Biology subjects

Ghosh, R.

Publications and source records attributed to Ghosh, R..

47 records · Page 3Linked to original sources

bioRxiv2021

Nanoceutical Fabric Prevents COVID-19 Spread through Expelled Respiratory Droplets: A Combined Computational, Spectroscopic and Anti-microbial Study

Centers for Disease Control and Prevention (CDC) warns the use of one-way valves or vents in free masks for potential threat of spreading COVID-19 through expelled respiratory droplets. Here, we have developed a nanoceutical cotton fabric duly sensitized with non-toxic zinc oxide nanomaterial for potential use as membrane filter in the one way valve for the ease of breathing without the threat of COVID-19 spreading. A detailed computational study revealed that zinc oxide nanoflowers (ZnO NF) with almost two-dimensional petals trap SARS-CoV-2 spike proteins, responsible to attach to ACE-2 receptors in human lung epithelial cells. The study also confirm significant denaturation of the spike proteins on the ZnO surface, revealing removal of virus upon efficient trapping. Following the computational study, we have synthesized ZnO NF on cotton matrix using hydrothermal assisted strategy. Electron microscopic, steady-state and picosecond resolved spectroscopic studies confirm attachment of ZnO NF to the cotton (i.e., cellulose) matrix at atomic level to develop the nanoceutical fabric. A detailed antimicrobial assay using Pseudomonas aeruginosa bacteria (model SARS-CoV-2 mimic) reveals excellent anti-microbial efficiency of the developed nanoceutical fabric. To our understanding the novel nanoceutical fabric used in one-way valve of a face mask would be the choice to assure breathing comfort along with source control of COVID-19 infection. The developed nanosensitized cloth can also be used as antibacterial/anti CoV-2 washable dress material in general. GRAPHICAL ABSTRACT O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY A novel nanoceutical cotton fabric duly sensitized with non-toxic zinc oxide nanoflower can potentially be used as membrane filter in the one way valve of face mask to assure breathing comfort along with source control of COVID-19 infection. The nanoceutical fabric denatures the SARS-CoV-2 spike protein and makes the microorganism ineffective.

microbiology↗

bioRxiv2021

A Nanoceutical Agent for Chemoprevention of Bilirubin Encephalopathy

BackgroundTargeted degradation of bilirubin in vivo may enable safer and more effective approach to manage incipient bilirubin encephalopathy consequent to severe neonatal hyperbilirubinemia (SNH). This report builds on the use of a spinel structured mixed-valence transition metal oxide (trimanganese tetroxide) nanoparticle duly functionalized with biocompatible ligand citrate (C-Mn3O4 NP) having the ability to degrade bilirubin without photo-activation. MethodThe efficiency of C-Mn3O4 NP in in vivo degradation of serum bilirubin and amelioration of severe bilirubin encephalopathy and associated neurobehavioral changes was evaluated in C57BL/6j animal model of SNH. ResultsOral single dose (0.25 mg kg-1 body weight) of the NPs efficiently reduced serum bilirubin levels (both conjugated and unconjugated) in study mice. It prevents bilirubin-induced neurotoxicity with reduction of SNH as observed by neurobehavioral and movement studies of SNH-mice. Pharmacokinetic data suggests intestinal reabsorption of the NPs and explain sustainable action. Biodistribution, pharmacokinetics, and biocompatibility of the NPs were tested during sub-chronic exposure. ConclusionThus, we report preliminary studies that explore an affordable chemoprevention mechanism to acutely prevent or minimize bilirubin neurotoxicity in newborn infants. IMPACT STATEMENTO_LIDespite several attempts, no pharmaco-therapeutics are available for the treatment of severe neonatal hyperbilirubinemia (SNH) and associated neurotoxicity. C_LIO_LIOur newly developed nanodrug, citrate functionalized Mn3O4 nanoparticles (C-Mn3O4 NPs), can efficiently ameliorate SNH and associated neurotoxicity as investigated in preclinical rodent model. C_LIO_LIChemoprevention effect of the nanodrug is found to be safe and sustainable. C_LIO_LIIf successfully translated into clinical trials, C-Mn3O4 NPs could become the first drug to treat SNH. C_LI

pharmacology and toxicology↗

bioRxiv2020

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit-- and revealed many critical ecosystem roles for viruses -- microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data ( enhancedviromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow (updated at protocols.io) can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a living document to facilitate dissemination of updates to keep pace with the rapid evolution of long read sequencing technology. Taken together, the addition of long-reads uniquely enabled the recovery of 22% of the most abundant viruses--that would have been missed in short-read only assemblies.

microbiology↗

bioRxiv2019

Parallel signaling through IRE1α and PERK regulates pancreatic neuroendocrine tumor growth and survival

