Biology subjects

Gupta, D.

Publications and source records attributed to Gupta, D..

102 records · Page 6Linked to original sources

bioRxiv2020

An approach for long-term, multi-probe Neuropixels recordings in unrestrained rats

The use of Neuropixels probes for chronic neural recordings is in its infancy and initial studies leave questions about long-term stability and probe reusability unaddressed. Here we demonstrate a new approach for chronic Neuropixels recordings over a period of months in freely moving rats. Our approach allows multiple probes per rat and multiple cycles of probe reuse. We found that hundreds of units could be recorded for multiple months, but that yields depended systematically on anatomical position. Explanted probes displayed a small increase in noise compared to unimplanted probes, but this was insufficient to impair future single-unit recordings. We conclude that cost-effective, multi-region, and multi-probe Neuropixels recordings can be carried out with high yields over multiple months in rats or other similarly sized animals. Our methods and observations may facilitate the standardization of chronic recording from Neuropixels probes in freely moving animals.

neuroscience↗

bioRxiv2020

Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis

The ongoing pandemic of the coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV2). We have performed an integrated sequence-based analysis of SARS-CoV2 genomes from different geographical locations in order to identify its unique features absent in SARS-CoV and other related coronavirus family genomes, conferring unique infection, facilitation of transmission, virulence and immunogenic features to the virus. The phylogeny of the genomes yields some interesting results. Systematic gene level mutational analysis of the genomes has enabled us to identify several unique features of the SARS-CoV2 genome, which includes a unique mutation in the spike surface glycoprotein (A930V (24351C>T)) in the Indian SARS-CoV2, absent in other strains studied here. We have also predicted the impact of the mutations in the spike glycoprotein function and stability, using computational approach. To gain further insights into host responses to viral infection, we predict that antiviral host-miRNAs may be controlling the viral pathogenesis. Our analysis reveals nine host miRNAs which can potentially target SARS-CoV2 genes. Interestingly, the nine miRNAs do not have targets in SARS and MERS genomes. Also, hsa-miR-27b is the only unique miRNA which has a target gene in the Indian SARS-CoV2 genome. We also predicted immune epitopes in the genomes

bioinformatics↗

bioRxiv2019

Plasmodium condensin core subunits (SMC2/SMC4) mediate atypical mitosis and are essential for parasite proliferation and transmission

Condensin is a multi-subunit protein complex regulating chromosome condensation and segregation during cell division. In Plasmodium spp., the causative agent of malaria, cell division is atypical and the role of condensin is unclear. Here we examine the role of SMC2 and SMC4, the core subunits of condensin, during endomitosis in schizogony and endoreduplication in male gametogenesis. During early schizogony SMC2/SMC4 localize to a distinct focus, identified as the centromeres by NDC80 fluorescence and ChIP-seq analyses, but do not form condensin I or II complexes. In mature schizonts and during male gametogenesis, there is a diffuse SMC2/SMC4 distribution on chromosomes and in the nucleus, and both condensin I and II complexes form at these stages. Knockdown of smc2 and smc4 gene expression revealed essential roles in parasite proliferation and transmission. The condensin core subunits (SMC2/SMC4) form different complexes and may have distinct functions at various stages of the parasite life cycle.

cell biology↗

bioRxiv2019

Classification models for Invasive Ductal Carcinoma Progression, based on gene expression data-trained supervised machine learning

