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Rao RSP, Ghate SD, Pinto L, Suravajhala P, Patil P, Shetty P, Ahsan N. Extent of Virulence and Antibiotic Resistance Genes in Helicobacter pylori and Campylobacteria. Curr Microbiol 2024; 81:154. [PMID: 38652129 DOI: 10.1007/s00284-024-03653-5] [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: 12/11/2023] [Accepted: 02/26/2024] [Indexed: 04/25/2024]
Abstract
Helicobacter pylori, a member of the clade campylobacteria, is the leading cause of chronic gastritis and gastric cancer. Virulence and antibiotic resistance of H. pylori are of great concern to public health. However, the relationship between virulence and antibiotic resistance genes in H. pylori in relation to other campylobacteria remains unclear. Using the virulence and comprehensive antibiotic resistance databases, we explored all available 354 complete genomes of H. pylori and compared it with 90 species of campylobacteria for virulence and antibiotic resistance genes/proteins. On average, H. pylori had 129 virulence genes, highest among Helicobacter spp. and 71 antibiotic resistance genes, one of the lowest among campylobacteria. Just 2.6% of virulence genes were shared by all campylobacterial members, whereas 9.4% were unique to H. pylori. The cytotoxin-associated genes (cags) seemed to be exclusive to H. pylori. Majority of the isolates from Asia and South America were cag2-negative and many antibiotic resistance genes showed isolate-specific patterns of occurrence. Just 15 (8.8%) antibiotic resistance genes, but 103 (66%) virulence genes including 25 cags were proteomically identified in H. pylori. Arcobacterial members showed large variation in the number of antibiotic resistance genes and there was a positive relation with the genome size. Large repository of antibiotic resistance genes in campylobacteria and a unique set of virulence genes might have important implications in shaping the course of virulence and antibiotic resistance in H. pylori.
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Affiliation(s)
- R Shyama Prasad Rao
- Center for Bioinformatics, NITTE Deemed to be University, Mangaluru, 575018, India.
| | - Sudeep D Ghate
- Center for Bioinformatics, NITTE Deemed to be University, Mangaluru, 575018, India.
| | - Larina Pinto
- Center for Bioinformatics, NITTE Deemed to be University, Mangaluru, 575018, India
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, 690525, India
| | - Prakash Patil
- Central Research Laboratory, KS Hegde Medical Academy (KSHEMA), NITTE Deemed to be University, Mangaluru, 575018, India
| | - Praveenkumar Shetty
- Central Research Laboratory, KS Hegde Medical Academy (KSHEMA), NITTE Deemed to be University, Mangaluru, 575018, India
- Department of Biochemistry, KS Hegde Medical Academy (KSHEMA), NITTE Deemed to be University, Mangaluru, 575018, India
| | - Nagib Ahsan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, OK, USA
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Kour B, Shukla N, Bhargava H, Sharma D, Sharma A, Singh A, Valadi J, Sadasukhi TC, Vuree S, Suravajhala P. Identification of Plausible Candidates in Prostate Cancer Using Integrated Machine Learning Approaches. Curr Genomics 2023; 24:287-306. [PMID: 38235353 PMCID: PMC10790336 DOI: 10.2174/0113892029240239231109082805] [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: 03/01/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 01/19/2024] Open
Abstract
Background Currently, prostate-specific antigen (PSA) is commonly used as a prostate cancer (PCa) biomarker. PSA is linked to some factors that frequently lead to erroneous positive results or even needless biopsies of elderly people. Objectives In this pilot study, we undermined the potential genes and mutations from several databases and checked whether or not any putative prognostic biomarkers are central to the annotation. The aim of the study was to develop a risk prediction model that could help in clinical decision-making. Methods An extensive literature review was conducted, and clinical parameters for related comorbidities, such as diabetes, obesity, as well as PCa, were collected. Such parameters were chosen with the understanding that variations in their threshold values could hasten the complicated process of carcinogenesis, more particularly PCa. The gathered data was converted to semi-binary data (-1, -0.5, 0, 0.5, and 1), on which machine learning (ML) methods were applied. First, we cross-checked various publicly available datasets, some published RNA-seq datasets, and our whole-exome sequencing data to find common role players in PCa, diabetes, and obesity. To narrow down their common interacting partners, interactome networks were analysed using GeneMANIA and visualised using Cytoscape, and later cBioportal was used (to compare expression level based on Z scored values) wherein various types of mutation w.r.t their expression and mRNA expression (RNA seq FPKM) plots are available. The GEPIA 2 tool was used to compare the expression of resulting similarities between the normal tissue and TCGA databases of PCa. Later, top-ranking genes were chosen to demonstrate striking clustering coefficients using the Cytoscape-cytoHubba module, and GEPIA 2 was applied again to ascertain survival plots. Results Comparing various publicly available datasets, it was found that BLM is a frequent player in all three diseases, whereas comparing publicly available datasets, GWAS datasets, and published sequencing findings, SPFTPC and PPIMB were found to be the most common. With the assistance of GeneMANIA, TMPO and FOXP1 were found as common interacting partners, and they were also seen participating with BLM. Conclusion A probabilistic machine learning model was achieved to identify key candidates between diabetes, obesity, and PCa. This, we believe, would herald precision scale modeling for easy prognosis.
