• The above-mentioned ab, of repetitive sequences in plant genomes (up to 99%), makes difficult the application of this technique for, mapping individual plant genes [40]. (centrocardiobogota.com)
  • The Rhodopsin family accounts for ~68% of the Ciona GPCR repertoire wherein the LGR-like subfamily exhibits a lineage specific gene expansion of a group of receptors that possess a novel domain organisation hitherto unobserved in metazoan genomes. (biomedcentral.com)
  • Valuable insight into these important enzymes has already emerged from the analysis of the yeast and worm genomes. (rupress.org)
  • of tandem repeats within their genomes [6, 17]. (scirp.org)
  • To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)
  • We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis . (asm.org)
  • The availability of the complete nucleotide sequences of several MTB genomes allows to use the comparative genomics as a tool to study the relationships of strains and differences in their evolutionary history including acquisition of drug-resistance. (ijpsr.com)
  • A genome-wide analysis resulted in the detection of more than eight hundred putative chitin synthases in proteomes associated with about 130 genomes. (biomedcentral.com)
  • Only patterns of short tandem repeats are stored in the NDNAD - not a person's full genomic sequence. (wikipedia.org)
  • An analysis of the Ciona repertoire of GPCRs from a comparative genomic perspective provides insight into the evolutionary origins of the GPCR signalling system in vertebrates. (biomedcentral.com)
  • Now, the genomic sequencing of organisms promises to be a major contributor to this field. (rupress.org)
  • To better understand the karyotype organization in Melipona and the relationship among the subgenera, we mapped repetitive sequences and analyzed previously reported cytogenetic data with the aim to identify cytogenetic markers to be used for investigating the phylogenetic relationships and chromosome evolution in the genus. (karger.com)
  • According to our phylogenetic analyses, the group constitutes a well-supported monophylum containing several distinct evolutionary lineages with high haplotype diversity. (podarcis.de)
  • Thus, sequencing of the Blastobotrys (Arxula) adeninivorans genome was of interest in order to generate an additional landmark in the basal portion of the hemiascomycete tree and possibly resolve phylogenetic relationships among basal species. (biomedcentral.com)
  • The first section introduces sequence-basedanalyses,includinggenefind-ing, gene family and phylogenetic analy-ses, and comparative genomics approaches. (centrocardiobogota.com)
  • Phylogenetic analyses reveal that Ciona GPCRs have homologous representatives from the five major GRAFS ( Glutamate, Rhodopsin, Adhesion, Frizzled and Secretin ) families concomitant with other vertebrate GPCR repertoires. (biomedcentral.com)
  • Phylogenetic analyses were performed with special care to avoid any pitfalls associated with the peculiarities of these sequences (e.g. highly variable regions, truncated or recombined sequences, long-branch attraction). (biomedcentral.com)
  • Sequences of previously described binding sites were collected for these five factors present in the cis-regulatory regions of known target genes. (sdbonline.org)
  • Genome-wide identification and expression analysis of the bZIP transcription factor family genes in response to abiotic stress in Nicotiana tabacum L. (biomedcentral.com)
  • To identify genes, signaling pathways and networks that are controlled by SRC-3 and potentially important for hormone-dependent decidualization, we performed RNA-sequencing on HESCs in which SRC-3 levels were significantly reduced at the time of administering the deciduogenic stimulus. (frontiersin.org)
  • Comparing HESC controls with HESCs deficient in SRC-3, gene enrichment analysis of the differentially expressed gene set revealed an overrepresentation of genes involved in chromatin remodeling, cell proliferation/motility, and programmed cell death. (frontiersin.org)
  • With 914 introns within 6116 genes, A. adeninivorans is one of the most intron-rich hemiascomycetes sequenced to date. (biomedcentral.com)
  • This is evident at the subfamily level comparisons since Ciona GPCR sequences are significantly analogous to vertebrate GPCR subfamilies even while exhibiting Ciona specific genes. (biomedcentral.com)
  • Gene Ontology (GO) enrichment analysis of differentially expressed genes between wild type plants and STTM159 transgenic plants showed that genes involved in cell division, auxin, cytokinin (CK) and brassinosteroids (BRs) biosynthesis and signaling are significantly down-regulated in STTM159 plants. (biomedcentral.com)
  • Further analysis from the RNA-seq data showed that the decreased cell divisions in STTM159 transgenic plants may result, at least partly from the lower expression of the genes involved in cell cycle and hormone homeostasis, which provides new insights of rice miR159-specific functions. (biomedcentral.com)
  • Some plant miRNA families have many members, and their mature miRNAs often have multiple target genes having similar complementary sequence. (biomedcentral.com)
  • 10,200 protein-encoding genes were predicted based on the genome sequence. (springeropen.com)
