• OvRFs are hypothesized to be used by viruses to encode proteins more compactly and to regulate transcription. (uwo.ca)
  • Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n = 744), demonstrating the viral proteins heterogeneous. (nature.com)
  • The Helicosporidium plastid genome is among the smallest known (37.5 kb), and like other plastids from non-photosynthetic organisms it lacks all genes for proteins that function in photosynthesis. (biomedcentral.com)
  • The co-occurrence analysis of core concepts in this stringent response, i.e. the (p)ppGpp nucleotides with gene products was also inspected and suggest that besides the enzymes RelA and SpoT that control the basal levels of (p)ppGpp nucleotides, many other proteins have a key role in this response. (biomedcentral.com)
  • All genes in the ANTP-C and BX-C code for homeodomain proteins. (sdbonline.org)
  • In Drosophila, the majority of Notch target genes known so far is located in the Enhancer of split complex , encoding small basic helix-loop-helix (bHLH) proteins that presumably act as transcriptional repressors. (sdbonline.org)
  • The five genes described in this paper are arrayed between mbeta and m7 , both coding for bHLH proteins. (sdbonline.org)
  • 10 Similarly, in recent studies, at least one third of genes in diverse organisms can exhibit alternative transcription, leading to the production of N-terminally extended proteins or alternative reading frames. (biorxiv.org)
  • Two genes encoding putative internalin proteins were chosen for further study. (omictools.com)
  • A particularly extreme case is the Drosophila dhc7 gene containing a ≥3.6 megabase (Mb) intron, which takes roughly three days to transcribe. (wikipedia.org)
  • The Enhancer of split complex (E[spl]-C) includes eight genes spread over 50 kilo bases on the Drosophila third chromosome. (sdbonline.org)
  • Other examples of Drosophila gene complexes include the Antennapedia complex (ANTP-C), the bithorax complex (BX-C) and the achaete-scute complex (AS-C). The hallmark of all these gene complexes, including the E(spl)-C is that within any complex the genes are evolutionarily related and jointly regulated. (sdbonline.org)
  • Further support to this similarity has been provided by the ability of the env-like gene of DmeGypV (the Gypsy endogenous retrovirus of Drosophila melanogaster) to promote infection of Drosophila cells by a pseudotyped vertebrate retrovirus vector. (lookformedical.com)
  • Latorre, A. and Moya, A. (1998) Mitochondrial DNA haplotype frequencies in natural and experimental populations of Drosophila subobscura. (uv.es)
  • Furthermore, our results of the preliminary epidemiological data on SARS-CoV-2 infections revealed that frequency of aa mutations were relatively higher in the SARS-CoV-2 genome sequences of Europe (43.07%) followed by Asia (38.09%), and North America (29.64%) while case fatality rates remained higher in the European temperate countries, such as Italy, Spain, Netherlands, France, England and Belgium. (nature.com)
  • Evaluating the frequency, prognosis and survival of RUNX1 and ASXL1 mutations in patients with acute myeloid leukaemia in northeastern Iran. (atlasgeneticsoncology.org)
  • RRResearch: Have bacteria evolved gene-specific rates of point mutations? (fieldofscience.com)
  • Although the classification of MDS/MPN relies largely on clinical features and peripheral blood and bone marrow morphology, studies have demonstrated that a large proportion of patients (~90%) with this disease harbor somatic mutations in a group of genes that are common across myeloid neoplasms. (encyclopedia.pub)
  • Although most of our variety comes from reshuffling of genes from our parents, new mutations are the ultimate source from which new variation is drawn. (uncommondescent.com)
  • Introns are rare in Bacteria and Archaea (prokaryotes), but most eukaryotic genes contain multiple splicesomal introns. (wikipedia.org)
  • Splicing of introns is required for the expression of most eukaryotic genes. (biomedcentral.com)
  • 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)
  • This gene encodes a member of the RecA/Rad51-related protein family that participates in homologous recombination to maintain chromosome stability and repair DNA damage. (cancerindex.org)
  • This gene encodes a protein with protease activity and is expressed in the placenta. (cancerindex.org)