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Affiliation(s)
- Bhumandeep Kour
- Department of Biotechnology, Lovely Professional University, Jalandhar, Punjab, India
- Bioclues.org, India
| | - Nidhi Shukla
- Bioclues.org, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, Rajasthan, India
| | - Harshita Bhargava
- Department of Computer Science, IIS University, Jaipur, Rajasthan, India
| | - Devendra Sharma
- Urology and Renal Transplant Department of Renal Sciences, Rukmani Birla Hospital, Jaipur, Rajasthan, India
| | - Amita Sharma
- Department of Computer Science, IIS University, Jaipur, Rajasthan, India
| | - Anjuvan Singh
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, Phagwara, 144001, India
| | - Jayaraman Valadi
- Department of Computer Science, FLAME University, Pune, Maharashtra, India
| | - Trilok Chand Sadasukhi
- Department of Urology and Renal Transplant, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur, Rajasthan, India
| | - Sugunakar Vuree
- Bioclues.org, India
- MNR Foundation for Research & Innovation, MNR Medical College and Hospital, MNR University, Telangana, India
| | - Prashanth Suravajhala
- Bioclues.org, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala, India
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Kishor PBK, Guddimalli R, Kulkarni J, Singam P, Somanaboina AK, Nandimandalam T, Patil S, Polavarapu R, Suravajhala P, Sreenivasulu N, Penna S. Impact of Climate Change on Altered Fruit Quality with Organoleptic, Health Benefit, and Nutritional Attributes. J Agric Food Chem 2023; 71:17510-17527. [PMID: 37943146 DOI: 10.1021/acs.jafc.3c03312] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
As a consequence of global climate change, acute water deficit conditions, soil salinity, and high temperature have been on the rise in their magnitude and frequency, which have been found to impact plant growth and development negatively. However, recent evidence suggests that many fruit plants that face moderate abiotic stresses can result in beneficial effects on the postharvest storage characters of the fruits. Salinity, drought, and high temperature conditions stimulate the synthesis of abscisic acid (ABA), and secondary metabolites, which are vital for fruit quality. The secondary metabolites like phenolic acids and anthocyanins that accumulate under abiotic stress conditions have antioxidant activity, and therefore, such fruits have health benefits too. It has been noticed that fruits accumulate more sugar and anthocyanins owing to upregulation of phenylpropanoid pathway enzymes. The novel information that has been generated thus far indicates that the growth environment during fruit development influences the quality components of the fruits. But the quality depends on the trade-offs between productivity, plant defense, and the frequency, duration, and intensity of stress. In this review, we capture the current knowledge of the irrigation practices for optimizing fruit production in arid and semiarid regions and enhancement in the quality of fruit with the application of exogenous ABA and identify gaps that exist in our understanding of fruit quality under abiotic stress conditions.
