Genomes and Genes
Experts and Doctors on dna sequence analysis in Houston, United States
Locale: Houston, United States
Topic: dna sequence analysis
- Wang L, Liu H, Zhang Z, Spitz M, Wei Q. Association of genetic variants of O6-methylguanine-DNA methyltransferase with risk of lung cancer in non-Hispanic Whites. Cancer Epidemiol Biomarkers Prev. 2006;15:2364-9 pubmed..Our findings suggest that non-synonymous SNPs in MGMT are associated with modestly increased risk of lung cancer in Caucasians and need to be further investigated. ..
- Kwon D, Woo J, Perng C, Go M, Graham D, el Zaatari F. The effect of galE gene inactivation on lipopolysaccharide profile of Helicobacter pylori. Curr Microbiol. 1998;37:144-8 pubmed..The LPS profile from the galE-knockout H. pylori strain showed a lower molecular weight than that of the parental strain, indicating the involvement of the galE gene in LPS biosynthesis of H. pylori...
- Anaya P, Evans S, Dai C, Lozano G, May G. Isolation of the Aspergillus nidulans sudD gene and its human homologue. Gene. 1998;211:323-9 pubmed..The predicted proteins are approximately 60000Da in mass and have a serine-plus-threonine content of about 11%. The evolutionary conservation of the proteins suggests an ancient origin and conserved function for these proteins. ..
- Vigil K, Johnson J, Johnston B, Kontoyiannis D, Mulanovich V, Raad I, et al. Escherichia coli Pyomyositis: an emerging infectious disease among patients with hematologic malignancies. Clin Infect Dis. 2010;50:374-80 pubmed publisher..Awareness of this emerging syndrome and the usual causative agent is important to ensure appropriate management when febrile, neutropenic patients with hematologic malignancy exhibit signs of localized muscle infection. ..
- Sohocki M, Sullivan L, Harrison W, Sodergren E, Elder F, Weinstock G, et al. Human glutamate pyruvate transaminase (GPT): localization to 8q24.3, cDNA and genomic sequences, and polymorphic sites. Genomics. 1997;40:247-52 pubmed..In addition, this will be a useful system for characterizing the telomeric region of 8q. Finally, determination of the molecular basis of the GPT isozyme variants will permit PCR-based detection of this world-wide polymorphism. ..
- Ansari Lari M, Oeltjen J, Schwartz S, Zhang Z, Muzny D, Lu J, et al. Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. Genome Res. 1998;8:29-40 pubmed....
- McLeod M, Qin X, Karpathy S, Gioia J, Highlander S, Fox G, et al. Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae. J Bacteriol. 2004;186:5842-55 pubmed..conorii) groups diverged. The three-way comparison allowed further in silico analysis of the SpoT split genes, leading us to propose that the stringent response system is still functional in these rickettsiae...
- Lu W, Zhu H, Wen S, Laurent C, Shaw G, Lammer E, et al. Screening for novel PAX3 polymorphisms and risks of spina bifida. Birth Defects Res A Clin Mol Teratol. 2007;79:45-9 pubmed..However, additional follow-up of the PAX3 gene variant T-1186C (rs16863657) and its related haplotype, TCTCCGCCC, may be important in other populations. ..
- Patel N, Hertel P, Estes M, De La Morena M, Petru A, Noroski L, et al. Vaccine-acquired rotavirus in infants with severe combined immunodeficiency. N Engl J Med. 2010;362:314-9 pubmed publisher..These infections raise concerns regarding the safety of rotavirus vaccine in severely immunocompromised patients. ..
- Zhou Y, Zheng J, Gu X, Li W, Saunders G. A novel Pax-6 binding site in rodent B1 repetitive elements: coevolution between developmental regulation and repeated elements?. Gene. 2000;245:319-28 pubmed....
- Nallapareddy S, Singh K, Okhuysen P, Murray B. A functional collagen adhesin gene, acm, in clinical isolates of Enterococcus faecium correlates with the recent success of this emerging nosocomial pathogen. Infect Immun. 2008;76:4110-9 pubmed publisher..faecium genogroup referred to as clonal complex 17 (CC17), which has emerged globally. Taken together, our findings support the hypothesis that Acm has contributed to the emergence of E. faecium and CC17 in nosocomial infections. ..
