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  • 1
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0133963, doi: 10.1371/journal.pone.0133963.
    Description: The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts.
    Description: This work was supported by grants from the Wellcome Trust (101480/Z/13/Z, http://www.wellcome.ac.uk/stellent/group​s/corporatesite/@msh_publishing_group/do​cuments/web_document/wts058331.pdf) and Biotechnology and Biological Sciences Research Council (BB/K019988/1, http://www.bbsrc.ac.uk/pa/grants/AwardDe​tails.aspx?FundingReference=BB/K019988/1) to the European Xenopus Resource Centre. This work was also supported by a Grant-in-Aid for Young Scientists (B) (No. 23710282, http://kaken.nii.ac.jp/d/p/23710282.en.h​tml) to TI from the Ministry of Education, Culture, Sports, Science and Technology, Japan and a Grant-in-Aid for Scientific Research (B) (No. 20510216, http://kaken.nii.ac.jp/d/p/24310173.en.h​tml) to MS from the Ministry of Education, Culture, Sports, Science and Technology, Japan.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Biology 12 (2014): e1001889, doi:10.1371/journal.pbio.1001889.
    Description: Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose.
    Description: This project was funded by the Gordon and Betty Moore Foundation (GBMF; Grants GBMF2637 and GBMF3111) to the National Center for Genome Resources (NCGR) and the National Center for Marine Algae and Microbiota (NCMA).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/msword
    Format: application/pdf
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  • 3
    Publication Date: 2018
    Description: 〈p〉Dynamic networks, where ties can be shed and new ties can be formed, promote the evolution of cooperation. Yet, past research has only compared networks where all ties can be severed to those where none can, confounding the benefits of fully dynamic networks with the presence of some dynamic ties within the network. Further, humans do not live in fully dynamic networks. Instead, in real-world networks, some ties are subject to change, while others are difficult to sever. Here, we consider whether and how cooperation evolves in networks containing both static and dynamic ties. We argue and find that the presence of dynamic ties in networks promotes cooperation even in static ties. Consistent with previous work demonstrating that cooperation cascades in networks, our results show that cooperation is enhanced in networks with both tie types because the higher rate of cooperation that occurs following the dynamics process "spills over" to those relations that are more difficult to alter. Thus, our findings demonstrate the critical role that dynamic ties play in promoting cooperation by altering behavioral outcomes even in non-dynamic relations.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 4
    Publication Date: 1999-04-24
    Description: The lack of an adequate hominid fossil record in eastern Africa between 2 and 3 million years ago (Ma) has hampered investigations of early hominid phylogeny. Discovery of 2.5 Ma hominid cranial and dental remains from the Hata beds of Ethiopia's Middle Awash allows recognition of a new species of Australopithecus. This species is descended from Australopithecus afarensis and is a candidate ancestor for early Homo. Contemporary postcranial remains feature a derived humanlike humeral/femoral ratio and an apelike upper arm-to-lower arm ratio.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Asfaw, B -- White, T -- Lovejoy, O -- Latimer, B -- Simpson, S -- Suwa, G -- New York, N.Y. -- Science. 1999 Apr 23;284(5414):629-35.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rift Valley Research Service, Post Office Box 5717, Addis Ababa, Ethiopia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10213683" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; Bones of Upper Extremity/anatomy & histology ; Dentition ; Ethiopia ; *Fossils ; History, Ancient ; Hominidae/anatomy & histology/*classification ; Humans ; Leg Bones/anatomy & histology ; Paleodontology ; Phylogeny ; Skull/anatomy & histology ; Terminology as Topic ; Tooth/anatomy & histology
    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: 2000-08-12
