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Datta, A.

Publications and source records attributed to Datta, A..

At least 73 records · Page 4Linked to original sources

Decisive Role of Polymer-BSA Interactions in Biofilm Substrates on Philicity and EPS Composition

Formation of extracellular polymeric substances (EPS) is a crucial step for bacterial biofilm growth. Dependence of EPS composition on the growth substrate and the conditioning of the latter is thus of primary importance. Here, we present results of studies on the growth of biofilms of two different strains each, of the Gram negative bacteria Escherichia coli and Klebsiella pneumoniae, on four polymers used commonly in indwelling medical devices - Polyethene, Polypropylene, Polycarbonate, and Polytetrafluoroethylene immersed in Bovine Serum Albumin (BSA) for 24 hrs. The polymer substrates are studied before and after immersing in BSA for 9 hrs and 24 hrs, using contact angle measurement (CAM) and Field Emission Scanning Electron Microscopy (FE-SEM) to extract, respectively, the philicity (defined as{phi} {equiv} sin ({theta}-90{degrees}), where{theta} is contact angle of the liquid on the solid at a particular temperature and ambient pressure) and spatial Hirsch parameter H (defined from the relation, F(r) ~ r2H, where F(r) is the mean squared density fluctuation at the sample surface). H =, <0.5 or >0.5 signifies no correlation, anti-correlation, and correlation, respectively. The substrates are seen to transform from large hydrophobicity to near amphiphilicity with the formation of BSA conditioning surface layer, and the H-values distinguish the length scales of ~ 100 nm, 500 nm, and 2000 nm, with the anti-correlation increasing with length scale. Biofilms grown on the BSA-covered surfaces are studied with CAM, FE-SEM, Fourier Transform Infrared (FTIR) and Surface Enhanced Raman Spectroscopy (SERS). Most notably, the{phi} -values are independent of the bacterial species and strain but dependent on the polymer, as is also shown strikingly by both types of spectra, while H-values show some bacterial variation. Thus, the EPS composition and consequently the wetting properties of the corresponding bacterial biofilms seems to be decided by the interaction of the conditioning BSA layer with a specific polymer used as the growth substrate.

biophysics↗

A study of Mutation in ATP7B gene and its correlation with clinical phenotype and radiological features in Wilson Disease patients

IntroductionWilson Disease (WD) is an autosomal recessive disease caused by mutations in the ATP7B gene. Clinical manifestations of WD are variable. Identification of prevalent mutations in a given population is necessary to provide mutation-based molecular diagnosis. Previous studies have detected common mutations in this part of the world and our study aimed to correlate genotype with clinical and radiological features. MethodsA descriptive cross-sectional observational study was conducted over a period of two years in a tertiary care hospital and neurology referral unit of Kolkata, India. All WD patients within the study period and meeting the inclusion criteria were included. Demographic data collection, clinical examination and relevant laboratory investigations were done. Magnetic resonance imaging of brain and cognitive assessment by Mini Mental Score Exam (MMSE) were also performed. Blood was collected for genetic analyses. PCR-Sanger sequencing of exons 2,4,6,8,10,14,16,18 of ATP7B gene was done based on previous reports of mutation hotspots of ATP7B gene for WD in Eastern India. Genotype phenotype correlation was attempted using two supervised machine learning methods, viz. logistic regression with an elastic-net penalty and the random forest. ResultsOf 52 WD patients were included in the study, 57.7% were males. The mean age at diagnosis was 13.96 years. Majority (61.8%) of the patients had dystonia on presentation, followed by dysarthria (41.2%), tremor (17.6%) and ataxia (11.8%). The mean MMSE and Frontal Assessment Battery score were 23.74 and 10.63 respectively and both were lower than the normal baseline values.Out of the total cohort of 52 patients,15(28.8%) harbored previously reported common mutations from this part of the country. Of the 15, 12 had the same mutation of c.813C>A(p.cys271Ter).The presence of common mutationswas associated with several distinct clinical phenotypes in the mathematical models but larger sample sizes are needed to corroborate the correlation. ConclusionsWD patients in eastern India have significant genotypic and phenotypic diversity. Further studies with larger samples and screening of remaining exons are warranted.

