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  • Molecular Sequence Data  (366)
  • American Association for the Advancement of Science (AAAS)  (366)
  • Annual Reviews
  • Society of Exploration Geophysicists (SEG)
  • 2005-2009  (98)
  • 1990-1994  (268)
  • 1980-1984
  • 2006  (98)
  • 1993  (268)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (366)
  • Annual Reviews
  • Society of Exploration Geophysicists (SEG)
Years
  • 2005-2009  (98)
  • 1990-1994  (268)
  • 1980-1984
Year
  • 1
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    An antigen produced by splicing of noncontiguous peptides in the reverse order (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-09
    Description: CD8-positive T lymphocytes recognize peptides that are usually derived from the degradation of cellular proteins and are presented by class I molecules of the major histocompatibility complex. Here we describe a human minor histocompatibility antigen created by a polymorphism in the SP110 nuclear phosphoprotein gene. The antigenic peptide comprises two noncontiguous SP110 peptide segments spliced together in reverse order to that in which they occur in the predicted SP110 protein. The antigenic peptide could be produced in vitro by incubation of precursor peptides with highly purified 20S proteasomes. Cutting and splicing probably occur within the proteasome by transpeptidation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Warren, Edus H -- Vigneron, Nathalie J -- Gavin, Marc A -- Coulie, Pierre G -- Stroobant, Vincent -- Dalet, Alexandre -- Tykodi, Scott S -- Xuereb, Suzanne M -- Mito, Jeffrey K -- Riddell, Stanley R -- Van den Eynde, Benoit J -- CA106512/CA/NCI NIH HHS/ -- CA18029/CA/NCI NIH HHS/ -- P01 CA018029/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2006 Sep 8;313(5792):1444-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16960008" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Motifs ; Amino Acid Sequence ; Amino Acid Substitution ; *Antigen Presentation ; B-Lymphocytes/immunology ; Cell Line, Transformed ; Cytotoxicity, Immunologic ; Electroporation ; HLA-A Antigens/immunology ; Humans ; Interferon-gamma/metabolism ; Male ; Middle Aged ; Minor Histocompatibility Antigens/genetics/*immunology/*metabolism ; Molecular Sequence Data ; Nuclear Proteins/chemistry/genetics/*immunology/*metabolism ; Peptide Fragments/metabolism ; Polymorphism, Single Nucleotide ; Proteasome Endopeptidase Complex/metabolism ; *Protein Splicing ; T-Lymphocytes, Cytotoxic/*immunology
    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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    Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-18
    Description: Using single-molecule DNA nanomanipulation, we show that abortive initiation involves DNA "scrunching"--in which RNA polymerase (RNAP) remains stationary and unwinds and pulls downstream DNA into itself--and that scrunching requires RNA synthesis and depends on RNA length. We show further that promoter escape involves scrunching, and that scrunching occurs in most or all instances of promoter escape. Our results support the existence of an obligatory stressed intermediate, with approximately one turn of additional DNA unwinding, in escape and are consistent with the proposal that stress in this intermediate provides the driving force to break RNAP-promoter and RNAP-initiation-factor interactions in escape.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754787/" 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/PMC2754787/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Revyakin, Andrey -- Liu, Chenyu -- Ebright, Richard H -- Strick, Terence R -- GM41376/GM/NIGMS NIH HHS/ -- R01 GM041376/GM/NIGMS NIH HHS/ -- R01 GM041376-15/GM/NIGMS NIH HHS/ -- R01 GM041376-16/GM/NIGMS NIH HHS/ -- R01 GM041376-17/GM/NIGMS NIH HHS/ -- R01 GM041376-18/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2006 Nov 17;314(5802):1139-43.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17110577" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Biomechanical Phenomena ; DNA/chemistry/*metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Promoter Regions, Genetic ; RNA/biosynthesis ; Transcription Initiation Site/physiology ; Transcription, Genetic/*physiology
    Print ISSN: 0036-8075
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  • 3
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    Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-25
    Description: The Dobzhansky-Muller model proposes that hybrid incompatibilities are caused by the interaction between genes that have functionally diverged in the respective hybridizing species. Here, we show that Lethal hybrid rescue (Lhr) has functionally diverged in Drosophila simulans and interacts with Hybrid male rescue (Hmr), which has functionally diverged in D. melanogaster, to cause lethality in F1 hybrid males. LHR localizes to heterochromatic regions of the genome and has diverged extensively in sequence between these species in a manner consistent with positive selection. Rapidly evolving heterochromatic DNA sequences may be driving the evolution of this incompatibility gene.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brideau, Nicholas J -- Flores, Heather A -- Wang, Jun -- Maheshwari, Shamoni -- Wang, Xu -- Barbash, Daniel A -- R01 GM074737-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 24;314(5803):1292-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17124320" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Chromosomal Proteins, Non-Histone/metabolism ; Chromosome Mapping ; Crosses, Genetic ; Drosophila/*genetics/physiology ; Drosophila Proteins/chemistry/*genetics/metabolism ; Drosophila melanogaster/*genetics/physiology ; *Evolution, Molecular ; Female ; *Genes, Insect ; Genetic Speciation ; *Hybridization, Genetic ; Male ; Molecular Sequence Data ; Selection, Genetic ; Transformation, Genetic ; Transgenes
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Structure and mechanism of the lantibiotic cyclase involved in nisin biosynthesis (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-11
    Description: Nisin is a posttranslationally modified antimicrobial peptide that is widely used as a food preservative. It contains five cyclic thioethers of varying sizes that are installed by a single enzyme, NisC. Reported here are the in vitro reconstitution of the cyclization process and the x-ray crystal structure of the NisC enzyme. The structure reveals similarities in fold and substrate activation with mammalian farnesyl transferases, suggesting that human homologs of NisC posttranslationally modify a cysteine of a protein substrate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Bo -- Yu, John Paul J -- Brunzelle, Joseph S -- Moll, Gert N -- van der Donk, Wilfred A -- Nair, Satish K -- GM58822/GM/NIGMS NIH HHS/ -- R01 GM079038/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Mar 10;311(5766):1464-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16527981" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anti-Bacterial Agents/*biosynthesis/chemistry ; Carbon-Sulfur Lyases/chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Farnesyltranstransferase/chemistry ; Humans ; Lactococcus lactis/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Nisin/*biosynthesis/chemistry ; Protein Conformation ; Protein Processing, Post-Translational ; Sequence Homology, Amino Acid ; Structure-Activity Relationship
    Print ISSN: 0036-8075
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  • 5
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    Rice domestication by reducing shattering (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-11
    Description: Crop domestication frequently began with the selection of plants that did not naturally shed ripe fruits or seeds. The reduction in grain shattering that led to cereal domestication involved genetic loci of large effect. The molecular basis of this key domestication transition, however, remains unknown. Here we show that human selection of an amino acid substitution in the predicted DNA binding domain encoded by a gene of previously unknown function was primarily responsible for the reduction of grain shattering in rice domestication. The substitution undermined the gene function necessary for the normal development of an abscission layer that controls the separation of a grain from the pedicel.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Changbao -- Zhou, Ailing -- Sang, Tao -- New York, N.Y. -- Science. 2006 Mar 31;311(5769):1936-9. Epub 2006 Mar 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16527928" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Amino Acid Substitution ; Biological Evolution ; Chromosome Mapping ; Computational Biology ; Crops, Agricultural/*genetics/growth & development ; Flowers/growth & development ; Gene Expression ; Genes, Plant ; Genotype ; Molecular Sequence Data ; Mutation ; Oryza/cytology/*genetics/growth & development ; Phenotype ; Plant Proteins/chemistry/*genetics ; Plants, Genetically Modified ; Quantitative Trait Loci ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transcription Factors/chemistry/*genetics ; Transformation, Genetic
    Print ISSN: 0036-8075
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  • 6
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    Structure of the vesicular stomatitis virus nucleoprotein-RNA complex (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-06-17
    Description: Vesicular stomatitis virus is a negative-stranded RNA virus. Its nucleoprotein (N) binds the viral genomic RNA and is involved in multiple functions including transcription, replication, and assembly. We have determined a 2.9 angstrom structure of a complex containing 10 molecules of the N protein and 90 bases of RNA. The RNA is tightly sequestered in a cavity at the interface between two lobes of the N protein. This serves to protect the RNA in the absence of polynucleotide synthesis. For the RNA to be accessed, some conformational change in the N protein should be necessary.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, Todd J -- Zhang, Xin -- Wertz, Gail W -- Luo, Ming -- AI050066/AI/NIAID NIH HHS/ -- R37 AI012464/AI/NIAID NIH HHS/ -- R37 AI012464-28/AI/NIAID NIH HHS/ -- R37 AI012464-29/AI/NIAID NIH HHS/ -- R37 AI012464-30/AI/NIAID NIH HHS/ -- R37 AI012464-31/AI/NIAID NIH HHS/ -- R37AI012464/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2006 Jul 21;313(5785):357-60. Epub 2006 Jun 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, School of Medicine, University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35294, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16778022" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleocapsid Proteins/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Viral/*chemistry/metabolism ; Ribonucleoproteins/*chemistry ; Sequence Alignment ; Vesicular stomatitis Indiana virus/*chemistry
    Print ISSN: 0036-8075
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  • 7
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    Ammonia channel couples glutaminase with transamidase reactions in GatCAB (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-01
    Description: The formation of glutaminyl transfer RNA (Gln-tRNA(Gln)) differs among the three domains of life. Most bacteria employ an indirect pathway to produce Gln-tRNA(Gln) by a heterotrimeric glutamine amidotransferase CAB (GatCAB) that acts on the misacylated Glu-tRNA(Gln). Here, we describe a series of crystal structures of intact GatCAB from Staphylococcus aureus in the apo form and in the complexes with glutamine, asparagine, Mn2+, and adenosine triphosphate analog. Two identified catalytic centers for the glutaminase and transamidase reactions are markedly distant but connected by a hydrophilic ammonia channel 30 A in length. Further, we show that the first U-A base pair in the acceptor stem and the D loop of tRNA(Gln) serve as identity elements essential for discrimination by GatCAB and propose a complete model for the overall concerted reactions to synthesize Gln-tRNA(Gln).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakamura, Akiyoshi -- Yao, Min -- Chimnaronk, Sarin -- Sakai, Naoki -- Tanaka, Isao -- New York, N.Y. -- Science. 2006 Jun 30;312(5782):1954-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16809541" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Amino Acid Sequence ; Aminoacyltransferases/metabolism ; Ammonia/*metabolism ; Apoenzymes/chemistry/metabolism ; Asparagine/metabolism ; Base Pairing ; Catalytic Domain ; Crystallography, X-Ray ; Glutaminase/metabolism ; Glutamine/*chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Magnesium/metabolism ; Manganese/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; RNA, Bacterial/chemistry/metabolism ; RNA, Transfer, Amino Acyl/chemistry/*metabolism ; RNA, Transfer, Gln/*chemistry/metabolism ; Staphylococcus aureus/*enzymology/genetics/metabolism
    Print ISSN: 0036-8075
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  • 8
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    Human hair growth deficiency is linked to a genetic defect in the phospholipase gene LIPH (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-11
    Description: The molecular mechanisms controlling human hair growth and scalp hair loss are poorly understood. By screening about 350,000 individuals in two populations from the Volga-Ural region of Russia, we identified a gene mutation in families who show an inherited form of hair loss and a hair growth defect. Affected individuals were homozygous for a deletion in the LIPH gene on chromosome 3q27, caused by short interspersed nuclear element-retrotransposon-mediated recombination. The LIPH gene is expressed in hair follicles and encodes a phospholipase called lipase H (alternatively known as membrane-associated phosphatidic acid-selective phospholipase A1alpha), an enzyme that regulates the production of bioactive lipids. These results suggest that lipase H participates in hair growth and development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kazantseva, Anastasiya -- Goltsov, Andrey -- Zinchenko, Rena -- Grigorenko, Anastasia P -- Abrukova, Anna V -- Moliaka, Yuri K -- Kirillov, Alexander G -- Guo, Zhiru -- Lyle, Stephen -- Ginter, Evgeny K -- Rogaev, Evgeny I -- K08-AR02179/AR/NIAMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):982-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, 303 Belmont Street, Worcester, MA 01604, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095700" target="_blank"〉PubMed〈/a〉
    Keywords: Alu Elements ; Amino Acid Sequence ; Base Sequence ; Chromosomes, Human, Pair 3/genetics ; Exons ; Female ; Gene Deletion ; Gene Expression ; Genetic Markers ; Hair/*growth & development ; Hair Follicle/enzymology ; Heterozygote ; Homozygote ; Humans ; Hypotrichosis/*genetics ; Lipase/chemistry/*genetics/metabolism ; Lipid Metabolism ; Lod Score ; Male ; Molecular Sequence Data ; Pedigree ; Protein Structure, Tertiary ; Recombination, Genetic ; Retroelements ; Russia ; Tandem Repeat Sequences
    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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  • 9
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    Global control of dimorphism and virulence in fungi (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-04-29
    Description: Microbial pathogens that normally inhabit our environment can adapt to thrive inside mammalian hosts. There are six dimorphic fungi that cause disease worldwide, which switch from nonpathogenic molds in soil to pathogenic yeast after spores are inhaled and exposed to elevated temperature. Mechanisms that regulate this switch remain obscure. We show that a hybrid histidine kinase senses host signals and triggers the transition from mold to yeast. The kinase also regulates cell-wall integrity, sporulation, and expression of virulence genes in vivo. This global regulator shapes how dimorphic fungal pathogens adapt to the mammalian host, which has broad implications for treating and preventing systemic fungal disease.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nemecek, Julie C -- Wuthrich, Marcel -- Klein, Bruce S -- New York, N.Y. -- Science. 2006 Apr 28;312(5773):583-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Microbiology and Immunology, University of Wisconsin Medical School, University of Wisconsin Hospital and Clinics, Madison, WI 53792, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16645097" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Blastomyces/cytology/enzymology/*genetics/*pathogenicity ; Blastomycosis/microbiology ; Coccidioides/enzymology/genetics/pathogenicity ; Fungal Proteins/genetics/physiology ; Gene Expression Regulation, Fungal ; Genes, Fungal ; Genetic Complementation Test ; Histoplasma/enzymology/genetics/pathogenicity ; Histoplasmosis/microbiology ; Lung Diseases, Fungal/microbiology ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Mutagenesis, Insertional ; Open Reading Frames ; Protein Kinases/chemistry/*genetics/*physiology ; RNA Interference ; Saccharomyces cerevisiae/genetics ; Soil Microbiology ; Spores, Fungal/physiology ; Temperature ; Virulence/genetics
    Print ISSN: 0036-8075
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  • 10
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    Evolutionary history of Salmonella typhi (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-25
    Description: For microbial pathogens, phylogeographic differentiation seems to be relatively common. However, the neutral population structure of Salmonella enterica serovar Typhi reflects the continued existence of ubiquitous haplotypes over millennia. In contrast, clinical use of fluoroquinolones has yielded at least 15 independent gyrA mutations within a decade and stimulated clonal expansion of haplotype H58 in Asia and Africa. Yet, antibiotic-sensitive strains and haplotypes other than H58 still persist despite selection for antibiotic resistance. Neutral evolution in Typhi appears to reflect the asymptomatic carrier state, and adaptive evolution depends on the rapid transmission of phenotypic changes through acute infections.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652035/" 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/PMC2652035/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roumagnac, Philippe -- Weill, Francois-Xavier -- Dolecek, Christiane -- Baker, Stephen -- Brisse, Sylvain -- Chinh, Nguyen Tran -- Le, Thi Anh Hong -- Acosta, Camilo J -- Farrar, Jeremy -- Dougan, Gordon -- Achtman, Mark -- 076962/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2006 Nov 24;314(5803):1301-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Infektionsbiologie, Department of Molecular Biology, Chariteplatz 1, 10117 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17124322" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Africa ; Alleles ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Asia ; *Biological Evolution ; Carrier State/*microbiology ; DNA Gyrase/genetics ; Drug Resistance, Bacterial ; Drug Resistance, Multiple, Bacterial ; Fluoroquinolones/pharmacology/therapeutic use ; *Genes, Bacterial ; Genetic Variation ; Haplotypes ; Humans ; Molecular Sequence Data ; Mutation ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Salmonella typhi/drug effects/*genetics ; Selection, Genetic ; Typhoid Fever/drug therapy/*microbiology
    Print ISSN: 0036-8075
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  • 11
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    Tequila, a neurotrypsin ortholog, regulates long-term memory formation in Drosophila (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-08-12
    Description: Mutations in the human neurotrypsin gene are associated with autosomal recessive mental retardation. To further understand the pathophysiological consequences of the lack of this serine protease, we studied Tequila (Teq), the Drosophila neurotrypsin ortholog, using associative memory as a behavioral readout. We found that teq inactivation resulted in a long-term memory (LTM)-specific defect. After LTM conditioning of wild-type flies, teq expression transiently increased in the mushroom bodies. Moreover, specific inhibition of teq expression in adult mushroom bodies resulted in a reversible LTM defect. Hence, the Teq pathway is essential for information processing in Drosophila.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Didelot, Gerard -- Molinari, Florence -- Tchenio, Paul -- Comas, Daniel -- Milhiet, Elodie -- Munnich, Arnold -- Colleaux, Laurence -- Preat, Thomas -- New York, N.Y. -- Science. 2006 Aug 11;313(5788):851-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genes et Dynamique des Systemes de Memoire, UMR CNRS 7637, Ecole Superieure de Physique et de Chimie Industrielles, 10 Rue Vauquelin 75005 Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16902143" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Conditioning, Classical ; Drosophila Proteins/chemistry/genetics/*physiology ; Drosophila melanogaster/genetics/*physiology ; Gene Expression ; Gene Expression Regulation ; Humans ; Learning ; *Memory ; Mifepristone/pharmacology ; Models, Animal ; Molecular Sequence Data ; Mushroom Bodies/anatomy & histology/physiology ; Mutation ; Odors ; RNA Interference ; RNA, Messenger/genetics/metabolism ; Serine Endopeptidases/chemistry/genetics/*physiology
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  • 12
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    Sequencing and analysis of Neanderthal genomic DNA (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-18
