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  • Articles  (36)
  • Mice  (23)
  • Phylogeny  (14)
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  • Articles  (36)
  • 1
    ISSN: 1433-4909
    Keywords: Key words Olive wastes ; Bacillus ; Alkaliphile ; Growth characteristics ; Lipid composition ; Phylogeny ; Adaptation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A novel Gram-positive facultatively alkaliphilic, sporulating, rod-shaped bacterium, designated as WW3-SN6, has been isolated from the alkaline washwaters derived from the preparation of edible olives. The bacterium is nonmotile, and flagella are not observed. It is oxidase positive and catalase negative. The facultative alkaliphile grows from pH 7.0 to 10.5, with a broad optimum from pH 8.0 to 9.0. It could grow in up to 15% (w/v) NaCl, and over the temperature range from 4° to 37°C, with an optimum between 27° and 32°C: therefore, it is both halotolerant and psychrotolerant. The bacterium is sensitive to a range of β-lactam, sulfonamide, and aminoglycoside antibiotics, but resistant to trimethoprim. The range of amino acids, sugars, and polyols utilized as growth substrates indicates that this alkaliphile is a heterotrophic bacterium. d(+)-glucose, d(+)-glucose-6-phosphate, d(+)-cellobiose, starch, or sucrose are the substrates best utilized. The major membrane lipids are phosphatidylglycerol and diphosphatidylglycerol, with smaller amounts of phosphatidylethanolamine and an unknown phospholipid. During growth at high pH, the proportion of phosphatidylglycerol is increased relative to phosphatidylethanolamine. The fatty acyl components in the membrane phospholipids are mainly branched chain, with 13-methyl tetradecanoic and 12-methyl tetradecanoic acids as the predominant components. The G + C content of the genomic DNA is 41.1 ± 1.0 mol%. The results of 16S ribosomal RNA sequence analysis place this alkaliphilic bacterium in a cluster, together with an unnamed alkaliphilic Bacillus species (98.2% similarity).
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 40 (1995), S. 487-498 
    ISSN: 1432-1432
    Keywords: Aminoacyl-tRNA synthetases ; Phylogeny ; Evolution of protein translation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Numerous aminoacyl-tRNA synthetase sequences have been aligned by computer and phylogenetic trees constructed from them for the two classes of these enzymes. Branching orders based on a consensus of these trees have been proposed for the two groups. Although the order of appearance can be rationalized to fit many different scenarios having to do with the genetic code, the invention of a system for translating nucleic acid sequences into polypeptide chains must have predated the existence of these proteins. In the past, a variety of schemes has been proposed for matching amino acids and tRNAs. Most of these have invoked direct recognition of one by the other, whether or not the anticodon was involved. Often ignored is the possibility of a nonprotein (presumably RNA) matchmaker for bringing the two into conjunction. If such had been the case, then the contemporary aminoacyl-tRNA synthetases could have entered the system gradually, each specific type replacing its matchmaking RNA counterpart in turn. A simple displacement scheme of this sort accommodates the existence of two different families of these enzymes, the second being introduced well before the first had undergone sufficient genetic duplications to specify the full gamut of amino acids. Such a scheme is also consistent with similar amino acids often, but not always, being the substrates of enzymes with the most similar amino acid sequences.
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 39 (1994), S. 631-643 
    ISSN: 1432-1432
    Keywords: Fibronectin type III ; Bacteria ; Glycohydrolases ; Phylogeny ; Horizontal gene transfers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolutionary spread of 22 fibronectin type III (Fn3) sequences among a dozen bacterial enzymes has been traced by searching databases with the non-Fn3 parts of the enzyme sequences. Numerous homologues were found that lacked the Fn3 domains. In each case the related sequences were aligned, phylogenetic trees were constructed, and the occurrences of Fn3 units on the trees were noted. Comparison with phylogenetic trees prepared from the Fn3 segments themselves allowed inferences to be made about when the Fn3 units were shuffled into their present positions.
