More and more ‘dry’ scientists are going into the wetlab. Today, Rinke showed students and Bob (on the right) around in our wetlab as part of the Workshop Mathematical Modelling (a third year course for VU and UvA Mathematics students). Will this be a one-time event or do they now never want to leave the wetlab…?
Willi, Brett, Frank and Bas have written a review on constraint-based modelling in the Journal of The Royal Society Interface
The paper can be found here
Jurgen is the senior author on a new book chapter that describes how mathematical modelling can help understand metabolism in parasites and guide drug target identification. The chapter focusses on recent advances for Trypanosoma brucei and Plasmodium Falciparum
The chapter is part of a book on “Comprehensive Analysis of Parasite Biology: From Metabolism to Drug Discovery: From Metabolism to Drug Discovery: From Metabolism to Drug Discovery” edited by Sylke Müller, Rachel Cerdan and Ovidiu Radulescu
Title: Attacking blood-borne parasites with mathematics
Authors: David D. van Niekerk, Gerald Penkler, François du Toit, Jacky L. Snoep, Barbara M. Bakker and Jurgen R. Haanstra
See also: http://onlinelibrary.wiley.com/doi/10.1002/9783527694082.ch22/summary
In July, Eva Mooij and Mariah Kes joint our lab to do a short research programme for their honours programme. They worked together with Marijke and Jurgen on glycogen, ammonium and urea measurements in liver cancer cell cultures. They did a great job and it was good to have them in our lab
(and thanks to Vera for taking the picture)
Jurgen co-authored a paper in BMC genomics that uses mathematical modelling to understand the gene expression cascade in Trypanosoma brucei. You can read it here.
The current analysis is a follow-up of two previous publications from Jurgen that describe the contruction of a model of the gene expression cascade in T. brucei (Haanstra et al., 2008) and the extension of this model to the entire genome (Fadda et al., 2014). Here, using genome-scale quantitative data on various levels of the gene expression cascade, we compared model-simulated mRNA abundances to the actual in vivo mRNA abundances on a per-gene basis.
This analyses revealed that levels of mRNAs in procyclic form trypanosomes (the life-stage inside the tsetse fly) are determined mainly by transcript length and mRNA decay, with some control of precursor processing. In bloodstream forms (when the parasite lives in the mammalian bloodstream) variations in nuclear events play a larger role in transcriptome regulation, suggesting aquisition of new control mechanisms during adaptation to mammalian parasitism.
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