• The differences are analyzed by DNA sequencing or by methods developed to quantify SNPs, such as Pyrosequencing (Biotage) or MassArray (Sequenom), measuring the relative amounts of C/T at the CG dinucleotide. (wikipedia.org)
  • After genotyping and applying various filters, researchers focused on three focal populations, pooling samples according to date (prior to DFTD or after DFTD introduction) in an attempt to identify single nucleotide polymorphisms (SNPs) and associated genes that had extreme allele frequency changes in response to DFTD. (reasons.org)
  • Two candidate regions-one on chromosome 2 and one on chromosome 3-were identified and contained nine unique SNPs that had allele frequency changes at or greater than the 97.5 percentile for the population harboring that specific SNP. (reasons.org)
  • The researchers admit that further investigation is absolutely necessary to identify which genetic changes and which genes may play a functional role in resistance to DFTD, as their findings point merely to disease-responsive SNPs. (reasons.org)
  • The advent of sequencing renewed interest in disease mechanisms less frequent but more penetrant than common single nucleotide polymorphisms (SNPs) of genome-wide association studies (GWAS). (biomedcentral.com)
  • In this study, we examined population substructures in a diverse set of over 1700 Han Chinese samples collected from 26 regions across China, each genotyped at approximately 160K single-nucleotide polymorphisms (SNPs). (nih.gov)
  • Assim, os objetivos deste trabalho foram obter as sequências dos genes - Phs e FRO1, acessar a frequência de SNPs em regiões codantes e não-codantes de ambos os genes, e avaliar a utilidade desses polimorfismos para investigar a diversidade genética em 31 genótipos cultivados de feijão comum e um acesso de P. lunatus. (usp.br)
  • During the past several years, hundreds of new variations in repetitive regions of DNA have been identified, leading researchers to believe that copy number variations (CNVs) are as important a component of genomic diversity as single nucleotide polymorphisms (SNPs). (nature.com)
  • The HapMap Project notes that CNVs encompass more nucleotide content per genome than SNPs, underscoring CNVs' significance to genetic diversity. (nature.com)
  • Dogs of various breeds, affected or unaffected with primary glaucoma, were genotyped for the Gly661Arg variant of ADAMTS10 , as well as 7 other nonsynonymous single nucleotide polymorphisms (SNPs) in other genes in the beagle POAG locus that segregate with disease. (arvojournals.org)
  • 1 Sequencing the entire locus revealed eight variants that segregated with disease and caused amino acid substitutions ( Fig. 1 ), all of which were single nucleotide polymorphisms (SNPs). (arvojournals.org)
  • 1 Genotyping the eight nonsynonymous SNPs in 48 control beagles showed that the Gly661Arg variant of ADAMTS10 had the lowest minor allele frequency (MAF). (arvojournals.org)
  • The locations of the eight nonsynonymous SNPs that segregate with disease in the POAG beagle colony are indicated by arrows labeled according to the gene in which the SNPs are located. (arvojournals.org)
  • Furthermore, they evaluated the face gene enrichment in 19,277 SNPs of 3,730 genes by applying a hypergeometric test and a 10,000 iterations Monte Carlo simulation. (news-medical.net)
  • Upon adding the reported face-associated SNPs to 19,277 SNPs, the authors observed that 11 of the 16 (68.7%) look-alike pairs clustered together, adding two new doubles. (news-medical.net)
  • Studies are generally limited to examination of individual regions or overlapping single-nucleotide polymorphisms (SNPs) and open chromatin peaks with limited investigation into how these regulatory elements combine to affect gene transcription 1 , 2 . (elifesciences.org)
  • It can be accessed online at www.helmholtz-hiri.de/en/datasets/enterococcus through an instance of the genomic viewer JBrowse. (frontiersin.org)
  • For the genomic information, the researchers ran single nucleotide polymorphisms (SNP) microarray that interrogated 4,327,108 genetic variants selected from the International HapMap and 1,000 Genomes Projects and targeted genetic variation down to 1% minor allele frequency (MAF). (news-medical.net)
  • Genomic analyses clustered only one couple together per copy number variation (CNVs). (news-medical.net)
  • VAAST's secret sauce, according to Reese, is that it is able to quickly mine genomic data, prioritize and identify disease-causing genes and their variants, and determine the statistical significance of any hits. (genomeweb.com)
  • At smaller genomic scales, promoter regions of hsp genes and the promoter region of CG18446 have been shown to accumulate TE insertions. (biomedcentral.com)
  • That the distances relating the number of identical base pairs to total HSP length (formula 2) behave differently indicates that the genomic similarities between T. velox, T. acidaminovorans and A. paucivorans are strongly restricted to more conserved sequences, a kind of saturation phenomenon [42]. (phosphorylase-signal.com)
  • The potential application of our method includes annotation of new genomic sequences and motif discovery. (biomedcentral.com)
  • Therefore, to address the growing volumes of available genomic sequence, a number of algorithms that identify putative cis-regulatory modules and transcription factor binding sites using evolutionary comparisons, whole-genome data, and known descriptions of transcription factor binding sites, have been successfully developed. (biomedcentral.com)
  • An allele is one of two or more versions of DNA sequence (a single base or a segment of bases) at a given genomic location. (genome.gov)
  • GEP studies also assess non-genetic throughput genomic techniques and the exposures, partly in recognition of the related bioinformatics to support GEN's importance of non-genetic factors in large-scale molecular epidemiology driving cancer incidence, and also to projects and other IARC genomics facilitate accurate assessment of gene- projects. (who.int)
