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  • Phylogeny  (38)
  • American Association for the Advancement of Science (AAAS)  (38)
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  • 11
    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 12
    Publication Date: 1998-06-06
    Description: Detection of human immunodeficiency virus-type 1 (HIV-1) on only one or a few occasions in infants born to infected mothers has been interpreted to indicate that infection may be transient rather than persistent. Forty-two cases of suspected transient HIV-1 viremia among 1562 perinatally exposed seroreverting infants and one mother were reanalyzed. HIV-1 env sequences were not found in specimens from 20; in specimens from 6, somatic genetic analysis revealed that specimens were mistakenly attributed to an infant; and in specimens from 17, phylogenetic analysis failed to demonstrate the expected linkage between the infant's and the mother's virus. These findings argue that transient HIV-1 infection, if it exists, will only rarely be satisfactorily documented.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frenkel, L M -- Mullins, J I -- Learn, G H -- Manns-Arcuino, L -- Herring, B L -- Kalish, M L -- Steketee, R W -- Thea, D M -- Nichols, J E -- Liu, S L -- Harmache, A -- He, X -- Muthui, D -- Madan, A -- Hood, L -- Haase, A T -- Zupancic, M -- Staskus, K -- Wolinsky, S -- Krogstad, P -- Zhao, J -- Chen, I -- Koup, R -- Ho, D -- Korber, B -- Apple, R J -- Coombs, R W -- Pahwa, S -- Roberts, N J Jr -- AI27757/AI/NIAID NIH HHS/ -- AI32910/AI/NIAID NIH HHS/ -- UO1-27658/PHS HHS/ -- etc. -- New York, N.Y. -- Science. 1998 May 15;280(5366):1073-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pediatrics, University of Rochester, Rochester, NY 14642, USA. lfrenkel@u.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9582120" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Viral/analysis/genetics ; Diagnostic Errors ; Equipment Contamination ; Female ; Genes, env ; HIV Infections/immunology/transmission/*virology ; HIV-1/*genetics/*isolation & purification ; Humans ; Infant ; Infant, Newborn ; Infectious Disease Transmission, Vertical ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Viral/analysis ; *Specimen Handling ; T-Lymphocytes, Cytotoxic/immunology ; Viremia/virology
    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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  • 13
    Publication Date: 1992-12-04
    Description: The doxorubicin-selected lung cancer cell line H69AR is resistant to many chemotherapeutic agents. However, like most tumor samples from individuals with this disease, it does not overexpress P-glycoprotein, a transmembrane transport protein that is dependent on adenosine triphosphate (ATP) and is associated with multidrug resistance. Complementary DNA (cDNA) clones corresponding to messenger RNAs (mRNAs) overexpressed in H69AR cells were isolated. One cDNA hybridized to an mRNA of 7.8 to 8.2 kilobases that was 100- to 200-fold more expressed in H69AR cells relative to drug-sensitive parental H69 cells. Overexpression was associated with amplification of the cognate gene located on chromosome 16 at band p13.1. Reversion to drug sensitivity was associated with loss of gene amplification and a marked decrease in mRNA expression. The mRNA encodes a member of the ATP-binding cassette transmembrane transporter superfamily.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cole, S P -- Bhardwaj, G -- Gerlach, J H -- Mackie, J E -- Grant, C E -- Almquist, K C -- Stewart, A J -- Kurz, E U -- Duncan, A M -- Deeley, R G -- New York, N.Y. -- Science. 1992 Dec 4;258(5088):1650-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research Laboratories, Queen's University, Kingston, Ontario, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1360704" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Chromosome Banding ; Chromosomes, Human, Pair 16 ; Doxorubicin/*pharmacology ; Drug Resistance/*genetics ; Gene Amplification ; Humans ; Lung/physiology ; Lung Neoplasms ; Male ; Membrane Glycoproteins/*genetics ; Molecular Sequence Data ; Multigene Family ; P-Glycoprotein ; Phylogeny ; RNA, Messenger/genetics ; Sequence Homology, Amino Acid ; Testis/physiology ; Tumor Cells, Cultured