    Description: Our knowledge of Neanderthals is based on a limited number of remains and artifacts from which we must make inferences about their biology, behavior, and relationship to ourselves. Here, we describe the characterization of these extinct hominids from a new perspective, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis. Several lines of evidence indicate that the 65,250 base pairs of hominid sequence so far identified in the library are of Neanderthal origin, the strongest being the ascertainment of sequence identities between Neanderthal and chimpanzee at sites where the human genomic sequence is different. These results enabled us to calculate the human-Neanderthal divergence time based on multiple randomly distributed autosomal loci. Our analyses suggest that on average the Neanderthal genomic sequence we obtained and the reference human genome sequence share a most recent common ancestor approximately 706,000 years ago, and that the human and Neanderthal ancestral populations split approximately 370,000 years ago, before the emergence of anatomically modern humans. Our finding that the Neanderthal and human genomes are at least 99.5% identical led us to develop and successfully implement a targeted method for recovering specific ancient DNA sequences from metagenomic libraries. This initial analysis of the Neanderthal genome advances our understanding of the evolutionary relationship of Homo sapiens and Homo neanderthalensis and signifies the dawn of Neanderthal genomics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2583069/" 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/PMC2583069/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Noonan, James P -- Coop, Graham -- Kudaravalli, Sridhar -- Smith, Doug -- Krause, Johannes -- Alessi, Joe -- Chen, Feng -- Platt, Darren -- Paabo, Svante -- Pritchard, Jonathan K -- Rubin, Edward M -- 1-F32-GM074367/GM/NIGMS NIH HHS/ -- HL066681/HL/NHLBI NIH HHS/ -- R01 HG002772/HG/NHGRI NIH HHS/ -- R01 HG002772-01/HG/NHGRI NIH HHS/ -- R01 HG002772-1/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 17;314(5802):1113-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17110569" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Bone and Bones ; Cell Nucleus ; DNA/*genetics/isolation & purification ; DNA, Mitochondrial ; *Fossils ; Gene Pool ; Genome ; Genome, Human ; Genomic Library ; History, Ancient ; Hominidae/*genetics ; Humans ; Male ; Molecular Sequence Data ; Pan troglodytes/genetics ; Polymerase Chain Reaction ; Sequence Alignment ; *Sequence Analysis, DNA/methods ; Time
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  • 13
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    Engineering cooperativity in biomotor-protein assemblies (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-11
    Description: A biosynthetic approach was developed to control and probe cooperativity in multiunit biomotor assemblies by linking molecular motors to artificial protein scaffolds. This approach provides precise control over spatial and elastic coupling between motors. Cooperative interactions between monomeric kinesin-1 motors attached to protein scaffolds enhance hydrolysis activity and microtubule gliding velocity. However, these interactions are not influenced by changes in the elastic properties of the scaffold, distinguishing multimotor transport from that powered by unorganized monomeric motors. These results highlight the role of supramolecular architecture in determining mechanisms of collective transport.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Diehl, Michael R -- Zhang, Kechun -- Lee, Heun Jin -- Tirrell, David A -- New York, N.Y. -- Science. 2006 Mar 10;311(5766):1468-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA. diehl@rice.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16527982" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry ; Amino Acid Sequence ; Elasticity ; Elastin/chemistry ; Hydrolysis ; Kinesin/chemistry ; Microtubules/physiology ; Models, Biological ; Molecular Motor Proteins/*physiology ; Molecular Sequence Data ; Protein Engineering ; Protein Structure, Tertiary ; Proteins/chemistry/*physiology ; Recombinant Proteins/chemistry ; Structure-Activity Relationship
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  • 14
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    A bacterial protein enhances the release and efficacy of liposomal cancer drugs (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-25
    Description: Clostridium novyi-NT is an anaerobic bacterium that can infect hypoxic regions within experimental tumors. Because C. novyi-NT lyses red blood cells, we hypothesized that its membrane-disrupting properties could be exploited to enhance the release of liposome-encapsulated drugs within tumors. Here, we show that treatment of mice bearing large, established tumors with C. novyi-NT plus a single dose of liposomal doxorubicin often led to eradication of the tumors. The bacterial factor responsible for the enhanced drug release was identified as a previously unrecognized protein termed liposomase. This protein could potentially be incorporated into diverse experimental approaches for the specific delivery of chemotherapeutic agents to tumors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheong, Ian -- Huang, Xin -- Bettegowda, Chetan -- Diaz, Luis A Jr -- Kinzler, Kenneth W -- Zhou, Shibin -- Vogelstein, Bert -- CA062924/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 24;314(5803):1308-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and the Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins Kimmel Comprehensive Cancer Center, Baltimore, MD 21231, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17124324" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antineoplastic Agents/*administration & dosage/pharmacokinetics/therapeutic use ; Bacterial Proteins/chemistry/genetics/*metabolism ; Base Sequence ; Camptothecin/administration & dosage/analogs & ; derivatives/pharmacokinetics/therapeutic use ; Cell Line, Tumor ; Cloning, Molecular ; Clostridium/*chemistry/genetics ; Colorectal Neoplasms/*drug therapy ; Doxorubicin/*administration & dosage/pharmacokinetics/therapeutic use ; Drug Carriers ; Humans ; Lipase/chemistry/genetics/*metabolism ; Lipid Bilayers/chemistry ; Liposomes/chemistry/*metabolism ; Mice ; Molecular Sequence Data ; Mutation ; Neoplasm Transplantation ; Protein Structure, Tertiary
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  • 15
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    Large-scale sequence analysis of avian influenza isolates (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-01-28
    Description: The spread of H5N1 avian influenza viruses (AIVs) from China to Europe has raised global concern about their potential to infect humans and cause a pandemic. In spite of their substantial threat to human health, remarkably little AIV whole-genome information is available. We report here a preliminary analysis of the first large-scale sequencing of AIVs, including 2196 AIV genes and 169 complete genomes. We combine this new information with public AIV data to identify new gene alleles, persistent genotypes, compensatory mutations, and a potential virulence determinant.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Obenauer, John C -- Denson, Jackie -- Mehta, Perdeep K -- Su, Xiaoping -- Mukatira, Suraj -- Finkelstein, David B -- Xu, Xiequn -- Wang, Jinhua -- Ma, Jing -- Fan, Yiping -- Rakestraw, Karen M -- Webster, Robert G -- Hoffmann, Erich -- Krauss, Scott -- Zheng, Jie -- Zhang, Ziwei -- Naeve, Clayton W -- AI95357/AI/NIAID NIH HHS/ -- CA 21765/CA/NCI NIH HHS/ -- R01 GM061739/GM/NIGMS NIH HHS/ -- R01 GM069916/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Mar 17;311(5767):1576-80. Epub 2006 Jan 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439620" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds/virology ; Computational Biology ; *Genes, Viral ; Genome, Viral ; Humans ; Influenza A Virus, H1N1 Subtype/genetics ; Influenza A Virus, H2N2 Subtype/genetics ; Influenza A Virus, H3N2 Subtype/genetics ; Influenza A Virus, H3N8 Subtype/genetics ; Influenza A Virus, H5N1 Subtype/chemistry/*genetics/pathogenicity ; Influenza A Virus, H5N2 Subtype/genetics ; Influenza A Virus, H7N7 Subtype/genetics ; Influenza A Virus, H9N2 Subtype/genetics ; Influenza A virus/chemistry/*genetics/isolation & purification/pathogenicity ; Influenza in Birds/virology ; Influenza, Human/virology ; Molecular Sequence Data ; Mutation ; Phylogeny ; RNA, Viral/genetics ; Reassortant Viruses/genetics ; Sequence Analysis, DNA ; Viral Nonstructural Proteins/*chemistry/genetics ; Viral Proteins/chemistry/genetics ; Virulence Factors/*chemistry/genetics
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  • 16
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    Molecular phylogeny and evolution of morphology in the social amoebas (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-10-28
    Description: The social amoebas (Dictyostelia) display conditional multicellularity in a wide variety of forms. Despite widespread interest in Dictyostelium discoideum as a model system, almost no molecular data exist from the rest of the group. We constructed the first molecular phylogeny of the Dictyostelia with parallel small subunit ribosomal RNA and a-tubulin data sets, and we found that dictyostelid taxonomy requires complete revision. A mapping of characters onto the phylogeny shows that the dominant trend in dictyostelid evolution is increased size and cell type specialization of fruiting structures, with some complex morphologies evolving several times independently. Thus, the latter may be controlled by only a few genes, making their underlying mechanisms relatively easy to unravel.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2173941/" 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/PMC2173941/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schaap, Pauline -- Winckler, Thomas -- Nelson, Michaela -- Alvarez-Curto, Elisa -- Elgie, Barrie -- Hagiwara, Hiromitsu -- Cavender, James -- Milano-Curto, Alicia -- Rozen, Daniel E -- Dingermann, Theodor -- Mutzel, Rupert -- Baldauf, Sandra L -- 057137/Wellcome Trust/United Kingdom -- 076618/Wellcome Trust/United Kingdom -- BB/D013453/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- COD16760/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2006 Oct 27;314(5799):661-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Life Sciences, University of Dundee, DD15EH Dundee, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17068267" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Dictyosteliida/*classification/*cytology/genetics/growth & development ; Dictyostelium/classification/cytology/genetics/growth & development ; Genes, Protozoan ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/genetics ; Spores, Protozoan/cytology ; Tubulin/genetics
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  • 17
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    Exploiting the reversibility of natural product glycosyltransferase-catalyzed reactions (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-02
    Description: Glycosyltransferases (GTs), an essential class of ubiquitous enzymes, are generally perceived as unidirectional catalysts. In contrast, we report that four glycosyltransferases from two distinct natural product biosynthetic pathways-calicheamicin and vancomycin-readily catalyze reversible reactions, allowing sugars and aglycons to be exchanged with ease. As proof of the broader applicability of these new reactions, more than 70 differentially glycosylated calicheamicin and vancomycin variants are reported. This study suggests the reversibility of GT-catalyzed reactions may be general and useful for generating exotic nucleotide sugars, establishing in vitro GT activity in complex systems, and enhancing natural product diversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Changsheng -- Griffith, Byron R -- Fu, Qiang -- Albermann, Christoph -- Fu, Xun -- Lee, In-Kyoung -- Li, Lingjun -- Thorson, Jon S -- AI52218/AI/NIAID NIH HHS/ -- CA84374/CA/NCI NIH HHS/ -- GM70637/GM/NIGMS NIH HHS/ -- U19 CA113297/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2006 Sep 1;313(5791):1291-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, National Cooperative Drug Discovery Group Program, University of Wisconsin (UW)-Madison, 777 Highland Avenue, Madison, WI 53705-2222, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16946071" target="_blank"〉PubMed〈/a〉
    Keywords: Aminoglycosides/biosynthesis/chemistry/*metabolism ; Carbohydrate Sequence ; Catalysis ; Enediynes ; Glucosyltransferases/*metabolism ; Glycosylation ; Glycosyltransferases/genetics/*metabolism ; Micromonospora/enzymology/genetics ; Molecular Sequence Data ; Molecular Structure ; Nucleoside Diphosphate Sugars/metabolism ; Pentoses/metabolism ; Thymine Nucleotides/metabolism ; Vancomycin/*analogs & derivatives/biosynthesis/chemistry/metabolism
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  • 18
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    Structural basis for double-stranded RNA processing by Dicer (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-01-18
    Description: The specialized ribonuclease Dicer initiates RNA interference by cleaving double-stranded RNA (dsRNA) substrates into small fragments about 25 nucleotides in length. In the crystal structure of an intact Dicer enzyme, the PAZ domain, a module that binds the end of dsRNA, is separated from the two catalytic ribonuclease III (RNase III) domains by a flat, positively charged surface. The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA. Thus, Dicer itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Macrae, Ian J -- Zhou, Kaihong -- Li, Fei -- Repic, Adrian -- Brooks, Angela N -- Cande, W Zacheus -- Adams, Paul D -- Doudna, Jennifer A -- New York, N.Y. -- Science. 2006 Jan 13;311(5758):195-8.〈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/16410517" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Conserved Sequence ; Crystallography, X-Ray ; Giardia lamblia/enzymology ; Humans ; Lanthanoid Series Elements/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; RNA Interference ; RNA, Double-Stranded/*metabolism ; RNA, Protozoan/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Ribonuclease III/*chemistry/metabolism ; Schizosaccharomyces/genetics ; Structure-Activity Relationship
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  • 19
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    Structure of tracheal cytotoxin in complex with a heterodimeric pattern-recognition receptor (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-25
    Description: Tracheal cytotoxin (TCT), a naturally occurring fragment of Gram-negative peptidoglycan, is a potent elicitor of innate immune responses in Drosophila. It induces the heterodimerization of its recognition receptors, the peptidoglycan recognition proteins (PGRPs) LCa and LCx, which activates the immune deficiency pathway. The crystal structure at 2.1 angstrom resolution of TCT in complex with the ectodomains of PGRP-LCa and PGRP-LCx shows that TCT is bound to and presented by the LCx ectodomain for recognition by the LCa ectodomain; the latter lacks a canonical peptidoglycan-docking groove conserved in other PGRPs. The interface, revealed in atomic detail, between TCT and the receptor complex highlights the importance of the anhydro-containing disaccharide in bridging the two ectodomains together and the critical role of diaminopimelic acid as the specificity determinant for PGRP interaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Chung-I -- Chelliah, Yogarany -- Borek, Dominika -- Mengin-Lecreulx, Dominique -- Deisenhofer, Johann -- New York, N.Y. -- Science. 2006 Mar 24;311(5768):1761-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX 75390-9050, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16556841" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Carrier Proteins/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Cytotoxins/*chemistry/metabolism ; Drosophila melanogaster ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Peptidoglycan/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 20
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    The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-06-17
    Description: The Xist noncoding RNA is the key initiator of the process of X chromosome inactivation in eutherian mammals, but its precise function and origin remain unknown. Although Xist is well conserved among eutherians, until now, no homolog has been identified in other mammals. We show here that Xist evolved, at least partly, from a protein-coding gene and that the loss of protein-coding function of the proto-Xist coincides with the four flanking protein genes becoming pseudogenes. This event occurred after the divergence between eutherians and marsupials, which suggests that mechanisms of dosage compensation have evolved independently in both lineages.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Duret, Laurent -- Chureau, Corinne -- Samain, Sylvie -- Weissenbach, Jean -- Avner, Philip -- New York, N.Y. -- Science. 2006 Jun 16;312(5780):1653-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire de Biometrie et Biologie Evolutive (UMR 5558), CNRS and Universite Lyon 1, 16 rue Raphael Dubois, 69622 Villeurbanne Cedex, France. duret@biomserv.univ-lyon1.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16778056" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cattle/genetics ; Chickens/genetics ; Dogs/genetics ; *Evolution, Molecular ; Exons ; Female ; Humans ; Male ; Mammals/*genetics ; Mice/genetics ; Molecular Sequence Data ; Opossums/genetics ; Phylogeny ; *Pseudogenes ; RNA, Long Noncoding ; RNA, Untranslated/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Vertebrates/*genetics ; X Chromosome Inactivation ; Xenopus/genetics
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  • 21
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    Escherichia coli induces DNA double-strand breaks in eukaryotic cells (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-08-12
    Description: Transient infection of eukaryotic cells with commensal and extraintestinal pathogenic Escherichia coli of phylogenetic group B2 blocks mitosis and induces megalocytosis. This trait is linked to a widely spread genomic island that encodes giant modular nonribosomal peptide and polyketide synthases. Contact with E. coli expressing this gene cluster causes DNA double-strand breaks and activation of the DNA damage checkpoint pathway, leading to cell cycle arrest and eventually to cell death. Discovery of hybrid peptide-polyketide genotoxins in E. coli will change our view on pathogenesis and commensalism and open new biotechnological applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nougayrede, Jean-Philippe -- Homburg, Stefan -- Taieb, Frederic -- Boury, Michele -- Brzuszkiewicz, Elzbieta -- Gottschalk, Gerhard -- Buchrieser, Carmen -- Hacker, Jorg -- Dobrindt, Ulrich -- Oswald, Eric -- New York, N.Y. -- Science. 2006 Aug 11;313(5788):848-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉INRA, UMR1225, Ecole Nationale Veterinaire de Toulouse, Toulouse F-31076, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16902142" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ataxia Telangiectasia Mutated Proteins ; Cell Cycle ; Cell Cycle Proteins/metabolism ; Cell Death ; Cell Line ; Cell Nucleus/chemistry ; Cytotoxins/*metabolism ; DNA/analysis ; *DNA Damage ; DNA-Binding Proteins/metabolism ; Escherichia coli/genetics/*pathogenicity/*physiology ; G2 Phase ; *Genomic Islands ; HeLa Cells ; Histones/metabolism ; Humans ; Intestinal Mucosa/cytology/microbiology ; Molecular Sequence Data ; Mutagenesis ; Mutagens/*metabolism ; Peptides/*metabolism ; Phosphorylation ; Polyketide Synthases/genetics ; Protein-Serine-Threonine Kinases/metabolism ; Rats ; Signal Transduction ; Tumor Suppressor Proteins/metabolism
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    Genome of Rice Cluster I archaea--the key methane producers in the rice rhizosphere (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-22
    Description: Rice fields are a global source of the greenhouse gas methane, which is produced by methanogenic archaea, and by methanogens of Rice Cluster I (RC-I) in particular. RC-I methanogens are not yet available in pure culture, and the mechanistic reasons for their prevalence in rice fields are unknown. We reconstructed a complete RC-I genome (3.18 megabases) using a metagenomic approach. Sequence analysis demonstrated an aerotolerant, H2/CO2-dependent lifestyle and enzymatic capacities for carbohydrate metabolism and assimilatory sulfate reduction, hitherto unknown among methanogens. These capacities and a unique set of antioxidant enzymes and DNA repair mechanisms as well as oxygen-insensitive enzymes provide RC-I with a selective advantage over other methanogens in its habitats, thereby explaining the prevalence of RC-I methanogens in the rice rhizosphere.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Erkel, Christoph -- Kube, Michael -- Reinhardt, Richard -- Liesack, Werner -- New York, N.Y. -- Science. 2006 Jul 21;313(5785):370-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16857943" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/biosynthesis/metabolism ; Carbohydrate Metabolism ; DNA Repair ; Euryarchaeota/classification/*genetics/metabolism/physiology ; *Genome, Archaeal ; Genomics ; Glycolysis ; Methane/*biosynthesis ; Methanomicrobiales/classification/genetics/metabolism/physiology ; Methanosarcinales/classification/genetics/metabolism/physiology ; Molecular Sequence Data ; Oryza/*microbiology ; Oxidative Stress ; Pyruvic Acid/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; *Soil Microbiology ; Sulfates/metabolism ; Sulfur/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Crystal structure of a divalent metal ion transporter CorA at 2.9 angstrom resolution (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-22
    Description: CorA family members are ubiquitously distributed transporters of divalent metal cations and are considered to be the primary Mg2+ transporter of Bacteria and Archaea. We have determined a 2.9 angstrom resolution structure of CorA from Thermotoga maritima that reveals a pentameric cone-shaped protein. Two potential regulatory metal binding sites are found in the N-terminal domain that bind both Mg2+ and Co2+. The structure of CorA supports an efflux system involving dehydration and rehydration of divalent metal ions potentially mediated by a ring of conserved aspartate residues at the cytoplasmic entrance and a carbonyl funnel at the periplasmic side of the pore.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eshaghi, Said -- Niegowski, Damian -- Kohl, Andreas -- Martinez Molina, Daniel -- Lesley, Scott A -- Nordlund, Par -- New York, N.Y. -- Science. 2006 Jul 21;313(5785):354-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden. Said.Eshaghi@ki.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16857941" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Cation Transport Proteins/*chemistry/metabolism ; Chlorides/analysis/metabolism ; Cobalt/chemistry/*metabolism ; Crystallography, X-Ray ; Hydrophobic and Hydrophilic Interactions ; Magnesium/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; Thermotoga maritima/*chemistry ; Water/chemistry
