59-616: CYCS may refer to: Cytochrome c , a protein Cyclorama (theater) plural - a large curtain or wall, often concave, positioned at the back of the stage area the ICAO code for Chesterfield Inlet Airport in Nunavut, Canada Topics referred to by the same term [REDACTED] This disambiguation page lists articles associated with the title CYCS . If an internal link led you here, you may wish to change
118-444: A nitrite reductase . Cytochrome c was also discovered in 1996 by Xiaodong Wang to have an intermediate role in apoptosis , a controlled form of cell death used to kill cells in the process of development or in response to infection or DNA damage. Cytochrome c binds to cardiolipin in the inner mitochondrial membrane, thus anchoring its presence and keeping it from releasing out of the mitochondria and initiating apoptosis. While
177-421: A book published in 1950, cladistics did not flourish until its translation into English in 1966 (Lewin 1997). Today, cladistics is the most popular method for inferring phylogenetic trees from morphological data. In the 1990s, the development of effective polymerase chain reaction techniques allowed the application of cladistic methods to biochemical and molecular genetic traits of organisms, vastly expanding
236-413: A cladistic analysis is a cladogram – a tree -shaped diagram ( dendrogram ) that is interpreted to represent the best hypothesis of phylogenetic relationships. Although traditionally such cladograms were generated largely on the basis of morphological characters and originally calculated by hand, genetic sequencing data and computational phylogenetics are now commonly used in phylogenetic analyses, and
295-422: A coarse impression of the complexity. A more detailed account will give details about fractions of introgressions between groupings, and even geographic variations thereof. This has been used as an argument for the use of paraphyletic groupings, but typically other reasons are quoted. Horizontal gene transfer is the mobility of genetic info between different organisms that can have immediate or delayed effects for
354-769: A dipole moment of approximately 320 debye while cytochromes c of plants and insects have a dipole moment of approximately 340 debye. Cytochrome c is an essential component of the respiratory electron transport chain in mitochondria. The heme group of cytochrome c accepts electrons from the bc 1 Complex III and transports them to Complex IV , while it transfers energy in the opposite direction. Cytochrome c can also catalyze several redox reactions such as hydroxylation and aromatic oxidation , and shows peroxidase activity by oxidation of various electron donors such as 2,2-azino- bis (3-ethylbenzthiazoline-6-sulphonic acid) ( ABTS ), 2-keto-4-thiomethyl butyric acid and 4-aminoantipyrine. A bacterial cytochrome c functions as
413-429: A few residues. In more than thirty species tested in one study, 34 of the 104 amino acids were conserved (identical at their characteristic position). For example, human cytochrome oxidase reacted with wheat cytochrome c , in vitro ; which held true for all pairs of species tested. In addition, the redox potential of +0.25 volts is the same in all cytochrome c molecules studied. Cytochrome c belongs to class I of
472-460: A hypothesis, a clade can be rejected only if some groupings were explicitly excluded. It may then be found that the excluded group did actually descend from the last common ancestor of the group, and thus emerged within the group. ("Evolved from" is misleading, because in cladistics all descendants stay in the ancestral group). To keep only valid clades, upon finding that the group is paraphyletic this way, either such excluded groups should be granted to
531-489: A large number and variety of different kinds of characters are viewed as more robust than those based on more limited evidence. Mono-, para- and polyphyletic taxa can be understood based on the shape of the tree (as done above), as well as based on their character states. These are compared in the table below. Cladistics, either generally or in specific applications, has been criticized from its beginnings. Decisions as to whether particular character states are homologous ,
590-473: A lot of possible trees. Assigning names to each possible clade may not be prudent. Furthermore, established names are discarded in cladistics, or alternatively carry connotations which may no longer hold, such as when additional groups are found to have emerged in them. Naming changes are the direct result of changes in the recognition of mutual relationships, which often is still in flux, especially for extinct species. Hanging on to older naming and/or connotations
649-510: A massive release of cyt c , which then acts in the positive feedback loop to maintain ER calcium release through the IP3Rs. This explains how the ER calcium release can reach cytotoxic levels. This release of cytochrome c in turn activates caspase 9 , a cysteine protease . Caspase 9 can then go on to activate caspase 3 and caspase 7 , which are responsible for destroying the cell from within. One of
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#1733092558556708-475: A particular method. Datasets are tables consisting of molecular , morphological, ethological and/or other characters and a list of operational taxonomic units (OTUs), which may be genes, individuals, populations, species, or larger taxa that are presumed to be monophyletic and therefore to form, all together, one large clade; phylogenetic analysis infers the branching pattern within that clade. Different datasets and different methods, not to mention violations of
