Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genome Components”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 991 records · Page 55Linked to original sources
PubMed2026

Whole-Genome Sequencing Reveals Population Structure, Genetic Diversity, and Selection Signatures in Kazakh Dromedary and Bactrian Camels.

Understanding the genomic basis of environmental adaptation is essential for the conservation and genetic improvement of domestic camels. In this study, we investigated the population structure, genetic diversity, and genomic variation potentially associated with environmental adaptation of Kazakh dromedary and Bactrian camels using whole-genome sequencing. Whole-genome sequencing data were generated for Kazakh camels (15 dromedaries and 16 Bactrian camels) and integrated with 131 publicly available genomes representing camel populations from the Arabian Peninsula, Iran, Xinjiang, Inner Mongolia, and Mongolian wild camels. Population structure, genetic diversity, and genome-wide selection were evaluated using principal component analysis, ADMIXTURE, nucleotide diversity, linkage disequilibrium, runs of homozygosity, genomic inbreeding (FROH), and selection scans based on FST, θπ ratio, and XP-EHH. Population genomic analyses revealed clear differentiation between dromedary and Bactrian camels, whereas Kazakh camel populations exhibited higher nucleotide diversity (θπ = 1.307-1.551 × 10-3), and lower genomic inbreeding (median FROH: 0.037-0.056) than Arabian populations. Genome-wide selection analyses identified MC4R as the prominent candidate gene in Kazakh dromedaries and RYR1 as a prominent candidate gene in Kazakh Bactrian camels. Functional enrichment analyses highlighted pathways related to energy metabolism, thermogenesis, calcium signaling, skeletal muscle function, mitochondrial activity, and oxidative stress response. These findings provide new insights into genomic variation potentially associated with environmental adaptation in Kazakh camels and offer valuable genomic resources for future conservation, breeding, and evolutionary studies.

MC4R↗
PubMed2003

Antigenic and genomic relation between human influenza viruses that circulated in Argentina in the period 1995-1999 and the corresponding vaccine components.

BACKGROUND: The analysis of epidemic influenza virus has been focused on antigenic and genomic characterization of the hemagglutinin (HA) glycoprotein in order to detect new variants for the recommendation of the vaccine strains in each season. Since October 1998, WHO organized a second meeting to evaluate the vaccine formula for the southern hemisphere. OBJECTIVES: (a) Present the antigenic and genomic characterization of influenza strains obtained from the Argentina surveillance network, (b) compare between strains collected in Argentina and other countries with the vaccine formula strains used in each season. STUDY DESIGN: Influenza strains were collected during a 5-year period (1995-1999). Initially, laboratory diagnosis was done by immunofluorescence (IF) assay on clinical samples, followed by viral isolation in Madin-Darby canine kidney (MDCK) cells. The isolates were characterized antigenically by hemagglutination-inhibition (HI) assay with post-infection ferret antisera. The genomic characterization consisted on RT-PCR followed by sequencing of the HA1 portion of the HA gene. The comparison between reference and circulating strains was analyzed by the construction of phylogenetic trees. RESULTS: The H3N2 circulating strains matched the corresponding vaccine component only in 1999, the first year when a vaccine recommended specifically for the southern hemisphere was used. Besides, H1N1 circulating strains matched the corresponding vaccine component only in 1998. Regarding to influenza B, only in 1995, the circulating strains showed no match to the B vaccine component. CONCLUSIONS: The results showed the usefulness of an intensified influenza laboratory surveillance to access the correct vaccine and the importance of having the necessary tools to characterize the circulating strains.

Animals↗
PubMed2002

DNA copy number changes in carcinoma in pleomorphic adenoma of the salivary gland: a comparative genomic hybridization study.

Pleomorphic adenoma is the most common benign tumor of the salivary glands and is rarely associated with concurrent epithelial malignancy, which is designated as carcinoma in pleomorphic adenoma (CPA). Genetic abnormalities potentially related to the development of CPA have not been fully investigated. We analyzed DNA copy number changes in each of the adenomatous and carcinomatous components of seven CPA by comparative genomic hybridization using DNA extracted from microdissected tissues of formalin-fixed, paraffin-embedded tumor samples. Carcinomatous components of CPA showed multiple DNA copy number changes at 1-18 different genomic sites (mean 13 sites). Adenomatous components displayed less frequent DNA copy number changes (0-13 sites; mean, 5). In both components, the majority of the changes were gains. The most common recurrent gains in carcinomatous components were seen at 6q (four cases in each), whereas gains at 13q1-2 and 15q1 were most frequently detected in adenomatous components (three cases in each). In five CPA, the same chromosomal regions were involved in the DNA copy number changes detected in both components. Our data suggest that an accumulated or increased number of chromosomal changes including 6q abnormalities may be associated with the development of carcinomatous components in a subset of CPA.

