Biology subjects

Roy, U.

Publications and source records attributed to Roy, U..

21 records · Page 2Linked to original sources

bioRxiv2020

Intermediate adhesion maximizes fluidity and migration velocity of multicellular clusters

Collections of cells exhibit coherent migration during morphogenesis, cancer metastasis, and wound healing. In many cases, bigger clusters split, smaller sub-clusters collide and reassemble, and gaps continually emerge. The connections between cell-level adhesion and cluster-level dynamics, as well as the resulting consequences for cluster properties such as migration velocity, remain poorly understood. Here we investigate collective migration of one- and two-dimensional cell clusters that collectively track chemical gradients using a mechanism based on contact inhibition of locomotion. We develop both a minimal description based on the lattice gas model of statistical physics, and a more realistic framework based on the cellular Potts model which captures cell shape changes and cluster rearrangement. In both cases, we find that cells have an optimal adhesion strength that maximizes cluster migration speed. The optimum negotiates a tradeoff between maintaining cell-cell contact and maintaining cluster fluidity, and we identify maximal variability in the cluster aspect ratio as a revealing signature. Our results suggest a collective benefit for intermediate cell-cell adhesion. SIGNIFICANCECells have been observed to migrate faster and more efficiently in clusters than as individuals. We conjecture that adhesion among cells and with the extracellular environment plays an important role in achieving higher-speed for the entire cluster. We carry out our analyses analytically and computationally, by employing a simplistic one-dimensional model and a realistic two-dimensional model which capture the essential features of multicellular migration. Our study demonstrates that an optimal cell-cell adhesion, which corresponds to maximal cellular rearrangement and loose packing, leads to a higher migration velocity for a multicellular cluster, acting as a crucial factor in effective movement of a collection of cells in a coordinated and directed fashion.

biophysics↗

bioRxiv2020

Bypass of DNA Interstrand crosslinks by a Rev1-DNA polymerase ζ complex

DNA polymerase {zeta} (Pol {zeta}) and Rev1 are essential for the repair of DNA interstrand crosslink (ICL) damage. We have used yeast DNA polymerases {eta}, {zeta}, and Rev1 to study translesion synthesis (TLS) past a nitrogen mustard-based ICL with an 8-atom linker between the crosslinked bases. The Rev1-Pol {zeta} complex was most efficient in complete bypass synthesis, by 2-3 fold, compared to Pol {zeta} alone or Pol {eta}. Rev1 protein, but not its catalytic activity, was required for efficient TLS. A dCMP residue was faithfully inserted across the ICL-G by Pol {eta}, Pol {zeta}, and Rev1-Pol {zeta}. Rev1-Pol {zeta}, and particularly Pol {zeta} alone showed a tendency to stall before the ICL, whereas Pol {eta} stalled just after insertion across the ICL. The stalling of Pol {eta} directly past the ICL is attributed to its autoinhibitory activity, caused by elongation of the short ICL-unhooked oligonucleotide (a six-mer in our study) by Pol {eta} providing a barrier to further elongation of the correct primer. No stalling by Rev1-Pol {zeta} directly past the ICL was observed, suggesting that the proposed function of Pol {zeta} as an extender DNA polymerase is also required for ICL repair.

biochemistry↗

bioRxiv2017

Ultrasensitivity and Fluctuations in the Barkai-Leibler Model of Chemotaxis Receptors in Escherichia coli

A stochastic version of the Barkai-Leibler model of chemotaxis receptors in Escherichia coli is studied here with the goal of elucidating the effects of intrinsic network noise in their conformational dynamics. The model was originally proposed to explain the robust and near-perfect adaptation of E. coli observed across a wide range of spatially uniform attractant/repellent (ligand) concentrations. In the model, a receptor is either active or inactive and can stochastically switch between the two states. The enzyme CheR methylates inactive receptors while CheB demethylates active receptors and the probability for a receptor to be active depends on its level of methylation and ligand occupation. In a simple version of the model with two methylation sites per receptor (M = 2), we show rigorously, under a quasi-steady state approximation, that the mean active fraction of receptors is an ultrasensitive function of [CheR]/[CheB] in the limit of saturating receptor concentration. Hence the model shows zero-order ultrasensitivity (ZOU), similar to the classical two-state model of covalent modification studied by Goldbeter and Koshland (GK). We also find that in the limits of extremely small and extremely large ligand concentrations, the system reduces to two different two-state GK modules. A quantitative measure of the spontaneous fluctuations in activity is provided by the variance [Formula] in the active fraction, which is estimated mathematically under linear noise approximation (LNA). It is found that [Formula] peaks near the ZOU transition. The variance is a non-monotonic, but weak function of ligand concentration and a decreasing function of receptor concentration. Gillespie simulations are also performed in models with M = 2, 3 and 4. For M = 2, simulations show excellent agreement with analytical results obtained under LNA. Numerical results for M = 3 and M = 4 are qualitatively similar to our mathematical results in M = 2; while all the models show ZOU in mean activity, the variance is found to be smaller for larger M. The magnitude of receptor noise deduced from available experimental data is consistent with our predictions. A simple analysis of the downstream signaling pathway shows that this noise is large enough to affect the motility of the organism, and may have a beneficial effect on it. The response of mean receptor activity to small time-dependent changes in the external ligand concentration is computed within linear response theory, and found to have a bilobe form, in agreement with earlier experimental observations.

biophysics↗