Genomes and Genes
Experts and Doctors on molecular sequence data in West Lafayette, Indiana, United States
Locale: West Lafayette, Indiana, United States
Topic: molecular sequence data
Publications248 found, 100 shown here
- Ward B, Seal B, Brophy C, Panitch A. Design of a bioactive cell-penetrating peptide: when a transduction domain does more than transduce. J Pept Sci. 2009;15:668-74 pubmed publisher..The results reported herein have wide implications for delivering therapeutics with CPPs and indicate that judicious choice of CPP is crucial to the ultimate therapeutic success. ..
- Na G, Salt D. Differential regulation of serine acetyltransferase is involved in nickel hyperaccumulation in Thlaspi goesingense. J Biol Chem. 2011;286:40423-32 pubmed publisher..goesingense...
- Waldbieser G, Aimi J, Dixon J. Cloning and characterization of the rat complementary deoxyribonucleic acid and gene encoding the neuroendocrine peptide 7B2. Endocrinology. 1991;128:3228-36 pubmed..The rat 7B2 gene and cDNA will be valuable tools for the identification of factors that regulate 7B2 gene expression. ..
- Gibbon B, Zonia L, Kovar D, Hussey P, Staiger C. Pollen profilin function depends on interaction with proline-rich motifs. Plant Cell. 1998;10:981-93 pubmed
- Keshvara L, Isaacson C, Yankee T, Sarac R, Harrison M, Geahlen R. Syk- and Lyn-dependent phosphorylation of Syk on multiple tyrosines following B cell activation includes a site that negatively regulates signaling. J Immunol. 1998;161:5276-83 pubmed..We propose that these sites are phosphorylated following the binding of Syk to immunoreceptor tyrosine-based activation motif. ..
- Mitin N, Ramocki M, Zullo A, Der C, Konieczny S, Taparowsky E. Identification and characterization of rain, a novel Ras-interacting protein with a unique subcellular localization. J Biol Chem. 2004;279:22353-61 pubmed..Taken together, these observations support a role for Rain as a novel protein that can serve as an effector of endomembrane-localized Ras. ..
- Kumar P, Gomez Gil L, Mohammadi M, Sylvestre M, Eltis L, Bolin J. Anaerobic crystallization and initial X-ray diffraction data of biphenyl 2,3-dioxygenase from Burkholderia xenovorans LB400: addition of agarose improved the quality of the crystals. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67:59-62 pubmed publisher..In the presence of agarose, wild-type BPDOLB400 crystals that diffracted to 2.4 Å resolution grew in space group P1. Crystals of the BPDOP4 and BPDORR41 variants of BPDOLB400 grew in space group P2(1). ..
- Weng J, Akiyama T, Ralph J, Chapple C. Independent recruitment of an O-methyltransferase for syringyl lignin biosynthesis in Selaginella moellendorffii. Plant Cell. 2011;23:2708-24 pubmed publisher..moellendorffii. Phylogenetic analysis reveals that Sm COMT, like F5H, evolved independently from its angiosperm counterparts...
- Luo M, Rossmann M, Palmenberg A. Prediction of three-dimensional models for foot-and-mouth disease virus and hepatitis A virus. Virology. 1988;166:503-14 pubmed..They also have large hydrophobic cavities within VP1 suggesting that it may be possible to inhibit their infectivity with suitably designed antiviral agents that block uncoating. ..
- Han S, Eltis L, Timmis K, Muchmore S, Bolin J. Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad. Science. 1995;270:976-80 pubmed..The iron atom has five ligands in square pyramidal geometry: one glutamate and two histidine side chains, and two water molecules...
- Taylor G, Liu Y, Baskerville C, Charbonneau H. The activity of Cdc14p, an oligomeric dual specificity protein phosphatase from Saccharomyces cerevisiae, is required for cell cycle progression. J Biol Chem. 1997;272:24054-63 pubmed..This COOH-terminal segment is not required for activity, for oligomerization, or for the critical cell cycle function of Cdc14p. ..
