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  • Allele
  • T (p.Glu172Asp) SNPs were found with variant allele frequencies of 12.9% (95% confidence interval: 11.0-15.0) and 7.2% (5.8-8.8). (nih.gov)
  • T (p.Ser486Phe) variant allele frequencies were 2.1% (1.4-3.1), 13.6% (11.7-15.7) and 2.8% (2.0-4.0), respectively. (nih.gov)
  • I/D refers to an insertion-deletion event in which a C was deleted at position (−31) in the most common allele, and IVS is intervening sequence (intron). (aacrjournals.org)
  • SNP calling and estimating the frequency of the minor allele from pooled samples, though, is a subtle exercise for at least three reasons. (nih.gov)
  • First, sequencing errors may have a much larger relevance than in individual SNP calling: while their impact in individual sequencing can be reduced by setting a restriction on a minimum number of reads per allele, this would have a strong and undesired effect in pools because it is unlikely that alleles at low frequency in the pool will be read many times. (nih.gov)
  • Second, the prior allele frequency for heterozygous sites in individuals is usually 0.5 (assuming one is not analyzing sequences coming from, e.g. cancer tissues), but this is not true in pools: in fact, under the standard neutral model, singletons (i.e. alleles of minimum frequency) are the most common class of variants because P(f) ∝ 1/f and they occur more often as the sample size increases. (nih.gov)
  • To improve upon existing theory and software packages, we have developed a Bayesian approach for minor allele frequency (MAF) computation and SNP calling in pools (and implemented it in a program called snape): the approach takes into account sequencing errors and allows users to choose different priors. (nih.gov)
  • cDNA
  • We sequenced a cDNA library constructed with mixed RNA from carnation leaves subjected to 42°C HS (0, 0.5, 1, and 2 h) and 46°C HS (0.5, 1, and 2 h), and obtained 45,604,882 high quality paired-end reads. (frontiersin.org)
  • The numbering scheme for nucleotide positions is based on assignment of the (+1) position to the "A" in the translation initiation codon, with nucleotides 5′ to that position assigned negative and those 3′ within the cDNA assigned positive numbers. (aacrjournals.org)
  • locus
  • Edwards argued that, even if the probability of misclassifying an individual based on the frequency of alleles at a single locus is as high as 30 percent (as Lewontin reported in 1972), the misclassification probability becomes close to zero if enough loci are studied. (wikipedia.org)
  • Gene density is estimated to be 1 locus per 7.5 Kb (compared with 9 Kb in fruit fly and 100 Kb in human). (biomedcentral.com)
  • Furthermore, the correlations between tRNA locus variation and transcription indicate that prediction of tRNA gene expression based on sequence variation data is possible. (pnas.org)
  • Humans
  • In addition to the Alu sequences in humans, about 3 percent of the fruit fly Drosophila melanogaster genome is made up of transposable element DNA. (encyclopedia.com)
  • We present evidence that transcription-associated mutagenesis and strong purifying selection are key determinants of patterns of sequence variation within and surrounding tRNA genes in humans and diverse model organisms. (pnas.org)
  • resistance genes
  • Knowledge of the diversity and evolution of antimicrobial resistance genes in natural populations is important for an understanding of the origin of resistance and of the evolution of, e.g., beta-lactamase catalytic activity ( 6 ). (asm.org)
  • Protein
  • This model consists of a selection process, which depends on two hydrophobicity parameters that can be computed from protein sequences without any fit, and a mutation process for which we consider various models. (biomedcentral.com)
  • The effective selection process that we propose reproduces well amino acid distributions as observed in the protein sequences in the PDB. (biomedcentral.com)
  • Protein sequences are considered either unviable or equivalent (neutral). (biomedcentral.com)
  • High temperatures typically stimulate the expression of heat shock protein genes (HSPs), and these can have key roles in enabling the survival of an individual in the face of potentially fatal high temperatures. (frontiersin.org)
  • In nondiabetic Pima Indians an A to G substitution in codon 54 of the fatty acid binding protein 2 (FABP2) gene has been shown to be associated with insulin resistance. (ahajournals.org)
  • 2013) published in the December 13 issue of Science presents strong evidence for one particular source of selection (unrelated to protein function) influencing coding regions, known as exons, of genes. (evmedreview.com)
  • The response of EF 4.1 mice to an I‐Ab‐associated epitope of the F‐Mu LV envelope protein is dominated by clones expressing a Vα2 gene segment, thus allowing a comprehensive analysis of the TCR α repertoire in a relatively large cohort of mice. (embopress.org)
  • Recently, several genome-wide association studies (GWASs) have reproduced the significant association of the single nucleotide polymorphism (SNP) rs1344706 (located in intron 2 of the zinc finger protein 804A (ZNF804A) on chromosome 2q32.1) with schizophrenia. (biomedsearch.com)
  • Furthermore, each discovery links the riboswitch ligand to the protein products of the genes under regulation. (pnas.org)
  • evolution
  • We used 454 sequencing and designed a novel phylogenetic method to model lineage evolution of the bnAbs PGT121-134 and found a positive correlation between the level of somatic hypermutation (SHM) and the development of neutralization breadth and potency. (nih.gov)
  • Although transposition occurs at a low frequency, evolution has provided ample time in which to transpose elements. (encyclopedia.com)
  • Gene duplication is a mechanism of evolution. (encyclopedia.com)
  • Phylogenetic analysis of the three genes studied revealed parallel evolution, with the SHV, OKP, and LEN beta-lactamase families corresponding to the phylogenetic groups KpI, KpII, and KpIII, respectively. (asm.org)
  • phylogenetic
