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Author (up) Arimoto-Kobayashi, S.; Sakata, H.; Mitsu, K.; Tanoue, H. file  url
  Title A possible photosensitizer: Tobacco-specific nitrosamine, 4-(N-methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), induced mutations, DNA strand breaks and oxidative and methylative damage with UVA Type Journal Article
  Year 2007 Publication Mutation Research Abbreviated Journal Mutat Res  
  Volume 632 Issue 1-2 Pages 111-120  
  Keywords Base Sequence; DNA Breaks; DNA Methylation--drug effects, radiation effects; Dose-Response Relationship, Drug; Models, Biological; Molecular Sequence Data; Mutation; Nitrosamines--toxicity; Oxidative Stress--drug effects, radiation effects; Photosensitizing Agents--toxicity; Salmonella typhimurium; Tobacco--chemistry; Ultraviolet Rays--adverse effects  
  Abstract We discovered the directly acting mutagenicity of the tobacco-specific nitrosamine, 4-(N-methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), with UVA light (320-400nm) in Ames bacteria and phage M13mp2 in the absence of metabolic activation. We have investigated the spectrum of mutations caused by UVA-activated NNK. The majority (57%) of induced sequence changes were comprised of GC to CG, GC to TA and GC to AT. This suggested that modification of guanine residues was responsible for these mutations. Hence, we explored the formation of 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxodG) and O(6)-methylguanine (O(6)meG) in the DNA. When calf thymus DNA was treated with NNK and UVA, the amount of 8-oxodG/dG and O(6)meG/G in the DNA increased up to 20-fold and 100-fold, respectively, compared with the untreated control. DNA strand breaks were observed following NNK and UVA treatment, and the strand breaks were suppressed in the presence of scavengers for oxygen and NO radical. The formation of NO was also observed in NNK solutions irradiated with UVA. We analyzed the photodynamic spectrum of mutation induction, 8-oxodG formation and NO formation using monochromatic radiation. The patterns of the action spectra were comparable to the absorption spectrum of NNK. We conclude that NNK may act as a photosensitizer in response to UVA to produce NO and other oxidative and alkylative intermediates following the formation of 8-oxodG and O(6)meG in DNA, which may lead to mutations and DNA strand breaks.  
  Call Number Serial 86  
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Author (up) Aveskamp, M.M.; Verkley, G.J.M.; de Gruyter, J.; Murace, M.A.; Perello, A.; Woudenberg, J.H.C.; Groenewald, J.Z.; Crous, P.W. file  url
  Title DNA phylogeny reveals polyphyly of Phoma section Peyronellaea and multiple taxonomic novelties Type Journal Article
  Year 2009 Publication Mycologia Abbreviated Journal Mycologia  
  Volume 101 Issue 3 Pages 363-382  
  Keywords Actins/analysis/genetics; Ascomycota/*classification/cytology/genetics; Biodiversity; DNA, Fungal/*analysis/genetics; DNA, Ribosomal Spacer/analysis/genetics; Genetic Speciation; Genetic Variation; Molecular Sequence Data; *Phylogeny; Polymerase Chain Reaction; Sequence Alignment; Sequence Analysis, DNA; Species Specificity; Tubulin/analysis/genetics  
  Abstract Species of the anamorph genus Phoma are commonly isolated from a wide range of ecological niches. They are notoriously difficult to identify due to the paucity of morphological features and the plasticity of these when cultivated on agar media. Species linked to Phoma section Peyronellaea are typified by the production of dictyochlamydospores and thus have additional characters to use in taxon delineation. However, the taxonomy of this section is still not fully understood. Furthermore the production of such chlamydospores also is known in some other sections of Phoma. DNA sequences were generated from three loci, namely ITS, actin, and 3-tubulin, to clarify the phylogeny of Phoma taxa that produce dictyochlamydospores. Results were unable to support section Peyronellaea as a taxonomic entity. Dictyochlamydospore formation appears to be a feature that developed, or was lost, many times during the evolution of Phoma. Furthermore, based on the multigene analyses, five new Phoma species could be delineated while a further five required taxonomic revision to be consistent with the genetic variation observed.  