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    Genome sequence diversity and clues to the evolution of variola (smallpox) virus (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-29
    Description: Comparative genomics of 45 epidemiologically varied variola virus isolates from the past 30 years of the smallpox era indicate low sequence diversity, suggesting that there is probably little difference in the isolates' functional gene content. Phylogenetic clustering inferred three clades coincident with their geographical origin and case-fatality rate; the latter implicated putative proteins that mediate viral virulence differences. Analysis of the viral linear DNA genome suggests that its evolution involved direct descent and DNA end-region recombination events. Knowing the sequences will help understand the viral proteome and improve diagnostic test precision, therapeutics, and systems for their assessment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Esposito, Joseph J -- Sammons, Scott A -- Frace, A Michael -- Osborne, John D -- Olsen-Rasmussen, Melissa -- Zhang, Ming -- Govil, Dhwani -- Damon, Inger K -- Kline, Richard -- Laker, Miriam -- Li, Yu -- Smith, Geoffrey L -- Meyer, Hermann -- Leduc, James W -- Wohlhueter, Robert M -- G0501257/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2006 Aug 11;313(5788):807-12. Epub 2006 Jul 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Preparedness, Detection, and Control of Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA. jesposito@cdc.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16873609" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Viral/*genetics ; Disease Outbreaks ; *Evolution, Molecular ; Gene Deletion ; *Genetic Variation ; *Genome, Viral ; Genomics ; Humans ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Proteome/analysis/genetics ; Recombination, Genetic ; Sequence Analysis, DNA ; Smallpox/epidemiology/mortality/*virology ; Variola virus/classification/*genetics/isolation & purification/pathogenicity ; Viral Proteins/chemistry/genetics ; Virulence/genetics
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    Aneuploidy and isochromosome formation in drug-resistant Candida albicans (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-07-22
    Description: Resistance to the limited number of available antifungal drugs is a serious problem in the treatment of Candida albicans. We found that aneuploidy in general and a specific segmental aneuploidy, consisting of an isochromosome composed of the two left arms of chromosome 5, were associated with azole resistance. The isochromosome forms around a single centromere flanked by an inverted repeat and was found as an independent chromosome or fused at the telomere to a full-length homolog of chromosome 5. Increases and decreases in drug resistance were strongly associated with gain and loss of this isochromosome, which bears genes expressing the enzyme in the ergosterol pathway targeted by azole drugs, efflux pumps, and a transcription factor that positively regulates a subset of efflux pump genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1717021/" 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/PMC1717021/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Selmecki, Anna -- Forche, Anja -- Berman, Judith -- DE10641-S/DE/NIDCR NIH HHS/ -- R01 AI062427/AI/NIAID NIH HHS/ -- R01 AIO62427/PHS HHS/ -- New York, N.Y. -- Science. 2006 Jul 21;313(5785):367-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Cell Biology, and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16857942" target="_blank"〉PubMed〈/a〉
    Keywords: *Aneuploidy ; Antifungal Agents/*pharmacology ; Azoles/pharmacology ; Candida albicans/*drug effects/*genetics/growth & development ; Centromere/ultrastructure ; Chromosomes, Fungal ; Cytochrome P-450 Enzyme System/genetics/metabolism ; Drug Resistance, Fungal/*genetics ; Ergosterol/biosynthesis ; Fluconazole/*pharmacology ; Fungal Proteins/genetics/metabolism ; Gene Dosage ; Gene Expression Profiling ; Genes, Fungal ; *Isochromosomes ; Karyotyping ; Molecular Sequence Data ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Transcription Factors/genetics/metabolism ; Trisomy
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    Anaphase inactivation of the spindle checkpoint (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-07-11
    Description: The spindle checkpoint delays cell cycle progression until microtubules attach each pair of sister chromosomes to opposite poles of the mitotic spindle. Following sister chromatid separation, however, the checkpoint ignores chromosomes whose kinetochores are attached to only one spindle pole, a state that activates the checkpoint prior to metaphase. We demonstrate that, in budding yeast, mutual inhibition between the anaphase-promoting complex (APC) and Mps1, an essential component of the checkpoint, leads to sustained inactivation of the spindle checkpoint. Mps1 protein abundance decreases in anaphase, and Mps1 is a target of the APC. Furthermore, expression of Mps1 in anaphase, or repression of the APC in anaphase, reactivates the spindle checkpoint. This APC-Mps1 feedback circuit allows cells to irreversibly inactivate the checkpoint during anaphase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Palframan, William J -- Meehl, Janet B -- Jaspersen, Sue L -- Winey, Mark -- Murray, Andrew W -- GM43987/GM/NIGMS NIH HHS/ -- GM51312/GM/NIGMS NIH HHS/ -- R37 GM043987/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Aug 4;313(5787):680-4. Epub 2006 Jul 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16825537" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anaphase/*physiology ; Anaphase-Promoting Complex-Cyclosome ; Cdc20 Proteins ; Cell Cycle Proteins/metabolism ; Chromosomes, Fungal/physiology ; Feedback, Physiological ; GTP-Binding Proteins/metabolism ; Kinetochores/physiology ; Mad2 Proteins ; Mitosis ; Molecular Sequence Data ; Nuclear Proteins/metabolism ; Phosphorylation ; Protein-Serine-Threonine Kinases/genetics/*metabolism ; Protein-Tyrosine Kinases/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/*cytology/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Securin ; Spindle Apparatus/*physiology ; Ubiquitin-Protein Ligase Complexes/*metabolism
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    Nitrogen fixation at 92 degrees C by a hydrothermal vent archaeon (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-12-16
    Description: A methanogenic archaeon isolated from deep-sea hydrothermal vent fluid was found to reduce N(2) to NH(3) at up to 92 degrees C, which is 28 degrees C higher than the current upper temperature limit of biological nitrogen fixation. The 16S ribosomal RNA gene of the hyperthermophilic nitrogen fixer, designated FS406-22, was 99% similar to that of non-nitrogen fixing Methanocaldococcus jannaschii DSM 2661. At its optimal growth temperature of 90 degrees C, FS406-22 incorporated (15)N(2) and expressed nifH messenger RNA. This increase in the temperature limit of nitrogen fixation could reveal a broader range of conditions for life in the subseafloor biosphere and other nitrogen-limited ecosystems than previously estimated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mehta, Mausmi P -- Baross, John A -- New York, N.Y. -- Science. 2006 Dec 15;314(5806):1783-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Oceanography, University of Washington, Seattle, WA 98195, USA. mausmi@alum.mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17170307" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Archaea/classification/genetics/*isolation & purification/*metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Base Sequence ; *Ecosystem ; Genes, Archaeal ; Genes, rRNA ; Geologic Sediments/microbiology ; *Hot Temperature ; Molecular Sequence Data ; Nitrogen/metabolism ; *Nitrogen Fixation/genetics ; Nitrogenase/chemistry/*genetics/metabolism ; Operon ; Oxidation-Reduction ; Oxidoreductases/chemistry/genetics/metabolism ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Volcanic Eruptions
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    Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-04-08
    Description: Biological responses to histone methylation critically depend on the faithful readout and transduction of the methyl-lysine signal by "effector" proteins, yet our understanding of methyl-lysine recognition has so far been limited to the study of histone binding by chromodomain and WD40-repeat proteins. The double tudor domain of JMJD2A, a Jmjc domain-containing histone demethylase, binds methylated histone H3-K4 and H4-K20. We found that the double tudor domain has an interdigitated structure, and the unusual fold is required for its ability to bind methylated histone tails. The cocrystal structure of the JMJD2A double tudor domain with a trimethylated H3-K4 peptide reveals that the trimethyl-K4 is bound in a cage of three aromatic residues, two of which are from the tudor-2 motif, whereas the binding specificity is determined by side-chain interactions involving amino acids from the tudor-1 motif. Our study provides mechanistic insights into recognition of methylated histone tails by tudor domains and reveals the structural intricacy of methyl-lysine recognition by two closely spaced effector domains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Ying -- Fang, Jia -- Bedford, Mark T -- Zhang, Yi -- Xu, Rui-Ming -- DK62248/DK/NIDDK NIH HHS/ -- GM 63718/GM/NIGMS NIH HHS/ -- GM68804/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 May 5;312(5774):748-51. Epub 2006 Apr 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16601153" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Histones/*chemistry/*metabolism ; Humans ; Hydrogen Bonding ; Jumonji Domain-Containing Histone Demethylases ; Lysine/metabolism ; Methylation ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Oxidoreductases, N-Demethylating ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Static Electricity ; Transcription Factors/*chemistry/genetics/*metabolism
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    BKCa-Cav channel complexes mediate rapid and localized Ca2+-activated K+ signaling (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-10-28
    Description: Large-conductance calcium- and voltage-activated potassium channels (BKCa) are dually activated by membrane depolarization and elevation of cytosolic calcium ions (Ca2+). Under normal cellular conditions, BKCa channel activation requires Ca2+ concentrations that typically occur in close proximity to Ca2+ sources. We show that BKCa channels affinity-purified from rat brain are assembled into macromolecular complexes with the voltage-gated calcium channels Cav1.2 (L-type), Cav2.1 (P/Q-type), and Cav2.2 (N-type). Heterologously expressed BKCa-Cav complexes reconstitute a functional "Ca2+ nanodomain" where Ca2+ influx through the Cav channel activates BKCa in the physiological voltage range with submillisecond kinetics. Complex formation with distinct Cav channels enables BKCa-mediated membrane hyperpolarization that controls neuronal firing pattern and release of hormones and transmitters in the central nervous system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berkefeld, Henrike -- Sailer, Claudia A -- Bildl, Wolfgang -- Rohde, Volker -- Thumfart, Jorg-Oliver -- Eble, Silke -- Klugbauer, Norbert -- Reisinger, Ellen -- Bischofberger, Josef -- Oliver, Dominik -- Knaus, Hans-Gunther -- Schulte, Uwe -- Fakler, Bernd -- New York, N.Y. -- Science. 2006 Oct 27;314(5799):615-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17068255" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Brain Chemistry ; CHO Cells ; Calcium/*metabolism ; Calcium Channels, L-Type/drug effects/isolation & purification/*metabolism ; Calcium Channels, N-Type/drug effects/isolation & purification/*metabolism ; Calcium Signaling ; Chromaffin Cells/drug effects/metabolism ; Cricetinae ; Cricetulus ; Egtazic Acid/analogs & derivatives/pharmacology ; Large-Conductance Calcium-Activated Potassium Channels/drug effects/isolation & ; purification/*metabolism ; Membrane Potentials/drug effects ; Molecular Sequence Data ; Patch-Clamp Techniques ; Potassium/*metabolism ; Rats ; *Signal Transduction ; Transfection ; Xenopus
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    Protrudin induces neurite formation by directional membrane trafficking (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-11-04
    Description: Guanosine triphosphatases of the Rab family are key regulators of membrane trafficking, with Rab11 playing a specific role in membrane recycling. We identified a mammalian protein, protrudin, that promoted neurite formation through interaction with the guanosine diphosphate (GDP)-bound form of Rab11. Phosphorylation of protrudin by extracellular signal-regulated kinase (ERK) in response to nerve growth factor promoted protrudin association with Rab11-GDP. Down-regulation of protrudin by RNA interference induced membrane extension in all directions and inhibited neurite formation. Thus, protrudin regulates Rab11-dependent membrane recycling to promote the directional membrane trafficking required for neurite formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shirane, Michiko -- Nakayama, Keiichi I -- New York, N.Y. -- Science. 2006 Nov 3;314(5800):818-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17082457" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Carrier Proteins/chemistry/genetics/*metabolism ; Cell Adhesion Molecules/metabolism ; Cell Line ; Cell Membrane/*metabolism ; Extracellular Signal-Regulated MAP Kinases/metabolism ; Guanosine Diphosphate/metabolism ; HeLa Cells ; Humans ; MAP Kinase Kinase 1/metabolism ; Membrane Proteins ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Nerve Growth Factor/pharmacology/physiology ; Neurites/*physiology ; PC12 Cells ; Phosphorylation ; RNA Interference ; Rats ; Recombinant Fusion Proteins/chemistry/metabolism ; Vesicular Transport Proteins ; rab GTP-Binding Proteins/metabolism
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    From the genome to the proteome: uncovering peptides in the Apis brain (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-10-28
    Description: Neuropeptides, critical brain peptides that modulate animal behavior by affecting the activity of almost every neuronal circuit, are inherently difficult to predict directly from a nascent genome sequence because of extensive posttranslational processing. The combination of bioinformatics and proteomics allows unprecedented neuropeptide discovery from an unannotated genome. Within the Apis mellifera genome, we have inferred more than 200 neuropeptides and have confirmed the sequences of 100 peptides. This study lays the groundwork for future molecular studies of Apis neuropeptides with the identification of 36 genes, 33 of which were previously unreported.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hummon, Amanda B -- Richmond, Timothy A -- Verleyen, Peter -- Baggerman, Geert -- Huybrechts, Jurgen -- Ewing, Michael A -- Vierstraete, Evy -- Rodriguez-Zas, Sandra L -- Schoofs, Liliane -- Robinson, Gene E -- Sweedler, Jonathan V -- DC006395/DC/NIDCD NIH HHS/ -- GM068946/GM/NIGMS NIH HHS/ -- NS31609/NS/NINDS NIH HHS/ -- P30 DA01830/DA/NIDA NIH HHS/ -- P30 DA018310/DA/NIDA NIH HHS/ -- R01 GM068946/GM/NIGMS NIH HHS/ -- R01 NS031609/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2006 Oct 27;314(5799):647-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Illinois, Urbana, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17068263" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bees/*chemistry/*genetics ; Brain Chemistry ; Codon ; Computational Biology ; *Genes, Insect ; Genome, Insect ; Insect Proteins/*chemistry/*genetics ; Mass Spectrometry ; Molecular Sequence Data ; Neuropeptides/*chemistry/*genetics ; Protein Precursors/chemistry/genetics ; Proteome
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    Autophagic fungal cell death is necessary for infection by the rice blast fungus (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-04-29
    Description: Rice blast is caused by the fungus Magnaporthe grisea, which elaborates specialized infection cells called appressoria to penetrate the tough outer cuticle of the rice plant Oryza sativa. We found that the formation of an appressorium required, sequentially, the completion of mitosis, nuclear migration, and death of the conidium (fungal spore) from which the infection originated. Genetic intervention during mitosis prevented both appressorium development and conidium death. Impairment of autophagy, by the targeted mutation of the MgATG8 gene, arrested conidial cell death but rendered the fungus nonpathogenic. Thus, the initiation of rice blast requires autophagic cell death of the conidium.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Veneault-Fourrey, Claire -- Barooah, Madhumita -- Egan, Martin -- Wakley, Gavin -- Talbot, Nicholas J -- New York, N.Y. -- Science. 2006 Apr 28;312(5773):580-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biosciences, University of Exeter, Washington Singer Laboratories, Perry Road, Exeter EX4 4QG, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16645096" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Autophagy ; Benomyl/pharmacology ; Cell Nucleus/physiology ; Cell Nucleus Division ; Genes, Fungal ; Hydroxyurea/pharmacology ; Magnaporthe/*cytology/genetics/pathogenicity/*physiology ; Microtubule-Associated Proteins/genetics/physiology ; Mitosis/drug effects ; Molecular Sequence Data ; Morphogenesis ; Mutation ; Oryza/*microbiology ; Plant Diseases/*microbiology ; Spores, Fungal/cytology/*physiology
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    Ancient noncoding elements conserved in the human genome (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-12-23
    Description: Cartilaginous fishes represent the living group of jawed vertebrates that diverged from the common ancestor of human and teleost fish lineages about 530 million years ago. We generated approximately 1.4x genome sequence coverage for a cartilaginous fish, the elephant shark (Callorhinchus milii), and compared this genome with the human genome to identify conserved noncoding elements (CNEs). The elephant shark sequence revealed twice as many CNEs as were identified by whole-genome comparisons between teleost fishes and human. The ancient vertebrate-specific CNEs in the elephant shark and human genomes are likely to play key regulatory roles in vertebrate gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Venkatesh, Byrappa -- Kirkness, Ewen F -- Loh, Yong-Hwee -- Halpern, Aaron L -- Lee, Alison P -- Johnson, Justin -- Dandona, Nidhi -- Viswanathan, Lakshmi D -- Tay, Alice -- Venter, J Craig -- Strausberg, Robert L -- Brenner, Sydney -- New York, N.Y. -- Science. 2006 Dec 22;314(5807):1892.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673. mcbbv@imcb.a-star.edu.sg〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185593" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; *Conserved Sequence ; DNA, Intergenic ; Enhancer Elements, Genetic ; Evolution, Molecular ; Genome ; *Genome, Human ; Humans ; Molecular Sequence Data ; *Regulatory Sequences, Nucleic Acid ; Sharks/*genetics ; Takifugu/genetics ; Zebrafish/genetics
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    P[acman]: a BAC transgenic platform for targeted insertion of large DNA fragments in D. melanogaster (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-02
    Description: We describe a transgenesis platform for Drosophila melanogaster that integrates three recently developed technologies: a conditionally amplifiable bacterial artificial chromosome (BAC), recombineering, and bacteriophage PhiC31-mediated transgenesis. The BAC is maintained at low copy number, facilitating plasmid maintenance and recombineering, but is induced to high copy number for plasmid isolation. Recombineering allows gap repair and mutagenesis in bacteria. Gap repair efficiently retrieves DNA fragments up to 133 kilobases long from P1 or BAC clones. PhiC31-mediated transgenesis integrates these large DNA fragments at specific sites in the genome, allowing the rescue of lethal mutations in the corresponding genes. This transgenesis platform should greatly facilitate structure/function analyses of most Drosophila genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Venken, Koen J T -- He, Yuchun -- Hoskins, Roger A -- Bellen, Hugo J -- GM067858-05/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Dec 15;314(5806):1747-51. Epub 2006 Nov 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17138868" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; *Chromosomes, Artificial, Bacterial ; Cloning, Molecular/*methods ; DNA Repair ; *DNA Transposable Elements ; Drosophila melanogaster/*genetics ; *Gene Transfer Techniques ; Genes, Insect ; Genetic Vectors ; Molecular Sequence Data ; Mutagenesis ; Plasmids ; Recombination, Genetic ; Siphoviridae/*genetics ; Transgenes ; Transposases/metabolism
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    JETLAG resets the Drosophila circadian clock by promoting light-induced degradation of TIMELESS (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-06-24
    Description: Organisms ranging from bacteria to humans synchronize their internal clocks to daily cycles of light and dark. Photic entrainment of the Drosophila clock is mediated by proteasomal degradation of the clock protein TIMELESS (TIM). We have identified mutations in jetlag-a gene coding for an F-box protein with leucine-rich repeats-that result in reduced light sensitivity of the circadian clock. Mutant flies show rhythmic behavior in constant light, reduced phase shifts in response to light pulses, and reduced light-dependent degradation of TIM. Expression of JET along with the circadian photoreceptor cryptochrome (CRY) in cultured S2R cells confers light-dependent degradation onto TIM, thereby reconstituting the acute response + of the circadian clock to light in a cell culture system. Our results suggest that JET is essential for resetting the clock by transmitting light signals from CRY to TIM.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2767177/" 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/PMC2767177/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koh, Kyunghee -- Zheng, Xiangzhong -- Sehgal, Amita -- NS048471/NS/NINDS NIH HHS/ -- R01 NS048471/NS/NINDS NIH HHS/ -- R01 NS048471-02/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2006 Jun 23;312(5781):1809-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Neuroscience, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16794082" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Cells, Cultured ; *Circadian Rhythm ; Cryptochromes ; Drosophila/chemistry/genetics/physiology ; Drosophila Proteins/chemistry/*genetics/*metabolism/*physiology ; Drosophila melanogaster/chemistry/*genetics/*physiology ; Eye Proteins/metabolism ; F-Box Proteins/chemistry/*genetics/*physiology ; Female ; *Light ; Male ; Models, Biological ; Molecular Sequence Data ; Mutation ; Protein Structure, Tertiary ; Receptors, G-Protein-Coupled/metabolism ; Transgenes ; Ubiquitin/metabolism
