Our lab is interested in the systems biology and evolution of epigenetic switches (bistability) and clocks (oscillators) in gene regulatory networks. We use experiment and theory, biology and physics, systems and synthetic biology to study the cell cycle, metabolic rhythms, and circadian clocks. How do oscillators with different frequencies co-exist in the same cell? Are there mechanisms and regulatory principles that ensure functional harmony between oscillators?
Selcan Aydin measured GAL1 gene expression at low galactose levels in single yeasts using timelapse luminescence microscope. Her data shows that the graded increase in GAL1 induction at the population level reflects a heterogeneous induction lag at the single cell level (click here to see movie). This work illustrates the power of single cell analysis using timelapse luminescence microscopy; see Mazo-Vargas et al, MBoC 2014. This was a quick collaboration with the Pascual-Ahuir and Proft labs.
Rienzo A, Poveda-Huertes D, Aydin S, Buchler NE, Pascual-Ahuir A, Proft M. Different mechanisms confer gradual control and memory at nutrient- and stress-regulated genes in yeast. Mol. Cell. Biol. 2015; 35: 3669-83.
Our lab was out in full force at the Ninth q-bio Conference in Blacksburg, Virginia.
- Heungwon Park, “A synthetic oscillator couples to the cell division cycle in budding yeast” [talk]
- Sargis Karapetyan “Redox rhythms reinforce the plant circadian clock” [poster]
- Tony Burnetti “The yeast metabolic cycle is coupled to cell division cycle Start across diverse strains” [poster].
This paper combined experiment and theory to demonstrate that newly discovered circadian redox rhythms regulate the plant circadian clock through NPR1, a master immune regulator. Sargis Karapetyan developed a mathematical model of the plant circadian clock to uncover new regulatory links (red arrows). We learned that NPR1 activates the expression of key circadian clock genes (TOC1, PRR7, LHY) in a “balanced” fashion, such that the amplitude is boosted with no change in period or phase during acute redox perturbation. This was a fun and productive collaboration with the Dong lab. Read more about it here on the Duke Today website.
Zhou M, Wang W, Karapetyan S, Mwimba M, Marques J, Buchler NE, Dong X. Redox rhythm reinforces circadian clock to gate immune response. Nature 523: 472 (2015)