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  • Base Sequence  (5)
  • Population Dynamics  (5)
  • Chemistry  (4)
  • American Association for the Advancement of Science (AAAS)  (14)
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  • 1
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    [Perspective] How to break down crystalline cellulose (2016)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2016-05-27
    Description: Biomass-degrading microorganisms use lytic polysaccharide monooxygenase (LPMO) enzymes to help digest cellulose, chitin, and starch. By cleaving otherwise inaccessible crystalline cellulose chains, these enzymes provide access to hydrolytic enzymes. LPMOs are of interest to biotechnology because efficient depolymerization of cellulose is a major bottleneck for the production of biologically based chemicals and fuels. On page 1098 of this issue, Kracher et al. (1) compare LPMO-reducing substrates in fungi from different taxonomic groups and lifestyles, based on both biochemical and genomic evidence. The results provide insights into reductive activation of LPMO that are important for developing more efficient industrial enzymes for lignocellulose biorefineries. Author: Angel T. Martínez
    Keywords: Chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-12-14
    Description: The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dehal, Paramvir -- Satou, Yutaka -- Campbell, Robert K -- Chapman, Jarrod -- Degnan, Bernard -- De Tomaso, Anthony -- Davidson, Brad -- Di Gregorio, Anna -- Gelpke, Maarten -- Goodstein, David M -- Harafuji, Naoe -- Hastings, Kenneth E M -- Ho, Isaac -- Hotta, Kohji -- Huang, Wayne -- Kawashima, Takeshi -- Lemaire, Patrick -- Martinez, Diego -- Meinertzhagen, Ian A -- Necula, Simona -- Nonaka, Masaru -- Putnam, Nik -- Rash, Sam -- Saiga, Hidetoshi -- Satake, Masanobu -- Terry, Astrid -- Yamada, Lixy -- Wang, Hong-Gang -- Awazu, Satoko -- Azumi, Kaoru -- Boore, Jeffrey -- Branno, Margherita -- Chin-Bow, Stephen -- DeSantis, Rosaria -- Doyle, Sharon -- Francino, Pilar -- Keys, David N -- Haga, Shinobu -- Hayashi, Hiroko -- Hino, Kyosuke -- Imai, Kaoru S -- Inaba, Kazuo -- Kano, Shungo -- Kobayashi, Kenji -- Kobayashi, Mari -- Lee, Byung-In -- Makabe, Kazuhiro W -- Manohar, Chitra -- Matassi, Giorgio -- Medina, Monica -- Mochizuki, Yasuaki -- Mount, Steve -- Morishita, Tomomi -- Miura, Sachiko -- Nakayama, Akie -- Nishizaka, Satoko -- Nomoto, Hisayo -- Ohta, Fumiko -- Oishi, Kazuko -- Rigoutsos, Isidore -- Sano, Masako -- Sasaki, Akane -- Sasakura, Yasunori -- Shoguchi, Eiichi -- Shin-i, Tadasu -- Spagnuolo, Antoinetta -- Stainier, Didier -- Suzuki, Miho M -- Tassy, Olivier -- Takatori, Naohito -- Tokuoka, Miki -- Yagi, Kasumi -- Yoshizaki, Fumiko -- Wada, Shuichi -- Zhang, Cindy -- Hyatt, P Douglas -- Larimer, Frank -- Detter, Chris -- Doggett, Norman -- Glavina, Tijana -- Hawkins, Trevor -- Richardson, Paul -- Lucas, Susan -- Kohara, Yuji -- Levine, Michael -- Satoh, Nori -- Rokhsar, Daniel S -- HD-37105/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2002 Dec 13;298(5601):2157-67.〈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/12481130" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Apoptosis ; Base Sequence ; Cellulose/metabolism ; Central Nervous System/physiology ; Ciona intestinalis/anatomy & histology/classification/*genetics/physiology ; Computational Biology ; Endocrine System/physiology ; Gene Dosage ; Gene Duplication ; Genes ; Genes, Homeobox ; *Genome ; Heart/embryology/physiology ; Immunity/genetics ; Molecular Sequence Data ; Multigene Family ; Muscle Proteins/genetics ; Organizers, Embryonic/physiology ; Phylogeny ; Polymorphism, Genetic ; Proteins/genetics/physiology ; *Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; Thyroid Gland/physiology ; Urochordata/genetics ; Vertebrates/anatomy & histology/classification/genetics/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Oncostatin M as a potent mitogen for AIDS-Kaposi's sarcoma-derived cells (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-03-13
