentially talking about fully-functional computers that can sense their surroundings, and then manipulate their host cells into doing just about anything. Biological computers might be used as an early-warning system for disease, or simply as a diagnostic tool ... Biological computers could tell their host cells to stop producing insulin, to pump out more adrenaline, to reproduce some healthy cells to combat disease, or to stop reproducing if cancer is detected. Biological computers will probably obviate the use of many pharmaceutical drugs. [ 1 ]
UC Berkeley biochemical engineer Jay Keasling said the transcriptor "clearly demonstrates the power of synthetic biology and could revolutionize how we compute in the future". [ 4 ] | https://en.wikipedia.org/wiki/Transcriptor |
A transcritical cycle is a closed thermodynamic cycle where the working fluid goes through both subcritical and supercritical states. In particular, for power cycles the working fluid is kept in the liquid region during the compression phase and in vapour and/or supercritical conditions during the expansion phase. The ultrasupercritical steam Rankine cycle represents a widespread transcritical cycle in the electricity generation field from fossil fuels , where water is used as working fluid. [ 1 ] Other typical applications of transcritical cycles to the purpose of power generation are represented by organic Rankine cycles , [ 2 ] which are especially suitable to exploit low temperature heat sources, such as geothermal energy , [ 3 ] heat recovery applications [ 4 ] or waste to energy plants. [ 5 ] With respect to subcritical cycles, the transcritical cycle exploits by definition higher pressure ratios , a feature that ultimately yields higher efficiencies for the majority of the working fluids . Considering then also supercritical cycles as a valid alternative to the transcritical ones, the latter cycles are capable of achieving higher specific works due to the limited relative importance of the work of compression work. [ 6 ] This evidences the extreme potential of transcritical cycles to the purpose of producing the most power (measurable in terms of the cycle specific work) with the least expenditure (measurable in terms of spent energy to compress the working fluid).
While in single level supercritical cycles both pressure levels are above the critical pressure of the working fluid, in transcritical cycles one pressure level is above the critical pressure and the other is below. In the refrigeration field carbon dioxide , CO 2 , is increasingly considered of interest as refrigerant . [ 7 ] [ 8 ] [ 9 ] [ 10 ]
In transcritical cycles, the pressure of the working fluid at the outlet of the pump is higher than the critical pressure, while the inlet conditions are close to the saturated liquid pressure at the given minimum temperature.
During the heating phase, which is typically considered an isobaric process , the working fluid overcomes the critical temperature , moving thus from the liquid to the supercritical phase without the occurrence of any evaporation process, a significant difference between subcritical and transcritical cycles. [ 11 ] Due to this significant difference in the heating phase, the heat injection into the cycle is significantly more efficient from a second law perspective, since the average temperature difference between the hot source and the working fluid is reduced. [ 12 ]
As a consequence, the maximum temperatures reached by the cold source can be higher at fixed hot source characteristics. Therefore, the expansion process can be accomplished exploiting higher pressure ratios, which yields higher power production. Modern ultrasupercritical Rankine cycles can reach maximum temperatures up to 620°C exploiting the optimized heat introduction process. [ 13 ]
As in any power cycle, the most important indicator of its performance is the thermal efficiency . The thermal efficiency of a transcritical cycle is computed as:
η c y c l e = W C y c l e Q i n {\displaystyle \eta _{cycle}={\frac {W_{Cycle}}{Q_{in}}}}
where Q i n {\displaystyle Q_{in}} is the thermal input of the cycle, provided by either combustion or with a heat exchanger , and W C y c l e {\displaystyle W_{Cycle}} is the power produced by the cycle.
The power produced is considered comprehensive of the produced power during the expansion process of the working fluid and the one consumed during the compression step.
The typical conceptual configuration of a transcritical cycle employs a single heater, [ 14 ] [ 15 ] thanks to the absence of drastic phase change from one state to another, being the pressure above the critical one. In subcritical cycles, instead, the heating process of the working fluid occurs in three different heat exchangers : [ 16 ] in economizers the working fluid is heated (while remaining in the liquid phase) up to a condition approaching the saturated liquid conditions. Evaporators accomplish fluid evaporation process (typically up to the saturated vapour conditions) and in superheaters the working fluid is heated form the saturated vapour conditions to a superheated vapor . Moreover, using Rankine cycles as bottoming cycles in the context of combined gas-steam cycles keeps the configuration of the former ones as always subcritical. Therefore, there will be multiple pressure levels and hence multiple evaporators, economizers and superheaters, which introduces a significant complication to the heat injection process in the cycle. [ 17 ]
Along adiabatic and isentropic processes, such as those theoretically associated with pumping processes in transcritical cycles, the enthalpy difference across both a compression and an expansion is computed as:
Δ h = ∫ P m i n P m a x v ⋅ d P {\displaystyle \Delta h=\int _{Pmin}^{Pmax}v\cdot dP}
Consequently, a working fluid with a lower specific volume (hence higher density ) can inevitably be compressed spending a lower mechanical work than one with low density (more gas like).
In transcritical cycles, the very high maximum pressures and the liquid conditions along the whole compression phase ensure a higher density and a lower specific volume with respect to supercritical counterparts. Considering the different physical phases though which compression processes occur, transcritical and supercritical cycles employ pumps (for liquids) and compressors (for gases), respectively, during the compression step.
In the expansion step of the working fluid in transcritical cycles, as in subcritical ones, the working fluid can be discharged either in wet or dry conditions.
Typical dry expansions are those involving organic or other unconventional working fluids, which are characterized by non-negligible molecular complexities and high molecular weights .
The expansion step occurs in turbines : depending on the application and on the nameplate power produced by the power plant, both axial turbines and radial turbines can be exploited during fluid expansion. Axial turbines favour lower rotational speed and higher power production, while radial turbines are suitable for limited powers produced and high rotational speed.
Organic cycles are appropriate choices for low enthalpy applications and are characterized by higher average densities across the expanders than those occurring in transcritical steam cycles: for this reason a low blade height is normally designed [ 18 ] and the volumetric flow rate is kept limited to relatively small values. On the other hand in large scale application scenarios the expander blades typically show heights that exceed one meter and that are exploited in the steam cycles. Here, in fact, the fluid density at the outlet of the last expansion stage is significantly low.
In general, the specific work of the cycle is expressed as:
w C y c l e = P o w e r e x p a n s i o n − P o w e r c o m p r e s s i o n m ˙ c o m p r e s s i o n {\displaystyle w_{Cycle}={\frac {Power_{expansion}-Power_{compression}}{{\dot {m}}_{compression}}}}
Even though the specific work of any cycle is strongly dependent on the actual working fluid considered in the cycle, transcritical cycles are expected to exhibit higher specific works than the corresponding subcritical and supercritical counterparts (i.e., that exploit the same working fluid). For this reason, at fixed boundary conditions, power produced and working fluid, a lower mass flow rate is expected in transcritical cycles than in other configurations.
In the last decades, the thermal efficiency of Rankine cycles increased drastically, especially for large scale applications fueled by coal : for these power plants, the application of ultrasupercritical layouts was the main factor to achieve the goal, since the higher pressure ratio ensures higher cycle efficiencies.
The increment in thermal efficiency of power plants fueled by dirty fuels became crucial also in the reduction of the specific emissions of the plants, both in therms of greenhouse gas and for pollutant such as sulfur dioxide or NOx .
In large scale applications, ultrasupercritical Rankine cycles employ up to 10 feedwater heaters , five on the high pressure side and five on the low pressure side, including the deaerator , helping in the increment of the temperature at the inlet of the boiler up to 300°C, allowing a significant regenerative air preheating , thus reducing the fuel consumption. Studies on the best performant configurations of supercritical rankine cycles (300 bar of maximum pressure, 600°C of maximum temperature and two reheats) show that such layouts can achieve a cycle efficiency higher than 50%, about 6% higher than subcritical configurations. [ 19 ]
Organic Rankine cycles are innovative power cycles which allow good performances for low enthalpy thermal sources [ 20 ] and ensure condensation above the atmospheric pressure, thus avoiding deaerators and large cross sectional area in the heat rejection units . Moreover, with respect to steam Rankine cycles , ORC have a higher flexibility in handling low power sizes, allowing significant compactness.
Typical applications of ORC cover: waste heat recovery plants , geothermal plants , biomass plants and waste to energy power plants .
Organic Rankine cycles use organic fluids (such as hydrocarbons , perfluorocarbons , chlorofluorocarbon , and many others) as working fluids. [ 21 ] Most of them have a critical temperature in the range of 100-200°C, [ 22 ] for this reason perfectly adaptable to transcritical cycles in low temperature applications. [ 23 ] Considering organic fluids, having a maximum pressure above the critical one can more than double the temperature difference across the turbine, with respect to the subcritical counterpart, and significantly increase both the cycle specific work and cycle efficiency.
A refrigeration cycle , also known as heat pump, is a thermodynamic cycle that allows the removal of heat from a low temperature heat source and the rejection of heat into a high temperature heat source, thanks to mechanical power consumption. [ 24 ] Traditional refrigeration cycles are subcritical, with the high pressure side (where heat rejection occurs) below the critical pressure. [ 25 ]
Innovative transcritical refrigeration cycles, instead, should use a working fluid whose critical temperature is around the ambient temperature. For this reason, carbon dioxide is chosen due to its favourable critical conditions. In fact, the critical point of carbon dioxide is 31°C, reasonably in between the hot source and cold source of traditional refrigeration applications, thus suitable for a transcritical applications.
In transcritical refrigeration cycles the heat is dissipated through a gas cooler instead of a desuperheater and a condenser [ 26 ] like in subcritical cycles. This limits the plant components, plant complexity and costs of the power block.
The advantages of using supercritical carbon dioxide as working fluid, instead of traditional refrigerant fluids (like HFC of HFO ), in refrigeration cycles is represented both by economic aspects and environmental ones. The cost of carbon dioxide is two order of magnitude lower than the ones of the average refrigerant working fluid and the environmental impact of carbon dioxide is very limited (with a GWP of 1 and an ODP of 0), the fluid is not reactive nor significantly toxic. No other working fluids for refrigeration is able to reach the same environmental favourable characteristics of carbon dioxide. [ 27 ] | https://en.wikipedia.org/wiki/Transcritical_cycle |
Transcytosis (also known as cytopempsis ) [ 1 ] is a type of transcellular transport in which various macromolecules are transported across the interior of a cell . Macromolecules are captured in vesicles on one side of the cell, drawn across the cell, and ejected on the other side. Examples of macromolecules transported include IgA , [ 2 ] transferrin , [ 3 ] and insulin . [ 4 ] While transcytosis is most commonly observed in epithelial cells , the process is also present elsewhere. Blood capillaries are a well-known site for transcytosis, [ 5 ] though it occurs in other cells, including neurons , [ 6 ] osteoclasts [ 7 ] and M cells of the intestine . [ 8 ]
The regulation of transcytosis varies greatly due to the many different tissues in which this process is observed. Various tissue-specific mechanisms of transcytosis have been identified. Brefeldin A , a commonly used inhibitor of ER -to- Golgi apparatus transport, has been shown to inhibit transcytosis in dog kidney cells, which provided the first clues as to the nature of transcytosis regulation. [ 9 ] Transcytosis in dog kidney cells has also been shown be regulated at the apical membrane by Rab17 , [ 10 ] as well as Rab11a and Rab25 . [ 11 ] Further work on dog kidney cells has shown that a signaling cascade involving the phosphorylation of EGFR by Yes leading to the activation of Rab11FIP5 by MAPK1 upregulates transcytosis. [ 12 ] Transcytosis has been shown to be inhibited by the combination of progesterone and estradiol followed by activation mediated by prolactin in the rabbit mammary gland during pregnancy . [ 13 ] In the thyroid , follicular cell transcytosis is regulated positively by TSH [ citation needed ] . The phosphorylation of caveolin 1 induced by hydrogen peroxide has been shown to be critical to the activation of transcytosis in pulmonary vascular tissue . [ 14 ] It can therefore be concluded that the regulation of transcytosis is a complex process that varies between tissues.
Due to the function of transcytosis as a process that transports macromolecules across cells, it can be a convenient mechanism by which pathogens can invade a tissue. Transcytosis has been shown to be critical to the entry of Cronobacter sakazakii across the intestinal epithelium as well as the blood–brain barrier . [ 15 ] Listeria monocytogenes has been shown to enter the intestinal lumen via transcytosis across goblet cells . [ 16 ] Shiga toxin secreted by enterohemorrhagic E. coli has been shown to be transcytosed into the intestinal lumen. [ 17 ] From these examples, it can be said that transcytosis is vital to the process of pathogenesis for a variety of infectious agents.
Transcytosis is also a suspected mechanism in atherosclerosis by which low density lipoprotein (LDL) macromolecules penetrate across endothelial cell monolayers of arterial walls, which is thought to occur via binding of LDL particles to scavenger receptor B1 and an eight amino-acid cytoplasmic domain on the receptor that recruits guanine nucleotide exchange factor dedicator of cytokinesis 4 (DOCK4). DOCK4 promotes the transport of LDL particles across the endothelial cell monolayers by activating RAC1 , a small signalling GTPase whose activation results in the coupling of LDL particles to scavenger receptor B1, allowing internalization of this complex and therefore delivery of LDL carriers of cholesterol into the arterial intima . [ 18 ] [ 19 ] [ 20 ]
Pharmaceutical companies, such as Lundbeck , are currently exploring the use of transcytosis as a mechanism for transporting therapeutic drugs across the human blood–brain barrier (BBB). [ citation needed ] Exploiting the body's own transport mechanism can help to overcome the high selectivity of the BBB, which typically blocks the uptake of most therapeutic antibodies into the brain and central nervous system (CNS). The pharmaceutical company Genentech , after having synthesized a therapeutic antibody that effectively inhibited BACE1 enzymatic function, experienced problems transferring adequate, efficient levels of the antibody within the brain. BACE1 is the enzyme which processes amyloid precursor proteins into amyloid-β peptides, including the species that aggregate to form amyloid plaques associated with Alzheimer's disease . [ citation needed ]
Molecules are transported across an epithelial or endothelial barrier by one of two routes: 1) a transcellular route through the intracellular compartment of the cell, or 2) a paracellular route through the extracellular space between adjacent cells. [ 21 ] The transcellular route is also called transcytosis. Transcytosis can be receptor-mediated and consists of three steps: 1) receptor-mediated endocytosis of the molecule on one side of the cell, e.g. the luminal side; 2) movement of the molecule through the intracellular compartment typically within the endosomal system; and 3) exocytosis of the molecule to the extracellular space on the other side of the cell, e.g. the abluminal side.
Transcytosis may be either unidirectional or bidirectional. Unidirectional transcytosis may occur selectively in the luminal to abluminal direction, or in the reverse direction, in the abluminal to luminal direction.
Transcytosis is prominent in brain microvascular peptide and protein transport, [ 22 ] because the brain microvascular endothelium, which forms the blood-brain barrier (BBB) in vivo, expresses unique, epithelial-like, high-resistance tight junctions . [ 23 ] The brain endothelial tight junctions virtually eliminate the paracellular pathway of solute transport across the microvascular endothelial wall in brain. In contrast, the endothelial barrier in peripheral organs does not express tight junctions, and solute movement through the paracellular pathway is prominent at the endothelial barrier in organs other than the brain or spinal cord. [ 24 ]
Receptor-mediated transcytosis, or RMT, across the BBB is a potential pathway for drug delivery to the brain , particularly for biologic drugs such as recombinant proteins. [ 25 ] The non-transportable drug, or therapeutic protein, is genetically fused to a transporter protein. The transporter protein may be an endogenous peptide, or peptidomimetic monoclonal antibody, which undergoes RMT across the BBB via transport on brain endothelial receptors such as the insulin receptor or transferrin receptor. The transporter protein acts as a molecular Trojan horse to ferry into brain the therapeutic protein that is genetically fused to the receptor-specific Trojan horse protein.
Monoclonal antibody Trojan horses that target the BBB insulin or transferrin receptor have been in drug development for over 10 years at ArmaGen, Inc., a biotechnology company in Los Angeles. ArmaGen has developed genetically engineered antibodies against both the insulin and transferrin receptors, and has fused to these antibodies different therapeutic proteins, including lysosomal enzymes, therapeutic antibodies, decoy receptors, and neurotrophins. [ 26 ] These therapeutic proteins alone do not cross the BBB, but following genetic fusion to the Trojan horse antibody, the therapeutic protein penetrates the BBB at a rate comparable to small molecules. In 2015, ArmaGen will be the first to enter human clinical trials with the BBB Trojan horse fusion proteins that delivery protein drugs to the brain via the transcytosis pathway. The human diseases initially targeted by ArmaGen are lysosomal storage diseases that adversely affect the brain. Inherited diseases create a condition where a specific lysosomal enzyme is not produced, leading to serious brain conditions including mental retardation, behavioral problems, and then dementia. Although the missing enzyme can be manufactured by drug companies, the enzyme drug alone does not treat the brain, because the enzyme alone does not cross the BBB. ArmaGen has re-engineered the missing lysosomal enzyme as a Trojan horse-enzyme fusion protein that crosses the BBB. The first clinical trials of the new Trojan horse fusion protein technology will treat the brain in lysosomal storage disorders, including one of the mucopolysaccharidosis type I diseases, (MPSIH), also called Hurler syndrome , and MPS Type II, also called Hunter syndrome .
Researchers at Genentech proposed the creation of a bispecific antibody that could bind the BBB membrane, induce receptor-mediated transcytosis, and release itself on the other side into the brain and CNS. They utilized a mouse bispecific antibody with two active sites performing different functions. One arm had a low-affinity anti- transferrin receptor binding site that induces transcytosis. A high-affinity binding site would result in the antibody not being able to release from the BBB membrane after transcytosis. This way, the amount of transported antibody is based on the concentration of antibody on either side of the barrier. The other arm had the previously developed high-affinity anti-BACE1 binding site that would inhibit BACE1 function and prevent amyloid plaque formation. Genentech was able to demonstrate in mouse models that the new bispecific antibody was able to reach therapeutic levels in the brain. [ 27 ] Genentech's method of disguising and transporting the therapeutic antibody by attaching it to a receptor-mediated transcytosis activator has been referred to as the "Trojan Horse" method. | https://en.wikipedia.org/wiki/Transcytosis |
Transdetermination is a concept in developmental biology to describe the process by which pluripotent stem cells change their fate from becoming one kind of specialized cell lineage to a different lineage. It is contrasted to transdifferentiation where a differentiated cell switches to another lineage without intermediate stages of dedifferentiation . [ 1 ] In Drosophila , it has been shown that imaginal disc cells could convert from eye to wing tissue through a factor called winged eye (wge) which induces histone modifications that lead to the altered fate. [ 2 ] | https://en.wikipedia.org/wiki/Transdetermination |
Transdifferentiation , also known as lineage reprogramming , [ 1 ] is the process in which one mature somatic cell is transformed into another mature somatic cell without undergoing an intermediate pluripotent state or progenitor cell type. [ 2 ] It is a type of metaplasia , which includes all cell fate switches, including the interconversion of stem cells. Current uses of transdifferentiation include disease modeling and drug discovery and in the future may include gene therapy and regenerative medicine . [ 3 ] The term 'transdifferentiation' was originally coined by Selman and Kafatos [ 4 ] in 1974 to describe a change in cell properties as cuticle-producing cells became salt-secreting cells in silk moths undergoing metamorphosis . [ 5 ]
Davis et al. 1987 reported the first instance (sight) of transdifferentiation where a cell changed from one adult cell type to another. Forcing mouse embryonic fibroblasts to express MyoD was found to be sufficient to turn those cells into myoblasts . [ 6 ]
The only [ 7 ] known instances where adult cells change directly from one lineage to another occurs in the species Turritopsis dohrnii (also known as the immortal jellyfish) and Turritopsis nutricula .
In newts , when the eye lens is removed, pigmented epithelial cells de-differentiate and then redifferentiate into the lens cells. [ 8 ] Vincenzo Colucci described this phenomenon in 1891 and Gustav Wolff described the same thing in 1894; the priority issue is examined in Holland (2021). [ 9 ]
In humans and mice, it has been demonstrated that alpha cells in the pancreas can spontaneously switch fate and transdifferentiate into beta cells. This has been demonstrated for both healthy and diabetic human and mouse pancreatic islets . [ 10 ] While it was previously believed that oesophageal cells were developed from the transdifferentiation of smooth muscle cells, that has been shown to be false. [ 11 ]
The first example of functional transdifferentiation has been provided by Ferber et al. [ 12 ] by inducing a shift in the developmental fate of cells in the liver and converting them into ' pancreatic beta-cell -like' cells. The cells induced a wide, functional and long-lasting transdifferentiation process that reduced the effects of hyperglycemia in diabetic mice. [ 13 ] Moreover, the trans-differentiated beta-like cells were found to be resistant to the autoimmune attack that characterizes type 1 diabetes . [ 14 ]
The second step was to undergo transdifferentiation in human specimens. By transducing liver cells with a single gene, Sapir et al. were able to induce human liver cells to transdifferentiate into human beta cells. [ 15 ]
This approach has been demonstrated in mice, rat, xenopus and human tissues. [ 16 ]
Schematic model of the hepatocyte -to-beta cell transdifferentiation process. Hepatocytes are obtained by liver biopsy from diabetic patient, cultured and expanded ex vivo , transduced with a PDX1 virus, transdifferentiated into functional insulin -producing beta cells, and transplanted back into the patient. [ 15 ]
Granulosa and theca cells in the ovaries of adult female mice can transdifferentiate to Sertoli and Leydig cells via induced knockout of the FOXL2 gene. [ 17 ] Similarly, Sertoli cells in the testes of adult male mice can transdifferentiate to granulosa cells via induced knockout of the DMRT1 gene. [ 18 ]
In this approach, transcription factors from progenitor cells of the target cell type are transfected into a somatic cell to induce transdifferentiation. [ 2 ] There exists two different means of determining which transcription factors to use: by starting with a large pool and narrowing down factors one by one [ 19 ] or by starting with one or two and adding more. [ 20 ] One theory to explain the exact specifics is that ectopic Transcriptional factors direct the cell to an earlier progenitor state and then redirects it towards a new cell type. Rearrangement of the chromatin structure via DNA methylation or histone modification may play a role as well. [ 21 ] Here is a list of in vitro examples and in vivo examples . In vivo methods of transfecting specific mouse cells utilize the same kinds of vectors as in vitro experiments, except that the vector is injected into a specific organ. Zhou et al. (2008) injected Ngn3, Pdx1 and Mafa into the dorsal splenic lobe (pancreas) of mice to reprogram pancreatic exocrine cells into β-cells in order to ameliorate hyperglycaemia. [ 22 ]
Somatic cells are first transfected with pluripotent reprogramming factors temporarily ( Oct4 , Sox2 , Nanog , etc.) before being transfected with the desired inhibitory or activating factors. [ 23 ] Here is a list of examples in vitro .
The DNA methylation inhibitor, 5-azacytidine is also known to promote phenotypic transdifferentiation of cardiac cells to skeletal myoblasts. [ 24 ]
In prostate cancer , treatment with androgen receptor targeted therapies induces neuroendocrine transdifferentiation in a subset of patients. [ 25 ] [ 26 ] No standard of care exists for these patients, and those diagnosed with treatment induced neuroendocrine carcinoma are typically treated palliatively. [ 27 ]
The transcription factors serve as a short term trigger to an irreversible process. The transdifferentiation liver cells observed 8 months after one single injection of pdx1. [ 13 ]
The ectopic transcription factors turn off the host repertoire of gene expression in each of the cells. However, the alternate desired repertoire is being turned on only in a subpopulation of predisposed cells. [ 28 ] Despite the massive dedifferentiation – lineage tracing approach indeed demonstrates that transdifferentiation originates in adult cells. [ 29 ]
Determining the unique set of cellular factors that is needed to be manipulated for each cell conversion is a long and costly process that involved much trial and error. As a result, this first step of identifying the key set of cellular factors for cell conversion is the major obstacle researchers face in the field of cell reprogramming. An international team of researchers have developed an algorithm, called Mogrify(1), that can predict the optimal set of cellular factors required to convert one human cell type to another. When tested, Mogrify was able to accurately predict the set of cellular factors required for previously published cell conversions correctly. To further validate Mogrify's predictive ability, the team conducted two novel cell conversions in the laboratory using human cells, and these were successful in both attempts solely using the predictions of Mogrify. [ 30 ] [ 31 ] [ 32 ] Mogrify has been made available online for other researchers and scientists.
When examining transdifferentiated cells, it is important to look for markers of the target cell type and the absence of donor cell markers which can be accomplished using green fluorescent protein or immunodetection. It is also important to examine the cell function, epigenome , transcriptome , and proteome profiles. Cells can also be evaluated based upon their ability to integrate into the corresponding tissue in vivo [ 19 ] and functionally replace its natural counterpart. In one study, transdifferentiating tail-tip fibroblasts into hepatocyte-like cells using transcription factors Gata4 , Hnf1α and Foxa3 , and inactivation of p19(Arf) restored hepatocyte-like liver functions in only half of the mice using survival as a means of evaluation. [ 33 ]
Generally transdifferentiation that occurs in mouse cells does not translate in effectiveness or speediness in human cells. Pang et al. found that while transcription factors Ascl1 , Brn2 and Myt1l turned mouse cells into mature neurons, the same set of factors only turned human cells into immature neurons. However, the addition of NeuroD1 was able to increase efficiency and help cells reach maturity. [ 34 ]
The order of expression of transcription factors can direct the fate of the cell. Iwasaki et al. (2006) showed that in hematopoietic lineages, the expression timing of Gata-2 and (C/EBPalpha) can change whether or not a lymphoid-committed progenitors can differentiate into granulocyte / monocyte progenitor, eosinophil , basophil or bipotent basophil / mast cell progenitor lineages. [ 35 ]
It has been found for induced pluripotent stem cells that when injected into mice, the immune system of the synergeic mouse rejected the teratomas forming. Part of this may be because the immune system recognized epigenetic markers of specific sequences of the injected cells. However, when embryonic stem cells were injected, the immune response was much lower. Whether or not this will occur within transdifferentiated cells remains to be researched. [ 3 ]
In order to accomplish transfection , one may use integrating viral vectors such as lentiviruses or retroviruses , non-integrating vectors such as Sendai viruses or adenoviruses , microRNAs and a variety of other methods including using proteins and plasmids ; [ 36 ] one example is the non-viral delivery of transcription factor-encoding plasmids with a polymeric carrier to elicit neuronal transdifferentiation of fibroblasts. [ 37 ] When foreign molecules enter cells, one must take into account the possible drawbacks and potential to cause tumorous growth. Integrating viral vectors have the chance to cause mutations when inserted into the genome. One method of going around this is to excise the viral vector once reprogramming has occurred, an example being Cre-Lox recombination [ 38 ] Non-integrating vectors have other issues concerning efficiency of reprogramming and also the removal of the vector. [ 39 ] Other methods are relatively new fields and much remains to be discovered. | https://en.wikipedia.org/wiki/Transdifferentiation |
In biophysics , transduction is the conveyance of energy from one electron (a donor) to another (a receptor), at the same time that the class of energy changes.
Photonic energy, the kinetic energy of a photon , may follow the following paths:
This biophysics -related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transduction_(biophysics) |
Transduction is the process by which foreign DNA is introduced into a cell by a virus or viral vector . [ 1 ] An example is the viral transfer of DNA from one bacterium to another and hence an example of horizontal gene transfer . [ 2 ] [ 3 ] [ page needed ] Transduction does not require physical contact between the cell donating the DNA and the cell receiving the DNA (which occurs in conjugation ), and it is DNase resistant ( transformation is susceptible to DNase). Transduction is a common tool used by molecular biologists to stably introduce a foreign gene into a host cell's genome (both bacterial and mammalian cells).
Transduction was discovered in Salmonella by Norton Zinder and Joshua Lederberg at the University of Wisconsin–Madison in 1952. [ 4 ]
Transduction happens through either the lytic cycle or the lysogenic cycle.