- Yang A, Estecio M, Doshi K, Kondo Y, Tajara E, Issa J. A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res. 2004;32:e38 pubmed..This method can be used as a surrogate marker of genome-wide methylation changes. In addition, it is less labor intensive and requires less DNA than previous methods of assessing global DNA methylation. ..
- Fohn L, Behringer R. ESX1L, a novel X chromosome-linked human homeobox gene expressed in the placenta and testis. Genomics. 2001;74:105-8 pubmed..The findings that there are similarities between ESXR1 and Esx1, yet differences between their encoded products, are consistent with the idea that placental genes evolve rapidly between mammalian species. ..
- Buyse I, Fang P, Hoon K, Amir R, Zoghbi H, Roa B. Diagnostic testing for Rett syndrome by DHPLC and direct sequencing analysis of the MECP2 gene: identification of several novel mutations and polymorphisms. Am J Hum Genet. 2000;67:1428-36 pubmed..We conclude that this two-tiered approach provides a sensitive, robust, and efficient strategy for RTT molecular diagnosis. ..
- Metzker M. Sequencing technologies - the next generation. Nat Rev Genet. 2010;11:31-46 pubmed publisher..I also outline the broad range of applications for NGS technologies, in addition to providing guidelines for platform selection to address biological questions of interest. ..
- Oeltjen J, Malley T, Muzny D, Miller W, Gibbs R, Belmont J. Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains. Genome Res. 1997;7:315-29 pubmed..These data show the usefulness of large scale sequence comparisons to focus investigation on regions of noncoding sequence that play essential roles in complex gene regulation. ..
- Stewart A, Lednicky J, Butel J. Sequence analyses of human tumor-associated SV40 DNAs and SV40 viral isolates from monkeys and humans. J Neurovirol. 1998;4:182-93 pubmed..There was no compelling evidence for human-specific strains of SV40 or for tumor type-specific associations, suggesting that SV40 has a relatively broad host range. The source of the viral DNA found in human tumors remains unknown. ..
- Petrosino J, Highlander S, Luna R, Gibbs R, Versalovic J. Metagenomic pyrosequencing and microbial identification. Clin Chem. 2009;55:856-66 pubmed publisher..Metagenomics, or genetic studies of microbial communities, may ultimately contribute to a more comprehensive understanding of human health, disease susceptibilities, and the pathophysiology of infectious and immune-mediated diseases. ..
- Sheng X, Koul D, Liu J, Liu T, Yung W. Promoter analysis of tumor suppressor gene PTEN: identification of minimum promoter region. Biochem Biophys Res Commun. 2002;292:422-6 pubmed..Interestingly, a p53 binding sequence is located within the 599 bp fragment (-1344/-745), although p53 expression had a minimal effect on PTEN, demonstrating its insignificant role in PTEN gene expression. ..
- McGuire A, Caulfield T, Cho M. Research ethics and the challenge of whole-genome sequencing. Nat Rev Genet. 2008;9:152-6 pubmed publisher..Although the issues are not new, we discuss their implications for personal genomics and provide recommendations for appropriate management in the context of research involving individual whole-genome sequencing. ..
- Burgess D, Matsuura T, Ashizawa T, Noebels J. Genetic localization of the Ca2+ channel gene CACNG2 near SCA10 on chromosome 22q13. Epilepsia. 2000;41:24-7 pubmed..In addition, our data clarify the relation between the physical and genetic linkage maps of this region and will facilitate isolation of the SCA10 gene. ..
- Bainbridge M, Wang M, Burgess D, Kovar C, Rodesch M, D Ascenzo M, et al. Whole exome capture in solution with 3 Gbp of data. Genome Biol. 2010;11:R62 pubmed publisher....
- Matin A, Nadeau J. Search for testicular cancer gene hits dead-end. Cell Cycle. 2005;4:1136-8 pubmed..The identity of Ter as Dead end and its function in PGCs will help clarify the role of editing in PGC biology and elucidate the causes of TGCTs in mice and humans. ..
- Shimmin L, Natarajan S, Ibarguen H, Montasser M, Kim D, Hanis C, et al. Corticotropin releasing hormone (CRH) gene variation: comprehensive resequencing for variant and molecular haplotype discovery in monosomic hybrid cell lines. DNA Seq. 2007;18:434-44 pubmed..6), likely reflecting disruptive selection in CRH evolution. Network analysis showed that AA have retained an ancestral CRH haplotype, while the most common EA haplotype is derived from a single recombination event. ..