Master regulators of the unfolded protein response (UPR)--IRE1 and PERK-- promote adaptation or apoptosis depending on levels of endoplasmic reticulum (ER) stress. While the UPR is activated in many cancers, its effects on tumor growth remain unclear. Derived from endocrine cells, pancreatic neuroendocrine tumors (PanNETs) universally hypersecrete one or more peptide hormones, likely sensitizing these cells to high ER protein-folding stress. For the nearly 1,500 Americans diagnosed with PanNETs annually, surgery is the only potentially curative treatment; however the five-year survival is extremely low for those who develop metastatic disease. To assess whether targeting the UPR is a viable therapeutic strategy, we analyzed human PanNET samples and found evidence of elevated ER stress and UPR activation. We then used genetic and pharmacologic approaches to modulate IRE1 and PERK in cultured cells and xenograft and spontaneous genetic (RIP-Tag2) mouse models of PanNETs. We found that UPR signaling is optimized for adaptation and that inhibiting either IRE1 or PERK leads to hyperactivation and apoptotic signaling through the reciprocal arm, thereby halting tumor growth and survival. Our results provide a strong rationale for therapeutically targeting the UPR in PanNETs and other cancers experiencing elevated ER stress.\n\nSignificanceThe unfolded protein response (UPR) is upregulated in human pancreatic neuroendocrine tumors and its genetic or pharmacological inhibition significantly reduces tumor growth in preclinical models, providing strong rationale for targeting the UPR in neoplasms with elevated ER stress.

cancer biology↗

bioRxiv2018

Small molecule inhibition of IRE1α kinase/RNase has anti-fibrotic effects in the lung

Endoplasmic reticulum stress (ER stress) has been implicated in the pathogenesis of idiopathic pulmonary fibrosis (IPF), a disease of progressive fibrosis and respiratory failure. ER stress activates a signaling pathway called the unfolded protein response (UPR) that either restores homeostasis or promotes apoptosis. The bifunctional kinase/RNase IRE1 is a UPR sensor that promotes apoptosis if ER stress remains high (i.e., a \"terminal\" UPR). Using multiple small molecule inhibitors against IRE1, we show that ER stress-induced apoptosis of murine alveolar epithelial cells can be mitigated in vitro. In vivo, we show that bleomycin exposure to murine lungs causes early ER stress to activate IRE1 and the terminal UPR prior to development of pulmonary fibrosis. Small-molecule IRE1 kinase-inhibiting RNase attenuators (KIRAs) that we developed were used to evaluate the importance of IRE1 activation in bleomycin-induced pulmonary fibrosis. One such KIRA--KIRA7--provided systemically to mice at the time of bleomycin exposure decreases terminal UPR signaling and prevents lung fibrosis. Administration of KIRA7 14 days after bleomycin exposure even promoted the reversal of established fibrosis. Finally, we show that KIRA8, a nanomolar-potent, monoselective KIRA compound derived from a completely different scaffold than KIRA7, likewise promoted reversal of established fibrosis. These results demonstrate that IRE1 may be a promising target in pulmonary fibrosis and that kinase inhibitors of IRE1 may eventually be developed into efficacious anti-fibrotic drugs.

molecular biology↗

bioRxiv2017

Failure through expanding voids in bacterial streamers

We investigate the failure of thick bacterial floc-mediated streamers in a microfluidic device with micro-pillars. We found that streamers could fail due to the growth of voids in the biomass that originate near the pillar walls. The quantification of void growth was made possible by the use of 200 nm fluorescent polystyrene beads. The beads get trapped in the extra-cellular matrix of the streamer biomass and act as tracers. Void growth time-scales could be characterized into short-time scales and long time-scales and the crack/void propagation showed several instances of fracture-arrest ultimately leading to a catastrophic failure of the entire streamer structure. This mode of fracture stands in strong contrast to necking-type instability observed before in streamers.

biophysics↗

bioRxiv2017

Allosteric Activation of p300 Autoacetylation by the Tumor Suppressor p53

The transcriptional coactivator p300 is essential for p53 transactivation, although its precise mechanism remains unclear. We report that, p53 allosterically activates the acetyltransferase activity of p300 through the enhancement of p300 autoacetylation. Cryo-electron microscopy revealed that the domain organization of p300 is substantially altered upon binding of p53, suggesting that a structural switch may underpin the activation. Acetylated p300 accumulates near the transcription start sites accompanied by a similar enrichment of activating histone marks near those sites. Disruption of p53-p300 interaction by a site-directed peptide inhibitor abolished autoacetylated p300-mediated enhanced histone acetylation, suggesting a crucial role played by the allosteric activation in p53-mediated gene regulation. Gain-of-function mutant p53, known to impart aggressive proliferative properties in tumor cells, also activate p300 autoacetylation. The same peptide abolished many of the gain-of-functions of mutant p53 as well. We conclude that allosteric activation of p300 by p53 underpins gene regulation by p53. Reversal of gain-of-function properties of mutant p53 suggests that molecules targeting the p53-p300 interface may be good candidates for anti-tumor drugs.

molecular biology↗

bioRxiv2017

Landscape of human miRNA variation and conservation using Annotative Database of miRNA Elements, ADmiRE