When bacteriophages (viruses that infect bacteria) that are lytic infect bacterial cells, they harness the replicational , transcriptional , and translation machinery of the host bacterial cell to make new viral particles ( virions ). The new phage particles are then released by lysis of the host. In the lysogenic cycle, the phage chromosome is integrated as a prophage into the bacterial chromosome, where it can stay dormant for extended periods of time. If the prophage is induced (by UV light for example), the phage genome is excised from the bacterial chromosome and initiates the lytic cycle, which culminates in lysis of the cell and the release of phage particles. Generalized transduction (see below) occurs in both cycles during the lytic stage, while specialized transduction (see below) occurs when a prophage is excised in the lysogenic cycle. [ citation needed ]
The packaging of bacteriophage DNA into phage capsids has low fidelity. Small pieces of bacterial DNA may be packaged into the bacteriophage particles. There are two ways that this can lead to transduction. [ citation needed ]
Generalized transduction occurs when random pieces of bacterial DNA are packaged into a phage. It happens when a phage is in the lytic stage, at the moment that the viral DNA is packaged into phage heads. If the virus replicates using 'headful packaging', it attempts to fill the head with genetic material. If the viral genome results in spare capacity, viral packaging mechanisms may incorporate bacterial genetic material into the new virion. Alternatively, generalized transduction may occur via recombination . Generalized transduction is a rare event and occurs on the order of 1 phage in 11,000. [ citation needed ]
The new virus capsule that contains part bacterial DNA then infects another bacterial cell. When the bacterial DNA packaged into the virus is inserted into the recipient cell three things can happen to it: [ citation needed ] [ 5 ]
Specialized transduction is the process by which a restricted set of bacterial genes is transferred to another bacterium. Those genes that are located adjacent to the prophage are transferred due to improper excision. Specialized transduction occurs when a prophage excises imprecisely from the chromosome so that bacterial genes lying adjacent to it are included in the excised DNA. The excised DNA along with the viral DNA is then packaged into a new virus particle, which is then delivered to a new bacterium when the phage attacks new bacterium. Here, the donor genes can be inserted into the recipient chromosome or remain in the cytoplasm, depending on the nature of the bacteriophage. [ citation needed ]
An example of specialized transduction is λ phage in Escherichia coli . [ 6 ]
Lateral transduction is the process by which very long fragments of bacterial DNA are transferred to another bacterium. So far, this form of transduction has been only described in Staphylococcus aureus , but it can transfer more genes and at higher frequencies than generalized and specialized transduction. In lateral transduction, the prophage starts its replication in situ before excision in a process that leads to replication of the adjacent bacterial DNA. After which, packaging of the replicated phage from its pac site (located around the middle of the phage genome) and adjacent bacterial genes occurs in situ, to 105% of a phage genome size. Successive packaging after initiation from the original pac site leads to several kilobases of bacterial genes being packaged into new viral particles that are transferred to new bacterial strains. If the transferred genetic material in these transducing particles provides sufficient DNA for homologous recombination, the genetic material will be inserted into the recipient chromosome.
Because multiple copies of the phage genome are produced during in situ replication, some of these replicated prophages excise normally (instead of being packaged in situ), producing normal infectious phages. [ 7 ]
Transduction with viral vectors can be used to insert or modify genes in mammalian cells. It is often used as a tool in basic research and is actively researched as a potential means for gene therapy . [ citation needed ]
In these cases, a plasmid is constructed in which the genes to be transferred are flanked by viral sequences that are used by viral proteins to recognize and package the viral genome into viral particles. This plasmid is inserted (usually by transfection ) into a producer cell together with other plasmids (DNA constructs) that carry the viral genes required for the formation of infectious virions . In these producer cells, the viral proteins expressed by these packaging constructs bind the sequences on the DNA/RNA (depending on the type of viral vector) to be transferred and insert it into viral particles. For safety, none of the plasmids used contains all the sequences required for virus formation, so that simultaneous transfection of multiple plasmids is required to get infectious virions. Moreover, only the plasmid carrying the sequences to be transferred contains signals that allow the genetic materials to be packaged in virions so that none of the genes encoding viral proteins are packaged. Viruses collected from these cells are then applied to the cells to be altered. The initial stages of these infections mimic infection with natural viruses and lead to expression of the genes transferred and (in the case of lentivirus /retrovirus vectors) insertion of the DNA to be transferred into the cellular genome. However, since the transferred genetic material does not encode any of the viral genes, these infections do not generate new viruses (the viruses are "replication-deficient"). [ citation needed ]
Some enhancers have been used to improve transduction efficiency such as polybrene , protamine sulfate , retronectin, and DEAE Dextran. [ 8 ] | https://en.wikipedia.org/wiki/Transduction_(genetics) |
In physiology , transduction is the translation of arriving stimulus into an action potential by a sensory receptor. It begins when stimulus changes the membrane potential of a sensory receptor .
A sensory receptor converts the energy in a stimulus into an electrical signal. [ 1 ] Receptors are broadly split into two main categories: exteroceptors, which receive external sensory stimuli, and interoceptors, which receive internal sensory stimuli. [ 2 ] [ 3 ]
In the visual system , sensory cells called rod and cone cells in the retina convert the physical energy of light signals into electrical impulses that travel to the brain . The light causes a conformational change in a protein called rhodopsin . [ 1 ] This conformational change sets in motion a series of molecular events that result in a reduction of the electrochemical gradient of the photoreceptor. [ 1 ] The decrease in the electrochemical gradient causes a reduction in the electrical signals going to the brain. Thus, in this example, more light hitting the photoreceptor results in the transduction of a signal into fewer electrical impulses, effectively communicating that stimulus to the brain. A change in neurotransmitter release is mediated through a second messenger system. The change in neurotransmitter release is by rods. Because of the change, a change in light intensity causes the response of the rods to be much slower than expected (for a process associated with the nervous system). [ 4 ]
In the auditory system , sound vibrations (mechanical energy) are transduced into electrical energy by hair cells in the inner ear. Sound vibrations from an object cause vibrations in air molecules, which in turn, vibrate the ear drum . The movement of the eardrum causes the bones of the middle ear (the ossicles ) to vibrate. [ 5 ] [ 6 ] These vibrations then pass into the cochlea , the organ of hearing. Within the cochlea, the hair cells on the sensory epithelium of the organ of Corti bend and cause movement of the basilar membrane. The membrane undulates in different sized waves according to the frequency of the sound. Hair cells are then able to convert this movement (mechanical energy) into electrical signals (graded receptor potentials) which travel along auditory nerves to hearing centres in the brain. [ 7 ]
In the olfactory system , odorant molecules in the mucus bind to G-protein receptors on olfactory cells. The G-protein activates a downstream signalling cascade that causes increased level of cyclic-AMP (cAMP), which trigger neurotransmitter release. [ 8 ]
In the gustatory system , perception of five primary taste qualities (sweet, salty, sour, bitter and umami [savoriness] ) depends on taste transduction pathways, through taste receptor cells, G proteins, ion channels, and effector enzymes. [ 9 ]
In the somatosensory system the sensory transduction mainly involves the conversion of the mechanical signal such as pressure, skin compression, stretch, vibration to electro-ionic impulses through the process of mechanotransduction . [ 10 ] It also includes the sensory transduction related to thermoception and nociception . | https://en.wikipedia.org/wiki/Transduction_(physiology) |
A transect is a path along which one counts and records occurrences of the objects of study (e.g. plants). [ citation needed ]
It requires an observer to move along a fixed path and to count occurrences along the path and, at the same time (in some procedures), obtain the distance of the object from the path. This results in an estimate of the area covered and an estimate of the way in which detectability increases from probability 0 (far from the path) towards 1 (near the path). Using the raw count and this probability function, one can arrive at an estimate of the actual density of objects.
The estimation of the abundance of populations (such as terrestrial mammal species) can be achieved using a number of different types of transect methods, such as strip transects, line transects , belt transects , point transects [ 1 ] [ page needed ] , gradsects and curved line transects. [ 2 ] | https://en.wikipedia.org/wiki/Transect |
Transfection is the process of deliberately introducing naked or purified nucleic acids into eukaryotic cells . [ 1 ] [ 2 ] It may also refer to other methods and cell types, although other terms are often preferred: " transformation " is typically used to describe non-viral DNA transfer in bacteria and non-animal eukaryotic cells, including plant cells. In animal cells, transfection is the preferred term, as the term "transformation" is also used to refer to a cell's progression to a cancerous state ( carcinogenesis ). Transduction is often used to describe virus-mediated gene transfer into prokaryotic cells. [ 2 ] [ 3 ]
The word transfection is a portmanteau of the prefix trans- and the word "infection." Genetic material (such as supercoiled plasmid DNA or siRNA constructs), may be transfected. Transfection of animal cells typically involves opening transient pores or "holes" in the cell membrane to allow the uptake of material. Transfection can be carried out using calcium phosphate (i.e. tricalcium phosphate ), by electroporation , by cell squeezing, or by mixing a cationic lipid with the material to produce liposomes that fuse with the cell membrane and deposit their cargo inside.
Transfection can result in unexpected morphologies and abnormalities in target cells.
The meaning of the term has evolved. [ 4 ] The original meaning of transfection was "infection by transformation", i.e., introduction of genetic material, DNA or RNA, from a prokaryote -infecting virus or bacteriophage into cells, resulting in an infection. For work with bacterial and archaeal cells transfection retains its original meaning as a special case of transformation. Because the term transformation had another sense in animal cell biology (a genetic change allowing long-term propagation in culture, or acquisition of properties typical of cancer cells), the term transfection acquired, for animal cells, its present meaning of a change in cell properties caused by introduction of DNA. [ citation needed ]
There are various methods of introducing foreign DNA into a eukaryotic cell : some rely on physical treatment (electroporation, cell squeezing, nanoparticles , magnetofection); others rely on chemical materials or biological particles (viruses) that are used as carriers. There are many different methods of gene delivery developed for various types of cells and tissues, from bacterial to mammalian. Generally, the methods can be divided into three categories: physical, chemical, and biological. [ 5 ]
Physical methods include electroporation , microinjection , gene gun , impalefection , hydrostatic pressure , continuous infusion, and sonication. Chemicals include methods such as lipofection , which is a lipid-mediated DNA-transfection process utilizing liposome vectors. It can also include the use of polymeric gene carriers (polyplexes). [ 6 ] Biological transfection is typically mediated by viruses , utilizing the ability of a virus to inject its DNA inside a host cell. A gene that is intended for delivery is packaged into a replication-deficient viral particle. Viruses used to date include retrovirus , lentivirus , adenovirus , adeno-associated virus , and herpes simplex virus . [ citation needed ]
Physical methods are the conceptually simplest, using some physical means to force the transfected material into the target cell's nucleus. The most widely used physical method is electroporation , where short electrical pulses disrupt the cell membrane, allowing the transfected nucleic acids to enter the cell. [ 5 ] Other physical methods use different means to poke holes in the cell membrane: Sonoporation uses high-intensity ultrasound (attributed mainly to the cavitation of gas bubbles interacting with nearby cell membranes), optical transfection uses a highly focused laser to form a ~1 μm diameter hole. [ 7 ]
Several methods use tools that force the nucleic acid into the cell, namely: microinjection of nucleic acid with a fine needle; [ 5 ] biolistic particle delivery , in which nucleic acid is attached to heavy metal particles (usually gold) and propelled into the cells at high speed; [ 8 ] and magnetofection , where nucleic acids are attached to magnetic iron oxide particles and driven into the target cells by magnets. [ 8 ]
Hydrodynamic delivery is a method used in mice and rats, in which nucleic acids can be delivered to the liver by injecting a relatively large volume in the blood in less than 10 seconds; nearly all of the DNA is expressed in the liver by this procedure. [ 9 ]
Chemical-based transfection can be divided into several kinds: cyclodextrin , [ 10 ] polymers, [ 11 ] liposomes, or nanoparticles [ 12 ] (with or without chemical or viral functionalization. See below).
DNA can also be introduced into cells using viruses as a carrier. In such cases, the technique is called transduction , and the cells are said to be transduced. Adenoviral vectors can be useful for viral transfection methods because they can transfer genes into a wide variety of human cells and have high transfer rates. [ 2 ] Lentiviral vectors are also helpful due to their ability to transduce cells not currently undergoing mitosis.
Protoplast fusion is a technique in which transformed bacterial cells are treated with lysozyme in order to remove the cell wall. Following this, fusogenic agents (e.g., Sendai virus, PEG, electroporation) are used in order to fuse the protoplast carrying the gene of interest with the target recipient cell. A major disadvantage of this method is that bacterial components are non-specifically introduced into the target cell as well.
Stable and transient transfection differ in their long term effects on a cell; a stably transfected cell will continuously express transfected DNA and pass it on to daughter cells , while a transiently transfected cell will express transfected DNA for a short amount of time and not pass it on to daughter cells.
For some applications of transfection, it is sufficient if the transfected genetic material is only transiently expressed. Since the DNA introduced in the transfection process is usually not integrated into the nuclear genome, the foreign DNA will be diluted through mitosis or degraded. [ 5 ] Cell lines expressing the Epstein–Barr virus (EBV) nuclear antigen 1 (EBNA1) or the SV40 large-T antigen allow episomal amplification of plasmids containing the viral EBV (293E) or SV40 (293T) origins of replication, greatly reducing the rate of dilution. [ 25 ]
If it is desired that the transfected gene actually remain in the genome of the cell and its daughter cells, a stable transfection must occur. To accomplish this, a marker gene is co-transfected, which gives the cell some selectable advantage, such as resistance towards a certain toxin . Some (very few) of the transfected cells will, by chance, have integrated the foreign genetic material into their genome. If the toxin is then added to the cell culture, only those few cells with the marker gene integrated into their genomes will be able to proliferate , while other cells will die. After applying this selective stress (selection pressure) for some time, only the cells with a stable transfection remain and can be cultivated further. [ 26 ]
Common agents for selecting stable transfection are:
RNA can also be transfected into cells to transiently express its coded protein, or to study RNA decay kinetics. RNA transfection is often used in primary cells that do not divide.
siRNAs can also be transfected to achieve RNA silencing (i.e. loss of RNA and protein from the targeted gene). This has become a major application in research to achieve " knock-down " of proteins of interests (e.g. Endothelin-1 [ 27 ] ) with potential applications in gene therapy. Limitation of the silencing approach are the toxicity of the transfection for cells and potential "off-target" effects on the expression of other genes/proteins.
RNA can be purified from cells after lysis or synthesized from free nucleotides either chemically, or enzymatically using an RNA polymerase to transcribe a DNA template. As with DNA, RNA can be delivered to cells by a variety of means including microinjection , electroporation , and lipid-mediated transfection . If the RNA encodes a protein , transfected cells may translate the RNA into the encoded protein. [ 28 ] If the RNA is a regulatory RNA (such as a miRNA ), the RNA may cause other changes in the cell (such as RNAi-mediated knockdown ).
Encapsulating the RNA molecule in lipid nanoparticles was a breakthrough for producing viable RNA vaccines , solving a number of key technical barriers in delivering the RNA molecule into the human cell. [ 29 ] [ 30 ]
RNA molecules shorter than about 25nt (nucleotides) largely evade detection by the innate immune system , which is triggered by longer RNA molecules. Most cells of the body express proteins of the innate immune system, and upon exposure to exogenous long RNA molecules, these proteins initiate signaling cascades that result in inflammation . This inflammation hypersensitizes the exposed cell and nearby cells to subsequent exposure. As a result, while a cell can be repeatedly transfected with short RNA with few non-specific effects, repeatedly transfecting cells with even a small amount of long RNA can cause cell death unless measures are taken to suppress or evade the innate immune system (see "Long-RNA transfection" below).
Short-RNA transfection is routinely used in biological research to knock down the expression of a protein of interest (using siRNA ) or to express or block the activity of a miRNA (using short RNA that acts independently of the cell's RNAi machinery, and therefore is not referred to as siRNA). While DNA-based vectors ( viruses , plasmids ) that encode a short RNA molecule can also be used, short-RNA transfection does not risk modification of the cell's DNA, a characteristic that has led to the development of short RNA as a new class of macromolecular drugs . [ 31 ]
Long-RNA transfection is the process of deliberately introducing RNA molecules longer than about 25nt into living cells. A distinction is made between short- and long-RNA transfection because exogenous long RNA molecules elicit an innate immune response in cells that can cause a variety of nonspecific effects including translation block, cell-cycle arrest, and apoptosis .
The innate immune system has evolved to protect against infection by detecting pathogen-associated molecular patterns (PAMPs), and triggering a complex set of responses collectively known as inflammation . Many cells express specific pattern recognition receptors (PRRs) for exogenous RNA including toll-like receptor 3,7,8 ( TLR3 , TLR7 , TLR8 ), [ 32 ] [ 33 ] [ 34 ] [ 35 ] the RNA helicase RIG1 (RARRES3) , [ 36 ] protein kinase R (PKR, a.k.a. EIF2AK2), [ 37 ] [ 38 ] members of the oligoadenylate synthetase family of proteins ( OAS1 , OAS2 , OAS3 ), and others. All of these proteins can specifically bind to exogenous RNA molecules and trigger an immune response.
The specific chemical, structural or other characteristics of long RNA molecules that are required for recognition by PRRs remain largely unknown despite intense study. At any given time, a typical mammalian cell may contain several hundred thousand mRNA and other, regulatory long RNA molecules. How cells distinguish exogenous long RNA from the large amount of endogenous long RNA is an important open question in cell biology . Several reports suggest that phosphorylation of the 5'-end of a long RNA molecule can influence its immunogenicity , and specifically that 5'-triphosphate RNA, which can be produced during viral infection, is more immunogenic than 5'-diphosphate RNA, 5'-monophosphate RNA or RNA containing no 5' phosphate. [ 39 ] [ 40 ] [ 41 ] [ 42 ] [ 43 ] [ 44 ] However, in vitro-transcribed (ivT) long RNA containing a 7-methylguanosine cap (present in eukaryotic mRNA) is also highly immunogenic despite having no 5' phosphate, [ 45 ] suggesting that characteristics other than 5'-phosphorylation can influence the immunogenicity of an RNA molecule.
Eukaryotic mRNA contains chemically modified nucleotides such as N 6 -methyladenosine , 5-methylcytidine , and 2'-O-methylated nucleotides. Although only a very small number of these modified nucleotides are present in a typical mRNA molecule, they may help prevent mRNA from activating the innate immune system by disrupting secondary structure that would resemble double-stranded RNA (dsRNA), [ 46 ] [ 34 ] a type of RNA thought to be present in cells only during viral infection.
The immunogenicity of long RNA has been used to study both innate and adaptive immunity .
Inhibiting only three proteins, interferon-β , STAT2 , and EIF2AK2 is sufficient to rescue human fibroblasts from the cell death caused by frequent transfection with long, protein-encoding RNA. [ 45 ] Inhibiting interferon signaling disrupts the positive-feedback loop that normally hypersensitizes cells exposed to exogenous long RNA. Researchers have recently used this technique to express reprogramming proteins in primary human fibroblasts . [ 47 ] | https://en.wikipedia.org/wiki/Transfection |
In statistical mechanics , the transfer-matrix method is a mathematical technique which is used to write the partition function into a simpler form. It was introduced in 1941 by Hans Kramers and Gregory Wannier . [ 1 ] [ 2 ] In many one dimensional lattice models , the partition function is first written as an n -fold summation over each possible microstate , and also contains an additional summation of each component's contribution to the energy of the system within each microstate.
Higher-dimensional models contain even more summations. For systems with more than a few particles, such expressions can quickly become too complex to work out directly, even by computer.
Instead, the partition function can be rewritten in an equivalent way. The basic idea is to write the partition function in the form
where v 0 and v N +1 are vectors of dimension p and the p × p matrices W k are the so-called transfer matrices . In some cases, particularly for systems with periodic boundary conditions, the partition function may be written more simply as
where "tr" denotes the matrix trace . In either case, the partition function may be solved exactly using eigenanalysis . If the matrices are all the same matrix W , the partition function may be approximated as the N th power of the largest eigenvalue of W , since the trace is the sum of the eigenvalues and the eigenvalues of the product of two diagonal matrices equals the product of their individual eigenvalues.
The transfer-matrix method is used when the total system can be broken into a sequence of subsystems that interact only with adjacent subsystems. For example, a three-dimensional cubical lattice of spins in an Ising model can be decomposed into a sequence of two-dimensional planar lattices of spins that interact only adjacently. The dimension p of the p × p transfer matrix equals the number of states the subsystem may have; the transfer matrix itself W k encodes the statistical weight associated with a particular state of subsystem k − 1 being next to another state of subsystem k .
Importantly, transfer matrix methods allow to tackle probabilistic lattice models from an algebraic perspective, allowing for instance the use of results from representation theory.
As an example of observables that can be calculated from this method, the probability of a particular state m {\displaystyle m} occurring at position x is given by:
Where P j {\displaystyle Pj} is the projection matrix for state m {\displaystyle m} , having elements P j μ ν = δ μ ν δ μ m {\displaystyle Pj_{\mu \nu }=\delta _{\mu \nu }\delta _{\mu m}}
Transfer-matrix methods have been critical for many exact solutions of problems in statistical mechanics , including the Zimm–Bragg and Lifson–Roig models of the helix-coil transition , transfer matrix models for protein-DNA binding , as well as the famous exact solution of the two-dimensional Ising model by Lars Onsager . | https://en.wikipedia.org/wiki/Transfer-matrix_method_(statistical_mechanics) |
The transfer DNA (abbreviated T-DNA ) is the transferred DNA of the tumor-inducing (Ti) plasmid of some species of bacteria such as Agrobacterium tumefaciens and Agrobacterium rhizogenes (actually an Ri plasmid) . The T-DNA is transferred from bacterium into the host plant's nuclear DNA genome . [ 1 ] The capability of this specialized tumor-inducing (Ti) plasmid is attributed to two essential regions required for DNA transfer to the host cell. The T-DNA is bordered by 25-base-pair repeats on each end. Transfer is initiated at the right border and terminated at the left border and requires the vir genes of the Ti plasmid.
The bacterial T-DNA is about 24,000 base pairs long [ 2 ] [ 3 ] and contains plant-expressed genes that code for enzymes synthesizing opines and phytohormones . By transferring the T-DNA into the plant genome, the bacterium essentially reprograms the plant cells to grow into a tumor and produce a unique food source for the bacteria. The synthesis of the plant hormones auxin and cytokinin by enzymes encoded in the T-DNA enables the plant cell to overgrow, thus forming the crown gall tumors typically induced by Agrobacterium tumefaciens infection. [ 4 ] Agrobacterium rhizogenes causes a similar infection known as hairy root disease . The opines are amino acid derivatives used by the bacterium as a source of carbon and energy. This natural process of horizontal gene transfer in plants is being utilized as a tool for fundamental and applied research in plant biology through Agrobacterium tumefaciens mediated foreign gene transformation and insertional mutagenesis. [ 5 ] [ 6 ] Plant genomes can be engineered by use of Agrobacterium for the delivery of sequences hosted in T-DNA binary vectors .
The infection process of T-DNA into the host cell and integration into its nucleus involve multiple steps. First, the bacteria multiply in the wound sap before infection and then attach to the plant cell walls. The bacterial virulence genes' expression of approximately 10 operons is activated by perception of phenolic compounds such as acetosyringone emitted by wounded plant tissue and follows cell-cell contact. Then this process proceeds with the macromolecular translocation from Agrobacterium to cytoplasm of host cell, transmission of T-DNA along with associated proteins (called T-complex ) to the host cell nucleus followed by disassembly of the T-complex, stable integration of T-DNA into host plant genome , and eventual expression of the transferred genes . The integration of T-DNA into a host genome involves the formation of a single-stranded nick in the DNA at the right border of the Ti plasmid. This nick creates a region of single stranded DNA from the left border of the T-DNA gene over to the right border which was cut. Then, single stranded binding proteins attach to the single stranded DNA. DNA synthesis displaces the single stranded region and then a second nick at the left border region releases the single stranded T-DNA fragment. Further this fragment can be incorporated into a host genome. [ 7 ]
Agrobacterium has been known to evolve a control system that uses plant host factors and cellular processes for several pathways of host-plant defense response to invade the host cell nucleus. For the integration of T-DNA into the target host genome, Agrobacterium carries out multiple interactions with host-plant factors. [ 7 ] To interact with host plant proteins many Agrobacterium virulence proteins encoded by vir genes. Agrobacterium vir gene expression occurs via the VirA-VirG sensor that results in generation of a mobile single-stranded T-DNA copy (T-strand). A processed form of VirB2 is the major component of the T-complex that is required for transformation. VirD2 is the protein that caps the 5′ end of the transferred T-strand by covalent attachment and is transported to the host cell cytoplasm. [ 8 ] [ 9 ] VirE2 is the single-stranded DNA binding protein that presumably coats the T- strand in the host cytoplasm by cooperative binding . It is then directed into the nucleus via interactions with the host cell proteins such as importin a, bacterial VirE3, and dynein-like proteins. Several other bacterial virulence effectors like VirB5, VirB7 (the minor components of the T-complex), VirD5, VirE2, VirE3, and VirF that may also interact with proteins of host plant cells. [ 10 ]
Agrobacterium -mediated T-DNA transfer is widely used as a tool in biotechnology . For more than two decades, Agrobacterium tumefaciens has been exploited for introducing genes into plants for basic research as well as for commercial production of transgenic crops . [ 11 ] In genetic engineering , the tumor-promoting and opine-synthesis genes are removed from the T-DNA and replaced with a gene of interest and/or a selection marker, which is required to establish which plants have been successfully transformed. Examples of selection markers include neomycin phosphotransferase, hygromycin B phosphotransferase (which both phosphorylate antibiotics) and phosphinothricin acetyltransferase (which acetylates and deactivates phosphinothricin , a potent inhibitor of glutamine synthetase ) or a herbicide formulations such as Basta or Bialophos. [ 12 ] Another selection system that can be employed is usage of metabolic markers such as phospho-mannose isomerase. [ 13 ] Agrobacterium is then used as a vector to transfer the engineered T-DNA into the plant cells where it integrates into the plant genome. This method can be used to generate transgenic plants carrying a foreign gene. Agrobacterium tumefaciens is capable of transferring foreign DNA to both monocotyledons and dicotyledonous plants efficiently while taking care of critically important factors like the genotype of plants, types and ages of tissues inoculated, kind of vectors, strains of Agrobacterium , selection marker genes and selective agents, and various conditions of tissue culture. [ 4 ]
The same procedure of T-DNA transfer can be used to disrupt genes via insertional mutagenesis . [ 6 ] Not only does the inserted T-DNA sequence create a mutation but its insertion also 'tags' [ 14 ] the affected gene, thus allowing for its isolation as T-DNA flanking sequences. A reporter gene can be linked to the right end of the T-DNA to be transformed along with a plasmid replicon and a selectable antibiotic (such as hygromycin )-resistance gene and can explicit approximately 30% of average efficiency having successful T-DNA inserts induced gene fusions in Arabidopsis thaliana . [ 15 ]
Reverse genetics involves testing the presumed function of a gene that is known by disrupting it and then looking for the effect of that induced mutation on the organismal phenotype. T-DNA tagging mutagenesis involves screening of populations by T-DNA insertional mutations. Collections of known T-DNA mutations provide resources to study the functions of individual genes, as developed for the model plant Arabidopsis thaliana . [ 16 ] [ 17 ] Examples of T-DNA insertion mutations in Arabidopsis thaliana include those associated many classes of phenotypes including seedling-lethals, size variants, pigment variants, embryo-defectives, reduced-fertility, and morphologically or physiologically aberrant plants. [ 18 ] | https://en.wikipedia.org/wiki/Transfer_DNA |
A transfer DNA ( T-DNA ) binary system is a pair of plasmids consisting of a T-DNA binary vector and a vir helper plasmid. [ 1 ] [ 2 ] The two plasmids are used together (thus binary [ 2 ] [ 3 ] ) to produce genetically modified plants . They are artificial vectors that have been derived from the naturally occurring Ti plasmid found in bacterial species of the genus Agrobacterium , such as A. tumefaciens . The binary vector is a shuttle vector , so-called because it is able to replicate in multiple hosts (e.g. Escherichia coli and Agrobacterium ).
Systems in which T-DNA and vir genes are located on separate replicons are called T-DNA binary systems. T-DNA is located on the binary vector (the non-T-DNA region of this vector containing origin(s) of replication that could function both in E. coli and Agrobacterium , and antibiotic resistance genes used to select for the presence of the binary vector in bacteria, became known as vector backbone sequences). The replicon containing the vir genes became known as the vir helper plasmid. The vir helper plasmid is considered disarmed if it does not contain oncogenes that could be transferred to a plant
The transfer DNA binary system is derived from the naturally occurring Agrobacterium tumefaciens infection mechanism of plants. [ 4 ] Agrobacterium is a parasitic bacterium that naturally occurs in soils and infects plant cells to utilize their biological processes and machinery, integrating its own genetic material into the genome of the plant cell to produce resources that support its survival. [ 5 ]
Agrobacterium contains a plasmid , a circular piece of DNA, called the "Tumor-inducing plasmid" ("Ti plasmid" for short). [ 4 ] The Ti plasmid contains the following elements:
The "T-DNA" region: The T-DNA region is the section of the plasmid that becomes integrated into the genome of the host plant cell. Agrobacterium utilizes the plant's transcription and translation machinery to express the genes located within the T-DNA region. [ 5 ] It contains the following elements:
Opine catabolism genes: The opine catabolism genes encode elements of the Agrobacterium 's opine catabolism pathway. [ 5 ] This pathway allows the bacterium to break down and use the opine as an energy source. [ 5 ] [ 6 ] Only members of the Agrobacterium genus are able to metabolize opine, providing them with a competitive advantage over other soil microbes. [ 5 ]
Vir genes cassette: The vir genes, or "virulence genes", encode elements that aid in the transfer of T-DNA from the Ti plasmid into the plant cell genome. [ 4 ] [ 5 ] There are 6 vir operons involved in the transfer of T-DNA: virA, virB, virG, virC, virD, and virE . [ 5 ] [ 6 ]
Ori : The ori is the "origin of replication", a site on the plasmid at which the two DNA strands begin to unwind to allow for DNA replication during cell division . [ 5 ] [ 8 ]
Bacteria are prokaryotic organisms and plants are eukaryotic organisms. Mechanisms of and machinery involved in gene expression differs in prokaryotic and eukaryotic organisms. [ 8 ] Agrobacterium has evolved to contain eukaryotic gene elements in the T-DNA region which allows for the genes encoded in the region to be expressed by the plant cells. [ 6 ] [ 8 ] The remaining Ti plasmid adheres to regular prokaryotic processes. [ 8 ]
In genetic engineering of plants, [ 6 ] the auxin, cytokinin, and opine genes are replaced with a "gene(s) of interest", the gene(s) to be inserted into the plant. [ 8 ] The opine catabolism genes are also removed. [ 8 ] The transfer of the gene(s) of interest from the Agrobacterium to the plant cell occurs via the natural infection mechanism of the bacterium. [ 6 ]
The natural mechanism of Agrobacterium infection of plant cells is mediated via the 6 vir genes located on the Ti plasmid. [ 4 ] The process of infection occurs in 2 general steps:
The T-DNA then integrates into a random location within the plant cell genome. [ 4 ] [ 6 ]
The table below is a summary of the vir genes and their function:
VirC1 binds to the overdrive sequence, a region near the RB, to aid in T-DNA processing. [ 6 ]
VirE2 ssDNA binding proteins coat the length of the T-DNA; Stabilize T-DNA to prevent degradation. [ 4 ] [ 6 ]
A binary vector is used in plant genetic engineering to transfer foreign genes into plant cells . The reason for having two separate plasmids is because it is easier to clone and manipulation of genes of interest in E. coli using the T-DNA vector because it is small and easy to work with, while the vir genes remain in Agrobacterium on the helper plasmid to help with plant transformation. [ 10 ] The components of the Binary Vector include:
The combination of these components makes binary vectors versatile and effective tools for plant genetic engineering, allowing researchers to modify and amplify plasmids efficiently in E. coli before introducing them into Agrobacterium for plant transformations.
