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Article ; Online: ENLIGHTENMENT: A Scalable Annotated Database of Genomics and NGS-Based Nucleotide Level Profiles.

Sinha, Rituparna / Pal, Rajat Kumar / De, Rajat K

IEEE/ACM transactions on computational biology and bioinformatics

2024 Volume 21, Issue 1, Page(s) 155–168

Abstract: The revolution in sequencing technologies has enabled human genomes to be sequenced at a very low cost and time leading to exponential growth in the availability of whole-genome sequences. However, the complete understanding of our genome and its ... ...

Abstract	The revolution in sequencing technologies has enabled human genomes to be sequenced at a very low cost and time leading to exponential growth in the availability of whole-genome sequences. However, the complete understanding of our genome and its association with cancer is a far way to go. Researchers are striving hard to detect new variants and find their association with diseases, which further gives rise to the need for aggregation of this Big Data into a common standard scalable platform. In this work, a database named Enlightenment has been implemented which makes the availability of genomic data integrated from eight public databases, and DNA sequencing profiles of H. sapiens in a single platform. Annotated results with respect to cancer specific biomarkers, pharmacogenetic biomarkers and its association with variability in drug response, and DNA profiles along with novel copy number variants are computed and stored, which are accessible through a web interface. In order to overcome the challenge of storage and processing of NGS technology-based whole-genome DNA sequences, Enlightenment has been extended and deployed to a flexible and horizontally scalable database HBase, which is distributed over a hadoop cluster, which would enable the integration of other omics data into the database for enlightening the path towards eradication of cancer.
MeSH term(s)	Humans ; Nucleotides ; Genomics/methods ; Sequence Analysis, DNA/methods ; Neoplasms/genetics ; Biomarkers ; High-Throughput Nucleotide Sequencing
Chemical Substances	Nucleotides ; Biomarkers
Language	English
Publishing date	2024-02-05
Publishing country	United States
Document type	Journal Article
ISSN	1557-9964
ISSN (online)	1557-9964
DOI	10.1109/TCBB.2023.3340067
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Article ; Online: Deciphering the conformational stability of MazE7 antitoxin in

Saha, Rituparna / Bhattacharje, Gourab / De, Soumya / Das, Amit Kumar

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–17

Abstract: MazEF Toxin-antitoxin (TA) systems are associated with the persistent phenotype of the pathogen, ...

Abstract	MazEF Toxin-antitoxin (TA) systems are associated with the persistent phenotype of the pathogen,
Language	English
Publishing date	2023-11-15
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2280675
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Article: Metagenomics: aid to combat antimicrobial resistance in diarrhea.

De, Rituparna

Gut pathogens

2019 Volume 11, Page(s) 47

Abstract: Antimicrobial resistance (AMR) has emerged as an obstacle in the supple administration of antimicrobial agents to critical diarrheal patients. Most diarrheal pathogens have developed resistance against the major classes of antibiotics commonly used for ... ...

Abstract	Antimicrobial resistance (AMR) has emerged as an obstacle in the supple administration of antimicrobial agents to critical diarrheal patients. Most diarrheal pathogens have developed resistance against the major classes of antibiotics commonly used for assuaging diarrheal symptoms. Antimicrobial resistance develops when pathogens acquire antimicrobial resistance genes (ARGs) through genetic recombination from commensals and pathogens. These are the constituents of the complex microbiota in all ecological niches. The recombination events may occur in the environment or in the gut. Containment of AMR can be achieved through a complete understanding of the complex and diverse structure and function of the microbiota. Its taxonomic entities serve as focal points for the dissemination of antimicrobial resistance genetic determinants. Molecular methods complemented with culture-based diagnostics have been historically implemented to document these natural events. However, the advent of next-generation sequencing has revolutionized the field of molecular epidemiology. It has revolutionized the method of addressing relevant problems like diagnosis and surveillance of infectious diseases and the issue of antimicrobial resistance. Metagenomics is one such next-generation technique that has proved to be a monumental advancement in the area of molecular taxonomy. Current understanding of structure, function and dysbiosis of microbiota associated with antimicrobial resistance was realized due to its conception. This review describes the major milestones achieved due to the advent and implementation of this new technique in the context of antimicrobial resistance. These achievements span a wide panorama from the discovery of novel microorganisms to invention of translational value.
Language	English
Publishing date	2019-10-14
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2478277-4
ISSN	1757-4749
ISSN	1757-4749
DOI	10.1186/s13099-019-0331-8
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Article ; Online: Role of the Microbiome in the Pathogenesis of COVID-19.

