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At least 1,189 records · Page 66Linked to original sources
PubMed1998

Characterization of a novel class of interspersed LTR elements in primate genomes: structure, genomic distribution, and evolution.

Retrovirus-like sequences and their solitary (solo) long terminal repeats (LTRs) are common repetitive elements in eukaryotic genomes. We reported previously that the tandemly arrayed genes encoding U2 snRNA (the RNU2 locus) in humans and apes contain a solo LTR (U2-LTR) which was presumably generated by homologous recombination between the two LTRs of an ancestral provirus that is retained in the orthologous baboon RNU2 locus. We have now sequenced the orthologous U2-LTRs in human, chimpanzee, gorilla, orangutan, and baboon and examined numerous homologs of the U2-LTR that are dispersed throughout the human genome. Although these U2-LTR homologs have been collectively referred to as LTR13 in the literature, they do not display sequence similarity to any known retroviral LTRs; however, the structure of LTR13 closely resembles that of other retroviral LTRs with a putative promoter, polyadenylation signal, and a tandemly repeated 53-bp enhancer-like element. Genomic blotting indicates that LTR13 is primate-specific; based on sequence analysis, we estimate there are about 2,500 LTR13 elements in the human genome. Comparison of the primate U2-LTR sequences suggests that the homologous recombination event that gave rise to the solo U2-LTR occurred soon after insertion of the ancestral provirus into the ancestral U2 tandem array. Phylogenetic analysis of the LTR13 family confirms that it is diverse, but the orthologous U2-LTRs form a coherent group in which chimpanzee is closest to the humans; orangutan is a clear outgroup of human, chimpanzee, and gorilla; and baboon is a distant relative of human, chimpanzee, gorilla, and orangutan. We compare the LTR13 family with other known LTRs and consider whether these LTRs might play a role in concerted evolution of the primate RNU2 locus.

Animals↗
PubMedDate not supplied

[Direct genetic manipulation and criminal code in Venezuela: absolute criminal law void?].

The judicial regulation of genetic biotechnology applied to the human genome is of big relevance currently in Venezuela due to the drafting of an innovative bioethical law in the country's parliament. This article will highlight the constitutional normative of Venezuela's 1999 Constitution regarding this subject, as it establishes the framework from which this matter will be legally regulated. The approach this article makes towards the genetic biotechnology applied to the human genome is made taking into account the Venezuelan penal law and by highlighting the violent genetic manipulations that have criminal relevance. The genetic biotechnology applied to the human genome has another important relevance as a consequence of the reformulation of the Venezuelan Penal Code discussed by the country's National Assembly. Therefore, a concise study of the country's penal code will be made in this article to better understand what judicial-penal properties have been protected by the Venezuelan penal legislation. This last step will enable us to identify the penal tools Venezuela counts on to face direct genetic manipulations. We will equally indicate the existing punitive loophole and that should be covered by the penal legislator. In conclusion, this essay concerns criminal policy, referred to the direct genetic manipulations on the human genome that haven't been typified in Venezuelan law, thus discovering a genetic biotechnology paradise.

Criminal Law↗
PubMed2006

Phycodnaviruses: a peek at genetic diversity.

The family Phycodnaviridae encompasses a diverse collection of large icosahedral, dsDNA viruses infecting algae. These viruses have genomes ranging from 160 to 560kb. The family consists of six genera based initially on host range and supported by sequence comparisons. The family is monophyletic with branches for each genus, but the phycodnaviruses have evolutionary roots that connect with several other families of large DNA viruses, referred to as the nucleocytoplasmic large DNA viruses (NCLDV). The genomes of members in three genera in the Phycodnaviridae have recently been sequenced and the purpose of this manuscript is to summarize these data. The viruses have diverse genome structures, some with large regions of non-coding sequence and others with regions of single-stranded DNA. Typically, phycodnaviruses have the coding capacity for hundreds of genes. The genome analyses have revealed in excess of 1000 unique genes, with only 14 homologous genes held in common among the three genera of the phycodnavirses sequenced to date. Thus, the gene diversity far exceeds the number of so-called "core" genes. Little is known about the replication of these viruses, but the consequences of these infections of the phytoplankton have global affects, including altered geochemical cycling and weather patterns.

DNA Viruses↗
PubMed1983

A recombinant DNA plasmid which inhibits bacteriophage T7 reproduction in escherichia coli.