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Affiliation(s)
- P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500 007, India
| | | | - Jayant Kulkarni
- Department of Botany, Savithribai Phule Pune University, Pune 411 007, India
| | - Prashant Singam
- Department of Genetics, Osmania University, Hyderabad 500 007, India
| | - Anil Kumar Somanaboina
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research Deemed to be University, Vadlamudi, Guntur 522 213, Andhra Pradesh, India
| | - Tejaswi Nandimandalam
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research Deemed to be University, Vadlamudi, Guntur 522 213, Andhra Pradesh, India
| | - Swaroopa Patil
- Department of Botany, Shivaji University, Kolhapur 416 004, Maharashtra, India
| | - Rathnagiri Polavarapu
- Genomix Molecular Diagnostics Pvt. Ltd., Pragathi Nagar, Kukatapally, Hyderabad 500 072, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwavidyapeetham, Clappana, 690 525, Amritapuri, Vallikavu, Kerala, India & Bioclues.org, Hyderabad, India
| | - Nese Sreenivasulu
- Consumer-Driven Grain Quality and Nutrition Research Unit, International Rice Research Institute, Los Banos, DAPO Box 7777, Metro Manil 1301, Philippines
| | - Suprasanna Penna
- Amity Centre for Nuclear Biotechnology, Amity Institute of Biotechnology, Amity University of Maharashtra, Mumbai 410 206, India
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Kugalingam N, De Silva D, Abeysekera H, Nanayakkara S, Tirimanne S, Ranaweera D, Suravajhala P, Chandrasekharan V. RB1 screening of retinoblastoma patients in Sri Lanka using targeted next generation sequencing (NGS) and gene ratio analysis copy enumeration PCR (GRACE-PCR). BMC Med Genomics 2023; 16:279. [PMID: 37932687 PMCID: PMC10626775 DOI: 10.1186/s12920-023-01721-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Retinoblastoma (RB) a tumour affecting those under 5 years, has a prevalence of 1 in 20,000, with around twenty new diagnoses per year in Sri Lanka. Unilateral and bilateral RB presents around 24 and 15 months respectively. Approximately 10% are familial. Systematic genetic testing for germline pathogenic variants of RB1, the only gene associated with an inherited risk of RB, is unavailable in Sri Lanka. Genetic testing optimizes management of affected children and at-risk siblings. This study aimed to develop accessible genetic testing to identify children with a germline pathogenic variant of RB1 in Sri Lanka. METHODS Targeted next generation sequencing (NGS) for detecting pathogenic sequence variants and Gene Ratio Analysis Copy Enumeration PCR (GRACE-PCR) for detecting RB1 copy number variations (CNVs) were performed for 49 consecutive RB patients treated between 2016 and 2020 at the designated RB care unit, Lady Ridgway hospital, Colombo. Patients (bilateral RB (n = 18; 37%), unilateral n = 31) were recruited following ethical clearance and informed consent. RESULTS There were 26 (53%) females. Mean age at diagnosis was 18 months. Thirty-five patients (71%) had undergone enucleation. Germline pathogenic variants of RB1 identified in 22/49 (45%) patients including 18 (37%; 12 bilateral and 6 unilateral) detected by targeted NGS (2 missense, 7 stop gained, 1 splice donor, 8 frameshift variants). Six were previously undescribed, likely pathogenic frameshift variants. Four bilateral RB patients had GRACE-PCR detected CNVs including one whole RB1, two intragenic deletions (exon 12/13; exon 11 and 23) and a partial duplication of exon 27. The only familial case (affected mother and child) shared the duplication. Only 2 of 4 CNVs and 10 of 18 pathogenic variants were confirmed by whole exome sequencing and Sanger sequencing respectively, due to funding limitations. CONCLUSIONS The study identified pathogenic or likely pathogenic germline RB1 sequence variants and copy number variants in 16/18 (89%) bilateral and 6/31(19%) unilateral cases, which is comparable to worldwide data (10-15% unilateral, 80-85% bilateral). Targeted NGS combined with GRACE-PCR significantly reduce the cost of RB1 testing in Sri Lanka, and may widen access for genetic diagnosis of RB patients in other low and middle income countries.
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Affiliation(s)
- Nirosha Kugalingam
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka.
