Biology subjects

Ray, S.

Publications and source records attributed to Ray, S..

At least 127 records · Page 7Linked to original sources

bioRxiv2020

Comparative assessment of allelopathic herbicidal actions and total phenolics content of seven Indian medicinal plants

Allelopathy is a vital ecological process that influences the dynamics of ecological succession, structure, and composition of plant communities. The present study aimed to evaluate a comparative account of allelopathic inhibitory actions in relation to total phenolic contents of aqueous extracts from seven traditionally used medicinal plants of India. Triticum aestivum and Cicer arietinum seedlings were used to test seed germination inhibition, seedling growth retardation and branch root sprouting inhibition. Allium cepa root tip cells were used for mitotic index inhibition and abnormal cell percentage analysis. The correlation between the total phenolics content and allelopathic activities was analyzed. The different extracts show the varied degree of allelopathic inhibitory activity. Out of these seven used extracts, Crinum asiaticum leaf extract (CaLAE) showed the highest allelopathic inhibitory action and it could reduce 94.3 and 79.59% root and shoot growth respectively at 96 h of treatment (1 mg/mL) and that was increased to 96.18 and 93.78% respectively with 2 mg/mL. The quantitative phytochemical analysis also revealed that CaLAE also possess relatively higher amounts of total phenolics. The growth retardation effects of the extract are in accordance with the mito-depression and increased chromosomal abnormality in A. cepa root tip cells. In conclusion, Crinum asiaticum may be considered as a prospective source of allelochemicals for plant growth regulation and a source of commercial herbicidal products.

plant biology↗

bioRxiv2020

RgCop-A regularized copula based method for gene selection in single cell rna-seq data

Gene selection in unannotated large single cell RNA sequencing (scRNA-seq) data is important and crucial step in the preliminary step of downstream analysis. The existing approaches are primarily based on high variation (highly variable genes) or significant high expression (highly expressed genes) failed to provide stable and predictive feature set due to technical noise present in the data. Here, we propose RgCop, a novel regularized copula based method for gene selection from large single cell RNA-seq data. RgCop utilizes copula correlation (Ccor), a robust equitable dependence measure that captures multivariate dependency among a set of genes in single cell expression data. We raise an objective function by adding a l1 regularization term with Ccor to penalizes the redundant co-efficient of features/genes, resulting non-redundant effective features/genes set. Results show a significant improvement in the clustering/classification performance of real life scRNA-seq data over the other state-of-the-art. RgCop performs extremely well in capturing dependence among the features of noisy data due to the scale invariant property of copula, thereby improving the stability of the method. Moreover, the differentially expressed (DE) genes identified from the clusters of scRNA-seq data are found to provide an accurate annotation of cells. Finally, the features/genes obtained from RgCop can able to annotate the unknown cells with high accuracy. AvailabilityCorresponding software is available in: https://github.com/Snehalikalall/RgCop Contactsumanta.ray@cwi.nl

bioinformatics↗

bioRxiv2020

Single-cell transcriptomics and cell-specific proteomics reveals molecular signatures of sleep

Every day, we sleep for a third of the day. Sleep is important for cognition, brain waste clearance, metabolism, and immune responses. The molecular mechanisms governing sleep are largely unknown. Here, we used a combination of single cell RNA sequencing and cell-type specific proteomics to interrogate the molecular underpinnings of sleep. Different cell types in three important brain regions for sleep (brainstem, cortex, and hypothalamus) exhibited diverse transcriptional responses to sleep need. Sleep restriction modulates astrocyte-neuron crosstalk and sleep need enhances expression of specific sets of transcription factors in different brain regions. In cortex, we also interrogated the proteome of two major cell types: astrocytes and neurons. Sleep deprivation differentially alters the expression of proteins in astrocytes and neurons. Similarly, phosphoproteomics revealed large shifts in cell-type specific protein phosphorylation. Our results indicate that sleep need regulates transcriptional, translational, and post-translational responses in a cell-specific manner.

neuroscience↗

bioRxiv2020

Comparative phytotoxicity and chironomid toxicity assessments of leaf successive extract fractions of Asiatic poison bulb, Crinum asiaticum L.