Escherichia coli plasmids carrying a DNA restriction fragment corresponding to the extreme right end of the T7 bacteriophage genome render cells incompetent to support reproduction of wild-type T7. Processing of intracellular concatemeric phage DNA and cell lysis are perturbed by one such plasmid, pRS148. The results are discussed with reference to the possibility that the right end of the T7 genome encodes a lysis-related function.

DNA Replication↗
PubMed1999

A growing family of receptor genes for lysophosphatidic acid (LPA) and other lysophospholipids (LPs).

A missing component in the experimental analysis of cell signaling by extracellular lysophospholipids such as lysophosphatidic acid (LPA) or sphingosine-1-phosphate (S1P) has been cloned receptors. Through studies on the developing brain, the first such receptor gene (referred to as vzg-1) was identified, representing a member of the G-protein coupled receptor (GPCR) super family (1). Here we review the neurobiological approach that led to both its cloning and identification as a receptor for LPA, along with related expression data. Summarized sequence and genomic structure analyses indicate that this first, functionally identified receptor is encoded by a member of a growing gene family that divides into at least two subgroups: genes most homologous to the high-affinity LPA receptor encoded by vzg-1, and those more homologous to an orphan receptor gene edg-1 that has recently been identified as a S1P receptor. A provisional nomenclature is proposed, based on published functional ligand actions, amino acid composition and genomic structure whereby the receptors encoded by these genes are referred to as lysophospholipid (LP) receptors, with subgroups distinguished by letter and number subscripts (e.g., LPA1 for Vzg-1, and LPB1 for Edg-1). Presented expression data support the recently published work indicating that members of the LPB1 subgroup are receptors for the structurally-related molecule, S1P. The availability of cloned LP receptors will enhance the analysis of the many documented LP effects, while their prominent expression in the nervous system indicates significant but as yet unknown roles in development, normal function, and neuropathology.

Base Sequence↗
PubMed1999

Efficient approach to unique single-nucleotide polymorphism discovery.

Single-nucleotide polymorphisms (SNPs) are the most frequently found DNA sequence variations in the human genome. It has been argued that a dense set of SNP markers can be used to identify genetic factors associated with complex disease traits. Because all high-throughput genotyping methods require precise sequence knowledge of the SNPs, any SNP discovery approach must involve both the determination of DNA sequence and allele frequencies. Furthermore, high-throughput genotyping also requires a genomic DNA amplification step, making it necessary to develop sequence-tagged sites (STSs) that amplify only the DNA fragment containing the SNP and nothing else from the rest of the genome. In this report, we demonstrate the utility of a SNP-screening approach that yields the DNA sequence and allele frequency information while screening out duplications with minimal cost and effort. Our approach is based on the use of a homozygous complete hydatidiform mole (CHM) as the reference. With this homozygous reference, one can identify and estimate the allele frequencies of common SNPs with a pooled DNA-sequencing approach (rather than having to sequence numerous individuals as is commonly done). More importantly, the CHM reference is preferable to a single individual reference because it reveals readily any duplicated regions of the genome amplified by the PCR assay before the duplicated sequences are found in GenBank. This approach reduces the cost of SNP discovery by 60% and eliminates the costly development of SNP markers that cannot be amplified uniquely from the genome.

Alleles↗
PubMed2000

Natural and biotech-derived therapeutic proteins: what is the future?

A myriad of novel proteins and ligands of unknown function will be generated by the Human Genomic Project. Due to differences in post-translational processing, proteins produced by recombinant DNA technology may not possess proper biological activity. One way to find their function is to search for their natural counterparts. Proteins are produced in the tissues, and many of them are secreted into plasma and excreted into urine. There is a virtually "unlimited" array of human proteins in our plasma and urine, many of them in a fully active form. They include small molecules like steroids, peptides, and large glycoproteins like human menopausal gonadotropin. A library of plasma and urinary proteins could be developed to serve as a reference for the novel proteins generated by the functional genomic projects.

Forecasting↗
PubMed2006

Genomic structure and phylogeny of the plant pathogen Ralstonia solanacearum inferred from gene distribution analysis.