  • Phylogenetic relationships of amphibian families inferred from DNA sequences of mitochondrial 12S and 16S ribosomal RNA genes. (nii.ac.jp)
  • We estimated the time since divergence of the phylogenetic groups KpI and KpIII at between 6 and 28 million years, confirming the ancient presence of the beta-lactamase gene in the genome of K. pneumoniae . (asm.org)
  • repertoire
  • Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. (biomedcentral.com)
  • We performed high-throughput sequencing of the expressed antibody heavy chain repertoire from adult torafugu. (frontiersin.org)
  • The CDR-H3 sequence repertoire observed in individuals is biased with the preferential use of a small number of VDJ, dominated by sequences containing inserted nucleotides. (frontiersin.org)
  • Control and Treg‐depleted EF 4.1 mice were immunized, and the extent of the Vα2‐bearing, antigen‐specific TCR repertoire was characterized by high‐throughput sequencing and spectratyping analysis. (embopress.org)
  • Findings
  • Findings: Genes encoding silver resistance were detected most frequently in Enterobacter spp. (pharmb.io)
  • Klebsiella
  • Also, the class A beta-lactamases of the OXY group seem to have diversified in parallel with housekeeping genes in Klebsiella oxytoca ( 17 , 18 ). (asm.org)
  • analysis
  • However, a specialised software is required for the rational analysis of massive data generated by next-generation sequencing. (biomedcentral.com)
  • tcR is an R package for the advanced analysis of T cell receptor repertoires after primary TR sequences extraction from raw sequencing reads. (biomedcentral.com)
  • Despite the absence of genotyping for founder individuals in the analysis, the previously identified candidate region on chromosome 1 was refined and led to the identification of a candidate gene. (biomedcentral.com)
  • Because the genetic basis of insulin resistance in FCHL is unknown, we screened the entire coding region of the FABP2 gene by SSCP analysis in 24 patients with FCHL and in 40 healthy men. (ahajournals.org)
  • The frequency of amino acid polymorphism in codon 54 of the FABP2 gene was also verified in 24 probands and in all 82 control subjects by restriction fragment length polymorphism analysis. (ahajournals.org)
  • Nevertheless, careful sequence analysis allowed us to predict a consensus sequence that would likely represent an active archetypal sequence. (asmscience.org)
  • To assess the degree of intra- and inter-specific genetic variability, we report the identification and analysis of C. intestinalis SNP (Single Nucleotide Polymorphism) markers. (biomedcentral.com)
  • Haplotypes
  • Luciferase activity levels for reporter gene constructs containing CDA 5′-flanking region haplotypes transfected into HEK293T ( A ) or PC-3 ( B ) cells. (aacrjournals.org)
  • archetypal
  • In C. intestinalis , these two genes have lost their archetypal topology within the cluster, such that Hox10 is located between Hox4 and Hox5 . (biomedcentral.com)
  • This latter result represents an important platform for future studies on Hox genes showing deviations from the archetypal topology. (biomedcentral.com)
  • Clusters
  • Sequences of the sil and pco clusters indicated that a single mutational event in the silS gene could have caused the phenotypic resistance. (pharmb.io)
  • Furthermore
  • Furthermore, we studied the association of the codon 54 polymorphism of this gene with insulin resistance and lipid and lipoprotein levels in 58 family members of patients with FCHL. (ahajournals.org)
  • alignments
  • Genotypes were called from the alignments of sequence data to the gorilla reference for each of the 14 individuals, with sites filtered on the basis of mapping quality and depth (Methods). (nih.gov)
  • This approach uses multiple-sequence alignments, atomic-resolution structural information, and riboswitch gene associations. (pnas.org)
  • molecules
  • Type VI secretion amidase effector (Tae) molecules (encoded by tae genes) can kill rival bacteria by degrading their cells walls when delivered into those competing cells. (evmedreview.com)
  • then changed the DNA sequence further to make billions of different versions of the nanobody, each one slightly different from the next in the region that binds to the target molecules. (elifesciences.org)
  • functional
  • Gene is a particular sequence of nucleotides along a molecule of DNA which represents a functional unit of inheritance, and it is not known to subdivide (Rieger et al. (dagris.info)
  • SB not only represents the first DNA-based transposon ever shown to be active in cells of vertebrates, but the first functional gene ever reconstructed from inactive, ancient genetic material, for which an active, naturally occurring copy either does not exist or has not yet been isolated. (asmscience.org)
  • transposable
  • The transposase coding region can be replaced by a gene of interest (yellow box) within the transposable element. (asmscience.org)
  • transposon ( transposable genetic element ) A mobile genetic element, known informally as a 'jumping gene', that can become integrated at many different sites in the genome, either by moving from place to place or by producing copies of itself that insert elsewhere in the genome. (encyclopedia.com)
  • high
  • High throughput sequencing of TCRs expressed by antigen‐stimulated CD 4 T cells demonstrates that Tregs control both the magnitude and the breadth of an immune response. (embopress.org)
  • found
  • Numerous genes were found to be induced in response to HS, the study of which may advance our understanding of heat response of carnation. (frontiersin.org)
  • 2014) presents a fascinating study of examples in which bacterial genes have found their way to a number of distinct eukaryotic lineages including ticks and mites, gastropod (e.g., snails and slugs) and bivalve mollusks (e.g. clams and oysters), and choanoflagellates (a subset of ptotozoans). (evmedreview.com)
  • Three groups of sequences were found, two of them corresponding to the families SHV (pI 7.6) and LEN (pI 7.1), respectively, and one, more heterogeneous, corresponding to a new family that we named OKP (for other K. pneumoniae beta-lactamase). (asm.org)