Early detection of breast cancer and its correct stage determination are important for prognosis and rendering appropriate personalized clinical treatment to breast cancer patients. However, despite considerable efforts and progress, there is a need to identify the specific genomic factors responsible for, or accompanying Invasive Ductal Carcinoma (IDC) progression stages, which can aid the determination of the correct cancer stages. We have developed two-class machine-learning classification models to differentiate the early and late stages of invasive ductal carcinoma. The prediction models are trained with RNA-seq gene expression profiles representing different IDC stages of 610 patients, obtained from The Cancer Genome Atlas (TCGA). Different supervised learning algorithms were trained and evaluated with an enriched model learning, facilitated by different feature selection methods. We also developed a machine-learning classifier trained on the same datasets with training sets reduced data corresponding to IDC driver genes. Based on these two classifiers, we have developed a web-server Duct-BRCA-CSP to predict early stage from late stages of IDC based on input RNA-seq gene expression profiles. The analysis conducted by us also enables deeper insights into the stage-dependent molecular events accompanying breast ductal carcinoma progression. The server is publicly available at http://bioinfo.icgeb.res.in/duct-BRCA-CSP.

bioinformatics↗

bioRxiv2019

HA Nanocarriers Mediate HepG2 Vaccine Induction of hGM-CSF Gene Antitumor effect study

This report developed a novel method to observe the anti-tumor effect of HA nanoparticle carrier-mediated HepG2 cell vaccine transfected with hGM-CSF gene in vitro, and provide evidence for the clinical application of hGM-CSF gene-modified HepG2 cell vaccine. HA nanoparticle-mediated hGM-CSF gene transfection of HepG2 cells was used to prepare HepG2 cell vaccine transfected with GMCSF gene. Human PBMC were isolated by density gradient centrifugation and human PBMC were induced in vitro. The proliferative activity of PBMC and the killing effect on HepG2 cells were determined by WST-1 method. The positive expression rates of CD4+ and CD8+ were analyzed by flow cytometry, and the secretion of INF-{gamma} was determined by ELISA. WST-1 results showed that the transgenic HepG2 vaccine induced PBMC proliferation, and its proliferation rate was better than that of wild-type vaccine. The induced PBMC had a higher killing rate against HepG2 than the wild-type vaccine group and each blank. In the control group, FCM results showed that the positive expression rates of CD4+ and CD8+ in the transgenic HepG2 vaccine group were higher than those in the wild-type vaccine group and each blank control group. The ELISA results showed that the IFN-{gamma} content in the transgenic PBMC culture supernatant was 1989.76. +/- 254.21 pg/ml, higher than the wild-type vaccine group and each blank control group.

bioengineering↗

bioRxiv2019

Preparation of Artesunate mPEG-PLGA Nanoparticles and Its Application to K562 Apoptosis of cells

The preparation process of artesunate-loaded polyethylene glycol monomethyl ether-polylactic acid-glycolic acid affinity block copolymer (mPEG-PLGA) nanoparticles and its growth inhibition on human leukemia K562 cells were investigated. METHODS: Artesunate mPEG-PLGA nanoparticles (Art-Nps) were prepared by modified self-emulsification method. The morphology of nanoparticles was characterized by scanning electron microscopy. The particle size distribution and zeta potential were measured by laser scattering particle size analyzer. The drug loading, encapsulation efficiency and in vitro release of Art-Nps were determined by chromatography. The proliferation and apoptosis of human leukemia K562 cells were observed by MTT assay and Hoechst staining. RESULTS: Art-Nps is a spherical solid particle with smooth surface, average particle size (156.70+/-1.01) nm, zeta potential of -(26.23+/-1.86) mV, average drug loading (14.51+/-0.20)%, average package. The sealing rate was (86.51+/-0.50)%, and the in vitro release law accorded with the Higuchi equation: Q=4.11t 1/2+27.05, R2=0.98. MTT assay showed that Art-Nps inhibited the proliferation of K562 cells in a time-dose-dependent manner, and the inhibition rate exceeded the artesunate-treated group after 72h, and sustained release. The number of cells was observed after cultured with different concentrations of Art-Nps for 48h. Significantly reduced, cell size is different, irregular shape, high magnification can be seen in the nucleus pyknosis, agglutination, and apoptotic bodies, and increased apoptotic bodies with increasing concentration.

bioengineering↗

bioRxiv2019

Preparation and in vitro release of fluorouracil polylactide glycolide-polyethylene glycol monomethyl ether nanoparticles