De, Rituparna / Dutta, Shanta

Frontiers in cellular and infection microbiology

2022 Volume 12, Page(s) 736397

Abstract: The ongoing pandemic coronavirus disease COVID-19 is caused by the highly contagious single-stranded RNA virus, SARS-coronavirus 2 (SARS-CoV-2), which has a high rate of evolution like other RNA viruses. The first genome sequences of SARS-CoV-2 were ... ...

Abstract	The ongoing pandemic coronavirus disease COVID-19 is caused by the highly contagious single-stranded RNA virus, SARS-coronavirus 2 (SARS-CoV-2), which has a high rate of evolution like other RNA viruses. The first genome sequences of SARS-CoV-2 were available in early 2020. Subsequent whole-genome sequencing revealed that the virus had accumulated several mutations in genes associated with viral replication and pathogenesis. These variants showed enhanced transmissibility and infectivity. Soon after the first outbreak due to the wild-type strain in December 2019, a genetic variant D614G emerged in late January to early February 2020 and became the dominant genotype worldwide. Thereafter, several variants emerged, which were found to harbor mutations in essential viral genes encoding proteins that could act as drug and vaccine targets. Numerous vaccines have been successfully developed to assuage the burden of COVID-19. These have different rates of efficacy, including, although rarely, a number of vaccinated individuals exhibiting side effects like thrombosis. However, the recent emergence of the Britain strain with 70% more transmissibility and South African variants with higher resistance to vaccines at a time when several countries have approved these for mass immunization has raised tremendous concern regarding the long-lasting impact of currently available prophylaxis. Apart from studies addressing the pathophysiology, pathogenesis, and therapeutic targets of SARS-CoV-2, analysis of the gut, oral, nasopharyngeal, and lung microbiome dysbiosis has also been undertaken to find a link between the microbiome and the pathogenesis of COVID-19. Therefore, in the current scenario of skepticism regarding vaccine efficacy and challenges over the direct effects of currently available drugs looming large, investigation of alternative therapeutic avenues based on the microbiome can be a rewarding finding. This review presents the currently available understanding of microbiome dysbiosis and its association with cause and consequence of COVID-19. Taking cues from other inflammatory diseases, we propose a hypothesis of how the microbiome may be influencing homeostasis, pro-inflammatory condition, and the onset of inflammation. This accentuates the importance of a healthy microbiome as a protective element to prevent the onset of COVID-19. Finally, the review attempts to identify areas where the application of microbiome research can help in reducing the burden of the disease.
MeSH term(s)	COVID-19 ; Dysbiosis ; Humans ; Microbiota ; SARS-CoV-2/genetics
Language	English
Publishing date	2022-03-31
Publishing country	Switzerland
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2022.736397
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Article ; Online: Lipid profile abnormalities & 10 yr risk of CVD assessment among adult in North East India

Nilratan Majumder / Rituparna Das / Ripan Debbarma / Nilanjan Majumder / Suranjana De

Indian Journal of Medical Research, Vol 158, Iss 3, Pp 269-

A cross-sectional study

2023 Volume 275

Abstract: Background & objectives: In India, lifestyle changes have contributed to increase in the number of people suffering from lipid profile abnormalities, which is a major risk factor for coronary artery diseases. The present study was aimed to estimate the ... ...