Adenocarcinoma↗
PubMed1998

Introduction to the post-Human Genome Project era, a target for interactions between polygenic and/or multiphenotypical components in cancer control in South America.

Epidemiological studies have suggested that the propensity to develop malignancy involves a complex mix of genetic and environmental determinants, however both older and innovative techniques display unresolved fundamental questions regarding etiology. Current barriers to achieving the potential benefit from this understanding are: 1) incomplete background on the various environmental and genetic factors involved in the carcinogenesis mechanism; 2) difficulties in accurately differentiating specific molecular subtypes and measuring the effective cellular exposure dose; and 3) difficulties in determining the multifactorial interaction between genetic and environmental factors. To extrapolate Human Genome Project research findings to the Post-Human Genome Project era, South America provides a large population and large-pedigree families, thus including genetically heterogeneous and less heterogeneous groups. An initial strategy might be to trace high risk populations and the respective exposures to which they are susceptible, such as: 1) migration, identifying rural migrant populations; 2) inherent susceptibility, studying "long term homogeneous populations" or large families living in similar rural environments; and 3) dissection of gene-environmental interaction

Environmental Exposure↗
PubMed1998

Evidence for the role of recombination in the regulatory evolution of Saccharomyces cerevisiae Ty elements.

The recent completion of the sequencing of the Saccharomyces cerevisiae genome provides a unique opportunity to analyze the evolutionary relationships existing among the entire complement of retrotransposons residing within a single genome. In this article we report the results of such an analysis of two closely related families of yeast long terminal repeat (LTR) retrotransposons, Ty1 and Ty2. In our study, we analyzed the molecular variation existing among the 32 Ty1 and 13 Ty2 elements present within the S. cerevisiae genome recently sequenced within the context of the yeast genome project. Our results indicate that while the Ty1 family is most likely ancestral to Ty2 elements, both families of elements are relatively recent components of the S. cerevisiae genome. Our results also indicate that both families of elements have been subject to purifying selection within their protein coding regions. Finally, and perhaps most interestingly, our results indicate that a relatively recent recombination event has occurred between Ty2 and a subclass of Ty1 elements involving the LTR regulatory region. We discuss the possible biological significance of these findings and, in particular, how they contribute to a better overall understanding of LTR retrotransposon evolution.

DNA, Fungal↗
PubMed2006

Sentra: a database of signal transduction proteins for comparative genome analysis.

Sentra (http://compbio.mcs.anl.gov/sentra), a database of signal transduction proteins encoded in completely sequenced prokaryotic genomes, has been updated to reflect recent advances in understanding signal transduction events on a whole-genome scale. Sentra consists of two principal components, a manually curated list of signal transduction proteins in 202 completely sequenced prokaryotic genomes and an automatically generated listing of predicted signaling proteins in 235 sequenced genomes that are awaiting manual curation. In addition to two-component histidine kinases and response regulators, the database now lists manually curated Ser/Thr/Tyr protein kinases and protein phosphatases, as well as adenylate and diguanylate cyclases and c-di-GMP phosphodiesterases, as defined in several recent reviews. All entries in Sentra are extensively annotated with relevant information from public databases (e.g. UniProt, KEGG, PDB and NCBI). Sentra's infrastructure was redesigned to support interactive cross-genome comparisons of signal transduction capabilities of prokaryotic organisms from a taxonomic and phenotypic perspective and in the framework of signal transduction pathways from KEGG. Sentra leverages the PUMA2 system to support interactive analysis and annotation of signal transduction proteins by the users.

Archaeal Proteins↗
PubMed1986

Reactions of sera from patients with rheumatoid arthritis, systemic lupus erythematosus and infectious mononucleosis to Epstein-Barr virus-induced polypeptides.

P3HR-1 and Ramos cells induced with sodium butyrate and 12-O-tetradecanoylphorbol 13-acetate were used in the protein immunoblot technique to identify Epstein-Barr virus (EBV)-specific antibodies present in sera from clinically normal individuals and patients with systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and infectious mononucleosis (IM). Sixteen EBV-specific polypeptides were detected ranging in mol. wt. from 22,000 (22K) to 140K. Many of the sera contained antibodies to different subsets of these antigens, and a high proportion expressed autoantibodies which reacted with cellular components from an EBV genome-negative cell line. About 50% of the sera from each category reacted with the 44K to 48K and 36K and 38K early antigen (EA) components. A high proportion of the SLE sera (64%) were found to contain anti-EA antibodies, suggesting an association between EBV and SLE. Almost all of the EBV-seropositive sera examined contained antibodies against a 22K late antigen, but none of the sera from IM patients reacted with this polypeptide.

