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  • Articles  (91)
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  • Articles  (91)
  • 1
    Publication Date: 2002-11-26
    Description: Neuronal PAS domain protein 2 (NPAS2) is a mammalian transcription factor that binds DNA as an obligate dimeric partner of BMAL1 and is implicated in the regulation of circadian rhythm. Here we show that both PAS domains of NPAS2 bind heme as a prosthetic group and that the heme status controls DNA binding in vitro. NPAS2-BMAL1 heterodimers, existing in either the apo (heme-free) or holo (heme-loaded) state, bound DNA avidly under favorably reducing ratios of the reduced and oxidized forms of nicotinamide adenine dinucleotide phosphate. Low micromolar concentrations of carbon monoxide inhibited the DNA binding activity of holo-NPAS2 but not that of apo-NPAS2. Upon exposure to carbon monoxide, inactive BMAL1 homodimers were formed at the expense of NPAS2-BMAL1 heterodimers. These results indicate that the heterodimerization of NPAS2, and presumably the expression of its target genes, are regulated by a gas through the heme-based sensor described here.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dioum, Elhadji M -- Rutter, Jared -- Tuckerman, Jason R -- Gonzalez, Gonzalo -- Gilles-Gonzalez, Marie-Alda -- McKnight, Steven L -- NIH5-T32-GM08-291-12/GM/NIGMS NIH HHS/ -- R01 HL640381/HL/NHLBI NIH HHS/ -- R01 MH5938805/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2002 Dec 20;298(5602):2385-7. Epub 2002 Nov 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Biochemistry and Plant Biology and Plant Biotechnology Center, The Ohio State University, 1060 Carmack Road, Columbus, OH 43210, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12446832" target="_blank"〉PubMed〈/a〉
    Keywords: ARNTL Transcription Factors ; Animals ; Basic Helix-Loop-Helix Transcription Factors ; Carbon Monoxide/*metabolism/pharmacology ; Circadian Rhythm ; DNA/*metabolism ; Dimerization ; Helix-Loop-Helix Motifs ; Heme/chemistry/*metabolism ; Ligands ; Myoglobin/metabolism ; NADP/metabolism ; Nerve Tissue Proteins/*chemistry/*metabolism ; Oxidation-Reduction ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Spectrophotometry, Ultraviolet ; Transcription Factors/*chemistry/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2007-10-13
    Description: Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Merchant, Sabeeha S -- Prochnik, Simon E -- Vallon, Olivier -- Harris, Elizabeth H -- Karpowicz, Steven J -- Witman, George B -- Terry, Astrid -- Salamov, Asaf -- Fritz-Laylin, Lillian K -- Marechal-Drouard, Laurence -- Marshall, Wallace F -- Qu, Liang-Hu -- Nelson, David R -- Sanderfoot, Anton A -- Spalding, Martin H -- Kapitonov, Vladimir V -- Ren, Qinghu -- Ferris, Patrick -- Lindquist, Erika -- Shapiro, Harris -- Lucas, Susan M -- Grimwood, Jane -- Schmutz, Jeremy -- Cardol, Pierre -- Cerutti, Heriberto -- Chanfreau, Guillaume -- Chen, Chun-Long -- Cognat, Valerie -- Croft, Martin T -- Dent, Rachel -- Dutcher, Susan -- Fernandez, Emilio -- Fukuzawa, Hideya -- Gonzalez-Ballester, David -- Gonzalez-Halphen, Diego -- Hallmann, Armin -- Hanikenne, Marc -- Hippler, Michael -- Inwood, William -- Jabbari, Kamel -- Kalanon, Ming -- Kuras, Richard -- Lefebvre, Paul A -- Lemaire, Stephane D -- Lobanov, Alexey V -- Lohr, Martin -- Manuell, Andrea -- Meier, Iris -- Mets, Laurens -- Mittag, Maria -- Mittelmeier, Telsa -- Moroney, James V -- Moseley, Jeffrey -- Napoli, Carolyn -- Nedelcu, Aurora M -- Niyogi, Krishna -- Novoselov, Sergey V -- Paulsen, Ian T -- Pazour, Greg -- Purton, Saul -- Ral, Jean-Philippe -- Riano-Pachon, Diego Mauricio -- Riekhof, Wayne -- Rymarquis, Linda -- Schroda, Michael -- Stern, David -- Umen, James -- Willows, Robert -- Wilson, Nedra -- Zimmer, Sara Lana -- Allmer, Jens -- Balk, Janneke -- Bisova, Katerina -- Chen, Chong-Jian -- Elias, Marek -- Gendler, Karla -- Hauser, Charles -- Lamb, Mary Rose -- Ledford, Heidi -- Long, Joanne C -- Minagawa, Jun -- Page, M Dudley -- Pan, Junmin -- Pootakham, Wirulda -- Roje, Sanja -- Rose, Annkatrin -- Stahlberg, Eric -- Terauchi, Aimee M -- Yang, Pinfen -- Ball, Steven -- Bowler, Chris -- Dieckmann, Carol L -- Gladyshev, Vadim N -- Green, Pamela -- Jorgensen, Richard -- Mayfield, Stephen -- Mueller-Roeber, Bernd -- Rajamani, Sathish -- Sayre, Richard T -- Brokstein, Peter -- Dubchak, Inna -- Goodstein, David -- Hornick, Leila -- Huang, Y Wayne -- Jhaveri, Jinal -- Luo, Yigong -- Martinez, Diego -- Ngau, Wing Chi Abby -- Otillar, Bobby -- Poliakov, Alexander -- Porter, Aaron -- Szajkowski, Lukasz -- Werner, Gregory -- Zhou, Kemin -- Grigoriev, Igor V -- Rokhsar, Daniel S -- Grossman, Arthur R -- GM07185/GM/NIGMS NIH HHS/ -- GM42143/GM/NIGMS NIH HHS/ -- R01 GM032843/GM/NIGMS NIH HHS/ -- R01 GM042143/GM/NIGMS NIH HHS/ -- R01 GM042143-09/GM/NIGMS NIH HHS/ -- R01 GM060992/GM/NIGMS NIH HHS/ -- R01 GM062915-06/GM/NIGMS NIH HHS/ -- R37 GM030626/GM/NIGMS NIH HHS/ -- R37 GM042143/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 12;318(5848):245-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17932292" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/*genetics/*physiology ; Animals ; *Biological Evolution ; Chlamydomonas reinhardtii/*genetics/physiology ; Chloroplasts/metabolism ; Computational Biology ; DNA, Algal/genetics ; Flagella/metabolism ; Genes ; *Genome ; Genomics ; Membrane Transport Proteins/genetics/physiology ; Molecular Sequence Data ; Multigene Family ; Photosynthesis/genetics ; Phylogeny ; Plants/genetics ; Proteome ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2008-10-11
    Description: Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schipper, Jan -- Chanson, Janice S -- Chiozza, Federica -- Cox, Neil A -- Hoffmann, Michael -- Katariya, Vineet -- Lamoreux, John -- Rodrigues, Ana S L -- Stuart, Simon N -- Temple, Helen J -- Baillie, Jonathan -- Boitani, Luigi -- Lacher, Thomas E Jr -- Mittermeier, Russell A -- Smith, Andrew T -- Absolon, Daniel -- Aguiar, John M -- Amori, Giovanni -- Bakkour, Noura -- Baldi, Ricardo -- Berridge, Richard J -- Bielby, Jon -- Black, Patricia Ann -- Blanc, J Julian -- Brooks, Thomas M -- Burton, James A -- Butynski, Thomas M -- Catullo, Gianluca -- Chapman, Roselle -- Cokeliss, Zoe -- Collen, Ben -- Conroy, Jim -- Cooke, Justin G -- da Fonseca, Gustavo A B -- Derocher, Andrew E -- Dublin, Holly T -- Duckworth, J W -- Emmons, Louise -- Emslie, Richard H -- Festa-Bianchet, Marco -- Foster, Matt -- Foster, Sabrina -- Garshelis, David L -- Gates, Cormack -- Gimenez-Dixon, Mariano -- Gonzalez, Susana -- Gonzalez-Maya, Jose Fernando -- Good, Tatjana C -- Hammerson, Geoffrey -- Hammond, Philip S -- Happold, David -- Happold, Meredith -- Hare, John -- Harris, Richard B -- Hawkins, Clare E -- Haywood, Mandy -- Heaney, Lawrence R -- Hedges, Simon -- Helgen, Kristofer M -- Hilton-Taylor, Craig -- Hussain, Syed Ainul -- Ishii, Nobuo -- Jefferson, Thomas A -- Jenkins, Richard K B -- Johnston, Charlotte H -- Keith, Mark -- Kingdon, Jonathan -- Knox, David H -- Kovacs, Kit M -- Langhammer, Penny -- Leus, Kristin -- Lewison, Rebecca -- Lichtenstein, Gabriela -- Lowry, Lloyd F -- Macavoy, Zoe -- Mace, Georgina M -- Mallon, David P -- Masi, Monica -- McKnight, Meghan W -- Medellin, Rodrigo A -- Medici, Patricia -- Mills, Gus -- Moehlman, Patricia D -- Molur, Sanjay -- Mora, Arturo -- Nowell, Kristin -- Oates, John F -- Olech, Wanda -- Oliver, William R L -- Oprea, Monik -- Patterson, Bruce D -- Perrin, William F -- Polidoro, Beth A -- Pollock, Caroline -- Powel, Abigail -- Protas, Yelizaveta -- Racey, Paul -- Ragle, Jim -- Ramani, Pavithra -- Rathbun, Galen -- Reeves, Randall R -- Reilly, Stephen B -- Reynolds, John E 3rd -- Rondinini, Carlo -- Rosell-Ambal, Ruth Grace -- Rulli, Monica -- Rylands, Anthony B -- Savini, Simona -- Schank, Cody J -- Sechrest, Wes -- Self-Sullivan, Caryn -- Shoemaker, Alan -- Sillero-Zubiri, Claudio -- De Silva, Naamal -- Smith, David E -- Srinivasulu, Chelmala -- Stephenson, Peter J -- van Strien, Nico -- Talukdar, Bibhab Kumar -- Taylor, Barbara L -- Timmins, Rob -- Tirira, Diego G -- Tognelli, Marcelo F -- Tsytsulina, Katerina -- Veiga, Liza M -- Vie, Jean-Christophe -- Williamson, Elizabeth A -- Wyatt, Sarah A -- Xie, Yan -- Young, Bruce E -- New York, N.Y. -- Science. 