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Dasgupta, A.

Publications and source records attributed to Dasgupta, A..

36 records · Page 2Linked to original sources

Semaphorin7A patterns neural circuitry in the lateral line of the zebrafish

In a developing nervous system, axonal arbors often undergo complex rearrangements before neural circuits attain their final innervation topology. In the lateral line sensory system of the zebrafish, developing sensory axons reorganize their terminal arborization patterns to establish precise neural microcircuits around the mechanosensory hair cells. However, a quantitative understanding of the changes in the sensory arbor morphology and the regulators behind the microcircuit assembly remain enigmatic. Here, we report that Semaphorin7A (Sema7A) acts as an important mediator of these processes. Utilizing a semi-automated three-dimensional neurite tracing methodology and computational techniques, we have identified and quantitatively analyzed distinct topological features that shape the network in wild-type and Sema7A loss-of-function mutants. In contrast to those of wild-type animals, the sensory axons in Sema7A mutants display aberrant arborizations with disorganized network topology and diminished contacts to hair cells. Moreover, ectopic expression of a secreted form of Sema7A by non-hair cells induces chemotropic guidance of sensory axons. Our findings propose that Sema7A likely functions both as a juxtracrine and as a secreted cue to pattern neural circuitry during sensory organ development.

neuroscience↗

RNASeq as a tool to understand dysregulation of potential biomarkers in HNSC

With its rising fatality rates, oral cancer is one of the most concerning public health issues. To reduce disease-related mortality and morbidity, advancements in screening and detection are critical. Finding specific biomarkers is one of the most successful approaches for screening, diagnosing, and staging this dreadful disease. In this study differentially expressed genes associated with oral cancer were analyzed using RNASeq to find the potential biomarkers. Functional enrichment of upregulated genes found that 253 genes were present in the plasma membrane. Three clusters were formed using KMean Clustering from the PPI networks, and highly connected hub genes were identified from each cluster. Eventually, expression and survival analyses of hub genes were performed using The Cancer Genome Atlas (TCGA) database targeting Head and Neck Squamous Cell Carcinoma. Among those genes, expression levels of eight genes SLC2A1, ITGA6, LAMC2, COL1A2, COL1A1, TNC, THY1, and CD276 have significantly changed in Head and Neck Squamous cell carcinoma. There are reports that suggest these genes were significantly dysregulated in Oral Squamous cell carcinoma and can be explored further as potential biomarkers for margin clearance.

cancer biology↗

In vitro and in vivo activity of Gepotidacin against drug-resistant mycobacterial infections

Mycobacterial pathogens including Non-tuberculous mycobacteria (NTM) and M. tuberculosis (Mtb), are pathogens of significant worldwide interest owing to inherent drug resistance to a wide variety of FDA-approved drugs as well as causing a broad range of serious infections. Identifying new antibiotics active against mycobacterial pathogens is an urgent unmet need, especially those antibiotics that can bypass existing resistance mechanisms. In this study, we demonstrate that Gepotidacin, a first-in-class triazaacenapthylene topoisomerase inhibitor, shows potent activity against Mtb and M. fortuitum as well as against other NTMs species, including fluoroquinolone-resistant M. abscessus. Furthermore, Gepotidacin exhibits concentration-dependent bactericidal activity against various mycobacterial pathogens, synergizes with several drugs utilized for their treatment, and reduces bacterial load in macrophages in the intracellular killing assay comparable to amikacin. Additionally, M. fortuitum ATCC 6841 was unable to generate resistance to Gepotidacin in vitro. When tested in a murine neutropenic M. fortuitum infection model, Gepotidacin caused a significant reduction in bacterial load in various organs at 10 fold lower concentration than amikacin. Taken together, Gepotidacin possesses a potentially new mechanism of action that enables it to escape existing resistance mechanisms. Thus, it can be projected as a potent novel lead for the treatment of mycobacterial infections, particularly for NTM, where present therapeutic interventions are very limited.

microbiology↗

Analysis of conditional colocalization relationships and hierarchies from three-color microscopy images

