Experts and Doctors on molecular sequence data in Corvallis, Oregon, United States

Summary

Locale: Corvallis, Oregon, United States
Topic: molecular sequence data

Top Publications

  1. Tsai C, Dreher T. Second-site suppressor mutations assist in studying the function of the 3' noncoding region of turnip yellow mosaic virus RNA. J Virol. 1992;66:5190-9 pubmed
    ..The A + 92 mutation enhanced the replication of mutant TYMC-G96 in protoplasts but was not a sufficiently potent suppressor to permit systemic spread of the A + 92/G-96 double mutant in plants. ..
  2. Gutenberger S, Giovannoni S, Field K, Fryer J, Rohovec J. A phylogenetic comparison of the 16S rRNA sequence of the fish pathogen, Renibacterium salmoninarum, to gram-positive bacteria. FEMS Microbiol Lett. 1991;61:151-6 pubmed
    ..A phylogenetic tree details the relationship of R. salmoninarum to ten actinomycetes from diverse environments...
  3. Parks T, Howard E, Wolpert T, Arp D, Dougherty W. Expression and purification of a recombinant tobacco etch virus NIa proteinase: biochemical analyses of the full-length and a naturally occurring truncated proteinase form. Virology. 1995;210:194-201 pubmed
    ..The truncated proteinase was approximately one-twentieth as efficient in proteolysis of the test peptide substrate as the full-length form. ..
  4. Hommes N, Sayavedra Soto L, Arp D. Mutagenesis and expression of amo, which codes for ammonia monooxygenase in Nitrosomonas europaea. J Bacteriol. 1998;180:3353-9 pubmed
    ..Northern blot analysis of transcription likewise showed that the slower-growing mutant had less full-sized AMO mRNA...
  5. Moerdyk Schauwecker M, Stein D, Eide K, Blouch R, Bildfell R, Iversen P, et al. Inhibition of HSV-1 ocular infection with morpholino oligomers targeting ICP0 and ICP27. Antiviral Res. 2009;84:131-41 pubmed publisher
    ..5-50% compared to controls. This study demonstrates that topically applied PPMO holds promise as an antiviral drug candidate against HSV-1 ocular infection...
  6. Quito Avila D, Jelkmann W, Tzanetakis I, Keller K, Martin R. Complete sequence and genetic characterization of Raspberry latent virus, a novel member of the family Reoviridae. Virus Res. 2011;155:397-405 pubmed publisher
    ..In addition, two nucleotide binding motifs, regarded as 'signature' sequences among turreted reoviruses, were also found in RpLV P8, suggesting that RpLV is a novel dicot-infecting reovirus in the subfamily Spinareovirinae...
  7. Cuesta Marcos A, Szucs P, Close T, Filichkin T, Muehlbauer G, Smith K, et al. Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure. BMC Genomics. 2010;11:707 pubmed publisher
    ..This provided sets of 247 accessions phenotyped for growth habit and 2,473 accessions phenotyped for inflorescence type. Each of the larger populations was genotyped with 3,072 SNPs derived from the original set of 4,608...
  8. Cooley R, Arp D, Karplus P. Symerythrin structures at atomic resolution and the origins of rubrerythrins and the ferritin-like superfamily. J Mol Biol. 2011;413:177-94 pubmed publisher
  9. Aagesen A, HASE C. Sequence analyses of type IV pili from Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus. Microb Ecol. 2012;64:509-24 pubmed publisher
    ..cholerae. Although the mechanism underlying this intriguing diversity has yet to be elucidated, our analyses are an important first step towards gaining insights into the various aspects of Vibrio ecology. ..

