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Counting fluorescence photobleaching steps is commonly used to infer the number n0 of monomeric units of individual oligomeric protein complexes or misfolded protein aggregates. We present a principled Bayesian approach for counting that incorporates the statistics of photobleaching. Our physics-based prior leads to a simple and efficient numerical scheme for maximum a posteriori probability (MAP) estimates of the initial fluorophore number n ^ 0 . Our focus here is on using a calibration to precisely estimate n ^ 0 , though our approach can also be used to calibrate the photophysics. Imaging noise increases with n ^ 0 , while bias is often introduced by temporal averaging. We examine the effects of fluorophore number n ^ 0 of the oligomer or aggregate, lifetime photon yield μeff of an individual fluorophore, and exposure time Δt of each image frame in a time-lapse experiment. We find that, in comparison with standard ratiometric approaches or with a "change-point" step-counting algorithm, our MAP approach is both more precise and less biased. [ABSTRACT FROM AUTHOR]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2007.09.045 Byline: Jun F. Allard (a), Alison L. Hill (b), Andrew D. Rutenberg (a) Keywords: Filamentous cyanobacteria; Anabaena; Heterocyst commitment; Lateral inhibition; Fixed nitrogen; Diazotrophic; Differentiation; Computational modeling; Pattern formation; Growth and division Abstract: We have quantitatively modeled heterocyst differentiation after fixed nitrogen step-down in the filamentous cyanobacterium Anabaena sp. PCC 7120 without lateral inhibition due to the patterning proteins PatS or HetN. We use cell growth and division together with fixed-nitrogen dynamics and allow heterocysts to differentiate upon the local exhaustion of available fixed nitrogen. Slow transport of fixed nitrogen along a shared periplasmic space allows for fast growing cells to differentiate ahead of their neighbors. Cell-to-cell variability in growth rate determines the initial heterocyst pattern. Early release of fixed nitrogen from committed heterocysts allows a significant fraction of vegetative cells to be retained at later times. We recover the experimental heterocyst spacing distributions and cluster size distributions of Khudyakov and Golden [Khudyakov, I.Y., Golden, J.W., 2004. Different functions of HetR, a master regulator of heterocyst differentiation in Anabaena sp PCC 7120, can be separated by mutation. Proc. Natl. Acad. Sci. U. S. A. 101, 16040-16045]. Author Affiliation: (a) Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1Z9 (b) Department of Physics, Queen's University, Kingston Ontario, Canada K7L 3N6 Article History: Received 25 April 2006; Revised 23 September 2007; Accepted 24 September 2007

Phage [lambda] lyses the host Escherichia coli at a precisely scheduled time after induction. Lysis timing is determined by the action of phage holins, which are small proteins that induce hole formation in the bacterium's cytoplasmic membrane. We present a two-stage nucleation model of lysis timing, with the nucleation of condensed holin rafts on the inner membrane followed by the nucleation of a hole within those rafts. The nucleation of holin rafts accounts for most of the delay of lysis after induction. Our simulations of this model recover the accurate lysis timing seen experimentally and show that the timing accuracy is optimal. An enhanced holin-holin interaction is needed in our model to recover experimental lysis delays after the application of membrane poison, and such early triggering of lysis is possible only after the inner membrane is supersaturated with holin. Antiholin reduces the delay between membrane depolarization and lysis and leads to an earlier time after which triggered lysis is possible.

We observed that the oscillation period of MinD within rod-like and filamentous cells of Escherichia coli varied by a factor of 4 in the temperature range from 20[degrees]C to 40[degrees]C. The detailed dependence was Arrhenius, with a slope similar to the overall temperature-dependent growth curve of E. coli. The detailed pattern of oscillation, including the characteristic wavelength in filamentous cells, remained independent of temperature. A quantitative model of MinDE oscillation exhibited similar behavior, with an activated temperature dependence of the MinE-stimulated MinD-ATPase rate.

COMPUTATIONAL INSIGHTS INTO FOLDED PROTEIN TRANSPORT BY DYNAMIC CHANNEL FORMATION IN BACTERIA. CHITRA NAYAK, DEPARTMENT OF PHYSICS, TUSKEGEE UNIVERSITY, AL 36832. AIDAN I BROWN, DALHOUSIE UNIVERSITY, NOVASCOTIA, CANADA, B3H3J5. ANDREW [...]