Research Topics
Genomes and Genes | Frederic D BushmanSummaryAffiliation: The Salk Institute Country: USA Publications
| Collaborators
|
Detail Information
Publications
Massively parallel pyrosequencing in HIV researchFrederic D Bushman
Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA
AIDS 22:1411-5. 2008- A new cellular system opposing HIV infection: implications for gene transfer?Frederic Bushman
Infectious Disease Laboratory, Salk Institute, 10010 North Torrey Pines Road, La Jolla, California, 92037, USA
Mol Ther 6:441-2. 2002 - Targeting retroviral integration?Frederic Bushman
Infectious Disease Laboratory, Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
Mol Ther 6:570-1. 2002 - RNA interference: applications in vertebratesFrederic Bushman
Infectious Disease Laboratory, Salk Institute, 10010 North Torreny Pines Road, La Jolla, CA 92037, USA
Mol Ther 7:9-10. 2003 - Targeting survival: integration site selection by retroviruses and LTR-retrotransposonsFrederic D Bushman
Infectious Disease Laboratory, The Salk Institute, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
Cell 115:135-8. 2003..Despite these differences, recent data hints at a common targeting mechanism-tethering of integration complexes to proteins bound at favorable sites... 
Selection of target sites for mobile DNA integration in the human genomeCharles Berry
Department of Family and Preventive Medicine, School of Medicine, University of California San Diego, La Jolla, California, United States of America
PLoS Comput Biol 2:e157. 2006....- RNA interference against retrovirusesWen-Yuan Hu
Infectious Disease Laboratory, The Salk Institute, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
Virus Res 102:59-64. 2004..Here we describe the use of RNA interference (RNAi) in live chick embryos to block replication of an avian retrovirus. We also describe inhibition of ASLV and HIV replication in cell culture with RNAi... - Retroviral DNA integration: viral and cellular determinants of target-site selectionMary K Lewinski
Infectious Disease Laboratory, The Salk Institute, La Jolla, California, USA
PLoS Pathog 2:e60. 2006.... - Single-particle image reconstruction of a tetramer of HIV integrase bound to DNAGang Ren
The Scripps Research Institute, Department of Cell Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
J Mol Biol 366:286-94. 2007..The asymmetry of the complex is a feature not incorporated in previous structural models and potentially provides the first view of an asymmetric reaction intermediate... - Roles of host cell factors in circularization of retroviral dnaJennifer M Kilzer
Infectious Disease Laboratory, The Salk Institute, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
Virology 314:460-7. 2003..None of the cellular mutations showed a strong effect on normal integration, consistent with the idea that the cellular pathways leading to circularization are not involved in productive integration... - Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replicationRenate König
Infectious and Inflammatory Disease Center, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
Cell 135:49-60. 2008..Taken together, the multiscale approach described here has uncovered multiprotein virus-host interactions that likely act in concert to facilitate the early steps of HIV-1 infection... - Modeling HIV-1 integrase complexes based on their hydrodynamic propertiesAlexei A Podtelezhnikov
Howard Hughes Medical Institute, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093 0365, USA
Biopolymers 68:110-20. 2003..Our model of the integrase tetramer bound to DNA may help to design anti-integrase inhibitors... - Inhibition of retroviral pathogenesis by RNA interferenceWen-Yuan Hu
Infectious Disease Laboratory, La Jolla, CA 92037, USA
Curr Biol 12:1301-11. 2002..CONCLUSIONS: RNAi can block retroviral infection in vertebrates. The tissue electroporation method described here should allow RNAi to be used widely to study gene function and control of infection in vertebrate animals... - Retroviral DNA integration--mechanism and consequencesMary K Lewinski
Infectious Disease Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92186, USA
Adv Genet 55:147-81. 2005..Research into the mechanisms of retroviral integration site selection has shed light on the phenomena of insertional mutagenesis and viral latency... - Estimating abundances of retroviral insertion sites from DNA fragment length dataCharles C Berry
Department of Family and Preventive Medicine, University of California, La Jolla, CA, USA
Bioinformatics 28:755-62. 2012..Consequently, it is advantageous to collect replicate samples to strengthen inferences about relative abundance... - Thalassiolins A-C: new marine-derived inhibitors of HIV cDNA integraseDavid C Rowley
Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
Bioorg Med Chem 10:3619-25. 2002..4 microM) and an antiviral IC50 of 30 microM. Molecular modeling studies indicate a favorable binding mode is probable at the catalytic core domain of HIV-1 integrase... - Human immunodeficiency virus cDNA metabolism: notable stability of two-long terminal repeat circlesScott L Butler
Infectious Disease Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
J Virol 76:3739-47. 2002..We also used the quantitative PCR methods to analyze the effects of MG132, a proteasome inhibitor, which revealed that viral complexes containing mostly completed cDNAs are the primary substrates for proteasome-mediated degradation... - Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferencesRick S Mitchell
Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
PLoS Biol 2:E234. 2004..Thus, each of the three retroviruses studied showed unique integration site preferences, suggesting that virus-specific binding of integration complexes to chromatin features likely guides site selection... - HTLV-1 integration into transcriptionally active genomic regions is associated with proviral expression and with HAM/TSPKiran N Meekings
