A collection of 200 wheat (Triticum aestivum L. cv ‘Chinese Spring’) cytogenetic stocks (nullisomic, tetrasomic, nulli-tetrasomic, ditelosomic and deletion lines, addition and substitution stocks from intra- and inter-specific crosses)... more
A collection of 200 wheat (Triticum aestivum L. cv ‘Chinese Spring’) cytogenetic stocks (nullisomic, tetrasomic, nulli-tetrasomic, ditelosomic and deletion lines, addition and substitution stocks from intra- and inter-specific crosses) was utilized to determine the proteins encoded by some of the wheat and barley dehydrin genes, using a western blot procedure. Proteins extracted from seeds were reacted with antibodies that recognize
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Research Interests: Genetics, Medicinal Plants, Multidisciplinary, Gene Mapping, Genetic linkage analysis, and 12 moreMolecular cloning, Electrolytes, Fabaceae, Environmental Stress, Genetic variation, Low Temperature, Amino Acid Sequence, Base Sequence, Amino Acid Substitution Rates, PLANT PROTEINS, Vigna Unguiculata, and Electrolyte Leakage
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... Dicktoo (the more tolerant cul-tivar) and Morex (the less tolerant) grown in Saskatoon, Canada expressed higher levels of expression of genes for ... of freezing tolerance, plants grown in Saskatoon were frozen and shipped to... more
... Dicktoo (the more tolerant cul-tivar) and Morex (the less tolerant) grown in Saskatoon, Canada expressed higher levels of expression of genes for ... of freezing tolerance, plants grown in Saskatoon were frozen and shipped to Riverside by Ping Fu and Lawrence Gusta (University ...
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A system has been developed to transcriptionally map plasmid DNA molecules in vivo. This system is based upon the activity of the Tn 9 Cm r gene whose product, chloramphenicol acetyltransferase (CAT), can be easily assayed enzymatically... more
A system has been developed to transcriptionally map plasmid DNA molecules in vivo. This system is based upon the activity of the Tn 9 Cm r gene whose product, chloramphenicol acetyltransferase (CAT), can be easily assayed enzymatically and identified phenotypically in Escherichia ...
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Research Interests:
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A maize dehydrin protein (Dhn1) containing 167 amino acids with a predicted molecular weight of 17.0 kDa was produced in the Escherichia coli overexpression strain BL21 (DE3)pLysS. Site-directed mutagenesis was used to construct a plasmid... more
A maize dehydrin protein (Dhn1) containing 167 amino acids with a predicted molecular weight of 17.0 kDa was produced in the Escherichia coli overexpression strain BL21 (DE3)pLysS. Site-directed mutagenesis was used to construct a plasmid with a protein coding region corresponding exactly to the original cDNA. Protein production was induced by IPTG. Dhn1 was enriched from total soluble protein by heat-fractionation and centrifugation and then purified by sequential cation exchange and hydrophobic interaction chromatography. The purified protein was visualized by SDS-PAGE and immunoblot analysis using a polyclonal antibody to the dehydrin consensus region. Expression in E. coli resulted in approximately 1.2 mg of purified protein per liter of induced culture.
Research Interests: Escherichia coli, Maize, Solubility, High Pressure Liquid Chromatography, Molecular cloning, and 11 moreProtein expression and purification, Zea mays, Time Factors, Molecular weight, Amino Acid Sequence, Base Sequence, Recombinant Proteins, Cation Exchange, PLANT PROTEINS, Biochemistry and cell biology, and Immunoblotting
... Tyler Close, Sujata Banerjee, Rick McGeer HP Labs Palo Alto, CA 94043 firstname.lastname @hp.com ... 2.1 S3: A Scalable Sensing Service S3 is a Scalable Sensing Service for real-time mon-itoring and management of large networked... more
... Tyler Close, Sujata Banerjee, Rick McGeer HP Labs Palo Alto, CA 94043 firstname.lastname @hp.com ... 2.1 S3: A Scalable Sensing Service S3 is a Scalable Sensing Service for real-time mon-itoring and management of large networked systems. ...
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. Direct percutaneous endoscopic jejunostomy (DPEJ) is an effective method of enteral feeding. However, failure rates with this procedure remain high due to various technical problems. We describe a case where modifications in the... more
. Direct percutaneous endoscopic jejunostomy (DPEJ) is an effective method of enteral feeding. However, failure rates with this procedure remain high due to various technical problems. We describe a case where modifications in the technique and ultrasound guidance assisted in a difficult DPEJ placement. This technique has the potential to improve the success rate of this procedure in selected cases.