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    Antibody class switching mediated by yeast endonuclease-generated DNA breaks (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-12-16
    Description: Antibody class switching in activated B cells uses class switch recombination (CSR), which joins activation-induced cytidine deaminase (AID)-dependent double-strand breaks (DSBs) within two large immunoglobulin heavy chain (IgH) locus switch (S) regions that lie up to 200 kilobases apart. To test postulated roles of S regions and AID in CSR, we generated mutant B cells in which donor Smu and accepter Sgamma1 regions were replaced with yeast I-SceI endonuclease sites. We found that site-specific I-SceI DSBs mediate recombinational IgH locus class switching from IgM to IgG1 without S regions or AID. We propose that CSR evolved to exploit a general DNA repair process that promotes joining of widely separated DSBs within a chromosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zarrin, Ali A -- Del Vecchio, Catherine -- Tseng, Eva -- Gleason, Megan -- Zarin, Payam -- Tian, Ming -- Alt, Frederick W -- 2P01AI031541-15/AI/NIAID NIH HHS/ -- P01CA092625-05/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2007 Jan 19;315(5810):377-81. Epub 2006 Dec 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Children's Hospital, CBR Institute for Biomedical Research, and Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17170253" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; B-Lymphocytes/*immunology ; Base Sequence ; Cell Line ; Cytidine Deaminase/*metabolism ; *DNA Breaks, Double-Stranded ; DNA Repair ; Deoxyribonucleases, Type II Site-Specific/genetics/*metabolism ; Embryonic Stem Cells ; Gene Targeting ; Genes, Immunoglobulin Heavy Chain ; Hybridomas ; *Immunoglobulin Class Switching ; Immunoglobulin G/biosynthesis/genetics ; Immunoglobulin M/biosynthesis/genetics ; *Immunoglobulin Switch Region ; Lymphocyte Activation ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Mutation ; Recombination, Genetic ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae Proteins
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    Untemplated oligoadenylation promotes degradation of RISC-cleaved transcripts (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-12-23
    Description: Double-stranded RNA, processed to small interfering RNAs (siRNAs) by Dicer and incorporated into the RNA-induced silencing complex (RISC), triggers gene silencing by a variety of pathways in eukaryotes. RNA interference involving the degradation of homologous transcripts is the best-characterized mechanism. However, the fate of the RNA fragments resulting from siRNA-directed cleavage is poorly understood. We have identified a gene (MUT68) in the unicellular green alga Chlamydomonas reinhardtii that is required for the efficient decay of siRNA-targeted transcripts. MUT68 encodes a noncanonical polyadenylate polymerase that adds untemplated adenines to the 5' RNA fragments after siRNA-mediated cleavage and appears to stimulate their exosome-dependent degradation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ibrahim, Fadia -- Rohr, Jennifer -- Jeong, Won-Joong -- Hesson, Jennifer -- Cerutti, Heriberto -- GM62915/GM/NIGMS NIH HHS/ -- R01 GM062915-06/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Dec 22;314(5807):1893.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biological Sciences and Plant Science Initiative, University of Nebraska, Lincoln, NE 68588, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185594" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine Nucleotides/*metabolism ; Animals ; Chlamydomonas reinhardtii/enzymology/*genetics/*metabolism ; Exoribonucleases/metabolism ; Molecular Sequence Data ; Oligoribonucleotides/*metabolism ; Polynucleotide Adenylyltransferase/genetics/*metabolism ; RNA, Messenger/genetics/*metabolism ; RNA, Small Interfering/metabolism ; RNA-Induced Silencing Complex/*metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Templates, Genetic ; Transgenes ; Tryptophan Synthase/genetics ; Uracil Nucleotides/metabolism
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    A plant peptide encoded by CLV3 identified by in situ MALDI-TOF MS analysis (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-08-12
    Description: The Arabidopsis CLAVATA3 (CLV3) gene encodes a stem cell-specific protein presumed to be a precursor of a secreted peptide hormone. Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) applied to in situ Arabidopsis tissues determined the structure of a modified 12-amino acid peptide (MCLV3), which was derived from a conserved motif in the CLV3 sequence. Synthetic MCLV3 induced shoot and root meristem consumption as cells differentiated into other organs, displaying the typical phenotype of transgenic plants overexpressing CLV3. These results suggest that the functional peptide of CLV3 is MCLV3.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kondo, Tatsuhiko -- Sawa, Shinichiro -- Kinoshita, Atsuko -- Mizuno, Satoko -- Kakimoto, Tatsuo -- Fukuda, Hiroo -- Sakagami, Youji -- New York, N.Y. -- Science. 2006 Aug 11;313(5788):845-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Bio-Agricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16902141" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis/*cytology/genetics/metabolism ; Arabidopsis Proteins/*chemistry/genetics/*metabolism/pharmacology ; Cell Differentiation ; Cells, Cultured ; Hydroxyproline/chemistry ; Meristem/*cytology/drug effects/metabolism ; Molecular Sequence Data ; Oligopeptides/chemistry/*metabolism/pharmacology ; Plant Roots/growth & development ; Plants, Genetically Modified ; Signal Transduction ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Stem Cells/cytology
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    An SNP caused loss of seed shattering during rice domestication (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-04-15
    Description: Loss of seed shattering was a key event in the domestication of major cereals. We revealed that the qSH1 gene, a major quantitative trait locus of seed shattering in rice, encodes a BEL1-type homeobox gene and demonstrated that a single-nucleotide polymorphism (SNP) in the 5' regulatory region of the qSH1 gene caused loss of seed shattering owing to the absence of abscission layer formation. Haplotype analysis and association analysis in various rice collections revealed that the SNP was highly associated with shattering among japonica subspecies of rice, implying that it was a target of artificial selection during rice domestication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Konishi, Saeko -- Izawa, Takeshi -- Lin, Shao Yang -- Ebana, Kaworu -- Fukuta, Yoshimichi -- Sasaki, Takuji -- Yano, Masahiro -- New York, N.Y. -- Science. 2006 Jun 2;312(5778):1392-6. Epub 2006 Apr 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of the Society for Techno-Innovation of Agriculture, Forestry, and Fisheries, 446-1 Ippaizuka, Kamiyokoba Tsukuba, Ibaraki 305-0854, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16614172" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*history ; Alleles ; Chromosome Mapping ; Chromosomes, Plant ; Crops, Agricultural/*genetics/history ; Genes, Plant ; History, Ancient ; Humans ; Molecular Sequence Data ; Oryza/*genetics/history ; Plant Proteins/genetics ; *Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; *Seeds ; Transcription Factors/genetics
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    Silk genes support the single origin of orb webs (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-06-24
    Description: The orb web is a spectacular evolutionary innovation that enables spiders to catch flying prey. This elegant, geometric structure is woven with silk fibers that are renowned for their superior mechanical properties. We used silk gland expression libraries to address a long-standing controversy concerning the evolution of the orb-web architecture. Contrary to the view that the orb-web design evolved multiple times, we found that the distribution and phylogeny of silk proteins support a single, ancient origin of the orb web at least 136 million years ago. Furthermore, we substantially expanded the repository of silk sequences that can be used for the synthesis of high-performance biomaterials.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garb, Jessica E -- Dimauro, Teresa -- Vo, Victoria -- Hayashi, Cheryl Y -- New York, N.Y. -- Science. 2006 Jun 23;312(5781):1762.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of California, Riverside, CA 92521, USA. jessica.garb@ucr.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16794073" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; DNA, Complementary ; Fibroins/*genetics ; *Genes ; Molecular Sequence Data ; Phylogeny ; Silk/*genetics ; Spiders/classification/*genetics/physiology
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    A virus reveals population structure and recent demographic history of its carnivore host (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-01-28
    Description: Directly transmitted parasites often provide substantial information about the temporal and spatial characteristics of host-to-host contact. Here, we demonstrate that a fast-evolving virus (feline immunodeficiency virus, FIV) can reveal details of the contemporary population structure and recent demographic history of its natural wildlife host (Puma concolor) that were not apparent from host genetic data and would be impossible to obtain by other means. We suggest that rapidly evolving pathogens may provide a complementary tool for studying population dynamics of their hosts in "shallow" time.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Biek, Roman -- Drummond, Alexei J -- Poss, Mary -- New York, N.Y. -- Science. 2006 Jan 27;311(5760):538-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA. rbiek@emory.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439664" target="_blank"〉PubMed〈/a〉
    Keywords: Alberta/epidemiology ; Animals ; Bayes Theorem ; British Columbia/epidemiology ; Ecosystem ; *Evolution, Molecular ; Genes, env ; Genes, pol ; Geography ; Immunodeficiency Virus, Feline/*classification/*genetics ; Lentivirus Infections/epidemiology/*veterinary/virology ; Microsatellite Repeats ; Molecular Sequence Data ; Montana/epidemiology ; Phylogeny ; Population Dynamics ; *Puma/genetics/virology ; Time Factors ; Wyoming/epidemiology
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    Sea urchin egg receptor for sperm: sequence similarity of binding domain and hsp70 (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-03-05
    Description: Fertilization depends on cell surface recognition proteins that interact and thereby mediate binding and subsequent fusion of the sperm and egg. Overlapping complementary DNA's encoding the egg plasma membrane receptor for sperm from the sea urchin Strongylocentrotus purpuratus were cloned and sequenced. Analysis of the deduced primary structure suggests that the receptor is a transmembrane protein with a short cytoplasmic domain. This domain showed no sequence similarity to known protein sequences. In contrast, the extracellular, sperm binding domain of the receptor did show sequence similarity to the heat shock protein 70 (hsp70) family of proteins. Recombinant protein representing this portion of the receptor bound to the sperm protein, binding, and also inhibited fertilization in a species-specific manner; beads coated with the protein became specifically bound to acrosome-reacted sperm. These data provide a basis for detailed investigations of molecular interactions that occur in gamete recognition and egg activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Foltz, K R -- Partin, J S -- Lennarz, W J -- HD18590/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 1993 Mar 5;259(5100):1421-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, University of California, Santa Barbara 93106.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8383878" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cloning, Molecular ; Female ; Fertilization ; Heat-Shock Proteins/*genetics ; Humans ; Male ; Molecular Sequence Data ; Ovum/physiology ; Receptors, Cell Surface/*genetics/metabolism ; Recombinant Proteins/metabolism ; Restriction Mapping ; Sea Urchins ; Sequence Homology, Amino Acid ; Sperm-Ovum Interactions ; Spermatozoa/cytology/physiology
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    Transcription factor TFIIB sites important for interaction with promoter-bound TFIID (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-07-23
    Description: Transcription initiation factor TFIIB recruits RNA polymerase II to the promoter subsequent to interaction with a preformed TFIID-promoter complex. The domains of TFIIB required for binding to the TFIID-promoter complex and for transcription initiation have been determined. The carboxyl-terminal two-thirds of TFIIB, which contains two direct repeats and two basic residue repeats, is sufficient for interaction with the TFIID-promoter complex. An extra 84-residue amino-terminal region, with no obvious known structural motifs, is required for basal transcription activity. Basic residues within the second basic repeat of TFIIB are necessary for stable interaction with the TFIID-promoter complex, whereas the basic character of the first basic repeat is not. Functional roles of other potential structural motifs are discussed in light of the present study.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yamashita, S -- Hisatake, K -- Kokubo, T -- Doi, K -- Roeder, R G -- Horikoshi, M -- Nakatani, Y -- AI27397/AI/NIAID NIH HHS/ -- CA42567/CA/NCI NIH HHS/ -- GM45258/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Jul 23;261(5120):463-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8332911" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; DNA-Binding Proteins/*metabolism ; Drosophila ; Molecular Sequence Data ; Mutation ; *Promoter Regions, Genetic ; Protein Binding ; Transcription Factor TFIIB ; Transcription Factor TFIID ; Transcription Factors/*chemistry/*metabolism
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    Origin recognition complex (ORC) in transcriptional silencing and DNA replication in S. cerevisiae (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-12-17
    Description: In Saccharomyces cerevisiae, the HMR-E silencer blocks site-specific interactions between proteins and their recognition sequences in the vicinity of the silencer. Silencer function is correlated with the firing of an origin of replication at HMR-E. An essential gene with a role in transcriptional silencing was identified by means of a screen for mutations affecting expression of HMR. This gene, known as ORC2, was shown to encode a component of the origin recognition complex that binds yeast origins of replication. A temperature-sensitive mutation in ORC2 disrupted silencing in cells grown at the permissive temperature. At the restrictive temperature, the orc2-1 mutation caused cell cycle arrest at a point in the cell cycle indicative of blocks in DNA replication. The orc2-1 mutation also resulted in the enhanced mitotic loss of a plasmid, suggestive of a defect in replication. These results provide strong evidence for an in vivo role of ORC in both chromosomal replication and silencing, and provide a link between the mechanism of silencing and DNA replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Foss, M -- McNally, F J -- Laurenson, P -- Rine, J -- GM31105/GM/NIGMS NIH HHS/ -- P30ES01896-12/ES/NIEHS NIH HHS/ -- New York, N.Y. -- Science. 1993 Dec 17;262(5141):1838-44.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8266071" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Cell Cycle ; Cloning, Molecular ; *DNA Replication ; DNA, Fungal/genetics/metabolism ; *DNA-Binding Proteins ; Fungal Proteins/chemistry/*genetics/metabolism ; *Gene Expression Regulation, Fungal ; *Genes, Fungal ; Molecular Sequence Data ; Mutation ; Origin Recognition Complex ; Phenotype ; Plasmids ; *Replicon ; Repressor Proteins/chemistry/*genetics/metabolism ; Saccharomyces cerevisiae/cytology/*genetics/metabolism ; Saccharomyces cerevisiae Proteins ; Transcription, Genetic
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    Rate and mechanism of nonhomologous recombination during a single cycle of retroviral replication (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-01-08
    Description: Oncogenes discovered in retroviruses such as Rous sarcoma virus were generated by transduction of cellular proto-oncogenes into the viral genome. Several different kinds of junctions between the viral and proto-oncogene sequences have been found in different viruses. A system of retrovirus vectors and a protocol that mimicked this transduction during a single cycle of retrovirus replication was developed. The transduction involved the formation of a chimeric viral-cellular RNA, strand switching of the reverse transcription growing point from an infectious retrovirus to the chimeric RNA, and often a subsequent deletion during the rest of viral DNA synthesis. A short region of sequence identity was frequently used for the strand switching. The rate of this process was about 0.1 to 1 percent of the rate of homologous retroviral recombination.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, J -- Temin, H M -- CA-07175/CA/NCI NIH HHS/ -- CA-22443/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1993 Jan 8;259(5092):234-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉McArdle Laboratory for Cancer Research, University of Wisconsin-Madison 53706.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8421784" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; *Cinnamates ; *DNA Replication ; DNA, Viral/chemistry/genetics ; Drug Resistance/genetics ; Genes, Viral ; Genetic Vectors ; Hygromycin B/analogs & derivatives ; Kinetics ; Mice ; Molecular Sequence Data ; Moloney murine leukemia virus/genetics ; Neomycin ; Plasmids ; *Proto-Oncogenes ; RNA, Viral/analysis/genetics ; *Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; Retroviridae/*genetics/physiology ; Transfection ; *Virus Replication
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    Mutations in the glucose-6-phosphatase gene that cause glycogen storage disease type 1a (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-10-22
    Description: Glycogen storage disease (GSD) type 1a is caused by the deficiency of D-glucose-6-phosphatase (G6Pase), the key enzyme in glucose homeostasis. Despite both a high incidence and morbidity, the molecular mechanisms underlying this deficiency have eluded characterization. In the present study, the molecular and biochemical characterization of the human G6Pase complementary DNA, its gene, and the expressed protein, which is indistinguishable from human microsomal G6Pase, are reported. Several mutations in the G6Pase gene of affected individuals that completely inactivate the enzyme have been identified. These results establish the molecular basis of this disease and open the way for future gene therapy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lei, K J -- Shelly, L L -- Pan, C J -- Sidbury, J B -- Chou, J Y -- New York, N.Y. -- Science. 1993 Oct 22;262(5133):580-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Genetics Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8211187" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Cell Line ; DNA, Complementary/genetics ; Exons ; Glucose-6-Phosphatase/*genetics/metabolism ; Glycogen Storage Disease Type I/enzymology/*genetics ; Glycosylation ; Humans ; Liver/enzymology ; Mice ; Molecular Sequence Data ; *Mutation ; Protein Conformation ; Transfection
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Multidrug resistance-associated protein: sequence correction (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-05-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cole, S P -- Deeley, R G -- New York, N.Y. -- Science. 1993 May 14;260(5110):879.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8098549" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Carrier Proteins/*chemistry ; Humans ; Membrane Glycoproteins/*chemistry ; Molecular Sequence Data ; P-Glycoprotein
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  • 48
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    Deletion of the paired alpha 5(IV) and alpha 6(IV) collagen genes in inherited smooth muscle tumors (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-08-27
    Description: The gene encoding alpha 6(IV) collagen, COL4A6, was identified on the human X chromosome in a head-to-head arrangement and within 452 base pairs of the alpha 5(IV) collagen gene, COL4A5. In earlier studies, intragenic deletions of COL4A5 were detected in a subset of patients with Alport syndrome (AS), a hereditary defect of basement membranes. In some families, AS cosegregates with diffuse leiomyomatosis (DL), a benign smooth muscle tumor diathesis. Here it is shown that patients with AS-DL harbor deletions that disrupt both COL4A5 and COL4A6. Thus, type IV collagen may regulate smooth muscle differentiation and morphogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, J -- Mochizuki, T -- Smeets, H -- Antignac, C -- Laurila, P -- de Paepe, A -- Tryggvason, K -- Reeders, S T -- New York, N.Y. -- Science. 1993 Aug 27;261(5125):1167-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536-0812.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8356449" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Cell Differentiation ; Collagen/chemistry/*genetics ; Exons ; Female ; Fetus/metabolism ; *Gene Deletion ; Genetic Linkage ; Humans ; Leiomyoma/*genetics ; Male ; Molecular Sequence Data ; Morphogenesis ; Muscle, Smooth/cytology ; Mutation ; Nephritis, Hereditary/*genetics ; RNA, Messenger/genetics/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 49
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    Expression cloning and signaling properties of the rat glucagon receptor (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-03-12