In the present study, we investigated the gene distribution among strains of the highly polymorphic plant pathogenic beta-proteobacterium Ralstonia solanacearum, paying particular attention to the status of known or candidate pathogenicity genes. Based on the use of comparative genomic hybridization on a pangenomic microarray for the GMI1000 reference strain, we have defined the conditions that allowed comparison of the repertoires of genes among a collection of 18 strains that are representative of the biodiversity of the R. solanacearum species. This identified a list of 2,690 core genes present in all tested strains. As a corollary, a list of 2,338 variable genes within the R. solanacearum species has been defined. The hierarchical clustering based on the distribution of variable genes is fully consistent with the phylotype classification that was previously defined from the nucleotide sequence analysis of four genes. The presence of numerous pathogenicity-related genes in the core genome indicates that R. solanacearum is an ancestral pathogen. The results establish the long coevolution of the two replicons that constitute the bacterial genome. We also demonstrate the clustering of variable genes in genomic islands. Most genomic islands are included in regions with an alternative codon usage, suggesting that they originate from acquisition of foreign genes through lateral gene transfers. Other genomic islands correspond to genes that have the same base composition as core genes, suggesting that they either might be ancestral genes lost by deletion in certain strains or might originate from horizontal gene transfers.

Chromosome Mapping↗
PubMed1999

A phylogenomic study of DNA repair genes, proteins, and processes.

The ability to recognize and repair abnormal DNA structures is common to all forms of life. Studies in a variety of species have identified an incredible diversity of DNA repair pathways. Documenting and characterizing the similarities and differences in repair between species has important value for understanding the origin and evolution of repair pathways as well as for improving our understanding of phenotypes affected by repair (e.g., mutation rates, lifespan, tumorigenesis, survival in extreme environments). Unfortunately, while repair processes have been studied in quite a few species, the ecological and evolutionary diversity of such studies has been limited. Complete genome sequences can provide potential sources of new information about repair in different species. In this paper, we present a global comparative analysis of DNA repair proteins and processes based upon the analysis of available complete genome sequences. We use a new form of analysis that combines genome sequence information and phylogenetic studies into a composite analysis we refer to as phylogenomics. We use this phylogenomic analysis to study the evolution of repair proteins and processes and to predict the repair phenotypes of those species for which we now know the complete genome sequence.

Adenosine Triphosphatases↗
PubMed2005

Integrative genetic analysis of transcription modules: towards filling the gap between genetic loci and inherited traits.

Genetic loci that regulate inherited traits are routinely identified using quantitative trait locus (QTL) mapping methods. However, the genotype-phenotype associations do not provide information on the gene expression program through which the genetic loci regulate the traits. Transcription modules are 'self-consistent regulatory units' and are closely related to the modular components of gene regulatory network [Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y. and Barkai, N. (2002) Revealing modular organization in the yeast transcriptional network. Nat. Genet., 31, 370-377; Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D. and Friedman, N. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet., 34, 166-176]. We used genome-wide genotype and gene expression data of a genetic reference population that consists of mice of 32 recombinant inbred strains to identify the transcription modules and the genetic loci regulating them. Twenty-nine transcription modules defined by genetic variations were identified. Statistically significant associations between the transcription modules and 18 classical physiological and behavioral traits were found. Genome-wide interval mapping showed that major QTLs regulating the transcription modules are often co-localized with the QTLs regulating the associated classical traits. The association and the possible co-regulation of the classical trait and transcription module indicate that the transcription module may be involved in the gene pathways connecting the QTL and the classical trait. Our results show that a transcription module may associate with multiple seemingly unrelated classical traits and a classical trait may associate with different modules. Literature mining results provided strong independent evidences for the relations among genes of the transcription modules, genes in the regions of the QTLs regulating the transcription modules and the keywords representing the classical traits.

Animals↗
PubMed1990

Prevalent enteric adenovirus variant not detected by commercial monoclonal antibody enzyme immunoassay.

A commercial monoclonal antibody enzyme immunoassay for the detection of enteric adenovirus type 40 and 41 (Ad40 and Ad41) in stool specimens was evaluated. Twenty-one stool specimens from children with gastroenteritis, with adenovirus particles visible by electron microscopy, and reference strains Ad40 Dugan and Ad41 Tak were tested by Ad40- and Ad41-specific and adenovirus group-reactive immunoassays. All stool specimens tested positive in the group-reactive immunoassay. However, only six specimens, containing isolates of Ad40 strain Hovi-X, an Ad40 genomic variant, and Ad41 strain Tak, reacted with the specific immunoassay, besides the reference strains. Fifteen stool specimens determined by restriction analysis to contain a genomic variant of Ad41 were negative by specific immunoassay. The positions of restriction site differences from the prototype strain Ad41 Tak were analyzed, and four mutations were mapped within the hexon gene; two others may occur in the fiber gene. The Ad41 genomic variant not detected by the enteric test is presently the most frequent cause of local adenoviral gastroenteritis. Highly specific monoclonal antibodies can fail to detect genomic variants of enteric adenoviruses, probably because of alteration of external neutralizable epitopes under immunological pressure to vary.