Representative series of binary vectors are listed below.
The vir helper plasmid contains the vir genes that originated from the Ti plasmid of Agrobacterium . These genes code for a series of proteins that cut the binary vector at the left and right border sequences, and facilitate transfer and integration of T-DNA to the plant's cells and genomes, respectively. [ 24 ]
Several vir helper plasmids have been reported, [ 25 ] and common Agrobacterium strains that include vir helper plasmids are:
The original Ti plasmid of Agrobacterium tumefaciens contains both the T-DNA region and the vir genes necessary for T-DNA processing and transfer. [ 26 ] The plasmid is large and can often exceed over 200kb in length and is structurally complex, leading to challenges for genetic manipulation and cloning. [ 26 ] [ 27 ] To overcome these limitations, two plasmids can be used over one: binary vector and a vir helper plasmid. [ 28 ] [ 29 ]
1) Binary vector plasmid : a small vector that contains the T-DNA border flanking the transgene of interest and selectable marker genes for both plant and bacterial selection. [ 26 ] [ 28 ] [ 30 ]
2) Vir helper plasmid : harbors the full complement of virulence genes but lacks the T-DNA sequence. It provides the necessary machinery to mediate T-DNA excision and transfer. It does not contribute to any foreign DNA to the plant genome. [ 26 ] [ 28 ] [ 27 ]
The adoption of the two-plasmid T-DNA binary system has revolutionized plant genetic engineering by improving flexibility and transformation efficiency. By separating the transgene cassette from the virulence machinery, researchers can conduct precise and genetic modification. These advantages have made the binary system the standard system for Agrobacterium mediated transformation in both academic and industrial settings [ 26 ] [ 28 ] [ 29 ] .
The pBIN19 vector was developed in the 1980s and is one of the first and most widely used binary vectors. The pGreen vector, which was developed in 2000, is a newer version of the binary vector that allows for a choice of promoters, selectable markers and reporter genes. Another distinguishing feature of pGreen is its large reduction in size (from about 11,7kbp to 4,6kbp) from pBIN19, therefore increasing its transformation efficiency . [ 33 ]
Along with higher transformation efficiency, pGreen has been engineered to ensure transformation integrity. Both pBIN19 and pGreen usually use the same selectable marker nptII , but pBIN19 has the selectable marker next to the right border, while pGreen has it close to the left border. Due to a polarity difference in the left and right borders, the right border of the T-DNA enters the host plant first. If the selectable marker is near the right border (as is the case with pBIN19) and the transformation process is interrupted, the resulting plant may have expression of a selectable marker but contain no T-DNA giving a false positive. The pGreen vector has the selectable marker entering the host last (due to its location next to the left border) so any expression of the marker will result in full transgene integration. [ 24 ]
The pGreen-based vectors are not autonomous and they will not replicate in Agrobacterium if pSoup is not present. Series of small binary vectors that autonomously replicate in E. coli and Agrobacterium include:
The T-DNA binary system has been an important instrumental application in plant genetic engineering. Its features of being versatile allows it for efficient delivery of transgenes into diverse plant species. [ 34 ] [ 35 ] With this concept, there are several key application areas that have benefited the real world.
T-DNA binary system was used to develop genetically modified (GM) crops with enhanced traits. [ 35 ] [ 36 ]
A binary system has been used to insert Bacillus thuringiensis (Bt) toxin genes into crops, conferring resistance to pests. [ 37 ] But toxins, such as Cry1Ac or Cry2Ab, are highly specific to certain insect pests and do not harm humans, beneficial insects, and other non-target organisms. [ 37 ] [ 38 ]
Bt action and steps: [ 38 ] [ 39 ]
T-DNA binary system was used to introduce multiple genes to engineer provitamin A biosynthesis in rice endosperm, addressing vitamin A deficiency in developing countries. [ 40 ] [ 41 ] Vitamins A deficiency is a major cause of preventable blindness and increases susceptibility to infectious disease as in children. [ 41 ] The two genes psy and crtl gene were inserted in the T-DNA region of a binary plasmid in the rice nuclear genome and placed in the control of an endosperm specific promoter, so that they are only expressed in the endosperm to ensure expression in the edible part of the grain. [ 40 ] This illustrates the power of the T-DNA binary system in engineering complex metabolic pathways in a tissue specific manner. [ 40 ] Using transformation strategies can be harnessed to produce nutritionally enhanced crops with significant public health benefits. [ 41 ] [ 42 ] The T-DNA binary system has enabled the precise and stable insertion of agriculturally important genes into crop genomes. [ 34 ] [ 36 ] Through the development of insect-resistant and nutritionally fortified crops, this technology has significantly contributed to sustainable agriculture, food security, and improved public health. [ 35 ] [ 36 ] [ 41 ] The real-world applications underscore the versatility and impact of the binary system as a foundational part form in part genetic engineering. [ 34 ] [ 35 ] [ 36 ] | https://en.wikipedia.org/wiki/Transfer_DNA_binary_system |
Transfer RNA-like structures ( tRNA-like structures ) are RNA sequences, which have a similar tertiary structure to tRNA; they frequently contain a pseudoknot close to the 3' end . [ 1 ] The presence of tRNA-like structures has been demonstrated in many plant virus RNA genomes . These tRNA-like structures are linked to regulation of plant virus replication. [ 1 ]
tRNA-like structures mimic some tRNA function, such as aminoacylation . There are three aminoacylation specificities, valine , histidine and tyrosine . For example, valine binds to the tRNA-like structure of the turnip yellow mosaic virus genome whilst tyrosine binds to the tRNA-like structure of the barley stripe mosaic virus genome. [ 2 ] tRNA-like structures which lack the 3' termini lack complete or partial tRNA mimicry.
tRNA-like structures are required for RNA encapsulation and increase RNA stability. They also act as 3'-translational enhancers [ 3 ] and regulators of minus strand synthesis. [ 1 ] | https://en.wikipedia.org/wiki/Transfer_RNA-like_structures |
Transfer entropy is a non-parametric statistic measuring the amount of directed (time-asymmetric) transfer of information between two random processes . [ 1 ] [ 2 ] [ 3 ] Transfer entropy from a process X to another process Y is the amount of uncertainty reduced in future values of Y by knowing the past values of X given past values of Y . More specifically, if X t {\displaystyle X_{t}} and Y t {\displaystyle Y_{t}} for t ∈ N {\displaystyle t\in \mathbb {N} } denote two random processes and the amount of information is measured using Shannon's entropy , the transfer entropy can be written as:
where H ( X ) is Shannon's entropy of X . The above definition of transfer entropy has been extended by other types of entropy measures such as Rényi entropy . [ 3 ] [ 4 ]
Transfer entropy is conditional mutual information , [ 5 ] [ 6 ] with the history of the influenced variable Y t − 1 : t − L {\displaystyle Y_{t-1:t-L}} in the condition:
Transfer entropy reduces to Granger causality for vector auto-regressive processes . [ 7 ] Hence, it is advantageous when the model assumption of Granger causality doesn't hold, for example, analysis of non-linear signals . [ 8 ] [ 9 ] However, it usually requires more samples for accurate estimation. [ 10 ] The probabilities in the entropy formula can be estimated using different approaches (binning, nearest neighbors) or, in order to reduce complexity, using a non-uniform embedding. [ 11 ] While it was originally defined for bivariate analysis , transfer entropy has been extended to multivariate forms, either conditioning on other potential source variables [ 12 ] or considering transfer from a collection of sources, [ 13 ] although these forms require more samples again.
Transfer entropy has been used for estimation of functional connectivity of neurons , [ 13 ] [ 14 ] [ 15 ] social influence in social networks [ 8 ] and statistical causality between armed conflict events. [ 16 ] Transfer entropy is a finite version of the directed information which was defined in 1990 by James Massey [ 17 ] as I ( X n → Y n ) = ∑ i = 1 n I ( X i ; Y i | Y i − 1 ) {\displaystyle I(X^{n}\to Y^{n})=\sum _{i=1}^{n}I(X^{i};Y_{i}|Y^{i-1})} , where X n {\displaystyle X^{n}} denotes the vector X 1 , X 2 , . . . , X n {\displaystyle X_{1},X_{2},...,X_{n}} and Y n {\displaystyle Y^{n}} denotes Y 1 , Y 2 , . . . , Y n {\displaystyle Y_{1},Y_{2},...,Y_{n}} . The directed information places an important role in characterizing the fundamental limits ( channel capacity ) of communication channels with or without feedback [ 18 ] [ 19 ] and gambling with causal side information. [ 20 ] | https://en.wikipedia.org/wiki/Transfer_entropy |
In chemistry , transfer hydrogenation is a chemical reaction involving the addition of hydrogen to a compound from a source other than molecular H 2 . It is applied in laboratory and industrial organic synthesis to saturate organic compounds and reduce ketones to alcohols , and imines to amines . It avoids the need for high-pressure molecular H 2 used in conventional hydrogenation . Transfer hydrogenation usually occurs at mild temperature and pressure conditions using organic or organometallic catalysts, many of which are chiral , allowing efficient asymmetric synthesis . It uses hydrogen donor compounds such as formic acid , isopropanol or dihydroanthracene , dehydrogenating them to CO 2 , acetone , or anthracene respectively. [ 1 ] Often, the donor molecules also function as solvents for the reaction. A large scale application of transfer hydrogenation is coal liquefaction using "donor solvents" such as tetralin . [ 2 ] [ 3 ]
In the area of organic synthesis , a useful family of hydrogen-transfer catalysts have been developed based on ruthenium and rhodium complexes, often with diamine and phosphine ligands. [ 4 ] A representative catalyst precursor is derived from (cymene)ruthenium dichloride dimer and the tosylated diphenylethylenediamine . These catalysts are mainly employed for the reduction of ketones and imines to alcohols and amines , respectively. The hydrogen-donor (transfer agent) is typically isopropanol , which converts to acetone upon donation of hydrogen. Transfer hydrogenations can proceed with high enantioselectivities when the starting material is prochiral :
where RR'C*H−OH is a chiral product. A typical catalyst is (cymene) R,R -HNCHPhCHPhNTs , where Ts refers to a tosyl group ( SO 2 C 6 H 4 Me ) and R,R refers to the absolute configuration of the two chiral carbon centers. This work was recognized with the 2001 Nobel Prize in Chemistry to Ryōji Noyori . [ 5 ]
Another family of hydrogen-transfer agents are those based on aluminium alkoxides, such as aluminium isopropoxide in the MPV reduction ; however their activities are relatively low by comparison with the transition metal-based systems.
The catalytic asymmetric hydrogenation of ketones was demonstrated with ruthenium-based complexes of BINAP . [ 6 ] [ 7 ]
Even though the BINAP-Ru dihalide catalyst could reduce functionalized ketones, the hydrogenation of simple ketones remained unsolved. This challenge was solved with precatalysts of the type RuCl 2 ( diphosphane )(diamine). [ 8 ] These catalysts preferentially reduce ketones and aldehydes, leaving olefins and many other substituents unaffected.
Prior to the development of catalytic hydrogenation, many methods were developed for the hydrogenation of unsaturated substrates. Many of these methods are only of historical and pedagogical interest. One prominent transfer hydrogenation agent is diimide or (NH) 2 , also called diazene. This becomes oxidized to the very stable N 2 :
The diimide can be generated from hydrazine or certain other organic precursors.
Two hydrocarbons that can serve as hydrogen donors are cyclohexene or cyclohexadiene . In this case, an alkane is formed, along with a benzene . The gain of aromatic stabilization energy when the benzene is formed is the driving force of the reaction. Pd can be used as a catalyst and a temperature of 100 °C is employed. More exotic transfer hydrogenations have been reported, including this intramolecular one:
Many reactions exist with alcohol or amines as the proton donors, and alkali metals as electron donors. Of continuing value is the sodium metal-mediated Birch reduction of arenes (another name for aromatic hydrocarbons ). Less important presently is the Bouveault–Blanc reduction of esters. The combination of magnesium and methanol is used in alkene reductions, e.g. the synthesis of asenapine : [ 11 ]
Organocatalytic transfer hydrogenation has been described by the group of List in 2004 in a system with a Hantzsch ester as hydride donor and an amine catalyst: [ 12 ]
In this particular reaction the substrate is an α,β-unsaturated carbonyl compound . The proton donor is oxidized to the pyridine form and resembles the biochemically relevant coenzyme NADH . In the catalytic cycle for this reaction the amine and the aldehyde first form an iminium ion , then proton transfer is followed by hydrolysis of the iminium bond regenerating the catalyst. By adopting a chiral imidazolidinone MacMillan organocatalyst an enantioselectivity of 81% ee was obtained:
[ 13 ]
In a case of stereoconvergence , both the E-isomer and the Z-isomer in this reaction yield the (S)- enantiomer .
Extending the scope of this reaction towards ketones or rather enones requires fine tuning of the catalyst (add a benzyl group and replace the t-butyl group by a furan ) and of the Hantzsch ester (add more bulky t-butyl groups): [ 14 ]
With another organocatalyst altogether, hydrogenation can also be accomplished for imines . One cascade reaction is catalyzed by a chiral phosphoric acid : [ 15 ]
The reaction proceeds via a chiral iminium ion . Traditional metal-based catalysts, hydrogenation of aromatic or heteroaromatic substrates tend to fail. | https://en.wikipedia.org/wiki/Transfer_hydrogenation |
In model theory , a transfer principle states that all statements of some language that are true for some structure are true for another structure. One of the first examples was the Lefschetz principle , which states that any sentence in the first-order language of fields that is true for the complex numbers is also true for any algebraically closed field of characteristic 0 .
An incipient form of a transfer principle was described by Leibniz under the name of "the Law of Continuity ". [ 1 ] Here infinitesimals are expected to have the "same" properties as appreciable numbers. The transfer principle can also be viewed as a rigorous formalization of the principle of permanence . Similar tendencies are found in Cauchy , who used infinitesimals to define both the continuity of functions (in Cours d'Analyse ) and a form of the Dirac delta function . [ 1 ] : 903
In 1955, Jerzy Łoś proved the transfer principle for any hyperreal number system. Its most common use is in Abraham Robinson 's nonstandard analysis of the hyperreal numbers , where the transfer principle states that any sentence expressible in a certain formal language that is true of real numbers is also true of hyperreal numbers.
The transfer principle concerns the logical relation between the properties of the real numbers R , and the properties of a larger field denoted * R called the hyperreal numbers . The field * R includes, in particular, infinitesimal ("infinitely small") numbers, providing a rigorous mathematical realisation of a project initiated by Leibniz.
The idea is to express analysis over R in a suitable language of mathematical logic , and then point out that this language applies equally well to * R . This turns out to be possible because at the set-theoretic level, the propositions in such a language are interpreted to apply only to internal sets rather than to all sets. As Robinson put it, the sentences of [the theory] are interpreted in * R in Henkin 's sense. [ 2 ]
The theorem to the effect that each proposition valid over R , is also valid over * R , is called the transfer principle.
There are several different versions of the transfer principle, depending on what model of nonstandard mathematics is being used.
In terms of model theory, the transfer principle states that a map from a standard model to a nonstandard model is an elementary embedding (an embedding preserving the truth values of all statements in a language), or sometimes a bounded elementary embedding (similar, but only for statements with bounded quantifiers ). [ clarification needed ]
The transfer principle appears to lead to contradictions if it is not handled correctly.
For example, since the hyperreal numbers form a non- Archimedean ordered field and the reals form an Archimedean ordered field, the property of being Archimedean ("every positive real is larger than 1 / n {\displaystyle 1/n} for some positive integer n {\displaystyle n} ") seems at first sight not to satisfy the transfer principle. The statement "every positive hyperreal is larger than 1 / n {\displaystyle 1/n} for some positive integer n {\displaystyle n} " is false; however the correct interpretation is "every positive hyperreal is larger than 1 / n {\displaystyle 1/n} for some positive hyperinteger n {\displaystyle n} ". In other words, the hyperreals appear to be Archimedean to an internal observer living in the nonstandard universe, but appear
to be non-Archimedean to an external observer outside the universe.
A freshman-level accessible formulation of the transfer principle is Keisler's book Elementary Calculus: An Infinitesimal Approach .
Every real x {\displaystyle x} satisfies the inequality x ≥ ⌊ x ⌋ , {\displaystyle x\geq \lfloor x\rfloor ,} where ⌊ ⋅ ⌋ {\displaystyle \lfloor \,\cdot \,\rfloor } is the integer part function. By a typical application of the transfer principle, every hyperreal x {\displaystyle x} satisfies the inequality x ≥ ∗ ⌊ x ⌋ , {\displaystyle x\geq {}^{*}\!\lfloor x\rfloor ,} where ∗ ⌊ ⋅ ⌋ {\displaystyle {}^{*}\!\lfloor \,\cdot \,\rfloor } is the natural extension of the integer part function. If x {\displaystyle x} is infinite, then the hyperinteger ∗ ⌊ x ⌋ {\displaystyle {}^{*}\!\lfloor x\rfloor } is infinite, as well.
Historically, the concept of number has been repeatedly generalized. The addition of 0 to the natural numbers N {\displaystyle \mathbb {N} } was a major intellectual accomplishment in its time. The addition of negative integers to form Z {\displaystyle \mathbb {Z} } already constituted a departure from the realm of immediate experience to the realm of mathematical models. The further extension, the rational numbers Q {\displaystyle \mathbb {Q} } , is more familiar to a layperson than their completion R {\displaystyle \mathbb {R} } , partly because the reals do not correspond to any physical reality (in the sense of measurement and computation) different from that represented by Q {\displaystyle \mathbb {Q} } . Thus, the notion of an irrational number is meaningless to even the most powerful floating-point computer. The necessity for such an extension stems not from physical observation but rather from the internal requirements of mathematical coherence. The infinitesimals entered mathematical discourse at a time when such a notion was required by mathematical developments at the time, namely the emergence of what became known as the infinitesimal calculus . As already mentioned above, the mathematical justification for this latest extension was delayed by three centuries. Keisler wrote:
The self-consistent development of the hyperreals turned out to be possible if every true first-order logic statement that uses basic arithmetic (the natural numbers , plus, times, comparison) and quantifies only over the real numbers was assumed to be true in a reinterpreted form if we presume that it quantifies over hyperreal numbers. For example, we can state that for every real number there is another number greater than it:
The same will then also hold for hyperreals:
Another example is the statement that if you add 1 to a number you get a bigger number:
which will also hold for hyperreals:
The correct general statement that formulates these equivalences is called the transfer principle. Note that, in many formulas in analysis, quantification is over higher-order objects such as functions and sets, which makes the transfer principle somewhat more subtle than the above examples suggest.
The transfer principle however doesn't mean that R and * R have identical behavior. For instance, in * R there exists an element ω such that
but there is no such number in R . This is possible because the nonexistence of this number cannot be expressed as a first order statement of the above type. A hyperreal number like ω is called infinitely large; the reciprocals of the infinitely large numbers are the infinitesimals.
The hyperreals * R form an ordered field containing the reals R as a subfield. Unlike the reals, the hyperreals do not form a standard metric space , but by virtue of their order they carry an order topology .
The hyperreals can be developed either axiomatically or by more constructively oriented methods. The essence of the axiomatic approach is to assert (1) the existence of at least one infinitesimal number, and (2) the validity of the transfer principle. In the following subsection we give a detailed outline of a more constructive approach. This method allows one to construct the hyperreals if given a set-theoretic object called an ultrafilter , but the ultrafilter itself cannot be explicitly constructed. Vladimir Kanovei and Shelah [ 3 ] give a construction of a definable, countably saturated elementary extension of the structure consisting of the reals and all finitary relations on it.
In its most general form, transfer is a bounded elementary embedding between structures.
The ordered field * R of nonstandard real numbers properly includes the real field R . Like all ordered fields that properly include R , this field is non-Archimedean . It means that some members x ≠ 0 of * R are infinitesimal , i.e.,
The only infinitesimal in R is 0. Some other members of * R , the reciprocals y of the nonzero infinitesimals, are infinite, i.e.,
The underlying set of the field * R is the image of R under a mapping A ↦ * A from subsets A of R to subsets of * R . In every case
with equality if and only if A is finite. Sets of the form * A for some A ⊆ R {\displaystyle \scriptstyle A\,\subseteq \,\mathbb {R} } are called standard subsets of * R . The standard sets belong to a much larger class of subsets of * R called internal sets. Similarly each function
extends to a function
these are called standard functions , and belong to the much larger class of internal functions . Sets and functions that are not internal are external .
The importance of these concepts stems from their role in the following proposition and is illustrated by the examples that follow it.
The transfer principle:
The appropriate setting for the hyperreal transfer principle is the world of internal entities. Thus, the well-ordering property of the natural numbers by transfer yields the fact that every internal subset of N {\displaystyle \mathbb {N} } has a least element. In this section internal sets are discussed in more detail. | https://en.wikipedia.org/wiki/Transfer_principle |
In chemistry , transferability is the assumption that a chemical property that is associated with an atom or a functional group in a molecule will have a similar (but not identical) value in a variety of different circumstances. [ 1 ] Examples of transferable properties include:
Transferable properties are distinguished from conserved properties , which are assumed to always have the same value whatever the chemical situation, e.g. standard atomic weight .
This chemistry -related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transferability_(chemistry) |
Transferable utility is a concept in cooperative game theory and in economics . Utility is transferable if one player can losslessly transfer part of its utility to another player. Such transfers are possible if the players have a common currency that is valued equally by all. Note that being able to transfer cash payoffs does not imply that utility is transferable: wealthy and poor players may derive a different utility from the same amount of money.
Transferable utility is assumed in many cooperative games, where the payoffs are not given for individual players, but only for coalitions . In this case the assumption implies that irrespective of the division of the coalitional payoff, members of the coalition enjoy the same total utility.
Myerson, Roger B. (1991). Game Theory: Analysis of Conflict . Cambridge, Massachusetts: Harvard University Press . p. 568. ISBN 0-674-34116-3 . | https://en.wikipedia.org/wiki/Transferable_utility |
The names for the chemical elements 104 to 106 were the subject of a major controversy starting in the 1960s, described by some nuclear chemists as the Transfermium Wars [ 1 ] [ 2 ] because it concerned the elements following fermium (element 100) on the periodic table .
This controversy arose from disputes between American scientists and Soviet scientists as to which had first isolated these elements. The final resolution of this controversy in 1997 also decided the names of elements 107 to 109.
By convention, naming rights for newly discovered chemical elements go to their discoverers. For elements 104, 105, and 106, there was a controversy between Soviet researchers at the Joint Institute for Nuclear Research and American researchers at Lawrence Berkeley National Laboratory regarding which group had discovered them first. Both parties suggested their own names for elements 104 and 105, not recognizing the other's name.
The American name of seaborgium for element 106 was also objectionable to some, because it referred to American chemist Glenn T. Seaborg who was still alive at the time this name was proposed. [ 3 ] ( Einsteinium and fermium had also been proposed as names of new elements while Albert Einstein and Enrico Fermi were still living, but only made public after their deaths, due to Cold War secrecy.)
The two principal groups which were involved in the conflict over element naming were:
and, as a kind of arbiter,
The German group at the Gesellschaft für Schwerionenforschung (GSI) in Darmstadt , who had (undisputedly) discovered elements 107 to 109, were dragged into the controversy when the Commission suggested that the name "hahnium", proposed for element 105 by the Americans, be used for GSI's element 108 instead.
The names suggested for the elements 107 to 109 by the German group were: [ 4 ]
In 1994, the IUPAC Commission on Nomenclature of Inorganic Chemistry proposed the following names:
This attempted to resolve the dispute by sharing the namings of the disputed elements between Russians and Americans, replacing the name for 104 with one honoring the Dubna research center , and not naming 106 after Seaborg.
This solution drew objections from the American Chemical Society (ACS) on the grounds that the right of the American group to propose the name for element 106 was not in question, and that group should have the right to name the element. Indeed, IUPAC decided that the credit for the discovery of element 106 should be awarded to Berkeley.
Along the same lines, the German group protested against naming element 108 by the American suggestion "hahnium", mentioning the long-standing convention that an element is named by its discoverers. [ 5 ]
In addition, given that many American books had already used rutherfordium and hahnium for 104 and 105, the ACS objected to those names being used for other elements.
In 1995, IUPAC abandoned the controversial rule and established a committee of national representatives aimed at finding a compromise. They suggested seaborgium for element 106 in exchange for the removal of all the other American proposals, except for the established name lawrencium for element 103. The equally entrenched name nobelium for element 102 was replaced by flerovium after Georgy Flyorov , following the recognition by the 1993 report that that element had been first synthesized in Dubna. This was rejected by American scientists and the decision was retracted. [ 6 ] The name flerovium was later used for element 114 . [ 7 ]
In 1996, IUPAC held another meeting, reconsidered all names in hand, and accepted another set of recommendations; finally, it was approved and published in 1997 on the 39th IUPAC General Assembly in Geneva , Switzerland. [ 8 ] Element 105 was named dubnium (Db), after Dubna in Russia, the location of the JINR; the American suggestions were used for elements 102, 103, 104, and 106. The name dubnium had been used for element 104 in the previous IUPAC recommendation. The American scientists "reluctantly" approved this decision. [ 9 ] IUPAC pointed out that the Berkeley laboratory had already been recognized several times, in the naming of berkelium , californium , and americium , and that the acceptance of the names rutherfordium and seaborgium for elements 104 and 106 should be offset by recognizing JINR's contributions to the discovery of elements 104, 105, and 106. [ 10 ]
The following names were agreed in 1997 on the 39th IUPAC General Assembly in Geneva , Switzerland:
Thus, the convention of the discoverer's right to name their elements was respected for elements 106 to 109, [ 11 ] and the two disputed claims were "shared" between the two opponents.
In some countries uninvolved in the dispute, such as Poland, Denmark, [ 12 ] India, [ 13 ] and Indonesia, [ 14 ] both kurchatovium for element 104 and hahnium for element 105 were used until 1997. | https://en.wikipedia.org/wiki/Transfermium_Wars |
4X1D , 1A8E , 1A8F , 1B3E , 1BP5 , 1BTJ , 1D3K , 1D4N , 1DTG , 1FQE , 1FQF , 1JQF , 1N7W , 1N7X , 1N84 , 1OQG , 1OQH , 1RYO , 1SUV , 2HAU , 2HAV , 2O7U , 2O84 , 3FGS , 3QYT , 3S9L , 3S9M , 3S9N , 3SKP , 3V83 , 3V89 , 3V8X , 3VE1 , 4H0W , 4X1B , 5DYH
7018
22041
ENSG00000091513
ENSMUSG00000032554
P02787
Q921I1
NM_001063 NM_001354704 NM_001354703
NM_133977
NP_001054 NP_001341633 NP_001341632
NP_598738
Transferrins are glycoproteins found in vertebrates which bind and consequently mediate the transport of iron (Fe) through blood plasma . [ 5 ] They are produced in the liver and contain binding sites for two Fe 3+ ions. [ 6 ] Human transferrin is encoded by the TF gene and produced as a 76 kDa glycoprotein. [ 7 ] [ 8 ]
Transferrin glycoproteins bind iron tightly, but reversibly. Although iron bound to transferrin is less than 0.1% (4 mg) of total body iron, it forms the most vital iron pool with the highest rate of turnover (25 mg/24 h). Transferrin has a molecular weight of around 80 kDa and contains two specific high-affinity Fe(III) binding sites. The affinity of transferrin for Fe(III) is extremely high ( association constant is 10 20 M −1 at pH 7.4) [ 9 ] but decreases progressively with decreasing pH below neutrality. Transferrins are not limited to only binding to iron but also to different metal ions. [ 10 ] These glycoproteins are located in various bodily fluids of vertebrates. [ 11 ] [ 12 ] Some invertebrates have proteins that act like transferrin found in the hemolymph . [ 11 ] [ 13 ]
When not bound to iron, transferrin is known as "apotransferrin" (see also apoprotein ).