More Information

Publications102 found, 100 shown here

  1. Xu J, Bently J, Beck L, Reed A, Miller Morgan T, Heidel J, et al. Analysis of koi herpesvirus latency in wild common carp and ornamental koi in Oregon, USA. J Virol Methods. 2013;187:372-9 pubmed publisher
  2. White C, Rivin C. Sequence and regulation of a late embryogenesis abundant group 3 protein of maize. Plant Physiol. 1995;108:1337-8 pubmed
  3. Gu Q, Beilstein M, Vendeland S, Lugade A, Ream W, Whanger P. Conserved features of selenocysteine insertion sequence (SECIS) elements in selenoprotein W cDNAs from five species. Gene. 1997;193:187-96 pubmed
    ..The selenoprotein W SECIS elements contained an additional highly conserved base-paired stem that may prevent inappropriate selenocysteine incorporation at the UGA stop codons. ..
  4. Connon S, Tovanabootr A, Dolan M, Vergin K, Giovannoni S, Semprini L. Bacterial community composition determined by culture-independent and -dependent methods during propane-stimulated bioremediation in trichloroethene-contaminated groundwater. Environ Microbiol. 2005;7:165-78 pubmed
    ..The dominant cultures from the air-sparged groundwater were from a novel beta-Proteobacterial clade, which we named after isolate HTCC333...
  5. Tzanetakis I, Price R, Martin R. Nucleotide sequence of the tripartite Fragaria chiloensis cryptic virus and presence of the virus in the Americas. Virus Genes. 2008;36:267-72 pubmed publisher
    ..More than 300 strawberry plants from North and South America were tested for FCCV, and the virus was only detected in plants from South America...
  6. Knaus B, Cronn R, Liston A, Pilgrim K, Schwartz M. Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore. BMC Ecol. 2011;11:10 pubmed publisher
    ..This message is timely because it highlights the new opportunities for basing conservation decisions on more accurate genetic information...
  7. Hasegawa H, HASE C. TetR-type transcriptional regulator VtpR functions as a global regulator in Vibrio tubiashii. Appl Environ Microbiol. 2009;75:7602-9 pubmed publisher
    ..Together, these findings establish that the V. tubiashii VtpR protein functions as a global regulator controlling an array of potential virulence factors. ..
  8. Bozarth C, Schwartz A, Shepardson J, Colwell F, Dreher T. Population turnover in a Microcystis bloom results in predominantly nontoxigenic variants late in the season. Appl Environ Microbiol. 2010;76:5207-13 pubmed publisher
    ..Toxicity (amount of microcystin per cell) and toxigenic potential (mcyB copy number) were lower during the second peak, and the mcyB copy number fell further as the bloom declined...
  9. Martinez Andujar C, Pluskota W, Bassel G, Asahina M, Pupel P, Nguyen T, et al. Mechanisms of hormonal regulation of endosperm cap-specific gene expression in tomato seeds. Plant J. 2012;71:575-86 pubmed publisher
    ..We propose that endosperm cap activation is caused by the ethylene response of this tissue, as a consequence of mechanosensing of the increase in embryonic growth potential by GA action. ..
  10. Weisz P, Solem M, Barnes D. Expression of a TGF beta regulated, brain-specific mRNA in serum-free mouse embryo (SFME) cells. Neurosci Lett. 1993;154:153-6 pubmed
    ..This mRNA was detected only in RNA preparations from brain among a number of tissues examined, and may provide an additional marker of TGF beta-regulated differentiation in these cells. ..
  11. Sayavedra Soto L, Arp D. In Azotobacter vinelandii hydrogenase, substitution of serine for the cysteine residues at positions 62, 65, 294, and 297 in the small (HoxK) subunit affects H2 oxidation [corrected]. J Bacteriol. 1993;175:3414-21 pubmed
    ..Mutation of the codons for Cys-294 and Cys-297 to Ser codons resulted in no hydrogenase activity. The results are consistent with alterations of the ligands of FeS clusters in the HoxK subunit of hydrogenase [corrected]. ..
  12. Nebenfuhr A, White T, Lomax T. The diageotropica mutation alters auxin induction of a subset of the Aux/IAA gene family in tomato. Plant Mol Biol. 2000;44:73-84 pubmed
    ..These results confirm that dgt plants can perceive auxin and suggest that a specific step in early auxin signal transduction is disrupted by the dgt mutation. ..
