BRENT LAB

Welcome to the Brent Lab

The lab studies the quantitative operation of the systems that living cells use to sense, represent, transmit, and act upon information to make appropriate responses. One system under study is a prototypic cell signaling system in budding yeast, the pheromone response system. When appropriate (which is frequently) experimental work proceeds in concert with efforts to account for observed quantitative behaviors by simulation. Work has recently led to some general insights into the information carried by cell signaling systems and how that is controlled. This work is benefitting from a deeper association with control theory and theorists. A recent outcome of this association is design and construction intracellular devices that can give much more precise control of chemically tuned gene expression, with one explicit goal being to give good gene control in mammalian cells to researchers worldwide.

Lab has extended similar work to systems operating in single cells of tissues in a metazoan, Caenorhabditis elegans. Because the lab studies system operation in single cells, we also study the causes and consequences of cell-to-cell variation in function of these systems, and the still-mysterious persistent cell physiological states that underlie much of this variation. Differences in these physiological states can have significant effects on the function of the organism that continue over the organism's life.

Work requires continual development and refinement of experimental and computational methods. One area is development of rapid means to generate new DNA constructions and make desired changes to the genomes of yeast and higher cells. Another is development of intracellular reporters to quantify particular molecular events in living cells, together with microscopic, flow cytometric, together with computational means to extract key quantities from these outputs. We expect that this technology development will continue to find relevance for more applied problems including cancer therapy and drug screening.

The lab also includes experimental social science component. Some of this work continues under the aegis of the Center for Biological Futures, a pilot project (2011-2014) that brought together biologists with scholars in the social sciences and humanities, including anthropologists and philosophers, to better understand how biological knowledge and capability are shaping human affairs in the 21st century. This work included a significant collaboration with investigators at the University of Washington, in the project Biological Futures in a Globalized World.  Work by researchers brought together by the Center continues.  Brent and other lab members are frequently able to participate in government and other advisorial settings to help shape the overall course of future research, and all lab members are encouraged to consider how the outcomes of their research and the ongoing increases in biological knowledge and capability might shape, and should shape, human affairs.
 

Recent news and publications

12 December 2016
Lab joins 21st century, posts work on bioRxiv

We've posted two major articles by Gustavo Pesce (et al.) on the bioRxiv preprint server.   These describe how Gus screened more than 1000 yeast strains deficient in different nonessential genes for those that affected cell-cell variation in signal transmitted through the pheromone response system, how different data suggest that the origin of the noise they introduce is due to the ends of cytoplasmic microtubules interacting with the site on inside of the cell membrane at which signal is generated, and how that noise degrades the accuracy of a cell fate decision.  We will describe the papers further when formally published.  These papers have now been under editorial review at Molecular Systems Biology for 2 months.  They represent revised versions of a single manuscript we originally submitted to that journal in July 2015.  We are also cross-publishing and doi-ing these Pesce et al. papers via our FHCRC archives.

C. Gustavo Pesce, William Peria, Stefan Zdraljevic, Dan Rockwell, Richard C. Yu, Alejandro Colman-Lerner, Roger Brent (2016).  Cell-to-cell variability in the yeast pheromone response: high throughput screen identifies genes with different effects on transmitted signal and response.  bioRxiv 093187; doi: http://dx.doi.org/10.1101/093187

C. Gustavo Pesce, Stefan Zdraljevic, Alan Bush, Victoria Repetto, William Peria, Richard C. Yu, Alejandro Colman-Lerner, Roger Brent (2016).  Cell-to-cell variability in the yeast pheromone response: Cytoplasmic microtubule function stabilizes signal generation and promotes accurate fate choice. bioRxiv 093195; doi: http://dx.doi.org/10.1101/093195

23 November 2016
Commentary on Andrews et al. by Weiße, Mannan, Oyarzún.

Description/ recapitulation and commentary on Andrews et al. Push-Pull paper in this issue of Cell Systems by Diego Oyarzún and coworkers at Imperial College London.  Authors argue for the importance of thinking about many kinds of systems in terms of input-output relationships. They also make a point that illustrates how critical precise definition will be for systems biology to progress beyond its current state, sometimes characterized by slogans and buzzwords, to generate important new scientific knowledge.  The authors note that because definitions of output differ among studies, different, the phrase "linear input-output relationship" covers a great deal of ground, and that serious attempts to infer general truths about "design principles" from studies of different systems will need to take such differences into account. 

