Theoretical Biology & Bioinformatics

Personalia

Name HWM (Hanneke) van Deutekom Position PhD student Research topics Immunological Bioinformatics Promotors Prof. dr. R.J. de Boer & dr. C. Kesmir (supervisor) Address Padualaan 8 3584 CH Utrecht the Netherlands Location Room Z529 Phone +31 30 2533812 Fax +31 30 2513655 Email H.W.M.vanDeutekom(at)uu(dot)nl

Research Project

Immunological Bioinformatics:
Detailed genetic analysis has demonstrated that the MHC class I repertoire in chimpanzees is severely reduced compared to humans which suggest that chimpanzees have gone through a selective sweep.
Studies on chimpanzees in captivity suggested that SIVcpz (a close relative to HIV-1) infected chimpanzees are quite resistant to develop AIDS.
Therefore it was proposed that an SIV-like virus could have been the selective agent during this selective sweep. However a recent paper presenting data on a wild chimpanzee population described higher death rates for SIVcpz infected animals compared to healthy ones.
We investigate whether or not SIVcpz is the most likely agent to have caused this selective sweep in chimpanzee population by performing a comparative study on predicted presentation of common primate viruses on frequent chimpanzee MHC molecules.

Theoretical Immunology:
The CTL immune response to acute HIV infection rapidly selects for viral mutants that have escaped CTL recognition. Some immune escapes were found to appear as early as 30-54 days after the peak of infection and rapidly replaced each other. Previously, we published a model with realistic virus dynamics, where CTL clones are stimulated by viral epitopes and interact with the virus population through cytotoxic killing of infected cells. However, we failed to obtain early escape mutants. Therefore we extended this model by enabling killing of cells in eclipse phase and changing the way CTL clones kill the infected cells, i.e. we removed the direct inhibitory effect amongst CTL clones in the killing rate. Furthermore, we investigated how the escape rates depend on the number of epitopes recognized by CTL clones.

Education and Employments

Publications

2011

van Deutekom HW, Hoof I, Bontrop RE, Keşmir C. A comparative analysis of viral peptides presented by contemporary human and chimpanzee MHC class I molecules. J Immunol. Dec 1;187(11):5995-6001. pubmed

Schellens IM, Navis M, van Deutekom HW, Boeser-Nunnink B, Berkhout B, Kootstra N, Miedema F, Keşmir C, Schuitemaker H, van Baarle D, Borghans JA. (2011) Loss of HIV-1 derived CTL epitopes restricted by protective HLA-B alleles during the HIV-1 epidemic. AIDS Sep 10;25(14):1691-700. pubmed

2010

Benschop JJ, Brabers N, van Leenen D, Bakker LV, van Deutekom HW, van Berkum NL, Apweiler E, Lijnzaad P, Holstege FC, Kemmeren P. (2010) A consensus of protein complex compositions for Saccharomyces cerevisiae. Mol Cell. Jun 25;38(6):916-28. pubmed

Buschow SI, Lasonder E, van Deutekom HW, Oud MM, Beltrame L, Huynen MA, de Vries IJ, Figdor CG, Cavalieri D. (2010) Dominant processes during human dendritic cell maturation revealed by integration of proteome and transcriptome at the pathway level. J Proteome Res. Apr 5;9(4):1727-37.pubmed

2008

Buitenhuis M, Verhagen LP, van Deutekom HW, Castor A, Verploegen S, Koenderman L, Jacobsen SE, Coffer PJ. (2008) Protein kinase B (C-AKT) regulates hematopoietic lineage choice decisions during myelopoiesis. Blood. Jan 1;111(1):112-21 pubmed

2005

Verploegen S, Ulfman L, van Deutekom HW, van Aalst C, Honing H, Lammers JW, Koenderman L, Coffer PJ. (2005) Characterization of the role of CaMKI-like kinase (CKLiK) in human granulocyte function. Blood. Aug 1;106(3):1076-83. pubmed

Buitenhuis M, van Deutekom HW, Verhagen LP, Castor A, Jacobsen SE, Lammers JW, Koenderman L, Coffer PJ. (2005) Differential regulation of granulopoiesis by the basic helix-loop-helix transcriptional inhibitors Id1 and Id2. Blood. Jun 1;105(11):4272-81. pubmed

2002

Verploegen S, van Leeuwen CM, van Deutekom HW, Lammers JW, Koenderman L, Coffer PJ. (2002) Role of Ca2+/calmodulin regulated signaling pathways in chemoattractant induced neutrophil effector functions. Comparison with the role of phosphotidylinositol-3 kinase. Eur J Biochem. Sep;269(18):4625-34. pubmed

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