• 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)
  • The complete sequences of the galago and rabbit beta-globin locus control regions: extended sequence and functional conservation outside the cores of DNase hypersensitive sites. (shengsci.com)
  • The locus control region (LCR) of mammalian beta-globin genes covers at least 17 kb at the 5' end of the gene cluster and has been implicated in chromatin domain opening, enhancement, and insulation from neighboring sequences. (shengsci.com)
  • Multiple copies of eBSV viral sequences have become integrated as direct and inverted tandem repeats at a single locus in the B genome of the host during viral infection 5 . (nature.com)
  • Common variants in UMOD have also been demonstrated in large genome-wide association studies (GWAS) to confer independent risk for both hypertension and kidney disease illustrating the shared risk for both phenotypes within this locus (see the GWAS in Nephrology team description for more). (medscape.com)
  • The locus at chromosome 1q21 was identified by linkage mapping in 1998, but the gene has only recently been discovered due to difficulty with sequencing this highly repetitive region and was previously missed using next-generation sequencing. (medscape.com)
  • In Colombia, the Beijing genotype was fi rst detected 2 readers and compared with SpolDB4.0 (Pasteur Institute in 1998 in 11 of 111 isolates from new and previously of Guadeloupe, Les Abymes, Guadeloupe) and MIRU- treated patients in Buenaventura ( 6 ). (cdc.gov)
  • 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)
  • High-throughput pyrosequencing of two L. monocytogenes isolates was used to rapidly provide the genome sequence of the primary outbreak strain and to investigate the extent of genetic diversity associated with a change of a single restriction enzyme fragment during PFGE. (biomedcentral.com)
  • Notably, these two isolates were found to harbor a 50 kbp putative mobile genomic island encoding translocation and efflux functions that has not been observed in other Listeria genomes. (biomedcentral.com)
  • These isolates, negative for IS 6110 by RFLP analysis, were from 1,180 Maryland cases. (cdc.gov)
  • 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)
  • Flp-mediated recombination, one of a family of site-specific recombination technologies, was used to integrate the DAT1 constructs into a common, transcriptionally-active region of the genome, eliminating several caveats associated with traditional reporter gene methodologies [ 36 ]. (biomedcentral.com)
  • Flp recombinase, the enzymatic basis of the system, is a Saccharomyces cerevisiae derived enzyme that utilizes a substrate Flp recombination target (FRT) sequence upstream of a gene of interest (GOI) to site-specifically insert the GOI into a target site in a host cell line, thereby providing a well-controlled approach to establishing the in vitro functional effect of the DAT1 VNTR polymorphism on the DAT [ 37 ]. (biomedcentral.com)
  • Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. (asm.org)
  • genetic analysis of cinnamyl alcohol dehydrogenase in loblolly pine: single gene inheritance, molecular characterization and evolution. (liverpool.ac.uk)
  • Whole exome sequencing revealed a de novo heterozygous missense variant in all three patients in the p.Glu209Lys variant of the PACS2 gene. (bvsalud.org)
  • 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)
  • 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)
  • The mouse biliary glycoprotein gene (Bgp): partial nucleotide sequence, expression, and chromosomal assignment. (shengsci.com)
  • Its sequence, when compared to those of members of the human carcinoembryonic antigen gene family, was most homologous to the sequence of the human biliary glycoprotein (BGP) gene. (shengsci.com)
  • The identification and sequence of KiSS-1 (HGMW-approved symbol, KISS1), a human malignant melanoma metastasis-suppressor gene, was recently published. (shengsci.com)
  • Wdr12, a mouse gene encoding a novel WD-Repeat Protein with a notchless-like amino-terminal domain. (shengsci.com)
  • The MyoD gene was duplicated during the teleost whole genome duplication and, while a second MyoD gene ( MyoD2 ) was subsequently lost from the genomes of some lineages (including zebrafish), many fish lineages (including Alcolapia species) have retained both MyoD paralogues. (mdpi.com)
  • Here, using Next Generation Sequencing we identified a novel gene fusion event between DAXX and the kinesin motor protein, KIFC3, leading to the translation of a chimeric DAXX-KIFC3 fusion protein. (oncotarget.com)
  • However, given the variety of DNMT3B mutations, a first-degree affected relative should first have both alleles of this gene sequenced. (biomedcentral.com)
  • A major challenge in interpreting genome sequences is understanding how the genome encodes the information that specifies when and where a gene will be expressed. (sdbonline.org)
  • Moreover, they demonstrated that phosphorylated NKCC2 levels rose in tandem with UMOD gene dosage. (medscape.com)
  • This disease, previously referred to as MCKD type 1, is due to a mutation in the variable-number tandem repeat region of the MUC1 (Mucin 1) gene. (medscape.com)