    Description: Oncostatin M, a cytokine produced by activated lymphoid cells, regulates the growth and differentiation of a number of tumor and normal cells. In contrast to its effects on normal endothelial and aortic smooth muscle cell cultures, Oncostatin M was a potent mitogen for cells derived from acquired immunodeficiency syndrome-related Kaposi's sarcoma (AIDS-KS). After exposure to Oncostatin M, AIDS-KS cells assumed a spindle morphology, had an increased ability to proliferate in soft agar, and secreted increased amounts of interleukin-6. Oncostatin M RNA and immunoreactive Oncostatin M protein were found in AIDS-KS-derived cell isolates. These results suggest that Oncostatin M may play a role in the pathogenesis of AIDS-KS.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miles, S A -- Martinez-Maza, O -- Rezai, A -- Magpantay, L -- Kishimoto, T -- Nakamura, S -- Radka, S F -- Linsley, P S -- AI27660/AI/NIAID NIH HHS/ -- CA 01588/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Mar 13;255(5050):1432-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UCLA AIDS Center 90024.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1542793" target="_blank"〉PubMed〈/a〉
    Keywords: Acquired Immunodeficiency Syndrome/*complications ; Base Sequence ; Cell Division/drug effects ; Growth Substances/biosynthesis/*physiology ; Humans ; Molecular Sequence Data ; Neoplasm Proteins/biosynthesis ; Oncostatin M ; Peptide Biosynthesis ; Peptides/*physiology ; Recombinant Proteins/pharmacology ; Sarcoma, Kaposi/etiology/metabolism/*pathology ; Tumor Cells, Cultured
    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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    Climate-driven basin-scale decadal oscillations of oceanic phytoplankton (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-12-08
    Description: Phytoplankton--the microalgae that populate the upper lit layers of the ocean--fuel the oceanic food web and affect oceanic and atmospheric carbon dioxide levels through photosynthetic carbon fixation. Here, we show that multidecadal changes in global phytoplankton abundances are related to basin-scale oscillations of the physical ocean, specifically the Pacific Decadal Oscillation and the Atlantic Multidecadal Oscillation. This relationship is revealed in approximately 20 years of satellite observations of chlorophyll and sea surface temperature. Interaction between the main pycnocline and the upper ocean seasonal mixed layer is one mechanism behind this correlation. Our findings provide a context for the interpretation of contemporary changes in global phytoplankton and should improve predictions of their future evolution with climate change.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Martinez, Elodie -- Antoine, David -- D'Ortenzio, Fabrizio -- Gentili, Bernard -- New York, N.Y. -- Science. 2009 Nov 27;326(5957):1253-6. doi: 10.1126/science.1177012.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UPMC University of Paris 06, UMR 7093, Laboratoire d'Oceanographie de Villefranche (LOV), 06230 Villefranche-sur-Mer, France. martinez@obs-vlfr.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965473" target="_blank"〉PubMed〈/a〉
    Keywords: Atlantic Ocean ; Biomass ; Chlorophyll/*analysis ; *Climate ; *Ecosystem ; Global Warming ; Indian Ocean ; Oceans and Seas ; Pacific Ocean ; Phytoplankton/*physiology ; Population Dynamics ; Seasons ; *Seawater/chemistry ; Temperature ; Time Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Ecology. Ecology for a crowded planet (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Palmer, Margaret -- Bernhardt, Emily -- Chornesky, Elizabeth -- Collins, Scott -- Dobson, Andrew -- Duke, Clifford -- Gold, Barry -- Jacobson, Robert -- Kingsland, Sharon -- Kranz, Rhonda -- Mappin, Michael -- Martinez, M Luisa -- Micheli, Fiorenza -- Morse, Jennifer -- Pace, Michael -- Pascual, Mercedes -- Palumbi, Stephen -- Reichman, O J -- Simons, Ashley -- Townsend, Alan -- Turner, Monica -- New York, N.Y. -- Science. 2004 May 28;304(5675):1251-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Maryland, College Park, MD, USA. mpalmer@umd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15166349" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Communicable Diseases/transmission ; Conservation of Natural Resources ; *Ecology ; *Ecosystem ; Environment ; Forecasting ; Fresh Water ; Health ; Human Activities ; Humans ; Population Dynamics ; *Research ; Urbanization