  13. Horton T, Molina R, Hood K. Douglas-fir ectomycorrhizae in 40- and 400-year-old stands: mycobiont availability to late successional western hemlock. Mycorrhiza. 2005;15:393-403 pubmed
    ..The trends revealed in this study corroborate earlier studies suggesting a predominance of multiple host fungi in mixed communities of EM plants. The role of host-specific fungi in these stands remains unclear...
  14. Tennessen J, Blouin M. Selection for antimicrobial peptide diversity in frogs leads to gene duplication and low allelic variation. J Mol Evol. 2007;65:605-15 pubmed
    ..Our data also support a pattern of enhanced synonymous site substitution in the mature peptide region of the gene, but we cannot conclude that this is due to an elevated mutation rate...
  15. Chung W, Miranda C, Stevens J, Maier C. Hop proanthocyanidins induce apoptosis, protein carbonylation, and cytoskeleton disorganization in human colorectal adenocarcinoma cells via reactive oxygen species. Food Chem Toxicol. 2009;47:827-36 pubmed publisher
    ..These findings suggest new modes of action for proanthocyandins as anticarcinogenic agents in human colon cancer cells, namely, promotion of protein oxidative modifications and cytoskeleton derangement. ..
  16. Tzanetakis I, Mackey I, Martin R. Strawberry necrotic shock virus is a distinct virus and not a strain of Tobacco streak virus. Arch Virol. 2004;149:2001-11 pubmed
    ..The CP genes of the 15 Fragaria and Rubus isolates that we studied form two distinct phylogenetic clusters that share about 95% amino acid sequence identity, while they only share 60-65% amino acid sequence identity with TSV-WC...
  17. Paredes Sabja D, Sarker N, Sarker M. Clostridium perfringens tpeL is expressed during sporulation. Microb Pathog. 2011;51:384-8 pubmed publisher
    ..In summary, these results indicate that TpeL is a sporulation-regulated C. perfringens toxin...
  18. Pang Q, Hays J, Rajagopal I. Two cDNAs from the plant Arabidopsis thaliana that partially restore recombination proficiency and DNA-damage resistance to E. coli mutants lacking recombination-intermediate-resolution activities. Nucleic Acids Res. 1993;21:1647-53 pubmed
    ..Both appear chloroplast targeted; Drt112 is highly homologous to Arabidopsis plastocyanin. DRT111 and DRT112 probes hybridize only to DNA from closely related plants. ..
  19. Gerwick L, Reynolds W, Bayne C. A precerebellin-like protein is part of the acute phase response in rainbow trout, Oncorhynchus mykiss. Dev Comp Immunol. 2000;24:597-607 pubmed
    ..However, it lacks the collagen portion of C1q with its characteristic Gly-X-Y repeats. The isolated protein seems to be involved in the inflammatory response but its physiological function is unknown. ..
  20. Tzanetakis I, Halgren A, Mosier N, Martin R. Identification and characterization of Raspberry mottle virus, a novel member of the Closteroviridae. Virus Res. 2007;127:26-33 pubmed
    ..The virus was detected in symptomatic raspberry plants in production areas in mixed infections with several other viruses, indicating that RMoV may impact raspberry production. ..
  21. Wei X, Sayavedra Soto L, Arp D. Characterization of the ferrioxamine uptake system of Nitrosomonas europaea. Microbiology. 2007;153:3963-72 pubmed
    ..For efficient acquisition of Fe-loaded ferrioxamine, N. europaea needs both ferrioxamine transporters FoxA(1) and FoxA(2). FoxA(1) probably regulates its own production, and it controls the production of FoxA(2) as well...
  22. Bartholomew J, Atkinson S, Hallett S, Lowenstine L, Garner M, Gardiner C, et al. Myxozoan parasitism in waterfowl. Int J Parasitol. 2008;38:1199-207 pubmed publisher
  23. Yoshinari S, Nagy P, Simon A, Dreher T. CCA initiation boxes without unique promoter elements support in vitro transcription by three viral RNA-dependent RNA polymerases. RNA. 2000;6:698-707 pubmed
    ..A framework is presented arguing that replication of viral RNA in the absence of unique promoter elements is feasible...