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Few, if any, complications have been reported with the nonoperative management of selected hepatic injuries diagnosed by computed tomographic (CT) scan in hemodynamically stable patients. This retrospective study was designed to evaluate... more
Few, if any, complications have been reported with the nonoperative management of selected hepatic injuries diagnosed by computed tomographic (CT) scan in hemodynamically stable patients. This retrospective study was designed to evaluate complications associated with this form of management. Twenty-six patients (21%) of 128 patients with blunt hepatic injuries were treated nonoperatively over a 3-year period. All patients were hemodynamically stable at the time of admission and had hepatic injuries identified by CT scans of the abdomen. Five patients (19%) developed complications associated with nonoperative therapy. Of these, two patients had minor hepatic injuries (grades 1-2) and three had major (grades 3-5) hepatic injuries. Two patients (one with minor and one with major hepatic injury), developed free intraperitoneal biliary leaks and required operative repair. Three patients (one with minor and two with major hepatic injuries) developed large subcapsular bilomas with resultant hepatic dysfunction. These patients were successfully managed with percutaneous CT-guided drainage. There were no deaths in our study population with nonoperative therapy. The complications of hepatic injuries initially managed by expectant observation were treated operatively or by percutaneous CT-guided drainage. Repeated CT evaluation to follow the progress of liver fracture and the occasional use of hepatobiliary scans for the identification of biliary leaks have proven useful in our experience.
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... Lauren Williams for rescue from crisis. ... Michael Butler, Tyler Close, John Corbett, M. Scott Doerrie, Jed Donnelley, K. Eric Drexler, Ian Grigg, Norm Hardy, Chris Hibbert, Jack High, Tad Hogg, David Hopwood, Jim Hopwood, Ted... more
... Lauren Williams for rescue from crisis. ... Michael Butler, Tyler Close, John Corbett, M. Scott Doerrie, Jed Donnelley, K. Eric Drexler, Ian Grigg, Norm Hardy, Chris Hibbert, Jack High, Tad Hogg, David Hopwood, Jim Hopwood, Ted Kaehler, Ken Kahn, Piotr Kaminski, Alan Karp ...
... Tyler Close, Sujata Banerjee, Rick McGeer HP Labs Palo Alto, CA 94043 firstname.lastname @hp.com ... 2.1 S3: A Scalable Sensing Service S3 is a Scalable Sensing Service for real-time mon-itoring and management of large networked... more
... Tyler Close, Sujata Banerjee, Rick McGeer HP Labs Palo Alto, CA 94043 firstname.lastname @hp.com ... 2.1 S3: A Scalable Sensing Service S3 is a Scalable Sensing Service for real-time mon-itoring and management of large networked systems. ...
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A rare complication of aortoiliac bypass procedure resulting in the formation of an acute ilio-iliac arteriovenous fistula was presented. The latter was a first manifestation of anastomotic iliac pseudoaneurysm. This is only the second... more
A rare complication of aortoiliac bypass procedure resulting in the formation of an acute ilio-iliac arteriovenous fistula was presented. The latter was a first manifestation of anastomotic iliac pseudoaneurysm. This is only the second such case reported in the English literature. Iliac anastomotic pseudoaneurysm although rarely detected, is a potentially lethal complication that has to be repaired close to the time of its detection.
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Research Interests:
... Soil Technol. 11:109-119. Risterucci, AM, Hippolyte, I, Perrier, X., Xia, L., Caig, V., Evers, M., Huttner, E., Kilian, A. and Glaszmann, JC 2009. Development and assessment of Diversity Arrays Technology for high-throughput DNA... more
... Soil Technol. 11:109-119. Risterucci, AM, Hippolyte, I, Perrier, X., Xia, L., Caig, V., Evers, M., Huttner, E., Kilian, A. and Glaszmann, JC 2009. Development and assessment of Diversity Arrays Technology for high-throughput DNA analyses in Musa. Theor. Appl. Genet. ...