Crinum asiaticum is an evergreen bulbous perennial shrub of Amaryllidaceae family with ethnomedicinal importance and our earlier study described a comparative account antimicrobial and antioxidant properties of the different solvent-mediated sequential extract fractions. The present study aimed to analyze their comparative account of induced phytotoxicity and chironomid toxicity. For phytotoxicity assessment, germination inhibition and seedlings root and shoot growth retardation effects on Triticum aestivum and Cicer arietinum were analyzed and for lethal concentration determination, the freshwater bottom-dwelling first instars chironomid larvae were used. The crude aqueous, petroleum ether and ethyl acetate extracts showed significant toxic effects on both meristematic tissue and aquatic midges. The phytotoxic assays indicate that the ethyl acetate fraction contains the most potent growth inhibitors, followed by the crude aqueous and petroleum ether fractions. The last aqueous fraction was found to be the least toxic, the highest LC50 and LT50 values and ethyl acetate extract fraction having highest toxicity. Thus the present study supplements to our earlier report, that indicated the last aqueous extract fraction of C. asiaticum has potent antioxidant and antibacterial potentials as well as its prospective use in livestock maintenance, as it is least toxic and the ethyl acetate extract, the most toxic fraction identified here, is needed to explore for pharmaceutical importance.

pharmacology and toxicology↗

bioRxiv2020

Pro-metaphase arrest, polyploidy, micronuclei, and mitotic abnormality inducing agents isolation from leaf aqueous extract of Clerodendrum viscosum Vent.

Clerodendrum viscosum is a traditionally used medicinal plant. The present study aimed to analyze cell cycle delay, pro-metaphase arrest, and c-metaphase inducing effects of the petroleum ether fraction (AQPEF) of leaf aqueous extract of C. Viscosum (LAECV). The LAECV was fractionated with petroleum ether and its metaphase arrest, cell cycle delay, and c-metaphase inducing activities were tested on A. cepa root tip cells. The AQPEF induced cell cycle delay, and colchicine like metaphase, c-metaphase, in A. cepa root tip cells. Thus, the present study explores AQPEF as an active fraction of LAECV having metaphase arresting, cell cycle delay, and c-metaphase inducing potentials.

pharmacology and toxicology↗

bioRxiv2020

Analysis of cell-type-specific chromatin modifications and gene expression in Drosophila neurons that direct reproductive behavior

Examining the role of chromatin modifications and gene expression in neurons is critical for understanding how the potential for behaviors are established and maintained. We investigate this question by examining Drosophila melanogaster fru P1 neurons that underlie reproductive behaviors in both sexes. We developed a method to purify cell-type-specific chromatin (Chromatag), using a tagged histone H2B variant that is expressed using the versatile Gal4/UAS gene expression system. Here, we use Chromatag to evaluate five chromatin modifications, at three life stages in both sexes. We find substantial changes in chromatin modification profiles across development and fewer differences between males and females. We generated cell-type-specific RNA-seq data sets, using translating ribosome affinity purification (TRAP), and identify actively translated genes in fru P1 neurons, revealing novel stage- and sex-differences in gene expression. We compare chromatin modifications to the gene expression data and find patterns of chromatin modifications associated with gene expression. An examination of the genic features where chromatin modifications resides shows certain chromatin modifications are maintained in the same genes across development, whereas others are more dynamic, which may point to modifications important for cell fate determination in neurons. Using a computational analysis to identify super-enhancer-containing genes we discovered differences across development, and between the sexes that are cell-type-specific. A set of super-enhancer-containing genes that overlapped with those determined to be expressed with the TRAP approach were validated as expressed in fru P1 neurons. Author SummaryDifferences in male and female reproductive behaviors are pervasive in nature and important for species propagation. Studies of sex differences in the fruit fly, Drosophila melanogaster, have been ongoing since the early 1900s, with many of the critical molecular and neural circuit determinates that create sexually dimorphic behavior identified. This system is a powerful model to understand fundamental principles about the underpinnings of complex behavior at high resolution. In this study, we examine the gene expression and chromatin modification differences specifically in a set of neurons that direct male and female reproductive behaviors in Drosophila. We describe differences across development and between the sexes with the goal of understanding how the potential for behavior is created and maintained.

genomics↗

bioRxiv2020

NASA GeneLab RNA-Seq Consensus Pipeline: Standardized Processing of Short-Read RNA-Seq Data

With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility and reusability of pipeline data, to provide a template for data processing of future spaceflight-relevant datasets, and to encourage cross-analysis of data from other databases with the data available in GeneLab.

