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Ghosh A, Kanta P, Ramola M, Mohindra R, Goyal K, Kishore R, Suri V, Lakshmi PVM, Chauhan C, Sharma M, Rakshit P, Ponnusamy K, Dikid T, Singh MP. Rapid Decline of SARS-CoV-2 Viral Load in Single vs. Double-Dose (Short-Interval <6 Weeks) ChAdOx nCoV-19 Vaccinated Health-Care Workers. Curr Microbiol 2024; 81:95. [PMID: 38353761 DOI: 10.1007/s00284-023-03603-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/26/2023] [Indexed: 02/16/2024]
Abstract
The present work was carried out during the emergence of Delta Variant of Concern (VoC) and aimed to study the change in SARS CoV-2 viral load in Covishield vaccinated asymptomatic/mildly symptomatic health-care workers (HCWs) to find out the optimum isolation period. The SARS CoV-2 viral load was carried out in sequential samples of 55 eligible HCWs which included unvaccinated (UnV; n = 11), single-dose vaccinated (SDV, n = 20) and double-dose vaccinated [DDV, n = 24; short-interval (<6 weeks)] subjects. The mean load of envelope (E) gene on day 5 in SDV [0.42 × 105 copies/reaction] was significantly lower as compared to DDV [6.3 × 105 copies/reaction, P = 0.005] and UnV [6.6 × 105 copies/reaction, P = 0.001] groups. The rate of decline of SARS CoV-2 viral load in the initial 5 days of PCR positivity was significantly higher in SDV as compared to that in DDV (Mean log decline 0.39 vs. 0.19; P < 0.001). This was possibly due to interference of adenoviral immunity of first dose of adenovirus-vectored vaccine in double-dose vaccinated HCWs who had received vaccines within a shorter interval (<6 weeks).
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Affiliation(s)
- Arnab Ghosh
- Department of Virology, Post-Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Poonam Kanta
- Department of Virology, Post-Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Manisha Ramola
- Department of Virology, Post-Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Ritin Mohindra
- Department of Internal Medicine, Post-Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Kapil Goyal
- Department of Virology, Post-Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Roop Kishore
- Department of Internal Medicine, Post-Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Vikas Suri
- Department of Internal Medicine, Post-Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - P V M Lakshmi
- Department of Community Medicine and School of Public Health, Post-Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Chanderkanta Chauhan
- Department of Community Medicine and School of Public Health, Post-Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Manisha Sharma
- Department of Community Medicine and School of Public Health, Post-Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Partha Rakshit
- National Centre for Disease Control (NCDC), New Delhi, India
| | | | - Tanzin Dikid
- National Centre for Disease Control (NCDC), New Delhi, India
| | - Mini P Singh
- Department of Virology, Post-Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India.
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Yadav A, Shinde PB, Dhar MS, Ponnusamy K, Marwal R, V S R, Sharma KK. Draft genome sequence of Kluyvera ascorbata HAK22 isolated from human feces. Microbiol Resour Announc 2024; 13:e0089023. [PMID: 38117067 DOI: 10.1128/mra.00890-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023] Open
Abstract
The whole genome sequence of rare human pathogen Kluyvera ascorbata strain HAK22 is reported. The K. ascorbata HAK22 was isolated from healthy human from Gurugram, Haryana, India. The draft genome has a length of 4.7 Mbp, with 54.36% GC content and 4,411 proteins, 4,470 genes, and 18 antimicrobial resistance genes.
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Affiliation(s)
- Asha Yadav
- Laboratory of Enzymology and Gut microbiology, Department of Microbiology, Maharshi Dayanand University , Rohtak, Haryana, India
| | - Pratik Balwant Shinde
- Laboratory of Enzymology and Gut microbiology, Department of Microbiology, Maharshi Dayanand University , Rohtak, Haryana, India
| | - Mahesh S Dhar
- Department of Biotechnology, National Centre for Disease Control , Delhi, India
| | | | - Robin Marwal
- Department of Biotechnology, National Centre for Disease Control , Delhi, India
| | - Radhakrishnan V S
- Department of Biotechnology, National Centre for Disease Control , Delhi, India
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Gut microbiology, Department of Microbiology, Maharshi Dayanand University , Rohtak, Haryana, India
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Kumar R, Madhavan T, Ponnusamy K, Sohn H, Haider S. Computational study of the motor neuron protein KIF5A to identify nsSNPs, bioactive compounds, and its key regulators. Front Genet 2023; 14:1282234. [PMID: 38028604 PMCID: PMC10667939 DOI: 10.3389/fgene.2023.1282234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Kinesin family member 5A (KIF5A) is a motor neuron protein expressed in neurons and involved in anterograde transportation of organelles, proteins, and RNA. Variations in the KIF5A gene that interfere with axonal transport have emerged as a distinguishing feature in several neurodegenerative disorders, including hereditary spastic paraplegia (HSP10), Charcot-Marie-Tooth disease type 2 (CMT2), and Amyotrophic Lateral Sclerosis (ALS). Methods: In this study, we implemented a computational structural and systems biology approach to uncover the role of KIF5A in ALS. Using the computational structural biology method, we explored the role of non-synonymous Single Nucleotide Polymorphism (nsSNPs) in KIF5A. Further, to identify the potential inhibitory molecule against the highly destabilizing structure variant, we docked 24 plant-derived phytochemicals involved in ALS. Results: We found KIF5AS291F variant showed the most structure destabilizing behavior and the phytocompound "epigallocatechin gallate" showed the highest binding affinity (-9.0 Kcal/mol) as compared to wild KIF5A (-8.4 Kcal/mol). Further, with the systems biology approach, we constructed the KIF5A protein-protein interaction (PPI) network to identify the associated Kinesin Families (KIFs) proteins, modules, and their function. We also constructed a transcriptional and post-transcriptional regulatory network of KIF5A. With the network topological parameters of PPIN (Degree, Bottleneck, Closeness, and MNC) using CytoHubba and computational knock-out experiment using Network Analyzer, we found KIF1A, 5B, and 5C were the significant proteins. The functional modules were highly enriched with microtubule motor activity, chemical synaptic transmission in neurons, GTP binding, and GABA receptor activity. In regulatory network analysis, we found KIF5A post-transcriptionally down-regulated by miR-107 which is further transcriptionally up-regulated by four TFs (HIF1A, PPARA, SREBF1, and TP53) and down-regulated by three TFs (ZEB1, ZEB2, and LIN28A). Discussion: We concluded our study by finding a crucial variant of KIF5A and its potential therapeutic target (epigallocatechin gallate) and KIF5A associated significant genes with important regulators which could decrypt the novel therapeutics in ALS and other neurodegenerative diseases.
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Affiliation(s)
- Rupesh Kumar
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Thirumurthy Madhavan
- Department of Genetic Engineering, Computational Biology Lab, SRM Institute of Science and Technology, Chennai, India
| | | | - Honglae Sohn
- Department of Chemistry and Department of Carbon Materials, Chosun University, Gwangju, Republic of Korea
| | - Shazia Haider
- Department of Biosciences, Jamia Millia University, New Delhi, India
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Shikha S, Jogi MK, Jha R, Kumar RA, Sah T, Singh P, Sagar R, Kumar A, Marwal R, Ponnusamy K, Agarwal SM, Kumar RS, Arif N, Bharadwaj M, Singh S, Kumar P. Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein. Front Immunol 2023; 14:1209513. [PMID: 37849762 PMCID: PMC10577267 DOI: 10.3389/fimmu.2023.1209513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/30/2023] [Indexed: 10/19/2023] Open
Abstract
The SARS-CoV-2 omicron variants keep accumulating a large number of mutations in the spike (S) protein, which contributes to greater transmissibility and a rapid rise to dominance within populations. The identification of mutations and their affinity to the cellular angiotensin-converting enzyme-2 (ACE-2) receptor and immune evasion in the Delhi NCR region was under-acknowledged. The study identifies some mutations (Y505 reversion, G339H, and R346T/N) in genomes from Delhi, India, and their probable implications for altering the immune response and binding affinity for ACE-2. The spike mutations have influenced the neutralizing activity of antibodies against the omicron variant, which shows partial immune escape. However, researchers are currently exploring various mitigation strategies to tackle the potential decline in efficacy or effectiveness against existing and future variants of SARS-CoV-2. These strategies include modifying vaccines to target specific variants, such as the omicron variant, developing multivalent vaccine formulations, and exploring alternative delivery methods. To address this, it is also necessary to understand the impact of these mutations from a different perspective, especially in terms of alterations in antigenic determinants. In this study, we have done whole genome sequencing (WGS) of SARS-CoV-2 in COVID-19 samples from Delhi, NCR, and analyzed the spike's mutation with an emphasis on antigenic alterations. The impact of mutation in terms of epitope formation, loss/gain of efficiency, and interaction of epitopes with antibodies has been studied. Some of the mutations or variant genomes seem to be the progenitors of the upcoming variants in India. Our analyses suggested that weakening interactions with antibodies may lead to immune resistance in the circulating genomes.
