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  • Base Sequence  (8)
  • Protein Structure, Tertiary  (7)
  • American Association for the Advancement of Science (AAAS)  (15)
  • American Institute of Physics (AIP)
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  • 1
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    Protein structure prediction and structural genomics (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-06
    Description: Genome sequencing projects are producing linear amino acid sequences, but full understanding of the biological role of these proteins will require knowledge of their structure and function. Although experimental structure determination methods are providing high-resolution structure information about a subset of the proteins, computational structure prediction methods will provide valuable information for the large fraction of sequences whose structures will not be determined experimentally. The first class of protein structure prediction methods, including threading and comparative modeling, rely on detectable similarity spanning most of the modeled sequence and at least one known structure. The second class of methods, de novo or ab initio methods, predict the structure from sequence alone, without relying on similarity at the fold level between the modeled sequence and any of the known structures. In this Viewpoint, we begin by describing the essential features of the methods, the accuracy of the models, and their application to the prediction and understanding of protein function, both for single proteins and on the scale of whole genomes. We then discuss the important role that protein structure prediction methods play in the growing worldwide effort in structural genomics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, D -- Sali, A -- GM 54762/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Oct 5;294(5540):93-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. dabaker@u.washington.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11588250" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; *Computational Biology ; Computer Simulation ; Databases, Factual ; *Genomics ; Humans ; Internet ; *Models, Molecular ; *Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Proteins/*chemistry/genetics/physiology ; Sequence Alignment ; Software ; Templates, Genetic
    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
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    Mapping of DNA instability at the fragile X to a trinucleotide repeat sequence p(CCG)n (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-06-21
    Description: The sequence of a Pst I restriction fragment was determined that demonstrate instability in fragile X syndrome pedigrees. The region of instability was localized to a trinucleotide repeat p(CCG)n. The sequence flanking this repeat were identical in normal and affected individuals. The breakpoints in two somatic cell hybrids constructed to break at the fragile site also mapped to this repeat sequence. The repeat exhibits instability both when cloned in a nonhomologous host and after amplification by the polymerase chain reaction. These results suggest variation in the trinucleotide repeat copy number as the molecular basis for the instability and possibly the fragile site. This would account for the observed properties of this region in vivo and in vitro.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kremer, E J -- Pritchard, M -- Lynch, M -- Yu, S -- Holman, K -- Baker, E -- Warren, S T -- Schlessinger, D -- Sutherland, G R -- Richards, R I -- New York, N.Y. -- Science. 1991 Jun 21;252(5013):1711-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cytogenetics and Molecular Genetics, Adelaide Children's Hospital, South Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1675488" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Blotting, Southern ; Chromosome Mapping ; Fragile X Syndrome/*genetics ; Humans ; Molecular Sequence Data ; Pedigree ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Repetitive Sequences, Nucleic Acid ; Restriction Mapping ; X Chromosome/ultrastructure
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  • 3
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    A multifunctional aqueous channel formed by CFTR (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-11-27