- Krahn J, Kim J, Burns M, Parry R, Zalkin H, Smith J. Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site. Biochemistry. 1997;36:11061-8 pubmed publisher..Different catalytic and inhibitory modes of divalent cation binding to the PRTase active site are revealed in the active conformer of the enzyme and in a feedback-inhibited GMP complex...
- Zhang Q, Ekhterae D, Kim K. Molecular cloning and characterization of P113, a mouse SNF2/SWI2-related transcription factor. Gene. 1997;202:31-7 pubmed..Using Northern blot analysis and the PAI-1 promoter/luciferase system, we demonstrated that P113 is a transcription factor that activates the transcription of the PAI-1 gene in 30A5 cells. ..
- Dudareva N, Murfitt L, Mann C, Gorenstein N, Kolosova N, Kish C, et al. Developmental regulation of methyl benzoate biosynthesis and emission in snapdragon flowers. Plant Cell. 2000;12:949-61 pubmed..Linear regression analysis revealed that production of methyl benzoate is regulated by the amount of benzoic acid and the amount of BAMT protein, which in turn is regulated at the transcriptional level. ..
- Baldwin J, Karthikeyan A, Raghothama K. LEPS2, a phosphorus starvation-induced novel acid phosphatase from tomato. Plant Physiol. 2001;125:728-37 pubmed..The bacterially (Escherichia coli) expressed protein exhibits phosphatase activity against the synthetic substrate p-nitrophenyl phosphate. The pH optimum of the enzyme activity suggests that LePS2 is an acid phosphatase. ..
- Krolikowski K, Victor J, Wagler T, Lolle S, Pruitt R. Isolation and characterization of the Arabidopsis organ fusion gene HOTHEAD. Plant J. 2003;35:501-11 pubmed..Furthermore, the sequence data unequivocally show that none of the alleles isolated are epigenetic alleles as suggested by genetic behavior previously observed at this locus. ..
- Zhang X, Tang J, Walker S, O Hara D, Nibert M, Duncan R, et al. Structure of avian orthoreovirus virion by electron cryomicroscopy and image reconstruction. Virology. 2005;343:25-35 pubmed..Overall, the results place ARVs between MRVs and aquareoviruses with respect to the highlighted features...
- Huang S, Gao L, Blanchoin L, Staiger C. Heterodimeric capping protein from Arabidopsis is regulated by phosphatidic acid. Mol Biol Cell. 2006;17:1946-58 pubmed..Such regulation may be important for the response of plant cells to extracellular stimuli as well as for the normal process of pollen tube tip growth. ..
- Liu H, Deng X, Shyu Y, Li J, Taparowsky E, Hu C. Mutual regulation of c-Jun and ATF2 by transcriptional activation and subcellular localization. EMBO J. 2006;25:1058-69 pubmed..Together, these findings demonstrate that ATF2 and c-Jun mutually regulate each other by altering the dynamics of subcellular localization and by positively impacting transcriptional activity. ..
- Sherman M, Guenther R, Tama F, Sit T, Brooks C, Mikhailov A, et al. Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release. J Virol. 2006;80:10395-406 pubmed..These results indicate that divalent cations play a central role in capsid dynamics and suggest a mechanism for the release of viral RNA in low-divalent-cation environments such as those found within the cytoplasm of a cell. ..
- Triant D, DeWoody J. Accelerated molecular evolution in Microtus (Rodentia) as assessed via complete mitochondrial genome sequences. Genetica. 2006;128:95-108 pubmed..The root cause of accelerated evolution in Microtus remains uncertain, but merits further investigation. ..
- Orlova I, Marshall Colon A, Schnepp J, Wood B, Varbanova M, Fridman E, et al. Reduction of benzenoid synthesis in petunia flowers reveals multiple pathways to benzoic acid and enhancement in auxin transport. Plant Cell. 2006;18:3458-75 pubmed..This suggests that BPBT is involved in metabolic processes in vegetative tissues as well...
- Jerke K, Nakatsu C, Beasley F, Konopka A. Comparative analysis of eight Arthrobacter plasmids. Plasmid. 2008;59:73-85 pubmed publisher..Comparison of a concatenation of all the maintenance genes from each plasmid suggests that the eight Arthrobacter plasmids represent multiple evolutionary pathways...
