Work distribution of a colloid in an elongational flow field and under Ornstein-Uhlenbeck noise.

The study of thermodynamic properties of microscopic systems, such as a colloid in a fluid, has been of great interest to researchers since the discovery of the fluctuation theorem and associated laws of stochastic thermodynamics. However, most of these studies confine themselves to systems where effective fluctuations acting on the colloid are in the form of delta-correlated Gaussian white noise (GWN). In this study, instead, we look into the work distribution function when a colloid trapped in a harmonic potential moves from one position to another in a fluid medium with an elongational flow field where the effective fluctuations are given by the Ornstein-Uhlenbeck noise, a type of colored noise.

Unveiling autophagy and aging through time-resolved imaging of lysosomal polarity with a delayed fluorescent emitter.

Detecting the lysosomal microenvironmental changes like viscosity, pH, and polarity during their dynamic interorganelle interactions remains an intriguing area that facilitates the elucidation of cellular homeostasis. The subtle variation of physiological conditions can be assessed by deciphering the lysosomal microenvironments during lysosome-organelle interactions, closely related to autophagic pathways leading to various cellular disorders. Herein, we shed light on the dynamic lysosomal polarity in live cells and a multicellular model organism, (), through time-resolved imaging employing a thermally activated delayed fluorescent probe, DC-Lyso.

Microfluidics based bioimaging with cost-efficient fabrication of multi-level micrometer-sized trenches.

Microfluidic devices, through their vast applicability as tools for miniaturized experimental setups, have become indispensable for cutting edge research and diagnostics. However, the high operational cost and the requirement of sophisticated equipment and clean room facility for the fabrication of these devices make their use unfeasible for many research laboratories in resource limited settings. Therefore, with the aim of increasing accessibility, in this article, we report a novel, cost-effective micro-fabrication technique for fabricating multi-layer microfluidic devices using only common wet-lab facilities, thereby significantly lowering the cost.

Lessons Learned from Two Decades of Modeling the Heat-Shock Response.

The Heat Shock Response (HSR) is a highly conserved genetic system charged with protecting the proteome in a wide range of organisms and species. Experiments since the early 1980s have elucidated key elements in these pathways and revealed a canonical mode of regulation, which relies on a titration feedback. This system has been subject to substantial modeling work, addressing questions about resilience, design and control.

Persistent Correlation in Cellular Noise Determines Longevity of Viral Infections.

The slowly decaying viral dynamics, even after 2-3 weeks from diagnosis, is one of the characteristics of COVID-19 infection that is still unexplored in theoretical and experimental studies. This long-lived characteristic of viral infections in the framework of inherent variations or noise present at the cellular level is often overlooked. Therefore, in this work, we aim to understand the effect of these variations by proposing a stochastic non-Markovian model that not only captures the coupled dynamics between the immune cells and the virus but also enables the study of the effect of fluctuations.

Transcription factors and chaperone proteins play a role in launching a faster response to heat stress and aggregation.

Proteins, under conditions of cellular stress, typically tend to unfold and form lethal aggregates leading to neurological diseases like Parkinson's and Alzheimer's. A clear understanding of the conditions that favor dis-aggregation and restore the cell to its healthy state after they have been stressed is therefore important in dealing with these diseases. The heat shock response (HSR) mechanism is a signaling network that deals with these undue protein aggregates and aids in the maintenance of homeostasis within a cell.

A near analytic solution of a stochastic immune response model considering variability in virus and T-cell dynamics.

Biological processes at the cellular level are stochastic in nature, and the immune response system is no different. Therefore, models that attempt to explain this system need to also incorporate noise or fluctuations that can account for the observed variability. In this work, a stochastic model of the immune response system is presented in terms of the dynamics of T cells and virus particles.

High prevalence of non-alcoholic fatty liver disease among healthy male blood donors of urban India.

Background: There is limited data on the community prevalence of non-alcoholic fatty liver disease (NAFLD). The present study evaluated the prevalence of NAFLD in a large number of healthy male blood donors of urban north India.

Methodology: In a prospective study performed over 18 months, voluntary blood donors fulfilling the requisite blood donation criteria and consenting to participate in the study were evaluated.

Redefining the Normal Values of Serum Aminotransferases in Healthy Indian Males.

Background: The normal range for Aspartate and Alanine Aminotransferases (AST and ALT) levels (<40 IU/L) were set in 1950s. Recent data from certain countries suggest lower levels of AST and ALT. Aim of the study was to redefine the normal values of aminotransferases in healthy Indian adults.

Biospark: scalable analysis of large numerical datasets from biological simulations and experiments using Hadoop and Spark.