  24. Cho J, Giovannoni S. Croceibacter atlanticus gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae. Syst Appl Microbiol. 2003;26:76-83 pubmed
    ..Therefore, it is proposed from the polyphasic studies that strain HTCC2559T (=ATCC BAA-628T = KCTC 12090T) belongs to a new genus and species named Croceibacter atlanticus gen. nov., sp. nov...
  25. Vergin K, Tripp H, Wilhelm L, Denver D, Rappé M, Giovannoni S. High intraspecific recombination rate in a native population of Candidatus pelagibacter ubique (SAR11). Environ Microbiol. 2007;9:2430-40 pubmed
    ..The eukaryotic model of species sharing a common pool of alleles is more apt for this SAR11 population than a strictly clonal model of inheritance in which allelic diversity is controlled by periodic selection. ..
  26. Schepetilnikov M, Solovyev A, Gorshkova E, Schiemann J, Prokhnevsky A, Dolja V, et al. Intracellular targeting of a hordeiviral membrane-spanning movement protein: sequence requirements and involvement of an unconventional mechanism. J Virol. 2008;82:1284-93 pubmed
    ..The determinants of targeting to plasmodesmata were localized to the C-terminal region of TGBp3, including the conserved hydrophilic and terminal membrane-spanning domains...
  27. Tamin A, Villarreal E, Weinrich S, Hruby D. Nucleotide sequence and molecular genetic analysis of the vaccinia virus HindIII N/M region encoding the genes responsible for resistance to alpha-amanitin. Virology. 1988;165:141-50 pubmed
    ..These results are discussed in relation to the drug-resistant phenotype and future experiments to identify the viral gene product responsible...
  28. Avram D, Bakalinsky A. SSU1 encodes a plasma membrane protein with a central role in a network of proteins conferring sulfite tolerance in Saccharomyces cerevisiae. J Bacteriol. 1997;179:5971-4 pubmed
  29. Tzanetakis I, Martin R. Strawberry chlorotic fleck: identification and characterization of a novel Closterovirus associated with the disease. Virus Res. 2007;124:88-94 pubmed
    ..Detection protocols have been developed and the virus was detected in several strawberry plants from production fields. ..
  30. Yan X, Pérez E, Leid M, Schimerlik M, de Lera A, Deinzer M. Deuterium exchange and mass spectrometry reveal the interaction differences of two synthetic modulators of RXRalpha LBD. Protein Sci. 2007;16:2491-501 pubmed
  31. Blouin M, Yowell C, Courtney C, Dame J. Haemonchus placei and Haemonchus contortus are distinct species based on mtDNA evidence. Int J Parasitol. 1997;27:1383-7 pubmed
    ..Furthermore, there was no evidence of introgressive hybridisation occurring in wild populations. ..
  32. Sayavedra Soto L, Hommes N, Arp D. Characterization of the gene encoding hydroxylamine oxidoreductase in Nitrosomonas europaea. J Bacteriol. 1994;176:504-10 pubmed
    ..Data bank searches did not reveal proteins with substantial similarities to HAO, but they did reveal similarities between Cyt c-554 and other c-type cytochromes. ..
  33. Hansen J, Kaattari S. The recombination activating gene 2 (RAG2) of the rainbow trout Oncorhynchus mykiss. Immunogenetics. 1996;44:203-11 pubmed
    ..In addition, the trout sequences may provide further insight into the evolution and origins of the RAG genes as well as that of the immune system itself. ..
  34. Dreher T, Goodwin J. Transfer RNA mimicry among tymoviral genomic RNAs ranges from highly efficient to vestigial. Nucleic Acids Res. 1998;26:4356-64 pubmed
    ..The range of tRNA mimicry within the tymovirus genus thus ranges from extremely highly developed to minimal. The implications on the role of the tRNA mimicry in viral biology are discussed...
