B Berkhout

Summary

Affiliation: Academic Medical Center
Country: The Netherlands

Publications

  1. pmc Hairpin-induced tRNA-mediated (HITME) recombination in HIV-1
    Pavlina Konstantinova
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Nucleic Acids Res 34:2206-18. 2006
  2. pmc Combinatorial RNAi against HIV-1 using extended short hairpin RNAs
    Ying Poi Liu
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
    Mol Ther 17:1712-23. 2009
  3. pmc Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron
    Ying Poi Liu
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Nucleic Acids Res 36:2811-24. 2008
  4. pmc HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome
    Ellen M Westerhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Nucleic Acids Res 33:796-804. 2005
  5. pmc The availability of the primer activation signal (PAS) affects the efficiency of HIV-1 reverse transcription initiation
    Marcel Ooms
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, The Netherlands
    Nucleic Acids Res 35:1649-59. 2007
  6. pmc Design of extended short hairpin RNAs for HIV-1 inhibition
    Ying Poi Liu
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, Amsterdam, The Netherlands
    Nucleic Acids Res 35:5683-93. 2007
  7. pmc RNAi-mediated inhibition of HIV-1 by targeting partially complementary viral sequences
    Ying Poi Liu
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam, Meibergdreef 15, Amsterdam, The Netherlands
    Nucleic Acids Res 37:6194-204. 2009
  8. pmc Destabilization of the TAR hairpin affects the structure and function of the HIV-1 leader RNA
    Martine M Vrolijk
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Nucleic Acids Res 36:4352-63. 2008
  9. pmc Circularization of the HIV-1 RNA genome
    Marcel Ooms
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, The Netherlands
    Nucleic Acids Res 35:5253-61. 2007
  10. pmc A systematic analysis of the effect of target RNA structure on RNA interference
    Ellen M Westerhout
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, The Netherlands
    Nucleic Acids Res 35:4322-30. 2007

Detail Information

Publications165 found, 100 shown here

  1. pmc Hairpin-induced tRNA-mediated (HITME) recombination in HIV-1
    Pavlina Konstantinova
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Nucleic Acids Res 34:2206-18. 2006
    ..The transient role of the cellular tRNA molecule as enhancer of retroviral recombination is illustrated by the eventual removal of inserted tRNA sequences by a subsequent recombination/deletion event...
  2. pmc Combinatorial RNAi against HIV-1 using extended short hairpin RNAs
    Ying Poi Liu
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
    Mol Ther 17:1712-23. 2009
    ..These results show that e-shRNAs can be used as a combinatorial RNAi approach to target error-prone viruses...
  3. pmc Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron
    Ying Poi Liu
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Nucleic Acids Res 36:2811-24. 2008
    ..These combined results indicate that a multiplex miRNA strategy may be a promising therapeutic approach to attack escape-prone viral pathogens...
  4. pmc HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome
    Ellen M Westerhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Nucleic Acids Res 33:796-804. 2005
    ..The results highlight the enormous genetic flexibility of HIV-1 and provide detailed molecular insight into the sequence specificity of RNAi and the impact of target RNA secondary structure...
  5. pmc The availability of the primer activation signal (PAS) affects the efficiency of HIV-1 reverse transcription initiation
    Marcel Ooms
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, The Netherlands
    Nucleic Acids Res 35:1649-59. 2007
    ..Furthermore, changes in PAS are critical to facilitate a primer-switch to a new tRNA species, demonstrating the importance of this enhancer element...
  6. pmc Design of extended short hairpin RNAs for HIV-1 inhibition
    Ying Poi Liu
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, Amsterdam, The Netherlands
    Nucleic Acids Res 35:5683-93. 2007
    ..These results provide building principles for the design of multi-siRNA hairpin constructs...
  7. pmc RNAi-mediated inhibition of HIV-1 by targeting partially complementary viral sequences
    Ying Poi Liu
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam, Meibergdreef 15, Amsterdam, The Netherlands
    Nucleic Acids Res 37:6194-204. 2009
    ..These data suggest that targeting imperfect target sites by antiviral miRNAs or shRNAs provides an alternative RNAi approach for inhibition of pathogenic viruses...
