• This involved firstly identifying a subset of 37,251 human deletions (hDELs) through pairwise comparisons of chimpanzee and macaque genomes. (wikipedia.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)
  • To gain in-depth insights into the viral population and to perform detailed characterization of viral genomes, we used a new approach combining long-range PCR with next-generation and third-generation sequencing which allowed near full-length sequencing of HEV-3 genomes. (nature.com)
  • Furthermore, we developed a targeted ultra-deep sequencing approach to assess the dynamics of clinically relevant mutations in the RdRp-region and to detect insertions in the HVR-domain in the HEV genomes. (nature.com)
  • Two recently sequenced rice genomes Oryza sativa L. var. (biomedcentral.com)
  • Enzymes with sequences sharing over 80% identity have been found in the genomes of macaque, mouse, rat, dog, and cow. (biomedcentral.com)
  • The Pseudomonas infecting PB1-like phages are widespread in nature and possess highly conserved genomes. (biomedcentral.com)
  • 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)
  • This is an actively progressing area, as more and more sequenced genomes appear. (biomedcentral.com)
  • The mechanisms and time of occurrence of hCONDELs are not entirely understood but given that conserved non-coding sequences play a major developmental role through regulation of genes, their loss in regions of deletions, it is expected that their loss in hCONDELs will result in developmental consequences that can be observed in human-specific traits. (wikipedia.org)
  • The reduced expression of most of these genes in htz1Delta cells was reversed by the deletion of SIR2 (sir2Delta) suggesting that H2A.Z antagonizes telomeric silencing. (sdbonline.org)
  • We, therefore constructed an in frame deletion mutant of dltX , without affecting the expression of the other genes of the operon. (frontiersin.org)
  • The sizes of genes, intergenic sequences, and indels are proportionally scaled down. (biomedcentral.com)
  • Gene structure analysis indicated that the maximum number of genes were intron-less and remained conserved during evolution. (nature.com)
  • Current diagnostic PCR assays target a variety of SARS CoV-2 genes and the vast majority target sequences in regions of the SARS CoV-2 genome that are highly conserved. (who.int)
  • Sequencing of a 2.5-kb chromosomal Sma I- Pst I fragment containing the structural gene revealed an open reading frame encoding 537 amino acids, homologous to known pckA genes. (asm.org)
  • Confirmed rat disease genes will be tested for conserved functions in humans. (europa.eu)
  • Deletion or mutations of their encoding genes usually severely impair either oogenesis or spermatogenesis or both. (ijbs.com)
  • These genes, encoding for RNA binding proteins, contain a highly conserved RNA recognition motif and at least one DAZ repeat encoding for a 24 amino acids sequence able to bind other mRNA binding proteins. (ijbs.com)
  • DAZ family genes are highly conserved. (ijbs.com)
  • Sequences of DNA in the genes that are located between the EXONS. (lookformedical.com)
  • Previous data for sequencing of 3 genes indicated that the Georgia 2007/1 isolate is closely related to isolates of genotype II, which has been identified in Mozambique, Madagascar, and Zambia. (cdc.gov)
  • 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)
  • Indeed, both whole-genome and exome sequencing strategies have identified disease-causing mutations in probands with Charcot-Marie Tooth disease , Miller syndrome , severe brain malformations , and a few other disorders. (massgenomics.org)
  • In order to identify optimal sites for primer design, we utilized 1020 whole genome sequences in public databases (NCBI, EMBL and DDBJ) and 103 sequences in our laboratory, and developed a program BxB to select conserved regions as candidates for primer design. (biomedcentral.com)
  • H. influenzae isolates were sent to the Centers for Disease Control and Prevention for species confirmation, serotyping, and whole genome sequencing of select isolates. (cdc.gov)
  • Background De novo mutations are emerging as an important cause of neurocognitive impairment, and whole exome sequencing of case-parent trios is a powerful way of detecting them. (bmj.com)
  • The purpose of the present study was to report the clinical features of a Chinese family with FAP and screen for novel mutations using the targeted next‑generation sequencing technology. (spandidos-publications.com)
  • All identified mutations occurred at highly conserved sequences, not only in the FGFR family of molecules, but also throughout evolution and clustered in the immunoglobulin-like loop-III domain, highlighting the functional importance of this domain. (aacrjournals.org)
  • Most, although not all, of the mutations causing skeletal abnormalities involve conserved residues that are predicted to play an important structural role in the correct folding of FGFRs, and substitutions with other residues result in constitutive activation of FGFRs with ligand-independent dimerization (11) . (aacrjournals.org)