  35. Bradford C, Walthers E, Stanley D, Baugh M, Moore F. Delta and mu opioid receptors from the brain of a urodele amphibian, the rough-skinned newt Taricha granulosa: cloning, heterologous expression, and pharmacological characterization. Gen Comp Endocrinol. 2006;146:275-90 pubmed
    ..Taricha granulosa expresses the same four subtypes (delta, mu, kappa, and ORL1) of opioid receptors found in other vertebrate classes, but ligand selectivity appears less stringent in the newt than has been documented in mammals. ..
  36. Pang Q, Hays J, Rajagopal I. A plant cDNA that partially complements Escherichia coli recA mutations predicts a polypeptide not strongly homologous to RecA proteins. Proc Natl Acad Sci U S A. 1992;89:8073-7 pubmed
    ..There are several tandemly repeated leucine-rich motifs. DNA from two closely related plants, but not from maize, hybridized strongly to a DRT100 cDNA probe. ..
  37. Vendeland S, Beilstein M, Yeh J, Ream W, Whanger P. Rat skeletal muscle selenoprotein W: cDNA clone and mRNA modulation by dietary selenium. Proc Natl Acad Sci U S A. 1995;92:8749-53 pubmed
    ..Dietary selenium at 0.1 ppm as selenite increased muscle mRNA 4-fold relative to a selenium-deficient diet. Higher dietary selenium produced no further increase in mRNA levels. ..
  38. Bannantine J, Rockey D. Use of primate model system to identify Chlamydia trachomatis protein antigens recognized uniquely in the context of infection. Microbiology. 1999;145 ( Pt 8):2077-85 pubmed
    ..Collectively, these studies identify two C. trachomatis proteins that are under-represented in EBs and are recognized uniquely in the context of infection...
  39. Martin R, Mok M, Habben J, Mok D. A maize cytokinin gene encoding an O-glucosyltransferase specific to cis-zeatin. Proc Natl Acad Sci U S A. 2001;98:5922-6 pubmed
    ..This finding indicates the existence of cis-specific regulatory elements in plants and suggests that cis-zeatin and derivatives may be more important in cytokinin homeostasis than currently recognized. ..
  40. Li Q, Dixon B, Al Fageeh M, Blum C, Dashwood R. Sequencing of the rat beta-catenin gene (Ctnnb1) and mutational analysis of liver tumors induced by 2-amino-3-methylimidazo[4,5-f]quinoline. Gene. 2002;283:255-62 pubmed
    ..Surprisingly, no mutations were found. The results are discussed in the context of the organ-specificity of IQ-induced mutations in beta-catenin, being highly prevalent in colon tumors, but much less common in liver tumors. ..
  41. Lawrence J, Johnson W. Lifson-Roig nucleation for alpha-helices in trifluoroethanol: context has a strong effect on the helical propensity of amino acids. Biophys Chem. 2002;101-102:375-85 pubmed
    ..Clearly, the prediction of alpha-helical secondary structure from protein sequence requires more than a single helical propensity for each amino acid...
  42. Tzanetakis I, Postman J, Martin R. Mint virus X: a novel potexvirus associated with symptoms in 'Variegata' mint. Arch Virol. 2006;151:143-53 pubmed
    ..All clones tested, obtained from nurseries around the United States were infected with MVX, making the virus a possible causal agent of the variegated symptoms. ..
  43. Skinner J, von Zitzewitz J, Szucs P, Marquez Cedillo L, Filichkin T, Amundsen K, et al. Structural, functional, and phylogenetic characterization of a large CBF gene family in barley. Plant Mol Biol. 2005;59:533-51 pubmed publisher
    ..These results suggest that in the Triticeae - as in Arabidopsis - members of the CBF gene family function as fundamental components of the winter hardiness regulon...
  44. Lupfer C, Stein D, Mourich D, Tepper S, Iversen P, Pastey M. Inhibition of influenza A H3N8 virus infections in mice by morpholino oligomers. Arch Virol. 2008;153:929-37 pubmed publisher
    ..These data indicate that PPMOs targeting highly conserved regions of FLUAV are promising novel therapeutic candidates. ..