767-720: A particular set of methods used in phylogenetic analysis, although it is now sometimes used to refer to the whole field. What is now called the cladistic method appeared as early as 1901 with a work by Peter Chalmers Mitchell for birds and subsequently by Robert John Tillyard (for insects) in 1921, and W. Zimmermann (for plants) in 1943. The term " clade " was introduced in 1958 by Julian Huxley after having been coined by Lucien Cuénot in 1940, "cladogenesis" in 1958, "cladistic" by Arthur Cain and Harrison in 1960, "cladist" (for an adherent of Hennig's school) by Ernst Mayr in 1965, and "cladistics" in 1966. Hennig referred to his own approach as "phylogenetic systematics". From
826-457: A period, many branches may have radiated, and it may take hundreds of millions of years for them to have whittled down to just two. Only then one can theoretically assign proper last common ancestors of groupings which do not inadvertently include earlier branches. The process of true cladistic bifurcation can thus take a much more extended time than one is usually aware of. In practice, for recent radiations, cladistically guided findings only give
885-444: A phylogenetic tree are used to justify decisions about character states, which are then used as evidence for the shape of the tree. Phylogenetics uses various forms of parsimony to decide such questions; the conclusions reached often depend on the dataset and the methods. Such is the nature of empirical science, and for this reason, most cladists refer to their cladograms as hypotheses of relationship. Cladograms that are supported by
944-535: A powerful way to test hypotheses about cross-cultural relationships among folktales. Literature : Cladistic methods have been used in the classification of the surviving manuscripts of the Canterbury Tales , and the manuscripts of the Sanskrit Charaka Samhita . Historical linguistics : Cladistic methods have been used to reconstruct the phylogeny of languages using linguistic features. This
1003-400: A precondition of their being synapomorphies, have been challenged as involving circular reasoning and subjective judgements. Of course, the potential unreliability of evidence is a problem for any systematic method, or for that matter, for any empirical scientific endeavor at all. Transformed cladistics arose in the late 1970s in an attempt to resolve some of these problems by removing
1062-406: A priori assumptions about phylogeny from cladistic analysis, but it has remained unpopular. The cladistic method does not identify fossil species as actual ancestors of a clade. Instead, fossil taxa are identified as belonging to separate extinct branches. While a fossil species could be the actual ancestor of a clade, there is no way to know that. Therefore, a more conservative hypothesis is that
1121-540: A protein-cage, which was different from enzyme in solution. This was attributed to local microenvironment provided by Dps nanocage's interior cavity which is different than bulk. Cladistics Cladistics ( / k l ə ˈ d ɪ s t ɪ k s / klə- DIST -iks ; from Ancient Greek κλάδος kládos 'branch') is an approach to biological classification in which organisms are categorized in groups (" clades ") based on hypotheses of most recent common ancestry . The evidence for hypothesized relationships
1180-401: A side-branch, not distinguishing whether an actual ancestor of other groupings was found. The techniques and nomenclature of cladistics have been applied to disciplines other than biology. (See phylogenetic nomenclature .) Cladistics findings are posing a difficulty for taxonomy , where the rank and (genus-)naming of established groupings may turn out to be inconsistent. Cladistics is now
1239-423: Is a small hemeprotein found loosely associated with the inner membrane of the mitochondrion where it plays a critical role in cellular respiration . It transfers electrons between Complexes III (Coenzyme Q – Cyt c reductase) and IV (Cyt c oxidase). Cytochrome c is highly water-soluble , unlike other cytochromes . It is capable of undergoing oxidation and reduction as its iron atom converts between
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#17330925585561298-555: Is a synapomorphy of the earliest taxa to be included within Tetrapoda: did all the earliest members of the Tetrapoda inherit four limbs from a common ancestor, whereas all other vertebrates did not, or at least not homologously? By contrast, for a group within the tetrapods, such as birds, having four limbs is a plesiomorphy. Using these two terms allows a greater precision in the discussion of homology, in particular allowing clear expression of
1357-440: Is correct, then the last common ancestor of turtles and birds, at the branch near the ▼ lived earlier than the last common ancestor of lizards and birds, near the ♦ . Most molecular evidence , however, produces cladograms more like this: lizards turtles crocodilians birds If this is accurate, then the last common ancestor of turtles and birds lived later than the last common ancestor of lizards and birds. Since
1416-574: Is counter-productive, as they typically do not reflect actual mutual relationships precisely at all. E.g. Archaea, Asgard archaea, protists, slime molds, worms, invertebrata, fishes, reptilia, monkeys, Ardipithecus , Australopithecus , Homo erectus all contain Homo sapiens cladistically, in their sensu lato meaning. For originally extinct stem groups, sensu lato generally means generously keeping previously included groups, which then may come to include even living species. A pruned sensu stricto meaning