This report demonstrates a novel strategy to prepare fluorouracil polylactide glycolide-polyethylene glycol monomethyl ether (PLGA-mPEG) nanoparticles and study their in vitro release characteristics. Fluorouracil PLGA-mPEG nanoparticles were prepared by nanoprecipitation method. The encapsulation efficiency was determined by high performance liquid chromatography. Based on the single factor experiment, the prescription and preparation process were optimized by orthogonal experiments. The in vitro release characteristics of nanoparticles were studied by dynamic membrane dialysis. Results The prepared nanoparticles were relatively uniform spheroidal particles with an average particle size of about 124. 3 nm, a Zeta potential of - 20. 6 mV, and an average encapsulation efficiency of (44.72 {+/-} 0.38%). In vitro drug release experiments showed that the particle burst release was less than 30% at 2 h, and the drug was slowly released within 48 h after burst release.

bioengineering↗

bioRxiv2019

Targeting study of HepG2 hepatoma cells in vitro by drug-loaded pectin-based nanoparticles

The biodegradable and biodegradable natural polysaccharide has always been used as a drug delivery system, and has the following advantages: It can prolong the biological half life of the drug and reduce the side effects of the drug. This experiment aimed to prepare a 5-fluorouracil (5-FU) nanoparticle (P-5-FU) drug-loading system based on pectin, and explored a large number of pectin-based nano drug-loading systems. The galactose residue is a natural target that targets human hepatoma cell HepG2. MTT assay was used to determine the proliferation inhibition effect of drug-loaded pectin-based nanoparticles on HepG2 and A549 cells. MTT assay showed that P-5-FU inhibited the proliferation of HepG2 cells in a dose-dependent manner, and the effect was stronger than 5-FU. P-5-FU also inhibited the proliferation of A549 cells in a dose-dependent manner, but there was no significant difference compared with 5-FU. High performance liquid chromatography (HPLC) on two kinds of cells loaded with drug-loaded nanoparticles the uptake and targeting were measured. The results of cell uptake showed that the uptake of P-5-FU by HepG2 cells was significantly higher than that of 5-FU, but there was no significant difference in the uptake of P-5-FU and 5-FU by A549 cells. There was no significant difference in the uptake of P-5-FU and 5-FU between the two cells after the galactose-saturated ASGPR binding site. The results indicate that pectin-based nano drug-loaded particles can specifically target highly expressed cells.

bioengineering↗

bioRxiv2019

ApicoTFdb: The comprehensive web repository of apicomplexan transcription factors and regulators.

Despite significant progress in apicomplexans genome sequencing and genomics, the current list of experimentally validated TFs in these genomes is incomplete and mainly consists of AP2 family of proteins, with only a limited number of non-AP2 family TFs and TAFs. We have performed systematic bioinformatics aided prediction of TFs and TAFs in apicomplexan genomes, and developed ApicoTFdb database which consists of experimentally validated as well as computationally predicted TFs and TAFs in 14 apicomplexan species. The predicted TFs are manually curated to complement the existing annotations. The current version of the database includes 1310 TFs, out of which 833 are novel and computationally predicted TFs, representing 22 distinct families across 14 apicomplexan species. The predictions include TFs of TUB, NAC, BSD, CCAAT, HTH, Cupin/Jumonji, winged-helix, and FHA family proteins, not reported earlier in the genomes. Apart from TFs, ApicoTFdb also classifies TAFs into three main subclasses-TRs, CRRs and RNARs, representing 3047 TAFs in 14 apicomplexan species are analyzed in this study. The database is equipped with a set of useful tools for comparative analysis of a user-defined list of the proteins. ApicoTFdb will be useful to the researchers interested in less-studied gene regulatory mechanisms mediating the complex life cycle of the apicomplexan parasites. The database will aid the discovery of novel drug targets to much needed combat the growing drug resistance in the parasites.

bioinformatics↗

bioRxiv2019

Cortical and Cardiovascular Regulation Support Adaptation to Ambient Sound Environment

