- Transversion
In molecular biology , transversion refers to the substitution of a purine for a pyrimidine or vice versa. ref http www.mun.ca biochem courses 3107 Topics Mutations.html Mutations & Mutagenesis ref It can only be reverted by a spontaneous reversion. Because this type of mutation changes the chemical structure dramatically, the consequences of this change tend to be more severe and less common than that of Transition genetics transitions . Transversions can be caused by ionizing radiation and alkylating agents. See also Transition genetics Transition References references External links http www.mun.ca biology scarr Transitions vs Transversions.html Diagram at mun.ca Mutation Category Mutation Molecular biology stub de Transversion pl Transwersja pt Transvers o ... more details
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- Transition (genetics)
Not to be confused with the evolutionary concept of a transitional fossil . In genetics, a transition is a point mutation that changes a purine nucleotide to another purine Adenine A Guanine G or a pyrimidine nucleotide to another pyrimidine Cytosine C Thymine T . Approximately two out of three single nucleotide polymorphism s SNPs are transitions. ref cite journal author Collins DW, Jukes TH title Rates of transition and transversion in coding sequences since the human rodent divergence journal Genomics volume 20 issue 3 pages 386 96 year 1994 month April pmid 8034311 doi 10.1006 geno.1994.1192 url http linkinghub.elsevier.com retrieve pii S0888 7543 84 71192 X ref Transitions can be caused by oxidative deamination and tautomerization . ref http www.mun.ca biochem courses 3107 Topics Mutations.html Mutations & Mutagenesis Bot generated title ref Although there are twice as many possible transversions , transitions appear more often in genomes, possibly due to the molecular mechanisms that generate them ref cite journal author Ebersberger I, Metzler D, Schwarz C, P bo S title Genomewide comparison of DNA sequences between humans and chimpanzees journal Am. J. Hum. Genet. volume 70 issue 6 pages 1490 7 year 2002 month June pmid 11992255 pmc 379137 doi 10.1086 340787 url http linkinghub.elsevier.com retrieve pii S0002 9297 07 60701 0 ref . 5 Methylcytosine is more prone to transition than unmethylated cytosine , due to spontaneous deamination . Fact taken from 5 Methylcytosine and deamination pages This mechanism is important because it dictates the rarity of CpG islands . See also Transversion References reflist External links http www.mun.ca biology scarr Transitions vs Transversions.html Diagram at mun.ca Cell biology stub Mutation Category Mutation bg de Transition Genetik es Transici n mutaci n ADN pl Tranzycja biologia pt Transi o ... more details
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- Depurination
Depurination is an alteration of DNA in which the purine base adenine or guanine is removed from the deoxyribose sugar by hydrolysis of the beta N glycosidic bond glycosidic link between them. After depurination, the sugar phosphate backbone remains and the sugar ring has a hydroxyl OH group in the place of the purine. Studies estimate that as many as 5,000 purines are lost this way each day in a typical human cell. ref name instability cite journal last Lindahl first T. date 22 April 1993 title Instability and decay of the primary structure of DNA journal Nature journal Nature volume 362 issue 6422 pages 709 715 issn 0028 0836 doi 10.1038 362709a0 pmid 8469282 url http www.nature.com nature journal v362 n6422 abs 362709a0.html ref One of the main causes of depurination is the presence of endogenous metabolites in cell undergoing chemical reactions. Depurinated bases in double stranded DNA are efficiently repaired by portions of the base excision repair pathway. Depurinated bases in single stranded DNA undergoing replication can lead to mutations , because in the absence of information from the complementary strand, BER can add an incorrect base at the apurinic site, resulting in either a Transition genetics transition or transversion mutation. ref cite web last Carr first Steven M. date 2009 title Depurination produces transversion mutations work http www.mun.ca biology scarr Directory.html www.mun.ca biology scarr publisher Memorial University of Newfoundland url http www.mun.ca biology scarr Depurination transversion.html accessdate 2010 08 19 ref Loss of pyrimidine bases Cytosine and Thymine occurs by a similar mechanism, but at a substantially lower rate. Hydrolytic depurination is one of the principal forms of damage to ancient DNA in fossil or subfossil material, since the base remains unrepaired. This results in both loss of information the base sequence , and difficulties in recovery and in vitro replication of the damaged molecule by the polymerase chain r ... more details