Abstract	Background & objectives: In India, lifestyle changes have contributed to increase in the number of people suffering from lipid profile abnormalities, which is a major risk factor for coronary artery diseases. The present study was aimed to estimate the prevalence of lipid profile abnormalities and 10 yr risk of cardiovascular disease (CVD) among the adult population in west Tripura district and to study the association of lipid profile abnormalities and increased CVD risk with sociodemography, body mass index (BMI), hypertension, random blood sugar (RBS) and haemoglobin level. Methods: This cross-sectional study was conducted amongst 445 adults of 20 to 60 yr of age from a randomly selected block in west Tripura district. The 10 yr risk of CVD was estimated using the Framingham Risk Assessment Tool. Results: The study revealed that overall 83.4 per cent adult population had lipid profile abnormalities, with 22.2, 42 and 70.3 per cent of participants having hypercholesterolaemia, hypertriglyceridaemia and low high-density lipoprotein level, respectively. Gender (P=0.02) and BMI (P<0.001) were the significant determinants of dyslipidaemia. Only 3.8 per cent of participants had intermediate or high risk of CVD, with all of them being males. Gender, age, occupation and RBS were significantly associated with increased CVD risk. Interpretation & conclusions: The study revealed a high burden of lipid profile abnormalities in the study population, with males having more risk of CVD. Hence, periodic screening of lipid profile abnormalities and risk of CVD should be incorporated at the primary care level to combat the CVD epidemic in India.
Keywords	cvd risk - framingham risk assessment - hypercholesterolaemia - hypertriglyceridaemia - lipid profile - hdl - risk ; Medicine ; R
Subject code	610
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Emerging resistome diversity in clinical Vibrio cholerae strains revealing their role as potential reservoirs of antimicrobial resistance.

De, Rituparna / Mukhopadhyay, Asish K / Ghosh, Manisha / Basak, Surajit / Dutta, Shanta

Molecular biology reports

2024 Volume 51, Issue 1, Page(s) 409

Abstract: Background: This is a unique and novel study delineating the genotyping and subsequent prediction of AMR determinants of Vibrio cholerae revealing the potential of contemporary strains to serve as precursors of severe AMR crisis in cholera.: Methods ... ...

Abstract	Background: This is a unique and novel study delineating the genotyping and subsequent prediction of AMR determinants of Vibrio cholerae revealing the potential of contemporary strains to serve as precursors of severe AMR crisis in cholera. Methods and results: Genotyping of representative strains, VC1 and VC2 was undertaken to characterize antimicrobial resistance genes (ARGs) against chloramphenicol, SXT, nalidixic acid and streptomycin against which they were found to be resistant by antibiogram analysis in our previous investigation. strAB, sxt, sul2, qace∆1-sul1 were detected by PCR. Genome annotation and identification of ARGs with WGS helped to detect the presence of almG, varG, strA (APH(3'')-Ib), strB (APH(6)-Id), sul2, catB9, floR, CRP, dfrA1 genes. Signatures of resistance determinants and protein domains involved in antimicrobial resistance, primarily, efflux of antibiotics were identified on the basis of 30-100% homology to reference proteins. These domains were predicted to be involved in other metabolic functions on the basis of 100% identity with 100% coverage with reference protein and nucleotide sequences and were predicted to be of a diverse taxonomic origin accentuating the influence of the microbiota on AMR acquisition. Sequence analysis of QRDR (quinolone resistance-determining region) revealed SNPs. Cytoscape v3.8.2 was employed to analyse protein-protein interaction of MDR proteins, MdtA and EmrD-2, with nodes of vital AMR pathways. Vital nodes involved in efflux of different classes of antibiotics were found to be absent in VC1 and VC2 justifying the sensitivity of these strains to most antibiotics. Conclusions: The study helped to examine the resistome of VC isolated from recent outbreaks to understand the underlying reason of sensitivity to most antibiotics and also to characterize the ARGs in their genome. It revealed that VC is a reservoir of signatures of resistance determinants and serving as precursors for severe AMR crisis in cholera. This is the first study, to our knowledge, which has scrutinized and presented systematically, information on prospective domains which bear the potential of serving as AMR determinants in VC with the help of bioinformatic tools. This pioneering approach may help in the prediction of AMR landfalls and benefit epidemiological surveillance and early warning systems.
MeSH term(s)	Humans ; Vibrio cholerae/genetics ; Cholera/drug therapy ; Cholera/epidemiology ; Anti-Bacterial Agents/pharmacology ; Prospective Studies ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2024-03-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-024-09313-y
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Article ; Online: GenSeg and MR-GenSeg: A Novel Segmentation Algorithm and its Parallel MapReduce Based Approach for Identifying Genomic Regions With Copy Number Variations.