Adaptation in complex biological systems is a consequence of sensitivity to environmental changes. We investigate how responses to unattended background sound changes are influenced by the interaction of external (pitch sequence context) and internal factors (biological regulation). Cortical responses (electroencephalograph Mismatch Negativity) demonstrated increased intensity and prolonged latency in unattended pitch changes in the context of the ascending pitch sequence compared with the descending pitch sequence. Moreover, ascending pitch context is associated with more activation of anterior cingula cortex and insula, suggesting arousal effect and internal regulation. However, the intensified and prolonged responses were supported by cortical and cardiovascular biomarkers for regulation respectively. These findings suggest that biological regulation may be associated with environmental context and play different roles in response sensitivity in terms of intensity and speed.

neuroscience↗

bioRxiv2018

Delays, behaviour and transmission: modelling the impact of effective private provider engagement on tuberculosis control in urban India

In India, the country with the worlds largest burden of tuberculosis (TB), most patients first seek care in the private healthcare sector, which is fragmented and unregulated. Ongoing initiatives are demonstrating effective approaches for engaging with this sector, and form a central part of Indias recent National Strategic Plan: here we aimed to address their potential impact on TB transmission in urban settings, when taken to scale. We developed a mathematical model of TB transmission dynamics, calibrated to urban populations in Mumbai and Patna, two major cities in India where pilot interventions are currently ongoing.\n\nWe found that, when taken to sufficient scale to capture 75% of patient-provider interactions, the intervention could reduce incidence by upto 21.3% (95% Bayesian credible interval (CrI) 13.0 - 32.5%) and 15.8% (95% CrI 7.8 - 28.2%) in Mumbai and Patna respectively, between 2018 and 2025. There is a stronger impact on TB mortality, with a reduction of up to 38.1% (95% CrI 20.0 - 55.1%) in the example of Mumbai. The incidence impact of this intervention alone may be limited by the amount of transmission that has already occurred by the time a patient first presents for care: model estimates suggest an initial patient delay of 4-5 months before first seeking care, followed by a diagnostic delay of 1-2 months before ultimately initiating TB treatment. Our results suggest that the transmission impact of such interventions could be maximised by additional measures to encourage early uptake of TB services.

systems biology↗

bioRxiv2018

mTORC1 Restricts Hepatitis C Virus Replication Through ULK1-mediated Suppression of miR-122 and Facilitates Post-replication Events

Mechanistic target of rapamycin (mTOR) is an important kinase that assimilates several upstream signals including viral infection and facilitates appropriate response by the cell through two unique complexes mTORC1 and mTORC2. Here, we demonstrate that mTORC1 is activated early during HCV infection as antiviral response. Pharmacological inhibition of mTORC1 promoted HCV replication as suggested by elevated levels of HCV (+) and (-) RNA strands. This was accompanied by significant drop in extracellular HCV RNA levels indicating defective post-replication stages. The increase in viral RNA levels failed to augment intracellular infectious virion levels, suggesting that mTORC1 inhibition is detrimental to post-replication steps. Lower infectivity of the supernatant confirmed this observation. Depletion of Raptor and ULK1 accurately reproduced these results suggesting that mTORC1 imparted these effects on HCV through mTORC1-ULK1 arm. Interestingly, ULK1 depletion resulted in increased levels of miR-122, a critical host factor for HCV replication, thus revealing a new mechanism of regulation by ULK1. The binary effect of mTORC1 on HCV replication and egress suggests that mTORC1-ULK1 could be critical in replication: egress balance. Interestingly we discover that ULK1 depletion did not interfere with autophagy in Huh7.5 cells and hence the effects on HCV replication and post-replication events are not resultant of involvement of autophagy. Our studies demonstrate an overall ULK1 mediated anti-HCV function of mTORC1 and identifies an ULK1-independent autophagy that allows HCV replication in spite of mTORC1 activation.

microbiology↗