Genomes and Genes
Experts and Doctors on molecular sequence data in Ames, Iowa, United States
Locale: Ames, Iowa, United States
Topic: molecular sequence data
Publications106 found, 100 shown here
- Gao M, Wanat J, Stinard P, James M, Myers A. Characterization of dull1, a maize gene coding for a novel starch synthase. Plant Cell. 1998;10:399-412 pubmed..We conclude that Du1 codes for a starch synthase, most likely SSII, and that secondary effects of du1- mutations, such as reduction of SBEIIa, result from the primary deficiency in this starch synthase. ..
- Bricker B, Ewalt D, Macmillan A, Foster G, Brew S. Molecular characterization of Brucella strains isolated from marine mammals. J Clin Microbiol. 2000;38:1258-62 pubmed..In keeping with historical precedent, the designation of several new Brucella species may be appropriate. ..
- Koev G, Liu S, Beckett R, Miller W. The 3prime prime or minute-terminal structure required for replication of Barley yellow dwarf virus RNA contains an embedded 3prime prime or minute end. Virology. 2002;292:114-26 pubmed..This 3prime prime or minute structure and the polymerase homologies suggest that genus Luteovirus is more closely related to the Tombusviridae family than to other Luteoviridae genera. ..
- Ji Y, Rath U, Girton J, Johansen K, Johansen J. D-Hillarin, a novel W180-domain protein, affects cytokinesis through interaction with the septin family member Pnut. J Neurobiol. 2005;64:157-69 pubmed..Based on these results we propose that D-hil may function as a regulator of septin function during cytokinesis in the developing nervous system. ..
- Terribilini M, Lee J, Yan C, Jernigan R, Honavar V, Dobbs D. Prediction of RNA binding sites in proteins from amino acid sequence. RNA. 2006;12:1450-62 pubmed..RNABindR is available as a Web tool from http://bindr.gdcb.iastate.edu.). ..
- Terribilini M, Sander J, Lee J, Zaback P, Jernigan R, Honavar V, et al. RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Res. 2007;35:W578-84 pubmed..RNABindR automatically displays 'high specificity' and 'high sensitivity' predictions of RNA-binding residues. RNABindR is freely available at http://bindr.gdcb.iastate.edu/RNABindR. ..
- Cheung A. Homologous recombination plays minor role in excision of unit-length viral genomes from head-to-tail direct tandem repeats of porcine circovirus during DNA replication in Escherichia coli. Arch Virol. 2007;152:1531-9 pubmed..Thus, in comparison with RCR, homologous recombination plays a minor role in the excision of unit-length PCV genomes from HTT constructs in Escherichia coli. ..
- Yu F, Liu X, Alsheikh M, Park S, Rodermel S. Mutations in SUPPRESSOR OF VARIEGATION1, a factor required for normal chloroplast translation, suppress var2-mediated leaf variegation in Arabidopsis. Plant Cell. 2008;20:1786-804 pubmed publisher..Our data indicate that defects in chloroplast rRNA processing are a common, but not universal, molecular phenotype associated with suppression of var2 variegation. ..
- Pan X, Zhao Y. Efficient construction of oligocholate foldamers via "click" chemistry and their tolerance of structural heterogeneity. Org Lett. 2009;11:69-72 pubmed publisher..Despite large structural perturbations, the clicked oligocholates folded similarly as the parent foldamers, demonstrating the robustness of the solvophobically driven folding mechanism. ..
- Brar H, Swaminathan S, Bhattacharyya M. The Fusarium virguliforme toxin FvTox1 causes foliar sudden death syndrome-like symptoms in soybean. Mol Plant Microbe Interact. 2011;24:1179-88 pubmed publisher..The requirement of light for foliar SDS-like symptom development indicates that FvTox1 induces foliar SDS in soybean, most likely through production of free radicals by interrupting photosynthesis. ..
