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Author (up) Ducey, T.F.; Jackson, L.; Orvis, J.; Dyer, D.W. file  url
doi  openurl
  Title Transcript analysis of nrrF, a Fur repressed sRNA of Neisseria gonorrhoeae Type Journal Article
  Year 2009 Publication Microbial Pathogenesis Abbreviated Journal Microb Pathog  
  Volume 46 Issue 3 Pages 166-170  
  Keywords Bacterial Proteins/*physiology; Base Sequence; Escherichia coli; Gene Expression Profiling; *Gene Expression Regulation, Bacterial; Models, Molecular; Molecular Sequence Data; Neisseria gonorrhoeae/*physiology; RNA, Bacterial/*genetics; RNA, Untranslated/*metabolism; Repressor Proteins/*physiology; Transcription Initiation Site  
  Abstract Like most microorganisms, Neisseria gonorrhoeae alters gene expression in response to iron availability. The ferric uptake regulator Fur has been shown to be involved in controlling this response, but the extent of this involvement remains unknown. It is known that in addition to working directly to repress gene expression, Fur may also work indirectly by controlling additional regulatory elements. Using in silico analysis, we identified a putative small RNA (sRNA) homolog of the meningococcal nrrF locus, and demonstrate that this sRNA is iron-repressible, suggesting that this is the gonococcal analog of the rhyB locus in Escherichia coli. Quantitative real-time RT-PCR analysis indicates that this transcript may also be temporally regulated. Transcript analysis identified the 5' start of the transcript, using a single reaction, fluorescent-based, primer extension assay. This protocol allows for the rapid identification of transcriptional start sites of RNA transcripts, and could be used for high-throughput transcript mapping.  
  Call Number Serial 417  
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Author (up) Kim, A.D.; Melick, C.H.; Clements, W.K.; Stachura, D.L.; Distel, M.; Panakova, D.; MacRae, C.; Mork, L.A.; Crump, J.G.; Traver, D. file  url
doi  openurl
  Title Discrete Notch signaling requirements in the specification of hematopoietic stem cells Type Journal Article
  Year 2014 Publication The EMBO Journal Abbreviated Journal Embo J  
  Volume 33 Issue 20 Pages 2363-2373  
  Keywords Animals; Cell Differentiation; *Gene Expression Regulation, Developmental; Hemangioblasts/cytology/physiology; Hematopoietic Stem Cells/cytology/*physiology; Homeodomain Proteins/genetics/*metabolism; Nerve Tissue Proteins/genetics/*metabolism; Receptor, Notch1/genetics/*metabolism; Receptors, Notch/genetics/*metabolism; Signal Transduction; Somites/cytology/embryology/physiology; Wnt Proteins/genetics/metabolism; Zebrafish/embryology/genetics/*physiology; Zebrafish Proteins/genetics/*metabolism; Notch; hematopoietic stem cell; hemogenic endothelium; somite  
  Abstract Hematopoietic stem cells (HSCs) require multiple molecular inputs for proper specification, including activity of the Notch signaling pathway. A requirement for the Notch1 and dispensability of the Notch2 receptor has been demonstrated in mice, but the role of the remaining Notch receptors has not been investigated. Here, we demonstrate that three of the four Notch receptors are independently required for the specification of HSCs in the zebrafish. The orthologues of the murine Notch1 receptor, Notch1a and Notch1b, are each required intrinsically to fate HSCs, just prior to their emergence from aortic hemogenic endothelium. By contrast, the Notch3 receptor is required earlier within the developing somite to regulate HSC emergence in a non-cell-autonomous manner. Epistatic analyses demonstrate that Notch3 function lies downstream of Wnt16, which is required for HSC specification through its regulation of two Notch ligands, dlc and dld. Collectively, these findings demonstrate for the first time that multiple Notch signaling inputs are required to specify HSCs and that Notch3 performs a novel role within the somite to regulate the neighboring precursors of hemogenic endothelium.  