1475-500: Is often adopted instead, but the group would need to be restricted to a single branch on the stem. Other branches then get their own name and level. This is commensurate to the fact that more senior stem branches are in fact closer related to the resulting group than the more basal stem branches; that those stem branches only may have lived for a short time does not affect that assessment in cladistics. The comparisons used to acquire data on which cladograms can be based are not limited to
1534-504: Is similar to the traditional comparative method of historical linguistics, but is more explicit in its use of parsimony and allows much faster analysis of large datasets ( computational phylogenetics ). Textual criticism or stemmatics : Cladistic methods have been used to reconstruct the phylogeny of manuscripts of the same work (and reconstruct the lost original) using distinctive copying errors as apomorphies. This differs from traditional historical-comparative linguistics in enabling
1593-474: Is typically shared derived characteristics ( synapomorphies ) that are not present in more distant groups and ancestors. However, from an empirical perspective, common ancestors are inferences based on a cladistic hypothesis of relationships of taxa whose character states can be observed. Theoretically, a last common ancestor and all its descendants constitute a (minimal) clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if
1652-739: The c-type cytochrome family and contains a characteristic CXXCH (cysteine-any-any-cysteine-histidine) amino acid motif that binds heme. This motif is located towards the N-terminus of the peptide chain and contains a histidine as the 5th ligand of the heme iron. The 6th ligand is provided by a methionine residue found towards the C-terminus . The protein backbone is folded into five α-helices that are numbered α1-α5 from N-terminus to C-terminus. Helices α3, α4 and α5 are referred to as 50s, 60s and 70s helices, respectively, when referring to mitochondrial cytochrome c. While most heme proteins are attached to
1711-525: The ferrous and ferric forms, but does not bind oxygen . It also plays a major role in cell apoptosis . In humans, cytochrome c is encoded by the CYCS gene . Cytochrome c is a highly conserved protein across the spectrum of eukaryotic species, found in plants, animals, fungi, and many unicellular organisms. This, along with its small size (molecular weight about 12,000 daltons ), makes it useful in studies of cladistics . Cytochrome c has been studied for
1770-409: The parsimony criterion has been abandoned by many phylogeneticists in favor of more "sophisticated" but less parsimonious evolutionary models of character state transformation. Cladists contend that these models are unjustified because there is no evidence that they recover more "true" or "correct" results from actual empirical data sets Every cladogram is based on a particular dataset analyzed with
1829-539: The amount of data available for phylogenetics. At the same time, cladistics rapidly became popular in evolutionary biology, because computers made it possible to process large quantities of data about organisms and their characteristics. The cladistic method interprets each shared character state transformation as a potential piece of evidence for grouping. Synapomorphies (shared, derived character states) are viewed as evidence of grouping, while symplesiomorphies (shared ancestral character states) are not. The outcome of
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1888-533: The cardiolipin–cytochrome c complex. The hemoprotein is then detached from the mitochondrial inner membrane and can be extruded into the soluble cytoplasm through pores in the outer membrane. The sustained elevation in calcium levels precedes cyt c release from the mitochondria. The release of small amounts of cyt c leads to an interaction with the IP3 receptor (IP3R) on the endoplasmic reticulum (ER), causing ER calcium release. The overall increase in calcium triggers
1947-441: The cell to culture medium, is a sensitive method to monitor the degree of apoptosis. However, detailed immuno-electronmicroscopic studies with rat tissues sections employing cytochrome c specific antibodies provide compelling evidence that cytochrome c under normal cellular conditions is also present at extramitochondrial locations. In pancreatic acinar cells and the anterior pituitary , strong and specific presence of cytochrome c
2006-422: The clade, or the group should be abolished. Branches down to the divergence to the next significant (e.g. extant) sister are considered stem-groupings of the clade, but in principle each level stands on its own, to be assigned a unique name. For a fully bifurcated tree, adding a group to a tree also adds an additional (named) clade, and a new level on that branch. Specifically, also extinct groups are always put on
2065-443: The cladograms show two mutually exclusive hypotheses to describe the evolutionary history, at most one of them is correct. The cladogram to the right represents the current universally accepted hypothesis that all primates , including strepsirrhines like the lemurs and lorises , had a common ancestor all of whose descendants are or were primates, and so form a clade; the name Primates is therefore recognized for this clade. Within
