Biology subjects

Das, P.

Publications and source records attributed to Das, P..

102 records · Page 6Linked to original sources

bioRxiv2020

Bioremediation Potential of Select Bacterial Species for the Neonicotinoid Insecticides, Thiamethoxam and Imidacloprid

The neonicotinoid insecticides, including thiamethoxam (THM) and imidacloprid (IMI), have become increasingly favored in the past decade due to their specificity as insect neurotoxicants. However, neonicotinoids have been implicated as a potential contributing factor in Colony Collapse Disorder (CCD), the widespread disappearance of honey bees, which affects produce production on a global scale. The environmental persistence of neonicotinoids underscores the importance of developing a sustainable, ecologically-friendly remediation technique to remove residual insecticides from the environment. The present study characterizes the neonicotinoid bioremediation potential of six bacterial species: Pseudomonas fluorescens, Pseudomonas putida, Pseudomonas aeruginosa, Alcaligenes faecalis, Escherichia coli, and Streptococcus lactis. In Phase I, we evaluated the utilization of IMI or THM as the sole carbon or nitrogen source by P. fluorescens, P. putida, and P. aeruginosa. All three species were better able to utilize THM over IMI as their sole carbon or nitrogen source, and better growth was noted when THM was used as the sole nitrogen source compared to the sole carbon source. Thus, further studies proceeded with THM only. In Phase II, we assessed the kinetics of THM removal from aqueous media by the six species. Significant (p<0.0001) reductions in 70 mg/L THM concentration were observed for P. fluorescens (67%), P. putida (65%), P. aeruginosa (52%), and A. faecalis (39%) over the 24-day study period, and for E. coli (60%) and S. lactis (12%) over the 14-day study period. The amount of time required to remove 50% of the THM in the media (T50) was: 12 days (d) (E. coli), 18 d (P. fluorescens), 19 d (P. putida), and 23 d (P. aeruginosa). Neither A. faecalis nor S. lactis achieved 50% removal during the study periods. The THM removal by all species followed a first-order kinetic reaction and half-lives were calculated accordingly. HPLC chromatograms of P. fluorescens, P. putida, and E. coli cultures revealed that as the area of the THM peak decreased over time, the area of an unidentified metabolite peak increased. In Phase II, we sought to characterize this metabolite and the overall metabolic efficiency of these three species. Maximal THM removal occurred at 30{degrees}C for all bacterial species assessed. Identification of the metabolite is currently underway, which will allow determination of whether the metabolite is less toxic than the parent compound, a prerequisite for this remediation technique to be viable. If the metabolite is found to be less hazardous than THM, further testing will follow to evaluate the use of this bioremediation technique in the field.

ecology↗

bioRxiv2020

Is Boldness in Climbing Perch (Anabas testudineus) Sensitive to the Apparatus Used for Measurement?

Swimway and open field are the two popular apparatus used for measuring boldness - the propensity to take risky decisions - in various piscine species. The present study compared boldness exhibited by an air breathing freshwater fish climbing perch in a swimway, rectangular open field, intermediate stages between these two apparatus and circular open field. Impact of the modification of the start chamber by providing substratum made up of cobbles and covering the water surface using water plant hydrilla, alone and in combinations on the boldness was also tested. Our results revealed that the apparatus has a significant impact on the boldness in climbing perch. The presence of a shelter in the experimental arena (swimway) and cobble substratum in the start chamber of the apparatus were found to be reducing boldness in this fish, while hydrilla cover on the water surface neutralised the impact of cobble substratum. Repeated exposure and resultant familiarity with the arena increased boldness of climbing perch but the pattern of modification of this behavioural trait exhibited during the course of experiment was divergent across the instruments. These results point towards the need for critically analyzing the influence of instruments used for measuring various behavioural traits and considering biological needs of the subject species while designing the apparatus.