    Description: Glucagon and the glucagon receptor are a primary source of control over blood glucose concentrations and are especially important to studies of diabetes in which the loss of control over blood glucose concentrations clinically defines the disease. A complementary DNA clone for the glucagon receptor was isolated by an expression cloning strategy, and the receptor protein was expressed in several kidney cell lines. The cloned receptor bound glucagon and caused an increase in the intracellular concentration of adenosine 3', 5'-monophosphate (cAMP). The cloned glucagon receptor also transduced a signal that led to an increased concentration of intracellular calcium. The glucagon receptor is similar to the calcitonin and parathyroid hormone receptors. It can transduce signals leading to the accumulation of two different second messengers, cAMP and calcium.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jelinek, L J -- Lok, S -- Rosenberg, G B -- Smith, R A -- Grant, F J -- Biggs, S -- Bensch, P A -- Kuijper, J L -- Sheppard, P O -- Sprecher, C A -- New York, N.Y. -- Science. 1993 Mar 12;259(5101):1614-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉ZymoGenetics Inc., Seattle, WA 98105.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8384375" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Calcium/pharmacology ; Cell Line ; Cloning, Molecular ; Cricetinae ; Cyclic AMP/metabolism ; Glucagon/metabolism/*pharmacology ; Kidney ; Kinetics ; Liver/*metabolism ; Molecular Sequence Data ; Rats ; Receptors, Gastrointestinal Hormone/genetics/metabolism/*physiology ; Receptors, Glucagon ; *Signal Transduction ; Transfection
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    Dialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-08-06
    Description: The structure of the bifunctional, pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase was determined to 2.1-angstrom resolution. Model building suggests that a single cleavage site catalyzes both decarboxylation and transamination by maximizing stereoelectronic advantages and providing electrostatic and general base catalysis. The enzyme contains two binding sites for alkali metal ions. One is located near the active site and accounts for the dependence of activity on potassium ions. The other is located at the carboxyl terminus of an alpha helix. These sites help show how proteins can specifically bind alkali metals and how these ions can exert functional effects.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Toney, M D -- Hohenester, E -- Cowan, S W -- Jansonius, J N -- GM13854/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Aug 6;261(5122):756-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, University of Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8342040" target="_blank"〉PubMed〈/a〉
    Keywords: Amination ; Amino Acid Sequence ; Binding Sites ; Carboxy-Lyases/*chemistry/metabolism ; Catalysis ; Computer Graphics ; Decarboxylation ; Metals, Alkali/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; X-Ray Diffraction
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Inhibition of Rev-mediated HIV-1 expression by an RNA binding protein encoded by the interferon-inducible 9-27 gene (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-02-26
    Description: Interferon inhibits expression of human immunodeficiency virus type-1 (HIV-1) through unknown mechanisms. A gene inducible by interferon-alpha (IFN-alpha) and interferon-gamma (IFN-gamma) was isolated by screening of a human complementary DNA library for proteins binding to the Rev-responsive element (RRE) of HIV-1. The product of this gene, RBP9-27, was shown to bind RNA in vitro and to inhibit HIV-1 expression after transfection into human cells. RBP9-27 primarily inhibited Rev-dependent posttranscriptional steps of viral gene expression. Thus, RBP9-27 is a cellular factor that antagonizes Rev function. These results suggest an interferon-induced antiviral mechanism operating through the induction of RNA binding proteins such as RBP9-27. Elucidation of RBP9-27 function may lead to a better understanding of the mechanism of interferon action during HIV-1 infection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Constantoulakis, P -- Campbell, M -- Felber, B K -- Nasioulas, G -- Afonina, E -- Pavlakis, G N -- N0-CO-74101/CO/NCI NIH HHS/ -- New York, N.Y. -- Science. 1993 Feb 26;259(5099):1314-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Retrovirus Section, National Cancer Institute-Frederick Cancer Research and Development Center, MD 21702.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7680491" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; *Gene Expression Regulation, Viral ; Genes, env ; *Genes, rev ; HIV-1/*genetics ; Humans ; Interferons/pharmacology ; *Membrane Proteins ; Molecular Sequence Data ; Oligodeoxyribonucleotides/chemistry ; RNA-Binding Proteins/*genetics ; Regulatory Sequences, Nucleic Acid
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    Disappearance of the lymphoid system in Bcl-2 homozygous mutant chimeric mice (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-09-17
    Description: The bcl-2 proto-oncogene can prevent the death of many cell types. Mice were generated that were chimeric for the homozygous inactivation of bcl-2. Lymphocytes without Bcl-2 differentiated into phenotypically mature cells. However, in vitro, the mature T cells that lacked Bcl-2 had shorter life-spans and increased sensitivity to glucocorticoids and gamma-irradiation. In contrast, stimulation of CD3 inhibited the death of these cells. T and B cells with no Bcl-2 disappeared from the bone marrow, thymus, and periphery by 4 weeks of age. Thus, Bcl-2 was dispensable for lymphocyte maturation, but was required for a stable immune system after birth.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakayama, K -- Negishi, I -- Kuida, K -- Shinkai, Y -- Louie, M C -- Fields, L E -- Lucas, P J -- Stewart, V -- Alt, F W -- AI 15322/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1993 Sep 17;261(5128):1584-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8372353" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD3/immunology ; Apoptosis ; B-Lymphocytes/cytology/*immunology ; Base Sequence ; Bone Marrow/immunology ; Bone Marrow Cells ; Cell Line ; Chimera ; Homozygote ; Humans ; Lymphoid Tissue/cytology/immunology ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Proto-Oncogene Proteins/genetics/*physiology ; Proto-Oncogene Proteins c-bcl-2 ; Proto-Oncogenes ; Receptors, Antigen, T-Cell/immunology ; T-Lymphocytes/cytology/*immunology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Microbial competition: Escherichia coli mutants that take over stationary phase cultures (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-03-19
    Description: Many microorganisms, including Escherichia coli, can survive extended periods of starvation. The properties of cells that survived prolonged incubation in stationary phase were studied by mixture of 10-day-old (aged) cultures with 1-day-old (young) cultures of the same strain of Escherichia coli. Mutants from the aged cultures that could grow eventually took over the population, which resulted in the death of the cells from the young cultures. This phenotype was conferred by mutations in rpoS, which encodes a putative stationary phase-specific sigma factor. These rapid population shifts have implications for the studies of microbial evolution and ecology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zambrano, M M -- Siegele, D A -- Almiron, M -- Tormo, A -- Kolter, R -- New York, N.Y. -- Science. 1993 Mar 19;259(5102):1757-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7681219" target="_blank"〉PubMed〈/a〉
    Keywords: Acridine Orange ; Alleles ; Amino Acid Sequence ; Cloning, Molecular ; Escherichia coli/*genetics/*growth & development/physiology ; Hydrogen Peroxide/metabolism ; Molecular Sequence Data ; *Mutation ; Peroxidase/metabolism ; Phenotype ; Sigma Factor/chemistry/*genetics ; Staining and Labeling ; Time Factors
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    Induction of G alpha i2-specific antisense RNA in vivo inhibits neonatal growth (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-05-14
    Description: Guanosine triphosphate-binding regulatory proteins (G proteins) are key elements in transmembrane signaling and have been implicated as regulators of more complex biological processes such as differentiation and development. The G protein G alpha i2 is capable of mediating the inhibitory control of adenylylcyclase and regulates stem cell differentiation to primitive endoderm. Here an antisense RNA to G alpha i2 was expressed in a hybrid RNA construct whose expression was both tissue-specific and induced at birth. Transgenic mice in which the antisense construct was expressed displayed a lack of normal development in targeted organs that correlated with the absence of G alpha i2. The loss of G alpha i2 expression in adipose tissue of the transgenic mice was correlated with a rise in basal levels of adenosine 3',5'-monophosphate (cAMP) and the loss of receptor-mediated inhibition of adenylylcyclase. These data expand our understanding of G protein function in vivo and demonstrate the necessity for G alpha i2 in the development of liver and fat.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moxham, C M -- Hod, Y -- Malbon, C C -- New York, N.Y. -- Science. 1993 May 14;260(5110):991-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Pharmacology, State University of New York (SUNY)/Stony Brook 11794-8651.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8493537" target="_blank"〉PubMed〈/a〉
    Keywords: Adipose Tissue/*growth & development/metabolism ; Animals ; Animals, Newborn/growth & development ; Base Sequence ; Body Weight ; GTP-Binding Proteins/biosynthesis/genetics/*physiology ; Growth/drug effects/*physiology ; Kidney/growth & development/metabolism ; Liver/*growth & development/metabolism ; Mice ; Mice, Transgenic ; Molecular Sequence Data ; Phosphoenolpyruvate Carboxykinase (GTP)/genetics ; RNA, Antisense/*genetics ; Transfection
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    Shutdown of class switch recombination by deletion of a switch region control element (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-02-12
    Description: Upon activation, B lymphocytes can change the class of the antibody they express by immunoglobulin class switch recombination. Cytokines can direct this recombination to distinct classes by the specific activation of repetitive recombinogenic DNA sequences, the switch regions. Recombination to a particular switch region (s gamma 1) was abolished in mice that were altered to lack sequences that are 5' to the s gamma 1 region. This result directly implicates the functional importance of 5' switch region flanking sequences in the control of class switch recombination. Mutant mice exhibit a selective agammaglobulinemia and may be useful in the assessment of the biological importance of immunoglobulin G1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jung, S -- Rajewsky, K -- Radbruch, A -- New York, N.Y. -- Science. 1993 Feb 12;259(5097):984-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genetics, University of Cologne, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8438159" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; B-Lymphocytes/*immunology ; Base Sequence ; Cell Line ; Chimera ; Drug Resistance/genetics ; Embryo, Mammalian ; *Gene Deletion ; Immunoglobulin G/genetics ; Immunoglobulin Heavy Chains/genetics ; Immunoglobulin Switch Region/*genetics ; Interleukin-4/pharmacology ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Mutagenesis ; Neomycin ; *Recombination, Genetic ; Stem Cells
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    Uncovering of functional alternative CTLA-4 counter-receptor in B7-deficient mice (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-11-05
    Description: B7 delivers a costimulatory signal through CD28, resulting in interleukin-2 secretion and T cell proliferation. Blockade of this pathway results in T cell anergy. The in vivo role of B7 was evaluated with B7-deficient mice. These mice had a 70 percent decrease in costimulation of the response to alloantigen. Despite lacking B7 expression, activated B cells from these mice bound CTLA-4 and GL1 monoclonal antibody, demonstrating that alternative CTLA-4 ligand or ligands exist. These receptors are functionally important because the residual allogenic mixed lymphocyte responses were blocked by CTLA4Ig. Characterization of these CTLA-4 ligands should lead to strategies for manipulating the immune response.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Freeman, G J -- Borriello, F -- Hodes, R J -- Reiser, H -- Hathcock, K S -- Laszlo, G -- McKnight, A J -- Kim, J -- Du, L -- Lombard, D B -- CA 40216/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1993 Nov 5;262(5135):907-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7694362" target="_blank"〉PubMed〈/a〉
    Keywords: Abatacept ; Animals ; Antigens, CD ; Antigens, CD80/genetics/*immunology/metabolism ; Antigens, Differentiation/immunology/*metabolism ; B-Lymphocytes/*immunology ; Base Sequence ; CTLA-4 Antigen ; Cell Line ; *Immunoconjugates ; Interleukin-2/secretion ; Isoantigens/immunology ; Lymphocyte Activation ; Lymphocyte Culture Test, Mixed ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Mice, Knockout ; Molecular Sequence Data ; Mutation ; T-Lymphocytes/*immunology ; Transfection
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    Cloning of B7-2: a CTLA-4 counter-receptor that costimulates human T cell proliferation (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-11-05
    Description: Although presentation of antigen to the T cell receptor is necessary for the initiation of an immune response, additional molecules expressed on antigen-presenting cells deliver essential costimulatory signals. T cell activation, in the absence of costimulation, results in T cell anergy. The B7-1 protein is a costimulator molecule that regulates interleukin-2 (IL-2) secretion by signaling through the pathway that uses CD28 and CTLA-4 (hereafter referred to as the CD28 pathway). We have cloned a counter-receptor of CD28 and CTLA-4, termed B7-2. Although only 26 percent identical to B7-1, B7-2 also costimulates IL-2 production and T cell proliferation. Unlike B7-1, B7-2 messenger RNA is constitutively expressed in unstimulated B cells. It is likely that B7-2 provides a critical early costimulatory signal determining if the T cell will contribute to an immune response or become anergic.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Freeman, G J -- Gribben, J G -- Boussiotis, V A -- Ng, J W -- Restivo, V A Jr -- Lombard, L A -- Gray, G S -- Nadler, L M -- CA 40216/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1993 Nov 5;262(5135):909-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Hematologic Malignancies, Dana-Farber Cancer Institute.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7694363" target="_blank"〉PubMed〈/a〉
    Keywords: Abatacept ; Amino Acid Sequence ; Animals ; *Antigens, CD ; Antigens, CD28/metabolism ; Antigens, CD80/chemistry/genetics/*immunology/metabolism ; Antigens, CD86 ; Antigens, Differentiation/*metabolism ; B-Lymphocytes/*immunology/metabolism ; CTLA-4 Antigen ; Cell Line ; *Cloning, Molecular ; DNA, Complementary/genetics ; Humans ; *Immunoconjugates ; *Lymphocyte Activation ; *Membrane Glycoproteins ; Molecular Sequence Data ; Sequence Alignment ; Signal Transduction ; T-Lymphocytes/*immunology
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  • 58
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    Convergent regulation of sodium channels by protein kinase C and cAMP-dependent protein kinase (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-09-10
    Description: The function of voltage-gated sodium channels that are responsible for action potential generation in mammalian brain neurons is modulated by phosphorylation by adenosine 3',5'-monophosphate (cAMP)-dependent protein kinase (cA-PK) and by protein kinase C (PKC). Reduction of peak sodium currents by cA-PK in intact cells required concurrent activation of PKC and was prevented by blocking phosphorylation of serine 1506, a site in the inactivation gate of the channel that is phosphorylated by PKC but not by cA-PK. Replacement of serine 1506 with negatively charged amino acids mimicked the effect of phosphorylation. Conversion of the consensus sequence surrounding serine 1506 to one more favorable for cA-PK enhanced modulation of sodium currents by cA-PK. Convergent modulation of sodium channels required phosphorylation of serine 1506 by PKC accompanied by phosphorylation of additional sites by cA-PK. This regulatory mechanism may serve to integrate neuronal signals mediated through these parallel signaling pathways.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, M -- West, J W -- Numann, R -- Murphy, B J -- Scheuer, T -- Catterall, W A -- R01-NS15751/NS/NINDS NIH HHS/ -- T32-GM07270/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Sep 10;261(5127):1439-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Washington, Seattle 98195.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8396273" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Amino Acid Sequence ; Animals ; CHO Cells ; Consensus Sequence ; Cricetinae ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Phosphorylation ; Protein Kinase C/*metabolism ; Protein Kinases/*metabolism ; Sodium/metabolism ; Sodium Channels/*metabolism
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    The Neurospora checkpoint kinase 2: a regulatory link between the circadian and cell cycles (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-01
    Description: The clock gene period-4 (prd-4) in Neurospora was identified by a single allele displaying shortened circadian period and altered temperature compensation. Positional cloning followed by functional tests show that PRD-4 is an ortholog of mammalian checkpoint kinase 2 (Chk2). Expression of prd-4 is regulated by the circadian clock and, reciprocally, PRD-4 physically interacts with the clock component FRQ, promoting its phosphorylation. DNA-damaging agents can reset the clock in a manner that depends on time of day, and this resetting is dependent on PRD-4. Thus, prd-4, the Neurospora Chk2, identifies a molecular link that feeds back conditionally from circadian output to input and the cell cycle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pregueiro, Antonio M -- Liu, Qiuyun -- Baker, Christopher L -- Dunlap, Jay C -- Loros, Jennifer J -- MH44651/MH/NIMH NIH HHS/ -- P01 GM068087/GM/NIGMS NIH HHS/ -- R01 GM034985/GM/NIGMS NIH HHS/ -- R37GM34985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Aug 4;313(5787):644-9. Epub 2006 Jun 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Dartmouth Medical School, Hanover, NH 03755, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16809488" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Cell Cycle ; Checkpoint Kinase 2 ; *Circadian Rhythm ; Cloning, Molecular ; DNA Damage ; Feedback, Physiological ; Fungal Proteins/chemistry/genetics/metabolism ; Gene Expression Regulation, Fungal ; Genes, Fungal ; Methyl Methanesulfonate/pharmacology ; Molecular Sequence Data ; Mutation ; Neurospora/*enzymology/genetics ; Neurospora crassa/cytology/*enzymology/*physiology ; Phosphorylation ; Protein-Serine-Threonine Kinases/chemistry/*genetics/*metabolism
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    A small microbial genome: the end of a long symbiotic relationship? (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-10-14
    Description: Intracellular bacteria are characterized by genome reduction. The 422,434-base pair genome of Buchnera aphidicola BCc, primary endosymbiont of the aphid Cinara cedri, is approximately 200 kilobases smaller than the previously sequenced B. aphidicola genomes. B. aphidicola BCc has lost most metabolic functions, including the ability to synthesize the essential amino acid tryptophan and riboflavin. In addition, most retained genes are evolving rapidly. Possibly, B. aphidicola BCc is losing its symbiotic capacity and is being complemented (and might be replaced) by the highly abundant coexisting secondary symbiont.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perez-Brocal, Vicente -- Gil, Rosario -- Ramos, Silvia -- Lamelas, Araceli -- Postigo, Marina -- Michelena, Jose Manuel -- Silva, Francisco J -- Moya, Andres -- Latorre, Amparo -- New York, N.Y. -- Science. 2006 Oct 13;314(5797):312-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartado Postal 22085, 46071 Valencia, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17038625" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/biosynthesis ; Animals ; Aphids/*microbiology/physiology ; Base Pairing ; Buchnera/*genetics/metabolism/physiology ; Chromosomes, Bacterial/genetics ; Evolution, Molecular ; Genes, Bacterial ; *Genome, Bacterial ; Molecular Sequence Data ; Sequence Analysis, DNA ; Serratia/genetics/metabolism/physiology ; *Symbiosis ; Tryptophan/biosynthesis
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    FG-rich repeats of nuclear pore proteins form a three-dimensional meshwork with hydrogel-like properties (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-11-04
    Description: Nuclear pore complexes permit rapid passage of cargoes bound to nuclear transport receptors, but otherwise suppress nucleocytoplasmic fluxes of inert macromolecules 〉/=30 kilodaltons. To explain this selectivity, a sieve structure of the permeability barrier has been proposed that is created through reversible cross-linking between Phe and Gly (FG)-rich nucleoporin repeats. According to this model, nuclear transport receptors overcome the size limit of the sieve and catalyze their own nuclear pore-passage by a competitive disruption of adjacent inter-repeat contacts, which transiently opens adjoining meshes. Here, we found that phenylalanine-mediated inter-repeat interactions indeed cross-link FG-repeat domains into elastic and reversible hydrogels. Furthermore, we obtained evidence that such hydrogel formation is required for viability in yeast.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frey, Steffen -- Richter, Ralf P -- Gorlich, Dirk -- New York, N.Y. -- Science. 2006 Nov 3;314(5800):815-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Zentrum fur Molekulare Biologie der Universitat Heidelberg (ZMBH), INF 282, D-69120 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17082456" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Amino Acid Motifs ; Amino Acid Sequence ; Biopolymers ; Calcium-Binding Proteins/*chemistry/genetics/*metabolism ; Fluorescence Recovery After Photobleaching ; HeLa Cells ; Humans ; Hydrogels ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Models, Biological ; Molecular Sequence Data ; Mutation ; Nuclear Pore/chemistry/*metabolism ; Nuclear Pore Complex Proteins/*chemistry/*metabolism ; Nuclear Proteins/*chemistry/genetics/*metabolism ; Nucleocytoplasmic Transport Proteins/*metabolism ; Permeability ; Phenylalanine/chemistry ; Protein Structure, Tertiary ; Repetitive Sequences, Amino Acid ; Saccharomyces cerevisiae/chemistry/physiology ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism
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    Evolutionary paths underlying flower color variation in Antirrhinum (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-08-19
    Description: To understand evolutionary paths connecting diverse biological forms, we defined a three-dimensional genotypic space separating two flower color morphs of Antirrhinum. A hybrid zone between morphs showed a steep cline specifically at genes controlling flower color differences, indicating that these loci are under selection. Antirrhinum species with diverse floral phenotypes formed a U-shaped cloud within the genotypic space. We propose that this cloud defines an evolutionary path that allows flower color to evolve while circumventing less-adaptive regions. Hybridization between morphs located in different arms of the U-shaped path yields low-fitness genotypes, accounting for the observed steep clines at hybrid zones.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Whibley, Annabel C -- Langlade, Nicolas B -- Andalo, Christophe -- Hanna, Andrew I -- Bangham, Andrew -- Thebaud, Christophe -- Coen, Enrico -- New York, N.Y. -- Science. 2006 Aug 18;313(5789):963-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16917061" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Alleles ; Antirrhinum/classification/*genetics ; Base Sequence ; *Biological Evolution ; Crosses, Genetic ; Flowers/*genetics ; Gene Flow ; Gene Frequency ; Genes, Plant ; *Genetic Speciation ; Genotype ; Haplotypes ; Hybridization, Genetic ; Models, Genetic ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Pigmentation/*genetics ; Pigments, Biological/genetics ; Principal Component Analysis ; Selection, Genetic
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    N- to C-terminal SNARE complex assembly promotes rapid membrane fusion (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-08-05
    Description: Assembly of the soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) syntaxin 1, SNAP-25, and synaptobrevin 2 is thought to be the driving force for the exocytosis of synaptic vesicles. However, whereas exocytosis is triggered at a millisecond time scale, the SNARE-mediated fusion of liposomes requires hours for completion, which challenges the idea of a key role for SNAREs in the final steps of exocytosis. We found that liposome fusion was dramatically accelerated when a stabilized syntaxin/SNAP-25 acceptor complex was used. Thus, SNAREs do have the capacity to execute fusion at a speed required for neuronal secretion, demonstrating that the maintenance of acceptor complexes is a critical step in biological fusion reactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pobbati, Ajaybabu V -- Stein, Alexander -- Fasshauer, Dirk -- P01 GM072694/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Aug 4;313(5787):673-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16888141" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Circular Dichroism ; Dimerization ; Exocytosis ; Liposomes/*chemistry ; *Membrane Fusion ; Molecular Sequence Data ; Peptide Fragments/chemistry/metabolism ; Protein Binding ; Protein Folding ; Protein Structure, Secondary ; Qa-SNARE Proteins/chemistry/*metabolism ; R-SNARE Proteins/chemistry/metabolism ; Rats ; Synaptosomal-Associated Protein 25/chemistry/*metabolism
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    Bacterial diversity in tree canopies of the Atlantic forest (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-07-01
    Description: We found an extraordinary level of bacterial biodiversity in the tree leaf canopy of a tropical Atlantic forest by using culture-independent molecular methods. Our survey suggests that each tree species selects for a distinct microbial community. Analysis of the bacterial 16S ribosomal RNA gene sequences revealed that about 97% of the bacteria were unknown species and that the phyllosphere of any one tree species carries at least 95 to 671 bacterial species. The tree canopies of tropical forests likely represent a large reservoir of unexplored microbial diversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lambais, M R -- Crowley, D E -- Cury, J C -- Bull, R C -- Rodrigues, R R -- New York, N.Y. -- Science. 2006 Jun 30;312(5782):1917.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Soils and Soil Science, University of Sao Paulo, Piracicaba, Sao Paulo, Brazil. mlambais@esalq.usp.br〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16809531" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*classification/genetics/*isolation & purification ; *Biodiversity ; Brazil ; DNA Fingerprinting ; *Ecosystem ; Genes, rRNA ; Molecular Sequence Data ; Plant Leaves/*microbiology ; RNA, Ribosomal, 16S/genetics ; Trees/*microbiology ; Tropical Climate
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    N-linked glycosylation of folded proteins by the bacterial oligosaccharyltransferase (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-11-18
    Description: N-linked protein glycosylation is found in all domains of life. In eukaryotes, it is the most abundant protein modification of secretory and membrane proteins, and the process is coupled to protein translocation and folding. We found that in bacteria, N-glycosylation can occur independently of the protein translocation machinery. In an in vitro assay, bacterial oligosaccharyltransferase glycosylated a folded endogenous substrate protein with high efficiency and folded bovine ribonuclease A with low efficiency. Unfolding the eukaryotic substrate greatly increased glycosylation. We propose that in the bacterial system, glycosylation sites are located in flexible parts of folded proteins, whereas the eukaryotic cotranslational glycosylation evolved to a mechanism presenting the substrate in a flexible form before folding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kowarik, Michael -- Numao, Shin -- Feldman, Mario F -- Schulz, Benjamin L -- Callewaert, Nico -- Kiermaier, Eva -- Catrein, Ina -- Aebi, Markus -- New York, N.Y. -- Science. 2006 Nov 17;314(5802):1148-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Microbiology, Department of Biology, Eidgenossische Technische Hochschule (ETH) Zurich, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17110579" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bacterial Proteins/*metabolism ; Campylobacter jejuni ; Cattle ; Escherichia coli ; Glycoproteins/*metabolism ; Glycosylation ; Hexosyltransferases/metabolism ; Membrane Proteins/metabolism ; Molecular Sequence Data ; *Protein Folding ; Protein Transport ; Recombinant Proteins/metabolism
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    Genomic islands and the ecology and evolution of Prochlorococcus (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-03-25
    Description: Prochlorococcus ecotypes are a useful system for exploring the origin and function of diversity among closely related microbes. The genetic variability between phenotypically distinct strains that differ by less that 1% in 16S ribosomal RNA sequences occurs mostly in genomic islands. Island genes appear to have been acquired in part by phage-mediated lateral gene transfer, and some are differentially expressed under light and nutrient stress. Furthermore, genome fragments directly recovered from ocean ecosystems indicate that these islands are variable among cooccurring Prochlorococcus cells. Genomic islands in this free-living photoautotroph share features with pathogenicity islands of parasitic bacteria, suggesting a general mechanism for niche differentiation in microbial species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Coleman, Maureen L -- Sullivan, Matthew B -- Martiny, Adam C -- Steglich, Claudia -- Barry, Kerrie -- Delong, Edward F -- Chisholm, Sallie W -- New York, N.Y. -- Science. 2006 Mar 24;311(5768):1768-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, 15 Vassar Street, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16556843" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Atlantic Ocean ; Bacteriophages/*genetics/physiology ; *Biological Evolution ; *Ecosystem ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; *Genomic Islands ; Light ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; Prochlorococcus/classification/*genetics/isolation & purification/*physiology ; Seawater/*microbiology
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    Metagenomic analysis of the human distal gut microbiome (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-06-03
    Description: The human intestinal microbiota is composed of 10(13) to 10(14) microorganisms whose collective genome ("microbiome") contains at least 100 times as many genes as our own genome. We analyzed approximately 78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction-amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-d-erythritol 4-phosphate pathway-mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3027896/" 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/PMC3027896/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gill, Steven R -- Pop, Mihai -- Deboy, Robert T -- Eckburg, Paul B -- Turnbaugh, Peter J -- Samuel, Buck S -- Gordon, Jeffrey I -- Relman, David A -- Fraser-Liggett, Claire M -- Nelson, Karen E -- AI51259/AI/NIAID NIH HHS/ -- DK70977/DK/NIDDK NIH HHS/ -- R01 AI051259/AI/NIAID NIH HHS/ -- R01 AI051259-04/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2006 Jun 2;312(5778):1355-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. srgill@buffalo.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16741115" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Bacteria/classification/*genetics/isolation & purification ; Bifidobacterium/genetics ; *DNA, Ribosomal ; Dietary Carbohydrates/metabolism ; Dietary Fiber/metabolism ; Feces/microbiology ; Female ; Fermentation ; *Genetic Variation ; Genome, Bacterial ; Genomics ; Humans ; Intestinal Mucosa/metabolism/microbiology ; Intestines/metabolism/*microbiology ; Male ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Xenobiotics/metabolism
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    Dodeca-CLE peptides as suppressors of plant stem cell differentiation (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-08-12
    Description: In plants and animals, small peptide ligands that signal in cell-cell communication have been suggested to be a crucial component of development. A bioassay of single-cell transdifferentation demonstrates that a dodecapeptide with two hydroxyproline residues is the functional product of genes from the CLE family, which includes CLAVATA3 in Arabidopsis. The dodecapeptide suppresses xylem cell development at a concentration of 10(-11) M and promotes cell division. An application, corresponding to all 26 Arabidopsis CLE protein family members, of synthetic dodecapeptides reveals two counteracting signaling pathways involved in stem cell fate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ito, Yasuko -- Nakanomyo, Ikuko -- Motose, Hiroyasu -- Iwamoto, Kuninori -- Sawa, Shinichiro -- Dohmae, Naoshi -- Fukuda, Hiroo -- New York, N.Y. -- Science. 2006 Aug 11;313(5788):842-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16902140" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/cytology ; Arabidopsis Proteins/chemistry/metabolism ; Asteraceae/*cytology ; Base Sequence ; Biological Assay ; Cell Communication ; *Cell Differentiation ; Cells, Cultured ; Ligands ; Meristem/cytology ; Molecular Sequence Data ; Oligopeptides/chemistry/isolation & purification/*metabolism/pharmacology ; Plant Proteins/chemistry/*metabolism ; Plant Roots/cytology/growth & development ; Plant Structures/*cytology ; *Signal Transduction ; Stem Cells/*cytology
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    Human lineage-specific amplification, selection, and neuronal expression of DUF1220 domains (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-09-02
    Description: Extreme gene duplication is a major source of evolutionary novelty. A genome-wide survey of gene copy number variation among human and great ape lineages revealed that the most striking human lineage-specific amplification was due to an unknown gene, MGC8902, which is predicted to encode multiple copies of a protein domain of unknown function (DUF1220). Sequences encoding these domains are virtually all primate-specific, show signs of positive selection, and are increasingly amplified generally as a function of a species' evolutionary proximity to humans, where the greatest number of copies (212) is found. DUF1220 domains are highly expressed in brain regions associated with higher cognitive function, and in brain show neuron-specific expression preferentially in cell bodies and dendrites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Popesco, Magdalena C -- Maclaren, Erik J -- Hopkins, Janet -- Dumas, Laura -- Cox, Michael -- Meltesen, Lynne -- McGavran, Loris -- Wyckoff, Gerald J -- Sikela, James M -- AA11853/AA/NIAAA NIH HHS/ -- New York, N.Y. -- Science. 2006 Sep 1;313(5791):1304-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Medical Genetics, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16946073" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Biological Evolution ; Brain/*metabolism ; Cognition ; Exons ; *Gene Amplification ; Gene Dosage ; Gene Duplication ; Gene Expression ; Genome, Human ; Humans ; Macaca mulatta/genetics ; Mice ; Molecular Sequence Data ; Neocortex/metabolism ; Neurons/*metabolism ; Pan troglodytes/genetics ; Phylogeny ; Polymerase Chain Reaction ; *Protein Structure, Tertiary ; Proteins/*chemistry/genetics ; Rats ; *Selection, Genetic
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    Brassinosteroids regulate dissociation of BKI1, a negative regulator of BRI1 signaling, from the plasma membrane (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-07-22
    Description: Brassinosteroids, the steroid hormones of plants, are perceived at the plasma membrane by a leucine-rich repeat receptor serine/threonine kinase called BRI1. We report a BRI1-interacting protein, BKI1, which is a negative regulator of brassinosteroid signaling. Brassinosteroids cause the rapid dissociation of BKI1-yellow fluorescent protein from the plasma membrane in a process that is dependent on BRI1-kinase. BKI1 is a substrate of BRI1 kinase and limits the interaction of BRI1 with its proposed coreceptor, BAK1, suggesting that BKI1 prevents the activation of BRI1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Xuelu -- Chory, Joanne -- New York, N.Y. -- Science. 2006 Aug 25;313(5790):1118-22. Epub 2006 Jul 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 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/16857903" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Brassinosteroids ; Cell Membrane/*metabolism ; Cholestanols/*metabolism/pharmacology ; Gene Expression Regulation, Plant ; Meristem/metabolism ; Molecular Sequence Data ; Nuclear Proteins/metabolism ; Phosphorylation ; Plants, Genetically Modified ; Protein Binding ; Protein Kinases/chemistry/genetics/*metabolism ; Protein Structure, Tertiary ; RNA Interference ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction ; Steroids, Heterocyclic/*metabolism/pharmacology ; Two-Hybrid System Techniques
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    South-seeking magnetotactic bacteria in the Northern Hemisphere (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-01-21
    Description: Magnetotactic bacteria contain membrane-bound intracellular iron crystals (magnetosomes) and respond to magnetic fields. Polar magnetotactic bacteria in vertical chemical gradients are thought to respond to high oxygen levels by swimming downward into areas with low or no oxygen (toward geomagnetic north in the Northern Hemisphere and geomagnetic south in the Southern Hemisphere). We identified populations of polar magnetotactic bacteria in the Northern Hemisphere that respond to high oxygen levels by swimming toward geomagnetic south, the opposite of all previously reported magnetotactic behavior. The percentage of magnetotactic bacteria with south polarity in the environment is positively correlated with higher redox potential. The coexistence of magnetotactic bacteria with opposing polarities in the same redox environment conflicts with current models of the adaptive value of magnetotaxis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simmons, Sheri L -- Bazylinski, Dennis A -- Edwards, Katrina J -- New York, N.Y. -- Science. 2006 Jan 20;311(5759):371-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts Institute of Technology-Woods Hole Oceanographic Institution (MIT-WHOI) Joint Program in Oceanography, Department of Marine Chemistry and Geochemistry, MS 52, WHOI, Woods Hole, MA 02543, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16424338" target="_blank"〉PubMed〈/a〉
    Keywords: Colony Count, Microbial ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Deltaproteobacteria/classification/cytology/isolation & purification/*physiology ; Geography ; In Situ Hybridization ; *Magnetics ; Molecular Sequence Data ; Movement ; Oxidation-Reduction ; Oxygen ; Water/chemistry ; *Water Microbiology
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    Isolation of new ribozymes from a large pool of random sequences [see comment] (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-09-10
    Description: An iterative in vitro selection procedure was used to isolate a new class of catalytic RNAs (ribozymes) from a large pool of random-sequence RNA molecules. These ribozymes ligate two RNA molecules that are aligned on a template by catalyzing the attack of a 3'-hydroxyl on an adjacent 5'-triphosphate--a reaction similar to that employed by the familiar protein enzymes that synthesize RNA. The corresponding uncatalyzed reaction also yields a 3',5'-phosphodiester bond. In vitro evolution of the population of new ribozymes led to improvement of the average ligation activity and the emergence of ribozymes with reaction rates 7 million times faster than the uncatalyzed reaction rate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bartel, D P -- Szostak, J W -- New York, N.Y. -- Science. 1993 Sep 10;261(5127):1411-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Massachusetts General Hospital, Boston 02114.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7690155" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Biological Evolution ; Catalysis ; Kinetics ; Magnesium/metabolism ; Molecular Sequence Data ; Mutation ; Oligoribonucleotides/metabolism ; RNA/*metabolism ; RNA Ligase (ATP)/chemistry/isolation & purification/metabolism ; RNA, Catalytic/chemistry/*isolation & purification/metabolism ; Temperature ; Templates, Genetic
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    Structure of the thiamine- and flavin-dependent enzyme pyruvate oxidase (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-02-12
    Description: Pyruvate oxidase from Lactobacillus plantarum is a tetrameric enzyme that decarboxylates pyruvate, producing hydrogen peroxide and the energy-storage metabolite acetylphosphate. Structure determination at 2.1 angstroms showed that the cofactors thiamine pyrophosphate (TPP) and flavin adenine dinucleotide (FAD) are bound at the carboxyl termini of six-stranded parallel beta sheets. The pyrophosphate moiety of TPP is bound to a metal ion and to a beta alpha alpha beta unit corresponding to an established sequence fingerprint. The spatial arrangement of TPP and FAD suggests that the oxidation of the oxyethyl intermediate does not occur by hydride displacement but rather by a two-step transfer of two electrons.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muller, Y A -- Schulz, G E -- New York, N.Y. -- Science. 1993 Feb 12;259(5097):965-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8438155" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Chemistry, Physical ; Crystallization ; Flavin-Adenine Dinucleotide/metabolism/*pharmacology ; Lactobacillus/*enzymology ; Macromolecular Substances ; Molecular Sequence Data ; Molecular Structure ; Physicochemical Phenomena ; Protein Structure, Secondary ; Pyruvate Oxidase/*chemistry/metabolism ; Thiamine Pyrophosphate/metabolism/*pharmacology ; X-Ray Diffraction
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    AI helps researchers find meaning in molecules (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-08-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Freedman, D -- New York, N.Y. -- Science. 1993 Aug 13;261(5123):844-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8346437" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Artificial Intelligence ; Base Sequence ; Collagen/chemistry/genetics/physiology ; DNA/chemistry/genetics ; Humans ; Molecular Sequence Data ; Mutation ; *Protein Structure, Secondary ; *Protein Structure, Tertiary ; *Sequence Analysis, DNA ; Software
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    Nucleosome disruption by transcription factor binding in yeast (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-12-03
    Description: Studies in vivo and in vitro have shown that the packaging of DNA into chromatin can affect gene expression. Here, binding of the yeast transcriptional activator GAL4 to DNA in chromatin has been investigated in vivo with a yeast episome. A positioned nucleosome that is present in cells grown in glucose and contains a single GAL4 binding site is disrupted by GAL4 binding in galactose. GAL4 can also bind to DNA in chromatin when the carboxyl-terminal activation domain of GAL4 is either masked by GAL80 or is absent. These results show that a transcription factor can bind to its site in vivo in what would appear to be a repressive chromatin structure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morse, R H -- New York, N.Y. -- Science. 1993 Dec 3;262(5139):1563-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8248805" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; DNA-Binding Proteins/*metabolism ; Fungal Proteins/*metabolism ; Galactose/metabolism ; Glucose/metabolism ; Molecular Sequence Data ; Nucleosomes/*metabolism ; Plasmids ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/*metabolism ; *Saccharomyces cerevisiae Proteins ; Transcription Factors/*metabolism