  8. pmc Destabilization of the TAR hairpin affects the structure and function of the HIV-1 leader RNA
    Martine M Vrolijk
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Nucleic Acids Res 36:4352-63. 2008
    ..Upon evolution of such mutant viruses, the replication capacity was repaired through the acquisition of additional TAR mutations that restore the local RNA folding, thus preventing the detrimental effect on the leader conformation...
  9. pmc Circularization of the HIV-1 RNA genome
    Marcel Ooms
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, The Netherlands
    Nucleic Acids Res 35:5253-61. 2007
    ..Phylogenetic analysis indicates that all HIV-1 subtypes can form the 5'/3' interaction despite considerable sequence divergence, suggesting an important role of RNA circularization in the HIV-1 replication cycle...
  10. pmc A systematic analysis of the effect of target RNA structure on RNA interference
    Ellen M Westerhout
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, The Netherlands
    Nucleic Acids Res 35:4322-30. 2007
    ....
  11. pmc Of Mice and Men: On the Origin of XMRV
    Antoinette Cornelia van der Kuyl
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands
    Front Microbiol 1:147. 2010
    ..We hypothesize that mouse cells or human cell lines used for vaccine production could have been contaminated with a replicating variant of the XMRV precursors encoded by the mouse genome...
  12. pmc Deep sequencing of virus-infected cells reveals HIV-encoded small RNAs
    Nick C T Schopman
    Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, The Netherlands
    Nucleic Acids Res 40:414-27. 2012
    ..These results suggest that HIV-1 triggers the production of vsiRNAs and vmiRNAs to modulate cellular and/or viral gene expression...
  13. pmc Dicer-independent processing of short hairpin RNAs
    Ying Poi Liu
    Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Nucleic Acids Res 41:3723-33. 2013
    ..Both the processing and subsequent RNAi activity of these AgoshRNAs are thus mediated by the RISC-component AGO2. These results have important implications for the future design of more specific RNAi therapeutics...
  14. pmc On the role of four small hairpins in the HIV-1 RNA genome
    Stefanie A Knoepfel
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center University of Amsterdam, Amsterdam, The Netherlands
    RNA Biol 10:540-52. 2013
    ..No major virus replication defects were scored, suggesting that these four hairpin structures do not play essential roles in HIV-1 replication...
  15. ncbi request reprint HIV, leukemia, and new horizons in molecular therapy
    Ben Berkhout
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands Electronic address
    J Formos Med Assoc 112:441-4. 2013
    ....
  16. pmc Cell-associated HIV RNA: a dynamic biomarker of viral persistence
    Alexander O Pasternak
    Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, Meibergdreef 15, Amsterdam 1105 AZ, The Netherlands
    Retrovirology 10:41. 2013
    ..Potential value of this biomarker for monitoring the response to ART and to novel HIV eradication therapies is highlighted...
  17. pmc The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus
    Antoinette C van der Kuyl
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, Amsterdam, AZ 1105, The Netherlands
    Retrovirology 9:92. 2012
    ....
  18. pmc Opening of the TAR hairpin in the HIV-1 genome causes aberrant RNA dimerization and packaging
    Atze T Das
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
    Retrovirology 9:59. 2012
    ..In this study, we set out to analyze which step of the HIV-1 replication cycle is affected by this conformational change of the leader RNA...
  19. pmc Obituary: Kuan-Teh Jeang
    Ben Berkhout
    Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, Meibergdreef 15, Amsterdam, 1105 AZ, The Netherlands
    Retrovirology 10:28. 2013
    ..Many of us came to know Teh as an energetic and gifted scientist for whom we had much respect and affection...
  20. doi request reprint Gene therapy as a vaccine for HIV-1
    Ben Berkhout
    University of Amsterdam, Center for Infection and Immunity Amsterdam, Academic Medical Center, Department of Medical Microbiology, Laboratory of Experimental Virology, Meibergdreef 15, K3 110, 1105 AZ Amsterdam, The Netherlands
    Expert Opin Biol Ther 12:1315-21. 2012
    ..HIV-1 vaccine research has encountered several false starts and a few causes for hope over the last 28 years, but no real success stories. Thus, it is time to think out of the box and design and test unorthodox vaccination strategies...