animal behavior and cognition↗

bioRxiv2019

Inferring Chromosome Radial Organization from Hi-CData

BackgroundThe nonrandom radial organization of eukaryotic chromosome territories (CTs) inside the nucleus plays an important role in nuclear functional compartmentalization. Increasingly, chromosome conformation capture (Hi-C) based approaches are being used to characterize the genome structure of many cell types and conditions. Computational methods to extract 3D arrangements of CTs from this type of pairwise contact data will thus increase our ability to analyze CT organization in a wider variety of biological situations. ResultsA number of full-scale polymer models have successfully reconstructed the 3D structure of chromosome territories from Hi-C. To supplement such methods, we explore alternative, direct, and less computationally intensive approaches to capture radial CT organization from Hi-C data. We show that we can infer relative chromo-some ordering using PCA on a thresholded inter-chromosomal contact matrix. We simulate an ensemble of possible CT arrangements using a force-directed network layout algorithm and propose an approach to integrate additional chromosome properties into our predictions. Our CT radial organization predictions have a high correlation with microscopy imaging data for various cell nucleus geometries (lymphoblastoid, skin fibroblast, and breast epithelial cells), and we can capture previously documented changes in senescent and progeria cells. ConclusionsOur analysis approaches provide rapid and modular approaches to screen for alterations in CT organization across widely available Hi-C data. We demon-strate which stages of the approach can extract meaningful information, and also de-scribe limitations of pairwise contacts alone to predict absolute 3D positions.

bioinformatics↗

bioRxiv2019

Constricted migration contributes to persistent 3D genome structure changes associated with an invasive phenotype in melanoma cells

To spread from a localized tumor, metastatic cancer cells must squeeze through constrictions that cause major nuclear deformations. Since chromosome structure affects nucleus stiffness, gene regulation and DNA repair, here we investigate the relationship between 3D genome structure and constricted migration in cancer cells. Using melanoma (A375) cells, we identify phenotypic differences in cells that have undergone multiple rounds of constricted migration. These cells display a stably higher migration efficiency, elongated morphology, and differences in the distribution of Lamin A/C and heterochromatin. Hi-C experiments reveal differences in chromosome spatial compartmentalization specific to cells that have passed through constrictions and related alterations in expression of genes associated with migration and metastasis. Certain features of the 3D genome structure changes, such as a loss of B compartment interaction strength, are consistently observed after constricted migration in clonal populations of A375 cells and in MDA-MB-231 breast cancer cells. Our observations suggest that consistent types of chromosome structure changes are induced or selected by passage through constrictions and that these may epigenetically encode stable differences in gene expression and cellular migration phenotype.

systems biology↗

bioRxiv2019

Neuro-Current Response Functions: A Unified Approach to MEG Source Analysis under the Continuous Stimuli Paradigm

Characterizing the neural dynamics underlying sensory processing is one of the central areas of investigation in systems and cognitive neuroscience. Neuroimaging techniques such as magnetoencephalography (MEG) and Electroencephalography (EEG) have provided significant insights into the neural processing of continuous stimuli, such as speech, thanks to their high temporal resolution. Existing work in the context of auditory processing suggests that certain features of speech, such as the acoustic envelope, can be used as reliable linear predictors of the neural response manifested in M/EEG. The corresponding linear filters are referred to as temporal response functions (TRFs). While the functional roles of specific components of the TRF are well-studied and linked to behavioral attributes such as attention, the cortical origins of the underlying neural processes are not as well understood. In this work, we address this issue by estimating a linear filter representation of cortical sources directly from neuroimaging data in the context of continuous speech processing. To this end, we introduce Neuro-Current Response Functions (NCRFs), a set of linear filters, spatially distributed throughout the cortex, that predict the cortical currents giving rise to the observed ongoing MEG (or EEG) data in response to continuous speech. NCRF estimation is cast within a Bayesian framework, which allows unification of the TRF and source estimation problems, and also facilitates the incorporation of prior information on the structural properties of the NCRFs. To generalize this analysis to M/EEG recordings which lack individual structural magnetic resonance (MR) scans, NCRFs are extended to free-orientation dipoles and a novel regularizing scheme is put forward to lessen reliance on fine-tuned coordinate co-registration. We present a fast estimation algorithm, which we refer to as the Champ-Lasso algorithm, by leveraging recent advances in optimization, and demonstrate its utility through application to simulated and experimentally recorded MEG data under auditory experiments. Our simulation studies reveal significant improvements over existing methods that typically operate in a two-stage fashion, in terms of spatial resolution, response function reconstruction, and recovering dipole orientations. The analysis of experimentally-recorded MEG data without MR scans corroborates existing findings, but also delineates the distinct cortical distribution of the underlying neural processes at high spatiotemporal resolution. In summary, we provide a principled modeling and estimation paradigm for MEG source analysis tailored to extracting the cortical origin of electrophysiological responses to continuous stimuli.

