PhD Candidate, Molecular and Cellular Biophysics
Department of Physics & Astronomy
University of Denver
2112 E Wesley Ave
Denver, CO 80208-0183
Competition and Noise in Biochemical Networks
Chemical reactions are often portrayed in terms of averages, which for in vitro experiments is perfectly fine. For instance, consider a simple complexation reaction (A + B --> AB), a fairly ubiquitous construct within biochemical networks. When dealing with a number of molecules on the same order of magnitude as Avogadro's number, any fluctuation around the average number of complexes is typically dwarfed in scale compared to the average value. However, for in vivo scenarios, where copy numbers of proteins can easily be in the range of one hundred or less, this fluctuation is no longer negligible and the entire probability distribution must be considered. Now, what happens when competition is introduced into this scenario, e.g. different types of molecules competing for limited resources of some shared complexation partner (A + C --> AC)? This competition actually facilitates further fluctuation even when accounting for the reduced amount of available resources due to the presence of the additional reactions. In fact, as long as the shared reactant remains limited, fluctuations can remain significant even when the competing molecules are infinite in number, a result in stark contrast to the single reaction scenario with no competition. We hope to apply these same principles to more complicated complexation networks in the future.
Modeling of Convergent Extension in Drosophila Melanogaster
During morphogenesis, many organisms tend to elongate along one axis and contract along another to produce their general shape as they progress through development. Until recent years, researchers could only observe as outsiders, but with advancements in microscopy and genetic sequencing, we can now actively probe the inner workings of the biological systems governing these basic morphological processes. An example of such a process can be found within the gut of fruit flies (Drosophila melanogaster) where cells reorganize and intercalate amongst themselves without any cell division in order to produce the elongation necessary for proper embryogenesis. This process is referred to as germ-band extension and is thought to be governed by tensile forces due to a higher concentration of a force-generating protein called myosin on contracting interfaces. Our research attempts to create a computational model of the tissue deformation caused by such a process to determine if these contractile forces along with basic cellular assumptions are sufficient to reproduce experimental observations or if an additional mechanism is necessary to produce the behaviors seen in experiment.