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Affiliation(s)
- Sristy Shikha
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Mukesh Kumar Jogi
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Ruchika Jha
- Department of Biotechnology, Vinoba Bhave University, Hazaribagh, Jharkhand, India
| | - Rana Amit Kumar
- Department of Biotechnology, Anugrah Narayan College, Patna, Bihar, India
| | - Tathagat Sah
- Department of Chemical Engineering and Biotechnology, Beant College of Engineering and Technology, Gurdaspur, Punjab, India
| | - Pushpendra Singh
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Ritu Sagar
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Anuj Kumar
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Robin Marwal
- Biotechnology Division, National Centre for Disease Control, Delhi, India
| | | | - Subhash Mohan Agarwal
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - R. Suresh Kumar
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Nazneen Arif
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Mausumi Bharadwaj
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Shalini Singh
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Pramod Kumar
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
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Khan MJ, Singh P, Jha P, Nayek A, Malik MZ, Bagler G, Kumar B, Ponnusamy K, Ali S, Chopra M, Dohare R, Singh IK, Syed MA. Investigating the link between miR-34a-5p and TLR6 signaling in sepsis-induced ARDS. 3 Biotech 2023; 13:282. [PMID: 37496978 PMCID: PMC10366072 DOI: 10.1007/s13205-023-03700-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/10/2023] [Indexed: 07/28/2023] Open
Abstract
Acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) are lung complications diagnosed by impaired gaseous exchanges leading to mortality. From the diverse etiologies, sepsis is a prominent contributor to ALI/ARDS. In the present study, we retrieved sepsis-induced ARDS mRNA expression profile and identified 883 differentially expressed genes (DEGs). Next, we established an ARDS-specific weighted gene co-expression network (WGCN) and picked the blue module as our hub module based on highly correlated network properties. Later we subjected all hub module DEGs to form an ARDS-specific 3-node feed-forward loop (FFL) whose highest-order subnetwork motif revealed one TF (STAT6), one miRNA (miR-34a-5p), and one mRNA (TLR6). Thereafter, we screened a natural product library and identified three lead molecules that showed promising binding affinity against TLR6. We then performed molecular dynamics simulations to evaluate the stability and binding free energy of the TLR6-lead molecule complexes. Our results suggest these lead molecules may be potential therapeutic candidates for treating sepsis-induced ALI/ARDS. In-silico studies on clinical datasets for sepsis-induced ARDS indicate a possible positive interaction between miR-34a and TLR6 and an antagonizing effect on STAT6 to promote inflammation. Also, the translational study on septic mice lungs by IHC staining reveals a hike in the expression of TLR6. We report here that miR-34a actively augments the effect of sepsis on lung epithelial cell apoptosis. This study suggests that miR-34a promotes TLR6 to heighten inflammation in sepsis-induced ALI/ARDS. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03700-1.
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Affiliation(s)
- Mohd Junaid Khan
- Translational Research Lab, Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, 110025 India
| | - Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025 India
| | - Prakash Jha
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, 110007 India
| | - Arnab Nayek
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Md. Zubbair Malik
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, 15462 Kuwait City, Kuwait
| | - Ganesh Bagler
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, 110020 India
| | - Bhupender Kumar
- Department of Microbiology, Swami Shraddhanand College, University of Delhi, New Delhi, 110036 India
| | - Kalaiarasan Ponnusamy
- Biotechnology and Viral Hepatitis Division, National Centre for Disease Control, Sham Nath Marg, New Delhi, 110054 India
| | - Shakir Ali
- Department of Biochemistry, School of Chemical and Life Sciences Jamia Hamdard, New Delhi, 110062 India
| | - Madhu Chopra
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, 110007 India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025 India
| | - Indrakant Kumar Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019 India
- DBC i4 Center, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019 India
| | - Mansoor Ali Syed
- Translational Research Lab, Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, 110025 India
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Gnanasekaran P, Gupta N, Ponnusamy K, Devendran R, George B, Chakraborty S. Betasatellite-encoded βC1 protein regulates helper virus accumulation by interfering with the ATP hydrolysis activity of geminivirus-encoded replication initiator protein. J Gen Virol 2023; 104. [PMID: 37326617 DOI: 10.1099/jgv.0.001866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Abstract
Geminivirus-betasatellite disease complexes are an epidemic threat to the majority of economically important crops across the world. Plant virus satellites including betasatellites are maintained by their associated helper virus. Geminivirus-betasatellites influence viral pathogenesis by substantially increasing or decreasing their helper virus accumulation. In the present study, we attempted to understand the mechanistic details of the geminivirus-betasatellite interaction. Here, we used tomato leaf curl Gujarat virus (ToLCGV) and tomato leaf curl Patna betasatellite (ToLCPaB) as a model system. This study reveals that ToLCGV can efficiently trans-replicate ToLCPaB in Nicotiana benthamiana plants, but ToLCPaB greatly reduced the accumulation of its helper virus DNA. For the first time, we have identified that the ToLCPaB-encoded βC1 protein is able to interact with ToLCGV-encoded replication initiator protein (Rep). In addition, we demonstrate that the C-terminal region of βC1 interacts with the C-terminus of Rep (RepC) protein. Our previous study had established that βC1 proteins encoded by diverse betasatellites possess a novel ATP hydrolysis activity and the conserved lysine/arginine residues at positions 49 and 91 are necessary for this function. Here, we show that mutating lysine at positions 49 to alanine of βC1 (βC1K49A) protein did not affect its ability to interact with RepC protein. Biochemical studies performed with ATP hydrolysis activity-deficient K49A mutated βC1 (βC1K49A) and RepC proteins revealed that Rep-βC1 interaction interferes with the ATP hydrolysis activity of Rep protein. Further, we demonstrate that βC1 protein is able to interact with D227A and D289A mutated RepC proteins but not with D262A, K272A or D286A mutated RepC proteins, suggesting that the βC1-interacting region of Rep protein encompasses its Walker-B and B' motifs. The results of docking studies supported that the βC1-interacting region of Rep protein encompasses its motifs associated with ATP binding and ATP hydrolysis activities. Docking studies also provided evidence that the Rep-βC1 interaction interferes with the ATP binding activity of Rep protein. Together, our findings suggest that βC1 protein regulates helper virus accumulation by interfering with the ATP hydrolysis activity of helper virus Rep protein.
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Affiliation(s)
- Prabu Gnanasekaran
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
| | - Neha Gupta
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
| | - Kalaiarasan Ponnusamy
- Biotechnology Division, National Centre for Disease Control, New Delhi-110 054, India
| | - Ragunathan Devendran
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
| | - Biju George
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
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Kumar R, Nagar S, Haider S, Sood U, Ponnusamy K, Dhingra GG, Anand S, Dua A, Singh M, Kumar R, Sengar M, Singh IK, Lal R. Monkeypox virus: phylogenomics, host-pathogen interactome and mutational cascade. Microb Genom 2023; 9. [PMID: 37043267 DOI: 10.1099/mgen.0.000987] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
While the world is still recovering from the Covid-19 pandemic, monkeypox virus (MPXV) awaits to cause another global outbreak as a challenge to all of mankind. However, the Covid-19 pandemic has taught us a lesson to speed up the pace of viral genomic research for the implementation of preventive and treatment strategies. One of the important aspects of MPXV that needs immediate insight is its evolutionary lineage based on genomic studies. Utilizing high-quality isolates from the GISAID (Global Initiative on Sharing All Influenza Data) database, primarily sourced from Europe and North America, we employed a SNP-based whole-genome phylogeny method and identified four major clusters among 628 MPXV isolates. Our findings indicate a distinct evolutionary lineage for the first MPXV isolate, and a complex epidemiology and evolution of MPXV strains across various countries. Further analysis of the host-pathogen interaction network revealed key viral proteins, such as E3, SPI-2, K7 and CrmB, that play a significant role in regulating the network and inhibiting the host's cellular innate immune system. Our structural analysis of proteins E3 and CrmB revealed potential disruption of stability due to certain mutations. While this study identified a large number of mutations within the new outbreak clade, it also reflected that we need to move fast with the genomic analysis of newly detected strains from around the world to develop better prevention and treatment methods.