Sinha, Rituparna / Pal, Rajat K / De, Rajat K

IEEE/ACM transactions on computational biology and bioinformatics

2022 Volume 19, Issue 1, Page(s) 443–454

Abstract: ... at https://github.com/rituparna-sinha/MapReduce-GENSEG. ...

Abstract	Identifying intragenic as well as intergenic sequences of the DNA, having structural alterations, is a significantly important research area, since this may be the root cause of many neurological and autoimmune diseases, including cancer. Working with whole genome NGS data has provided a new insight in this regard, but has lead to huge explosion of data that is growing exponentially. Hence, the challenges lie in efficient means of storage and processing this big data. In this study, we have developed a novel segmentation algorithm, called GenSeg, and its parallel MapReduce based algorithm, called MR-GenSeg, for detecting copy number variations. In order to annotate CNVs (variants), segments formed by GenSeg/MR-GenSeg have been represented in a novel way using a binary tree, where each node is a CNV event. GenSeg considers each position specific data of whole genome DNA sequence, so that precise identification of breakpoints is possible. GenSeg/MR-GenSeg has been compared with twelve popular CNV detection algorithms, where it has outperformed the others in terms of sensitivity, and has achieved a good F-score value. MR-GenSeg has excelled in terms of SpeedUp, when compared with these algorithms. The effect of CNVs on immunoglobulin (IG) genes has also been analysed in this study. Availability: The source codes are available at https://github.com/rituparna-sinha/MapReduce-GENSEG.
MeSH term(s)	Algorithms ; DNA Copy Number Variations/genetics ; Genome, Human/genetics ; Genomics ; Humans ; Software
Language	English
Publishing date	2022-02-03
Publishing country	United States
Document type	Journal Article
ISSN	1557-9964
ISSN (online)	1557-9964
DOI	10.1109/TCBB.2020.3000661
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Article: Lipid profile abnormalities & 10 yr risk of CVD assessment among adult in North East India: A cross-sectional study.

Majumder, Nilratan / Das, Rituparna / Debbarma, Ripan / Majumder, Nilanjan / De, Suranjana

The Indian journal of medical research

2023 Volume 158, Issue 3, Page(s) 269–275

Abstract	Background & objectives: In India, lifestyle changes have contributed to increase in the number of people suffering from lipid profile abnormalities, which is a major risk factor for coronary artery diseases. The present study was aimed to estimate the prevalence of lipid profile abnormalities and 10 yr risk of cardiovascular disease (CVD) among the adult population in west Tripura district and to study the association of lipid profile abnormalities and increased CVD risk with sociodemography, body mass index (BMI), hypertension, random blood sugar (RBS) and haemoglobin level. Methods: This cross-sectional study was conducted amongst 445 adults of 20 to 60 yr of age from a randomly selected block in west Tripura district. The 10 yr risk of CVD was estimated using the Framingham Risk Assessment Tool. Results: The study revealed that overall 83.4 per cent adult population had lipid profile abnormalities, with 22.2, 42 and 70.3 per cent of participants having hypercholesterolaemia, hypertriglyceridaemia and low high-density lipoprotein level, respectively. Gender (P=0.02) and BMI (P<0.001) were the significant determinants of dyslipidaemia. Only 3.8 per cent of participants had intermediate or high risk of CVD, with all of them being males. Gender, age, occupation and RBS were significantly associated with increased CVD risk. Interpretation & conclusions: The study revealed a high burden of lipid profile abnormalities in the study population, with males having more risk of CVD. Hence, periodic screening of lipid profile abnormalities and risk of CVD should be incorporated at the primary care level to combat the CVD epidemic in India.
MeSH term(s)	Adult ; Female ; Humans ; Male ; Cardiovascular Diseases/epidemiology ; Cross-Sectional Studies ; Hypertension ; Lipids ; Risk Factors ; Young Adult ; Middle Aged
Chemical Substances	Lipids
Language	English
Publishing date	2023-10-10
Publishing country	India
Document type	Journal Article
ZDB-ID	390883-5
ISSN	0971-5916 ; 0019-5340
ISSN	0971-5916 ; 0019-5340
DOI	10.4103/ijmr.ijmr_2683_21
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Article ; Online: The gut microbiome of the healthy population in Kolkata, India, is a reservoir of antimicrobial resistance genes emphasizing the need of enforcing antimicrobial stewardship.

