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PubMed2000

Selecting protein targets for structural genomics of Pyrobaculum aerophilum: validating automated fold assignment methods by using binary hypothesis testing.

Three-dimensional protein folds were assigned to all ORFs of the recently sequenced genome of the hyperthermophilic archaeon Pyrobaculum aerophilum. Binary hypothesis testing was used to estimate a confidence level for each assignment. A separate test was conducted to assign a probability for whether each sequence has a novel fold-i.e., one that is not yet represented in the experimental database of known structures. Of the 2,130 predicted nontransmembrane proteins in this organism, 916 matched a fold at a cumulative 90% confidence level, and 245 could be assigned at a 99% confidence level. Likewise, 286 proteins were predicted to have a previously unobserved fold with a 90% confidence level, and 14 at a 99% confidence level. These statistically based tools are combined with homology searches against the Online Mendelian Inheritance in Man (OMIM) human genetics database and other protein databases for the selection of attractive targets for crystallographic or NMR structure determination. Results of these studies have been collated and placed at http://www.doe-mbi.ucla.edu/people/parag/P A_HOME/, the University of California, Los Angeles-Department of Energy Pyrobaculum aerophilum web site.

Algorithms↗
PubMed2000

Unusual polymorphisms in human immunodeficiency virus type 1 associated with nonprogressive infection.

Factors accounting for long-term nonprogression may include infection with an attenuated strain of human immunodeficiency virus type 1 (HIV-1), genetic polymorphisms in the host, and virus-specific immune responses. In this study, we examined eight individuals with nonprogressing or slowly progressing HIV-1 infection, none of whom were homozygous for host-specific polymorphisms (CCR5-Delta32, CCR2-64I, and SDF-1-3'A) which have been associated with slower disease progression. HIV-1 was recovered from seven of the eight, and recovered virus was used for sequencing the full-length HIV-1 genome; full-length HIV-1 genome sequences from the eighth were determined following amplification of viral sequences directly from peripheral blood mononuclear cells (PBMC). Longitudinal studies of one individual with HIV-1 that consistently exhibited a slow/low growth phenotype revealed a single amino acid deletion in a conserved region of the gp41 transmembrane protein that was not seen in any of 131 envelope sequences in the Los Alamos HIV-1 sequence database. Genetic analysis also revealed that five of the eight individuals harbored HIV-1 with unusual 1- or 2-amino-acid deletions in the Gag sequence compared to subgroup B Gag consensus sequences. These deletions in Gag have either never been observed previously or are extremely rare in the database. Three individuals had deletions in Nef, and one had a 4-amino-acid insertion in Vpu. The unusual polymorphisms in Gag, Env, and Nef described here were also found in stored PBMC samples taken 3 to 11 years prior to, or in one case 4 years subsequent to, the time of sampling for the original sequencing. In all, seven of the eight individuals exhibited one or more unusual polymorphisms; a total of 13 unusual polymorphisms were documented in these seven individuals. These polymorphisms may have been present from the time of initial infection or may have appeared in response to immune surveillance or other selective pressures. Our results indicate that unusual, difficult-to-revert polymorphisms in HIV-1 can be found associated with slow progression or nonprogression in a majority of such cases.

Amino Acid Sequence↗
PubMed2025

Influence of ADRB2 variants on bronchodilator response and asthma control in a mixed population.

OBJECTIVE: Given that b2 agonists constitute the primary treatment for asthma and that treatment response varies as a result of polymorphisms in the ADRB2 gene, we sought to investigate the associations between ADRB2 gene variants and bronchodilator response (BDR) in asthma patients. METHODS: A genetic database comprising 813 individuals was analyzed for variants in the ADRB2 gene. A longitudinal analysis of severe asthma patients was performed to evaluate changes in BDR over time. RESULTS: The rs1042713, rs1042714, and rs1042717 variants were associated with age-related changes in BDR in patients with severe asthma. The G allele (rs1042714) and the A allele (rs1042717) were associated with uncontrolled asthma, with carriers of the G46/G79/A252 alleles showing a higher risk of difficult-to-control asthma. Notably, no association was found between these variants and ADRB2 expression levels. CONCLUSIONS: Our findings suggest that a genetic panel including ADRB2 variants, as well as age-related differences in BDR, is a useful complementary tool in asthma management.

Humans↗
PubMed1999

Population genetic data on loci LDLR, GYPA, HBGG, D7S8 and GC in the Bangkok population compared with rural Thais from Trat province.

