5 results on '"Abhay Deep Pandey"'
Search Results
2. Insights into the human gut virome by sampling a population from the Indian subcontinent
- Author
-
Kanchan Bhardwaj, Anjali Garg, Abhay Deep Pandey, Himani Sharma, Manish Kumar, and Sudhanshu Vrati
- Subjects
Virome ,Virology ,Viruses ,Animals ,Humans ,Bacteriophages ,Genome, Viral ,Metagenomics - Abstract
Gut virome plays an important role in human physiology but remains poorly understood. This study reports an investigation of the human gut DNA-virome of a previously unexplored ethnic population through metagenomics of faecal samples collected from individuals residing in Northern India. Analysis shows that, similar to the populations investigated earlier, majority of the identified virome belongs to bacteriophages and a smaller fraction (< 20%) consists of viruses that infect animals, archaea, protists, multiple domains or plants. However, crAss-like phages, in this population, are dominated by the genera VII, VIII and VI. Interestingly, it also reveals the presence of a virus family, Sphaerolipoviridae, which has not been detected in the human gut earlier. Viral families, Siphoviridae, Myoviridae, Podoviridae, Microviridae, Herelleviridae and Phycodnaviridae are detected in all of the analyzed individuals, which supports the existence of a core virome. Lysogeny-associated genes were found in less than 10% of the assembled genomes and a negative correlation was observed in the richness of bacterial and free-viral species, suggesting that the dominant lifestyle of gut phage is not lysogenic. This is in contrast to some of the earlier studies. Further, several hundred high-quality viral genomes were recovered. Detailed characterization of these genomes would be useful for understanding the biology of these viruses and their significance in human physiology.ImportanceViruses are important constituents of the human gut microbiome but it remains poorly understood. The Indian subcontinent is a unique biogeographic region and the Indian population is known to harbour a distinct bacterial microbiome. However, the gut virome in this population has not been investigated earlier. Therefore, in this study, we investigated fecal samples of 12 healthy individuals to analyze their gut virome, through metagenomics.
- Published
- 2022
3. High-Throughput RNA Sequencing Analysis of Plasma Samples Reveals Circulating microRNA Signatures with Biomarker Potential in Dengue Disease Progression
- Author
-
Vishnampettai G. Ramachandran, Vikas Sood, Bhaswati Bandyopadhyay, Sudhanshu Vrati, Abhay Deep Pandey, Jaya Saini, Shukla Das, and Arup Banerjee
- Subjects
0301 basic medicine ,Small RNA ,Physiology ,Dengue virus ,medicine.disease_cause ,Biochemistry ,Microbiology ,Dengue fever ,Host-Microbe Biology ,03 medical and health sciences ,0302 clinical medicine ,microRNA ,Genetics ,Medicine ,plasma microRNA ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Respiratory distress ,business.industry ,RNA sequencing ,medicine.disease ,dengue ,QR1-502 ,Fold change ,Computer Science Applications ,circulating miRNA ,Circulating MicroRNA ,030104 developmental biology ,030220 oncology & carcinogenesis ,Modeling and Simulation ,Immunology ,Biomarker (medicine) ,business ,Research Article - Abstract
Dengue virus (DENV) infection usually causes dengue fever (DF) with flu-like illness affecting infants, young children, and adults. The DF occasionally evolves into a potentially lethal complication called dengue severe (DS) leading to a rapid fall in platelet count along with plasma leakage, fluid accumulation, respiratory distress, and severe bleeding. The diverse clinical spectrum of dengue disease, as well as its significant similarity to other febrile viral illnesses, makes early identification more challenging in this high-risk group. microRNAs (miRNAs) are small (∼19 to 21 nucleotides [nt] in length), noncoding RNAs, extremely stable and easily detectable in the plasma; thus, they have potential as biomarkers for diagnosing and monitoring human diseases. This study provides a comprehensive analysis of miRNAs circulating in plasma of dengue virus-infected patients and identifies the miRNA signatures that have biomarker potential for dengue infection and disease progression., The circulating microRNA (miRNA) profile has been widely used for identifying potential biomarkers against viral infections. However, data on circulating microRNA expression patterns in dengue patients are scanty. Considering the impact of severity caused by dengue infection, circulating miRNA profiles in plasma of dengue patients may prove to be valuable for developing early prognostic markers for the disease severity. Here, we described an in-depth analytical study of small RNA sequencing data obtained from the plasma of 39 dengue patients. Integrating bioinformatics and in vitro studies, we identified differentially expressed miRNAs (DEMs) (log2 fold change ≥1.5, P
- Published
- 2020
4. Correlation of altered expression of a long non-coding RNA, NEAT1, in peripheral blood mononuclear cells with dengue disease progression
- Author
-