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Comment on "Foraging adaptation and the relationship between food-web complexity and stability" (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brose, Ulrich -- Williams, Richard J -- Martinez, Neo D -- New York, N.Y. -- Science. 2003 Aug 15;301(5635):918; author reply 918.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Romberg Tiburon Center, Department of Biology, San Francisco State University, 3152 Paradise Drive, Tiburon, CA 94920, USA. brose@sfsu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12920282" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Biological ; Animals ; *Ecosystem ; *Feeding Behavior ; *Food Chain ; *Models, Biological ; Population Dynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Imaging CF3I conical intersection and photodissociation dynamics with ultrafast electron diffraction (2018)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2018-07-06
    Description: Conical intersections play a critical role in excited-state dynamics of polyatomic molecules because they govern the reaction pathways of many nonadiabatic processes. However, ultrafast probes have lacked sufficient spatial resolution to image wave-packet trajectories through these intersections directly. Here, we present the simultaneous experimental characterization of one-photon and two-photon excitation channels in isolated CF 3 I molecules using ultrafast gas-phase electron diffraction. In the two-photon channel, we have mapped out the real-space trajectories of a coherent nuclear wave packet, which bifurcates onto two potential energy surfaces when passing through a conical intersection. In the one-photon channel, we have resolved excitation of both the umbrella and the breathing vibrational modes in the CF 3 fragment in multiple nuclear dimensions. These findings benchmark and validate ab initio nonadiabatic dynamics calculations.
    Keywords: Chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Community genomics among stratified microbial assemblages in the ocean's interior (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-01-28
    Description: Microbial life predominates in the ocean, yet little is known about its genomic variability, especially along the depth continuum. We report here genomic analyses of planktonic microbial communities in the North Pacific Subtropical Gyre, from the ocean's surface to near-sea floor depths. Sequence variation in microbial community genes reflected vertical zonation of taxonomic groups, functional gene repertoires, and metabolic potential. The distributional patterns of microbial genes suggested depth-variable community trends in carbon and energy metabolism, attachment and motility, gene mobility, and host-viral interactions. Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeLong, Edward F -- Preston, Christina M -- Mincer, Tracy -- Rich, Virginia -- Hallam, Steven J -- Frigaard, Niels-Ulrik -- Martinez, Asuncion -- Sullivan, Matthew B -- Edwards, Robert -- Brito, Beltran Rodriguez -- Chisholm, Sallie W -- Karl, David M -- New York, N.Y. -- Science. 2006 Jan 27;311(5760):496-503.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts Institute of Technology, Cambridge, MA 02139, USA. delong@mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439655" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Archaea/classification/*genetics/metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Bacteriophages/genetics ; Base Sequence ; Cloning, Molecular ; Cluster Analysis ; Computational Biology ; Cosmids ; DNA, Viral/chemistry/genetics ; Ecosystem ; Gene Library ; *Genes, Archaeal ; *Genes, Bacterial ; Genes, rRNA ; *Genomics ; Molecular Sequence Data ; Pacific Ocean ; Seawater/*microbiology ; Sequence Analysis, DNA ; Water Microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-04-10