- Fan C, Bobik T. The N-terminal region of the medium subunit (PduD) packages adenosylcobalamin-dependent diol dehydratase (PduCDE) into the Pdu microcompartment. J Bacteriol. 2011;193:5623-8 pubmed publisher..Immunoprecipitation tests indicated that the fusion proteins were encapsulated inside the MCP shell. ..
- Xiao C, Halbur P, Opriessnig T. Complete genome sequence of a newly identified porcine astrovirus genotype 3 strain US-MO123. J Virol. 2012;86:13126 pubmed publisher..Sequence comparison and phylogenetic analysis showed that PAstV3 has the closest relationship with mink AstV and the human AstV strains VA1, VA2, and SG, indicating the same ancestral origin and zoonotic potential of the virus. ..
- Srivastava R, Deng Y, Shah S, Rao A, Howell S. BINDING PROTEIN is a master regulator of the endoplasmic reticulum stress sensor/transducer bZIP28 in Arabidopsis. Plant Cell. 2013;25:1416-29 pubmed publisher..Thus, the dissociation of BiP from the C-terminal tail of bZIP28 is a major switch that activates one arm of the unfolded protein response signaling pathway in plants. ..
- Kappes M, Miller C, Faaberg K. Highly divergent strains of porcine reproductive and respiratory syndrome virus incorporate multiple isoforms of nonstructural protein 2 into virions. J Virol. 2013;87:13456-65 pubmed publisher..Together, these data identify nsp2 as a virion-associated structural PRRSV protein and reveal that nsp2 exists in or on viral particles as multiple isoforms. ..
- Zuerner R, Alt D, Bolin C. IS1533-based PCR assay for identification of Leptospira interrogans sensu lato serovars. J Clin Microbiol. 1995;33:3284-9 pubmed..These results demonstrate that this assay is selective enough to be used for typing leptospiral serovars from clinical material and thus allows leptospiral typing without isolation of the bacteria in pure culture. ..
- Rath U, Wang D, Ding Y, Xu Y, Qi H, Blacketer M, et al. Chromator, a novel and essential chromodomain protein interacts directly with the putative spindle matrix protein skeletor. J Cell Biochem. 2004;93:1033-47 pubmed..These findings suggest that Chromator is a nuclear protein that plays a role in proper spindle dynamics during mitosis. ..
- Walker D, Wang D, Jin Y, Rath U, Wang Y, Johansen J, et al. Skeletor, a novel chromosomal protein that redistributes during mitosis provides evidence for the formation of a spindle matrix. J Cell Biol. 2000;151:1401-12 pubmed..Thus, the identification and characterization of skeletor represents the first direct molecular evidence for the existence of a complete spindle matrix that forms within the nucleus before microtubule spindle formation. ..
- Trent J, Hargrove M. A ubiquitously expressed human hexacoordinate hemoglobin. J Biol Chem. 2002;277:19538-45 pubmed..The discovery of histoglobin demonstrates that humans, like plants, differentially express multiple hexacoordinate hemoglobins. ..
- Patton T, Scupham A, Bearson S, Carlson S. Characterization of fecal microbiota from a Salmonella endemic cattle herd as determined by oligonucleotide fingerprinting of rDNA genes. Vet Microbiol. 2009;136:285-92 pubmed publisher..Finally, this study did not identify species that prevented Salmonella colonization or resulted from Salmonella colonization. ..
- Stanton T, Humphrey S, Bayles D, Zuerner R. Identification of a divided genome for VSH-1, the prophage-like gene transfer agent of Brachyspira hyodysenteriae. J Bacteriol. 2009;191:1719-21 pubmed publisher..6-kb cluster. The location and transcription direction of these genes relative to those of the previously described VSH-1 16.3-kb gene operon indicate that the gene transfer agent VSH-1 has a noncontiguous, divided genome. ..
- Zhao X, Dittmer K, Blair H, Thompson K, Rothschild M, Garrick D. A novel nonsense mutation in the DMP1 gene identified by a genome-wide association study is responsible for inherited rickets in Corriedale sheep. PLoS ONE. 2011;6:e21739 pubmed publisher..Affected sheep could be used as animal models for this form of human rickets, and for further investigation of the role of DMP1 in phosphate homeostasis. ..
