Experts and Doctors on sequence alignment in United States

Summary

Locale: United States
Topic: sequence alignment

Top Publications

  1. Lafreniere R, Carrel L, Willard H. A novel transmembrane transporter encoded by the XPCT gene in Xq13.2. Hum Mol Genet. 1994;3:1133-9 pubmed
    ..Thus, a chromosomal switch in inactivation pattern occurs between these two genes on the X chromosome. ..
  2. Quiram P, Ohno K, Milone M, Patterson M, Pruitt N, Brengman J, et al. Mutation causing congenital myasthenia reveals acetylcholine receptor beta/delta subunit interaction essential for assembly. J Clin Invest. 1999;104:1403-10 pubmed
    ..The findings imply that the mutated residues are positioned at the interface between beta and delta subunits and demonstrate contribution of this local region of the long cytoplasmic loop to AChR assembly...
  3. Ma W, Kaiser M, Lyamicheva N, Schaefer J, Allawi H, Takova T, et al. RNA template-dependent 5' nuclease activity of Thermus aquaticus and Thermus thermophilus DNA polymerases. J Biol Chem. 2000;275:24693-700 pubmed
    ..The application of the enzymes with improved RNA-dependent 5' nuclease activity for RNA detection using the invasive signal amplification assay is discussed. ..
  4. Maslov D, Zíková A, Kyselová I, Lukes J. A putative novel nuclear-encoded subunit of the cytochrome c oxidase complex in trypanosomatids. Mol Biochem Parasitol. 2002;125:113-25 pubmed
    ..brucei and promastigote Leishmania mexicana amazonensis. However, the trCOIV gene, the mRNA and the polypeptide could not be detected in a respiration-deficient trypanosomatid Phytomonas serpens. ..
  5. Palladino M, Bower J, Kreber R, Ganetzky B. Neural dysfunction and neurodegeneration in Drosophila Na+/K+ ATPase alpha subunit mutants. J Neurosci. 2003;23:1276-86 pubmed
    ..Our data show that maintenance of neuronal viability is dependent on normal sodium pump activity and establish Drosophila as a useful model for investigating the role of the pump in human neurodegenerative and seizure disorders. ..
  6. Brigstock D. Regulation of angiogenesis and endothelial cell function by connective tissue growth factor (CTGF) and cysteine-rich 61 (CYR61). Angiogenesis. 2002;5:153-65 pubmed
  7. Wang C, Lefkowitz E. SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters. BMC Bioinformatics. 2004;5:171 pubmed
    ..Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist. ..
  8. Chavatte L, Brown B, Driscoll D. Ribosomal protein L30 is a component of the UGA-selenocysteine recoding machinery in eukaryotes. Nat Struct Mol Biol. 2005;12:408-16 pubmed
    ..We propose a model in which SBP2 and L30 carry out different functions in the UGA recoding mechanism, with the SECIS acting as a molecular switch upon protein binding. ..
  9. Kim J, Fahad A, Shanmukhappa K, Kapil S. Defining the cellular target(s) of porcine reproductive and respiratory syndrome virus blocking monoclonal antibody 7G10. J Virol. 2006;80:689-96 pubmed
    ..These results suggest that vimentin is part of the PRRSV receptor complex and that it plays an important role in PRRSV binding with the other cytoskeletal filaments that mediate transportation of the virus in the cytosol. ..

More Information

Publications618 found, 100 shown here

  1. Grdzelishvili V, Smallwood S, Tower D, Hall R, Hunt D, Moyer S. Identification of a new region in the vesicular stomatitis virus L polymerase protein which is essential for mRNA cap methylation. Virology. 2006;350:394-405 pubmed
    ..J. Virol. 79, 13373-13384], a new region between L amino acids 1450-1481 was identified which is critical for mRNA cap methylation. ..
  2. Porter F, Bochkov Y, Albee A, Wiese C, Palmenberg A. A picornavirus protein interacts with Ran-GTPase and disrupts nucleocytoplasmic transport. Proc Natl Acad Sci U S A. 2006;103:12417-22 pubmed
    ..To our knowledge, L is the first viral picornaviral protein to interact directly with Ran and modulate the Ran-dependent nucleocytoplasmic pathway. ..
  3. Nguyen K, Ritz D, Gu J, Alexander D, Chu M, Miao V, et al. Combinatorial biosynthesis of novel antibiotics related to daptomycin. Proc Natl Acad Sci U S A. 2006;103:17462-7 pubmed
    ..This study established a robust combinatorial biosynthesis platform to produce novel peptide antibiotics in sufficient quantities for antimicrobial screening and drug development. ..