  21. pmc Inhibition of HIV-1 replication with stable RNAi-mediated knockdown of autophagy factors
    Julia Jm Eekels
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Virol J 9:69. 2012
    ..Stable knockdown of several autophagy factors inhibit HIV-1 replication without any apparent cytotoxicity. We therefore propose that targeting of the autophagy pathway can be a novel therapeutic approach against HIV-1...
  22. doi request reprint Is there a future for antiviral fusion inhibitors?
    Ben Berkhout
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam, The Netherlands
    Curr Opin Virol 2:50-9. 2012
    ..Here, we will review the field of HIV-1 fusion inhibitors...
  23. pmc Human coronavirus 229E encodes a single ORF4 protein between the spike and the envelope genes
    Ronald Dijkman
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, The Netherlands
    Virol J 3:106. 2006
    ....
  24. pmc Genome structure and transcriptional regulation of human coronavirus NL63
    Krzysztof Pyrc
    Department of Human Retrovirology, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
    Virol J 1:7. 2004
    ..In this study, we describe the genome structure and the transcription strategy of HCoV-NL63 by experimental analysis of the viral subgenomic mRNAs...
  25. pmc Occult hepatitis B infection: an evolutionary scenario
    Formijn J van Hemert
    Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
    Virol J 5:146. 2008
    ..To gain insight into the mechanism of the development of occult infection, we compared the full-length HBV genome from a blood donor carrying an occult infection (d4) with global genotype D genomes...
  26. pmc Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function
    Formijn J van Hemert
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, The Netherlands
    Virol J 4:25. 2007
    ..Analyses of synonymous substitutions displayed a loss of tree structure, suggesting either saturation of the substitution model or a deviant pattern of synonymous substitutions in certain virus species...
  27. pmc Latency profiles of full length HIV-1 molecular clone variants with a subtype specific promoter
    Renee M van der Sluis
    Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Retrovirology 8:73. 2011
    ..Latency differences may influence establishment and size of viral reservoirs as well as the possibility to clear the virus by therapeutic intervention...
  28. pmc A stabilized HIV-1 envelope glycoprotein trimer fused to CD40 ligand targets and activates dendritic cells
    Mark Melchers
    Laboratory of Experimental Virology, Department of Medical Microbiology Center for Infection and Immunity Amsterdam, Netherlands
    Retrovirology 8:48. 2011
    ..We have previously stabilized soluble trimeric mimics of Env by introducing a disulfide bond between gp120 and gp41 and adding a trimer stabilizing mutation in gp41 (SOSIP.R6 gp140)...
  29. pmc Efficient inhibition of HIV-1 expression by LNA modified antisense oligonucleotides and DNAzymes targeted to functionally selected binding sites
    Martin R Jakobsen
    Department of Molecular Biology, University of Aarhus C F Møllers Allé, Arhus C, Denmark
    Retrovirology 4:29. 2007
    ..Using a library selection approach to define the most accessible sites for 20-mer oligonucleotides annealing within the highly structured 5'-UTR of the HIV-1 genome we have shown that there are at least four optimal targets available...
  30. pmc Differential susceptibility of naïve, central memory and effector memory T cells to dendritic cell-mediated HIV-1 transmission
    Fedde Groot
    Dept, of Cell Biology and Histology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
    Retrovirology 3:52. 2006
    ..The TEM cell subset, which can be further divided into effector Th1 and Th2 cells, has been shown to be the prime target for viral replication after HIV-1 infection, and is abundantly present in mucosal tissues...
  31. pmc The virion-associated incoming HIV-1 RNA genome is not targeted by RNA interference
    Ellen M Westerhout
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, The Netherlands Westerhout
    Retrovirology 3:57. 2006
    ..There have been conflicting results on whether RNAi can target the RNA genome of infecting HIV-1 particles. We have addressed this issue with HIV-1-based lentiviral vectors...
  32. pmc Modification of the Tet-On regulatory system prevents the conditional-live HIV-1 variant from losing doxycycline-control
    Xue Zhou
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Retrovirology 3:82. 2006
    ..However, subsequent dox-withdrawal may impose a selection for virus variants with reduced dox-dependence...