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- Covarion
genetics transition and transversion genetics transversion mutations, is the rate of transition ... more details
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- Slipped strand mispairing
Slipped strand mispairing SSM is a mutation process which occurs during DNA replication . It involves Denaturation biochemistry denaturation and displacement of the DNA strands, resulting in mispairing of the complementary bases. Slipped strand mispairing is one explanation for the origin and evolution of Repeated sequence DNA repetitive DNA sequences . ref name Levinson cite journal author Levinson, G. & Gutman, G. A. year 1987 title Slipped Strand Mispairing A Major Mechanism for DNA Sequence Evolution journal Mol. Biol. Evol. volume 4 issue 3 pages 203 221 pmid 3328815 ref Slipped Strand Mispairing has also been shown to function as a Phase variation mechanism in certain bacteria. ref name Torres Cruz cite journal author Torres Cruz, Joshua and van der Woude, Marjan W. year 2003 title Slipped Strand Mispairing Can Function as a Phase Variation Mechanism in Escherichia coli journal Journal of Bacteriology pages 6990 6994 doi 10.1128 JB.185.23.6990 6994.2003 volume 185 pmid 14617664 issue 23 pmc 262711 ref Self acceleration SSM events can result in either insertions or deletions. Insertions are thought to be self accelerating as repeats grow longer, the probability of subsequent mispairing events increases. Insertions can expand simple tandem repeats by one or more units. In long repeats, expansions may involve two or more units. For example, insertion of a single repeat unit in GAGAGA expands the sequence to GAGAGAGA, while insertion of two repeat units in GA sub 6 sub would produce GA sub 8 sub . Evolution of diverse adjacent repeats The combination of SSM events with point mutation is thought to account for the evolution of more complex repeat units. Mutations followed by expansion would result in the formation of new types of adjacent short tandem repeat units. For example, a transversion could change the simple two base repeat GA sub 10 sub to GA sub 4 sub GATA GA sub 2 sub . This could then be expanded to GA sub 4 sub GATA sub 3 sub GA sub 2 sub by two subseq ... more details
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- Palmitoyl protein thioesterase
Pfam box Symbol Palm thioest Name Palmitoyl protein thioesterase image 1eh5 opm.gif width caption Palmitoyl protein thioesterase 1. Red plane shows hydrocarbon boundary of the lipid bilayer Pfam PF02089 Pfam clan CL0028 InterPro IPR002472 SMART Prosite SCOP 1exw TCDB OPM family 135 OPM protein 1eh5 PDB PDB3 1eh5 A 28 306 PDB3 1ei9 A 28 306 PDB3 1exw A 28 306 PDB3 1pja A 32 302 enzyme Name palmitoyl protein hydrolase EC number 3.1.2.22 CAS number 150605 49 5 IUBMB EC number 3 1 2 22 GO code 0008474 image width caption Palmitoyl protein thioesterases are enzymes EC number 3.1.2.22 that remove thioester linked fatty acyl groups such as palmitate from modified cysteine residues in proteins or peptides during lysosome lysosomal degradation . neuronal ceroid lipofuscinosis Neuronal ceroid lipofuscinoses NCL represent a group of encephalopathies that occur in 1 in 12,500 children. Mutations in the palmitoyl protein thioesterase gene causing infantile neuronal ceroid lipofuscinosis ref name PUB00004218 cite journal author Hofmann SL, Vesa J, Hellsten E, Verkruyse LA, Camp LA, Rapola J, Santavuori P, Peltonen L title Mutations in the palmitoyl protein thioesterase gene causing infantile neuronal ceroid lipofuscinosis journal Nature volume 376 issue 6541 pages 584 587 year 1995 pmid 7637805 doi 10.1038 376584a0 ref . The most common mutation results in intracellular accumulation of the polypeptide and undetectable enzyme activity in the brain. Direct sequencing of cDNAs derived from brain RNA of INCL patients has shown a mis sense transversion of A to T at nucleotide position 364, which results in substitution of Trp for Arg at position 122 in the protein Arg 122 is immediately adjacent to a lipase consensus sequence that contains the putative active site Ser of PPT. The occurrence of this and two other independent mutations in the PPT gene strongly suggests that defects in this gene cause INCL. Examples Human proteins containing this domain include protein Name PPT1 palmitoy ... more details
