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  • Articles  (21)
  • Base Sequence
  • American Association for the Advancement of Science (AAAS)  (21)
  • 2000-2004  (21)
  • 2004  (21)
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  • Articles  (21)
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  • American Association for the Advancement of Science (AAAS)  (21)
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  • 2000-2004  (21)
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  • 1
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    Ultraconserved elements in the human genome (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-08
    Description: There are 481 segments longer than 200 base pairs (bp) that are absolutely conserved (100% identity with no insertions or deletions) between orthologous regions of the human, rat, and mouse genomes. Nearly all of these segments are also conserved in the chicken and dog genomes, with an average of 95 and 99% identity, respectively. Many are also significantly conserved in fish. These ultraconserved elements of the human genome are most often located either overlapping exons in genes involved in RNA processing or in introns or nearby genes involved in the regulation of transcription and development. Along with more than 5000 sequences of over 100 bp that are absolutely conserved among the three sequenced mammals, these represent a class of genetic elements whose functions and evolutionary origins are yet to be determined, but which are more highly conserved between these species than are proteins and appear to be essential for the ontogeny of mammals and other vertebrates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bejerano, Gill -- Pheasant, Michael -- Makunin, Igor -- Stephen, Stuart -- Kent, W James -- Mattick, John S -- Haussler, David -- 1P41HG02371/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2004 May 28;304(5675):1321-5. Epub 2004 May 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA. jill@soe.ucsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131266" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Animals ; Base Sequence ; Chickens/genetics ; Computational Biology ; *Conserved Sequence ; DNA, Intergenic ; Dogs/genetics ; Evolution, Molecular ; Exons ; Gene Expression Regulation ; Genes ; Genome ; *Genome, Human ; Humans ; Introns ; Mice/genetics ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; RNA/chemistry/genetics/metabolism ; Rats/genetics ; Takifugu/genetics
    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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  • 2
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    The Biology of Genomes meeting. The case of the disappearing DNA hotspots (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-06-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2004 Jun 11;304(5677):1590.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15192195" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Biological Evolution ; *Genome ; *Genome, Human ; Humans ; Pan troglodytes/*genetics ; *Polymorphism, Single Nucleotide ; *Recombination, 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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  • 3
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    Recruitment and spreading of the C. elegans dosage compensation complex along X chromosomes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-21
    Description: To achieve X-chromosome dosage compensation, organisms must distinguish X chromosomes from autosomes. We identified multiple, cis-acting regions that recruit the Caenorhabditis elegans dosage compensation complex (DCC) through a search for regions of X that bind the complex when detached from X. The DCC normally assembles along the entire X chromosome, but not all detached regions recruit the complex, despite having genes known to be dosage compensated on the native X. Thus, the DCC binds first to recruitment sites, then spreads to neighboring X regions to accomplish chromosome-wide gene repression. From a large chromosomal domain, we defined a 793-base pair fragment that functions in vivo as an X-recognition element to recruit the DCC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Csankovszki, Gyorgyi -- McDonel, Patrick -- Meyer, Barbara J -- F32-GM065007/GM/NIGMS NIH HHS/ -- R37-GM30702/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 20;303(5661):1182-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3204, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14976312" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; Base Sequence ; Binding Sites ; Caenorhabditis elegans/*genetics/metabolism ; Caenorhabditis elegans Proteins/*metabolism ; Carrier Proteins/metabolism ; Chromosomes/metabolism ; Cosmids ; DNA-Binding Proteins/metabolism ; Disorders of Sex Development ; *Dosage Compensation, Genetic ; Female ; In Situ Hybridization, Fluorescence ; Male ; Models, Genetic ; Molecular Sequence Data ; Nuclear Proteins/metabolism ; Repetitive Sequences, Nucleic Acid ; X Chromosome/*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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  • 4