  45. Shenvi S, Smith E, Hagen T. Transcriptional regulation of rat gamma-glutamate cysteine ligase catalytic subunit gene is mediated through a distal antioxidant response element. Pharmacol Res. 2009;60:229-36 pubmed publisher
    ..This is the first report showing that rat Gclc is under the transcriptional control of the Nrf2-ARE pathway on a constitutive basis. ..
  46. Martin R, Zhou J, Tzanetakis I. Blueberry latent virus: an amalgam of the Partitiviridae and Totiviridae. Virus Res. 2011;155:175-80 pubmed publisher
  47. Eide K, Miller Morgan T, Heidel J, Bildfell R, Jin L. Results of total DNA measurement in koi tissue by Koi Herpes Virus real-time PCR. J Virol Methods. 2011;172:81-4 pubmed publisher
    ..This study demonstrated that KHV genomic DNA can be detected in normal koi exposed previously to KHV and suggests that KHV becomes latent in fish...
  48. Dreher T. Viral tRNAs and tRNA-like structures. Wiley Interdiscip Rev RNA. 2010;1:402-14 pubmed publisher
    ..The structures and roles of these TLSs are discussed, emphasizing the variety in both structure and function. ..
  49. Kiemnec Tyburczy K, Woodley S, Watts R, Arnold S, Houck L. Expression of vomeronasal receptors and related signaling molecules in the nasal cavity of a caudate amphibian (Plethodon shermani). Chem Senses. 2012;37:335-46 pubmed publisher
    ..Thus, some aspects of mRNA expression of vomeronasal receptors and related molecules differ between salamanders and frogs, and between salamanders and mice. ..
  50. Spatafora J, Owensby C, Douhan G, Boehm E, Schoch C. Phylogenetic placement of the ectomycorrhizal genus Cenococcum in Gloniaceae (Dothideomycetes). Mycologia. 2012;104:758-65 pubmed publisher
    ..Glonium is a genus of saprobic Dothideomycetes that produces darkly pigmented, carbonaceous, hysteriate apothecia and is not known to be biotrophic. Evolution of ectomycorhizae, Cenococcum and Dothideomycetes is discussed...
  51. Putman T, Suchland R, Ivanovitch J, Rockey D. Culture-independent sequence analysis of Chlamydia trachomatis in urogenital specimens identifies regions of recombination and in-patient sequence mutations. Microbiology. 2013;159:2109-17 pubmed publisher
    ..trachomatis, and that this approach can be used to examine genomic variation within this species. ..
  52. Dolja V, Kreuze J, Valkonen J. Comparative and functional genomics of closteroviruses. Virus Res. 2006;117:38-51 pubmed
    ..The evolutionary processes that have shaped the complex and fluid genomes of the large RNA viruses might be similar to those that have been involved in evolution of genomic complexity in other divisions of life...
  53. Ito T, Roongsawang N, Shirasaka N, Lu W, Flatt P, Kasanah N, et al. Deciphering pactamycin biosynthesis and engineered production of new pactamycin analogues. Chembiochem. 2009;10:2253-65 pubmed publisher
    ..The new compounds showed equivalent cytotoxic and antibacterial activities with the corresponding parent molecules and shed more light on the structure-activity relationship of pactamycin...
  54. Tripathy S, Torres Gonzalez M, Jump D. Elevated hepatic fatty acid elongase-5 activity corrects dietary fat-induced hyperglycemia in obese C57BL/6J mice. J Lipid Res. 2010;51:2642-54 pubmed publisher
    ..Our findings establish a link between fatty acid elongation and hepatic glucose metabolism and suggest a role for regulators of Elovl5 activity in the treatment of diet-induced hyperglycemia. ..