    Description: The cystic fibrosis gene product (CFTR) is a complex protein that functions as an adenosine 3,5-monophosphate (cAMP)-stimulated ion channel and possibly as a regulator of intracellular processes. In order to determine whether the CFTR molecule contains a functional aqueous pathway, anion, water, and urea transport were measured in Xenopus oocytes expressing CFTR. Cyclic AMP agonists induced a Cl- conductance of 94 microsiemens and an increase in water permeability of 4 x 10(-4) centimeter per second that was inhibited by a Cl- channel blocker and was dependent on anion composition. CFTR has a calculated single channel water conductance of 9 x 10(-13) cubic centimeter per second, suggesting a pore-like aqueous pathway. Oocytes expressing CFTR also showed cAMP-stimulated transport of urea but not the larger solute sucrose. Thus CFTR contains a cAMP-stimulated aqueous pore that can transport anions, water, and small solutes. The results also provide functional evidence for water movement through an ion channel.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hasegawa, H -- Skach, W -- Baker, O -- Calayag, M C -- Lingappa, V -- Verkman, A S -- DK35124/DK/NIDDK NIH HHS/ -- DK43840/DK/NIDDK NIH HHS/ -- HL42368/HL/NHLBI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1992 Nov 27;258(5087):1477-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, University of California, San Francisco 94143-0532.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1279809" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Biological Transport/physiology ; Chlorides/metabolism ; Cyclic AMP/physiology ; Cystic Fibrosis Transmembrane Conductance Regulator ; Female ; Humans ; In Vitro Techniques ; Ion Channels/*physiology ; Membrane Proteins/*physiology ; Molecular Sequence Data ; Oocytes ; Urea/metabolism ; Water/metabolism ; Xenopus
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  • 4
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    Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-08
    Description: Many bacterial pathogens have long, slender pili through which they adhere to host cells. The crystal structure of the major pilin subunit from the Gram-positive human pathogen Streptococcus pyogenes at 2.2 angstroms resolution reveals an extended structure comprising two all-beta domains. The molecules associate in columns through the crystal, with each carboxyl terminus adjacent to a conserved lysine of the next molecule. This lysine forms the isopeptide bonds that link the subunits in native pili, validating the relevance of the crystal assembly. Each subunit contains two lysine-asparagine isopeptide bonds generated by an intramolecular reaction, and we find evidence for similar isopeptide bonds in other cell surface proteins of Gram-positive bacteria. The present structure explains the strength and stability of such Gram-positive pili and could facilitate vaccine development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, Hae Joo -- Coulibaly, Fasseli -- Clow, Fiona -- Proft, Thomas -- Baker, Edward N -- New York, N.Y. -- Science. 2007 Dec 7;318(5856):1625-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18063798" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Asparagine/chemistry ; Chemistry, Physical ; Crystallography, X-Ray ; Fimbriae Proteins/*chemistry ; Fimbriae, Bacterial/*chemistry/ultrastructure ; Hydrogen Bonding ; Lysine/chemistry ; Models, Molecular ; Molecular Sequence Data ; Peptides/chemistry ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Streptococcus pyogenes/*chemistry/metabolism/*ultrastructure
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  • 5
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    A Burkholderia pseudomallei toxin inhibits helicase activity of translation factor eIF4A (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-11-15
    Description: The structure of BPSL1549, a protein of unknown function from Burkholderia pseudomallei, reveals a similarity to Escherichia coli cytotoxic necrotizing factor 1. We found that BPSL1549 acted as a potent cytotoxin against eukaryotic cells and was lethal when administered to mice. Expression levels of bpsl1549 correlate with conditions expected to promote or suppress pathogenicity. BPSL1549 promotes deamidation of glutamine-339 of the translation initiation factor eIF4A, abolishing its helicase activity and inhibiting translation. We propose to name BPSL1549 Burkholderia lethal factor 1.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3364511/" 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/PMC3364511/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cruz-Migoni, Abimael -- Hautbergue, Guillaume M -- Artymiuk, Peter J -- Baker, Patrick J -- Bokori-Brown, Monika -- Chang, Chung-Te -- Dickman, Mark J -- Essex-Lopresti, Angela -- Harding, Sarah V -- Mahadi, Nor Muhammad -- Marshall, Laura E -- Mobbs, George W -- Mohamed, Rahmah -- Nathan, Sheila -- Ngugi, Sarah A -- Ong, Catherine -- Ooi, Wen Fong -- Partridge, Lynda J -- Phillips, Helen L -- Raih, M Firdaus -- Ruzheinikov, Sergei -- Sarkar-Tyson, Mitali -- Sedelnikova, Svetlana E -- Smither, Sophie J -- Tan, Patrick -- Titball, Richard W -- Wilson, Stuart A -- Rice, David W -- 085162/Wellcome Trust/United Kingdom -- BB/D011795/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/D524975/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E025293/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- WT085162AIA/Wellcome Trust/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2011 Nov 11;334(6057):821-4. doi: 10.1126/science.1211915.