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    Multiple Ebola virus transmission events and rapid decline of central African wildlife (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-17
    Description: Several human and animal Ebola outbreaks have occurred over the past 4 years in Gabon and the Republic of Congo. The human outbreaks consisted of multiple simultaneous epidemics caused by different viral strains, and each epidemic resulted from the handling of a distinct gorilla, chimpanzee, or duiker carcass. These animal populations declined markedly during human Ebola outbreaks, apparently as a result of Ebola infection. Recovered carcasses were infected by a variety of Ebola strains, suggesting that Ebola outbreaks in great apes result from multiple virus introductions from the natural host. Surveillance of animal mortality may help to predict and prevent human Ebola outbreaks.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leroy, Eric M -- Rouquet, Pierre -- Formenty, Pierre -- Souquiere, Sandrine -- Kilbourne, Annelisa -- Froment, Jean-Marc -- Bermejo, Magdalena -- Smit, Sheilag -- Karesh, William -- Swanepoel, Robert -- Zaki, Sherif R -- Rollin, Pierre E -- New York, N.Y. -- Science. 2004 Jan 16;303(5656):387-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Recherche pour le Developpement, UR034, Centre International de Recherches Medicales de Franceville, BP 769 Franceville, Gabon. Eric.Leroy@ird.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14726594" target="_blank"〉PubMed〈/a〉
    Keywords: Africa, Central/epidemiology ; Animals ; Animals, Wild/*virology ; Ape Diseases/*epidemiology/virology ; Base Sequence ; *Disease Outbreaks/veterinary ; Disease Reservoirs ; Ebolavirus/classification/*genetics/isolation & purification ; Gabon/epidemiology ; Genes, Viral ; Gorilla gorilla/virology ; Hemorrhagic Fever, Ebola/*epidemiology/transmission/*veterinary/virology ; Humans ; Molecular Sequence Data ; Pan troglodytes/virology ; Population Density ; Population Surveillance ; Ruminants/virology ; Viral Envelope Proteins/genetics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    The complete genome sequence of Propionibacterium acnes, a commensal of human skin (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-08-03
    Description: Propionibacterium acnes is a major inhabitant of adult human skin, where it resides within sebaceous follicles, usually as a harmless commensal although it has been implicated in acne vulgaris formation. The entire genome sequence of this Gram-positive bacterium encodes 2333 putative genes and revealed numerous gene products involved in degrading host molecules, including sialidases, neuraminidases, endoglycoceramidases, lipases, and pore-forming factors. Surface-associated and other immunogenic factors have been identified, which might be involved in triggering acne inflammation and other P. acnes-associated diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bruggemann, Holger -- Henne, Anke -- Hoster, Frank -- Liesegang, Heiko -- Wiezer, Arnim -- Strittmatter, Axel -- Hujer, Sandra -- Durre, Peter -- Gottschalk, Gerhard -- New York, N.Y. -- Science. 2004 Jul 30;305(5684):671-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gottingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Gottingen, Grisebachstrasse 8, 37077 Gottingen, Germany. hbruegg@pasteur.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15286373" target="_blank"〉PubMed〈/a〉
    Keywords: Acne Vulgaris/immunology/microbiology ; Amino Acid Motifs ; Amino Acid Sequence ; Antigens, Bacterial/chemistry/genetics ; Bacterial Proteins/chemistry/genetics/immunology ; Base Sequence ; Chromosomes, Bacterial/genetics ; Computational Biology ; Energy Metabolism ; Esterases/genetics/metabolism ; Genes, Bacterial ; *Genome, Bacterial ; Heat-Shock Proteins/chemistry/genetics ; Humans ; Hydrolases/genetics/metabolism ; Lipase/genetics/metabolism ; Molecular Sequence Data ; Oxidative Phosphorylation ; Propionibacterium acnes/*genetics/immunology/physiology ; *Sequence Analysis, DNA ; Skin/*microbiology
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  • 6
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    RNA-mediated metal-metal bond formation in the synthesis of hexagonal palladium nanoparticles (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-17