2008 Oct 10;322(5899):225-30. doi: 10.1126/science.1165115.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉International Union for Conservation of Nature (IUCN) Species Programme, IUCN, 28 Rue Mauverney, 1196 Gland, Switzerland. jan.schipper@iucn.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18845749" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Body Size ; Conservation of Natural Resources ; Databases, Factual ; Ecosystem ; *Extinction, Biological ; *Mammals/anatomy & histology/classification/physiology ; Marine Biology ; Phylogeny ; Population Dynamics ; Seawater
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    ISSN: 0749-503X
    Keywords: Saccharomyces cerevisiae ; chromosome XI ; UBI2 ; MPLI ; ORF ; myosin ; USO1 ; Nopp140 ; membrane protein ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: As part of the EEC yeast genome program, a fragment of 15 820 bp from the right arm of Saccharomyces cerevisiae chromosome XI has been sequenced. This fragment corresponds roughly to the centromere-distal half of cosmid pUKG046 and to a small fragment of cosmid pUKG096, which are located approximately 150 kb from the centromere. It contains four open reading frames (ORFs) which encode potential proteins of more than 100 amino acid residues, as well as the UBI2 gene which carries an intron and does not show up as an ORF in the sequence analysis programs. One of the putative proteins, YKR412, is very rich in serine and has significant homology at the carboxyl end to Nopp140 phosphoprotein. YKR413 has several predicted transmembrane domains. YKR15, which has been recently cloned as the MPL1 gene, encodes a polypeptide that shows homologies to myosin heavy chain and to the cytoskeleton protein Uso1.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 9 (1993), S. 1065-1073 
    ISSN: 0749-503X
    Keywords: Permeases ; amino acids ; nitrogen regulation ; Saccharomyces cerevisiae ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: In the yeast Saccharomyces cerevisiae, there is a general amino acid permease, regulated by nitrogen catabolite repression, and several specific permeases whose nitrogen regulation is not well understood. In this study, we used continuous cultures to analyse the effect of nitrogen limitation and pH on the activity of general and several specific amino acid permeases. General permease activity was maximal in severe nitrogen limitation and diminished 400-fold in cells grown under nitrogen excess. For the specific permeases, the maximal uptake activity was found between mild limitation and nitrogen excess, while very small activity was detected under strict limitation. These results indicate that the nitrogen regulation of the general and the specific amino acid carriers is coordinated in such a way that no redundancy exists in amino acid transport. The regulation of the specific permeases was similar to that found for a system with anabolic function in nitrogen metabolism.All of these permeases are supposed to work through a proton symport mechanism, and thus rely on pH gradients to carry out their function. We studied the effect of pH on the kinetic constants of the general permease. Our results show that the effect of pH on the Km was different for acidic, neutral and basic amino acids, while the effect on Vmax was independent of the electrical charge of the amino acids.