  • He also noted concern regarding delays in referring specimens to the laboratory for testing, and emphasized the need for improvement in timeliness of reporting and tracking of the viruses referred for genomic sequencing. (who.int)
  • He thanked the regional and global specialized laboratories for their efforts to provide timely results of the genomic sequencing of wild polioviruses, and for their help in planning and monitoring polio eradication activities in the Region. (who.int)
  • Simply put, population genetics is the study of genetic variation within populations and assessment of changes in the frequencies of genetic variations and alleles in populations. (livemint.com)
  • Alleles are nucleotide bases (A, T, G and C) found in the DNA in different combinations and demonstrate genetic variations. (livemint.com)
  • These alleles collectively form a cluster known as the gene pool of a certain population. (livemint.com)
  • Are most adaptive alleles new mutations or pre-existing alleles segregating at low to moderate frequency within a species? (unc.edu)
  • A way to improve the drought tolerance of crops is to discover new genes and alleles that allow plants to continue to grow and maintain or increase grain yield under water-limited growing conditions. (biomedcentral.com)
  • For phylogenetic analysis, nucleotide sequences identified in this study were deposited in GISAID (www.gisaid.org) and GenBank (www.ncbi.nlm.nih.gov/genomes/FLU). (cdc.gov)
  • Our understanding of the ecology of oral microbes surged thanks to the Human Microbiome Project (HMP) [ 20 ], which generated extensive sequencing data from 9 oral sites sampled from 200 healthy individuals and over 300 reference genomes for bacteria isolated from the human oral cavity. (biomedcentral.com)
  • Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13-15]. (deepdyve.com)
  • He told BioInform 's sister publication Clinical Sequencing News that the platform will be used to clinically annotate both whole genomes and more targeted data such as exomes or gene panels ( CSN 06/29/11 ). (genomeweb.com)
  • Unlike analysis methods developed for GWAS, "which evaluate the statistical significance of frequency differences for individual variants in cases vs. controls, VAAST evaluates the likelihood of observing the aggregate genotype of a feature given a background dataset of control genomes," the authors note, adding that this approach "greatly improves statistical power, in part because it bypasses the need for large statistical corrections for multiple tests. (genomeweb.com)
  • These data will provide new insight into how genomes evolve, which types of genes are evolving most rapidly, the relationships between recombination, DNA divergence, and DNA polymorphism, and details about the spatial and organizational evolution of genomes. (unc.edu)
  • The comparison of the number of genes belonging to different COG categories revealed no large differences in the genomes of T. velox and T. acidaminovorans, with only 0.2% deviation between the same COG categories on average. (phosphorylase-signal.com)
  • This is an actively progressing area, as more and more sequenced genomes appear. (biomedcentral.com)
  • One feature in which virus genomes are usually rich, is the presence of overlapping reading frames (OvRFs) - portions of the genome where the same nucleotide sequence encodes more than one protein. (uwo.ca)
  • Further, I retrieved n = 8, 586 protein-coding sequences from n = 1, 224 reference genomes, and used an alignment-free method to cluster these sequences within virus families. (uwo.ca)
  • I also used these net- works to generate a high-level visualization of how overlapping genes are distributed among virus genomes in the same family. (uwo.ca)
  • In particular, understanding the impact of OvRFs on the evolution of virus genomes will provide us with crucial pieces of a significant puzzle - under- standing the origin of new genes in virus genomes, and thereby virus diversity. (uwo.ca)
  • Many viral genomes have a type of gene arrangement known as overlapping reading frames (OvRFs), where the same sequence encodes multiple pro- teins. (uwo.ca)
  • OvRFs are thought to be used by viruses to increase the amount of information contained in smaller genomes, regulate transcription, and contribute to the creation of new genes. (uwo.ca)
  • Understanding the role of OvRFs in virus genomes provides valuable insights into the origin of new genes and the diversity of viruses. (uwo.ca)
  • Genomes of M. tuberculosis cultures from a relatively high and low incidence region in Guangxi have been sequenced. (biomedcentral.com)
  • We sequenced SARS-CoV-2 genomes for patients and healthcare workers (HCWs) across multiple geographically distinct UK hospitals, obtaining 173 high-quality SARS-CoV-2 genomes. (cdc.gov)
  • Sequence Analysis of 20,453 SARS-CoV-2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern. (cdc.gov)
  • A maximum-likelihood tree was estimated by using MEGA7 and the Hasegawa-Kishino-Yano model of nucleotide substitution with gamma-distributed rate variation among sites with 4 rate categories. (cdc.gov)
  • To unravel the effects of OvRFs on virus evolution, I developed HexSE, a simulation model of nucleotide sequence evolution along a phylogeny that tracks the substitution rates at every nucleotide site. (uwo.ca)
  • Thus, the first step in identifying the disease-susceptibility genes should involve identification of candidate genes. (livemint.com)
  • Candidate genes for T2DM include genes responsible for pancreatic cell (Beta cell), insulin action/glucose metabolism, or other metabolic conditions that increase T2DM risk (eg, energy intake/expenditure, lipid metabolism). (livemint.com)
  • More than 50 candidate genes for T2DM have been studied worldwide. (livemint.com)
  • The simplest forms of filters are minor allele frequency (MAF), candidate genes or variants, or considering the exome. (biomedcentral.com)
  • Candidate genes with changes in expression are identified through microarray and other expression studies. (unc.edu)