  4. Drevland R, Waheed A, Graham D. Enzymology and evolution of the pyruvate pathway to 2-oxobutyrate in Methanocaldococcus jannaschii. J Bacteriol. 2007;189:4391-400 pubmed publisher
  5. Yu J, Wei M, Boyd Z, Lehmann E, Trotta R, Mao H, et al. Transcriptional control of human T-BET expression: the role of Sp1. Eur J Immunol. 2007;37:2549-61 pubmed
  6. Choi K, Kim S. ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts. BMC Bioinformatics. 2008;9:145 pubmed publisher
    ..ComPath is an interactive workbench for pathway reconstruction, annotation, and analysis where experts can perform various sequence, domain, context analysis, using an intuitive and interactive spreadsheet-style interface. ..
  7. Singh S, Tokhunts R, Baubet V, Goetz J, Huang Z, Schilling N, et al. Sonic hedgehog mutations identified in holoprosencephaly patients can act in a dominant negative manner. Hum Genet. 2009;125:95-103 pubmed publisher
  8. Campbell M, Gottlieb G, Hawes S, Nickle D, Wong K, Deng W, et al. HIV-1 superinfection in the antiretroviral therapy era: are seroconcordant sexual partners at risk?. PLoS ONE. 2009;4:e5690 pubmed publisher
    ..In some cases, HIV-1 superinfection may become apparent when recombinant viral strains are detected. ..
  9. Davie J, Earl J, de Vries S, Ahmed A, Hu F, Bootsma H, et al. Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates. BMC Genomics. 2011;12:70 pubmed publisher
    ..catarrhalis pathogenesis that will aid in the development of novel therapeutic regimens. ..
  10. Aglyamova G, Hunt M, Modi C, Matz M. Multi-colored homologs of the green fluorescent protein from hydromedusa Obelia sp. Photochem Photobiol Sci. 2011;10:1303-9 pubmed publisher
    ..The discovery of Obelia FPs fills the four-decade-old gap in the knowledge of cnidarian bioluminescence and provides experimental material to further investigate the details of its molecular mechanism. ..
  11. Yuan H, Dragnea V, Wu Q, Gardner K, Bauer C. Mutational and structural studies of the PixD BLUF output signal that affects light-regulated interactions with PixE. Biochemistry. 2011;50:6365-75 pubmed publisher
  12. Meyer A, Wilke C. Integrating sequence variation and protein structure to identify sites under selection. Mol Biol Evol. 2013;30:36-44 pubmed publisher
    ..Our method is broadly applicable to any protein sequences for which structural data are available or can be obtained via homology modeling or threading. ..
  13. Hasnain G, Frelin O, Roje S, Ellens K, Ali K, Guan J, et al. Identification and characterization of the missing pyrimidine reductase in the plant riboflavin biosynthesis pathway. Plant Physiol. 2013;161:48-56 pubmed publisher
    ..The role of the COG3236 domain remains mysterious; no evidence was obtained for the possibility that it catalyzes the dephosphorylation that follows pyrimidine reduction. ..
  14. Shaw T, Srivastava A, Chou W, Liu L, Hawkinson A, Glenn T, et al. Transcriptome sequencing and annotation for the Jamaican fruit bat (Artibeus jamaicensis). PLoS ONE. 2012;7:e48472 pubmed publisher
    ..The Jamaican fruit bat transcriptome dataset is a resource that should provide additional candidate markers for studying bat evolution and ecology, and tools for analysis of the host response and pathology of disease. ..
  15. Stevens S, Abelson J. Purification of the yeast U4/U6.U5 small nuclear ribonucleoprotein particle and identification of its proteins. Proc Natl Acad Sci U S A. 1999;96:7226-31 pubmed
  16. Li Q, Suprenant K. Molecular characterization of the 77-kDa echinoderm microtubule-associated protein. Homology to the beta-transducin family. J Biol Chem. 1994;269:31777-84 pubmed
    ..Alternatively, the EMAP may be an important link between signal transduction events and a change in microtubule organization during the cell cycle...
  17. Saksena N, Herv V, Sherman M, Durand J, Mathiot C, M ller M, et al. Sequence and phylogenetic analyses of a new STLV-I from a naturally infected tantalus monkey from Central Africa. Virology. 1993;192:312-20 pubmed
    ..The data also indicate that interspecies transmission occurred several times on different continents over prolonged periods of time...
  18. Moe O, Baker Malcolm J, Wang W, Kang C, Fromm H, Colman R. Involvement of arginine 143 in nucleotide substrate binding at the active site of adenylosuccinate synthetase from Escherichia coli. Biochemistry. 1996;35:9024-33 pubmed
    ..These results indicate that both subunits of dimeric adenylosuccinate synthetase contribute to each active site and that Arg-143 plays an important role in nucleotide binding. ..