| | - Deepthi De Silva
- Department of Physiology, Faculty of Medicine, University of Kelaniya, Kelaniya, Sri Lanka
| | | | | | - Shamala Tirimanne
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | - Dinali Ranaweera
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
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G VCVS, Reddy PVJ, Suravajhala P, Suravajhala R, V UK, Pb KK, Tc V, Polavarapu R. Performance evaluation of in-house developed Covid-19 IgG/IgM antibody rapid diagnostic kit. AMB Express 2023; 13:116. [PMID: 37848586 PMCID: PMC10581998 DOI: 10.1186/s13568-023-01620-0] [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: 05/29/2023] [Accepted: 10/03/2023] [Indexed: 10/19/2023] Open
Abstract
In the interest of preventing the Coronavirus Disease 2019 (COVID-19) pandemic from spreading, it is crucial to promptly identify and confine afflicted patients. Serological antibody testing is a significant diagnostic technique that is increasingly employed in clinics, however its clinical use is still being investigated. The present study was carried out to scrutinize how well Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) antibody testing using in-house developed rapid antibody assay worked against the chemiluminescence (CLIA) assay. Either IgG positive (IgG + IgM-) or IgM positive (IgM + IgG-); both IgG and IgM positive (IgM + IgG+); and negatives (IgM- IgG-) have been evaluated. A total of 300 samples with diverse age and sexual identity data were included. The combined sensitivities for IgG + IgM+, IgM + IgG-, IgG + IgM- and IgG-IgM- were evaluated. More accurate diagnostic results may be obtained using molecular diagnostic tools. The Antibody Rapid Diagnostic kit's (in-house developed) performance was satisfactory for determining the presence of Covid-19 infection with IgG and IgM positivity. The IgG and IgM positivity helped evaluate the immune response in the individual for the COVID-19 infection. These results lend support to the additional utilisation of serological antibody tests in the COVID-19 diagnosis.
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Affiliation(s)
- Vinaya Chandu Vidya Sagar G
- Genomix CARL Pvt. Ltd, Pulivendula, Andhra Pradesh, 516 390, India
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research Deemed to be University, Vadlamudi, Guntur, Andhra Pradesh, 522 213, India
| | | | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, 690525, India.
- Bioclues.org, Hyderabad, India.
| | - Renuka Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, 690525, India
| | - Uday Kiran V
- Genomix CARL Pvt. Ltd, Pulivendula, Andhra Pradesh, 516 390, India
| | - Kavi Kishor Pb
- Department of Genetics, Osmania University, Hyderabad, Telangana, 500 007, India
| | - Venkateswarulu Tc
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research Deemed to be University, Vadlamudi, Guntur, Andhra Pradesh, 522 213, India
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Soy S, Lakra U, Prakash P, Suravajhala P, Nigam VK, Sharma SR, Bayal N. Exploring microbial diversity in hot springs of Surajkund, India through 16S rRNA analysis and thermozyme characterization from endogenous isolates. Sci Rep 2023; 13:14221. [PMID: 37648773 PMCID: PMC10469164 DOI: 10.1038/s41598-023-41515-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/28/2023] [Indexed: 09/01/2023] Open
Abstract
Hot springs are a valuable source of biologically significant chemicals due to their high microbial diversity. To investigate the possibilities for industrial uses of these bacteria, researchers collected water and sediment samples from variety of hot springs. Our investigation employed both culture-dependent and culture-independent techniques, including 16S-based marker gene analysis of the microbiota from the hot springs of Surajkund, Jharkhand. In addition, we cultivated thermophilic isolates and screened for their ability to produce amylase, xylanase, and cellulase. After the optimized production of amylase the enzyme was partially purified and characterized using UPLC, DLS-ZP, and TGA. The retention time for the amylase was observed to be around 0.5 min. We confirmed the stability of the amylase at higher temperatures through observation of a steady thermo gravimetric profile at 400 °C. One of the thermophilic isolates obtained from the kund, demonstrated the potential to degrade lignocellulosic agricultural waste.