  Call Number Serial 1048  
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Author (up) Law, R.D.; Crafts-Brandner, S.J. file  url
openurl 
  Title High temperature stress increases the expression of wheat leaf ribulose-1,5-bisphosphate carboxylase/oxygenase activase protein Type Journal Article
  Year 2001 Publication Archives of Biochemistry and Biophysics Abbreviated Journal Arch Biochem Biophys  
  Volume 386 Issue 2 Pages 261-267  
  Keywords Blotting, Southern; Blotting, Western; Enzyme Induction; *Gene Expression Regulation, Plant; Isoenzymes/biosynthesis/chemistry/genetics/metabolism; Molecular Weight; Plant Diseases; Plant Leaves/*enzymology/genetics; Plant Proteins/*biosynthesis/chemistry/genetics; Protein Subunits; RNA, Messenger/genetics/metabolism; RNA, Plant/genetics/metabolism; Ribulose-Bisphosphate Carboxylase/biosynthesis/chemistry/genetics; Temperature; Time Factors; Triticum/*enzymology/genetics  
  Abstract The effect of high temperature stress on the expression of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activase was examined in wheat (Triticum aestivum L.) leaves, which normally possess 46- and 42-kDa activase forms. Heat stress at 38 degrees C significantly reduced total activase mRNA levels compared to controls, and recovery of activase transcription was only marginal 24 h after alleviating heat stress. In contrast to transcript abundance, immunoblot analysis indicated that heat stress increased the accumulation of the 42-kDa activase and induced a putative 41-kDa form. Heat stress did not affect the amounts of the 46- and 42-kDa activase forms (present as 51- and 45-kDa preproteins) recovered after their immunoprecipitation from in vitro translation products. De novo protein synthesis in vivo in the presence of [35S]Met/Cys showed an increase in the amount of newly synthesized 42-kDa subunit after 4 h of heat stress, and synthesis of the putative 41-kDa activase was apparent. In contrast to activase, heat stress led to a rapid and large reduction in the de novo synthesis of the large and small subunits of Rubisco. Long-term (48-h) heat stress further increased the amounts of de novo synthesized 42- and 41-kDa activase forms. After 24 h of recovery from heat stress, de novo synthesis of the 42-kDa activase returned to control levels, while a small amount of 41-kDa protein was still expressed. Southern analysis suggested the presence of a single activase gene. These results indicate that heat stress alters activase expression, most likely posttranscriptionally, and suggest that the heat-induced expression of the 42- and 41-kDa subunits of wheat leaf Rubisco activase may be related to the maintenance and acclimation of photosynthetic CO2 fixation during high temperature stress in wheat.  
  Call Number Serial 1802  
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Author (up) Parsons, A.B.; Brost, R.L.; Ding, H.; Li, Z.; Zhang, C.; Sheikh, B.; Brown, G.W.; Kane, P.M.; Hughes, T.R.; Boone, C. file  url
doi  openurl
  Title Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways Type Journal Article
  Year 2004 Publication Nature Biotechnology Abbreviated Journal Nat Biotechnol  
  Volume 22 Issue 1 Pages 62-69  
  Keywords Biotechnology/*methods; Cluster Analysis; Drug Industry/*methods; *Drug Resistance; Fungal Proteins/metabolism; Gene Deletion; *Gene Expression Regulation; Mutation; Pharmacogenetics; Proton-Translocating ATPases/metabolism; Saccharomyces cerevisiae/*genetics; Software  
  Abstract Bioactive compounds can be valuable research tools and drug leads, but it is often difficult to identify their mechanism of action or cellular target. Here we investigate the potential for integration of chemical-genetic and genetic interaction data to reveal information about the pathways and targets of inhibitory compounds. Taking advantage of the existing complete set of yeast haploid deletion mutants, we generated drug-hypersensitivity (chemical-genetic) profiles for 12 compounds. In addition to a set of compound-specific interactions, the chemical-genetic profiles identified a large group of genes required for multidrug resistance. In particular, yeast mutants lacking a functional vacuolar H(+)-ATPase show multidrug sensitivity, a phenomenon that may be conserved in mammalian cells. By filtering chemical-genetic profiles for the multidrug-resistant genes and then clustering the compound-specific profiles with a compendium of large-scale genetic interaction profiles, we were able to identify target pathways or proteins. This method thus provides a powerful means for inferring mechanism of action.  