    Description: Ecosystems are capital assets: When properly managed, they yield a flow of vital goods and services. Relative to other forms of capital, however, ecosystems are poorly understood, scarcely monitored, and--in many important cases--undergoing rapid degradation. The process of economic valuation could greatly improve stewardship. This potential is now being realized with innovative financial instruments and institutional arrangements.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Daily, G C -- Soderqvist, T -- Aniyar, S -- Arrow, K -- Dasgupta, P -- Ehrlich, P R -- Folke, C -- Jansson, A -- Jansson, B -- Kautsky, N -- Levin, S -- Lubchenco, J -- Maler, K G -- Simpson, D -- Starrett, D -- Tilman, D -- Walker, B -- New York, N.Y. -- Science. 2000 Jul 21;289(5478):395-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA. gdaily@leland.stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10939949" target="_blank"〉PubMed〈/a〉
    Keywords: Australia ; Commerce ; Conservation of Natural Resources/*economics ; Costa Rica ; *Ecosystem ; Industry ; Investments
    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
    Publication Date: 2000-03-25
    Description: The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Adams, M D -- Celniker, S E -- Holt, R A -- Evans, C A -- Gocayne, J D -- Amanatides, P G -- Scherer, S E -- Li, P W -- Hoskins, R A -- Galle, R F -- George, R A -- Lewis, S E -- Richards, S -- Ashburner, M -- Henderson, S N -- Sutton, G G -- Wortman, J R -- Yandell, M D -- Zhang, Q -- Chen, L X -- Brandon, R C -- Rogers, Y H -- Blazej, R G -- Champe, M -- Pfeiffer, B D -- Wan, K H -- Doyle, C -- Baxter, E G -- Helt, G -- Nelson, C R -- Gabor, G L -- Abril, J F -- Agbayani, A -- An, H J -- Andrews-Pfannkoch, C -- Baldwin, D -- Ballew, R M -- Basu, A -- Baxendale, J -- Bayraktaroglu, L -- Beasley, E M -- Beeson, K Y -- Benos, P V -- Berman, B P -- Bhandari, D -- Bolshakov, S -- Borkova, D -- Botchan, M R -- Bouck, J -- Brokstein, P -- Brottier, P -- Burtis, K C -- Busam, D A -- Butler, H -- Cadieu, E -- Center, A -- Chandra, I -- Cherry, J M -- Cawley, S -- Dahlke, C -- Davenport, L B -- Davies, P -- de Pablos, B -- Delcher, A -- Deng, Z -- Mays, A D -- Dew, I -- Dietz, S M -- Dodson, K -- Doup, L E -- Downes, M -- Dugan-Rocha, S -- Dunkov, B C -- Dunn, P -- Durbin, K J -- Evangelista, C C -- Ferraz, C -- Ferriera, S -- Fleischmann, W -- Fosler, C -- Gabrielian, A E -- Garg, N S -- Gelbart, W M -- Glasser, K -- Glodek, A -- Gong, F -- Gorrell, J H -- Gu, Z -- Guan, P -- Harris, M -- Harris, N L -- Harvey, D -- Heiman, T J -- Hernandez, J R -- Houck, J -- Hostin, D -- Houston, K A -- Howland, T J -- Wei, M H -- Ibegwam, C -- Jalali, M -- Kalush, F -- Karpen, G H -- Ke, Z -- Kennison, J A -- Ketchum, K A -- Kimmel, B E -- Kodira, C D -- Kraft, C -- Kravitz, S -- Kulp, D -- Lai, Z -- Lasko, P -- Lei, Y -- Levitsky, A A -- Li, J -- Li, Z -- Liang, Y -- Lin, X -- Liu, X -- Mattei, B -- McIntosh, T C -- McLeod, M P -- McPherson, D -- Merkulov, G -- Milshina, N V -- Mobarry, C -- Morris, J -- Moshrefi, A -- Mount, S M -- Moy, M -- Murphy, B -- Murphy, L -- Muzny, D M -- Nelson, D L -- Nelson, D R -- Nelson, K A -- Nixon, K -- Nusskern, D R -- Pacleb, J M -- Palazzolo, M -- Pittman, G S -- Pan, S -- Pollard, J -- Puri, V -- Reese, M G -- Reinert, K -- Remington, K -- Saunders, R D -- Scheeler, F -- Shen, H -- Shue, B C -- Siden-Kiamos, I -- Simpson, M -- Skupski, M P -- Smith, T -- Spier, E -- Spradling, A C -- Stapleton, M -- Strong, R -- Sun, E -- Svirskas, R -- Tector, C -- Turner, R -- Venter, E -- Wang, A H -- Wang, X -- Wang, Z Y -- Wassarman, D A -- Weinstock, G M -- Weissenbach, J -- Williams, S M -- WoodageT -- Worley, K C -- Wu, D -- Yang, S -- Yao, Q A -- Ye, J -- Yeh, R F -- Zaveri, J S -- Zhan, M -- Zhang, G -- Zhao, Q -- Zheng, L -- Zheng, X H -- Zhong, F N -- Zhong, W -- Zhou, X -- Zhu, S -- Zhu, X -- Smith, H O -- Gibbs, R A -- Myers, E W -- Rubin, G M -- Venter, J C -- P50-HG00750/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2000 Mar 24;287(5461):2185-95.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10731132" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Transport/genetics ; Chromatin/genetics ; Cloning, Molecular ; Computational Biology ; Contig Mapping ; Cytochrome P-450 Enzyme System/genetics ; DNA Repair/genetics ; DNA Replication/genetics ; Drosophila melanogaster/*genetics/metabolism ; Euchromatin ; Gene Library ; Genes, Insect ; *Genome ; Heterochromatin/genetics ; Insect Proteins/chemistry/genetics/physiology ; Nuclear Proteins/genetics ; Protein Biosynthesis ; *Sequence Analysis, DNA ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2007-09-11