neuroscience↗

Advanced Biophysical Model to Capture Channel Variability for EQS Capacitive HBC

Human Body Communication (HBC) has come up as a promising alternative to traditional radio frequency (RF) Wireless Body Area Network (WBAN) technologies. This is essentially due to HBC providing a broadband communication channel with enhanced signal security in the physical layer due to lower radiation from the human body as compared to its RF counterparts. An in-depth understanding of the mechanism for the channel loss variability and associated biophysical model needs to be developed before EQS-HBC can be used more frequently in WBAN consumer and medical applications. Biophysical models characterizing the human body as a communication channel didnt exist in literature for a long time. Recent developments have shown models that capture the channel response for fixed transmitter and receiver positions on the human body. These biophysical models do not capture the variability in the HBC channel for varying positions of the devices with respect to the human body. In this study, we provide a detailed analysis of the change in path loss in a capacitive-HBC channel in the electroquasistatic (EQS) domain. Causes of channel loss variability namely: inter-device coupling and effects of fringe fields due to bodys shadowing effects are investigated. FEM based simulation results are used to analyze the channel response of human body for different positions and sizes of the device which are further verified using measurement results to validate the developed biophysical model. Using the bio-physical model, we develop a closed form equation for the path loss in a capacitive HBC channel which is then analyzed as a function of the geometric properties of the device and the position with respect to the human body which will help pave the path towards future EQS-HBC WBAN design.

bioengineering↗

Network Modeling and Inference of Peroxisome Proliferator-Activated Receptor Pathway in High fat diet-linked Obesity

Systems biology aims to understand how holistic systems theory can be used to explain the observable living system characteristics, and mathematical modeling tools have been successful in understanding the intricate relationships underlying cellular functions. Lately, researchers have been interested in understanding molecular mechanisms underlying obesity, which is a major health concern worldwide and has been linked to several diseases. Various mechanisms such as peroxisome proliferator-activated receptors (PPARs) are known to modulate obesity-induced inflammation and its consequences. In this study, we have modeled the PPAR pathway using a Bayesian model and inferred the sub-pathways that are potentially responsible for the activation of the output processes that are associated with high fat diet (HFD)-induced obesity. We examined a previously published dataset from a study that compared gene expression profiles of 40 mice maintained on HFD against 40 mice fed with chow diet (CD). Our simulations have highlighted that GPCR and FATCD36 sub-pathways were aberrantly active in HFD mice and are therefore favorable targets for anti-obesity strategies. We further cross-validated our observations with experimental results from the literature. We believe that mathematical models such as those presented in the present study can help in inferring other pathways and deducing significant biological relationships.

bioinformatics↗

Targeting Oncogenic Mutations in Colorectal Cancer using Cryptotanshinone

Colorectal cancer (CRC) is one of the most prevalent types of cancer in the world and ranks second in cancer deaths in the US. Despite the recent improvements in screening and treatment, the number of deaths associated with CRC is still very significant. The complexities involved in CRC therapy stem from multiple oncogenic mutations and crosstalk between abnormal pathways. This calls for using advanced molecular genetics to understand the underlying pathway interactions responsible for this cancer. In this paper, we construct the CRC pathway from the literature and using an existing public dataset on healthy vs tumor colon cells, we identify the genes/pathways that are mutated and are possibly responsible for the disease progression. We then introduce drugs in the CRC pathway, and using a boolean modeling technique, we deduce the drug combinations that produce maximum cell death. Our theoretical simulations demonstrate the effectiveness of Cryptotanshinone, a traditional Chinese herb derivative, achieved by targeting critical oncogenic mutations and enhancing cell death. Finally, we validate our theoretical results using wet lab experiments on HT29 and HCT116 human colorectal carcinoma cell lines.

systems biology↗

Patterns of roost site use by Asian hornbills and implications for seed dispersal