- Hafenstein S, Bowman V, Sun T, Nelson C, Palermo L, Chipman P, et al. Structural comparison of different antibodies interacting with parvovirus capsids. J Virol. 2009;83:5556-66 pubmed publisher..Most of the exposed surface area was antigenic, although each of the antibodies had a common area of overlap that coincided with the positions of the previously mapped escape mutations...
- Lei M, La H, Lu K, Wang P, Miki D, Ren Z, et al. Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns. Proc Natl Acad Sci U S A. 2014;111:527-32 pubmed publisher..Our results thus increase the understanding of antisilencing, genome methylation patterns, and regulation of alternative RNA processing by intronic heterochromatin...
- Cui J, Somerville R. Physical map location and transcriptional orientation of the tyrR gene of Escherichia coli K-12. J Bacteriol. 1992;174:3832-3 pubmed
- Hinterberger T, Mays J, Konieczny S. Structure and myofiber-specific expression of the rat muscle regulatory gene MRF4. Gene. 1992;117:201-7 pubmed..5 and 5.0 kb upstream from the coding region play a role in regulating the expression of this muscle-specific gene. ..
- Ostanin K, Pokalsky C, Wang S, Van Etten R. Cloning and characterization of a Saccharomyces cerevisiae gene encoding the low molecular weight protein-tyrosine phosphatase. J Biol Chem. 1995;270:18491-9 pubmed..cerevisiae. ..
- Weng M, Nagy P, Zalkin H. Identification of the Bacillus subtilis pur operon repressor. Proc Natl Acad Sci U S A. 1995;92:7455-9 pubmed..In addition, purR is autoregulated. There is no structural or mechanistic similarity between the B. subtilis and Escherichia coli purine repressors. ..
- Zhang J, Fitz James P, Aronson A. Cloning and characterization of a cluster of genes encoding polypeptides present in the insoluble fraction of the spore coat of Bacillus subtilis. J Bacteriol. 1993;175:3757-66 pubmed..These proteins, as part of the coat insoluble fraction, appear to be localized to the outer coat and influence spore hydrophobicity as well as the accessibility of germinants. ..
- Meyer N, Johansen L, Tae H, Budde P, Williams K, Taparowsky E. Genomic organization of human B-ATF, a target for regulation by EBV and HTLV-1. Mamm Genome. 1998;9:849-52 pubmed
- Chittur S, Klem T, Shafer C, Davisson V. Mechanism for acivicin inactivation of triad glutamine amidotransferases. Biochemistry. 2001;40:876-87 pubmed..Stabilization of the imine-thioether intermediate by the oxyanion hole in triad glutamine amidotransferases appears to confer the high degree of specificity for acivicin inhibition and relates to a common mechanism for inactivation...
- Gong Z, Koiwa H, Cushman M, Ray A, Bufford D, Kore eda S, et al. Genes that are uniquely stress regulated in salt overly sensitive (sos) mutants. Plant Physiol. 2001;126:363-75 pubmed..The pivotal function of the SOS signal pathway to mediate ion homeostasis and salt tolerance implicates AD06C08/unknown, VSP2, SAMT, 6.6/KIN2, STZ, and CCR1 as determinates that are involved in salt adaptation. ..
- Akin A, Lin T, Wu C, Bryan T, Hooper T, Schrader D. Nucleocapsid protein gene sequence analysis reveals close genomic relationship between turkey coronavirus and avian infectious bronchitis virus. Acta Virol. 2001;45:31-8 pubmed..1-94.1% at the N gene level. It was also observed that the N gene of eight TCV isolates originating from various regions of the USA could not be amplified by the primers designed from the N gene of bovine coronavirus (BCV). ..
- Reid G, Shang H, Hogan J, Lee G, McLuckey S. Gas-phase concentration, purification, and identification of whole proteins from complex mixtures. J Am Chem Soc. 2002;124:7353-62 pubmed..The identification of these proteins illustrates the potential of this "top-down" protein identification approach to reduce the reliance on condensed-phase chemistries and extensive separations for complex protein mixture analysis...
