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Co-Authors

Santi Ranjan Dey
Pankaj K. Singh
Mitu De
Meesha Singh
Mahashweta Mitra Ghosh
Rajdeep Das
Bidisha Mallick
Debleena Roy
Suchita Sinha
Rajat Banerjee
Sarmishta Mukhopadhyay
Santanu Chakrabarti
Wrick Chakraborty
Paramita Nandy (Datta)
Saptarshi Bhattacharyya
Saptaki De
Souradip Basu
Gaurab Aditya Dhar
Souptik Ghosh
Nabarun Dawn
Sohini Ganguli Gupta
Arunima Bhattacharya

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Journal of Environment and Sociobiology

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Ganguli, Sayak

Seri - Bioinformatics : To Enhance Silken Touch

Abstract Views :369 | PDF Views:0

Authors

Santi Ranjan Dey ¹, Pankaj K. Singh ², Sayak Ganguli ³, Mitu De ⁴

Affiliations
1 Department of Zoology, Rammohan College, Kolkata 700010, IN
2 Computational Biology Division, The Biome-Kolkata-700064, IN
3 Theoretical and Computational Biology Division, Amplicon Biosciences, Palta-743122, IN
4 Department of Botany, Gurudas College, Kolkata-700054, IN

Source

Journal of Environment and Sociobiology, Vol 13, No 2 (2016), Pagination: 207-216

Abstract

Computational Biology has emerged as one of the leading interdisciplinary realms having applications and analytical implications in every branch of biological sciences. The efforts to understand silkworm or its interactions with other organisms have generated a plethora of information which has been converted into different types of electronic databases. Application of modern methodologies, such as, next generation sequencing - comparative modelling and simulation, docking and design of specific molecules which not only provide insight on disease incidence and progression in silkworms but also provides us with necessary information for enhancement of silk fibre quality for enhancing that silken touch. These seri-bioinformatics databases are a valuable seri-bioresource. In this paper, we have reviewed some of the available online resources on silkworm and its related organisms, including databases as well as informative websites. Designed as a basic platform and accompanied by the SilkDB, MorusDB and strives to be a comprehensive platform for the silkworm-mulberry interaction studies. Some of the other seri-databases reviewed are BmMDB, MulSatDB and SilkTransDB. Application of bioinformatics tools and techniques not only facilitated detection of proteomic and genomic diversity among the species/strains but also resulted in finding a gap in the silkworm genome sequence of a strain that diverged during the course of domestication.

Keywords

Next Generation Sequencing, Mulberry, Silkworm, Seri-Databases, MorusDB.

Full Text

References

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Antimicrobial and Computational Assessment of Christella dentata Crude Extracts Against Multidrug Resistant Bacterial Cultures and Targets

Abstract Views :361 | PDF Views:1

Authors

Meesha Singh ¹, Sayak Ganguli ², Sayak Ganguli ², Mahashweta Mitra Ghosh ¹, Mahashweta Mitra Ghosh ¹

Affiliations
1 Department of Microbiology, St. Xavier’s College, Kolkata-700016, IN
2 Department of Biotechnology, St. Xavier’s College, Kolkata-700016, IN

Source

Journal of Environment and Sociobiology, Vol 17, No 1 (2020), Pagination: 1-10

Abstract

There has been an abrupt increase in the emergence of antibiotic resistant bacteria and related infections throughout the globe. There is a dire need to explore novel botanicals with the purpose of identifying potential antibacterial compounds effective against such drug resistant bacteria. This study focuses on the screening of crude ethanolic extracts of an edible fern, Christella dentata. The biochemical tests and antibacterial efficacy assay against cultures of E. coli, Salmonella, Pseudomonas, Bacillus and Lactobacillus indicate the potency of the crude extracts. The study was further extended by text and literature-based identification of active principles from the plant under study. The identified compounds were then tested for their druggabilities and docked against reported targets of multidrug resistant (MDR) strains of E. coli, Klebsiella pneumoniae and Staphylococcus aureus. Results indicate that some of these active compounds can be explored as potential leads for inhibiting the protein targets and preventing the spread of these MDR strains.

Keywords

Ferns, Hospital effluent, Multidrug Resistance, Phytochemicals, Molecular docking, Computational Study.