    Description: The Hayward fault, located on the east side of the San Francisco Bay, represents a natural laboratory for seismologists, because it does not sleep silently between major earthquakes. In his Perspective, Simpson discusses the study by Burgmann et al., who have used powerful new techniques to study the fault. The results indicate that major earthquakes cannot originate in the northern part of the fault. However, surface-rupturing earthquakes have occurred in the area, suggesting that they originated to the north or south of the segment studied by Burgmann et al. Fundamental questions remain regarding the mechanism by which plate tectonic stresses are transferred to the Hayward fault.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simpson, R W -- New York, N.Y. -- Science. 2000 Aug 18;289(5482):1147-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17833401" target="_blank"〉PubMed〈/a〉
    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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  • 8
    Publication Date: 2001-04-28
    Description: Slit is secreted by cells at the midline of the central nervous system, where it binds to Roundabout (Robo) receptors and functions as a potent repellent. We found that migrating mesodermal cells in vivo respond to Slit as both an attractant and a repellent and that Robo receptors are required for both functions. Mesoderm cells expressing Robo receptors initially migrate away from Slit at the midline. A few hours after migration, these same cells change their behavior and require Robo to extend toward Slit-expressing muscle attachment sites. Thus, Slit functions as a chemoattractant to provide specificity for muscle patterning.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kramer, S G -- Kidd, T -- Simpson, J H -- Goodman, C S -- NS18366/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2001 Apr 27;292(5517):737-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Molecular and Cell Biology, 519 Life Sciences Addition, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11326102" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Body Patterning ; Cell Fusion ; Cell Movement ; Drosophila/embryology/genetics ; *Drosophila Proteins ; Embryo, Nonmammalian/cytology/metabolism ; Epidermis/embryology/metabolism ; Mesoderm/*cytology/metabolism ; Microscopy, Confocal ; Muscles/*cytology/embryology/metabolism ; Mutation ; Nerve Tissue Proteins/genetics/*metabolism ; Receptors, Immunologic/genetics/*metabolism ; Signal Transduction ; Stem Cells/metabolism/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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  • 9
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2001-07-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simpson, S -- Marshall, E -- New York, N.Y. -- Science. 2001 Jul 13;293(5528):233.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11452107" target="_blank"〉PubMed〈/a〉
    Keywords: Allergy and Immunology/trends ; Humans ; *Immunity ; Immunization Programs ; *Immunologic Memory ; *Vaccines/administration & dosage/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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  • 10
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2002-04-16
    Description: Multiple environmental and endogenous inputs regulate when plants flower. The molecular genetic dissection of flowering time control in Arabidopsis has identified an integrated network of pathways that quantitatively control the timing of this developmental switch. This framework provides the basis to understand the evolution of different reproductive strategies and how floral pathways interact through seasonal progression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simpson, Gordon G -- Dean, Caroline -- New York, N.Y. -- Science. 2002 Apr 12;296(5566):285-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11951029" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics/growth & development/*physiology ; Arabidopsis Proteins/genetics/*metabolism ; Circadian Rhythm ; DNA-Binding Proteins/genetics/physiology ; *Gene Expression Regulation, Plant ; Genes, Plant ; Gibberellins/metabolism ; Meristem/physiology ; Mutation ; Photoperiod ; Plant Structures/physiology ; Seasons ; Temperature ; Time Factors ; Transcription Factors/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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