- Bout S, Vermerris W. A candidate-gene approach to clone the sorghum Brown midrib gene encoding caffeic acid O-methyltransferase. Mol Genet Genomics. 2003;269:205-14 pubmed..Molecular markers were developed for each of the three mutant alleles to facilitate the use of these mutant alleles in genetic studies and breeding programs. ..
- Zhu J, Shi H, Lee B, Damsz B, Cheng S, Stirm V, et al. An Arabidopsis homeodomain transcription factor gene, HOS9, mediates cold tolerance through a CBF-independent pathway. Proc Natl Acad Sci U S A. 2004;101:9873-8 pubmed..Together, these results suggest that HOS9 is important for plant growth and development, and for a part of freezing tolerance, by affecting the activity of genes independent of the CBF pathway. ..
- Wu J, Bera A, Kuhn R, Smith J. Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing. J Virol. 2005;79:10268-77 pubmed..The third, C-terminal domain has a unique structure and is proposed to function in RNA and protein recognition. The organization of the three domains indicates that cleavage of the viral polyprotein NS3-NS4A junction occurs in trans. ..
- Miura K, Jin J, Lee J, Yoo C, Stirm V, Miura T, et al. SIZ1-mediated sumoylation of ICE1 controls CBF3/DREB1A expression and freezing tolerance in Arabidopsis. Plant Cell. 2007;19:1403-14 pubmed..SIZ1-dependent sumoylation of ICE1 may activate and/or stabilize the protein, facilitating expression of CBF3/DREB1A and repression of MYB15, leading to low temperature tolerance...
- Baxter I, Muthukumar B, Park H, Buchner P, Lahner B, Danku J, et al. Variation in molybdenum content across broadly distributed populations of Arabidopsis thaliana is controlled by a mitochondrial molybdenum transporter (MOT1). PLoS Genet. 2008;4:e1000004 pubmed publisher..This work provides the first molecular insight into the processes that regulate Mo accumulation in plants and shows that novel loci can be detected by association mapping. ..
- Zheng Z, Qualley A, Fan B, Dudareva N, Chen Z. An important role of a BAHD acyl transferase-like protein in plant innate immunity. Plant J. 2009;57:1040-53 pubmed publisher..These results suggest that there is natural variation among Arabidopsis ecotypes with respect to the antagonistic cross-talk between defense signaling pathways against various types of microbial pathogens. ..
- Varadarajan J, Guilleminot J, Saint Jore Dupas C, Piegu B, Chaboute M, Gomord V, et al. ATR3 encodes a diflavin reductase essential for Arabidopsis embryo development. New Phytol. 2010;187:67-82 pubmed publisher..Together these results demonstrated that ATR3 belongs to the NR1 subfamily of diflavin reductases whose characterized members are involved in essential cellular functions. ..
- Joshi R, Ho K, Tenney K, Chen J, Golden B, Gimble F. Evolution of I-SceI homing endonucleases with increased DNA recognition site specificity. J Mol Biol. 2011;405:185-200 pubmed publisher..This biochemical and structural analysis defines one pathway by which site specificity is augmented for a homing endonuclease. ..
- Banks J, Nishiyama T, Hasebe M, Bowman J, Gribskov M, DePamphilis C, et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science. 2011;332:960-3 pubmed publisher..Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes...
- Ruzzini A, Bhowmik S, Yam K, Ghosh S, Bolin J, Eltis L. The lid domain of the MCP hydrolase DxnB2 contributes to the reactivity toward recalcitrant PCB metabolites. Biochemistry. 2013;52:5685-5695 pubmed publisher..Finally, an increased mobility of the DxnB2 lid may contribute to the enzyme's ability to hydrolyze PCB metabolites, highlighting how lid architecture contributes to substrate specificity in α/β-hydrolases. ..
