Genomes and Genes
Experts and Doctors on sequence alignment in College Station, Texas, United States
Locale: College Station, Texas, United States
Topic: sequence alignment
- Wu X, Guarino L. Autographa californica nucleopolyhedrovirus orf69 encodes an RNA cap (nucleoside-2'-O)-methyltransferase. J Virol. 2003;77:3430-40 pubmed..Immunoblot analysis confirmed that MTase1 was not synthesized in these cells, and single-step growth curves revealed that the rate of virus replication in tissue culture was not affected by the absence of MTase1. ..
- Credille K, Venta P, Breen M, Lowe J, Murphy K, Ostrander E, et al. DNA sequence and physical mapping of the canine transglutaminase 1 gene. Cytogenet Cell Genet. 2001;93:73-6 pubmed..Characterizing the coding region of canine TGM1 is a first step in examining the role of this enzyme in normal and defective cornification in the dog. ..
- Thapa H, Tang S, Sacchettini J, Devarenne T. Tetraterpene Synthase Substrate and Product Specificity in the Green Microalga Botryococcus braunii Race L. ACS Chem Biol. 2017;12:2408-2416 pubmed publisher..These studies also offer insights into tetraterpene hydrocarbon metabolism in B. braunii and provide a foundation for engineering LOS for robust production of specific hydrocarbons of a desired chain length. ..
- Miles G, Bayley H, Cheley S. Properties of Bacillus cereus hemolysin II: a heptameric transmembrane pore. Protein Sci. 2002;11:1813-24 pubmed publisher..Although they share limited primary sequence identity (30%), these data confirm that HlyII is a structural and functional homolog of staphylococcal alpha-hemolysin...
- Qiu W, Scholthof K. In vitro- and in vivo-generated defective RNAs of satellite panicum mosaic virus define cis-acting RNA elements required for replication and movement. J Virol. 2000;74:2247-54 pubmed..5-kDa SPMV CP. This represents the first report of a D-RNA associated with a satellite virus...
- Kochan K, Amaral M, Agarwala R, Schäffer A, Riggs P. Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis) chromosome 20. BMC Genomics. 2008;9:544 pubmed publisher..To improve sensitivity and efficiency of radiation hybrid panel analysis in comparison to gel-based methods, we adapted fluorescence-based real-time PCR and dissociation curve analysis for use as a novel scoring method...
- Dash B, Phillips T. Molecular characterization of a catalase from Hydra vulgaris. Gene. 2012;501:144-52 pubmed publisher..These results indicated that the HvCatalase gene is involved in the cellular stress response and (anti)oxidative processes triggered by stressor and contaminant exposure. ..
- Choi I, Hash S, Collisson E. Molecular cloning and expression of feline CD28 and CTLA-4 cDNA. Vet Immunol Immunopathol. 2000;76:45-59 pubmed..Expression of feline CD28 and CTLA-4 mRNA in freshly isolated feline PBMC was demonstrated by RT-PCR. Stimulation of PBMC with Con-A similarly increased the expression of both CD28 and CTLA-4 mRNA. ..
- Janecka J, Miller W, Pringle T, Wiens F, Zitzmann A, Helgen K, et al. Molecular and genomic data identify the closest living relative of primates. Science. 2007;318:792-4 pubmed..Our data show that colugos are the closest living relatives of primates and indicate that their divergence occurred in the Cretaceous...
- Wood E, Tamborero S, Mingarro I, Esteve Gassent M. BB0172, a Borrelia burgdorferi outer membrane protein that binds integrin ?3?1. J Bacteriol. 2013;195:3320-30 pubmed publisher..This is the first report of a borrelial adhesin with a metal ion-dependent adhesion site (MIDAS) motif that is similar to those observed in eukaryotic integrins and has a similar function. ..
