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Oct 29 2021

Biophysics Seminar- Chaitra Agrahar & Ganesh Pandey

Biophysics Seminar

October 29, 2021

2:00 PM - 3:00 PM


2214 SES- Alternate Zoom link:


845 W. Taylor St., Chicago, IL 60612

Molecular Implementations of Positive and Negative Feedback Inform Robustness in Biological Oscillator Motifs.
Chaitra Agrahar (Rust Lab, UChicago)
Abstract: Biological Oscillators like the cell-cycle, the circadian cycle, etc. are vital to an organism's survival. Biological oscillator circuits are typically classified based on the net logic of regulatory connections between interacting molecules. However, in a genetic network, a positive logic of regulation can be implemented either by enhancing the production of a component, or by inhibiting its degradation. We show that these logically equivalent alternatives have vastly different dynamical outcomes, in that the probability of obtaining stable limit cycles varies substantially based on the regulatory implementations of the circuit topology. Nullcline analyses, and linear stability arguments predict the dynamical outcomes of differential regulatory implementations of a topology. Robust regulatory implementations not only enhance the probability of obtaining stable limit cycles over larger ranges of parameter variations, but also exhibit an increased resilience of oscillations to stochasticity. We further show that there are preferred regulatory implementations for particular biological functions, and that the
most robust regulatory implementations of a topology are realized in naturally occuring oscillator systems where high phase-coherence is desired.


Studying chromatin scaffolds of transcription condensates with single molecule localization microscopy.

Ganesh Pandey (Spille Lab, UIC Physics)
Abstract: Regulatory chromatin regions (enhancer and promoter) control transcription of a gene. They recruit dozens of factors, including the coactivator Mediator complex and RNA Polymerase II. Mediator and Pol II form condensates by phase separation. Enhancers are characterized by acetylation of histone protein H3, forming H3K27ac. H3K27ac is required for the maintenance of transcription condensates, highlighting the importance of the chromatin scaffold in understanding transcription condensates. ChIPseq data obtained from populations of cells suggests that transcription condensates form at super-enhancers with particularly strong H3K27ac marks. I will discuss how multicolor single molecule localization microscopy data challenges this model and sheds new light on the connection between clusters of H3K27ac and transcription condensates.


Physics Office

Date posted

Oct 25, 2021

Date updated

Oct 25, 2021