Prior to the introduction of any DNA marker as a tool for person identification and paternity test in certain ethnic groups, a population genetic database should be constructed. Using multiplex primers in single tube polymerase chain amplification, 5 loci of unrelated genes in the PM Amplitype kit (Perkin Elmer) were studied in two Thai population groups: 228 DNA samples were extracted from blood collected at the Borai rural area in Trat province; another 123 DNA samples were collected at the outpatient clinic, Department of Forensic Medicine, King Chulalongkorn Memorial Hospital, Bangkok. Analysis of alleles and genotypes was performed after reversed dot blot hybridization of PCR products to allelic sequence specific probes immobilized on the membrane strip followed by nonradioisotopic detection according to the manufacturer's protocol. Population genetic statistic parameters including discrimination power (DP), the probability of matching (PM), power of exclusion for trio (PE trio) and typical paternity index (PI typical) were computed. Both Thai population groups showed no significant deviation from the Hardy Weinberg Expectation (HWE). The combined DP of all 5 loci in the PM Amplitype markers was 0.993636 for rural Thais and 0.994409 for Thais from Bangkok. The combined PM for rural Thais and those living in Bangkok was 0.006364 and 0.005591, respectively. The combined PE trio was 0.696825 and 0.698875 in both Thai population groups and the combined PI typical values were < 1.0. In conclusion, person identification using PM Amplitype DNA markers was efficient and satisfactory within certain limits. Hence, the application of PM Amplitype DNA markers for paternity tests should be cautiously considered and applied in combination with other parameters.

Alleles↗
PubMed2002

Regulatory context is a crucial part of gene function.

Information about the time and place of gene transcription, which until recently was only possible by extensive experimental analysis, can now be predicted through in silico analysis. Using the human RANTES/CCL5 promoter, we show that organizational features of promoters derived from promoter sequences contain information about the spatial and temporal 'functional context' of expression.

Animals↗
PubMed2002

Comparison of the small molecule metabolic enzymes of Escherichia coli and Saccharomyces cerevisiae.

The comparison of the small molecule metabolism pathways in Escherichia coli and Saccharomyces cerevisiae (yeast) shows that 271 enzymes are common to both organisms. These common enzymes involve 384 gene products in E. coli and 390 in yeast, which are between one half and two thirds of the gene products of small molecule metabolism in E. coli and yeast, respectively. The arrangement and family membership of the domains that form all or part of 374 E. coli sequences and 343 yeast sequences was determined. Of these, 70% consist entirely of homologous domains, and 20% have homologous domains linked to other domains that are unique to E. coli, yeast, or both. Over two thirds of the enzymes common to the two organisms have sequence identities between 30% and 50%. The remaining groups include 13 clear cases of nonorthologous displacement. Our calculations show that at most one half to two thirds of the gene products involved in small molecule metabolism are common to E. coli and yeast. We have shown that the common core of 271 enzymes has been largely conserved since the separation of prokaryotes and eukaryotes, including modifications for regulatory purposes, such as gene fusion and changes in the number of isozymes in one of the two organisms. Only one fifth of the common enzymes have nonhomologous domains between the two organisms. Around the common core very different extensions have been made to small molecule metabolism in the two organisms.

Databases, Genetic↗
PubMedDate not supplied

Parental decision-making differences between patients in two healthcare systems for choroid plexus cysts.

OBJECTIVE: We evaluated the medical-sociological implications of parental perception of risk and decision-making choices for prenatally ascertained choroid plexus cysts (CPCs) between two obstetric populations with similar clinical situations. METHODS: The Wayne State University (WSU) Reproductive Genetics database and the Madigan Army Medical Center (MAMC) experience were reviewed to compare the rates of aneuploidy and invasive testing for cases with CPC. Aneuploidy rates were compared between those with isolated CPC, CPC with advanced maternal age (AMA), and CPC associated with multiple anomalies. RESULTS: 186 cases were identified in the WSU cohort, of whom 27 (15%) declined invasive fetal testing. In the remaining 159 cases, aneuploidy was present in 2/132 (1.5%) isolated CPCs, 3/11 (27%) CPCs with AMA, and 15/16 (93%) CPCs with multiple anomalies. 107 cases were identified in the MAMC cohort, of whom 99 (92%) declined invasive fetal testing. No cases of aneuploidy were found in the 3/12 AMA cases or 5/95 non-AMA cases who underwent amniocentesis. CONCLUSIONS: The 2 cases of aneuploidy with isolated CPC cannot be ignored, and provide an estimated attributable risk of at least 0.8%, a higher risk than 38 years of age. However, the parental sociologic context may be as important as the genetic-prognostic risk for decision-making.

Academic Medical Centers↗
PubMed2000

Parental decision-making differences between patients in two healthcare systems for choroid plexus cysts.