  19. Liao Y, Lal A, Moremen K. Cloning, expression, purification, and characterization of the human broad specificity lysosomal acid alpha-mannosidase. J Biol Chem. 1996;271:28348-58 pubmed
    ..L., and Schmidt, M. C. (1994) Biochem. Biophys. Res. Commun. 200, 239-245) and several differences were found relative to the functional lysosomal alpha-mannosidase encoded by the 3-kb spleen cDNA. ..
  20. Lupashin V, Pokrovskaya I, McNew J, Waters M. Characterization of a novel yeast SNARE protein implicated in Golgi retrograde traffic. Mol Biol Cell. 1997;8:2659-76 pubmed
    ..We propose that Vti1p, along with Ykt6p and perhaps Sft1p, acts as a retrograde v-SNARE capable of interacting with the cis-Golgi t-SNARE Sed5p. ..
  21. Voos W, Stevens T. Retrieval of resident late-Golgi membrane proteins from the prevacuolar compartment of Saccharomyces cerevisiae is dependent on the function of Grd19p. J Cell Biol. 1998;140:577-90 pubmed
    ..We conclude that Grd19p is a component of the retrieval machinery that functions by direct interaction with the cytosolic tails of certain TGN membrane proteins during the sorting/budding process at the prevacuolar compartment. ..
  22. Erbeznik M, Strobel H, Dawson K, Jones C. The D-xylose-binding protein, XylF, from Thermoanaerobacter ethanolicus 39E: cloning, molecular analysis, and expression of the structural gene. J Bacteriol. 1998;180:3570-7 pubmed
    ..ethanolicus. This is the first report of a gene encoding a xylose-binding protein in a gram-positive or thermophilic bacterium...
  23. Lee M, Lu K, Hazard S, Yu H, Shulenin S, Hidaka H, et al. Identification of a gene, ABCG5, important in the regulation of dietary cholesterol absorption. Nat Genet. 2001;27:79-83 pubmed
    ..H.L. et al., manuscript submitted). We now report that a new member of the ABC transporter family, ABCG5, is mutant in nine unrelated sitosterolemia patients...
  24. Yang H, Clendenin W, Wong D, Demple B, Slupska M, Chiang J, et al. Enhanced activity of adenine-DNA glycosylase (Myh) by apurinic/apyrimidinic endonuclease (Ape1) in mammalian base excision repair of an A/GO mismatch. Nucleic Acids Res. 2001;29:743-52 pubmed
    ..Consequently, Ape1 preserves the Myh preference for A/GO over A/G and improves overall glycosylase efficiency. Our study suggests that protein-protein interactions may occur in vivo to achieve efficient BER of A/GO. ..
  25. Wang X, Babu J, Harden J, Jablonski S, Gazi M, Lingle W, et al. The mitotic checkpoint protein hBUB3 and the mRNA export factor hRAE1 interact with GLE2p-binding sequence (GLEBS)-containing proteins. J Biol Chem. 2001;276:26559-67 pubmed
    ..Our findings demonstrate that GLEBS motifs reside in mammalian nucleoporins and mitotic checkpoint proteins and apparently serve as specific binding sites for either BUB3, RAE1, or both. ..
  26. Hamilton S, Stapleton D, O Donnell J, Kung J, Dalal S, Kemp B, et al. An activating mutation in the gamma1 subunit of the AMP-activated protein kinase. FEBS Lett. 2001;500:163-8 pubmed
    ..These data illustrate the importance of the gamma1 subunit in the regulation of AMPK and its modulation by AMP. ..
  27. Zou Z, Jiang H. Manduca sexta serpin-6 regulates immune serine proteinases PAP-3 and HP8. cDNA cloning, protein expression, inhibition kinetics, and function elucidation. J Biol Chem. 2005;280:14341-8 pubmed
    ..These results suggest that serpin-6 plays important roles in the regulation of immune proteinases in the hemolymph. ..
  28. Merhige P, Both Kim D, Robida M, Hollingsworth M. RNA-protein complexes that form in the spinach chloroplast atpI 5' untranslated region can be divided into two subcomplexes, each comprised of unique cis-elements and trans-factors. Curr Genet. 2005;48:256-64 pubmed
    ..These data support the hypothesis that there are at least two unique polypeptides involved in these 5'UTR-protein complexes, each binding specifically to a different site within the 5'UTR. ..