bioinformatics↗

bioRxiv2020

Identification of key immune regulatory genes in HIV-1Progression

In the last few decades, application of DNA microarray technology has sprung up as a powerful technique for discovering stage specific changes in expression pattern of a disease progression. Human Immunodeficiency Virus (HIV) infection causes Acquired Immunodeficiency Syndrome (AIDS) which is one of the most devastating diseases affecting humankind. Here, we have proposed a framework to examine the difference among microarray gene expression data of uninfected and three different HIV-1 infection stages using module preservation statistics. Initially, we detected differentially expressed genes among all the stages and identified coexpression modules by using topological overlap as a dissimilarity measure. To examine relationship among co-expression modules, we have compiled a module eigenegene network for each sample category which models similarity among all coexpression modules. To further examine the network, we have found clusters in it which are termed as meta-modules. Different module preservation statistics with two composite statistics: "Zsummary" and "MedianRank" are utilized to examine changes in structure of coexpression modules. We have applied our proposed methodology to discover modular changes between uninfected and acute samples, acute and chronic samples, chronic and AIDS samples. We have found several interesting results on preservation characteristics of gene modules across different stages. Some genes are identified to be preserved in a pair of stages while alter their characteristics across other stages. We further validated the obtained results using permutation test and classification techniques. Biological significance of the obtained modules have been examined using gene ontology and pathway based analysis. Additionally, we have detected key immune regulatory hub genes in the associated protein-protein interaction networks (PPINs) of the differentially expressed genes (DEGs) using twelve topological and centrality analysis methods. Moreover, we have analyzed the key immune regulatory genes which interacts with HIV-1 proteins inside the preserved and perturbed meta-modules across different HIV-1 stages and thus likely to act as potential biomarkers in HIV-1 progression.

bioinformatics↗

bioRxiv2020

sc-REnF: An entropy guided robust feature selection for clustering of single-cell rna-seq data

Many single-cell typing methods require pure clustering of cells, which is susceptible towards the technical noise, and heavily dependent on high quality informative genes selected in the preliminary steps of downstream analysis. Techniques for gene selection in single-cell RNA sequencing (scRNA-seq) data are seemingly simple which casts problems with respect to the resolution of (sub-)types detection, marker selection and ultimately impacts towards cell annotation. We introduce sc-REnF, a novel and robust entropy based feature (gene) selection method, which leverages the landmark advantage of Renyi and Tsallis entropy achieved in their original application, in single cell clustering. Thereby, gene selection is robust and less sensitive towards the technical noise present in the data, producing a pure clustering of cells, beyond classifying independent and unknown sample with utmost accuracy. The corresponding software is available at: https://github.com/Snehalikalall/sc-REnF

bioinformatics↗

bioRxiv2020

Discovering Key Transcriptomic Regulators in Pancreatic Ductal Adenocarcinoma using Dirichlet Process Gaussian Mixture Model

Pancreatic Ductal Adenocarcinoma (PDAC) is the most lethal type of pancreatic cancer (PC), late detection of which leads to its therapeutic failure. This study aims to find out key regulatory genes and their impact on the progression of the disease helping the etiology of the disease which is still largely unknown. We leverage the landmark advantages of time-series gene expression data of this disease, and thereby the identified key regulators capture the characteristics of gene activity patterns in the progression of the cancer. We have identified the key modules and predicted gene functions of top genes from the compiled gene association network (GAN). Here, we have used the natural cubic spline regression model (splineTimeR) to identify differentially expressed genes (DEG) from the PDAC microarray time-series data downloaded from gene expression omnibus (GEO). First, we have identified key transcriptomic regulators (TR) and DNA binding transcription factors (DbTF). Subsequently, the Dirichlet process and Gaussian process (DPGP) mixture model is utilized to identify the key gene modules. A variation of the partial correlation method is utilized to analyze GAN, which is followed by a process of gene function prediction from the network. Finally, a panel of key genes related to PDAC is highlighted from each of the analyses performed. Please note: Abbreviations should be introduced at the first mention in the main text - no abbreviations lists. Suggested structure of main text (not enforced) is provided below.