We evaluated the medical-sociological implications of parental perception of risk and decision-making choices for prenatally ascertained choroid plexus cysts (CPC) between two obstetric populations. The Wayne State University (WSU) Reproductive Genetics database and the Madigan Army Medical Center (MAMC) experience were reviewed to compare the rates of aneuploidy and invasive testing for cases with CPC. Aneuploidy rates were compared between those with isolated CPC, CPC with advanced maternal age (AMA), and CPC associated with multiple anomalies. In the WSU cohort 186 cases were identified, of whom 27 (15%) declined invasive fetal testing. In the remaining 159 cases, aneuploidy was present in 2/132 (1.5%) isolated CPC, 3/11 (27%) CPC with AMA, and 15/16 (93%) CPC with multiple anomalies. In the MAMC cohort 107 cases were identified, of whom 99 (92%) declined invasive fetal testing. No aneuploidy cases were found in the 3/12 AMA cases or 5/95 non-AMA cases that underwent amniocentesis. The two cases of aneuploidy with isolated CPC cannot be ignored, and provide an estimated attributable risk of at least 0.8%, a higher risk than 38 years of age. However, the parental sociologic context may be as important for decision-making as the genetic-prognostic risk.

Abnormalities, Multiple↗
PubMed2002

[Phylogenetic relationship of mitochondrial DNA in salmonids of the subfamily Salmoninae: analysis of the cytochrome b gene sequences].

On the basis of comparison of the cytochrome b gene nucleotide sequences from genetic databases, the possible phylogenetic relationships of mitochondrial DNA (mtDNA) among all major lineages of Salmoninae (Brachymystax, Parahucho, Salvelinus, Salmo, Parasalmo, and Oncorhynchus) were examined. Three different phylogenetic methods (UPGMA, NJ, and ML) yielded phylogenetic trees of essentially the same topology: (((Brachymystax, Parahucho), Salvelinus, Salmo), (Parasalmo, Oncorhynchus)). The results obtained using the maximum parsimony method were less clear. Apparently, the divergence of the main salmonid lineages occurred during a relatively short time period; hence, the number of synapomorphs marking the order of their divergence was extremely low. This may account for the relative failure to use the maximum parsimony method of phylogenetic reconstruction. The problem of concordance of mtDNA and species phylogenetic schemes is discussed. Their discrepancy in salmonids may be caused by interspecific introgressive hybridization.

Animals↗
PubMed1987

Applications of the MEGADATS database system in medical genetics.

The MEGADATS relational database system has many useful applications in the field of medical genetics. Some of these applications include storage, retrieval, and display of pedigree information; retrieval of sets of individuals, sibships, or families who meet given criteria; storage of necessary information for mailing lists, clinic data, etc; and combination of pedigree information and genotype information into the format needed for linkage analysis packages.

Genetics, Medical↗
PubMed2003

The European Bioinformatics Institute's data resources.

As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics Institute (EBI) hosts six core databases, which store information on DNA sequences (EMBL-Bank), protein sequences (SWISS-PROT and TrEMBL), protein structure (MSD), whole genomes (Ensembl) and gene expression (ArrayExpress). But just as a cell would be useless if it couldn't transcribe DNA or translate RNA, our resources would be compromised if each existed in isolation. We have therefore developed a range of tools that not only facilitate the deposition and retrieval of biological information, but also allow users to carry out searches that reflect the interconnectedness of biological information. The EBI's databases and tools are all available on our website at www.ebi.ac.uk.

Animals↗
PubMed1995

A study of five variable number tandem repeat (VNTR) loci in the Greek population.

The use of hypervariable tandem repeat loci for population genetic studies, genetic analysis of inherited disease and individual identification purposes requires establishment of a genetic database for each reference population. In the present study we have analysed variability at five tandem repeat loci (D1S80, D17S5, 3'-hvr/apoB, F8vWF and D6S89)in a representative sample (88 to 156 individuals of greek ancestry), using polymerase chain reaction amplification. Between nine and 19 alleles were resolved throughout the five polymorphic loci. Heterozygosity indices for these loci in the greek population ranged from 0.68 to 0.85. Allele frequencies follow a bimodal discrimination (pd) and allelic diversity (h) values ranged from 0.84 to 0.94 and 0.85 to 0.91, respectively, and indicated that these loci are highly informative and can be used for population studies, forensic purposes and parentage and family testing. Comparison of observed and expected genotype frequencies by the conventional chi-square test indicated conformity to Hardy-Weinberg predictions.

Alleles↗
PubMed2002

Identification of new herpesvirus gene homologs in the human genome.

Viruses are intracellular parasites that use many cellular pathways during their replication. Large DNA viruses, such as herpesviruses, have captured a repertoire of cellular genes to block or mimic host immune responses, apoptosis regulation, and cell-cycle control mechanisms. We have conducted a systematic search for all homologs of herpesvirus proteins in the human genome using position-specific scoring matrices representing herpesvirus protein sequence domains, and pair-wise sequence comparisons. The analysis shows that approximately 13% of the herpesvirus proteins have clear sequence similarity to products of the human genome. Different human herpesviruses vary in their numbers of human homologs, indicating distinct rates of gene acquisition in different lineages. Our analysis has identified new families of herpesvirus/human homologs from viruses including human herpesvirus 5 (human cytomegalovirus; HCMV) and human herpesvirus 8 (Kaposi's sarcoma-associated herpesvirus; KSHV), which may play important roles in host-virus interactions.