  29. Yin H, Laguna K, Li G, Kuret J. Dysbindin structural homologue CK1BP is an isoform-selective binding partner of human casein kinase-1. Biochemistry. 2006;45:5297-308 pubmed
    ..These data suggest that the acidic domain of dysbindin and its paralogs in humans may function to recruit casein kinase-1 isoforms to protein complexes involved in multiple biological functions. ..
  30. Giles T, Graham D. Characterization of an acid-dependent arginine decarboxylase enzyme from Chlamydophila pneumoniae. J Bacteriol. 2007;189:7376-83 pubmed
    ..These genes are the first evidence that obligately intracellular chlamydiae may encounter acidic conditions. Alternatively, this system could reduce the host cell arginine concentration and produce inhibitors of nitric oxide synthase. ..
  31. Mattiacio J, Read L. Evidence for a degradosome-like complex in the mitochondria of Trypanosoma brucei. FEBS Lett. 2009;583:2333-8 pubmed publisher
    ..This is the first report of a mitochondrial degradosome-like complex outside of yeast. Our data indicate an early evolutionary origin for the mitochondrial SUV3/DSS-1 containing complex. ..
  32. Rha G, Wu G, Shoelson S, Chi Y. Multiple binding modes between HNF4alpha and the LXXLL motifs of PGC-1alpha lead to full activation. J Biol Chem. 2009;284:35165-76 pubmed publisher
  33. Siler C, Diesmos A, Alcala A, Brown R. Phylogeny of Philippine slender skinks (Scincidae: Brachymeles) reveals underestimated species diversity, complex biogeographical relationships, and cryptic patterns of lineage diversification. Mol Phylogenet Evol. 2011;59:53-65 pubmed publisher
  34. Ruffalo M, LaFramboise T, Koyutürk M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics. 2011;27:2790-6 pubmed publisher
    ..g. identification of genomic variants). Seal is available as open source at http://compbio.case.edu/seal/. matthew.ruffalo@case.edu Supplementary data are available at Bioinformatics online. ..
  35. Siler C, Brown R. Evidence for repeated acquisition and loss of complex body-form characters in an insular clade of Southeast Asian semi-fossorial skinks. Evolution. 2011;65:2641-63 pubmed publisher
    ..The results of our study join a nascent body of literature showing strong statistical support for character loss, followed by evolutionary re-acquisition of complex structures associated with a generalized pentadactyl body form. ..
  36. Amunugama R, He Y, Willcox S, Forties R, Shim K, Bundschuh R, et al. RAD51 protein ATP cap regulates nucleoprotein filament stability. J Biol Chem. 2012;287:8724-36 pubmed publisher
    ..These studies suggest that the HsRAD51(Asp-316) salt bridge may function as a conformational sensor that enhances turnover at the expense of recombinase activity...
  37. Pesci E, Pickett C. Genetic organization and enzymatic activity of a superoxide dismutase from the microaerophilic human pathogen, Helicobacter pylori. Gene. 1994;143:111-6 pubmed
    ..Assays for SOD activities, accompanied by inhibition studies, demonstrated that Hp produces an FeSOD. No other SOD activities were seen...
  38. Semrau J, Chistoserdov A, Lebron J, Costello A, Davagnino J, Kenna E, et al. Particulate methane monooxygenase genes in methanotrophs. J Bacteriol. 1995;177:3071-9 pubmed
    ..These results suggest that the 45- and 27-kDa pMMO-associated polypeptides of methanotrophs are subunits of the pMMO and are present in duplicate gene copies in methanotrophs. ..
  39. Pappan K, Qin W, Dyer J, Zheng L, Wang X. Molecular cloning and functional analysis of polyphosphoinositide-dependent phospholipase D, PLDbeta, from Arabidopsis. J Biol Chem. 1997;272:7055-61 pubmed
  40. Gonzalez D, Karaveg K, Vandersall Nairn A, Lal A, Moremen K. Identification, expression, and characterization of a cDNA encoding human endoplasmic reticulum mannosidase I, the enzyme that catalyzes the first mannose trimming step in mammalian Asn-linked oligosaccharide biosynthesis. J Biol Chem. 1999;274:21375-86 pubmed
    ..Enzyme reactions using a combination of human ER mannosidase I and recombinant Golgi mannosidase IA indicated that that these two enzymes are complementary in their cleavage of Man(9)GlcNAc(2) oligosaccharides to Man(5)GlcNAc(2). ..