    Description: RNA sequences have been discovered that mediate the growth of hexagonal palladium nanoparticles. In vitro selection techniques were used to evolve an initial library of approximately 10(14) unique RNA sequences through eight cycles of selection to yield several active sequence families. Of the five families, all representative members could form crystalline hexagonal palladium platelets. The palladium particle growth occurred in aqueous solution at ambient temperature, without any endogenous reducing agent, and at low concentrations of metal precursor (100 micromolar). Relative to metal precursor, the RNA concentration was significantly lower (1 micromolar), yet micrometer-size crystalline hexagonal palladium particles were formed rapidly (7.5 to 1 minutes).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gugliotti, Lina A -- Feldheim, Daniel L -- Eaton, Bruce E -- New York, N.Y. -- Science. 2004 May 7;304(5672):850-2. Epub 2004 Apr 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15087507" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Chemistry, Physical ; Crystallization ; DNA, Complementary ; DNA-Directed RNA Polymerases/metabolism ; *Nanotubes ; Palladium/*chemistry ; Particle Size ; Physicochemical Phenomena ; Polymerase Chain Reaction ; RNA/*chemistry ; Temperature ; Transcription, Genetic ; Viral Proteins
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-31
    Description: Sixty-one SARS coronavirus genomic sequences derived from the early, middle, and late phases of the severe acute respiratory syndrome (SARS) epidemic were analyzed together with two viral sequences from palm civets. Genotypes characteristic of each phase were discovered, and the earliest genotypes were similar to the animal SARS-like coronaviruses. Major deletions were observed in the Orf8 region of the genome, both at the start and the end of the epidemic. The neutral mutation rate of the viral genome was constant but the amino acid substitution rate of the coding sequences slowed during the course of the epidemic. The spike protein showed the strongest initial responses to positive selection pressures, followed by subsequent purifying selection and eventual stabilization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chinese SARS Molecular Epidemiology Consortium -- New York, N.Y. -- Science. 2004 Mar 12;303(5664):1666-9. Epub 2004 Jan 29.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14752165" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Amino Acid Substitution ; Animals ; Base Sequence ; Carnivora/virology ; China/epidemiology ; Cluster Analysis ; Coronavirus/genetics/isolation & purification ; *Disease Outbreaks ; *Evolution, Molecular ; *Genome, Viral ; Genotype ; Humans ; Membrane Glycoproteins/genetics ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; Point Mutation ; RNA, Viral/genetics ; SARS Virus/*genetics/isolation & purification/physiology ; Selection, Genetic ; Sequence Deletion ; Severe Acute Respiratory Syndrome/*epidemiology/*virology ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins/genetics ; Viral Matrix Proteins/chemistry/genetics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    The ubiquitin ligase SCFFbw7 antagonizes apoptotic JNK signaling (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-24
    Description: Jun N-terminal kinases (JNKs) are essential for neuronal microtubule assembly and apoptosis. Phosphorylation of the activating protein 1 (AP1) transcription factor c-Jun, at multiple sites within its transactivation domain, is required for JNK-induced neurotoxicity. We report that in neurons the stability of c-Jun is regulated by the E3 ligase SCF(Fbw7), which ubiquitinates phosphorylated c-Jun and facilitates c-Jun degradation. Fbw7 depletion resulted in accumulation of phosphorylated c-Jun, stimulation of AP1 activity, and neuronal apoptosis. SCF(Fbw7) therefore antagonizes the apoptotic c-Jun-dependent effector arm of JNK signaling, allowing neurons to tolerate potentially neurotoxic JNK activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nateri, Abdolrahman S -- Riera-Sans, Lluis -- Da Costa, Clive -- Behrens, Axel -- New York, N.Y. -- Science. 2004 Feb 27;303(5662):1374-8. Epub 2004 Jan 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Mammalian Genetics Laboratory, Cancer Research UK, London Research Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3PX, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14739463" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Apoptosis ; Base Sequence ; Cell Cycle Proteins/genetics/*metabolism ; Cell Line ; F-Box Proteins/genetics/*metabolism ; Humans ; JNK Mitogen-Activated Protein Kinases ; MAP Kinase Signaling System ; Mice ; Mitogen-Activated Protein Kinases/*metabolism ; Molecular Sequence Data ; Neurons/*physiology ; PC12 Cells ; Phosphorylation ; Proto-Oncogene Proteins c-jun/*metabolism ; RNA, Small Interfering/metabolism ; Rats ; Transcription Factor AP-1/metabolism ; Transfection ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/genetics/*metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    MicroRNA-directed cleavage of HOXB8 mRNA (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-24