MicroRNAs (miRNAs) are the most abundant class of non-coding RNAs that regulate expression of >60% genes and are frequently deregulated in many human diseases. Sequence variants in miRNAs are expected to have a high impact on miRNA function. However, the lack of miRNA variant annotation and prioritization guidelines has hampered this analysis from whole genome/exome sequencing (WGS/WES) studies. Through the development of an Annotative Database of miRNA Elements, ADmiRE workflow, we re-annotated the publicly available population dataset of gnomAD 15,596 WGS and 123,136 WES and describe 26,094 precursor-miRNA variants. AdmiRE annotates twice the miRNA variants predicted by existing tools which prioritize variation relative to protein coding regions. We provide the allele frequency distribution of miRNA variation which is comparable to variation in exonic regions. This distribution is similar for miRNAs located in the intragenic and intergenic genomic context. Moreover, high confidence miRNAs (designated by miRBase) harbor less variation (the majority contributed by rare variants) compared with the remaining miRNAs. We identify 279 miRNAs highly constrained with little or no variation in gnomAD. We further describe the evolutionary conservation of miRNAs across 100 vertebrates and identify 434 highly conserved miRNAs. We demonstrate that these constraint and conservation metrics (now incorporated into the ADmiRE workflow) characterize miRNAs previously implicated in human diseases. In conclusion, through the development of ADmiRE, we comprehensively analyze the landscape of miRNA sequence variation in large human population datasets and provide miRNA vertebrate conservation scores to aid future studies of miRNA variation in human diseases.

genomics↗

bioRxiv2017

Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines

BackgroundThe American College of Medical Genetics and American College of Pathologists (ACMG/AMP) variant classification guidelines for clinical reporting are widely used in diagnostic laboratories for variant interpretation. The ACMG/AMP guidelines recommend complete concordance of predictions among all in silico algorithms used without specifying the number or types of algorithms. The subjective nature of this recommendation contributes to discordance of variant classification among clinical laboratories and prevents definitive classification of variants.\n\nResultsUsing 14,819 benign or pathogenic missense variants from the ClinVar database, we compared performance of 25 algorithms across datasets differing in distinct biological and technical variables. There was wide variability in concordance among different combinations of algorithms with particularly low concordance for benign variants. We also identify a previously unreported source of error in variant interpretation where in silico predictions are opposite to the evidence provided by other sources. We identified recently developed algorithms with high predictive power and robust to variables like disease mechanism, gene constraint and mode of inheritance, although poorer performing algorithms are more frequently used based on review of the clinical genetics literature (2011-2017).\n\nConclusionsOur analyses identify algorithms with high performance characteristics independent of underlying disease mechanisms. We describe combinations of algorithms with increased concordance that should improve in silico algorithm usage during assessment of clinically relevant variants using the ACMG/AMP guidelines.

bioinformatics↗

bioRxiv2017

A fluorogenic nanobody array tag for prolonged single molecule imaging in live cells

Prolonged single molecule imaging in live cells requires labels that do not aggregate, have high contrast, and are photo-stable. To address these requirements, we have generated arrays of modular protein domains that function as fluorophore recruitment platforms. ArrayG, a linear repeat of GFP-nanobodies, recruits free monomeric wild-type GFP, which brightens ~15-fold upon binding the array. The fluorogenic ArrayG tag effectively eliminates background fluorescence from free binders, a major impediment to high-throughput acquisition of long trajectories in recruitment based imaging strategies. The photo-stability of ArrayG and consistently low background made it possible to continuously track single integrins for as long as 105 seconds (2100 frames). Prolonged tracking of both kinesin and integrin revealed repeated state-switching events, a measurement capability that is crucial to a mechanistic understanding of complex cellular processes. We also report an orthogonal array tag, based on a DHFR-nanobody, for prolonged dual color imaging of single molecules.

biophysics↗

bioRxiv2017

Evaluating the clinical validity of gene-disease associations: an evidence-based framework developed by the Clinical Genome Resource

With advances in genomic sequencing technology, the number of reported gene-disease relationships has rapidly expanded. However, the evidence supporting these claims varies widely, confounding accurate evaluation of genomic variation in a clinical setting. Despite the critical need to differentiate clinically valid relationships from less well-substantiated relationships, standard guidelines for such evaluation do not currently exist. The NIH-funded Clinical Genome Resource (ClinGen) has developed a framework to define and evaluate the clinical validity of gene-disease pairs across a variety of Mendelian disorders. In this manuscript we describe a proposed framework to evaluate relevant genetic and experimental evidence supporting or contradicting a gene-disease relationship, and the subsequent validation of this framework using a set of representative gene-disease pairs. The framework provides a semi-quantitative measurement for the strength of evidence of a gene-disease relationship which correlates to a qualitative classification: \"Definitive\", \"Strong\", \"Moderate\", \"Limited\", \"No Reported Evidence\" or \"Conflicting Evidence.\" Within the ClinGen structure, classifications derived using this framework are reviewed and confirmed or adjusted based on clinical expertise of appropriate disease experts. Detailed guidance for utilizing this framework and access to the curation interface is available on our website. This evidence-based, systematic method to assess the strength of gene-disease relationships will facilitate more knowledgeable utilization of genomic variants in clinical and research settings.

genetics↗