noise

Noise in synthetic genetic oscillators

This paper focuses on characterizing the stochastic dynamics of previously described synthetic genetic oscillators. It is a very nice combination of experimental and computational work. The computational aspect includes both image analysis and parameter estimation. They breakdown the noise into different components including intrinsic noise, cell cycle noise, and parameter variability by looking at the expression […]

Entrainment of a genetic oscillator

This paper from Bill Mather group in the Physics Department at Virginia Tech shows how a genetic oscillator responds to noisy signals. The authors show that the oscillator gets entrained despite the noise affecting the input signal. This is a nice use of an existing oscillator developed in Jeff Hasty’s group. After demonstrating this property […]

Leave it to chance or not

leave it to chance cover

Carolyn Beans wrote a blog post about our project to develop stochastic models of the regulatory network controlling cell division.  She was particularly interested in aspects of cell physiology that are affected by random events and how cells manage to remain healthy despite the vagaries of molecular interactions. Read her post on the NIGMS Biobeat […]

Cell Cycle Model

cell cycle regulator mRNA

Cell cycle model: a noisy yet robust network A cell cycle model can help better understand the property of this complex regulatory network. The cell cycle is the process by which a growing cell replicates its genome and partitions the two copies of each chromosome to two daughter cells at division. It is of utmost […]

Measurement and modeling of transcriptional noise in the cell cycle regulatory network

Fifty years of genetic and molecular experiments have revealed a wealth of molecular interactions involved in the control of cell division. In light of the complexity of this control system, mathematical modeling has proved useful in analyzing biochemical hypotheses that can be tested experimentally. Stochastic modeling has been especially useful in understanding the intrinsic variability […]

Measurements modeling transcription noise makes the cover of Cell Cycle

The October issue of Cell Cycle includes an article reporting our efforts to measure and model the transcriptional noise affecting the the regulatory network controlling the cell cycle in the baker yeast (Saccharomyces cerevisiae). The journal cover page features an image derived from this work.   Cell Cycle. 2013 Sep 4;12(19). [Epub ahead of print] Measurement […]

Controlling Gene Expression Noise by Preventing Interchromosomal Interactions

In this paper, the authors examine intrinsic and extrinsic noise in the yeast pheromone response MAP kinase pathway. The transcription factor Ste12 is regulated by this kinase pathway, and there are two partially redundant repressors, Dig1 and Dig2, that interact with Ste12 and inhibit transcriptional activation at Ste12-dependent promoters. The authors confirmed that single gene […]

Control of Stochasticity in Eukaryotic Gene Expression

This paper uses the dual reporter approach to measuring gene expression developed by Elowitz (see this journal club entry). The authors look at different promoters. In all cases, the intrinsic noise was a small fraction of the total noise. The largest noise component was non-gene specific extrinsic noise. The authors show that different mechanisms of […]