- Karamysheva Z, Surovtseva Y, Vespa L, Shakirov E, Shippen D. A C-terminal Myb extension domain defines a novel family of double-strand telomeric DNA-binding proteins in Arabidopsis. J Biol Chem. 2004;279:47799-807 pubmed..Thus, Myb-ext is required for binding plant telomeric DNA and defines a novel class of proteins in Arabidopsis. ..
- Ahn J, Guarino L, Zhu Salzman K. Seven-up facilitates insect counter-defense by suppressing cathepsin B expression. FEBS J. 2007;274:2800-14 pubmed
- Oubre C, D Hondt E, Moore R, Hargis B, Berghman L. The chicken pituitary expresses an ovoinhibitor-like protein in subpopulations of some, but not all, hormone-producing cell types. Domest Anim Endocrinol. 2003;25:389-97 pubmed
- Daubner S, McGinnis J, Gardner M, Kroboth S, Morris A, Fitzpatrick P. A flexible loop in tyrosine hydroxylase controls coupling of amino acid hydroxylation to tetrahydropterin oxidation. J Mol Biol. 2006;359:299-307 pubmed..The V/K(tyr) to V/K(phe) ratios for these variants were altered significantly, but the results did not suggest that F184 of TyrH or Y138 of PheH plays a dominant role in determining amino acid substrate specificity. ..
- Zhang L, DeRider M, McCornack M, Jao S, Isern N, Ness T, et al. Solution structure of the complex between poxvirus-encoded CC chemokine inhibitor vCCI and human MIP-1beta. Proc Natl Acad Sci U S A. 2006;103:13985-90 pubmed..This structure reveals the strategy used by vCCI to tightly bind numerous chemokines while retaining selectivity for the CC chemokine subfamily...
- Nachman R, Russell W, Coast G, Russell D, Miller J, Predel R. Identification of PVK/CAP2b neuropeptides from single neurohemal organs of the stable fly and horn fly via MALDI-TOF/TOF tandem mass spectrometry. Peptides. 2006;27:521-6 pubmed..The identification of these novel neuropeptides adds to our knowledge of the peptidomes of flies, and can aid in the development of neuropeptide-based control strategies of these insect pests. ..
- Mulenga A, Khumthong R. Silencing of three Amblyomma americanum (L.) insulin-like growth factor binding protein-related proteins prevents ticks from feeding to repletion. J Exp Biol. 2010;213:1153-61 pubmed publisher..The data are discussed with reference to advances in tick molecular biology and the potential of the three proteins as targets for immunizing animals against tick feeding. ..
- Morishige D, Childs K, Moore L, Mullet J. Targeted analysis of orthologous phytochrome A regions of the sorghum, maize, and rice genomes using comparative gene-island sequencing. Plant Physiol. 2002;130:1614-25 pubmed..Within genomic regions where micro-colinearity of genes is absolutely conserved, gene-island sequencing is a particularly useful tool for comparative analysis of genomes between related species. ..
- Ramel M, Buckles G, Lekven A. Conservation of structure and functional divergence of duplicated Wnt8s in pufferfish. Dev Dyn. 2004;231:441-8 pubmed publisher..This finding suggests that zebrafish (and possibly teleost in general) Wnt8 receptors are able to discriminate between highly related ligands...
- Karamyshev A, Patrick A, Karamysheva Z, Griesemer D, Hudson H, Tjon Kon Sang S, et al. Inefficient SRP interaction with a nascent chain triggers a mRNA quality control pathway. Cell. 2014;156:146-57 pubmed publisher..The results reveal a previously unappreciated general mechanism of translational quality control, in which specific mRNA degradation preemptively regulates aberrant protein production (RAPP). ..
- Bishop M, Xenoulis P, Levinski M, Suchodolski J, Steiner J. Identification of variants of the SPINK1 gene and their association with pancreatitis in Miniature Schnauzers. Am J Vet Res. 2010;71:527-33 pubmed publisher..In healthy dogs of other breeds, only the 2 exon variants were identified. Variants of the SPINK1 gene may be associated with the development of pancreatitis in Miniature Schnauzers. ..
