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Topic: Silent mutations

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Point mutation

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	Mutations
		Recessive mutations (most of them are) will not be seen except on the rare occasions that both parents contribute a mutation at the same locus to their child.
		The significance of mutations is profoundly influenced by the distinction between germline and soma.
		Whatever the effect, the ultimate fate of that somatic mutation is to disappear when the cell in which it occurred, or its owner, dies.
	users.rcn.com /jkimball.ma.ultranet/BiologyPages/M/Mutations.html (2842 words)

	Mutation - Wikipedia, the free encyclopedia
		Mutations can be caused by copying errors in the genetic material during cell division and by exposure to ultraviolet or ionizing radiation, chemical mutagens, or viruses, or can occur deliberately under cellular control during processes such as meiosis or hypermutation.
		Mutations create variation in the gene pool, and the less favorable (or deleterious) mutations are removed from the gene pool by natural selection, while more favorable (beneficial or advantageous) ones tend to accumulate, resulting in evolutionary change.
		One theory for the etiology of the relatively high frequency of CCR5-32 in the euopean population is that is conferred resistance to the bubonic plague in mid-14th century Europe [2].
	en.wikipedia.org /wiki/Mutations (1920 words)

	mutation.html
		Neutral mutations are a type of missense mutation in which the new amino acid is chmically similar to the one it is replacing.
		Silent mutations are a type of substitution mutations in which a base substitution in the DNA template results no change in the amino acid.
		A nonsense mutation is a mutation that replaces a codon for an amino acid with one of the three stop codons.
	staff.jccc.net /pdecell/evolution/mutations/mutation.html (2525 words)

	PMG 2002 List 5
		What then occurs is that a point mutation that produces a stop codon, which would normally produce a nonfunctional prematurely terminated protein, now would produce a protein with some random amino acid at the point of mutation.
		Silent mutation: There is no change in translation, therefore there is no change in protein function.
		Silent mutation, in this context, means that the protein is still functional, so there is no expression of the mutation on the phenotype.
	utminers.utep.edu /rwebb/html/pmg_2002_list_5.html (773 words)

	MCDB 2150 -- Lecture 25
		Mutation: A mutation is any change in genetic information relative to a reference "wild-type" genome, including changes that affect expression of genes without altering their coding sequences and changes that do not cause any detectable phenotypic difference (silent mutations).
		Gene mutations are defined as those that occur entirely within one gene (and its upstream regulatory sequences) and may be either point mutations or other small disruptions of normal chromosomal structure that occur entirely within one gene.
		Somatic and germ-line mutations: The mutations that we normally deal with in genetics are those that occur in the germ-line and are thus passed on to subsequent generations.
	www.colorado.edu /MCDB/MCDB2150Fall/notes/L25.html (3937 words)

	Silent mutation - Wikipedia, the free encyclopedia
		Silent mutations are DNA mutations that do not result in a change to the amino acid sequence of a protein.
		The phrase silent mutation is often used interchangeably with the phrase synonymous mutation; however, synonymous mutations are a subcategory of the former, occurring only within exons.
		"A silent mutation induces exon skipping in the phenylalanine hydroxylase gene in phenylketonuria".
	en.wikipedia.org /wiki/Silent_mutations (280 words)

	Silent mutation - Information, Resources, Links and Reference (Site not responding. Last check: 2007-10-26)
		Silent mutations are DNA mutations that do not result in a change to the amino acid sequence of a protein.
		The phrase silent mutation is often used interchangeably with the phrase synonymous mutation; however, synonymous mutations are a subcategory of the former, occurring only within exons.
		Because silent mutations do not alter protein function they are often treated as though they are evolutionarily neutral.
	www.cyberpedia.net /info.php?title=Silent_mutation (312 words)

	Are Mutations Harmful?
		Quite often a mutation occurs within a population and then disappears because the organism had no offspring or didn't happen to pass the mutation on to its offspring; this can happen even if the mutation is beneficial.
		Moreover a mutation may be favorable in the sense that it permits survival in an unfavorable environment and yet be unfavorable in a better environment.
		A common effect of mutations conferring resistance to predators and parasites seems to be a lowering of the maximum growth rate of the mutant bacteria.
	www.talkorigins.org /faqs/mutations.html (8632 words)

	Human Prion Point Mutations
		Compound and homozygous prion mutations Predicting missing CJD mutations: predictions from CpG effect.
		Hsiao observed in N Engl J Med 1991 Apr 18;324(16):1091-7 that "one patient was homozygous for the lysine mutation [E200K], and her clinical course did not differ from that of the patients heterozygous for the mutation....
		The similarity of the clinical courses of the patient homozygous for this mutation and the patients heterozygous for it argues that familial Creutzfeldt-Jakob disease is a true dominant disorder.
	www.mad-cow.org /prion_point_mutations.html (4916 words)