- Szafranski P, Schaaf C, Person R, Gibson I, Xia Z, Mahadevan S, et al. Structures and molecular mechanisms for common 15q13.3 microduplications involving CHRNA7: benign or pathological?. Hum Mutat. 2010;31:840-50 pubmed publisher..Nevertheless, if they prove to have a pathological effects, their high frequency could make them a common risk factor for many neurobehavioral disorders. ..
- Chang S, Heacock P, Mileykovskaya E, Voelker D, Dowhan W. Isolation and characterization of the gene (CLS1) encoding cardiolipin synthase in Saccharomyces cerevisiae. J Biol Chem. 1998;273:14933-41 pubmed..These results definitively identify the gene encoding the CL synthase of yeast. ..
- Eichler E, Lu F, Shen Y, Antonacci R, Jurecic V, Doggett N, et al. Duplication of a gene-rich cluster between 16p11.1 and Xq28: a novel pericentromeric-directed mechanism for paralogous genome evolution. Hum Mol Genet. 1996;5:899-912 pubmed....
- Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski E, et al. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res. 2010;20:273-80 pubmed publisher..Validation results show that Atlas-SNP2 achieves a false-positive rate of lower than 10%, with an approximately 5% or lower false-negative rate. ..
- Daines B, Wang H, Li Y, Han Y, Gibbs R, Chen R. High-throughput multiplex sequencing to discover copy number variants in Drosophila. Genetics. 2009;182:935-41 pubmed publisher..The approach we describe is immediately applicable to the systematic exploration of copy number variation in model organisms and humans. ..
- Moldovan S, DeMayo F, Brunicardi F. Cloning of the mouse SSTR5 gene. J Surg Res. 1998;76:57-60 pubmed..This gene will be important for use in gene regulation and gene ablation studies to determine the molecular events controlled by SSTR5 in regulating murine physiology and development. ..
- Han Z, Riefler G, Saam J, Mango S, Schumacher J. The C. elegans Tousled-like kinase contributes to chromosome segregation as a substrate and regulator of the Aurora B kinase. Curr Biol. 2005;15:894-904 pubmed....
- Rijnkels M, Elnitski L, Miller W, Rosen J. Multispecies comparative analysis of a mammalian-specific genomic domain encoding secretory proteins. Genomics. 2003;82:417-32 pubmed..The conserved regions might have biological importance for the regulation of genes in this genomic "neighborhood." ..
- Jayakumar A, Tai M, Huang W, al Feel W, Hsu M, Abu Elheiga L, et al. Human fatty acid synthase: properties and molecular cloning. Proc Natl Acad Sci U S A. 1995;92:8695-9 pubmed..This altered sequence is also present in HepG2 genomic DNA. The origin and significance of this sequence variance in the HepG2 FAS gene are unclear, but the variance apparently does not contribute to the lower activity of HepG2 FAS. ..
- Sampson M, Lovell R, Davison D, Craigen W. A novel mouse mitochondrial voltage-dependent anion channel gene localizes to chromosome 8. Genomics. 1996;36:192-6 pubmed..The phylogenetic relationship of the eukaryotic VDAC genes is presented. ..
- Whitworth D, Pask A, Shaw G, Marshall Graves J, Behringer R, Renfree M. Characterization of steroidogenic factor 1 during sexual differentiation in a marsupial. Gene. 2001;277:209-19 pubmed..Thus, although the structure of tammar SF1 is divergent from that of eutherians, its expression profile is similar, supporting a conserved role in gonadal development and steroidogenesis. ..
- Noveroske J, Hardy R, Dapper J, Vogel H, Justice M. A new ENU-induced allele of mouse quaking causes severe CNS dysmyelination. Mamm Genome. 2005;16:672-82 pubmed..Because the qk(v) allele is a large deletion that affects the expression of three genes, the new neurologic qk(e5) allele is an important addition to this allelic series. ..
- Ji J, Dimmock D, Tang L, Descartes M, Gomez R, Rutledge S, et al. A novel c.592-4_c.592-3delTT mutation in DGUOK gene causes exon skipping. Mitochondrion. 2010;10:188-91 pubmed publisher..The parents were subsequently confirmed to be carriers of this mutation. In summary, we have demonstrated that c.592-4_c.592-3delTT is a pathogenic splice acceptor site mutation leading to DGUOK deficiency. ..
