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  • 1
    Publication Date: 2016-01-07
    Description: The MetaCyc database ( MetaCyc.org ) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. The majority of MetaCyc pathways are small-molecule metabolic pathways that have been experimentally determined. MetaCyc contains more than 2400 pathways derived from 〉46 000 publications, and is the largest curated collection of metabolic pathways. BioCyc ( BioCyc.org ) is a collection of 5700 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems, and pathway-hole fillers. The BioCyc website offers a variety of tools for querying and analyzing PGDBs, including Omics Viewers and tools for comparative analysis. This article provides an update of new developments in MetaCyc and BioCyc during the last two years, including addition of Gibbs free energy values for compounds and reactions; redesign of the primary gene/protein page; addition of a tool for creating diagrams containing multiple linked pathways; several new search capabilities, including searching for genes based on sequence patterns, searching for databases based on an organism's phenotypes, and a cross-organism search; and a metabolite identifier translation service.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2013-01-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pereira, H M -- Ferrier, S -- Walters, M -- Geller, G N -- Jongman, R H G -- Scholes, R J -- Bruford, M W -- Brummitt, N -- Butchart, S H M -- Cardoso, A C -- Coops, N C -- Dulloo, E -- Faith, D P -- Freyhof, J -- Gregory, R D -- Heip, C -- Hoft, R -- Hurtt, G -- Jetz, W -- Karp, D S -- McGeoch, M A -- Obura, D -- Onoda, Y -- Pettorelli, N -- Reyers, B -- Sayre, R -- Scharlemann, J P W -- Stuart, S N -- Turak, E -- Walpole, M -- Wegmann, M -- New York, N.Y. -- Science. 2013 Jan 18;339(6117):277-8. doi: 10.1126/science.1229931.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centro de Biologia Ambiental, Faculdade de Ciencias da Universidade de Lisboa, Lisboa, Portugal. hpereira@fc.ul.pt〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23329036" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; *Biodiversity ; *Environmental Monitoring ; Genetic Variation ; Population
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2014-04-18
    Description: The equilibrium theory of island biogeography is the basis for estimating extinction rates and a pillar of conservation science. The default strategy for conserving biodiversity is the designation of nature reserves, treated as islands in an inhospitable sea of human activity. Despite the profound influence of islands on conservation theory and practice, their mainland analogues, forest fragments in human-dominated landscapes, consistently defy expected biodiversity patterns based on island biogeography theory. Countryside biogeography is an alternative framework, which recognizes that the fate of the world's wildlife will be decided largely by the hospitality of agricultural or countryside ecosystems. Here we directly test these biogeographic theories by comparing a Neotropical countryside ecosystem with a nearby island ecosystem, and show that each supports similar bat biodiversity in fundamentally different ways. The island ecosystem conforms to island biogeographic predictions of bat species loss, in which the water matrix is not habitat. In contrast, the countryside ecosystem has high species richness and evenness across forest reserves and smaller forest fragments. Relative to forest reserves and fragments, deforested countryside habitat supports a less species-rich, yet equally even, bat assemblage. Moreover, the bat assemblage associated with deforested habitat is compositionally novel because of predictable changes in abundances by many species using human-made habitat. Finally, we perform a global meta-analysis of bat biogeographic studies, spanning more than 700 species. It generalizes our findings, showing that separate biogeographic theories for countryside and island ecosystems are necessary. A theory of countryside biogeography is essential to conservation strategy in the agricultural ecosystems that comprise roughly half of the global land surface and are likely to increase even further.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mendenhall, Chase D -- Karp, Daniel S -- Meyer, Christoph F J -- Hadly, Elizabeth A -- Daily, Gretchen C -- England -- Nature. 2014 May 8;509(7499):213-7. doi: 10.1038/nature13139. Epub 2014 Apr 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Center for Conservation Biology, Stanford University, Stanford, California 94305, USA [2] Department of Biology, Stanford University, Stanford, California 94305, USA. ; 1] Center for Conservation Biology, Stanford University, Stanford, California 94305, USA [2] Department of Biology, Stanford University, Stanford, California 94305, USA [3] Department of Environmental Science, Policy & Management, University of California, Berkeley, California 94720, USA [4] The Nature Conservancy, Berkeley, California 94705, USA. ; 1] Institute of Experimental Ecology, University of Ulm, 89069 Ulm, Germany [2] Centre for Environmental Biology, University of Lisbon, 1749-016 Lisbon, Portugal. ; Department of Biology, Stanford University, Stanford, California 94305, USA. ; 1] Center for Conservation Biology, Stanford University, Stanford, California 94305, USA [2] Department of Biology, Stanford University, Stanford, California 94305, USA [3] Woods Institute for the Environment, Stanford University, Stanford, California 94305, USA [4] Global Economic Dynamics and the Biosphere, Royal Swedish Academy of Sciences, Stockholm, SE-104 05, Sweden [5] Stockholm Resilience Centre, University of Stockholm, Stockholm, SE-106 91, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24739971" target="_blank"〉PubMed〈/a〉
    Keywords: *Agriculture/methods ; Animals ; *Biodiversity ; Chiroptera/physiology ; *Conservation of Natural Resources ; Costa Rica ; Extinction, Biological ; *Geography ; Islands ; Lakes ; Models, Biological ; Population Dynamics ; Trees/*growth & development
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2014-09-13
