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  • *Biological Evolution  (69)
  • Binding Sites  (61)
  • Chemistry
  • American Association for the Advancement of Science (AAAS)  (131)
  • 2000-2004  (131)
  • 1945-1949
  • 2004  (131)
  • 1945
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (131)
  • Wiley-Blackwell  (263)
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  • 2000-2004  (131)
  • 1945-1949
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  • 1
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    CCR5 promoter alleles and specific DNA binding factors (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bream, J H -- Young, H A -- Rice, N -- Martin, M P -- Smith, M W -- Carrington, M -- O'Brien, S J -- New York, N.Y. -- Science. 1999 Apr 9;284(5412):223.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Experimental Immunology, National Cancer Institute-Frederick Cancer, Research and Development Center (NCI-FCRDC), Frederick, MD 21702, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15224670" target="_blank"〉PubMed〈/a〉
    Keywords: Acquired Immunodeficiency Syndrome/genetics/immunology/mortality/*physiopathology ; *Alleles ; Binding Sites ; Cell Nucleus/metabolism ; DNA-Binding Proteins/*metabolism ; Disease Progression ; Electrophoretic Mobility Shift Assay ; Humans ; Nuclear Proteins/*metabolism ; Oligodeoxyribonucleotides/metabolism ; Polymorphism, Single Nucleotide ; *Promoter Regions, Genetic ; Receptors, CCR5/*genetics ; Survival Rate ; T-Lymphocytes ; Transcription Factors/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
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    Crystal structure of the long-chain fatty acid transporter FadL (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-06-05
    Description: The mechanisms by which hydrophobic molecules, such as long-chain fatty acids, enter cells are poorly understood. In Gram-negative bacteria, the lipopolysaccharide layer in the outer membrane is an efficient barrier for fatty acids and aromatic hydrocarbons destined for biodegradation. We report crystal structures of the long-chain fatty acid transporter FadL from Escherichia coli at 2.6 and 2.8 angstrom resolution. FadL forms a 14-stranded beta barrel that is occluded by a central hatch domain. The structures suggest that hydrophobic compounds bind to multiple sites in FadL and use a transport mechanism that involves spontaneous conformational changes in the hatch.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van den Berg, Bert -- Black, Paul N -- Clemons, William M Jr -- Rapoport, Tom A -- New York, N.Y. -- Science. 2004 Jun 4;304(5676):1506-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA. lvandenberg@hms.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15178802" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*chemistry/metabolism ; Binding Sites ; Biological Transport ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; Fatty Acid Transport Proteins ; Fatty Acids/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
    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
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    Cope's rule, hypercarnivory, and extinction in North American canids (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-02
    Description: Over the past 50 million years, successive clades of large carnivorous mammals diversified and then declined to extinction. In most instances, the cause of the decline remains a puzzle. Here we argue that energetic constraints and pervasive selection for larger size (Cope's rule) in carnivores lead to dietary specialization (hypercarnivory) and increased vulnerability to extinction. In two major clades of extinct North American canids, the evolution of large size was associated with a dietary shift to hypercarnivory and a decline in species durations. Thus, selection for attributes that promoted individual success resulted in progressive evolutionary failure of their clades.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Van Valkenburgh, Blaire -- Wang, Xiaoming -- Damuth, John -- New York, N.Y. -- Science. 2004 Oct 1;306(5693):101-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA 90095-1606, USA. bvanval@ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15459388" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Body Constitution ; Body Weight ; *Carnivora/anatomy & histology/classification/physiology ; Cuspid/anatomy & histology ; *Diet ; *Fossils ; Incisor/anatomy & histology ; Jaw/anatomy & histology ; Molar/anatomy & histology ; North America ; Paleodontology ; Population Density ; Population Dynamics ; Predatory Behavior ; Principal Component Analysis ; Selection, Genetic
    Print ISSN: 0036-8075
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  • 4
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    In vivo activation of the p53 pathway by small-molecule antagonists of MDM2 (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-06
    Description: MDM2 binds the p53 tumor suppressor protein with high affinity and negatively modulates its transcriptional activity and stability. Overexpression of MDM2, found in many human tumors, effectively impairs p53 function. Inhibition of MDM2-p53 interaction can stabilize p53 and may offer a novel strategy for cancer therapy. Here, we identify potent and selective small-molecule antagonists of MDM2 and confirm their mode of action through the crystal structures of complexes. These compounds bind MDM2 in the p53-binding pocket and activate the p53 pathway in cancer cells, leading to cell cycle arrest, apoptosis, and growth inhibition of human tumor xenografts in nude mice.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vassilev, Lyubomir T -- Vu, Binh T -- Graves, Bradford -- Carvajal, Daisy -- Podlaski, Frank -- Filipovic, Zoran -- Kong, Norman -- Kammlott, Ursula -- Lukacs, Christine -- Klein, Christian -- Fotouhi, Nader -- Liu, Emily A -- New York, N.Y. -- Science. 2004 Feb 6;303(5659):844-8. Epub 2004 Jan 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Discovery Oncology, Roche Research Center, Hoffmann-La Roche, Inc., Nutley, NJ 07110, USA. lyubomir.vassilev@roche.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14704432" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis/*drug effects ; Binding Sites ; Cell Cycle/drug effects ; Cell Division/*drug effects ; Cell Line ; Cell Line, Tumor ; Cell Survival/drug effects ; Crystallization ; Crystallography, X-Ray ; Cyclin-Dependent Kinase Inhibitor p21 ; Cyclins/metabolism ; Dose-Response Relationship, Drug ; Gene Expression ; Genes, p53 ; Humans ; Hydrophobic and Hydrophilic Interactions ; Imidazoles/chemistry/metabolism/*pharmacology ; Mice ; Mice, Nude ; Models, Molecular ; Molecular Weight ; NIH 3T3 Cells ; Neoplasm Transplantation ; Neoplasms, Experimental/drug therapy/metabolism/*pathology ; *Nuclear Proteins ; Phosphorylation ; Piperazines/chemistry/metabolism/*pharmacology ; Protein Conformation ; Proto-Oncogene Proteins/*antagonists & inhibitors/chemistry/metabolism ; Proto-Oncogene Proteins c-mdm2 ; Stereoisomerism ; Transplantation, Heterologous ; Tumor Suppressor Protein p53/*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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  • 5
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    Genetics. A ruff theory of evolution: gene stutters drive dog shape (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2004 Dec 24;306(5705):2172.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15618495" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Breeding ; Dogs/*anatomy & histology/*genetics/growth & development ; Genetic Variation ; Hindlimb ; Neoplasm Proteins/genetics ; Nose/anatomy & histology ; Phenotype ; Selection, Genetic ; Skull/anatomy & histology ; *Tandem Repeat Sequences ; Toes/anatomy & histology ; Transcription Factors/genetics
    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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  • 6
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    Developmental biology. Worm's light-sensing proteins suggest eye's single origin (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2004 Oct 29;306(5697):796-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15514125" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Brain/cytology ; Circadian Rhythm ; *Eye ; Gene Duplication ; Genome ; Homeodomain Proteins/*analysis ; Humans ; Light ; Photoreceptor Cells, Invertebrate/chemistry/*cytology ; Photoreceptor Cells, Vertebrate/chemistry/cytology ; Polychaeta/chemistry/*cytology/*genetics ; Retinal Ganglion Cells/cytology ; Rod Opsins/analysis/*chemistry/*genetics
    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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  • 7
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    Old World fossil record of modern-type hummingbirds (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-08
    Description: I report on tiny skeletons of stem-group hummingbirds from the early Oligocene of Germany that are of essentially modern appearance and exhibit morphological specializations toward nectarivory and hovering flight. These are the oldest fossils of modern-type hummingbirds, which had not previously been reported from the Old World. The findings demonstrate that early hummingbird evolution was not restricted to the New World. They further suggest that bird-flower coevolution dates back to the early Oligocene and open another view on the origin of ornithophily in Old World plants.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mayr, Gerald -- New York, N.Y. -- Science. 2004 May 7;304(5672):861-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Forschungsinstitut Senckenberg, Division of Ornithology, Senckenberganlage 25, D-60325 Frankfurt a.M., Germany. Gerald.Mayr@senckenberg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131303" target="_blank"〉PubMed〈/a〉
    Keywords: Americas ; Animals ; *Biological Evolution ; *Birds/anatomy & histology/classification ; Bone and Bones/anatomy & histology ; Europe ; Flight, Animal ; Flowers ; *Fossils ; Germany
    Print ISSN: 0036-8075
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  • 8
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    Natural history museums. Museums that made a master (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2004 Jul 2;305(5680):37.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15232086" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Awards and Prizes ; Berlin ; *Biological Evolution ; Biology/history ; Birds ; History, 20th Century ; History, 21st Century ; Museums/*history ; United States
    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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  • 9
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    Evolutionary biology. Changing a fish's bony armor in the wink of a gene (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-06-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2004 Jun 18;304(5678):1736.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15205506" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Alleles ; Animals ; *Biological Evolution ; Breeding ; Crosses, Genetic ; Environment ; Extremities/growth & development ; Fresh Water ; Gene Expression Regulation ; Genes ; Genome ; Homeodomain Proteins/*genetics/metabolism ; Mutation ; Paired Box Transcription Factors ; Seawater ; Selection, Genetic ; Smegmamorpha/*anatomy & histology/*genetics ; Transcription Factors/*genetics/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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  • 10
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    The structure and receptor binding properties of the 1918 influenza hemagglutinin (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-07
    Description: The 1918 influenza pandemic resulted in about 20 million deaths. This enormous impact, coupled with renewed interest in emerging infections, makes characterization of the virus involved a priority. Receptor binding, the initial event in virus infection, is a major determinant of virus transmissibility that, for influenza viruses, is mediated by the hemagglutinin (HA) membrane glycoprotein. We have determined the crystal structures of the HA from the 1918 virus and two closely related HAs in complex with receptor analogs. They explain how the 1918 HA, while retaining receptor binding site amino acids characteristic of an avian precursor HA, is able to bind human receptors and how, as a consequence, the virus was able to spread in the human population.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gamblin, S J -- Haire, L F -- Russell, R J -- Stevens, D J -- Xiao, B -- Ha, Y -- Vasisht, N -- Steinhauer, D A -- Daniels, R S -- Elliot, A -- Wiley, D C -- Skehel, J J -- AI-13654/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1838-42. Epub 2004 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14764886" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Birds ; Crystallography, X-Ray ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/*metabolism ; History, 20th Century ; Humans ; Hydrogen Bonding ; Influenza A virus/*immunology/metabolism/pathogenicity ; Influenza, Human/epidemiology/history/*virology ; Membrane Glycoproteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Virus/*metabolism ; Sequence Alignment ; Sialic Acids/metabolism ; Species Specificity ; Swine
    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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  • 11
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    Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-04
    Description: DNA photolyases use light energy to repair DNA that comprises ultraviolet-induced lesions such as the cis-syn cyclobutane pyrimidine dimers (CPDs). Here we report the crystal structure of a DNA photolyase bound to duplex DNA that is bent by 50 degrees and comprises a synthetic CPD lesion. This CPD lesion is flipped into the active site and split there into two thymines by synchrotron radiation at 100 K. Although photolyases catalyze blue light-driven CPD cleavage only above 200 K, this structure apparently mimics a structural substate during light-driven DNA repair in which back-flipping of the thymines into duplex DNA has not yet taken place.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mees, Alexandra -- Klar, Tobias -- Gnau, Petra -- Hennecke, Ulrich -- Eker, Andre P M -- Carell, Thomas -- Essen, Lars-Oliver -- New York, N.Y. -- Science. 2004 Dec 3;306(5702):1789-93.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, Butenandt-Strasse 5-13, Ludwig Maximilians University, D-81377 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15576622" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/*chemistry/metabolism ; *DNA Damage ; *DNA Repair ; DNA, Single-Stranded/chemistry/metabolism ; Deoxyribodipyrimidine Photo-Lyase/*chemistry/metabolism ; Flavin-Adenine Dinucleotide/metabolism ; Hydrogen Bonding ; Nucleic Acid Conformation ; Protein Conformation ; Pyrimidine Dimers/*chemistry/metabolism ; Synechococcus/*enzymology ; Thymine/chemistry
    Print ISSN: 0036-8075
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  • 12
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    Biochemistry. How active sites communicate in thiamine enzymes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jordan, Frank -- GM-50380/GM/NIGMS NIH HHS/ -- GM-62330/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Oct 29;306(5697):818-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Rutgers University, Newark, NJ 07102, USA. frjordan@newark.rutgers.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15514144" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Binding Sites ; Dihydrolipoyllysine-Residue Acetyltransferase ; Dimerization ; Geobacillus stearothermophilus/*enzymology ; Glutamic Acid/chemistry ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Kinetics ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits ; Protons ; Pyruvate Dehydrogenase (Lipoamide)/*chemistry/*metabolism ; Pyruvate Dehydrogenase Complex/*chemistry/*metabolism ; Thiamine Pyrophosphate/chemistry/*metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 13
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    Living with the past: evolution, development, and patterns of disease (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-18
    Description: Epidemiological observations have led to the hypothesis that the risk of developing some chronic noncommunicable diseases in adulthood is influenced not only by genetic and adult life-style factors but also by environmental factors acting in early life. Research in evolutionary biology, developmental biology, and animal and human physiology provides support for this idea and suggests that environmental processes influencing the propensity to disease in adulthood operate during the periconceptual, fetal, and infant phases of life. This "developmental origins of health and disease" concept may have important biological, medical, and socioeconomic implications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gluckman, Peter D -- Hanson, Mark A -- New York, N.Y. -- Science. 2004 Sep 17;305(5691):1733-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Liggins Institute, University of Auckland and National Research Centre for Growth and Development, 2-6 Park Avenue, Grafton, Private Bag 92019, Auckland, New Zealand. pd.gluckman@auckland.ac.nz〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15375258" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Birth Weight ; *Chronic Disease ; Cues ; Disease/*etiology ; *Disease Susceptibility ; *Embryonic and Fetal Development ; *Environment ; Female ; Humans ; Infant, Newborn ; Life Style ; Nutritional Physiological Phenomena ; Pregnancy ; Prenatal Exposure Delayed Effects ; Risk Factors