Shaoli Das, Arup Banerjee, Nandita Basu, Abhay Deep Pandey, Manisha Pal, Shweta Shukla, Suman Ghosal, Vikas Sood, Priyanka Pandey, Bhaswati Bandyopadhyay, Sudhanshu Vrati, Saptamita Goswami, Vishnampettai G. Ramachandran, and Jayprokas Chakrabarti
- Subjects
Adult ,Male ,0301 basic medicine ,Microbiology (medical) ,Adolescent ,Biology ,Peripheral blood mononuclear cell ,Dengue fever ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Humans ,Computer Simulation ,Severe Dengue ,Child ,Gene ,Aged ,Receiver operating characteristic ,Sequence Analysis, RNA ,Area under the curve ,Membrane Proteins ,RNA ,Dengue Virus ,Middle Aged ,medicine.disease ,Phenotype ,Long non-coding RNA ,030104 developmental biology ,Infectious Diseases ,ROC Curve ,030220 oncology & carcinogenesis ,Immunology ,Disease Progression ,Leukocytes, Mononuclear ,Regression Analysis ,Female ,RNA, Long Noncoding ,Biomarkers - Abstract
Summary The association of long non-coding RNAs (lncRNAs) with dengue disease progression is currently unknown. Therefore, the present study aimed to identify lncRNAs in different categories of dengue patients and evaluate their association with dengue disease progression. Herein, we examined the expression profiles of lncRNAs and protein-coding genes between other febrile illness (OFI) and different grade of dengue patients through high-throughput RNA sequencing. We identified Nuclear Enriched Abundant Transcript 1 ( NEAT1 ) as one of the differentially expressed lncRNAs (adjusted P ≤ 0.05 and log-fold change ≥ 2) and subsequently validated the expression by qRT-PCR. The co-expression analysis further revealed that NEAT1 and the coding gene IFI27 were highly co-expressed and negatively correlated with dengue severity. Using regression analysis, we observed that NEAT1 expression was significantly dependent on disease progression (Coefficient = −0.27750, SE Coefficient = 0.07145, and t = −3.88).Further, receiver operating characteristic (ROC) curve revealed that NEAT1 expression could discriminate DI from DS (sensitivity and specificity of 100% (95%CI: 85.69 – 97.22) and area under the curve (AUC) = 0.97). Overall, the results of this study offer the first experimental evidence demonstrating the correlation between lncRNAs and severe dengue phenotype. Monitoring NEAT1and IFI27 expression in PBMC may be useful in understanding dengue virus-induced disease progression.
- Published
- 2017
5. RNA-Seq analysis of peripheral blood mononuclear cells reveals unique transcriptional signatures associated with disease progression in dengue patients
- Author
-
Nandita Basu, Abhay Deep Pandey, Vikas Sood, Srima Adhikari, Mehebubar Rahman, Saptamita Goswami, Bhaswati Bandyopadhyay, Sudhanshu Vrati, Shatakshee Chatterjee, Shweta Shukla, Priyanka Pandey, Arjun Malhotra, Nemai Bhattacharya, Amitesh Agarwal, Vishnampettai G. Ramachandran, Shukla Das, and Arup Banerjee
- Subjects
0301 basic medicine ,Adult ,Male ,Adolescent ,Transcription, Genetic ,Disease ,Dengue virus ,Biology ,medicine.disease_cause ,Peripheral blood mononuclear cell ,Dengue fever ,Transcriptome ,Dengue ,03 medical and health sciences ,Young Adult ,Immunity ,Physiology (medical) ,medicine ,Humans ,Child ,Regulation of gene expression ,Base Sequence ,Biochemistry (medical) ,Public Health, Environmental and Occupational Health ,General Medicine ,Dengue Virus ,medicine.disease ,Virology ,030104 developmental biology ,Gene Expression Regulation ,Immunology ,Leukocytes, Mononuclear ,RNA ,Female ,Extracellular matrix organization - Abstract
Patients infected with Dengue virus usually present a mild, self-limiting febrile dengue infection (DI) that occasionally leads to a potentially lethal complication, called the severe dengue (DS). The ability to identify the prognostic markers of DS could allow an improved disease intervention and management. To identify the transcriptional signatures associated with the dengue disease progression, we carried out the high-throughput sequencing of the RNA isolated from the peripheral blood mononuclear cells (PBMCs) of the dengue patients of varying severity and compared with that in the patients with other febrile illnesses (OFIs) or the healthy controls. The transcriptional signatures that discriminated the DS patients from OFI and DI patients were broadly related to the pathways involving glycine, serine, and threonine metabolisms, extracellular matrix organization, ubiquitination, and cytokines and inflammatory response. Several upregulated genes in the inflammatory process (MPO, DEFA4, ELANE, AUZ1, CTSG, OLFM4, SLC16A14, and CRISP3) that were associated with the dengue disease progression are known to facilitate leukocyte-mediated migration, and neutrophil activation and degranulation process. High activity of MPO and ELANE in the plasma samples of the follow-up and recovered dengue patients, as well as and the presence of a larger amount of cell-free dsDNA in the DS patients, suggested an association of neutrophil-mediated immunity with dengue disease progression. Careful monitoring of some of these gene transcripts, and control of the activity of proteins encoded by them, may have a great translational significance for the prognosis and management of the dengue patients.
- Published
- 2017
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.