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Affiliation(s)
- S Soy
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - U Lakra
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - P Prakash
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - P Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
- Systems Genomics Lab, Bioclues.org, Hyderabad, India
| | - V K Nigam
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - S R Sharma
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
| | - N Bayal
- National Centre for Cell Science, Ganeshkhind, Pune, India
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Işık EB, Brazas MD, Schwartz R, Gaeta B, Palagi PM, van Gelder CWG, Suravajhala P, Singh H, Morgan SL, Zahroh H, Ling M, Satagopam VP, McGrath A, Nakai K, Tan TW, Gao G, Mulder N, Schönbach C, Zheng Y, De Las Rivas J, Khan AM. Grand challenges in bioinformatics education and training. Nat Biotechnol 2023; 41:1171-1174. [PMID: 37568018 DOI: 10.1038/s41587-023-01891-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Affiliation(s)
- Esra Büşra Işık
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul, Turkey
- APBioNET.org, Singapore, Singapore
| | - Michelle D Brazas
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Bioinformatics.ca, Toronto, Ontario, Canada
| | | | - Bruno Gaeta
- School of Computer Science and Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | | | | | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, India
- Bioclues.org, Hyderabad, India
| | - Harpreet Singh
- APBioNET.org, Singapore, Singapore
- Bioclues.org, Hyderabad, India
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, India
| | - Sarah L Morgan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Hilyatuz Zahroh
- APBioNET.org, Singapore, Singapore
- Genetics Research Centre, Universitas YARSI, Jakarta, Indonesia
| | - Maurice Ling
- APBioNET.org, Singapore, Singapore
- School of Applied Science, Temasek Polytechnic, Singapore, Singapore
| | - Venkata P Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- International Society for Computational Biology, Leesburg, VA, USA
| | | | - Kenta Nakai
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Tin Wee Tan
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
- National Supercomputing Centre, Singapore, Singapore
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Biomedical Pioneering Innovative Center and Beijing Advanced Innovation Center for Genomics, Center for Bioinformatics, Peking University, Beijing, China
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Christian Schönbach
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Yun Zheng
- School of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Javier De Las Rivas
- Cancer Research Center, Spanish National Research Council, University of Salamanca & Institute for Biomedical Research of Salamanca, Salamanca, Spain
| | - Asif M Khan
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul, Turkey.
- APBioNET.org, Singapore, Singapore.
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia.
- College of Computing and Information Technology, University of Doha for Science and Technology, Doha, Qatar.
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Karumanchi AR, Sivan P, Kummari D, Rajasheker G, Kumar SA, Reddy PS, Suravajhala P, Podha S, Kishor PBK. Root and Leaf Anatomy, Ion Accumulation, and Transcriptome Pattern under Salt Stress Conditions in Contrasting Genotypes of Sorghum bicolor. Plants (Basel) 2023; 12:2400. [PMID: 37446963 DOI: 10.3390/plants12132400] [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: 04/26/2023] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023]
Abstract
Roots from salt-susceptible ICSR-56 (SS) sorghum plants display metaxylem elements with thin cell walls and large diameter. On the other hand, roots with thick, lignified cell walls in the hypodermis and endodermis were noticed in salt-tolerant CSV-15 (ST) sorghum plants. The secondary wall thickness and number of lignified cells in the hypodermis have increased with the treatment of sodium chloride stress to the plants (STN). Lignin distribution in the secondary cell wall of sclerenchymatous cells beneath the lower epidermis was higher in ST leaves compared to the SS genotype. Casparian thickenings with homogenous lignin distribution were observed in STN roots, but inhomogeneous distribution was evident in SS seedlings treated with sodium chloride (SSN). Higher accumulation of K+ and lower Na+ levels were noticed in ST compared to the SS genotype. To identify the differentially expressed genes among SS and ST genotypes, transcriptomic analysis was carried out. Both the genotypes were exposed to 200 mM sodium chloride stress for 24 h and used for analysis. We obtained 70 and 162 differentially expressed genes (DEGs) exclusive to SS and SSN and 112 and 26 DEGs exclusive to ST and STN, respectively. Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis unlocked the changes in metabolic pathways in response to salt stress. qRT-PCR was performed to validate 20 DEGs in each SSN and STN sample, which confirms the transcriptomic results. These results surmise that anatomical changes and higher K+/Na+ ratios are essential for mitigating salt stress in sorghum apart from the genes that are differentially up- and downregulated in contrasting genotypes.