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 14
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    Recruitment and spreading of the C. elegans dosage compensation complex along X chromosomes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-21
    Description: To achieve X-chromosome dosage compensation, organisms must distinguish X chromosomes from autosomes. We identified multiple, cis-acting regions that recruit the Caenorhabditis elegans dosage compensation complex (DCC) through a search for regions of X that bind the complex when detached from X. The DCC normally assembles along the entire X chromosome, but not all detached regions recruit the complex, despite having genes known to be dosage compensated on the native X. Thus, the DCC binds first to recruitment sites, then spreads to neighboring X regions to accomplish chromosome-wide gene repression. From a large chromosomal domain, we defined a 793-base pair fragment that functions in vivo as an X-recognition element to recruit the DCC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Csankovszki, Gyorgyi -- McDonel, Patrick -- Meyer, Barbara J -- F32-GM065007/GM/NIGMS NIH HHS/ -- R37-GM30702/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 20;303(5661):1182-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3204, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14976312" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; Base Sequence ; Binding Sites ; Caenorhabditis elegans/*genetics/metabolism ; Caenorhabditis elegans Proteins/*metabolism ; Carrier Proteins/metabolism ; Chromosomes/metabolism ; Cosmids ; DNA-Binding Proteins/metabolism ; Disorders of Sex Development ; *Dosage Compensation, Genetic ; Female ; In Situ Hybridization, Fluorescence ; Male ; Models, Genetic ; Molecular Sequence Data ; Nuclear Proteins/metabolism ; Repetitive Sequences, Nucleic Acid ; X Chromosome/*metabolism
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  • 15
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    Large shifts in pathogen virulence relate to host population structure (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-07
    Description: Theory on the evolution of virulence generally predicts selection for an optimal level of virulence determined by trade-offs with transmission and/or recovery. Here we consider the evolution of pathogen virulence in hosts who acquire long-lived immunity and live in a spatially structured population. We show theoretically that large shifts in virulence may occur in pathogen populations as a result of a bistability in evolutionary dynamics caused by the local contact or social population structure of the host. This model provides an explanation for the rapid emergence of the highly virulent strains of rabbit hemorrhagic disease virus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boots, M -- Hudson, P J -- Sasaki, A -- New York, N.Y. -- Science. 2004 Feb 6;303(5659):842-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK. m.boots@sheffield.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14764881" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Caliciviridae Infections/epidemiology/*veterinary/virology ; *Communicable Diseases/epidemiology/immunology/transmission ; Disease Susceptibility ; Hemorrhagic Disease Virus, Rabbit/genetics/*pathogenicity ; Humans ; Immunity, Active ; Mathematics ; Models, Biological ; Molecular Epidemiology ; Mutation ; Recombination, Genetic ; *Virulence/genetics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Derivatives of erythropoietin that are tissue protective but not erythropoietic (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-13
    Description: Erythropoietin (EPO) is both hematopoietic and tissue protective, putatively through interaction with different receptors. We generated receptor subtype-selective ligands allowing the separation of EPO's bioactivities at the cellular level and in animals. Carbamylated EPO (CEPO) or certain EPO mutants did not bind to the classical EPO receptor (EPOR) and did not show any hematopoietic activity in human cell signaling assays or upon chronic dosing in different animal species. Nevertheless, CEPO and various nonhematopoietic mutants were cytoprotective in vitro and conferred neuroprotection against stroke, spinal cord compression, diabetic neuropathy, and experimental autoimmune encephalomyelitis at a potency and efficacy comparable to EPO.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leist, Marcel -- Ghezzi, Pietro -- Grasso, Giovanni -- Bianchi, Roberto -- Villa, Pia -- Fratelli, Maddalena -- Savino, Costanza -- Bianchi, Marina -- Nielsen, Jacob -- Gerwien, Jens -- Kallunki, Pekka -- Larsen, Anna Kirstine -- Helboe, Lone -- Christensen, Soren -- Pedersen, Lars O -- Nielsen, Mette -- Torup, Lars -- Sager, Thomas -- Sfacteria, Alessandra -- Erbayraktar, Serhat -- Erbayraktar, Zubeyde -- Gokmen, Necati -- Yilmaz, Osman -- Cerami-Hand, Carla -- Xie, Qiao-Wen -- Coleman, Thomas -- Cerami, Anthony -- Brines, Michael -- New York, N.Y. -- Science. 2004 Jul 9;305(5681):239-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉H. Lundbeck A/S, 2500 Valby, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15247477" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis ; Binding Sites ; Cells, Cultured ; Diabetic Neuropathies/drug therapy ; Drug Design ; Encephalomyelitis, Autoimmune, Experimental/drug therapy ; Erythropoiesis ; Erythropoietin/*analogs & ; derivatives/chemistry/genetics/metabolism/pharmacology/*therapeutic use ; Female ; Hematocrit ; Humans ; Ligands ; Mice ; Mice, Inbred C3H ; Mutagenesis ; Nervous System Diseases/*drug therapy ; Neurons/metabolism ; Neuroprotective Agents/chemistry/metabolism/pharmacology/*therapeutic use ; Rats ; Rats, Sprague-Dawley ; Receptors, Erythropoietin/metabolism ; Recombinant Proteins ; Signal Transduction ; Spinal Cord Compression/drug therapy ; Stroke/drug therapy ; Structure-Activity Relationship
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Evolution of a protochordate allorecognition locus (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉De Tomaso, Anthony W -- Weissman, Irving L -- AI10332/AI/NIAID NIH HHS/ -- AI41588/AI/NIAID NIH HHS/ -- R01 AI041588/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 13;303(5660):977.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA. tdet@stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963321" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; *Biological Evolution ; Cloning, Molecular ; Crosses, Genetic ; Heterozygote ; Homozygote ; Immunogenetics ; *Polymorphism, Genetic ; Urochordata/*genetics/growth & development/immunology
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  • 18
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    Structure of the uncleaved human H1 hemagglutinin from the extinct 1918 influenza virus (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-07
    Description: The 1918 "Spanish" influenza pandemic represents the largest recorded outbreak of any infectious disease. The crystal structure of the uncleaved precursor of the major surface antigen of the extinct 1918 virus was determined at 3.0 angstrom resolution after reassembly of the hemagglutinin gene from viral RNA fragments preserved in 1918 formalin-fixed lung tissues. A narrow avian-like receptor-binding site, two previously unobserved histidine patches, and a less exposed surface loop at the cleavage site that activates viral membrane fusion reveal structural features primarily found in avian viruses, which may have contributed to the extraordinarily high infectivity and mortality rates observed during 1918.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stevens, James -- Corper, Adam L -- Basler, Christopher F -- Taubenberger, Jeffery K -- Palese, Peter -- Wilson, Ian A -- AI058113/AI/NIAID NIH HHS/ -- AI42266/AI/NIAID NIH HHS/ -- AI50619/AI/NIAID NIH HHS/ -- CA55896/CA/NCI NIH HHS/ -- P50-GM 62411/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1866-70. Epub 2004 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14764887" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Carbohydrate Conformation ; Cloning, Molecular ; Crystallography, X-Ray ; Glycosylation ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/metabolism ; Histidine/chemistry/metabolism ; History, 20th Century ; Humans ; Hydrogen Bonding ; Influenza A virus/classification/*immunology/pathogenicity ; Influenza, Human/epidemiology/history/virology ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Virus/metabolism ; Sialic Acids/metabolism
    Print ISSN: 0036-8075
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    Evolution. Transitions from nonliving to living matter (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rasmussen, Steen -- Chen, Liaohai -- Deamer, David -- Krakauer, David C -- Packard, Norman H -- Stadler, Peter F -- Bedau, Mark A -- New York, N.Y. -- Science. 2004 Feb 13;303(5660):963-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Los Alamos National Laboratory, Los Alamos, NM 87545, USA. steen@lanl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963315" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Biopolymers ; Catalysis ; *Cells ; Combinatorial Chemistry Techniques ; Computer Simulation ; *Evolution, Chemical ; Genetic Engineering ; *Life ; Lipid Metabolism ; Lipids/chemistry ; Liposomes ; Mycoplasma genitalium/genetics/metabolism ; *Origin of Life ; Peptide Nucleic Acids/chemistry/metabolism ; RNA/chemistry/metabolism ; Selection, Genetic ; Thermodynamics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    In silico genetics: identification of a functional element regulating H2-Ealpha gene expression (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-23
    Description: Computational tools can markedly accelerate the rate at which murine genetic models can be analyzed. We developed a computational method for mapping phenotypic traits that vary among inbred strains onto haplotypic blocks. This method correctly predicted the genetic basis for strain-specific differences in several biologically important traits. It was also used to identify an allele-specific functional genomic element regulating H2-Ealpha gene expression. This functional element, which contained the binding sites for YY1 and a second transcription factor that is probably serum response factor, is located within the first intron of the H2-Ealpha gene. This computational method will greatly improve our ability to identify the genetic basis for a variety of phenotypic traits, ranging from qualitative trait information to quantitative gene expression data, which vary among inbred mouse strains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liao, Guochun -- Wang, Jianmei -- Guo, Jingshu -- Allard, John -- Cheng, Janet -- Ng, Anh -- Shafer, Steve -- Puech, Anne -- McPherson, John D -- Foernzler, Dorothee -- Peltz, Gary -- Usuka, Jonathan -- 1 R01 HG02322-01/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2004 Oct 22;306(5696):690-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and Genomics, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304-1397, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15499019" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Binding Sites ; *Computational Biology ; Electrophoretic Mobility Shift Assay ; Gene Expression Profiling ; *Gene Expression Regulation ; Genes, MHC Class II ; Genetic Variation ; H-2 Antigens/*genetics ; Haplotypes ; Hydrocarbons, Aromatic/pharmacology ; Introns ; Liver/metabolism ; Lung/metabolism ; Major Histocompatibility Complex ; Mice ; Mice, Inbred Strains ; Oligodeoxyribonucleotides/metabolism ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Polymorphism, Single Nucleotide ; Receptors, Aryl Hydrocarbon/chemistry/genetics/metabolism ; Regulatory Sequences, Nucleic Acid ; Serum Response Factor/metabolism ; Transcription Factors/metabolism
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    Comment on "The evolution of modern eukaryotic phytoplankton" (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keeling, Patrick J -- Archibald, John M -- Fast, Naomi M -- Palmer, Jeffrey D -- New York, N.Y. -- Science. 2004 Dec 24;306(5705):2191; author reply 2191.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada. pkeeling@interchange.ubc.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15618503" target="_blank"〉PubMed〈/a〉
    Keywords: Biodiversity ; *Biological Evolution ; Chlorophyta/genetics/physiology ; *Eukaryota/genetics/physiology ; Gene Transfer, Horizontal ; Phylogeny ; *Phytoplankton/genetics ; Plastids/genetics/physiology ; Rhodophyta/genetics/physiology ; Symbiosis
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Society of Vertebrate Paleontology meeting. Timing complicates history of horses (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2004 Nov 26;306(5701):1467.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15567833" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Extremities/anatomy & histology ; Feeding Behavior ; *Fossils ; *Horses/anatomy & histology ; Paleodontology ; *Poaceae ; Time ; Tooth/*anatomy & histology ; Trees
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    Comment on "Molecular phylogenies link rates of evolution and speciation" (I) (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Witt, Christopher C -- Brumfield, Robb T -- New York, N.Y. -- Science. 2004 Jan 9;303(5655):173; author reply 173.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences and, Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA. cwitt@lsu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14715994" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Evolution, Molecular ; Genes ; Genetics, Population ; Mathematics ; Models, Statistical ; *Phylogeny ; Plants/classification/genetics ; Sampling Studies ; Selection Bias
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    Paleontology. 400-million-year-old wounds reveal a time when predators romped (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2004 Sep 3;305(5689):1386.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15353767" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Echinodermata/*physiology ; Fishes ; *Fossils ; *Predatory Behavior ; *Regeneration
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 25
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    Phospholipid metabolism regulated by a transcription factor sensing phosphatidic acid (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-06-12
    Description: Cells regulate the biophysical properties of their membranes by coordinated synthesis of different classes of lipids. Here, we identified a highly dynamic feedback mechanism by which the budding yeast Saccharomyces cerevisiae can regulate phospholipid biosynthesis. Phosphatidic acid on the endoplasmic reticulum directly bound to the soluble transcriptional repressor Opi1p to maintain it as inactive outside the nucleus. After the addition of the lipid precursor inositol, this phosphatidic acid was rapidly consumed, releasing Opi1p from the endoplasmic reticulum and allowing its nuclear translocation and repression of target genes. Thus, phosphatidic acid appears to be both an essential ubiquitous metabolic intermediate and a signaling lipid.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Loewen, C J R -- Gaspar, M L -- Jesch, S A -- Delon, C -- Ktistakis, N T -- Henry, S A -- Levine, T P -- BBS/E/B/0000F969/Biotechnology and Biological Sciences Research Council/United Kingdom -- GM-19629/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jun 11;304(5677):1644-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Cell Biology, Institute of Ophthalmology, Bath Street, London EC1V 9EL, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15192221" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Animals ; Binding Sites ; COS Cells ; Cell Membrane/metabolism ; Cell Nucleus/metabolism ; Cercopithecus aethiops ; Cytidine Diphosphate Diglycerides/metabolism ; Endoplasmic Reticulum/metabolism ; Inositol/*metabolism ; Liposomes/metabolism ; Mutation ; Nuclear Envelope/metabolism ; Phosphatidic Acids/*metabolism ; Phosphatidylinositols/metabolism ; Phospholipids/biosynthesis/*metabolism ; Recombinant Fusion Proteins/metabolism ; Repressor Proteins/chemistry/genetics/*metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Signal Transduction
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    Prospects for building the tree of life from large sequence databases (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-11-13