Colocalization analysis of multicolor microscopy images is a cornerstone approach in cell biology. It provides information on the localization of molecules within various subcellular compartments and allows the interrogation of molecular interactions in their cellular context. However, almost all colocalization analyses are designed for two-color images. This limits their applicability and the type of information that they reveal, leading to underutilization of multicolor microscopy images. Here we describe an approach, termed "conditional colocalization analysis," for analyzing the colocalization relationships between three molecular entities in three-color microscopy images. Going beyond the question of whether colocalization is present or not, it addresses the question of whether the colocalization between two entities is influenced, positively or negatively, by their colocalization with a third entity. We showcase two applications of conditional colocalization analysis, one addressing the question of compartmentalization of molecular interactions, and one investigating the hierarchy of molecular interactions in a multimolecular complex. The software for conditional colocalization analysis is available at https://github.com/kjaqaman/conditionalColoc.

cell biology↗

STED super-resolution imaging of membrane packing and dynamics by exchangeable polarity-sensitive dyes

Understanding the plasma membrane nano-scale organisation and dynamics in living cells requires microscopy techniques with high spatial and temporal resolution, permitting for long acquisition times, and that allow for the quantification of membrane biophysical properties such as lipid ordering. Among the most popular super-resolution techniques, stimulated emission depletion (STED) microscopy offers one of the highest temporal resolutions, ultimately defined by the scanning speed. However, monitoring live processes using STED microscopy is significantly limited by photobleaching, which recently has been circumvented by exchangeable membrane dyes that only temporarily reside in the membrane. Here, we show that NR4A, a polarity-sensitive exchangeable plasma membrane probe based on Nile Red, permits the super-resolved quantification of membrane biophysical parameters in real time with high temporal and spatial resolution as well as long acquisition times. The potential of this polarity-sensitive exchangeable dye is showcased by live-cell real-time 3D-STED recordings of bleb formation and lipid exchange during membrane fusion, as well as by STED-fluorescence correlation spectroscopy (STED-FCS) experiments for the simultaneous quantification of membrane dynamics and lipid packing, which correlate in model and live-cell membranes.

biophysics↗

Semiconducting bacterial biofilm based on graphene-MoS2 template and component dependent gating behavior

In this paper, we report for the first time, the synthesis of a semiconducting biofilm. Photosynthetic bacterial biofilm has been used to weave together MoS2 nanosheets into an adherent film grown on interdigitated electrodes. Liquid-phase exfoliation of bulk MoS2 powder was used to obtain MoS2 nanosheets. A synchronous-fluorescence scan revealed the presence of two emission maxima at 682nm and 715nm for the MoS2 suspension. Such maxima with bandgap energy 1.82 and 1.73 eV corresponded to the single and double layer of MoS2. The presence of such single and multi-layered structures was confirmed by Raman spectroscopy, FTIR studies, and electron microscopy. The current-voltage (I-V) studies of such a bio-nano hybrid revealed the emergence of the gated nature of the current flow. This Schottky diode like behavior, reported earlier for Graphene-biofilm junctions, is also observed in this case. Gating voltage depended on the composition of the biofilm. The semiconductor biofilms, when studied using electrochemical impedance spectroscopy, revealed characteristic Nyquist and Bode plots, suggesting special circuit-equivalence for each film. While Mos2 was marked with stability with respect to variations in RMS voltage and bias voltage, the graphene biofilm was unique by the absence of any Warburg element.

synthetic biology↗

Rates of gene conversions between Escherichia coli ribosomal operons

Due to their universal presence and high sequence conservation, rRNA sequences are used widely in phylogenetics for inferring evolutionary relationships between microbes and in metagenomics for analyzing the composition of microbial communities. Most microbial genomes encode multiple copies of ribosomal RNA (rRNA) genes to supply cells with sufficient capacity for protein synthesis. These copies typically undergo concerted evolution that keeps their sequences identical, or nearly so, due to gene conversion, a type of intragenomic recombination that changes one copy of a homologous sequence to exactly match another. Widely varying rates of rRNA gene conversion have previously been estimated by comparative genomics methods and using genetic reporter assays. To more directly measure rates of rRNA intragenomic recombination, we sequenced the seven Escherichia coli rRNA operons in 15 lineages of cells that were evolved for ~13,750 generations with frequent single-cell bottlenecks that reduce the effects of selection. We identified 34 gene conversion events and estimate an overall rate of intragenomic recombination events between rRNA copies of 3.2 x 10-4 per generation or 5.3 x 10-5 per potential donor sequence. This rate varied only slightly from random expectations between different portions of the rRNA genes and between rRNA operons located at different locations in the genome. This accurate estimate of the rate of rRNA gene conversions fills a gap in our quantitative understanding of how ribosomal sequences and other multicopy elements diversify and homogenize during microbial genome evolution.