Animals spend a significant amount of time roosting. Therefore, understanding roosting patterns and the processes that influence roosting behaviour and roost site choice is essential. Hornbills exhibit interesting roosting patterns with some species roosting communally in large flocks. They are important seed dispersers and patterns of roost site use can have a significant influence on seed dispersal distributions and thereby on plant recruitment. We documented roost site use by four Great Hornbills (Buceros bicornis) and one Wreathed Hornbill (Rhyticeros undulatus) at a site in north-east India using GPS telemetry. We examined the influence of riverine habitats, nests and foraging range on roost selection. We determined the proportion of seeds that hornbills disperse at roosts and the dispersal distances of seeds dispersed at roosts from the source trees. Through telemetry, we found that roosts of Great Hornbills were generally in forested habitats. Our telemetry data showed that Wreathed Hornbill roosts were close to the river. These results were corroborated by observational data from roost sites where we had regular detections of relatively large flocks of Wreathed Hornbills and occasionally Great Hornbills. The roost sites were not close to the nest sites and were generally within the 95% kernel density diurnal activity ranges. Hornbills dispersed a small proportion of seeds at roost sites. Seeds dispersed at roost sites had almost twice the dispersal distances compared to those dispersed at non-roost sites. This study highlights variation in roost site pattern across individual hornbills and its implications for seed dispersal.

ecology↗

Phosphoproteomic Identification of Vasopressin-Regulated Protein Kinases in Collecting Duct Cells

Background and PurposeThe peptide hormone vasopressin regulates water transport in the renal collecting duct largely via the V2 receptor, which triggers a cAMP-mediated activation of a protein kinase A (PKA)-dependent signaling network. The protein kinases downstream from PKA have not been fully identified or mapped to regulated phosphoproteins. Experimental ApproachWe carried out systems-level analysis of large-scale phosphoproteomic data quantifying vasopressin-induced changes in phosphorylation in aquaporin-2-expressing cultured collecting duct cells (mpkCCD). Quantification was done using stable isotope labeling (SILAC method). Key Results9640 phosphopeptides were quantified. Stringent statistical analysis identified significant changes in response to vasopressin in 429 of these phosphopeptides. The corresponding phosphoproteins were mapped to known vasopressin-regulated cellular processes. The vasopressin-regulated sites were classified according to the sequences surrounding the phosphorylated amino acids giving 11 groups distinguished predominantly by the amino acids at positions +1, -3, -2 and -5 relative to the phosphorylated amino acid. Among the vasopressin-regulated phosphoproteins were 25 distinct protein kinases. Among these, six of them plus PKA appeared to account for phosphorylation of more than 80% of the 313 vasopressin-regulated phosphorylation sites. The six downstream kinases were salt-inducible kinase 2 (Sik2), cyclin-dependent kinase 18 (PCTAIRE-3, Cdk18), calmodulin-dependent kinase kinase 2 (Camkk2), protein kinase D2 (Prkd2), mitogen-activated kinase 3 (ERK1; Mapk3), and myosin light chain kinase (Mylk). Conclusion and ImplicationsIn V2 receptor-mediated signaling, PKA is at the head of a complex network that includes at least 6 downstream vasopressin-regulated protein kinases that are prime targets for future study. The extensive phosphoproteomic data generated in this study is provided as a web-based data resource for future studies of G-protein coupled receptors.

systems biology↗

Comprehensive Live-cell Imaging Analysis of Cryptotanshinone and Synergistic Drug-Screening Effects in Various Human and Canine Cancer Cell Lines

ABSTRACTBackground Several studies have highlighted both the extreme anticancer effects of Cryptotanshinone (CT), a Stat3 crippling component from Salvia miltiorrhiza, as well as other STAT3 inhibitors to fight cancer.Methods Data presented in this experiment incorporates 2 years of in vitro studies applying a comprehensive live-cell drug-screening analysis of human and canine cancer cells exposed to CT at 20 μM concentration, as well as to other drug combinations. As previously observed in other studies, dogs are natural cancer models, given to their similarity in cancer genetics, epidemiology and disease progression compared to humans.Results Results obtained from several types of human and canine cancer cells exposed to CT and varied drug combinations, verified CT efficacy at combating cancer by achieving an extremely high percentage of apoptosis within 24 hours of drug exposure.Conclusions CT anticancer efficacy in various human and canine cancer cell lines denotes its ability to interact across different biological processes and cancer regulatory cell networks, driving inhibition of cancer cell survival.View Full Text