Weiße, A. Y, Mannan, A. A., and Oyarzún, D. A.  (2016) Signaling tug-of-war delivers the whole message. Cell Systems 3, 415-416

http://dx.doi.org/10.1016/j.cels.2016.11.003

https://authors.elsevier.com/a/1U5pm8YyDfNNuu

27 October 2016 (epub) and 23 November 2016 (pub)
Andrews et al. Push-Pull now out/ up/ published in Cell Systems

In this paper, we asked how cell signaling systems, including the yeast pheromone response system, might exhibit ‘‘Dose-Response Alignment’’ (DoRA), in which output of one or more downstream steps closely matches the fraction of occupied receptors, and preserve this relationship throughout changes in the number of protein components.  Systems with DoRA transmit information optimally. We found a non-feedback based, non-closed loop mechanism, Push-Pull, in which the nominally inactive form of upstream components actually reduces downstream activity, can generate DoRA. Although key aspects of the open-loop control enabled by Push-Pull are inferior to the closed-loop feedback control that would have been used by human (or other sentient) engineers, Push-Pull seems to be widespread throughout evolved eukaryotic signaling systems (even plants).  Our work suggests means to detect when Push-Pull and closed-loop feedback control might be operating, and means by which synthetic closed-loop feedback control in signaling systems might be engineered.

Andrews, S.,  Peria, W., Yu. R,. C., Colman-Lerner, A., and Brent, R. (2016).  Feedback and push-pull mechanisms can align signaling system outputs with inputs.  Cell Systems 3 (5):  444-455.e2

http://dx.doi.org/10.1016/j.cels.2016.10.002

https://authors.elsevier.com/a/1U5pm8YyDfNNng


22 September 2016
More from the vaults

We've published and doi-ed via FHCRC archives a number of previously unavailable papers from the lab.  The first (Ptashne et al. 2003) is a review on modular transcription activators from ergito.com, a now-defunct web textbook.  The second (Finley et al. 2003) is our original paper on a Drosophila gene and protein we called Cdi4, which interacted with Cdk2 and Cyclin E, and now called decapo.  The reasons we were unable to publish that work contemporaneously have to do with the occasional failure of peer review when the reviewers are untenured faculty members who view their work as competitive. 

Ptashne, M., Gill, G. and Brent, R.  (2003).   Modularity of eukaryotic transcription activators. doi: 10.6076/J7RN35SF

Finley, R. L. Jr., Cohen, B. and Brent, R. (2003) Drosophila Cdi4 is a p21/p27/p57-like cyclin-dependent kinase inhibitor with specificity for cyclin E complexes.  doi:10.6076/J7WD3XHS12

15 July 2016

New controller design from Khammash lab

We know from our unpublished work that consideration of early 20th century control systems (Mindell 2002) has been helpful in understanding how evolved cell signaling systems like the yeast PRS operate.  We are now testing a related idea, that collaboration with living 21st century control engineers at ETHZ may help us learn more about evolved systems and build better artificial ones.  Work from our collaborator Mustafa Khammash illustrates the promise of such engagement.  In a just published paper (Briat et al. 2016a), Khammash and his coworkers show a new and simple design for an integral controller that gives robust "perfect adaptation", but at the price of sensitivity to stochastic intracellular events.  This result stands in contrast with a second recently articulated design from the Khammash lab (Briat et al. 2016b), whose workings are robust to intracellular stochastic events, and our lab is seeking to understand this difference in natural language terms.

Mindell, D.A. (2002). Between Human and Machine (Baltimore: Johns Hopkins University Press).

Briat, C., Zechner, C. and Khammash, M (2016a).  Design of a Synthetic Integral Feedback Circuit: Dynamic Analysis and DNA Implementation.  ACS Synth Biol. Article ASAP 2016 Jul 8. PMID: 27345033 DOI: 10.1021/acssynbio.6b00014

Briat, C., Gupta, A., and Khammash, M. (2016b). Antithetic Integral Feedback Ensures Robust Perfect Adaptation in Noisy Biomolecular Networks.  Cell Systems 2(1): 15-26. doi: 10.1016/j.cels.2016.01.004.