  • The genes and proteins were predicted and annotated based on the genome sequence. (springeropen.com)
  • The first stage involved identifying, in unrelated subjects showing linkage to 2q24-q33, genetic variants in exons and flanking sequence within candidate genes and comparing the frequency of the variants between autistic and unrelated nonautistic subjects. (neurotransmitter.net)
  • A substantial portion of the regulatory interactions in the higher eukaryotic cell are mediated by simple sequence motifs in the regulatory segments of genes and (pre-)mRNAs, and in the intrinsically disordered regions of proteins. (biomedcentral.com)
  • We sequenced the worm's ~ 688-Mb haploid genome with an overall completeness of ~ 95% and discovered that L. luymesi lacks many genes essential in amino acid biosynthesis, obligating them to products provided by symbionts. (biomedcentral.com)
  • We also found an expansion of hemoglobin B1 genes, many of which possess a free cysteine residue which is hypothesized to function in sulfide binding. (biomedcentral.com)
  • Ankyrin repeats are tandemly repeated modules of about 33 amino acids. (embl.de)
  • However, methods for detecting it, and especially determining the proportion and identities of the underlying strains, from WGS (whole-genome sequencing) data, have been limited. (microbiologyresearch.org)
  • Based on the multi locus sequence typing (MLST) scheme, the strains were classified in 27 sequence types (STs), including ST26 that causes food poisoning. (bvsalud.org)
  • In our study, online resources for comparative genomics analysis between strains by using databases such as MGDD (Mycobacterial Genome Divergence Database), Biohealth base, GenomycDB, Mycobacterium tuberculosis database, and TBDB (Tuberculosis Database). (ijpsr.com)
  • Since 2014 sixteen loci of the DNA-17 system are analysed, resulting in a string of 32 numbers, being two allele repeats from each of the sixteen loci. (wikipedia.org)
  • of 6 short tandem repeat loci demon- tarandi than females? (cdc.gov)
  • Short tandem repeats (STRs) compose approximately 3% of the genome, and mutations at STR loci have been linked to dozens of human diseases including amyotrophic lateral sclerosis, Friedreich ataxia, Huntington disease, and fragile X syndrome. (biomedcentral.com)
  • To estimate the genome-wide pattern of mutations at STR loci, we analyze blood-derived whole-genome sequencing data for 544 individuals from 29 three-generation CEPH pedigrees. (biomedcentral.com)
  • Due to the repetitive structure of STRs and their high mutability, sequencing and genotyping these loci is difficult, especially using short-read sequencing data. (biomedcentral.com)
  • Some of these tools are designed to detect STR expansions at disease-related loci, while others detect expansions and contractions of STRs genome-wide but are constrained by sequencing read length and the STR motif size. (biomedcentral.com)
  • PWMs are a useful way to represent binding specificities and provide a statistical framework for searching for novel instances of the motif in genome sequences (Berman, 2002). (sdbonline.org)
  • those containing only the DAT1 coding region or the coding region flanked by a truncated 3' UTR resulted in greater DAT density than either of the naturalistic 9- and 10-repeat variants. (biomedcentral.com)
  • the complete genome sequence of Mycobacterium tuberculosis continues to provide an invaluable resource to understand tuberculosis (TB), the leading cause of global infectious disease mortality. (jci.org)
  • While the genome sequence was already transformative at the time, the past 25 years of progress have substantially increased its impact on TB taxonomy, drug discovery, resistance mechanisms, epidemiology, vaccine development, and pathogenesis. (jci.org)
  • Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission. (microbiologyresearch.org)
  • The binding sequences for each factor were aligned by using the motif-assembly program, and the binding specificities of each factor were modeled with position weight matrices (PWMs). (sdbonline.org)
  • Sequences of ARF-GAP domains show no recognizable similarity to those of other GAPs, and contain a characteristic Cys-X(2)-Cys-X(16-17)-Cys-X(2)-Cys motif. (embl.de)
  • The term motif denotes a repeated figure or design and, in motif biology, the occurrence of a given class of motif in a set of unrelated biomolecules led to the appropriation of the term to refer to a recurrent pattern of nucleotides or amino acids that corresponds to an autonomous functional module. (biomedcentral.com)
  • Short tandem repeats (STRs), or microsatellites, are 1-6 base pair (bp) motifs of repeating units of DNA. (biomedcentral.com)
  • The ankyrin repeat is one of the most common protein-protein interaction motifs in nature. (embl.de)
  • While whole gene duplications and deletions are relatively well-studied, the biology of subexonic ( i.e. , within coding exon sequences), copy number variation remains elusive. (nature.com)
  • Several large species-specific families appear to result from multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not yet described in yeasts. (biomedcentral.com)