  • 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)
  • Southern blot analysis of EcoRI-digested mouse cellular DNA with this probe detected four restriction fragments, all of which appear to be located on mouse chromosome 7, Northern blot analysis using the mouse probe demonstrated that related mRNA species were expressed in some normal adult mouse tissues. (shengsci.com)
  • A bacterial artificial chromosome (BAC) library has been constructed for use in bovine genome mapping using constructed for use in bovine genome mapping using the pBeloBAC11 vector. (shengsci.com)
  • During DNA REPLICATION, chromosome ends loose some of their telomere sequence (TELOMERE SHORTENING. (lookformedical.com)
  • 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)
  • Improving our understanding of these mutations would increase our knowledge of the mutational dynamics of the genome and may uncover additional loci that contribute to disease. (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)
  • Approximately 30% of new STR mutations occur within Alu elements, which compose only 11% of the genome, but only 10% are found in LINE-1 insertions, which compose 17% of the genome. (biomedcentral.com)
  • We estimate the average number of de novo genome-wide STR mutations per individual to be approximately 85, which is similar to the average number of observed de novo single nucleotide variants. (biomedcentral.com)
  • 7- 9 All reported mutations are single nucleotide alterations leading to splice site, missense, nonsense, or frameshift mutations, or intra-exonic deletions and insertions of up to four nucleotides, which have been detected through exonic PCR amplifications and sequencing. (bmj.com)
  • 3, 10 However, analyses of SDHC in four series of patients with paraganglioma or pheochromocytoma 6, 8, 11, 12 yielded no definitive SDHC mutations. (bmj.com)
  • The regenerated genome-edited events of Gonja Manjaya showed mutations in the targeted sites with the potential to prevent proper transcription or/and translational into functional viral proteins. (nature.com)
  • The genome-edited events of plantain Gonja Manjaya were generated with mutations in the targeted sites of integrated eBSV sequences in the host genome. (nature.com)
  • The analysis gives an upper-bound on the performance of genome assemblers for de novo reconstruction of genomes across a wide range of read lengths. (biomedcentral.com)
  • GENETICS AND GENEALOGY: Y Polymorphism and mtDNA Analyses", by Kevin F. Duerinck, Esq. (duerinck.com)
  • Actually, no, because the women whom you have traced using the mtDNA analysis were not the ones married to the males you traced in the y polymorphism analysis. (duerinck.com)
  • High-throughput genome sequencing provided a more detailed real-time assessment of genetic traits characteristic of the outbreak strains than could be achieved with routine subtyping methods. (biomedcentral.com)
  • 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)
  • The variable number of tandem repeats (VNTR) typing method was employed, as previously described, to further investigate these strains ( 11 ). (cdc.gov)
  • To resolve a well-supported eumalacostracan phylogeny and obtain a robust tree, it will be necessary to look beyond the most commonly utilized sources of data (nuclear ribosomal and mitochondrial sequences). (wikipedia.org)
  • The second method is called mitochondrial DNA, or mtDNA analysis. (duerinck.com)
  • Again, please understand that the molecular biology techniques used in mitochondrial DNA analysis should not be confused with DNA fingerprinting which is carried out on nuclear DNA. (duerinck.com)
  • BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. (biomedcentral.com)
  • Heterogeneous cDNAs can be amplified with PCR by appending known sequences to one or both ends of the cDNA so primers with known sequences can be used to amplify the heterogeneous cDNAs. (github.io)
  • 2003. Genome-scale design of PCR primers and long oligomers for DNA microarrays. (ojp.gov)
  • Microsatellites were observed only in euchromatin regions, whereas the (TTAGG) 6 repeats were found at telomeric sites in both groups. (karger.com)
  • Teixeira LSR, Seger KG, Targueta CP, Orrico VGD, Lourenço LB (2016) Comparative cytogenetics of tree frogs of the Dendropsophus marmoratus (Laurenti, 1768) group: conserved karyotypes and interstitial telomeric sequences. (pensoft.net)
  • Though the species of this group show a high degree of karyotypic similarity, D. soaresi was unique in presenting large blocks of het- ITSs (heterochromatic internal telomeric sequences) in the majority of the centromeres. (pensoft.net)
  • ALT is a recombination-based mechanism where one telomere uses other chromosomal, or extrachromosomal, telomeric DNA sequences as a template for telomere elongation. (oncotarget.com)
  • It is structurally different from TELOMERIC REPEAT BINDING PROTEIN 2 in that it contains acidic N-terminal amino acid residues. (lookformedical.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)
  • Short tandem repeats (STRs), or microsatellites, are 1-6 base pair (bp) motifs of repeating units of DNA. (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)
  • Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome. (biomedcentral.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)
  • 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)
  • Sequences of previously described binding sites were collected for these five factors present in the cis-regulatory regions of known target genes. (sdbonline.org)
  • Further, we demonstrate that the majority of genes in prokaryotic genomes can be reconstructed uniquely using very short reads even if the genomes themselves cannot. (biomedcentral.com)
  • This study confirms that the latest generation of DNA sequencing technologies can be applied during high priority public health events, and laboratories need to prepare for this inevitability and assess how to properly analyze and interpret whole genome sequences in the context of molecular epidemiology. (biomedcentral.com)
  • We describe an application of de Bruijn graphs to analyze the global repeat structure of prokaryotic genomes. (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)
  • The potential application of our method includes annotation of new genomic sequences and motif discovery. (biomedcentral.com)
  • 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)
  • The common ancestor of the salmonids experienced a whole genome duplication event, making extant salmonids such as the rainbow trout an excellent model for studying the evolution of tetraploidization and re-diploidization in vertebrates. (biomedcentral.com)
  • A whole genome duplication event occurred 25 to 100 million years ago in the common ancestor of the salmonids. (biomedcentral.com)
  • 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 first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and identified almost 59.5% of the BES database in base-pairs as repetitive sequence. (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)
  • Identification of putative transmembrane receptor sequences homologous to the calcium-sensing G-protein-coupled receptor. (shengsci.com)
  • We find that this type of non-canonical fork convergence in fission yeast is prone to trigger deletions between repetitive DNA sequences via a mechanism we call Inter-Fork Strand Annealing (IFSA) that depends on the recombination proteins Rad52, Exo1 and Mus81, and is countered by the FANCM-related DNA helicase Fml1. (elifesciences.org)
  • 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)
  • Here, we examined the genetic diversity, distribution and mobilisation of iuc and iro loci amongst 2503 K . pneumoniae genomes using comparative genomics approaches and developed tools for tracking them via genomic surveillance. (biomedcentral.com)
  • DNA isolation, genotyping of simple tandem repeat polymorphisms, PCR amplification and sequencing were performed using standard techniques 2 and all simple tandem repeat polymorphisms were amplified in the presence of 10% glycerol and 5% DMSO after labelling one oligonucleotide primer with 32 P and analysed on a 6% polyacrylamide gel. (bmj.com)
  • In this case, the basic principle is to detect specific DNA and RNA sequences via hybridization of a probe, detecting any complementary sequence on the cDNA of this bacterium. (australiaessays.com)
  • Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission. (microbiologyresearch.org)
  • The fractions of the 97,846 non-repetitive trout BES reads that had significant BLASTN hits against the zebrafish, medaka and stickleback genome databases were 15%, 16.2% and 17.9%, respectively, while the fractions of the non-repetitive BES reads that had significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 10.7%, 9.5% and 9.5%, respectively. (biomedcentral.com)
  • The study of biological complexity is a new frontier that requires high-throughput molecular technology, high speed computer memory, new approaches to data analysis, and the integration of interdisciplinary skills. (intechopen.com)
  • At present, DNA molecular marker techniques are widely applied in the fields of germplasm identification, phylogenetics, and genetic structural analysis. (biomedcentral.com)
  • The major burden of iuc and iro amongst the genomes analysed was due to two linked lineages ( iuc1 / iro1 74% and iuc2 / iro2 14%), each carried by a distinct non-self-transmissible IncFIB K virulence plasmid type that we designate KpVP-1 and KpVP-2. (biomedcentral.com)
  • 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)
  • In this report, we present a corrected genomic sequence, genomic structure, and refined chromosomal location for KiSS-1. (shengsci.com)
  • We can therefore amplify nucleotide sequences from infinitesimal amounts of DNA extract. (intechopen.com)
  • A comparative analysis of the available cytogenetic data for the family Osmeridae reveals diploid numbers higher than 48 and high fundamental numbers. (scielo.br)
  • Its principle is based on the use of DNA polymerase which is an in vitro replication of specific DNA sequences. (intechopen.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)
  • Ultimately, this task is accomplished experimentally using techniques such as empirical deletion analysis, direct binding measurements, and co-precipitation of protein-DNA complexes. (biomedcentral.com)