- Gao H, Narayanan N, Ellison L, Bhattacharyya M. Two classes of highly similar coiled coil-nucleotide binding-leucine rich repeat genes isolated from the Rps1-k locus encode Phytophthora resistance in soybean. Mol Plant Microbe Interact. 2005;18:1035-45 pubmed..Analyses of independent R0, R1, R2, and R3 progeny populations suggested that both gene classes confer Phytophthora resistance in soybean. A possible evolutionary mechanism for the Class I gene family is proposed. ..
- Poland B, Bruns C, Fromm H, Honzatko R. Entrapment of 6-thiophosphoryl-IMP in the active site of crystalline adenylosuccinate synthetase from Escherichia coli. J Biol Chem. 1997;272:15200-5 pubmed..The direct observation of 6-thiophosphoryl-IMP in the active site is consistent with the putative generation of 6-phosphoryl-IMP along the reaction pathway of the synthetase. ..
- Suarez D, Whetstone C. Size variation within the second hypervariable region of the surface envelope gene of the bovine lentivirus BIV in experimentally and naturally infected cattle. J Virol. 1997;71:2482-6 pubmed..Similar to other lentiviruses, BIV appears to mutate rapidly, which may be important in viral persistence and pathogenesis. ..
- Stickney J, Buss J. Murine guanylate-binding protein: incomplete geranylgeranyl isoprenoid modification of an interferon-gamma-inducible guanosine triphosphate-binding protein. Mol Biol Cell. 2000;11:2191-200 pubmed..The C20-selective impairment in prenylation also identifies mGBP1 as an important model for the study of substrate/geranylgeranyl transferase I interactions. ..
- McGrail M, Hatler J, Kuang X, Liao H, Nannapaneni K, Watt K, et al. Somatic mutagenesis with a Sleeping Beauty transposon system leads to solid tumor formation in zebrafish. PLoS ONE. 2011;6:e18826 pubmed publisher..The zebrafish T2/OncZ cancer model will be useful for identifying novel and conserved genetic drivers of human cancers. ..
- Beck B, Tabatabai L, Mayfield J. A protein isolated from Brucella abortus is a Cu-Zn superoxide dismutase. Biochemistry. 1990;29:372-6 pubmed..The high degree of conservation between Photobacterium and Brucella Cu-Zn SOD supports the hypothesis of a separately evolved prokaryotic and eukaryotic Cu-Zn SOD gene. ..
- Williams T, Zhang C, Scott J, Bazylinski D. Evidence for autotrophy via the reverse tricarboxylic acid cycle in the marine magnetotactic coccus strain MC-1. Appl Environ Microbiol. 2006;72:1322-9 pubmed..These results are consistent with the operation of the rTCA cycle in MC-1. Strain MC-1 appears to be the first known representative of the alpha-Proteobacteria to use the rTCA cycle for autotrophy. ..
- Kirthi N, Roy Chaudhuri B, Kelley T, Culver G. A novel single amino acid change in small subunit ribosomal protein S5 has profound effects on translational fidelity. RNA. 2006;12:2080-91 pubmed..This study highlights the importance of S5 in ribosome function and cell physiology, and suggests that translational fidelity can be regulated in multiple ways. ..
- Chen Q, Li G, Stasko J, Thomas J, Stensland W, Pillatzki A, et al. Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States. J Clin Microbiol. 2014;52:234-43 pubmed publisher..Phylogenetic analyses using different genes of PEDV suggested that the full-length spike gene or the S1 portion is appropriate for sequencing to study the genetic relatedness of these viruses. ..
- Shen C, Shao Z, Powell Coffman J. The Caenorhabditis elegans rhy-1 gene inhibits HIF-1 hypoxia-inducible factor activity in a negative feedback loop that does not include vhl-1. Genetics. 2006;174:1205-14 pubmed..Collectively, these data support models in which RHY-1 and EGL-9 function in VHL-1-independent pathway(s) to repress HIF-1 transcriptional activity. ..