  55. Thrash J, Boyd A, Huggett M, Grote J, Carini P, Yoder R, et al. Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Sci Rep. 2011;1:13 pubmed publisher
  56. Ray N, Mathews C. Nucleoside diphosphokinase: a functional link between intermediary metabolism and nucleic acid synthesis. Curr Top Cell Regul. 1992;33:343-57 pubmed
  57. Chiba M, Reed J, Prokhnevsky A, Chapman E, Mawassi M, Koonin E, et al. Diverse suppressors of RNA silencing enhance agroinfection by a viral replicon. Virology. 2006;346:7-14 pubmed
    ..The members of this family are predicted to have RNA silencing suppressor activity...
  58. Solem M, Rawson C, Lindburg K, Barnes D. Transforming growth factor beta regulates cystatin C in serum-free mouse embryo (SFME) cells. Biochem Biophys Res Commun. 1990;172:945-51 pubmed
  59. Johansen I, Keller K, Dougherty W, Hampton R. Biological and molecular properties of a pathotype P-1 and a pathotype P-4 isolate of pea seed-borne mosaic virus. J Gen Virol. 1996;77 ( Pt 6):1329-33 pubmed
    ..The nucleotide sequence and deduced amino acid sequence of NY were determined and compared to the corresponding sequences of DPD1. ..
  60. Ivanchenko M, Vejlupkova Z, Quatrano R, Fowler J. Maize ROP7 GTPase contains a unique, CaaX box-independent plasma membrane targeting signal. Plant J. 2000;24:79-90 pubmed
    ..Our analysis suggests that the ROP7 HVR directs PM localization by a mechanism independent of a C-terminal CaaX motif; this mechanism may have evolved through addition of 3' intron/exon sequences to a rop progenitor. ..
  61. Skinner M, Trempy J. Expression of clpX, an ATPase subunit of the Clp protease, is heat and cold shock inducible in Lactococcus lactis. J Dairy Sci. 2001;84:1783-5 pubmed publisher
    ..8 kDa. Analysis of the relative levels of clpX transcript revealed that in addition to a role in proteolysis of heat damaged proteins, ClpX may also be involved in cryoprotection...
  62. Alzhanova D, Napuli A, Creamer R, Dolja V. Cell-to-cell movement and assembly of a plant closterovirus: roles for the capsid proteins and Hsp70 homolog. EMBO J. 2001;20:6997-7007 pubmed
  63. Napuli A, Alzhanova D, Doneanu C, Barofsky D, Koonin E, Dolja V. The 64-kilodalton capsid protein homolog of Beet yellows virus is required for assembly of virion tails. J Virol. 2003;77:2377-84 pubmed
    ..These results reveal the dual function of p64 in tail assembly and BYV motility and support the concept of the virion tail as a specialized device for BYV cell-to-cell movement. ..
  64. Wood Z, Poole L, Karplus P. Peroxiredoxin evolution and the regulation of hydrogen peroxide signaling. Science. 2003;300:650-3 pubmed publisher
    ..We suggest this adaptation allows 2-Cys Prxs to act as floodgates, keeping resting levels of hydrogen peroxide low, while permitting higher levels during signal transduction...
  65. Bennett S, Chen C, Mosbaugh D. Escherichia coli nucleoside diphosphate kinase does not act as a uracil-processing DNA repair nuclease. Proc Natl Acad Sci U S A. 2004;101:6391-6 pubmed
    ..coli uracil-DNA glycosylase (Ung). Collectively, these observations demonstrate that the E. coli Ndk polypeptide does not possess inherent uracil-DNA glycosylase activity. ..
  66. Corley Smith G, Su H, Wang Buhler J, Tseng H, Hu C, Hoang T, et al. CYP3C1, the first member of a new cytochrome P450 subfamily found in zebrafish (Danio rerio). Biochem Biophys Res Commun. 2006;340:1039-46 pubmed
    ..TCDD, dexamethasone, and rifampicin, which up-regulated CYP3A65 mRNA in zebrafish larvae, did not alter the CYP3C1 transcript levels suggesting regulatory differences between CYP3A and CYP3C enzymes in this species. ..