bioinformatics↗

bioRxiv2020

MarkerCapsule: Explainable Single Cell Typing using Capsule Networks

Many single cell typing methods require manual annotation which casts problems with respect to resolution of (sub-)types, manpower resources and bias towards existing human knowledge. The integration of heterogeneous data and biologically meaningful interpretation of results are further current key challenges. We introduce MarkerCapsule, which leverages the landmark advantages of capsule networks achieved in their original applications in single cell typing. Thereby, the small amount of labeled data required and the naturally arising, biologically meaningful interpretation of cell types in terms of characteristic gene activity patterns are exemplary strengths, beyond outperforming the state of the art in terms of basic typing accuracy. MarkerCapsule is available at: https://github.com/sumantaray/MarkerCapsule.

bioinformatics↗

bioRxiv2020

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↗

bioRxiv2020

Human belief state-based exploration and exploitation in an information-selective reversal bandit task

Humans often face sequential decision-making problems, in which information about the environmental reward structure is detached from rewards for a subset of actions. In the current exploratory study, we introduce an information-selective symmetric reversal bandit task to model such situations and obtained choice data on this task from 24 participants. To arbitrate between different decision-making strategies that participants may use on this task, we developed a set of probabilistic agent-based behavioral models, including exploitative and explorative Bayesian agents, as well as heuristic control agents. Upon validating the model and parameter recovery properties of our model set and summarizing the participants choice data in a descriptive way, we used a maximum likelihood approach to evaluate the participants choice data from the perspective of our model set. In brief, we provide quantitative evidence that participants employ a belief state-based hybrid explorative-exploitative strategy on the information-selective symmetric reversal bandit task, lending further support to the finding that humans are guided by their subjective uncertainty when solving exploration-exploitation dilemmas.

neuroscience↗

bioRxiv2020

Decoding of attentional state using high-frequency local field potential is as accurate as using spikes

Local field potentials (LFPs) in visual cortex are reliably modulated when the subjects focus of attention is cued into versus out of the receptive field of the recorded sites, similar to modulation of spiking activity. However, human psychophysics studies have used an additional attention condition, neutral cueing, for decades. The effect of neutral cueing on spiking responses was examined recently and found to be intermediate between cued and uncued conditions. However, whether LFPs are also precise enough to represent graded states of attention is unknown. We found that LFPs during neutral cueing were intermediate between cued and uncued conditions, and, for a single electrode, attention was more discriminable using high frequency (>30 Hz) LFP power than spikes. Surprisingly, spikes did not outperform LFPs even when discriminability was computed using multiple electrodes. These results constrain the spatial scale attention operates over and highlight the usefulness of LFPs in studying attention.

neuroscience↗

bioRxiv2020

Gamma oscillations in primate primary visual cortex are severely attenuated by small stimulus discontinuities

Gamma oscillations have been hypothesized to play an important role in feature binding, based on the observation that continuous long bars induce stronger gamma in the visual cortex than bars with a small gap. Recently, many studies have shown that natural images, that have discontinuities in several low-level features, do not induce strong gamma oscillations, questioning their role in feature binding. However, the effect of different discontinuities on gamma has not been well studied. To address this, we recorded spikes and local field potential from two monkeys while they were shown gratings with discontinuities in space, orientation, phase or contrast. Gamma, but not spiking activity, drastically reduced with small discontinuities in all cases, suggesting that gamma could be a resonant phenomenon. An excitatory-inhibitory population model with stimulus-tuned recurrent inputs showed such resonant properties. Therefore, gamma could be a signature of excitation-inhibition balance, which gets disrupted due to discontinuities.

neuroscience↗

bioRxiv2020

RNAseq analysis of rodent spaceflight experiments is confounded by sample collection techniques

To understand the physiological changes that occur in response to spaceflight, mice are transported to the International Space Station (ISS) and housed for variable periods of time before euthanasia on-orbit or return to Earth. Sample collection under such difficult conditions introduces confounding factors that need to be identified and addressed. We found large changes in the transcriptome of mouse tissues dissected and preserved on-orbit compared to tissues from mice euthanized on-orbit, preserved, and dissected after return to Earth. Changes due to preservation method eclipsed those between flight and ground samples making it difficult to identify spaceflight-specific changes. Follow-on experiments to interrogate the roles of euthanasia methods, tissue and carcass preservation protocols, and library preparation methods suggested that differences due to preservation protocols are exacerbated when coupled with polyA selection. This has important implications for the interpretation of existing datasets and the design of future experiments.

systems biology↗

bioRxiv2020

APEX2 proximity proteomics resolves flagellum subdomains and identifies flagellum tip-specific proteins in Trypanosoma brucei