  • We previously identified a compound tandem repeat located within the breakpoints of a microdeletion in intron 2 of DCDC2 as a risk variant (Marino et al. (springer.com)
  • The frequencies of CNVs in these populations were analyzed by oligonucleotide array comparative genome hybridization, quantitative PCR, PCR, DNA sequencing across breakpoints, and single-worm PCR. (biomedcentral.com)
  • Despite its high frequency in the general population [ 7 ] and an absence of studies addressing possible effects of the VNTR on measures of DAT physiology and pharmacology, the 10-repeat DAT1 allele has become generally recognized as a "high risk" allele for ADHD. (biomedcentral.com)
  • The data held on the NDNAD is owned by the police authority which submitted the sample for analysis. (wikipedia.org)
  • Sha J , Almagro G , Mc V . Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data. (microbiologyresearch.org)
  • Build data systems that link various data sources and allow for automated, more efficient data analysis and visualization. (cdc.gov)
  • Analyses of WGS data enabled the identification of three members of the B. cereus group: B. cereus sensu stricto, B. mosaicus and B. thuringiensis. (bvsalud.org)
  • Analysis of published expression data suggested that COMMD3 is normally expressed in the mammary ducts and lobules, that expression is lost in some tumours and that loss is associated with lower survival probability. (biomedcentral.com)
  • Sequencing data will be deposited in a controlled access repository according to accepted standards and complete pathway analyses made available with the publication. (bmj.com)
  • In order to clarify the biological and pharmacological mechanisms of O. sinensis , we carried out the genome sequencing of H. sinensis, anamorph of O. sinensis , for the first time, described the annotation and gene expression, and analyzed the complete sequencing data (Li et al. (springeropen.com)
  • Last, molecular clock analyses based on phylogenomic data suggest modern siboglinid diversity originated in 267 mya (± 70 my) support previous hypotheses indicating a Late Mesozoic or Cenozoic origins of approximately 50-126 mya for vestimentiferans. (biomedcentral.com)
  • Data analyses used standard statistical approaches. (cdc.gov)
  • On a broader scale, our study highlights variable subexonic repeats as a primary source for modular evolutionary innovation that lead to rapid functional adaptation. (nature.com)
  • A major expansion to include all known active offenders was funded between April 2000 and March 2005 at a cost of over £300 million. (wikipedia.org)
  • The sequencing of strain LS3 revealed that the nuclear genome of A. adeninivorans is 11.8 Mb long and consists of four chromosomes with regional centromeres. (biomedcentral.com)
  • results can serve as an important argument in favour of the proposal to develop a special program for sequencing the genome chromosomes and for, To estimate the possibility of plant genome mapping using human genome probes, the probes fluorescent in situ hybridization (FISH) of human 18S-28S rDNA (clon 22F9 from the LA-13NCO1 library) was carried out on chromosomes of the spring barleyHordeum vulgareL. (centrocardiobogota.com)
  • A meta-analysis from 2017 connected low levels of vitamin D with a higher risk of respiratory tract infections [ 7 ]. (karger.com)
  • We report our analysis of MyoD1 and MyoD2 protein sequences from 54 teleost species, and show that O. alcalica , along with some other teleosts, include a polyserine repeat between the amino terminal transactivation domains (TAD) and the cysteine-histidine rich region (H/C) in MyoD1. (mdpi.com)
  • The bZIP protein sequence contains 2 conserved bZIP domains with a total length of ~ 60-80 amino acids. (biomedcentral.com)
  • Though the VNTR resides in the 3'UTR and therefore does not affect the protein's amino acid sequence, regulatory factors such as mRNA stability and nuclear transport, and protein synthesis are potentially regulated by such variations [ 11 - 14 ]. (biomedcentral.com)
  • We performed immunohistochemical analysis of an independent tumour cohort to investigate relationships between COMMD3 protein expression, phenotypic markers and disease-specific survival. (biomedcentral.com)
  • Sequences that Confer Response to a Particular Stimulus Consensus Sequences CTNGAATNTT CTAGA Response to Heat Protein Factor Heat-shock transcription Gene Containing Sequences hsp70, hsp83, has a ring of glutamates near the inner entryway of the channel (Brelidze et al. (forextipsnow.com)
  • Crystal structure of the ARF-GAP domain and ankyrin repeats of PYK2-associated protein beta. (embl.de)
  • PAPbeta, a protein that binds to and is phosphorylated by the non-receptor tyrosine kinase PYK2, contains several modular signaling domains including a pleckstrin homology domain, an SH3 domain, ankyrin repeats and an ARF-GAP domain. (embl.de)
  • Alternative splicing of MAPT pre-mRNA generates six major tau isoforms in the adult central nervous system resulting in tau proteins with three or four microtubule-binding repeat domains. (biomedcentral.com)
  • A recent study has shown that, despite the high intrinsic mutability of subexonic repeats, the vast majority of thousands of subexonic repeats remain strongly conserved among mammals 4 . (nature.com)