  41. Ramamurthy V, Swann S, Paulson J, Spedaliere C, Mueller E. Critical aspartic acid residues in pseudouridine synthases. J Biol Chem. 1999;274:22225-30 pubmed
  42. Emmenegger E, Meyers T, Burton T, Kurath G. Genetic diversity and epidemiology of infectious hematopoietic necrosis virus in Alaska. Dis Aquat Organ. 2000;40:163-76 pubmed
    ..This information could be used to determine the source of an IHN outbreak and to facilitate decisions in fisheries management of Alaskan salmonid stocks. ..
  43. Keeler S, Boettger C, Haynes J, Kuches K, Johnson M, Thureen D, et al. Acquired thermotolerance and expression of the HSP100/ClpB genes of lima bean. Plant Physiol. 2000;123:1121-32 pubmed
  44. von Bülow G, Russell H, Copeland N, Gilbert D, Jenkins N, Bram R. Molecular cloning and functional characterization of murine transmembrane activator and CAML interactor (TACI) with chromosomal localization in human and mouse. Mamm Genome. 2000;11:628-32 pubmed
    ..This work identifies conserved domains within TACI that may mediate the cellular distribution and signal transduction function of the protein and extend the details of homology between mouse Chr 11 and human 17p. ..
  45. Halleck M, Lawler JF J, Blackshaw S, Gao L, Nagarajan P, Hacker C, et al. Differential expression of putative transbilayer amphipath transporters. Physiol Genomics. 1999;1:139-50 pubmed
    ..These results suggest that the genes are expressed in a tissue-specific manner, are not simply redundant, and may represent isoforms that transport a variety of different amphipaths...
  46. King N, O Brian M. Evidence for direct interaction between enzyme I(Ntr) and aspartokinase to regulate bacterial oligopeptide transport. J Biol Chem. 2001;276:21311-6 pubmed publisher
    ..The findings demonstrate a role for a PTS protein in the transport of a non-sugar solute and suggest an unusual regulatory function for aspartokinase in regulating the phosphorylation state of EI(Ntr)...
  47. Liu G, Zhao S, Bailey J, Sahinalp S, Alkan C, Tuzun E, et al. Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Res. 2003;13:358-68 pubmed
    ..Assuming that the primate genome sequence we have sampled is representative, we estimate that human euchromatin has expanded 30 Mb and 550 Mb compared to the primate genomes of chimpanzee and lemur, respectively...
  48. Ersahin C, Szpaderska A, Simmons W. Rat and mouse membrane aminopeptidase P: structure analysis and tissue distribution. Arch Biochem Biophys. 2003;417:131-40 pubmed
    ..The tissue-specific expression of mAPP was studied using the polymerase chain reaction. The mAPP gene is widely, but variably, expressed in adult tissues of the rat and mouse and in mouse embryos. ..
  49. Singh D, Griffin D, Pacyniak E, Jackson M, Werle M, Wisdom B, et al. The presence of the casein kinase II phosphorylation sites of Vpu enhances the CD4(+) T cell loss caused by the simian-human immunodeficiency virus SHIV(KU-lbMC33) in pig-tailed macaques. Virology. 2003;313:435-51 pubmed
  50. Tilmann C, Kimble J. Cyclin D regulation of a sexually dimorphic asymmetric cell division. Dev Cell. 2005;9:489-99 pubmed
    ..We propose that cyclin D and other canonical regulators of the G1/S transition coordinate key regulators of axis formation and sex determination with cell cycle progression to achieve the sexually dimorphic SGP asymmetric division. ..
  51. Subramanya A, Yang C, Zhu X, Ellison D. Dominant-negative regulation of WNK1 by its kidney-specific kinase-defective isoform. Am J Physiol Renal Physiol. 2006;290:F619-24 pubmed
    ..These observations suggest that KS-WNK1 plays an essential role in the renal molecular switch regulating Na+ and K+ balance; they provide insight into the kidney-specific phenotype of FHHt. ..
  52. Crisp M, Liu Q, Roux K, Rattner J, Shanahan C, Burke B, et al. Coupling of the nucleus and cytoplasm: role of the LINC complex. J Cell Biol. 2006;172:41-53 pubmed
    ..2005), support a model in which Sun proteins tether nesprins in the ONM via interactions spanning the PNS. In this way, Sun proteins and nesprins form a complex that links the nucleoskeleton and cytoskeleton (the LINC complex). ..
  53. Zhang H, Zhou Y, Bao H, Liu H. Vi antigen biosynthesis in Salmonella typhi: characterization of UDP-N-acetylglucosamine C-6 dehydrogenase (TviB) and UDP-N-acetylglucosaminuronic acid C-4 epimerase (TviC). Biochemistry. 2006;45:8163-73 pubmed publisher
    ..These results set the stage for future in vitro biosynthesis of Vi antigen. These enzymes may also be drug targets to inhibit Vi antigen production...