    Description: We assess the phylogenetic potential of approximately 300,000 protein sequences sampled from Swiss-Prot and GenBank. Although only a small subset of these data was potentially phylogenetically informative, this subset retained a substantial fraction of the original taxonomic diversity. Sampling biases in the databases necessitate building phylogenetic data sets that have large numbers of missing entries. However, an analysis of two "supermatrices" suggests that even data sets with as much as 92% missing data can provide insights into broad sections of the tree of life.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Driskell, Amy C -- Ane, Cecile -- Burleigh, J Gordon -- McMahon, Michelle M -- O'meara, Brian C -- Sanderson, Michael J -- New York, N.Y. -- Science. 2004 Nov 12;306(5699):1172-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA 95616, USA. acdriskell@ucdavis.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15539599" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anopheles/classification/genetics ; Biodiversity ; *Biological Evolution ; Classification ; Computational Biology ; *Databases, Nucleic Acid ; *Databases, Protein ; Multigene Family ; *Phylogeny ; Plant Proteins/genetics ; Plants/classification/genetics ; Spodoptera/classification/genetics
    Print ISSN: 0036-8075
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    ABAD directly links Abeta to mitochondrial toxicity in Alzheimer's disease (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-04-17
    Description: Mitochondrial dysfunction is a hallmark of beta-amyloid (Abeta)-induced neuronal toxicity in Alzheimer's disease (AD). Here, we demonstrate that Abeta-binding alcohol dehydrogenase (ABAD) is a direct molecular link from Abeta to mitochondrial toxicity. Abeta interacts with ABAD in the mitochondria of AD patients and transgenic mice. The crystal structure of Abeta-bound ABAD shows substantial deformation of the active site that prevents nicotinamide adenine dinucleotide (NAD) binding. An ABAD peptide specifically inhibits ABAD-Abeta interaction and suppresses Abeta-induced apoptosis and free-radical generation in neurons. Transgenic mice overexpressing ABAD in an Abeta-rich environment manifest exaggerated neuronal oxidative stress and impaired memory. These data suggest that the ABAD-Abeta interaction may be a therapeutic target in AD.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lustbader, Joyce W -- Cirilli, Maurizio -- Lin, Chang -- Xu, Hong Wei -- Takuma, Kazuhiro -- Wang, Ning -- Caspersen, Casper -- Chen, Xi -- Pollak, Susan -- Chaney, Michael -- Trinchese, Fabrizio -- Liu, Shumin -- Gunn-Moore, Frank -- Lue, Lih-Fen -- Walker, Douglas G -- Kuppusamy, Periannan -- Zewier, Zay L -- Arancio, Ottavio -- Stern, David -- Yan, Shirley ShiDu -- Wu, Hao -- 1K07AG00959/AG/NIA NIH HHS/ -- AG16736/AG/NIA NIH HHS/ -- AG17490/AG/NIA NIH HHS/ -- NS42855/NS/NINDS NIH HHS/ -- P50AG08702/AG/NIA NIH HHS/ -- New York, N.Y. -- Science. 2004 Apr 16;304(5669):448-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Reproductive Sciences and Department of Obstetrics and Gynecology, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15087549" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Hydroxyacyl CoA Dehydrogenases/chemistry/*metabolism ; Aged ; Aged, 80 and over ; Alzheimer Disease/*metabolism ; Amino Acid Sequence ; Amyloid beta-Peptides/chemistry/genetics/*metabolism ; Animals ; Binding Sites ; Brain/*metabolism ; Brain Chemistry ; Carrier Proteins/chemistry/*metabolism ; Cells, Cultured ; Cerebral Cortex/chemistry/metabolism ; Crystallization ; DNA Fragmentation ; Hippocampus/physiology ; Humans ; Learning ; Memory ; Mice ; Mice, Transgenic ; Microscopy, Confocal ; Microscopy, Immunoelectron ; Mitochondria/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; NAD/metabolism ; Neurons/metabolism ; Protein Binding ; Protein Conformation ; Reactive Oxygen Species/metabolism
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  • 28
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    Extensive gene traffic on the mammalian X chromosome (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-01-24
    Description: Mammalian sex chromosomes have undergone profound changes since evolving from ancestral autosomes. By examining retroposed genes in the human and mouse genomes, we demonstrate that, during evolution, the mammalian X chromosome has generated and recruited a disproportionately high number of functional retroposed genes, whereas the autosomes experienced lower gene turnover. Most autosomal copies originating from X-linked genes exhibited testis-biased expression. Such export is incompatible with mutational bias and is likely driven by natural selection to attain male germline function. However, the excess recruitment is consistent with a combination of both natural selection and mutational bias.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Emerson, J J -- Kaessmann, Henrik -- Betran, Esther -- Long, Manyuan -- GM-065429-01A1/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 23;303(5657):537-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14739461" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Chromosomes, Human/genetics ; Chromosomes, Human, X/*genetics ; Chromosomes, Mammalian/genetics ; Computational Biology ; Dosage Compensation, Genetic ; Female ; Gene Expression Profiling ; Genes, Duplicate ; Genetic Linkage ; Genome ; Genome, Human ; Humans ; Introns ; Male ; Mice ; Monte Carlo Method ; Mutation ; Oligonucleotide Array Sequence Analysis ; Ovary/metabolism ; Pseudogenes/*genetics ; *Recombination, Genetic ; Retroelements/*genetics ; Selection, Genetic ; Sex Characteristics ; Testis/metabolism ; X Chromosome/*genetics
    Print ISSN: 0036-8075
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    The mentality of crows: convergent evolution of intelligence in corvids and apes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-14
    Description: Discussions of the evolution of intelligence have focused on monkeys and apes because of their close evolutionary relationship to humans. Other large-brained social animals, such as corvids, also understand their physical and social worlds. Here we review recent studies of tool manufacture, mental time travel, and social cognition in corvids, and suggest that complex cognition depends on a "tool kit" consisting of causal reasoning, flexibility, imagination, and prospection. Because corvids and apes share these cognitive tools, we argue that complex cognitive abilities evolved multiple times in distantly related species with vastly different brain structures in order to solve similar socioecological problems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Emery, Nathan J -- Clayton, Nicola S -- New York, N.Y. -- Science. 2004 Dec 10;306(5703):1903-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sub-Department of Animal Behaviour, University of Cambridge, CB3 8AA, UK. nje23@cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15591194" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Behavior, Animal ; *Biological Evolution ; Brain/anatomy & histology/physiology ; *Cognition ; *Crows/anatomy & histology/physiology ; Hominidae/physiology ; Imagination ; *Intelligence ; Memory ; Social Behavior
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    Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-14
    Description: The first structure of an ammonia channel from the Amt/MEP/Rh protein superfamily, determined to 1.35 angstrom resolution, shows it to be a channel that spans the membrane 11 times. Two structurally similar halves span the membrane with opposite polarity. Structures with and without ammonia or methyl ammonia show a vestibule that recruits NH4+/NH3, a binding site for NH4+, and a 20 angstrom-long hydrophobic channel that lowers the NH4+ pKa to below 6 and conducts NH3. Favorable interactions for NH3 are seen within the channel and use conserved histidines. Reconstitution of AmtB into vesicles shows that AmtB conducts uncharged NH3.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Khademi, Shahram -- O'Connell, Joseph 3rd -- Remis, Jonathan -- Robles-Colmenares, Yaneth -- Miercke, Larry J W -- Stroud, Robert M -- GM24485/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Sep 10;305(5690):1587-94.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, S412C Genentech Hall, University of California-San Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15361618" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Ammonia/*metabolism ; Binding Sites ; Biological Transport ; Cation Transport Proteins/*chemistry/genetics/metabolism ; Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry/metabolism ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Liposomes ; Membrane Potentials ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Quaternary Ammonium Compounds/metabolism ; Rh-Hr Blood-Group System/chemistry/metabolism ; Sequence Alignment ; Water/chemistry/metabolism
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    Abiotic forcing of plankton evolution in the Cenozoic (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-13
    Description: We characterize the evolutionary radiation of planktic foraminifera by the test size distributions of entire assemblages in more than 500 Cenozoic marine sediment samples, including more than 1 million tests. Calibration of Holocene size patterns with environmental parameters and comparisons with Cenozoic paleoproxy data show a consistently positive correlation between test size and surface-water stratification intensity. We infer that the observed macroevolutionary increase in test size of planktic foraminifera through the Cenozoic was an adaptive response to intensifying surface-water stratification in low latitudes, which was driven by polar cooling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmidt, Daniela N -- Thierstein, Hans R -- Bollmann, Jorg -- Schiebel, Ralf -- New York, N.Y. -- Science. 2004 Jan 9;303(5655):207-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, Eidgenossische Technische Hochschule (ETH) Zurich, and University of Zurich, ETH-Zentrum, CH-8092 Zurich, Switzerland. d.schmidt@gl.rhul.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14716007" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Climate ; Ecosystem ; Eukaryota/chemistry/cytology ; Geography ; Oxygen Isotopes/analysis ; *Plankton/chemistry/cytology ; Seawater ; Temperature ; Time ; Zooplankton/chemistry/cytology
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    Evolution. Insights into innovation (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Erwin, Douglas H -- Krakauer, David C -- New York, N.Y. -- Science. 2004 May 21;304(5674):1117-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Paleobiology, Smithsonian Institution, Washington, DC 20560, USA. erwin@santafe.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15155937" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Diffusion of Innovation ; Economics ; Ecosystem ; *Engineering ; Environment ; Epigenesis, Genetic ; Gene Duplication ; Gene Transfer, Horizontal ; Genotype ; Mutation ; Phenotype ; Selection, Genetic ; *Technology
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    Common and distinct elements in cellular signaling via EGF and FGF receptors (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-30
    Description: Signaling pathways that are activated by epidermal growth factor (EGF) or fibroblast growth factor (FGF) receptors have been identified and compared (detailed Connections Maps are available at Science's Signal Transduction Knowledge Environment). Both receptors stimulate a similar complement of intracellular signaling pathways. However, whereas activated EGF receptors (EGFRs) function as the main platform for recruitment of signaling proteins, signaling through the FGF receptors (FGFRs) is mediated primarily by assembly of a multidocking protein complex. Moreover, FGFR signaling is subject to additional intracellular and extracellular control mechanisms that do not affect EGFR signaling. The differential circuitry of the intracellular networks that are activated by EGFR and FGFR may affect signal specificity and physiological responses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schlessinger, Joseph -- R01-AR051448-01/AR/NIAMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Nov 26;306(5701):1506-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA. joseph.schlessinger@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15567848" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/metabolism ; Binding Sites ; Dimerization ; Epidermal Growth Factor/metabolism ; Fibroblast Growth Factors/metabolism ; Heparan Sulfate Proteoglycans/metabolism ; Humans ; Ligands ; Phosphorylation ; Receptor, Epidermal Growth Factor/chemistry/*metabolism ; Receptors, Fibroblast Growth Factor/chemistry/*metabolism ; Second Messenger Systems ; *Signal Transduction ; Tyrosine/metabolism
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    Evolution of behavior. Seeking the key to music (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balter, Michael -- New York, N.Y. -- Science. 2004 Nov 12;306(5699):1120-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15539578" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; *Biological Evolution ; Cooperative Behavior ; *Cultural Evolution ; Emotions ; Endorphins/physiology ; Female ; Humans ; Language ; Male ; Maternal Behavior ; *Music ; Nonverbal Communication ; Object Attachment ; Selection, Genetic ; Sexual Behavior ; *Social Behavior
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    Species interactions and the evolution of sex (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-05-15
    Description: The Red Queen hypothesis posits that sex has evolved in response to the shifting adaptive landscape generated by the evolution of interacting species. Previous studies supporting the Red Queen hypothesis have considered a narrow region of parameter space and only a subset of ecological and genetic interactions. Here, we develop a population genetics model that circumscribes a broad array of ecological and genetic interactions among species and derive the first general analytical conditions for the impact of species interactions on the evolution of sex. Our results show that species interactions typically select against sex. We conclude that, although the Red Queen favors sex under certain circumstances, it alone does not account for the ubiquity of sex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Otto, Sarah P -- Nuismer, Scott L -- F32 GM65620-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 May 14;304(5673):1018-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. otto@zoology.ubc.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15143283" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; *Biological Evolution ; Epistasis, Genetic ; Gene Frequency ; Genetic Linkage ; Genetics, Population ; Genotype ; Linkage Disequilibrium ; Mathematics ; Models, Genetic ; Recombination, Genetic ; Reproduction, Asexual ; Selection, Genetic ; *Sex
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    A glycine-dependent riboswitch that uses cooperative binding to control gene expression (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-09
    Description: We identified a previously unknown riboswitch class in bacteria that is selectively triggered by glycine. A representative of these glycine-sensing RNAs from Bacillus subtilis operates as a rare genetic on switch for the gcvT operon, which codes for proteins that form the glycine cleavage system. Most glycine riboswitches integrate two ligand-binding domains that function cooperatively to more closely approximate a two-state genetic switch. This advanced form of riboswitch may have evolved to ensure that excess glycine is efficiently used to provide carbon flux through the citric acid cycle and maintain adequate amounts of the amino acid for protein synthesis. Thus, riboswitches perform key regulatory roles and exhibit complex performance characteristics that previously had been observed only with protein factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mandal, Maumita -- Lee, Mark -- Barrick, Jeffrey E -- Weinberg, Zasha -- Emilsson, Gail Mitchell -- Ruzzo, Walter L -- Breaker, Ronald R -- New York, N.Y. -- Science. 2004 Oct 8;306(5694):275-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, Yale University, Post Office Box 208103, New Haven, CT 06520-8103, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15472076" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions/chemistry/*metabolism ; Allosteric Regulation ; Allosteric Site ; Bacillus subtilis/*genetics/metabolism ; Base Pairing ; Base Sequence ; Binding Sites ; *Gene Expression Regulation, Bacterial ; Glycine/*metabolism ; Ligands ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Operon ; RNA, Bacterial/chemistry/*metabolism ; RNA, Messenger/chemistry/*metabolism ; Transcription, Genetic ; Vibrio cholerae/*genetics/metabolism