  Call Number Serial 1999  
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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) Birchall, P.S.; Fishpool, R.M.; Albertson, D.G. file  url
  Title Expression patterns of predicted genes from the C. elegans genome sequence visualized by FISH in whole organisms Type Journal Article
  Year 1995 Publication Nature Genetics Abbreviated Journal Nat Genet  
  Volume 11 Issue 3 Pages 314-320  
  Keywords Animals; Base Sequence; Caenorhabditis/cytology/*genetics; *Gene Expression; *Genome; Helminth Proteins/genetics; In Situ Hybridization, Fluorescence/*methods; Molecular Sequence Data; Muscle Proteins/genetics; RNA, Messenger/analysis  
  Abstract More than 10 megabases of contiguous genome sequence have been submitted to the databases by the Caenorhabditis elegans Genome Sequencing Consortium. To characterize the genes predicted from the sequence, we have developed high resolution FISH for visualization of mRNA distributions in whole animals. The high resolution and sensitivity afforded by the use of directly fluorescently labelled probes and confocal imaging permitted mRNA distributions to be recorded at the cellular and subcellular level. Expression patterns were obtained for 8 out of 10 genes in an initial test set of predicted gene sequences, indicating that FISH is an effective means of characterizing predicted genes in C. elegans.  
  Call Number Serial 172  
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Author (up) Cho, J.H.; Bandyopadhyay, J.; Lee, J.; Park, C.S.; Ahnn, J. file  url
  Title Two isoforms of sarco/endoplasmic reticulum calcium ATPase (SERCA) are essential in Caenorhabditis elegans Type Journal Article
  Year 2000 Publication Gene Abbreviated Journal Gene  
  Volume 261 Issue 2 Pages 211-219  
  Keywords Alternative Splicing; Amino Acid Sequence; Animals; Caenorhabditis elegans/embryology/enzymology/*genetics; Calcium-Transporting ATPases/*genetics/metabolism; Embryo, Nonmammalian/drug effects/enzymology; Embryonic Development; Gene Expression Regulation, Enzymologic; Green Fluorescent Proteins; Isoenzymes/genetics/metabolism; Luminescent Proteins/genetics/metabolism; Microscopy, Fluorescence; Molecular Sequence Data; Phenotype; Promoter Regions, Genetic/genetics; RNA, Double-Stranded/administration & dosage/genetics; Recombinant Fusion Proteins/genetics/metabolism; Sarcoplasmic Reticulum Calcium-Transporting ATPases; Sequence Homology, Amino Acid; Tissue Distribution  
  Abstract SERCA (Sarco/Endoplasmic Reticulum Calcium ATPase), a membrane bound Ca(2+)- /Mg(2+)- dependent ATPase that sequesters Ca(2+) into the SR/ER lumen, is one of the essential components for the maintenance of intracellular Ca(2+) homeostasis. Here we describe the identification and functional characterization of a C. elegans SERCA gene (ser-1). ser-1 is a single gene alternatively spliced at its carboxyl terminus to form two isoforms (SER-1A and SER-1B) and displays a high homology (70% identity, 80% similarity) with mammalian SERCAs. Green fluorescent protein (GFP) and whole-mount immunostaining analyses reveal that SER-1 expresses in neuronal cells, body-wall muscles, pharyngeal and vulval muscles, excretory cells, and vulva epithelial cells. Furthermore, SER-1::GFP expresses during embryonic stages and the expression is maintained through the adult stages. Double-stranded RNA injection (also known as RNAi) targeted to each SER-1 isoform results in severe phenotypic defects: ser-1A(RNAi) animals show embryonic lethality, whereas ser-1B(RNAi) results in L1 larval arrest phenotype. These findings suggest that both isoforms of C. elegans SERCA, like in mammals, are essential for embryonic development and post-embryonic growth and survival.  