  54. Cox M, Layton S, Jiang T, Cole K, Hargis B, Berghman L, et al. Scarless and site-directed mutagenesis in Salmonella enteritidis chromosome. BMC Biotechnol. 2007;7:59 pubmed
    ..Furthermore, this method should be applicable in other gram-negative bacterial species where Red recombinase enzymes can be functionally expressed. ..
  55. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics. 2008;9:40 pubmed publisher
    ..The I-TASSER server is freely available to the academic community at http://zhang.bioinformatics.ku.edu/I-TASSER. ..
  56. Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher M. PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes. BMC Bioinformatics. 2008;9:170 pubmed publisher
    ..Access to the public web server and instructions for obtaining source code can be found at http://www.nwrce.org/psat. ..
  57. Aikins M, Schooley D, Begum K, Detheux M, Beeman R, Park Y. Vasopressin-like peptide and its receptor function in an indirect diuretic signaling pathway in the red flour beetle. Insect Biochem Mol Biol. 2008;38:740-8 pubmed publisher
  58. Stombaugh J, Zirbel C, Westhof E, Leontis N. Frequency and isostericity of RNA base pairs. Nucleic Acids Res. 2009;37:2294-312 pubmed publisher
    ..In order to improve the statistics from the 3D structures, we also derive base pair occurrence frequencies from rRNA sequence alignments. ..
  59. Doyle M, Amasino R. A single amino acid change in the enhancer of zeste ortholog CURLY LEAF results in vernalization-independent, rapid flowering in Arabidopsis. Plant Physiol. 2009;151:1688-97 pubmed publisher
    ..Furthermore, FRI appears to affect CLF occupancy at FLC; thus, our work provides insight into the molecular role that FRI plays in delaying the onset of flowering. ..
  60. Meredith R, Pires M, Reznick D, Springer M. Molecular phylogenetic relationships and the coevolution of placentotrophy and superfetation in Poecilia (Poeciliidae: Cyprinodontiformes). Mol Phylogenet Evol. 2011;59:148-57 pubmed publisher
    ..Within P. (Pamphorichthys), superfetation evolved in ?9 million years on the P. (Pamphorichthys) hasemani branch, and placentotrophy evolved in ?10 million years in the common ancestor of this subgenus. ..
  61. Eletsky A, Ruyechan W, Xiao R, Acton T, Montelione G, Szyperski T. Solution NMR structure of MED25(391-543) comprising the activator-interacting domain (ACID) of human mediator subunit 25. J Struct Funct Genomics. 2011;12:159-66 pubmed publisher
  62. Nie S, Kee Y, Bronner Fraser M. Caldesmon regulates actin dynamics to influence cranial neural crest migration in Xenopus. Mol Biol Cell. 2011;22:3355-65 pubmed publisher
    ..Taken together, these results suggest that the actin-modulating activity of CaD may underlie its critical function and is regulated by distinct signaling pathways during normal neural crest migration...
  63. Sousa D, Stagg S, Stroupe M. Cryo-EM structures of the actin:tropomyosin filament reveal the mechanism for the transition from C- to M-state. J Mol Biol. 2013;425:4544-55 pubmed publisher
  64. Lefurgy S, Malashkevich V, Aguilan J, Nieves E, Mundorff E, Biju B, et al. Analysis of the Structure and Function of FOX-4 Cephamycinase. Antimicrob Agents Chemother. 2016;60:717-28 pubmed publisher
  65. Opperman T, Richardson J. Phylogenetic analysis of sequences from diverse bacteria with homology to the Escherichia coli rho gene. J Bacteriol. 1994;176:5033-43 pubmed
    ..Since functionally defective mutants for E. coli Rho exist in all three of these segments, they represent important parts of Rho that have undergone adaptive evolution...
  66. Stewart M, Denell R. Mutations in the Drosophila gene encoding ribosomal protein S6 cause tissue overgrowth. Mol Cell Biol. 1993;13:2524-35 pubmed
    ..Surprisingly, these mutations are due to P element insertions in the 5' regulatory region of the Drosophila gene encoding ribosomal protein S6 and cause a reduction of S6 transcript abundance in mutant larvae. ..
  67. Kopan R, Weintraub H. Mouse notch: expression in hair follicles correlates with cell fate determination. J Cell Biol. 1993;121:631-41 pubmed
    ..This is a novel finding and suggests that mNotch is important for follicular differentiation and possibly cell fate selection within the follicle. ..