- Kleiboeker S. Sequence analysis of the fiber genomic region of a porcine adenovirus predicts a novel fiber protein. Virus Res. 1995;39:299-309 pubmed..Thus the predicted amino acid sequence of the NADC-1 fiber head is unique among adenoviruses for which the sequence of the fiber protein is known. ..
- Cheung A. Rolling-circle replication of an animal circovirus genome in a theta-replicating bacterial plasmid in Escherichia coli. J Virol. 2006;80:8686-94 pubmed
- Hemken P, Bellin R, Sernett S, Becker B, Huiatt T, Robson R. Molecular characteristics of the novel intermediate filament protein paranemin. Sequence reveals EAP-300 and IFAPa-400 are highly homologous to paranemin. J Biol Chem. 1997;272:32489-99 pubmed..Antibody labeling of these cells suggests that paranemin does not form IFs by itself, but rather is incorporated into heteropolymeric IFs with vimentin. ..
- Carter C, Thornburg R. The nectary-specific pattern of expression of the tobacco Nectarin I promoter is regulated by multiple promoter elements. Plant Mol Biol. 2003;51:451-7 pubmed..Analysis in transgenic plants revealed that the nectary-specific expression is the result of multiple promoter elements and suggests that nectar secretion and flower opening may be coordinately regulated. ..
- Messer L, Wang L, Tuggle C, Yerle M, Chardon P, Pomp D, et al. Mapping of the melatonin receptor 1a (MTNR1A) gene in pigs, sheep, and cattle. Mamm Genome. 1997;8:368-70 pubmed
- Li J, Harper L, Golubovskaya I, Wang C, Weber D, Meeley R, et al. Functional analysis of maize RAD51 in meiosis and double-strand break repair. Genetics. 2007;176:1469-82 pubmed..The finding that maize rad51 double mutant embryos are extremely susceptible to radiation-induced DSBs demonstrates a conserved role for RAD51 in the repair of mitotic DSBs in plants, vertebrates, and yeast. ..
- Valenzuela N. Multivariate expression analysis of the gene network underlying sexual development in turtle embryos with temperature-dependent and genotypic sex determination. Sex Dev. 2010;4:39-49 pubmed publisher..mutica, consistent with the hypothesis that sexual development is a more canalized process in A. mutica, as would be expected if GSD evolved in this lineage through directional selection from its TSD ancestor...
- Duncan S, Sirkanungo R, Miller L, Phillips G. DraGnET: software for storing, managing and analyzing annotated draft genome sequence data. BMC Bioinformatics. 2010;11:100 pubmed publisher..dragnet.cvm.iastate.edu and includes example files for examining the functionalities, a link for downloading the DraGnET setup package and a link to the DraGnET source code hosted with full documentation on SourceForge. ..
- Kim S, Bassham D. TNO1 is involved in salt tolerance and vacuolar trafficking in Arabidopsis. Plant Physiol. 2011;156:514-26 pubmed publisher..These data demonstrate that TNO1 is involved in vacuolar trafficking and salt tolerance, potentially via roles in vesicle fusion and in maintaining TGN structure or identity. ..
- Bannantine J, Lingle C, Stabel J, Ramyar K, Garcia B, Raeber A, et al. MAP1272c encodes an NlpC/P60 protein, an antigen detected in cattle with Johne's disease. Clin Vaccine Immunol. 2012;19:1083-92 pubmed publisher..These tools provide additional means to study a strong antigen of M. avium subsp. paratuberculosis. ..
- Joseph R, Norris F. Substrate specificity and recognition is conferred by the pleckstrin homology domain of the Dbl family guanine nucleotide exchange factor P-Rex2. J Biol Chem. 2005;280:27508-12 pubmed..Thus substrate recognition can now be added to the growing list of functions that are being attributed to the PH domain of Dbl family GEFs. ..