  • Candidate genes with structural changes are identified using population genetic data and positional cloning. (unc.edu)
  • Subsequently, candidate genes and their regulatory regions are analyzed in order to pinpoint the genetic changes that have occurred and how they have evolved. (unc.edu)
  • This finding is a step-forward in understanding the function of these loci and identifying candidate genes to accelerate positional cloning of yield QTL in wheat under drought. (biomedcentral.com)
  • We propose an approach for low-resolution, yet accurate, early detection of specific variants of concern through clustered interspaced short palindromic repeats (CRISPR) diagnostics. (cdc.gov)
  • In this study, DNA fragment of the mitochondrial cytochrome c oxidase subunit I (COXI) gene of H. Lepturus for the molecular phylogenetic analysis was amplified. (ac.ir)
  • After sequencing of the PCR products, the phylogenetic analysis was performed using the neighbor-joining method with 1000 replicates of bootstrapping using the MEGA7 software. (ac.ir)
  • The candidate regions identified in chromosomes 2 and 3 correspond to regions harboring five genes (one on chromosome 2 and four on chromosome 3) associated with immune function or cancer in other mammals. (reasons.org)
  • The researchers speculate that the cereblon gene on chromosome 2 (a myeloma treatment target in humans) and two genes on chromosome 3, CD146 and THY1 (immune system regulators involved in cell-to-cell communication and cellular adhesion in humans), are likely to be of greatest interest. (reasons.org)
  • A 'chromosome walk' experiment allowed the isolation of clones indicating a tandem of arrangement of clusters on the chromosome. (bl.uk)
  • Since hundreds of genes are present on chromosome arms, high-quality inferences of aneuploidy can be made from scRNA-seq datasets. (techscience.com)
  • Aneuploidy, the loss or gain of chromosome arms, appears less prevalent in normal tissue in these clonal mutant next-generation sequencing analyses. (techscience.com)
  • Lateral gene transfers resulted in different linkages between the ospC gene and loci of the chromosome or other plasmids. (cdc.gov)
  • The Kimura 2- parameter (K2P) genetic distance, average nucleotide frequencies, nucleotide substitution patterns and phylogenetic trees were reconstructed using neighbour joining (NJ) method. (notulaebiologicae.ro)
  • The Gly661Arg variant of ADAMTS10 was identified as the likely cause of POAG in the beagle colony because it was the only rare nonsynonymous variant that caused a highly nonconservative amino acid substitution in a highly conserved region of a gene. (arvojournals.org)
  • Evolution in overlapping genes is complicated because the effect of a nucleotide substitution has multiple contexts. (uwo.ca)
  • In HexSE, I implemented a customized data structure to efficiently track the substitution rates at every nucleotide site. (uwo.ca)
  • By simulating nucleotide sequence evolution in hepatitis B virus, I discovered consistent drops in synonymous substitution rates within overlapping gene regions. (uwo.ca)
  • All of these focal populations come from a single genetic cluster, of which there are only two. (reasons.org)
  • Gene drives have enormous potential for the control of insect populations of medical and agricultural relevance. (imperial.ac.uk)
  • Analysis of genetic relationships between populations reveals three main clusters of populations in space of two first PCs reflecting the differential presence of ancient West-Eurasian Caucasoid, Proto-Uralic and Paleoasiatic components. (blogspot.com)
  • The natural populations from China with specific genetic characteristics enriched the gene pools of global A. thaliana collections. (biomedcentral.com)
  • In another study, the trnL - trnF cpDNA intergenic spacer region of 475 individuals from 167 A. thaliana populations in its native range was sequenced and 16 haplotypes were identified [ 8 ]. (biomedcentral.com)
  • We found that the distributions and frequencies of types of OspC genes differed between populations of B. burgdorferi in the Northeast, the Midwest, and California. (cdc.gov)
  • This article discusses approaches that filtered or prioritized genetic variants, regions, or genes. (biomedcentral.com)
  • Authors are encouraged to attempt these aneuploid analyses when reporting scRNA-seq data, much like copy-number variants are commonly reported in bulk genome sequencing data. (techscience.com)
  • Nowadays, it is still unclear as to the number of genes or their variants that are necessary for effective screening. (mdpi.com)
  • This paper describes the development of a carrier screening custom panel for cystic fibrosis, phenylketonuria, alpha-1 antitrypsin deficiency, and sensorineural hearing loss consisting of 116 variants in the CFTR , PAH , SERPINA1, and GJB2 genes. (mdpi.com)
  • As a result, evaluating sequence variants "in the context of pre-existing gene annotations" is gaining in importance, but tools that were developed to analyze data from SNP arrays and genome-wide association studies fall short. (genomeweb.com)
  • VAAST scores variants by combining "variant frequency data with AAS effect information on a feature-by-feature basis," where a feature is defined as "one or more user-defined region - [genes and conserved sequence regions for example] - of the genome," the researchers explain in the paper. (genomeweb.com)
  • Based on our extensive genome sequencing program involving 20,453 COVID-19 patient samples collected from March 2020 to February 2021, we report identification of all six of these SARS-CoV-2 variants among Houston Methodist Hospital patients residing in the greater metropolitan area. (cdc.gov)
  • Although these variants are currently at relatively low frequency (aggregate of 1.1%) in the population, they are geographically widespread. (cdc.gov)
  • Houston is the first city in the United States in which active circulation of all six current variants of concern has been documented by genome sequencing. (cdc.gov)
