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  • 1
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    Computational prediction of N-linked glycosylation incorporating structural properties and patterns (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-25
    Description: Motivation: N-linked glycosylation occurs predominantly at the N-X-T/S motif, where X is any amino acid except proline. Not all N-X-T/S sequons are glycosylated, and a number of web servers for predicting N-linked glycan occupancy using sequence and/or residue pattern information have been developed. None of the currently available servers, however, utilizes protein structural information for the prediction of N -glycan occupancy. Results: Here, we describe a novel classifier algorithm, NGlycPred, for the prediction of glycan occupancy at the N-X-T/S sequons. The algorithm utilizes both structural as well as residue pattern information and was trained on a set of glycosylated protein structures using the Random Forest algorithm. The best predictor achieved a balanced accuracy of 0.687 under 10-fold cross-validation on a curated dataset of 479 N-X-T/S sequons and outperformed sequence-based predictors when evaluated on the same dataset. The incorporation of structural information, including local contact order, surface accessibility/composition and secondary structure thus improves the prediction accuracy of glycan occupancy at the N-X-T/S consensus sequon. Availability and Implementation: NGlycPred is freely available to non-commercial users as a web-based server at http://exon.niaid.nih.gov/nglycpred/ . Contact: ivelin.georgiev@nih.gov Supplementary Information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Regulation of the proinflammatory effects of Fas ligand (CD95L) (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-11-30
    Description: Fas ligand (CD95L) inhibits T cell function in immune-privileged organs such as the eye and testis, yet in most tissues CD95L expression induces potent inflammatory responses. With a stably transfected colon carcinoma cell line, CT26-CD95L, the molecular basis for these divergent responses was defined. When injected subcutaneously, rejection of CT26-CD95L was caused by neutrophils activated by CD95L. CT26-CD95L survived in the intraocular space because of the presence of transforming growth factor-beta (TGF-beta), which inhibited neutrophil activation. Providing TGF-beta to subcutaneous sites protected against tumor rejection. Thus, these cytokines together generate a microenvironment that promotes immunologic tolerance, which may aid in the amelioration of allograft rejection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, J J -- Sun, Y -- Nabel, G J -- New York, N.Y. -- Science. 1998 Nov 27;282(5394):1714-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of Michigan Medical Center, Departments of Internal Medicine and Biological Chemistry, 1150 West Medical Center Drive, 4520 Medical Science Research Building I, Ann Arbor, MI 48109-0650, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9831564" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anterior Chamber ; Apoptosis ; Calcium-Calmodulin-Dependent Protein Kinases/antagonists & inhibitors/metabolism ; Cytotoxicity, Immunologic ; Fas Ligand Protein ; Female ; Graft Rejection ; Humans ; Immune Tolerance ; Inflammation/*immunology ; Jurkat Cells ; Membrane Glycoproteins/*physiology ; Mice ; Mice, Inbred BALB C ; *Mitogen-Activated Protein Kinases ; Neoplasm Transplantation ; Neoplasms, Experimental/*immunology/pathology ; *Neutrophil Activation ; Neutrophils/immunology ; Transfection ; Transforming Growth Factor beta/pharmacology ; Tumor Cells, Cultured ; p38 Mitogen-Activated Protein Kinases
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Distinct cellular interactions of secreted and transmembrane Ebola virus glycoproteins (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-03-07
    Description: The mechanisms by which Ebola virus evades detection and infects cells to cause hemorrhagic fever have not been defined, though its glycoprotein, synthesized in either a secreted or transmembrane form, is likely involved. Here the secreted glycoprotein was found to interact with neutrophils through CD16b, the neutrophil-specific form of the Fc gamma receptor III, whereas the transmembrane glycoprotein was found to interact with endothelial cells but not neutrophils. A murine retroviral vector pseudotyped with the transmembrane glycoprotein preferentially infected endothelial cells. Thus, the secreted glycoprotein inhibits early neutrophil activation, which likely affects the host response to infection, whereas binding of the transmembrane glycoprotein to endothelial cells may contribute to the hemorrhagic symptoms of this disease.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Z -- Delgado, R -- Xu, L -- Todd, R F -- Nabel, E G -- Sanchez, A -- Nabel, G J -- New York, N.Y. -- Science. 1998 Feb 13;279(5353):1034-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9461435" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; Ebolavirus/genetics/metabolism/*pathogenicity/physiology ; Endothelium, Vascular/cytology/*metabolism/virology ; Genes, Viral ; Genetic Vectors ; Glycoproteins/genetics/*metabolism/secretion ; Hemorrhagic Fever, Ebola/virology ; Humans ; L-Selectin/metabolism ; Membrane Glycoproteins/genetics/*metabolism ; Moloney murine leukemia virus/genetics/physiology ; Neutrophil Activation ; Neutrophils/immunology/*metabolism ; Receptors, IgG/metabolism ; Transfection ; Tumor Cells, Cultured ; Viral Matrix Proteins/genetics/*metabolism ; Viral Proteins/genetics/*metabolism/secretion
    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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    Alternative mechanisms for activation of human immunodeficiency virus enhancer in T cells (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-03-11