- Register K, Yersin A. Analytical verification of a PCR assay for identification of Bordetella avium. J Clin Microbiol. 2005;43:5567-73 pubmed..Sequence analysis of the B. avium PCR amplicons identified only three occasional sequence polymorphisms. These data indicate the B. avium PCR assay can provide clinically significant results...
- Meng Y, Moscou M, Wise R. Blufensin1 negatively impacts basal defense in response to barley powdery mildew. Plant Physiol. 2009;149:271-85 pubmed publisher..Collectively, these data suggest that the grass-specific Bln1 negatively impacts basal defense against Bgh...
- Liu J, Howell S. bZIP28 and NF-Y transcription factors are activated by ER stress and assemble into a transcriptional complex to regulate stress response genes in Arabidopsis. Plant Cell. 2010;22:782-96 pubmed publisher..Thus, in response to ER stress, bZIP28 is mobilized by proteolysis and recruits NF-Y subunits to form a transcriptional complex that upregulates the expression of ER stress-induced genes. ..
- Iancu C, Borza T, Choe J, Fromm H, Honzatko R. Recombinant mouse muscle adenylosuccinate synthetase: overexpression, kinetics, and crystal structure. J Biol Chem. 2001;276:42146-52 pubmed..Observed differences in ligand recognition among adenylosuccinate synthetases may be due in part to conformational variations in the IMP pocket of the ligand-free enzymes. ..
- Zhang W, Wang Y, Long J, Girton J, Johansen J, Johansen K. A developmentally regulated splice variant from the complex lola locus encoding multiple different zinc finger domain proteins interacts with the chromosomal kinase JIL-1. J Biol Chem. 2003;278:11696-704 pubmed..Thus, genetic interaction assays provide direct evidence that gene products from the lola locus function within the same pathway as the chromosomal kinase JIL-1. ..
- Gao X, Vander Velden K, Voytas D, Gu X. SplitTester: software to identify domains responsible for functional divergence in protein family. BMC Bioinformatics. 2005;6:137 pubmed..From the analysis of retroelements reverse transcriptase family, we successfully identified the regions splitting this family according to the primer specificity, implying their functions in the specific primer selection. ..
- Fan C, Fromm H, Bobik T. Kinetic and functional analysis of L-threonine kinase, the PduX enzyme of Salmonella enterica. J Biol Chem. 2009;284:20240-8 pubmed publisher..The studies reported here are the first to investigate the kinetic and catalytic mechanisms of l-threonine kinase from any organism. ..
- Meyer M, Lichti C, Townsend R, Rao A. Identification of in vitro autophosphorylation sites and effects of phosphorylation on the Arabidopsis CRINKLY4 (ACR4) receptor-like kinase intracellular domain: insights into conformation, oligomerization, and activity. Biochemistry. 2011;50:2170-86 pubmed publisher..Sedimentation velocity and gel filtration experiments indicate that the ICD has a propensity to oligomerize and that this property is lost upon autophosphorylation. ..
- Yu C, Zhang J, Peterson T. Genome rearrangements in maize induced by alternative transposition of reversed ac/ds termini. Genetics. 2011;188:59-67 pubmed publisher..These results document the types and frequencies of genome rearrangements induced by alternative transposition of reversed Ac/Ds termini in maize...
- Shen H, Halbur P, Opriessnig T. Prevalence and phylogenetic analysis of the current porcine circovirus 2 genotypes after implementation of widespread vaccination programmes in the USA. J Gen Virol. 2012;93:1345-55 pubmed publisher..The data generated in this study provide novel information on the distribution of PCV2 genotypes in vaccinated pig populations...
- Messer L, Wang L, Yelich J, Pomp D, Geisert R, Rothschild M. Linkage mapping of the retinol-binding protein 4 (RBP4) gene to porcine chromosome 14. Mamm Genome. 1996;7:396 pubmed
- Bergmann D, Zahn J, Hooper A, DiSpirito A. Cytochrome P460 genes from the methanotroph Methylococcus capsulatus bath. J Bacteriol. 1998;180:6440-5 pubmed..capsulatus Bath indicated that the expression level of cytochrome P460 was not affected either by expression of the two different methane monooxygenases or by addition of ammonia to the culture medium...