genetics↗

Direct Supercritical Angle Localization Microscopy for Nanometer 3D Superresolution

3D single molecule localization microscopy (SMLM) is an emerging superresolution method for structural cell biology, as it allows probing precise positions of proteins in cellular structures. Supercritical angle fluorescence strongly depends on the z-position of the fluorophore and can be used for z localization in a method called supercritical angle localization microscopy (SALM). Here, we realize the full potential of SALM by directly splitting supercritical and undercritical emission, using an ultra-high NA objective, and applying new fitting routines to extract precise intensities of single emitters, resulting in a four-fold improved z-resolution compared to the state of the art. We demonstrate nanometer isotropic localization precision on DNA origami structures, and on clathrin coated vesicles and microtubules in cells, illustrating the potential of SALM for cell biology.

biophysics↗

Endothelial Cells stimulate proliferation of CD140a sorted human Glial Progenitor Cells and their specification towards astrocytic lineage.

Homeostasis in stem cell niche is established by fine-tuning between interacting signaling pathways of all resident cell types that constitute the niche. In this context, the exact contribution of human endothelial cells in biology of PDGFR positive human glial progenitor cells (hGPCs) in niche environment is not well understood. Towards the same, insert co-culture system with human umbilical vein endothelial cells (HUVECs) has been adopted. In co-culture with HUVECs, under proliferative condition, hGPCs show increased proliferation and sphere formation, while under differentiating condition hGPCs show increased differentiation to astrocytes with concomitant decrease in differentiation to oligodendrocytes with respect to no co-culture controls. Transcript assay for selected humoral factors reveals bone morphogenic proteins (BMPs), endothelin1, growth arrest specific 6 and interleukin 6 to be in higher abundance in HUVECS than hGPCs, of which BMP4 transcripts were most abundant, indicating possibilities of its being the key mediator of endothelial mediated effects. Concurrently, noggin effectively attenuates HUVEC mediated astrocytic differentiation of PDGFR sorted fetal hGPCs The results have implication towards safety of transplantation therapies with PDGFR sorted fetal hGPCs. It is postulated that proliferation and differentiation response as seen in this co-culture system could have defining implications towards the genesis of glioma.

neuroscience↗

G-domain prediction across the diversity of G protein families

Guanine nucleotide binding proteins are characterized by a structurally and mechanistically conserved GTP-binding domain, indispensable for binding GTP. The G domain comprises of five adjacent consensus motifs called G boxes, which are separated by amino acid spacers of different lengths. Several G proteins, discovered over time, are characterized by diverse function and sequence. This sequence diversity is also observed in the G box motifs (specifically the G5 box) as well as the inter-G box spacer length. The Spacers and Mismatch Algorithm (SMA) introduced in this study, can predict G-domains in a given G protein sequence, based on user-specified constraints for approximate G-box patterns and inter-box gaps in each G protein family. The SMA parameters can be customized as more G proteins are discovered and characterized structurally. Family-specific G box motifs including the less characterized G5 motif as well as G domain boundaries were predicted with higher precision. Overall, our analysis suggests the possible classification of G protein families based on family-specific G box sequences and lengths of inter-G box spacers. Significance StatementIt is difficult to define the boundaries of a G domain as well as predict G boxes and important GTP-binding residues of a G protein, if structural information is not available. Sequence alignment and phylogenetic methods are often unsuccessful, given the sequence diversity across G protein families. SMA is a unique method which uses approximate pattern matching as well as inter-motif separation constraints to predict the locations of G-boxes. It is able to predict all G boxes including the less characterized G5 motif which marks the carboxy-terminal boundary of a G domain. Thus, SMA can be used to predict G domain boundaries within a large multi-domain protein as long as the user-specified constraints are satisfied. ClassificationBiological Sciences/Biophysics and Computational Biology