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    Creationism. Georgia backs off a bit, but in other states battles heat up (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holden, Constance -- New York, N.Y. -- Science. 2004 Feb 27;303(5662):1268.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14988522" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Biological Science Disciplines/education ; *Curriculum ; Georgia ; Natural Science Disciplines/education ; *Religion and Science ; Textbooks as Topic ; United States
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    The evolution of modern eukaryotic phytoplankton (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-07-17
    Description: The community structure and ecological function of contemporary marine ecosystems are critically dependent on eukaryotic phytoplankton. Although numerically inferior to cyanobacteria, these organisms are responsible for the majority of the flux of organic matter to higher trophic levels and the ocean interior. Photosynthetic eukaryotes evolved more than 1.5 billion years ago in the Proterozoic oceans. However, it was not until the Mesozoic Era (251 to 65 million years ago) that the three principal phytoplankton clades that would come to dominate the modern seas rose to ecological prominence. In contrast to their pioneering predecessors, the dinoflagellates, coccolithophores, and diatoms all contain plastids derived from an ancestral red alga by secondary symbiosis. Here we examine the geological, geochemical, and biological processes that contributed to the rise of these three, distantly related, phytoplankton groups.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Falkowski, Paul G -- Katz, Miriam E -- Knoll, Andrew H -- Quigg, Antonietta -- Raven, John A -- Schofield, Oscar -- Taylor, F J R -- New York, N.Y. -- Science. 2004 Jul 16;305(5682):354-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road, New Brunswick, NJ 08540, USA. falko@imcs.rutgers.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15256663" target="_blank"〉PubMed〈/a〉
    Keywords: Biodiversity ; *Biological Evolution ; *Ecosystem ; Fossils ; Phylogeny ; *Phytoplankton/classification/cytology/physiology ; Plastids/physiology
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    Testing predator-driven evolution with Paleozoic crinoid arm regeneration (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-09
    Description: Regenerating arms of crinoids represent direct evidence of nonlethal attacks by predators and provide an opportunity for exploring the importance of predation through geologic time. Analysis of 11 Paleozoic crinoid Lagerstatten revealed a significant increase in arm regeneration during the Siluro-Devonian. During this interval, referred to as the Middle Paleozoic Marine Revolution, the diversity of shell-crushing predators increased, and antipredatory morphologies among invertebrate prey, such as crinoids, became more common. Crinoid arm regeneration data suggest an increase in nonlethal attacks at this time and represent a causal link between those patterns, which implies an important role for predator-driven evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baumiller, Tomasz K -- Gahn, Forest J -- New York, N.Y. -- Science. 2004 Sep 3;305(5689):1453-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Michigan Museum of Paleontology, Ann Arbor, MI 48105, USA. tomaszb@umich.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15353799" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Echinodermata/*physiology ; Fishes ; *Fossils ; *Predatory Behavior ; *Regeneration
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    Semaphorin 3E and plexin-D1 control vascular pattern independently of neuropilins (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-20
    Description: The development of a patterned vasculature is essential for normal organogenesis. We found that signaling by semaphorin 3E (Sema3E) and its receptor plexin-D1 controls endothelial cell positioning and the patterning of the developing vasculature in the mouse. Sema3E is highly expressed in developing somites, where it acts as a repulsive cue for plexin-D1-expressing endothelial cells of adjacent intersomitic vessels. Sema3E-plexin-D1 signaling did not require neuropilins, which were previously presumed to be obligate Sema3 coreceptors. Moreover, genetic ablation of Sema3E or plexin-D1 but not neuropilin-mediated Sema3 signaling disrupted vascular patterning. These findings reveal an unexpected semaphorin signaling pathway and define a mechanism for controlling vascular patterning.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gu, Chenghua -- Yoshida, Yutaka -- Livet, Jean -- Reimert, Dorothy V -- Mann, Fanny -- Merte, Janna -- Henderson, Christopher E -- Jessell, Thomas M -- Kolodkin, Alex L -- Ginty, David D -- CA23767-24/CA/NCI NIH HHS/ -- MH59199-06/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2005 Jan 14;307(5707):265-8. Epub 2004 Nov 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15550623" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Blood Vessels/*embryology/metabolism ; Body Patterning ; COS Cells ; Cercopithecus aethiops ; Chick Embryo ; Endothelial Cells/cytology/physiology ; Endothelium, Vascular/cytology/embryology ; Glycoproteins/*metabolism ; In Situ Hybridization ; Ligands ; Membrane Glycoproteins/*metabolism ; Membrane Proteins/*metabolism ; Mice ; Morphogenesis ; Mutation ; Nerve Tissue Proteins/*metabolism ; Neuropilin-1/metabolism ; Neuropilin-2/metabolism ; Phenotype ; Protein Binding ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Somites/*metabolism ; Transfection
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    Anthropology. The earliest hominins--is less more? (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-03-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Begun, David R -- New York, N.Y. -- Science. 2004 Mar 5;303(5663):1478-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anthropology, University of Toronto, Toronto, Ontario M5S 3G3, Canada. begun@chass.utoronto.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15001766" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bicuspid/anatomy & histology ; *Biological Evolution ; Cooperative Behavior ; Cuspid/anatomy & histology ; Dental Enamel/anatomy & histology ; Ethiopia ; *Fossils ; *Hominidae/anatomy & histology/classification ; Humans ; Locomotion ; Lower Extremity/anatomy & histology ; Molar/anatomy & histology ; Paleodontology ; Pan troglodytes/anatomy & histology ; Skull/anatomy & histology ; Tooth/*anatomy & histology
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    Searching for the genome's second code (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-10-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2004 Oct 22;306(5696):632-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15499005" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Biological Evolution ; Computational Biology ; Drosophila/embryology/genetics ; Echinodermata/embryology/genetics ; *Enhancer Elements, Genetic ; *Gene Expression Regulation ; Gene Expression Regulation, Developmental ; Genetic Code ; *Genome ; Humans ; *Regulatory Sequences, Nucleic Acid ; Silencer Elements, Transcriptional ; Transcription Factors/metabolism
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    Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-06
    Description: The crystal structure of biotin synthase from Escherichia coli in complex with S-adenosyl-L-methionine and dethiobiotin has been determined to 3.4 angstrom resolution. This structure addresses how "AdoMet radical" or "radical SAM" enzymes use Fe4S4 clusters and S-adenosyl-L-methionine to generate organic radicals. Biotin synthase catalyzes the radical-mediated insertion of sulfur into dethiobiotin to form biotin. The structure places the substrates between the Fe4S4 cluster, essential for radical generation, and the Fe2S2 cluster, postulated to be the source of sulfur, with both clusters in unprecedented coordination environments.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456065/" 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/PMC1456065/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berkovitch, Frederick -- Nicolet, Yvain -- Wan, Jason T -- Jarrett, Joseph T -- Drennan, Catherine L -- NSLS X25/NS/NINDS NIH HHS/ -- R01 GM059175/GM/NIGMS NIH HHS/ -- R01-GM59175/GM/NIGMS NIH HHS/ -- R01-GM65337/GM/NIGMS NIH HHS/ -- T32-GM07229/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 2;303(5654):76-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14704425" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Biotin/*analogs & derivatives/*chemistry/metabolism ; Catalysis ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Escherichia coli/*enzymology ; Escherichia coli Proteins/*chemistry/*metabolism ; Hydrogen/chemistry ; Hydrogen Bonding ; Iron/chemistry ; Ligands ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; S-Adenosylmethionine/*chemistry/metabolism ; Sulfur/chemistry ; Sulfurtransferases/*chemistry/*metabolism
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    Evolutionary ecology of the prezygotic stage (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-14
    Description: The life cycles of sexually reproducing animals and flowering plants begin with male and female gametes and their fusion to form a zygote. Selection at this earliest stage is crucial for offspring quality and raises similar evolutionary issues, yet zoology and botany use dissimilar approaches. There are striking parallels in the role of prezygotic competition for sexual selection on males, cryptic female choice, sexual conflict, and against selfish genetic elements and genetic incompatibility. In both groups, understanding the evolution of sex-specific and reproductive traits will require an appreciation of the effects of prezygotic competition on fitness.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bernasconi, G -- Ashman, T-L -- Birkhead, T R -- Bishop, J D D -- Grossniklaus, U -- Kubli, E -- Marshall, D L -- Schmid, B -- Skogsmyr, I -- Snook, R R -- Taylor, D -- Till-Bottraud, I -- Ward, P I -- Zeh, D W -- Hellriegel, B -- New York, N.Y. -- Science. 2004 Feb 13;303(5660):971-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Environmental Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland. bernasco@uwinst.unizh.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963320" target="_blank"〉PubMed〈/a〉
    Keywords: Angiosperms/*physiology ; Animals ; *Biological Evolution ; Competitive Behavior ; Copulation ; Female ; Gene Expression ; Male ; Pollen/*physiology ; *Reproduction ; Selection, Genetic ; Sex Characteristics ; *Sexual Behavior, Animal ; Spermatozoa/*physiology
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    Human origins. Louse DNA suggests close contact between early humans (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2004 Oct 8;306(5694):210.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15472046" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Genetics, Population ; History, Ancient ; *Hominidae/classification/parasitology ; Humans ; Lice Infestations/history/transmission ; Pediculus/classification/*genetics/physiology ; Population Dynamics ; Species Specificity ; Time
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    Happy birthday: 80 years of watching the evolutionary scenery (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mayr, Ernst -- New York, N.Y. -- Science. 2004 Jul 2;305(5680):46-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA. emayr@oeb.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15232092" target="_blank"〉PubMed〈/a〉
    Keywords: Biodiversity ; *Biological Evolution ; Biology/*history ; Classification ; Genetics, Population ; Germany ; History, 20th Century ; History, 21st Century ; Mutation ; Selection, Genetic
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    Evolution. Sex...only if really necessary in a feminine monarchy (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gadagkar, Raghavendra -- New York, N.Y. -- Science. 2004 Dec 3;306(5702):1694-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Ecological Sciences, Indian Institute of Science, 560 012 Bangalore, India. ragh@ces.iisc.ernet.in〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15576600" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Ants/genetics/*physiology ; Bees/genetics/physiology ; Behavior, Animal ; *Biological Evolution ; Diploidy ; Female ; Genes, Insect ; Genetic Variation ; Haploidy ; Male ; *Parthenogenesis ; Reproduction ; Sex Determination Processes ; Sexual Behavior, Animal ; Social Behavior
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    Evolution of developmental diversity meeting. RNAi takes Evo-Devo world by storm (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2004 Apr 16;304(5669):384.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15087524" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; DNA-Binding Proteins/genetics/physiology ; *Developmental Biology ; Drosophila/embryology/genetics/physiology ; Drosophila Proteins ; *Genes ; Insects/embryology/genetics/physiology ; Nuclear Proteins ; Planarians/genetics/physiology ; *RNA Interference ; Regeneration ; Stem Cells/physiology ; Transcription Factors
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    Human evolution. The primate bite: brawn versus brain? (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2004 Mar 26;303(5666):1957.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15044775" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Brain/anatomy & histology/*growth & development ; Gorilla gorilla/anatomy & histology/genetics/growth & development ; *Hominidae/anatomy & histology/genetics/growth & development ; Humans ; Macaca/anatomy & histology/genetics/growth & development ; Masticatory Muscles/anatomy & histology/growth & development ; Myosin Heavy Chains/*genetics ; Pan troglodytes/anatomy & histology/genetics/growth & development ; Primates/anatomy & histology/genetics/growth & development ; *Sequence Deletion ; Skull/anatomy & histology/growth & development
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    Runcaria, a middle devonian seed plant precursor (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-30
    Description: The emergence of the seed habit in the Middle Paleozoic was a decisive evolutionary breakthrough. Today, seed plants are the most successful plant lineage, with more than 250,000 living species. We have identified a middle Givetian (385 million years ago) seed precursor from Belgium predating the earliest seeds by about 20 million years. Runcaria is a small, radially symmetrical, integumented megasporangium surrounded by a cupule. The megasporangium bears an unopened distal extension protruding above the multilobed integument. This extension is assumed to be involved in anemophilous pollination. Runcaria sheds new light on the sequence of character acquisition leading to the seed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gerrienne, P -- Meyer-Berthaud, B -- Fairon-Demaret, M -- Streel, M -- Steemans, P -- New York, N.Y. -- Science. 2004 Oct 29;306(5697):856-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departement de Geologie, B18, Universite de Liege, Sart Tilman, Liege 1, Belgique. p.gerrienne@ulg.ac.be〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15514154" target="_blank"〉PubMed〈/a〉
    Keywords: Belgium ; *Biological Evolution ; Fossils ; Plant Physiological Phenomena ; Plant Structures/*anatomy & histology ; Plants/*anatomy & histology/classification ; Pollen ; *Seeds ; Time
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    Anabaena sensory rhodopsin: a photochromic color sensor at 2.0 A (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-02
    Description: Microbial sensory rhodopsins are a family of membrane-embedded photoreceptors in prokaryotic and eukaryotic organisms. Structures of archaeal rhodopsins, which function as light-driven ion pumps or photosensors, have been reported. We present the structure of a eubacterial rhodopsin, which differs from those of previously characterized archaeal rhodopsins in its chromophore and cytoplasmic-side portions. Anabaena sensory rhodopsin exhibits light-induced interconversion between stable 13-cis and all-trans states of the retinylidene protein. The ratio of its cis and trans chromophore forms depends on the wavelength of illumination, thus providing a mechanism for a single protein to signal the color of light, for example, to regulate color-sensitive processes such as chromatic adaptation in photosynthesis. Its cytoplasmic half channel, highly hydrophobic in the archaeal rhodopsins, contains numerous hydrophilic residues networked by water molecules, providing a connection from the photoactive site to the cytoplasmic surface believed to interact with the receptor's soluble 14-kilodalton transducer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vogeley, Lutz -- Sineshchekov, Oleg A -- Trivedi, Vishwa D -- Sasaki, Jun -- Spudich, John L -- Luecke, Hartmut -- R01-GM067808/GM/NIGMS NIH HHS/ -- R01-GM59970/GM/NIGMS NIH HHS/ -- R37-GM27750/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Nov 19;306(5700):1390-3. Epub 2004 Sep 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15459346" target="_blank"〉PubMed〈/a〉