  • 6 The gene is located at chromosome 21q21.22 and encodes for a transmembrane protein that is normally processed into amyloid fragments. (touchneurology.com)
  • This process is not complete, however, as all known plastids have retained a residual genome that encodes a handful of RNA and protein-coding genes, which typically include many of the key components of photosystems I and II [ 2 ]. (biomedcentral.com)
  • The word intron is derived from the term intragenic region, i.e., a region inside a gene. (wikipedia.org)
  • must be replaced by that of a transcription unit containing regions which will be lost from the mature messenger - which I suggest we call introns (for intragenic regions) - alternating with regions which will be expressed - exons. (wikipedia.org)
  • Acute myeloid leukemia in a child with familial platelet disorder and a cryptic runx1 intragenic deletion. (atlasgeneticsoncology.org)
  • Intragenic recombination among ospC genes is known, but the extent to which recombination extended beyond the ospC locus itself is undefined. (cdc.gov)
  • Introns are found in the genes of most organisms and many viruses and they can be located in both protein-coding genes and genes that function as RNA (noncoding genes). (wikipedia.org)
  • Introns are now known to occur within a wide variety of genes throughout organisms, bacteria, and viruses within all of the biological kingdoms. (wikipedia.org)
  • The frequency of introns within different genomes is observed to vary widely across the spectrum of biological organisms. (wikipedia.org)
  • Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. (biorxiv.org)
  • However, recent studies in many organisms and in humans have revealed significant protein sequence variation due to the presence of somatically acquired genetic variants, alternative transcription, and mRNA splicing, which are not necessarily annotated in reference databases. (biorxiv.org)
  • In most organisms, the opened euchromatin is enriched in tri-methylation of lysine 4 and lysine 36 (H3K4me3 and H3K36me3), two concomitant modifications associated with active transcription [ 2 ]. (biomedcentral.com)
  • We investigated a panel of 34 known high/moderate-risk cancer genes, including 16 related to breast or ovarian cancer (BC/OC) genes, and 63 candidate genes to BC/OC in 192 clinically suspicious of hereditary breast/ovarian cancer (HBOC) Spanish families without pathogenic variants in BRCA1 or BRCA2 (BRCA1/2). (cancerindex.org)
  • The phenomenon of a group of genes with the same function and location on the chromosome signifies a so-called gene complex. (sdbonline.org)
  • DNA methylation is an epigenetic modification that plays an important role in gene regulation. (uni-wuerzburg.de)
  • In this study, we performed quantitative methylation analyses of six differentially methylated imprinted genes (H19, MEG3, LIT1, NESP55, PEG3 and SNRPN), one hypermethylated pluripotency gene (OCT4) and one hypomethylated tumor suppressor gene (APC) in chorionic villus, fetal and adult cortex, and adult blood samples. (uni-wuerzburg.de)
  • Both average methylation level and range of methylation variation depended on the gene locus, tissue type and/or developmental stage. (uni-wuerzburg.de)
  • Examples of 2-omics analyses include expression quantitative trait locus eQTL (Franke & Jansen, 2009) and methylation quantitative trait locus meQTL (Smith, Kilaru, Kocak, Almli, & Mercer, 2014) that, respectively, assess the influence of genetic and epigenetic markers on gene expression. (researchgate.net)
  • Integration of gene expression and methylation to unravel biological networks in glioblastoma patients: Gadaleta et al. (researchgate.net)
  • In this work, we describe Regression2Net, a computational approach that is able to integrate gene expression and genomic or methylation data in two steps. (researchgate.net)
  • When applying our approach, Regression2Net to gene expression and methylation profiles for individuals with glioblastoma multiforme, we identified, respectively, 284 and 447 potentially interesting genes in relation to glioblastoma pathology. (researchgate.net)
  • Filters or priors on genes may be derived from methylation or expression data if available in the same individuals. (biomedcentral.com)