- Borras E, Cantó E, Choi M, Maria Villar L, Alvarez Cermeño J, Chiva C, et al. Protein-Based Classifier to Predict Conversion from Clinically Isolated Syndrome to Multiple Sclerosis. Mol Cell Proteomics. 2016;15:318-28 pubmed publisher..Our results are of special relevance for patients affected by multiple sclerosis as early treatment can prevent brain damage and slow down the disease progression. ..
- Zhou J, Goldsbrough P. Structure, organization and expression of the metallothionein gene family in Arabidopsis. Mol Gen Genet. 1995;248:318-28 pubmed..MT1b and MT2b map to separate loci on chromosome V, and MT2a is located on chromosome III. The locations of these MT genes are different from that of CAD1, a gene involved in cadmium tolerance in Arabidopsis. ..
- Zhang J, Aronson A. A Bacillus subtilis bglA gene encoding phospho-beta-glucosidase is inducible and closely linked to a NADH dehydrogenase-encoding gene. Gene. 1994;140:85-90 pubmed..subtilis chromosome. Disruption of these genes by insertion of a neomycin-resistance-encoding gene (neo) did not result in any phenotypic changes comparable to those found in E. coli mutants. ..
- Nagy P, McCorkle G, Zalkin H. purU, a source of formate for purT-dependent phosphoribosyl-N-formylglycinamide synthesis. J Bacteriol. 1993;175:7066-73 pubmed..On the basis of the growth of purU, purN, and purU purN mutants, it appears that PurU provides the major source of formate for the purT-dependent synthesis of FGAR...
- Ha J, Lee J, Kim K, Witters L, Kim K. Cloning of human acetyl-CoA carboxylase-beta and its unique features. Proc Natl Acad Sci U S A. 1996;93:11466-70 pubmed..A fragment of ACC-beta cDNA was expressed in Escherichia coli and antibodies against the peptide were generated to establish that the cDNA sequence that we cloned is that for ACC-beta. ..
- Zhang H, Carrell C, Huang D, Sled V, Ohnishi T, Smith J, et al. Characterization and crystallization of the lumen side domain of the chloroplast Rieske iron-sulfur protein. J Biol Chem. 1996;271:31360-6 pubmed..1 A, b = 31.9 A, c = 35.8 A, alpha = 95.6 degrees, beta = 107.1 degrees, gamma = 117.3 degrees. ..
- Bell Lelong D, Cusumano J, Meyer K, Chapple C. Cinnamate-4-hydroxylase expression in Arabidopsis. Regulation in response to development and the environment. Plant Physiol. 1997;113:729-38 pubmed..A modest increase in C4H expression was observed in the tt8 mutant of Arabidopsis. ..
- Liang W, Bidwell C, Williams S, Mills S. Rapid communication: molecular cloning of the porcine beta 2-adrenergic receptor gene. J Anim Sci. 1997;75:2824 pubmed
- Peterson P, Smith T. The structure of bovine glutamate dehydrogenase provides insights into the mechanism of allostery. Structure. 1999;7:769-82 pubmed..Extensive contacts between antennae within the crystal lattice may represent hexamer interactions in solution and, perhaps, with other enzymes within the mitochondrial matrix. ..
- Qiu J, Jilk R, Marks M, Szymanski D. The Arabidopsis SPIKE1 gene is required for normal cell shape control and tissue development. Plant Cell. 2002;14:101-18 pubmed..The assembly of laterally clustered foci of microtubules and polarized growth are early events in cotyledon development, and both processes are misregulated in spike1 epidermal cells. ..
- Lin T, Loa C, Wu C. Existence of gene 5 indicates close genomic relationship of Turkey coronavirus to infectious bronchitis virus. Acta Virol. 2002;46:107-16 pubmed..4% to 94.0%. The results indicate the existence of gene 5 in the genome of TCV and a close relatedness of the TCV gene 5 to the IBV gene 5 in location and nucleotide sequence. ..
- Jeong J, Johns J, Sinclair C, Park J, Rossie S. Characterization of Saccharomyces cerevisiae protein Ser/Thr phosphatase T1 and comparison to its mammalian homolog PP5. BMC Cell Biol. 2003;4:3 pubmed..The observation that Ppt1p is most highly expressed during early log phase growth suggests that this enzyme is involved in cell growth or its expression is controlled by metabolic or nutritional signals. ..
