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

Signal One and Two Blockade Are Both Critical for Non-Myeloablative Murine HSCT across a Major Histocompatibility Complex Barrier

Non-myeloablative allogeneic haematopoietic stem cell transplantation (HSCT) is rarely achievable clinically, except where donor cells have selective advantages. Murine non-myeloablative conditioning regimens have limited clinical success, partly through use of clinically unachievable cell doses or strain combinations permitting allograft acceptance using immunosuppression alone. We found that reducing busulfan conditioning in murine syngeneic HSCT, increases bone marrow (BM):blood SDF-1 ratio and total donor cells homing to BM, but reduces the proportion of donor cells engrafting. Despite this, syngeneic engraftment is achievable with non-myeloablative busulfan (25 mg/kg) and higher cell doses induce increased chimerism. Therefore we investigated regimens promoting initial donor cell engraftment in the major histocompatibility complex barrier mismatched CBA to C57BL/6 allo-transplant model. This requires full myeloablation and immunosuppression with non-depleting anti-CD4/CD8 blocking antibodies to achieve engraftment of low cell doses, and rejects with reduced intensity conditioning (≤75 mg/kg busulfan). We compared increased antibody treatment, G-CSF, niche disruption and high cell dose, using reduced intensity busulfan and CD4/8 blockade in this model. Most treatments increased initial donor engraftment, but only addition of co-stimulatory blockade permitted long-term engraftment with reduced intensity or non-myeloablative conditioning, suggesting that signal 1 and 2 T-cell blockade is more important than early BM niche engraftment for transplant success

Cross-over in polymer solutions

Using a small-angle neutron scattering experiment, we measured the pair correlation function P(r) in polymer solutions in the interval 3 RG ≥ r ≥ l, where RG is the radius of gyration and I the step length. At the theta temperature, this function is known to follow the characteristic Debye law P(r) ∼ r-1. In good solvents (high temperature limit) and in the limit of zero polymer concentration this function is uniformly proportional to r-4/3, as predicted by S. F. Edwards. We observe however, that at higher concentrations or intermediate temperatures, P(r) exhibits both characteristic behaviours, depending on the range of r. The cross-over distances r* which separate the patterns are found to depend upon concentration and temperature. The scaling of r* is related to the scaling of the screening length ξ and the radius R G in the temperature-concentration diagram.La fonction de corrélation de paire P(r) pour les polymères en solution a été mesurée par diffusion de neutrons aux petits angles dans l'intervalle 3 RG ≥ r ≥ l où RG est le rayon de giration et l la longueur du monomère. A la température thêta cette fonction est décrite par la loi de Debye 1/r. En bon solvant (limite haute température) et à la limite de la concentration nulle, S. F. Edwards prédit que cette fonction est uniformément proportionnelle à r-4/3 . Cependant le résultat expérimental montre que pour des concentrations assez élevées ou pour des températures intermédiaires la fonction P(r) présente les deux comportements. On trouve qu'ils sont séparés par des longueurs de cross-over r* qui dépendent de la température et de la concentration. Le scaling de r* est relié au scaling de la longueur de corrélation ξ et du rayon RG dans le diagramme température-concen tration