I presented our recent theoretical work on optimisation of biomass yield and growth rate by bacteria, which metabolic subnetworks give rise to optimality and how optimality depends on the kinetics of the associated metabolic enzymes.
See this link. In this paper, we describe a stochastic model that describes the stochastic diffusion, sliding, and biochemical activities of histone-modifying enzymes along the body of a gene. We find a wide pattern of dynamic behaviours, including spontaneous bistable switching between active and inactive gene states, and coherence of nucleosome modification along the body of a gene. This work suggests that the stochastic activity of single genes in single eukaryotic cells may not only stem from transcription factor and transcription initiation fluctuations but equally well from fluctuations in the nucleosome modification state along the gene.
Stefan Mueller visited us last week to introduce us to the main results of chemical reaction network theory (Feinberg’s formalism), discuss how this theory can be applied to metabolic pathways, and to discuss some of the optimisation problems relevant for metabolic networks.
at the TU Delft (Delft, Netherlands). I had a marvellous time while speaking to several of the researchers there! Definitely an institute to keep informed about!
This paper discusses a supply and demand perspective on understanding the regulatory structure of glycolysis.
Our university appoints every year a few URC positions. In this way, associate professors are awarded for their quality of research. Such a position lasts for five years. After this period, the associated faculty offers the awardee a full professorship; provided the awardee meets certain criteria. See this link for more information.
Obviously, I am really happy with this appointment! I would like to thank all the group members and collaborators for the great scientific collaborations!
See the great movie on YouTube: http://youtu.be/6w-NTWU6CwY?list=UUesNt4_Z-Pm41RzpAClfVcg
I upload this here because of the current epidemic of ebola in Africa, which is a growing concern.
This movie given some more information about the working of the virus.
You can find it here. We describe a biophysical model of a G-protein coupled receptor (GPCR) that changes conformation of its global structure and of its intracellular binding domains in response to extracellular signals and their combinations. This model reproduces several experimentally found phenomena, such as modulation of affinity, magnitude and sensitivity; all associated with the surprisingly pervasive ligand-bias of GPCRs.
See the link.
At the Lorentz Centre in Leiden, Susanne and I participated in a GPCR meeting this week. It covered a broad range of topics from structural aspects to spatiotemporal signaling and in vivo studies. We presented our work on GPCR modeling – recently published – and FRET-sensors – current work; collaboration with Kobus van Unen, Joachim Goedhart and Dorus Gadella.