2124-402: The development of cultures or artifacts using groups of cultural traits or artifact features. Comparative mythology and folktale use cladistic methods to reconstruct the protoversion of many myths. Mythological phylogenies constructed with mythemes clearly support low horizontal transmissions (borrowings), historical (sometimes Palaeolithic) diffusions and punctuated evolution. They also are
2183-408: The electron transport chain and cell apoptosis, according to a recent study cytochrome c can also act as an antioxidative enzyme in the mitochondria; it does so by removing superoxide ( O − 2 ) and hydrogen peroxide (H 2 O 2 ) from mitochondria . Therefore, not only is cytochrome c required in the mitochondria for cellular respiration, but it is also needed in the mitochondria to limit
2242-601: The electron transport chain. Cytochrome C has also been widely studied as an enzyme with peroxidase-like activity. Cytochrome C was conjugated to charged polymer to test its peroxidase-like activity. Inspired from natural examples of enzyme encapsulation in protein-based cage structures (Example: Carboxysomes, Ferritin and Encapsulin), Cytochrome C was encapsulated in a 9 nm small self-assembling DNA binding protein from nutrient starved cells (Dps) protein cage using chimeric self-assembly approach. Authors observed unique catalytic activity behavior upon encapsulating enzyme inside
2301-410: The exact historic relationships between the groups. The following terms, coined by Hennig, are used to identify shared or distinct character states among groups: The terms plesiomorphy and apomorphy are relative; their application depends on the position of a group within a tree. For example, when trying to decide whether the tetrapods form a clade, an important question is whether having four limbs
2360-512: The field of biology. Any group of individuals or classes that are hypothesized to have a common ancestor, and to which a set of common characteristics may or may not apply, can be compared pairwise. Cladograms can be used to depict the hypothetical descent relationships within groups of items in many different academic realms. The only requirement is that the items have characteristics that can be identified and measured. Anthropology and archaeology : Cladistic methods have been used to reconstruct
2419-481: The fossil taxon is related to other fossil and extant taxa, as implied by the pattern of shared apomorphic features. An otherwise extinct group with any extant descendants, is not considered (literally) extinct, and for instance does not have a date of extinction. Anything having to do with biology and sex is complicated and messy, and cladistics is no exception. Many species reproduce sexually, and are capable of interbreeding for millions of years. Worse, during such
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2478-433: The glimpse it gives into evolutionary biology. Cytochrome c has a primary structure consisting of a chain of about 100 amino acids . Many higher-order organisms possess a chain of 104 amino acids. The sequence of cytochrome c in humans is identical to that of chimpanzees (our closest relatives), but differs from that of horses. Cytochrome c has an amino acid sequence that is highly conserved in eukaryotes, varying by only
2537-407: The hierarchical relationships among different homologous features. It can be difficult to decide whether a character state is in fact the same and thus can be classified as a synapomorphy, which may identify a monophyletic group, or whether it only appears to be the same and is thus a homoplasy, which cannot identify such a group. There is a danger of circular reasoning: assumptions about the shape of
2596-410: The initial attraction between cardiolipin and cytochrome c is electrostatic due to the extreme positive charge on cytochrome c, the final interaction is hydrophobic, where a hydrophobic tail from cardiolipin inserts itself into the hydrophobic portion of cytochrome c. During the early phase of apoptosis, mitochondrial ROS production is stimulated, and cardiolipin is oxidized by a peroxidase function of
2655-487: The latter contains Tarsiiformes and Anthropoidea. Lemurs and tarsiers may have looked closely related to humans, in the sense of being close on the evolutionary tree to humans. However, from the perspective of a tarsier, humans and lemurs would have looked close, in the exact same sense. Cladistics forces a neutral perspective, treating all branches (extant or extinct) in the same manner. It also forces one to try to make statements, and honestly take into account findings, about
2714-596: The link to point directly to the intended article. Retrieved from " https://en.wikipedia.org/w/index.php?title=CYCS&oldid=633089815 " Category : Disambiguation pages Hidden categories: Short description is different from Wikidata All article disambiguation pages All disambiguation pages Cytochrome c 1J3S , 3NWV , 3ZCF , 3ZOO , 2N9J , 2N9I 54205 13063 ENSG00000172115 ENSMUSG00000063694 P99999 P62897 NM_018947 NM_007808 NP_061820 NP_031834 The cytochrome complex , or cyt c ,
2773-419: The mentioned assumptions, often result in different cladograms. Only scientific investigation can show which is more likely to be correct. Until recently, for example, cladograms like the following have generally been accepted as accurate representations of the ancestral relations among turtles, lizards, crocodilians, and birds: turtles lizards crocodilians birds If this phylogenetic hypothesis