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Affiliation(s)
- Roshan Kumar
- Post-Graduate Department of Zoology, Magadh University, Bodh Gaya, Bihar 824234, India
| | - Shekhar Nagar
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, Delhi 110019, India
| | - Shazia Haider
- Department of Biotechnology, Jaypee Institute of Information and Technology, Uttar Pradesh, Noida 201309, India
| | - Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi 110007, India
| | - Kalaiarasan Ponnusamy
- Biotechnology and Viral Hepatitis Division, National Centre for Disease Control, New Delhi 110054, India
| | - Gauri Garg Dhingra
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi 110007, India
| | - Shailly Anand
- Deen Dayal Upadhyaya College, University of Delhi, New Delhi 110078, India
| | - Ankita Dua
- Shivaji College, University of Delhi, New Delhi 110027, India
| | - Mona Singh
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, Delhi 110019, India
| | - Roushan Kumar
- Post-Graduate Department of Zoology, Magadh University, Bodh Gaya, Bihar 824234, India
| | - Manisha Sengar
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, Delhi 110019, India
| | - Indrakant Kumar Singh
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, Delhi 110019, India
- Institute of Eminence, Delhi School of Public Health, University of Delhi, Delhi 110007, India
| | - Rup Lal
- Phixgen Pvt. Ltd., Sector 55, Noida, Uttar Pradesh, India
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
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Kumar R, Mahmoud MM, Tashkandi HM, Haque S, Harakeh S, Ponnusamy K, Haider S. Combinatorial Network of Transcriptional and miRNA Regulation in Colorectal Cancer. Int J Mol Sci 2023; 24:ijms24065356. [PMID: 36982429 PMCID: PMC10048903 DOI: 10.3390/ijms24065356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
Colorectal cancer is one of the leading causes of cancer-associated mortality across the worldwide. One of the major challenges in colorectal cancer is the understanding of the regulatory mechanisms of biological molecules. In this study, we aimed to identify novel key molecules in colorectal cancer by using a computational systems biology approach. We constructed the colorectal protein–protein interaction network which followed hierarchical scale-free nature. We identified TP53, CTNBB1, AKT1, EGFR, HRAS, JUN, RHOA, and EGF as bottleneck-hubs. The HRAS showed the largest interacting strength with functional subnetworks, having strong correlation with protein phosphorylation, kinase activity, signal transduction, and apoptotic processes. Furthermore, we constructed the bottleneck-hubs’ regulatory networks with their transcriptional (transcription factor) and post-transcriptional (miRNAs) regulators, which exhibited the important key regulators. We observed miR-429, miR-622, and miR-133b and transcription factors (EZH2, HDAC1, HDAC4, AR, NFKB1, and KLF4) regulates four bottleneck-hubs (TP53, JUN, AKT1 and EGFR) at the motif level. In future, biochemical investigation of the observed key regulators could provide further understanding about their role in the pathophysiology of colorectal cancer.
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Affiliation(s)
- Rupesh Kumar
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector 62, Noida 201309, India;
| | - Maged Mostafa Mahmoud
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo 12622, Egypt
| | - Hanaa M. Tashkandi
- Department of General Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut 13-5053, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman P.O. Box 346, United Arab Emirates
| | - Steve Harakeh
- King Fahd Medical Research Center, and Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Kalaiarasan Ponnusamy
- Biotechnology Division, National Centre for Disease Control, New Delhi 110054, India
- Correspondence: (K.P.); (S.H.)
| | - Shazia Haider
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector 62, Noida 201309, India;
- Correspondence: (K.P.); (S.H.)
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Kashyap J, Kumari N, Ponnusamy K, Tyagi RK. Hereditary Vitamin D-Resistant Rickets (HVDRR) associated SNP variants of vitamin D receptor exhibit malfunctioning at multiple levels. Biochim Biophys Acta Gene Regul Mech 2023; 1866:194891. [PMID: 36396100 DOI: 10.1016/j.bbagrm.2022.194891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/11/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
Vitamin D receptor (VDR) is a member of the nuclear receptor superfamily. It is a primary regulator of calcium and phosphate homeostasis required for skeleton and bone mineralization. Vitamin D in active form 1α,25 dihydroxyvitamin-D3 mediates its cellular functions by binding to VDR. Active VDR forms heterodimers with partner RXR (retinoid X receptor) to execute its physiological actions. HVDRR (Hereditary Vitamin D-Resistant Rickets) is a rare genetic disorder that occurs because of generalized resistance to the 1α,25(OH)2D3. HVDRR is caused by the polymorphic variations in VDR gene leading to defective intestinal calcium absorption and mineralization of newly forming bones. Using point and deletion SNPs of VDR we have studied several HVDRR-associated SNP variants for their subcellular dynamics, transcriptional functions, 'genome bookmarking', heterodimeric interactions with RXR, and receptor stability. We previously reported that VDR is a 'mitotic bookmarking factor' that remains constitutively associated with the mitotic chromatin to inherit 'transcriptional memory', however the mechanistic details remained unclear. We document that 'genome bookmarking' property by VDR is critically impaired by naturally occurring HVDRR-associated point and deletion variants found in patients. Furthermore, these HVDRR-associated SNP variants of VDR were found to be compromised in transcriptional function, nuclear translocation, protein stability and intermolecular interactions with its heterodimeric partner RXR. Intriguingly, majority of these disease-allied functional defects failed to be rescued by RXR. Our findings suggest that the HVDRR-associated SNP variations influence the normal functioning of the receptor, and this derived understanding may help in the management of disease with precisely designed small molecule modulators.
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Affiliation(s)
- Jyoti Kashyap
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Neha Kumari
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | | | - Rakesh K Tyagi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India; Special Centre for Systems Medicine (Concurrent Faculty), Jawaharlal Nehru University, New Delhi 110067, India.
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10
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Kumar R, Malik Z, Singh M, Rachana R, Mani S, Ponnusamy K, Haider S. Amyotrophic Lateral Sclerosis Risk Genes and Suppressor. Curr Gene Ther 2023; 23:148-162. [PMID: 36366843 DOI: 10.2174/1566523223666221108113330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/24/2022] [Accepted: 09/01/2022] [Indexed: 11/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that leads to death by progressive paralysis and respiratory failure within 2-4 years of onset. About 90-95% of ALS cases are sporadic (sALS), and 5-10% are inherited through family (fALS). Though the mechanisms of the disease are still poorly understood, so far, approximately 40 genes have been reported as ALS causative genes. The mutations in some crucial genes, like SOD1, C9ORF72, FUS, and TDP-43, are majorly associated with ALS, resulting in ROS-associated oxidative stress, excitotoxicity, protein aggregation, altered RNA processing, axonal and vesicular trafficking dysregulation, and mitochondrial dysfunction. Recent studies show that dysfunctional cellular pathways get restored as a result of the repair of a single pathway in ALS. In this review article, our aim is to identify putative targets for therapeutic development and the importance of a single suppressor to reduce multiple symptoms by focusing on important mutations and the phenotypic suppressors of dysfunctional cellular pathways in crucial genes as reported by other studies.
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Affiliation(s)
- Rupesh Kumar
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
| | - Zubbair Malik
- School of Computational and Integrative Science, Jawaharlal Nehru University, New Delhi-110067, India
| | - Manisha Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
| | - R Rachana
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
| | - Shalini Mani
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
| | | | - Shazia Haider
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
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11
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Pathak AK, Mishra GP, Uppili B, Walia S, Fatihi S, Abbas T, Banu S, Ghosh A, Kanampalliwar A, Jha A, Fatma S, Aggarwal S, Dhar MS, Marwal R, Radhakrishnan VS, Ponnusamy K, Kabra S, Rakshit P, Bhoyar RC, Jain A, Divakar MK, Imran M, Faruq M, Sowpati DT, Thukral L, Raghav SK, Mukerji M. Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes. Nucleic Acids Res 2022; 50:1551-1561. [PMID: 35048970 PMCID: PMC8860616 DOI: 10.1093/nar/gkab1297] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/09/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying variants of concern (VOC). Viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host single nucleotide variations (iSNVs). Analysing 1347 samples collected till June 2020, we recorded 16 410 iSNV sites throughout the SARS-CoV-2 genome. We found ∼42% of the iSNV sites to be reported as SNVs by 30 September 2020 in consensus sequences submitted to GISAID, which increased to ∼80% by 30th June 2021. Following this, analysis of another set of 1774 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) lineage-defining variations appeared as iSNVs before getting fixed in the population. Besides, mutations in RdRp as well as RNA-editing by APOBEC and ADAR deaminases seem to contribute to the differential prevalence of iSNVs in hosts. We also observe hyper-variability at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions.