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Affiliation(s)
- Appa Rao Karumanchi
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522 209, India
| | - Pramod Sivan
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Albanova University Center, SE-10691 Stockholm, Sweden
| | - Divya Kummari
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - G Rajasheker
- Department of Genetics, Osmania University, Hyderabad 500 007, India
| | - S Anil Kumar
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research (Deemed to Be University), Guntur 522 213, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | | | - Sudhakar Podha
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522 209, India
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500 007, India
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Gupta S, Mathur P, Mishra AK, Medicherla KM, Bandapalli OR, Suravajhala P. Whole Exome-Trio Analysis Reveals Rare Variants Associated with Congenital Pouch Colon. Children (Basel) 2023; 10:children10050902. [PMID: 37238450 DOI: 10.3390/children10050902] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023]
Abstract
Anorectal malformations (ARM) are individually common, but Congenital Pouch Colon (CPC) is a rare anorectal anomaly that causes a dilated pouch and communication with the genitourinary tract. In this work, we attempted to identify de novo heterozygous missense variants, and further discovered variants of unknown significance (VUS) which could provide insights into CPC manifestation. From whole exome sequencing (WES) performed earlier, the trio exomes were analyzed from those who were admitted to J.K. Lon Hospital, SMS Medical College, Jaipur, India, between 2011 and 2017. The proband exomes were compared with the unaffected sibling/family members, and we sought to ask whether any variants of significant interest were associated with the CPC manifestation. The WES data from a total of 64 samples including 16 affected neonates (11 male and 5 female) with their parents and unaffected siblings were used for the study. We examined the role of rare allelic variation associated with CPC in a 16 proband/parent trio family, comparing the mutations to those of their unaffected parents/siblings. We also performed RNA-Seq as a pilot to find whether or not the genes harboring these mutations were differentially expressed. Our study revealed extremely rare variants, viz., TAF1B, MUC5B and FRG1, which were further validated for disease-causing mutations associated with CPC, further closing the gaps of surgery by bringing intervention in therapies.
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Affiliation(s)
- Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India
- Amity Institute of Biotechnology, Amity University Rajasthan, Kant Kalwar, Jaipur 303002, India
| | - Praveen Mathur
- Department of Pediatric Surgery, SMS Medical College and Hospital, JLN Marg, Jaipur 302004, India
| | | | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India
- Department of Bioengineering, Birla Institute of Technology, Mesra, Jaipur Campus, 27-Malaviya Industrial, Area, Jaipur 302017, India
| | | | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita University, Vallikavu, Clappana P.O. Box 690525, Kerala, India
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10
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Shukla N, Kour B, Sharma D, Vijayvargiya M, Sadasukhi TC, Medicherla KM, Malik B, Bissa B, Vuree S, Lohiya NK, Suravajhala P. Towards Understanding the Key Signature Pathways Associated from Differentially Expressed Gene Analysis in an Indian Prostate Cancer Cohort. Diseases 2023; 11:diseases11020072. [PMID: 37218885 DOI: 10.3390/diseases11020072] [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: 02/20/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent cancers among men in India. Although studies on PCa have dealt with genetics, genomics, and the environmental influence in the causality of PCa, not many studies employing the Next Generation Sequencing (NGS) approaches of PCa have been carried out. In our previous study, we identified some causal genes and mutations specific to Indian PCa using Whole Exome Sequencing (WES). In the recent past, with the help of different cancer consortiums such as The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC), along with differentially expressed genes (DEGs), many cancer-associated novel non-coding RNAs have been identified as biomarkers. In this work, we attempt to identify differentially expressed genes (DEGs) including long non-coding RNAs (lncRNAs) associated with signature pathways from an Indian PCa cohort using the RNA-sequencing (RNA-seq) approach. From a cohort of 60, we screened six patients who underwent prostatectomy; we performed whole transcriptome shotgun sequencing (WTSS)/RNA-sequencing to decipher the DEGs. We further normalized the read counts using fragments per kilobase of transcript per million mapped reads (FPKM) and analyzed the DEGs using a cohort of downstream regulatory tools, viz., GeneMANIA, Stringdb, Cytoscape-Cytohubba, and cbioportal, to map the inherent signatures associated with PCa. By comparing the RNA-seq data obtained from the pairs of normal and PCa tissue samples using our benchmarked in-house cuffdiff pipeline, we observed some important genes specific to PCa, such as STEAP2, APP, PMEPA1, PABPC1, NFE2L2, and HN1L, and some other important genes known to be involved in different cancer pathways, such as COL6A1, DOK5, STX6, BCAS1, BACE1, BACE2, LMOD1, SNX9, CTNND1, etc. We also identified a few novel lncRNAs such as LINC01440, SOX2OT, ENSG00000232855, ENSG00000287903, and ENST00000647843.1 that need to be characterized further. In comparison with publicly available datasets, we have identified characteristic DEGs and novel lncRNAs implicated in signature PCa pathways in an Indian PCa cohort which perhaps have not been reported. This has set a precedent for us to validate candidates further experimentally, and we firmly believe this will pave a way toward the discovery of biomarkers and the development of novel therapies.