    Description: The expression of human immunodeficiency virus (HIV) after T cell activation is regulated by NF-kappa B, an inducible DNA-binding protein that stimulates transcription. Proteins encoded by a variety of DNA viruses are also able to activate expression from the HIV enhancer. To determine how this activation occurs, specific genes from herpes simplex virus type 1 and adenovirus that activate HIV in T lymphoma cells have been identified. The cis-acting regulatory sequences in the HIV enhancer that mediate their effect have also been characterized. The relevant genes are those for ICP0-an immediate-early product of herpes simplex virus type 1-and the form of E1A encoded by the 13S messenger RNA of adenovirus. Activation of HIV by adenovirus E1A was found to depend on the TATA box, whereas herpesvirus ICP0 did not work through a single defined cis-acting element. These findings suggest multiple pathways that can be used to bypass normal cellular activation of HIV, and they raise the possibility that infection by herpes simplex virus or adenovirus may directly contribute to the activation of HIV in acquired immunodeficiency syndrome by mechanisms independent of antigenic stimulation in T cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nabel, G J -- Rice, S A -- Knipe, D M -- Baltimore, D -- AI20530/AI/NIAID NIH HHS/ -- F32GM11224/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Mar 11;239(4845):1299-302.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Cambridge, MA 02142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2830675" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviruses, Human/genetics ; *Enhancer Elements, Genetic ; Genes, Regulator ; *Genes, Viral ; HIV/*genetics/growth & development ; Humans ; *Lymphocyte Activation ; Plasmids ; Simplexvirus/genetics ; T-Lymphocytes/*immunology ; Transcription, Genetic ; Virus Activation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Recombinant gene expression in vivo within endothelial cells of the arterial wall (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-06-16
    Description: A technique for the transfer of endothelial cells and expression of recombinant genes in vivo could allow the introduction of proteins of therapeutic value in the management of cardiovascular diseases. Porcine endothelial cells expressing recombinant beta-galactosidase from a murine amphotropic retroviral vector were introduced with a catheter into denuded iliofemoral arteries of syngeneic animals. Arterial segments explanted 2 to 4 weeks later contained endothelial cells expressing beta-galactosidase, an indication that they were successfully implanted on the vessel wall.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nabel, E G -- Plautz, G -- Boyce, F M -- Stanley, J C -- Nabel, G J -- New York, N.Y. -- Science. 1989 Jun 16;244(4910):1342-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor 48109-0650.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2499928" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Catheterization, Peripheral ; DNA, Recombinant ; Endothelium, Vascular/*cytology/enzymology/transplantation ; Female ; Galactosidases/*biosynthesis ; Genetic Vectors ; Iliac Artery/cytology ; Retroviridae ; Swine ; Swine, Miniature ; beta-Galactosidase/*biosynthesis
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Regulation of gene expression with double-stranded phosphorothioate oligonucleotides (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-11-16
    Description: Alteration of gene transcription by inhibition of specific transcriptional regulatory proteins is necessary for determining how these factors participate in cellular differentiation. The functions of these proteins can be antagonized by several methods, each with specific limitations. Inhibition of sequence-specific DNA-binding proteins was achieved with double-stranded (ds) phosphorothioate oligonucleotides that contained octamer or kappa B consensus sequences. The phosphorothioate oligonucleotides specifically bound either octamer transcription factor or nuclear factor (NF)-kappa B. The modified oligonucleotides accumulated in cells more effectively than standard ds oligonucleotides and modulated gene expression in a specific manner. Octamer-dependent activation of a reporter plasmid or NF-kappa B-dependent activation of the human immunodeficiency virus (HIV) enhancer was inhibited when the appropriate phosphorothioate oligonucleotide was added to a transiently transfected B cell line. Addition of phosphorothioate oligonucleotides that contained the octamer consensus to Jurkat T leukemia cells inhibited interleukin-2 (IL-2) secretion to a degree similar to that observed with a mutated octamer site in the IL-2 enhancer. The ds phosphorothioate oligonucleotides probably compete for binding of specific transcription factors and may provide anti-viral, immunosuppressive, or other therapeutic effects.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bielinska, A -- Shivdasani, R A -- Zhang, L Q -- Nabel, G J -- AI26865/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1990 Nov 16;250(4983):997-1000.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor 48109-0650.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2237444" target="_blank"〉PubMed〈/a〉
    Keywords: DNA-Binding Proteins/metabolism ; *Gene Expression Regulation ; Gene Expression Regulation, Neoplastic ; Gene Expression Regulation, Viral ; HIV Enhancer ; Host Cell Factor C1 ; Humans ; Interleukin-2/antagonists & inhibitors ; Leukemia, T-Cell/genetics ; NF-kappa B/metabolism ; Octamer Transcription Factor-1 ; Oligonucleotides/*genetics ; T-Lymphocytes ; Thionucleotides/*genetics ; Transcription Factors/metabolism ; Tumor Cells, Cultured
    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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    Site-specific gene expression in vivo by direct gene transfer into the arterial wall (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-09-14