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  • 6
    ISSN: 0749-503X
    Keywords: Saccharomyces cerevisiae ; yeast genome ; genome sequencing ; chromosome VII ; QCR9 ; UBR1 ; TYS1 ; TFG1 ; HGH1 ; BUB1 ; tRNALeu3 ; tRNATrp ; tRNALys1 ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We report the sequence of a 23 002 bp fragment located on the right arm of Saccharomyces cerevisiae chromosome VII. Analysis of this region revealed 14 complete open reading frames (ORFs) with more than 300 base pairs. Six of them correspond to previously known genes. G7164 is the QCR9 gene coding for subunit 9 of the cytochrome c reductase; G7168 is UBR1, encoding an ubiquitin protein ligase; G7522 is the TYS1 gene, which encodes for the tyrosyl tRNA synthetase; G7526 is TFG1, the gene coding for the RNA polymerase transcription initiation factor TFIIF (factor G); G7538 is the gene HGH1 which encodes a protein related to the mammalian HMG1 and HMG2 proteins. G7542 is the BUB1 gene which encodes a ser/thr protein kinase involved in spindle assembly during the cell cycle. One of the ORFs, G7553, shares significant homologies with the gene UTR2 from S. cerevisiae. None of the seven remaining ORFs shows similarity to any of the sequences within the public databases. Three ORFs are internal ORFs of the above-described known genes, and two small ORFs are completely contained in larger ORFs on the complementary strand, and therefore probably do not correspond to real genes. This region also contains three genes specifying tRNAs for Leu, Lys and Trp, and several LTR elements. The sequence described in this paper has been deposited in the EMBL data library under the Accession Number X99074. © 1997 John Wiley & Sons, Ltd.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 13 (1997), S. 961-971 
    ISSN: 0749-503X
    Keywords: Kluyveromyces lactis ; HEM1 ; 5-aminolevulinate synthase ; transcription regulation ; heme-responsive element ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The KlHEM1 gene from Kluyveromyces lactis encodes a functional 5-aminolevulinate synthase (δALA synthase), as confirmed by complementation of a hem1 mutant Saccharomyces cerevisiae strain, homology search, and detection of a 2·3 kb transcript. The gene is highly homologous to the ScHEM1 gene, and the sequence of the promoter region contains a complex combination of putative regulatory signals. Some of them are related to phospholipid biosynthesis, glycolytic metabolism, and regulation by carbon source. Transcription of KlHEM1 increased significantly in response to limited oxygen, and only slightly with the change from repressed (glucose) to derepressed conditions (glycerol). The δALA synthase from K. lactis contains, in the amino-terminal region, two heme-responsive elements that are not present in the protein from Saccharomyces cerevisiae. The complete nucleotide sequence has been entered in the EMBL data library under Accession Number X92944. © 1997 John Wiley & Sons, Ltd.
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  • 8
    ISSN: 0749-503X
    Keywords: yeast ; Candida utilis ; URA3 ; orotidine 5′-monophosphate decarboxylase ; transformation system ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The URA3 gene of Candida utilis encoding orotidine-5′-phosphate decarboxylase enzyme was isolated by complementation in Escherichia coli pyrF mutation. The deduced amino-acid sequence is highly similar to that of the Ura3 proteins from other yeast and fungal species. An extensive analysis of the family of orotidine-5′-phosphate decarboxylase is shown. The URA3 gene of C. utilis was able to complement functionally the ura3 mutation of Saccharomyces cerevisiae. The sequence presented here has been deposited in the EMBL data library under Accession Number Y12660. © 1998 John Wiley & Sons, Ltd.
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  • 9
    ISSN: 0749-503X
    Keywords: yeast genome ; chromosome VII ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We report the sequence of a 9000 bp fragment from the right arm of Saccharomyces cerevisiae chromosome VII. Analysis of the sequence revealed four complete previously unknown open reading frames, which were named G7587, G7589, G7591 and G7594 following standard rules for provisional nomenclature. Outstanding features of some of these proteins were the homology of the putative protein coded by G7589 with proteins involved in transcription regulation and the transmembrane domains predicted in the putative protein coded by G7591. The sequence reported has been deposited in the EMBL data library under Accession Number X82775.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 13 (1997), S. 1347-1355 
    ISSN: 0749-503X
    Keywords: yeast metabolism ; metabolite extraction ; metabolic engineering ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: A simple and reliable method for the efficient inactivation of metabolism and for quantitative metabolite extraction from yeast cells is presented. It is based on the use of a boiling solution made of 75% ethanol (volume/final volume) buffered with 70 mm-Hepes (final concentration), pH 7·5, to guarantee the stability throughout the whole procedure of a large variety of metabolites, including all glycolytic intermediates, nucleotides, pyridine nucleotides and organic acids compounds. The extraction is fast, requiring only 3 min incubation of yeast cells in the ethanol-buffered mixture maintained at 80°C. It can be carried out either directly by spraying the cells into the boiling mixture, or after quenching the whole culture in 60% methanol kept at -40°C. Extracts are subsequently concentrated by evaporation under partial vacuum and the residue is resuspended in a small volume of water. This concentration step and the use of a highly sensitive analytical method allow us to quantify metabolites in less than 10 mg dry weight cells. This method, which can be applied to other fungi, could be very helpful for the determination of true metabolites in mutants generated through the EUROFAN programme and for metabolic flux analysis. © 1997 John Wiley & Sons, Ltd.
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