  Call Number Serial 451  
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Author (up) Denner, E.B.; Mark, B.; Busse, H.J.; Turkiewicz, M.; Lubitz, W. file  url
doi  openurl
  Title Psychrobacter proteolyticus sp. nov., a psychrotrophic, halotolerant bacterium isolated from the Antarctic krill Euphausia superba Dana, excreting a cold-adapted metalloprotease Type Journal Article
  Year 2001 Publication Systematic and Applied Microbiology Abbreviated Journal Syst Appl Microbiol  
  Volume 24 Issue 1 Pages 44-53  
  Keywords Adaptation, Biological/*physiology; Animals; Antarctic Regions; Bacterial Proteins/isolation & purification; Bacterial Typing Techniques; Cold Temperature; Crustacea/*microbiology; DNA, Ribosomal/genetics; Drug Resistance, Microbial; Fatty Acids/analysis; Gammaproteobacteria/classification/enzymology/*isolation & purification; Gram-Negative Aerobic Rods and Cocci/enzymology/*isolation & purification; Metalloendopeptidases/*secretion; Molecular Sequence Data; RNA, Ribosomal, 16S/genetics; Salts/pharmacology  
  Abstract An Antarctic marine bacterium (strain 116) excreting an extracellular cold-adapted metalloprotease was subjected to a detailed polyphasic taxonomic investigation. Strain 116 was previously isolated from the stomach of a specimen of the Antarctic krill Euphasia superba Dana and tentatively characterized as Sphingomonas paucimobilis 116. The 16S rDNA sequence analysis showed that the strain is in fact related to species of the genus Psychrobacter, next to Psychrobacter glacincola (97.4% similarity). Sequence similarities between strain 116 and other Psychrobacter species ranged from 96.9% (with P. urativorans) to 95.4% (with P. immobilis). Key phenotypic characteristics as well as chemotaxonomic features of the bacterium were congruent with the description of the genus Psychrobacter i.e. cells were strictly aerobic, strongly oxidase-positive, psychrotrophic, halotolerant, gram-negative non-motile coccobacilli, with ubiquinone-8 as the main respiratory lipoquinone and 18:1 cis 9, 16:1 cis and 17:1 (omega8c being the predominant cellular fatty acids. The G+C content of the DNA was 43.6 mol%. DNA-DNA hybridization studies showed that the relatedness between strain 116 and Psychrobacter glacinola is only 62.2%. Further differences were apparent in whole-cell SDS-PAGE protein pattern, cellular fatty acid profile and in a number of physiological and biochemical characteristics as well as in enzymatic activities. Tolerance to 5% bile salts, nitrate reduction, citrate utilization, acid production from carbohydrates, alkaline phosphatase, acid phosphatase, C4 esterase, C14 lipase and valine arylamidase were found to differentiate strain 116 from Psychrobacter glacincola. On the basis of this phenotypic and molecular evidences, strain 116, previously known as Sphingomonas paucimobilis 116, was recognized as a new species of the genus Psychrobacter for which the name Psychrobacter proteolyticus is proposed. Strain 116 has been deposited in the Collection de l'Institut Pasteur, France, as CIP106830T and in the Deutsche Sammlung von Mikroorganismen and Zellkulturen, as DSM13887.  
  Call Number Serial 436  
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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) Fliss, H.; Menard, M. file  url
  Title Hypochlorous acid-induced mobilization of zinc from metalloproteins Type Journal Article
  Year 1991 Publication Archives of Biochemistry and Biophysics Abbreviated Journal Arch Biochem Biophys  
  Volume 287 Issue 1 Pages 175-179  
  Keywords Amino Acid Sequence; Animals; Horses; Hypochlorous Acid--metabolism; Kinetics; Metalloproteins--metabolism; Molecular Sequence Data; Oligopeptides--metabolism; Resorcinols--metabolism; Zinc--metabolism  
  Abstract Hypochlorous acid (HOCl), a neutrophil oxidant, can contribute to tissue injury at sites of inflammation by its reactivity with protein sulfhydryls. The present study shows that physiological concentrations (50-200 microM) of HOCl can displace Zn2+ from metalloproteins, such as metallothionein and alcohol dehydrogenase, in which the metal is bound to sulfhydryls by means of thiolate (S-Zn) bonds. No mobilization of Zn2+ was observed from superoxide dismutase in which the metal is not bound to cysteine, suggesting that HOCl reacts selectively with thiolate bonds. Zn2+ mobilization, measured spectrophotometrically with the metallochromic indicator 4-(2-pyridylazo)resorcinol, was also observed from complexes of this metal with other thiol-containing compounds such as 2,3-dimercaptopropanol and metallothionein fragment 56-61. HOCl cleavage of the thiolate bonds was confirmed by the decrease in absorbance at 250 nm. This study shows for the first time that HOCl can mobilize protein-bound Zn2+ and suggests that neutrophil oxidant injury may be partially mediated by the mobilization of cellular Zn2+.  