  • The diversity among GPCRs primarily stem from the presence of characteristic N-terminal extracellular domains and C-terminal intracellular domains and to a relatively lesser extent from the connecting loops which share limited sequence similarity. (biomedcentral.com)
  • In addition to the highly conserved miRNAs, many more of new and species-specific miRNAs have been identified in various crops through high-throughput sequencing technology. (biomedcentral.com)
  • This comprehensive multi-species analysis contributes to the classification of fungal CHS, in particular by optimizing its robustness, consensuality and accessibility. (biomedcentral.com)
  • First, MUC7 carries subexonic repeats that are 69 bp (23 amino acids) long and are copy number variable in humans 5 . (nature.com)
  • Ankyrin repeats are about 33 amino acids long and occur in at least four consecutive copies. (embl.de)
  • These repeats can be particularly well studied in this gene because the repeats are relatively short and few in number compared to other mucins. (nature.com)
  • STTM (Short Tandem Target Mimic) is an effective tool to block the activity of endogenous mature miRNA activity in plant. (biomedcentral.com)
  • Evidence for linkage was supported by linkage analysis with the two SNPs, with a maximal multipoint nonparametric linkage score of 1.57 and a maximal multipoint heterogeneity lod score of 2.11. (neurotransmitter.net)
  • An analysis of the genome and its transcriptome revealed enzymes with biotechnological potential, such as two extracellular tannases (Atan1p and Atan2p) of the tannic-acid catabolic route, and a new pathway for the assimilation of n-butanol via butyric aldehyde and butyric acid. (biomedcentral.com)
  • Our comparative analyses also suggest the Toll-like receptor pathway may be essential for tolerance/sensitivity to symbionts and pathogens. (biomedcentral.com)
  • This paper discusses the sequencing of the genome of Arxula adeninivorans, a yeast of biotechnological interest. (biomedcentral.com)
  • This sequencing bias remains despite the number of recent publications of yeast genome sequences. (biomedcentral.com)
  • The sequences also show an The conventional and marker-assisted breeding (MAB) are the two approaches used to accomplish plant breeding (Breseghello and Coelho, 2013). (centrocardiobogota.com)
  • The salivary MUC7 gene provides an opportunity for studying such variation, as it harbors copy number variable subexonic repeat sequences that encode for densely O-glycosylated domains (PTS-repeats) with microbe-binding properties. (nature.com)
  • Second, the subexonic repeats of MUC7 code for densely O-glycosylated proline-, threonine-, and serine-rich (PTS) tandem repeat domains. (nature.com)
  • It shows a stack of six IkappaBalpha ankyrin repeats facing the C-terminal domains of the NF-kappaB Rel homology regions. (embl.de)
  • Though the VNTR resides in a region encoding the 3' untranslated region (UTR) and does not alter the protein's amino acid sequence, the prevalent 10-repeat variant has shown both linkage and association to Attention Deficit Hyperactivity Disorder (ADHD). (biomedcentral.com)
  • Through extensive biochemical and genetic analysis, we now know that pathways are not simply switched on with kinases and off with phosphatases. (rupress.org)
  • However, there is no study to our knowledge that specifically investigated the evolution of copy number variable subexonic repeats from their initial emergence as functional units to the adaptive constraints and mutational properties that contributed to their extant variation in primates. (nature.com)
  • In this study, we identified members of B. cereus groups in 65% of the ice cream samples analyzed, which were characterized based on multi locus variable number tandem repeats analysis (MLVA) and whole genome sequencing (WGS). (bvsalud.org)
  • A 40-bp variable number of tandem repeats (VNTR) polymorphism exists in the 15th exon of DAT1 , the gene encoding the human dopamine transporter (DAT). (biomedcentral.com)
  • However, the cis-regulatory sequence controlling this posterior expression pattern has not been precisely identified. (sdbonline.org)
  • Our analysis provides a framework to perform future experimental and comparative studies to understand the roles of the ancestral chordate versions of GPCRs that predated the divergence of the urochordates and the vertebrates. (biomedcentral.com)
  • MUC7 provides an opportunity to assess the broader implications of subexonic repeat variation within the context of the functional evolution of the mucin functional group and primate salivary adaptation. (nature.com)
  • Here, we focus on the salivary mucin-7 gene ( MUC7 ) to study the evolution and functional impact of subexonic repeats. (nature.com)
  • In this study, we investigated the chromatin dynamics and arrangement with DNA damage in Arabidopsis thaliana by live-cell imaging with the lacO /LacI-EGFP system and simulation analysis. (nature.com)
  • These results were validated by paired TCR and single cell RNA sequencing, which elucidated transcriptomic profiles distinct to neoantigen-specific CD4 + TIL. (bmj.com)
  • Four ankyrin repeats are also present, the first two of which form an extensive interface with the ARF-GAP domain. (embl.de)