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    Long-range photoinduced electron transfer through a DNA helix (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-11-12
    Description: Rapid photoinduced electron transfer is demonstrated over a distance of greater than 40 angstroms between metallointercalators that are tethered to the 5' termini of a 15-base pair DNA duplex. An oligomeric assembly was synthesized in which the donor is Ru(phen)2dppz2+ (phen, phenanthroline, and dppz, dipyridophenazine) and the acceptor is Rh(phi)2phen3+ (phi, phenanthrenequinone diimine). These metal complexes are intercalated either one or two base steps in from the helix termini. Although the ruthenium-modified oligonucleotide hybridized to an unmodified complement luminesces intensely, the ruthenium-modified oligomer hybridized to the rhodium-modified oligomer shows no detectable luminescence. Time-resolved studies point to a lower limit of 10(9) per second for the quenching rate. No quenching was observed upon metallation of two complementary octamers by Ru(phen)3(2+) and Rh(phen)3(3+) under conditions where the phen complexes do not intercalate. The stacked aromatic heterocycles of the DNA duplex therefore serve as an efficient medium for coupling electron donors and acceptors over very long distances.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murphy, C J -- Arkin, M R -- Jenkins, Y -- Ghatlia, N D -- Bossmann, S H -- Turro, N J -- Barton, J K -- GM49216/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Nov 12;262(5136):1025-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Beckman Institute, California Institute of Technology, Pasadena 91125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7802858" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA/*chemistry ; *Electrons ; Intercalating Agents/*chemistry ; Lasers ; Luminescence ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/*chemistry ; Organometallic Compounds/chemistry ; Phenanthrenes/chemistry ; Phenanthrolines/chemistry ; Photochemistry
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    A detailed genetic map for the X chromosome of the malaria vector, Anopheles gambiae (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-07-30
    Description: Anopheles gambiae, the primary vector of human malaria in Africa, is responsible for approximately a million deaths per year, mostly of children. Despite its significance in disease transmission, this mosquito has not been studied extensively by genetic or molecular techniques. To facilitate studies on this vector, a genetic map has been developed that covers the X chromosome at an average resolution of 2 centimorgans. This map has been integrated with the chromosome banding pattern and used to localize a recessive, sex-linked mutation (white eye) to within 1 centimorgan of flanking markers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zheng, L -- Collins, F H -- Kumar, V -- Kafatos, F C -- New York, N.Y. -- Science. 1993 Jul 30;261(5121):605-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Developmental Biology, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8342025" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Anopheles/*genetics ; Base Sequence ; Chromosome Banding ; *Chromosome Mapping ; Crosses, Genetic ; DNA, Satellite/genetics ; Female ; *Genes, Insect ; Genes, Recessive ; Genetic Markers ; Insect Vectors/*genetics ; Malaria/transmission ; Male ; Molecular Sequence Data ; Mutation ; Recombination, Genetic ; *X Chromosome
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    Generation of allospecific natural killer cells by stimulation across a polymorphism of HLA-C (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-05-21
    Description: The cytotoxicity of human natural killer (NK) cells is modulated by the major histocompatibility complex human leukocyte antigen (HLA)-C molecules on the surface of the target cell. Alloreactive NK cells specific for the NK-1 alloantigen could be reproducibly generated from individuals that were homozygous for HLA-C with asparagine at residue 77 and lysine at residue 80 [HLA-C(Asn77,Lys80)] by stimulation with target cells that were homozygous for HLA-C(Ser77,Asn80); the reciprocal stimulation yielded NK cells specific for the NK-2 alloantigen. However, neither homozygous target cell stimulated the generation of alloreactive NK cells from heterozygous individuals. Thus, these data reveal an unanticipated difference between human NK alloreactivity defined by this system and murine "hybrid resistance."〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Colonna, M -- Brooks, E G -- Falco, M -- Ferrara, G B -- Strominger, J L -- CA 47554/CA/NCI NIH HHS/ -- KO8 AI01064/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1993 May 21;260(5111):1121-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Immunogenetics, Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8493555" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Base Sequence ; Cell Line ; *Cytotoxicity, Immunologic ; Genotype ; HLA-C Antigens/genetics/*immunology ; Heterozygote ; Homozygote ; Humans ; Isoantigens/*immunology ; Killer Cells, Natural/*immunology ; Mice ; Molecular Sequence Data ; Oligodeoxyribonucleotides ; Polymorphism, Genetic
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    Systemic gene expression after intravenous DNA delivery into adult mice (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-07-09
    Description: Direct gene transfer into adult animals resulting in generalized or tissue-specific expression would facilitate rapid analysis of transgene effects and allow precise in vivo manipulation of biologic processes at the molecular level. A single intravenous injection of expression plasmid:cationic liposome complexes into adult mice efficiently transfected virtually all tissues. In addition to vascular endothelial cells, most of the extravascular parenchymal cells present in many tissues including the lung, spleen, lymph nodes, and bone marrow expressed the transgene without any apparent treatment-related toxicity. The transgene was still expressed in large numbers of cells in multiple tissues for at least 9 weeks after a single injection. Expression could be targeted to specific tissues and cell types, depending on the promoter element used.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, N -- Liggitt, D -- Liu, Y -- Debs, R -- New York, N.Y. -- Science. 1993 Jul 9;261(5118):209-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research Institute, University of California, San Francisco 94143-0128.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7687073" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Bone Marrow/metabolism ; Chloramphenicol O-Acetyltransferase/genetics ; Cystic Fibrosis/genetics ; Cystic Fibrosis Transmembrane Conductance Regulator ; Cytomegalovirus/genetics ; Female ; *Gene Expression ; Injections, Intravenous ; Liposomes ; Liver/metabolism ; Lung/metabolism ; Lung Neoplasms/genetics ; Lymphoid Tissue/metabolism ; Membrane Proteins/genetics ; Mice ; Mice, Inbred ICR ; Mice, Transgenic ; Molecular Sequence Data ; Myocardium/metabolism ; Oligodeoxyribonucleotides ; Phosphatidylethanolamines/chemistry ; Plasmids ; Quaternary Ammonium Compounds ; *Transfection
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    Mineralocorticoids, glucocorticoids, receptors and response elements (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-02-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Funder, J W -- New York, N.Y. -- Science. 1993 Feb 19;259(5098):1132-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Baker Medical Research Institute, Prahran, Victoria, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8382375" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; DNA/*metabolism ; DNA-Binding Proteins/*metabolism ; Gene Expression Regulation ; Glucocorticoids/*physiology ; Mineralocorticoids/*physiology ; Models, Biological ; Molecular Sequence Data ; Receptors, Glucocorticoid/*metabolism ; Receptors, Mineralocorticoid ; Receptors, Steroid/*metabolism ; *Transcription, Genetic
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    Binding of L-selectin to the vascular sialomucin CD34 (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-10-15
    Description: The adhesive interactions between leukocyte L-selectin and the endothelium are involved in the migration of lymphocytes through peripheral lymph nodes and of neutrophils to sites of inflammation. A recombinant L-selectin stains high endothelial venules (HEVs) in lymph nodes and recognizes sulfated carbohydrates found on two endothelial glycoproteins, Sgp50 and Sgp90. Amino acid sequencing of purified Sgp90 revealed a protein core identical to that CD34, a sialomucin expressed on hematopoietic stem cells and endothelium. A polyclonal antiserum to recombinant murine CD34 stains peripheral lymph node endothelium and recognizes Sgp90 that is functionally bound by L-selectin. Thus, an HEV glycoform of CD34 can function as a ligand for L-selectin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baumheter, S -- Singer, M S -- Henzel, W -- Hemmerich, S -- Renz, M -- Rosen, S D -- Lasky, L A -- GM 23547/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Oct 15;262(5132):436-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, Genentech, Inc., South San Francisco, CA 94080.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7692600" target="_blank"〉PubMed〈/a〉
    Keywords: 3T3 Cells ; Amino Acid Sequence ; Animals ; Antigens, CD/*metabolism ; Antigens, CD34 ; Cell Adhesion Molecules/*metabolism ; Clusterin ; Endothelium, Vascular/*metabolism ; Glycoproteins/*metabolism ; L-Selectin ; Lymph Nodes/*blood supply ; Mice ; *Molecular Chaperones ; Molecular Sequence Data ; Mucins/*metabolism ; Recombinant Proteins/metabolism ; Sialomucins
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    Distinct functions of SR proteins in alternative pre-mRNA splicing (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-04-09
    Description: Alternative splicing of precursor messenger RNAs (pre-mRNAs) is a common mechanism of regulating gene expression. SR proteins are a family of pre-mRNA splicing factors that are structurally related and evolutionarily conserved. Any member of the SR family can complement a splicing-deficient extract that lacks the entire family of SR proteins. Here it is demonstrated that particular SR proteins have distinct functions in alternative pre-mRNA splicing in vitro. In addition, SR proteins are differentially expressed in a variety of tissues. These results suggest a fundamental role for SR proteins in the regulation of alternative splicing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zahler, A M -- Neugebauer, K M -- Lane, W S -- Roth, M B -- 42786-02/PHS HHS/ -- New York, N.Y. -- Science. 1993 Apr 9;260(5105):219-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98104.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8385799" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Amino Acid Sequence ; Cell Extracts ; HeLa Cells ; Humans ; Molecular Sequence Data ; RNA Precursors/*genetics ; RNA Splicing ; RNA, Viral/genetics ; RNA-Binding Proteins/*physiology ; Simian virus 40/genetics
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    Mutation of glycine receptor subunit creates beta-alanine receptor responsive to GABA (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-10-08
    Description: The amino acid at position 160 of the ligand-binding subunit, alpha 1, is an important determinant of agonist and antagonist binding to the glycine receptor. Exchange of the neighboring residues, phenylalanine at position 159 and tyrosine at position 161, increased the efficacy of amino acid agonists. Whereas wild-type alpha 1 channels expressed in Xenopus oocytes required 0.7 millimolar beta-alanine for a half-maximal response, the doubly mutated (F159Y,Y161F) alpha 1 subunit had an affinity for beta-alanine (which was more potent than glycine) that was 110-fold that of the wild type. Also, gamma-aminobutyric acid and D-serine, amino acids that do not activate wild-type alpha 1 receptors, efficiently gated the mutant channel. Thus, aromatic hydroxyl groups are crucial for ligand discrimination at inhibitory amino acid receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmieden, V -- Kuhse, J -- Betz, H -- New York, N.Y. -- Science. 1993 Oct 8;262(5131):256-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurochemistry, Max Planck Institute for Brain Research, Frankfurt, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8211147" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Female ; Glycine/metabolism ; Ion Channel Gating/drug effects ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Oocytes ; Receptors, GABA/chemistry/metabolism ; Receptors, Glycine/chemistry/genetics/*metabolism ; Serine/pharmacology ; Taurine/pharmacology ; Xenopus ; beta-Alanine/*metabolism/pharmacology ; gamma-Aminobutyric Acid/*metabolism/pharmacology
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    Selective and ATP-dependent translocation of peptides by the MHC-encoded transporter (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-08-06
    Description: Major histocompatibility complex (MHC) class I molecules present peptides derived from nuclear and cytosolic proteins to CD8+ T cells. These peptides are translocated into the lumen of the endoplasmic reticulum (ER) to associate with class I molecules. Two MHC-encoded putative transporter proteins, TAP1 and TAP2, are required for efficient assembly of class I molecules and presentation of endogenous peptides. Expression of TAP1 and TAP2 in a mutant cell line resulted in the delivery of an 11-amino acid oligomer model peptide to the ER. Peptide translocation depended on the sequence of the peptide, was adenosine triphosphate (ATP)-dependent, required ATP hydrolysis, and was inhibited in a concentration-dependent manner.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Neefjes, J J -- Momburg, F -- Hammerling, G J -- New York, N.Y. -- Science. 1993 Aug 6;261(5122):769-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Netherlands Cancer Institute, Amsterdam.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8342042" target="_blank"〉PubMed〈/a〉
    Keywords: *ATP-Binding Cassette Transporters ; Adenosine Triphosphate/*metabolism ; Amino Acid Sequence ; Animals ; Biological Transport ; Carrier Proteins/*metabolism ; Cell Line ; Cell Membrane Permeability ; Endoplasmic Reticulum/metabolism ; Glycosylation ; Histocompatibility Antigens Class II/*metabolism ; Molecular Sequence Data ; Oligopeptides/*metabolism ; Rats ; T-Lymphocytes, Cytotoxic/*metabolism ; Transfection
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    Structure of DNA polymerase I Klenow fragment bound to duplex DNA (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-04-16
    Description: Klenow fragment of Escherichia coli DNA polymerase I, which was cocrystallized with duplex DNA, positioned 11 base pairs of DNA in a groove that lies at right angles to the cleft that contains the polymerase active site and is adjacent to the 3' to 5' exonuclease domain. When the fragment bound DNA, a region previously referred to as the "disordered domain" became more ordered and moved along with two helices toward the 3' to 5' exonuclease domain to form the binding groove. A single-stranded, 3' extension of three nucleotides bound to the 3' to 5' exonuclease active site. Although this cocrystal structure appears to be an editing complex, it suggests that the primer strand approaches the catalytic site of the polymerase from the direction of the 3' to 5' exonuclease domain and that the duplex DNA product may bend to enter the cleft that contains the polymerase catalytic site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beese, L S -- Derbyshire, V -- Steitz, T A -- GM28550/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Apr 16;260(5106):352-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8469987" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Crystallization ; DNA/chemistry/*metabolism ; DNA Polymerase I/*chemistry/metabolism ; DNA Replication ; DNA, Single-Stranded/chemistry/metabolism ; Escherichia coli/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Templates, Genetic
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  • 86
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    Cloning the differences between two complex genomes (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-02-12
    Description: The analysis of the differences between two complex genomes holds promise for the discovery of infectious agents and probes useful for genetic studies. A system was developed in which subtractive and kinetic enrichment was used to purify restriction endonuclease fragments present in one population of DNA fragments but not in another. Application of this method to DNA populations of reduced complexity ("representations") resulted in the isolation of probes to viral genomes present as single copies in human DNA, and probes that detect polymorphisms between two individuals. In principle, this system, called representational difference analysis (RDA), may also be used for isolating probes linked to sites of genomic rearrangements, whether occurring spontaneously and resulting in genetic disorders or cancer, or programmed during differentiation and development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lisitsyn, N -- Wigler, M -- New York, N.Y. -- Science. 1993 Feb 12;259(5097):946-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, NY 11724.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8438152" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviridae/genetics ; Bacteriophage lambda/genetics ; Base Sequence ; *Cloning, Molecular ; DNA/*chemistry ; DNA Probes ; DNA, Viral ; Female ; Gene Deletion ; Genetic Diseases, Inborn/genetics ; Humans ; Male ; Molecular Sequence Data ; Neoplasms/genetics ; Nucleic Acid Hybridization/methods ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Sequence Homology, Nucleic Acid
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  • 87
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    Fusion between transcription factor CBF beta/PEBP2 beta and a myosin heavy chain in acute myeloid leukemia (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-08-20
    Description: The pericentric inversion of chromosome 16 [inv(16)(p13q22)] is a characteristic karyotypic abnormality associated with acute myeloid leukemia, most commonly of the M4Eo subtype. The 16p and 16q breakpoints were pinpointed by yeast artificial chromosome and cosmid cloning, and the two genes involved in this inversion were identified. On 16q the inversion occurred near the end of the coding region for CBF beta, also known as PEBP2 beta, a subunit of a heterodimeric transcription factor regulating genes expressed in T cells; on 16p a smooth muscle myosin heavy chain (SMMHC) gene (MYH11) was interrupted. In six of six inv(16) patient samples tested, an in-frame fusion messenger RNA was demonstrated that connected the first 165 amino acids of CBF beta with the tail region of SMMHC. The repeated coiled coil of SMMHC may result in dimerization of the CBF beta fusion protein, which in turn would lead to alterations in transcriptional regulation and contribute to leukemic transformation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, P -- Tarle, S A -- Hajra, A -- Claxton, D F -- Marlton, P -- Freedman, M -- Siciliano, M J -- Collins, F S -- CA55164/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1993 Aug 20;261(5124):1041-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor 48109.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8351518" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; *Chromosome Inversion ; *Chromosomes, Human, Pair 16 ; Cloning, Molecular ; Core Binding Factor Alpha 1 Subunit ; Core Binding Factor beta Subunit ; Core Binding Factors ; Cosmids ; DNA-Binding Proteins/*genetics ; Humans ; In Situ Hybridization, Fluorescence ; Leukemia, Myelomonocytic, Acute/*genetics ; Molecular Sequence Data ; Muscle, Smooth/chemistry ; Myosins/*genetics ; *Neoplasm Proteins ; Polymerase Chain Reaction ; Protein Multimerization ; Restriction Mapping ; Transcription Factor AP-2 ; Transcription Factors/*genetics
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  • 88
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    Benzodiazepine peptidomimetics: potent inhibitors of Ras farnesylation in animal cells (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-06-25
    Description: Oncogenic Ras proteins transform animal cells to a malignant phenotype only when modified by farnesyl residues attached to cysteines near their carboxyl termini. The farnesyltransferase that catalyzes this reaction recognizes tetrapeptides of the sequence CAAX, where C is cysteine, A is an aliphatic amino acid, and X is a carboxyl-terminal methionine or serine. Replacement of the two aliphatic residues with a benzodiazepine-based mimic of a peptide turn generated potent inhibitors of farnesyltransferase [50 percent inhibitory concentration (IC50) 〈 1 nM]. Unlike tetrapeptides, the benzodiazepine peptidomimetics enter cells and block attachment of farnesyl to Ras, nuclear lamins, and several other proteins. At micromolar concentrations, these inhibitors restored a normal growth pattern to Ras-transformed cells. The benzodiazepine peptidomimetics may be useful in the design of treatments for tumors in which oncogenic Ras proteins contribute to abnormal growth, such as that of the colon, lung, and pancreas.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉James, G L -- Goldstein, J L -- Brown, M S -- Rawson, T E -- Somers, T C -- McDowell, R S -- Crowley, C W -- Lucas, B K -- Levinson, A D -- Marsters, J C Jr -- HL 20948/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1993 Jun 25;260(5116):1937-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas 75235.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8316834" target="_blank"〉PubMed〈/a〉