Transferrins are glycoproteins that are often found in biological fluids of vertebrates. When a transferrin protein loaded with iron encounters a transferrin receptor on the surface of a cell , e.g., erythroid precursors in the bone marrow, it binds to it and is transported into the cell in a vesicle by receptor-mediated endocytosis . [ 14 ] The pH of the vesicle is reduced by hydrogen ion pumps ( H + ATPases ) to about 5.5, causing transferrin to release its iron ions. [ 11 ] Iron release rate is dependent on several factors including pH levels, interactions between lobes, temperature, salt, and chelator. [ 14 ] The receptor with its ligand bound transferrin is then transported through the endocytic cycle back to the cell surface, ready for another round of iron uptake.
Each transferrin molecule has the ability to carry two iron ions in the ferric form ( Fe 3+ ). [ 13 ]
The liver is the main site of transferrin synthesis but other tissues and organs, including the brain, also produce transferrin. A major source of transferrin secretion in the brain is the choroid plexus in the ventricular system . [ 15 ] The main role of transferrin is to deliver iron from absorption centers in the duodenum and white blood cell macrophages to all tissues. Transferrin plays a key role in areas where erythropoiesis and active cell division occur. [ 16 ] The receptor helps maintain iron homeostasis in the cells by controlling iron concentrations. [ 16 ]
The gene coding for transferrin in humans is located in chromosome band 3q21. [ 7 ]
Medical professionals may check serum transferrin level in iron deficiency and in iron overload disorders such as hemochromatosis .
Drosophila melanogaster has three transferrin genes and is highly divergent from all other model clades, Ciona intestinalis one, Danio rerio has three highly divergent from each other, as do Takifugu rubripes and Xenopus tropicalis and Gallus gallus , while Monodelphis domestica has two divergent orthologs , and Mus musculus has two relatively close and one more distant ortholog. Relatedness and orthology/ paralogy data are also available for Dictyostelium discoideum , Arabidopsis thaliana , and Pseudomonas aeruginosa . [ 17 ]
In humans, transferrin consists of a polypeptide chain containing 679 amino acids and two carbohydrate chains. The protein is composed of alpha helices and beta sheets that form two domains . [ 18 ] The N- and C- terminal sequences are represented by globular lobes and between the two lobes is an iron-binding site. [ 12 ]
The amino acids which bind the iron ion to the transferrin are identical for both lobes; two tyrosines , one histidine , and one aspartic acid . For the iron ion to bind, an anion is required, preferably carbonate ( CO 2− 3 ). [ 18 ] [ 13 ]
Transferrin also has a transferrin iron-bound receptor ; it is a disulfide-linked homodimer . [ 16 ] In humans, each monomer consists of 760 amino acids. It enables ligand bonding to the transferrin, as each monomer can bind to one or two atoms of iron. Each monomer consists of three domains: the protease, the helical, and the apical domains. The shape of a transferrin receptor resembles a butterfly based on the intersection of three clearly shaped domains. [ 18 ] Two main transferrin receptors found in humans denoted as transferrin receptor 1 (TfR1) and transferrin receptor 2 (TfR2). Although both are similar in structure, TfR1 can only bind specifically to human TF where TfR2 also has the capability to interact with bovine TF. [ 8 ]
Transferrin is also associated with the innate immune system . It is found in the mucosa and binds iron, thus creating an environment low in free iron that impedes bacterial survival in a process called iron withholding. The level of transferrin decreases in inflammation. [ 21 ]
An increased plasma transferrin level is often seen in patients with iron deficiency anemia , during pregnancy, and with the use of oral contraceptives, reflecting an increase in transferrin protein expression. When plasma transferrin levels rise, there is a reciprocal decrease in percent transferrin iron saturation, and a corresponding increase in total iron binding capacity in iron deficient states [ 22 ]
A decreased plasma transferrin level can occur in iron overload diseases and protein malnutrition. An absence of transferrin results from a rare genetic disorder known as atransferrinemia , a condition characterized by anemia and hemosiderosis in the heart and liver that leads to heart failure and many other complications as well as to H63D syndrome .
Studies reveal that a transferrin saturation (serum iron concentration ÷ total iron binding capacity) over 60 percent in men and over 50 percent in women identified the presence of an abnormality in iron metabolism (Hereditary hemochromatosis, heterozygotes and homozygotes) with approximately 95 percent accuracy. This finding helps in the early diagnosis of Hereditary hemochromatosis, especially while serum ferritin still remains low. The retained iron in Hereditary hemochromatosis is primarily deposited in parenchymal cells, with reticuloendothelial cell accumulation occurring very late in the disease. This is in contrast to transfusional iron overload in which iron deposition occurs first in the reticuloendothelial cells and then in parenchymal cells. This explains why ferritin levels remain relative low in Hereditary hemochromatosis, while transferrin saturation is high. [ 23 ] [ 24 ]
Transferrin and its receptor have been shown to diminish tumour cells when the receptor is used to attract antibodies . [ 16 ]
Many drugs are hindered when providing treatment when crossing the blood-brain barrier yielding poor uptake into areas of the brain. Transferrin glycoproteins are able to bypass the blood-brain barrier via receptor-mediated transport for specific transferrin receptors found in the brain capillary endothelial cells. [ 25 ] Due to this functionality, it is theorized that nanoparticles acting as drug carriers bound to transferrin glycoproteins can penetrate the blood-brain barrier allowing these substances to reach the diseased cells in the brain. [ 26 ] Advances with transferrin conjugated nanoparticles can lead to non-invasive drug distribution in the brain with potential therapeutic consequences of central nervous system (CNS) targeted diseases (e.g. Alzheimer's or Parkinson's disease). [ 27 ]
Carbohydrate deficient transferrin increases in the blood with heavy ethanol consumption and can be monitored through laboratory testing. [ 28 ]
Transferrin is an acute phase protein and is seen to decrease in inflammation, cancers, and certain diseases (in contrast to other acute phase proteins, e.g., C-reactive protein, which increase in case of acute inflammation). [ 29 ]
Atransferrinemia is associated with a deficiency in transferrin.
In nephrotic syndrome, urinary loss of transferrin, along with other serum proteins such as thyroxine-binding globulin, gammaglobulin, and anti-thrombin III, can manifest as iron-resistant microcytic anemia .
An example reference range for transferrin is 204–360 mg/dL. [ 30 ] Laboratory test results should always be interpreted using the reference range provided by the laboratory that performed the test [ citation needed ] .
A high transferrin level may indicate an iron deficiency anemia . Levels of serum iron and total iron binding capacity (TIBC) are used in conjunction with transferrin to specify any abnormality. See interpretation of TIBC . Low transferrin likely indicates malnutrition .
Transferrin has been shown to interact with insulin-like growth factor 2 [ 31 ] and IGFBP3 . [ 32 ] Transcriptional regulation of transferrin is upregulated by retinoic acid . [ 33 ]
Members of the family include blood serotransferrin (or siderophilin, usually simply called transferrin); lactotransferrin (lactoferrin); milk transferrin; egg white ovotransferrin (conalbumin); and membrane-associated melanotransferrin . [ 34 ] | https://en.wikipedia.org/wiki/Transferrin |
In computer technology, transfers per second and its more common secondary terms gigatransfers per second (abbreviated as GT/s ) and megatransfers per second ( MT/s ) are informal language that refer to the number of operations transferring data that occur in each second in some given data-transfer channel . It is also known as sample rate , i.e. the number of data samples captured per second, each sample normally occurring at the clock edge. The terms are neutral with respect to the method of physically accomplishing each such data-transfer operation; nevertheless, they are most commonly used in the context of transmission of digital data. 1 MT/s is 10 6 or one million transfers per second; similarly, 1 GT/s means 10 9 , or equivalently in the US/ short scale , one billion transfers per second.
These terms alone do not specify the bit rate at which binary data is being transferred because they do not specify the number of bits transferred in each transfer operation (known as the channel width or word length ). In order to calculate the data transmission rate, one must multiply the transfer rate by the information channel width. For example, a data bus eight-bytes wide (64 bits) by definition transfers eight bytes in each transfer operation; at a transfer rate of 1 GT/s, the data rate would be 8 × 10 9 B /s, i.e. 8 GB/s, or approximately 7.45 GiB /s. The bit rate for this example is 64 Gbit/s (8 × 8 × 10 9 bit/s).
The formula for a data transfer rate is: Channel width (bits/transfer) × transfers/second = bits/second .
Expanding the width of a channel, for example that between a CPU and a northbridge , increases data throughput without requiring an increase in the channel's operating frequency (measured in transfers per second). This is analogous to increasing throughput by increasing bandwidth but leaving latency unchanged.
The units usually refer to the "effective" number of transfers, or transfers perceived from "outside" of a system or component, as opposed to the internal speed or rate of the clock of the system. One example is a computer bus running at double data rate where data is transferred on both the rising and falling edge of the clock signal. If its internal clock runs at 100 MHz, then the effective rate is 200 MT/s, because there are 100 million rising edges per second and 100 million falling edges per second of a clock signal running at 100 MHz.
Buses like SCSI and PCI fall in the megatransfer range of data transfer rate, while newer bus architectures like the PCI-X , PCI Express , Ultra Path , and HyperTransport / Infinity Fabric operate at the gigatransfer rate.
The choice of the symbol T for transfer conflicts with the International System of Units , in which T is the symbol for the tesla , a unit of magnetic flux density (so "megatesla per second" (MT/s) would be a reasonable unit to describe the rate of a rapidly changing magnetic field, such as in a pulsed field magnet or kicker magnet ). | https://en.wikipedia.org/wiki/Transfers_per_second |
Transfersome is a proprietary drug delivery technology, an artificial vesicle designed to exhibit the characteristics of a cell vesicle suitable for controlled and potentially targeted drug delivery . Some evidence has shown efficacy for its use for drug delivery without causing skin irritation, [ 1 ] potentially being used to treat skin cancer. [ 2 ] Transfersome is made by the German company IDEA AG. | https://en.wikipedia.org/wiki/Transfersome |
A transfluxor was a specialised type of magnetic core memory element in which each core had two holes, one for writing and another for reading. It had the unusual property that a core's state could be read without erasing it. [ 1 ] [ 2 ] In addition to binary data, transfluxors could also store analog values, with no need to drive them into core saturation. [ 3 ] [ 4 ]
The technology is described in U.S. patent 3048828. [ 5 ]
Transfluxors were used in the ARMA Micro Computer . [ 1 ]
This computing article is a stub . You can help Wikipedia by expanding it .
This electronics-related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transfluxor |
In broad terms, transformation design is a human-centered , interdisciplinary process that seeks to create desirable and sustainable changes in behavior and form – of individuals, systems and organizations. It is a multi-stage, iterative process of applying design principles to large and complex systems.
Its practitioners examine problems holistically rather than reductively to understand relationships as well as components to better frame the challenge. They then prototype small-scale systems – composed of objects, services, interactions and experiences – that support people and organizations in achievement of a desired change. Successful prototypes are then scaled.
Because transformation design is about applying design skills in non-traditional territories, it often results in non-traditional design outputs. 3 Projects have resulted in the creation of new roles, new organizations, new systems and new policies. These designers are just as likely to shape a job description, as they are a new product. 3
This emerging field draws from a variety of design disciplines - service design , user-centered design , participatory design , concept design , information design , industrial design , graphic design , systems design , interactive design , experience design - as well as non-design disciplines including cognitive psychology and perceptual psychology , linguistics , cognitive science , architecture , haptics , information architecture , ethnography , storytelling and heuristics .
Though academics have written about the economic value of and need for transformations over the years 7,8 , its practice first emerged in 2004 when The Design Council , the UK's national strategic body for design, formed RED : a self-proclaimed "do-tank" challenged to bring design thinking to the transformation of public services. 1
This move was in response to Prime Minister Tony Blair's desire to have public services "redesigned around the needs of the user, the patients, the passenger, the victim of crime". 3
The RED team, led by Hilary Cottam , studied these big, complex problems to determine how design thinking and design techniques could help government rethink the systems and structures within public services and possibly redesign them from beginning to end. 3
Between 2004 and 2006, the RED team, in collaboration with many other people and groups, developed techniques, processes and outputs that were able to "transform" social issues such as preventing illness, managing chronic illnesses, senior citizen care, rural transportation, energy conservation, re-offending prisoners and public education.
In 2015 Braunschweig University of Art / Germany has launched a new MA in Transformation Design . In 2016 The Glasgow School of Art launched another masters program "M.Des in Design Innovation and Transformation Design". In 2019 the University of Applied Sciences Augsburg / Germany launched a masters program in Transformation Design .
Transformation design, like user-centered design, starts from the perspective of the end user. Designers spend a great deal of time not only learning how users currently experience the system and how they want to experience the system, but also co-creating with them the designed solutions.
Because transformation design tackles complex issues involving many stakeholders and components, more expertise beyond the user and the designer is always required. People such as, but not limited to, policy makers, sector analysts, psychologists, economists, private businesses, government departments and agencies, front-line workers and academics are invited to participate in the entire design process - from problem definition to solution development. 6
With so many points-of-view brought into the process, transformation designers are not always 'designers.' Instead, they often play the role of moderator. Though varying methods of participation and co-creation, these moderating designers create hands-on, collaborative workshops (a.k.a. charrette ) that make the design process accessible to the non-designers.
Ideas from workshops are rapidly prototyped and beta-tested in the real world with a group of real end users. Their experience with and opinions of the prototypes are recorded and fed back into the workshops and development of the next prototype. | https://en.wikipedia.org/wiki/Transformation_design |
Transformation efficiency refers to the ability of a cell to take up and incorporate exogenous DNA, such as plasmids , during a process called transformation . The efficiency of transformation is typically measured as the number of transformants (cells that have taken up the exogenous DNA ) per microgram of DNA added to the cells. A higher transformation efficiency means that more cells are able to take up the DNA, and a lower efficiency means that fewer cells are able to do so.
In molecular biology , transformation efficiency is a crucial parameter, it is used to evaluate the ability of different methods to introduce plasmid DNA into cells and to compare the efficiency of different plasmid , vectors and host cells. This efficiency can be affected by a number of factors, including the method used for introducing the DNA, the type of cell and plasmid used, and the conditions under which the transformation is performed. Therefore, measuring and optimizing transformation efficiency is an important step in many molecular biology applications, including genetic engineering , gene therapy and biotechnology .
By measuring the transformation efficiency, we can utilize the information from our experiment to evaluate how effectively our transformation went. This is a quantification of how many cells were altered by 1 μg of plasmid DNA. In essence, it is a sign that the transformation experiment was successful. [ 1 ] It should be determined under conditions of cell excess. [ 2 ]
Transformation efficiency is typically measured as the number of transformed cells per total number of cells. It can be represented as a percentage or as colony forming units (CFUs) per microgram of DNA. [ citation needed ]
One of the most common ways to measure transformation efficiency is by performing a colony forming assay. Here is an example of how to calculate transformation efficiency using colony forming units (CFUs): [ 3 ]
For example, if you plate 1x 10 7 cells and count 1000 colonies, the transformation efficiency is: (1000/1x 10 7 ) x 100 = 0.1% [ citation needed ]
Alternatively, CFUs can be reported per microgram of DNA used for the transformation. This can be calculated by multiplying the number of colonies by the volume of the culture plated and dividing by the amount of DNA used. [ citation needed ]
Quantitative PCR (qPCR) - This method utilizes the fact that the plasmid DNA will have a specific gene or sequence that is not present in the host cell genome, and therefore can be used as a target for qPCR. By quantifying the number of copies of this specific gene or sequence in the transformed cells, it is possible to determine the amount of plasmid DNA present in the cell, and thus the transformation efficiency. [ 4 ]
Fluorescent assay - This method relies on the use of a plasmid that contains a fluorescent protein or reporter gene. The transformed cells are then analyzed by flow cytometry or fluorescence microscopy to determine the number of cells that express the fluorescent protein . The transformation efficiency is then calculated as the percentage of cells that express the fluorescent protein. [ 5 ]
The number of viable cells in a preparation for a transformation reaction may range from 2×10 8 to 10 11 ; most common methods of E. coli preparation yield around 10 10 viable cells per reaction. The standard plasmids used for determination of transformation efficiency in Escherichia coli are pBR322 or other similarly sized or smaller vectors, such as the pUC series of vectors. Different vectors however may be used to determine their transformation efficiency. 10–100 pg of DNA may be used for transformation, more DNA may be necessary for low-efficiency transformation (generally saturation level is reached at over 10 ng). [ 6 ]
After transformation, 1% and 10% of the cells are plated separately, the cells may be diluted in media as necessary for ease of plating. Further dilution may be used for high efficiency transformation. [ citation needed ]
A transformation efficiency of 1×10 8 cfu/μg for a small plasmid like pUC19 is roughly equivalent to 1 in 2000 molecules of the plasmid used being introduced into cells. In E. coli , the theoretical limit of transformation efficiency for most commonly used plasmids would be over 1×10 11 cfu/μg. In practice the best achievable result may be around 2–4×10 10 cfu/μg for a small plasmid like pUC19, and considerably lower for large plasmids. [ citation needed ]
Individual cells are capable of taking up many DNA molecules, but the presence of multiple plasmids does not significantly affect the occurrence of successful transformation events. [ 7 ] A number of factors may affect the transformation efficiency: [ 2 ]
Plasmid size – A study done in E. coli found that transformation efficiency declines linearly with increasing plasmid size, i.e. larger plasmids transform less well than smaller plasmids. [ 7 ] [ 8 ] [ 9 ]
Forms of DNA – Supercoiled plasmid have a slightly better transformation efficiency than relaxed plasmids – relaxed plasmids are transformed at around 75% efficiency of supercoiled ones. [ 7 ] Linear and single-stranded DNA however have much lower transformation efficiency. Single-stranded DNAs are transformed at 10 4 lower efficiency than double-stranded ones.
Media composition – The composition of the media used in the transformation process can affect the efficiency. For example, certain media supplements can increase the natural competence of cells. [ 10 ]
Genotype of cells – Cloning strains may contain mutations that improve the transformation efficiency of the cells. For example, E. coli K12 strains with the deoR mutation, originally found to confer an ability of cell to grow in minimum media using inosine as the sole carbon source, have 4-5 times the transformation efficiency of similar strains without. For linear DNA, which is poorly transformed in E. coli , the recBC or recD mutation can significantly improve the efficiency of its transformation. [ 11 ]
Culture conditions – E. coli cells are more susceptible to be made competent when it is growing rapidly, cells are therefore normally harvested in the early log phase of cell growth when preparing competent cells. The optimal optical density for harvesting cells normally lies around 0.4, although it may vary with different cell strains. A higher value of 0.94-0.95 has also been found to produce good yield of competent cells, but this can be impractical when cell growth is rapid. [ 12 ]
Presence of antibiotics – The presence of antibiotics can increase the efficiency of transformation by inhibiting the growth of non-transformed cells and selecting for transformed cells that are resistant to the antibiotic. For instance, the use of β-lactam antibiotics has been shown for glutamate-producing bacteria to increase its transformation efficiencies. [ 13 ] [ 14 ] [ 15 ]
Plasmid origin of replication – The origin of replication of the plasmid used in the transformation process can affect the efficiency in several ways. The copy number of the plasmid in the cell, the activity of the origin of replication in the host cells, and the expression of the genes on the plasmid can all affect the efficiency. The plasmid with a high copy number origin of replication will generally have a higher transfection efficiency than one with a low copy number origin, using a plasmid with an origin of replication that is active in the host cell can lead to a higher transfection efficiency. [ 16 ] [ 17 ]
Transformation conditions – The method of preparation of competent cells, the length of time of heat shock , temperature of heat shock, incubation time after heat shock, growth medium used, pH and various additives, all can affect the transformation efficiency of the cells. The presence of contaminants as well as ligase in a ligation mixture can reduce the transformation efficiency in electroporation , [ 18 ] and inactivation of ligase or chloroform extraction of DNA may be necessary for electroporation, alternatively only use a tenth of the ligation mixture to reduce the amount of contaminants. Normal preparation of competent cells can yield transformation efficiency ranging from 10 6 to 10 8 cfu/μg DNA. Protocols for chemical method however exist for making super competent cells that may yield a transformation efficiency of over 1 x 10 9 . [ 19 ]
Damage to DNA – Exposure of DNA to UV radiation in standard preparative agarose gel electrophoresis procedure for as little as 45 seconds can damage the DNA, and this can significantly reduce the transformation efficiency. [ 20 ] Adding cytidine or guanosine to the electrophoresis buffer at 1 mM concentration however may protect the DNA from damage. A higher-wavelength UV radiation (365 nm) which cause less damage to DNA should be used if it is necessary work for work on the DNA on a UV transilluminator for an extended period of time. This longer wavelength UV produces weaker fluorescence with the ethidium bromide intercalated into the DNA, therefore if it is necessary to capture images of the DNA bands, a shorter wavelength (302 or 312 nm) UV radiations may be used. Such exposure however should be limited to a very short time if the DNA is to be recovered later for ligation and transformation.
The method used for introducing the DNA have a significant impact on the transformation efficiency. [ 21 ]
Electroporation tends to be more efficient than chemical methods and can be applied to a wide range of species and to strains that were previously resistant and recalcitrant to transformation techniques. [ 22 ] [ 23 ]
Electroporation has been found to have an average yield typically between 10 4 - 10 8 CFU/ug . However, a transformation efficiencies as high as 0.5-5 x 10 10 colony forming units (CFU) per microgram of DNA for E. coli . For samples that are hard to handle, like cDNA libraries , gDNA , and plasmids larger than 30 kb, it is suggested to use electrocompetent cells that have transformation efficiencies of over 1 x 10 10 CFU/μg. This will ensure a high success rate in introducing the DNA and forming a large number of colonies. [ 24 ] It is important to adjust and optimize the electroporation buffer (Increasing the concentration of the electroporation buffer can result in increased transformation efficiencies ) and the shape, strength, number, and number of pulses these electrical parameters play a key role in transformation efficiency. [ 25 ]
Chemical transformation or heat shock can be performed in a simple laboratory setup, typically yielding transformation efficiencies that are adequate for cloning and subcloning applications, approximately 10 6 CFU/μg. One of the early methods used was a combination of CaCl 2 and MgCl 2 to treat the cells. However, these methods resulted in transformation efficiencies, with a maximum of 10 5 - 10 6 colony forming units (CFU) per microgram of plasmid DNA. [ 24 ] Later research found that certain cations, such as Mn 2+ , Ca 2+ , Ba 2+ , Sr 2+ and Mg 2+ could have a positive effect on transformation efficiencies, with Mn 2+ showing the greatest effect. [ 26 ]
Some bacterial cells have restriction-modification systems that can degrade exogenous plasmids that are foreign to the host cell. This can greatly reduce the efficiency of transformation. [ 27 ] [ 21 ] This is due to restriction systems in the recipient cells that target and destroy exogenous DNA. These systems recognize exogenous DNA based on differences in methylation patterns. To address this problem, strategies such as altering the methylation of the exogenous DNA using commercial methylases or reducing the restriction activity in the recipient cells have been applied. [ 28 ] [ 29 ] For example, using methylation-negative mutants or temporarily inactivating the restriction system with heat can reduce the recipient cell's ability to impose restrictions on the exogenous DNA. [ 30 ] | https://en.wikipedia.org/wiki/Transformation_efficiency |
In mathematics , transformation geometry (or transformational geometry ) is the name of a mathematical and pedagogic take on the study of geometry by focusing on groups of geometric transformations , and properties that are invariant under them. It is opposed to the classical synthetic geometry approach of Euclidean geometry , that focuses on proving theorems .
For example, within transformation geometry, the properties of an isosceles triangle are deduced from the fact that it is mapped to itself by a reflection about a certain line. This contrasts with the classical proofs by the criteria for congruence of triangles . [ 1 ]
The first systematic effort to use transformations as the foundation of geometry was made by Felix Klein in the 19th century, under the name Erlangen programme . For nearly a century this approach remained confined to mathematics research circles. In the 20th century efforts were made to exploit it for mathematical education . Andrei Kolmogorov included this approach (together with set theory ) as part of a proposal for geometry teaching reform in Russia . [ 2 ] These efforts culminated in the 1960s with the general reform of mathematics teaching known as the New Math movement.
An exploration of transformation geometry often begins with a study of reflection symmetry as found in daily life. The first real transformation is reflection in a line or reflection against an axis . The composition of two reflections results in a rotation when the lines intersect, or a translation when they are parallel. Thus through transformations students learn about Euclidean plane isometry . For instance, consider reflection in a vertical line and a line inclined at 45° to the horizontal. One can observe that one composition yields a counter-clockwise quarter-turn (90°) while the reverse composition yields a clockwise quarter-turn. Such results show that transformation geometry includes non-commutative processes.
An entertaining application of reflection in a line occurs in a proof of the one-seventh area triangle found in any triangle.
Another transformation introduced to young students is the dilation . However, the reflection in a circle transformation seems inappropriate for lower grades. Thus inversive geometry , a larger study than grade school transformation geometry, is usually reserved for college students.
Experiments with concrete symmetry groups make way for abstract group theory . Other concrete activities use computations with complex numbers , hypercomplex numbers , or matrices to express transformation geometry.
Such transformation geometry lessons present an alternate view that contrasts with classical synthetic geometry . When students then encounter analytic geometry , the ideas of coordinate rotations and reflections follow easily. All these concepts prepare for linear algebra where the reflection concept is expanded.
Educators have shown some interest and described projects and experiences with transformation geometry for children from kindergarten to high school. In the case of very young age children, in order to avoid introducing new terminology and to make links with students' everyday experience with concrete objects, it was sometimes recommended to use words they are familiar with, like "flips" for line reflections, "slides" for translations, and "turns" for rotations, although these are not precise mathematical language. In some proposals, students start by performing with concrete objects before they perform the abstract transformations via their definitions of a mapping of each point of the figure. [ 3 ] [ 4 ] [ 5 ] [ 6 ]
In an attempt to restructure the courses of geometry in Russia, Kolmogorov suggested presenting it under the point of view of transformations, so the geometry courses were structured based on set theory . This led to the appearance of the term "congruent" in schools, for figures that were before called "equal": since a figure was seen as a set of points, it could only be equal to itself, and two triangles that could be overlapped by isometries were said to be congruent . [ 2 ]
One author expressed the importance of group theory to transformation geometry as follows: | https://en.wikipedia.org/wiki/Transformation_geometry |
In linear algebra , linear transformations can be represented by matrices . If T {\displaystyle T} is a linear transformation mapping R n {\displaystyle \mathbb {R} ^{n}} to R m {\displaystyle \mathbb {R} ^{m}} and x {\displaystyle \mathbf {x} } is a column vector with n {\displaystyle n} entries, then there exists an m × n {\displaystyle m\times n} matrix A {\displaystyle A} , called the transformation matrix of T {\displaystyle T} , [ 1 ] such that: T ( x ) = A x {\displaystyle T(\mathbf {x} )=A\mathbf {x} } Note that A {\displaystyle A} has m {\displaystyle m} rows and n {\displaystyle n} columns, whereas the transformation T {\displaystyle T} is from R n {\displaystyle \mathbb {R} ^{n}} to R m {\displaystyle \mathbb {R} ^{m}} . There are alternative expressions of transformation matrices involving row vectors that are preferred by some authors. [ 2 ] [ 3 ]
Matrices allow arbitrary linear transformations to be displayed in a consistent format, suitable for computation. [ 1 ] This also allows transformations to be composed easily (by multiplying their matrices).
Linear transformations are not the only ones that can be represented by matrices. Some transformations that are non-linear on an n-dimensional Euclidean space R n can be represented as linear transformations on the n +1-dimensional space R n +1 . These include both affine transformations (such as translation ) and projective transformations . For this reason, 4×4 transformation matrices are widely used in 3D computer graphics . These n +1-dimensional transformation matrices are called, depending on their application, affine transformation matrices , projective transformation matrices , or more generally non-linear transformation matrices . With respect to an n -dimensional matrix, an n +1-dimensional matrix can be described as an augmented matrix .
In the physical sciences , an active transformation is one which actually changes the physical position of a system , and makes sense even in the absence of a coordinate system whereas a passive transformation is a change in the coordinate description of the physical system ( change of basis ). The distinction between active and passive transformations is important. By default, by transformation , mathematicians usually mean active transformations, while physicists could mean either.
Put differently, a passive transformation refers to description of the same object as viewed from two different coordinate frames.
If one has a linear transformation T ( x ) {\displaystyle T(x)} in functional form, it is easy to determine the transformation matrix A by transforming each of the vectors of the standard basis by T , then inserting the result into the columns of a matrix. In other words, A = [ T ( e 1 ) T ( e 2 ) ⋯ T ( e n ) ] {\displaystyle A={\begin{bmatrix}T(\mathbf {e} _{1})&T(\mathbf {e} _{2})&\cdots &T(\mathbf {e} _{n})\end{bmatrix}}}
For example, the function T ( x ) = 5 x {\displaystyle T(x)=5x} is a linear transformation. Applying the above process (suppose that n = 2 in this case) reveals that: T ( x ) = 5 x = 5 I x = [ 5 0 0 5 ] x {\displaystyle T(\mathbf {x} )=5\mathbf {x} =5I\mathbf {x} ={\begin{bmatrix}5&0\\0&5\end{bmatrix}}\mathbf {x} }
The matrix representation of vectors and operators depends on the chosen basis; a similar matrix will result from an alternate basis. Nevertheless, the method to find the components remains the same.