  Call Number Serial 339  
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Author (up) Shanks, R.M.Q.; Lahr, R.M.; Stella, N.A.; Arena, K.E.; Brothers, K.M.; Kwak, D.H.; Liu, X.; Kalivoda, E.J. file  url
openurl 
  Title A Serratia marcescens PigP homolog controls prodigiosin biosynthesis, swarming motility and hemolysis and is regulated by cAMP-CRP and HexS Type Journal Article
  Year 2013 Publication PloS one Abbreviated Journal PLoS One  
  Volume 8 Issue 3 Pages e57634  
  Keywords Bacterial Proteins/*genetics/metabolism; Depsipeptides/*biosynthesis/genetics/pharmacology; Erythrocytes/drug effects; *Gene Expression Regulation, Bacterial; Genetic Complementation Test; Hemolysis/drug effects; Hexosyltransferases/genetics/metabolism; Humans; Membrane Proteins/genetics/metabolism; Movement/drug effects; Mutation; Operon; Prodigiosin/*biosynthesis; Sequence Homology, Amino Acid; Serratia marcescens/*genetics/metabolism; Signal Transduction; Transcription Factors/*genetics/metabolism  
  Abstract Swarming motility and hemolysis are virulence-associated determinants for a wide array of pathogenic bacteria. The broad host-range opportunistic pathogen Serratia marcescens produces serratamolide, a small cyclic amino-lipid, that promotes swarming motility and hemolysis. Serratamolide is negatively regulated by the transcription factors HexS and CRP. Positive regulators of serratamolide production are unknown. Similar to serratamolide, the antibiotic pigment, prodigiosin, is regulated by temperature, growth phase, HexS, and CRP. Because of this co-regulation, we tested the hypothesis that a homolog of the PigP transcription factor of the atypical Serratia species ATCC 39006, which positively regulates prodigiosin biosynthesis, is also a positive regulator of serratamolide production in S. marcescens. Mutation of pigP in clinical, environmental, and laboratory strains of S. marcescens conferred pleiotropic phenotypes including the loss of swarming motility, hemolysis, and severely reduced prodigiosin and serratamolide synthesis. Transcriptional analysis and electrophoretic mobility shift assays place PigP in a regulatory pathway with upstream regulators CRP and HexS. The data from this study identifies a positive regulator of serratamolide production, describes novel roles for the PigP transcription factor, shows for the first time that PigP directly regulates the pigment biosynthetic operon, and identifies upstream regulators of pigP. This study suggests that PigP is important for the ability of S. marcescens to compete in the environment.  
  Call Number Serial 1612  
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Author (up) Zhang, Y.; Griffiths, M.W. file  url
openurl 
  Title Induced expression of the heat shock protein genes uspA and grpE during starvation at low temperatures and their influence on thermal resistance of Escherichia coli O157:H7 Type Journal Article
  Year 2003 Publication Journal of Food Protection Abbreviated Journal J Food Prot  
  Volume 66 Issue 11 Pages 2045-2050  
  Keywords Adaptation, Physiological; Bacterial Proteins/biosynthesis/*genetics; Colony Count, Microbial; Escherichia coli O157/genetics/metabolism/*physiology; *Escherichia coli Proteins; Fluorescence; Food Microbiology; *Gene Expression Regulation, Bacterial; Heat-Shock Proteins/biosynthesis/*genetics; Hot Temperature; Starvation; Time Factors  
  Abstract Heat shock proteins play an important role in protecting bacterial cells against several stresses, including starvation. In this study, the promoters for two genes encoding heat shock proteins involved in many stress responses, UspA and GrpE, were fused with the green fluorescent protein (gfp) gene. Thus, the expression of the two genes could be quantified by measuring the fluorescence emitted by the cells under different environmental conditions. The heat resistance levels of starved and nonstarved cells during storage at 5, 10, and 37 degrees C were compared with the levels of expression of the uspA and grpE genes. D52-values (times required for decimal reductions in count at 52 degrees C) increased by 11.5, 14.6, and 18.5 min when cells were starved for 3 h at 37 degrees C, for 24 h at 10 degrees C, and for 2 days at 5 degrees C, respectively. In all cases, these increases were significant (P < 0.01), indicating that the stress imposed by starvation altered the ability of E. coli O157:H7 to survive subsequent heat treatments. Thermal tolerance was correlative with the induction of UspA and GrpE. At 5 degrees C, the change in the thermal tolerance of the pathogen was positively linked to the induced expression of the grpE gene but negatively related to the expression of the uspA gene. The results obtained in this study indicate that UspA plays an important role in starvation-induced thermal tolerance at 37 degrees C but that GrpE may be more involved in regulating this response at lower temperatures. An improvement in our understanding of the molecular mechanisms involved in these cross-protection responses may make it possible to devise strategies to limit their effects.  
  Call Number Serial 312  
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