Adenovirus Infections, Human↗
PubMed1995

The maize mitochondrial genome: dynamic, yet functional.

The organization of the mitochondrial genome of higher plants is complex. It has two striking features: a large size that can vary among plant species; and the ability to undergo homologous recombination that results in variation within species. From cosmid clone mapping studies, the total genetic information of the plant mitochondrial genome can be arranged into a single circular molecule that is referred to as the master chromosome. This circular DNA molecule contains repeated sequences that can generate, via intramolecular recombination, either isomeric forms of the master chromosome or smaller subgenomic circular DNA molecules. The maize mitochondrial genome is the most complex and largest mitochondrial genome for which a physical map is presently available. Its organization varies considerably among the different maize cytotypes. In an attempt to understand the numerous different mitochondrial DNA rearrangements encountered among those cytotypes, we have proposed a general model of genome evolution that can explain a multitude of genomic rearrangements, not only for the maize mitochondrial DNA but also for other higher plant mitochondrial genomes as well.

Biological Evolution↗
PubMed2005

PoMaMo--a comprehensive database for potato genome data.

A database for potato genome data (PoMaMo, Potato Maps and More) was established. The database contains molecular maps of all twelve potato chromosomes with about 1000 mapped elements, sequence data, putative gene functions, results from BLAST analysis, SNP and InDel information from different diploid and tetraploid potato genotypes, publication references, links to other public databases like GenBank (http://www.ncbi.nlm.nih.gov/) or SGN (Solanaceae Genomics Network, http://www.sgn.cornell.edu/), etc. Flexible search and data visualization interfaces enable easy access to the data via internet (https://gabi.rzpd.de/PoMaMo.html). The Java servlet tool YAMB (Yet Another Map Browser) was designed to interactively display chromosomal maps. Maps can be zoomed in and out, and detailed information about mapped elements can be obtained by clicking on an element of interest. The GreenCards interface allows a text-based data search by marker-, sequence- or genotype name, by sequence accession number, gene function, BLAST Hit or publication reference. The PoMaMo database is a comprehensive database for different potato genome data, and to date the only database containing SNP and InDel data from diploid and tetraploid potato genotypes.

Chromosome Mapping↗
PubMed1986

Genomic and antigenic comparison of an equine herpesvirus 1 (EHV 1) isolate from the 1983 Lippizan abortion storm with EHV 1 reference strains.

An EHV 1 isolate from the Lippizan Stud at Piber, which caused the abortion and paresis outbreak in 1983, was investigated using 3 known subtype 1 and 2 subtype 2 strains for comparison. Broad-scale restriction enzyme analysis as well as cross-neutralization with hyperimmune sera produced in rabbits were performed, and SDS-PAGE of infected cell proteins was conducted on a limited scale. The Piber isolate was clearly classified as a subtype 1 strain of EHV 1, and showed closest resemblance in its restriction patterns with a British EHV 1 strain, which originated from an outbreak with paretic symptoms. A second Piber isolate from the same outbreak examined to limited extent only was practically indistinguishable from the first one, as could have been expected. A thoroughly controlled systematic vaccination program with existing commercial vaccines against EHV 1 should protect the endangered Lippizan horses population against the abortigenic and less certainly against the paretic syndromes caused by this virus. According to data presented, a protection against respiratory disease is less probable.

Animals↗
PubMedDate not supplied

Tests of six cotton (Gossypium hirsutum L.) mutants for association with aneuploids.

Genetic mutants are useful tools for basic and applied research to elucidate the developmental and regulatory processes of the cotton plant (Gossypium hirsutum L.). Their value is enhanced with knowledge of their location in the genome. The results of aneuploid tests used to locate mutant loci on specific chromosomes in G. hirsutum L. are reported. Thirty-four monosomes and telosomes, representing 18 of the 26 chromosomes, were used in combination with six mutants that were associated with nine loci. The mutant loci were glandless stem and boll (gl1gl6), immature fiber (im), Ligon lintless-2 (Li2), methylation (me), nonpinking (np1np2), and Raimondal (Ra1Ra2). We found that im was associated with chromosome 3 that contains linkage group VI (accessory involucre and frego bract); Li2 was associated with chromosome 18 that contains linkage group XVI (open bud and yellow pollen-2); and me was associated with chromosome 9. The remaining three mutants were not associated with the aneuploids in the tests. Knowledge of these chromosome assignments provides a valuable reference for specific studies of mutants and for further genome mapping efforts.