To elaborate, vector v {\displaystyle \mathbf {v} } can be represented in basis vectors, E = [ e 1 e 2 ⋯ e n ] {\displaystyle E={\begin{bmatrix}\mathbf {e} _{1}&\mathbf {e} _{2}&\cdots &\mathbf {e} _{n}\end{bmatrix}}} with coordinates [ v ] E = [ v 1 v 2 ⋯ v n ] T {\displaystyle [\mathbf {v} ]_{E}={\begin{bmatrix}v_{1}&v_{2}&\cdots &v_{n}\end{bmatrix}}^{\mathrm {T} }} : v = v 1 e 1 + v 2 e 2 + ⋯ + v n e n = ∑ i v i e i = E [ v ] E {\displaystyle \mathbf {v} =v_{1}\mathbf {e} _{1}+v_{2}\mathbf {e} _{2}+\cdots +v_{n}\mathbf {e} _{n}=\sum _{i}v_{i}\mathbf {e} _{i}=E[\mathbf {v} ]_{E}}
Now, express the result of the transformation matrix A upon v {\displaystyle \mathbf {v} } , in the given basis: A ( v ) = A ( ∑ i v i e i ) = ∑ i v i A ( e i ) = [ A ( e 1 ) A ( e 2 ) ⋯ A ( e n ) ] [ v ] E = A ⋅ [ v ] E = [ e 1 e 2 ⋯ e n ] [ a 1 , 1 a 1 , 2 ⋯ a 1 , n a 2 , 1 a 2 , 2 ⋯ a 2 , n ⋮ ⋮ ⋱ ⋮ a n , 1 a n , 2 ⋯ a n , n ] [ v 1 v 2 ⋮ v n ] {\displaystyle {\begin{aligned}A(\mathbf {v} )&=A\left(\sum _{i}v_{i}\mathbf {e} _{i}\right)=\sum _{i}{v_{i}A(\mathbf {e} _{i})}\\&={\begin{bmatrix}A(\mathbf {e} _{1})&A(\mathbf {e} _{2})&\cdots &A(\mathbf {e} _{n})\end{bmatrix}}[\mathbf {v} ]_{E}=A\cdot [\mathbf {v} ]_{E}\\[3pt]&={\begin{bmatrix}\mathbf {e} _{1}&\mathbf {e} _{2}&\cdots &\mathbf {e} _{n}\end{bmatrix}}{\begin{bmatrix}a_{1,1}&a_{1,2}&\cdots &a_{1,n}\\a_{2,1}&a_{2,2}&\cdots &a_{2,n}\\\vdots &\vdots &\ddots &\vdots \\a_{n,1}&a_{n,2}&\cdots &a_{n,n}\\\end{bmatrix}}{\begin{bmatrix}v_{1}\\v_{2}\\\vdots \\v_{n}\end{bmatrix}}\end{aligned}}}
The a i , j {\displaystyle a_{i,j}} elements of matrix A are determined for a given basis E by applying A to every e j = [ 0 0 ⋯ ( v j = 1 ) ⋯ 0 ] T {\displaystyle \mathbf {e} _{j}={\begin{bmatrix}0&0&\cdots &(v_{j}=1)&\cdots &0\end{bmatrix}}^{\mathrm {T} }} , and observing the response vector A e j = a 1 , j e 1 + a 2 , j e 2 + ⋯ + a n , j e n = ∑ i a i , j e i . {\displaystyle A\mathbf {e} _{j}=a_{1,j}\mathbf {e} _{1}+a_{2,j}\mathbf {e} _{2}+\cdots +a_{n,j}\mathbf {e} _{n}=\sum _{i}a_{i,j}\mathbf {e} _{i}.}
This equation defines the wanted elements, a i , j {\displaystyle a_{i,j}} , of j -th column of the matrix A . [ 4 ]
Yet, there is a special basis for an operator in which the components form a diagonal matrix and, thus, multiplication complexity reduces to n . Being diagonal means that all coefficients a i , j {\displaystyle a_{i,j}} except a i , i {\displaystyle a_{i,i}} are zeros leaving only one term in the sum ∑ a i , j e i {\textstyle \sum a_{i,j}\mathbf {e} _{i}} above. The surviving diagonal elements, a i , i {\displaystyle a_{i,i}} , are known as eigenvalues and designated with λ i {\displaystyle \lambda _{i}} in the defining equation, which reduces to A e i = λ i e i {\displaystyle A\mathbf {e} _{i}=\lambda _{i}\mathbf {e} _{i}} . The resulting equation is known as eigenvalue equation . [ 5 ] The eigenvectors and eigenvalues are derived from it via the characteristic polynomial .
With diagonalization , it is often possible to translate to and from eigenbases.
Most common geometric transformations that keep the origin fixed are linear, including rotation, scaling, shearing, reflection, and orthogonal projection; if an affine transformation is not a pure translation it keeps some point fixed, and that point can be chosen as origin to make the transformation linear. In two dimensions, linear transformations can be represented using a 2×2 transformation matrix.
A stretch in the xy -plane is a linear transformation which enlarges all distances in a particular direction by a constant factor but does not affect distances in the perpendicular direction. We only consider stretches along the x-axis and y-axis. A stretch along the x-axis has the form x' = kx ; y' = y for some positive constant k . (Note that if k > 1 , then this really is a "stretch"; if k < 1 , it is technically a "compression", but we still call it a stretch. Also, if k = 1 , then the transformation is an identity, i.e. it has no effect.)
The matrix associated with a stretch by a factor k along the x-axis is given by: [ k 0 0 1 ] {\displaystyle {\begin{bmatrix}k&0\\0&1\end{bmatrix}}}
Similarly, a stretch by a factor k along the y-axis has the form x' = x ; y' = ky , so the matrix associated with this transformation is [ 1 0 0 k ] {\displaystyle {\begin{bmatrix}1&0\\0&k\end{bmatrix}}}
If the two stretches above are combined with reciprocal values, then the transformation matrix represents a squeeze mapping : [ k 0 0 1 / k ] . {\displaystyle {\begin{bmatrix}k&0\\0&1/k\end{bmatrix}}.} A square with sides parallel to the axes is transformed to a rectangle that has the same area as the square. The reciprocal stretch and compression leave the area invariant.
For rotation by an angle θ counterclockwise (positive direction) about the origin the functional form is x ′ = x cos θ − y sin θ {\displaystyle x'=x\cos \theta -y\sin \theta } and y ′ = x sin θ + y cos θ {\displaystyle y'=x\sin \theta +y\cos \theta } . Written in matrix form, this becomes: [ 6 ] [ x ′ y ′ ] = [ cos θ − sin θ sin θ cos θ ] [ x y ] {\displaystyle {\begin{bmatrix}x'\\y'\end{bmatrix}}={\begin{bmatrix}\cos \theta &-\sin \theta \\\sin \theta &\cos \theta \end{bmatrix}}{\begin{bmatrix}x\\y\end{bmatrix}}}
Similarly, for a rotation clockwise (negative direction) about the origin, the functional form is x ′ = x cos θ + y sin θ {\displaystyle x'=x\cos \theta +y\sin \theta } and y ′ = − x sin θ + y cos θ {\displaystyle y'=-x\sin \theta +y\cos \theta } the matrix form is: [ x ′ y ′ ] = [ cos θ sin θ − sin θ cos θ ] [ x y ] {\displaystyle {\begin{bmatrix}x'\\y'\end{bmatrix}}={\begin{bmatrix}\cos \theta &\sin \theta \\-\sin \theta &\cos \theta \end{bmatrix}}{\begin{bmatrix}x\\y\end{bmatrix}}}
These formulae assume that the x axis points right and the y axis points up.
For shear mapping (visually similar to slanting), there are two possibilities.
A shear parallel to the x axis has x ′ = x + k y {\displaystyle x'=x+ky} and y ′ = y {\displaystyle y'=y} . Written in matrix form, this becomes: [ x ′ y ′ ] = [ 1 k 0 1 ] [ x y ] {\displaystyle {\begin{bmatrix}x'\\y'\end{bmatrix}}={\begin{bmatrix}1&k\\0&1\end{bmatrix}}{\begin{bmatrix}x\\y\end{bmatrix}}}
A shear parallel to the y axis has x ′ = x {\displaystyle x'=x} and y ′ = y + k x {\displaystyle y'=y+kx} , which has matrix form: [ x ′ y ′ ] = [ 1 0 k 1 ] [ x y ] {\displaystyle {\begin{bmatrix}x'\\y'\end{bmatrix}}={\begin{bmatrix}1&0\\k&1\end{bmatrix}}{\begin{bmatrix}x\\y\end{bmatrix}}}
For reflection about a line that goes through the origin, let l = ( l x , l y ) {\displaystyle \mathbf {l} =(l_{x},l_{y})} be a vector in the direction of the line. Then the transformation matrix is: A = 1 ‖ l ‖ 2 [ l x 2 − l y 2 2 l x l y 2 l x l y l y 2 − l x 2 ] {\displaystyle \mathbf {A} ={\frac {1}{\lVert \mathbf {l} \rVert ^{2}}}{\begin{bmatrix}l_{x}^{2}-l_{y}^{2}&2l_{x}l_{y}\\2l_{x}l_{y}&l_{y}^{2}-l_{x}^{2}\end{bmatrix}}}
To project a vector orthogonally onto a line that goes through the origin, let u = ( u x , u y ) {\displaystyle \mathbf {u} =(u_{x},u_{y})} be a vector in the direction of the line. Then the transformation matrix is: A = 1 ‖ u ‖ 2 [ u x 2 u x u y u x u y u y 2 ] {\displaystyle \mathbf {A} ={\frac {1}{\lVert \mathbf {u} \rVert ^{2}}}{\begin{bmatrix}u_{x}^{2}&u_{x}u_{y}\\u_{x}u_{y}&u_{y}^{2}\end{bmatrix}}}
As with reflections, the orthogonal projection onto a line that does not pass through the origin is an affine, not linear, transformation.
Parallel projections are also linear transformations and can be represented simply by a matrix. However, perspective projections are not, and to represent these with a matrix, homogeneous coordinates can be used.
The matrix to rotate an angle θ about any axis defined by unit vector ( x , y , z ) is [ 7 ] [ x x ( 1 − cos θ ) + cos θ y x ( 1 − cos θ ) − z sin θ z x ( 1 − cos θ ) + y sin θ x y ( 1 − cos θ ) + z sin θ y y ( 1 − cos θ ) + cos θ z y ( 1 − cos θ ) − x sin θ x z ( 1 − cos θ ) − y sin θ y z ( 1 − cos θ ) + x sin θ z z ( 1 − cos θ ) + cos θ ] . {\displaystyle {\begin{bmatrix}xx(1-\cos \theta )+\cos \theta &yx(1-\cos \theta )-z\sin \theta &zx(1-\cos \theta )+y\sin \theta \\xy(1-\cos \theta )+z\sin \theta &yy(1-\cos \theta )+\cos \theta &zy(1-\cos \theta )-x\sin \theta \\xz(1-\cos \theta )-y\sin \theta &yz(1-\cos \theta )+x\sin \theta &zz(1-\cos \theta )+\cos \theta \end{bmatrix}}.}
To reflect a point through a plane a x + b y + c z = 0 {\displaystyle ax+by+cz=0} (which goes through the origin), one can use A = I − 2 N N T {\displaystyle \mathbf {A} =\mathbf {I} -2\mathbf {NN} ^{\mathrm {T} }} , where I {\displaystyle \mathbf {I} } is the 3×3 identity matrix and N {\displaystyle \mathbf {N} } is the three-dimensional unit vector for the vector normal of the plane. If the L 2 norm of a {\displaystyle a} , b {\displaystyle b} , and c {\displaystyle c} is unity, the transformation matrix can be expressed as: A = [ 1 − 2 a 2 − 2 a b − 2 a c − 2 a b 1 − 2 b 2 − 2 b c − 2 a c − 2 b c 1 − 2 c 2 ] {\displaystyle \mathbf {A} ={\begin{bmatrix}1-2a^{2}&-2ab&-2ac\\-2ab&1-2b^{2}&-2bc\\-2ac&-2bc&1-2c^{2}\end{bmatrix}}}
Note that these are particular cases of a Householder reflection in two and three dimensions. A reflection about a line or plane that does not go through the origin is not a linear transformation — it is an affine transformation — as a 4×4 affine transformation matrix, it can be expressed as follows (assuming the normal is a unit vector): [ x ′ y ′ z ′ 1 ] = [ 1 − 2 a 2 − 2 a b − 2 a c − 2 a d − 2 a b 1 − 2 b 2 − 2 b c − 2 b d − 2 a c − 2 b c 1 − 2 c 2 − 2 c d 0 0 0 1 ] [ x y z 1 ] {\displaystyle {\begin{bmatrix}x'\\y'\\z'\\1\end{bmatrix}}={\begin{bmatrix}1-2a^{2}&-2ab&-2ac&-2ad\\-2ab&1-2b^{2}&-2bc&-2bd\\-2ac&-2bc&1-2c^{2}&-2cd\\0&0&0&1\end{bmatrix}}{\begin{bmatrix}x\\y\\z\\1\end{bmatrix}}} where d = − p ⋅ N {\displaystyle d=-\mathbf {p} \cdot \mathbf {N} } for some point p {\displaystyle \mathbf {p} } on the plane, or equivalently, a x + b y + c z + d = 0 {\displaystyle ax+by+cz+d=0} .
If the 4th component of the vector is 0 instead of 1, then only the vector's direction is reflected and its magnitude remains unchanged, as if it were mirrored through a parallel plane that passes through the origin. This is a useful property as it allows the transformation of both positional vectors and normal vectors with the same matrix. See homogeneous coordinates and affine transformations below for further explanation.
One of the main motivations for using matrices to represent linear transformations is that transformations can then be easily composed and inverted.
Composition is accomplished by matrix multiplication . Row and column vectors are operated upon by matrices, rows on the left and columns on the right. Since text reads from left to right, column vectors are preferred when transformation matrices are composed:
If A and B are the matrices of two linear transformations, then the effect of first applying A and then B to a column vector x {\displaystyle \mathbf {x} } is given by: B ( A x ) = ( B A ) x . {\displaystyle \mathbf {B} (\mathbf {A} \mathbf {x} )=(\mathbf {BA} )\mathbf {x} .}
In other words, the matrix of the combined transformation A followed by B is simply the product of the individual matrices.
When A is an invertible matrix there is a matrix A −1 that represents a transformation that "undoes" A since its composition with A is the identity matrix . In some practical applications, inversion can be computed using general inversion algorithms or by performing inverse operations (that have obvious geometric interpretation, like rotating in opposite direction) and then composing them in reverse order. Reflection matrices are a special case because they are their own inverses and don't need to be separately calculated.
To represent affine transformations with matrices, we can use homogeneous coordinates . This means representing a 2-vector ( x , y ) as a 3-vector ( x , y , 1), and similarly for higher dimensions. Using this system, translation can be expressed with matrix multiplication. The functional form x ′ = x + t x ; y ′ = y + t y {\displaystyle x'=x+t_{x};y'=y+t_{y}} becomes: [ x ′ y ′ 1 ] = [ 1 0 t x 0 1 t y 0 0 1 ] [ x y 1 ] . {\displaystyle {\begin{bmatrix}x'\\y'\\1\end{bmatrix}}={\begin{bmatrix}1&0&t_{x}\\0&1&t_{y}\\0&0&1\end{bmatrix}}{\begin{bmatrix}x\\y\\1\end{bmatrix}}.}
All ordinary linear transformations are included in the set of affine transformations, and can be described as a simplified form of affine transformations. Therefore, any linear transformation can also be represented by a general transformation matrix. The latter is obtained by expanding the corresponding linear transformation matrix by one row and column, filling the extra space with zeros except for the lower-right corner, which must be set to 1. For example, the counter-clockwise rotation matrix from above becomes: [ cos θ − sin θ 0 sin θ cos θ 0 0 0 1 ] {\displaystyle {\begin{bmatrix}\cos \theta &-\sin \theta &0\\\sin \theta &\cos \theta &0\\0&0&1\end{bmatrix}}}
Using transformation matrices containing homogeneous coordinates, translations become linear, and thus can be seamlessly intermixed with all other types of transformations. The reason is that the real plane is mapped to the w = 1 plane in real projective space, and so translation in real Euclidean space can be represented as a shear in real projective space. Although a translation is a non- linear transformation in a 2-D or 3-D Euclidean space described by Cartesian coordinates (i.e. it can't be combined with other transformations while preserving commutativity and other properties), it becomes , in a 3-D or 4-D projective space described by homogeneous coordinates, a simple linear transformation (a shear ).
More affine transformations can be obtained by composition of two or more affine transformations. For example, given a translation T' with vector ( t x ′ , t y ′ ) , {\displaystyle (t'_{x},t'_{y}),} a rotation R by an angle θ counter-clockwise , a scaling S with factors ( s x , s y ) {\displaystyle (s_{x},s_{y})} and a translation T of vector ( t x , t y ) , {\displaystyle (t_{x},t_{y}),} the result M of T'RST is: [ 8 ] [ s x cos θ − s y sin θ t x s x cos θ − t y s y sin θ + t x ′ s x sin θ s y cos θ t x s x sin θ + t y s y cos θ + t y ′ 0 0 1 ] {\displaystyle {\begin{bmatrix}s_{x}\cos \theta &-s_{y}\sin \theta &t_{x}s_{x}\cos \theta -t_{y}s_{y}\sin \theta +t'_{x}\\s_{x}\sin \theta &s_{y}\cos \theta &t_{x}s_{x}\sin \theta +t_{y}s_{y}\cos \theta +t'_{y}\\0&0&1\end{bmatrix}}}
When using affine transformations, the homogeneous component of a coordinate vector (normally called w ) will never be altered. One can therefore safely assume that it is always 1 and ignore it. However, this is not true when using perspective projections.
Another type of transformation, of importance in 3D computer graphics , is the perspective projection . Whereas parallel projections are used to project points onto the image plane along parallel lines, the perspective projection projects points onto the image plane along lines that emanate from a single point, called the center of projection. This means that an object has a smaller projection when it is far away from the center of projection and a larger projection when it is closer (see also reciprocal function ).
The simplest perspective projection uses the origin as the center of projection, and the plane at z = 1 {\displaystyle z=1} as the image plane. The functional form of this transformation is then x ′ = x / z {\displaystyle x'=x/z} ; y ′ = y / z {\displaystyle y'=y/z} . We can express this in homogeneous coordinates as: [ x c y c z c w c ] = [ 1 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 ] [ x y z 1 ] = [ x y z z ] {\displaystyle {\begin{bmatrix}x_{c}\\y_{c}\\z_{c}\\w_{c}\end{bmatrix}}={\begin{bmatrix}1&0&0&0\\0&1&0&0\\0&0&1&0\\0&0&1&0\end{bmatrix}}{\begin{bmatrix}x\\y\\z\\1\end{bmatrix}}={\begin{bmatrix}x\\y\\z\\z\end{bmatrix}}}
After carrying out the matrix multiplication , the homogeneous component w c {\displaystyle w_{c}} will be equal to the value of z {\displaystyle z} and the other three will not change. Therefore, to map back into the real plane we must perform the homogeneous divide or perspective divide by dividing each component by w c {\displaystyle w_{c}} : [ x ′ y ′ z ′ 1 ] = 1 w c [ x c y c z c w c ] = [ x / z y / z 1 1 ] {\displaystyle {\begin{bmatrix}x'\\y'\\z'\\1\end{bmatrix}}={\frac {1}{w_{c}}}{\begin{bmatrix}x_{c}\\y_{c}\\z_{c}\\w_{c}\end{bmatrix}}={\begin{bmatrix}x/z\\y/z\\1\\1\end{bmatrix}}}
More complicated perspective projections can be composed by combining this one with rotations, scales, translations, and shears to move the image plane and center of projection wherever they are desired. | https://en.wikipedia.org/wiki/Transformation_matrix |
Transformation optics is a branch of optics which applies metamaterials to produce spatial variations, derived from coordinate transformations , which can direct chosen bandwidths of electromagnetic radiation . This can allow for the construction of new composite artificial devices , which probably could not exist without metamaterials and coordinate transformation. Computing power that became available in the late 1990s enables prescribed quantitative values for the permittivity and permeability , the constitutive parameters , which produce localized spatial variations. The aggregate value of all the constitutive parameters produces an effective value , which yields the intended or desired results.
Hence, complex artificial materials, known as metamaterials , are used to produce transformations in optical space.
The mathematics underpinning transformation optics is similar to the equations that describe how gravity warps space and time, in general relativity . However, instead of space and time , these equations show how light can be directed in a chosen manner, analogous to warping space. For example, one potential application is collecting sunlight with novel solar cells by concentrating the light in one area. Hence, a wide array of conventional devices could be markedly enhanced by applying transformation optics. [ 1 ] [ 2 ] [ 3 ] [ 4 ] [ 5 ]
Transformation optics has its beginnings in two research endeavors, and their conclusions. They were published on May 25, 2006, in the same issue of the peer-reviewed journal Science . The two papers describe tenable theories on bending or distorting light to electromagnetically conceal an object. Both papers notably map the initial configuration of the electromagnetic fields on to a Cartesian mesh. Twisting the Cartesian mesh, in essence, transforms the coordinates of the electromagnetic fields, which in turn conceal a given object. Hence, with these two papers, transformation optics is born. [ 5 ]
Transformation optics subscribes to the capability of bending light , or electromagnetic waves and energy , in any preferred or desired fashion, for a desired application. Maxwell's equations do not vary even though coordinates transform. Instead values of chosen parameters of materials "transform", or alter, during a certain time period. Transformation optics developed from the capability to choose which parameters for a given material, known as a metamaterial. Hence, since Maxwell's equations retain the same form, it is the successive values of permittivity and permeability that change, over time. Permittivity and permeability are in a sense responses to the electric and magnetic fields of a radiated light source respectively, among other descriptions. The precise degree of electric and magnetic response can be controlled in a metamaterial, point by point. Since so much control can be maintained over the responses of the material, this leads to an enhanced and highly flexible gradient-index material. Conventionally predetermined refractive index of ordinary materials become independent spatial gradients, that can be controlled at will. Therefore, transformation optics is a new method for creating novel and unique optical devices . [ 1 ] [ 2 ] [ 6 ] [ 7 ]
Transformation optics can go beyond cloaking (mimic celestial mechanics) because its control of the trajectory and path of light is highly effective. Transformation optics is a field of optical and material engineering and science embracing nanophotonics , plasmonics , and optical metamaterials .
Developments in this field focus on advances in research of transformation optics. Transformation optics is the foundation for exploring a diverse set of theoretical , numerical , and experimental developments, involving the perspectives of the physics and engineering communities . The multi-disciplinary perspectives for inquiry and designing of materials develop understanding of their behaviors, properties, and potential applications for this field.
If a coordinate transformation can be derived or described, a ray of light (in the optical limit) will follow lines of a constant coordinate. There are constraints on the transformations, as listed in the references. In general, however, a particular goal can be accomplished using more than one transformation. The classic cylindrical cloak (first both simulated and demonstrated experimentally) can be created with many transformations. The simplest, and most often used, is a linear coordinate mapping in the radial coordinate. There is significant ongoing research into determining advantages and disadvantages of particular types of transformations, and what attributes are desirable for realistic transformations. One example of this is the broadband carpet cloak: the transformation used was quasi-conformal. Such a transformation can yield a cloak that uses non-extreme values of permittivity and permeability , unlike the classic cylindrical cloak, which required some parameters to vary towards infinity at the inner radius of the cloak.
General coordinate transformations can be derived which compress or expand space, bend or twist space, or even change the topology (e.g. by mimicking a wormhole ). Much current interest involves designing invisibility cloaks , event cloaks , field concentrators, or beam-bending waveguides .
The interactions of light and matter with spacetime , as predicted by general relativity , can be studied using the new type of artificial optical materials that feature extraordinary abilities to bend light (which is actually electromagnetic radiation). This research creates a link between the newly emerging field of artificial optical metamaterials to that of celestial mechanics , thus opening a new possibility to investigate astronomical phenomena in a laboratory setting. The recently introduced, new class, of specially designed optical media can mimic the periodic , quasi-periodic and chaotic motions observed in celestial objects that have been subjected to gravitational fields . [ 8 ] [ 9 ] [ 10 ]
Hence, a new class of metamaterials introduced with the nomenclature “continuous-index photon traps” (CIPTs). CIPTz have applications as optical cavities. As such, CIPTs can control, slow and trap light in a manner similar to celestial phenomena such as black holes , strange attractors , and gravitational lenses . [ 8 ] [ 9 ]
A composite of air and the dielectric Gallium Indium Arsenide Phosphide ( GaInAsP ), operated in the infrared spectral range and featured a high refractive index with low absorptions. [ 8 ] [ 11 ]
This opens an avenue to investigate light phenomena that imitates orbital motion , strange attractors and chaos in a controlled laboratory environment by merging the study of optical metamaterials with classical celestial mechanics. [ 9 ]
If a metamaterial could be produced that did not have high intrinsic loss and a narrow frequency range of operation then it could be employed as a type of media to simulate light motion in a curved spacetime vacuum . Such a proposal is brought forward, and metamaterials become prospective media in this type of study. The classical optical-mechanical analogy renders the possibility for the study of light propagation in homogeneous media as an accurate analogy to the motion of massive bodies, and light, in gravitational potentials. A direct mapping of the celestial phenomena is accomplished by observing photon motion in a controlled laboratory environment. The materials could facilitate periodic, quasi-periodic and chaotic light motion inherent to celestial objects subjected to complex gravitational fields. [ 8 ]
Twisting the optical metamaterial effects its "space" into new coordinates. The light that travels in real space will be curved in the twisted space, as applied in transformational optics. This effect is analogous to starlight when it moves through a closer gravitational field and experiences curved spacetime or a gravitational lensing effect. This analogue between classic electromagnetism and general relativity, shows the potential of optical metamaterials to study relativity phenomena such as the gravitational lens. [ 8 ] [ 11 ]
Observations of such celestial phenomena by astronomers can sometimes take a century of waiting. Chaos in dynamic systems is observed in areas as diverse as molecular motion, population dynamics and optics. In particular, a planet around a star can undergo chaotic motion if a perturbation, such as another large planet, is present. However, owing to the large spatial distances between the celestial bodies, and the long periods involved in the study of their dynamics, the direct observation of chaotic planetary motion has been a challenge. The use of the optical-mechanical analogy may enable such studies to be accomplished in a bench-top laboratory setting at any prescribed time. [ 8 ] [ 11 ]
The study also points toward the design of novel optical cavities and photon traps for application in microscopic devices and lasers systems. [ 8 ]
Matter propagating in a curved spacetime is similar to the electromagnetic wave propagation in a curved space and in an in homogeneous metamaterial, as stated in the previous section. Hence a black hole can possibly be simulated using electromagnetic fields and metamaterials. In July 2009 a metamaterial structure forming an effective black hole was theorized, and numerical simulations showed a highly efficient light absorption . [ 10 ] [ 12 ]
The first experimental demonstration of electromagnetic black hole at microwave frequencies occurred in October 2009. The proposed black hole was composed of non-resonant, and resonant, metamaterial structures, which can absorb electromagnetic waves efficiently coming from all directions due to the local control of electromagnetic fields. It was constructed of a thin cylinder at 21.6 centimeters in diameter comprising 60 concentric rings of metamaterials . This structure created a gradient index of refraction , necessary for bending light in this way. However, it was characterized as being artificially inferior substitute for a real black hole. The characterization was justified by an absorption of only 80% in the microwave range, and that it has no internal source of energy . It is singularly a light absorber. The light absorption capability could be beneficial if it could be adapted to technologies such as solar cells. However, the device is limited to the microwave range. [ 13 ] [ 14 ]
Also in 2009, transformation optics were employed to mimic a black hole of Schwarzschild form . Similar properties of photon sphere were also found numerically for the metamaterial black hole. Several reduced versions of the black hole systems were proposed for easier implementations. [ 15 ]
MIT computer simulations by Fung along with lab experiments are designing a metamaterial with a multilayer sawtooth structure that slows and absorbs light over a wide range of wavelength frequencies, and at a wide range of incident angles, at 95% efficiency. This has an extremely wide window for colors of light.
Engineering optical space with metamaterials could be useful to reproduce an accurate laboratory model of the physical multiverse. " This ‘metamaterial landscape’ may include regions in which one or two spatial dimensions are compactified. " Metamaterial models appear to be useful for non-trivial models such as 3D de Sitter space with one compactified dimension, 2D de Sitter space with two compactified dimensions, 4D de Sitter dS4, and anti-de Sitter AdS4 spaces. [ 10 ] [ 16 ]
Transformation optics is employed to increase capabilities of gradient index lenses.