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Affiliation(s)
- Ankit K Pathak
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | | | - Bharathram Uppili
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Safal Walia
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Saman Fatihi
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Tahseen Abbas
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sofia Banu
- CSIR - Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Arup Ghosh
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | | | - Atimukta Jha
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Sana Fatma
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Shifu Aggarwal
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Mahesh Shanker Dhar
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Robin Marwal
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | | | - Kalaiarasan Ponnusamy
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Sandhya Kabra
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Partha Rakshit
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Rahul C Bhoyar
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Abhinav Jain
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohit Kumar Divakar
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohamed Imran
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohammed Faruq
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Divya Tej Sowpati
- CSIR - Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Lipi Thukral
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Sunil K Raghav
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Mitali Mukerji
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Indian Institute of Technology (IIT), Jodhpur, India
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12
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Jha P, Singh P, Arora S, Sultan A, Nayek A, Ponnusamy K, Syed MA, Dohare R, Chopra M. Integrative multiomics and in silico analysis revealed the role of ARHGEF1 and its screened antagonist in mild and severe COVID-19 patients. J Cell Biochem 2022; 123:673-690. [PMID: 35037717 PMCID: PMC9015317 DOI: 10.1002/jcb.30213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 12/22/2022]
Abstract
COVID‐19 is a sneaking deadly disease caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). The rapid increase in the number of infected patients worldwide enhances the exigency for medicines. However, precise therapeutic drugs are not available for COVID‐19; thus, exhaustive research is critically required to unscramble the pathogenic tools and probable therapeutic targets for the development of effective therapy. This study utilizes a chemogenomics strategy, including computational tools for the identification of viral‐associated differentially expressed genes (DEGs), and molecular docking of potential chemical compounds available in antiviral, anticancer, and natural product‐based libraries against these DEGs. We scrutinized the messenger RNA expression profile of SARS‐CoV‐2 patients, publicly available on the National Center for Biotechnology Information–Gene Expression Omnibus database, stratified them into different groups based on the severity of infection, superseded by identification of overlapping mild and severe infectious (MSI)‐DEGs. The profoundly expressed MSI‐DEGs were then subjected to trait‐linked weighted co‐expression network construction and hub module detection. The hub module MSI‐DEGs were then exposed to enrichment (gene ontology + pathway) and protein–protein interaction network analyses where Rho guanine nucleotide exchange factor 1 (ARHGEF1) gene conjectured in all groups and could be a probable target of therapy. Finally, we used the molecular docking and molecular dynamics method to identify inherent hits against the ARHGEF1 gene from antiviral, anticancer, and natural product‐based libraries. Although the study has an identified significant association of the ARHGEF1 gene in COVID19; and probable compounds targeting it, using in silico methods, these targets need to be validated by both in vitro and in vivo methods to effectively determine their therapeutic efficacy against the devastating virus.
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Affiliation(s)
- Prakash Jha
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
| | - Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shweta Arora
- Department of Biotechnology, Translational Research Lab, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Armiya Sultan
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Arnab Nayek
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Kalaiarasan Ponnusamy
- Synthetic Biology Lab, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Mansoor Ali Syed
- Department of Biotechnology, Translational Research Lab, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Madhu Chopra
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
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13
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Dhar MS, Marwal R, VS R, Ponnusamy K, Jolly B, Bhoyar RC, Sardana V, Naushin S, Rophina M, Mellan TA, Mishra S, Whittaker C, Fatihi S, Datta M, Singh P, Sharma U, Ujjainiya R, Bhatheja N, Divakar MK, Singh MK, Imran M, Senthivel V, Maurya R, Jha N, Mehta P, A V, Sharma P, VR A, Chaudhary U, Soni N, Thukral L, Flaxman S, Bhatt S, Pandey R, Dash D, Faruq M, Lall H, Gogia H, Madan P, Kulkarni S, Chauhan H, Sengupta S, Kabra S, Gupta RK, Singh SK, Agrawal A, Rakshit P. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science 2021; 374:995-999. [PMID: 34648303 PMCID: PMC7612010 DOI: 10.1126/science.abj9932] [Citation(s) in RCA: 160] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/06/2021] [Indexed: 01/16/2023]
Abstract
Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.
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Affiliation(s)
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | | | | | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Rahul C. Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Viren Sardana
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Salwa Naushin
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Thomas A. Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Saman Fatihi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | - Uma Sharma
- National Centre for Disease Control, Delhi, India
| | - Rajat Ujjainiya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Nitin Bhatheja
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Ranjeet Maurya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Neha Jha
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Priyanka Mehta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Vivekanand A
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Pooja Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Arvinden VR
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Namita Soni
- National Centre for Disease Control, Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Samir Bhatt
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Hemlata Lall
- National Centre for Disease Control, Delhi, India
| | - Hema Gogia
- National Centre for Disease Control, Delhi, India
| | - Preeti Madan
- National Centre for Disease Control, Delhi, India
| | | | | | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - The Indian SARS-CoV-2 Genomics Consortium (INSACOG)‡
- National Centre for Disease Control, Delhi, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Department of Mathematics, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Ravindra K. Gupta
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | | | - Anurag Agrawal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
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14
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Dhar MS, Marwal R, Vs R, Ponnusamy K, Jolly B, Bhoyar RC, Sardana V, Naushin S, Rophina M, Mellan TA, Mishra S, Whittaker C, Fatihi S, Datta M, Singh P, Sharma U, Ujjainiya R, Bhatheja N, Divakar MK, Singh MK, Imran M, Senthivel V, Maurya R, Jha N, Mehta P, A V, Sharma P, Vr A, Chaudhary U, Soni N, Thukral L, Flaxman S, Bhatt S, Pandey R, Dash D, Faruq M, Lall H, Gogia H, Madan P, Kulkarni S, Chauhan H, Sengupta S, Kabra S, Gupta RK, Singh SK, Agrawal A, Rakshit P, Nandicoori V, Tallapaka KB, Sowpati DT, Thangaraj K, Bashyam MD, Dalal A, Sivasubbu S, Scaria V, Parida A, Raghav SK, Prasad P, Sarin A, Mayor S, Ramakrishnan U, Palakodeti D, Seshasayee ASN, Bhat M, Shouche Y, Pillai A, Dikid T, Das S, Maitra A, Chinnaswamy S, Biswas NK, Desai AS, Pattabiraman C, Manjunatha MV, Mani RS, Arunachal Udupi G, Abraham P, Atul PV, Cherian SS. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science 2021; 374:995-999. [PMID: 34648303 DOI: 10.1101/2021.06.02.21258076] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.
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Affiliation(s)
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | | | | | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Viren Sardana
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Salwa Naushin
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Thomas A Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Saman Fatihi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | - Uma Sharma
- National Centre for Disease Control, Delhi, India
| | - Rajat Ujjainiya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Nitin Bhatheja
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Ranjeet Maurya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Neha Jha
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Priyanka Mehta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Vivekanand A
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Pooja Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Arvinden Vr
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Namita Soni
- National Centre for Disease Control, Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Samir Bhatt
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Hemlata Lall
- National Centre for Disease Control, Delhi, India
| | - Hema Gogia
- National Centre for Disease Control, Delhi, India
| | - Preeti Madan
- National Centre for Disease Control, Delhi, India
| | | | | | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Ravindra K Gupta
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | | | - Anurag Agrawal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
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Mlcochova P, Kemp SA, Dhar MS, Papa G, Meng B, Ferreira IATM, Datir R, Collier DA, Albecka A, Singh S, Pandey R, Brown J, Zhou J, Goonawardane N, Mishra S, Whittaker C, Mellan T, Marwal R, Datta M, Sengupta S, Ponnusamy K, Radhakrishnan VS, Abdullahi A, Charles O, Chattopadhyay P, Devi P, Caputo D, Peacock T, Wattal C, Goel N, Satwik A, Vaishya R, Agarwal M, Mavousian A, Lee JH, Bassi J, Silacci-Fegni C, Saliba C, Pinto D, Irie T, Yoshida I, Hamilton WL, Sato K, Bhatt S, Flaxman S, James LC, Corti D, Piccoli L, Barclay WS, Rakshit P, Agrawal A, Gupta RK. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 2021; 599:114-119. [PMID: 34488225 DOI: 10.1101/2021.05.08.443253] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/23/2021] [Indexed: 05/23/2023]
Abstract
The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)1. In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era.
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Affiliation(s)
- Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- University College London, London, UK
| | | | - Guido Papa
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Dami A Collier
- Department of Medicine, University of Cambridge, Cambridge, UK
- University College London, London, UK
| | - Anna Albecka
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Sujeet Singh
- National Centre for Disease Control, Delhi, India
| | - Rajesh Pandey
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Jonathan Brown
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Jie Zhou
- Department of Infectious Diseases, Imperial College London, London, UK
| | | | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Thomas Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | | | | | - Adam Abdullahi
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Priti Devi
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Tom Peacock
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | - Joo Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Takashi Irie
- Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Isao Yoshida
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Kei Sato
- Division of Systems Virology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
| | - Samir Bhatt
- National Centre for Disease Control, Delhi, India
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Leo C James
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Wendy S Barclay
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | | | - Anurag Agrawal
- CSIR Institute of Genomics and Integrative Biology, Delhi, India.
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Africa Health Research Institute, Durban, South Africa.