  67. Kraus J, Tzanetakis I, Putnam M, Martin R. Complete nucleotide sequence of an isolate of coleus vein necrosis virus from verbena. Arch Virol. 2008;153:381-4 pubmed
  68. Hoffman P, Curtis M, Iwai S, Hays J. Biochemical evolution of DNA polymerase eta: properties of plant, human, and yeast proteins. Biochemistry. 2008;47:4583-96 pubmed publisher
    ..The depressed ( N - 1) insertion upstream of T[CPD]T (but not T-T) may reduce the extent of gratuitous error-prone insertion. ..
  69. Tzanetakis I, Tsai C, Martin R, Dreher T. A tymovirus with an atypical 3'-UTR illuminates the possibilities for 3'-UTR evolution. Virology. 2009;392:238-45 pubmed publisher
    ..These experiments suggest the way in which DuMV may have evolved from a typical tymovirus, and illuminate the ways in which viral 3'-UTRs in general can evolve...
  70. Hall A, Sankaran B, Poole L, Karplus P. Structural changes common to catalysis in the Tpx peroxiredoxin subfamily. J Mol Biol. 2009;393:867-81 pubmed publisher
    ..The involvement of the dimer interface in stabilizing active-site folding and in forming the hydrophobic collar implies that Tpx is an obligate homodimer and explains the high conservation of interface residues. ..
  71. Cuperus J, Montgomery T, Fahlgren N, Burke R, Townsend T, Sullivan C, et al. Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing. Proc Natl Acad Sci U S A. 2010;107:466-71 pubmed publisher
  72. Thrash J, Cho J, Ferriera S, Johnson J, Vergin K, Giovannoni S. Genome sequences of strains HTCC2148 and HTCC2080, belonging to the OM60/NOR5 clade of the Gammaproteobacteria. J Bacteriol. 2010;192:3842-3 pubmed publisher
    ..Isolated from coastal Oregon water, Gammaproteobacteria HTCC2148 and HTCC2080 are two members of this important clade. Here we present the genome sequences of the OM60 Gammaproteobacteria HTCC2148 and HTCC2080...
  73. Varsani A, Kraberger S, Jennings S, Porzig E, Julian L, Massaro M, et al. A novel papillomavirus in Adélie penguin (Pygoscelis adeliae) faeces sampled at the Cape Crozier colony, Antarctica. J Gen Virol. 2014;95:1352-65 pubmed publisher
    ..This is the first report, to our knowledge, of a papillomavirus associated with a penguin species. ..
  74. Dreher T, Tsai C, Florentz C, Giege R. Specific valylation of turnip yellow mosaic virus RNA by wheat germ valyl-tRNA synthetase determined by three anticodon loop nucleotides. Biochemistry. 1992;31:9183-9 pubmed
    ..The mechanism by which anticodon mutations are discriminated also appears to vary, being affinity-based for the wheat germ enzyme, and kinetically-based for the yeast enzyme [Florentz et al. (1991) Eur. J. Biochem. 195, 229-234]. ..
  75. Hansen J, Kaattari S. The recombination activation gene 1 (RAG1) of rainbow trout (Oncorhynchus mykiss): cloning, expression, and phylogenetic analysis. Immunogenetics. 1995;42:188-95 pubmed
    ..This data forms the basis for a proposal that the thymus of teleost species plays an essential developmental role in lymphopoiesis and thus can be regarded as a primary lymphoid organ...
  76. Malencik D, Zhao Z, Anderson S. Preparation and functional characterization of a catalytically active fragment of phosphorylase kinase. Mol Cell Biochem. 1993;127-128:31-43 pubmed
    ..1 mol/mol. In the former case, phosphorylation occurs primarily at Ser30 while in the latter an additional reaction takes place at Ser81. The phosphopeptides correspond to sequences occurring in the gamma-subunit of phosphorylase kinase. ..
  77. Lindquist J, Barofsky E, McFadden P. Determination of two sites of automethylation in bovine erythrocyte protein (D-aspartyl/L-isoaspartyl) carboxyl methyltransferase. J Protein Chem. 1996;15:115-22 pubmed
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