  • This article discusses approaches that filtered or prioritized genetic variants, regions, or genes. (biomedcentral.com)
  • In this case, standing genetic variants are present in the population at low frequencies, maintained by neutral or slightly negative selection. (biomedcentral.com)
  • 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)
  • This thesis explores the cryptic information contained in viral genomes to help explain the evolutionary processes that shape them. (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)
  • 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)
  • This project aims to decipher the cryptic information contained within viral genomes to shed light on the evolutionary processes shaping them. (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)
  • In most plastid genomes, the vast majority of genes encode products involved in either gene expression or photosynthesis. (biomedcentral.com)
  • The Helicosporidium plastid genome is also highly structured, with each half of the circular genome containing nearly all genes on one strand. (biomedcentral.com)
  • When photosynthesis is lost, so are most or all of the related genes, leading to dramatic changes in the plastid genome in size, coding capacity, and often also structure. (biomedcentral.com)
  • The E. virginiana plastid is about half the size of typical angiosperm plastids, having lost all its photosynthetic genes, but is otherwise similar to its relatives in many ways including non-coding DNA content, synteny of remaining genes and overall structure [ 4 ]. (biomedcentral.com)
  • Likewise, E. longa has lost most of the photosynthetic genes found in the plastid of its close relative Euglena gracilis , but they share many features that are unique to euglenids, such as three tandem repeats of the RNA operon and a multitude of distinctive introns [ 5 ]. (biomedcentral.com)
  • 1q23.1 homozygous deletion and downregulation of Fc receptor-like family genes confer poor prognosis in chronic lymphocytic leukemia. (cancerindex.org)
  • Deletion of either gene (GBAA0552 or GBAA1340) resulted in attenuation in a murine model of infection. (omictools.com)
  • virulence genes, and intimin types of Shi- tion. (cdc.gov)
  • DOI: aortic valve and its frequent associa- verifying serotypes and virulence genes. (cdc.gov)
  • Genome-wide transcript analysis showed that B. anthracis undergoes considerable changes in gene expression during growth in iron-depleted media, including the regulation of known and candidate virulence factors. (omictools.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 finding further highlights the importance of DMRT1 gene in sex determination and differentiation in males. (biomedcentral.com)
  • Genes of the E(spl)-C and AS-C regulate neurogenesis and related differentiation pathways. (sdbonline.org)
  • The expression patterns suggest that both genes are under the same regulatory control as are the E(spl) bHLH genes and thus, might play a part in Notch mediated cell differentiation. (sdbonline.org)
  • In contrast, the 'facultative' heterochromatin corresponds to the deposition of H3K27me3 on gene-rich regions, whose silencing is transient and dynamic across developmental processes, allowing cell type-specific differentiation and rapid adaptation of gene expression [ 5 ]. (biomedcentral.com)
  • Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. (duke.edu)
  • Introns were first discovered in protein-coding genes of adenovirus, and were subsequently identified in genes encoding transfer RNA and ribosomal RNA genes. (wikipedia.org)
  • For example, introns are extremely common within the nuclear genome of jawed vertebrates (e.g. humans, mice, and pufferfish (fugu)), where protein-coding genes almost always contain multiple introns, while introns are rare within the nuclear genes of some eukaryotic microorganisms, for example baker's/brewer's yeast (Saccharomyces cerevisiae). (wikipedia.org)
  • What does this gene/protein do? (cancerindex.org)
  • The candidate genes exhibit expression patterns in lung and heart similar to that of known PAH risk genes, and most variants occur in conserved protein domains. (biomedcentral.com)
  • Genes responsible for familial AD include the amyloid precursor protein ( APP ), presenilin 1 ( PS1 ) and presenilin 2 ( PS2 ), whereas the main genes responsible for familial FTLD are microtubule-associated protein tau gene ( MAPT ) and progranulin ( GRN ). (touchneurology.com)