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Mlcochova P, Kemp SA, Dhar MS, Papa G, Meng B, Ferreira IATM, Datir R, Collier DA, Albecka A, Singh S, Pandey R, Brown J, Zhou J, Goonawardane N, Mishra S, Whittaker C, Mellan T, Marwal R, Datta M, Sengupta S, Ponnusamy K, Radhakrishnan VS, Abdullahi A, Charles O, Chattopadhyay P, Devi P, Caputo D, Peacock T, Wattal C, Goel N, Satwik A, Vaishya R, Agarwal M, Mavousian A, Lee JH, Bassi J, Silacci-Fegni C, Saliba C, Pinto D, Irie T, Yoshida I, Hamilton WL, Sato K, Bhatt S, Flaxman S, James LC, Corti D, Piccoli L, Barclay WS, Rakshit P, Agrawal A, Gupta RK. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 2021; 599:114-119. [PMID: 34488225 PMCID: PMC8566220 DOI: 10.1038/s41586-021-03944-y] [Citation(s) in RCA: 810] [Impact Index Per Article: 270.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/23/2021] [Indexed: 12/26/2022]
Abstract
The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)1. In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era.
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Affiliation(s)
- Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- University College London, London, UK
| | | | - Guido Papa
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Dami A Collier
- Department of Medicine, University of Cambridge, Cambridge, UK
- University College London, London, UK
| | - Anna Albecka
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Sujeet Singh
- National Centre for Disease Control, Delhi, India
| | - Rajesh Pandey
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Jonathan Brown
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Jie Zhou
- Department of Infectious Diseases, Imperial College London, London, UK
| | | | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Thomas Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | | | | | - Adam Abdullahi
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Priti Devi
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Tom Peacock
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | - Joo Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Takashi Irie
- Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Isao Yoshida
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Kei Sato
- Division of Systems Virology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
| | - Samir Bhatt
- National Centre for Disease Control, Delhi, India
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Leo C James
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Wendy S Barclay
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | | | - Anurag Agrawal
- CSIR Institute of Genomics and Integrative Biology, Delhi, India.
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Africa Health Research Institute, Durban, South Africa.
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Chakravarty R, Ponnusamy K, Sendhil R. Micro-level evaluation of socio-technological interventions to address climate change-induced stresses in dairy enterprises. IJDS 2021. [DOI: 10.33785/ijds.2021.v74i05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bhat ZI, Naseem A, Kumar B, Ponnusamy K, Tiwari RR, Sharma GD, Rizvi MMA. Association of PARK-2 Non-synonyms Polymorphisms and Their In Silico Validation Among North Indian Colorectal Cancer Patients. J Gastrointest Cancer 2021; 53:674-682. [PMID: 34467515 DOI: 10.1007/s12029-021-00693-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2021] [Indexed: 11/25/2022]
Abstract
PURPOSE PARK2 is a potential tumour suppressor gene and its genetic alterations (regionic loss) are common across many human cancers. The association of PARK2 germline variations (SNPs) with Parkinson's has been shown, but their association in development and progression of cancer remains elusive. The aim of this study was to identify association of PARK2 polymorphisms (rs1801474, rs1801334) with colorectal cancer in a case control study design. METHODS This case control study included a total of 650 genetically unrelated subjects comprising 300 colorectal cancer cases and 350 healthy controls belonging to North Indian. Both SNPs were analyzed using the PCR-RFLP assay. Statistical analysis for describing risk and association was performed using SPSS-17 software. Structural deviations due to non- synonymous substitutions (S167N and D394N) were analyzed using MD simulations. RESULTS The genotype distributions of both the SNPs were in Hardy-Weinberg equilibrium. For both the polymorphisms, the allelic model showed statistically significant risk with OR ~ 1.3. Many of the associations remained significant even after Bonferroni correction (P < 0.00125). The result suggested that both S167N and D394N were deviated from wild type and structures and were stable after 5 ns. The average value of RMSD for backbone atoms was calculated from 5 to 10 ns molecular dynamics simulation data. CONCLUSION In conclusion, our study revealed a significant association of PARK2 SNPs with colorectal cancer as well as their relations with other clinical parameters highlighting their contribution towards colorectal cancer susceptibility in North Indian population.
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Affiliation(s)
- Zafar Iqbal Bhat
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Afreen Naseem
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Bhupender Kumar
- Department of Biochemistry, Institute of Home Economics, University of Delhi, Delhi, India
| | - Kalaiarasan Ponnusamy
- Synthetic Biology Lab, School ofBiotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Raj Ranjan Tiwari
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - G D Sharma
- Department of Zoology, P.M.B Gujarati Science College, Indore, India
| | - M Moshahid Alam Rizvi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India.
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Gnanasekaran P, Gupta N, Ponnusamy K, Chakraborty S. Geminivirus Betasatellite-Encoded βC1 Protein Exhibits Novel ATP Hydrolysis Activity That Influences Its DNA-Binding Activity and Viral Pathogenesis. J Virol 2021; 95:e0047521. [PMID: 34132576 PMCID: PMC8354231 DOI: 10.1128/jvi.00475-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/09/2021] [Indexed: 11/20/2022] Open
Abstract
Plant virus satellites are maintained by their associated helper viruses, and satellites influence viral pathogenesis. Diseases caused by geminivirus-betasatellite complexes can become epidemics and therefore have become a threat to economically important crops across the world. Here, we identified a novel molecular function of the betasatellite-encoded pathogenicity determinant βC1. The tomato leaf curl Patna betasatellite (ToLCPaB)-encoded βC1 protein was found to exhibit novel ATPase activity in the presence of the divalent metal ion cofactor MgCl2. Moreover, ATPase activity was confirmed to be ubiquitously displayed by βC1 proteins encoded by diverse betasatellites. Mutational and sequence analysis showed that conserved lysine/arginine residues at positions 49/50 and 91 of βC1 proteins are essential for their ATPase activity. Biochemical studies revealed that the DNA-binding activity of the βC1 protein was interfered with by the binding of ATP to the protein. Mutating arginine 91 of βC1 to alanine reduced its DNA-binding activity. The results of docking studies provided evidence for an overlap of the ATP-binding and DNA-binding regions of βC1 and for the importance of arginine 91 for both ATP-binding and DNA-binding activities. A mutant betasatellite with a specifically βC1-ATPase dominant negative mutation was found to induce symptoms on Nicotiana benthamiana plants similar to those induced by wild-type betasatellite infection. The ATPase function of βC1 was found to be negatively associated with geminivirus-betasatellite DNA accumulation, despite the positive influence of this ATPase function on the accumulation of replication-associated protein (Rep) and βC1 transcripts. IMPORTANCE Most satellites influence the pathogenesis of their helper viruses. Here, we characterized the novel molecular function of βC1, a nonstructural pathogenicity determinant protein encoded by a betasatellite. We demonstrated the display of ATPase activity by this βC1 protein. Additionally, we confirmed the ubiquitous display of ATPase activity by βC1 proteins encoded by diverse betasatellites. The lysine/arginine residues conserved at positions 49 and 91 of βC1 were found to be crucial for its ATPase function. DNA-binding activity of βC1 was found to be reduced in the presence of ATP. Inhibition of ATPase activity of βC1 in the presence of an excess concentration of cold ATP, GTP, CTP, or UTP suggested that the purified βC1 can also hydrolyze other cellular nucleoside triphosphates (NTPs) besides ATP in vitro. These results established the importance of the ATPase and DNA-binding activities of the βC1 protein in regulating geminivirus-betasatellite DNA accumulation in the infected plant cell.
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Affiliation(s)
- Prabu Gnanasekaran
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru Universitygrid.10706.30, New Delhi, India
| | - Neha Gupta
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru Universitygrid.10706.30, New Delhi, India
| | | | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru Universitygrid.10706.30, New Delhi, India
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Mohapatra S, R S, Singh A, Dixit AK, Malhotra R, Ponnusamy K. An economic analysis of milk production in Haryana. IJDS 2021. [DOI: 10.33785/ijds.2021.v74i02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Nagar S, Talwar C, Haider S, Puri A, Ponnusamy K, Gupta M, Sood U, Bajaj A, Lal R, Kumar R. Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae. Front Microbiol 2020; 11:1725. [PMID: 33013721 PMCID: PMC7500135 DOI: 10.3389/fmicb.2020.01725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/30/2020] [Indexed: 11/28/2022] Open
Abstract
The genus Parapedobacter was established to describe a novel genus within the family Sphingobacteriaceae and derives its name from Pedobacter, with which it is shown to be evolutionarily related. Despite this, Parapedobacter and Pedobacter do not share very high 16S rRNA gene sequence similarities. Therefore, we hypothesized whether these substantial differences at the 16S rRNA gene level depict the true phylogeny or that these genomes have actually diverged. Thus, we performed genomic analysis of the four available genomes of Parapedobacter to better understand their phylogenomic position within family Sphingobacteriaceae. Our results demonstrated that Parapedobacter is more closely related to species of Olivibacter, as opposed to the genus Pedobacter. Further, we identified a significant class of enzymes called pectinases with potential industrial applications within the genomes of Parapedobacter luteus DSM 22899T and Parapedobacter composti DSM 22900T. These enzymes, specifically pectinesterases and pectate lyases, are presumed to have largely different catalytic activities based on very low sequence similarities to already known enzymes and thus may be exploited for industrial applications. We also determined the complete Bacteroides aerotolerance (Bat) operon (batA, batB, batC, batD, batE, hypothetical protein, moxR, and pa3071) within the genome of Parapedobacter indicus RK1T. This expands the definition of genus Parapedobacter to containing members that are able to tolerate oxygen stress using encoded oxidative stress responsive systems. By conducting a signal propagation network analysis, we determined that BatD, BatE, and hypothetical proteins are the major controlling hubs that drive the expression of Bat operon. As a key metabolic difference, we also annotated the complete iol operon within the P. indicus RK1T genome for utilization of all three stereoisomers of inositol, namely myo-inositol, scyllo-inositol, and 1D-chiro-inositol, which are abundant sources of organic phosphate found in soils. The results suggest that the genus Parapedobacter holds promising applications owing to its environmentally relevant genomic adaptations, which may be exploited in the future.