Full Text

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Insights into Rhizospheric Bacterial Abundance of Bruguiera gymnorhiza (l.) LAM. from the Indian Sunderbans

Abstract Views :276 | PDF Views:2

Authors

Rajdeep Das ¹, Bidisha Mallick ¹, Debleena Roy ¹, Suchita Sinha ¹, Rajat Banerjee ², Sayak Ganguli ³

Affiliations
1 Department of Botany, Lady Brabourne College, Kolkata-700017, West Bengal, IN
2 Department of Biotechnology, University of Calcutta, Kolkata-700019, West Bengal, IN
3 Department of Biotechnology, St. Xavier’s College, Kolkata-700016, West Bengal, IN

Source

Journal of Environment and Sociobiology, Vol 17, No 1 (2020), Pagination: 43-47

Abstract

The sturdiness of mangrove plants, such as Bruguiera gymnorhiza (L.) Lam, has been related to their inherent physiological resistance and beneficial interactions with associated and specific microbial communities. Development in metagenomics provides a more complete picture of rhizosphere microbiome. In this work we analysed bacterial community of ischolar_main rhizosphere of B. gymnorhiza using 16s rRNA metagenome next generation sequencing (Oxford Nanopore minion platfrom) and found Candidatus, Ectothiorhodospira, Holophaga, Nitrospira, Pelagibius, Sulfitobacter, Thioalkalivibrio, Vicinamibacter, Woeseia to be most abundant genera, which provides a new insight into the functional and microbial diversity of the rhizospheric assemblage of the plant under study.

Keywords

Bruguiera gymnorhiza, Metagenomics, Microbiome, Oxford Nanopore, 16s rRNA

Full Text

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Functional Annotation of Pathogenesis Proteins in Shigella flexneri using Comparative Genomics

Abstract Views :239 | PDF Views:1

Authors

Sarmishta Mukhopadhyay ¹, Sayak Ganguli ², Santanu Chakrabarti ¹

Affiliations
1 Department of Zoology, Government General Degree College, Singur, West Bengal, IN
2 Department of Biotechnology, St. Xavier’s College, Kolkata- 700016, IN

Source

Journal of Environment and Sociobiology, Vol 17, No 1 (2020), Pagination: 65-78

Abstract

The Gram-negative bacteria, Shigella species, is a predominant diarrheal pathogen and itself accounts for 15% of the diarrheal episodes occurring globally. Shigella enters the human body through ingestion of contaminated food and water and on reaching the intestine, dismantles the epithelial barrier, generating symptoms varying from mild to severe bloody diarrhea. Widespread diversity of Shigella species and the emergence of multi-drug resistant strains in recent years has made it extremely enigmatic to design a successful drug to combat shigellosis. This work focusses on comparative genomics methods to identify and annotate hypothetical proteins from the Shigella flexneri genome in quest of identifying novel druggable targets.

Keywords

Shigellosis, Hypothetical Proteins, Comparative Genomics, Drug Targets.

Full Text

References

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Rhizospheric Metagenome Dataset of the Terrestrial Mangrove Nypa fruticans Wurmb. from Indian Sunderbans

Abstract Views :265 | PDF Views:1

Authors

Wrick Chakraborty ¹, Sayak Ganguli ², Paramita Nandy (Datta) ¹

Affiliations
1 Department of Botany, Sister Nibedita Government General Degree College for Girls, 20B, Judges Court Road, Kolkata-700027, West Bengal, IN
2 Department of Biotechnology, St. Xavier’s College (Autonomous), Kolkata-700016, IN

Source

Journal of Environment and Sociobiology, Vol 17, No 1 (2020), Pagination: 79-82

Abstract

Microorganisms that colonize the rhizosphere help plants to cope with infection, toxic compounds, and other sources of stress. This work attempts to analyse the rhizospheric abundance of microorganisms around Nypa fruticans Wurmb. to characterise the optimum microbial content for proper survivability of the mangrove species. This is the first study which reports Nypa fruticans Wurmb. rhizospheric association of microorganisms.

Keywords

Nypa Fruticans, Indian Sunderbans, Rhizospheric Metagenome.