neuroscience↗

bioRxiv2019

Prey capturing and feeding apparatus of dragonfly nymph

Aquatic predatory insects, like the nymphs of a dragonfly, use rapid movements to catch their prey. Dragonfly nymphs are voracious predators that feed on smaller aquatic organisms. In this study, we examine dragonfly nymph (Libellulidae: Insecta: Odonata) mouthparts that are used in prey capturing and feeding. In particular, we characterise the morphology of the labium and mechanical properties of the mandibles of the nymph. Additionally, we record and analyse the preying mechanism using high-speed photography. The morphological details suggest that the prey capturing mechanism is a complex grasping mechanism with additional sensory organs that might aid in sensing the surroundings. The times taken for the extension and retraction of labial organ during prey capture was 187{+/-}54 ms. The Youngs modulus and hardness of the mandibles samples were 9.1{+/-}1.9 GPa and 0.85{+/-}0.13 GPa. Gradation in the mechanical properties was also observed in the mandible tip regions with increased properties at the tip end. The overall mechanism with its sensory capabilities provides a unique design to develop bioinspired underwater deployable mechanisms.

bioengineering↗

bioRxiv2019

Mesenchymal stem cells (MSCs) offer a drug tolerant and immune-privileged niche to Mycobacterium tuberculosis

Anti-tuberculosis (TB) drugs while being highly potent in vitro require prolonged treatment to control Mycobacterium tuberculosis (Mtb) infections in vivo. We report here, mesenchymal stem cells (MSCs) shelter Mtb to help tolerate anti-TB drugs. MSCs uptake Mtb readily and allow them grow unabated despite having functional innate pathway of phagosome maturation. Unlike macrophage-resident ones, MSC-resident Mtb tolerates anti-TB drugs remarkably well, a phenomenon requiring proteins ABCC1, ABCG2 and vacuolar-type H+ATPases. Additionally, contrary to what is classically known, IFN{gamma} and TNF aid mycobacterial growth within MSCs. Mechanistically, evading drugs and inflammatory cytokines by MSC-resident Mtb is dependent on elevated PGE2 signaling, which we subsequently verified in vivo analyzing sorted CD45-CD73+SCA1+-MSCs from the lungs of infected mice. Moreover granulomas from human pulmonary and extra-pulmonary TB show presence of MSCs co-inhabiting with Mtb. Together the results show targeting the immune-privileged niche, provided by MSCs to Mtb, can revolutionize tuberculosis prevention and cure.

immunology↗

bioRxiv2018

A gradient in inner pressure of germline cells controls overlaying epithelial cell morphogenesis

It is unknown how growth in one tissue impacts morphogenesis in a neighboring tissue. To address this, we used the Drosophila ovarian follicle, where a cluster of 15 nurse cells and a posteriorly located oocyte are surrounded by a layer of epithelial cells. It is known that as the nurse cells grow, the overlying epithelial cells flatten in a wave that begins in the anterior. Here, we demonstrate that an anterior to posterior gradient of decreasing cytoplasmic pressure is present across the nurse cells and that this gradient acts through TGF{beta} to control both the triggering and the progression of the wave of epithelial cell flattening. Our data indicate that intrinsic nurse cell growth is important to control proper nurse cell pressure. Finally, we reveal that nurse cell pressure and subsequent TGF{beta} activity in the StC combine to increase follicle elongation in the anterior, which is crucial for allowing nurse cell growth and pressure control. More generally, our results reveal that during development, inner cytoplasmic pressure in individual cells has an important role in shaping their neighbors. Impact StatementCell shape change depends on extrinsic forces exerted by cytoplasmic pressure in neighbouring cells.

developmental biology↗

bioRxiv2018

MiR-146a-dependent regulation of CD24/AKT/β-catenin axis drives stem cell phenotype in oral cancer