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 14
    Publication Date: 2007-11-03
    Description: A full understanding of primate morphological and genomic evolution requires the identification of their closest living relative. In order to resolve the ancestral relationships among primates and their closest relatives, we searched multispecies genome alignments for phylogenetically informative rare genomic changes within the superordinal group Euarchonta, which includes the orders Primates, Dermoptera (colugos), and Scandentia (treeshrews). We also constructed phylogenetic trees from 14 kilobases of nuclear genes for representatives from most major primate lineages, both extant colugos, and multiple treeshrews, including the pentail treeshrew, Ptilocercus lowii, the only living member of the family Ptilocercidae. A relaxed molecular clock analysis including Ptilocercus suggests that treeshrews arose approximately 63 million years ago. Our data show that colugos are the closest living relatives of primates and indicate that their divergence occurred in the Cretaceous.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Janecka, Jan E -- Miller, Webb -- Pringle, Thomas H -- Wiens, Frank -- Zitzmann, Annette -- Helgen, Kristofer M -- Springer, Mark S -- Murphy, William J -- HG02238/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 2;318(5851):792-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17975064" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Dna ; Evolution, Molecular ; Fossils ; Genome ; Humans ; Mammals/classification/genetics ; Molecular Sequence Data ; Phylogeny ; Primates/classification/*genetics ; Scandentia/classification/genetics ; Sequence Alignment
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  • 15
    Publication Date: 2007-09-29
    Description: The genome of the eukaryotic protist Giardia lamblia, an important human intestinal parasite, is compact in structure and content, contains few introns or mitochondrial relics, and has simplified machinery for DNA replication, transcription, RNA processing, and most metabolic pathways. Protein kinases comprise the single largest protein class and reflect Giardia's requirement for a complex signal transduction network for coordinating differentiation. Lateral gene transfer from bacterial and archaeal donors has shaped Giardia's genome, and previously unknown gene families, for example, cysteine-rich structural proteins, have been discovered. Unexpectedly, the genome shows little evidence of heterozygosity, supporting recent speculations that this organism is sexual. This genome sequence will not only be valuable for investigating the evolution of eukaryotes, but will also be applied to the search for new therapeutics for this parasite.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morrison, Hilary G -- McArthur, Andrew G -- Gillin, Frances D -- Aley, Stephen B -- Adam, Rodney D -- Olsen, Gary J -- Best, Aaron A -- Cande, W Zacheus -- Chen, Feng -- Cipriano, Michael J -- Davids, Barbara J -- Dawson, Scott C -- Elmendorf, Heidi G -- Hehl, Adrian B -- Holder, Michael E -- Huse, Susan M -- Kim, Ulandt U -- Lasek-Nesselquist, Erica -- Manning, Gerard -- Nigam, Anuranjini -- Nixon, Julie E J -- Palm, Daniel -- Passamaneck, Nora E -- Prabhu, Anjali -- Reich, Claudia I -- Reiner, David S -- Samuelson, John -- Svard, Staffan G -- Sogin, Mitchell L -- AI42488/AI/NIAID NIH HHS/ -- AI43273/AI/NIAID NIH HHS/ -- AI51687/AI/NIAID NIH HHS/ -- R01 AI043273/AI/NIAID NIH HHS/ -- R01 AI048082/AI/NIAID NIH HHS/ -- R01 HG004164/HG/NHGRI NIH HHS/ -- R01 HG004164-01/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 28;317(5846):1921-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Marine Biological Laboratory, Woods Hole, MA 02543-1015, USA. morrison@mbl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17901334" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Biological Evolution ; DNA Replication/genetics ; *Eukaryotic Cells ; Gene Transfer, Horizontal ; Genes, Protozoan ; *Genome, Protozoan ; Genomics ; Giardia lamblia/classification/*genetics/physiology ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Kinases/genetics/metabolism ; Protozoan Proteins/chemistry/genetics/metabolism ; RNA Processing, Post-Transcriptional ; Signal Transduction ; Transcription, Genetic
