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Identifying novel herpesvirus-host interactions using genome-wide RNAi screens in human cells

Thursday 17 January 2013

Project
Upon infecting a host, viruses are confronted by a multi-faceted immune response. Evolutionary combat between viruses and their hosts has shaped the host’s development of a formidable innate and adaptive immune defense arsenal. In turn, viruses have acquired effective means to evade the immune system. Elucidation of the mode of action of the immune evasion proteins encoded by viruses has not only provided new insights into viral pathogenesis, but has also led to the discovery of hitherto unknown cell biological and immunological phenomena. Moreover, understanding the molecular basis of viral immune evasion strategies is vital for the development of effective new vaccines and anti-viral therapies.

We are studying the fascinating interplay between virus and host, thereby focusing on strategies that herpesviruses have evolved to evade the host’s immune response. To do this, we have recently developed a state-of-the-art RNAinterference (RNAi) library screenings system (see reference for proof of concept) that enables us to perform loss-of-function screens in human cells. Using a genome-wide shRNA library we are currently performing screens to identify cellular and viral gene products that are involved in essential viral processes, such as cell binding and entry, replication and release of viral progeny. A recently performed screen identified many human genes that are potentially involved in such processes and we are currently following up on these discoveries. We are looking for an enthusiastic undergrad student to help in these endeavors. If we’ve raised your interest, please drop us a line and we’ll be happy to explain the project(s) in more detail.

Techniques
DNA techniques (DNA isolations, cloning, rescrition analysis,, miniprep, PCR, sequencing, etc); RNA techniques (RNA isolations, cDNA synthesis, qPCR, etc); Protein work (protein gels, Western blots, immunoprecipitation, etc); Tissue culture (standard cell maintenance, transfections, cell cloning, lentiviral transductions, etc); FACS; RNAi screens; Deep-sequencing (Illumina massive parallel sequencing)

Duration
6 and 9 months

Contact
Dr Ir. Robert Jan Lebbink, r.j.lebbink-2@umcutrecht.nl
Prof. dr Emmanuel Wiertz: E.Wiertz@umcutrecht.nl

References
Bassik* MC, Lebbink* RJ, Churchman LS, Ingolia NT, Patena W, LeProust EM, Schuldiner M, Weissman JS, McManus MT. (2009). Rapid creation and quantitative monitoring of high coverage shRNA libraries. Nat Methods 6: 443-5

Bassik MC, Kampmann M, Lebbink RJ, Wang S, Hein MY, Poser I, Weibezahn J, Horlbeck MA, Chen S, Mann M, Hyman AA, Leproust EM, McManus MT, Weissman JS. A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility.
Cell. 2013 Feb 14;152(4):909-22.

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