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Dehydrins are a family of desiccation proteins that were identified originally in plants (T.J. Close, A.A. Kortt, P.M. Chandler [1989] Plant Mol Biol 13: 95-108; G. Galau, T.J. Close [1992] Plant Physiol 98: 1523-1525). Dehydrins are... more
Dehydrins are a family of desiccation proteins that were identified originally in plants (T.J. Close, A.A. Kortt, P.M. Chandler [1989] Plant Mol Biol 13: 95-108; G. Galau, T.J. Close [1992] Plant Physiol 98: 1523-1525). Dehydrins are characterized by the consensus amino acid sequence domain EKKGIMDKIKEKLPG found at or near the carboxy terminus; the core of this domain (KIKEKLPG) may be repeated from one to many times within the complete polypeptide. Dehydrins generally accumulate in plants in response to dehydration stress, regardless of whether the stimulus is evaporation, chilling, or a decrease in external osmotic potential. Polyclonal antibodies highly specific to the consensus carboxy terminus of plant dehydrins were used to search for dehydrins in cyanobacteria, many of which are known to survive desiccation. A 40-kD osmotic-stress-induced protein was identified in Anabaena sp. strain PCC 7120. The 40-kD protein was usually not detected in logarithmic cultures and was induced by shifting the growth medium to higher solute concentrations. Several solutes have inductive effects, including sucrose, sorbitol, and polyethylene glycol (PEG). Measurements of osmotic potential suggest that a shift of -0.5 MPa (sucrose and PEG) or -1.2 MPa (sorbitol) is sufficient to induce synthesis of the 40-kD protein. Glycerol, which is highly permeable, was not an inducer at -1.2 MPa (0.5 M), nor was the plant hormone abscisic acid. Induction appears to be evoked by a shift in osmotic potential approximately equal in absolute magnitude to the expected turgor pressure of bacterial cells in logarithmic phase growth. A dehydrin-like polypeptide was also identified among osmotically induced proteins from two other filamentous, heterocyst-forming cyano-bacteria. A 40-kD protein was observed in Calothrix sp. strain PCC 7601, and in Nostoc sp. strain Mac-R2, an osmotic-induced doublet at 39 and 40 kD was observed. From these data, it appears that cyanobacteria produce a dehydrin-like protein under osmotic stress.
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Dehydrins (DHNs; late embryogenesis abundant D11 family) are a family of intrinsically unstructured plant proteins that accumulate in the late stages of seed development and in vegetative tissues subjected to water deficit, salinity, low... more
Dehydrins (DHNs; late embryogenesis abundant D11 family) are a family of intrinsically unstructured plant proteins that accumulate in the late stages of seed development and in vegetative tissues subjected to water deficit, salinity, low temperature, or abscisic acid treatment. We demonstrated previously that maize (Zea mays) DHNs bind preferentially to anionic phospholipid vesicles; this binding is accompanied by an increase in alpha-helicity of the protein, and adoption of alpha-helicity can be induced by sodium dodecyl sulfate. All DHNs contain at least one "K-segment," a lysine-rich 15-amino acid consensus sequence. The K-segment is predicted to form a class A2 amphipathic alpha-helix, a structural element known to interact with membranes and proteins. Here, three K-segment deletion proteins of maize DHN1 were produced. Lipid vesicle-binding assays revealed that the K-segment is required for binding to anionic phospholipid vesicles, and adoption of alpha-helicity of the K-segment accounts for most of the conformational change of DHNs upon binding to anionic phospholipid vesicles or sodium dodecyl sulfate. The adoption of structure may help stabilize cellular components, including membranes, under stress conditions.
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In recent years, access to complete genomic sequences, coupled with rapidly accumulating data related to RNA and protein expression patterns, has made it possible to determine comprehensively how genes contribute to complex phenotypes.... more
In recent years, access to complete genomic sequences, coupled with rapidly accumulating data related to RNA and protein expression patterns, has made it possible to determine comprehensively how genes contribute to complex phenotypes. However, for major crop plants, publicly available, standard platforms for parallel expression analysis have been limited. We report the conception and design of the new publicly available, 22K Barley1 GeneChip probe array, a model for plants without a fully sequenced genome. Array content was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley (Hordeum vulgare) gene sequences from the National Center for Biotechnology Information nonredundant database. Conserved sequences expressed in seedlings of wheat (Triticum aestivum), oat (Avena strigosa), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays) were identified that will be valuable in the design of arrays across grasses. To enhance the usability of the data, BarleyBase, a MIAME-compliant, MySQL relational database, serves as a public repository for raw and normalized expression data from the Barley1 GeneChip probe array. Interconnecting links with PlantGDB and Gramene allow BarleyBase users to perform gene predictions using the 21,439 non-redundant Barley1 exemplar sequences or cross-species comparison at the genome level, respectively. We expect that this first generation array will accelerate hypothesis generation and gene discovery in disease defense pathways, responses to abiotic stresses, development, and evolutionary diversity in monocot plants.