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  • 16
    Publication Date: 2008-04-26
    Description: Correlated gene arrangements among taxa provide a valuable framework for inference of shared ancestry of genes and for the utilization of findings from model organisms to study less-well-understood systems. In angiosperms, comparisons of gene arrangements are complicated by recurring polyploidy and extensive genome rearrangement. New genome sequences and improved analytical approaches are clarifying angiosperm evolution and revealing patterns of differential gene loss after genome duplication and differential gene retention associated with evolution of some morphological complexity. Because of variability in DNA substitution rates among taxa and genes, deviation from collinearity might be a more reliable phylogenetic character.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tang, Haibao -- Bowers, John E -- Wang, Xiyin -- Ming, Ray -- Alam, Maqsudul -- Paterson, Andrew H -- New York, N.Y. -- Science. 2008 Apr 25;320(5875):486-8. doi: 10.1126/science.1153917.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18436778" target="_blank"〉PubMed〈/a〉
    Keywords: Angiosperms/classification/*genetics ; Biological Evolution ; Chromosomes, Plant/genetics ; Gene Duplication ; Gene Order ; Gene Rearrangement ; *Genome, Plant ; Genomics ; Karyotyping ; Phylogeny ; Polyploidy ; Sequence Analysis, DNA ; *Synteny
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  • 17
    Publication Date: 2009-11-07
    Description: We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785132/" 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/PMC3785132/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wade, C M -- Giulotto, E -- Sigurdsson, S -- Zoli, M -- Gnerre, S -- Imsland, F -- Lear, T L -- Adelson, D L -- Bailey, E -- Bellone, R R -- Blocker, H -- Distl, O -- Edgar, R C -- Garber, M -- Leeb, T -- Mauceli, E -- MacLeod, J N -- Penedo, M C T -- Raison, J M -- Sharpe, T -- Vogel, J -- Andersson, L -- Antczak, D F -- Biagi, T -- Binns, M M -- Chowdhary, B P -- Coleman, S J -- Della Valle, G -- Fryc, S -- Guerin, G -- Hasegawa, T -- Hill, E W -- Jurka, J -- Kiialainen, A -- Lindgren, G -- Liu, J -- Magnani, E -- Mickelson, J R -- Murray, J -- Nergadze, S G -- Onofrio, R -- Pedroni, S -- Piras, M F -- Raudsepp, T -- Rocchi, M -- Roed, K H -- Ryder, O A -- Searle, S -- Skow, L -- Swinburne, J E -- Syvanen, A C -- Tozaki, T -- Valberg, S J -- Vaudin, M -- White, J R -- Zody, M C -- Broad Institute Genome Sequencing Platform -- Broad Institute Whole Genome Assembly Team -- Lander, E S -- Lindblad-Toh, K -- 098051/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Nov 6;326(5954):865-7. doi: 10.1126/science.1178158.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA. c.wade@usyd.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19892987" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Domestic/genetics ; Centromere/genetics ; Chromosome Mapping ; Chromosomes, Mammalian/*genetics ; Computational Biology ; DNA Copy Number Variations ; Dogs ; Evolution, Molecular ; Female ; Genes ; *Genome ; Haplotypes ; Horses/*genetics ; Humans ; Molecular Sequence Data ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Synteny
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  • 18
    Publication Date: 2011-09-03
    Description: Ice Age megafauna have long been known to be associated with global cooling during the Pleistocene, and their adaptations to cold environments, such as large body size, long hair, and snow-sweeping structures, are best exemplified by the woolly mammoths and woolly rhinos. These traits were assumed to have evolved as a response to the ice sheet expansion. We report a new Pliocene mammal assemblage from a high-altitude basin in the western Himalayas, including a primitive woolly rhino. These new Tibetan fossils suggest that some megaherbivores first evolved in Tibet before the beginning of the Ice Age. The cold winters in high Tibet served as a habituation ground for the megaherbivores, which became preadapted for the Ice Age, successfully expanding to the Eurasian mammoth steppe.