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Article ; Online: Serum Chemerin Levels Correlate With Severity of Dysglycemia in Young Adult Women With Polycystic Ovary Syndrome.

Bose, Chiranjit / Mukherjee, Bidisha / Mukherjee, Ananya / Pramanik, Subhasish / Saha, Chinmay / Mondal, Asif / Mukhopadhyay, Satinath

Journal of the Endocrine Society

2024 Volume 8, Issue 4, Page(s) bvae023

Abstract: Context: A subset of polycystic ovary syndrome (PCOS) individuals also have type 2 diabetes (T2D); an unmet need to identify this subgroup exists.: Objective: We looked at the potential role of serum chemerin, a proinflammatory adipokine, in ... ...

Abstract	Context: A subset of polycystic ovary syndrome (PCOS) individuals also have type 2 diabetes (T2D); an unmet need to identify this subgroup exists. Objective: We looked at the potential role of serum chemerin, a proinflammatory adipokine, in identifying dysglycemic PCOS. Methods: A total of 93 PCOS and 33 healthy controls were classified, based on fasting and 2-hour plasma glucose levels (2hPGPG) and glycated hemoglobin A Results: Metabolic syndrome was present in 9.7% (National Cholesterol Education Program) of PCOS. Waist circumference, body fat (%), 2hPGPG, and HbA Conclusion: Elevated serum chemerin levels reliably identify PCOS individuals with dysglycemia. Further, longitudinal studies with larger samples are required to confirm this association.
Language	English
Publishing date	2024-03-01
Publishing country	United States
Document type	Journal Article
ISSN	2472-1972
ISSN (online)	2472-1972
DOI	10.1210/jendso/bvae023
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Article ; Online: Co-Regulation of Protein Coding Genes by Transcription Factor and Long Non-Coding RNA in SARS-CoV-2 Infected Cells: An In Silico Analysis.

Saha, Chinmay / Laha, Sayantan / Chatterjee, Raghunath / Bhattacharyya, Nitai P

Non-coding RNA

2021 Volume 7, Issue 4

Abstract: Altered expression of protein coding gene (PCG) and long non-coding RNA (lncRNA) have been identified in SARS-CoV-2 infected cells and tissues from COVID-19 patients. The functional role and mechanism (s) of transcriptional regulation of deregulated ... ...

Abstract	Altered expression of protein coding gene (PCG) and long non-coding RNA (lncRNA) have been identified in SARS-CoV-2 infected cells and tissues from COVID-19 patients. The functional role and mechanism (s) of transcriptional regulation of deregulated genes in COVID-19 remain largely unknown. In the present communication, reanalyzing publicly available gene expression data, we observed that 66 lncRNA and 5491 PCG were deregulated in more than one experimental condition. Combining our earlier published results and using different publicly available resources, it was observed that 72 deregulated lncRNA interacted with 3228 genes/proteins. Many targets of deregulated lncRNA could also interact with SARS-CoV-2 coded proteins, modulated by IFN treatment and identified in CRISPR screening to modulate SARS-CoV-2 infection. The majority of the deregulated lncRNA and PCG were targets of at least one of the transcription factors (TFs), interferon responsive factors (IRFs), signal transducer, and activator of transcription (STATs), NFκB, MYC, and RELA/p65. Deregulated 1069 PCG was joint targets of lncRNA and TF. These joint targets are significantly enriched with pathways relevant for SARS-CoV-2 infection indicating that joint regulation of PCG could be one of the mechanisms for deregulation. Over all this manuscript showed possible involvement of lncRNA and mechanisms of deregulation of PCG in the pathogenesis of COVID-19.
Language	English
Publishing date	2021-11-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2813993-8
ISSN	2311-553X ; 2311-553X
ISSN (online)	2311-553X
ISSN	2311-553X
DOI	10.3390/ncrna7040074
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Article: Decreased Levels of miR-126 and miR-132 in Plasma and Vitreous Humor of Non-Proliferative Diabetic Retinopathy Among Subjects with Type-2 Diabetes Mellitus.

Pramanik, Subhasish / Saha, Chinmay / Chowdhury, Subhankar / Bose, Chiranjit / Bhattacharyya, Nitai P / Mondal, Lakshmi Kanta

Diabetes, metabolic syndrome and obesity : targets and therapy

2022 Volume 15, Page(s) 345–358

Abstract: Purpose: Diabetic retinopathy (DR), the leading cause of blindness among working adults, is an urgent public health problem as diabetes mellitus (DM) is increasing at an alarming rate. Hyperglycemia-induced endothelial dysfunction is the principal ... ...