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- Syrmaticus
NOTOC Taxobox image Syrmaticus humiae.jpg image caption Hume s Pheasant Syrmaticus humiae br female left and male image width 240px regnum Animal ia phylum Chordata classis Aves subclassis Neornithes infraclassis Galloanserae ordo Galliformes superfamilia Phasianoidea familia Phasianidae subfamilia Phasianinae genus Syrmaticus genus authority Johann Georg Wagler Wagler , 1832 subdivision ranks Species subdivision Reeves s Pheasant S. reevesii br Copper Pheasant S. soemmerringii br Mikado Pheasant S. mikado br Elliot s Pheasant S. ellioti br Hume s Pheasant S. humiae The genus Syrmaticus contains the five species of long tailed pheasant s . The males have short spurs and usually red facial wattle s, but otherwise differ wildly in appearance. The hens females and chicks pattern of all the species have a rather conservative and plesiomorphic drab brown color pattern. ref name zhanzhang2005 Zhan & Zhang 2005 ref 5 species are generally accepted in this genus. ref name zhanzhang2005 File Stavenn Syrmaticus soemmerringii 00.jpg thumb left At first glance, the Copper Pheasant S. soemmerringii resembles a female Common Pheasant Phasianus colchicus Systematics and taxonomy The genus is occasionally included in Phasianus based on DNA sequence data, but this does not seem well warranted the molecular evolution in this genus has been unusual and can easily mislead molecular phylogenetic studies and makes molecular clock s unreliable. At least in the cytochrome b cytochrome b sequence Transition genetics transition s have outnumbered transversion s to an extent rarely seen in other bird s. Transition transversion frequencies in mtDNA control region are by contrast more like those usually seen in birds, but this region of the mitochondrial genome has been evolving unusually slowly in Syrmaticus . ref name zhanzhang2005 Still, the phylogeny and evolution of the long tailed pheasants can be considered resolved to satisfaction by now. It was long accepted that the three southeastern ... more details
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- Models of DNA evolution
and the top right and bottom left 2 × 2 blocks corresponds to transversion probabilities ... to purine, or C T, i.e. from pyrimidine to pyrimidine and transversion s from purine to pyrimidine ... to 1 and use &kappa to denote the transition transversion rate ratio as is done below . The K80 model ... genetics transitions and transversion s using the &kappa parameter , and it allows unequal base ... title Estimation of the number of nucleotide substitutions when there are strong transition transversion ... when there are strong transition transversion and G C content biases, as in the case of Drosophila ... i.e. A G is allowed to have a different rate to C T . Transversion s are all assumed to occur ... more details
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- CYP2C9*13
Cytochrome P450 2C9 CYP2C9 , a member of the CYP2C enzyme subfamily, ranks amongst the most important drug metabolizing enzymes in humans. Human CYP2C9 has been shown to exhibit genetic Polymorphism biology polymorphism . In addition to the wild type protein CYP2C9 1, at least 30 single nucleotide polymorphisms SNPs have been reported within the coding region of the CYP2C9 gene producing the variant allozymes. CYP2C9 13 is one of them. It involves a T to C transversion at nucleotide position 269 causing a mutation at codon 90, which results in a Leu Pro substitution. Frequency analysis indicated approximately 2 of the Chinese population carry the allele. ref Si Dayong, Guo Yingjie, Zhang Yifan, Yang Lei, Zhou Hui , Zhong Dafang. http p4502c.googlepages.com my.pdf Identification of a novel variant CYP2C9 allele in Chinese . Pharmacogenetics. 2004 Jul 14 7 465 9. ref ref Zhang Yifan, Zhong Dafang , Si Dayong, Guo Yingjie, Chen Xiaoyan, Zhou Hui. http p4502c.googlepages.com bcp.pdf Lornoxicam pharmacokinetics in relation to cytochrome P450 2C9 genotype. The British Journal of Clinical Pharmacology. 2005 Jan 59 1 14 7. ref CYP2C9 13 was found in Japanese people Japanese and Korean people Korean ref Allele and genotype frequencies of CYP2C9 in a Korean population. Br J Clin Pharmacol. 2005 Oct 60 4 418 22 ref ref Tong YIN, Keiko MAEKAWA, Kei KAMIDE, Yoshiro SAITO, Hironori HANADA, Kotaro MIYASHITA, Yoshihiro KOKUBO, Yasuhisa AKAIWA, Ryoichi OTSUBO, Kazuyuki NAGATSUKA, Toshiho OTSUKI, Takeshi HORIO, Shin TAKIUCHI, Yuhei KAWANO, Kazuo MINEMATSU, Hiroaki NARITOMI, Hitonobu TOMOIKE, Jun ichi SAWADA, and Toshiyuki MIYATA1 , Genetic Variations of CYP2C9 in 724 Japanese Individuals and Their Impact on the Antihypertensive Effects of Losartan, Hypertens Res Vol. 31, No. 8 2008 , 1149 57 ref ref J Clin Pharm Ther. 2011 Jan 5. doi 10.1111 j.1365 2710.2010.01238.x. Epub ahead of print Frequency of CYP2C9 variant alleles, including CYP2C9 13 in a Korean population and effect on glim ... more details