bioinformatics↗

A cost-efficient open source laser engine for microscopy

Scientific-grade lasers are costly components of modern microscopes. For high-power applications, such as single-molecule localization microscopy, their price can become prohibitive. Here, we present an open-source high-power laser engine that can be built for a fraction of the cost. It uses affordable, yet powerful laser diodes at wavelengths of 405 nm, 488 nm and 640 nm and optionally a 561 nm diode-pumped solid-state laser. The light is delivered to the microscope via an agitated multimode fiber in order to suppress speckles. We provide the part lists, CAD files and detailed descriptions, allowing any research group to build their own laser engine.

biophysics↗

Single-molecule study of the dynamic organization of Vascular Endothelial Growth Factor Receptor 2 on the endothelial cell surface

The nanoscale organization of cell surface receptors plays an important role in signaling. We determined this organization and its relation to receptor activation for VEGF Receptor-2 (VEGFR-2), a critical receptor tyrosine kinase in endothelial cells (ECs), by combining live-cell single-molecule imaging of endogenous VEGFR-2 with rigorous computational analysis. We found that surface VEGFR-2 can be mobile or immobile/confined, and monomeric or non-monomeric, with a complex interplay between the two. The mobility and interaction heterogeneity of VEGFR-2 in the basal state led to heterogeneity in the sequence of steps leading to VEGFR-2 activation by VEGF. Specifically, we found that VEGF can bind to both monomeric and non-monomeric VEGFR-2, and, when binding to monomeric VEGFR-2, promotes dimer formation but only for immobile/confined receptors. Overall, our study highlights the dynamic and heterogeneous nature of cell surface receptor organization and its complex relationships with receptor activation and signaling.

biophysics↗

Symmetry breaking during morphogenesis of a mechanosensory organ

Actively regulated symmetry breaking, which is ubiquitous in biological cells, underlies phenomena such as directed cellular movement and morphological polarization. Here we investigate how an organ-level polarity pattern emerges through symmetry breaking at the cellular level during the formation of a mechanosensory organ. Combining theory, genetic perturbations, and in vivo imaging assisted by deep learning, we study the development and regeneration of the fluid-motion sensors in the zebrafishs lateral line. We find that two interacting symmetry-breaking events -- one mediated by biochemical signaling and the other by cellular mechanics -- give rise to a novel form of collective cell migration, which produces a mirror-symmetric polarity pattern in the receptor organ.

biophysics↗

Catestatin improves insulin sensitivity in diet-induced obese mice: in vivo and in silico validation

Obesity is characterized by a state of chronic, unresolved inflammation in insulin-targeted tissues. Obesity-induced inflammation accumulates proinflammatory macrophages in adipose tissue and liver. Proinflammatory cytokines released from tissue macrophages inhibits insulin sensitivity. Chromogranin A (CgA) peptide catestatin (CST: hCgA352-372) improves obesity-induced hepatic insulin resistance by reducing inflammation and inhibiting proinflammatory macrophage infiltration. Obesity leads to inflammation-induced endoplasmic reticulum (ER) stress and insulin resistance. We reasoned that the anti-inflammatory effects of CST would alleviate ER stress. CST decreased obesity-induced ER dilation in hepatocytes and macrophages. CST reduced phosphorylation of UPR signaling molecules and increased phosphorylation of insulin signaling molecules. We developed an in silico state space model mimicking dynamics of integrated ER stress and insulin pathways. Proportional-Integral-Derivative (PID) controllers helped in checking whether the reduction of phosphorylated PERK resulting in attenuation of ER stress, resembling CST effect, could enhance insulin sensitivity. The simulation results showed CST not only decreased ER stress but also enhanced insulin sensitivity. Simulation results also revealed that enhancement of AKT phosphorylation overcame effects of high ER stress to achieve insulin sensitivity.