Trypanosoma brucei is the protozoan parasite responsible for sleeping sickness, a lethal vector-borne disease. T. brucei has a single flagellum that plays critical roles in parasite biology, transmission and pathogenesis. An emerging concept in flagellum biology is that the organelle is organized into subdomains, each having specialized composition and function. Overall flagellum proteome has been well-studied, but a critical gap in knowledge is the protein composition of individual flagellum subdomains. We have therefore used APEX-based proximity proteomics to examine protein composition of T. brucei flagellum subdomains. To assess effectiveness of APEX-based proximity labeling, we fused APEX2 to the DRC1 subunit of the nexin-dynein regulatory complex, an axonemal complex distributed along the flagellum. We found that DRC1-APEX2 directs flagellum-specific biotinylation and purification of biotinylated proteins yields a DRC1 "proximity proteome" showing good overlap with proteomes obtained from purified axonemes. We next employed APEX2 fused to a flagellar membrane protein that is restricted to the flagellum tip, adenylate cyclase 1 (AC1), or a flagellar membrane protein that is excluded from the flagellum tip, FS179. Principal component analysis demonstrated the pools of biotinylated proteins in AC1-APEX2 and FS179-APEX2 samples are distinguished from each other. Comparing proteins in these two pools allowed us to identify an AC1 proximity proteome that is enriched for flagellum tip proteins and includes several proteins involved in signal transduction. Our combined results demonstrate that APEX2-based proximity proteomics is effective in T. brucei and can be used to resolve proteome composition of flagellum subdomains that cannot themselves be readily purified. IMPORTANCESleeping sickness is a neglected tropical disease, caused by the protozoan parasite Trypanosoma brucei. The disease disrupts the sleep-wake cycle, leading to coma and death if left untreated. T. brucei motility, transmission, and virulence depend on its flagellum (aka cilium), which consists of several different specialized subdomains. Given the essential and multifunctional role of the T. brucei flagellum, there is need of approaches that enable proteomic analysis of individual subdomains. Our work establishes that APEX2 proximity labeling can, indeed, be implemented in the biochemical environment of T. brucei, and has allowed identification of proximity proteomes for different subdomains. This capacity opens the possibility to study the composition and function of other compartments. We further expect that this approach may be extended to other eukaryotic pathogens, and will enhance the utility of T. brucei as a model organism to study ciliopathies, heritable human diseases in which cilia function is impaired.

microbiology↗

bioRxiv2019

Atypical Protein Kinase C iota (PKC{lambda}/{iota}) Ensures Mammalian Development by Establishing the Maternal-Fetal Exchange Interface

In utero mammalian development relies on the establishment of the maternal-fetal exchange interface, which ensures transportation of nutrients and gases between the mother and the fetus. This exchange interface is established via development of multinucleated syncytiotrophoblast cells (SynTs) during placentation. In mouse, SynTs develop via differentiation of the trophoblast progenitor cells (TSPCs) of the placenta primordium and in human, SynTs are developed via differentiation of villous cytotrophoblast (CTB) progenitors. Despite the critical need in pregnancy progression, conserved signaling mechanisms that ensure SynT development are poorly understood. Herein, we show that Atypical Protein Kinase C iota (PKC{lambda}/I) plays an essential role in establishing the SynT differentiation program in trophoblast progenitors. Loss of PKC{lambda}/I in the mouse TSPCs abrogates SynT development leading to embryonic death at ~E9.0. We also show that PKC{lambda}/I-mediated priming of trophoblast progenitors for SynT differentiation is a conserved event during human placentation. PKC{lambda}/I is selectively expressed in the first-trimester CTBs of a developing human placenta. Furthermore, loss of PKC{lambda}/I in CTB-derived human trophoblast stem cells (Human TSCs) impairs their SynT differentiation potential both in vitro and after transplantation in immunocompromised mice. Our mechanistic analyses indicate that PKC{lambda}/I signaling maintains expression of GCM1, GATA2, and PPAR{gamma}, which are key transcription factors to instigate SynT differentiation programs in both mouse and human trophoblast progenitors. Our study uncovers a conserved molecular mechanism, in which PKC{lambda}/I signaling regulates establishment of the maternal-fetal exchange surface by promoting trophoblast progenitor to SynT transition during placentation.

developmental biology↗