Abhishekh Gupta

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BACKGROUND In Escherichia coli the mean and cell-to-cell diversity in RNA numbers of different genes vary widely. This is likely due to different kinetics of transcription initiation, a complex process with multiple rate-limiting steps that affect RNA production. RESULTS We measured the in vivo kinetics of production of individual RNA molecules under the(More)
The kinetics of transcription initiation in Escherichia coli depend on the duration of two rate-limiting steps, the closed and the open complex formation. In a lac promoter variant, P(lac/ara-1), the kinetics of these steps is controlled by IPTG and arabinose. From in vivo single-RNA measurements, we find that induction affects the mean and normalized(More)
MOTIVATION Cell growth and division affect the kinetics of internal cellular processes and the phenotype diversity of cell populations. Since the effects are complex, e.g. different cellular components are partitioned differently in cell division, to account for them in silico, one needs to simulate these processes in great detail. RESULTS We present(More)
Attractors represent the long-term behaviors of Random Boolean Networks. We study how the amount of information propagated between the nodes when on an attractor, as quantified by the average pairwise mutual information (I(A)), relates to the robustness of the attractor to perturbations (R(A)). We find that the dynamical regime of the network affects the(More)
Even single-celled organisms, such as Escherichia coli, possess a far from random internal organization, as the cytoplasm is a crowded, heterogeneous environment. Some proteins preferentially locate at the cell poles (e.g. those involved in chemo-taxis), while others, e.g. involved in gene expression, locate at mid-cell, within a structure known as(More)
Recent evidence suggests that cells employ functionally asymmetric partitioning schemes in division to cope with aging. We explore various schemes in silico, with a stochastic model of Escherichia coli that includes gene expression, non-functional proteins generation, aggregation and polar retention, and molecule partitioning in division. The model is(More)
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