A Coarse-Grained Biophysical Model of E. coli and Its Application to Perturbation of the rRNA Operon Copy Number

We propose a biophysical model of Escherichia coli that predicts growth rate and an effective cellular composition from an effective, coarse-grained representation of its genome. We assume that E. coli is in a state of balanced exponential steadystate growth, growing in a temporally and spatially constant environment, rich in resources. We apply this model to a series of past measurements, where the growth rate and rRNA-to-protein ratio have been measured for seven E. coli strains with an rRNA operon copy number ranging from one to seven (the wild-type copy number). These experiments show that growth rate markedly decreases for strains with fewer than six copies. Using the model, we were able to reproduce these measurements. We show that the model that best fits these data suggests that the volume fraction of macromolecules inside E. coli is not fixed when the rRNA operon copy number is varied. Moreover, the model predicts that increasing the copy number beyond seven results in a cytoplasm densely packed with ribosomes and proteins. Assuming that under such overcrowded conditions prolonged diffusion times tend to weaken binding affinities, the model predicts that growth rate will not increase substantially beyond the wild-type growth rate, as indicated by other experiments. Our model therefore suggests that changing the rRNA operon copy number of wild-type E. coli cells growing in a constant rich environment does not substantially increase their growth rate. Other observations regarding strains with an altered rRNA operon copy number, such as nucleoid compaction and the rRNA operon feedback response, appear to be qualitatively consistent with this model. In addition, we discuss possible design principles suggested by the model and propose further experiments to test its validity

What determines cell size?

AbstractFirst paragraph (this article has no abstract) For well over 100 years, cell biologists have been wondering what determines the size of cells. In modern times, we know all of the molecules that control the cell cycle and cell division, but we still do not understand how cell size is determined. To check whether modern cell biology has made any inroads on this age-old question, BMC Biology asked several heavyweights in the field to tell us how they think cell size is controlled, drawing on a range of different cell types. The essays in this collection address two related questions - why does cell size matter, and how do cells control it

Factors affecting visual recovery after successful repair of macula-off retinal detachments:findings from a large prospective UK cohort study

OBJECTIVE: To identify risk factors affecting visual outcomes in successfully re-attached macula-off rhegmatogenous retinal detachment (RD) surgery. DESIGN: A prospective study, using online databases, of visual outcomes for 2074 macula-off retinal detachments that were successfully re-attached by vitrectomy and internal tamponade. The database included detailed retinal diagrams of each detachment. MAIN OUTCOME MEASURE: The probability of achieving a post-operative visual acuity (VA) of ≤0.30 LogMAR (Snellen 6/12 or better). RESULTS: Male patients accounted for 64.9% of the sample and the median age was 63 years old. The median pre-operative VA was counting fingers (LogMAR 1.98); this improved to 0.41 LogMAR post-operatively. A post-operative VA of ≤0.30 LogMAR was achieved for 1012 (48.8%) eyes and the factors affecting this were the patient age and gender, pre-operative VA, duration of central vision loss, PVR grade, lens status, total RD and the presence of any ocular co-pathology where the model area under the receiver operator curve was 71.6%. CONCLUSIONS: From the identified risk factors that decrease the probability of achieving a post-operative visual acuity of ≤0.30 LogMAR, the most important modifiable risk factor was the duration of central vision loss. Recent macula-off retinal detachments should be repaired within 72 h of the loss of central vision