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 34 (1992), S. 175-184 
    ISSN: 1432-1432
    Keywords: Superoxide dismutase ; Phylogeny ; Evolutionary rates ; Horizontal gene transfers ; Molecular clock
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Phylogenetic trees were constructed for 25 Cu-Zn superoxide dismutases and 31 Mn/Fe superoxide dismutases. The latter set includes seven new sequences that we determined in an effort to make the two phylogenies equally representative. We analyzed all pairwise differences in each set in an attempt to estimate rates of change. As reported by others, the Cu-Zn enzyme has experienced significant changes in its evolutionary rate. In contrast, the clock for the Mn/Fe enzyme is ticking quite regularly. The comparison of these two independently evolved superoxide dismutases that catalyze the same reaction and occur together throughout much of the biological world suggests that adaptation to environmental stress is not the basis for the erratic rate of change observed in the Cu-Zn enzyme.
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Plant systematics and evolution 200 (1996), S. 213-224 
    ISSN: 1615-6110
    Keywords: Bryophytes ; Takakia ; mosses ; liverworts ; hornworts ; Phylogeny ; 18S rRNA gene ; parsimony analysis ; maximum-likelihood analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We investigate phylogenetic relationships among hornworts, liverworts and mosses, and their relationships to other green plant groups, by analysis of nucleotide variation in complete 18s rRNA gene sequences of three green algae, two hornworts, seven liverworts, nine mosses, and six tracheophytes. Parsimony and maximum-likelihood analyses yield a single optimal tree in which the hornworts are resolved as the basal group among land plants, and the liverworts and mosses are sister taxa that together form the sister clade to the tracheophytes. This phylogeny is internally robust as indicated by decay indices and by comparison (using both parsimony and likelihood criteria) to topologies representing five alternative hypotheses of bryophyte relationships. We discuss some possible reasons for differences between the phylogeny inferred from the rRNA data and those inferred from other character sets.
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  • 6
    Publication Date: 1998-11-13
    Description: The ectodomains of numerous proteins are released from cells by proteolysis to yield soluble intercellular regulators. The responsible protease, tumor necrosis factor-alpha converting enzyme (TACE), has been identified only in the case when tumor necrosis factor-alpha (TNFalpha) is released. Analyses of cells lacking this metalloproteinase-disintegrin revealed an expanded role for TACE in the processing of other cell surface proteins, including a TNF receptor, the L-selectin adhesion molecule, and transforming growth factor-alpha (TGFalpha). The phenotype of mice lacking TACE suggests an essential role for soluble TGFalpha in normal development and emphasizes the importance of protein ectodomain shedding in vivo.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Peschon, J J -- Slack, J L -- Reddy, P -- Stocking, K L -- Sunnarborg, S W -- Lee, D C -- Russell, W E -- Castner, B J -- Johnson, R S -- Fitzner, J N -- Boyce, R W -- Nelson, N -- Kozlosky, C J -- Wolfson, M F -- Rauch, C T -- Cerretti, D P -- Paxton, R J -- March, C J -- Black, R A -- CA43793/CA/NCI NIH HHS/ -- DK53804/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1998 Nov 13;282(5392):1281-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Immunex Corporation, Seattle, WA 98101, USA. peschon@immunex.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9812885" target="_blank"〉PubMed〈/a〉