cancer biology↗

Control of filament length by a depolymerizing gradient

Cells assemble microns-long filamentous structures from protein monomers that are nanometers in size. These structures are often highly dynamic, yet in order for them to function properly, cells maintain precise filament lengths. In this paper, we investigate length dependent depolymerization as a mechanism of length control. This mechanism has been recently proposed for flagellar length control in the single cell organisms Chlamydomonas and Giardia. Length dependent depolymerization can arise from a concentration gradient of a depolymerizing protein, such as kinesin-13 in Giardia, along the length of the flagellum. Two possible scenarios are considered, that of a linear and an exponential gradient of depolymerizing proteins. We compute analytically the probability distributions of filament lengths for both scenarios and show how these distributions are controlled by key biochemical parameters through a dimensionless number that we identify. In Chlamydomonas cells it has been well documented that the assembly dynamics of its two flagella are coupled via a shared pool of molecular components, and so we investigate the effect of a limiting monomer pool on the length distributions. Finally, we compare our calculations to experiments. While the computed mean lengths are consistent with observations, the noise is two orders of magnitude smaller than the observed length fluctuations.

biophysics↗

Persistent loss of biologically-rich tropical forests in the Indian Eastern Himalaya

Deforestation is a major cause of biodiversity loss in Asia. Using fine-resolution satellite imagery we assessed the change in forest cover of a state-managed Reserved Forest located in Indias Eastern Himalaya biodiversity hot-spot. Thirty-two square kilometers of forest cover was lost from 2013 and 2017 with a 5% decline in total forest area over four years. Hornbills are a key functionally important species found in the area. We therefore assessed the habitat around 29 hornbill nest trees in this Reserved Forest and estimated that there was a loss of 35% of forest cover from 2011 to 2019. We identify illegal logging (despite a ban by the Supreme Court of India) as the main driver that is depleting forest cover within this important area. Our results highlight the ongoing threats to biologically-rich forests and the need for urgent measures to halt this loss. We suggest that this study has practical implications for the governance of non-PA state-managed forests in Arunachal Pradesh. The ongoing deforestation appears to be due to organized crime, institutional inadequacy from a combination of limited resources, bureaucratic apathy, and/or ambiguity in use and ownership of forest land compared to other community forests which appear to have robust governance systems.

ecology↗

multiSLIDE: a query-driven heatmap visualization tool for multi-omics data

Emerging multi-omics experiments pose new challenges for exploration of quantitative data sets. We present multiSLIDE, a web-based interactive tool for simultaneous heatmap visualization of interconnected molecular features in multi-omics data sets. multiSLIDE operates by keyword search for visualizing biologically connected molecular features, such as genes in pathways and Gene Ontologies, offering convenient functionalities to rearrange, filter, and cluster data sets on a web browser in a real time basis. Various built-in querying mechanisms make it adaptable to diverse omics types, and visualizations are fully customizable. We demonstrate the versatility of the tool through three example studies, each of which showcases its applicability to a wide range of multi-omics data sets, ability to visualize the links between molecules at different granularities of measurement units, and the interface to incorporate inter-molecular relationship from external data sources into the visualization. Online and standalone versions of multiSLIDE are available at https://github.com/soumitag/multiSLIDE.

bioinformatics↗

Optimized Interferential Stimulation of Human Brains

ObjectiveInterferential stimulation (IFS) has generated considerable interest recently because of its potential to achieve focal electric fields in deep brain areas with transcranial currents. Conventionally, IFS applies sinusoidal currents through two electrode pairs with close-by frequencies. Here we propose to use an array of electrodes instead of just two electrode pairs; and to use algorithmic optimization to identify the currents required at each electrode to target a desired location in the brain. ApproachWe formulate rigorous optimization criteria for IFS to achieve either maximal modulation-depth or maximally focal stimulation. We find the solution for optimal modulation-depth analytically and maximize for focal stimulation numerically. Main resultsMaximal modulation is achieved when IFS equals conventional high-definition multi-electrode transcranial electrical stimulation (HD-TES) with a modulated current source. This optimal solution can be found directly from a current-flow model, i.e. the "lead field" without the need for algorithmic optimization. Once currents are optimized numerically to achieve optimal focal stimulation, we find that IFS can indeed be more focal than conventional HD-TES, both at the cortical surface and deep in the brain. Generally, however, stimulation intensity of IFS is weak and the locus of highest intensity does not match the locus of highest modulation. SignificanceThis proof-of-principle study shows the potential of IFS over HD-TES for focal non-invasive deep brain stimulation. Future work will be needed to improve on intensity of stimulation and convergence of the optimization procedure.