Full Text

References

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Insights Into The Structure And Dynamics Of Shigella Invasion Proteins For Use As Potential Drug Targets

Abstract Views :132 | PDF Views:0

Authors

Sarmishta Mukhopadhyay ¹, Sayak Ganguli ¹, Santanu Chakrabarti ²

Affiliations
1 Department of Biotechnology, St. Xavier’s College (Autonomous), Kolkata-700016, IN
2 Department of Zoology, Government General Degree College, Singur, West Bengal, IN

Source

Journal of Environment and Sociobiology, Vol 19, No 1 (2022), Pagination: 37-42

Abstract

The Gram-negative bacteria, Shigella spp. has always been a pathogen of concern in the context of global burden of diarrheal diseases, with recent surveys taking the annual incidence of shigellosis to roughly 125 million cases worldwide. The scenario has been further worsened by the frequent reports on isolation of multi drug resistant (MDR) Shigella strains, showing resistance against potent antibiotics including the 3rd generation cephalosporins as well. With the recent years witnessing a growing interest in the discovery of novel drugs, this work has scrutinized the structural nitty-gritty of the predominant virulence factors in Shigella, viz. the invasion plasmid antigens IpaA, IpaB, IpaC and IpaD, that are evidenced to have multifaceted role in the pathogenesis cascade, to explore their potential as promising therapeutic targets. In this work we report the 3D models of the different invasion proteins using comparative modeling and a comprehensive structural evaluation protocol for evaluating their stability as drug targets. Our data suggest significant potential of these invasion proteins to serve as future drug targets, thus opening up the avenue for further investigations.

Keywords

Shigella, Invasion proteins, Structural analysis, Drug targets, In-silico.

Full Text

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Comparative Profiling of Rice Endospheric Bacterial Assemblages to Identify Climate Independent Core

Abstract Views :132 | PDF Views:3

Authors

Saptarshi Bhattacharyya ¹, Saptaki De ¹, Souradip Basu ², Gaurab Aditya Dhar ³, Sayak Ganguli ¹

Affiliations
1 Post Graduate Department of Biotechnology, St. Xavier’s College (Autonomous), Kolkata., IN
2 Post Graduate Department of Microbiology, St. Xavier’s College (Autonomous), Kolkata., IN
3 Post Graduate Department of Botany, Lady Brabourne College, Kolkata, India., IN

Source

Journal of Environment and Sociobiology, Vol 19, No 2 (2022), Pagination: 137-145

Abstract

Microbial communities present in plant roots have a significant impact on plant nourishment and output. Although it has been hypothesized that increased atmospheric CO₂ and heat will alter above- and below-ground plant activities, it is still undetermined how root-associated microbial population will react to these changes, particularly in agroecosystems. Recently, several technologies related to the variety and microbiome of plants have been used, including sequencing, metagenomics, and bioinformatics. Minimal research has been conducted on the variables that affect how plant microorganisms are composed. Microbial communities are effective biogeochemical cycle regulators, which makes them a superior strategy for reducing the effects of shifting climatic patterns and enables optimum usage of greenhouse gases for metabolic processes. Okibacterium, Catellicoccus, Acinetobacter and Massilia are found to be of highest dominance in the root endosphere which help in development of the plants. Recently, studies are conducted on the root microbiome to check their responses to the gradual changing climate. This in turn can provide us with the knowledge on microbial supplementation which can be used for various challenging conditions that hinder the growth of plants

Keywords

Rice Endosphere, Metagenomics, Climate Change, Greenhouse Gases.

Full Text

References

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Microbial Enrichment in Global Wastewater Niches Under Impact of Climate Change – A Computational Study

Abstract Views :188 | PDF Views:0

Authors

Souptik Ghosh ¹, Nabarun Dawn ¹, Souradip Basu ², Sayak Ganguli ¹

Source

Journal of Environment and Sociobiology, Vol 19, No 2 (2022), Pagination: 221-243

Abstract

With rise in industrialization and human activities, global warming and eventually climate change concerns are looming large on the face of humankind. Wastewater, being the sink for local microbial community can be assessed and analyzed as an indicator for climate change. Impacts of global warming are far-reaching and cause changes in life processes occurring in Nature, which gets reflected on the abundance of microorganisms detected in the wastewater. Greenhouse gases like Methane and Nitrous oxide, are the major players of global warming. The data used in our research was collected from rural, urban and delta region of India, regions of São Paulo, Brazil, along with domestic and industrial regions of Henan, China. The data were analyzed after thorough metagenomics study. Changes in nutrient cycling, such as carbon and nitrogen cycling, rise of several diseases and antibiotic resistance amongst the microorganisms have been detected. Increase in mean temperature of earth will also cause changes in the life processes of microorganisms and the ones which can survive outside the temperature niche of initial habitat can survive. Thus, by observing these six data sets, we aim to investigate the roles of microbes present in wastewater as an indicator for climate change.