Antibodies, Viral↗
PubMed2001

Antigenic and genomic relation between human influenza A (H3N2) viruses circulating in Argentina during 1998 and the H3N2 vaccine component.

OBJECTIVE: Due to the lack of correlation from 1994 to 1997 between the A H3N2 component of the influenza vaccine recommended for this period and the circulating viruses in Argentina, we decided to study the antigenic and genomic relationships of the 1998 A H3N2 Argentine circulating strains with the corresponding vaccine component for that year as recommended by the World Health Organization (WHO). METHODS: We selected 18 influenza A H3N2 strains isolated in Argentina during 1998 to carry out an antigenic and genomic study of their hemagglutinin (HA) and neuraminidase (NA) proteins. For the genomic study we added 3 isolates from Uruguay. We compared the Argentine and Uruguayan strains with available reference strains. RESULTS: We found that all 18 strains from Argentina were similar to the A/Sydney/5/97 (H3N2) strain, as opposed to the A/Wuhan/359/95 (H3N2) strain, which was the vaccine component. This result was confirmed by the genomic study. CONCLUSIONS: The approach that we applied in Argentina has improved the quality and quantity of information about influenza in the country. This type of work should be encouraged in other countries in order to help choose the most appropriate vaccine components each year and provide individuals with the best possible protection against influenza.

Antigens, Viral↗
PubMed2006

[Nutrigenomics. Scientific basis, status and perspectives of application].

Nutrigenomics investigates the interaction between nutrition and the genome, thereby combining nutritional research with functional genomics. Its aims are (1) to correlate heterogeneous effects of nutrients with sequence variations in the genome and (2) to investigate the effects of nutrients and other food components on gene expression at a genome-wide scale (mRNA profiling), and on patterns of metabolite alterations in serum (metabolite profiling). The field will provide important information as to the biological effects of food components, and to the functional consequences of genetic variance. This information will improve the prevention of nutrition-related diseases, e. g. by establishing personalised nutritional recommendations.

Adult↗
PubMed1995

Immunodetection, expression strategy and complementation of turnip crinkle virus p28 and p88 replication components.

The plus-sense RNA genome of turnip crinkle virus (TCV) encodes at its 5' end a 28-kDa protein of unspecified function. Readthrough suppression of the p28 stop codon allows for the production of an 88-kDa product which is required for genome replication. Immunological analysis of the expression of p28 and p88 demonstrated that: (i) the genome directs the synthesis of polypeptides of approximately 28 and 88 kDa, (ii) the 88-kDa protein is immunologically related to p28, consistent with p88 being a readthrough product, and (iii) p28, but not p88, is detectable in vivo. An in vivo assay, in which readthrough is linked to the expression of a beta-glucuronidase reporter gene, showed that readthrough of the p28 amber stop codon occurs with an efficiency of approximately 1%. A similar efficiency of readthrough was observed when an altered context from the nonviable TCV mutant, mA2, containing a disrupted secondary structure (FfFa) spanning the p28 termination codon, was tested. This result suggests that the defective phenotype of mA2 is likely not linked to an alteration in readthrough efficiency. Additional studies demonstrated that complementation occurs in coinoculations with two nonviable TCV mutants, RT and APA, which are unable to express either p28 or p88, respectively. This result verifies that p28 is essential for TCV genome replication and provides the first definitive evidence for the role of a 5'-proximal open reading frame for any member of the family Tombusviridae.

Base Sequence↗
PubMed2002

Interference by toxic metal ions with zinc-dependent proteins involved in maintaining genomic stability.

