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Author (up) Baylis, H.A.; Furuichi, T.; Yoshikawa, F.; Mikoshiba, K.; Sattelle, D.B. file  url
  Title Inositol 1,4,5-trisphosphate receptors are strongly expressed in the nervous system, pharynx, intestine, gonad and excretory cell of Caenorhabditis elegans and are encoded by a single gene (itr-1) Type Journal Article
  Year 1999 Publication Journal of Molecular Biology Abbreviated Journal J Mol Biol  
  Volume 294 Issue 2 Pages 467-476  
  Keywords Amino Acid Sequence; Animals; Animals, Genetically Modified; Binding Sites; Caenorhabditis elegans/*genetics; Calcium Channels/*genetics/*metabolism; Cell Membrane/genetics/metabolism; Conserved Sequence; Gene Expression Profiling; Gonads/metabolism; Helminth Proteins/*genetics/*metabolism; Inositol 1,4,5-Trisphosphate Receptors; Intestines/metabolism; Molecular Sequence Data; Nervous System/metabolism; Pharynx/metabolism; RNA, Messenger; Receptors, Cytoplasmic and Nuclear/*genetics/*metabolism; Rectum/cytology/metabolism  
  Abstract Inositol 1,4,5-trisphosphate (InsP3) activates receptors (InsP3Rs) that mediate intracellular Ca(2+ )release, thereby modulating intracellular calcium signals and regulating important aspects of cellular physiology and gene expression. To further our understanding of InsP3Rs we have characterised InsP3Rs and the InsP3R gene, itr-1, from the model organism Caenorhabditis elegans. cDNAs encoding InsP3Rs were cloned enabling us to: (a) identify three putative transcription start sites that result in alternative mRNA 5' ends: (b) detect alternative splicing at three sites and: (c) determine the full genomic organisation of the itr-1 gene. The InsP3R protein (ITR-1) is approximately 42 % identical with known InsP3Rs and possesses conserved structural features. When the putative InsP3 binding domain was expressed in Escherichia coli, specific binding of InsP3 was detected. Using antibodies against ITR-1 we detected a protein of 220 kDa in C. elegans membranes. These antibodies and itr-1::GFP (green fluorescent protein) reporter constructs were used to determine the expression pattern of itr-1 in C. elegans. Strong expression was observed in the intestine, pharynx, nerve ring, excretory cell and gonad. These results demonstrate the high degree of structural and functional conservation of InsP3Rs from nematodes to mammals and the utility of C. elegans as a system for studies on InsP3R mediated signalling.  
  Call Number Serial 309  
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Author (up) Biron, D.; Shibuya, M.; Gabel, C.; Wasserman, S.M.; Clark, D.A.; Brown, A.; Sengupta, P.; Samuel, A.D.T. file  url
  Title A diacylglycerol kinase modulates long-term thermotactic behavioral plasticity in C. elegans Type Journal Article
  Year 2006 Publication Nature Neuroscience Abbreviated Journal Nat Neurosci  
  Volume 9 Issue 12 Pages 1499-1505  
  Keywords Animals; Association Learning/physiology; Behavior, Animal/*physiology; Body Temperature Regulation/physiology; Caenorhabditis elegans/*enzymology/genetics; Caenorhabditis elegans Proteins/genetics/*metabolism; Diacylglycerol Kinase/genetics/*metabolism; Gene Expression Profiling; Mutation; Neurons/enzymology; Thermosensing/*physiology  
  Abstract A memory of prior thermal experience governs Caenorhabditis elegans thermotactic behavior. On a spatial thermal gradient, C. elegans tracks isotherms near a remembered temperature we call the thermotactic set-point (T(S)). The T(S) corresponds to the previous cultivation temperature and can be reset by sustained exposure to a new temperature. The mechanisms underlying this behavioral plasticity are unknown, partly because sensory and experience-dependent components of thermotactic behavior have been difficult to separate. Using newly developed quantitative behavioral analyses, we demonstrate that the T(S) represents a weighted average of a worm's temperature history. We identify the DGK-3 diacylglycerol kinase as a thermal memory molecule that regulates the rate of T(S) resetting by modulating the temperature range of synaptic output, but not temperature sensitivity, of the AFD thermosensory neurons. These results provide the first mechanistic insight into the basis of experience-dependent plasticity in this complex behavior.  