  33. pmc Retroviral superinfection resistance
    Micha Nethe
    Dept of Human Retrovirology, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
    Retrovirology 2:52. 2005
    ..As primate models of SIV infection closely resemble HIV infection, a better knowledge of SIR-induced mechanisms could contribute to the development of an HIV vaccine or other antiviral strategies...
  34. pmc It's the virus, stupid--part 2
    Ben Berkhout
    Retrovirology 2:78. 2005
    ..This editorial presents Retrovirology's choice for the best basic science "retrovirus paper of the year 2005"...
  35. pmc Trans-inhibition of HIV-1 by a long hairpin RNA expressed within the viral genome
    Pavlina Konstantinova
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
    Retrovirology 4:15. 2007
    ..In order to solve this problem, we constructed an HIV-1 variant with a 300 bp long hairpin structure in the 3' part of the genome corresponding to the Nef gene (HIV-lhNef)...
  36. pmc SIVdrl detection in captive mandrills: are mandrills infected with a third strain of simian immunodeficiency virus?
    Antoinette C van der Kuyl
    Department of Human Retrovirology, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Retrovirology 1:36. 2004
    ..This suggests that mandrills are the first primate species to be infected with three strains of SIV: SIVmnd1, SIVmnd2, and SIVdrl...
  37. pmc Dendritic cell-mediated HIV-1 transmission to T cells of LAD-1 patients is impaired due to the defect in LFA-1
    Fedde Groot
    Department of Cell Biology and Histology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
    Retrovirology 3:75. 2006
    ..To corroborate the importance of the ICAM-1- LFA-1 interaction, we performed transmission experiments to LFA-1 negative leukocytes from Leukocyte Adhesion Deficiency type 1 (LAD-1) patients...
  38. pmc Factor correction as a tool to eliminate between-session variation in replicate experiments: application to molecular biology and retrovirology
    Jan M Ruijter
    Department of Anatomy and Embryology, Academic Medical Centre, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Retrovirology 3:2. 2006
    ..Normalisation, however, adds variation because the control value is not without error, while standardisation is biased if the data set is incomplete...
  39. pmc Optimization of the doxycycline-dependent simian immunodeficiency virus through in vitro evolution
    Atze T Das
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, The Netherlands
    Retrovirology 5:44. 2008
    ..Since macaque studies will likely require an efficiently replicating variant, we set out to optimize SIV-rtTA through in vitro viral evolution...
  40. pmc Towards a genetic AIDS vaccine
    Antonia V Bordería
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infectious Diseases and Immunology Amsterdam, Academic Medical Center, University of Amsterdam, The Netherlands
    Retrovirology 6:93. 2009
    ..Nat. Med. 2009, 15: 901-906) in which an effective HIV-1 vaccine was designed that is based on gene therapy. The introduced gene produces an antibody-like immunoadhesin in the blood that neutralizes the virus...
  41. pmc Destabilization of the TAR hairpin leads to extension of the polyA hairpin and inhibition of HIV-1 polyadenylation
    Martine M Vrolijk
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Retrovirology 6:13. 2009
    ..We recently described that the replication of an HIV-1 variant that does not need TAR for transcription was severely impaired by destabilization of the TAR hairpin, even though a complete TAR deletion was acceptable...
  42. pmc HIV-1 latency in actively dividing human T cell lines
    Rienk E Jeeninga
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, The Netherlands
    Retrovirology 5:37. 2008
    ..Exploring the molecular details of viral latency will provide new insights for eventual future therapeutics that aim at viral eradication...
  43. pmc The HIV RNA setpoint theory revisited
    Ronald B Geskus
    Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
    Retrovirology 4:65. 2007
    ..Both markers were evaluated on a scale that is directly related to AIDS risk...
  44. pmc Evolution of the HIV-1 envelope glycoproteins with a disulfide bond between gp120 and gp41
    Rogier W Sanders
    Dept of Human Retrovirology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
    Retrovirology 1:3. 2004
    ..The modified Env protein antigenically mimics the functional wild-type Env complex. Here, we explore the effects of the covalent gp120 - gp41 interaction on virus replication and evolution...