biophysics↗

Variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibility

Neutrophils play fundamental roles in innate inflammatory response, shape adaptive immunity1, and have been identified as a potentially causal cell type underpinning genetic associations with immune system traits and diseases2,3 The majority of these variants are non-coding and the underlying mechanisms are not fully understood. Here, we profiled the binding of one of the principal myeloid transcriptional regulators, PU.1, in primary neutrophils across nearly a hundred volunteers, and elucidate the coordinated genetic effects of PU.1 binding variation, local chromatin state, promoter-enhancer interactions and gene expression. We show that PU.1 binding and the associated chain of molecular changes underlie genetically-driven differences in cell count and autoimmune disease susceptibility. Our results advance interpretation for genetic loci associated with neutrophil biology and immune disease.

genetics↗

Factors affecting the survival of tree seedlings following shifting cultivation in the Eastern Himalaya

O_LIThe seedling stage is considered an important bottleneck determining forest community composition during succession. Seedling growth and survival are known to be affected by factors such as light availability, herbivory and competition with existing vegetation. A shifting cultivation landscape with a cycle of clearing and regeneration provides an experimental setup to understand secondary succession.\nC_LIO_LIWe introduced tree seedlings of three species with differing life history strategies in an uncut forest and in sites formed 2, 6, 12, 25, 50 and 100 years following shifting cultivation in a subtropical landscape in the Eastern Himalaya. Seedlings of a pioneer species Saurauia nepalensis, a mid-successional species Terminalia myriocarpa and a mature forest species Castanopsis indica were introduced in plots with a control and three treatments: shading (light manipulated), clearing of vegetation (reduced competition), and exclosures (mammal herbivory excluded) and monitored for 18, 22 and 23 months, respectively.\nC_LIO_LISaurauia survived relatively well in all sites, Terminalia seedlings survived relatively well in the 12 and 25 year sites, and Castanopsis seedlings survived well in the 100 year site and the uncut forest. In the early successional site, survival of Saurauia was higher within exclosures indicating negative effects of herbivory. In the same site, clearing vegetation improved the survival of Terminalia, implying competition with existing vegetation. Castanopsis had the highest survival in uncut forest and survival was almost nil in the early successional site.\nC_LIO_LISynthesis: Seedling survival in a successional landscape depended on species-as well as site-specific factors. The existing vegetation in an early successional site had a negative effect on the survival of the mid-successional species, while herbivory had a negative effect on the pioneer species. Survival of the mature forest species in the early successional site was negligible but was high in old successional and uncut forest sites, indicating that mature forest species can colonize sites and survive only after certain physical and biotic aspects of the environment have been met. Our experiments were useful to examine factors that affect survival of tree species with differing life history strategies in a shifting cultivation landscape.\nC_LI

ecology↗

Epigenomic and functional dynamics of human bone marrow myeloid differentiation to mature blood neutrophils

Neutrophils are short-lived blood cells that play a critical role in host defense against infections. To better comprehend neutrophil functions and their regulation, we provide a complete epigenetic and functional overview of their differentiation stages from bone marrow-residing progenitors to mature circulating cells. Integration of epigenetic and transcriptome dynamics reveals an enforced regulation of differentiation, through cellular functions such as: release of proteases, respiratory burst, cell cycle regulation and apoptosis. We observe an early establishment of the cytotoxic capability, whilst the signaling components that activate antimicrobial mechanisms are transcribed at later stages, outside the bone marrow, thus preventing toxic effects in the bone marrow niche. Altogether, these data reveal how the developmental dynamics of the epigenetic landscape orchestrate the daily production of large number of neutrophils required for innate host defense and provide a comprehensive overview of the epigenomes of differentiating human neutrophils.\n\nKey pointsO_LIDynamic acetylation enforces human neutrophil progenitor differentiation.\nC_LI\n\nO_LINeutrophils cytotoxic capability is established early at the (pro)myelocyte stage.\nC_LI\n\nO_LICoordinated signaling component expression prevents unwanted toxic effects to the bone marrow niche.\nC_LI