- Hou Z, Cashel M, Fromm H, Honzatko R. Effectors of the stringent response target the active site of Escherichia coli adenylosuccinate synthetase. J Biol Chem. 1999;274:17505-10 pubmed..Conceivably, synthetase activity in vivo during the stringent response may be sensitive to the relative concentrations of several effectors, which together exercise precise control over the de novo synthesis of AMP. ..
- Baccam P, Thompson R, Li Y, Sparks W, Belshan M, Dorman K, et al. Subpopulations of equine infectious anemia virus Rev coexist in vivo and differ in phenotype. J Virol. 2003;77:12122-31 pubmed..A quasispecies model with multiple subpopulations may provide additional insight into the nature of lentivirus reservoirs and the evolution of antigenic and drug-resistant variants...
- Shen R, Miller W. The 3' untranslated region of tobacco necrosis virus RNA contains a barley yellow dwarf virus-like cap-independent translation element. J Virol. 2004;78:4655-64 pubmed..We propose a new class of cap-independent TE called BYDV-like TE...
- Iancu C, Zhou Y, Borza T, Fromm H, Honzatko R. Cavitation as a mechanism of substrate discrimination by adenylosuccinate synthetases. Biochemistry. 2006;45:11703-11 pubmed..At an approximate energy cost of 2.2 kcal/mol, the unfavorable thermodynamics of cavity formation may be the major factor in destabilizing ligands at the L-aspartate pocket. ..
- Sahin O, Plummer P, Jordan D, Sulaj K, Pereira S, Robbe Austerman S, et al. Emergence of a tetracycline-resistant Campylobacter jejuni clone associated with outbreaks of ovine abortion in the United States. J Clin Microbiol. 2008;46:1663-71 pubmed publisher..Together, these results indicate that a single tetracycline-resistant C. jejuni clone has emerged as the major cause of Campylobacter-associated sheep abortion in the United States...
- Zuerner R, Alt D. Variable nucleotide tandem-repeat analysis revealing a unique group of Leptospira interrogans serovar Pomona isolates associated with California sea lions. J Clin Microbiol. 2009;47:1202-5 pubmed publisher..Significantly, California sea lion isolates formed a unique group, providing evidence that these animals are maintenance hosts of serovar Pomona...
- Jin H, Kanthasamy A, Anantharam V, Rana A, Kanthasamy A. Transcriptional regulation of pro-apoptotic protein kinase Cdelta: implications for oxidative stress-induced neuronal cell death. J Biol Chem. 2011;286:19840-59 pubmed publisher..Collectively, our findings may have implications for development of new translational strategies against oxidative damage. ..
- Zamanian M, Agbedanu P, Wheeler N, McVeigh P, Kimber M, Day T. Novel RNAi-mediated approach to G protein-coupled receptor deorphanization: proof of principle and characterization of a planarian 5-HT receptor. PLoS ONE. 2012;7:e40787 pubmed publisher..Future work can help optimize and adapt this protocol for higher-throughput platforms as well as other phyla...
- Liu S, Chougule N, Vijayendran D, Bonning B. Deep sequencing of the transcriptomes of soybean aphid and associated endosymbionts. PLoS ONE. 2012;7:e45161 pubmed publisher..The soybean aphid has significantly impacted soybean production in the U.S. Transcriptomic analyses were conducted for further insight into leads for potential novel management strategies...
- Wang W, Gorrell A, Honzatko R, Fromm H. A study of Escherichia coli adenylosuccinate synthetase association states and the interface residues of the homodimer. J Biol Chem. 1997;272:7078-84 pubmed..Our results suggest that IMP binding induces enzyme dimerization and that two residues in the interface region, Arg143 and Asp231, play significant roles in IMP and GTP binding. ..