2832-451: The most commonly used method to classify organisms. The original methods used in cladistic analysis and the school of taxonomy derived from the work of the German entomologist Willi Hennig , who referred to it as phylogenetic systematics (also the title of his 1966 book); but the terms "cladistics" and "clade" were popularized by other researchers. Cladistics in the original sense refers to
2891-405: The possibility of the existence of yet-unidentified specific mechanisms for protein translocation from mitochondria to other cellular destinations. Cytochrome c has been used to detect peroxide production in biological systems. As superoxide is produced, the number of oxidised cytochrome c increases, and reduced cytochrome c decreases. However, superoxide is often produced with nitric oxide. In
2950-483: The presence of nitric oxide, the reduction of cytochrome c is inhibited. This leads to the oxidisation of cytochrome c to cytochrome c by peroxynitrous acid , an intermediate made through the reaction of nitric oxide and superoxide. Presence of peroxynitrite or H 2 O 2 and nitrogen dioxide NO 2 in the mitochondria can be lethal since they nitrate tyrosine residues of cytochrome c, which leads to disruption of cytochrome c's function as an electron carrier in
3009-444: The primates, all anthropoids (monkeys, apes, and humans) are hypothesized to have had a common ancestor all of whose descendants are or were anthropoids, so they form the clade called Anthropoidea. The "prosimians", on the other hand, form a paraphyletic taxon. The name Prosimii is not used in phylogenetic nomenclature , which names only clades; the "prosimians" are instead divided between the clades Strepsirhini and Haplorhini , where
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#17330925585563068-473: The production of O − 2 and H 2 O 2 . Cytochrome c is widely believed to be localised solely in the mitochondrial intermembrane space under normal physiological conditions. The release of cytochrome c from mitochondria to the cytosol, where it activates the caspase family of proteases , is believed to be the primary trigger leading to the onset of apoptosis. Measuring the amount of cytochrome c leaking from mitochondria to cytosol, and out of
3127-413: The proper directions and enhancing their abilities to bind to other molecules. The dipole moment of cytochrome c results from a cluster of negatively charged amino acid side chains at the "back" of the enzyme. Despite variations in the number of bound heme groups and variations in sequence, the dipole moment of vertebrate cytochromes c is remarkably conserved. For example, vertebrate cytochromes c all have
3186-493: The prosthetic group through iron ion ligation and tertiary interactions, the heme group of cytochrome c makes thioether bonds with two cysteine side chains of the protein. One of the main properties of heme c, which allows cytochrome c to have variety of functions, is its ability to have different reduction potentials in nature. This property determines the kinetics and thermodynamics of an electron transfer reaction. The dipole moment has an important role in orienting proteins to
3245-432: The reciprocal host. There are several processes in nature which can cause horizontal gene transfer . This does typically not directly interfere with ancestry of the organism, but can complicate the determination of that ancestry. On another level, one can map the horizontal gene transfer processes, by determining the phylogeny of the individual genes using cladistics. If there is unclarity in mutual relationships, there are
3304-461: The terms worms or fishes were used within a strict cladistic framework, these terms would include humans. Many of these terms are normally used paraphyletically , outside of cladistics, e.g. as a ' grade ', which are fruitless to precisely delineate, especially when including extinct species. Radiation results in the generation of new subclades by bifurcation, but in practice sexual hybridization may blur very closely related groupings. As
3363-410: The time of his original formulation until the end of the 1970s, cladistics competed as an analytical and philosophical approach to systematics with phenetics and so-called evolutionary taxonomy . Phenetics was championed at this time by the numerical taxonomists Peter Sneath and Robert Sokal , and evolutionary taxonomy by Ernst Mayr . Originally conceived, if only in essence, by Willi Hennig in
3422-416: The ways cell apoptosis is activated is by release of cytochrome c from the mitochondria into cytosol. A study has shown that cells are able to protect themselves from apoptosis by blocking the release of cytochrome c using Bcl-x L . Another way that cells can control apoptosis is by phosphorylation of Tyr48, which would turn cytochrome c into an anti-apoptotic switch. In addition to its well-known roles in
3481-530: Was detected in zymogen granules and in growth hormone granules, respectively. In the pancreas, cytochrome c was also found in condensing vacuoles and in the acinar lumen . The extramitochondrial localisation of cytochrome c was shown to be specific as it was completely abolished upon adsorption of the primary antibody with purified cytochrome c. Besides cytochrome c, extramitochondrial localisation has also been observed for large numbers of other proteins including those encoded by mitochondrial DNA. This raises
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