  68. Martinez P, Davidson E. SpHmx, a sea urchin homeobox gene expressed in embryonic pigment cells. Dev Biol. 1997;181:213-22 pubmed
    ..This more general expression resolves to a dramatic pigment cell-specific pattern in prism and pluteus stages. SpHmx apparently encodes a cell-type-specific transcription factor of embryonic pigment cells. ..
  69. Korte J, Salo W, Cabrera V, Wright P, Felskie A, Anderson P. Expression of carbamoyl-phosphate synthetase III mRNA during the early stages of development and in muscle of adult rainbow trout (Oncorhynchus mykiss). J Biol Chem. 1997;272:6270-7 pubmed
    ..The pyrimidine nucleotide pathway-related CPSase II mRNA was expressed in all tissues...
  70. King G, Shih Y, Maciejewski M, Bains N, Pan B, Rowland S, et al. Structural basis for the topological specificity function of MinE. Nat Struct Biol. 2000;7:1013-7 pubmed publisher
    ..Structure-directed mutagenesis of conserved surface residues has enabled us to identify a spatially restricted site on the surface of the protein that is critical for the topological specificity function of MinE...
  71. Capehart A, Kern C. Identification of gammaA-like protocadherin expressed during chick development. J Cell Biochem. 2003;90:608-18 pubmed
    ..As for protocadherins described in other species, these results suggest that this novel gammaA-like protocadherin may also play a role in chick neural development. ..
  72. Liang P, Jones C, Bisgrove B, Song L, Glenn S, Yost H, et al. Genomic characterization and expression analysis of the first nonmammalian renin genes from zebrafish and pufferfish. Physiol Genomics. 2004;16:314-22 pubmed publisher
  73. Park H, Suquet C, Satterlee J, Kang C. Insights into signal transduction involving PAS domain oxygen-sensing heme proteins from the X-ray crystal structure of Escherichia coli Dos heme domain (Ec DosH). Biochemistry. 2004;43:2738-46 pubmed
    ..These changes provide insight to the mechanism of signal propagation within the heme domain following initiation due to O(2) dissociation. ..
  74. De La Fuente J, Passos L, Van Den Bussche R, Ribeiro M, Facury Filho E, Kocan K. Genetic diversity and molecular phylogeny of Anaplasma marginale isolates from Minas Gerais, Brazil. Vet Parasitol. 2004;121:307-16 pubmed
    ..marginale isolates, while MSP1a was found not to be a useful marker for phylogeographic characterization of A. marginale isolates. ..
  75. Jiang D, Ghabrial S. Molecular characterization of Penicillium chrysogenum virus: reconsideration of the taxonomy of the genus Chrysovirus. J Gen Virol. 2004;85:2111-21 pubmed publisher
    ..This study represents the first report on molecular characterization of a chrysovirus and the results suggest the creation of a new family of mycoviruses with multipartite dsRNA genomes to accommodate PcV and related viruses...
  76. Bundschuh R. Computational prediction of RNA editing sites. Bioinformatics. 2004;20:3214-20 pubmed
    ..Nevertheless, knowledge of these editing sites is crucial for understanding the editing machinery of these organisms...
  77. Raychaudhuri A, Jerga A, Tipton P. Chemical mechanism and substrate specificity of RhlI, an acylhomoserine lactone synthase from Pseudomonas aeruginosa. Biochemistry. 2005;44:2974-81 pubmed
  78. Held P, Olivares E, Aguilar C, Finegold M, Calos M, Grompe M. In vivo correction of murine hereditary tyrosinemia type I by phiC31 integrase-mediated gene delivery. Mol Ther. 2005;11:399-408 pubmed
    ..The stability of transgene expression, relatively high integration frequency, and significant site specificity that characterize the phiC31 integration system suggest that it may have utility in many gene therapy settings...
  79. Neff A, King M, Harty M, Nguyen T, Calley J, Smith R, et al. Expression of Xenopus XlSALL4 during limb development and regeneration. Dev Dyn. 2005;233:356-67 pubmed
    ..We show for the first time that a SAL family member (XlSALL4) is expressed at the right place and time to play a role regulating both digit identity along the anterior/posterior axis and epimorphic limb regeneration. ..
  80. Wang Y, Zou Z, Jiang H. An expansion of the dual clip-domain serine proteinase family in Manduca sexta: gene organization, expression, and evolution of prophenoloxidase-activating proteinase-2, hemolymph proteinase 12, and other related proteinases. Genomics. 2006;87:399-409 pubmed
    ..Comparison with HP15, HP23, and PAP-3 sequences suggested an evolutionary pathway of the dual clip-domain serine proteinases in M. sexta. ..