Metal ions are essential components of biological systems; nevertheless, even essential elements may have toxic or carcinogenic properties. Thus, besides As(III) and Cd(II), also Ni(II) and Co(II) have been shown previously to disturb different types of DNA repair systems at low, non-cytotoxic concentrations. Since some metals exert high affinities for SH groups, we investigated whether zinc finger structures in DNA-binding motifs of DNA repair proteins are potential targets for toxic metal ions. The bacterial formamidopyrimidine-DNA glycosylase (Fpg protein) involved in base excision repair was inhibited by Cd(II), Cu(II) and Hg(II) with increasing efficiencies, whereas Co(II), As(III), Pb(II) and Ni(II) had no effect. Furthermore, Cd(II) still disturbed enzyme function when bound to metallothionein. Strong inhibition was also observed in the presence of phenylselenyl chloride, followed by selenocystine, while selenomethionine was not inhibitory. Regarding the mammalian XPA protein involved in the recognition of DNA lesions during nucleotide excision repair, its DNA-binding capacity was diminished by Cd(II), Cu(II), Ni(II) and Co(II), while Hg(II), Pb(II) and As(III) were ineffective. Finally, the H(2)O(2)-induced activation of the poly(ADP-ribose)polymerase (PARP) involved in DNA strand break detection and apoptosis was greatly reduced by Cd(II), Co(II), Ni(II) and As(III). Similarly, the disruption of correct p53 folding and DNA binding by Cd(II), Ni(II) and Co(II) has been shown by other authors. Therefore, zinc-dependent proteins involved in DNA repair and cell-cycle control may represent sensitive targets for some toxic metals such as Cd(II), Ni(II), Co(II) and Cu(II), as well as for some selenium compounds. Relevant mechanisms of inhibition appear to be the displacement of zinc by other transition metals as well as redox reactions leading to thiol/disulfide interchange.

Cations, Divalent↗
PubMed2001

Cytochrome oxidase subunit VI of Trypanosoma brucei is imported without a cleaved presequence and is developmentally regulated at both RNA and protein levels.

Mitochondrial respiration in the African trypanosome undergoes dramatic developmental stage regulation. This requires co-ordinated control of components encoded by both the nuclear genome and the kinetoplast, the unusual mitochondrial genome of these parasites. As a model for understanding the co-ordination of these genomes, we have examined the regulation and mitochondrial import of a nuclear-encoded component of the cytochrome oxidase complex, cytochrome oxidase subunit VI (COXVI). By generating transgenic trypanosomes expressing intact or mutant forms of this protein, we demonstrate that COXVI is not imported using a conventional cleaved presequence and show that sequences at the N-terminus of the protein are necessary for correct mitochondrial sorting. Analyses of endogenous and transgenic COXVI mRNA and protein expression in parasites undergoing developmental stage differentiation demonstrates a temporal order of control involving regulation in the abundance of, first, mRNA and then protein. This represents the first dissection of the regulation and import of a nuclear-encoded protein into the cytochrome oxidase complex in these organisms, which were among the earliest eukaryotes to possess a mitochondrion.

Amino Acid Sequence↗
PubMed2001

[Ocular changes associated with connective tissue disorders: role of the elastic and collagen components].

Every day, the emerging fields of genomics and proteomics provide new information about both normal and pathological processes, among which, the extracellular matrix appears to play a significant role. Over the past decade, the classic fibrillar components of the matrix, collagen and elastin, have been the subject of extensive research leading to a wealth of information which is far form being fully interpreted. Although the basic composition and structure of the matrix components has been well established, today more than twenty five different varieties of collagen have been described, and elastic fibers are currently described as polymeric complexes, composed of at least 19 different proteins in their microfibrillar and amorphic portions. Mutations in three of the genes coding for some of the most abundant proteins in the elastic fibers give rise to a wide range of elastic tissue phenotypes, from skeletal or dermal anomalies to vascular or ocular defects. In this review, our aim was to gain insight into the fibrillar component of the extracellular matrix in an attempt to improve our understanding of certain ocular disorders.

Collagen↗
PubMed1985

Nucleotide sequence and structural features of a novel US-a junction present in a defective herpes simplex virus genome.

Defective genomes generated during serial propagation of herpes simplex virus type 1 (Justin) consist of tandem reiterations of sequences that are colinear with a portion of the S component of the standard viral genome. We determined the structure of the novel US-a junction, at which the US sequences of one repeat unit join the a sequences of the adjacent repeat unit. Comparison of the nucleotide sequence at this junction with the nucleotide sequence of the corresponding US region of the standard virus genome indicated that the defective genome repeat unit arose by a single recombinational event between an L-S junction a sequence and the US region. The recombinational process might have been mediated by limited sequence homology. The sequences retained within the US-a junction further define the signal for cleavage and packaging of viral DNA.

Base Sequence↗
PubMed1989

Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome.

