In enzymatic reactions, the reverse reaction reduces product noise.

Enzymatic reactions are essential for most cellular reactions and ubiquitous in living organisms. In the present study, we explore the pivotal role of the reverse reaction in enzymatic reactions. It is a powerful noise-buffering motif.

A comprehensive study on flocculation of anionic dyes using the bioflocculant produced by Bacillus thuringiensis: Kinetics, affecting factors, and perspectives.

Bioflocculants have received more and more attention as alternatives to chemical flocculants because of their innocuousness, environmental friendliness, and high effectiveness. This study aims to investigate various factors that influence the performance of the novel bioflocculant produced by Bacillus thuringiensis (BF-TWB10) and analyze its adsorption kinetics to optimize its flocculation performance for real applications. The best-fit kinetic model was pseudo-second order with R  = 0.

Dimerization induces bimodality in protein number distributions.

We examined gene expression with DNA switching between two states, active and inactive. Subpopulations emerge from mechanisms that do not arise from trivial transcriptional heterogeneity. Although the RNA demonstrates a unimodal distribution, dimerization intriguingly causes protein bimodality.

The switch of DNA states filtering the extrinsic noise in the system of frequency modulation.

There is a special node, which the large noise of the upstream element may not always lead to a broad distribution of downstream elements. This node is DNA, with upstream element TF and downstream elements mRNA and proteins. By applying the stochastic simulation algorithm (SSA) on gene circuits inspired by the fim operon in Escherichia coli, we found that cells exchanged the distribution of the upstream transcription factor (TF) for the transitional frequency of DNA.

Exposure to One Antibiotic Leads to Acquisition of Resistance to Another Antibiotic Quorum Sensing Mechanisms.

The vancomycin-resistant Enterococci (VRE) have progressively become a severe medical problem. Although clinics have started to reduce vancomycin prescription, vancomycin resistance has not been contained. We found that the transfer of vancomycin resistance in increased more than 30-fold upon treatment by streptomycin.

Author Correction: The Reaction of Dimerization by Itself Reduces the Noise Intensity of the Protein Monomer.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The Reaction of Dimerization by Itself Reduces the Noise Intensity of the Protein Monomer.

Because of the small particle number of intracellular species participating in genetic circuits, stochastic fluctuations are inevitable. This intracellular noise is detrimental to precise regulation. To maintain the proper function of a cell, some natural motifs attenuate the noise at the protein level.

The Insight into Protein-Ligand Interactions, a Novel Way of Buffering Protein Noise in Gene Expression.

Random fluctuations are often considered detrimental in the context of gene regulation. Studies aimed at discovering the noise-buffering strategies are important. In this study, we demonstrated a novel design of attenuating noise at protein-level.

Inhibitors Alter the Stochasticity of Regulatory Proteins to Force Cells to Switch to the Other State in the Bistable System.

The cellular behaviors under the control of genetic circuits are subject to stochastic fluctuations, or noise. The stochasticity in gene regulation, far from a nuisance, has been gradually appreciated for its unusual function in cellular activities. In this work, with Chemical Master Equation (CME), we discovered that the addition of inhibitors altered the stochasticity of regulatory proteins.

Driving Cells to the Desired State in a Bimodal Distribution through Manipulation of Internal Noise with Biologically Practicable Approaches.

The stochastic nature of gene regulatory networks described by Chemical Master Equation (CME) leads to the distribution of proteins. A deterministic bistability is usually reflected as a bimodal distribution in stochastic simulations. Within a certain range of the parameter space, a bistable system exhibits two stable steady states, one at the low end and the other at the high end.

On speeding up stochastic simulations by parallelization of random number generation.

This paper adds to the tool kit of stochastic simulations based on a very simple idea. Applicable to both SSA and Tau-leap algorithms, it can notably reduce computational times. Stochastic simulations are based on computing sample paths based on the generation of random numbers with either exactly stipulated distribution functions as in SSA (Gillespie, 1977) or in the method of interval of quiescence (Shah et al.

New "Tau-Leap" Strategy for Accelerated Stochastic Simulation.

The "Tau-Leap" strategy for stochastic simulations of chemical reaction systems due to Gillespie and co-workers has had considerable impact on various applications. This strategy is reexamined with Chebyshev's inequality for random variables as it provides a rigorous probabilistic basis for a measured τ-leap thus adding significantly to simulation efficiency. It is also shown that existing strategies for simulation times have no probabilistic assurance that they satisfy the τ-leap criterion while the use of Chebyshev's inequality leads to a specified degree of certainty with which the τ-leap criterion is satisfied.

Role of intracellular stochasticity in biofilm growth. Insights from population balance modeling.

There is increasing recognition that stochasticity involved in gene regulatory processes may help cells enhance the signal or synchronize expression for a group of genes. Thus the validity of the traditional deterministic approach to modeling the foregoing processes cannot be without exception. In this study, we identify a frequently encountered situation, i.

Antagonistic self-sensing and mate-sensing signaling controls antibiotic-resistance transfer.

Conjugation is one of the most common ways bacteria acquire antibiotic resistance, contributing to the emergence of multidrug-resistant "superbugs." Bacteria of the genus Enterococcus faecalis are highly antibiotic-resistant nosocomial pathogens that use the mechanism of conjugation to spread antibiotic resistance between resistance-bearing donor cells and resistance-deficient recipient cells. Here, we report a unique quorum sensing-based communication system that uses two antagonistic signaling molecules to regulate conjugative transfer of tetracycline-resistance plasmid pCF10 in E.

MODELING OF GENE REGULATORY PROCESSES BY POPULATION MEDIATED SIGNALING. NEW APPLICATIONS OF POPULATION BALANCES.

Population balance modeling is considered for cell populations in gene regulatory processes in which one or more intracellular variables undergo stochastic dynamics as determined by Ito stochastic differential equations. This paper addresses formulation and computational issues with sample applications to the spread of drug resistance among bacterial cells. It is shown that predictions from population balances can display qualitative differences from those made with single cell models which are usually encountered in the literature.

Bistability versus bimodal distributions in gene regulatory processes from population balance.

In recent times, stochastic treatments of gene regulatory processes have appeared in the literature in which a cell exposed to a signaling molecule in its environment triggers the synthesis of a specific protein through a network of intracellular reactions. The stochastic nature of this process leads to a distribution of protein levels in a population of cells as determined by a Fokker-Planck equation. Often instability occurs as a consequence of two (stable) steady state protein levels, one at the low end representing the "off" state, and the other at the high end representing the "on" state for a given concentration of the signaling molecule within a suitable range.

Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation.

Convergent gene pairs with head-to-head configurations are widespread in both eukaryotic and prokaryotic genomes and are speculated to be involved in gene regulation. Here we present a unique mechanism of gene regulation due to convergent transcription from the antagonistic prgX/prgQ operon in Enterococcus faecalis controlling conjugative transfer of the antibiotic resistance plasmid pCF10 from donor cells to recipient cells. Using mathematical modeling and experimentation, we demonstrate that convergent transcription in the prgX/prgQ operon endows the system with the properties of a robust genetic switch through premature termination of elongating transcripts due to collisions between RNA polymerases (RNAPs) transcribing from opposite directions and antisense regulation between complementary counter-transcripts.