- Perera R, Navaratnarajah C, Kuhn R. A heterologous coiled coil can substitute for helix I of the Sindbis virus capsid protein. J Virol. 2003;77:8345-53 pubmed
- Negre F, Kish C, Boatright J, Underwood B, Shibuya K, Wagner C, et al. Regulation of methylbenzoate emission after pollination in snapdragon and petunia flowers. Plant Cell. 2003;15:2992-3006 pubmed
- Hogan J, Pitteri S, McLuckey S. Phosphorylation site identification via ion trap tandem mass spectrometry of whole protein and peptide ions: bovine alpha-crystallin A chain. Anal Chem. 2003;75:6509-16 pubmed..Fragmentation of the doubly charged phosphopeptide, formed by ion/ion proton-transfer reactions, positively identified the phosphorylation site as serine-122. ..
- Basu D, Le J, El Essal S, Huang S, Zhang C, Mallery E, et al. DISTORTED3/SCAR2 is a putative arabidopsis WAVE complex subunit that activates the Arp2/3 complex and is required for epidermal morphogenesis. Plant Cell. 2005;17:502-24 pubmed..These results demonstrate the utility of the Arabidopsis trichome system to understand how the WAVE and ARP2/3 complexes translate signaling inputs into a coordinated morphogenetic response. ..
- Yi Z, Vitek O, Qasim M, Lu S, Lu W, Ranjbar M, et al. Functional evolution within a protein superfamily. Proteins. 2006;63:697-708 pubmed
- Messner D, Romeo C, Boynton A, Rossie S. Inhibition of PP2A, but not PP5, mediates p53 activation by low levels of okadaic acid in rat liver epithelial cells. J Cell Biochem. 2006;99:241-55 pubmed..In contrast, specific blockade of PP2A mimics p53-related responses to OA in T51B cells, suggesting that PP2A is the target for this response to OA. ..
- Mirzaei H, Regnier F. Identification and quantification of protein carbonylation using light and heavy isotope labeled Girard's P reagent. J Chromatogr A. 2006;1134:122-33 pubmed
- Sun J, Cai Y, Moll W, Guo P. Controlling bacteriophage phi29 DNA-packaging motor by addition or discharge of a peptide at N-terminus of connector protein that interacts with pRNA. Nucleic Acids Res. 2006;34:5482-90 pubmed
- Zhang P, Mueller S, Morais M, Bator C, Bowman V, Hafenstein S, et al. Crystal structure of CD155 and electron microscopic studies of its complexes with polioviruses. Proc Natl Acad Sci U S A. 2008;105:18284-9 pubmed publisher..These results provide a detailed analysis of how a nonenveloped virus can enter its host cell. ..
- Abuqamar S, Luo H, Laluk K, Mickelbart M, Mengiste T. Crosstalk between biotic and abiotic stress responses in tomato is mediated by the AIM1 transcription factor. Plant J. 2009;58:347-60 pubmed publisher..Together, our data suggest SlAIM1 integrates plant responses to pathogens and abiotic stresses by modulating responses to ABA...
- Benatti T, Valicente F, Aggarwal R, Zhao C, Walling J, Chen M, et al. A neo-sex chromosome that drives postzygotic sex determination in the hessian fly (Mayetiola destructor). Genetics. 2010;184:769-77 pubmed publisher..The inversions are the functional equivalent of the sciarid X-prime chromosomes. We speculate that W' chromosomes exist in a variety of species that produce unisexual broods. ..
- Plevka P, Hafenstein S, Harris K, Cifuente J, Zhang Y, Bowman V, et al. Interaction of decay-accelerating factor with echovirus 7. J Virol. 2010;84:12665-74 pubmed publisher..This suggests that there is an advantage for these viruses to recognize DAF during the initial process of infection. ..
- Lai Z, Li Y, Wang F, Cheng Y, Fan B, Yu J, et al. Arabidopsis sigma factor binding proteins are activators of the WRKY33 transcription factor in plant defense. Plant Cell. 2011;23:3824-41 pubmed publisher..These results suggest that dual-targeted SIB1 and SIB2 function as activators of WRKY33 in plant defense against necrotrophic pathogens. ..