  • Even where sequencing is being done, CRISPR diagnostics can help to isolate variants in the first instance, which can then be sequenced to validate and map coexisting mutations (appendix). (cdc.gov)
  • The present study analyzed the sequence data from four genes (Cytb, CO1, 16S and 12S rRNA) of mitochondrial genome for the attempt to estimate the relationships among five species such as Elops saurus, E. affinis, E. smithi, E. machnata and E. hawaiensis and to assess the phylogenetic utility of these markers. (notulaebiologicae.ro)
  • Phylogenetic relationships inferred from an alignment of small nuclear ribosomal subunit rRNA gene sequences using maximum likelihood. (ajtmh.org)
  • METHODS: Culture-dependent and -independent (16S rRNA gene clone libraries were constructed) methods were used to determine the composition of LAB in fermented cabbage. (who.int)
  • RESULTS: Ninety LAB isolated from fermented cabbage were identified as species of Lactobacillus and Leuconostoc, whereas 115 clones of the 16S rRNA gene sequence from fermented cabbage DNA were identified as Lactobacillus, Weissella, Pediococcus and Leuconostoc. (who.int)
  • Here, using the dRNA-seq technique in combination with ANNOgesic analysis, we successfully mapped and annotated transcription start sites (TSS) of both E. faecalis V583 and E. faecium AUS0004 at single nucleotide resolution. (frontiersin.org)
  • This comprehensive global TSS mapping atlas provides a valuable resource for RNA biology and gene expression analysis in the Enterococci. (frontiersin.org)
  • With genetic analysis, a person can benefit from timely interventions and gene-targeted treatments. (livemint.com)
  • Additionally, it can knock out genes, facilitating efforts to elucidate gene functions through the analysis of mutant phenotypes. (mdpi.com)
  • This prompted more detailed analysis of histone gene arrangements in X. borealis, which is the subject of this thesis. (bl.uk)
  • Analysis of these clones indicated one class containing the major cluster, and a second, minor class which appeared to be cloned at high frequency. (bl.uk)
  • Microinjection analysis again showed the genes were functional. (bl.uk)
  • Diversity analysis in common bean (Phaseolus vulgaris L.), based on morphological traits and molecular markers, has revealed the existence of two major gene pools, the Mesoamerican and Andean pools, which differ in several features, including the grain morphology and physiology. (usp.br)
  • Bioinformatic analysis of differential biology within the population of cells studied relies on inferences and grouping of cells due to the spotty nature of data within individual cell scRNA-seq gene counts. (techscience.com)
  • For microbiome analysis, they performed ribosomal ribonucleic acid (RNA) direct sequencing. (news-medical.net)
  • In RNA seq, this indicates the sequence but also the frequency of the RNA molecule, giving way to expression level analysis. (canopybiosciences.com)
  • Interested in the Differential Gene Expression Analysis pipeline? (canopybiosciences.com)
  • Let us sort through it and provide an organized report highlighting the sequencing run, the comparison data between your treatment groups, significant changes in gene expression and pathway analysis. (canopybiosciences.com)
  • VAAST's ability to incorporate AAS information, meantime, sets it apart from variant aggregation approaches such as CMC and Kernel Based Adaptive Cluster methods, both of which were developed by researchers at Baylor university and recently incorporated into the sequence analysis module of Golden Helix' next-generation sequence analysis software ( BI 05/20/2011 ). (genomeweb.com)
  • The analysis of the nucleotide sequences showed that the 77 accessions of A. thaliana were partitioned into two major differentiated haplotype classes (MDHCs). (biomedcentral.com)
  • Arbitrary genome sequences as well as genic sequences were used for this purpose. (usp.br)
  • Efforts are underway to produce whole genome sequences for several other species of Drosophila (see the UC Davis - DPGP project site for details). (unc.edu)
  • Genome sequences of 358 bacterial cultures have been determined with WGS. (biomedcentral.com)
  • Scale bars indicate nucleotide substitutions per site. (cdc.gov)
  • Percentages of replicate trees in which associated taxa clustered together in the bootstrap test (1,000 replicates) are shown next to branches. (cdc.gov)
  • The gene fragment of Hl-Kh formed a cluster relative to the only scorpion of H. Lepturus (Hl) from Izeh, Iran with a good bootstrap score of 96. (ac.ir)
  • More recently, nine roo insertions were also described in the promoter region of another stress response gene, CG18446 that encodes a nucleic acid binding protein [ 10 ]. (biomedcentral.com)
  • The sequence of the four nucleotide bases encodes DNA's information. (genome.gov)
  • 87(5): 1663-1667] Specifically, the investigators started by priming whole cerebellar RNA with a synthetic oligonucleotide containing a T7 RNA polymerase promoter sequence. (genomicglossaries.com)
  • GEN's projects usual y involve extensive may have a larger effect than common fieldwork in col aboration with external single-nucleotide polymorphisms but investigators in order to develop large- that are not sufficiently frequent to scale epidemiological studies with be captured by current genome-wide appropriate clinical and exposure data, association genotyping arrays. (who.int)
  • The vast diversity of possible T-cell receptors (TCR) is generated by the random recombination of genes in the third complimentary determining regions (CDR3) within a TCR's α and β chains. (biorxiv.org)
  • In the recombination process of the β chain, loci of the variable (V), diversity (D), and joining (J) regions are randomly spliced together with non-templated insertions and deletions occurring between each junction, resulting in up to 10 11 possible sequences ( 3 , 4 ). (biorxiv.org)
  • Recombination of the TCRα chain includes only V and J gene segments, resulting in fewer possible rearrangements and making the TCRβ chain a more suitable target for identifying unique T cells, and thus the focus of this paper. (biorxiv.org)