    Keywords: ADAM Proteins ; Amino Acid Sequence ; Animals ; Catalytic Domain ; Cell Membrane/*metabolism ; Cells, Cultured ; Crosses, Genetic ; *Embryonic and Fetal Development ; L-Selectin/metabolism ; Ligands ; Membrane Proteins/*metabolism ; Metalloendopeptidases/chemistry/genetics/*metabolism ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Mutation ; Phenotype ; Protein Processing, Post-Translational ; Receptors, Tumor Necrosis Factor/metabolism ; Transforming Growth Factor alpha/metabolism ; Tumor Necrosis Factor-alpha/*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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  • 7
    Publication Date: 2009-07-07
    Description: Activator protein 1 (AP-1, also known as JUN) transcription factors are dimers of JUN, FOS, MAF and activating transcription factor (ATF) family proteins characterized by basic region and leucine zipper domains. Many AP-1 proteins contain defined transcriptional activation domains, but BATF and the closely related BATF3 (refs 2, 3) contain only a basic region and leucine zipper, and are considered to be inhibitors of AP-1 activity. Here we show that Batf is required for the differentiation of IL17-producing T helper (T(H)17) cells. T(H)17 cells comprise a CD4(+) T-cell subset that coordinates inflammatory responses in host defence but is pathogenic in autoimmunity. Batf(-/-) mice have normal T(H)1 and T(H)2 differentiation, but show a defect in T(H)17 differentiation, and are resistant to experimental autoimmune encephalomyelitis. Batf(-/-) T cells fail to induce known factors required for T(H)17 differentiation, such as RORgamma t (encoded by Rorc) and the cytokine IL21 (refs 14-17). Neither the addition of IL21 nor the overexpression of RORgamma t fully restores IL17 production in Batf(-/-) T cells. The Il17 promoter is BATF-responsive, and after T(H)17 differentiation, BATF binds conserved intergenic elements in the Il17a-Il17f locus and to the Il17, Il21 and Il22 (ref. 18) promoters. These results demonstrate that the AP-1 protein BATF has a critical role in T(H)17 differentiation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2716014/" 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/PMC2716014/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schraml, Barbara U -- Hildner, Kai -- Ise, Wataru -- Lee, Wan-Ling -- Smith, Whitney A-E -- Solomon, Ben -- Sahota, Gurmukh -- Sim, Julia -- Mukasa, Ryuta -- Cemerski, Saso -- Hatton, Robin D -- Stormo, Gary D -- Weaver, Casey T -- Russell, John H -- Murphy, Theresa L -- Murphy, Kenneth M -- AI035783/AI/NIAID NIH HHS/ -- AR049293/AR/NIAMS NIH HHS/ -- GM07200/GM/NIGMS NIH HHS/ -- HG00249/HG/NHGRI NIH HHS/ -- R01 HG000249/HG/NHGRI NIH HHS/ -- R01 HG000249-20/HG/NHGRI NIH HHS/ -- T32 GM008802/GM/NIGMS NIH HHS/ -- T32 GM008802-08/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Jul 16;460(7253):405-9. doi: 10.1038/nature08114. Epub 2009 Jul 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, Missouri 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19578362" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Basic-Leucine Zipper Transcription Factors/deficiency/genetics/*metabolism ; *Cell Differentiation ; Encephalomyelitis, Autoimmune, Experimental/genetics ; Female ; Gene Expression Regulation ; Genetic Predisposition to Disease ; Interleukin-17/biosynthesis/genetics/*metabolism ; Interleukins/genetics/metabolism/pharmacology ; Lymph Nodes/metabolism ; Male ; Mice ; Nuclear Receptor Subfamily 1, Group F, Member 3 ; Promoter Regions, Genetic/genetics ; Receptors, Retinoic Acid/genetics/metabolism ; Receptors, Thyroid Hormone/genetics/metabolism ; T-Lymphocytes, Helper-Inducer/*cytology/*metabolism ; Transcription Factor AP-1/deficiency/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2007-03-03