    Keywords: Anabaena/*chemistry ; Archaeal Proteins/chemistry ; Bacterial Proteins/chemistry ; Binding Sites ; Chemistry, Physical ; Crystallography, X-Ray ; Cytoplasm/chemistry ; Hydrogen Bonding ; Light ; Lipid Bilayers/chemistry ; Models, Molecular ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Secondary ; Sensory Rhodopsins/*chemistry ; Water
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    The early evolution of the tetrapod humerus (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-06
    Description: A tetrapod humerus from the Late Devonian of Pennsylvania has a novel mix of primitive and derived characters. A comparative analysis of this fossil and other relevant humeri from the Devonian shows that the role of the limb in propping the body arose first in fish fins, not tetrapod limbs. The functional diversity of the earliest known limbs includes several different kinds of appendage design. This functional diversity was achieved with a humeral architecture that was remarkably conserved during the Devonian.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shubin, Neil H -- Daeschler, Edward B -- Coates, Michael I -- New York, N.Y. -- Science. 2004 Apr 2;304(5667):90-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA. nshubin@uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15064415" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Biomechanical Phenomena ; Extremities/*anatomy & histology ; Fishes/anatomy & histology/physiology ; *Fossils ; Humerus/*anatomy & histology ; Locomotion ; Movement ; Pennsylvania ; Vertebrates/*anatomy & histology/physiology
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    Biochemistry. Completing the view of transcriptional regulation (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Hippel, Peter H -- GM-15792/GM/NIGMS NIH HHS/ -- GM-29158/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jul 16;305(5682):350-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403, USA. petevh@molbio.uoregon.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15256661" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/*metabolism ; Binding Sites ; DNA, Bacterial/*chemistry/*metabolism ; Diffusion ; Dimerization ; Escherichia coli/chemistry/genetics/metabolism ; Escherichia coli Proteins/chemistry/metabolism ; *Gene Expression Regulation, Bacterial ; Hydrogen Bonding ; Kinetics ; Lac Operon ; Lac Repressors ; Models, Genetic ; Models, Molecular ; Nucleic Acid Conformation ; Operator Regions, Genetic ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/*metabolism ; Static Electricity ; Thermodynamics ; *Transcription, Genetic
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    Community assembly through adaptive radiation in Hawaiian spiders (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-01-17
    Description: Communities arising through adaptive radiation are generally regarded as unique, with speciation and adaptation being quite different from immigration and ecological assortment. Here, I use the chronological arrangement of the Hawaiian Islands to visualize snapshots of evolutionary history and stages of community assembly. Analysis of an adaptive radiation of habitat-associated, polychromatic spiders shows that (i) species assembly is not random; (ii) within any community, similar sets of ecomorphs arise through both dispersal and evolution; and (iii) species assembly is dynamic with maximum species numbers in communities of intermediate age. The similar patterns of species accumulation through evolutionary and ecological processes suggest universal principles underlie community assembly.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gillespie, Rosemary -- New York, N.Y. -- Science. 2004 Jan 16;303(5656):356-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Insect Biology, University of California, 201 Wellman Hall, Berkeley, CA94720-3112, USA. gillespi@nature.berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14726588" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; Biodiversity ; *Biological Evolution ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; *Ecosystem ; Electron Transport Complex IV/genetics ; Environment ; Feeding Behavior ; Hawaii ; Isoenzymes/genetics ; Phylogeny ; Population Density ; RNA, Ribosomal, 16S/genetics ; *Spiders/anatomy & histology/classification/genetics/physiology
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    Phosphoryl transfer and calcium ion occlusion in the calcium pump (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-06-12
    Description: A tight coupling between adenosine triphosphate (ATP) hydrolysis and vectorial ion transport has to be maintained by ATP-consuming ion pumps. We report two crystal structures of Ca2+-bound sarco(endo)plasmic reticulum Ca2+-adenosine triphosphatase (SERCA) at 2.6 and 2.9 angstrom resolution in complex with (i) a nonhydrolyzable ATP analog [adenosine (beta-gamma methylene)-triphosphate] and (ii) adenosine diphosphate plus aluminum fluoride. SERCA reacts with ATP by an associative mechanism mediated by two Mg2+ ions to form an aspartyl-phosphorylated intermediate state (Ca2-E1 approximately P). The conformational changes that accompany the reaction with ATP pull the transmembrane helices 1 and 2 and close a cytosolic entrance for Ca2+, thereby preventing backflow before Ca2+ is released on the other side of the membrane.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sorensen, Thomas Lykke-Moller -- Moller, Jesper Vuust -- Nissen, Poul -- New York, N.Y. -- Science. 2004 Jun 11;304(5677):1672-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15192230" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/*analogs & derivatives/*metabolism ; Aluminum Compounds/metabolism ; Animals ; Binding Sites ; Calcium/*metabolism ; Calcium-Transporting ATPases/*chemistry/*metabolism ; Crystallization ; Crystallography, X-Ray ; Cytosol/metabolism ; Fluorides/metabolism ; Models, Molecular ; Muscle Fibers, Fast-Twitch/*enzymology ; Phosphorylation ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rabbits ; Sarcoplasmic Reticulum Calcium-Transporting ATPases
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    Dioxygen binds end-on to mononuclear copper in a precatalytic enzyme complex (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-08
    Description: Copper active sites play a major role in enzymatic activation of dioxygen. We trapped the copper-dioxygen complex in the enzyme peptidylglycine-alphahydroxylating monooxygenase (PHM) by freezing protein crystals that had been soaked with a slow substrate and ascorbate in the presence of oxygen. The x-ray crystal structure of this precatalytic complex, determined to 1.85-angstrom resolution, shows that oxygen binds to one of the coppers in the enzyme with an end-on geometry. Given this structure, it is likely that dioxygen is directly involved in the electron transfer and hydrogen abstraction steps of the PHM reaction. These insights may apply to other copper oxygen-activating enzymes, such as dopamine beta-monooxygenase, and to the design of biomimetic complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prigge, Sean T -- Eipper, Betty A -- Mains, Richard E -- Amzel, L Mario -- DK32949/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2004 May 7;304(5672):864-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Molecular Immunology, The Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131304" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Catalysis ; Catalytic Domain ; Copper/*metabolism ; Crystallization ; Crystallography, X-Ray ; Dipeptides/chemistry/metabolism ; Electron Transport ; Glycine/chemistry/metabolism ; Hydrogen/metabolism ; Hydrogen Bonding ; Ligands ; Mixed Function Oxygenases/*chemistry/*metabolism ; Models, Molecular ; Multienzyme Complexes/*chemistry/*metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Peptides/metabolism ; Protein Conformation ; Rats ; Water/metabolism
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    Michael Majerus profile. In defense of Darwin and a former icon of evolution (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-06-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Proffitt, Fiona -- New York, N.Y. -- Science. 2004 Jun 25;304(5679):1894-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15218121" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Birds ; England ; History, 20th Century ; History, 21st Century ; *Moths/anatomy & histology/physiology ; Pigmentation ; Predatory Behavior ; *Selection, Genetic
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    Comment on "Molecular phylogenies link rates of evolution and speciation" (II) (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brower, Andrew V Z -- New York, N.Y. -- Science. 2004 Jan 9;303(5655):173; author reply 173.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, Oregon State University, Corvallis, OR 97331, USA. browera@science.oregonstate.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14715995" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Evolution, Molecular ; Genes ; Mathematics ; Models, Statistical ; *Phylogeny ; Sampling Studies
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Integrins regulate Rac targeting by internalization of membrane domains (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-07
    Description: Translocation of the small GTP-binding protein Rac1 to the cell plasma membrane is essential for activating downstream effectors and requires integrin-mediated adhesion of cells to extracellular matrix. We report that active Rac1 binds preferentially to low-density, cholesterol-rich membranes, and specificity is determined at least in part by membrane lipids. Cell detachment triggered internalization of plasma membrane cholesterol and lipid raft markers. Preventing internalization maintained Rac1 membrane targeting and effector activation in nonadherent cells. Regulation of lipid rafts by integrin signals may regulate the location of membrane domains such as lipid rafts and thereby control domain-specific signaling events in anchorage-dependent cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉del Pozo, Miguel A -- Alderson, Nazilla B -- Kiosses, William B -- Chiang, Hui-Hsien -- Anderson, Richard G W -- Schwartz, Martin A -- GM52016/GM/NIGMS NIH HHS/ -- HL 20948/HL/NHLBI NIH HHS/ -- R01 GM47214/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 6;303(5659):839-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. mdelpozo@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14764880" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD29/metabolism ; Binding Sites ; Cell Adhesion ; Cell Line ; Cell Membrane/*metabolism ; Cells, Cultured ; Cholera Toxin/metabolism ; Cholesterol/metabolism ; G(M1) Ganglioside/metabolism ; Glycosylphosphatidylinositols/metabolism ; Guanosine Triphosphate/metabolism ; Humans ; Integrins/*metabolism ; Liposomes/metabolism ; Membrane Microdomains/*metabolism ; Mice ; NIH 3T3 Cells ; Rats ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Transfection ; rac1 GTP-Binding Protein/genetics/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Biochemistry. De novo design of an enzyme (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-06-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sterner, Reinhard -- Schmid, Franz X -- New York, N.Y. -- Science. 2004 Jun 25;304(5679):1916-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Universitat Regensburg, Institut fur Biophysik und Physikalische Biochemie, D-93040 Regensburg, Germany. reinhard.sterner@biologie.uni-regensburg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15218133" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Substitution ; Binding Sites ; Catalysis ; Computational Biology ; Computer Simulation ; Directed Molecular Evolution ; *Escherichia coli Proteins/chemistry/genetics/metabolism ; Glutamic Acid/chemistry ; Glyceraldehyde 3-Phosphate/metabolism ; Histidine/chemistry ; Hydrogen Bonding ; Lysine/chemistry ; Models, Molecular ; *Periplasmic Binding Proteins/chemistry/genetics/metabolism ; Protein Conformation ; *Protein Engineering ; *Triose-Phosphate Isomerase/chemistry/metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Evolution. Retrospective: in memory of John Maynard Smith (1920-2004) (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lewontin, Richard -- New York, N.Y. -- Science. 2004 May 14;304(5673):979.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15143272" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; England ; Game Theory ; History, 20th Century ; History, 21st Century ; Selection, Genetic
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    Cofolding organizes alfalfa mosaic virus RNA and coat protein for replication (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-18
    Description: Alfalfa mosaic virus genomic RNAs are infectious only when the viral coat protein binds to the RNA 3' termini. The crystal structure of an alfalfa mosaic virus RNA-peptide complex reveals that conserved AUGC repeats and Pro-Thr-x-Arg-Ser-x-x-Tyr coat protein amino acids cofold upon interacting. Alternating AUGC residues have opposite orientation, and they base pair in different adjacent duplexes. Localized RNA backbone reversals stabilized by arginine-guanine interactions place the adenosines and guanines in reverse order in the duplex. The results suggest that a uniform, organized 3' conformation, similar to that found on viral RNAs with transfer RNA-like ends, may be essential for replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1500904/" 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/PMC1500904/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guogas, Laura M -- Filman, David J -- Hogle, James M -- Gehrke, Lee -- AI20566/AI/NIAID NIH HHS/ -- GM42504/GM/NIGMS NIH HHS/ -- R01 AI020566/AI/NIAID NIH HHS/ -- R01 GM042504/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Dec 17;306(5704):2108-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15604410" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; Alfalfa mosaic virus/*chemistry/*physiology ; Amino Acid Sequence ; Base Pairing ; Base Sequence ; Binding Sites ; Capsid Proteins/*chemistry/metabolism ; Crystallization ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Folding ; Protein Structure, Secondary ; RNA, Viral/*chemistry/metabolism ; Repetitive Sequences, Nucleic Acid ; *Virus Replication
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Late Miocene teeth from Middle Awash, Ethiopia, and early hominid dental evolution (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-06
    Description: Late Miocene fossil hominid teeth recovered from Ethiopia's Middle Awash are assigned to Ardipithecus kadabba. Their primitive morphology and wear pattern demonstrate that A. kadabba is distinct from Ardipithecus ramidus. These fossils suggest that the last common ancestor of apes and humans had a functionally honing canine-third premolar complex. Comparison with teeth of Sahelanthropus and Orrorin, the two other named late Miocene hominid genera, implies that these putative taxa are very similar to A. kadabba. It is therefore premature to posit extensive late Miocene hominid diversity on the basis of currently available samples.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haile-Selassie, Yohannes -- Suwa, Gen -- White, Tim D -- New York, N.Y. -- Science. 2004 Mar 5;303(5663):1503-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cleveland Museum of Natural History, 1 Wade Oval Drive, Cleveland, OH 44106, USA. yhailese@cmnh.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15001775" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bicuspid/*anatomy & histology ; *Biological Evolution ; Cuspid/*anatomy & histology ; Dental Enamel/anatomy & histology ; Dentition ; Ethiopia ; *Fossils ; *Hominidae/anatomy & histology/classification ; Humans ; Paleodontology
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    Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-14
    Description: The structure of the general transcription factor IIB (TFIIB) in a complex with RNA polymerase II reveals three features crucial for transcription initiation: an N-terminal zinc ribbon domain of TFIIB that contacts the "dock" domain of the polymerase, near the path of RNA exit from a transcribing enzyme; a "finger" domain of TFIIB that is inserted into the polymerase active center; and a C-terminal domain, whose interaction with both the polymerase and with a TATA box-binding protein (TBP)-promoter DNA complex orients the DNA for unwinding and transcription. TFIIB stabilizes an early initiation complex, containing an incomplete RNA-DNA hybrid region. It may interact with the template strand, which sets the location of the transcription start site, and may interfere with RNA exit, which leads to abortive initiation or promoter escape. The trajectory of promoter DNA determined by the C-terminal domain of TFIIB traverses sites of interaction with TFIIE, TFIIF, and TFIIH, serving to define their roles in the transcription initiation process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bushnell, David A -- Westover, Kenneth D -- Davis, Ralph E -- Kornberg, Roger D -- AI21144/AI/NIAID NIH HHS/ -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 13;303(5660):983-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963322" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Hybridization ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/chemistry/metabolism ; RNA Polymerase II/*chemistry/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; TATA Box ; TATA-Box Binding Protein/chemistry/metabolism ; Templates, Genetic ; Transcription Factor TFIIB/*chemistry/metabolism ; Transcription Factors, TFII/chemistry/metabolism ; *Transcription, Genetic ; Zinc/chemistry