- Bahrmand A, Titov L, Tasbiti A, Yari S, Graviss E. High-level rifampin resistance correlates with multiple mutations in the rpoB gene of pulmonary tuberculosis isolates from the Afghanistan border of Iran. J Clin Microbiol. 2009;47:2744-50 pubmed publisher....
- BUCASAS K, Pandya G, Pradhan S, Fleischmann R, Peterson S, Belmont J. Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping. BMC Genet. 2009;10:85 pubmed publisher....
- Britton R, Lupski J. Isolation and characterization of suppressors of two Escherichia coli dnaG mutations, dnaG2903 and parB. Genetics. 1997;145:867-75 pubmed..The sdgG suppressor is likely a mutation in one of three genes: ubiC, ubiA or yjbI. The sdgH class affects rpsF, which encodes the ribosomal protein S6. Possible mechanisms of suppression by these different classes are discussed. ..
- Lee B, Thirunavukkarasu K, Zhou L, Pastore L, Baldini A, Hecht J, et al. Missense mutations abolishing DNA binding of the osteoblast-specific transcription factor OSF2/CBFA1 in cleidocranial dysplasia. Nat Genet. 1997;16:307-10 pubmed..Thus, these results together suggest that CCD is produced by haploinsufficiency of OSF2/CBFA1 and provide direct genetic evidence that the phenotype is secondary to an alteration of osteoblast differentiation...
- Sohocki M, Malone K, Sullivan L, Daiger S. Localization of retina/pineal-expressed sequences: identification of novel candidate genes for inherited retinal disorders. Genomics. 1999;58:29-33 pubmed..This combination of database analysis and laboratory investigation has localized several EST clusters that are potential candidates for genes causing inherited retinopathy. ..
- Dias Neto E, Nunes D, Giordano R, Sun J, Botz G, Yang K, et al. Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis. PLoS ONE. 2009;4:e8338 pubmed publisher..Overall, qPhage plus pyrosequencing is superior to TU-counting plus Sanger sequencing and is proposed as the method of choice over a broad range of phage display applications in vitro, in cells, and in vivo. ..
- Galloway Peña J, Nallapareddy S, Arias C, Eliopoulos G, Murray B. Analysis of clonality and antibiotic resistance among early clinical isolates of Enterococcus faecium in the United States. J Infect Dis. 2009;200:1566-73 pubmed publisher....
- Han K, Millar N, Davis R. A novel octopamine receptor with preferential expression in Drosophila mushroom bodies. J Neurosci. 1998;18:3650-8 pubmed..The preferential expression of OAMB in mushroom bodies and its capacity to produce cAMP accumulation suggest an important role in synaptic modulation underlying behavioral plasticity. ..
- Srivatsan A, Han Y, Peng J, Tehranchi A, Gibbs R, Wang J, et al. High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet. 2008;4:e1000139 pubmed publisher....
- Shi X, Bennett G. Plasmids bearing hfq and the hns-like gene stpA complement hns mutants in modulating arginine decarboxylase gene expression in Escherichia coli. J Bacteriol. 1994;176:6769-75 pubmed....
- Shen L, Kondo Y, Guo Y, Zhang J, Zhang L, Ahmed S, et al. Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet. 2007;3:2023-36 pubmed....
- Boettger Tong H, Rohozinski J, Agoulnik A, Dohmae K, Nishimune Y, Levy N, et al. Identification and sequencing the juvenile spermatogonial depletion critical interval on mouse chromosome 1 reveals the presence of eight candidate genes. Biochem Biophys Res Commun. 2001;288:1129-35 pubmed..The critical 0.4 cM jsd interval corresponds to a physical distance of approximately 1.5 Mb. Eight genes have been identified in this interval, two of which appear to be possible candidates for the jsd mutation. ..
- Matthews K, Mueller Ortiz S, Wetsel R. Carboxypeptidase N: a pleiotropic regulator of inflammation. Mol Immunol. 2004;40:785-93 pubmed..The future use of gene ablation technology may be the most appropriate way to understand the function of CPN in vivo. ..
- Qin X, Singh K, Weinstock G, Murray B. Effects of Enterococcus faecalis fsr genes on production of gelatinase and a serine protease and virulence. Infect Immun. 2000;68:2579-86 pubmed..These results suggest that sprE and agr-like genes contribute to the virulence of E. faecalis OG1RF in this model...