- Chen C, Spencer T, Bazer F. Fibroblast growth factor-10: a stromal mediator of epithelial function in the ovine uterus. Biol Reprod. 2000;63:959-66 pubmed..The nonoverlapping spatial patterns of expression for FGF-10 and FGF-7 in ovine uterus and conceptus suggest independent roles in uterine function and conceptus development. ..
- Predel R, Russell W, Tichy S, Russell D, Nachman R. Mass spectrometric analysis of putative capa-gene products in Musca domestica and Neobellieria bullata. Peptides. 2003;24:1487-91 pubmed..The species-specific peptide sequences differ remarkably between the related dipteran species. These differences could make it possible to develop peptide-analogs with group- or species-specific efficacy...
- Williamson K, SCHNEIDER V, Jordan R, Mueller J, Henderson Pozzi M, Bryk M. Catalytic and functional roles of conserved amino acids in the SET domain of the S. cerevisiae lysine methyltransferase Set1. PLoS ONE. 2013;8:e57974 pubmed publisher..Further, the results suggest that the attributes of Set1 required for trimethylation of histone H3 are those required for Pol II gene silencing at the rDNA and kinetochore function. ..
- Hash S, Brown W, Rice Ficht A. Characterization of a cDNA encoding bovine interleukin 10: kinetics of expression in bovine lymphocytes. Gene. 1994;139:257-61 pubmed..8-kb transcript, reaching maximal levels between 8 and 24 h, in ConA-stimulated peripheral T-cells, and weak expression in lipopolysaccharide-activated macrophages. ..
- Mateos M, Hurtado L, Santamaria C, Leignel V, Guinot D. Molecular systematics of the deep-sea hydrothermal vent endemic Brachyuran family Bythograeidae: a comparison of three Bayesian species tree methods. PLoS ONE. 2012;7:e32066 pubmed publisher..Our species tree analyses reveal differences in how each of the three methods weighs conflicting phylogenetic signal from different gene partitions and how limits on the number of outgroup taxa may affect the results. ..
- Shakirov E, McKnight T, Shippen D. POT1-independent single-strand telomeric DNA binding activities in Brassicaceae. Plant J. 2009;58:1004-15 pubmed publisher..thaliana and its close relatives, underscoring the remarkable functional divergence of POT1 proteins from plants and other eukaryotes. ..
- Lee J, Page R, García Contreras R, Palermino J, Zhang X, Doshi O, et al. Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance. J Mol Biol. 2007;373:11-26 pubmed..Therefore, this protein, which clearly has a critical role in acid-resistance in E. coli, has been renamed as AriR for regulator of acid resistance influenced by indole. ..
- Ranjith Kumar C, Miller W, Sun J, Xiong J, Santos J, Yarbrough I, et al. Effects of single nucleotide polymorphisms on Toll-like receptor 3 activity and expression in cultured cells. J Biol Chem. 2007;282:17696-705 pubmed..They were also reduced in their ability to act in a dominant negative fashion on the wild type TLR3 allele. These observations suggest that N284I and L412F affect the activities of TLR3 needed for proper signaling. ..
- Gokulan K, Aggarwal A, Shipman L, Besra G, Sacchettini J. Mycobacterium tuberculosis acyl carrier protein synthase adopts two different pH-dependent structural conformations. Acta Crystallogr D Biol Crystallogr. 2011;67:657-69 pubmed publisher..0 than at pH values above 6.5, where the activity drops owing to the change in conformation. The results show that apo-AcpS and AcpS-ADP adopt different conformations depending upon the pH conditions of the crystallization solution. ..