  Call Number Serial 74  
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Author (up) Foltz, D.R.; Jansen, L.E.T.; Black, B.E.; Bailey, A.O.; Yates, J.R. 3rd; Cleveland, D.W. url  doi
  Title The human CENP-A centromeric nucleosome-associated complex Type Journal Article
  Year 2006 Publication Nature Cell Biology Abbreviated Journal Nat Cell Biol  
  Volume 8 Issue 5 Pages 458-469  
  Keywords Amino Acid Sequence; Autoantigens--chemistry, isolation & purification; metabolism; Centromere--metabolism; Chromatin Assembly Factor-1; Chromatin Assembly and Disassembly--genetics; Chromosomal Proteins, Non-Histone--chemistry, isolation & purification, metabolism; Chromosomes, Human genetics; DNA-Binding Proteins--metabolism; HeLa Cells; Histones--chemistry; Humans; Mitosis--genetics; Molecular Sequence Data; Nucleosomes--metabolism; Protein Binding; Signal Transduction  
  Abstract The basic element for chromosome inheritance, the centromere, is epigenetically determined in mammals. The prime candidate for specifying centromere identity is the array of nucleosomes assembled with CENP-A, the centromere-specific histone H3 variant. Here, we show that CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of three new human centromere proteins (CENP-M, CENP-N and CENP-T), along with CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Facilitates chromatin transcription (FACT) and nucleophosmin-1 (previously implicated in transcriptional chromatin remodelling and as a multifunctional nuclear chaperone, respectively) are absent from histone H3-containing nucleosomes, but are stably recruited to CENP-A nucleosomes independent of CENP-A NAC. Seven new CENP-A-nucleosome distal (CAD) centromere components (CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S) are identified as assembling on the CENP-A NAC. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival despite continued centromere-derived mitotic checkpoint signalling.  
  Call Number Serial 13  
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Author (up) Gregg-Jolly, L.A.; Ornston, L.N. file  url
  Title Properties of Acinetobacter calcoaceticus recA and its contribution to intracellular gene conversion Type Journal Article
  Year 1994 Publication Molecular Microbiology Abbreviated Journal Mol Microbiol  
  Volume 12 Issue 6 Pages 985-992  
  Keywords Acinetobacter calcoaceticus/*genetics/metabolism; Amino Acid Sequence; *Bacterial Proteins; Base Sequence; Cloning, Molecular; DNA Transposable Elements; *DNA-Binding Proteins; Escherichia coli/genetics; Gene Conversion/*physiology; Genes, Bacterial/*genetics; Genetic Complementation Test; Genomic Library; Molecular Sequence Data; Mutation/physiology; Rec A Recombinases/chemistry/*genetics/metabolism; Restriction Mapping; Sequence Analysis, DNA; Sequence Homology, Amino Acid; Transformation, Bacterial  
  Abstract The Acinetobacter calcoaceticus pcaJ and catJ genes, nearly identical in DNA sequence, differ in transcriptional control and are separated by more than 20 kb of chromosomal DNA. The pcaJ3125 mutation is repaired frequently in organisms containing the wild-type catJ gene. This high-frequency repair is eliminated in strains lacking the catJ gene, which suggests that recombination between the homologous catJ and pcaJ genes contributes to the high-frequency repair of the pcaJ3125 mutation. We report here that the high-frequency repair also requires a functional recA gene. The A. calcoaceticus recA gene was cloned in Escherichia coli by complementation of a recA mutation in the host strain. The nucleotide sequence of a 1506 bp DNA fragment containing A. calcoaceticus recA was determined. The amino acid sequences of RecA from E. coli and A. calcoaceticus shared 71% identity. The DNA sequences differed in that a consensus binding site for binding of LexA repressor, represented upstream from recA in E. coli, is not evident in the corresponding region of the A. calcoaceticus DNA sequence. A Tn5 insertion was introduced into the A. calcoaceticus recA gene. Selection for Tn5-encoded kanamycin resistance allowed the inactivated recA gene to be recombined by natural transformation into the A. calcoaceticus chromosome. Strains that had acquired the mutant gene were sensitive to both MMS and u.v. light, were deficient in natural transformation, and failed to carry out catJ-dependent high-frequency repair of the pcaJ3125 mutation.  
  Call Number Serial 299  
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