- Zhou L, Lacroute F, Thornburg R. Cloning, expression in Escherichia coli, and characterization of Arabidopsis thaliana UMP/CMP kinase. Plant Physiol. 1998;117:245-54 pubmed..The optimal pH for the enzyme is 6.5. P1, P5-di(adenosine-5') pentaphosphate was found to be a competitive inhibitor of both ATP and UMP. ..
- Wu D, Wright D, Wetzel C, Voytas D, Rodermel S. The IMMUTANS variegation locus of Arabidopsis defines a mitochondrial alternative oxidase homolog that functions during early chloroplast biogenesis. Plant Cell. 1999;11:43-55 pubmed
- Chang C, Yoon K, Zimmerman J, Harmon K, Dixon P, Dvorak C, et al. Evolution of porcine reproductive and respiratory syndrome virus during sequential passages in pigs. J Virol. 2002;76:4750-63 pubmed..Although no epitopic changes were detected under the conditions of this experiment, PRRS virus was shown to evolve continuously in infected pigs, with different genes of the viral genome undergoing various degrees of change. ..
- Borza T, Iancu C, Pike E, Honzatko R, Fromm H. Variations in the response of mouse isozymes of adenylosuccinate synthetase to inhibitors of physiological relevance. J Biol Chem. 2003;278:6673-9 pubmed..Fructose 1,6-bisphosphate and IMP together may be dynamic regulators of the basic isozyme in muscle, causing potent inhibition of the synthetase under conditions of high AMP deaminase activity. ..
- Dinges J, Colleoni C, James M, Myers A. Mutational analysis of the pullulanase-type debranching enzyme of maize indicates multiple functions in starch metabolism. Plant Cell. 2003;15:666-80 pubmed..Therefore, pullulanase-type DBE partially compensates for the defect in isoamylase-type DBE, suggesting a function during starch synthesis as well as degradation. ..
- Humphries J, Kimber M, Barton Y, Hsu W, Marks N, Greer B, et al. Structure and bioactivity of neuropeptide F from the human parasites Schistosoma mansoni and Schistosoma japonicum. J Biol Chem. 2004;279:39880-5 pubmed
- El Manzalawy Y, Dobbs D, Honavar V. On evaluating MHC-II binding peptide prediction methods. PLoS ONE. 2008;3:e3268 pubmed publisher..These results underscore the importance of using similarity-reduced datasets in rigorously comparing the performance of alternative MHC-II peptide prediction methods. ..
- Hewezi T, Howe P, Maier T, Hussey R, Mitchum M, Davis E, et al. Cellulose binding protein from the parasitic nematode Heterodera schachtii interacts with Arabidopsis pectin methylesterase: cooperative cell wall modification during parasitism. Plant Cell. 2008;20:3080-93 pubmed publisher..These data indicate that CBP directly interacts with PME3 thereby activating and potentially targeting this enzyme to aid cyst nematode parasitism. ..
- Xu M, Brar H, Grosic S, Palmer R, Bhattacharyya M. Excision of an active CACTA-like transposable element from DFR2 causes variegated flowers in soybean [Glycine max (L.) Merr.]. Genetics. 2010;184:53-63 pubmed publisher..The highly active endogenous transposon, Tgm9, should facilitate genomics studies specifically that relate to legume biology. ..
- Sturms R, Kakar S, Trent J, Hargrove M. Trema and parasponia hemoglobins reveal convergent evolution of oxygen transport in plants. Biochemistry. 2010;49:4085-93 pubmed publisher..These results demonstrate distinct mechanisms for convergent evolution of oxygen transport in different phylogenetic classes of plant hemoglobins...
- Scupham A, Jones J, Rettedal E, Weber T. Antibiotic manipulation of intestinal microbiota to identify microbes associated with Campylobacter jejuni exclusion in poultry. Appl Environ Microbiol. 2010;76:8026-32 pubmed publisher..Examination of the constituents of the derived communities via the array-based method oligonucleotide fingerprinting of rRNA genes detected a subtype of Megamonas hypermegale specific to the C. jejuni-suppressive treatments...