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield S10 2TN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22076380" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Bacterial Proteins/*chemistry/genetics/metabolism/*toxicity ; Bacterial Toxins/*chemistry/genetics/metabolism/*toxicity ; Burkholderia pseudomallei/*chemistry/*pathogenicity ; Catalytic Domain ; Cell Line ; Crystallography, X-Ray ; Cytotoxins/chemistry/genetics/metabolism/toxicity ; Escherichia coli Proteins/chemistry ; Eukaryotic Initiation Factor-4A/*antagonists & inhibitors/metabolism ; Glutamine/metabolism ; Humans ; Mice ; Mice, Inbred BALB C ; Models, Molecular ; Mutant Proteins/toxicity ; Peptide Chain Initiation, Translational/drug effects ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 6
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    Toward high-resolution de novo structure prediction for small proteins (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-17
    Description: The prediction of protein structure from amino acid sequence is a grand challenge of computational molecular biology. By using a combination of improved low- and high-resolution conformational sampling methods, improved atomically detailed potential functions that capture the jigsaw puzzle-like packing of protein cores, and high-performance computing, high-resolution structure prediction (〈1.5 angstroms) can be achieved for small protein domains (〈85 residues). The primary bottleneck to consistent high-resolution prediction appears to be conformational sampling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bradley, Philip -- Misura, Kira M S -- Baker, David -- New York, N.Y. -- Science. 2005 Sep 16;309(5742):1868-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Washington, Department of Biochemistry, and Howard Hughes Medical Institute, Box 357350, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16166519" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chemistry, Physical ; *Computational Biology ; Computer Simulation ; Hydrogen Bonding ; Models, Molecular ; Monte Carlo Method ; Physicochemical Phenomena ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry ; Sequence Alignment ; Thermodynamics
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  • 7
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    Control of cell fate by a deubiquitinating enzyme encoded by the fat facets gene (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-15
    Description: Ubiquitin is a highly conserved polypeptide found in all eukaryotes. The major function of ubiquitin is to target proteins for complete or partial degradation by a multisubunit protein complex called the proteasome. Here, the Drosophila fat facets gene, which is required for the appropriate determination of particular cells in the fly eye, was shown to encode a ubiquitin-specific protease (Ubp), an enzyme that cleaves ubiquitin from ubiquitin-protein conjugates. The Fat facets protein (FAF) acts as a regulatory Ubp that prevents degradation of its substrate by the proteasome. Flies bearing fat facets gene mutations were used to show that a Ubp is cell type--and substrate-specific and a regulator of cell fate decisions in a multicellular organism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Y -- Baker, R T -- Fischer-Vize, J A -- New York, N.Y. -- Science. 1995 Dec 15;270(5243):1828-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Texas, Austin 78712, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8525378" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; *Cell Differentiation/genetics ; Cysteine/metabolism ; Drosophila/embryology/enzymology/genetics ; Endopeptidases/genetics/*metabolism ; Escherichia coli ; Eye/embryology ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Oligodeoxyribonucleotides ; Recombinant Fusion Proteins/genetics/metabolism ; Ubiquitins/*metabolism ; beta-Galactosidase/genetics
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  • 8
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    Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-10-18