  • These results indicate the region with high-pairing probabilities may be a more fundamental factor affecting HIV-1 recombination than sequence similarity in natural HIV-1 infections. (biomedcentral.com)
  • Intragenic recombination among ospC genes is known, but the extent to which recombination extended beyond the ospC locus itself is undefined. (cdc.gov)
  • A better understanding of how these species cause disease and spread antibiotic resistance requires a knowledge of how its genes are controlled, on both the DNA and the RNA level. (frontiersin.org)
  • Tools like ANNOVAR additionally provide variant annotation to genes and to regions such as conserved regions among species, predicted transcription factor binding sites, and segmental duplication regions. (biomedcentral.com)
  • The four mitochondrial marker genes used in this study showed different type of cluster and we could not confirm the relationship between the five Elops species. (notulaebiologicae.ro)
  • Colonization of the gut starts just after birth when pioneering species interact, through surface receptors, with gut cells to promote the expression of a specific set of host genes and favour the colonization of commensal microorganisms [6]. (deepdyve.com)
  • Sequences of Angiostrongylus species obtained from GenBank are indicated with the accession no. and the country code (ISO 3166-1 alpha-3 code). (ajtmh.org)
  • Phylogenetic relationships inferred from an alignment of ITS2 region sequences using maximum likelihood (ML). Sequences of Angiostrongylus species obtained from GenBank are indicated with the accession no. and the country code (ISO 3166-1 alpha-3 code). (ajtmh.org)
  • Phylogenetic relationships inferred from an alignment of COI gene sequences using maximum likelihood (ML). Sequences of Angiostrongylus species obtained from GenBank are indicated with the accession no. and the country code (ISO 3166-1 alpha-3 code). (ajtmh.org)
  • Once these genes are cloned, I can explore the genetic mechanism of attraction behavior and see if homologs of these genes are involved in the olfactory behavior of other species. (unc.edu)
  • At present, I am helping to develop the data structure and tools to process, analyze, and represent the sequence data from these species. (unc.edu)
  • For discovering new VH genes, for example, you need to get the IGHV, IGHD and IGHJ files of your species. (gitlab.io)
  • Performance of phylogenetic foot-printing depends on the evolutionary distance between given species and on the conservation level of individual genes. (biomedcentral.com)
  • Although the sample size in Cluster B is not large enough to draw a final conclusion, the percentage of sequence divergence was high enough for interspecific comparisons to provide separation of species. (ac.ir)
  • Given that aneuploidy is (a) known to contribute to cell biology and (b) is present at some detectable level in many cell types, it is valuable for single-cell sequencing studies to include aneuploidy information in their analyses. (techscience.com)
  • Based on these population analyses, some genes have also been reported to accumulate many TE insertions, such as the 106.5 kb klarsicht , and the 24 kb derailed-2 that were analyzed in 146 strains of the Drosophila Synthetic Population Resource [ 5 , 6 ]. (biomedcentral.com)
  • 2006). Perhaps the best-defined and most widely known CNVs are the trinucleotide repeats (TNRs), which consist of three nucleotides repeating in tandem. (nature.com)
  • Therefore, the aims of this study were to sequence the -Phs and FRO1 genes, to assess SNP frequencies in coding and non-coding regions of both genes, and to assess the possible use of these polymorphisms for investigating the genetic diversity of 31 cultivated genotypes of common bean and one of P. lunatus. (usp.br)
  • Because alternative RNA splicing allows different types of mRNA molecules to be created from a single gene, it generates the diversity of protein function and structure that is essential to complex organisms. (genomicglossaries.com)
  • Forty-nine haplotypes were detected among the 77 accessions, which exhibited nucleotide diversity (π) of 0.00169. (biomedcentral.com)
  • Visitors to the website are encouraged to explore the intricacies of the most complex blood group gene locus. (karger.com)
  • Any step of gene expression may be modulated, from signaling to transcription to post-translational modification of a protein. (wikipedia.org)
  • In general, the density of its packing is indicative of the frequency of transcription. (wikipedia.org)
  • Transcription of a gene by RNA polymerase can be regulated by several mechanisms. (wikipedia.org)
  • Full-length genome sequencing of A/Mandarin_duck/Korea/K16-187-3/2016(H5N6) virus was performed by using conventional reverse transcription PCR and Sanger sequencing. (cdc.gov)
  • While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. (biomedcentral.com)
  • They are likely to have conserved DNA sequence elements, called transcription factor binding motifs (TFBMs), in their promoter regions. (biomedcentral.com)
  • TFBMs act as binding sites for transcription factors and coordinate the expression of the genes in whose promoter regions they appear. (biomedcentral.com)
  • They are about 6-8 nucleotides (nt) in length and occur upstream of the gene transcription start site (TSS). (biomedcentral.com)
  • Yet the interacting effects that genetic and epigenetic factors produce on gene transcription are rarely studied at a genome-wide scale, leaving us without global information on a key step between the genetic code and the phenotype. (elifesciences.org)
  • The transcription rate of genes is dictated primarily by interactions between DNA-binding transcription factors. (biomedcentral.com)
  • Comparatively short sequences (several hundred to several thousand base pairs, depending on thespecies) upstream or downstream of the transcription start site often play a major role in the regulation of gene expression. (biomedcentral.com)