  81. Herdendorf T, Miziorko H. Phosphomevalonate kinase: functional investigation of the recombinant human enzyme. Biochemistry. 2006;45:3235-42 pubmed
  82. Jacobson M, Lin G, Raphael B, Andreadis J, Johnson E. Analysis of neurotoxin cluster genes in Clostridium botulinum strains producing botulinum neurotoxin serotype A subtypes. Appl Environ Microbiol. 2008;74:2778-86 pubmed publisher
    ..The degree of similarity of the sequences of the ntnh genes and corresponding amino acid sequences correlated with the neurotoxin cluster type to which the ntnh gene was assigned...
  83. McBride K, Riley M, Zender G, Fitzgerald Butt S, Towbin J, Belmont J, et al. NOTCH1 mutations in individuals with left ventricular outflow tract malformations reduce ligand-induced signaling. Hum Mol Genet. 2008;17:2886-93 pubmed publisher
    ..These results also establish for the first time that AVS, COA and HLHS can share a common pathogenetic mechanism at the molecular level, explaining observations of these defects co-occurring within families. ..
  84. Patel V, Wang J, Setia S, Verma A, Warden C, Zhang K. On comparing two structured RNA multiple alignments. J Bioinform Comput Biol. 2010;8:967-80 pubmed
    ..The BlockMatch algorithm is implemented into a web server, accessible at http://bioinformatics.njit.edu/blockmatch. A jar file of the program is also available for download from the web server. ..
  85. Cady K, O Toole G. Non-identity-mediated CRISPR-bacteriophage interaction mediated via the Csy and Cas3 proteins. J Bacteriol. 2011;193:3433-45 pubmed publisher
    ..This work demonstrates how the interaction between P. aeruginosa strain UCBPP-PA14 and bacteriophage DMS3 can be used to further our understanding of the diverse roles of CRISPR system function in bacteria...
  86. Janosi L, Keer H, Cogdell R, Ritz T, Kosztin I. In silico predictions of LH2 ring sizes from the crystal structure of a single subunit using molecular dynamics simulations. Proteins. 2011;79:2306-15 pubmed publisher
    ..One finds that X and ACI very likely form a 9-ring, while MOLI is more likely to form an 8-ring than a 9-ring. Finally, we discuss both the merits and limitations of all three prediction methods. ..
  87. Wang Z, Cao R, Cheng J. Three-level prediction of protein function by combining profile-sequence search, profile-profile search, and domain co-occurrence networks. BMC Bioinformatics. 2013;14 Suppl 3:S3 pubmed publisher
  88. Kitaoka S, Morielli A, Zhao F. FGT-1 is a mammalian GLUT2-like facilitative glucose transporter in Caenorhabditis elegans whose malfunction induces fat accumulation in intestinal cells. PLoS ONE. 2013;8:e68475 pubmed publisher
    ..Our results indicated that in C. elegans, FGT-1 is mainly a mammalian GLUT2-like intestinal glucose transporter and is involved in lipid metabolism...
  89. Patel King R, Gilberti R, Hom E, King S. WD60/FAP163 is a dynein intermediate chain required for retrograde intraflagellar transport in cilia. Mol Biol Cell. 2013;24:2668-77 pubmed publisher
    ..The few remaining approximately full-length cilia had a chaotic beat with a frequency reduced from 24 to ?10 Hz. Thus WD60/FAP163 is a dynein IC that is absolutely required for retrograde IFT and ciliary assembly...
  90. Chai K, Chao J, Chao L. Molecular cloning and sequence analysis of the mouse kallikrein-binding protein gene. Biochim Biophys Acta. 1991;1129:127-30 pubmed
    ..The MKBP gene encodes a prepeptide of 417 amino acid residues which exhibits 71% homology with RKBP. A TATA box sequence was located in the 5' flanking region of the MKBP gene by similarity with the consensus sequence TATAAAA. ..
  91. D Souza I, Schellenberg G. Determinants of 4-repeat tau expression. Coordination between enhancing and inhibitory splicing sequences for exon 10 inclusion. J Biol Chem. 2000;275:17700-9 pubmed
    ..Thus splicing of tau E10 is regulated by a complex set of cis-acting elements that span nearly the entire exon and also include intronic sequences. ..
  92. Maurer J, Elmore D, Lester H, Dougherty D. Comparing and contrasting Escherichia coli and Mycobacterium tuberculosis mechanosensitive channels (MscL). New gain of function mutations in the loop region. J Biol Chem. 2000;275:22238-44 pubmed
    ..coli MscL by sequence alignment. Taken together, these results indicate that caution should be exercised in using the M. tuberculosis MscL crystal structure to analyze previous functional studies of E. coli MscL. ..