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Hybridization using overgo probes is an established approach for screening arrayed bacterial artificial chromosome (BAC) libraries. We have improved the use of overgos by increasing the yield of positive clones using reduced levels of... more
Hybridization using overgo probes is an established approach for screening arrayed bacterial artificial chromosome (BAC) libraries. We have improved the use of overgos by increasing the yield of positive clones using reduced levels of radioisotopes and enzyme. The strategy involves labeling with all four radiolabeled nucleotides in a hot pulse followed by a cold nucleotide chase and then extending the exposure time to compensate for reduced specific activity of the probes. The resulting cost savings and reduced human exposure to radiation make the use of highly pooled overgo probes a more attractive approach for screening of BAC libraries from organisms with large genomes.
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Mutants with Tn5 insertions in the vir region of the Agrobacterium tumefaciens TiC58 plasmid are unable to form crown-gall tumors. Complementation tests of these vir region mutants were carried out by constructing merodiploids in a... more
Mutants with Tn5 insertions in the vir region of the Agrobacterium tumefaciens TiC58 plasmid are unable to form crown-gall tumors. Complementation tests of these vir region mutants were carried out by constructing merodiploids in a recombination-deficient strain. Each merodiploid possessed a mutant TiC58 plasmid and a recombinant plasmid containing either the homologous wild-type DNA region or the homologous region containing a second Tn5 insertion. The analysis identified six complementation groups. Mutations in one of these complementation groups were not complemented in trans and represent a cis-dominant locus. The mutation in one complementation group showed variation in host range.
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We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley (Hordeum vulgare) gene pool extends, on average, for... more
We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley (Hordeum vulgare) gene pool extends, on average, for <1-5 cM. Based on this information, we have developed a platform for whole genome association studies that comprises a collection of elite lines that we have characterized at 3060 genome-wide single nucleotide polymorphism (SNP) marker loci. Interrogating this data set shows that significant population substructure is present within the elite gene pool and that diversity and LD vary considerably across each of the seven barley chromosomes. However, we also show that a subpopulation comprised of only the two-rowed spring germplasm is less structured and well suited to whole genome association studies without the need for extensive statistical intervention to account for structure. At the current marker density, the two-rowed spring population is suited for fine mapping simple traits that are located outside of the genetic centromeres with a resolution that is sufficient for candidate gene identification by exploiting conservation of synteny with fully sequenced model genomes and the emerging barley physical map.
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Plant microspores can be reprogrammed from their normal pollen development to an embryogenic route in a process termed microspore embryogenesis or androgenesis. Stress treatment has a critical role in this process, inducing the... more
Plant microspores can be reprogrammed from their normal pollen development to an embryogenic route in a process termed microspore embryogenesis or androgenesis. Stress treatment has a critical role in this process, inducing the dedifferentiation of microspores and conditioning the following androgenic response. In this study, we have used three barley doubled haploid lines with similar genetic background but different androgenic response. The Barley1 GeneChip was used for transcriptome comparison of these lines after mannitol stress treatment, allowing the identification of 213 differentially expressed genes. Most of these genes belong to the functional categories "cell rescue, defense, and virulence"; "metabolism"; "transcription"; and "transport". These genes were grouped into clusters according to their expression profiles among lines. A principal component analysis allowed us to associate specific gene expression clusters to phenotypic variables. Genes associated with the ability of microspores to divide and form embryos were mainly involved in changes in the structure and function of membranes, efficient use of available energy sources, and cell fate. Genes related to stress response, transcription and translation regulation, and degradation of pollen-specific proteins were associated with green plant production, while expression of genes related to plastid development was associated with albino plant regeneration.
Research Interests: Bioinformatics, Genetics, Pigmentation, Principal Component Analysis, Life Sciences, and 28 moreStress, Cell Biology, Gene expression, Translation, Transcription, Embryo, Protein Structure and Function, Phylogeny, Androgenesis, Assignment, Pollen, Stress response, Albinism, Cluster Analysis, Lines, Gene, Genes, Gen, Embryonic Development, Gramineae, Plant Regeneration, Plant production, Energy Source, Cell Fate, Embryos, Embryogenesis, PLANT PROTEINS, and Gene expression profiling
Timothy Close 1, Nils Rostoks 2, Luke Ramsay 2, Jan Svensson 1, Prasanna Bhat 1, Mikeal Roose 1, Robbie Waugh 2, Patrick Hayes 3, Peter Szucs 3, and Gary Muehlbauer 4.(1) University of California-Riverside, Department of Botany and Plant... more
Timothy Close 1, Nils Rostoks 2, Luke Ramsay 2, Jan Svensson 1, Prasanna Bhat 1, Mikeal Roose 1, Robbie Waugh 2, Patrick Hayes 3, Peter Szucs 3, and Gary Muehlbauer 4.(1) University of California-Riverside, Department of Botany and Plant Sciences, Riverside, ...