  Call Number Serial 1679  
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Author (up) Cleary, M.D.; Meiering, C.D.; Jan, E.; Guymon, R.; Boothroyd, J.C. file  url
  Title Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay Type Journal Article
  Year 2005 Publication Nature Biotechnology Abbreviated Journal Nat Biotechnol  
  Volume 23 Issue 2 Pages 232-237  
  Keywords Animals; Gene Expression Profiling/*methods; Gene Expression Regulation/*physiology; Humans; Metabolic Clearance Rate; Oligonucleotide Array Sequence Analysis/*methods; Pentosyltransferases/chemistry/*metabolism; RNA, Messenger/chemistry/*genetics/*metabolism; Signal Transduction/physiology; Staining and Labeling/methods; Toxoplasma/genetics/metabolism; Transcription Factors/*metabolism; Transcriptional Activation/*physiology  
  Abstract Standard microarrays measure mRNA abundance, not mRNA synthesis, and therefore cannot identify the mechanisms that regulate gene expression. We have developed a method to overcome this limitation by using the salvage enzyme uracil phosphoribosyltransferase (UPRT) from the protozoan Toxoplasma gondii. T. gondii UPRT has been well characterized because of its application in monitoring parasite growth: mammals lack this enzyme activity and thus only the parasite incorporates (3)H-uracil into its nucleic acids. In this study we used RNA labeling by UPRT to determine the roles of mRNA synthesis and decay in the control of gene expression during T. gondii asexual development. We also used this approach to specifically label parasite RNA during a mouse infection and to incorporate thio-substituted uridines into the RNA of human cells engineered to express T. gondii UPRT, indicating that engineered UPRT expression will allow cell-specific analysis of gene expression in organisms other than T. gondii.  
  Call Number Serial 1344  
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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) Frols, S.; White, M.F.; Schleper, C. file  url
  Title Reactions to UV damage in the model archaeon Sulfolobus solfataricus Type Journal Article
  Year 2009 Publication Biochemical Society Transactions Abbreviated Journal Biochem Soc Trans  
  Volume 37 Issue Pt 1 Pages 36-41  
  Keywords DNA Damage; DNA Repair--genetics; Gene Expression Profiling; Models, Biological; Sulfolobus solfataricus--cytology, genetics, radiation effects; Ultraviolet Rays  
  Abstract Mechanisms involved in DNA repair and genome maintenance are essential for all organisms on Earth and have been studied intensively in bacteria and eukaryotes. Their analysis in extremely thermophilic archaea offers the opportunity to discover strategies for maintaining genome integrity of the relatively little explored third domain of life, thereby shedding light on the diversity and evolution of these central and important systems. These studies might also reveal special adaptations that are essential for life at high temperature. A number of investigations of the hyperthermophilic and acidophilic crenarchaeote Sulfolobus solfataricus have been performed in recent years. Mostly, the reactions to DNA damage caused by UV light have been analysed. Whole-genome transcriptomics have demonstrated that a UV-specific response in S. solfataricus does not involve the transcriptional induction of DNA-repair genes and it is therefore different from the well-known SOS response in bacteria. Nevertheless, the UV response in S. solfataricus is impressively complex and involves many different levels of action, some of which have been elucidated and shed light on novel strategies for DNA repair, while others involve proteins of unknown function whose actions in the cell remain to be elucidated. The present review summarizes and discusses recent investigations on the UV response of S. solfataricus on both the molecular biological and the cellular levels.  
  Call Number Serial 15  
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