    Description: The Escherichia coli DNA binding protein RuvA acts in concert with the helicase RuvB to drive branch migration of Holliday intermediates during recombination and DNA repair. The atomic structure of RuvA was determined at a resolution of 1.9 angstroms. Four monomers of RuvA are related by fourfold symmetry in a manner reminiscent of a four-petaled flower. The four DNA duplex arms of a Holliday junction can be modeled in a square planar configuration and docked into grooves on the concave surface of the protein around a central pin that may facilitate strand separation during the migration reaction. The model presented reveals how a RuvAB-junction complex may also accommodate the resolvase RuvC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rafferty, J B -- Sedelnikova, S E -- Hargreaves, D -- Artymiuk, P J -- Baker, P J -- Sharples, G J -- Mahdi, A A -- Lloyd, R G -- Rice, D W -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 1996 Oct 18;274(5286):415-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK. d.rice@sheffield.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8832889" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Base Composition ; Crystallography, X-Ray ; DNA Helicases/metabolism ; DNA, Bacterial/chemistry/*metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Endodeoxyribonucleases/metabolism ; Escherichia coli ; *Escherichia coli Proteins ; Hydrogen Bonding ; Models, Molecular ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Recombination, Genetic
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  • 9
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    Relation of phenotype evolution of HIV-1 to envelope V2 configuration (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-06-04
    Description: Biological variability of human immunodeficiency virus type-1 (HIV-1) is involved in the pathogenesis of acquired immunodeficiency syndrome (AIDS). Syncytium-inducing (SI) HIV-1 variants emerge in 50 percent of infected individuals during infection, preceding accelerated CD4+ T cell loss and rapid progression to AIDS. The V1 to V2 and V3 region of the viral envelope glycoprotein gp120 contained the major determinants of SI capacity. The configuration of a hypervariable locus in the V2 domain appeared to be predictive for non-SI to SI phenotype conversion. Early prediction of HIV-1 phenotype evolution may be useful for clinical monitoring and treatment of asymptomatic infection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Groenink, M -- Fouchier, R A -- Broersen, S -- Baker, C H -- Koot, M -- van't Wout, A B -- Huisman, H G -- Miedema, F -- Tersmette, M -- Schuitemaker, H -- New York, N.Y. -- Science. 1993 Jun 4;260(5113):1513-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Clinical Viro-Immunology, Central Laboratory of the Netherlands Red Cross Blood Transfusion Service, Amsterdam.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8502996" target="_blank"〉PubMed〈/a〉
    Keywords: Acquired Immunodeficiency Syndrome/microbiology ; Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Consensus Sequence ; Genetic Variation ; Giant Cells/microbiology ; HIV Envelope Protein gp120/*chemistry ; HIV Seropositivity/microbiology ; HIV-1/*chemistry/*genetics/pathogenicity ; Humans ; Male ; Molecular Sequence Data ; Phenotype ; Protein Conformation ; Recombination, Genetic
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  • 10
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    Lineages of acidophilic archaea revealed by community genomic analysis (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-23
    Description: Novel, low-abundance microbial species can be easily overlooked in standard polymerase chain reaction (PCR)-based surveys. We used community genomic data obtained without PCR or cultivation to reconstruct DNA fragments bearing unusual 16S ribosomal RNA (rRNA) and protein-coding genes from organisms belonging to novel archaeal lineages. The organisms are minor components of all biofilms growing in pH 0.5 to 1.5 solutions within the Richmond Mine, California. Probes specific for 16S rRNA showed that the fraction less than 0.45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of 〈0.006 cubic micrometer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Brett J -- Tyson, Gene W -- Webb, Richard I -- Flanagan, Judith -- Hugenholtz, Philip -- Allen, Eric E -- Banfield, Jillian F -- New York, N.Y. -- Science. 2006 Dec 22;314(5807):1933-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185602" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; *Biofilms ; California ; Cell Membrane/ultrastructure ; DNA Transposable Elements ; DNA, Archaeal ; Databases, Genetic ; *Ecosystem ; *Euryarchaeota/genetics/physiology/ultrastructure ; Genes, Archaeal ; Genes, rRNA ; *Genome, Archaeal ; Hydrogen-Ion Concentration ; Microscopy, Electron, Transmission ; Mining ; Molecular Sequence Data ; Oligonucleotide Probes ; Phylogeny ; Pyrophosphatases/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Temperature
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