  • E-cadherin is a cell-cell adhesion protein encoded by CDH1 tumor-suppressor gene. (oncotarget.com)
  • At the genomic level, this integration involved the loss of many genes and the transfer of many more to the host nuclear genome, the protein products of which are targeted back to the organelle [ 1 ]. (biomedcentral.com)
  • 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)
  • 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)
  • and (iv) genes harboring germline non-silent variants presumed to confer a risk of sporadic ALL. (haematologica.org)
  • Acquisitions of OspC genes that are novel for the region confer to recipients unique identities to host immune systems and, presumably, selective advantage when immunity to existing types is widespread among hosts. (cdc.gov)
  • Chromosome 9pter aberrations, such as ring chromosome have been reported to cause 46,XY disorders of sex development (DSD), due to involvement of DMRT1 gene located at the 9p24.3 region. (biomedcentral.com)
  • Sex reversal due to haploinsufficiency of DMRT1 gene in ring chromosome 9 structures is exceedingly rare with only a handful of cases ever reported. (biomedcentral.com)
  • Sex determination and development in males occurs during the embryonic period, and is initiated by the expression of SRY gene located on the short arm of the Y chromosome. (biomedcentral.com)
  • This terminal region of chromosome 9p (9p24.3 region) contains 3 types of DMRT genes ( DMRT1 - 3 ). (biomedcentral.com)
  • In 1987, a region of linkage with AD was reported on the long arm of chromosome 21, which encompassed a region harboring the β- APP gene, a compelling candidate for AD. (touchneurology.com)
  • Genes are often organized by function on the chromosome. (sdbonline.org)
  • Lateral gene transfers resulted in different linkages between the ospC gene and loci of the chromosome or other plasmids. (cdc.gov)
  • Indeed, the identification of biologically relevant concepts in free text, namely genes, tRNAs, mRNAs, gene products and small molecules, is crucial to capture the structure and functioning of different responses. (biomedcentral.com)
  • We propose to name IERV-K and IERV-S these two major subgroups of Insect Endogenous Retro Viruses (or Insect ERrantiVirus, according to the ICTV nomenclature) which respectively use Lys and Ser tRNAs to prime reverse transcription. (lookformedical.com)
  • The segregation ratios of these families were consistent with expression of major gene resistance (MGR) controlled by a dominant R locus. (frontiersin.org)
  • To identify new risk genes, we utilized an international consortium of 4241 PAH cases with exome or genome sequencing data from the National Biological Sample and Data Repository for PAH, Columbia University Irving Medical Center, and the UK NIHR BioResource - Rare Diseases Study. (biomedcentral.com)
  • Genetic analyses of larger cohorts using gene panels, exome sequencing (ES), or genome sequencing (GS) have further defined the frequency of individuals with deleterious variants in PAH risk genes and have identified novel candidate risk genes. (biomedcentral.com)
  • The latest revolution in genome sequencing know-how allows the buildup of huge quantities of knowledge on biosynthetic genes, the blueprint of the molecular building. (mygentaur.com)
  • Summary: Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. (omictools.com)
  • We established genome-wide patterns of H3K27me3 and H3K9me3 modifications, and found these marks mutually exclusive within gene-rich regions but not within repeats. (biomedcentral.com)
  • These associated SNPs were located in genes involved in multiple molecular mechanisms potentially underlying limber pine MGR to C. ribicola , including NBS-LRR genes for recognition of C. ribicola effectors, signaling components, and a large set of defense-responsive genes with potential functions in plant effector-triggered immunity (ETI). (frontiersin.org)
  • A total of 110 clinical isolates of A. baumannii , collected in a recent 2-year period, were tested for carbapenem antibiotic susceptibility, followed by a molecular analysis of carbapenemase genes. (frontiersin.org)