    Description: Transcription factors (TFs) direct gene expression by binding to DNA regulatory regions. To explore the evolution of gene regulation, we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine experimentally the genome-wide occupancy of two TFs, CCAAT/enhancer-binding protein alpha and hepatocyte nuclear factor 4 alpha, in the livers of five vertebrates. Although each TF displays highly conserved DNA binding preferences, most binding is species-specific, and aligned binding events present in all five species are rare. Regions near genes with expression levels that are dependent on a TF are often bound by the TF in multiple species yet show no enhanced DNA sequence constraint. Binding divergence between species can be largely explained by sequence changes to the bound motifs. Among the binding events lost in one lineage, only half are recovered by another binding event within 10 kilobases. Our results reveal large interspecies differences in transcriptional regulation and provide insight into regulatory evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008766/" 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/PMC3008766/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmidt, Dominic -- Wilson, Michael D -- Ballester, Benoit -- Schwalie, Petra C -- Brown, Gordon D -- Marshall, Aileen -- Kutter, Claudia -- Watt, Stephen -- Martinez-Jimenez, Celia P -- Mackay, Sarah -- Talianidis, Iannis -- Flicek, Paul -- Odom, Duncan T -- 062023/Wellcome Trust/United Kingdom -- 079643/Wellcome Trust/United Kingdom -- 15603/Cancer Research UK/United Kingdom -- 202218/European Research Council/International -- A15603/Cancer Research UK/United Kingdom -- WT062023/Wellcome Trust/United Kingdom -- WT079643/Wellcome Trust/United Kingdom -- Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2010 May 21;328(5981):1036-40. doi: 10.1126/science.1186176. Epub 2010 Apr 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20378774" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; Base Sequence ; Binding Sites ; Biological Evolution ; CCAAT-Enhancer-Binding Protein-alpha/*metabolism ; Chickens/genetics ; Chromatin Immunoprecipitation ; DNA/genetics/metabolism ; Dogs ; *Evolution, Molecular ; *Gene Expression Regulation ; *Genome ; Genome, Human ; Hepatocyte Nuclear Factor 4/*metabolism ; Humans ; Liver/*metabolism ; Mice ; Opossums/genetics ; Protein Binding ; Regulatory Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Species Specificity ; Vertebrates/*genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Erosion of lizard diversity by climate change and altered thermal niches (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-15
    Description: It is predicted that climate change will cause species extinctions and distributional shifts in coming decades, but data to validate these predictions are relatively scarce. Here, we compare recent and historical surveys for 48 Mexican lizard species at 200 sites. Since 1975, 12% of local populations have gone extinct. We verified physiological models of extinction risk with observed local extinctions and extended projections worldwide. Since 1975, we estimate that 4% of local populations have gone extinct worldwide, but by 2080 local extinctions are projected to reach 39% worldwide, and species extinctions may reach 20%. Global extinction projections were validated with local extinctions observed from 1975 to 2009 for regional biotas on four other continents, suggesting that lizards have already crossed a threshold for extinctions caused by climate change.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sinervo, Barry -- Mendez-de-la-Cruz, Fausto -- Miles, Donald B -- Heulin, Benoit -- Bastiaans, Elizabeth -- Villagran-Santa Cruz, Maricela -- Lara-Resendiz, Rafael -- Martinez-Mendez, Norberto -- Calderon-Espinosa, Martha Lucia -- Meza-Lazaro, Rubi Nelsi -- Gadsden, Hector -- Avila, Luciano Javier -- Morando, Mariana -- De la Riva, Ignacio J -- Victoriano Sepulveda, Pedro -- Rocha, Carlos Frederico Duarte -- Ibarguengoytia, Nora -- Aguilar Puntriano, Cesar -- Massot, Manuel -- Lepetz, Virginie -- Oksanen, Tuula A -- Chapple, David G -- Bauer, Aaron M -- Branch, William R -- Clobert, Jean -- Sites, Jack W Jr -- New York, N.Y. -- Science. 2010 May 14;328(5980):894-9. doi: 10.1126/science.1184695.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA. lizardrps@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20466932" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization ; Animals ; *Biodiversity ; Biological Evolution ; Body Temperature ; *Climate Change ; *Ecosystem ; *Extinction, Biological ; Female ; Forecasting ; Geography ; Global Warming ; *Lizards/genetics/physiology ; Male ; Mexico ; Models, Biological ; Phylogeny ; Population Dynamics ; Reproduction ; Seasons ; Selection, Genetic ; Temperature
    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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