B Berkhout

Summary

Affiliation: Academic Medical Center
Country: The Netherlands

Publications

  1. Gao Z, Herrera Carrillo E, Berkhout B. RNA Polymerase II Activity of Type 3 Pol III Promoters. Mol Ther Nucleic Acids. 2018;12:135-145 pubmed publisher
    ..These mechanistic insights are important for optimal use of Pol III promoters, and they offer additional flexibility for biotechnology applications of these genetic elements. ..
  2. van Bel N, Das A, Cornelissen M, Abbink T, Berkhout B. A short sequence motif in the 5' leader of the HIV-1 genome modulates extended RNA dimer formation and virus replication. J Biol Chem. 2014;289:35061-74 pubmed publisher
  3. van der Velden Y, Villaudy J, Siteur van Rijnstra E, van der Linden C, Franklin E, Weijer K, et al. Protective efficacy of broadly neutralizing antibody PGDM1400 against HIV-1 challenge in humanized mice. AIDS Res Hum Retroviruses. 2018;: pubmed publisher
    ..The results demonstrate that PGDM1400 might be a promising component of strategies to prevent HIV-1 infection, and provide support for the pursuit of vaccines that induce PGDM1400-like bNAbs. ..
  4. Berkhout B. RNAi-mediated antiviral immunity in mammals. Curr Opin Virol. 2018;32:9-14 pubmed publisher
    ..Thus, the presence of multiple antiviral response mechanisms seems standard outside the plant world and we will specifically discuss the interactions between these antiviral programs. ..
  5. Darcis G, Das A, Berkhout B. Tackling HIV Persistence: Pharmacological versus CRISPR-Based Shock Strategies. Viruses. 2018;10: pubmed publisher
    ..We will review the benefits and drawbacks of these different cure strategies. ..
  6. Berkhout B, Bukrinsky M. Jan van der Noordaa (1934-2015); A Virologist Pur Sang. Viruses. 2015;7:5016-7 pubmed publisher
    ..Our loyal friend and colleague, Jan van der Noordaa, passed away unexpectedly at the age of 80 on the evening of 17 June 2015. [...]. ..
  7. Berkhout B, Van Hemert F. On the biased nucleotide composition of the human coronavirus RNA genome. Virus Res. 2015;202:41-7 pubmed publisher
    ..The relevance for evolution of the novel human pathogens MERS and SARS is discussed. ..
  8. Das A, Berkhout B. Conditionally replicating HIV and SIV variants. Virus Res. 2016;216:66-75 pubmed publisher
    ..These viruses can be used as a tool in HIV and SIV biology studies and in vaccine research. We review how HIV-rtTA and SIV-rtTA were used to study the role of the viral TAR and Tat elements in virus replication. ..
  9. Berkhout B, Das A. On the primer binding site mutation that appears and disappears during HIV and SIV replication. Retrovirology. 2015;12:75 pubmed publisher
    ..The presence of a variant tRNA species explains the rapid appearance and disappearance of a variant PBS sequence. ..