  45. pmc ESF-EMBO symposium: antiviral applications of RNA interference
    Olivier Ter Brake
    Department of Medical Microbiology, Center of Infection and Immunity Amsterdam, Laboratory of Experimental Virology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
    Retrovirology 5:81. 2008
  46. pmc HIV-1 drug-resistance and drug-dependence
    Chris Baldwin
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, The Netherlands
    Retrovirology 4:78. 2007
    ..Second, a compensatory mutation that repairs the protein function, but in the presence of the drug, which becomes an intrinsic part of the mechanism. The clinical relevance of drug-dependent HIV-1 variants is also discussed...
  47. pmc Analysis of infectious virus clones from two HIV-1 superinfection cases suggests that the primary strains have lower fitness
    Antoinette C van der Kuyl
    Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam CINIMA, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
    Retrovirology 7:60. 2010
    ..The use of isolate-specific primer sets indicated that the primary and secondary strains co-exist in plasma at all time points after the moment of superinfection...
  48. pmc Second site escape of a T20-dependent HIV-1 variant by a single amino acid change in the CD4 binding region of the envelope glycoprotein
    Chris E Baldwin
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, The Netherlands
    Retrovirology 3:84. 2006
    ....
  49. pmc Construction of doxycyline-dependent mini-HIV-1 variants for the development of a virotherapy against leukemias
    Rienk E Jeeninga
    Laboratory of Experimental Virology, Department of Medical Microbiology Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
    Retrovirology 3:64. 2006
    ..The therapeutic viruses use CD4 and CXCR4 for cell entry and could potentially be used against CXCR4 expressing malignancies such as T-lymphoblastic leukemia/lymphoma, NK leukemia and some myeloid leukemias...
  50. pmc The carbohydrate at asparagine 386 on HIV-1 gp120 is not essential for protein folding and function but is involved in immune evasion
    Rogier W Sanders
    Laboratory of Experimental Virology, Dept, Medical Microbiology, Center of Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
    Retrovirology 5:10. 2008
    ..Here we studied the role of the carbohydrate at position 386. We identified a virus variant that had lost the 386 glycan in an evolution study of a mutant virus lacking the disulfide bond at the base of the V4 domain...
  51. pmc A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium
    Elien Moës
    Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Belgium
    BMC Infect Dis 5:6. 2005
    ..In this study we explored the incidence of HCoV-NL63 infection in children diagnosed with respiratory tract infections in Belgium...
  52. pmc Improved single-chain transactivators of the Tet-On gene expression system
    Xue Zhou
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
    BMC Biotechnol 7:6. 2007
    ..Unfortunately, the activity of the single-chain rtTA (sc-rtTA) is reduced when compared with the regular rtTA, which might limit its application...
  53. doi request reprint Toward a durable anti-HIV gene therapy based on RNA interference
    Ben Berkhout
    Laboratory of Experimental Virology, Academic Medical Center, University of Amsterdam, The Netherlands
    Ann N Y Acad Sci 1175:3-14. 2009
    ..Combinatorial RNAi strategies are required to prevent viral escape...
  54. ncbi request reprint The interplay between virus infection and the cellular RNA interference machinery
    Ben Berkhout
    Department of Human Retrovirology, K3 110, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
    FEBS Lett 580:2896-902. 2006
    ..Here, we summarize the latest news on virus-RNAi interactions and RNAi based antiviral therapy...
  55. doi request reprint New pathogenic viruses and novel antiviral drugs
    Ben Berkhout
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center of the University of Amsterdam, K3 110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
    Expert Rev Anti Infect Ther 9:161-3. 2011
    ..Approximately 220 participants representing 36 countries attended the congress, which covered topics such as emerging viruses, virus-host interactions, new antiviral drugs and antiviral resistance...
  56. pmc Directed HIV-1 evolution of protease inhibitor resistance by second-generation short hairpin RNAs
    Nick C T Schopman
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
    Antimicrob Agents Chemother 56:479-86. 2012
    ..These results are of importance for a deeper understanding of HIV-1 evolution under combined drug and RNAi pressure and may be used to design future therapeutic approaches...
  57. ncbi request reprint HIV-1 as RNA evolution machine
    Ben Berkhout
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infectivity and Immunity Amsterdam CINIMA, Academic Medical Center AMC, University of Amsterdam, The Netherlands
    RNA Biol 8:225-9. 2011
    ....
