Biology subjects

Sinha, B.

Publications and source records attributed to Sinha, B..

4 recordsLinked to original sources

bioRxiv2018

Development of an interactive open source software application (RadaR) for infection management / antimicrobial stewardship

ObjectivesAnalysing process and outcome measures for patients suspected of or having an infection in an entire hospital requires processing large datasets and accounting for numerous patient parameters and treatment guidelines. Rapid, reproducible and adaptable analyses usually need substantial technical expertise but can yield valuable insight for infection management and antimicrobial stewardship (AMS) teams. We describe a software application (RadaR - Rapid analysis of diagnostic and antimicrobial patterns in R) for infection management allowing user-friendly, intuitive and interactive analysis of large datasets without prior in-depth statistical or software knowledge.\n\nMethods and ResultsRadaR was built in R, an open source programming language, making it free to use and adaptable to different settings. Shiny, an additional open source package to implement web-application frameworks in R, was used to develop the application. RadaR was developed in the context of a 1339-bed academic tertiary referral hospital to handle data of more than 180,000 admissions.\n\nRadaR visualizes analytical graphs and statistical summaries in an interactive manner within seconds. Users can filter large patient groups by 17 different criteria and investigate antimicrobial use, microbiological diagnostic use and results, and outcome in length of stay. Results can easily be stratified and grouped to compare individually defined patient groups. Finally, datasets of identified patients / groups can be downloaded for further analyses.\n\nConclusionRadaR facilitates understanding and communication of trends in antimicrobial use, diagnostic use and patient outcome by linking and aggregating individual patient data in one user-friendly application. RadaR can produce aggregated data analysis while preserving patients features in the data to adjust and stratify results in detail. AMS teams can use RadaR to identify areas, both for diagnostic and therapeutic procedures, within their institutions that might benefit from increased support and to target their interventions.

bioinformatics↗

bioRxiv2018

Lack of functional caveolae in Cav3 mutated human dystrophic myotubes results in deficient mechanoprotection and IL6/STAT3 mechanosignaling.

Caveolin-3 is the major structural protein of caveolae in muscle cells. Mutations in the CAV3 gene cause different type of muscle disorders mostly characterized by defects in membrane integrity and repair, deregulation in the expression of various muscle proteins and deregulation of several muscle associated signaling pathways. We show here that myotubes derived from patients bearing the CAV3 P28L and R26Q mutations present a lack of functional caveolae at the plasma membrane which results in an abnormal mechanoresponse. Mutant myotubes can no longer buffer the increase of membrane tension induced by mechanical stress and present an hyperactivation of the IL6/STAT3 signaling pathway at rest and under mechanical stress. The impaired mechanical regulation of the IL6/STAT3 signaling pathway by caveolae leads to chronic activation and a higher expression of muscle specific genes. These defects could be reversed by reassembling a pool of functional caveolae through expression of wild type Cav3. Our findings bring more mechanistic insight into human Cav3 associated muscle disorders and show a general defect in the mechanoresponse of CAV3 P28L and R26Q myotubes.

cell biology↗

bioRxiv2018

Cholesterol depletion by MβCD enhances membrane tension, its heterogeneity and affects cellular integrity.

Cholesterol depletion in cells by M{beta}CD remodels the plasma membranes mechanics and its interactions with the underlying cytoskeleton. Decoupling the two effects and studying various alterations to the membranes mechanical parameters is important for understanding cholesterols role in cellular response to stress. By mapping membrane height fluctuations in single cells, we report that M{beta}CD treatment reduces temporal fluctuations and flattens out the membrane - but does not supress activity-driven fluctuations. We find that membrane tension increase contributes most to the altered fluctuations, among the multiple mechanical parameters computed. Maps also reveal an enhanced long-range heterogeneity within single cells, both in amplitude of fluctuations and membrane tension on cholesterol depletion. To check if this alters the tenacity of membrane to mechanical stress we use hypo-osmotic shock. We find that on M{beta}CD treatment, cells are more prone to rupture than control cells, and this is not hindered by actomyosin perturbations. We report increased rupture sizes on cholesterol depletion and argue that, together, this indicates decreased lysis and line tension. Therefore, we show that cholesterol depletion directly affects cell membranes not only by enhancing membrane-cytoskeleton interactions, but also by increasing membrane tension while reducing lysis tension - hence making cells prone to rupture.

biophysics↗

bioRxiv2017

Regulation of thickness of actomyosin cortex in well-spread cells by contractility and spread area

The contractile cortical actomyosin cytoskeleton (or cortex) in interphase cells confers rigidity to cells, but also lead to shape dynamics. Regulation of its thickness, although well studied in rounded cells, is less explored in well-spread cells. In this paper, we quantify the variations in thickness and study the contribution of actin polymerization, myosin II activity and spread area of cells. We report an increase in cortex thickness and its variations on disrupting actin network by actin depolymerizing agents or reducing contractility by inhibiting motor activity of myosin II. On spread area reduction by substrate micropatterning, we find reduced cell volume and increased mean & variability of thickness. To validate, we follow cells through de-adhesion with EDTA. The thickness of cortex increases (and oscillates) while the volume of cells reduces with 5-15 mins timescales. Moreover, total internal reflection fluorescence (TIRF) imaging reveals stress fibre dissolution and events of their buckling along with a growing population of micron-sized mobile filaments. We believe that the cytoskeleton responds to the loss of adhesion by contracting and fragmenting, hence leading to cortex thickening. Limiting volume reduction does not suppress cortex thickening on de-adhesion, suggesting that decreased traction stress may be primarily responsible for the cortex thickening.

biophysics↗