Optical elements (lenses) perform a variety of functions, ranging from image formation, to light projection or light collection. The performance of these systems is frequently limited by their optical elements, which dominate system weight and cost, and force tradeoffs between system parameters such as focal length, field of view (or acceptance angle), resolution, and range. [ 17 ]
Conventional lenses are ultimately limited by geometry. Available design parameters are a single index of refraction (n) per lens element, variations in the element surface profile, including continuous surfaces (lens curvature) and/or discontinuous surfaces (diffractive optics). Light rays undergo refraction at the surfaces of each element, but travel in straight lines within the lens. Since the design space of conventional optics is limited to a combination of refractive index and surface structure, correcting for aberrations (for example through the use of achromatic or diffractive optics) leads to large, heavy, complex designs, and/or greater losses, lower image quality, and manufacturing difficulties. [ 17 ]
Gradient index lenses (or GRIN lenses) as the name implies, are optical elements whose index of refraction varies within the lens. Control of the internal refraction allows the steering of light in curved trajectories through the lens. GRIN optics thus increase the design space to include the entire volume of the optical elements, providing the potential for dramatically reduced size, weight, element count, and assembly cost, as well as opening up new space to trade between performance parameters. However, past efforts to make large aperture GRIN lenses have had limited success due to restricted refractive index change, poor control over index profiles, and/or severe limitations in lens diameter. [ 17 ]
Recent steps forward in material science have led to at least one method for developing large (>10 mm) GRIN lenses with 3-dimensional gradient indexes. There is a possibility of adding expanded deformation capabilities to the GRIN lenses. This translates into controlled expansion, contraction, and shear (for variable focus lenses or asymmetric optical variations). These capabilities have been demonstrated. Additionally, recent advances in transformation optics and computational power provide a unique opportunity to design, assemble and fabricate elements in order to advance the utility and availability of GRIN lenses across a wide range of optics-dependent systems, defined by needs. A possible future capability could be to further advance lens design methods and tools, which are coupled to enlarged fabrication processes. [ 17 ]
Transformation optics has potential applications for the battlefield. The versatile properties of metamaterials can be tailored to fit almost any practical need, and transformation optics shows that space for light can be bent in almost any arbitrary way. This is perceived as providing new capabilities to soldiers in the battlefield. For battlefield scenarios benefits from metamaterials have both short term and long-term impacts. [ 18 ]
For example, determining whether a cloud in the distance is harmless or an aerosol of enemy chemical or biological warfare is very difficult to assess quickly. However, with the new metamaterials being developed, the ability exists to see things smaller than the wavelength of light – something which has yet to be achieved in the far field . Using metamaterials in the creation of a new lens may allow soldiers to be able to see pathogens and viruses that are impossible to detect with any visual device. [ 18 ]
Harnessing subwavelength capabilities then allow for other advancements which appear to be beyond the battlefield. All kinds of materials could be manufactured with nano-manufacturing, which could go into electronic and optical devices from night vision goggles to distance sensors to other kinds of sensors. Longer-term views include the possibility for cloaking materials, which would provide "invisibility" by redirecting light around a cylindrical shape. [ 18 ] | https://en.wikipedia.org/wiki/Transformation_optics |
Transformed cladistics , also known as pattern cladistics is an epistemological approach to the cladistic method of phylogenetic inference and classification that makes no a priori assumptions about common ancestry . It was advocated by Norman Platnick , Colin Patterson , Ronald Brady and others in the 1980s, but has few modern proponents. The book, Foundations of Systematics and Biogeography [ 1 ] by David Williams and Malte Ebach provides a thoughtful history of the origins of this point of view.
The traditional approach to cladistics, which traces back to Willi Hennig , [ 2 ] [ 3 ] groups together organisms based on whether or not they share derived characters or character states that are assumed to be descended from a common ancestor. Transformed cladists maintain that the assumption of common descent is uninformative and/or potentially misleading, and that therefore cladistic methods should be free from evolutionary process assumptions, and based only on parsimonious interpretation of empirical data:
"If classifications (that is, our knowledge of patterns) are ever to provide an adequate test of theories of evolutionary processes their construction must be independent of any particular theory of process." (Platnick, 1979) [ 4 ]
In other words, pattern cladists argue that the fewer evolutionary assumptions a classification presupposes, the fewer errors creep in, and greater transparency results. They draw a distinction between patterns, which are observed, and processes, which may be inferred from patterns, but which should not be presupposed. Before the emergence of cladistics as a school, Joseph Henry Woodger criticized phylogenetic systematics on the grounds that homology by way of common ancestry is "putting the cart before the horse, because descent from a common ancestor is something assumed, not observed. It belongs to theory, whereas morphological correspondence is observed.". [ 5 ] Colin Patterson later wrote similarly:
"We must remember the distinction between the cart--the explanation--and the horse--the data. And where models are introduced in phylogenetic reconstruction, we should prefer models dictated by features of the data to models derived from explanatory theories." [ 6 ]
Pattern cladists, like traditional cladists, think that classifications should be isomorphic to cladograms, recognizing groups based on nested patterns of synapomorphies , but they argue that the discovery of characters is not dependent on apriori considerations about common ancestry:
"[T]o state a cladogram is a synapomorphy scheme invites the rejoinder that a cladogram must, therefore be a phyletic concept. Not so, for by ‘synapomorphy’ we mean ‘defining character’ of an inclusive taxon." [ 7 ]
Nelson & Platnick (1981) also noted that: " all of Hennig’s groups correspond by definition to patterns of synapomorphy. Indeed, Hennig’s trees are frequently called synapomorphy schemes. The concept of ‘patterns within patterns’ seems, therefore, an empirical generalization.” Pattern cladists hence regard synapomorphies to be patterns free of processes.
A frequent (but false) accusation against pattern cladistics is that its proponents claim that systematics should be "theory free." At some point in the 1960s and '70s pheneticists may have believed that, but pattern cladists are not pheneticists. Obviously, rejecting a priori evolutionary process theories is not the same thing as categorically rejecting "theory" in toto. Furthermore, pattern cladists do not reject post hoc evolutionary explanations for cladograms, they simply think that the evidence is independent of the explanation. [ 8 ] Nevertheless, some philosophers with a background conciliatory towards evolutionary taxonomy continue to offer criticisms in this vein:
"Pattern cladistics has remained on the fringe because of, first, its implausible assumption that there can be pure observation untainted by theory; and second, its rejection of the evolution assumption. Few systematists now think that a classification not based on evolutionary branching and history has any real signification or justification. The developing consensus is that Darwin was right – a natural classification must be genealogical." [ 9 ]
Of course, the distinction between the phenomenon and its explanation was clear to Darwin: "the grand fact in natural history of the subordination of group under group, which from its familiarity, does not always sufficiently strike us, is in my judgment fully explained." [ 10 ] But, "“we have no written pedigrees; we have to make out community of descent by resemblances of any kind." [ 11 ] For pattern cladists, it is not just "any kind" of resemblance, but synapomorphy, that reveals community of descent.
Brady [ 12 ] [ 13 ] introduced to systematics the terms explanandum for empirical patterns (the phenomenon to be explained) and explanans for process theory (the explanation), writing: "by making our explanation into the definition of the condition [data] to be explained, we express not scientific hypothesis but belief". In the above quote, Darwin's "fact" is the explanandum ; his theory of descent with modification is the explanans .
In this view, whatever the characters imply as the preferred hypothesis of relationships becomes, de facto, "genealogical" when we explain it as a result of evolution. [ 14 ]
As noted, transformed cladistics does not deny common ancestry , rather it argues a logical precedence: theories regarding processes should only be formulated after patterns are discovered. Creationists have distorted this to argue that there are pattern cladists who are skeptical about whether evolution occurs.
In November, 1981, Patterson delivered a seminar to the Systematics Discussion Group in the American Museum of Natural History. [ 15 ] In the talk, Patterson asked provocatively: "Can you tell me anything about evolution, any one thing that is true?", and remarked:
"As I understand it, cladistics is theoretically neutral so far as evolution is concerned. It has nothing to say about evolution. You don’t need to know about evolution, or believe in it, to do cladistic analysis. All that cladistics demands is that groups have characters."
A creationist in the audience taped segments of Patterson's talk to imply he was "agnostic" on the subject of evolution. [ 16 ] To his dismay, Patterson soon found his name quoted in creationist publications:
"I was too naive and foolish to guess what might happen: the talk was taped by a creationist who passed the tape to Luther Sunderland [...] Since, in my view, the tape was obtained unethically, I asked Sunderland to stop circulating the transcript, but of course to no effect. There is not much point in my going through the article point by point. I was putting a case for discussion, as I thought off the record, and was speaking only about systematics, a specialized field. I do not support the creationist movement in any way, and in particular I am opposed to their efforts to modify school curricula. In short the article does not fairly represent my views. But even if it did, so what? The issue should be resolved by rational discussion, and not by quoting 'authorities,' which seems to be the creationists' principal mode of argument." (Letter from Colin Patterson to Steven W. Binkley, June 17, 1982)
"Unfortunately, and unknown to me, there was a creationist in my audience with a hidden tape recorder. A transcript of my talk was produced and circulated among creationists, and the talk has since been widely, and often inaccurately, quoted in creationist literature." (Patterson, 1994)
(Note that a transcript of Patterson's talk has been published in the Linnean 18(2), and may be downloaded from the Linnean Society).
"Because creationists lack scientific research to support such theories as a young earth ... a world-wide flood ... or separate ancestry for humans and apes, their common tactic is to attack evolution by hunting out debate or dissent among evolutionary biologists. ... I learned that one should think carefully about candour in argument (in publications, lectures, or correspondence) in case one was furnishing creationist campaigners with ammunition in the form of 'quotable quotes', often taken out of context." [ 17 ]
A notable contemporary pattern cladist is Andrew V. Z. Brower. [ 18 ] [ 19 ] [ 20 ] | https://en.wikipedia.org/wiki/Transformed_cladistics |
In electrical engineering , a transformer is a passive component that transfers electrical energy from one electrical circuit to another circuit, or multiple circuits . A varying current in any coil of the transformer produces a varying magnetic flux in the transformer's core, which induces a varying electromotive force (EMF) across any other coils wound around the same core. Electrical energy can be transferred between separate coils without a metallic (conductive) connection between the two circuits. Faraday's law of induction , discovered in 1831, describes the induced voltage effect in any coil due to a changing magnetic flux encircled by the coil.
Transformers are used to change AC voltage levels, such transformers being termed step-up or step-down type to increase or decrease voltage level, respectively. Transformers can also be used to provide galvanic isolation between circuits as well as to couple stages of signal-processing circuits. Since the invention of the first constant-potential transformer in 1885, transformers have become essential for the transmission , distribution , and utilization of alternating current electric power. [ 2 ] A wide range of transformer designs is encountered in electronic and electric power applications. Transformers range in size from RF transformers less than a cubic centimeter in volume, to units weighing hundreds of tons used to interconnect the power grid .
Ideal transformer equations
By Faraday's law of induction :
where V {\displaystyle V} is the instantaneous voltage , N {\displaystyle N} is the number of turns in a winding, dΦ/dt is the derivative of the magnetic flux Φ through one turn of the winding over time ( t ), and subscripts P and S denotes primary and secondary.
Combining the ratio of eq. 1 & eq. 2:
where for a step-up transformer a < 1 and for a step-down transformer a > 1. [ 4 ]
By the law of conservation of energy , apparent , real and reactive power are each conserved in the input and output:
where S {\displaystyle S} is apparent power and I {\displaystyle I} is current .
Combining Eq. 3 & Eq. 4 with this endnote [ b ] [ 5 ] gives the ideal transformer identity :
where L P {\displaystyle L_{\text{P}}} is the primary winding self-inductance and L S {\displaystyle L_{\text{S}}} is the secondary winding self-inductance.
By Ohm's law and ideal transformer identity:
where Z L {\displaystyle Z_{\text{L}}} is the load impedance of the secondary circuit & Z L ′ {\displaystyle Z'_{\text{L}}} is the apparent load or driving point impedance of the primary circuit, the superscript ′ {\displaystyle '} denoting referred to the primary.
An ideal transformer is linear , lossless and perfectly coupled . Perfect coupling implies infinitely high core magnetic permeability and winding inductance and zero net magnetomotive force (i.e. i p n p − i s n s = 0). [ 4 ] [ c ]
A varying current in the transformer's primary winding creates a varying magnetic flux in the transformer core, which is also encircled by the secondary winding. This varying flux at the secondary winding induces a varying electromotive force or voltage in the secondary winding. This electromagnetic induction phenomenon is the basis of transformer action and, in accordance with Lenz's law , the secondary current so produced creates a flux equal and opposite to that produced by the primary winding.
The windings are wound around a core of infinitely high magnetic permeability so that all of the magnetic flux passes through both the primary and secondary windings. With a voltage source connected to the primary winding and a load connected to the secondary winding, the transformer currents flow in the indicated directions and the core magnetomotive force cancels to zero.
According to Faraday's law , since the same magnetic flux passes through both the primary and secondary windings in an ideal transformer, a voltage is induced in each winding proportional to its number of turns. The transformer winding voltage ratio is equal to the winding turns ratio. [ 7 ]
An ideal transformer is a reasonable approximation for a typical commercial transformer, with voltage ratio and winding turns ratio both being inversely proportional to the corresponding current ratio.
The load impedance referred to the primary circuit is equal to the turns ratio squared times the secondary circuit load impedance. [ 8 ]
The ideal transformer model neglects many basic linear aspects of real transformers, including unavoidable losses and inefficiencies. [ 9 ]
(a) Core losses, collectively called magnetizing current losses, consisting of [ 10 ]
(b) Unlike the ideal model, the windings in a real transformer have non-zero resistances and inductances associated with:
(c) similar to an inductor , parasitic capacitance and self-resonance phenomenon due to the electric field distribution. Three kinds of parasitic capacitance are usually considered and the closed-loop equations are provided [ 11 ]
Inclusion of capacitance into the transformer model is complicated, and is rarely attempted; the 'real' transformer model's equivalent circuit shown below does not include parasitic capacitance. However, the capacitance effect can be measured by comparing open-circuit inductance, i.e. the inductance of a primary winding when the secondary circuit is open, to a short-circuit inductance when the secondary winding is shorted.
The ideal transformer model assumes that all flux generated by the primary winding links all the turns of every winding, including itself. In practice, some flux traverses paths that take it outside the windings. [ 12 ] Such flux is termed leakage flux , and results in leakage inductance in series with the mutually coupled transformer windings. [ 13 ] Leakage flux results in energy being alternately stored in and discharged from the magnetic fields with each cycle of the power supply. It is not directly a power loss, but results in inferior voltage regulation , causing the secondary voltage not to be directly proportional to the primary voltage, particularly under heavy load. [ 12 ] Transformers are therefore normally designed to have very low leakage inductance.
In some applications increased leakage is desired, and long magnetic paths, air gaps, or magnetic bypass shunts may deliberately be introduced in a transformer design to limit the short-circuit current it will supply. [ 13 ] Leaky transformers may be used to supply loads that exhibit negative resistance , such as electric arcs , mercury- and sodium- vapor lamps and neon signs or for safely handling loads that become periodically short-circuited such as electric arc welders . [ 10 ] : 485
Air gaps are also used to keep a transformer from saturating, especially audio-frequency transformers in circuits that have a DC component flowing in the windings. [ 14 ] A saturable reactor exploits saturation of the core to control alternating current.
Knowledge of leakage inductance is also useful when transformers are operated in parallel. It can be shown that if the percent impedance [ e ] and associated winding leakage reactance-to-resistance ( X / R ) ratio of two transformers were
the same, the transformers would share the load power in proportion to their respective ratings. However, the impedance tolerances of commercial transformers are significant. Also, the impedance and X/R ratio of different capacity transformers tends to vary. [ 16 ]
Referring to the diagram, a practical transformer's physical behavior may be represented by an equivalent circuit model, which can incorporate an ideal transformer. [ 17 ]
Winding joule losses and leakage reactance are represented by the following series loop impedances of the model:
In normal course of circuit equivalence transformation, R S and X S are in practice usually referred to the primary side by multiplying these impedances by the turns ratio squared, ( N P / N S ) 2 = a 2 .
Core loss and reactance is represented by the following shunt leg impedances of the model:
R C and X M are collectively termed the magnetizing branch of the model.
Core losses are caused mostly by hysteresis and eddy current effects in the core and are proportional to the square of the core flux for operation at a given frequency. [ 10 ] : 142–143 The finite permeability core requires a magnetizing current I M to maintain mutual flux in the core. Magnetizing current is in phase with the flux, the relationship between the two being non-linear due to saturation effects. However, all impedances of the equivalent circuit shown are by definition linear and such non-linearity effects are not typically reflected in transformer equivalent circuits. [ 10 ] : 142 With sinusoidal supply, core flux lags the induced EMF by 90°. With open-circuited secondary winding, magnetizing branch current I 0 equals transformer no-load current. [ 17 ]
The resulting model, though sometimes termed 'exact' equivalent circuit based on linearity assumptions, retains a number of approximations. [ 17 ] Analysis may be simplified by assuming that magnetizing branch impedance is relatively high and relocating the branch to the left of the primary impedances. This introduces error but allows combination of primary and referred secondary resistances and reactance by simple summation as two series impedances.
Transformer equivalent circuit impedance and transformer ratio parameters can be derived from the following tests: open-circuit test , short-circuit test , winding resistance test, and transformer ratio test.
If the flux in the core is purely sinusoidal , the relationship for either winding between its rms voltage E rms of the winding, and the supply frequency f , number of turns N , core cross-sectional area A in m 2 and peak magnetic flux density B peak in Wb/m 2 or T (tesla) is given by the universal EMF equation: [ 10 ]
A dot convention is often used in transformer circuit diagrams, nameplates or terminal markings to define the relative polarity of transformer windings. Positively increasing instantaneous current entering the primary winding's 'dot' end induces positive polarity voltage exiting the secondary winding's 'dot' end. Three-phase transformers used in electric power systems will have a nameplate that indicate the phase relationships between their terminals. This may be in the form of a phasor diagram, or using an alpha-numeric code to show the type of internal connection (wye or delta) for each winding.
The EMF of a transformer at a given flux increases with frequency. [ 10 ] By operating at higher frequencies, transformers can be physically more compact because a given core is able to transfer more power without reaching saturation and fewer turns are needed to achieve the same impedance. However, properties such as core loss and conductor skin effect also increase with frequency. Aircraft and military equipment employ 400 Hz power supplies which reduce core and winding weight. [ 18 ] Conversely, frequencies used for some railway electrification systems were much lower (e.g. 16.7 Hz and 25 Hz) than normal utility frequencies (50–60 Hz) for historical reasons concerned mainly with the limitations of early electric traction motors . Consequently, the transformers used to step-down the high overhead line voltages were much larger and heavier for the same power rating than those required for the higher frequencies.
Operation of a transformer at its designed voltage but at a higher frequency than intended will lead to reduced magnetizing current. At a lower frequency, the magnetizing current will increase. Operation of a large transformer at other than its design frequency may require assessment of voltages, losses, and cooling to establish if safe operation is practical. Transformers may require protective relays to protect the transformer from overvoltage at higher than rated frequency.
One example is in traction transformers used for electric multiple unit and high-speed train service operating across regions with different electrical standards. The converter equipment and traction transformers have to accommodate different input frequencies and voltage (ranging from as high as 50 Hz down to 16.7 Hz and rated up to 25 kV).
At much higher frequencies the transformer core size required drops dramatically: a physically small transformer can handle power levels that would require a massive iron core at mains frequency. The development of switching power semiconductor devices made switch-mode power supplies viable, to generate a high frequency, then change the voltage level with a small transformer.
Transformers for higher frequency applications such as SMPS typically use core materials with much lower hysteresis and eddy-current losses than those for 50/60 Hz. Primary examples are iron-powder and ferrite cores. The lower frequency-dependant losses of these cores often is at the expense of flux density at saturation. For instance, ferrite saturation occurs at a substantially lower flux density than laminated iron.
Large power transformers are vulnerable to insulation failure due to transient voltages with high-frequency components, such as caused in switching or by lightning.
Transformer energy losses are dominated by winding and core losses. Transformers' efficiency tends to improve with increasing transformer capacity. [ 19 ] The efficiency of typical distribution transformers is between about 98 and 99 percent. [ 19 ] [ 20 ]
As transformer losses vary with load, it is often useful to tabulate no-load loss , full-load loss, half-load loss, and so on. Hysteresis and eddy current losses are constant at all load levels and dominate at no load, while winding loss increases as load increases. The no-load loss can be significant, so that even an idle transformer constitutes a drain on the electrical supply. Designing energy efficient transformers for lower loss requires a larger core, good-quality silicon steel , or even amorphous steel for the core and thicker wire, increasing initial cost. The choice of construction represents a trade-off between initial cost and operating cost. [ 21 ]
Transformer losses arise from:
Closed-core transformers are constructed in 'core form' or 'shell form'. When windings surround the core, the transformer is core form; when windings are surrounded by the core, the transformer is shell form. [ 25 ] Shell form design may be more prevalent than core form design for distribution transformer applications due to the relative ease in stacking the core around winding coils. [ 25 ] Core form design tends to, as a general rule, be more economical, and therefore more prevalent, than shell form design for high voltage power transformer applications at the lower end of their voltage and power rating ranges (less than or equal to, nominally, 230 kV or 75 MVA). At higher voltage and power ratings, shell form transformers tend to be more prevalent. [ 25 ] [ 26 ] [ 27 ] Shell form design tends to be preferred for extra-high voltage and higher MVA applications because, though more labor-intensive to manufacture, shell form transformers are characterized as having inherently better kVA-to-weight ratio, better short-circuit strength characteristics and higher immunity to transit damage. [ 27 ]
Transformers for use at power or audio frequencies typically have cores made of high permeability silicon steel . [ 28 ] The steel has a permeability many times that of free space and the core thus serves to greatly reduce the magnetizing current and confine the flux to a path which closely couples the windings. [ 29 ] Early transformer developers soon realized that cores constructed from solid iron resulted in prohibitive eddy current losses, and their designs mitigated this effect with cores consisting of bundles of insulated iron wires. [ 30 ] Later designs constructed the core by stacking layers of thin steel laminations, a principle that has remained in use. Each lamination is insulated from its neighbors by a thin non-conducting layer of insulation. [ 31 ] The transformer universal EMF equation can be used to calculate the core cross-sectional area for a preferred level of magnetic flux. [ 10 ]
The effect of laminations is to confine eddy currents to highly elliptical paths that enclose little flux, and so reduce their magnitude. Thinner laminations reduce losses, [ 28 ] but are more laborious and expensive to construct. [ 32 ] Thin laminations are generally used on high-frequency transformers, with some of very thin steel laminations able to operate up to 10 kHz.
One common design of laminated core is made from interleaved stacks of E-shaped steel sheets capped with I-shaped pieces, leading to its name of E-I transformer . [ 32 ] Such a design tends to exhibit more losses, but is very economical to manufacture. The cut-core or C-core type is made by winding a steel strip around a rectangular form and then bonding the layers together. It is then cut in two, forming two C shapes, and the core assembled by binding the two C halves together with a steel strap. [ 32 ] They have the advantage that the flux is always oriented parallel to the metal grains, reducing reluctance.
A steel core's remanence means that it retains a static magnetic field when power is removed. When power is then reapplied, the residual field will cause a high inrush current until the effect of the remaining magnetism is reduced, usually after a few cycles of the applied AC waveform. [ 33 ] Overcurrent protection devices such as fuses must be selected to allow this harmless inrush to pass.
On transformers connected to long, overhead power transmission lines, induced currents due to geomagnetic disturbances during solar storms can cause saturation of the core and operation of transformer protection devices. [ 34 ]
Distribution transformers can achieve low no-load losses by using cores made with low-loss high-permeability silicon steel or amorphous (non-crystalline) metal alloy . The higher initial cost of the core material is offset over the life of the transformer by its lower losses at light load. [ 35 ]
Powdered iron cores are used in circuits such as switch-mode power supplies that operate above mains frequencies and up to a few tens of kilohertz. These materials combine high magnetic permeability with high bulk electrical resistivity . For frequencies extending beyond the VHF band , cores made from non-conductive magnetic ceramic materials called ferrites are common. [ 32 ] Some radio-frequency transformers also have movable cores (sometimes called 'slugs') which allow adjustment of the coupling coefficient (and bandwidth ) of tuned radio-frequency circuits.
Toroidal transformers are built around a ring-shaped core, which, depending on operating frequency, is made from a long strip of silicon steel or permalloy wound into a coil, powdered iron, or ferrite . [ 36 ] A strip construction ensures that the grain boundaries are optimally aligned, improving the transformer's efficiency by reducing the core's reluctance . The closed ring shape eliminates air gaps inherent in the construction of an E-I core. [ 10 ] : 485 The cross-section of the ring is usually square or rectangular, but more expensive cores with circular cross-sections are also available. The primary and secondary coils are often wound concentrically to cover the entire surface of the core. This minimizes the length of wire needed and provides screening to minimize the core's magnetic field from generating electromagnetic interference .
Toroidal transformers are more efficient than the cheaper laminated E-I types for a similar power level. Other advantages compared to E-I types, include smaller size (about half), lower weight (about half), less mechanical hum (making them superior in audio amplifiers), lower exterior magnetic field (about one tenth), low off-load losses (making them more efficient in standby circuits), single-bolt mounting, and greater choice of shapes. The main disadvantages are higher cost and limited power capacity (see Classification parameters below). Because of the lack of a residual gap in the magnetic path, toroidal transformers also tend to exhibit higher inrush current, compared to laminated E-I types.
Ferrite toroidal cores are used at higher frequencies, typically between a few tens of kilohertz to hundreds of megahertz, to reduce losses, physical size, and weight of inductive components. A drawback of toroidal transformer construction is the higher labor cost of winding. This is because it is necessary to pass the entire length of a coil winding through the core aperture each time a single turn is added to the coil. As a consequence, toroidal transformers rated more than a few kVA are uncommon. Relatively few toroids are offered with power ratings above 10 kVA, and practically none above 25 kVA. Small distribution transformers may achieve some of the benefits of a toroidal core by splitting it and forcing it open, then inserting a bobbin containing primary and secondary windings. [ 37 ]
A transformer can be produced by placing the windings near each other, an arrangement termed an "air-core" transformer. An air-core transformer eliminates loss due to hysteresis in the core material. [ 13 ] The magnetizing inductance is drastically reduced by the lack of a magnetic core, resulting in large magnetizing currents and losses if used at low frequencies. Air-core transformers are unsuitable for use in power distribution, [ 13 ] but are frequently employed in radio-frequency applications. [ 38 ] Air cores are also used for resonant transformers such as tesla coils , where they can achieve reasonably low loss despite the low magnetizing inductance.
The electrical conductor used for the windings depends upon the application, but in all cases the individual turns must be electrically insulated from each other to ensure that the current travels throughout every turn. For small transformers, in which currents are low and the potential difference between adjacent turns is small, the coils are often wound from enameled magnet wire . Larger power transformers may be wound with copper rectangular strip conductors insulated by oil-impregnated paper and blocks of pressboard . [ 39 ]
High-frequency transformers operating in the tens to hundreds of kilohertz often have windings made of braided Litz wire to minimize the skin-effect and proximity effect losses. [ 40 ] Large power transformers use multiple-stranded conductors as well, since even at low power frequencies non-uniform distribution of current would otherwise exist in high-current windings. [ 39 ] Each strand is individually insulated, and the strands are arranged so that at certain points in the winding, or throughout the whole winding, each portion occupies different relative positions in the complete conductor. The transposition equalizes the current flowing in each strand of the conductor, and reduces eddy current losses in the winding itself. The stranded conductor is also more flexible than a solid conductor of similar size, aiding manufacture. [ 39 ]
The windings of signal transformers minimize leakage inductance and stray capacitance to improve high-frequency response. Coils are split into sections, and those sections interleaved between the sections of the other winding.
Power-frequency transformers may have taps at intermediate points on the winding, usually on the higher voltage winding side, for voltage adjustment. Taps may be manually reconnected, or a manual or automatic switch may be provided for changing taps. Automatic on-load tap changers are used in electric power transmission or distribution, on equipment such as arc furnace transformers, or for automatic voltage regulators for sensitive loads. Audio-frequency transformers, used for the distribution of audio to public address loudspeakers, have taps to allow adjustment of impedance to each speaker. A center-tapped transformer is often used in the output stage of an audio power amplifier in a push-pull circuit . Modulation transformers in AM transmitters are very similar.
It is a rule of thumb that the life expectancy of electrical insulation is halved for about every 7 °C to 10 °C increase in operating temperature (an instance of the application of the Arrhenius equation ). [ 41 ]
Small dry-type and liquid-immersed transformers are often self-cooled by natural convection and radiation heat dissipation. As power ratings increase, transformers are often cooled by forced-air cooling, forced-oil cooling, water-cooling, or combinations of these. [ 42 ] Large transformers are filled with transformer oil that both cools and insulates the windings. [ 43 ] Transformer oil is often a highly refined mineral oil that cools the windings and insulation by circulating within the transformer tank. The mineral oil and paper insulation system has been extensively studied and used for more than 100 years. It is estimated that 50% of power transformers will survive 50 years of use, that the average age of failure of power transformers is about 10 to 15 years, and that about 30% of power transformer failures are due to insulation and overloading failures. [ 44 ] [ 45 ] Prolonged operation at elevated temperature degrades insulating properties of winding insulation and dielectric coolant, which not only shortens transformer life but can ultimately lead to catastrophic transformer failure. [ 41 ] With a great body of empirical study as a guide, transformer oil testing including dissolved gas analysis provides valuable maintenance information.