systems biology↗

Notch-Mediated Polarity Decisions in Mechanosensory Hair Cells

The development of mechanosensory epithelia, such as those of the auditory and vestibular systems, results in the precise orientation of mechanosensory hair cells and consequently directional sensitivity. After division of a precursor cell in the zebrafishs lateral line, the daughter hair cells differentiate with opposite mechanical sensitivity. Through a combination of theoretical and experimental approaches, we show that Notch1a-mediated lateral inhibition produces a bistable switch that reliably gives rise to cell pairs of opposite polarity. Using our mathematical model of the process, we predict the outcome of several genetic and chemical alterations to the system, which we then confirm experimentally. We show that Notch1a downregulates the expression of Emx2, a transcription factor known to be involved in polarity specification, and acts in parallel with the planar-cell-polarity system to determine the orientation of hair bundles. By analyzing the effect of simultaneous genetic perturbations to Notch1a and Emx2 we infer that the generegulatory network determining cell polarity includes undiscovered polarity effectors.

developmental biology↗

Asymmetric cell volume changes regulate epithelial morphogenesis in zebrafish Kupffers vesicle

How epithelial cell behaviors are coordinately regulated to sculpt tissue architecture is a fundamental question in biology. Kupffer's vesicle (KV), a transient organ with a fluid - filled lumen, provides a simple system to investigate the interplay between intrinsic cellular mechanisms and external forces during epithelial morphogenesis. Using 3 - dimensional (3D) analyses of single cells we identify asymmetric cell volume changes along the anteroposterior axis of KV that coincide with asymmetric cell shape changes. Blocking ion flux prevents these cell volume changes and cell shape changes. Vertex simulations suggest cell shape changes do not depend on lumen expansion. Consistent with this prediction, asymmetric changes in KV cell volume and shape occur normally when KV lumen growth fails due to leaky cell adhesions. These results indicate ion flux mediates asymmetric cell volume changes that contribute to asymmetric cell shape changes in KV, and that these changes in epithelial morphology are separable from lumen - generated forces.

cell biology↗

Cooling Induced by Uphill Energy Transport in Plant Photosystems

The uphill energy transfer in photosystems implies input energy at higher wavelength leading to energy output at lower wavelength. Briefly, energy is uphill transported from photosystem I (PSI) to photosystem II (PSII), the latter having a lower wavelength emission. This uphill energy transport involves absorption of thermal energy from the surroundings. While such cooling effects have been reported in laser systems we report for the first time a white light driven cooling in thylakoid suspension. The cooling of the surrounding medium by appropriate illumination was illustrated using thermal measurements. Again cooling is inhibited by agents like 3-(3,4-Dichlorophenyl)-1,1-dimethylurea,that block the linear electron flow between the photocenters, implying a dependence of the cooling on interplay between such centers. Furthermore, it is possible to modulate the cooling pattern by addition of external agents like nanopaticles, some favoring further cooling (e.g., Ag nanoparticle) and some like Au or chlorophyll nanoparticles, showing insignificant or even reverse trends. Interestingly, the cooling is invariably associated with the 77K spectra of the thylakoid suspension. With reference to the dark control, an agent causing cooling always increases PSII to PSI ratio and vice versa i.e.,the uphill energy transport. Importantly, the cooling effect, apart from its import role in plant physiology can be exploited artificially for energy saving in post-harvest or food preservation.

bioengineering↗

The E. coli molecular phenotype under different growth conditions

Modern systems biology requires extensive, carefully curated measurements of cellular components in response to different environmental conditions. While high-throughput methods have made transcriptomics and proteomics datasets widely accessible and relatively economical to generate, systematic measurements of both mRNA and protein abundances under a wide range of different conditions are still relatively rare. Here we present a detailed, genome-wide transcriptomics and proteomics dataset of E. coli grown under 34 different conditions. We manipulate concentrations of sodium and magnesium in the growth media, and we consider four different carbon sources glucose, gluconate, lactate, and glycerol. Moreover, samples are taken both in exponential and stationary phase, and we include two extensive time-courses, with multiple samples taken between 3 hours and 2 weeks. We find that exponential-phase samples systematically differ from stationary-phase samples, in particular at the level of mRNA. Regulatory responses to different carbon sources or salt stresses are more moderate, but we find numerous differentially expressed genes for growth on gluconate and under salt and magnesium stress. Our data set provides a rich resource for future computational modeling of E. coli gene regulation, transcription, and translation.

bioinformatics↗