  • The WD-repeat protein family consists of a large group of structurally related yet functionally diverse proteins found predominantly in eukaryotic cells. (shengsci.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)
  • Since the disease is prone to recurrence after surgery, HGF patients must undergo repeated surgical procedures of gingival resection, which brings a heavy psychological and economic burden to HGF patients and their families. (nature.com)
  • In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents. (biomedcentral.com)
  • The capelin, Mallotus villosus (Müller, 1776), is a smeltlike fish species widely distributed in sub arctic waters (Gjøsæter, 1998). (scielo.br)
  • 2005). The species appears to be semelparous (Gjøsæter and Loeng, 1987), although females from fjord populations may survive to spawn a second time (Christiansen and Siikavuopio, 1998). (scielo.br)
  • Methods of this type assume that regulatory regions are highly conserved in cross-genomic comparison, and conserved segments can be extracted from evolutionary related genomes. (biomedcentral.com)
  • Furthermore, it is still an open question as to how many genomes are sufficient for reliable extraction of regulatory regions. (biomedcentral.com)
  • The first step in this process is the identification of regions of the genome that contain regulatory information. (sdbonline.org)
  • However, the cis-regulatory sequence controlling this posterior expression pattern has not been precisely identified. (sdbonline.org)
  • When the banana plants are stressed, the eBSV recombines to produce a functional episomal viral genome and infectious viral particles and as a result the plant develops disease symptoms. (nature.com)
  • Sha J , Almagro G , Mc V . Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data. (microbiologyresearch.org)
  • These data highlight a potentially unrecognized mechanism of DAXX inactivation in ALT positive osteosarcoma and provide rationale for thorough and comprehensive analyses of ATRX/DAXX/H3.3 proteins in ALT positive cancers. (oncotarget.com)
  • Build data systems that link various data sources and allow for automated, more efficient data analysis and visualization. (cdc.gov)
  • The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. (biomedcentral.com)
  • Approximately 55% of the BES reads (97,846) had more than 100 base pairs of contiguous non-repetitive sequences. (biomedcentral.com)
  • After Alu I digestion, the DNA was transferred to a nylon membrane for polymorphic guanine cytosine-rich repetitive sequence (PGRS) Southern blotting. (cdc.gov)
  • Indeed, if the sequence of interest is present in the DNA extract, it is possible to selectively replicate it (we speak of amplification) in very large numbers. (intechopen.com)
  • We provide the first survey of the repeat structure of a large number of genomes. (biomedcentral.com)
  • This method can generate tens of billions of copies of a particular DNA fragment (the sequence of interest, DNA of interest, or target DNA) from a DNA extract (DNA template). (intechopen.com)
  • A total of 176,485 high quality BES, were generated, representing approximately 4% of the trout genome. (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)
  • Metabolites were quantified using reversed-phase ultra-high performance liquid chromatography and electrospray ionization tandem mass spectrometry. (cdc.gov)
  • This study paves the way for the improvement of B genome germplasm and its use in breeding programs to produce hybrids that can be globally disseminated. (nature.com)
  • In this study, CRISPR/Cas9-based genome-editing technology was applied to inactivate eBSV sequences in the host plantain genome. (nature.com)
  • In this paper, we study an idealized instance of the short-read assembly problem and attempt to estimate the ability of these technologies to reconstruct genomes. (biomedcentral.com)
  • Instead of approximately 1000 nucleotide reads common with traditional Sanger sequencing, these technologies generate reads of only about 25-400 consecutive nucleotides. (biomedcentral.com)
  • Upon discovery of a new disease, careful analysis on the disease must be done before initiating screening, diagnosis and treatment methods to be used. (australiaessays.com)
  • Scientific Working Group on DNA Analysis Methods (SWGDAM) Y-STR Subcommittee. (ojp.gov)
  • 2004. Report on the current activities of the Scientific Working Group on DNA Analysis Methods Y-STR Subcommittee. (ojp.gov)
  • 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)
  • At the 25-year anniversary of this accomplishment, we describe how insights gleaned from the M. tuberculosis genome have led to vital tools for TB research, epidemiology, and clinical practice. (jci.org)
  • The M. tuberculosis genome has ushered in a quarter century of substantial clinical and public health advancements. (jci.org)
  • These MGEs, most typically plasmids and integrative and conjugative elements (ICEs), are therefore important constituents of the accessory genome that imbue K . pneumoniae organisms with their distinct HA or CA clinical profiles. (biomedcentral.com)
  • It also restricts germplasm movement of genotypes with the B genome worldwide due to this potential activation of eBSV into the episomal infectious form of virus. (nature.com)