  • We describe the clinical and molecular features of a child who presented with a large abdominal mass, AML, and a new CK, involving chromosomes 11, 16, and 19 leading to a KMT2A-MLLT1 fusion and 2 extra copies of the ELL gene, thus resulting in the concurrent overexpression of MLLT1 and ELL. (cancerindex.org)
  • The identification of causal or predictive variants/genes/mechanisms for disease-associated traits is characterized by 'complex' networks of molecular phenotypes. (researchgate.net)
  • We now have carried out in vacuo Molecular Dynamics simulations to validate their implementation in opposition to quantum mechanical frequency calculations. (mygentaur.com)
  • Firstly no members were predicted to reside on the eight uncharitableest dispensable chromosomes stand foring their redundant (or at least currently cryptic) roles in infection. (upb.ro)
  • Given that the minor spliceosome is ubiquitously expressed, we hypothesized that these restricted phenotypes might be caused by the tissue-specific regulation of the minor spliceosome targets, i.e. minor intron-containing genes (MIGs). (biomedcentral.com)
  • Many of the above-listed tools also provide information on regulatory elements that control gene activity. (biomedcentral.com)
  • Using the established heterologous expression system, activation of the pathway-specific transcription issue coupled with a knockout technique, and manipulating the worldwide regulatory gene, the biosynthetic genes have been exploited to activate biosynthetic pathways and decipher the encoded enzyme features. (mygentaur.com)
  • Evolution in overlapping genes is complicated because the effect of a nucleotide substitution has multiple contexts. (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)
  • An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. (wikipedia.org)
  • These rates are determined by the stationary nucleotide frequencies, transition bias, and the distribution of selection biases (dN and dS) in the respective reading frames. (uwo.ca)
  • Based on linkage disequilibrium (LD)-based association mapping used to detect single nucleotide polymorphism (SNP) markers associated with MGR against C. ribicola , MGR in these seed families appears to be controlled by Cr4 or other R genes in very close proximity to Cr4 . (frontiersin.org)
  • Concerning sporadic AD, it is known that the presence of the ε4 allele of the apolipoprotein E gene is a susceptibility factor. (touchneurology.com)
  • The simplest forms of filters are minor allele frequency (MAF), candidate genes or variants, or considering the exome. (biomedcentral.com)
  • Notably, residues of receptor-binding domain (RBD) showing crucial interactions with angiotensin-converting enzyme 2 (ACE2) and cross-reacting neutralizing antibody were found to be conserved among the analyzed virus strains, except for replacement of lysine with arginine at 378th position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320). (nature.com)
  • GM sugarcane strains with built-in Cry1Ab and EPSPS overseas genes have been used for GM sugar manufacturing. (mygentaur.com)
  • Over time, OspC genes were transferred between strains through recombinations involving the whole or parts of the gene and one or both flanks. (cdc.gov)
  • However, for patients with a KMT2A rearrangement (KMT2A-r), the prognosis appears to depend on the fusion partner gene rather than the karyotype structure. (cancerindex.org)
  • The Set2/Rpd3S pathway suppresses cryptic transcription without regard to gene length or transcription frequency. (duke.edu)
  • These data suggest that additional genetic, epigenetic, environmental factors, and gene × environment interactions contribute to disease. (biomedcentral.com)
  • Pérez-Ortín, J.E. y García-Martínez, J. (2004) Evaluation of transcription rates at the genomic level. (uv.es)
  • The fact that genes were split or interrupted by introns was discovered independently in 1977 by Phillip Allen Sharp and Richard J. Roberts, for which they shared the Nobel Prize in Physiology or Medicine in 1993. (wikipedia.org)
  • Although introns are sometimes called intervening sequences, the term "intervening sequence" can refer to any of several families of internal nucleic acid sequences that are not present in the final gene product, including inteins, untranslated regions (UTR), and nucleotides removed by RNA editing, in addition to introns. (wikipedia.org)