Cancer stem cells (CSCs) are known to potentiate tumor initiation and maintenance in Oral Squamous Cell Carcinoma (OSCC). Increasing evidences suggest that CD44highCD24low population in OSCC are potential CSCs. MicroRNAs (miRNAs) have emerged as crucial players in tumor development. However, their role in maintenance of OSCC stem cells remains unclear. Here we report that CD44highCD24low population within OSCC cells and primary HNSCC tumors have an elevated expression of miR-146a. Moreover, over-expression of miR-146a results in enhanced stemness phenotype by augmenting CD44highCD24low population. We demonstrate that miR-146a induces stemness by stabilizing {beta}-catenin with concomitant loss of E-cadherin and CD24. Interestingly, CD24 is identified as a novel functional target of miR-146a and ectopic expression of CD24 abrogates miR-146a driven potential CSC phenotype. Mechanistic analysis reveals that higher CD24 levels inhibit AKT phosphorylation leading to {beta}-catenin degradation. Using stably expressing miR-146a/CD24 OSCC cell lines, we also validate that the miR-146a/ CD24/AKT loop significantly alters tumorigenic ability in vivo. Furthermore, we confirmed that {beta}-catenin trans-activates miR-146a, thereby forming a positive feedback loop contributing to stem cell maintenance. Collectively, our study demonstrates that miR-146a regulate CSCs in OSCC through CD24-AKT-{beta}-catenin axis.\n\nHighlightsO_LIMiR-146a induces cancer stem cell characteristics in OSCC by targeting CD24\nC_LIO_LICD24 abrogates miR-146a mediated stemness via {beta}-catenin degradation in non-CSCs\nC_LIO_LIAkt/Wnt pathway is critical for sustenance of miR-146a driven potential CSCs\nC_LIO_LIThe miR-146a/CD24/AKT loop significantly alters tumorigenic ability in vivo\nC_LI

cancer biology↗

bioRxiv2018

Dose Escalation for Locally Advanced Pancreatic Cancer: How High Can We Go?

Introduction Introduction Methods Results Discussion References Locally advanced pancreatic cancer (LAPC) is particularly difficult to treat given that it exhibits a poor response to chemotherapy and is by definition unresectable. A large proportion of patients experience significant morbidity and mortality due to local progression. As systemic therapy improves with the advent of gemcitabine/ abraxane1 and FOLFIRINOX2, the burden of local disease will only increase. Standard radiation therapy doses have failed to improve survival, which is not unexpected given anatomical and technical limitations. Although the LAP-07 trial3 failed to show an overall survival benefit to radiation at standard doses, it did show benefits in terms of local control and t ...

clinical trials↗

bioRxiv2017

Early warning signals regarding environmental suitability in the Drosophila antenna

HighlightsO_LIA novel geotaxis assay showed high intensity odorant exposures are harmful to flies\nC_LIO_LIRepulsion at high odor intensities can be a protective mechanism\nC_LIO_LIOlfactory receptor neuron (ORN) excitability abruptly changes with odor intensity\nC_LIO_LIA linear combination of ORN activities can robustly predict intensity-dependent behavioral repulsion\nC_LI\n\nSummaryThe olfactory system is uniquely positioned to warn an organism of environmental threats. Whether and how it encodes such information is not understood. Here, we examined this issue in the fruit fly Drosophila melanogaster. We found that intensity-dependent repulsion to chemicals safeguarded flies from harmful, high-intensity vapor exposures. To understand how sensory input changed as the odor valence switched from innocuous to threatening, we recorded from olfactory receptor neurons (ORNs) in the fly antenna. Primarily, we observed two response non-linearities: recruitment of non-active ORNs at higher intensities, and abrupt transitions in neural excitability from regular spiking to high-firing oscillatory regime. Although non-linearities observed in any single ORN was not a good indicator, a simple linear combination of firing events from multiple neurons provided robust recognition of threating/repulsive olfactory stimuli. In sum, our results reveal how information necessary to avoid environmental threats may also be encoded in the insect antenna.

neuroscience↗

bioRxiv2017

SUPERMAN prevents stamen formation and promotes stem cell termination in the fourth whorl of the Arabidopsis flower

The molecular and genetic networks underlying the determination of floral organ identity are well studied, but much less is known about how the flower is partitioned into four developmentally distinct whorls. The SUPERMAN gene is required for proper specification of the boundary between stamens in whorl 3 and carpels in whorl 4, as superman mutants exhibit supernumerary stamens but usually lack carpels. However, it has remained unclear whether extra stamens in superman mutants originate from an organ identity change in whorl 4 or the overproliferation of whorl 3. Using live confocal imaging, we show that the extra stamens in superman mutants arise from cells in whorl 4, which change their fate from female to male, while floral stem cells proliferate longer, allowing for the production of additional stamens.

developmental biology↗