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Affiliation(s)
- Shekhar Nagar
- Department of Zoology, University of Delhi, Delhi, India
| | - Chandni Talwar
- Department of Zoology, University of Delhi, Delhi, India
| | - Shazia Haider
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Akshita Puri
- Department of Zoology, University of Delhi, Delhi, India.,P.G.T.D, Zoology, R.T.M Nagpur University, Nagpur, India
| | | | - Madhuri Gupta
- Department of Zoology, University of Delhi, Delhi, India
| | - Utkarsh Sood
- Department of Zoology, University of Delhi, Delhi, India.,The Energy and Resources Institute, New Delhi, India
| | - Abhay Bajaj
- Department of Zoology, University of Delhi, Delhi, India.,Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India.,The Energy and Resources Institute, New Delhi, India
| | - Roshan Kumar
- Department of Zoology, University of Delhi, Delhi, India.,P.G. Department of Zoology, Magadh University, Bodh Gaya, India
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Raj K, Ponnusamy K, Yadav R, CN K, Begum M. Effectiveness of Public Private Partnership model of dairy farming in Haryana. IJDS 2020. [DOI: 10.33785/ijds.2020.v73i01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Haider S, Ponnusamy K, Singh RKB, Chakraborti A, Bamezai RNK. Hamiltonian energy as an efficient approach to identify the significant key regulators in biological networks. PLoS One 2019; 14:e0221463. [PMID: 31442253 PMCID: PMC6707611 DOI: 10.1371/journal.pone.0221463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/07/2019] [Indexed: 12/27/2022] Open
Abstract
The topological characteristics of biological networks enable us to identify the key nodes in terms of modularity. However, due to a large size of the biological networks with many hubs and functional modules across intertwined layers within the network, it often becomes difficult to accomplish the task of identifying potential key regulators. We use for the first time a generalized formalism of Hamiltonian Energy (HE) with a recursive approach. The concept, when applied to the Apoptosis Regulatory Gene Network (ARGN), helped us identify 11 Motif hubs (MHs), which influenced the network up to motif levels. The approach adopted allowed to classify MHs into 5 significant motif hubs (S-MHs) and 6 non-significant motif hubs (NS-MHs). The significant motif hubs had a higher HE value and were considered as high-active key regulators; while the non-significant motif hubs had a relatively lower HE value and were considered as low-active key regulators, in network control mechanism. Further, we compared the results of the HE analyses with the topological characterization, after subjecting to the three conditions independently: (i) removing all MHs, (ii) removing only S-MHs, and (iii) removing only NS-MHs from the ARGN. This procedure allowed us to cross-validate the role of 5 S-MHs, NFk-B1, BRCA1, CEBPB, AR, and POU2F1 as the potential key regulators. The changes in HE calculations further showed that the removal of 5 S-MHs could cause perturbation at all levels of the network, a feature not discernible by topological analysis alone.
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Affiliation(s)
- Shazia Haider
- Department of Neurology, All India Institute of Medical Science (AIIMS), New Delhi, India
| | | | - R. K. Brojen Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail: (RKBS); (AC); (RNKB)
| | - Anirban Chakraborti
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail: (RKBS); (AC); (RNKB)
| | - Rameshwar N. K. Bamezai
- Formerly at National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail: (RKBS); (AC); (RNKB)
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Gnanasekaran P, Ponnusamy K, Chakraborty S. A geminivirus betasatellite encoded βC1 protein interacts with PsbP and subverts PsbP-mediated antiviral defence in plants. Mol Plant Pathol 2019; 20:943-960. [PMID: 30985068 PMCID: PMC6589724 DOI: 10.1111/mpp.12804] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Geminivirus disease complexes potentially interfere with plants physiology and cause disastrous effects on a wide range of economically important crops throughout the world. Diverse geminivirus betasatellite associations exacerbate the epidemic threat for global food security. Our previous study showed that βC1, the pathogenicity determinant of geminivirus betasatellites induce symptom development by disrupting the ultrastructure and function of chloroplasts. Here we explored the betasatellite-virus-chloroplast interaction in the scope of viral pathogenesis as well as plant defence responses, using Nicotiana benthamiana-Radish leaf curl betasatellite (RaLCB) as the model system. We have shown an interaction between RaLCB-encoded βC1 and one of the extrinsic subunit proteins of oxygen-evolving complex of photosystem II both in vitro and in vivo. Further, we demonstrate a novel function of the Nicotiana benthamiana oxygen-evolving enhancer protein 2 (PsbP), in that it binds DNA, including geminivirus DNA. Transient silencing of PsbP in N. benthamiana plants enhances pathogenicity and viral DNA accumulation. Overexpression of PsbP impedes disease development during the early phase of infection, suggesting that PsbP is involved in generation of defence response during geminivirus infection. In addition, βC1-PsbP interaction hampers non-specific binding of PsbP to the geminivirus DNA. Our findings suggest that betasatellite-encoded βC1 protein accomplishes counter-defence by physical interaction with PsbP reducing the ability of PsbP to bind geminivirus DNA to establish infection.
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Affiliation(s)
- Prabu Gnanasekaran
- Molecular Virology Laboratory, School of Life SciencesJawaharlal Nehru UniversityNew Delhi110 067India
| | - Kalaiarasan Ponnusamy
- Synthetic Biology Laboratory, School of BiotechnologyJawaharlal Nehru UniversityNew Delhi110 067India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life SciencesJawaharlal Nehru UniversityNew Delhi110 067India
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Singh SK, Yende AS, Ponnusamy K, Tyagi RK. A comprehensive evaluation of anti-diabetic drugs on nuclear receptor PXR platform. Toxicol In Vitro 2019; 60:347-358. [PMID: 31233785 DOI: 10.1016/j.tiv.2019.06.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 06/09/2019] [Accepted: 06/20/2019] [Indexed: 10/26/2022]
Abstract
Pregnane & Xenobiotic Receptor (PXR), one of the members of nuclear receptor superfamily, acts as a 'master-regulator' of drug metabolism and disposition machinery (DMD). Activation of PXR enables detoxification and elimination of toxic xenobiotics/endobiotics, and defends our body against chemical insults. On the contrary, PXR activation also imposes a serious concern for drug-drug interactions (DDIs). Such DDIs could either decrease the efficacy or lead to accumulation of co-administered drugs at toxic level. Therefore, it is desirable that during drug development process the small drug molecules are screened on PXR-platform prior to their clinical trial and prevent late stage failures. In view of this, we have selected a group of anti-diabetic drug molecules to examine if the success and potential failure of small molecule modulators can be pre-assessed and judiciously correlated on PXR platform. For this purpose, we have examined the PXR activation potential of the selected anti-diabetic drugs. Subsequent to screening of these anti-diabetic drugs, we elaborated the study further with rosiglitazone and pioglitazone (thiazolidinediones, TZDs) which are oral anti-diabetic formulations and have been in controversy owing to their association with cardiotoxicity and bladder cancer respectively. Our study revealed that some of the selected anti-diabetic drugs possess PXR activation potential, implying that these can up-regulate the expression of CYP3A4, UGT1A1, MDR1 and thereby can be predicted to inflict undesirable consequences.
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Affiliation(s)
- Shashi Kala Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ashutosh S Yende
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | | | - Rakesh K Tyagi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India.