    Description: A hallmark of mammalian immunity is the heterogeneity of cell fate that exists among pathogen-experienced lymphocytes. We show that a dividing T lymphocyte initially responding to a microbe exhibits unequal partitioning of proteins that mediate signaling, cell fate specification, and asymmetric cell division. Asymmetric segregation of determinants appears to be coordinated by prolonged interaction between the T cell and its antigen-presenting cell before division. Additionally, the first two daughter T cells displayed phenotypic and functional indicators of being differentially fated toward effector and memory lineages. These results suggest a mechanism by which a single lymphocyte can apportion diverse cell fates necessary for adaptive immunity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, John T -- Palanivel, Vikram R -- Kinjyo, Ichiko -- Schambach, Felix -- Intlekofer, Andrew M -- Banerjee, Arnob -- Longworth, Sarah A -- Vinup, Kristine E -- Mrass, Paul -- Oliaro, Jane -- Killeen, Nigel -- Orange, Jordan S -- Russell, Sarah M -- Weninger, Wolfgang -- Reiner, Steven L -- AI007532/AI/NIAID NIH HHS/ -- AI042370/AI/NIAID NIH HHS/ -- AI053827/AI/NIAID NIH HHS/ -- AI055428/AI/NIAID NIH HHS/ -- AI061699/AI/NIAID NIH HHS/ -- AI069380/AI/NIAID NIH HHS/ -- CA114114/CA/NCI NIH HHS/ -- CA87812/CA/NCI NIH HHS/ -- DK007066/DK/NIDDK NIH HHS/ -- GM007170/GM/NIGMS NIH HHS/ -- R01 AI061699/AI/NIAID NIH HHS/ -- T32 AI055428/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2007 Mar 23;315(5819):1687-91. Epub 2007 Mar 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Abramson Family Cancer Research Institute and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17332376" target="_blank"〉PubMed〈/a〉
    Keywords: Adoptive Transfer ; Animals ; Antigen Presentation ; Antigens, CD/analysis ; Antigens, CD8/analysis ; CD8-Positive T-Lymphocytes/*cytology/*immunology ; Cell Differentiation ; *Cell Division ; Cell Lineage ; Cell Polarity ; Dendritic Cells/immunology ; *Immunologic Memory ; Intracellular Signaling Peptides and Proteins/metabolism ; Listeria monocytogenes/immunology ; Listeriosis/immunology ; Lymphocyte Activation ; Membrane Proteins/analysis ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Mitosis ; Nerve Tissue Proteins/analysis ; Protein Kinase C/metabolism ; Receptors, Antigen, T-Cell/immunology ; Receptors, Interferon/analysis ; Signal Transduction ; T-Lymphocyte Subsets/*cytology/*immunology ; T-Lymphocytes, Helper-Inducer/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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  • 9
    Publication Date: 2008-04-19
    Description: Antigenic and genetic analysis of the hemagglutinin of approximately 13,000 human influenza A (H3N2) viruses from six continents during 2002-2007 revealed that there was continuous circulation in east and Southeast Asia (E-SE Asia) via a region-wide network of temporally overlapping epidemics and that epidemics in the temperate regions were seeded from this network each year. Seed strains generally first reached Oceania, North America, and Europe, and later South America. This evidence suggests that once A (H3N2) viruses leave E-SE Asia, they are unlikely to contribute to long-term viral evolution. If the trends observed during this period are an accurate representation of overall patterns of spread, then the antigenic characteristics of A (H3N2) viruses outside E-SE Asia may be forecast each year based on surveillance within E-SE Asia, with consequent improvements to vaccine strain selection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Russell, Colin A -- Jones, Terry C -- Barr, Ian G -- Cox, Nancy J -- Garten, Rebecca J -- Gregory, Vicky -- Gust, Ian D -- Hampson, Alan W -- Hay, Alan J -- Hurt, Aeron C -- de Jong, Jan C -- Kelso, Anne -- Klimov, Alexander I -- Kageyama, Tsutomu -- Komadina, Naomi -- Lapedes, Alan S -- Lin, Yi P -- Mosterin, Ana -- Obuchi, Masatsugu -- Odagiri, Takato -- Osterhaus, Albert D M E -- Rimmelzwaan, Guus F -- Shaw, Michael W -- Skepner, Eugene -- Stohr, Klaus -- Tashiro, Masato -- Fouchier, Ron A M -- Smith, Derek J -- DP1-OD000490-01/OD/NIH HHS/ -- MC_U117512723/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Apr 18;320(5874):340-6. doi: 10.1126/science.1154137.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Cambridge, Cambridge, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18420927" target="_blank"〉PubMed〈/a〉