    Description: MicroRNAs (miRNAs) are endogenous approximately 22-nucleotide RNAs, some of which are known to play important regulatory roles in animals by targeting the messages of protein-coding genes for translational repression. We find that miR-196, a miRNA encoded at three paralogous locations in the A, B, and C mammalian HOX clusters, has extensive, evolutionarily conserved complementarity to messages of HOXB8, HOXC8, and HOXD8. RNA fragments diagnostic of miR-196-directed cleavage of HOXB8 were detected in mouse embryos. Cell culture experiments demonstrated down-regulation of HOXB8, HOXC8, HOXD8, and HOXA7 and supported the cleavage mechanism for miR-196-directed repression of HOXB8. These results point to a miRNA-mediated mechanism for the posttranscriptional restriction of HOX gene expression during vertebrate development and demonstrate that metazoan miRNAs can repress expression of their natural targets through mRNA cleavage in addition to inhibiting productive translation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yekta, Soraya -- Shih, I-Hung -- Bartel, David P -- New York, N.Y. -- Science. 2004 Apr 23;304(5670):594-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15105502" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; Animals ; Base Sequence ; Down-Regulation ; *Genes, Homeobox ; Genes, Reporter ; HeLa Cells ; Homeodomain Proteins/*genetics ; Humans ; Mice ; MicroRNAs/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Neoplasm Proteins/genetics ; RNA, Messenger/chemistry/*genetics/*metabolism ; Sequence Alignment ; Transcription Factors/genetics ; Transfection
    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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    Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8 (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-21
    Description: Double-stranded ribonucleic acid (dsRNA) serves as a danger signal associated with viral infection and leads to stimulation of innate immune cells. In contrast, the immunostimulatory potential of single-stranded RNA (ssRNA) is poorly understood and innate immune receptors for ssRNA are unknown. We report that guanosine (G)- and uridine (U)-rich ssRNA oligonucleotides derived from human immunodeficiency virus-1 (HIV-1) stimulate dendritic cells (DC) and macrophages to secrete interferon-alpha and proinflammatory, as well as regulatory, cytokines. By using Toll-like receptor (TLR)-deficient mice and genetic complementation, we show that murine TLR7 and human TLR8 mediate species-specific recognition of GU-rich ssRNA. These data suggest that ssRNA represents a physiological ligand for TLR7 and TLR8.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heil, Florian -- Hemmi, Hiroaki -- Hochrein, Hubertus -- Ampenberger, Franziska -- Kirschning, Carsten -- Akira, Shizuo -- Lipford, Grayson -- Wagner, Hermann -- Bauer, Stefan -- New York, N.Y. -- Science. 2004 Mar 5;303(5663):1526-9. Epub 2004 Feb 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Medical Microbiology, Immunology and Hygiene, Technische Universitat Munchen, Trogerstr. 9, D - 81675 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14976262" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing ; Animals ; Antigens, Differentiation/metabolism ; Base Sequence ; Cytokines/biosynthesis ; Dendritic Cells/*immunology ; Fatty Acids, Monounsaturated ; Genetic Complementation Test ; Guanosine/analysis ; HIV-1/genetics/*immunology ; Humans ; Interferon-alpha/biosynthesis ; Leukocytes, Mononuclear/immunology ; Macrophages/*immunology ; Membrane Glycoproteins/genetics/*metabolism ; Mice ; Mice, Inbred C57BL ; Myeloid Differentiation Factor 88 ; Oligoribonucleotides/chemistry/*immunology ; Quaternary Ammonium Compounds ; RNA, Viral/chemistry/*immunology/metabolism ; Receptors, Cell Surface/genetics/*metabolism ; Receptors, Immunologic/metabolism ; Species Specificity ; Thionucleotides/chemistry/immunology ; Toll-Like Receptor 7 ; Toll-Like Receptor 8 ; Toll-Like Receptors ; Transfection ; Uridine/analysis
    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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