Department of Immunology, Wright Fleming Institute, Imperial College London, London, United Kingdom
PLoS Pathog 4:e1000027. 2008.... - Gene transfer in humans using a conditionally replicating lentiviral vectorBruce L Levine
Abramson Family Cancer Research Institute, University of Pennsylvania Cancer Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
Proc Natl Acad Sci U S A 103:17372-7. 2006..There is no evidence for insertional mutagenesis after 21-36 months of observation. Immune function improved in four subjects. Lentiviral vectors appear promising for gene transfer to humans... - Retroviral integration and human gene therapyFrederic D Bushman
Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104 6076, USA
J Clin Invest 117:2083-6. 2007.... - DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transferGary P Wang
University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104 6076, USA
Nucleic Acids Res 36:e49. 2008..The methods described here should allow integration site populations from human gene therapy to be deeply characterized with spatial and temporal resolution... - Retroviral DNA integration: HIV and the role of LEDGF/p75Angela Ciuffi
University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104 6076, USA
Trends Genet 22:388-95. 2006..Understanding viral integration will help improve the safety of retrovirus-based vectors used in gene therapy... - Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1Salima Hacein-Bey-Abina
Department of Biotherapy, Hopital Necker Enfants Malades, Assistance Publique Hopitaux de Paris AP HP, Universite Rene Descartes, Paris, France
J Clin Invest 118:3132-42. 2008..Successful chemotherapy was associated with restoration of polyclonal transduced T cell populations. As a result, the treated patients continued to benefit from therapeutic gene transfer... - Role of PSIP1/LEDGF/p75 in lentiviral infectivity and integration targetingHeather M Marshall
Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
PLoS ONE 2:e1340. 2007..A cellular protein, PSIP1/LEDGF/p75, binds tightly to the lentiviral-encoded integrase protein (IN), and has been reported to be important for HIV infectivity and integration targeting... - The interferon response inhibits HIV particle production by induction of TRIM22Stephen D Barr
Department of Medical Microbiology and Immunology, University of Alberta, Alberta Institute for Viral Immunology, Edmonton, Alberta, Canada
PLoS Pathog 4:e1000007. 2008..Mutational analyses of TRIM22 showed that the catalytic amino acids Cys15 and Cys18 of the RING domain are required for TRIM22 antiviral activity. These data disclose a pathway by which Type 1 interferons obstruct HIV replication... - DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutationsChristian Hoffmann
Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104 6076, USA
Nucleic Acids Res 35:e91. 2007.... - HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modificationsGary P Wang
University of Pennsylvania, School of Medicine, Department of Microbiology, Philadelphia, PA 19104 6076, USA
Genome Res 17:1186-94. 2007..The pyrosequencing and bioinformatic methods described here should be useful for investigating many aspects of retroviral DNA integration... - Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomesNana Minkah
Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 6076, USA
Virology 365:60-9. 2007..These data define the full variola virus topoisomerase recognition site and provide a new window on topoisomerase function in vivo... - Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genomeStephen D Barr
University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104 6076, USA
J Virol 79:12035-44. 2005..Further analysis indicated that ERVs in humans, mice, and rats showed similar distributions, suggesting purifying selection dictated their distributions as well... - Regulation of catalysis by the smallpox virus topoisomeraseYoung Hwang
Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
J Biol Chem 281:38052-60. 2006..These findings help elucidate the amino acid side chains involved in DNA binding and catalysis and provide guidance for designing topoisomerase poisons for use as smallpox antivirals... - Modulating target site selection during human immunodeficiency virus DNA integration in vitro with an engineered tethering factorAngela Ciuffi
Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6076, USA
Hum Gene Ther 17:960-7. 2006.... - Division of labor within human immunodeficiency virus integrase complexes: determinants of catalysis and target DNA captureTracy L Diamond
University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA
J Virol 79:15376-87. 2005..These data specify the ligands bound at the catalytically relevant IN monomer and allow more-specific modeling of the mechanism of inhibitors that also bind this surface of IN... - DNA cleavage by the A22R resolvase of vaccinia virusMatthew J Culyba
Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA
Virology 352:466-76. 2006..Analysis of the reaction products revealed that A22R cleaves to leave a 3' hydroxyl at the cleaved phosphodiester bond... - HIV integration site selection: targeting in macrophages and the effects of different routes of viral entryStephen D Barr
Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, 19104-6076, USA
Mol Ther 14:218-25. 2006..Analysis of additional published integration site sequences also indicated that the route of entry did not affect integration site selection for other viral envelopes as well... - A statistical method for comparing viral growth curvesGary P Wang
Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA
J Virol Methods 135:118-23. 2006..A web-based tutorial for implementing this method is available at http://microb230.med.upenn.edu/tutorials/wangTutorial...