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Patel D, Ponnusamy K. Development and validation of extension strategies for effective management of reproductive problems of dairy animals. IJDS 2019. [DOI: 10.33785/ijds.2019.v72i02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rana M, Dash AK, Ponnusamy K, Tyagi RK. Nuclear localization signal region in nuclear receptor PXR governs the receptor association with mitotic chromatin. Chromosome Res 2018; 26:255-276. [DOI: 10.1007/s10577-018-9583-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/28/2018] [Accepted: 07/02/2018] [Indexed: 12/17/2022]
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Mahida DP, Sendhil R, Sirohi S, Chandel BS, Ponnusamy K, Sankhala G. Tracking the Disparities in Gujarat Dairy Development – An Application of Biplot Analysis. CURR SCI INDIA 2018. [DOI: 10.18520/cs/v114/i10/2151-2155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Aggarwal S, Nayek A, Pradhan D, Verma R, Yadav M, Ponnusamy K, Jain AK. dbGAPs: A comprehensive database of genes and genetic markers associated with psoriasis and its subtypes. Genomics 2017; 110:S0888-7543(17)30115-5. [PMID: 29031638 DOI: 10.1016/j.ygeno.2017.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/04/2017] [Accepted: 10/10/2017] [Indexed: 01/12/2023]
Abstract
Psoriasis is a systemic hyperproliferative inflammatory skin disorder, although rarely fatal but significantly reduces quality of life. Understanding the full genetic component of the disease association may provide insight into biological pathways as well as targets and biomarkers for diagnosis, prognosis and therapy. Studies related to psoriasis associated genes and genetic markers are scattered and not easily amendable to data-mining. To alleviate difficulties, we have developed dbGAPs an integrated knowledgebase representing a gateway to psoriasis associated genomic data. The database contains annotation for 202 manually curated genes associated with psoriasis and its subtypes with cross-references. Functional enrichment of these genes, in context of Gene Ontology and pathways, provide insight into their important role in psoriasis etiology and pathogenesis. The dbGAPs interface is enriched with an interactive search engine for data retrieval along with unique customized tools for Single Nucleotide Polymorphism (SNP)/indel detection and SNP/indel annotations. dbGAPs is accessible at http://www.bmicnip.in/dbgaps/.
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Affiliation(s)
- Shweta Aggarwal
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | - Arnab Nayek
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | - Dibyabhaba Pradhan
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | - Rashi Verma
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | - Monika Yadav
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | | | - Arun Kumar Jain
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India.
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Ravikumar RK, Thakur D, Choudhary H, Kumar V, Kinhekar AS, Garg T, Ponnusamy K, Bhojne GR, Shetty VM, Kumar V. Social engineering of societal knowledge in livestock science: Can we be more empathetic? Vet World 2017; 10:86-91. [PMID: 28246452 PMCID: PMC5301184 DOI: 10.14202/vetworld.2017.86-91] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/09/2016] [Indexed: 11/25/2022] Open
Abstract
Questions are raised in effective utilization of farmer’s wisdom by communities in their farming. Planners support to livelihood emphasize mostly of inputs from outside and not setting up sustainable goals. Formal institutions and planners of program are finding constraints and sceptical in wider dissemination of indigenous knowledge research system (IKRS). This is in spite of evidence that considerable number of farmer’s in livestock sector depends on IKRS. In this context, it is pertinent to showcase dissemination potential of these knowledge system(s) in larger geographical areas. The review illustrates different challenges encountered while control of livestock ailments like ectoparasite infestation through IKRS. Several times, it was opinioned to provide or share IKRS to thwart ailments in a specific region. This is interesting as it was narrated how formal system is unable to recognize farmer’s problem and challenges in integrating these sustainable practices. It has to be noted that disseminating activities seldom takes into account the experimental potential of farmers. This review paper articulates various evidences generated in enhancing diffusion thereby dissemination of IKRS. The nature of support extended by IKRS in entrepreneurial activity of smallholder farming units did not get adequate recognition. There needs to be minimum standard protocol in deriving benefit from such low-cost alternative technologies. This will enrich incremental innovation activities as per location specific need and provide scope for wider dissemination.
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Affiliation(s)
- R K Ravikumar
- National Innovation Foundation-India, Satellite Complex, Ahmedabad 380 015 Gujarat, India
| | - Devesh Thakur
- Department of Veterinary and Animal Husbandry Extension Education, Dr. GC Negi College of Veterinary and Animal Sciences, CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur - 176 062, Himachal Pradesh, India
| | - Hardev Choudhary
- National Innovation Foundation-India, Satellite Complex, Ahmedabad 380 015 Gujarat, India
| | - Vivek Kumar
- National Innovation Foundation-India, Satellite Complex, Ahmedabad 380 015 Gujarat, India
| | - Amol S Kinhekar
- National Innovation Foundation-India, Satellite Complex, Ahmedabad 380 015 Gujarat, India
| | - Tushar Garg
- National Innovation Foundation-India, Satellite Complex, Ahmedabad 380 015 Gujarat, India
| | - K Ponnusamy
- Division of Dairy Extension, ICAR- National Dairy Research Institute, Karnal - 132 001, Haryana, India
| | - G R Bhojne
- Department of Clinical Medicine, Ethics & Jurisprudence, Nagpur Veterinary College, Maharashtra Animal & Fishery Sciences University, Nagpur - 440 001, Maharashtra, India
| | - Vasanth M Shetty
- Dean, Veterinary College, Karnataka Veterinary, Animal and Fisheries Sciences University, Hassan - 573 202, Karnataka, India
| | - Vipin Kumar
- National Innovation Foundation-India, Satellite Complex, Ahmedabad 380 015 Gujarat, India
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Ponnusamy K, Munilkumar S, Das S, Verma A, Venkitesan R, Pal A. Shellfish resources around Madras Atomic Power Station Kalpakkam, Southeast India. Journal of Asia-Pacific Biodiversity 2017. [DOI: 10.1016/j.japb.2016.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Chandra Mangalhara K, Manvati S, Saini SK, Ponnusamy K, Agarwal G, Abraham SK, Bamezai RNK. ERK2-ZEB1-miR-101-1 axis contributes to epithelial-mesenchymal transition and cell migration in cancer. Cancer Lett 2017; 391:59-73. [PMID: 28109909 DOI: 10.1016/j.canlet.2017.01.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/06/2017] [Accepted: 01/11/2017] [Indexed: 12/17/2022]
Abstract
Regulation of metastasis continues to remain enigmatic despite our improved understanding of cancer. Identification of microRNAs associated with metastasis in the recent past has provided a new hope. Here, we show how microRNA-101 (miR-101) regulates two independent processes of cellular metastasis by targeting pro-metastatic upstream regulatory transcription factors, ZEB1 and ZEB2, and downstream effector-actin modulators, RHOA and RAC1, providing a single target for therapeutic intervention. Further, we depict how down-regulation of miR-101 by extracellular signal-regulated kinase-2 (ERK2) is vital for MAP kinase pathway induced cellular migration and mesenchymal transition. Importantly, EKR2 induced expression of ZEB1 seems essential for down-regulation of miR-101-1 and induction of EMT. Given the role of EMT in metastasis, we also observe a significant correlation between miR-101 expression and lymph node metastasis; and identify the ERK2-ZEB1-miR-101-1 pathway active in breast cancer tissues, with an apparent clinicopathological implication.
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Affiliation(s)
| | - Siddharth Manvati
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Sunil Kumar Saini
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Kalaiarasan Ponnusamy
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Gaurav Agarwal
- Department of Endocrine & Breast Surgery, Sanjay Gandhi Post-Graduate Institute of Medical Sciences (SGPGIMS), Lucknow 226014, India
| | - Suresh K Abraham
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Rameshwar N K Bamezai
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India.
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Abdelhameed AS, Ajmal MR, Ponnusamy K, Subbarao N, Khan RH. Interaction of the recently approved anticancer drug nintedanib with human acute phase reactant α 1-acid glycoprotein. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.02.048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Nafis S, Ponnusamy K, Husain M, Singh RKB, Bamezai RNK. Identification of key regulators and their controlling mechanism in a combinatorial apoptosis network: a systems biology approach. Mol BioSyst 2016; 12:3357-3369. [DOI: 10.1039/c6mb00526h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
NFKB1, SP1 and hsa-let-7a, were identified as key regulators of apoptosis, by network theory through probability of signal propagation, hub-removal and motif analysis.
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Affiliation(s)
- Shazia Nafis
- Department of Biotechnology
- Jamia Millia Islamia (Central University)
- New Delhi
- India
- School of Computational and Integrative Sciences
| | - Kalaiarasan Ponnusamy
- National Centre of Applied Human Genetics
- School of Life Sciences
- Jawaharlal Nehru University
- New Delhi
- India
| | - Mohammad Husain
- Department of Biotechnology
- Jamia Millia Islamia (Central University)
- New Delhi
- India
| | - R. K. Brojen Singh
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi
- India
| | - Rameshwar N. K. Bamezai
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi
- India
- National Centre of Applied Human Genetics
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Ramachandran V, Padmanaban E, Ponnusamy K, Naidu S, Natesan M. Pharmacophore based virtual screening for identification of marine bioactive compounds as inhibitors against macrophage infectivity potentiator (Mip) protein of Chlamydia trachomatis. RSC Adv 2016. [DOI: 10.1039/c5ra24999f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Macrophage infectivity potentiator (Mip) is the virulence factor fromChlamydia trachomatisthat is primarily responsible for causing sexually transmitted diseases (STDs) and blindness.