- Guimaraes A, Toth B, Santos A, do Nascimento N, Kritchevsky J, Messick J. Genome sequence of "Candidatus Mycoplasma haemolamae" strain purdue, a red blood cell pathogen of alpacas (Vicugna pacos) and llamas (Lama glama). J Bacteriol. 2012;194:6312-3 pubmed publisher..3% G+C content, and 925 coding sequences (CDSs). A great proportion (49.1%) of these CDSs are organized into paralogous gene families, which can now be further explored with regard to antigenic variation. ..
- Balasubramaniam D, Eissler C, Stauffacher C, Hall M. Use of selected reaction monitoring data for label-free quantification of protein modification stoichiometry. Proteomics. 2010;10:4301-5 pubmed publisher..Use of selected reaction monitoring is advantageous with complex biological samples and we show this approach can be used to quantify multiple PTMs independently on a single peptide. ..
- Vaidya T, Rhodes S, Moore J, Sherman D, Konieczny S, Taparowsky E. Isolation and structural analysis of the rat MyoD gene. Gene. 1992;116:223-30 pubmed..The high degree of identity between the amino acid sequence of rat MyoD and the MyoD proteins isolated from other vertebrates indicates that this muscle regulatory protein has been evolutionarily conserved. ..
- Steczko J, Donoho G, Clemens J, Dixon J, Axelrod B. Conserved histidine residues in soybean lipoxygenase: functional consequences of their replacement. Biochemistry. 1992;31:4053-7 pubmed..The inactive mutants, H499Q, H504Q, H504S, and H690Q, become insoluble when heated for 3 min at 65 degrees C, as does H522Q. The other mutants and the wild-type are stable under these conditions.(ABSTRACT TRUNCATED AT 250 WORDS) ..
- Behm M, Lowman H, Ng S, Bina M. Analysis of temperature-sensitive mutations in the simian virus 40 gene encoding virion protein 1. Proc Natl Acad Sci U S A. 1988;85:9421-5 pubmed..We summarize the behavior of the SV40 ts mutants and discuss the possible relationship between the ts phenotype and amino acid substitutions. ..
- Davis J, Zhou M, Van Etten R. Kinetic and site-directed mutagenesis studies of the cysteine residues of bovine low molecular weight phosphotyrosyl protein phosphatase. J Biol Chem. 1994;269:8734-40 pubmed..The C17A mutant had a 4-fold higher phosphate Ki and slightly higher Km values for p-nitrophenyl phosphate suggesting that Cys-17 may be important for optimal positioning of the substrate phosphate moiety. ..
- Metcalf W, Wanner B. Evidence for a fourteen-gene, phnC to phnP locus for phosphonate metabolism in Escherichia coli. Gene. 1993;129:27-32 pubmed..This was done by testing the effect of phn::uidA insertions in or near the 3' end of phnP on Pn use. Altogether, these results show that all genes required for Pn use are in the 10.9-kb, fourteen-gene, phnCDEFGHIJKLMNOP locus. ..
- Klem T, Davisson V. Imidazole glycerol phosphate synthase: the glutamine amidotransferase in histidine biosynthesis. Biochemistry. 1993;32:5177-86 pubmed..The mechanistic significance of this glutaminase activity compared to other trpG type glutamine amidotransferases is discussed. ..
- Chapman M, Rossmann M. Structure, sequence, and function correlations among parvoviruses. Virology. 1993;194:491-508 pubmed
- Sarria R, Lyznik A, Vallejos C, Mackenzie S. A cytoplasmic male sterility-associated mitochondrial peptide in common bean is post-translationally regulated. Plant Cell. 1998;10:1217-28 pubmed..Our data suggest that ORF239 was undetected in vegetative tissue due to rapid turnover by at least one mitochondrial protease that acts against ORF239 post-translationally. ..