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Affiliation(s)
- Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302001, India
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur 303007, India
| | - Bhumandeep Kour
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144001, India
| | - Devendra Sharma
- Department of Urology, Rukmani Birla Hospital, Jaipur 302018, India
| | - Maneesh Vijayvargiya
- Department of Pathology, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur 302022, India
| | - T C Sadasukhi
- Department of Urology, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur 302022, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302001, India
- Department of Bioengineering, Birla Institute of Technology, Mesra Jaipur Campus, 27-Malaviya Industrial Area, Jaipur 302017, India
| | - Babita Malik
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur 303007, India
| | - Bhawana Bissa
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India
| | - Sugunakar Vuree
- Bioclues.org, Hyderabad 500072, India
- MNR Foundation for Research & Innovation, MNR University, Sangareddy 502294, India
| | - Nirmal Kumar Lohiya
- Department of Zoology, Center for Advanced Studies, University of Rajasthan, Jaipur 302004, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
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11
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Do DN, Suravajhala P. Editorial: Role of Non-Coding RNAs in Animals. Animals (Basel) 2023; 13:ani13050805. [PMID: 36899662 PMCID: PMC10000048 DOI: 10.3390/ani13050805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/10/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
The importance of non-coding RNAs (ncRNAs), such as microRNAs (miRNA), long non-coding RNAs (lncRNA), and circular RNAs (circRNA), in gene regulation is increasingly being appreciated in many species [...].
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Affiliation(s)
- Duy Ngoc Do
- Faculty of Veterinary Medicine, Viet Nam National University of Agriculture, Hanoi 100000, Vietnam
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
- Correspondence: (D.N.D.); (P.S.)
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana 690525, India
- Correspondence: (D.N.D.); (P.S.)
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12
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Kumar S, Choudhary N, Faruq M, Kumar A, Saran RK, Indercanti PK, Singh V, Sait H, Jaitley S, Valis M, Kuca K, Polipalli SK, Kumar M, Singh T, Suravajhala P, Sharma R, Kapoor S. Anastrozole-mediated modulation of mitochondrial activity by inhibition of mitochondrial permeability transition pore opening: an initial perspective. J Biomol Struct Dyn 2023; 41:14063-14079. [PMID: 36815262 DOI: 10.1080/07391102.2023.2176927] [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: 09/12/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023]
Abstract
The mitochondrial permeability transition pore (mtPTP) plays a vital role in altering the structure and function of mitochondria. Cyclophilin D (CypD) is a mitochondrial protein that regulates mtPTP function and a known drug target for therapeutic studies involving mitochondria. While the effect of aromatase inhibition on the mtPTP has been studied previously, the effect of anastrozole on the mtPTP has not been completely elucidated. The role of anastrozole in modulating the mtPTP was evaluated by docking, molecular dynamics and network-guided studies using human CypD data. The peripheral blood mononuclear cells (PBMCs) of patients with mitochondrial disorders and healthy controls were treated with anastrozole and evaluated for mitochondrial permeability transition pore (mtPTP) function and apoptosis using a flow cytometer. Spectrophotometry was employed for estimating total ATP levels. The anastrozole-CypD complex is more stable than cyclosporin A (CsA)-CypD. Anastrozole performed better than cyclosporine in inhibiting mtPTP. Additional effects included inducing mitochondrial membrane depolarization and a reduction in mitochondrial swelling and superoxide generation, intrinsic caspase-3 activity and cellular apoptosis, along with an increase in ATP levels. Anastrozole may serve as a potential therapeutic agent for mitochondrial disorders and ameliorate the clinical phenotype by regulating the activity of mtPTP. However, further studies are required to substantiate our preliminary findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Somesh Kumar
- Pediatrics Genetics & Research Laboratory, Department of Pediatrics, Maulana Azad Medical College & Associated LN Hospital, Delhi, India
| | - Neha Choudhary
- Centre for Computational Biology and Bioinformatics, Central University of Himachal Pradesh, Dharamsala, India
| | - Mohammed Faruq
- Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Arun Kumar
- Department of Emergency Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi, India
| | - Ravindra K Saran
- Department of Pathology, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research, Delhi, India
| | | | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, Central University of Himachal Pradesh, Dharamsala, India