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    Regulation of gene expression by a metabolic enzyme (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-16
    Description: Gene expression in eukaryotes is normally believed to be controlled by transcriptional regulators that activate genes encoding structural proteins and enzymes. To identify previously unrecognized DNA binding activities, a yeast proteome microarray was screened with DNA probes; Arg5,6, a well-characterized mitochondrial enzyme involved in arginine biosynthesis, was identified. Chromatin immunoprecipitation experiments revealed that Arg5,6 is associated with specific nuclear and mitochondrial loci in vivo, and Arg5,6 binds to specific fragments in vitro. Deletion of Arg5,6 causes altered transcript levels of both nuclear and mitochondrial target genes. These results indicate that metabolic enzymes can directly regulate eukaryotic gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hall, David A -- Zhu, Heng -- Zhu, Xiaowei -- Royce, Thomas -- Gerstein, Mark -- Snyder, Michael -- New York, N.Y. -- Science. 2004 Oct 15;306(5695):482-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8005, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15486299" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Oxidoreductases/*metabolism ; Binding Sites ; Cell Nucleus/metabolism ; Culture Media ; DNA Probes ; DNA, Fungal/*metabolism ; DNA, Mitochondrial/metabolism ; DNA, Single-Stranded/metabolism ; *Gene Expression Regulation, Fungal ; Genes, Fungal ; Introns ; Multienzyme Complexes/*metabolism ; Oligonucleotide Array Sequence Analysis ; Phosphotransferases (Carboxyl Group Acceptor)/*metabolism ; Polymerase Chain Reaction ; Precipitin Tests ; Proteome ; RNA, Fungal/metabolism ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/*enzymology/*genetics ; Transcription, Genetic
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    Biophysics. Catching copper in the act (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aboelella, Nermeen W -- Reynolds, Anne M -- Tolman, William B -- New York, N.Y. -- Science. 2004 May 7;304(5672):836-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131298" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Copper/*metabolism ; Crystallography, X-Ray ; Dipeptides/chemistry/metabolism ; Electron Spin Resonance Spectroscopy ; Hydroxylation ; Mixed Function Oxygenases/*chemistry/metabolism ; Models, Chemical ; Models, Molecular ; Multienzyme Complexes/*chemistry/metabolism ; Nitric Oxide/*metabolism ; Nitrite Reductases/*chemistry/metabolism ; Nitrites/metabolism ; Oxidation-Reduction ; Oxygen/*metabolism
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    Nutrient availability regulates SIRT1 through a forkhead-dependent pathway (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-12-18
    Description: Nutrient availability regulates life-span in a wide range of organisms. We demonstrate that in mammalian cells, acute nutrient withdrawal simultaneously augments expression of the SIRT1 deacetylase and activates the Forkhead transcription factor Foxo3a. Knockdown of Foxo3a expression inhibited the starvation-induced increase in SIRT1 expression. Stimulation of SIRT1 transcription by Foxo3a was mediated through two p53 binding sites present in the SIRT1 promoter, and a nutrient-sensitive physical interaction was observed between Foxo3a and p53. SIRT1 expression was not induced in starved p53-deficient mice. Thus, in mammalian cells, p53, Foxo3a, and SIRT1, three proteins separately implicated in aging, constitute a nutrient-sensing pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nemoto, Shino -- Fergusson, Maria M -- Finkel, Toren -- New York, N.Y. -- Science. 2004 Dec 17;306(5704):2105-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cardiovascular Branch, National Heart, Lung, and Blood Institute (NHLBI), Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15604409" target="_blank"〉PubMed〈/a〉
    Keywords: Adipose Tissue/metabolism ; Animals ; Binding Sites ; Culture Media ; Culture Media, Serum-Free ; DNA-Binding Proteins/*metabolism ; Forkhead Transcription Factors ; Gene Deletion ; Genes, p53 ; Glucose ; HeLa Cells ; Humans ; Mice ; Mice, Inbred C57BL ; Mutation ; PC12 Cells ; Promoter Regions, Genetic ; RNA, Small Interfering/pharmacology ; Rats ; Recombinant Fusion Proteins/metabolism ; Recombinant Proteins/metabolism ; Serum ; Sirtuin 1 ; Sirtuins/genetics/*metabolism ; *Starvation ; Transcription Factors/*metabolism ; Transcription, Genetic ; Tumor Suppressor Protein p53/metabolism
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    The bacterial condensin MukBEF compacts DNA into a repetitive, stable structure (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-06-05
    Description: Condensins are conserved proteins containing SMC (structural maintenance of chromosomes) moieties that organize and compact chromosomes in an unknown mechanism essential for faithful chromosome partitioning. We show that MukBEF, the condensin in Escherichia coli, cooperatively compacts a single DNA molecule into a filament with an ordered, repetitive structure in an adenosine triphosphate (ATP) binding-dependent manner. When stretched to a tension of approximately 17 piconewtons, the filament extended in a series of repetitive transitions in a broad distribution centered on 45 nanometers. A filament so extended and held at a lower force recondensed in steps of 35 nanometers or its multiples; this cycle was repeatable even in the absence of ATP and free MukBEF. Remarkably, the pattern of transitions displayed by a given filament during the initial extension was identical in every subsequent extension. Hence, after being deformed micrometers in length, each filament returned to its original compact structure without the addition of energy. Incubation with topoisomerase I increased the rate of recondensation and allowed the structure to extend and reform almost reversibly, indicating that supercoiled DNA is trapped in the condensed structure. We suggest a new model for how MukBEF organizes the bacterial chromosome in vivo.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Case, Ryan B -- Chang, Yun-Pei -- Smith, Steven B -- Gore, Jeff -- Cozzarelli, Nicholas R -- Bustamante, Carlos -- GM31655/GM/NIGMS NIH HHS/ -- GM32543/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jul 9;305(5681):222-7. Epub 2004 Jun 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15178751" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Binding Sites ; Chemistry, Physical ; Chromosomal Proteins, Non-Histone/chemistry/*metabolism ; DNA Topoisomerases, Type I/metabolism ; DNA, Bacterial/*chemistry/*metabolism ; DNA, Superhelical/chemistry/metabolism ; Dimerization ; Escherichia coli/genetics ; Escherichia coli Proteins/chemistry/*metabolism ; Lasers ; Microspheres ; Models, Chemical ; Models, Molecular ; *Nucleic Acid Conformation ; Physicochemical Phenomena ; Protein Binding ; Protein Conformation ; Protein Subunits ; Repressor Proteins/chemistry/*metabolism
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    Comment on "The early evolution of the tetrapod humerus" (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ahlberg, P E -- New York, N.Y. -- Science. 2004 Sep 17;305(5691):1715; author reply 1715.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Evolutionary Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18A752 36 Uppsala, Sweden. per.ahlberg@ebc.uu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15375249" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Fossils ; Humerus/*anatomy & histology ; Scotland ; Vertebrates/*anatomy & histology
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    Stathmin-tubulin interaction gradients in motile and mitotic cells (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-03-20
    Description: The spatial organization of the microtubule cytoskeleton is thought to be directed by steady-state activity gradients of diffusible regulatory molecules. We visualized such intracellular gradients by monitoring the interaction between tubulin and a regulator of microtubule dynamics, stathmin, using a fluorescence resonance energy transfer (FRET) biosensor. These gradients were observed both during interphase in motile membrane protrusions and during mitosis around chromosomes, which suggests that a similar mechanism may contribute to the creation of polarized microtubule structures. These interaction patterns are likely to reflect phosphorylation of stathmin in these areas.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Niethammer, Philipp -- Bastiaens, Philippe -- Karsenti, Eric -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1862-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15031504" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacterial Proteins ; Binding Sites ; Cell Line ; *Cell Movement ; Chromosomes/metabolism ; Cytosol/metabolism ; Fluorescence Resonance Energy Transfer ; Green Fluorescent Proteins ; Interphase ; Luminescent Proteins ; *Microtubule Proteins ; Microtubules/metabolism/ultrastructure ; *Mitosis ; Mutation ; Phosphoprotein Phosphatases/metabolism ; Phosphoproteins/genetics/*metabolism ; Phosphorylation ; Protein Binding ; Recombinant Fusion Proteins/metabolism ; Spindle Apparatus/ultrastructure ; Stathmin ; Swine ; Tetradecanoylphorbol Acetate/pharmacology ; Transfection ; Tubulin/*metabolism ; Xenopus ; Xenopus Proteins
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    KIF1A alternately uses two loops to bind microtubules (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-08-03
    Description: The motor protein kinesin moves along microtubules, driven by adenosine triphosphate (ATP) hydrolysis. However, it remains unclear how kinesin converts the chemical energy into mechanical movement. We report crystal structures of monomeric kinesin KIF1A with three transition-state analogs: adenylyl imidodiphosphate (AMP-PNP), adenosine diphosphate (ADP)-vanadate, and ADP-AlFx (aluminofluoride complexes). These structures, together with known structures of the ADP-bound state and the adenylyl-(beta,gamma-methylene) diphosphate (AMP-PCP)-bound state, show that kinesin uses two microtubule-binding loops in an alternating manner to change its interaction with microtubules during the ATP hydrolysis cycle; loop L11 is extended in the AMP-PNP structure, whereas loop L12 is extended in the ADP structure. ADP-vanadate displays an intermediate structure in which a conformational change in two switch regions causes both loops to be raised from the microtubule, thus actively detaching kinesin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nitta, Ryo -- Kikkawa, Masahide -- Okada, Yasushi -- Hirokawa, Nobutaka -- New York, N.Y. -- Science. 2004 Jul 30;305(5684):678-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology and Anatomy, University of Tokyo, Graduate School of Medicine, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15286375" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Adenylyl Imidodiphosphate/metabolism ; Aluminum/metabolism ; Animals ; Binding Sites ; Crystallography, X-Ray ; Fluorides/metabolism ; Hydrogen Bonding ; Kinesin/*chemistry/*metabolism ; Mice ; Microtubules/*metabolism ; Models, Molecular ; Nerve Tissue Proteins/*chemistry/*metabolism ; Phosphates/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Vanadates/metabolism
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    Ancient invasions: from endosymbionts to organelles (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-10
    Description: The acquisitions of mitochondria and plastids were important events in the evolution of the eukaryotic cell, supplying it with compartmentalized bioenergetic and biosynthetic factories. Ancient invasions by eubacteria through symbiosis more than a billion years ago initiated these processes. Advances in geochemistry, molecular phylogeny, and cell biology have offered insight into complex molecular events that drove the evolution of endosymbionts into contemporary organelles. In losing their autonomy, endosymbionts lost the bulk of their genomes, necessitating the evolution of elaborate mechanisms for organelle biogenesis and metabolite exchange. In the process, symbionts acquired many host-derived properties, lost much of their eubacterial identity, and were transformed into extraordinarily diverse organelles that reveal complex histories that we are only beginning to decipher.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dyall, Sabrina D -- Brown, Mark T -- Johnson, Patricia J -- AI27857/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Apr 9;304(5668):253-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, 405 Hilgard Avenue, Los Angeles, CA 90095-1489, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15073369" target="_blank"〉PubMed〈/a〉
    Keywords: Alphaproteobacteria/genetics/physiology ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Chloroplasts/physiology ; Cyanobacteria/genetics/physiology ; Evolution, Molecular ; Genome ; Genome, Bacterial ; Mitochondria/*physiology ; Organelles/*physiology ; Origin of Life ; Plastids/*physiology ; Proteins/chemistry/metabolism ; *Symbiosis
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Computational design of a biologically active enzyme (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-06-26
    Description: Rational design of enzymes is a stringent test of our understanding of protein chemistry and has numerous potential applications. Here, we present and experimentally validate the computational design of enzyme activity in proteins of known structure. We have predicted mutations that introduce triose phosphate isomerase activity into ribose-binding protein, a receptor that normally lacks enzyme activity. The resulting designs contain 18 to 22 mutations, exhibit 10(5)- to 10(6)-fold rate enhancements over the uncatalyzed reaction, and are biologically active, in that they support the growth of Escherichia coli under gluconeogenic conditions. The inherent generality of the design method suggests that many enzymes can be designed by this approach.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dwyer, Mary A -- Looger, Loren L -- Hellinga, Homme W -- New York, N.Y. -- Science. 2004 Jun 25;304(5679):1967-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15218149" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Binding Sites ; Catalysis ; Catalytic Domain ; Computational Biology ; Computer Simulation ; Dihydroxyacetone Phosphate/metabolism ; Dimerization ; Directed Molecular Evolution ; Enzyme Stability ; Escherichia coli/genetics/growth & development/metabolism ; *Escherichia coli Proteins/chemistry/genetics/metabolism ; Glyceraldehyde 3-Phosphate/metabolism ; Glycerol/metabolism ; Hydrogen Bonding ; Kinetics ; Lactates/metabolism ; Ligands ; Models, Molecular ; Molecular Conformation ; Mutation ; *Periplasmic Binding Proteins/chemistry/genetics/metabolism ; Protein Conformation ; *Protein Engineering ; Protons ; *Triose-Phosphate Isomerase/chemistry/metabolism
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    Microbiology. We get by with a little help from our (little) friends (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ruby, Edward -- Henderson, Brian -- McFall-Ngai, Margaret -- New York, N.Y. -- Science. 2004 Feb 27;303(5662):1305-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pacific Biomedical Research Center, Kewalo Marine Laboratory, University of Hawaii, Honolulu, HI 96813, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14988540" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacteria/genetics/pathogenicity ; Bacterial Infections/microbiology ; *Bacterial Physiological Phenomena ; *Biological Evolution ; *Ecosystem ; Humans ; Immune System/physiology ; Invertebrates/*microbiology/physiology ; Models, Biological ; Vertebrates/*microbiology/physiology ; Virulence Factors/physiology
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    A reversible synthetic rotary molecular motor (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-11-30
    Description: The circumrotation of a submolecular fragment in either direction in a synthetic molecular structure is described. The movement of a small ring around a larger one occurs through positional displacements arising from biased Brownian motion that are kinetically captured and then directionally released. The sense of rotation is governed solely by the order in which a series of orthogonal chemical transformations is performed. The minimalist nature of the [2]catenane flashing ratchet design permits certain mechanistic comparisons with the Smoluchowski-Feynman ratchet and pawl. Even when no work has to be done against an opposing force and no net energy is used to power the motion, a finite conversion of energy is intrinsically required for the molecular motor to undergo directional rotation. Nondirectional rotation has no such requirement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hernandez, Jose V -- Kay, Euan R -- Leigh, David A -- New York, N.Y. -- Science. 2004 Nov 26;306(5701):1532-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JJ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15567858" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catenanes/chemical synthesis/*chemistry ; Chemistry, Physical ; Isomerism ; Magnetic Resonance Spectroscopy ; Models, Chemical ; Molecular Motor Proteins/chemical synthesis/*chemistry ; Molecular Structure ; Motion ; Physicochemical Phenomena ; Rotation ; Thermodynamics