Unlabelled: Data-parallel programming techniques can dramatically decrease the time needed to analyze large datasets. While these methods have provided significant improvements for sequencing-based analyses, other areas of biological informatics have not yet adopted them. Here, we introduce Biospark, a new framework for performing data-parallel analysis on large numerical datasets.

Gradient sensing by a bistable regulatory motif enhances signal amplification but decreases accuracy in individual cells.

Many vital eukaryotic cellular functions require the cell to respond to a directional gradient of a signaling molecule. The first two steps in any eukaryotic chemotactic/chemotropic pathway are gradient detection and cell polarization. Like many processes, such chemotactic and chemotropic decisions are made using a relatively small number of molecules and are thus susceptible to internal and external fluctuations during signal transduction.

Dynamics of simple gene-network motifs subject to extrinsic fluctuations.

Cellular processes do not follow deterministic rules; even in identical environments genetically identical cells can make random choices leading to different phenotypes. This randomness originates from fluctuations present in the biomolecular interaction networks. Most previous work has been focused on the intrinsic noise (IN) of these networks.

Interfacial growth as a model of tube-width heterogeneities in concentrated solutions of stiff polymers.

Recent experimental measurements of the distribution P(w) of transverse chain fluctuations w in concentrated solutions of F-actin filaments [B. Wang, J Guan, S. M.

Efficacy and safety of autologous bone marrow-derived stem cell transplantation in patients with type 2 diabetes mellitus: a randomized placebo-controlled study.

There is a growing interest in cell-based therapies in T2DM as β-cell failure is progressive and inexorable with the advancing duration of disease. This prospective, randomized, single-blinded placebo-controlled study evaluates the efficacy and safety of autologous bone marrow-derived stem cell transplantation (ABMSCT) in T2DM. Twenty-one patients with triple oral antidiabetic drug failure and requiring insulin ≥0.

Subdiffusion in hair bundle dynamics: the role of protein conformational fluctuations.

The detection of sound signals in vertebrates involves a complex network of different mechano-sensory elements in the inner ear. An especially important element in this network is the hair bundle, an antenna-like array of stereocilia containing gated ion channels that operate under the control of one or more adaptation motors. Deflections of the hair bundle by sound vibrations or thermal fluctuations transiently open the ion channels, allowing the flow of ions through them, and producing an electrical signal in the process, eventually causing the sensation of hearing.

Confinement and viscoelastic effects on chain closure dynamics.

Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to cellular biochemistry--the diffusion-limited cyclization of long chain polymers--is influenced by such confinement and crowding effects. More specifically, starting from the Rouse model of polymer dynamics, and invoking the Wilemski-Fixman approximation, we determine the scaling relationship between the mean closure time t(c) of a flexible chain (no excluded volume or hydrodynamic interactions) and the length N of its contour under the following separate conditions: (a) confinement of the chain to a sphere of radius d and (b) modulation of its dynamics by colored Gaussian noise.

Microsomal Epoxide Hydrolase Polymorphisms and Haplotypes as Determinants of Hepatitis B Virusand Hepatitis C Virus-related Liver Disease in Indian Population.

Background: Hepatocellular carcinoma (HCC) is the fifth most common cancer and third leading cause of death worldwide. Main causes of HCC are hepatitis B virus (HBV) and hepatitis C virus (HCV) infections. mEPHX, a xenobiotic metabolizing enzyme, exhibits a dual role of procarcinogen detoxification and activation, hence considered as a cancer risk factor as well as a protective factor.

Distribution of transverse chain fluctuations in harmonically confined semiflexible polymers.

Two different experimental studies of polymer dynamics based on single-molecule fluorescence imaging have recently found evidence of heterogeneities in the widths of the putative tubes that surround filaments of F-actin during their motion in concentrated solution. In one [J. Glaser, D.

Work fluctuations in an elastic dumbbell model of polymers in planar elongational flow.

We use a path-integral approach to calculate the distribution P(w,t) of the fluctuations in the work w at time t of a polymer molecule (modeled as an elastic dumbbell in a viscous solvent) that is acted on by an elongational flow field having a flow rate ̇γ. We find that P(w,t) is non-Gaussian and that, at long times, the ratio P(w,t)/P(-w,t) is equal to exp[w/(k(B)T)], independent of ̇γ. On the basis of this finding, we suggest that polymers in elongational flows satisfy a fluctuation theorem.

Polymer melt dynamics: microscopic roots of fractional viscoelasticity.

The rheological properties of polymer melts and other complex macromolecular fluids are often successfully modeled by phenomenological constitutive equations containing fractional differential operators. We suggest a molecular basis for such fractional equations in terms of the generalized Langevin equation (GLE) that underlies the renormalized Rouse model developed by Schweizer [J. Chem.