  • Overall, these assays and approaches detect specific mutations or features such as insertions, deletions and point mutations in the SARS CoV-2 genome that are characteristic of a particular VOC/VOI using PCR. (who.int)
  • This identified 14 non-coding de novo mutations affecting a 42bp conserved region encompassed by a regulatory. (exeter.ac.uk)
  • Specific gene mutations and chromosomal anomalies including translocations, deletions, and duplications have also been documented in patients with syndromic, non-syndromic, and isolated PRS. (biomedcentral.com)
  • RNA editing refers to post-transcriptional processes that alter the nucleotide sequence of an RNA transcript by insertion, deletion or nucleotide conversion. (biomedcentral.com)
  • When this conversion occurs in the coding region of mRNA, it results in an altered nucleotide codon and, therefore, can change the amino acid sequence of the coded protein in what is referred to as a re-coding editing event. (biomedcentral.com)
  • The considerable number of HBV isolates with rather divergent nucleotide sequences and the partially double-stranded characteristic of HBV impose the need for extreme care in the choice of primers for both full length and fragment amplification. (biomedcentral.com)
  • It is also called nucleotide sequence. (lookformedical.com)
  • Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)
  • Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. (lookformedical.com)
  • The human immunodeficiency virus-1 (HIV-1) nucleocapsid protein (NCp7) is a nucleic acid chaperone protein with two highly conserved zinc fingers. (bvsalud.org)
  • Methods The Deciphering Developmental Disorders study is using whole exome sequencing in family trios to investigate children with severe, sporadic, undiagnosed developmental delay. (bmj.com)
  • Whole exome sequencing of the genomic DNA and polymerase chain reaction were conducted for all the controls and family members to verify the variants. (biomedcentral.com)
  • Chimpanzee sequences highly conserved in other species were then identified by pairwise alignment of chimpanzee with macaque, mouse and chicken sequences with BLASTZ followed by multiple alignment of the pairwise alignments done with MULTIZ. (wikipedia.org)
  • Multiple MTG8-related sequences are found in several vertebrate species, from fish to mammals, albeit not in a urodele. (embl-heidelberg.de)
  • We conducted a phylogenetic analysis of the section, including samples of all species, using sequences of the ITS and ETS regions of nuclear ribosomal DNA. (bioone.org)
  • Similar enzymes have been found in the genomic sequences of several species, but neither systematic analyses of their distribution nor modeling of their structures have been previously attempted. (biomedcentral.com)
  • We have analyzed the presence of orthologs of human CLN2 in the genomic sequences of a number of eukaryotic species. (biomedcentral.com)
  • Promoter sequences of other Brassicaceae species were able to partially complement the A. thaliana bb-1 mutant, suggesting that at least within the Brassicaceae family the regulatory pathways are conserved. (biomedcentral.com)
  • The possibility for developing such probes specifically painting homoeologous chromosomes in allopolyploid species has been questioned since that chromosomes belonging to the same homoeologous group share highly conserved sequences. (arborbiosci.com)
  • In some invertebrate species, BOULE protein play a pivotal role in germline specification and a conserved regulatory role in meiosis. (ijbs.com)
  • Formins are multidomain proteins conserved from plants to fungi and vertebrates. (biomedcentral.com)
  • ADARs are highly conserved across vertebrates and are essential for normal development in mammals. (biomedcentral.com)
  • Ancestral Boule is present from sea anemones through humans and Dazl is conserved among vertebrates. (ijbs.com)
  • Of the 510 identified hCONDELs, only one of these deletions has been shown to remove a 92 bp sequence that is part of a protein-coding region in the human sequence. (wikipedia.org)
  • The deletion that affects the protein coding region in humans results in a frameshift mutation in the CMAH gene which codes for the cytidine monophosphate-N-acetylneurminic acid hydroxylase-like protein, an enzyme involved in the production of N-glycolylneuraminic acid, one type of sialic acid. (wikipedia.org)
  • by fusion of mouse constructs fused to basal promoter with LacZ expression for hCONDELs near the androgen receptor (AR) locus and the growth arrest and DNA-damage-inducible protein GADD45 gamma (GADD45G) locus suggest a role in deletions that affect regulatory sequences in humans. (wikipedia.org)
  • PURA encodes Pur-α, a highly conserved multifunctional protein that has an important role in normal postnatal brain development in animal models. (bmj.com)