Abstract	Purpose: Diabetic retinopathy (DR), the leading cause of blindness among working adults, is an urgent public health problem as diabetes mellitus (DM) is increasing at an alarming rate. Hyperglycemia-induced endothelial dysfunction is the principal contributing factor leading to the development of microangiopathy. Altered levels of microRNA (miR), the negative regulator of protein-coding genes, have been observed and considered to be markers for DR. Present study aimed to find out whether miR levels in plasma could be effective biomarkers to differentiate between type 2 diabetes mellitus (T2DM) with non-proliferative retinopathy (NPDR) from T2DM with no-DR (DNR). Methods: We recruited 50 T2DM subjects comprising 31 NPDR and 19 DNR individuals. Surrogate markers of systemic oxidative stress and vascular endothelial growth factor (VEGF) were measured in plasma. Levels of miR-126 and miR-132 were determined in plasma and vitreous fluid using real-time PCR. Results: We observed that levels of miR-126 and miR-132 were decreased in NPDR subjects in comparison to DNR. Plasma levels of miRs were inversely correlated with secreted levels of VEGF and oxidative stress marker. The levels of these miRs showed discriminating ability between NPDR and DNR. Conclusion: Circulating miRs 126 and 132 in plasma or vitreous may serve as biomarkers for early diabetic retinopathy risk prediction, provided validated in a larger cohort and other forms of retinal vasculopathy or retinopathy in the future.
Language	English
Publishing date	2022-02-04
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2494854-8
ISSN	1178-7007
ISSN	1178-7007
DOI	10.2147/DMSO.S346097
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Article: Early changes in shoot transcriptome of rice in response to Rhodotorula mucilaginosa JGTA-S1.

Saha, Chinmay / Seal, Anindita

Genomics data

2015 Volume 6, Page(s) 237–240

Abstract: Yeasts of Rhodotorula genus have been reported to show endophytic colonization in different plants. Some of the Rhodotorula species are found to exhibit plant growth promoting activities and also have been reported to protect plants against invading ... ...

Abstract	Yeasts of Rhodotorula genus have been reported to show endophytic colonization in different plants. Some of the Rhodotorula species are found to exhibit plant growth promoting activities and also have been reported to protect plants against invading pathogens. A yeast strain closely related to Rhodotorula mucilaginosa was isolated from the endosphere of Typha angustifolia collected from a Uranium mine. A microarray analysis was performed to investigate the early changes in rice shoot transcripts in response to this yeast (R. mucilaginosa JGTA-S1). Transcriptional changes were monitored in 6 h and 24 h treated rice plant shoots as compared to 0 h control. The microarray data has been submitted to the NCBI GEO repository under the accession number of GSE64321.
Language	English
Publishing date	2015-10-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2751131-5
ISSN	2213-5960
ISSN	2213-5960
DOI	10.1016/j.gdata.2015.09.023
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Article: Early changes in shoot transcriptome of rice in response to Rhodotorula mucilaginosa JGTA-S1

Saha, Chinmay / Seal, Anindita

Genomics Data. 2015 Dec., v. 6

2015

Abstract	Yeasts of Rhodotorula genus have been reported to show endophytic colonization in different plants. Some of the Rhodotorula species are found to exhibit plant growth promoting activities and also have been reported to protect plants against invading pathogens. A yeast strain closely related to Rhodotorula mucilaginosa was isolated from the endosphere of Typha angustifolia collected from a Uranium mine. A microarray analysis was performed to investigate the early changes in rice shoot transcripts in response to this yeast (R. mucilaginosa JGTA-S1). Transcriptional changes were monitored in 6h and 24h treated rice plant shoots as compared to 0h control. The microarray data has been submitted to the NCBI GEO repository under the accession number of GSE64321.
Keywords	Rhodotorula rubra ; Typha angustifolia ; endophytes ; microarray technology ; pathogens ; plant growth ; rice ; shoots ; transcription (genetics) ; transcriptome ; uranium ; yeasts
Language	English
Dates of publication	2015-12
Size	p. 237-240.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2751131-5
ISSN	2213-5960
ISSN	2213-5960
DOI	10.1016/j.gdata.2015.09.023
Database	NAL-Catalogue (AGRICOLA)

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Article: In silico

Laha, Sayantan / Saha, Chinmay / Dutta, Susmita / Basu, Madhurima / Chatterjee, Raghunath / Ghosh, Sujoy / Bhattacharyya, Nitai P

Heliyon

2021 Volume 7, Issue 3, Page(s) e06395

Abstract: Altered expression of long noncoding RNA (lncRNA), longer than 200 nucleotides without potential for coding protein, has been observed in diverse human diseases including viral diseases. It is largely unknown whether lncRNA would deregulate in SARS-CoV-2 ...