Genes for DNA-dependent RNA polymerase components B, A, and C from the archaebacterium Sulfolobus acidocaldarius and for components B", B', A, and C from the archaebacterium Halobacterium halobium were cloned and sequenced. They are organized in gene clusters in the order above, which corresponds to the order of the homologous rpoB and rpoC genes in the corresponding operon of the Escherichia coli genome. Derived amino acid sequences of archaebacterial components A and C were aligned with each other and with the sequences of corresponding (largest) subunits from the archaebacterium Methanobacterium thermoautotrophicum, with sequences of various eukaryotic nuclear RNA polymerases I, II, and III, and with the sequence of the beta' component from E. coli polymerase. The archaebacterial genes for component A are homologous to about the first two-thirds of genes for the eukaryotic component A and the eubacterial component beta', and the archaebacterial genes for component C are homologous to the last third of the genes for the eukaryotic component A and the eubacterial component beta'. Unrooted phylogenetic dendrograms derived from both distance matrix and parsimony analyses show the archaebacteria are a coherent group closely related to the eukaryotic nuclear RNA polymerase II and/or III lineages. The eukaryotic polymerase I lineage appears to arise separately from a bifurcation with the eubacterial beta' component lineage.

Amino Acid Sequence↗
PubMed2006

GeneTrees: a phylogenomics resource for prokaryotes.

The GeneTrees phylogenomics system pursues comparative genomic analyses from the perspective of gene phylogenies for individual genes. The GeneTrees project has the goal of providing detailed evolutionary models for all protein-coding gene components of the fully sequenced genomes. Currently, a database of alignments and trees for all protein sequences for 325 fully sequenced and annotated prokaryote genomes is available. The prokaryote database contains 890,000 protein sequences organized into over 100,000 alignments, each described by a phylogenetic tree. An original homology group discovery tool assembles sets of related proteins from all versus all pairwise alignments. Multiple alignments for each homology group are stored and subjected to phylogenetic tree inference. A graphical web interface provides visual exploration of the GeneTrees database. Homology groups can be queried by sequence identifiers or annotation terms. Genomes can be browsed visually on a gene map of each chromosome or plasmid. Phylogenetic trees with support values are displayed in conjunction with the associated sequence alignment. A variety of classes of information can be selected to label the tree tips to aid in visual evaluation of annotation and gene function. This web interface is available at http://genetrees.vbi.vt.edu.

Bacterial Proteins↗
PubMed2001

Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside.

The recent release of the complete euchromatic genome sequence of Drosophila melanogaster offers a unique opportunity to explore the evolutionary history of transposable elements (TEs) within the genome of a higher eukaryote. In this report, we describe the annotation and phylogenetic comparison of 178 full-length long terminal repeat (LTR) retrotransposons from the sequenced component of the D. melanogaster genome. We report the characterization of 17 LTR retrotransposon families described previously and five newly discovered element families. Phylogenetically, these families can be divided into three distinct lineages that consist of members from the canonical Copia and Gypsy groups as well as a newly discovered third group containing BEL, mazi, and roo elements. Each family consists of members with average pairwise identities > or =99% at the nucleotide level, indicating they may be the products of recent transposition events. Consistent with the recent transposition hypothesis, we found that 70% (125/178) of the elements (across all families) have identical intra-element LTRs. Using the synonymous substitution rate that has been calculated previously for Drosophila (.016 substitutions per site per million years) and the intra-element LTR divergence calculated here, the average age of the remaining 30% (53/178) of the elements was found to be 137,000 +/-89,000 yr. Collectively, these results indicate that many full-length LTR retrotransposons present in the D. melanogaster genome have transposed well after this species diverged from its closest relative Drosophila simulans, 2.3 +/-.3 million years ago.

Amino Acid Sequence↗
PubMed1997

Transduction potential of human retroviruses in highly proliferating small-cell lung cancer cells as well as non-proliferating hematopoietic stem cells.

Direct gene transfer to solid tissues or metastatic cancer cells requires vectors capable of in vivo transduction to specific cells. The predominant retroviral vectors of murine origin are inactivated by human complement, which precludes their use in vivo. Such inactivation does not take place with vectors based on human retroviruses. Murine retroviral vectors are also limited to proliferating cells, which human retroviruses are not. In this study we examined whether or not a vector using components from the human retroviruses HIV-1 and HTLV-1 could infect small-cell lung cancer cells and resting CD34+ hematopoietic stem cells. While HIV-1 itself was unable to infect cells lacking the CD4-membrane molecule, chimeric viral particles (pseudotype virus) with HIV-1 genome and HTLV-1 envelope components were able to infect both CD4-containing lymphocytic cells, CD4-negative tumour cells and hematopoietic stem cells. After infection with the pseudotype vector, the RNA genome was reverse transcribed and integrated. Transduction efficiency and gene expression under the HIV-1 LTR promoter in both tumour and stem cells were found to be of a similar or greater magnitude than in lymphocytic cells. These results suggest that gene transfer targeting proliferating as well as resting cells in vivo may be realized using components from human retroviruses.

Antigens, CD34↗