  58. doi request reprint Molecular strategies to design an escape-proof antiviral therapy
    Ben Berkhout
    Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, The Netherlands
    Antiviral Res 92:7-14. 2011
    ..Several options for a combinatorial RNAi attack to prevent viral escape will be discussed. The simultaneous use of multiple RNAi inhibitors turns out to be the most effective and durable strategy...
  59. ncbi request reprint Towards a durable RNAi gene therapy for HIV-AIDS
    Ben Berkhout
    Academic Medical Center of the University of Amsterdam, Center for Infection and Immunity Amsterdam CINIMA, Department of Medical Microbiology, Laboratory of Experimental Virology, Amsterdam, The Netherlands
    Expert Opin Biol Ther 9:161-70. 2009
    ..RNA interference (RNAi) can be employed as a potent antiviral mechanism...
  60. ncbi request reprint Infectious diseases of the nervous system: pathogenesis and worldwide impact
    Ben Berkhout
    University of Amsterdam, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, K3 110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
    IDrugs 11:791-5. 2008
    ..This meeting fostered worldwide interactions between scientists and stimulated the exchange of the latest research results on these neglected neurotropic pathogens...
  61. pmc 6th international symposium on retroviral nucleocapsid
    Ben Berkhout
    LaboRetro INSERM 758, Ecole Normale Superieure de Lyon, IFR 128 Biosciences Lyon Gerland, 69364 Lyon Cedex 07, France
    Retrovirology 5:21. 2008
    ..All aspects of NC biology, from structure to function and to anti-HIV vaccination, were covered during this meeting...
  62. ncbi request reprint Third European Congress of Virology. 1-5 September 2007, Nuremberg, Germany
    Ben Berkhout
    University of Amsterdam, Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, K3 110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
    IDrugs 10:772-4. 2007
  63. pmc Forced evolution of a regulatory RNA helix in the HIV-1 genome
    B Berkhout
    Academic Medical Center, University of Amsterdam, Department of Human Retrovirology, PO Box 22700, 1100 DE Amsterdam, The Netherlands
    Nucleic Acids Res 25:940-7. 1997
    ..These experiments also highlight some general principles of RNA structure building...
  64. ncbi request reprint Codon and amino acid usage in retroviral genomes is consistent with virus-specific nucleotide pressure
    Ben Berkhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
    AIDS Res Hum Retroviruses 18:133-41. 2002
    ..For instance, the typical trends in nucleotide usage could influence the molecular phylogenetic reconstruction of the family Retroviridae...
  65. ncbi request reprint Characterization of the anti-HIV effects of native lactoferrin and other milk proteins and protein-derived peptides
    Ben Berkhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
    Antiviral Res 55:341-55. 2002
    ..These results demonstrate that bLF targets the HIV-1 entry process...
  66. pmc The leader of the HIV-1 RNA genome forms a compactly folded tertiary structure
    B Berkhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands
    RNA 6:282-95. 2000
    ..The putative biological function of this conformational polymorphism as molecular RNA switch in the HIV-1 replication cycle is discussed...
  67. pmc Aggressive HIV-1?
    Ben Berkhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Retrovirology 2:13. 2005
    ..Is the panic justified?..
  68. ncbi request reprint The antiviral activity of the milk protein lactoferrin against the human immunodeficiency virus type 1
    Ben Berkhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Biometals 17:291-4. 2004
    ..In this manuscript, we review the antiviral properties of the milk protein lactoferrin (LF). In particular, we will describe its antiviral activity against the human immunodeficiency virus type 1 (HIV-1)...
  69. ncbi request reprint HIV-1 evolution under pressure of protease inhibitors: climbing the stairs of viral fitness
    B Berkhout
    Department of Human Retrovirology, Academic Medical Center, Amsterdam, The Netherlands
    J Biomed Sci 6:298-305. 1999
    ..The possibility to restrict HIV-1 fitness is discussed in relation to the control of HIV-1 pathogenesis...
  70. ncbi request reprint In vitro evidence that the untranslated leader of the HIV-1 genome is an RNA checkpoint that regulates multiple functions through conformational changes
    Ben Berkhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    J Biol Chem 277:19967-75. 2002
    ..This in vitro result should be verified in subsequent in vivo studies with HIV-infected cells...