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- Human mitochondrial molecular clock
Ma CH transversions, br small 15 1 transition transversion small style background fcfcfc style background ... methods To overcome the affects of saturation genetic saturation , HVR analysis relied on the transversion ... Harpending Kocher 1989 ref A Transition genetics transition to transversion ratio was applied to this distance ... Feldhofer I Neanderthal revealed that there was also a transversion between humans and Neanderthals ... was an underestimate of the likely number of transversion events. The year 1991 study also used a transition to transversion ratio from the study of old world monkeys of 15 1. Citation needed date ... more details
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- Benzo(a)pyrene
cycle and hence functions as a tumor suppressor . By inducing G guanine to T thymidine transversion s in transversion hotspots within p53 , there is a probability that benzo a pyrene diol epoxide ... more details
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- Ka/Ks ratio
transversion rates are substantially more reliable than those that do not. ref name Yang2000 Limitations ... more details
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- Intrinsic immunity
stranded DNA which introduces transversion mutations into the HIV genome during reverse transcription ... more details
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- Sobp
S449fsX490 . In the jc sup 2J sup allele, the mutation is a nonsense transversion of a guanine to a thymidine ... more details
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- Substitution model
for the transversion rate and in 1981, Felsenstein ref cite journal author Felsenstein J title ... transition transversion and G C content biases journal Mol. Biol. Evol. volume 9 issue 4 pages ... more details
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- Retinal Degeneration (Rhodopsin Mutation)
SP. Autosomal dominant sectoral retinitis pigmentosa two families with transversion mutation in codon ... findings associated with a rhodopsin gene codon 58 transversion mutation in autosomal dominant ... more details
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- Index of molecular biology articles
transposition transposon transversion Spin triplet triplet trisomy tRNA tumor suppressor tumor ... more details
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- Frataxin
pedigrees with the ATG to ATT transversion points to a unique common ancestor. journal Hum. Genet ... more details
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- NPC1
Pick disease is caused by a G3097 T transversion in NPC1. journal Am. J. Hum. Genet. volume ... more details
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- NUDT1
of A T to C G transversion. journal Genomics volume 24 issue 3 pages 485 90 year 1995 pmid 7713500 doi ... more details
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- Chargaff's rules
spontaneously slowly deaminates to adenosine a C to A transversion . The longer the strands are separated ... more details
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- Haplogroup H (Y-DNA)
M52 A C transversion was reported in the Vlax Roma Romani subgroup Roma Kalaydjieva et al. 2001 and India ... more details
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- DSC3
were Zygosity Homozygous homozygous for a 2129T G transversion in exon 14 of the DSC3 ... more details
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- Computational phylogenetics
genetics transitions and transversion s in nucleotide sequences. The use of substitution models ... advanced models distinguish between transition genetics transitions and transversion s. The most general ... more details
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- Aflatoxin
cite journal author F Aguilar, S P Hussain and P Cerutti title Aflatoxin B1 induces the transversion ... more details
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