  • Regulatory regions of higher eukaryotes can be subdivided into proximal regulatory units - promoters - which are located close to and upstream of the gene, and distal transcription regulatory units called enhancers or cis-regulatory modules. (biomedcentral.com)
  • This approach exploits the clustering of known, cooperatively-acting transcription factors (TFs). (biomedcentral.com)
  • Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes. (genomicglossaries.com)
  • More than half of all human genes are alternatively spliced, so it is expected that alternative pre- mRNA splicing will be responsible for the identification of more than 90 percent of all human proteins. (genomicglossaries.com)
  • High- fidelity mRNA amplification for gene profiling. (genomicglossaries.com)
  • More specifically, antisense oligonucleotides that are useful as reagents for target validation , or as drugs, are engineered molecules that differ from natural RNA but that have a base sequence that is recognized as being complementary to a very specific mRNA sequence. (genomicglossaries.com)
  • A complementary RNA sequence that binds to a naturally occurring (sense) mRNA molecule, thus blocking its translation. (genomicglossaries.com)
  • Highly specific and effective gene silencing of any disease can be achieved by an accurate knowledge of the target mRNA sequence and rational design of its complementary antisense agents for the downregulation of its protein message. (genomicglossaries.com)
  • An anticodon is a trinucleotide sequence located at one end of a transfer RNA (tRNA) molecule, which is complementary to a corresponding codon in a messenger RNA (mRNA) sequence. (genome.gov)
  • DNA is typically methylated by methyltransferase enzymes on cytosine nucleotides in a CpG dinucleotide sequence (also called "CpG islands" when densely clustered). (wikipedia.org)
  • Adenine (A) is one of the four nucleotide bases in DNA, with the other three being cytosine (C), guanine (G) and thymine (T). Within a double-stranded DNA molecule, adenine bases on one strand pair with thymine bases on the opposite strand. (genome.gov)
  • Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). (wikipedia.org)
  • Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. (genomicglossaries.com)
  • We know little about the mechanisms, frequency, or patterns underlying these events. (unc.edu)
  • The work will be of broad interest to geneticists and those working to understand the basic mechanisms of gene expression. (elifesciences.org)
  • Local regulatory mechanisms within the genome and their interaction with chromatin structure give rise to subtle variations in gene expression. (elifesciences.org)
  • Understanding the scope and landscape of these interactions on a genome-wide scale is a vital step towards deciphering the genetic regulation of gene expression and, in turn, the mechanisms of non-coding variation on phenotypic outcomes. (elifesciences.org)
  • The major mechanisms for balancing selection are heterozygote advantage, frequency-dependent selection, or environmental heterogeneity. (biomedcentral.com)
  • Still, the RH antigens resisted many attempts to characterize their molecular basis: discussions continued whether all RH antigens derived from a single gene or whether there were three genes coding for C, D, or E. It was not until 1990 that the sequence of the Rh protein was elucidated [ 7,8 ]. (karger.com)
  • A novel approach to estimating genetic variability is in silico mining for single nucleotide polymorphisms (SNP). (usp.br)
  • Recruiting metagenomic short reads using single-copy core genes, Donati et al. (biomedcentral.com)
  • Single-cell sequencing data has transformed the understanding of biological heterogeneity. (techscience.com)
  • While many flavors of single-cell sequencing have been developed, single-cell RNA sequencing (scRNA-seq) is currently the most prolific form in published literature. (techscience.com)
  • One biologically relevant variable is readily inferred from scRNA-seq gene count tables regardless of individual gene representation within single cells: aneuploidy. (techscience.com)
  • VAAST combines variant frequency information and AAS information into a single unified likelihood framework," Reese said. (genomeweb.com)
  • Dominant" means that a single copy of the mutated gene (from one parent) is enough to cause the disorder. (genome.gov)
  • By contrast, an autosomal dominant disorder requires only a single copy of the mutated gene from one parent to cause the disorder. (genome.gov)
  • These authors found considerable variation existed among the non-coding single-copy sequences in the chloroplast genome of A. thaliana . (biomedcentral.com)
  • We found that five single nucleotide polymorphisms within TMPRSS2 and near MX1 gene show associations with severe COVID-19. (cdc.gov)
  • 1 The research is relatively vague in regard to what may actually be providing some Tasmanian devils with resistance to a transmissible form of cancer known as DFTD (devil facial tumor disease), but data points to changes in allele frequencies in two regions of chromosomes 2 and 3. (reasons.org)
  • The researchers speculate that genes in these regions may end up being key in providing Tasmanian devils with resistance to the aggressive and easily transmitted form of cancer that has wiped out 80 percent of the population in just two decades. (reasons.org)
  • Based on characteristics of DFTD, the allele frequency changes in these regions, and localized genes and the homologous gene product function in other mammals, the researchers suggest that these allele changes are indicative of an adaptive immune response to DFTD cells. (reasons.org)
  • Major cluster clone XbHW302 was restriction site mapped, and certain regions sequenced. (bl.uk)
  • The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf . (biomedcentral.com)
  • 2016) [ 10 ] other similar clusters of roo insertions in gene promoter regions are present in the genome. (biomedcentral.com)
  • Extracting clustered recognition motifs is one of the most reliable techniques, but is limited to the recognition of similarly regulated cis-regulatory regions. (biomedcentral.com)