  • hNoL12 is a highly conserved 25 kDa nucleolar RNA-binding protein implicated in the 5'end processing of ribosomal RNA in the nucleolus and thus in the assembly and maturation of ribosomes. (bvsalud.org)
  • Molecular cloning of cDNA indicated that the AML1-MTG8-binding protein (MTGR1) is highly related to MTG8 and similar to Drosophila Nervy. (embl-heidelberg.de)
  • GRP78 is a highly conserved protein that is essential for cell viability.The highly conserved sequence Lys-Asp-Glu-Leu (KDEL) is present at the C terminus of GRP78and other resident ER proteins including glucose regulated protein 94 (GRP 94) and proteindisulfide isomerase (PDI). (exposed-skin-care.net)
  • This region of the protein associating with Dss1 is highly conserved in sequence and by comparison with mammalian BRCA2 corresponds to a part of the DNA binding domain with characteristic OB folds. (cornell.edu)
  • 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)
  • AbstractSummaryCurrent tools to annotate the predicted effect of genetic variants are heavily biased towards protein-coding sequence. (exeter.ac.uk)
  • We report the complete genomic coding sequence of the Georgia 2007/1 isolate and comparison with other isolates. (cdc.gov)
  • Experimental infections of pigs confirmed that isolates obtained after introduction of ASF into Armenia and the Russian Federation cause acute disease and result in high mortality rates ( www.efsa.europa.eu/en/scdocs/scdoc/1556.htm ). (cdc.gov)
  • Advances in genome resources and gene targeting have increased the attractiveness of the rat model for genetic studies but progress has been hampered by absence of relevant rat genome sequences. (europa.eu)
  • The histone H2A.F/Z (H2AZ) variant is a functionally distinct, highly conserved histone subgroup that likely represents a separate evolutionary lineage of histone H2A proteins. (sdbonline.org)
  • Formins are multidomain proteins defined by a conserved FH2 (formin homology 2) domain with actin nucleation activity preceded by a proline-rich FH1 (formin homology 1) domain. (biomedcentral.com)
  • This intronic deletion spans a highly conserved binding domain to which several developmentally important proteins bind. (upenn.edu)
  • These proteins have a highly conserved RNA recognition motif (RRM) for binding target mRNAs and at least one characteristic sequence of 24 amino acids, which are termed as DAZ repeats [ 1 ]. (ijbs.com)
  • Combining with other proteins, DAZ family members play a crucial role in male and female gametogenesis conserved throughout the evolution. (ijbs.com)
  • Sequencing of the phage genome revealed that the phage JG024 is highly related to the ubiquitous and conserved PB1-like phages. (biomedcentral.com)
  • These represent a new class of regulatory sequences and may have played an important role in the development of specific traits and behavior that distinguish closely related organisms from each other. (wikipedia.org)
  • The region of DNA which borders the 3' end of a transcription unit and where a variety of regulatory sequences are located. (lookformedical.com)
  • Population-based Sanger sequencing has been shown to miss minor variants with a frequency below 20% 20 . (nature.com)
  • Highly conserved regions are less likely to mutate, therefore there is a high likelihood that the diagnostic test will remain accurate in the presence of variants. (who.int)
  • Next, the authors developed a method ("Syzygy") to model sequencing error and call variants at very low frequencies. (massgenomics.org)
  • These sequence variants, along with variants controlling dysregulated gene expression that we characterised previously, most likely include the major determinants of SHR cardiovascular and metabolic disease phenotypes. (europa.eu)
  • We shall determine the functional consequences of these variants by creating and phenotyping transgenic and knockout rats on the SHR and WKY genetic backgrounds, using transposon-mediated transgenesis and zinc-finger nuclease-mediated gene deletion recently shown to be highly efficient in rats. (europa.eu)
  • Matthew has developed a keen interest in novel data analysis methods for short read sequencing data, particularly for extracting information (such as copy number variants, homozygosity mapping, and relatedness) from sequence reads that would otherwise be unused. (exeter.ac.uk)
  • While the genomic sequence of DcAOX2a was previously described, we characterize here the complete genomic sequence of DcAOX1 . (frontiersin.org)
  • A comparison of the two predicted amino acid sequences revealed a highly conserved N-terminal region, which is presumed to be the catalytic domain, and a variable C-terminal region containing multiple Cys residues, which is proposed to be involved in activation of the enzyme by metal ions. (archive.org)
  • however, validation of these predicated regions of deletions through polymerase chain reaction methods produces 510 hCONDELs. (wikipedia.org)
  • Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. (lookformedical.com)
  • Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. (lookformedical.com)
  • Such rearrangements include insertion/deletion (indel), duplication and transposition. (biomedcentral.com)
  • DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom. (lookformedical.com)
  • In this study, the potential use of PCR was investigated using the primers Pt8-Pt9 based on the insertion sequence IS 6110 of the Mycobacterium tuberculosis complex (Kolk etal, 1992). (who.int)
  • Based on an established filtering strategy and data analyses, along with confirmation by Sanger sequencing and co‑segregation, a novel frameshift mutation c.1317delA (p.Ala440LeufsTer14) in exon 10 of the APC gene was identified. (spandidos-publications.com)
  • Major distinctions in the gene sequences between SARS‑CoV and SARS‑CoV‑2 include the spike gene, open reading frame (ORF) 3b and ORF 8. (spandidos-publications.com)
  • More than 68 percent had less than 5 copies of the IS sequence suggesting that our local M.tuberculosis strains have a fewer number of copies compared to data shown in most countries. (who.int)
  • To investigate the upstream regulation of BB we combined a promoter deletion analysis with a phylogenetic footprinting approach. (biomedcentral.com)
  • Primer extension analysis identified a transcriptional start site 72 bp upstream of the pckA initiation codon and an upstream sequence similar to ς 70 promoters. (asm.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)
  • There are many superfamilies of Znf motifs, varying in both sequence and structure. (embl.de)
  • Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. (lu.se)
  • Analysis with C-terminal deletion mutants of AML1-MTG8 indicated that the region of 51 residues (488 to 538), which contains NHR2, is essential for the induction of G-CSF-dependent cell proliferation. (embl-heidelberg.de)
  • hCONDELs, on average, remove about 95 base pairs (bp) of highly conserved sequences from the human genome. (wikipedia.org)
  • The highly-conserved Grainyhead-like (Grhl) transcription factors are critical regulators of embryogenesis that regulate cellular survival, proliferation, migration and epithelial integrity, especially during the formation of the craniofacial skeleton. (doe.gov)
  • The median size of these 510 validated CONDELs is about 2,804 bp, thus showing a diverse range in length of the characteristic deletions. (wikipedia.org)
  • The highly heterogenic characteristic of viruses is the major obstacle to efficient DNA amplification. (biomedcentral.com)
  • The highly conserved chimpanzee sequences were searched against the human genome using BLAT to identify conserved regions not present in humans. (wikipedia.org)
  • The loss of this gene is evident in the undetectable levels of sialic acid in humans but highly present in mouse, pig, chimpanzee and other mammal tissues and may provide more insight into the historic background of human evolution. (wikipedia.org)
  • Plague is a zoonotic disease, endemic throughout the world, and highly infectious in humans. (asm.org)
  • By analysing iNKT cells from lymphoid tissues of mice and humans we demonstrate that their T cell receptor (TCR) repertoire is highly diverse and is distinct for cells from various tissues resulting in differential lipid-antigen recognition. (elifesciences.org)
  • Deletion of DAZ gene is the most common causes of infertility in humans. (ijbs.com)
  • The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). (lookformedical.com)
  • In most fungal and metazoan formins the FH1-FH2 core is accompanied by a less well conserved N-terminal FH3 (formin homology 3) domain involved in targeting [ 14 ]. (biomedcentral.com)
  • Sequence homology is an indication of the genetic relatedness of different organisms and gene function. (lookformedical.com)
  • Therefore, to capture the heterogeneity of the HEV quasispecies, including recombination events and SNP that occur with very low frequencies, we developed new sequencing approaches for HEV genotype 3 based on the amplification of the near full-length genome of HEV by long-range PCR (lrPCR) followed by subsequent next-generation sequencing (NGS) and third-generation sequencing. (nature.com)
  • Taking advantage of the large number of virus DNA sequences in public databases to select conserved sites for primer design is an optimal way to tackle the difficulties in virus genome amplification. (biomedcentral.com)
  • Because of the existence of quasispecies, the only way to obtain HBV haplotype sequences is through full length genome amplification and clone-sequencing instead of assembling the PCR sequences of several amplified fragments of the genome. (biomedcentral.com)