immunology↗

Bayesian estimation of MSM population size in Côte d’Ivoire

Cote dIvoire has one of the largest HIV epidemics in West Africa with around half million people living with HIV. Key populations like gay men and other men who have sex with men (MSM) are often disproportionately burdened with HIV due to specific acquisition and transmission risks. Quantifying the MSM population sizes at subnational level is critical to improving the HIV prevention interventions. While survey-based direct estimates of MSM numbers are available at a few urban centers in C{circumflex}ote dIvoire, no data on MSM population size exists at other areas without any community infrastructure to facilitate sufficient access to the MSM community. We use this limited data in a Bayesian regression setup to produce first empirically calculated estimates of the numbers of MSM in all areas of C{circumflex}ote dIvoire prioritized in the HIV response. Our hierarchical model imputes missing covariates using geospatial information and allows for proper uncertainty quantification leading to meaningful confidence bounds for the predicted MSM population size estimates. The intended impact of this process is to increase uptake and use of high quality, comprehensive epidemiologic and interventional data in program planning. These estimates will help design future surveys and support the planning of the scale and content of HIV prevention and treatment programs for MSM in C{circumflex}ote dIvoire.

epidemiology↗

Realistic vOlumetric-Approach to Simulate Transcranial Electric Stimulation -- ROAST -- a fully automated open-source pipeline

Research in the area of transcranial electrical stimulation (TES) often relies on computational models of current flow in the brain. Models are built based on the magnetic resonance images (MRI) of the human head to capture detailed individual anatomy. To simulate current flow on an individual, the subjects MRI is segmented, virtual electrodes are placed on this anatomical model, the volume is tessellated into a mesh, and a finite element model (FEM) is solved numerically to estimate the current flow. Various software tools are available for each step, as well as processing pipelines that connect these tools for automated or semi-automated processing. The goal of the present tool - ROAST - is to provide an end-to-end pipeline that can automatically process individual heads with realistic volumetric anatomy leveraging open-source software and custom scripts to improve segmentation and execute electrode placement. The electric field estimated with the open-source tools used by ROAST differ little from the results obtained with commercial meshing and FEM solving software. We also do not find large differences between the various automated segmentation methods used by ROAST and SimNIBS, a well-established open-source modeling pipeline. However, we do find large differences when volumetric segmentation are converted into surfaces that are used in SimNIBS to generate volumetric meshes. Evaluation on intracranial recordings from human subjects suggests that ROAST outperforms newer versions of SimNIBS in predicting field distribution and magnitudes, but that an older version of SimNIBS performs similarly. We hope that the detailed comparisons presented here of various choices in this modeling pipeline can provide guidance for future tool development. We release ROAST as an open-source, easy-to-install and fully-automated pipeline for individualized TES modeling at https://www.parralab.org/roast/.

biophysics↗

Fibroblast-derived HGF drives acinar lung cancer cell polarization through integrin-dependent RhoA-ROCK1 inhibition.

The formation of lumens in epithelial tissues requires apical-basal polarization of cells, and the co-ordination of this individual polarity collectively around a contiguous lumen. Signals from the Extracellular Matrix (ECM) instruct epithelia as to the orientation of where basal, and thus consequently apical, surfaces should be formed. We report that this pathway is normally absent in Calu-3 human lung adenocarcinoma cells in 3-Dimensional culture, but that paracrine signals from MRC5 lung fibroblasts can induce correct orientation of polarity and acinar morphogenesis. We identify HGF, acting through the c-Met receptor, as the key polarity-inducing morphogen, which acts to activate {beta}1-integrin-dependent adhesion. HGF and ECM-derived integrin signals co-operate via a c-Src-dependent inhibition of the RhoA-ROCK1 signalling pathway via p190A RhoGAP. This occurred via controlling localization of these signalling pathways to the ECM-abutting surface of cells in 3-Dimensional culture. Thus, stromal derived signals can influence morphogenesis in epithelial cells by controlling activation and localization of cell polarity pathways.

cell biology↗