Amino Acid Sequence↗
PubMed1999

HP0333, a member of the dprA family, is involved in natural transformation in Helicobacter pylori.

Helicobacter pylori is naturally competent for DNA transformation, but the mechanism by which transformation occurs is not known. For Haemophilus influenzae, dprA is required for transformation by chromosomal but not plasmid DNA, and the complete genomic sequence of H. pylori 26695 revealed a dprA homolog (HP0333). Examination of genetic databases indicates that DprA homologs are present in a wide variety of bacterial species. To examine whether HP0333 has a function similar to dprA of H. influenzae, HP0333, present in each of 11 strains studied, was disrupted in two H. pylori isolates. For both mutants, the frequency of transformation by H. pylori chromosomal DNA was markedly reduced, but not eliminated, compared to their wild-type parental strains. Mutation of HP0333 also resulted in a marked decrease in transformation frequency by a shuttle plasmid (pHP1), which differs from the phenotype described in H. influenzae. Complementation of the mutant with HP0333 inserted in trans in the chromosomal ureAB locus completely restored the frequency of transformation to that of the wild-type strain. Thus, while dprA is required for high-frequency transformation, transformation also may occur independently of DprA. The presence of DprA homologs in bacteria known not to be naturally competent suggests a broad function in DNA processing.

Amino Acid Sequence↗
PubMed1996

Molecular cloning and functional analysis of a novel macrolide-resistance determinant, mefA, from Streptococcus pyogenes.

Several streptococcal strains had an uncharacterized mechanism of macrolide resistance that differed from those that had been reported previously in the literature. This novel mechanism conveyed resistance to 14- and 15-membered macrolides, but not to 16-membered macrolides, lincosamides or analogues of streptogramin B. The gene encoding this phenotype was cloned by standard methods from total genomic digests of Streptococcus pyogenes 02C1064 as a 4.7 kb heterologous insert into the low-copy vector, pACYC177, and expressed in several Escherichia coli K-12 strains. The location of the macrolide-resistance determinant was established by functional analysis of deletion derivatives and sequencing. A search for homologues in the genetic databases confirmed that the gene is a novel one with homology to membrane-associated pump proteins. The macrolide-resistance coding sequence was subcloned into a pET23a vector and expressed from the inducible T7 promoter on the plasmid in E. coli BL21(DE3). Physiological studies of the cloned determinant, which has been named mefA for macrolide efflux, provide evidence for its mechanism of action in host bacteria. E.coli strains containing the cloned determinant maintain lower levels of intracellular erythromycin when this compound is added to the external medium than isogenic clones without mefA. Furthermore, intracellular accumulation of [14C]-erythromycin in the original S. pyogenes strain was always lower than that observed in erythromycin-sensitive strains. This is consistent with a hypothesis that the gene encodes a novel antiporter function which pumps erythromycin out of the cell. The gene appears to be widely distributed in S. pyogenes strains, as demonstrated by primer-specific synthesis using the polymerase chain reaction.

Bacterial Proteins↗
PubMed1997

Significance of a false-positive trisomy 18 multiple-marker screening test.

OBJECTIVE: To determine if a false-positive trisomy 18 multiple-marker screening test (all three analytes low: maternal serum alpha-fetoprotein [AFP] at most 0.75 multiples of the median [MoM], unconjugated estriol at most 0.60 MoM, and hCG at most 0.55 MoM) indicates increased risk for obstetric complications or is related to maternal weight. METHODS: We accessed our genetic database to obtain multiple-marker screening test results, fetal karyotypes, and pregnancy outcomes from all patients with a normal multiple-marker screening test (n = 3900) and from all patients with a positive trisomy 18 screening test (n = 103) seen in the prenatal diagnosis clinic from 1992 to 1996. During this period, only maternal serum AFP was adjusted for maternal weight. RESULTS: A positive trisomy 18 screen identified five of 12 trisomy 18 fetuses. Women with a false-positive trisomy 18 screen were heavier (175.6 +/- 43.8 lb versus 159.9 +/- 37.9 lb, P < .001) and younger (29.7 +/- 6.5 years versus 32.3 +/- 6.5 years, P < .001) than women with a normal multiple-marker screening test, but were not at increased risk for pregnancy complications. Weight-adjusting all three analytes reduced the false-positive trisomy 18 screen rate by 42% (from 1.9% to 1.1%) but did not change the trisomy 18 detection rate. CONCLUSION: A false-positive trisomy 18 screening test does not indicate increased risk to develop pregnancy complications and may be related to inadequate correction for increased maternal weight.

Adult↗