  71. pmc Identification of an active reverse transcriptase enzyme encoded by a human endogenous HERV-K retrovirus
    B Berkhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
    J Virol 73:2365-75. 1999
    ..The endogenous RT activity may also have been involved in the shaping of the human genome, e.g., by formation of pseudogenes...
  72. ncbi request reprint Conditional virus replication as an approach to a safe live attenuated human immunodeficiency virus vaccine
    Ben Berkhout
    Department of Human Retrovirology, University of Amsterdam, Academic Medical Center, Amsterdam, The Netherlands
    J Neurovirol 8:134-7. 2002
    ..The optimised Tet system may be of particular use in other applications such as inducible expression of gene therapy vectors in the brain...
  73. ncbi request reprint RNA interference as an antiviral approach: targeting HIV-1
    Ben Berkhout
    University of Amsterdam, Department of Human Retrovirology, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Curr Opin Mol Ther 6:141-5. 2004
    ..This review describes the antiviral RNAi field, which is barely two years-old, with an emphasis on recent studies aimed at suppression of HIV-1...
  74. ncbi request reprint RNAi Europe 2005
    Ben Berkhout
    University of Amsterdam, Academisch Medisch Centrum, Department of Human Retrovirology, Academic Medical Center K3 106c, The Netherlands
    IDrugs 8:978-81. 2005
  75. pmc Genetic instability of live, attenuated human immunodeficiency virus type 1 vaccine strains
    B Berkhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
    J Virol 73:1138-45. 1999
    ..This insight may guide future efforts to develop more stable anti-HIV vaccines...
  76. ncbi request reprint Control over HIV-1 replication by an antibiotic; a novel vaccination strategy with a drug-dependent virus
    Ben Berkhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands
    Virus Res 82:103-8. 2002
  77. ncbi request reprint Structural and functional analysis of negatively charged milk proteins with anti-HIV activity
    B Berkhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands
    AIDS Res Hum Retroviruses 13:1101-7. 1997
    ....
  78. pmc The primer binding site on the RNA genome of human and simian immunodeficiency viruses is flanked by an upstream hairpin structure
    B Berkhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, PO Box 22700, 1100 DE Amsterdam, The Netherlands
    Nucleic Acids Res 25:4013-7. 1997
    ....
  79. pmc Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription
    B Berkhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands
    RNA 7:1097-114. 2001
    ..Base pairing can occur between the complementary loops ("loop-loop kissing"), and strand transfer is completed by the subsequent formation of an extended RNA-cDNA duplex...
  80. doi request reprint Increased virus replication in mammalian cells by blocking intracellular innate defense responses
    W de Vries
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam, Meibergdreef, Amsterdam, The Netherlands
    Gene Ther 15:545-52. 2008
    ..These results can be employed for improving the production of viral gene transfer vectors and viral vaccine strains...
  81. ncbi request reprint Optimization of the Tet-On system for regulated gene expression through viral evolution
    X Zhou
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Gene Ther 13:1382-90. 2006
    ..Importantly, these rtTA variants show no activity in the absence of dox. The optimized rtTA variants are particularly useful for in vivo applications that require a more sensitive or more active Tet-On system...
  82. ncbi request reprint Silencing of HIV-1 with RNA interference: a multiple shRNA approach
    Olivier Ter Brake
    Department of Human Retrovirology, University of Amsterdam, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands
    Mol Ther 14:883-92. 2006
    ..These results confirm that RNAi has great potential as an antiviral gene therapy approach and support our efforts to develop this strategy for treatment of HIV-1-infected individuals...
  83. ncbi request reprint Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA
    P Konstantinova
    Department of Human Retrovirology, Academic Medical Center K3 110, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Gene Ther 13:1403-13. 2006
    ..Our results show that DNA constructs encoding virus-specific lhRNAs are capable of inhibiting HIV-1 production in a sequence-specific manner, without inducing the class I interferon genes...
  84. doi request reprint Autoregulatory lentiviral vectors allow multiple cycles of doxycycline-inducible gene expression in human hematopoietic cells in vivo
    M Centlivre
    Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center of the University of Amsterdam AMC UvA, Amsterdam, The Netherlands
    Gene Ther 17:14-25. 2010
    ..These findings are of major interest for gene therapy and basic research settings that require inducible gene expression...