Building regulations in many jurisdictions require indoor liquid-filled transformers to either use dielectric fluids that are less flammable than oil, or be installed in fire-resistant rooms. [ 19 ] Air-cooled dry transformers can be more economical where they eliminate the cost of a fire-resistant transformer room.
The tank of liquid-filled transformers often has radiators through which the liquid coolant circulates by natural convection or fins. Some large transformers employ electric fans for forced-air cooling, pumps for forced-liquid cooling, or have heat exchangers for water-cooling. [ 43 ] An oil-immersed transformer may be equipped with a Buchholz relay , which, depending on severity of gas accumulation due to internal arcing, is used to either trigger an alarm or de-energize the transformer. [ 33 ] Oil-immersed transformer installations usually include fire protection measures such as walls, oil containment, and fire-suppression sprinkler systems.
Polychlorinated biphenyls (PCBs) have properties that once favored their use as a dielectric coolant , though concerns over their environmental persistence led to a widespread ban on their use. [ 46 ] Today, non-toxic, stable silicone -based oils, or fluorinated hydrocarbons may be used where the expense of a fire-resistant liquid offsets additional building cost for a transformer vault. [ 19 ] [ 47 ] However, the long life span of transformers can mean that the potential for exposure can be high long after banning. [ 48 ]
Some transformers are gas-insulated. Their windings are enclosed in sealed, pressurized tanks and often cooled by nitrogen or sulfur hexafluoride gas. [ 47 ]
Experimental power transformers in the 500–1,000 kVA range have been built with liquid nitrogen or helium cooled superconducting windings, which eliminates winding losses without affecting core losses. [ 49 ] [ 50 ]
Insulation must be provided between the individual turns of the windings, between the windings, between windings and core, and at the terminals of the winding.
Inter-turn insulation of small transformers may be a layer of insulating varnish on the wire. Layer of paper or polymer films may be inserted between layers of windings, and between primary and secondary windings. A transformer may be coated or dipped in a polymer resin to improve the strength of windings and protect them from moisture or corrosion. The resin may be impregnated into the winding insulation using combinations of vacuum and pressure during the coating process, eliminating all air voids in the winding. In the limit, the entire coil may be placed in a mold, and resin cast around it as a solid block, encapsulating the windings. [ 51 ]
Large oil-filled power transformers use windings wrapped with insulating paper, which is impregnated with oil during assembly of the transformer. Oil-filled transformers use highly refined mineral oil to insulate and cool the windings and core.
Construction of oil-filled transformers requires that the insulation covering the windings be thoroughly dried of residual moisture before the oil is introduced. Drying may be done by circulating hot air around the core, by circulating externally heated transformer oil, or by vapor-phase drying (VPD) where an evaporated solvent transfers heat by condensation on the coil and core. For small transformers, resistance heating by injection of current into the windings is used.
Larger transformers are provided with high-voltage insulated bushings made of polymers or porcelain. A large bushing can be a complex structure since it must provide careful control of the electric field gradient without letting the transformer leak oil. [ 52 ]
Transformers can be classified in many ways, such as the following:
Various specific electrical application designs require a variety of transformer types . Although they all share the basic characteristic transformer principles, they are customized in construction or electrical properties for certain installation requirements or circuit conditions.
In electric power transmission , transformers allow transmission of electric power at high voltages, which reduces the loss due to heating of the wires. This allows generating plants to be located economically at a distance from electrical consumers. [ 53 ] All but a tiny fraction of the world's electrical power has passed through a series of transformers by the time it reaches the consumer. [ 23 ]
In many electronic devices, a transformer is used to convert voltage from the distribution wiring to convenient values for the circuit requirements, either directly at the power line frequency or through a switch mode power supply .
Signal and audio transformers are used to couple stages of amplifiers and to match devices such as microphones and record players to the input of amplifiers. Audio transformers allowed telephone circuits to carry on a two-way conversation over a single pair of wires. A balun transformer converts a signal that is referenced to ground to a signal that has balanced voltages to ground , such as between external cables and internal circuits. Isolation transformers prevent leakage of current into the secondary circuit and are used in medical equipment and at construction sites. Resonant transformers are used for coupling between stages of radio receivers, or in high-voltage Tesla coils.
Electromagnetic induction , the principle of the operation of the transformer, was discovered independently by Michael Faraday in 1831 and Joseph Henry in 1832. [ 55 ] [ 56 ] [ 57 ] [ 58 ] Only Faraday furthered his experiments to the point of working out the equation describing the relationship between EMF and magnetic flux now known as Faraday's law of induction :
where | E | {\displaystyle |{\mathcal {E}}|} is the magnitude of the EMF in volts and Φ B is the magnetic flux through the circuit in webers . [ 59 ]
Faraday performed early experiments on induction between coils of wire, including winding a pair of coils around an iron ring, thus creating the first toroidal closed-core transformer. [ 58 ] [ 60 ] However he only applied individual pulses of current to his transformer, and never discovered the relation between the turns ratio and EMF in the windings.
The first type of transformer to see wide use was the induction coil , invented by Irish-Catholic Rev. Nicholas Callan of Maynooth College , Ireland in 1836. [ 58 ] He was one of the first researchers to realize the more turns the secondary winding has in relation to the primary winding, the larger the induced secondary EMF will be. Induction coils evolved from scientists' and inventors' efforts to get higher voltages from batteries. Since batteries produce direct current (DC) rather than AC, induction coils relied upon vibrating electrical contacts that regularly interrupted the current in the primary to create the flux changes necessary for induction. Between the 1830s and the 1870s, efforts to build better induction coils, mostly by trial and error, slowly revealed the basic principles of transformers.
By the 1870s, efficient generators producing alternating current (AC) were available, and it was found AC could power an induction coil directly, without an interrupter .
In 1876, Russian engineer Pavel Yablochkov invented a lighting system based on a set of induction coils where the primary windings were connected to a source of AC. The secondary windings could be connected to several 'electric candles' (arc lamps) of his own design. The coils Yablochkov employed functioned essentially as transformers. [ 61 ]
In 1878, the Ganz factory , Budapest, Hungary, began producing equipment for electric lighting and, by 1883, had installed over fifty systems in Austria-Hungary. Their AC systems used arc and incandescent lamps, generators, and other equipment. [ 58 ] [ 62 ]
In 1882, Lucien Gaulard and John Dixon Gibbs first exhibited a device with an initially widely criticized laminated plate open iron core called a 'secondary generator' in London, then sold the idea to the Westinghouse company in the United States in 1886. [ 30 ] They also exhibited the invention in Turin, Italy in 1884, where it was highly successful and adopted for an electric lighting system. [ 63 ] Their open-core device used a fixed 1:1 ratio to supply a series circuit for the utilization load (lamps). However, the voltage of their system was controlled by moving the iron core in or out. [ 64 ]
Induction coils with open magnetic circuits are inefficient at transferring power to loads . Until about 1880, the paradigm for AC power transmission from a high voltage supply to a low voltage load was a series circuit. Open-core transformers with a ratio near 1:1 were connected with their primaries in series to allow use of a high voltage for transmission while presenting a low voltage to the lamps. The inherent flaw in this method was that turning off a single lamp (or other electric device) affected the voltage supplied to all others on the same circuit. Many adjustable transformer designs were introduced to compensate for this problematic characteristic of the series circuit, including those employing methods of adjusting the core or bypassing the magnetic flux around part of a coil. [ 63 ] Efficient, practical transformer designs did not appear until the 1880s, but within a decade, the transformer would be instrumental in the war of the currents , and in seeing AC distribution systems triumph over their DC counterparts, a position in which they have remained dominant ever since. [ 65 ]
In the autumn of 1884, Károly Zipernowsky , Ottó Bláthy and Miksa Déri (ZBD), three Hungarian engineers associated with the Ganz Works , had determined that open-core devices were impracticable, as they were incapable of reliably regulating voltage. [ 62 ] The Ganz factory had also in the autumn of 1884 made delivery of the world's first five high-efficiency AC transformers, the first of these units having been shipped on September 16, 1884. [ 66 ] This first unit had been manufactured to the following specifications: 1,400 W, 40 Hz, 120:72 V, 11.6:19.4 A, ratio 1.67:1, one-phase, shell form. [ 66 ] In their joint 1885 patent applications for novel transformers (later called ZBD transformers), they described two designs with closed magnetic circuits where copper windings were either wound around an iron wire ring core or surrounded by an iron wire core. [ 63 ] The two designs were the first application of the two basic transformer constructions in common use to this day, termed "core form" or "shell form" . [ 67 ]
In both designs, the magnetic flux linking the primary and secondary windings traveled almost entirely within the confines of the iron core, with no intentional path through air (see Toroidal cores below). The new transformers were 3.4 times more efficient than the open-core bipolar devices of Gaulard and Gibbs. [ 68 ] The ZBD patents included two other major interrelated innovations: one concerning the use of parallel connected, instead of series connected, utilization loads, the other concerning the ability to have high turns ratio transformers such that the supply network voltage could be much higher (initially 1,400 to 2,000 V) than the voltage of utilization loads (100 V initially preferred). [ 69 ] [ 70 ] When employed in parallel connected electric distribution systems, closed-core transformers finally made it technically and economically feasible to provide electric power for lighting in homes, businesses and public spaces. Bláthy had suggested the use of closed cores, Zipernowsky had suggested the use of parallel shunt connections , and Déri had performed the experiments; [ 71 ] In early 1885, the three engineers also eliminated the problem of eddy current losses with the invention of the lamination of electromagnetic cores. [ 72 ]
Transformers today are designed on the principles discovered by the three engineers. They also popularized the word 'transformer' to describe a device for altering the EMF of an electric current [ 73 ] although the term had already been in use by 1882. [ 74 ] [ 75 ] In 1886, the ZBD engineers designed, and the Ganz factory supplied electrical equipment for, the world's first power station that used AC generators to power a parallel connected common electrical network, the steam-powered Rome-Cerchi power plant. [ 76 ]
Building on the advancement of AC technology in Europe, [ 77 ] George Westinghouse founded the Westinghouse Electric in Pittsburgh, Pennsylvania, on January 8, 1886. [ 78 ] The new firm became active in developing alternating current (AC) electric infrastructure throughout the United States.
The Edison Electric Light Company held an option on the US rights for the ZBD transformers, requiring Westinghouse to pursue alternative designs on the same principles. George Westinghouse had bought Gaulard and Gibbs' patents for $50,000 in February 1886. [ 79 ] He assigned to William Stanley the task of redesign the Gaulard and Gibbs transformer for commercial use in United States. [ 80 ] Stanley's first patented design was for induction coils with single cores of soft iron and adjustable gaps to regulate the EMF present in the secondary winding (see image). This design [ 81 ] was first used commercially in the US in 1886 [ 82 ] but Westinghouse was intent on improving the Stanley design to make it (unlike the ZBD type) easy and cheap to produce. [ 81 ]
Westinghouse, Stanley and associates soon developed a core that was easier to manufacture, consisting of a stack of thin 'E‑shaped' iron plates insulated by thin sheets of paper or other insulating material. Pre-wound copper coils could then be slid into place, and straight iron plates laid in to create a closed magnetic circuit. Westinghouse obtained a patent for the new low-cost design in 1887. [ 71 ]
In 1889, Russian-born engineer Mikhail Dolivo-Dobrovolsky developed the first three-phase transformer at the Allgemeine Elektricitäts-Gesellschaft ('General Electricity Company') in Germany. [ 83 ]
In 1891, Nikola Tesla invented the Tesla coil , an air-cored, dual-tuned resonant transformer for producing very high voltages at high frequency. [ 84 ]
Audio frequency transformers (" repeating coils ") were used by early experimenters in the development of the telephone . [ 85 ]
General links : | https://en.wikipedia.org/wiki/Transformer |
Transformer oil or insulating oil is an oil that is stable at high temperatures and has excellent electrical insulating properties. It is used in oil-filled wet transformers, [ 1 ] some types of high-voltage capacitors , fluorescent lamp ballasts , and some types of high-voltage switches and circuit breakers. It functions to insulate , suppress corona discharge and arcing, and serves as a coolant.
Most often, transformer oil is based on mineral oil , but alternative formulations - with different engineering or environmental properties - are growing in popularity.
Transformer oil's primary functions are to insulate and cool a transformer . It must therefore have high dielectric strength , thermal conductivity , and chemical stability , and must keep these properties when held at high temperatures for extended periods. [ 2 ] Typically, they have a flash point greater than 140 °C (284 °F), pour point less than −40 °C (−40 °F), and a dielectric breakdown at greater than 28 kV RMS . [ 3 ] To improve cooling of large power transformers, the oil-filled tank may have external radiators through which the oil circulates by natural convection . Power transformers with capacities of thousands of kilovolt-ampere may also have cooling fans , oil pumps, and even oil-to-water heat exchangers . [ 4 ]
Power transformers undergo prolonged drying processes, using electrical self-heating, the application of a vacuum , or both to ensure that the transformer is completely free of water vapor before the insulating oil is introduced. This helps prevent corona formation and subsequent electrical breakdown under load.
Oil filled transformers with a conservator oil reservoir may have a gas detector relay like a Buchholz relay . These safety devices detect the buildup of gas inside the transformer due to corona discharge , overheating, or an internal electric arc . On a slow accumulation of gas, or rapid pressure rise, these devices can trip a protective circuit breaker to remove power from the transformer. Transformers without conservators are usually equipped with sudden pressure relays, which perform a similar function as the Buchholz relay.
Mineral oil is generally effective as a transformer oil, but it has some disadvantages, one of which is its relatively low flashpoint versus some alternatives. If a transformer leaks mineral oil, it can potentially start a fire. Fire codes often require that transformers inside buildings use a less flammable liquid, or the use of dry-type transformers with no liquid at all. Mineral oil is also an environmental contaminant, and its insulating properties are rapidly degraded by even small amounts of water. Transformers are well equipped to keep water outside the oil for this reason.
Pentaerythritol tetra fatty acid synthetic and natural esters have emerged as an increasingly common mineral oil alternative, especially in high-fire-risk applications such as indoors due to their high fire point , which are over 300 °C (572 °F). [ 5 ] They are biodegradable , but are more expensive than mineral oil. Natural esters have lower oxidation stability in the 120C oxygen saturated test of approximately 48-hours compared to 500-hours for Mineral oils, and are therefore used in closed transformers.
Hermetic seals are important for larger transformers due to thermal expansion and contraction. Mid-size and large power transformers will typically have a conservator and employ a rubber bag with the use of natural ester to reduce oxygen ingress and prevent the natural ester from experiencing a faster oxidation than utilities are accustomed to with mineral oils. Silicone or fluorocarbon -based oils, which are even less flammable, are also used, but they are more expensive than esters. [ citation needed ]
There are over 3 million transformers in service with vegetable-based formulations, using soy or rapeseed based formulations in up to 500 kV transformers so far. However, coconut oil -based formulations are unsuitable for use in cold climates or for voltages over 230 kV. [ 7 ] Researchers are also investigating nanofluids for transformer use; these would be used as additives to improve the stability and thermal and electrical properties of the oil. [ 8 ]
Polychlorinated biphenyls (PCB) are synthetic dielectrics first made over a century ago and found to have desirable properties that led to their widespread use. [ 9 ] Polychlorinated biphenyls were formerly used as transformer oil, since they have high dielectric strength and are not flammable. Unfortunately, they are also toxic , bioaccumulative , not at all biodegradable, and difficult to dispose of safely. When burned, they form even more toxic products, such as chlorinated dioxins and chlorinated dibenzofurans .
Beginning in the 1970s, production and new uses of PCBs were banned in many countries, due to concerns about the accumulation of PCBs and toxicity of their byproducts. For instance, in the USA, production of PCBs was banned in 1979 under the Toxic Substances Control Act . [ 10 ] In many countries significant programs are in place to reclaim and safely destroy PCB contaminated equipment. [ citation needed ] One method that can be used to reclaim PCB contaminated transformer oil is the application of a PCB removal system, also called a PCB dechlorination system.
PCB removal systems use an alkali dispersion to strip the chlorine atoms from the other molecules in a chemical reaction. This forms PCB-free transformer oil and a PCB-free sludge. The two can then be separated via a centrifuge. The sludge can be disposed as regular non-PCB industrial waste. The treated transformer oil is fully restored, meeting the required standards, without any detectable PCB content. It can, thus, be used as the insulating fluid in transformers again. [ 11 ]
PCBs and mineral oil are miscible in all proportions, and sometimes the same equipment (drums, pumps, hoses, and so on) was used for either type of liquid, so PCB contamination of transformer oil continues to be a concern. For instance, under present regulations, concentrations of PCBs exceeding 5 parts per million can cause an oil to be classified as hazardous waste in California. [ 12 ]
Transformer oils are subject to electrical and mechanical stresses while a transformer is in operation. In addition there is contamination caused by chemical interactions with windings and other solid insulation, catalyzed by high operating temperature . The original chemical properties of transformer oil change gradually, rendering it ineffective for its intended purpose after many years. [ 13 ] Oil in large transformers and electrical apparatus is periodically tested for its electrical and chemical properties, to make sure it is suitable for further use. Sometimes oil condition can be improved by filtration and treatment. Tests can be divided into:
The details of conducting these tests are available in standards released by International Electrotechnical Commission , ASTM International , International standard , British Standards , and testing can be done by any of the methods. The Furan and DGA tests are specifically not for determining the quality of transformer oil, but for determining any abnormalities in the internal windings of the transformer or the paper insulation of the transformer, which cannot be otherwise detected without a complete overhaul of the transformer. Suggested intervals for these test are:
Some transformer oil tests can be carried out in the field, using portable test apparatus. Other tests, such as dissolved gas, normally require a sample to be sent to a laboratory. Electronic on-line dissolved gas detectors can be connected to important or distressed transformers to continually monitor gas generation trends.
To determine the insulating property of the dielectric oil, an oil sample is taken from the device under test, and its breakdown voltage is measured on-site according to the following test sequence: | https://en.wikipedia.org/wiki/Transformer_oil |
The transformer ratio arm bridge or TRA bridge is a type of bridge circuit for measuring electronic components, using a.c. It can be designed to work in terms of either impedance or admittance . It can be used on resistors, capacitors and inductors, measuring minor as well as major terms, e.g. series resistance in capacitors. It is probably the most accurate type of bridge available, being capable of the precision needed, for example, when checking secondary component standards against national standards. [ 1 ]
Like all bridges, the TRA bridge involves comparing an unknown component against a standard. Like all a.c. bridges, it requires a signal source and a null detector. The accuracy of this class of bridge depends on the ratio of the turns on one or more transformers . A notable advantage is that normal stray capacitance across the transformer, including lead capacitance, may affect the sensitivity of the bridge but does not affect its measuring accuracy. [ 2 ]
The invention of the TRA bridge is credited to Alan Blumlein in his UK patent 323037 (published 1929), [ 3 ] and this class of bridge is sometimes known as a Blumlein bridge , although links to earlier types of bridge can be seen. Blumlein's first patent was for a capacitance-measuring bridge: Fig. 1 is redrawn from one of the diagrams in the patent.
Subsequently the ratio arm principle was applied more generally, to other classes of electronic components and at frequencies up to r.f. , and with many variations in how the unknown component was connected to the transformer or transformers. [ 4 ]
Blumlein himself was responsible for several further related patents. [ 5 ] He made his first bridge while employed by the British company Standard Telephones and Cables , which did not manufacture test instruments. TRA bridges have since been made by many specialist manufacturers, [ 1 ] including Boonton , ESI (formerly Brown Engineering and BECO), General Radio , Marconi Instruments , H. W. Sullivan (now part of Megger ) and Wayne Kerr. [ 6 ]
One possible configuration using two transformers is shown in Fig. 2. [ 7 ] (The two transformers allow both the signal source and the null detector to be isolated from the measured component.) The unknown Z x {\displaystyle Z_{x}} and the standard Z s {\displaystyle Z_{s}} are both driven by T1, feeding currents to the primary of T2. Because of the winding sense of the two halves of the T2 primary, these currents are in antiphase .
If Z x {\displaystyle Z_{x}} and Z s {\displaystyle Z_{s}} have the same value and are fed from the same tap on T1, the antiphase currents cancel out perfectly and the null detector will show balance. When Z x {\displaystyle Z_{x}} and Z s {\displaystyle Z_{s}} are unequal, balance can be approached by connecting Z s {\displaystyle Z_{s}} to a different tap on the T1 secondary. An exact balance may be achieved by using two or more standards connected to suitable taps.
Fig. 2 shows Z x {\displaystyle Z_{x}} and Z s {\displaystyle Z_{s}} as single components. Fig. 3 shows separate standards for conductance G {\displaystyle G} and susceptance B {\displaystyle B} , allowing minor as well as major terms of Y x {\displaystyle Y_{x}} to be resolved. [ 2 ] The standards are shown as variable components connected to fixed taps on the T1 secondary, but bridges can equally be made with fixed standards connected to variable taps.
The unknown component too may be connected to a tap part-way along the T1 secondary. Also the numbers of turns on the two arms of the T1 secondary are not necessarily equal, and likewise those on the T2 primary. Combinations of these various options offer great flexibility of construction, allowing measurements over a wide range of values while using only a small number of standards – essentially one per significant figure of the resistance or conductance value and one per significant figure of the reactance or susceptance value. [ 8 ]
In Fig. 3, [ 2 ] at balance
The bridge may be balanced (nulled) by manual switching of the standards, but "autobalance" bridges, in which the switching is wholly or partially automated, are also made.
The operation of a universal TRA bridge [ 8 ] is best explained on the basis of an actual product, the Wayne Kerr B221 bridge, dating from the 1950s. [ 7 ] It used valve (vacuum tube) technology. The following description is simplified.
The bridge is based on two transformers (Fig. 4): T1 is described as the voltage transformer, and is driven by the signal source in the usual way. T2, the "current transformer", compares the two arms of the circuit – for the unknown Z x {\displaystyle Z_{x}} and the various standards – and drives the null detector, which takes the form of a phase-sensitive detector with adjustable sensitivity, feeding two magic eyes . (Later versions of the instrument, with transistorised circuitry, used a moving-coil meter as the display for the null detector.)
Taps at 1, 10, 100 and 1000 turns are shown on the T1 secondary and on T2 primary P2a. Four-way selector switches are shown, but the tap selections are actually combined on a single switch to give seven measuring ranges. Full-scale limits at full accuracy (specified as ±0.1%) are 100 MΩ, 11.1 pF and 10 kH for the least sensitive range, and 100 Ω, 11.1 μF and 10 mH for the most sensitive range. Each range can be extended in the direction of higher resistance, higher inductance or lower capacitance at reduced accuracy. The voltage applied by T1 to Z x {\displaystyle Z_{x}} is about 30 V r.m.s. on the least sensitive range, 30 mV on the two most sensitive.
The most significant figures of the major and minor components of Z x {\displaystyle Z_{x}} are obtained by switching the resistance standard R s1 and the capacitance standard C s1 to one of taps 0 to 10 on the secondary of T1. The second significant figures are obtained by switching R s2 and C s2 in the same way. Continuous ("vernier") fine adjustment to give third and fourth significant figures is provided by R s3 and C s3 . R s3 and C s3 are shown connected to tap 10 on T1, but in practice these two standards may be connected to any convenient tap, as appropriate to their values.
Primary P2b on T2 provides 100-turn taps of both polarities. Switching the capacitance standards between the positive and negative taps selects between capacitance measurements and inductance measurements. Similarly the polarity of the resistance standard can be reversed, so that measurements can be made in all four quadrants.
Besides the main balance controls described above, the front panel of the instrument has zero adjustments for both resistance and capacitance. The inductive elements of the wire-wound resistance standards are compensated by trimming capacitors. All these and other trimming components are omitted in Fig. 4.
This bridge measures conductance and susceptance in parallel. The susceptance reading is displayed as capacitance, and inductance must be calculated as a reciprocal using
To simplify the arithmetic, the bridge operates at 1592 Hz so that ω 2 is 10 8 s −2 . The readings can be converted to resistance and capacitance in series. On the most sensitive ranges, readings must be adjusted to take account of lead resistance and inductance.
The external link allows two-, three- or four-terminal measurements to be made. Besides conventional component measurements, the bridge can also be used to measure attenuator performance, transformer turns ratio and the effectiveness of transformer screening. Subject to conditions, in-situ (in-circuit) measurement of a component is possible. With additional external components, capacitors with a polarising voltage or inductors with a standing direct current can be measured.
An optional low-impedance adaptor extends the measuring range downwards by another four orders of magnitude, giving full-scale readings down to 10 mΩ, 5 F and 1 μH at ±1% basic accuracy.
Henry P. Hall, A History of Impedance Measurements , based on a draft for an unpublished book . | https://en.wikipedia.org/wiki/Transformer_ratio_arm_bridge |
The transformer utilization factor (TUF) of a rectifier circuit is defined as the ratio of the DC power available at the load resistor to the AC rating of the secondary coil of a transformer . [ 1 ] [ 2 ]
T . U . F = P o d c V A r a t i n g o f t r a n s f o r m e r {\displaystyle T.U.F={\frac {P_{odc}}{VA\ rating\ of\ transformer}}}
The V A {\displaystyle VA} rating of the transformer can be defined as: V A = V r . m . s I ˙ r . m . s ( F o r s e c o n d a r y c o i l . ) {\displaystyle VA=V_{r.m.s}{\dot {I}}_{r.m.s}(For\ secondary\ coil.)} TRANSFORMER utilization factor for half wave rectifier is .287 or .3.
This article about electric power is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transformer_utilization_factor |
Transforming growth factor ( [ attribution needed ] , or TGF ) is used to describe two classes of polypeptide growth factors , TGFα and TGFβ .
The name "Transforming Growth Factor" is somewhat arbitrary, since the two classes of TGFs are not structurally or genetically related to one another, and they act through different receptor mechanisms . Furthermore, they do not always induce cellular transformation, and are not the only growth factors that induce cellular transformation.
These proteins were originally characterized by their capacity to induce oncogenic transformation in a specific cell culture system, rat kidney fibroblasts. Application of the transforming growth factors to normal rat kidney fibroblasts induces the cultured cells to proliferate and overgrow, no longer subject to the normal inhibition caused by contact between cells. [ 6 ] [ 7 ] | https://en.wikipedia.org/wiki/Transforming_growth_factor |
A transgene is a gene that has been transferred naturally, or by any of a number of genetic engineering techniques, from one organism to another. The introduction of a transgene, in a process known as transgenesis , has the potential to change the phenotype of an organism. Transgene describes a segment of DNA containing a gene sequence that has been isolated from one organism and is introduced into a different organism. This non-native segment of DNA may either retain the ability to produce RNA or protein in the transgenic organism or alter the normal function of the transgenic organism's genetic code. In general, the DNA is incorporated into the organism's germ line . For example, in higher vertebrates this can be accomplished by injecting the foreign DNA into the nucleus of a fertilized ovum . This technique is routinely used to introduce human disease genes or other genes of interest into strains of laboratory mice to study the function or pathology involved with that particular gene.
The construction of a transgene requires the assembly of a few main parts. The transgene must contain a promoter , which is a regulatory sequence that will determine where and when the transgene is active, an exon , a protein coding sequence (usually derived from the cDNA for the protein of interest), and a stop sequence. These are typically combined in a bacterial plasmid and the coding sequences are typically chosen from transgenes with previously known functions. [ 1 ]
Transgenic or genetically modified organisms , be they bacteria, viruses or fungi, serve many research purposes. Transgenic plants , insects, fish and mammals (including humans) have been bred. Transgenic plants such as corn and soybean have replaced wild strains in agriculture in some countries (e.g. the United States). Transgene escape has been documented for GMO crops since 2001 with persistence and invasiveness. Transgenetic organisms pose ethical questions and may cause biosafety problems.
The idea of shaping an organism to fit a specific need is not a new science. However, until the late 1900s farmers and scientists could breed new strains of a plant or organism only from closely related species because the DNA had to be compatible for offspring to be able to reproduce. [ citation needed ]
In the 1970 and 1980s, scientists passed this hurdle by inventing procedures for combining the DNA of two vastly different species with genetic engineering . The organisms produced by these procedures were termed transgenic. Transgenesis is the same as gene therapy in the sense that they both transform cells for a specific purpose. However, they are completely different in their purposes, as gene therapy aims to cure a defect in cells, and transgenesis seeks to produce a genetically modified organism by incorporating the specific transgene into every cell and changing the genome . Transgenesis will therefore change the germ cells, not only the somatic cells, in order to ensure that the transgenes are passed down to the offspring when the organisms reproduce. Transgenes alter the genome by blocking the function of a host gene; they can either replace the host gene with one that codes for a different protein, or introduce an additional gene. [ 2 ]
The first transgenic organism was created in 1974 when Annie Chang and Stanley Cohen expressed Staphylococcus aureus genes in Escherichia coli . [ 3 ] In 1978, yeast cells were the first eukaryotic organisms to undergo gene transfer. [ 4 ] Mouse cells were first transformed in 1979, followed by mouse embryos in 1980. Most of the very first transmutations were performed by microinjection of DNA directly into cells. Scientists were able to develop other methods to perform the transformations, such as incorporating transgenes into retroviruses and then infecting cells; using electroinfusion, which takes advantage of an electric current to pass foreign DNA through the cell wall; biolistics , which is the procedure of shooting DNA bullets into cells; and also delivering DNA into the newly fertilized egg. [ 5 ]
The first transgenic animals were only intended for genetic research to study the specific function of a gene, and by 2003, thousands of genes had been studied.