- Yantiri F, Morre D. Isolation and characterization of a tumor-associated NADH oxidase (tNOX) from the HeLa cell surface. Arch Biochem Biophys. 2001;391:149-59 pubmed..The tNOX form from the surface of HeLa cells yielded N-terminal sequence consistent with a coidentity of the cell surface and serum forms of the two activities. ..
- Sang T, Ready D. Eyes closed, a Drosophila p47 homolog, is essential for photoreceptor morphogenesis. Development. 2002;129:143-54 pubmed..Loss of Eyc function results in a lethal failure of nuclear envelope assembly in early zygotic divisions. Phenotypes resulting from eyc mutations provide the first in vivo evidence for a role for p47 in membrane biogenesis. ..
- Kanamaru S, Leiman P, Kostyuchenko V, Chipman P, Mesyanzhinov V, Arisaka F, et al. Structure of the cell-puncturing device of bacteriophage T4. Nature. 2002;415:553-7 pubmed..The amino-terminal, antiparallel beta-barrel domain of gp5 is inserted into a cylinder formed by three gp27 monomers, which may serve as a channel for DNA ejection. ..
- Guo P. Structure and function of phi29 hexameric RNA that drives the viral DNA packaging motor: review. Prog Nucleic Acid Res Mol Biol. 2002;72:415-72 pubmed..This article reviews the structure and function of this pRNA and focuses on novel methods and unique approaches that lead to the illumination of its structure and function. ..
- Kourtev P, Nakatsu C, Konopka A. Responses of the anaerobic bacterial community to addition of organic C in chromium(VI)- and iron(III)-amended microcosms. Appl Environ Microbiol. 2006;72:628-37 pubmed..The studied Cr(VI)-contaminated soil contained a viable anaerobic bacterial community; however, Cr(VI) altered its composition, which could affect the soil biodegradation potential. ..
- Xu X, Chen C, Fan B, Chen Z. Physical and functional interactions between pathogen-induced Arabidopsis WRKY18, WRKY40, and WRKY60 transcription factors. Plant Cell. 2006;18:1310-26 pubmed..cinerea. These results indicate that the three WRKY proteins interact both physically and functionally in a complex pattern of overlapping, antagonistic, and distinct roles in plant responses to different types of microbial pathogens. ..
- Nakatsu C, Hristova K, Hanada S, Meng X, Hanson J, Scow K, et al. Methylibium petroleiphilum gen. nov., sp. nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria. Int J Syst Evol Microbiol. 2006;56:983-9 pubmed..On the basis of the morphological, physiological, biochemical and genetic information, a new genus and species, Methylibium petroleiphilum gen. nov., sp. nov., is proposed, with PM1T (=ATCC BAA-1232T=LMG 22953T) as the type strain...
- Chu H, Low P. Mapping of glycolytic enzyme-binding sites on human erythrocyte band 3. Biochem J. 2006;400:143-51 pubmed..Taken together, these results argue that band 3 provides a nucleation site for the GE complex on the human erythrocyte membrane and that other components near band 3 must also participate in organizing the enzyme complex. ..
- Jung K, Cho W, Regnier F. Glycoproteomics of plasma based on narrow selectivity lectin affinity chromatography. J Proteome Res. 2009;8:643-50 pubmed publisher..Although the number of cancer patients examined was too small to validate cancer marker candidates, they are clearly worth examining in a larger, more diverse patient population. ..
- Hill C, Guerrero F, Van Zee J, Geraci N, Walling J, Stuart J. The position of repetitive DNA sequence in the southern cattle tick genome permits chromosome identification. Chromosome Res. 2009;17:77-89 pubmed publisher..microplus. We present evidence that R. microplus has holocentric chromosomes and explore the implications of these findings for tick chromosome biology and genomic research. ..
- Xing D, Lai Z, Zheng Z, Vinod K, Fan B, Chen Z. Stress- and pathogen-induced Arabidopsis WRKY48 is a transcriptional activator that represses plant basal defense. Mol Plant. 2008;1:459-70 pubmed publisher..These results suggest that WRKY48 is a negative regulator of PR gene expression and basal resistance to the bacterial pathogen P. syringae. ..