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Affiliation(s)
- Vijayan Ramachandran
- Department of Marine Science
- School of Marine Sciences
- Bharathidasan University
- Trichy-620024
- India
| | - Elavarasi Padmanaban
- Department of Marine Science
- School of Marine Sciences
- Bharathidasan University
- Trichy-620024
- India
| | - Kalaiarasan Ponnusamy
- National Centre for Applied Human Genetics
- School of Life Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Subbarao Naidu
- Centre for Computational Biology and Bioinformatics
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Manoharan Natesan
- Department of Marine Science
- School of Marine Sciences
- Bharathidasan University
- Trichy-620024
- India
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Ponnusamy K, Kohrs N, Ptasinska A, Assi SA, Herold T, Hiddemann W, Lausen J, Bonifer C, Henschler R, Wichmann C. RUNX1/ETO blocks selectin-mediated adhesion via epigenetic silencing of PSGL-1. Oncogenesis 2015; 4:e146. [PMID: 25867177 PMCID: PMC5399174 DOI: 10.1038/oncsis.2015.6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/08/2015] [Accepted: 02/11/2015] [Indexed: 12/21/2022] Open
Abstract
RUNX1/ETO (RE), the t(8;21)-derived leukemic transcription factor associated with acute myeloid leukemia (AML) development, deregulates genes involved in differentiation, self-renewal and proliferation. In addition, these cells show differences in cellular adhesion behavior whose molecular basis is not well understood. Here, we demonstrate that RE epigenetically silences the gene encoding P-Selectin Glycoprotein Ligand-1 (PSGL-1) and downregulates PSGL-1 expression in human CD34+ and murine lin− hematopoietic progenitor cells. Levels of PSGL-1 inversely and dose-dependently correlate with RE oncogene levels. However, a DNA-binding defective mutant fails to downregulate PSGL-1. We show by ChIP experiments that the PSGL-1 promoter is a direct target of RE and binding is accompanied by high levels of the repressive chromatin mark histone H3K27me3. In t(8;21)+ Kasumi-1 cells, PSGL-1 expression is completely restored at both the mRNA and cell surface protein levels following RE downregulation with short hairpin RNA (shRNA) or RE inhibition with tetramerization-blocking peptides, and at the promoter H3K27me3 is replaced by the activating chromatin mark H3K9ac as well as by RNA polymerase II. Upregulation of PSGL-1 restores the binding of cells to P- and E-selectin and re-establishes myeloid-specific cellular adhesion while it fails to bind to lymphocyte-specific L-selectin. Overall, our data suggest that the RE oncoprotein epigenetically represses PSGL-1 via binding to its promoter region and thus affects the adhesive behavior of t(8;21)+ AML cells.
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Affiliation(s)
- K Ponnusamy
- 1] Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, Ludwig-Maximilian University Hospital, Munich, Germany [2] Institute of Transfusion Medicine and Immunohematology, Goethe University, Frankfurt, Germany
| | - N Kohrs
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Germany
| | - A Ptasinska
- School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | - S A Assi
- School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | - T Herold
- Department of Internal Medicine 3, Ludwig-Maximilian University Hospital, Munich, Germany
| | - W Hiddemann
- Department of Internal Medicine 3, Ludwig-Maximilian University Hospital, Munich, Germany
| | - J Lausen
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Germany
| | - C Bonifer
- School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | - R Henschler
- 1] Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, Ludwig-Maximilian University Hospital, Munich, Germany [2] Institute of Transfusion Medicine and Immunohematology, Goethe University, Frankfurt, Germany
| | - C Wichmann
- 1] Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, Ludwig-Maximilian University Hospital, Munich, Germany [2] Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Germany
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Ponnusamy K, Kappachery S, Thekeettle M, Song JH, Kweon JH. Anti-biofouling property of vanillin on Aeromonas hydrophila initial biofilm on various membrane surfaces. World J Microbiol Biotechnol 2013; 29:1695-703. [PMID: 23539151 DOI: 10.1007/s11274-013-1332-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 03/20/2013] [Indexed: 11/29/2022]
Abstract
Biofouling is a serious problem on filter membranes of water purification systems due to formation of bacterial biofilms, which can be detrimental to the membrane performance. Biofouling occurs on membrane surface and therefore greatly influences the physical and chemical aspects of the surface. Several membranes including microfiltration, ultrafiltration, and reverse osmosis (RO) membranes were used to learn about the anti-biofouling properties of vanillin affecting the membrane performances. Vanillin has been recognized as a potential quorum quenching compound for Aeromonas hydrophila biofilms. The initial attachment and dynamics of biofilm growth were monitored using scanning electron microscopy and confocal laser scanning microscopy. Biofilm quantities were measured using a plate count method and total protein determinations. Vanillin addition was effective in the prevention of biofilm formation on the tested membrane surfaces. Among the membranes, RO membranes made with cellulose acetate showed the most substantial reduction of biofilm formation by addition of vanillin. The biofilm reduction was confirmed by the results of surface coverage, biomass and protein accumulation. The HPLC spectrum of the spent culture with vanillin addition showed that vanillin may interfere with quorum sensing molecules and thus prevent the formation of the biofilms.
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Affiliation(s)
- K Ponnusamy
- Department of Environmental Engineering, Konkuk University, 1 Hwayang Dong, Gwangjin Gu, Seoul 143-701, Republic of Korea.
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Ponnusamy K, Naidu J. 3.237 NEUROPROTECTIVE RFFECT OF L-CARNITINE AND CENTELLA ASIATICA EXTRACT ON 6-HYDROXYDOPAMINE (6-OHDA)-INDUCED CHANGES IN THE REPAIR-MECHANISM AND GENOTOXICITY IN AGED RATS. Parkinsonism Relat Disord 2012. [DOI: 10.1016/s1353-8020(11)70909-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Ponnusamy K, Jose S, Savarimuthu I, Michael G, Redenbach M. Genetic diversity study of Chromobacterium violaceum isolated from Kolli hills by amplified ribosomal DNA restriction analysis (ARDRA) and random amplified polymorphic DNA (RAPD). Lett Appl Microbiol 2011; 53:341-9. [DOI: 10.1111/j.1472-765x.2011.03115.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ponnusamy K, Mohan M, Nagaraja HS. Protective antioxidant effect of Centella asiatica bioflavonoids on lead acetate induced neurotoxicity. Med J Malaysia 2008; 63 Suppl A:102. [PMID: 19025005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Lead (Pb) is a neurotoxic heavy metal and children in the developmental stage are particularly susceptible to toxic effects of lead exposure. The brain is the key organ involved in interpreting and responding to potential stressors. Epidemiological investigations have established the relationship between chronic lead exposure and cognitive impairments in young children. Excessive production of radical species plays an important role in neuronal pathology resulting from excitotoxic insults, therefore one plausible neuroprotective mechanism of bioflavonoids is partly relevant to their metal chelating and antioxidant properties. Centella asiatica (CA) is a tropical medicinal plant enriched with bioflavonoids and triterpenes and selenium, reported to rejuvenate the cells and promote physical and mental health. Bioflavonoids are claimed to be exert antimutagenic, neurotrophic and xenobiotics ameliorating and membrane molecular stabilizing effects. The objective of the present work is to study the protective antioxidant effect of pretreatment of CA extract (CAE) on lead acetate induced changes in oxidative biomarkers in the central nervous system (CNS) of mice.
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Affiliation(s)
- K Ponnusamy
- Department of Human Biology, International Medical University, Kuala Lumpur, Malaysia
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Mahto M, Ponnusamy K, Schuhwerk M, Richens J, Lambert N, Wilkins E, Churchill DR, Miller RF, Behrens RH. Knowledge, attitudes and health outcomes in HIV-infected travellers to the USA. HIV Med 2006; 7:201-4. [PMID: 16630031 DOI: 10.1111/j.1468-1293.2006.00371.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND The USA bans entry to non-citizens unless they obtain a waiver visa. AIM To establish how many people with HIV infection travelled to the USA, whether they were aware of the travel restriction, whether they travelled with a waiver visa and HIV inclusive medical insurance and how they managed with their antiretroviral medication (ARV). DESIGN Collation of data from cross-sectional studies conducted independently at three different medical centres, Manchester, Brighton and London, using a structured self-completion questionnaire. RESULTS The overall response rate was 66.6% (1113 respondents). 349 (31%) had travelled to the USA since testing HIV positive, of whom only 14.3% travelled with a waiver visa. 64% and 62% of the respondents at Manchester and Brighton were aware of the need of a waiver visa. 68.5% (212) were on ARV medication at the time of travel and, of these, 11.3% stopped their medication. Of those taking ARV medication, only 25% took a doctors' letter, 11.7% posted their medication in advance. Of those discontinuing treatment (n=27), 55.5% sought medical advice before stopping, 11 were on NNRTI-based regimen and one developed NNRTI-based mutation. Only 27% took up HIV inclusive medical insurance. Many patients reported negative practical and emotional experiences resulting from travel restrictions. CONCLUSION The majority of HIV patients travel to the USA without the waiver visa, with nearly half doing so with insufficient planning and advice. A significant minority (11.3%) stop their medication in an unplanned manner, risking the development of drug resistance.
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