A variety of transgenic plants have been designed for agriculture to produce genetically modified crops , such as corn, soybean, rapeseed oil, cotton, rice and more. As of 2012 [update] , these GMO crops were planted on 170 million hectares globally. [ 6 ]
One example of a transgenic plant species is golden rice . In 1997, [ citation needed ] five million children developed xerophthalmia , a medical condition caused by vitamin A deficiency, in Southeast Asia alone. [ 7 ] Of those children, a quarter million went blind. [ 7 ] To combat this, scientists used biolistics to insert the daffodil phytoene synthase gene into Asia indigenous rice cultivars . [ 8 ] The daffodil insertion increased the production of β-carotene . [ 8 ] The product was a transgenic rice species rich in vitamin A, called golden rice . Little is known about the impact of golden rice on xerophthalmia because anti-GMO campaigns have prevented the full commercial release of golden rice into agricultural systems in need. [ 9 ]
The escape of genetically-engineered plant genes via hybridization with wild relatives was first discussed and examined in Mexico [ 10 ] and Europe in the mid-1990s. There is agreement that escape of transgenes is inevitable, even "some proof that it is happening". [ 6 ] Up until 2008 there were few documented cases. [ 6 ] [ 11 ]
Corn sampled in 2000 from the Sierra Juarez, Oaxaca , Mexico contained a transgenic 35S promoter, while a large sample taken by a different method from the same region in 2003 and 2004 did not. A sample from another region from 2002 also did not, but directed samples taken in 2004 did, suggesting transgene persistence or re-introduction. [ 12 ] A 2009 study found recombinant proteins in 3.1% and 1.8% of samples, most commonly in southeast Mexico. Seed and grain import from the United States could explain the frequency and distribution of transgenes in west-central Mexico, but not in the southeast. Also, 5.0% of corn seed lots in Mexican corn stocks expressed recombinant proteins despite the moratorium on GM crops. [ 13 ]
In 2011, transgenic cotton was found in Mexico among wild cotton, after 15 years of GMO cotton cultivation. [ 14 ]
Transgenic rapeseed Brassicus napus – hybridized with a native Japanese species, Brassica rapa – was found in Japan in 2011 [ 15 ] after having been identified in 2006 in Québec , Canada. [ 16 ] They were persistent over a six-year study period, without herbicide selection pressure and despite hybridization with the wild form. This was the first report of the introgression —the stable incorporation of genes from one gene pool into another—of an herbicide-resistance transgene from Brassica napus into the wild form gene pool. [ 17 ]
Transgenic creeping bentgrass , engineered to be glyphosate -tolerant as "one of the first wind-pollinated, perennial, and highly outcrossing transgenic crops", was planted in 2003 as part of a large (about 160 ha) field trial in central Oregon near Madras, Oregon . In 2004, its pollen was found to have reached wild growing bentgrass populations up to 14 kilometres away. Cross-pollinating Agrostis gigantea was even found at a distance of 21 kilometres. [ 18 ] The grower, Scotts Company could not remove all genetically engineered plants, and in 2007, the U.S. Department of Agriculture fined Scotts $500,000 for noncompliance with regulations. [ 19 ]
The long-term monitoring and controlling of a particular transgene has been shown not to be feasible. [ 20 ] The European Food Safety Authority published a guidance for risk assessment in 2010. [ 21 ]
Genetically modified mice are the most common animal model for transgenic research. [ 22 ] Transgenic mice are currently being used to study a variety of diseases including cancer, obesity, heart disease, arthritis, anxiety, and Parkinson's disease. [ 23 ] The two most common types of genetically modified mice are knockout mice and oncomice . Knockout mice are a type of mouse model that uses transgenic insertion to disrupt an existing gene's expression. In order to create knockout mice, a transgene with the desired sequence is inserted into an isolated mouse blastocyst using electroporation . Then, homologous recombination occurs naturally within some cells, replacing the gene of interest with the designed transgene. Through this process, researchers were able to demonstrate that a transgene can be integrated into the genome of an animal, serve a specific function within the cell, and be passed down to future generations. [ 24 ]
Oncomice are another genetically modified mouse species created by inserting transgenes that increase the animal's vulnerability to cancer. Cancer researchers utilize oncomice to study the profiles of different cancers in order to apply this knowledge to human studies. [ 24 ]
Multiple studies have been conducted concerning transgenesis in Drosophila melanogaster , the fruit fly. This organism has been a helpful genetic model for over 100 years, due to its well-understood developmental pattern. The transfer of transgenes into the Drosophila genome has been performed using various techniques, including P element , Cre-loxP , and ΦC31 insertion. The most practiced method used thus far to insert transgenes into the Drosophila genome utilizes P elements. The transposable P elements, also known as transposons , are segments of bacterial DNA that are translocated into the genome, without the presence of a complementary sequence in the host's genome. P elements are administered in pairs of two, which flank the DNA insertion region of interest. Additionally, P elements often consist of two plasmid components, one known as the P element transposase and the other, the P transposon backbone. The transposase plasmid portion drives the transposition of the P transposon backbone, containing the transgene of interest and often a marker, between the two terminal sites of the transposon. Success of this insertion results in the nonreversible addition of the transgene of interest into the genome. While this method has been proven effective, the insertion sites of the P elements are often uncontrollable, resulting in an unfavorable, random insertion of the transgene into the Drosophila genome. [ 25 ]
To improve the location and precision of the transgenic process, an enzyme known as Cre has been introduced. Cre has proven to be a key element in a process known as recombinase-mediated cassette exchange (RMCE). While it has shown to have a lower efficiency of transgenic transformation than the P element transposases, Cre greatly lessens the labor-intensive abundance [ clarification needed ] of balancing random P insertions. Cre aids in the targeted transgenesis of the DNA gene segment of interest, as it supports the mapping of the transgene insertion sites, known as loxP sites. These sites, unlike P elements, can be specifically inserted to flank a chromosomal segment of interest, aiding in targeted transgenesis. The Cre transposase is important in the catalytic cleavage of the base pairs present at the carefully positioned loxP sites, permitting more specific insertions of the transgenic donor plasmid of interest. [ 26 ]
To overcome the limitations and low yields that transposon-mediated and Cre-loxP transformation methods produce, the bacteriophage ΦC31 has recently been utilized. Recent breakthrough studies involve the microinjection of the bacteriophage ΦC31 integrase, which shows improved transgene insertion of large DNA fragments that are unable to be transposed by P elements alone. This method involves the recombination between an attachment (attP) site in the phage and an attachment site in the bacterial host genome (attB). Compared to usual P element transgene insertion methods, ΦC31 integrates the entire transgene vector, including bacterial sequences and antibiotic resistance genes. Unfortunately, the presence of these additional insertions has been found to affect the level and reproducibility of transgene expression.
One agricultural application is to selectively breed animals for particular traits: Transgenic cattle with an increased muscle phenotype has been produced by overexpressing a short hairpin RNA with homology to the myostatin mRNA using RNA interference . [ 27 ] Transgenes are being used to produce milk with high levels of proteins or silk from the milk of goats. Another agricultural application is to selectively breed animals, which are resistant to diseases or animals for biopharmaceutical production. [ 27 ]
The application of transgenes is a rapidly growing area of molecular biology . As of 2005 it was predicted that in the next two decades, 300,000 lines of transgenic mice will be generated. [ 28 ] Researchers have identified many applications for transgenes, particularly in the medical field. Scientists are focusing on the use of transgenes to study the function of the human genome in order to better understand disease, adapting animal organs for transplantation into humans, and the production of pharmaceutical products such as insulin , growth hormone , and blood anti-clotting factors from the milk of transgenic cows. [ citation needed ]
As of 2004 there were five thousand known genetic diseases , and the potential to treat these diseases using transgenic animals is, perhaps, one of the most promising applications of transgenes. There is a potential to use human gene therapy to replace a mutated gene with an unmutated copy of a transgene in order to treat the genetic disorder. This can be done through the use of Cre-Lox or knockout . Moreover, genetic disorders are being studied through the use of transgenic mice, pigs, rabbits, and rats. Transgenic rabbits have been created to study inherited cardiac arrhythmias, as the rabbit heart markedly better resembles the human heart as compared to the mouse. [ 29 ] [ 30 ] More recently, scientists have also begun using transgenic goats to study genetic disorders related to fertility . [ 31 ]
Transgenes may be used for xenotransplantation from pig organs. Through the study of xeno-organ rejection, it was found that an acute rejection of the transplanted organ occurs upon the organ's contact with blood from the recipient due to the recognition of foreign antibodies on endothelial cells of the transplanted organ. Scientists have identified the antigen in pigs that causes this reaction, and therefore are able to transplant the organ without immediate rejection by removal of the antigen. However, the antigen begins to be expressed later on, and rejection occurs. Therefore, further research is being conducted. [ citation needed ] Transgenic microorganisms capable of producing catalytic proteins or enzymes which increase the rate of industrial reactions.
Transgene use in humans is currently fraught with issues. Transformation of genes into human cells has not been perfected yet. The most famous example of this involved certain patients developing T-cell leukemia after being treated for X-linked severe combined immunodeficiency (X-SCID). [ 32 ] This was attributed to the close proximity of the inserted gene to the LMO2 promoter, which controls the transcription of the LMO2 proto-oncogene. [ 33 ] | https://en.wikipedia.org/wiki/Transgene |
Transgene S.A. is a French biotechnology company founded in 1979. It is based in Illkirch-Graffenstaden , near Strasbourg , Alsace . The company develops and manufactures immunotherapies for the treatment of cancer. Based on viral vectors, these therapies stimulate the immune defenses of patients to specifically target cancer cells.
Transgene has two technological platforms based on these respective approaches: individual therapeutic vaccines, shared antigens cancer vaccines oncolytic viruses .
Transgene’s portfolio consists of four products currently in clinical development. Its lead product TG4050, a neoantigen individualized therapeutic cancer vaccine is currently being developed in a randomized Phase I/II trial in the adjuvant treatment of head and neck cancer.
The company is listed on the regulated market of Euronext in Paris . [ 1 ]
Transgene was founded in 1979, on the initiative of Pierre Chambon and Philippe Kourilsky. Jean-Pierre Lecocq was the first Scientific Director of Transgene in 1980. [ 2 ]
Dr Alessandro Riva, MD, joined Transgene in 2022 as Chairman of the Board of Directors. In May 2023 the board appointed him Chairman adn Chief Executive Officer of the company [ 3 ] , . [ 4 ]
Transgene owns two technological platforms:
The Company has several clinical-stage products in its portfolio.
1- TG4050 : This neoantigen individualized therapeutic cancer vaccine is currently being developed in a randomized Phase I/II trial in the adjuvant treatment of head and neck cancer. [ 11 ]
2- TG4001 : is a therapeutic vaccine designed to express the E6 and E7 antigens of the HPV-16 virus (human papillomavirus type 16). [ 12 ] Transgene is currently evaluating the full study results in detail to determine the best way forward for this program. [ 13 ]
3- Oncolytic viruses : TG6050 and BT-001. Transgene’s oncolytic viruses are designed to directly and selectively destroy the cancer cells by using an oncolysis mechanism, while also inducing immune responses against tumor cells. In addition, during their replication, the virus expresses the payloads integrated in its genome and therefore allows the expression of immunomodulators and/or therapeutic agents specifically in the tumors [ 14 ] , [ 15 ] , [ 16 ] , [ 17 ] , . [ 18 ] [ 19 ]
4- Transgene and AstraZeneca have been collaborating since 2019 to co-develop oncolytic viruses from the Invir.IO™ platform. [ 20 ] [ 21 ] [ 22 ]
Transgene’s Management Committee is composed of the following members: | https://en.wikipedia.org/wiki/Transgene_(company) |
Cnidarians such as Hydra have become attractive model organisms to study the evolution of immunity . However, despite long-term efforts, stably transgenic animals could not be generated, severely limiting the functional analysis of genes . For analytical purposes, therefore, an important technical breakthrough in the field was the development of a transgenic procedure for generation of stably transgenic lines by embryo microinjection .
Hydra polyps are small and transparent which makes it possible to trace single cells in vivo . In addition, transgenic Hydra provide a ready system for generating gain-of-function phenotypes. With the use of transgenes producing dominant-negative versions of proteins , one should be able to obtain loss-of-function phenotypes as well.
Current technology allows generation of reporter constructs using promoters of various Hydra genes fused to fluorescent proteins.
Since transgenic Hydra lines have become an important tool to dissect molecular mechanisms of development, a “Hydra Transgenic Facility” has been established at the Christian-Albrechts-University of Kiel (Germany). | https://en.wikipedia.org/wiki/Transgenic_hydra |
Transgranular fracture is a type of fracture that occurs through the crystal grains of a material. In contrast to intergranular fractures , which occur when a fracture follows the grain boundaries, this type of fracture traverses the material's microstructure directly through individual grains. This type of fracture typically results from a combination of high stresses and material defects, such as voids or inclusions, that create a path for crack propagation through the grains. A broad range of ductile or brittle materials, including metals, ceramics, and polymers, can experience transgranular fracture. When examined under scanning electron microscopy , this type of fracture reveals cleavage steps, river patterns, feather markings, dimples, and tongues. [ 1 ] The fracture may change directions somewhat when entering a new grain in order to follow the new lattice orientation of that grain but this is a less severe direction change then would be required to follow the grain boundary. This results in a fairly smooth looking fracture with fewer sharp edges than one that follows the grain boundaries. [ 2 ] This can be visualized as a jigsaw puzzle cut from a single sheet of wood with the wood grain showing. A transgranular fracture follows the grains in the wood, not the jigsaw edges of the puzzle pieces. This is in contrast to an intergranular fracture which, in this analogy, would follow the jigsaw edges, not the wood grain.
The mechanism of transgranular fracture may vary depending on the material and surrounding conditions under which the fracture occurs. [ 3 ] However, some general steps are typically involved in the transgranular fracture process:
In ductile metals, the plastic deformation of the material can be a critical factor in the transgranular fracture process, while in brittle materials such as ceramics, the formation and growth of cracks can be influenced by factors such as grain size, porosity, and the presence of impurities or other defects.
The fracture behavior of materials can be significantly changed by the use of precipitation-based grain boundary design. For example, Meindlhumer et. al. [ 9 ] produced a thin film of AlCrN containing a specific distribution of precipitates within the grain boundaries in precipitation-based grain boundary design. The precipitates acted as a barrier to crack propagation, increasing the material's resistance to intergranular cracking. Additionally, the precipitates altered the stress distribution within the material, promoting transgranular crack propagation instead. Furthermore, smaller precipitates with a more uniform distribution have been shown to be more effective at promoting transgranular fracture. | https://en.wikipedia.org/wiki/Transgranular_fracture |
In algebraic topology, a transgression map is a way to transfer cohomology classes.
It occurs, for example in the inflation-restriction exact sequence in group cohomology , and in integration in fibers . It also naturally arises in many spectral sequences ; see spectral sequence#Edge maps and transgressions .
The transgression map appears in the inflation-restriction exact sequence , an exact sequence occurring in group cohomology . Let G be a group , N a normal subgroup , and A an abelian group which is equipped with an action of G , i.e., a homomorphism from G to the automorphism group of A . The quotient group G / N {\displaystyle G/N} acts on
Then the inflation-restriction exact sequence is:
The transgression map is the map H 1 ( N , A ) G / N → H 2 ( G / N , A N ) {\displaystyle H^{1}(N,A)^{G/N}\to H^{2}(G/N,A^{N})} .
Transgression is defined for general n ∈ N {\displaystyle n\in \mathbb {N} } ,
only if H i ( N , A ) G / N = 0 {\displaystyle H^{i}(N,A)^{G/N}=0} for i ≤ n − 1 {\displaystyle i\leq n-1} . [ 1 ]
This algebra -related article is a stub . You can help Wikipedia by expanding it .
This topology-related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transgression_map |
In genetics, transgressive segregation is the formation of extreme phenotypes , or transgressive phenotypes, observed in segregated hybrid populations compared to phenotypes observed in the parental lines. [ 1 ] The appearance of these transgressive (extreme) phenotypes can be either positive or negative in terms of fitness . If both parents' favorable alleles come together, it will result in a hybrid having a higher fitness than the two parents. The hybrid species will show more genetic variation and variation in gene expression than their parents. As a result, the hybrid species will have some traits that are transgressive (extreme) in nature. Transgressive segregation can allow a hybrid species to populate different environments/niches in which the parent species do not reside, or compete in the existing environment with the parental species.
Genetic
There are many causes for transgressive segregation in hybrids. One cause can be due to recombination of additive alleles. Recombination results in new pairs of alleles at two or more loci. These different pairs of alleles can give rise to new phenotypes if gene expression has been changed at these loci. Another cause can be elevated mutation rate . When mutation rates are high, it is more probable that a mutation will occur and cause an extreme phenotypic change. Reduced developmental stability is another cause for transgressive segregation. Developmental stability refers to the capability of a genotype to go through a constant development of a phenotype in a certain environmental setting. If there is a disturbance due to genetic or environmental factors, the genotype will be more sensitive to phenotypic changes. Another cause arises from the interaction between two alleles of two different genes, also known as the epistatic effect . Epistasis is the event when one allele at a locus prevents an allele at another locus to express its product as if it is masking its effect. Therefore, epistasis can be related to gene over dominance caused by heterozygosity at specific loci.[2] What this means is that the heterozygote (hybrid) when compared to the homozygote (parent) is better adapted and therefore shows more transgressive, extreme phenotypes. All of these causes lead to the appearance of these extreme phenotypes and creates a hybrid species that will deviate away from the parent species niche and eventually create an individual "hybrid" species.
Environmental
Other than the genetic factors solely causing transgressive segregation, environmental factors can cause genetic factors to take place. Environmental factors that cause transgressive segregation can be influenced by human activity and climate change . Both human activity and climate change have the capability to force species of a specific genome to interact with other species with different genomes.
For example, if a bridge is built that connects two isolated areas to one another, a gene flow door would open. This open door will increase the interactions between different species with different genomes can create hybrid species that can potentially show transgressive phenotypes. Human activity can open the gene flow door by pursuing harmful actions such as cutting down forests and pollution. Climate change on the other hand can open the gene flow door by breaking climate and environmental barriers that were present before. This convergence between species can give rise to a hybrid species that will have more phenotypic variation when compared to the parent species. This increase in phenotypic variation has the potential for transgressive segregation to occur. [ 2 ]
In Kenya, there is a fungus called septoria tritici blotch (STB) that diminishes yield in wheat crop. The parent species of wheat had little resistance toward STB, but the hybrid species due to transgressive segregation showed a higher resistance toward STB and therefore a higher fitness. You can create a higher resistance to STB by crossing genes together that are efficient. In result, out of 36 crosses there were 31 that showed a higher mean fitness than the control, parent value. These 31 crosses indicate a higher resistance to STB. The crosses used were from other commercial wheat's that were high yielding which is advantageous because there is a lower chance of deleterious (unwanted traits) appearing and therefore an increase in beneficial traits. Transgressive segregation has been found to be useful to create a resistance toward this organism in order to increase the yield of wheat crop. [ 3 ]
Rieseberg used sunflowers to show the transgressive segregation of parental traits. Helianthus annuus and Helianthus petiolaris are the two parent groups for the hybrids. Ultimately there were three hybrid sunflower species. When compared to the fitness of the parents, the hybrids showed a higher tolerance in areas which the parent species would not be able to survive i.e. salt marsh, sand dunes, and deserts. Transgressive segregation allowed these hybrids to survive in areas that the parent would not be able to. Therefore, the hybrids were populated in areas where the parent species were not. This is due to hybrid species showing more gene expression (phenotypes) than their parents and also having some genes that are transgressive (extreme) in nature. [ 4 ]
There are many ways to test if transgressive segregation occurred within a population. One common way to test for transgressive segregation is to use a Dunnett's test . This test looks at whether the hybrid species' performance was different from the control group by looking whether or not the mean of the control group (parent species) differs significantly from mean of the other groups. If there is a difference, that is an indication of transgressive segregation. [ 5 ] Another commonly used test is the use of quantitative trait loci (QTL) to assess transgressive segregation. Alleles with QTL that were opposed (either by overdominance or underdominance) of the parental parent QTL indicate that transgressive segregation occurred. Alleles with QTL that was the same as the predicted parent QTL showed that there was no transgressive segregation. [ 6 ]
Transgressive segregation creates an opportunity for new hybrid species to arise that are more fit than their ancestors. As seen with the STB in Kenya and Rieseberg's sunflowers, transgressive segregation can be used to create a species that is more adaptable and resistant in areas where there is environmental stress. Transgressive segregation can be seen as genetic engineering in the way that the goal for each of these events is to create an organism that is more fit than the last. | https://en.wikipedia.org/wiki/Transgressive_segregation |
Transhalogenation is a substitution reaction in which the halide of a halide compound is exchanged for another halide. [ 1 ]
A common method is halide metathesis. An example is the conversion of alkyl chloride into alkyl fluoride :
This kind of reaction is called Finkelstein reaction . [ 2 ] However, it is also possible, for example, to produce phosphorus fluoride compounds by transhalogenating chlorine, bromine or iodine bound to phosphorus with a metal fluoride. [ 3 ]
As a halogen source for transhalogenation, metal halides (such as sodium fluoride or lithium fluoride ) are often used, but also the use of onium halides is possible. [ 2 ] Transhalogenation has been described as a gentle method for the synthesis of fluoroorganylboranes. [ 4 ] It is also possible to produce aryliodides from the corresponding aryl chlorides or aryl bromides. [ 5 ]
One investigation showed a possibility to perform transhalogenation by means of genetically modified enzymes (haloalkanes dehalogenases, HLDs). [ 6 ] | https://en.wikipedia.org/wiki/Transhalogenation |
In nuclear physics , transient equilibrium is a situation in which equilibrium is reached by a parent-daughter radioactive isotope pair where the half-life of the daughter is shorter than the half-life of the parent. Contrary to secular equilibrium , the half-life of the daughter is not negligible compared to parent's half-life. An example of this is a molybdenum-99 generator producing technetium-99 for nuclear medicine diagnostic procedures. Such a generator is sometimes called a cow because the daughter product, in this case technetium-99, is milked at regular intervals. [ 1 ] Transient equilibrium occurs after four half-lives, on average. [ 2 ]
The activity of the daughter is given by the Bateman equation:
where A P {\displaystyle A_{P}} and A d {\displaystyle A_{d}} are the activity of the parent and daughter, respectively. T P {\displaystyle T_{P}} and T d {\displaystyle T_{d}} are the half-lives (inverses of reaction rates λ {\displaystyle \lambda } in the above equation modulo ln(2)) of the parent and daughter, respectively, and BR is the branching ratio .
In transient equilibrium, the Bateman equation cannot be simplified by assuming the daughter's half-life is negligible compared to the parent's half-life. The ratio of daughter-to-parent activity is given by:
In transient equilibrium, the daughter activity increases and eventually reaches a maximum value that can exceed the parent activity. The time of maximum activity is given by:
where T P {\displaystyle T_{P}} and T d {\displaystyle T_{d}} are the half-lives of the parent and daughter, respectively. In the case of Tc 99 m − 99 Mo {\displaystyle {\ce {^{99\!m}Tc-^{99}Mo}}} generator, the time of maximum activity ( t max {\displaystyle t_{\max }} ) is approximately 24 hours, which makes it convenient for medical use. [ 3 ]
This radioactivity –related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Transient_equilibrium |
Transient expression , more frequently referred to " transient gene expression ", is the temporary expression of genes that are expressed for a short time after nucleic acid , most frequently plasmid DNA encoding an expression cassette , has been introduced into eukaryotic cells with a chemical delivery agent like calcium phosphate (CaPi) or polyethyleneimine (PEI). [ 1 ] However, unlike "stable expression," the foreign DNA does not fuse with the host cell DNA, resulting in the inevitable loss of the vector after several cell replication cycles. [ 2 ] The majority of transient gene expressions are done with cultivated animal cells. The technique is also used in plant cells; however, the transfer of nucleic acids into these cells requires different methods than those with animal cells. In both plants and animals, transient expression should result in a time-limited use of transferred nucleic acids, since any long-term expression would be called "stable expression."
Methodology varies depending on the organism to transform . While plants can be transformed with a construct introduced into Agrobacterium tumefaciens via agroinfiltration or floral dip, most animal cells would require a viral vector . In humans, the field of transient transformation advanced rapidly during the 2020–2021 COVID-19 pandemic with major COVID-19 vaccines using either direct mRNA transfer into human or adenovirus vectors, with the RNA being expressed in the host human to produce spike proteins that induce an immune response.
When choosing between inducing transient or stable expression in cells, time frame and experimental goal must be taken into consideration. Transiently transfected cells are often used to study the effects of short-term gene expression, perform RNA interference (RNAi)‑mediated gene silencing, or quickly generate small-scale recombinant proteins. [ 3 ] This rapid generation small quantities of recombinant proteins can be applied towards evaluating their potential as drug candidates or examining their integrity of constructs during stages of vector development. Additionally, transient expression can be a useful tool when aiming to optimize selected parameters before undergoing the time-consuming process of scale-up in stably transfected cells. [ 4 ] Typically, the cells are harvested within 1-4 days after successful transfection. For even quicker results, replacing DNA with mRNA can result in transient expression within minutes after successful transfection in some systems; this process bypasses translocation to the nucleus and transcription . [ 5 ]
If stable, long-term gene expression is desired, stable transfection of cells is more useful. However, since successful integration of a DNA vector into the chromosome is a rare occurrence, this process is more difficult and time-consuming, and is reserved for large-scale protein production, gene therapies, and long-term pharmacology studies.
The dominant technology used for the production of transgenic plants for transient expression is Agrobacterium -mediated genetic transformation, or "agroinfiltration," and virus expression machinery. [ 6 ] Agrobacterium tumefaciens and related Agrobacterium species are well-known plant pathogens that have been engineered to efficiently transfer specific pieces of DNA (called transfer DNA, or T-DNA) into the plant nucleus using binary vector systems , which consists of a T-DNA binary vector and a vir helper plasmid. [ 7 ] This binary vector separates T-DNA from trans -acting virulence proteins that help mediate the transfer. [ 8 ] Advantages of this method include modularity of broad host-range plasmids of small size through standard molecular biology techniques. Furthermore, since the parent tumor-inducing plasmid in Agrobacterium strains have been disarmed and only non-reproductive cells have been modified (as opposed to germ-line modifications), the process is considered environmentally harmless. [ 6 ]
Applications of this process has resulted in advancements made in the use of plants to synthetic biology. Plant-derived bioproducts show promise of high competitiveness towards traditional mammalian cell expression systems.
Mammalian cell expression systems are essential for the transient production of recombinant proteins and their complementary post-translational modifications. In fact, approximately half of the current commercially available therapeutic proteins are produced in mammalian cells. However, mammalian cell systems' slow growth, precise growth requirements, and potential risk of infection by animal viruses present a number of challenges. As a result, a growing number of mammalian cell lines have been established to serve as hosts for transient recombinant protein production. [ 2 ]
Although other cells lines, such as African green monkey kidney (COS) and baby hamster kidney (BHK), can be used for recombinant protein production, the most commonly employed host system in transient expression of mammalian cells involves derivatives of the HEK293 cell line, which is based on the human embryonic kidney cell line established in 1977 by Graham et al. [ 9 ] The HEK293 cell line was created via transformation with sheared Adenovirus 5 DNA. [ 10 ] Advantages of using this cell line include their high rates of transfection and ability to grow in a serum-free medium, which results in reduced cost and lowered risk of contamination with animal-derived material typically found in serum. [ 2 ]
Several engineered sublines were later developed by incorporating viral elements derived from mammalian viruses, such as SV40 virus or Epstein–Barr virus (EBV), which are notable for their high retention of plasmid DNA in an episomal state and their capacity to increase transcription and translation via specific viral properties. [ 11 ] These later sublines were consequently identified to have two interacting components: the SV40 large T-antigen binding to the SV20 origin of replication (SV40 ori ) and the EBV-derived nuclear antigen-1 ( EBNA-1 ) protein to its associated origin of replication ( oriP). [ 11 ]
Typical historical yields of transient expression in HEK293 cells transfected using PEI-25kDa was 20-40 mg/L of recombinant antibody protein. In 2008, Backliwal et. al reported for the first time yields crossing 1 g/L of recombinant antibody protein. [ 12 ]
Traditionally, Chinese hamster ovary (CHO) cells are associated with the establishment of stable cell lines for biologics. Recently, however, attempts to engineer CHO cells for transient protein production have garnered recognition. CHO cells were among the earliest established cell lines for in vitro cultivation, and their potential as a host for production and manufacturing of biological products remains popular. [ 11 ] CHO cells are preferable for transient expression due to their easy industrial scale-up, versatility for the production of diverse biomolecules, and low risk of infection of human viruses, among other advantages. [ 13 ] Three primary expression systems have been established: | https://en.wikipedia.org/wiki/Transient_expression |
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