More Information

Publications30

  1. Gao Z, Herrera Carrillo E, Berkhout B. Delineation of the Exact Transcription Termination Signal for Type 3 Polymerase III. Mol Ther Nucleic Acids. 2018;10:36-44 pubmed publisher
    ..We next improved these crRNAs by insertion of the HDV ribozyme to avoid U-tails. This study provides detailed design guidelines for small RNA expression cassettes based on Pol III. ..
  2. van Hemert F, Zaaijer H, Berkhout B. In silico prediction of ebolavirus RNA polymerase inhibition by specific combinations of approved nucleotide analogues. J Clin Virol. 2015;73:89-94 pubmed publisher
    ..Any nucleotide analogue on its own did not reduce ligand-protein interaction energies. This prediction encourages specific drug testing efforts and guides future strategies to inhibit ebolavirus replication. ..
  3. Berkhout B, van der Velden Y. ABX464: a good drug candidate instead of a magic bullet. Retrovirology. 2015;12:64 pubmed publisher
    ..Although ABX464 may remain an important new addition to the anti-HIV arsenal, we do present a sobering alternative explanation for the long-lasting reduction in viral load after treatment cessation. ..
  4. Herrera Carrillo E, Berkhout B. Bone Marrow Gene Therapy for HIV/AIDS. Viruses. 2015;7:3910-36 pubmed publisher
    ..Finally, a potent combination of anti-HIV genes based on our own research program is described. ..
  5. Mueller N, van Bel N, Berkhout B, Das A. HIV-1 splicing at the major splice donor site is restricted by RNA structure. Virology. 2014;468-470:609-20 pubmed publisher
    ..The 5'ss region of different HIV-1 isolates and the related SIVmac239 can fold a similar structure. This evolutionary conservation supports the importance of this structure in viral replication. ..
  6. van Bel N, Ghabri A, Das A, Berkhout B. The HIV-1 leader RNA is exquisitely sensitive to structural changes. Virology. 2015;483:236-52 pubmed publisher
  7. Berkhout B, Sanders R. Gene therapy as a vaccine for HIV-1. Expert Opin Biol Ther. 2012;12:1315-21 pubmed publisher
    ..VIP is a prolonged form of passive immunization by means of a gene therapy. We will discuss the ins and outs of VIP and the therapeutic possibilities and challenges. ..
  8. Harwig A, Das A, Berkhout B. Retroviral microRNAs. Curr Opin Virol. 2014;7:47-54 pubmed publisher
    ..An intricate scenario of multi-layer virus-host interactions becomes apparent with small RNAs as the regulatory molecules. ..
  9. request reprint
    Berkhout B. HIV-1 as RNA evolution machine. RNA Biol. 2011;8:225-9 pubmed
  10. Van Hemert F, Berkhout B. Nucleotide composition of the Zika virus RNA genome and its codon usage. Virol J. 2016;13:95 pubmed publisher
    ..We discuss the evolutionary scenarios and molecular mechanisms that may be responsible for these distinctive ZIKV RNA genome features. ..
  11. Berkhout B, van Wamel J. The leader of the HIV-1 RNA genome forms a compactly folded tertiary structure. RNA. 2000;6:282-95 pubmed
    ..The putative biological function of this conformational polymorphism as molecular RNA switch in the HIV-1 replication cycle is discussed. ..
  12. request reprint
    Berkhout B, van Wamel J, Beljaars L, Meijer D, Visser S, Floris R. Characterization of the anti-HIV effects of native lactoferrin and other milk proteins and protein-derived peptides. Antiviral Res. 2002;55:341-55 pubmed
    ..These results demonstrate that bLF targets the HIV-1 entry process. ..
  13. request reprint
    Berkhout B, Floris R, Recio I, Visser S. The antiviral activity of the milk protein lactoferrin against the human immunodeficiency virus type 1. Biometals. 2004;17:291-4 pubmed
    ..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). ..
  14. Berkhout B, Gorelick R, Summers M, Mely Y, Darlix J. 6th international symposium on retroviral nucleocapsid. Retrovirology. 2008;5:21 pubmed publisher
    ..All aspects of NC biology, from structure to function and to anti-HIV vaccination, were covered during this meeting. ..
  15. Amadori C, van der Velden Y, Bonnard D, Orlov I, van Bel N, Le Rouzic E, et al. The HIV-1 integrase-LEDGF allosteric inhibitor MUT-A: resistance profile, impairment of virus maturation and infectivity but without influence on RNA packaging or virus immunoreactivity. Retrovirology. 2017;14:50 pubmed publisher
    ..These inactivated viruses might form an attractive new approach in vaccine research in an attempt to study if this new type of immunogen could elicit an immune response against HIV-1 in animal models. ..
  16. Harwig A, Landick R, Berkhout B. The Battle of RNA Synthesis: Virus versus Host. Viruses. 2017;9: pubmed publisher
    ..Subsequently, we use the distinct stages (initiation, elongation, termination) to describe the latest insights into nascent RNA-mediated regulation in the context of each relevant stage. ..
  17. Klaver B, van der Velden Y, Van Hemert F, van der Kuyl A, Berkhout B. HIV-1 tolerates changes in A-count in a small segment of the pol gene. Retrovirology. 2017;14:43 pubmed publisher
    ..This survey also provided clues that silent codon changes, in particular from G-to-A, determine the subtype-specific sequence signatures. ..
  18. Wang G, Zhao N, Berkhout B, Das A. A Combinatorial CRISPR-Cas9 Attack on HIV-1 DNA Extinguishes All Infectious Provirus in Infected T Cell Cultures. Cell Rep. 2016;17:2819-2826 pubmed publisher
    ..These results provide a proof-of-principle that HIV-1-infected cells can be functionally cured by dual-gRNA CRISPR/Cas9 treatment. ..
  19. Mueller N, Das A, Berkhout B. A Phylogenetic Survey on the Structure of the HIV-1 Leader RNA Domain That Encodes the Splice Donor Signal. Viruses. 2016;8: pubmed publisher
    ..We therefore inspected the sequence of natural HIV-1 isolates in search for support, in the form of base pair (bp) co-variations, for the different RNA conformations. ..
  20. Turrini F, Marelli S, Kajaste Rudnitski A, Lusic M, Van Lint C, Das A, et al. HIV-1 transcriptional silencing caused by TRIM22 inhibition of Sp1 binding to the viral promoter. Retrovirology. 2015;12:104 pubmed publisher
    ..TRIM22 acts as a suppressor of basal HIV-1 LTR-driven transcription by preventing Sp1 binding to the HIV-1 promoter. ..
  21. request reprint
    Berkhout B, Derksen G, Back N, Klaver B, de Kruif C, Visser S. Structural and functional analysis of negatively charged milk proteins with anti-HIV activity. AIDS Res Hum Retroviruses. 1997;13:1101-7 pubmed