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    Biochemistry. Oily barbarians breach ion channel gates (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hilgemann, Donald W -- New York, N.Y. -- Science. 2004 Apr 9;304(5668):223-4. Epub 2004 Mar 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, University of Texas Southwestern, Dallas, TX 75235, USA. donald.hilgemann@utsouthwestern.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15031439" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Membrane/metabolism ; Cytoplasm/metabolism ; Eicosanoic Acids/*metabolism/pharmacology ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers ; Membrane Lipids/*metabolism ; Micelles ; Models, Biological ; Phosphatidylinositol 4,5-Diphosphate/*metabolism/pharmacology ; Potassium Channels, Voltage-Gated/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Signal Transduction ; Sodium-Calcium Exchanger/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-02
    Description: Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Armbrust, E Virginia -- Berges, John A -- Bowler, Chris -- Green, Beverley R -- Martinez, Diego -- Putnam, Nicholas H -- Zhou, Shiguo -- Allen, Andrew E -- Apt, Kirk E -- Bechner, Michael -- Brzezinski, Mark A -- Chaal, Balbir K -- Chiovitti, Anthony -- Davis, Aubrey K -- Demarest, Mark S -- Detter, J Chris -- Glavina, Tijana -- Goodstein, David -- Hadi, Masood Z -- Hellsten, Uffe -- Hildebrand, Mark -- Jenkins, Bethany D -- Jurka, Jerzy -- Kapitonov, Vladimir V -- Kroger, Nils -- Lau, Winnie W Y -- Lane, Todd W -- Larimer, Frank W -- Lippmeier, J Casey -- Lucas, Susan -- Medina, Monica -- Montsant, Anton -- Obornik, Miroslav -- Parker, Micaela Schnitzler -- Palenik, Brian -- Pazour, Gregory J -- Richardson, Paul M -- Rynearson, Tatiana A -- Saito, Mak A -- Schwartz, David C -- Thamatrakoln, Kimberlee -- Valentin, Klaus -- Vardi, Assaf -- Wilkerson, Frances P -- Rokhsar, Daniel S -- New York, N.Y. -- Science. 2004 Oct 1;306(5693):79-86.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Oceanography, University of Washington, Seattle, WA 98195, USA. armbrust@ocean.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15459382" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Algal Proteins/chemistry/genetics/physiology ; Animals ; *Biological Evolution ; Cell Nucleus/genetics ; Chromosomes ; DNA/genetics ; Diatoms/chemistry/cytology/*genetics/metabolism ; *Ecosystem ; Energy Metabolism ; *Genome ; Iron/metabolism ; Light ; Light-Harvesting Protein Complexes/chemistry/genetics/metabolism ; Mitochondria/genetics ; Molecular Sequence Data ; Nitrogen/metabolism ; Photosynthesis ; Plastids/genetics ; Restriction Mapping ; Sequence Alignment ; *Sequence Analysis, DNA ; Silicic Acid/metabolism ; Symbiosis ; Urea/metabolism
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    Evolutionary dynamics of biological games (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-07
    Description: Darwinian dynamics based on mutation and selection form the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short- and long-term evolution in phenotype space and have found applications ranging from animal behavior and ecology to speciation, macroevolution, and human language. Evolutionary game theory is an essential component of a mathematical and computational approach to biology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nowak, Martin A -- Sigmund, Karl -- New York, N.Y. -- Science. 2004 Feb 6;303(5659):793-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program for Evolutionary Dynamics, Department of Mathematics, Department of Organismic and Evolutionary Biology, Harvard University, 1 Brattle Square, Cambridge, MA 02138, USA. martin_nowak@harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14764867" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Algorithms ; Animals ; *Biological Evolution ; Ecosystem ; Evolution, Molecular ; Female ; *Game Theory ; Genetics, Population ; Humans ; Male ; Mathematics ; Selection, Genetic
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    Adaptive radiation from resource competition in digital organisms (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-07-03
    Description: Species richness often peaks at intermediate productivity and decreases as resources become more or less abundant. The mechanisms that produce this pattern are not completely known, but several previous studies have suggested environmental heterogeneity as a cause. In experiments with evolving digital organisms and populations of fixed size, maximum species richness emerges at intermediate productivity, even in a spatially homogeneous environment, owing to frequency-dependent selection to exploit an influx of mixed resources. A diverse pool of limiting resources is sufficient to cause adaptive radiation, which is manifest by the origin and maintenance of phenotypically and phylogenetically distinct groups of organisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chow, Stephanie S -- Wilke, Claus O -- Ofria, Charles -- Lenski, Richard E -- Adami, Christoph -- New York, N.Y. -- Science. 2004 Jul 2;305(5680):84-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Digital Life Laboratory 136-93, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15232105" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Biological ; Algorithms ; *Biodiversity ; *Biological Evolution ; *Computer Simulation ; Ecosystem ; Genome ; *Models, Biological ; Mutation ; Phylogeny ; *Software ; User-Computer Interface
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    Functional adaptation of BabA, the H. pylori ABO blood group antigen binding adhesin (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-27
    Description: Adherence by Helicobacter pylori increases the risk of gastric disease. Here, we report that more than 95% of strains that bind fucosylated blood group antigen bind A, B, and O antigens (generalists), whereas 60% of adherent South American Amerindian strains bind blood group O antigens best (specialists). This specialization coincides with the unique predominance of blood group O in these Amerindians. Strains differed about 1500-fold in binding affinities, and diversifying selection was evident in babA sequences. We propose that cycles of selection for increased and decreased bacterial adherence contribute to babA diversity and that these cycles have led to gradual replacement of generalist binding by specialist binding in blood group O-dominant human populations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aspholm-Hurtig, Marina -- Dailide, Giedrius -- Lahmann, Martina -- Kalia, Awdhesh -- Ilver, Dag -- Roche, Niamh -- Vikstrom, Susanne -- Sjostrom, Rolf -- Linden, Sara -- Backstrom, Anna -- Lundberg, Carina -- Arnqvist, Anna -- Mahdavi, Jafar -- Nilsson, Ulf J -- Velapatino, Billie -- Gilman, Robert H -- Gerhard, Markus -- Alarcon, Teresa -- Lopez-Brea, Manuel -- Nakazawa, Teruko -- Fox, James G -- Correa, Pelayo -- Dominguez-Bello, Maria Gloria -- Perez-Perez, Guillermo I -- Blaser, Martin J -- Normark, Staffan -- Carlstedt, Ingemar -- Oscarson, Stefan -- Teneberg, Susann -- Berg, Douglas E -- Boren, Thomas -- P30 DK52574/DK/NIDDK NIH HHS/ -- R01 AI38166/AI/NIAID NIH HHS/ -- R01 DK53727/DK/NIDDK NIH HHS/ -- R01 DK63041/DK/NIDDK NIH HHS/ -- R03 AI49161/AI/NIAID NIH HHS/ -- R0IGM62370/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jul 23;305(5683):519-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Odontology, section of Oral Microbiology, Umea University, SE-901 87 Umea, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15273394" target="_blank"〉PubMed〈/a〉
    Keywords: ABO Blood-Group System/*metabolism ; Adaptation, Biological ; Adhesins, Bacterial/chemistry/*genetics/immunology/*metabolism ; Alleles ; *Bacterial Adhesion ; Base Sequence ; Binding Sites ; Evolution, Molecular ; Fucose/metabolism ; Gastric Mucosa/microbiology ; Helicobacter Infections/microbiology ; Helicobacter pylori/genetics/immunology/*physiology ; Humans ; Indians, South American ; Lewis Blood-Group System/metabolism ; Molecular Sequence Data ; Mutation ; Peru ; Phenotype ; Phylogeny ; Protein Binding ; Selection, Genetic ; Transformation, Bacterial
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    Genome sequence of a polydnavirus: insights into symbiotic virus evolution (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-09
    Description: Little is known of the fate of viruses involved in long-term obligatory associations with eukaryotes. For example, many species of parasitoid wasps have symbiotic viruses to manipulate host defenses and to allow development of parasitoid larvae. The complete nucleotide sequence of the DNA enclosed in the virus particles injected by a parasitoid wasp revealed a complex organization, resembling a eukaryote genomic region more than a viral genome. Although endocellular symbiont genomes have undergone a dramatic loss of genes, the evolution of symbiotic viruses appears to be characterized by extensive duplication of virulence genes coding for truncated versions of cellular proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Espagne, Eric -- Dupuy, Catherine -- Huguet, Elisabeth -- Cattolico, Laurence -- Provost, Bertille -- Martins, Nathalie -- Poirie, Marylene -- Periquet, Georges -- Drezen, Jean Michel -- New York, N.Y. -- Science. 2004 Oct 8;306(5694):286-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 6035, UFR Sciences et Techniques, Parc de Grandmont, 37200 Tours, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15472078" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Ankyrin Repeat ; Base Composition ; *Biological Evolution ; Cysteine Proteinase Inhibitors/genetics ; Genes, Viral ; *Genome, Viral ; Introns ; Manduca/parasitology/virology ; Molecular Sequence Data ; Polydnaviridae/*genetics ; Protein Tyrosine Phosphatases/genetics ; *Sequence Analysis, DNA ; *Symbiosis ; Viral Proteins/chemistry/genetics ; Virulence Factors/genetics ; Wasps/*virology
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    Human evolution. Faster than a hyena? Running may make humans special (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-11-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zimmer, Carl -- New York, N.Y. -- Science. 2004 Nov 19;306(5700):1283.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15550638" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anthropometry ; *Biological Evolution ; Biomechanical Phenomena ; Body Size ; Buttocks/anatomy & histology ; Hominidae/anatomy & histology/*physiology ; Humans ; Ligaments/anatomy & histology ; *Physical Endurance ; *Running/physiology ; Tendons/anatomy & histology
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    Side-on copper-nitrosyl coordination by nitrite reductase (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-05-08
    Description: A copper-nitrosyl intermediate forms during the catalytic cycle of nitrite reductase, the enzyme that mediates the committed step in bacterial denitrification. The crystal structure of a type 2 copper-nitrosyl complex of nitrite reductase reveals an unprecedented side-on binding mode in which the nitrogen and oxygen atoms are nearly equidistant from the copper cofactor. Comparison of this structure with a refined nitrite-bound crystal structure explains how coordination can change between copper-oxygen and copper-nitrogen during catalysis. The side-on copper-nitrosyl in nitrite reductase expands the possibilities for nitric oxide interactions in copper proteins such as superoxide dismutase and prions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tocheva, Elitza I -- Rosell, Federico I -- Mauk, A Grant -- Murphy, Michael E P -- New York, N.Y. -- Science. 2004 May 7;304(5672):867-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131305" target="_blank"〉PubMed〈/a〉
    Keywords: Alcaligenes faecalis/enzymology ; Ascorbic Acid/metabolism ; Binding Sites ; Catalysis ; Copper/*metabolism ; Crystallization ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Hydrogen Bonding ; Models, Chemical ; Models, Molecular ; Nitric Oxide/*metabolism ; Nitrite Reductases/*chemistry/*metabolism ; Nitrites/*metabolism ; Oxidation-Reduction ; Oxygen/metabolism
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    The significance of few versus many in the tree of life (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scotland, Robert W -- Sanderson, Michael J -- New York, N.Y. -- Science. 2004 Jan 30;303(5658):643.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Sciences, Oxford University, Oxford, OX1 3RB, UK. robert.scotland@plants.ox.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14752153" target="_blank"〉PubMed〈/a〉
    Keywords: Angiosperms/*classification ; Animals ; *Biodiversity ; *Biological Evolution ; Birds/*classification ; Classification ; Computer Simulation ; Models, Biological ; *Phylogeny
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  • 85
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    Protein displacement by DExH/D "RNA helicases" without duplex unwinding (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-01
    Description: Members of the DExH/D superfamily of nucleic acid-activated nucleotide triphosphatases are essential for virtually all aspects of RNA metabolism, including pre-messenger RNA splicing, RNA interference, translation, and nucleocytoplasmic trafficking. Physiological substrates for these enzymes are thought to be regions of double-stranded RNA, because several DExH/D proteins catalyze strand separation in vitro. These "RNA helicases" can also disrupt RNA-protein interactions, but it is unclear whether this activity is coupled to duplex unwinding. Here we demonstrate that two unrelated DExH/D proteins catalyze protein displacement independently of duplex unwinding. Therefore, the essential functions of DExH/D proteins are not confined to RNA duplexes but can be exerted on a wide range of ribonucleoprotein substrates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fairman, Margaret E -- Maroney, Patricia A -- Wang, Wen -- Bowers, Heath A -- Gollnick, Paul -- Nilsen, Timothy W -- Jankowsky, Eckhard -- R01 GM067700/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Apr 30;304(5671):730-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15118161" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Bacterial Proteins/metabolism ; Binding Sites ; Cell Cycle Proteins/*metabolism ; DEAD-box RNA Helicases ; Exons ; Fungal Proteins/*metabolism ; Nucleic Acid Conformation ; Protein Binding ; RNA/chemistry/metabolism ; RNA Helicases/*metabolism ; RNA Precursors/chemistry/*metabolism ; RNA Splicing ; RNA, Double-Stranded/chemistry/*metabolism ; RNA, Messenger/chemistry/*metabolism ; RNA-Binding Proteins/metabolism ; Ribonucleoproteins/*metabolism ; Transcription Factors/metabolism ; Vaccinia virus/enzymology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 86
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    Molecular biology. RNAs turn on in tandem (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Famulok, Michael -- New York, N.Y. -- Science. 2004 Oct 8;306(5694):233-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Kekule Institut fur Organische Chemie und Biochemie, D-53121 Bonn, Germany. m.famulok@uni-bonn.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15472064" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Allosteric Site ; Binding Sites ; *Gene Expression Regulation, Bacterial ; Glycine/*metabolism ; Ligands ; Nucleic Acid Conformation ; RNA, Bacterial/chemistry/*metabolism ; RNA, Messenger/chemistry/metabolism ; Untranslated Regions/*metabolism ; Vibrio cholerae/genetics/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 87
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    Virology. 1918 and all that (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holmes, Edward C -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1787-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Oxford, Oxford OX1 3PS, UK. edward.holmes@zoo.ox.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15031487" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Birds ; Carbohydrate Conformation ; Crystallography, X-Ray ; Disease Outbreaks/history ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/*metabolism ; History, 20th Century ; Humans ; Influenza A virus/*immunology/metabolism/pathogenicity ; Influenza, Human/epidemiology/*history/*virology ; Membrane Glycoproteins/chemistry/metabolism ; Protein Conformation ; RNA, Viral/chemistry/genetics/isolation & purification ; Receptors, Virus/chemistry/metabolism ; Sialic Acids/metabolism ; Virulence