- Agoulnik A, Lu B, Zhu Q, Truong C, Ty M, Arango N, et al. A novel gene, Pog, is necessary for primordial germ cell proliferation in the mouse and underlies the germ cell deficient mutation, gcd. Hum Mol Genet. 2002;11:3047-53 pubmed..Thus, in addition to being necessary for PGC proliferation, Pog may have a wider significance in early embryonic development. ..
- Eldon E, Kooyer S, D Evelyn D, Duman M, Lawinger P, Botas J, et al. The Drosophila 18 wheeler is required for morphogenesis and has striking similarities to Toll. Development. 1994;120:885-99 pubmed..The data suggest that the 18W protein participates in the developmental program specified by segmentation and homeotic genes as a cell adhesion or receptor molecule that facilitates cell movements. ..
- de Conciliis L, Marchitiello A, Wapenaar M, Borsani G, Giglio S, Mariani M, et al. Characterization of Cxorf5 (71-7A), a novel human cDNA mapping to Xp22 and encoding a protein containing coiled-coil alpha-helical domains. Genomics. 1998;51:243-50 pubmed....
- Martínez Alcántara A, Ballesteros E, Feng C, Rojas M, Koshinsky H, Fofanov V, et al. PIQA: pipeline for Illumina G1 genome analyzer data quality assessment. Bioinformatics. 2009;25:2438-9 pubmed publisher..The PIQA pipeline, installation instructions and examples are available at the supplementary web site (http://bioinfo.uh.edu/PIQA). ..
- Larsen M, Ressler S, Gerdes M, Lu B, Byron M, Lawrence J, et al. The WFDC1 gene encoding ps20 localizes to 16q24, a region of LOH in multiple cancers. Mamm Genome. 2000;11:767-73 pubmed..Identification and characterization of the WFDC1 gene may aid in better understanding the potential role of this gene and ps20 in prostate biology and carcinogenesis. ..
- Dryden S, Dowhan W. Isolation and expression of the Rhodobacter sphaeroides gene (pgsA) encoding phosphatidylglycerophosphate synthase. J Bacteriol. 1996;178:1030-8 pubmed..coli pgsA. Overexpression of PgsARs in either E. coli or R. sphaeroides did not have dramatic effects on the phospholipid composition of the cells, suggesting regulation of the activity of this enzyme in both organisms. ..
- Nichols B, Avery S, Sen P, Swallow D, Hahn D, Sterchi E. The maltase-glucoamylase gene: common ancestry to sucrase-isomaltase with complementary starch digestion activities. Proc Natl Acad Sci U S A. 2003;100:1432-7 pubmed..The complementary human enzyme activities allow digestion of the starches of plant origin that make up two-thirds of most diets. ..
- Li X, Chuang C, Mao C, Angerer L, Klein W. Two Otx proteins generated from multiple transcripts of a single gene in Strongylocentrotus purpuratus. Dev Biol. 1997;187:253-66 pubmed publisher..These results demonstrate that novel forms of Otx are produced in sea urchins by differential promoter utilization and alternative splicing. It may be that similar regulatory mechanisms lead to diverse forms of Otx in vertebrates...
- Probst F, Cooper M, Cheung S, Justice M. Genotype, phenotype, and karyotype correlation in the XO mouse model of Turner Syndrome. J Hered. 2008;99:512-7 pubmed publisher..This work lays the foundation for the use of this strain to study Turner Syndrome in particular and the X chromosome in general. ..
- Biesinger T, Yu Kimata M, Kimata J. Changes in simian immunodeficiency virus reverse transcriptase alleles that appear during infection of macaques enhance infectivity and replication in CD4+ T cells. Virology. 2008;370:184-93 pubmed..Taken together, our data underscore the importance of RT determinants for pathogenicity of SIV and for the capacity to replicate in CD4(+) T cell populations...
- Cardnell R, Nogare D, Ganetzky B, Stern M. In vivo analysis of a gain-of-function mutation in the Drosophila eag-encoded K+ channel. Genetics. 2006;172:2351-8 pubmed..We hypothesize that the G297E substitution may cause premature, prolonged, or constitutive opening of the Eag channels by favoring the "unlocked" state of the channel. ..