	[No title] (Site not responding. Last check: 2007-10-26)
		Obviously, silent mutations that do not even change the amino acid (silent) are not maintained by selection - these differences in the DNA are invisible to selection.
		Mutations at the second position change amino acids, and these changes are deleterious.
		This strongly suggests that, although silent mutations in DNA tick along neutrally, the actual sequence of amino acids in the proteins is highly conserved and of significant selective value.
	facweb.furman.edu /~wworthen/bio55/neutral.htm (1424 words)

	Mutate a DNA Sentence! (Site not responding. Last check: 2007-10-26)
		Point mutations are single nucleotide base changes in a gene's DNA sequence.
		Missense mutations are point mutations that result in a single amino acid change within the protein.
		Silent mutations are point mutations that do not cause amino acid changes within the protein.
	learn.genetics.utah.edu /units/disorders/mutations/mutatedna.cfm (493 words)

	Evolution - A-Z - Silent mutations
		Silent base changes are mutations which do not alter the amino acid.
		If silent codon positions were selectively unconstrained, they should show pan-neutral evolution.
		This suggests that silent alternative codons are not all functionally equivalent.
	www.blackwellpublishing.com /ridley/a-z/Silent_mutations.asp (138 words)

	Tau mutations in familial frontotemporal dementia -- Spillantini and Goedert 123 (5): 857 -- Brain (Site not responding. Last check: 2007-10-26)
		Eight missense mutations, one deletion mutation and two silent mutations in the coding region are shown.
		Seven mutations that reduce the stability of this tau exon 10 splicing regulatory element RNA are shown.
		Progressive supranuclear palsy pathology caused by a novel silent mutation in exon 10 of the tau gene.
	brain.oxfordjournals.org /cgi/content/full/123/5/857 (1635 words)

	The Scientist : "Silent" mutations are not always silent
		They focused on the C3435T, a single nucleotide polymorphism (SNP) that is synonymous or silent, encoding for the same amino acid as the gene's wild-type version.
		The idea that synonymous mutations might lead to differently folded proteins was proposed by Ian Purvis at the University of Glasgow and his colleagues and, independently, by Anton Komar, now at Cleveland State University in Ohio.
		Gottesman and his colleagues speculate that synonymous mutations represent rare codons for which translation machinery is not optimized.
	www.the-scientist.com /news/home/38329 (1263 words)

	Strand asymmetry of CpG transitions as indicator of G1 phase-dependent origin of multiple tumorigenic p53 mutations in ...
		Mutations in dividing cells are replication dependent (Rd), whereas those in nondividing cells are time dependent (Td) (1-4).
		Silent p53 mutations are invisible to selection and may appear in tumors exclusively as neutral hitchhikers.
		However, this scheme is inconsistent with the fact that one of the mutations in p53 doublets is a hitchhiker (14).
	www.pnas.org /cgi/content/full/95/20/11927 (3946 words)

	Silent mutations in secondary Shine-Dalgarno sequences in the cDNA of human serum amyloid A4 promotes expression of ... (Site not responding. Last check: 2007-10-26)
		Silent mutations in secondary Shine-Dalgarno sequences in the cDNA of human serum amyloid A4 promotes expression of recombinant protein in Escherichia coli -- Hrzenjak et al.
		Mutations of rbs-like sequences in SAA4 cDNA by PCR.
		To mutate sequences from SAA4 cDNA which are similar to rbs from pT7-7 vector, three silent point mutations (underlined) were introduced by PCR using a specific 5' primer (primer A [mut/+]).
	peds.oxfordjournals.org /cgi/content/full/14/12/949 (2497 words)

	Gefitinib-Sensitive Mutations of the Epidermal Growth Factor Receptor Tyrosine Kinase Domain in Chinese Patients with ...
		mutation, we assessed mutations from exons 18 to 21 in 54 Chinese
		Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib.
		EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib.
	clincancerres.aacrjournals.org /cgi/content/full/11/12/4289 (2975 words)

	Mutations (Site not responding. Last check: 2007-10-26)
		Mutations are changes in the genotype which may or may not affect the phenotype
		Silent mutation: base change results in no change of the amino acid sequence of the translated protein
		Mutation rate is the probability that a gene will mutate when the cell divides
	microvet.arizona.edu /Courses/vsc610/mic205/mutations.html (632 words)

	Hypermutability in Carcinogenesis -- Strauss 148 (4): 1619 -- Genetics
		mutations in a tumor is the result of these different forces.
		Silent mutations are defined as nucleotide substitutions that
		, 1995 Somatic mutations in the BRCA1 gene in sporadic ovarian tumours.
	www.genetics.org /cgi/content/full/148/4/1619 (5103 words)