  • In an investigation on the maternal origins of A. suecica , 12 cpDNA regions were sequenced for 25 A. thaliana accessions, which were mainly collected from Scandinavia [ 25 ]. (biomedcentral.com)
  • Virtually any step of gene expression can be modulated, from transcriptional initiation, to RNA processing, and to the post-translational modification of a protein. (wikipedia.org)
  • The transcriptome of the Pf asexual intraerythrocytic developmental cycle (IDC) has been analysed and transcriptional regulation has been shown to orchestrate a continuous cascade of gene expression, with genes being induced once per cycle, in a "just-in-time" manner, only when the gene product is required by the cell [ 3 ]. (biomedcentral.com)
  • These results indicate that TosR is a transcriptional activator that increases expression of the flhDC operon genes, contributing to flagellar expression and optimal virulence. (bvsalud.org)
  • In addition, OvRFs might be a source of gene novelty, facilitating the creation of new open reading frames (ORF) within the transcriptional context of existing ones. (uwo.ca)
  • A slightly higher fraction of genes belonging to the categories amino acid metabolism (T. velox 11.8%, T. acidaminovorans 11.4%), carbohydrate metabolism (T. velox 5. (phosphorylase-signal.com)
  • A protein consists of one or more chains of amino acids (called polypeptides) whose sequence is encoded in a gene. (genome.gov)
  • A codon is a DNA or RNA sequence of three nucleotides (a trinucleotide) that forms a unit of genetic information encoding a particular amino acid. (genome.gov)
  • Alternate allele frequencies were calculated with 95% confidence intervals and comparisons made to expected allele frequency relative to disease prevalence or between cases and controls. (arvojournals.org)
  • The Gly661Arg variant of ADAMTS10 was the only variant with minor allele frequency consistent with the prevalence of primary glaucoma in the general beagle population. (arvojournals.org)
  • Repressors bind to the Operator, coding sequences on the DNA strand that are close to or overlapping the promoter region, impeding RNA polymerase's progress along the strand, thus impeding the expression of the gene. (wikipedia.org)
  • Moreover, we found that the roo insertional cluster in the CG18446 promoter region is unique: no other promoter region in the genome contains a similar number of roo insertions. (biomedcentral.com)
  • We found that, similar to hsp gene promoters, chromatin accessibility could be one of the factors explaining the recurrent insertions of roo elements in CG18446 promoter region. (biomedcentral.com)
  • The accumulation of TEs in the promoter of hsp genes was explained by the chromatin conformation of this particular region, and by selection favoring the retention of TEs because of their effect on gene expression [ 8 ]. (biomedcentral.com)
  • Considerable effort has gone into identifying genes involved in olfactory perception however little progress has been made in the genetics of behavior driven by olfactory information. (unc.edu)
  • Additionally, the investigation of nucleotide sequences that code for important proteins, such as phaseolin and iron-reductase, encoded respectively by the Phs and FRO1 genes, should allow new and informative markers to be generated, helping us to gain a better understanding of intraspecific variation in P. vulgaris. (usp.br)
  • In addition, we sequenced 99 ospC flanking sequences from different lineages and compared the complete cp26 sequences of 11 strains as well as the cp26 bbb02 loci of 56 samples. (cdc.gov)
  • Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility and adaptability of an organism by allowing the cell to express protein when needed. (wikipedia.org)
  • Maximum-likelihood phylogenetic trees for A) hemagglutinin (HA) and B) neuraminidase (NA) genes of avian influenza viruses. (cdc.gov)
  • Maximum-likelihood phylogenetic trees for polymerase basic 2 (PB2), PB1, acidic polymerase (PA), nucleoprotein (NP), matrix (M), and nonstructural protein (NS) genes of avian influenza viruses. (cdc.gov)
  • For example, +2 frameshifts are predominantly found in dsDNA viruses, whereas +0 frameshifts in RNA viruses tend to involve longer overlaps, which may increase the selective burden of the same nucleotide positions within codons. (uwo.ca)
  • Patients within [patient contact clusters] carried viruses more genetically identical to HCWs in the same ward location. (cdc.gov)
  • Gene expression is known to be affected by interactions between local genetic variation and DNA accessibility, with the latter organized into three-dimensional chromatin structures. (elifesciences.org)
  • With 176 samples profiled for genotype, gene expression, and open chromatin, we used regression modeling to infer genetic-epigenetic interactions on a genome-wide scale. (elifesciences.org)
  • In stem cells, open chromatin participating in the most significant regression models demonstrated an enrichment for developmental genes and the TAD-forming CTCF binding complex, providing an opportunity for statistical inference of shifting TAD boundaries operating during early development. (elifesciences.org)
  • This important work substantially advances our understanding of the interplay between genetic variation, chromatin, and genes within topologically associated domains and how this interplay regulates gene expression. (elifesciences.org)
  • Sophisticated programs of gene expression are widely observed in biology, for example to trigger developmental pathways, respond to environmental stimuli, or adapt to new food sources. (wikipedia.org)
  • We sequenced small RNA libraries representing 11 developmental stages of B. germanica ontogeny (with especial emphasis on embryogenesis) and the changes in miRNA expression were examined. (biomedcentral.com)
  • The goal of my research is to identify, clone, and characterize the evolution of genes underlying natural adaptations in order to determine the types of genes involved, how many and what types of genetic changes occurred, and the evolutionary history of these changes. (unc.edu)