    Keywords: Antigenic Variation ; Asia/epidemiology ; Asia, Southeastern/epidemiology ; *Disease Outbreaks ; Europe/epidemiology ; Evolution, Molecular ; Forecasting ; Hemagglutinin Glycoproteins, Influenza Virus/genetics/*immunology ; Humans ; *Influenza A Virus, H3N2 Subtype/classification/genetics/immunology/isolation & ; purification ; Influenza Vaccines ; Influenza, Human/*epidemiology/virology ; North America/epidemiology ; Oceania ; Phylogeny ; Population Surveillance ; Seasons ; South America/epidemiology
    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
    Publication Date: 2010-05-15
    Description: Mycobacterium tuberculosis has a penetrance of its host population that would be the envy of most human pathogens. About one-third of the human population would have a positive skin test for the infection and is thus thought to harbor the bacterium. Globally, 22 "high-burden" countries account for more than 80% of the active tuberculosis cases in the world, which shows the inequitable distribution of the disease. There is no effective vaccine against infection, and current drug therapies are fraught with problems, predominantly because of the protracted nature of the treatment and the increasing occurrence of drug resistance. Here we focus on the biology of the host-pathogen interaction and discuss new and evolving strategies for intervention.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872107/" 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/PMC2872107/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Russell, David G -- Barry, Clifton E 3rd -- Flynn, JoAnne L -- AI057086/AI/NIAID NIH HHS/ -- AI067027/AI/NIAID NIH HHS/ -- AI080651/AI/NIAID NIH HHS/ -- AI50732/AI/NIAID NIH HHS/ -- HL055936/HL/NHLBI NIH HHS/ -- HL075845/HL/NHLBI NIH HHS/ -- HL092883/HL/NHLBI NIH HHS/ -- HL100928/HL/NHLBI NIH HHS/ -- HL71241/HL/NHLBI NIH HHS/ -- R01 AI037859/AI/NIAID NIH HHS/ -- R01 AI050732/AI/NIAID NIH HHS/ -- R01 AI050732-07/AI/NIAID NIH HHS/ -- R01 AI057086/AI/NIAID NIH HHS/ -- R01 AI057086-06A2/AI/NIAID NIH HHS/ -- R01 AI067027/AI/NIAID NIH HHS/ -- R01 AI067027-05/AI/NIAID NIH HHS/ -- R01 AI080651/AI/NIAID NIH HHS/ -- R01 AI080651-02/AI/NIAID NIH HHS/ -- R01 HL055936/HL/NHLBI NIH HHS/ -- R01 HL055936-14/HL/NHLBI NIH HHS/ -- R01 HL075845/HL/NHLBI NIH HHS/ -- R01 HL075845-05/HL/NHLBI NIH HHS/ -- R01 HL100928/HL/NHLBI NIH HHS/ -- R01 HL100928-01/HL/NHLBI NIH HHS/ -- R33 HL092883/HL/NHLBI NIH HHS/ -- R33 HL092883-02/HL/NHLBI NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 May 14;328(5980):852-6. doi: 10.1126/science.1184784.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA. dgr8@cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20466922" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Antitubercular Agents/pharmacology/therapeutic use ; *BCG Vaccine/administration & dosage/immunology ; Biomarkers ; Disease Models, Animal ; Drug Discovery ; Drug Therapy, Combination ; Host-Pathogen Interactions ; Humans ; Mice ; *Mycobacterium tuberculosis/growth & development/immunology/metabolism ; Public Health Practice ; *Tuberculosis/drug therapy/immunology/microbiology/prevention & control ; Vaccination
    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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