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Sudeepto Bhattacharya

Bio: Sudeepto Bhattacharya is an academic researcher from Shiv Nadar University. The author has contributed to research in topics: Wildlife corridor & Population. The author has an hindex of 5, co-authored 12 publications receiving 62 citations.

Papers
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Journal ArticleDOI
07 Sep 2018-PLOS ONE
TL;DR: Meta-analysis and co-expression network comparison of drought and cold stress response in Arabidopsis thaliana and gene ontology-based enrichment analysis identified shared biological processes and molecular mechanisms such as—‘photosynthesis’, ‘respiratory burst’ and ‘response to hormone’ which were affected under cold and drought stress.
Abstract: Multiple environmental stresses adversely affect plant growth and development. Plants under multiple stress condition trigger cascade of signals and show response unique to specific stress as well as shared responses, common to individual stresses. Here, we aim to identify common and unique genetic components during stress response mechanisms liable for cross-talk between stresses. Although drought and cold stress have been widely studied, insignificant information is available about how their combination affects plants. To that end, we performed meta-analysis and co-expression network comparison of drought and cold stress response in Arabidopsis thaliana by analyzing 390 microarray samples belonging to 29 microarray studies. We observed 6120 and 7079 DEGs (differentially expressed genes) under drought and cold stress respectively, using Rank Product methodology. Statistically, 28% (2890) DEGs were found to be common in both the stresses (i.e.; drought and cold stress) with most of them having similar expression pattern. Further, gene ontology-based enrichment analysis have identified shared biological processes and molecular mechanisms such as—‘photosynthesis’, ‘respiratory burst’, ‘response to hormone’, ‘signal transduction’, ‘metabolic process’, ‘response to water deprivation’, which were affected under cold and drought stress. Forty three transcription factor families were found to be expressed under both the stress conditions. Primarily, WRKY, NAC, MYB, AP2/ERF and bZIP transcription factor family genes were highly enriched in all genes sets and were found to regulate 56% of common genes expressed in drought and cold stress. Gene co-expression network analysis by WGCNA (weighted gene co-expression network analysis) revealed 21 and 16 highly inter-correlated gene modules with specific expression profiles under drought and cold stress respectively. Detection and analysis of gene modules shared between two stresses revealed the presence of four consensus gene modules.

54 citations

Journal ArticleDOI
TL;DR: In this article, a graph theoretic network approach has been used to model the potential connectivity of the natural areas in Darjeeling Himalayas which provide connectivity to the invasive species Maling bamboo ( Yushania maling ).

23 citations

Journal ArticleDOI
01 Jan 2020-Genomics
TL;DR: A stress-specific TF-miRNA-gene network was built for Arabidopsis under drought, cold, salt and waterlogging stress using data from reliable publically available databases; and transcriptome and degradome sequence data analysis by meta-analysis approach elucidated significantly dense, scale-free, small world and hierarchical backbone of interactions.

13 citations

Journal ArticleDOI
TL;DR: Game theory and graph theory are used to model and design a wildlife corridor in the Central India – Eastern Ghats landscape complex, with tiger as the focal species and a cost matrix is constructed to indicate the cost incurred by the tiger for passage between the habitat patches in the landscape.

12 citations

Journal ArticleDOI
TL;DR: In this paper, the authors have constructed multiple abiotic stresses responsive TF-miRNA-gene regulatory network for Oryza sativa using transcriptome and degradome sequencing data meta-analysis approach.
Abstract: Climate changes and environmental stresses have a consequential association with crop plant growth and yield that raise the necessity to cultivate crops having tolerance towards changing climate and environmental disturbances such as water stress, temperature fluctuation, salt toxicity. Recent studies have shown miRNAs and transcription factors; the trans-acting regulatory elements is emerging as a promising tool for engineering naive improved crop varieties, having tolerance for multiple environmental stresses and enhanced quality as well as yield. However, the interwoven complex regulatory function of transcription factors (TF) and miRNAs at transcriptional and post-transcriptional levels is unexplored in Oryza sativa. To this end, we have constructed multiple abiotic stresses responsive TF-miRNA-gene regulatory network for Oryza sativa using transcriptome and degradome sequencing data meta-analysis approach. The theoretical network approach has shown the networks to be dense, scale-free, and small-world that makes the network stable, invariant to scale change where an efficient, quick transmission of biological signals occurs within the network on extrinsic hindrance. The analysis also deciphered the existence of communities (cluster of TF, miRNA, and genes) working together to help plant in acclimatizing with multiple stresses. It highlighted genes, TFs, and miRNAs shared by multiple stresses conditions that work as a hub or bottlenecks for signal propagation, for example, during interaction between stress-responsive genes (TFs/miRNAs/ other genes) and genes involved in floral development pathways under multiple environmental stresses. Thus, this study further highlights the questions: how the fine-tuning feedback mechanism works for balancing stress tolerance and timely flowering to survive the adverse condition. As a component of this study, we developed the abiotic stress-responsive regulatory network, APRegNet database (http://lms.snu.edu.in/APRegNet), which may help the researchers studying the roles of miRNAs and transcription factors. Furthermore, this study will advance the current understanding of multiple abiotic stress tolerance mechanisms.