De, Rituparna / Kanungo, Suman / Mukhopadhyay, Asish Kumar / Dutta, Shanta

FEMS microbiology letters

2023 Volume 370

Abstract: Antimicrobial resistance (AMR) alleviation warrants antimicrobial stewardship (AS) entailing the indispensability of epidemiological surveillance. We undertook a small-scale surveillance in Kolkata to detect the presence of antimicrobial resistance genes ...

Abstract	Antimicrobial resistance (AMR) alleviation warrants antimicrobial stewardship (AS) entailing the indispensability of epidemiological surveillance. We undertook a small-scale surveillance in Kolkata to detect the presence of antimicrobial resistance genes (ARGs) in the healthy gut microbiome. We found that it was a reservoir of ARGs against common antibiotics. A targeted Polymerase Chain Reaction (PCR) and sequencing-based ARGs detection against tetracyclines, macrolides, trimethoprim, sulfamethoxazole, aminoglycosides, amphenicol, and mobile genetic element (MGE) markers were deployed in 25 fecal samples. Relative abundance and frequency of ARGs were calculated. We detected markers against all these classes of antibiotics. 100% samples carried aminoglycoside resistance marker and int1U. A comparison with our previously published diarrheal resistome from the same spatial and temporal frame revealed that a higher diversity of ARGs were detected in the community and a higher rate of isolation of tetC, msrA, tmp, and sul-2 was found. The presence of common markers in the two cohorts proves that the gut microbiome has been contaminated with ARGs and which are being disseminated among different ecosystems. This is an issue of discerning concern for public health. The study raises an alarming picture of the AMR crisis in low-middle and emergent economies. It emphasizes the strict enforcement of AS in the community.
Language	English
Publishing date	2023-09-11
Publishing country	England
Document type	Journal Article
ZDB-ID	752343-9
ISSN	1574-6968 ; 0378-1097
ISSN (online)	1574-6968
ISSN	0378-1097
DOI	10.1093/femsle/fnad090
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Article ; Online: Crystal structure of a mycobacterial secretory protein Rv0398c and in silico prediction of its export pathway.

Saha, Rituparna / Mukherjee, Somnath / Singh, Bina / De, Soumya / Weiss, Manfred S / Das, Amit Kumar

Biochemical and biophysical research communications

2023 Volume 672, Page(s) 45–53

Abstract: Secretory proteins are used by pathogenic bacteria to manipulate the host systems and compete with other microorganisms, thereby enabling their survival in their host. Similar to other bacteria, secretory proteins of Mycobacterium tuberculosis also play ... ...

Abstract	Secretory proteins are used by pathogenic bacteria to manipulate the host systems and compete with other microorganisms, thereby enabling their survival in their host. Similar to other bacteria, secretory proteins of Mycobacterium tuberculosis also play a pivotal role in evading immune response within hosts, thereby leading to acute and latent tuberculosis infection. Prokaryotes have several classes of bacterial secretory systems out of which the Sec and Tat pathways are the most conserved in Mtb to transport proteins across the cytoplasmic membrane. Here, we report the crystal structure of a secretory protein, Rv0398c determined to 1.9 Å resolution. The protein comprises a core of antiparallel β sheets surrounded by α helices adopting a unique β sandwich fold. Structural comparison with other secretory proteins in Mtb and other pathogenic bacteria reveals that Rv0398c may be secreted via the Sec pathway. Our structural and in silico analyses thus provide mechanistic insights into the pathway adopted by Mtb to transport out secretory protein, Rv0398c which will facilitate the invasion to the host immune system.
MeSH term(s)	Bacterial Proteins/metabolism ; Membrane Transport Proteins/metabolism ; Mycobacterium tuberculosis/metabolism ; Carrier Proteins/metabolism ; Biological Transport
Chemical Substances	Bacterial Proteins ; Membrane Transport Proteins ; Carrier Proteins
Language	English
Publishing date	2023-06-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2023.06.029
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