- Razvi A, Scholtz J. A thermodynamic comparison of HPr proteins from extremophilic organisms. Biochemistry. 2006;45:4084-92 pubmed
- Tirloni L, Seixas A, Mulenga A, Vaz I, Termignoni C. A family of serine protease inhibitors (serpins) in the cattle tick Rhipicephalus (Boophilus) microplus. Exp Parasitol. 2014;137:25-34 pubmed publisher..microplus serpins in this study retain the consensus secondary of typical serpins. This descriptive study enlarges the knowledge on the molecular biology of R. microplus, an important tick species. ..
- Holman P, Madeley J, Craig T, Allsopp B, Allsopp M, Petrini K, et al. Antigenic, phenotypic and molecular characterization confirms Babesia odocoilei isolated from three cervids. J Wildl Dis. 2000;36:518-30 pubmed..odocoilei. A phylogenetic tree constructed from SSU rRNA gene sequences shows that B. odocoilei is most closely related to Babesia divergens, both of which branch together in the true babesia clade. ..
- Summer E, Liu M, Gill J, Grant M, Chan Cortes T, Ferguson L, et al. Genomic and functional analyses of Rhodococcus equi phages ReqiPepy6, ReqiPoco6, ReqiPine5, and ReqiDocB7. Appl Environ Microbiol. 2011;77:669-83 pubmed publisher..Application of DocB7 lysates to soils amended with a host strain of R. equi reduced recoverable bacterial CFU, suggesting that phage may be useful in limiting R. equi load in the environment while foals are susceptible to infection. ..
- Waters P, Snowden K, Holman P. A comparison of homologous genes encoding aminopeptidases among bird and human Encephalitozoon hellem isolates and a rabbit E. cuniculi isolate. Parasitol Res. 2004;93:410-8 pubmed..cuniculi glutamyl aminopeptidase. The conservation of this aminopeptidase between species and divergence from mammalian aminopeptidases indicate that this enzyme may be a valid target for drug therapy...
- Devarenne T. The plant cell death suppressor Adi3 interacts with the autophagic protein Atg8h. Biochem Biophys Res Commun. 2011;412:699-703 pubmed publisher..Cosilencing Adi3 with several autophagy genes lead to the same run away cell death suggesting Adi3 may be involved in autophagic regulation of PCD. ..
- Knapp G, Hu J. The oligomerization of CynR in Escherichia coli. Protein Sci. 2009;18:2307-15 pubmed publisher..Oligomerization was assayed by the ability of mutant lambda repressor-CynR fusions to assemble in E. coli revealing interesting similarities and differences between OxyR and CynR...
- Berridge B, Bercovier H, Frelier P. Streptococcus agalactiae and Streptococcus difficile 16S-23S intergenic rDNA: genetic homogeneity and species-specific PCR. Vet Microbiol. 2001;78:165-73 pubmed..The sequence data generated were also used to construct a pair of species-specific PCR primers for use in molecular detection and identification schemes. ..
- Holman P, Carroll J, Pugh R, Davis D. Molecular detection of Babesia bovis and Babesia bigemina in white-tailed deer (Odocoileus virginianus) from Tom Green County in central Texas. Vet Parasitol. 2011;177:298-304 pubmed publisher..Clarification of the possible role of white-tailed deer as reservoir hosts in maintaining these important pathogens of cattle is critical to understanding whether or not deer contribute to the epidemiology of bovine babesiosis...
- Hosking E, Manson M. Clusters of charged residues at the C terminus of MotA and N terminus of MotB are important for function of the Escherichia coli flagellar motor. J Bacteriol. 2008;190:5517-21 pubmed publisher..Charge-altering mutations affecting these residues impair motility but do not diminish Mot protein levels. The motility defects are reversed by second-site mutations targeting the same or partner protein. ..
- Farmer J, Burghardt R, Jousan F, Hansen P, Bazer F, Spencer T. Galectin 15 (LGALS15) functions in trophectoderm migration and attachment. FASEB J. 2008;22:548-60 pubmed publisher..Collectively, these results support the hypothesis that LGALS15 stimulates trophectoderm cell migration and attachment via integrin binding and activation which are critical to blastocyst elongation and implantation...
