The Seven Stones

q-bio 2010 Conference on Cellular Information Processing

This last August 11-14, systems biologists convened in beautiful Santa Fe, New Mexico, for the Fourth Annual q-bio Conference on Cellular Information Processing. The conference brought together a potent mix of theoretical and quantitative experimental biology across a wide range of topics. The full program and abstracts for each talk can be browsed on the conference’s Wiki page.

St. John’s College, the q-bio venue

Highlighting the value of systems-level analysis, many of the talks revealed the functional importance of features of biological systems that may often be tempting to disregard:

  • Thierry Emonet showed that noise in the chemotactic signaling pathways actually acts to help coordinate the bacteria’s multiple flagella.  (In fact, chemotaxis and bacterial swarming were popular topics. See also the talks by Jan Liphardt, Ned Wingreen, Victor Sourjik, Bonnie Bassler, Christopher Rao, and Yi Jiang).
  • Talks by Anat Burger and Narendra Maheshri explored the ways that non-functional transcription factor binding sites (sites that do not directly affect gene regulation) can nonetheless have dramatic effects on the dynamics of gene regulatory circuits.
  • Debora Marks discussed her work showing that saturation and competition play a potentially important role in determining the efficiency of siRNA and microRNA target gene repression. (See also her recent work in Molecular Systems Biology, Arvey et al. 2010).

The conference also hosted several excellent talks on cell cycle regulation — a classical model in systems biology research — including a closing lecture by James Ferrell and a talk by John Tyson describing his detailed stochastic model of the eukaryotic cell cycle (recently published in Molecular Systems Biology, Barik et al. 2010). See also talks by Jan Skotheim, Silvia Santos, and Xiaojing Yang. Galit Lahav also provided some exciting insights into another extremely well-studied system — p53 signaling (see Loewer et al. 2010).

In addition, two researchers studying HIV1 provided some of the most thought-provoking presentations:

    • Leor Weinberger proposed a way to treat HIV1 with a transmissible therapeutic agent, and described both cell culture experiments demonstrating the ability of their agent to slow HIV1 propagation, and computational modeling showing how this agent could spread through the human population.
  • Alex Sigal used a combination of modeling and cell culture experiments to make a compelling case that direct cell-to-cell transmission of HIV1 may help maintain a low-level “smoldering infection” during anti-retroviral drug treatment.

Naturally, these are just a few highlights from the conference, which hosted many other excellent talks. Once again, we encourage you to browse the full program and abstracts on the conference’s Wiki page.

Barik D, Baumann WT, Paul MR, Novak B, Tyson JJ (2010) A model of yeast cell-cycle regulation based on multisite phosphorylation. Mol Syst Biol 6:405

Arvey A, Larsson E, Sander C, Leslie CS, Marks DS (2010) Target mRNA abundance dilutes microRNA and siRNA activity. Mol Syst Biol 6:363

Loewer A, Batchelor E, Gaglia G, Lahav G (2010) Basal Dynamics of p53 Reveal Transcriptionally Attenuated Pulses in Cycling Cells. Cell 142:89-100


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