- Xiao C, Giménez Lirola L, Jiang Y, Halbur P, Opriessnig T. Characterization of a novel porcine parvovirus tentatively designated PPV5. PLoS ONE. 2013;8:e65312 pubmed publisher..The high similarity to PPV4 and the lack of ORF3 may suggest PPV5 is an intermediate of PPV4 during the evolution of parvoviruses in pigs. ..
- Ellingson J, Bolin C, Stabel J. Identification of a gene unique to Mycobacterium avium subspecies paratuberculosis and application to diagnosis of paratuberculosis. Mol Cell Probes. 1998;12:133-42 pubmed publisher..paratuberculosis. The dOH method could be a good alternative to existing assays and will be adapted for specific identification of M. paratuberculosis from faecal samples, mixed bacteriologic cultures, tissue specimens and whole blood...
- Coats S, Booden M, Buss J. Transient palmitoylation supports H-Ras membrane binding but only partial biological activity. Biochemistry. 1999;38:12926-34 pubmed..Farnesyl may be important for signaling, especially transformation, while palmitates may provide potentially dynamic regulation of membrane binding. ..
- Townsend J, Wright D, Winfrey R, Fu F, Maeder M, Joung J, et al. High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature. 2009;459:442-5 pubmed publisher..More than 40% of recombinant plants had modifications in multiple SuR alleles. The observed high frequency of gene targeting indicates that it is now possible to efficiently make targeted sequence changes in endogenous plant genes. ..
- Gao Y, Shen L, Honzatko R. Central cavity of fructose-1,6-bisphosphatase and the evolution of AMP/fructose 2,6-bisphosphate synergism in eukaryotic organisms. J Biol Chem. 2014;289:8450-61 pubmed publisher..Taken together, these observations suggest the evolution of AMP/Fru-2,6-P2 synergism in eukaryotic FBPases from an ancestral FBPase having a central aqueous cavity and exhibiting synergistic feedback inhibition by AMP and Fru-6-P. ..
- Ernst C, Kapke P, Yerle M, Rothschild M. The leptin receptor gene (LEPR) maps to porcine chromosome 6. Mamm Genome. 1997;8:226 pubmed
- Adams K, Percifield R, Wendel J. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics. 2004;168:2217-26 pubmed publisher..These results provide a detailed portrayal of gene silencing events that can occur following allopolyploidization and suggest epigenetic causal factors...
- Fatland B, Nikolau B, Wurtele E. Reverse genetic characterization of cytosolic acetyl-CoA generation by ATP-citrate lyase in Arabidopsis. Plant Cell. 2005;17:182-203 pubmed
- Fu A, Park S, Rodermel S. Sequences required for the activity of PTOX (IMMUTANS), a plastid terminal oxidase: in vitro and in planta mutagenesis of iron-binding sites and a conserved sequence that corresponds to Exon 8. J Biol Chem. 2005;280:42489-96 pubmed..Chloroplast import assays revealed that mutant enzymes lacking Exon 8 have enhanced turnover. We conclude that the Exon 8 domain is required not only for PTOX activity but also for its stability. ..
- Shao Z, Graf S, Chaga O, Lavrov D. Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule encoding a putative DNA-dependent DNA polymerase. Gene. 2006;381:92-101 pubmed publisher..The acquisition of mitochondrial genomic data for the second class of Cnidaria allows us to reconstruct characteristic features of mitochondrial evolution in this animal phylum...
- Fu Y, Wen T, Ronin Y, Chen H, Guo L, Mester D, et al. Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize. Genetics. 2006;174:1671-83 pubmed publisher..Detection of two-locus gamete disequilibrium provides another means to extract functional genomic data from well-characterized plant RILs...
- Hawkins J, Kim H, Nason J, Wing R, Wendel J. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res. 2006;16:1252-61 pubmed..Like maize, Gossypium has undergone a threefold increase in genome size due to the accumulation of LTR retrotransposons over the 5-10 Myr since its origin. ..