  • In these minor intron-containing genes (MIGs), the majority of introns are usually spliced by the major spliceosome, with only one or two introns being spliced by the minor spliceosome. (biomedcentral.com)
  • While genetic drift has certainly contributed to this, we implement gene ontology, association analysis and population simulations to increase our confidence in candidate selective sweeps. (biomedcentral.com)
  • malpha and m4 embyonic expression patterns are nearly indistinguishable, and appear very similar to those of E(spl)-C bHLH genes, particularly m5, m7 and m8 . (sdbonline.org)
  • Since U4atac snRNA is ubiquitously expressed, mutation in this gene is expected to result in systemic inhibition of the minor spliceosome. (biomedcentral.com)
  • Chlorambucil-conjugated PI-polyamides (Chb-M'), a transcription inhibitor of RUNX family, has an anti-tumor activity against SHH-type medulloblastoma with p53 mutation. (atlasgeneticsoncology.org)
  • concludes that E. coli genes have different mutation rates. (fieldofscience.com)
  • That phenomenon has been shown to not be due to changes in the mutation rate (considered per base pair), but to initially unsuspected cryptic growth on the sugar and changes in the number of copies of the gene under selection. (fieldofscience.com)
  • Two SNPs in X-Ray Repair Cross Complementing 2 gene (XRCC2) rs2040639 and interferon gamma (IFNG) rs2069705 genes were found to be associated with ARSR. (cancerindex.org)
  • However, the B3galtl gene is subject to transcriptional silencing via IAP-induced heterochromatin. (prolekarniky.cz)
  • Hence, although rare, IAP-induced local heterochromatin spreading into nearby genes may influence expression and, in turn, host fitness. (prolekarniky.cz)
  • The compact architecture of heterochromatin limits the accessibility of the transcription machinery to the embedded DNA, thereby silencing gene expression. (biomedcentral.com)
  • Accordingly, H3K9me3-dependent heterochromatin is considered as a barrier to cell fate changes, by preventing some transcription factors to bind DNA [ 18 ]. (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)
  • Cryptic chloroplasts are similar to the chloroplasts found in plant cells, but unlike plants the compartments in apicomplexans are unable to harvest energy from sunlight. (elifesciences.org)
  • We found significant increases in the MN frequency and induced chromosomal aberrations in the lymphocytes of only one donor after ethyl-paraben exposure in the presence of S9 after a short exposure. (metasystems-probes.com)
  • In-depth biological analysis of connected genes in ANDnet and XORnet revealed genes that are related to energy metabolism, cell cycle control (AATF), immune system response, and several cancer types. (researchgate.net)
  • It seems that the expansion of numbers of genes evolving by duplication to handle the ever increasing complexities of neurogenesis, has been matched by a similar expansion of genes, also by duplication, to suppress or regulate neurogenesis. (sdbonline.org)
  • Rare variant analysis of a large international consortium identified two new candidate genes- FBLN2 and PDGFD . (biomedcentral.com)
  • Three strong candidate genes, MHC , SEMA5A and TGFBR2 , are also presented. (biomedcentral.com)
  • Within an altered environment, these standing variants will gain a selective advantage and increase in frequency in the population to reach fixation. (biomedcentral.com)
  • The number of genes underlying an adaptive process often belies the complexity of the selective environment. (biomedcentral.com)
  • Selective gene silencing is key to development. (biomedcentral.com)
  • However, at least three lineages of apicomplexans have independently lost their cryptic chloroplasts. (elifesciences.org)
  • Reverse sequence analysis showed that the MLLT1 gene was fused to the 16p11.2 region. (cancerindex.org)
  • These evidences are often based on the derivation of standard measures of association, linking (epi-)genetic markers to gene expression combined with gene expression analysis (Wagner, Busche, Ge, Kwan, & Pastinen, 2014). (researchgate.net)
  • This serotype can also cause antigen gene cluster ( rfb -RFLP). (cdc.gov)
  • Each gene in any given cluster or complex of genes will have a similar function and structure to the others in its group. (sdbonline.org)