    Keywords: *Alkyl and Aryl Transferases ; Amino Acid Sequence ; Animals ; Antineoplastic Agents/chemistry/*pharmacology ; Benzodiazepinones/chemistry/*pharmacology ; CHO Cells ; Cell Division/drug effects ; Cell Line, Transformed ; Cell Transformation, Neoplastic/drug effects ; Cricetinae ; Drug Design ; Farnesyltranstransferase ; Molecular Sequence Data ; Oligopeptides/pharmacology ; Oncogene Proteins/*metabolism ; Protein Prenylation/*drug effects ; Transferases/*antagonists & inhibitors
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  • 89
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    Isolation of ORC6, a component of the yeast origin recognition complex by a one-hybrid system (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-12-17
    Description: Here a method is described to identify genes encoding proteins that recognize a specific DNA sequence. A bank of random protein segments tagged with a transcriptional activation domain is screened for proteins that can activate a reporter gene containing the sequence in its promoter. This strategy was used to identify an essential protein that interacts in vivo with the yeast origin of DNA replication. Matches between its predicted amino acid sequence and peptide sequence obtained from the 50-kilodalton subunit of the yeast origin recognition complex (ORC) established that the gene isolated here, ORC6, encodes this subunit. These observations provide evidence that ORC recognizes yeast replication origins in vivo.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, J J -- Herskowitz, I -- AI18738/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1993 Dec 17;262(5141):1870-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8266075" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Cell Cycle ; *DNA Replication ; DNA, Fungal/metabolism ; DNA-Binding Proteins/chemistry/*genetics/metabolism ; Fungal Proteins/chemistry/*genetics/metabolism ; *Genes, Fungal ; Genes, Reporter ; Molecular Sequence Data ; Open Reading Frames ; Origin Recognition Complex ; Promoter Regions, Genetic ; *Replicon ; Repressor Proteins/chemistry/*genetics/metabolism ; Saccharomyces cerevisiae/cytology/*genetics/metabolism ; Saccharomyces cerevisiae Proteins
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  • 90
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    Electrostatic screening of charge and dipole interactions with the helix backbone (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-04-09
    Description: Electrostatic interactions in proteins are potentially quite strong, but these interactions are mitigated by the screening effects of water, ions, and nearby protein atoms. The early work of Kirkwood and Westheimer on small organic molecules showed that the extent of the screening may depend on whether charged or dipolar groups are involved. The dielectric and ionic screening of the interactions between the dipolar backbone amide groups of monomeric alpha helices and either (i) solvent-exposed charges or (ii) solvent-exposed dipoles at the amino terminus was measured. The dielectric screening effects are an order of magnitude greater for the backbone-charge interactions than for the backbone-dipole interactions, and the ionic strength dependence is substantially different in the two cases. These results suggest that interactions that involve the dipolar groups of proteins may be relatively more important for stability and function than is generally thought.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lockhart, D J -- Kim, P S -- New York, N.Y. -- Science. 1993 Apr 9;260(5105):198-202.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge Center 02142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8469972" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Circular Dichroism ; Electrochemistry ; Hydrogen-Ion Concentration ; Magnetic Resonance Spectroscopy ; Molecular Sequence Data ; Osmolar Concentration ; Peptides/*chemistry ; Protein Structure, Secondary ; Thermodynamics
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  • 91
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    Phosphatidylinositol 3-kinase encoded by yeast VPS34 gene essential for protein sorting (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-04-02
    Description: The VPS34 gene product (Vps34p) is required for protein sorting to the lysosome-like vacuole of the yeast Saccharomyces cerevisiae. Vps34p shares significant sequence similarity with the catalytic subunit of bovine phosphatidylinositol (PI) 3-kinase [the 110-kilodalton (p110) subunit of PI 3-kinase], which is known to interact with activated cell surface receptor tyrosine kinases. Yeast strains deleted for the VPS34 gene or carrying vps34 point mutations lacked detectable PI 3-kinase activity and exhibited severe defects in vacuolar protein sorting. Overexpression of Vps34p resulted in an increase in PI 3-kinase activity, and this activity was specifically precipitated with antisera to Vps34p. VPS34 encodes a yeast PI 3-kinase, and this enzyme appears to regulate intracellular protein trafficking decisions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schu, P V -- Takegawa, K -- Fry, M J -- Stack, J H -- Waterfield, M D -- Emr, S D -- New York, N.Y. -- Science. 1993 Apr 2;260(5104):88-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8385367" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Brain/enzymology ; Cattle ; Chromatography, High Pressure Liquid ; Fungal Proteins/*metabolism ; Gene Deletion ; Gene Expression ; *Genes, Fungal ; Lysosomes/metabolism ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Phosphatidylinositol 3-Kinases ; Phosphotransferases/chemistry/*genetics/metabolism ; Point Mutation ; Saccharomyces cerevisiae/enzymology/*genetics ; Sequence Homology, Amino Acid ; Signal Transduction ; Vacuoles/metabolism
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  • 92
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    Genetic identification of a hantavirus associated with an outbreak of acute respiratory illness (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-11-05
    Description: A mysterious respiratory illness with high mortality was recently reported in the southwestern United States. Serologic studies implicated the hantaviruses, rodent-borne RNA viruses usually associated elsewhere in the world with hemorrhagic fever with renal syndrome. A genetic detection assay amplified hantavirus-specific DNA fragments from RNA extracted from the tissues of patients and deer mice (Peromyscus maniculatus) caught at or near patient residences. Nucleotide sequence analysis revealed the associated virus to be a new hantavirus and provided a direct genetic link between infection in patients and rodents.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nichol, S T -- Spiropoulou, C F -- Morzunov, S -- Rollin, P E -- Ksiazek, T G -- Feldmann, H -- Sanchez, A -- Childs, J -- Zaki, S -- Peters, C J -- New York, N.Y. -- Science. 1993 Nov 5;262(5135):914-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Viral and Rickettsial Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8235615" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Bunyaviridae Infections/epidemiology/*microbiology/veterinary ; DNA Primers ; *Disease Outbreaks ; *Disease Reservoirs ; *Genome, Viral ; Hantavirus/classification/*genetics/isolation & purification ; Humans ; Lung Diseases/epidemiology/*microbiology ; Molecular Sequence Data ; Peromyscus/*microbiology ; Phylogeny ; Polymerase Chain Reaction ; Rodent Diseases/epidemiology/microbiology ; Sequence Homology, Nucleic Acid ; Southwestern United States/epidemiology
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  • 93
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    A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-11-26
    Description: A DNA sequence rich in (A+T), located upstream of the -10, -35 region of the Escherichia coli ribosomal RNA promoter rrnB P1 and called the UP element, stimulates transcription by a factor of 30 in vivo, as well as in vitro in the absence of protein factors other than RNA polymerase (RNAP). When fused to other promoters, such as lacUV5, the UP element also stimulates transcription, indicating that it is a separate promoter module. Mutations in the carboxyl-terminal region of the alpha subunit of RNAP prevent stimulation of these promoters by the UP element although the mutant enzymes are effective in transcribing the "core" promoters (those lacking the UP element). Protection of UP element DNA by the mutant RNAPs is severely reduced in footprinting experiments, suggesting that the selective decrease in transcription might result from defective interactions between alpha and the UP element. Purified alpha binds specifically to the UP element, confirming that alpha acts directly in promoter recognition. Transcription of three other promoters was also reduced by the COOH-terminal alpha mutations. These results suggest that UP elements comprise a third promoter recognition region (in addition to the -10, -35 recognition hexamers, which interact with the sigma subunit) and may account for the presence of (A+T)-rich DNA upstream of many prokaryotic promoters. Since the same alpha mutations also block activation by some transcription factors, mechanisms of promoter stimulation by upstream DNA elements and positive control by certain transcription factors may be related.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ross, W -- Gosink, K K -- Salomon, J -- Igarashi, K -- Zou, C -- Ishihama, A -- Severinov, K -- Gourse, R L -- AI90035/AI/NIAID NIH HHS/ -- GM49242/GM/NIGMS NIH HHS/ -- R01 GM37048/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Nov 26;262(5138):1407-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bacteriology, University of Wisconsin-Madison 53706.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8248780" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Carrier Proteins/metabolism ; DNA, Bacterial/*metabolism ; DNA-Binding Proteins/metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Escherichia coli/enzymology/*genetics ; *Escherichia coli Proteins ; Integration Host Factors ; Molecular Sequence Data ; *Promoter Regions, Genetic ; Transcription Factors/metabolism ; Transcription, Genetic ; *rRNA Operon
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  • 94
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    Identification of the von Hippel-Lindau disease tumor suppressor gene (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-05-28
    Description: A gene discovered by positional cloning has been identified as the von Hippel-Lindau (VHL) disease tumor suppressor gene. A restriction fragment encompassing the gene showed rearrangements in 28 of 221 VHL kindreds. Eighteen of these rearrangements were due to deletions in the candidate gene, including three large nonoverlapping deletions. Intragenic mutations were detected in cell lines derived from VHL patients and from sporadic renal cell carcinomas. The VHL gene is evolutionarily conserved and encodes two widely expressed transcripts of approximately 6 and 6.5 kilobases. The partial sequence of the inferred gene product shows no homology to other proteins, except for an acidic repeat domain found in the procyclic surface membrane glycoprotein of Trypanosoma brucei.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Latif, F -- Tory, K -- Gnarra, J -- Yao, M -- Duh, F M -- Orcutt, M L -- Stackhouse, T -- Kuzmin, I -- Modi, W -- Geil, L -- New York, N.Y. -- Science. 1993 May 28;260(5112):1317-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Immunobiology, National Cancer Institute-Frederick Cancer Research and Development Center (NCI-FCRDC), Frederick, MD 21702-1201.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8493574" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Carcinoma, Renal Cell/genetics ; Chromosomes, Human, Pair 3 ; Cloning, Molecular ; Gene Deletion ; *Genes, Tumor Suppressor ; Humans ; Kidney Neoplasms/genetics ; Membrane Glycoproteins/chemistry/*genetics ; Molecular Sequence Data ; Mutation ; Open Reading Frames ; Pedigree ; Polymorphism, Genetic ; Tumor Cells, Cultured ; von Hippel-Lindau Disease/*genetics
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  • 95
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    Association of the APC gene product with beta-catenin (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-12-10
    Description: Mutations in the human APC gene are linked to familial adenomatous polyposis and to the progression of sporadic colorectal and gastric tumors. To gain insight into APC function, APC-associated proteins were identified by immunoprecipitation experiments. Antibodies to APC precipitated a 95-kilodalton protein that was purified and identified by sequencing as beta-catenin, a protein that binds to the cell adhesion molecule E-cadherin. An antibody specific to beta-catenin also recognized the 95-kilodalton protein in the immunoprecipitates. These results suggest that APC is involved in cell adhesion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rubinfeld, B -- Souza, B -- Albert, I -- Muller, O -- Chamberlain, S H -- Masiarz, F R -- Munemitsu, S -- Polakis, P -- New York, N.Y. -- Science. 1993 Dec 10;262(5140):1731-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Onyx Pharmaceuticals, Richmond, CA 94806.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8259518" target="_blank"〉PubMed〈/a〉
    Keywords: Adenomatous Polyposis Coli Protein ; Amino Acid Sequence ; Antibodies ; Cadherins/*metabolism ; Cell Adhesion ; Cell Line ; Colonic Neoplasms/genetics/*metabolism ; Cytoskeletal Proteins/chemistry/isolation & purification/*metabolism ; *Genes, APC ; Humans ; Molecular Sequence Data ; Neoplasm Proteins/genetics/immunology/*metabolism ; Precipitin Tests ; *Trans-Activators ; Tumor Cells, Cultured ; beta Catenin
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  • 96
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    Crystal structure of the repetitive segments of spectrin (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-12-24
    Description: The elongated proteins of the spectrin family (dystrophin, alpha-actinin, and spectrin) contain tandemly repeated segments and form resilient cellular meshworks by cross-linking actin filaments. The structure of one of the repetitive segments of alpha-spectrin was determined at a 1.8 angstrom resolution. A segment consists of a three-helix bundle. A model of the interface between two tandem segments suggests that hydrophobic interactions between segments may constrain intersegment flexibility. The helix side chain interactions explain how mutations that are known to produce hemolytic anemias disrupt spectrin associations that sustain the integrity of the erythrocyte membrane.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yan, Y -- Winograd, E -- Viel, A -- Cronin, T -- Harrison, S C -- Branton, D -- CA 13202/CA/NCI NIH HHS/ -- HL 17411/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1993 Dec 24;262(5142):2027-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8266097" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Crystallization ; Drosophila ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Spectrin/*chemistry
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    Alterations of a zinc finger-encoding gene, BCL-6, in diffuse large-cell lymphoma (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-10-29
    Description: The molecular pathogenesis of diffuse large-cell lymphoma (DLCL), the most frequent and clinically relevant type of lymphoma, is unknown. A gene was cloned from chromosomal translocations affecting band 3q27, which are common in DLCL. This gene, BCL-6, codes for a 79-kilodalton protein that is homologous with zinc finger-transcription factors. In 33 percent (13 of 39) of DLCL samples, but not in other types of lymphoid malignancies, the BCL-6 gene is truncated within its 5' noncoding sequences, suggesting that its expression is deregulated. Thus, BCL-6 may be a proto-oncogene specifically involved in the pathogenesis of DLCL.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ye, B H -- Lista, F -- Lo Coco, F -- Knowles, D M -- Offit, K -- Chaganti, R S -- Dalla-Favera, R -- CA 44029/CA/NCI NIH HHS/ -- CA 48236/CA/NCI NIH HHS/ -- EY 06337/EY/NEI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1993 Oct 29;262(5134):747-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, College of Physicians and Surgeons, Columbia University, New York, NY 10032.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8235596" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Line ; Chromosomes, Human, Pair 3 ; DNA, Complementary ; DNA-Binding Proteins/genetics ; Exons ; Gene Rearrangement ; Humans ; Introns ; Lymphoma, Large B-Cell, Diffuse/*genetics ; Molecular Sequence Data ; Proto-Oncogene Proteins/genetics ; Proto-Oncogene Proteins c-bcl-6 ; Proto-Oncogenes/*genetics ; Sequence Homology, Amino Acid ; Transcription Factors/genetics ; Translocation, Genetic ; Zinc Fingers/*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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  • 98
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    Induction by EGF and interferon-gamma of tyrosine phosphorylated DNA binding proteins in mouse liver nuclei (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-09-24
    Description: Intraperitoneal injection of epidermal growth factor (EGF) into mice resulted in the appearance in liver nuclei of three tyrosine phosphorylated proteins (84, 91, and 92 kilodaltons) within minutes after administration of EGF. Administration of interferon-gamma (IFN-gamma) resulted in the appearance in liver nuclei of two tyrosine phosphorylated proteins (84 and 91 kilodaltons). The 84- and 91-kilodalton proteins detected after either EGF or IFN-gamma administration were identified as the IFN-gamma activation factors (GAF). Furthermore, gel shift analysis revealed that these GAF proteins, detected after either EGF or IFN-gamma administration, specifically bound to the sis-inducible element of the c-fos promoter. Thus, GAF proteins participate in nuclear signaling in both IFN-gamma and EGF pathways.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ruff-Jamison, S -- Chen, K -- Cohen, S -- HD-00700/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 1993 Sep 24;261(5129):1733-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8378774" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Cell Nucleus/drug effects/*metabolism ; DNA-Binding Proteins/*metabolism ; Epidermal Growth Factor/*pharmacology ; Genes, fos ; Interferon-Stimulated Gene Factor 3 ; Interferon-gamma/*pharmacology ; Liver/drug effects/metabolism ; Mice ; Molecular Sequence Data ; Phosphorylation ; Promoter Regions, Genetic ; STAT1 Transcription Factor ; *Trans-Activators ; Transcription Factors/*metabolism ; Tyrosine/*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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  • 99
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    Structure of the retinoid X receptor alpha DNA binding domain: a helix required for homodimeric DNA binding (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-05-21
    Description: The three-dimensional solution structure of the DNA binding domain (DBD) of the retinoid X receptor alpha (RXR alpha) was determined by nuclear magnetic resonance spectroscopy. The two zinc fingers of the RXR DBD fold to form a single structural domain that consists of two perpendicularly oriented helices and that resembles the corresponding regions of the glucocorticoid and estrogen receptors (GR and ER, respectively). However, in contrast to the DBDs of the GR and ER, the RXR DBD contains an additional helix immediately after the second zinc finger. This third helix mediates both protein-protein and protein-DNA interactions required for cooperative, dimeric binding of the RXR DBD to DNA. Identification of the third helix in the RXR DBD thus defines a structural feature required for selective dimerization of the RXR on hormone response elements composed of half-sites (5'-AGGTCA-3') arranged as tandem repeats.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, M S -- Kliewer, S A -- Provencal, J -- Wright, P E -- Evans, R M -- New York, N.Y. -- Science. 1993 May 21;260(5111):1117-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8388124" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; DNA/*metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Nuclear Proteins/*chemistry/metabolism ; Oligodeoxyribonucleotides ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Cell Surface/*chemistry/metabolism ; *Receptors, Retinoic Acid ; Repetitive Sequences, Nucleic Acid ; Retinoid X Receptors ; *Transcription Factors ; Zinc Fingers
    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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  • 100
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    Molecular mapping and detoxification of the lipid A binding site by synthetic peptides (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-01-15
    Description: Endotoxin [lipopolysaccharide (LPS)], the major antigen of the outer membrane of Gram-negative bacteria, consists of a variable-size carbohydrate chain that is covalently linked to N,O-acylated beta-1,6-D-glucosamine disaccharide 1,4'-bisphosphate (lipid A). The toxic activity of LPS resides in the lipid A structure. The structural features of synthetic peptides that bind to lipid A with high affinity, detoxify LPS in vitro, and prevent LPS-induced cytokine release and lethality in vivo were defined. The binding thermodynamics were comparable to that of an antigen-antibody reaction. Such synthetic peptides may provide a strategy for prophylaxis and treatment of LPS-mediated diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rustici, A -- Velucchi, M -- Faggioni, R -- Sironi, M -- Ghezzi, P -- Quataert, S -- Green, B -- Porro, M -- New York, N.Y. -- Science. 1993 Jan 15;259(5093):361-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biosynth Research Laboratories, Siena, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8420003" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding, Competitive ; Bordetella pertussis/chemistry ; Escherichia coli/chemistry ; Hydrogen-Ion Concentration ; Limulus Test ; Lipid A/chemistry/*metabolism/toxicity ; Lipopolysaccharides/chemistry/*metabolism/toxicity ; Mice ; Mice, Inbred BALB C ; Micelles ; Microscopy, Electron ; Molecular Sequence Data ; Peptides/chemical synthesis/chemistry/*metabolism ; Polymyxin B/chemistry/*metabolism ; Protein Conformation ; Temperature
    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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