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deng, Tao -- Wang, Xiaoming -- Fortelius, Mikael -- Li, Qiang -- Wang, Yang -- Tseng, Zhijie J -- Takeuchi, Gary T -- Saylor, Joel E -- Saila, Laura K -- Xie, Guangpu -- New York, N.Y. -- Science. 2011 Sep 2;333(6047):1285-8. doi: 10.1126/science.1206594.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Key Laboratory of Evolutionary Systematics of Vertebrates, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21885780" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization ; *Altitude ; Animals ; *Biological Evolution ; *Cold Climate ; *Fossils ; *Ice Cover ; Mammals/*anatomy & histology/classification ; Mandible/anatomy & histology ; Perissodactyla/*anatomy & histology/classification ; Phylogeny ; Seasons ; Skull/anatomy & histology ; Tibet ; Tooth/anatomy & histology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 19
    Publication Date: 2012-06-16
    Description: Ecosystems worldwide are rapidly losing taxonomic, phylogenetic, genetic, and functional diversity as a result of human appropriation of natural resources, modification of habitats and climate, and the spread of pathogenic, exotic, and domestic plants and animals. Twenty years of intense theoretical and empirical research have shown that such biotic impoverishment can markedly alter the biogeochemical and dynamic properties of ecosystems, but frontiers remain in linking this research to the complexity of wild nature, and in applying it to pressing environmental issues such as food, water, energy, and biosecurity. The question before us is whether these advances can take us beyond merely invoking the precautionary principle of conserving biodiversity to a predictive science that informs practical and specific solutions to mitigate and adapt to its loss.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Naeem, Shahid -- Duffy, J Emmett -- Zavaleta, Erika -- New York, N.Y. -- Science. 2012 Jun 15;336(6087):1401-6. doi: 10.1126/science.1215855.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027, USA. sn2121@columbia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22700920" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Conservation of Natural Resources ; *Ecosystem ; Environment ; *Extinction, Biological ; Humans ; Phylogeny ; Plants ; Research
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 20
    Publication Date: 2012-11-20
    Description: Unlike other Salmonellae, the intracellular bacterial human pathogen Salmonella Typhi exhibits strict host specificity. The molecular bases for this restriction are unknown. Here we found that the expression of a single type III secretion system effector protein from broad-host Salmonella Typhimurium allowed Salmonella Typhi to survive and replicate within macrophages and tissues from mice, a nonpermissive host. This effector proteolytically targeted Rab32, which controls traffic to lysosome-related organelles in conjunction with components of the biogenesis of lysosome-related organelle complexes (BLOCs). RNA interference-mediated depletion of Rab32 or of an essential component of a BLOC complex was sufficient to allow S. Typhi to survive within mouse macrophages. Furthermore, S. Typhi was able to survive in macrophages from mice defective in BLOC components.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693731/" 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/PMC3693731/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spano, Stefania -- Galan, Jorge E -- AI055472/AI/NIAID NIH HHS/ -- AI079022/AI/NIAID NIH HHS/ -- R01 AI055472/AI/NIAID NIH HHS/ -- R01 AI079022/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2012 Nov 16;338(6109):960-3. doi: 10.1126/science.1229224.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbial Pathogenesis, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23162001" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bacterial Secretion Systems/genetics/*physiology ; COS Cells ; Cercopithecus aethiops ; *Host-Pathogen Interactions ; Humans ; Lysosomes/metabolism ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Phylogeny ; RNA Interference ; Salmonella typhi/genetics/*physiology ; rab GTP-Binding Proteins/classification/genetics/*physiology
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