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 88
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    Reconstitution of Ca2+-regulated membrane fusion by synaptotagmin and SNAREs (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-27
    Description: We investigated the effect of synaptotagmin I on membrane fusion mediated by neuronal SNARE proteins, SNAP-25, syntaxin, and synaptobrevin, which were reconstituted into vesicles. In the presence of Ca2+, the cytoplasmic domain of synaptotagmin I (syt) strongly stimulated membrane fusion when synaptobrevin densities were similar to those found in native synaptic vesicles. The Ca2+ dependence of syt-stimulated fusion was modulated by changes in lipid composition of the vesicles and by a truncation that mimics cleavage of SNAP-25 by botulinum neurotoxin A. Stimulation of fusion was abolished by disrupting the Ca2+-binding activity, or by severing the tandem C2 domains, of syt. Thus, syt and SNAREs are likely to represent the minimal protein complement for Ca2+-triggered exocytosis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tucker, Ward C -- Weber, Thomas -- Chapman, Edwin R -- GM 56827/GM/NIGMS NIH HHS/ -- GM 66313/GM/NIGMS NIH HHS/ -- MH 61876/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2004 Apr 16;304(5669):435-8. Epub 2004 Mar 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15044754" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Calcium/*metabolism ; *Calcium-Binding Proteins ; Exocytosis ; Fluorescence Resonance Energy Transfer ; Lipid Bilayers ; Lipids/analysis ; Liposomes/chemistry/metabolism ; *Membrane Fusion ; Membrane Glycoproteins/chemistry/*metabolism ; Membrane Proteins/chemistry/*metabolism ; Mice ; Mutation ; Nerve Tissue Proteins/chemistry/*metabolism ; Protein Structure, Tertiary ; Qa-SNARE Proteins ; R-SNARE Proteins ; Rats ; Synaptic Vesicles/chemistry/metabolism ; Synaptosomal-Associated Protein 25 ; Synaptotagmin I ; Synaptotagmins
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 89
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    Illuminating the evolutionary history of chlamydiae (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-10
    Description: Chlamydiae are the major cause of preventable blindness and sexually transmitted disease. Genome analysis of a chlamydia-related symbiont of free-living amoebae revealed that it is twice as large as any of the pathogenic chlamydiae and had few signs of recent lateral gene acquisition. We showed that about 700 million years ago the last common ancestor of pathogenic and symbiotic chlamydiae was already adapted to intracellular survival in early eukaryotes and contained many virulence factors found in modern pathogenic chlamydiae, including a type III secretion system. Ancient chlamydiae appear to be the originators of mechanisms for the exploitation of eukaryotic cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Horn, Matthias -- Collingro, Astrid -- Schmitz-Esser, Stephan -- Beier, Cora L -- Purkhold, Ulrike -- Fartmann, Berthold -- Brandt, Petra -- Nyakatura, Gerald J -- Droege, Marcus -- Frishman, Dmitrij -- Rattei, Thomas -- Mewes, Hans-Werner -- Wagner, Michael -- New York, N.Y. -- Science. 2004 Apr 30;304(5671):728-30. Epub 2004 Apr 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbial Ecology, Institute of Ecology and Conservation Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. horn@microbial-ecology.net〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15073324" target="_blank"〉PubMed〈/a〉
    Keywords: Acanthamoeba/microbiology ; Animals ; Bacterial Proteins/analysis/genetics/metabolism ; *Biological Evolution ; Cell Membrane/chemistry ; Cell Wall/chemistry ; Chlamydia/classification/genetics/metabolism/pathogenicity ; Chlamydiales/*classification/*genetics/metabolism/pathogenicity ; Chlamydophila/classification/genetics/metabolism/pathogenicity ; Electron Transport ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Molecular Sequence Data ; Nucleotide Transport Proteins/metabolism ; Phylogeny ; Symbiosis ; Virulence ; Virulence Factors/genetics/metabolism
    Print ISSN: 0036-8075
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  • 90
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    Heterodimeric GTPase core of the SRP targeting complex (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-17
    Description: Two structurally homologous guanosine triphosphatase (GTPase) domains interact directly during signal recognition particle (SRP)-mediated cotranslational targeting of proteins to the membrane. The 2.05 angstrom structure of a complex of the NG GTPase domains of Ffh and FtsY reveals a remarkably symmetric heterodimer sequestering a composite active site that contains two bound nucleotides. The structure explains the coordinate activation of the two GTPases. Conformational changes coupled to formation of their extensive interface may function allosterically to signal formation of the targeting complex to the signal-sequence binding site and the translocon. We propose that the complex represents a molecular "latch" and that its disengagement is regulated by completion of assembly of the GTPase active site.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3546161/" 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/PMC3546161/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Focia, Pamela J -- Shepotinovskaya, Irina V -- Seidler, James A -- Freymann, Douglas M -- GM58500/GM/NIGMS NIH HHS/ -- R01 GM058500/GM/NIGMS NIH HHS/ -- RR07707/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 16;303(5656):373-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14726591" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Dimerization ; Guanosine Triphosphate/*analogs & derivatives/metabolism ; Heterotrimeric GTP-Binding Proteins/*chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Receptors, Cytoplasmic and Nuclear/*chemistry/metabolism ; Signal Recognition Particle/*chemistry/metabolism ; Thermus/*chemistry
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  • 91
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    A molecular switch and proton wire synchronize the active sites in thiamine enzymes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-30
    Description: Thiamine diphosphate (ThDP) is used as a cofactor in many key metabolic enzymes. We present evidence that the ThDPs in the two active sites of the E1 (EC 1.2.4.1) component of the pyruvate dehydrogenase complex communicate over a distance of 20 angstroms by reversibly shuttling a proton through an acidic tunnel in the protein. This "proton wire" permits the co-factors to serve reciprocally as general acid/base in catalysis and to switch the conformation of crucial active-site peptide loops. This synchronizes the progression of chemical events and can account for the oligomeric organization, conformational asymmetry, and "ping-pong" kinetic properties of E1 and other thiamine-dependent enzymes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frank, Rene A W -- Titman, Christopher M -- Pratap, J Venkatesh -- Luisi, Ben F -- Perham, Richard N -- New York, N.Y. -- Science. 2004 Oct 29;306(5697):872-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15514159" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Dihydrolipoyllysine-Residue Acetyltransferase ; Geobacillus stearothermophilus/*enzymology ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Mutation ; Phosphorylation ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Protons ; Pyruvate Dehydrogenase (Lipoamide)/*chemistry/genetics/*metabolism ; Pyruvate Dehydrogenase Complex/*chemistry/*metabolism ; Pyruvic Acid/metabolism ; Thiamine Pyrophosphate/*metabolism
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  • 92
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    Evolution. Ice ages may explain ancient bison's boom-bust history (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2004 Nov 26;306(5701):1454.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15567821" target="_blank"〉PubMed〈/a〉
    Keywords: Alaska ; Animals ; *Biological Evolution ; *Bison/classification/genetics ; Canada ; *Climate ; DNA, Mitochondrial/genetics ; *Fossils ; Genetic Variation ; Human Activities ; Humans ; Population Dynamics ; Sequence Analysis, DNA ; Time
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 93
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    A fast and furious hunt for gene regulators (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2004 Oct 22;306(5696):635.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15499006" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Computational Biology ; *Enhancer Elements, Genetic ; *Gene Expression Regulation ; Oligonucleotide Array Sequence Analysis ; *Promoter Regions, Genetic ; Regulatory Sequences, Nucleic Acid ; Software
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  • 94
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    Evolutionary biology. The birth of the nucleus (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-08-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2004 Aug 6;305(5685):766-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15297641" target="_blank"〉PubMed〈/a〉
    Keywords: Archaea/cytology/*physiology ; Bacteria/cytology/ultrastructure ; *Bacterial Physiological Phenomena ; *Biological Evolution ; *Cell Nucleus/metabolism/ultrastructure ; Eukaryotic Cells/*physiology/ultrastructure ; Genes, Archaeal ; Genes, Bacterial ; Intracellular Membranes/ultrastructure ; Myxococcales/cytology/physiology ; Nuclear Envelope/physiology/ultrastructure ; Symbiosis ; *Virus Physiological Phenomena ; Viruses/ultrastructure
    Print ISSN: 0036-8075
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  • 95
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    Overriding imatinib resistance with a novel ABL kinase inhibitor (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-17
    Description: Resistance to the ABL kinase inhibitor imatinib (STI571 or Gleevec) in chronic myeloid leukemia (CML) occurs through selection for tumor cells harboring BCR-ABL kinase domain point mutations that interfere with drug binding. Crystallographic studies predict that most imatinib-resistant mutants should remain sensitive to inhibitors that bind ABL with less stringent conformational requirements. BMS-354825 is an orally bioavailable ABL kinase inhibitor with two-log increased potency relative to imatinib that retains activity against 14 of 15 imatinib-resistant BCR-ABL mutants. BMS-354825 prolongs survival of mice with BCR-ABL-driven disease and inhibits proliferation of BCR-ABL-positive bone marrow progenitor cells from patients with imatinib-sensitive and imatinib-resistant CML. These data illustrate how molecular insight into kinase inhibitor resistance can guide the design of second-generation targeted therapies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shah, Neil P -- Tran, Chris -- Lee, Francis Y -- Chen, Ping -- Norris, Derek -- Sawyers, Charles L -- New York, N.Y. -- Science. 2004 Jul 16;305(5682):399-401.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Hematology and Oncology, Department of Medicine, The David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15256671" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Antineoplastic Agents/metabolism/*pharmacology/therapeutic use ; Benzamides ; Binding Sites ; Cell Division/drug effects ; Cell Line ; Clinical Trials, Phase I as Topic ; Dasatinib ; Drug Resistance, Neoplasm ; Enzyme Inhibitors/metabolism/pharmacology/therapeutic use ; Fusion Proteins, bcr-abl/*antagonists & inhibitors/chemistry/genetics/metabolism ; Hematopoietic Stem Cells/drug effects ; Humans ; Imatinib Mesylate ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/*drug therapy ; Mice ; Mice, SCID ; Mutation ; Piperazines/*pharmacology/therapeutic use ; Protein Conformation ; Pyrimidines/metabolism/*pharmacology/therapeutic use ; Thiazoles/metabolism/*pharmacology/therapeutic use ; Transfection
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  • 96
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    Neuroscience. Calcium and CREST for healthy dendrites (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jefferis, Gregory S X E -- Komiyama, Takaki -- Luo, Liqun -- New York, N.Y. -- Science. 2004 Jan 9;303(5655):179-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences and Neurosciences Program, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14715999" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; CREB-Binding Protein ; Calcium/*metabolism ; Calcium Signaling ; Calcium-Calmodulin-Dependent Protein Kinases/metabolism ; Cell Nucleus/metabolism ; Cells, Cultured ; Cyclic AMP Response Element-Binding Protein/metabolism ; DNA-Binding Proteins/metabolism ; Dendrites/*physiology/ultrastructure ; Mice ; Neurons/physiology/ultrastructure ; Nuclear Proteins/metabolism ; Rats ; Recombinant Fusion Proteins/metabolism ; Trans-Activators/chemistry/genetics/*metabolism ; Transcription Factors/metabolism ; *Transcription, Genetic ; *Transcriptional Activation ; Transfection
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  • 97
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    Evolution of developmental diversity meeting. The genes that change the cichlid jaws (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2004 Apr 16;304(5669):383.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15087522" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Cichlids/*anatomy & histology/*genetics/growth & development ; Crosses, Genetic ; *Genes ; Mandible/*anatomy & histology/growth & development ; *Quantitative Trait Loci
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  • 98
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    RNAi-independent heterochromatin nucleation by the stress-activated ATF/CREB family proteins (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-06-26
    Description: At the silent mating-type interval of fission yeast, the RNA interference (RNAi) machinery cooperates with cenH, a DNA element homologous to centromeric repeats, to initiate heterochromatin formation. However, in RNAi mutants, heterochromatin assembly can still occur at low efficiency. Here, we report that Atf1 and Pcr1, two ATF/CREB family proteins, act in a parallel mechanism to the RNAi pathway for heterochromatin nucleation. Deletion of atf1 or pcr1 alone has little effect on silencing at the mating-type region, but when combined with RNAi mutants, double mutants fail to nucleate heterochromatin assembly. Moreover, deletion of atf1 or pcr1 in combination with cenH deletion causes loss of silencing and heterochromatin formation. Furthermore, Atf1 and Pcr1 bind to the mating-type region and target histone H3 lysine-9 methylation and the Swi6 protein essential for heterochromatin assembly. These analyses link ATF/CREB family proteins, involved in cellular response to environmental stresses, to nucleation of constitutive heterochromatin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jia, Songtao -- Noma, Ken-ichi -- Grewal, Shiv I S -- New York, N.Y. -- Science. 2004 Jun 25;304(5679):1971-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15218150" target="_blank"〉PubMed〈/a〉
    Keywords: Activating Transcription Factor 1 ; Activating Transcription Factors ; Binding Sites ; Chromosomal Proteins, Non-Histone/metabolism ; DNA, Fungal/metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Gene Deletion ; Genes, Fungal ; Genes, Mating Type, Fungal ; Heterochromatin/*metabolism ; Histones/metabolism ; Hydroxamic Acids/pharmacology ; Methylation ; Mutation ; Phosphoproteins/chemistry/genetics/*metabolism ; Protein Structure, Tertiary ; *RNA Interference ; Schizosaccharomyces/*genetics/*metabolism ; Schizosaccharomyces pombe Proteins/chemistry/genetics/*metabolism ; Transcription Factors/chemistry/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Behavioral evolution. The evolution of the golden rule (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vogel, Gretchen -- New York, N.Y. -- Science. 2004 Feb 20;303(5661):1128-31.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14976292" target="_blank"〉PubMed〈/a〉
    Keywords: Altruism ; Animals ; *Biological Evolution ; Brain/*physiology ; *Cooperative Behavior ; Culture ; Games, Experimental ; Humans ; Magnetic Resonance Imaging ; Prefrontal Cortex/physiology ; Primates/psychology ; Punishment ; Reproductive Behavior ; Social Behavior
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Evolution. Genomic databases and the tree of life (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crandall, Keith A -- Buhay, Jennifer E -- New York, N.Y. -- Science. 2004 Nov 12;306(5699):1144-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA. keith_crandall@byu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15539592" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Biological Evolution ; Computational Biology ; Computer Simulation ; *Databases, Nucleic Acid ; *Databases, Protein ; Multigene Family ; *Phylogeny ; Plants/classification/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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