  • Despite the high intra-ethnic variation (Gst=0.03 on average), the inter-ethnic differences were five times higher (Gst=0.15), revealing dominance of inter-ethnic variation in structuring the paternal gene pool in Europe. (blogspot.com)
  • They also found that the amplicons were similar in size distribution to the parent cDNA and showed sequence heterogeneity. (genomicglossaries.com)
  • By means of DNA sequencing of a large sample collection of the pathogen from across the United States, we studied the gene for the bacterium's highly diverse OspC protein, protective immunity against which develops in animals. (cdc.gov)
  • The purified recombinant TosR does not bind to fliC and fliA but to the upstream region of the flhD gene. (bvsalud.org)
  • The characteristic AT-rich sequence exists 550-578 bases upstream of the flhD gene. (bvsalud.org)
  • These may be located far upstream or downstream of the target gene, and are much more difficult to recognise. (biomedcentral.com)
  • We have recently developed gene drives based on CRISPR nuclease constructs that are designed to disrupt key genes essential for female fertility in the malaria mosquito. (imperial.ac.uk)
  • Both isolates had active-on-imipenem metallo-beta-lactamase emase genes. (cdc.gov)
  • CRPA isolates for carbapenemase genes and implementation of occupied room X while receiving mechanical ventilation for sink hygiene interventions, was critical in the identification of 4 weeks. (cdc.gov)
  • Often, one gene regulator controls another, and so on, in a gene regulatory network. (wikipedia.org)
  • Many of the above-listed tools also provide information on regulatory elements that control gene activity. (biomedcentral.com)
  • This paper addresses the problem of recognising DNA cis-regulatory modules which are located far from genes. (biomedcentral.com)
  • These insertions, deletions, inversions, and duplications result in changes in the physical arrangement of genes on chromosomes. (nature.com)
  • Autosomal" means that the gene in question is located on one of the numbered, or non-sex, chromosomes. (genome.gov)
  • In multicellular organisms, gene regulation drives cellular differentiation and morphogenesis in the embryo, leading to the creation of different cell types that possess different gene expression profiles from the same genome sequence. (wikipedia.org)
  • Hence these modifications may up or down regulate the expression of a gene. (wikipedia.org)
  • Some of these modifications that regulate gene expression are inheritable and are referred to as epigenetic regulation. (wikipedia.org)
  • Such modifications are considered to be responsible for more or less permanent changes in gene expression levels. (wikipedia.org)
  • The combination of the two seems to be a signal for DNA to be packed more densely, lowering gene expression. (wikipedia.org)
  • We examined the changes in miRNA expression over the ontogeny of the German cockroach Blattella germanica , using 11 small RNA libraries prepared and sequenced in our laboratory, representing developmentally important stages. (biomedcentral.com)
  • can be based on biological knowledge or predicted variant function, or even be used to integrate gene expression or other omics data. (biomedcentral.com)
  • Indeed, power improved when gene expression data for FDR-controlled informative weighting of association test p values of genes was used. (biomedcentral.com)
  • Filters or priors on genes may be derived from methylation or expression data if available in the same individuals. (biomedcentral.com)
  • Regulation of gene expression in Plasmodium falciparum (Pf) remains poorly understood. (biomedcentral.com)
  • The question then arises as to how such fine-tuned regulation of gene expression is achieved in this extreme parasite. (biomedcentral.com)
  • Sequencing RNA provides both abundance and sequence information yielding a deep understanding of gene expression. (canopybiosciences.com)
  • Changes within these genes are calculated, clustered and the expression profile is created. (canopybiosciences.com)
  • A biological process that is crucial for gene expression in most animal life, including humans. (genomicglossaries.com)
  • presents an opportunity to manipulate gene expression within the cells to treat various diseases, and acts as a powerful tool for studying gene function utilizing antisense agents to manage the diseases by regulating the expression of the specific factor that actually causes the particular disease. (genomicglossaries.com)
  • Microinjection of the major cluster clones in to Xenopus oocytes, confirmed that these genes were functional. (bl.uk)
  • Analyzing bacteria in late exponential phase, we capture ~40% ( E. faecalis ) and 43% ( E. faecium ) of the annotated protein-coding genes, determine 5′ and 3′ UTR (untranslated region) length, and detect instances of leaderless mRNAs. (frontiersin.org)
  • One of the few antigens against which mammals develop protective immunity is the highly polymorphic OspC protein, encoded by the ospC gene on the cp26 plasmid. (cdc.gov)
  • Often, DNA methylation and histone deacetylation work together in gene silencing. (wikipedia.org)
  • A previous study showed that unlike X. laevis, X. borealis contains a predominant or major histone gene cluster, which contains 70% of the 80-90 copies of the H4 genes in the genome (Turner & Woodland 1983 (Nucl. (bl.uk)
  • Clones containing histone genes were isolated from a library prepared for this purpose. (bl.uk)
  • Extensive DNA sequence comparisons between various Xenopus histone gene clusters were undertaken. (bl.uk)
  • The picture of histone gene cluster structure in X. borealis that emerges from these studies, is compared at the nucleotide, gene, and chromosomal levels with X. laevis. (bl.uk)
  • It may even have come from swine - there are some closely related swine-sequences from Hong Kong 2002. (flutrackers.com)
  • Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. (biomedcentral.com)