- Chowdhary B, Raudsepp T, Kata S, Goh G, Millon L, Allan V, et al. The first-generation whole-genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes. Genome Res. 2003;13:742-51 pubmed
- Mulenga A, Blandon M, Khumthong R. The molecular basis of the Amblyomma americanum tick attachment phase. Exp Appl Acarol. 2007;41:267-87 pubmed..Identification of genes in this study provides the framework for future studies to elucidate molecular signaling cascades that regulate early molecular events during the tick attachment phase. ..
- Maldonado Mendoza I, Nessler C. Cloning and expression of a plant homologue of the small subunit of the Golgi-associated clathrin assembly protein AP19 from Camptotheca acuminata. Plant Mol Biol. 1996;32:1149-53 pubmed..DNA blot analysis suggests that the AP19S of C. acuminata are encoded by a small gene family. CAP19 was expressed ubiquitously throughout the plant suggesting that it may be involved in general Golgi-mediated secretion. ..
- Mulenga A, Khumthong R, Chalaire K. Ixodes scapularis tick serine proteinase inhibitor (serpin) gene family; annotation and transcriptional analysis. BMC Genomics. 2009;10:217 pubmed publisher..scapularis. Although the paper is descriptive, this study provides the first step toward a comprehensive understanding of serpins in tick physiology. ..
- Matthee C, Burzlaff J, Taylor J, Davis S. Mining the mammalian genome for artiodactyl systematics. Syst Biol. 2001;50:367-90 pubmed..The nuclear DNA data suggest that the Antilocaprinae account for a unique evolutionary lineage, the Cervidae and Bovidae are sister taxa, and the Giraffidae are more primitive...
- Murphy W, Pearks Wilkerson A, Raudsepp T, Agarwala R, Sch ffer A, Stanyon R, et al. Novel gene acquisition on carnivore Y chromosomes. PLoS Genet. 2006;2:e43 pubmed publisher..Specific plans to identify the male-specific genes encoded in the Y chromosome of mammals should be a priority...
- Myers Payne S, Fontaine R, Loeffler A, Pu L, Rao A, Kier A, et al. Effects of chronic ethanol consumption on sterol transfer proteins in mouse brain. J Neurochem. 1996;66:313-20 pubmed..Changes in the amount of SCP-2 may contribute to membrane tolerance to ethanol. ..
- Sahraeian S, Yoon B. PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach. BMC Bioinformatics. 2011;12 Suppl 1:S38 pubmed publisher..PicXAA-R source code is freely available at: http://www.ece.tamu.edu/~bjyoon/picxaa/. ..
- Giedroc D, Chen X, Apuy J. Metal response element (MRE)-binding transcription factor-1 (MTF-1): structure, function, and regulation. Antioxid Redox Signal. 2001;3:577-96 pubmed..This review summarizes recent progress that has been made toward understanding the structure, function, and metalloregulation of mammalian MTF-1. ..
- Kannan K, Nelson A, Shippen D. Dyskerin is a component of the Arabidopsis telomerase RNP required for telomere maintenance. Mol Cell Biol. 2008;28:2332-41 pubmed publisher..We conclude that dyskerin is a conserved component of the telomerase RNP complex in higher eukaryotes that is required for maximal enzyme activity in vivo. ..
- Seabury C, Derr J. Identification of a novel ovine PrP polymorphism and scrapie-resistant genotypes for St. Croix White and a related composite breed. Cytogenet Genome Res. 2003;102:85-8 pubmed..0123; S.E. = 0.00113). Additionally, the majority of the SCW (66.7%) and CMP (65.4%) sampled possessed genotypes considered resistant or nearly resistant to scrapie and experimental BSE (bovine spongiform encephalopathy. ..