  85. pmc In vitro evolution of a highly replicating, doxycycline-dependent HIV for applications in vaccine studies
    G Marzio
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
    Proc Natl Acad Sci U S A 98:6342-7. 2001
    ..These results suggest that this in vitro evolved, doxycycline-dependent HIV might represent a useful tool toward the development of a safer, live-attenuated HIV vaccine...
  86. ncbi request reprint The native structure of the human immunodeficiency virus type 1 RNA genome is required for the first strand transfer of reverse transcription
    B Berkhout
    Academic Medical Center, University of Amsterdam, Meibergdreef 15, Amsterdam, The Netherlands
    Virology 249:211-8. 1998
    ..The results suggest that the conformation of the dimeric RNA genome facilitates the first strand-transfer reaction of the reverse transcription mechanism...
  87. ncbi request reprint A conditionally replicating HIV-based vector that stably expresses an antiviral shRNA against HIV-1 replication
    Ellen M Westerhout
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Mol Ther 14:268-75. 2006
    ..Because the shRNA targets viral sequences that are removed from the vector construct, there is no self-targeting, yet there is specific shutdown of HIV-1 replication...
  88. pmc Two alternating structures of the HIV-1 leader RNA
    H Huthoff
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands
    RNA 7:143-57. 2001
    ..This structural rearrangement is facilitated by the viral nucleocapsid protein NC. We propose that this structural polymorphism of the HIV-1 leader RNA acts as a molecular switch in the viral replication cycle...
  89. pmc Mutations in the TAR hairpin affect the equilibrium between alternative conformations of the HIV-1 leader RNA
    H Huthoff
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Nucleic Acids Res 29:2594-600. 2001
    ..We also demonstrate that the change in conformation of the leader RNA due to TAR truncations severely affects formation of the HIV-1 RNA dimer...
  90. pmc Strict control of human immunodeficiency virus type 1 replication by a genetic switch: Tet for Tat
    K Verhoef
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
    J Virol 75:979-87. 2001
    ..g., selection and optimization experiments, with the E. coli-derived Tet reagents in a eukaryotic background. Furthermore, such viruses may represent improved vaccine candidates because their replication can be turned on and off at will...
  91. pmc Forced selection of a human immunodeficiency virus type 1 variant that uses a non-self tRNA primer for reverse transcription: involvement of viral RNA sequences and the reverse transcriptase enzyme
    Truus E M Abbink
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    J Virol 78:10706-14. 2004
    ..We demonstrate that both the PAS and RT mutations improve the replication capacity of the tRNA(1,2)(Lys)-using virus...
  92. ncbi request reprint Evolutionary relationships within a subgroup of HERV-K-related human endogenous retroviruses
    J Zsiros
    Department of Pediatric Oncology, Academic Medical Center, University of Amsterdam, The Netherlands
    J Gen Virol 79:61-70. 1998
    ..The evolution of this class of endogenous retroelements is discussed...
  93. pmc Evolution of the human immunodeficiency virus type 1 long terminal repeat promoter by conversion of an NF-kappaB enhancer element into a GABP binding site
    K Verhoef
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
    J Virol 73:1331-40. 1999
    ..This typical LTR promoter configuration may provide these viruses with unique biological properties...
  94. ncbi request reprint Evolution of AZT resistance in HIV-1: the 41-70 intermediate that is not observed in vivo has a replication defect
    R E Jeeninga
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands
    Virology 283:294-305. 2001
    ..Because we could select for these changes without drug pressure, these changes are likely to improve the RT enzyme function and the HIV-1 replication capacity...
  95. pmc Switching the in vitro tRNA usage of HIV-1 by simultaneous adaptation of the PBS and PAS
    Nancy Beerens
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands
    RNA 8:357-69. 2002
    ..These results indicate that the PAS-antiPAS interaction is important for both primer selection and efficient reverse transcription...
  96. ncbi request reprint A conditionally replicating virus as a novel approach toward an HIV vaccine
    Atze T Das
    Department of Human Retrovirology, Academic Medical Center, Amsterdam, The Netherlands
    Methods Enzymol 388:359-79. 2004