Keywords

Climate Change, Wastewater, Global warming, Methane, Nitrous oxide.

Full Text

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Repetitive Sequences in Monocot MICRORNAs – Targets for Future Bioengineering Strategies for Climate Resilient Crops

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Authors

Sohini Ganguli Gupta ¹, Souradip Basu ², Sayak Ganguli ³

Affiliations
1 Post Graduate Department of Botany, Barasat Government College, Barasat., IN
2 Post Graduate Department of Microbiology, St. Xavier’s College (Autonomous), Kolkata., IN
3 Department of Biotechnology, St. Xavier’s College (Autonomous), Kolkata., IN

Source

Journal of Environment and Sociobiology, Vol 19, No 2 (2022), Pagination: 295-306

Abstract

miRNAs are a de novo class of endogenous, small, non-coding RNAs (19–21 nucleotides long) that are evolutionarily conserved and have a direct impact on the processes of development, differentiation, growth, metabolism, and disease resistance. Micro (mi)RNAs having high base- pair complementarity exert their effect by post-transcriptional silencing of targets. miRNAs functions by acting upon target mRNA induce cleavage and subsequent degradation of it. Further more, they can also repress the translational targets. mRNA deadenylation and their subsequent degradation is caused by the induction of translational repression of miRNAs in animals. Plant miRNA not only differ in their mechanism of gene regulation but they also differ from biogenesis point of view. Majority of the miRNAs function as negative switches to control the expression of important genes, like transcription factors, which affects how the body reacts to stress and during development. With the impact of climate change the mean average temperatures are on the rise. Thus, the need of the hour is to identify or develop crops that can be grown in areas even under above normal temperatures. For this the microRNA regulatory pathways offers us with the necessary tweaking cascade that can be explored further. This work focuses on the identification of internal repeats in microRNA sequences which not only enables us to identify and map the occurrence of the specific molecules but also enables us to formulate methods for their regulation. Results indicate that there is a strong correlation between the occurrence of internal repeats and miRNA stability.

Keywords

Climate Change, MicroRNAs, Internal Repeats.

Full Text

References

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Predicting Drug Targets from Hypothetical Proteins of Pseudomonas Sp. Released from Permafrost Thawing under Impact of Climate Change

Abstract Views :126 | PDF Views:0

Authors

Arunima Bhattacharya ¹, Sarmishta Mukhopadhyay ¹, Sayak Ganguli ¹

Affiliations
1 Post-Graduate Department of Biotechnology, St. Xavier’s College (Autonomous), Kolkata, West Bengal, IN

Source

Journal of Environment and Sociobiology, Vol 19, No 2 (2022), Pagination: 153-170

Abstract

One of the major consequences of the increase in global temperature is the thawing of permafrost, which is predicted to cause huge imbalances in natural ecosystems. The results of permafrost thawing is the resurface of quiescent psychrotolerant microbes which have been shown to be storehouses of antibiotic resistance genes (ARGs). Such superbugs, even if non-pathogenic, can transfer the ARGs to active pathogens, aggravating the existing public health crisis of antibiotic resistance. It is thus imperative to explore novel drug targets. Like most other organisms, bacteria possess coding sequences in the genome whose cellular and biochemical functions remain to be predicted. Functional annotation of such hypothetical proteins and their subsequent exploration as drug targets can thus be attempted as a novel computer-aided drug discovery approach. In this paper, we propose an in-silico pipeline for characterisation and functional annotation of hypothetical proteins using Pseudomonas aeruginosa, a multidrug-resistant WHO-listed critical priority pathogen. We then explore their potential as drug targets with small molecules of plant origin. Our results show considerable interactions between the proteins and the small molecules, including successful molecular docking, establishing a successful pipeline which may be useful in small molecule-based drug discovery in the near future.

Keywords

Permafrost thawing, Antibiotic resistance, Pseudomonas aeruginosa, Hypothetical protein

Full Text

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