Aneuploidy↗
PubMed1995

Taxonomy of Corynebacterium diphtheriae and related taxa, with recognition of Corynebacterium ulcerans sp. nov. nom. rev.

Levels of genomic DNA relatedness were determined using a S1 nuclease procedure for reference bacteria identified as biotypes of Corynebacterium diphtheriae, biovars of Corynebacterium pseudotuberculosis, and 'Corynebacterium ulcerans'. These results showed that the three species are separate taxa at the genomospecies level whereas biotypes and biovars are closely related genomically within each species. Phylogenetic analyses of small-subunit rDNA sequences revealed that 'Corynebacterium ulcerans' forms a tight cluster with Corynebacterium pseudotuberculosis within the robust branch that groups all Corynebacterium sequenced to date. Therefore, we propose that the species incertae sedis 'C. ulcerans' should be conclusively recognized as a distinct species within the genus Corynebacterium with strain CCUG 2708 = NCTC 7910 as type strain. This species is characterized by urease production and fermentation of glycogen.

Base Composition↗
PubMed1994

Functional and structural changes of porcine alveolar macrophages induced by sublytic doses of a heat-labile, hemolytic, cytotoxic substance produced by Actinobacillus pleuropneumoniae.

Alterations in the size and functions of porcine alveolar macrophages exposed to sublytic amounts of heat-labile, hemolytic cytotoxin produced by Actinobacillus pleuropneumoniae (App) serotype 1, strain HS54 into the culture medium were studied in vitro. Alveolar macrophages were sensitive to the cytotoxin; treatment of the macrophages with low concentrations of cytotoxin (0.016 hemolytic unit) resulted in severe, irreversible cell swelling. However, high doses of cytotoxin (2.0 hemolytic units) were required to cause substantial cell death, as indicated by the influx of propidium iodide into and release of lactate dehydrogenase from cells. Macrophages exposed to low, sublytic doses of cytotoxin failed to migrate toward chemoattractant, were unable to attach to glass, and failed to phagocytize optimally opsonized erythrocytes. Macrophages already attached to glass surfaces detached when exposed to sublytic doses of cytotoxin. The swelling and impairment of functions of alveolar macrophages observed in this study could not be attributed to endotoxic effects, because heat treatment of the cytotoxin preparation for 60 minutes at 60 C resulted in complete loss of cytotoxicity. We conclude that sublytic doses of heat-labile, hemolytic cytotoxic substances produced by App depress alveolar macrophage function at concentrations likely to develop in association with acute pulmonary infection with App. The Apx (A pleuropneumoniae Rtx toxins) exotoxins secreted by the bacteria into culture medium were considered responsible for the toxic activity of the cytotoxin preparation. The Apx of the App field strain used in this study were likely to be similar to those of serotype-1 reference strain (S4707). Analysis by use of DNA-DNA hybridization indicated that genomic DNA of the field strain contained sequences similar to those encoding structural protein of ApxI (apxIA) and ApxII (apxIIA) of the serotype-1 reference strain. Therefore, Apx produced by the field strain of App used in this study are likely to be of similar pathogenic importance worldwide.

Actinobacillus pleuropneumoniae↗
PubMed1994

Genomic fingerprinting of Yersinia enterocolitica species by degenerate oligonucleotide-primed polymerase chain reaction.

A novel version of the polymerase chain reaction (PCR) termed degenerate oligonucleotide-primed PCR (DOP-PCR) was used to fingerprint the bacterial genome of Yersinia enterocolitica species. Eight well-characterized reference strains of Y. enterocolitica (ribotype, serotype, biotype and zymotype) were examined. Optimal experimental conditions for reproducibility, sensitivity and specificity were obtained using a single DOP-primer. All the strains gave distinct DOP-PCR profiles composed of 12 to 19 fragments with sizes from 200 to 1.500 bp. Thus, the DOP-PCR, which has so far been used to fingerprint human, mouse, fruitfly and plant DNA, is also well-suited to bacterial DNA.

Base Sequence↗