    Description: A recombinant beta-galactosidase gene has been expressed in a specific arterial segment in vivo by direct infection with a murine amphotropic retroviral vector or by DNA transfection with the use of liposomes. Several cell types in the vessel wall were transduced, including endothelial and vascular smooth muscle cells. After retroviral infection, a recombinant reporter gene was expressed for at least 5 months, and no helper virus was detected. Recombinant gene expression achieved by direct retroviral infection or liposome-mediated DNA transfection was limited to the site of infection and was absent from liver, lung, kidney, and spleen. These results demonstrate that site-specific gene expression can be achieved by direct gene transfer in vivo and could be applied to the treatment of such human diseases as atherosclerosis or cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nabel, E G -- Plautz, G -- Nabel, G J -- AI 29179/AI/NIAID NIH HHS/ -- DK 42706/DK/NIDDK NIH HHS/ -- GM-13457/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Sep 14;249(4974):1285-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Internal Medicine, Howard Hughes Medical Institute, University of Michigan Medical Center, Ann Arbor 48109-0650.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2119055" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/genetics ; Animals ; Arteries/*metabolism ; Catheterization, Peripheral ; *Gene Expression ; Hexadimethrine Bromide ; Liposomes ; Methods ; Moloney murine leukemia virus/genetics ; Promoter Regions, Genetic/genetics ; Swine ; *Transfection ; beta-Galactosidase/biosynthesis/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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  • 8
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    Public health. Rethinking influenza (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-10-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rappuoli, Rino -- Del Giudice, Giuseppe -- Nabel, Gary J -- Osterhaus, Albert D M E -- Robinson, Robin -- Salisbury, David -- Stohr, Klaus -- Treanor, John J -- New York, N.Y. -- Science. 2009 Oct 2;326(5949):50. doi: 10.1126/science.1179475.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Novartis Vaccines and Diagnostics Srl, 53100 Siena, Italy. rino.rappuoli@novartis.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19797644" target="_blank"〉PubMed〈/a〉
    Keywords: Adjuvants, Immunologic ; Animals ; Antiviral Agents/therapeutic use ; Developed Countries ; Developing Countries ; *Disease Outbreaks/prevention & control ; Humans ; *Influenza A Virus, H1N1 Subtype/immunology ; *Influenza Vaccines/adverse effects/immunology ; *Influenza, Human/epidemiology/prevention & control/virology ; Mass Vaccination ; *Orthomyxoviridae/immunology ; Population Surveillance
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Philosophy of science. The coordinates of truth (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-10-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nabel, Gary J -- New York, N.Y. -- Science. 2009 Oct 2;326(5949):53-4. doi: 10.1126/science.1177637.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. gnabel@nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19797647" target="_blank"〉PubMed〈/a〉
    Keywords: *Biomedical Research ; Human Genome Project ; Humans ; National Institutes of Health (U.S.) ; Peer Review, Research ; *Philosophy ; Research ; Research Design ; Research Support as Topic ; *Science ; Systems Biology ; United States
    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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    Induction of broadly neutralizing H1N1 influenza antibodies by vaccination (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-07-22
    Description: The rapid dissemination of the 2009 pandemic influenza virus underscores the need for universal influenza vaccines that elicit protective immunity to diverse viral strains. Here, we show that vaccination with plasmid DNA encoding H1N1 influenza hemagglutinin (HA) and boosting with seasonal vaccine or replication-defective adenovirus 5 vector encoding HA stimulated the production of broadly neutralizing influenza antibodies. This prime/boost combination increased the neutralization of diverse H1N1 strains dating from 1934 to 2007 as compared to either component alone and conferred protection against divergent H1N1 viruses in mice and ferrets. These antibodies were directed to the conserved stem region of HA and were also elicited in nonhuman primates. Cross-neutralization of H1N1 subtypes elicited by this approach provides a basis for the development of a universal influenza vaccine for humans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wei, Chih-Jen -- Boyington, Jeffrey C -- McTamney, Patrick M -- Kong, Wing-Pui -- Pearce, Melissa B -- Xu, Ling -- Andersen, Hanne -- Rao, Srinivas -- Tumpey, Terrence M -- Yang, Zhi-Yong -- Nabel, Gary J -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Aug 27;329(5995):1060-4. doi: 10.1126/science.1192517. Epub 2010 Jul 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892-3005, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20647428" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Neutralizing/biosynthesis/*immunology ; Antibodies, Viral/biosynthesis/*immunology ; *Cross Protection ; Female ; Ferrets ; Genetic Vectors ; Hemagglutinin Glycoproteins, Influenza Virus/genetics/*immunology ; Humans ; Immunization, Secondary ; Influenza A Virus, H1N1 Subtype/*immunology ; Influenza A Virus, H2N2 Subtype/immunology ; Influenza A Virus, H3N2 Subtype/immunology ; Influenza A Virus, H5N1 Subtype/immunology ; Influenza Vaccines/*administration & dosage/*immunology ; Influenza, Human/immunology/prevention & control ; Macaca mulatta ; Male ; Mice ; Mice, Inbred BALB C ; Mutant Proteins/immunology ; Orthomyxoviridae Infections/immunology/prevention & control ; Plasmids ; Vaccination ; Vaccines, DNA/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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