Abstract	Altered expression of long noncoding RNA (lncRNA), longer than 200 nucleotides without potential for coding protein, has been observed in diverse human diseases including viral diseases. It is largely unknown whether lncRNA would deregulate in SARS-CoV-2 infection, causing ongoing pandemic COVID-19. To identify, if lncRNA was deregulated in SARS-CoV-2 infected cells, we analyzed in silico the data in GSE147507. It was revealed that expression of 20 lncRNA like MALAT1, NEAT1 was increased and 4 lncRNA like PART1, TP53TG1 was decreased in at least two independent cell lines infected with SARS-CoV-2. Expression of NEAT1 was also increased in lungs tissue of COVID-19 patients. The deregulated lncRNA could interact with more than 2800 genes/proteins and 422 microRNAs as revealed from the database that catalogs experimentally determined interactions. Analysis with the interacting gene/protein partners of deregulated lncRNAs revealed that these genes/proteins were associated with many pathways related to viral infection, inflammation and immune functions. To find out whether these lncRNAs could be regulated by STATs and interferon regulatory factors (IRFs), we used ChIPBase v2.0 that catalogs experimentally determined binding from ChIP-seq data. It was revealed that any one of the transcription factors IRF1, IRF4, STAT1, STAT3 and STAT5A had experimentally determined binding at regions within -5kb to +1kb of the deregulated lncRNAs in at least 2 independent cell lines/conditions. Our analysis revealed that several lncRNAs could be regulated by IRF1, IRF4 STAT1 and STAT3 in response to SARS-CoV-2 infection and lncRNAs might be involved in antiviral response. However, these in silico observations are necessary to be validated experimentally.
Language	English
Publishing date	2021-02-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2021.e06395
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Article ; Online: A unique life-strategy of an endophytic yeast Rhodotorula mucilaginosa JGTA-S1-a comparative genomics viewpoint.

Sen, Diya / Paul, Karnelia / Saha, Chinmay / Mukherjee, Gairik / Nag, Mayurakshi / Ghosh, Samrat / Das, Abhishek / Seal, Anindita / Tripathy, Sucheta

DNA research : an international journal for rapid publication of reports on genes and genomes

2019 Volume 26, Issue 2, Page(s) 131–146

Abstract: Endophytic yeasts of genus Rhodotorula are gaining importance for their ability to improve plant growth. The nature of their interaction with plants, however, remains unknown. Rhodotorula mucilaginosa JGTA-S1 was isolated as an endophyte of Typha ... ...

Abstract	Endophytic yeasts of genus Rhodotorula are gaining importance for their ability to improve plant growth. The nature of their interaction with plants, however, remains unknown. Rhodotorula mucilaginosa JGTA-S1 was isolated as an endophyte of Typha angustifolia and promoted growth in the host. To investigate the life-strategy of the yeast from a genomics perspective, we used Illumina and Oxford Nanopore reads to generate a high-quality annotated draft assembly of JGTA-S1 and compared its genome to three other Rhodotorula yeasts and the close relative Rhodosporidium toruloides. JGTA-S1 is a haploid yeast possessing several genes potentially facilitating its endophytic lifestyle such as those responsible for solubilizing phosphate and producing phytohormones. An intact mating-locus in JGTA-S1 raised the possibility of a yet unknown sexual reproductive cycle in Rhodotorula yeasts. Additionally, JGTA-S1 had functional anti-freezing genes and was also unique in lacking a functional nitrate-assimilation pathway-a feature that is associated with obligate biotrophs. Nitrogen-fixing endobacteria were found within JGTA-S1 that may circumvent this defective N-metabolism. JGTA-S1 genome data coupled with experimental evidence give us an insight into the nature of its beneficial interaction with plants.
MeSH term(s)	Bacteria/metabolism ; Endophytes ; Genome, Fungal ; Genomics ; Metabolic Networks and Pathways ; Nitrogen/metabolism ; Pseudomonas stutzeri/metabolism ; Rhodotorula/genetics ; Rhodotorula/metabolism ; Rhodotorula/physiology ; Sequence Analysis, DNA ; Symbiosis ; Typhaceae
Chemical Substances	Nitrogen (N762921K75)
Language	English
Publishing date	2019-01-07
Publishing country	England
Document type	Journal Article
ZDB-ID	1212508-8
ISSN	1756-1663 ; 1340-2838
ISSN (online)	1756-1663
ISSN	1340-2838
DOI	10.1093/dnares/dsy044
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Article ; Online: Author Correction: An Endophytic Bacterial Consortium modulates multiple strategies to improve Arsenic Phytoremediation Efficacy in Solanum nigrum.