- Wales M, Madison L, Glaser S, Wild J. Divergent allosteric patterns verify the regulatory paradigm for aspartate transcarbamylase. J Mol Biol. 1999;294:1387-400 pubmed..coli, exhibited no response to ATP. The conserved structure and diverged functional characteristics of the E. herbicola enzyme provides an opportunity for a new evaluation of the common paradigm involving allosteric control of ATCase. ..
- Guo J, Rasmussen J, Wunschmann A, de la Concha Bermejillo A. Genetic characterization of orf viruses isolated from various ruminant species of a zoo. Vet Microbiol. 2004;99:81-92 pubmed
- Davis B, Li G, Murphy W. Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivora: Felidae). Mol Phylogenet Evol. 2010;56:64-76 pubmed publisher..These results highlight new avenues for the study of speciation genomics and understanding the historical events surrounding the origin of the members of this lineage...
- Lu D, Wu S, Gao X, Zhang Y, Shan L, He P. A receptor-like cytoplasmic kinase, BIK1, associates with a flagellin receptor complex to initiate plant innate immunity. Proc Natl Acad Sci U S A. 2010;107:496-501 pubmed publisher..Thus, BIK1 is an essential component in MAMP signal transduction, which links the MAMP receptor complex to downstream intracellular signaling. ..
- Holman P, Swift P, Frey R, Bennett J, Cruz D, Wagner G. Genotypically unique Babesia spp. isolated from reindeer (Rangifer tarandus tarandus) in the United States. Parasitol Res. 2002;88:405-11 pubmed..The SSU rRNA gene showed 94.2% identity to that of B. bigemina. Further studies are needed to determine whether these parasites are the same as the Babesia spp. previously documented in Siberian reindeer. ..
- Takahashi T, Yawata M, Raudsepp T, Lear T, Chowdhary B, Antczak D, et al. Natural killer cell receptors in the horse: evidence for the existence of multiple transcribed LY49 genes. Eur J Immunol. 2004;34:773-784 pubmed publisher..We also show that horse spleen expresses ILT-like genes with unique domain organizations. Radiation hybrid mapping and fluorescence in situ hybridization localized horse LY49 and KIR/ILT genes to chromosomes 6q13 and 10p12, respectively...
- Liu T, Golden J, Giedroc D. A zinc(II)/lead(II)/cadmium(II)-inducible operon from the Cyanobacterium anabaena is regulated by AztR, an alpha3N ArsR/SmtB metalloregulator. Biochemistry. 2005;44:8673-83 pubmed
- Shakirov E, Perroud P, Nelson A, Cannell M, Quatrano R, Shippen D. Protection of Telomeres 1 is required for telomere integrity in the moss Physcomitrella patens. Plant Cell. 2010;22:1838-48 pubmed publisher..We conclude that the telomere capping function of POT1 is conserved in early diverging land plants but is subsequently lost in Arabidopsis...
- Kim S, Jones R, Yoo K, Pike L. Gold color in onions (Allium cepa): a natural mutation of the chalcone isomerase gene resulting in a premature stop codon. Mol Genet Genomics. 2004;272:411-9 pubmed..Inactivation of CHI results in a block in the flavonoid biosynthesis pathway and the accumulation of chalcone derivatives, including a yellow pigment which might be responsible for the gold color in onions. ..
- Lu Y, Sze S. Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. Nucleic Acids Res. 2009;37:463-72 pubmed publisher..Unlike previous algorithms, consistent average improvements can be obtained across all identity levels. ..
- Murphy W, Pringle T, Crider T, Springer M, Miller W. Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res. 2007;17:413-21 pubmed..We discuss the impacts of this topology on earlier phylogenetic reconstructions and repeat-based inferences of phylogeny...
- B umler A, Norris T, Lasco T, Voight W, Reissbrodt R, Rabsch W, et al. IroN, a novel outer membrane siderophore receptor characteristic of Salmonella enterica. J Bacteriol. 1998;180:1446-53 pubmed..These results suggest that the iroA locus functions in iron acquisition in S. enterica...