    Description: Habitat conversion is the primary driver of biodiversity loss, yet little is known about how it is restructuring the tree of life by favoring some lineages over others. We combined a complete avian phylogeny with 12 years of Costa Rican bird surveys (118,127 detections across 487 species) sampled in three land uses: forest reserves, diversified agricultural systems, and intensive monocultures. Diversified agricultural systems supported 600 million more years of evolutionary history than intensive monocultures but 300 million fewer years than forests. Compared with species with many extant relatives, evolutionarily distinct species were extirpated at higher rates in both diversified and intensive agricultural systems. Forests are therefore essential for maintaining diversity across the tree of life, but diversified agricultural systems may help buffer against extreme loss of phylogenetic diversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frishkoff, Luke O -- Karp, Daniel S -- M'Gonigle, Leithen K -- Mendenhall, Chase D -- Zook, Jim -- Kremen, Claire -- Hadly, Elizabeth A -- Daily, Gretchen C -- New York, N.Y. -- Science. 2014 Sep 12;345(6202):1343-6. doi: 10.1126/science.1254610.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Stanford University, Stanford, CA 94305, USA. Center for Conservation Biology, Stanford University, Stanford, CA 94305, USA. frishkol@stanford.edu dkarp@berkeley.edu. ; Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA. Nature Conservancy, Berkeley, CA 94705, USA. frishkol@stanford.edu dkarp@berkeley.edu. ; Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA. ; Department of Biology, Stanford University, Stanford, CA 94305, USA. Center for Conservation Biology, Stanford University, Stanford, CA 94305, USA. ; Union de Ornitologos de Costa Rica, Apartado 182-4200, Naranjo de Alajuela, Costa Rica. ; Department of Biology, Stanford University, Stanford, CA 94305, USA. ; Department of Biology, Stanford University, Stanford, CA 94305, USA. Center for Conservation Biology, Stanford University, Stanford, CA 94305, USA. Woods Institute for the Environment, Stanford University, Stanford, CA 94305, USA. Global Economic Dynamics and the Biosphere, Royal Swedish Academy of Sciences, SE-104 05 Stockholm, Sweden. Stockholm Resilience Center, University of Stockholm, SE-106 91 Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25214627" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*trends ; Animals ; *Biodiversity ; Birds/*classification ; Conservation of Natural Resources ; Costa Rica ; *Extinction, Biological ; Phylogeny ; Species Specificity ; Trees
    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
    Publication Date: 2011-12-12
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 6
    Publication Date: 2019
    Description: 〈p〉Human land use threatens global biodiversity and compromises multiple ecosystem functions critical to food production. Whether crop yield–related ecosystem services can be maintained by a few dominant species or rely on high richness remains unclear. Using a global database from 89 studies (with 1475 locations), we partition the relative importance of species richness, abundance, and dominance for pollination; biological pest control; and final yields in the context of ongoing land-use change. Pollinator and enemy richness directly supported ecosystem services in addition to and independent of abundance and dominance. Up to 50% of the negative effects of landscape simplification on ecosystem services was due to richness losses of service-providing organisms, with negative consequences for crop yields. Maintaining the biodiversity of ecosystem service providers is therefore vital to sustain the flow of key agroecosystem benefits to society.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 7
    Publication Date: 2015-11-04
    Description: Kirchhoff (1) highlights inherent difficulties in organizing the rationales that motivate conservation. The author provides two critiques: first, that our conservation objective typology aggregates conflicting subgoals, and second that the objectives are not mutually exclusive (2). We contend that homogenous and mutually exclusive typologies are neither feasible nor desirable for...
    Keywords: Letters, Sustainability Science
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 8
    Publication Date: 2011-12-28
    Description: The consequences of biodiversity decline in intensified agricultural landscapes hinge on surviving biotic assemblages. Maintaining crucial ecosystem processes and services requires resilience to natural and anthropogenic disturbances. However, the resilience and stability of surviving biological communities remain poorly quantified. From a 10-y dataset comprising 2,880 bird censuses across a land-use gradient, we present three key findings concerning the resilience and stability of Costa Rican bird communities. First, seed dispersing, insect eating, and pollinating guilds were more resilient to low-intensity land use than high-intensity land use. Compared with forest assemblages, bird abundance, species richness, and diversity were all ∼15% lower in low-intensity land use and ∼50% lower in high-intensity land use. Second, patterns in species richness generally correlated with patterns in stability: guilds exhibited less variation in abundance in low-intensity land use than in high-intensity land use. Finally, interspecific differences in reaction to environmental change (response diversity) and possibly the portfolio effect, but not negative covariance of species abundances, conferred resilience and stability. These findings point to the changes needed in agricultural production practices in the tropics to better sustain bird communities and, possibly, the functional and service roles that they play.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 9
    Publication Date: 2015-09-02
    Description: Diverse motivations for preserving nature both inspire and hinder its conservation. Optimal conservation strategies may differ radically depending on the objective. For example, creating nature reserves may prevent extinctions through protecting severely threatened species, whereas incentivizing farmland hedgerows may benefit people through bolstering pest-eating or pollinating species. Win-win interventions that...
    Keywords: Sustainability Science
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
    Publication Date: 2015-09-02
    Description: In 2006, a deadly Escherichia coli O157:H7 outbreak in bagged spinach was traced to California’s Central Coast region, where 〉70% of the salad vegetables sold in the United States are produced. Although no definitive cause for the outbreak could be determined, wildlife was implicated as a disease vector. Growers were...
    Keywords: Sustainability Science
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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