	Seed: The Sound of Silence
		Chava Kimchi-Sarfaty and her colleagues at the National Institutes of Health were trying to understand why certain silent mutations occurred with unusual frequency in a gene called multidrug resistance 1 (MDR1), found in human cancer cells.
		This mechanism, which they call "translational pausing," is actually just one of several ways in which silent mutations have very recently been shown to affect protein function—and, more broadly, the fitness of an organism.
		It turns out that silent mutations can also change the stability of mRNA, one of the important intermediates in the transfer of information from DNA to proteins, and disrupt gene splicing, the process by which the DNA that contains genes is trimmed away from the rest of the genome.
	www.seedmagazine.com /news/2007/03/the_sound_of_silence.php (624 words)

	EMBOSS: silent
		silent does a scan of a nucleic acid sequence for silent mutation restriction enzyme sites.
		silent finds positions in a sequence where a point mutation could be made to introduce a specified restriction enzyme recognition site without changing the translation.
		silent finds sites where a restriction enzyme site can be introduced without changing the translation in frame 1 of the sequence.
	www.psc.edu /general/software/packages/emboss/silent.html (402 words)

	WatCut: An on-line tool for restriction analysis, silent mutation scanning, SNP-RFLP analysis
		Silent mutation analysis is intended for use with oligonucleotide sequences.
		Mutations must not be introduced directly adjoining to the polymorphic site, since that would be the 3' end of the oligonucleotide.
		Allowing more than one mutation and having a gap of less than 3 base pairs is probably not a good idea.
	watcut.uwaterloo.ca /watcut/watcut/template.php?act=help (4687 words)

	Zen of Mutagenesis (Site not responding. Last check: 2007-10-26)
		Spontaneous mutations in a particular gene are typically very rare.
		However, many "hits" result in silent mutations -- for example, some mutations do not change the amino acid sequence of the resulting polypeptide, some mutations do not affect critical amino acid residues of the resulting polypeptide, and some mutations will be in unessential, noncoding sequences.
		Following heavy mutagenesis, it is important to move a desired mutation into an unmutagenized cell to separate the desired mutation from multiple other mutations in the original mutagenized cell.
	www.sci.sdsu.edu /~smaloy/MicrobialGenetics/topics/mutations/zen.html (539 words)

	Protocadherin Ii Cell Suraface Receptor For Normal Prion
		While none of the silent mutations is a smoking gun, it is not at all safe to assume that they are neutral.
		The webmaster updated the point mutation collection to reflect these 7 additions to known point mutations, bringing the total to 28 different sites (7 silent, 3 neutral coding, 18 causative).
		Genetic analysis of the mutated allele revealed a sequence of five extra octapeptide repeats, distinct from those of the two previously reported families with an insertion of this size.
	www.mad-cow.org /protocad.html (9347 words)

	The Frequency Distribution of Nucleotide Variation in Drosophila simulans -- Begun 18 (7): 1343 -- Molecular Biology ...
		mutation can be used in certain analyses, but not in others.
		mutations is similar to the ratio for unpreferred mutations
		Li W.-H., 1987 Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons J. Mol.
	mbe.oxfordjournals.org /cgi/content/full/18/7/1343 (4937 words)

	Silent and non - silent mutations
		In the above example, the second codon ACT in the master codes for Threonine and the corresponding codon in the query ACC also codes for the same, hence this is shown as a silent mutation.
		Whereas, the 3rd codon in the master codes for amino acid Asparagine and the corresponding codon in the query GTT codes for valine, hence this is shown as a non - silent mutation.
		While using IUPAC codes, the tool ignores all codons that have an IUPAC character in it no matter which choice is selected for the IUPAC codes but marks the amino-acid in that position with an X in the downloadable protein sequence.
	hiv-web.lanl.gov /content/hiv-db/HIGHLIGHT/silentNonSilent.html (247 words)

	Evidence of Selection on Silent Site Base Composition in Mammals: Potential Implications for the Evolution of Isochores ...
		GC mutations are on average segregating at higher or lower frequencies
		The pattern of silent polymorphism in MHC genes
		The proportion of neutral mutations segregating in a population that would be classified as an AT mutation, when the G + C content is 80%, as a function of the nucleotide diversity (see Appendix 1, Equation A3 and Equation A4).
	www.genetics.org /cgi/content/full/152/2/675 (5371 words)

	GCK Tutorial 6: Cloning a DNA Segment and Silent Mutations
		GCK Tutorial 6: Cloning a DNA Segment and Silent Mutations
		An alternative is to eliminate the middle BamHI site through a silent mutation, which will eliminate the BamHI site but not change the coding information.
		To make a silent mutation you first need to specify the reading frame to which you are referring.
	www.textco.com /support/gck-tutorials/gck_tutorial_06.html (912 words)

	Forensic Mathematics
		Multiple mutations, covert mutations, and false exclusions in paternity casework May05
		Symbolic Kinship Program – description and history Jan02
		Strategies and calculations in DNA kinship cases rev Apr00
	dna-view.com (399 words)

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