Mukherjee, Gairik / Saha, Chinmay / Naskar, Nabanita / Mukherjee, Abhishek / Mukherjee, Arghya / Lahiri, Susanta / Majumder, Arun Lahiri / Seal, Anindita

Scientific reports

2018 Volume 8, Issue 1, Page(s) 16365

Abstract: A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper. ...

Abstract	A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Language	English
Publishing date	2018-10-31
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-33707-1
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Article ; Online: An Endophytic Bacterial Consortium modulates multiple strategies to improve Arsenic Phytoremediation Efficacy in Solanum nigrum.

Mukherjee, Gairik / Saha, Chinmay / Naskar, Nabanita / Mukherjee, Abhishek / Mukherjee, Arghya / Lahiri, Susanta / Majumder, Arun Lahiri / Seal, Anindita

Scientific reports

2018 Volume 8, Issue 1, Page(s) 6979

Abstract: Endophytic microbes isolated from plants growing in contaminated habitats possess specialized properties that help their host detoxify the contaminant/s. The possibility of using microbe-assisted phytoremediation for the clean-up of Arsenic (As) ... ...

Abstract	Endophytic microbes isolated from plants growing in contaminated habitats possess specialized properties that help their host detoxify the contaminant/s. The possibility of using microbe-assisted phytoremediation for the clean-up of Arsenic (As) contaminated soils of the Ganga-Brahmaputra delta of India, was explored using As-tolerant endophytic microbes from an As-tolerant plant Lantana camara collected from the contaminated site and an intermediate As-accumulator plant Solanum nigrum. Endophytes from L. camara established within S. nigrum as a surrogate host. The microbes most effectively improved plant growth besides increasing bioaccumulation and root-to-shoot transport of As when applied as a consortium. Better phosphate nutrition, photosynthetic performance, and elevated glutathione levels were observed in consortium-treated plants particularly under As-stress. The consortium maintained heightened ROS levels in the plant without any deleterious effect and concomitantly boosted distinct antioxidant defense mechanisms in the shoot and root of As-treated plants. Increased consortium-mediated As(V) to As(III) conversion appeared to be a crucial step in As-detoxification/translocation. Four aquaporins were differentially regulated by the endophytes and/or As. The most interesting finding was the strong upregulation of an MRP transporter in the root by the As + endophytes, which suggested a major alteration of As-detoxification/accumulation pattern upon endophyte treatment that improved As-phytoremediation.
MeSH term(s)	Arsenic/metabolism ; Biodegradation, Environmental ; Endophytes/growth & development ; Endophytes/metabolism ; Glutathione/metabolism ; India ; Lantana/microbiology ; Microbial Consortia ; Oxidative Stress ; Phosphates/metabolism ; Photosynthesis ; Reactive Oxygen Species/metabolism ; Soil Pollutants/metabolism ; Solanum nigrum/growth & development ; Solanum nigrum/metabolism ; Solanum nigrum/microbiology ; Stress, Physiological
Chemical Substances	Phosphates ; Reactive Oxygen Species ; Soil Pollutants ; Glutathione (GAN16C9B8O) ; Arsenic (N712M78A8G)
Language	English
Publishing date	2018-05-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-25306-x
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Article: Epidemiological challenges in pandemic coronavirus disease (COVID-19): Role of artificial intelligence.

Wiley interdisciplinary reviews. Data mining and knowledge discovery

2022 Volume 12, Issue 4, Page(s) e1462

Abstract: World is now experiencing a major health calamity due to the coronavirus disease (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus clade 2. The foremost challenge facing the scientific community is to explore the growth and ...

Abstract	World is now experiencing a major health calamity due to the coronavirus disease (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus clade 2. The foremost challenge facing the scientific community is to explore the growth and transmission capability of the virus. Use of artificial intelligence (AI), such as deep learning, in (i) rapid disease detection from x-ray or computed tomography (CT) or high-resolution CT (HRCT) images, (ii) accurate prediction of the epidemic patterns and their saturation throughout the globe, (iii) forecasting the disease and psychological impact on the population from social networking data, and (iv) prediction of drug-protein interactions for repurposing the drugs, has attracted much attention. In the present study, we describe the role of various AI-based technologies for rapid and efficient detection from CT images complementing quantitative real-time polymerase chain reaction and immunodiagnostic assays. AI-based technologies to anticipate the current pandemic pattern, prevent the spread of disease, and face mask detection are also discussed. We inspect how the virus transmits depending on different factors. We investigate the deep learning technique to assess the affinity of the most probable drugs to treat COVID-19. This article is categorized under:Application Areas > Health CareAlgorithmic Development > Biological Data MiningTechnologies > Machine Learning.
Language	English
Publishing date	2022-06-28
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1942-4787
ISSN	1942-4787
DOI	10.1002/widm.1462
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