  • In conclution, DNA amplification is a rapid, reliable and accurate method with a high degree of sensitivity and specificity for the detection of Mycobacterium tuberculosis DNA sequences and it can replace the conventional culture method in the diagnosis of extra pulmonary tuberculosis and tuberculosis meningitis except in the situation when antibiotic sensitivity results are required. (who.int)
  • SRSF3 emerged as the most potent NXF1 adaptor, conferring sequence specificity to RNA binding by NXF1 in last exons. (uni-frankfurt.de)
  • Their requirement for Htz1 can be bypassed by sir2Delta or by a deletion encompassing the silencing nucleation sites in HMR. (sdbonline.org)
  • We have reported previously that Short Interspersed Degenerate Retroposons of the SIDER2 subfamily, largely located within 3'UTRs of Leishmania transcripts, promote rapid turnover of mRNAs through endonucleolytic cleavage within the highly conserved second tandem 79-nt hallmark sequence (79-nt SII). (uni-frankfurt.de)
  • Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. (embl.de)
  • The model presented here indicates a very open and accessible active site that is almost completely conserved among all known CLN2 enzymes. (biomedcentral.com)
  • All of these enzymes contain a conserved deaminase domain, shown in blue. (biomedcentral.com)
  • Comparison of the three predicted human MTG8-related polypeptides to their Drosophila counterpart (nervy) highlights four separate regions of sequence conservation that may correspond to distinct domains. (embl-heidelberg.de)
  • The migration of ATP7A appears to involve amino acid sequences in the carboxyl terminus, utilizing both clathrin-dependent and clathrin-independent endocytosis. (medscape.com)
  • Phylogeny based on concatenated sequences of 125 conserved ORFs showed that this isolate clustered most closely with the Mkuzi 1979 isolate. (cdc.gov)
  • Although human disease is rare, Y. pestis is dangerous and highly infectious and thus has been identified as having potential for use in bioterrorism or as a biological weapon. (asm.org)
  • When it comes to massively parallel sequencing, few areas of human health stand to benefit as much as rare genetic diseases. (massgenomics.org)
  • Since 2022, despite the wide geographic spread of highly pathogenic avian influenza (HPAI) A(H5N1) viruses in wild birds and to poultry worldwide, with sporadic spillover to mammals, only a small number of sporadic human cases of A(H5N1) have been identified. (cdc.gov)
  • The objective of this document is to outline the available methods and tools for screening and sequencing patient specimens for the detection of VOC or VOI, with a focus on those that offer a rapid turn-around time so as to support rapid implementation of public health actions for COVID 19 control. (who.int)
  • however, recombinant HAdV-14p1 fi ber regions containing the depending on the infecting HAdV serotype and tropism 2-aa deletion did not demonstrate substantial phenotypic resulting from differential host receptor use, the wide differences between the new agent and the prototype virus variety of symptoms can include pneumonia, febrile ( 12 ). (cdc.gov)
  • Almost all of these deletions fall within regions that perform non-coding functions. (wikipedia.org)
  • This identified 583 regions of deletions that were then referred to as hCONDELs. (wikipedia.org)
  • The BxB program based on multiple sequence alignment not only can be used as a separate tool but also can be integrated in any open source primer design software to select conserved regions for primer design. (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)
  • We present a detailed sequence analysis of the 10 formins (ForA to J) identified in the genome of the social amoeba Dictyostelium discoideum . (biomedcentral.com)
  • Sequence analysis revealed that all affected dogs share a homozygous deletion of 7.8 kb in the NHEJ1 gene. (upenn.edu)
  • In the present study, we attempted to construct a wheat chromosome 4D-specific oligo probe library by selecting 4D-specific sequences in reference genome of common wheat cv. (arborbiosci.com)
  • Pierre Robin sequence (PRS) is a condition present at birth. (biomedcentral.com)
  • We found that short deletions of 8-nt spanning the two predicted cleavage sites block degradation of SIDER2-containing transcripts, leading to mRNA accumulation. (uni-frankfurt.de)
  • Now, the Barnes laboratory investigates viral-host interactions and translates knowledge of the structural correlates of antibody-mediated neutralization of viruses into the rational development of highly protective antibodies. (stanford.edu)
  • Dotted line represents where a sequence in one line cannot be aligned with a sequence at the corresponding position in the other line. (biomedcentral.com)
  • citation needed] The 60.7kb hCONDEL which is located near the AR locus has been found to be responsible for removing a 5 kb sequence that codes for an enhancer for the AR locus. (wikipedia.org)
  • Sequences of DNA or RNA that occur in multiple copies. (lookformedical.com)
  • TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES). (lookformedical.com)