7 citations


Cited by
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Proceedings ArticleDOI
22 Jan 2006
TL;DR: Some of the major results in random graphs and some of the more challenging open problems are reviewed, including those related to the WWW.
Abstract: We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

7,116 citations

30 Apr 1984
TL;DR: A review of the literature on optimal foraging can be found in this article, with a focus on the theoretical developments and the data that permit tests of the predictions, and the authors conclude that the simple models so far formulated are supported by available data and that they are optimistic about the value both now and in the future.
Abstract: Beginning with Emlen (1966) and MacArthur and Pianka (1966) and extending through the last ten years, several authors have sought to predict the foraging behavior of animals by means of mathematical models. These models are very similar,in that they all assume that the fitness of a foraging animal is a function of the efficiency of foraging measured in terms of some "currency" (Schoener, 1971) -usually energy- and that natural selection has resulted in animals that forage so as to maximize this fitness. As a result of these similarities, the models have become known as "optimal foraging models"; and the theory that embodies them, "optimal foraging theory." The situations to which optimal foraging theory has been applied, with the exception of a few recent studies, can be divided into the following four categories: (1) choice by an animal of which food types to eat (i.e., optimal diet); (2) choice of which patch type to feed in (i.e., optimal patch choice); (3) optimal allocation of time to different patches; and (4) optimal patterns and speed of movements. In this review we discuss each of these categories separately, dealing with both the theoretical developments and the data that permit tests of the predictions. The review is selective in the sense that we emphasize studies that either develop testable predictions or that attempt to test predictions in a precise quantitative manner. We also discuss what we see to be some of the future developments in the area of optimal foraging theory and how this theory can be related to other areas of biology. Our general conclusion is that the simple models so far formulated are supported are supported reasonably well by available data and that we are optimistic about the value both now and in the future of optimal foraging theory. We argue, however, that these simple models will requre much modification, espicially to deal with situations that either cannot easily be put into one or another of the above four categories or entail currencies more complicated that just energy.

2,709 citations

Journal ArticleDOI
TL;DR: In this article, the authors used Land Change Modeller (LCM)-Markov Chain models to simulate urban expansion in three cities (Kuala Lumpur, Metro Manila and Jakarta), all experiencing rapid urban expansion, and identify which are the main drivers, including spatial planning, in the resulting spatial patterns.

138 citations

01 Jan 2014
TL;DR: In this article, the authors used individual-based genetic analysis in combination with landscape permeability models to identify and prioritize movement corridors across seven tiger populations within the Central Indian Landscape, and found that the covariates that best explained tiger occupancy were large, remote, dense forest patches; large ungulate abundance, and low human footprint.
Abstract: Even with global support for tiger (Panthera tigris) conservation their survival is threatened by poaching, habitat loss and isolation. Currently about 3,000 wild tigers persist in small fragmented populations within seven percent of their historic range. Identifying and securing habitat linkages that connect source populations for maintaining landscape-level gene flow is an important long-term conservation strategy for endangered carnivores. However, habitat corridors that link regional tiger populations are often lost to development projects due to lack of objective evidence on their importance. Here, we use individual based genetic analysis in combination with landscape permeability models to identify and prioritize movement corridors across seven tiger populations within the Central Indian Landscape. By using a panel of 11 microsatellites we identified 169 individual tigers from 587 scat and 17 tissue samples. We detected four genetic clusters within Central India with limited gene flow among three of them. Bayesian and likelihood analyses identified 17 tigers as having recent immigrant ancestry. Spatially explicit tiger occupancy obtained from extensive landscape-scale surveys across 76,913 km2 of forest habitat was found to be only 21,290 km2. After accounting for detection bias, the covariates that best explained tiger occupancy were large, remote, dense forest patches; large ungulate abundance, and low human footprint. We used tiger occupancy probability to parameterize habitat permeability for modeling habitat linkages using least-cost and circuit theory pathway analyses. Pairwise genetic differences (F ST) between populations were better explained by modeled linkage costs (r>0.5, p<0.05) compared to Euclidean distances, which was in consonance with observed habitat fragmentation. The results of our study highlight that many corridors may still be functional as there is evidence of contemporary migration. Conservation efforts should provide legal status to corridors, use smart green infrastructure to mitigate development impacts, and restore habitats where connectivity has been lost.

70 citations

Journal ArticleDOI
TL;DR: In this paper, a review describes the rapid expansion of bamboo hectarage, both intentional and by encroachment, in native and non-native countries, and details of the influence of bamboo invasion on biodiversity and soil processes as well as potential ecological risk.

67 citations