| | - Haseena Sait
- Pediatrics Genetics & Research Laboratory, Department of Pediatrics, Maulana Azad Medical College & Associated LN Hospital, Delhi, India
| | - Sunita Jaitley
- Department of Biomedical Sciences, Acharya Narendra Dev College, University of Delhi, Delhi, India
| | - Martin Valis
- Department of Neurology of the Medical Faculty of Charles University and University Hospital in Hradec Králové, Hradec Králové, Czech Republic
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - Sunil K Polipalli
- Pediatrics Genetics & Research Laboratory, Department of Pediatrics, Maulana Azad Medical College & Associated LN Hospital, Delhi, India
| | - Manoj Kumar
- Department of Emergency Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
- Department of Microbiology, World College of Medical Science and Research, Jhajjar, Haryana, India
| | - Tejveer Singh
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | | | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Seema Kapoor
- Pediatrics Genetics & Research Laboratory, Department of Pediatrics, Maulana Azad Medical College & Associated LN Hospital, Delhi, India
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13
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Chot E, Suravajhala P, Medicherla KM, Reddy MS. Characterization and genome-wide sequence analysis of an ectomycorrhizal fungus Pisolithus albus, a potential source for reclamation of degraded lands. 3 Biotech 2023; 13:58. [PMID: 36714549 PMCID: PMC9873894 DOI: 10.1007/s13205-023-03483-5] [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: 08/26/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023] Open
Abstract
Pisolithus albus is a ubiquitous ectomycorrhizal fungus that establishes symbiosis with a wide range of woody plants around the globe. The symbiotic association of this fungus plays a crucial role in the nutrient cycling of their host plants and enables them to thrive in adverse environmental conditions. Based on its ecological importance and lack of genomic studies, whole-genome sequencing was carried out to analyze P. albus sequences through an Illumina HiSeq X system. The functional annotations were performed against various databases to explore genomic patterns and traits possibly attributing to its specialization. Comparative genomics of P. albus with phylogenetically related Pisolithus microcarpus and Pisolithus tinctorius (only available genomes of Pisolithus at NCBI till now) led to the identification of their unique and shared basic functional and stress adaptation capabilities. The de novo assembled genome of 56.15 Mb with 91.8% BUSCO completeness is predicted to encode 23,035 genes. The study is aimed to generate solid genomic data resources for P. albus, forming the theoretical basis for future transcriptomic, proteomic and metabolomic studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03483-5.
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Affiliation(s)
- Eetika Chot
- Thapar Institute of Engineering and Technology, Bhadson Road, Patiala, Punjab 147004 India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana P.O, Kollam, Kerala 690525 India
| | | | - Mondem Sudhakara Reddy
- Thapar Institute of Engineering and Technology, Bhadson Road, Patiala, Punjab 147004 India
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14
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Vidyasagar GVC, Reddy PVJ, Kumar S, Polipalli SK, Jaiswal RM, Venkateswarulu TC, Kishor PBK, Suravajhala P, Polavarapu R. Perspectives on Rapid Antigen Tests for Downstream Validation and Development of Theranostics. Adv Exp Med Biol 2023; 1412:285-310. [PMID: 37378774 DOI: 10.1007/978-3-031-28012-2_16] [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] [Indexed: 06/29/2023]
Abstract
Point-of-care SARS-CoV-2 rapid antigen tests have proven to be useful over the years and have become more apparent to the public eye during COVID-19 pandemic due to their ease of use, rapid processing and result times, and low cost. Here, we have assessed the effectiveness and accuracy of rapid antigen tests in comparison to the standard real-time polymerase chain reaction analyses of the same samples.
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Affiliation(s)
- G Vinaya Chandu Vidyasagar
- Genomix CARL Pvt. Ltd., Pulivendula, AP, India
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Guntur, AP, India
| | | | - Somesh Kumar
- Genome Sequencing Laboratory, Lok Nayak Hospital, Jawaharlal Nehru Marg, New Delhi, India
- Bioclues.org, Hyderabad, Telangana, India
| | - Sunil Kumar Polipalli
- Genome Sequencing Laboratory, Lok Nayak Hospital, Jawaharlal Nehru Marg, New Delhi, India
- Bioclues.org, Hyderabad, Telangana, India
| | - Ram Mohan Jaiswal
- Blood Centre and Transplantation Immunology Lab, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur, Rajasthan, India
| | - T C Venkateswarulu
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Guntur, AP, India
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, Telangana, India.
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India.
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15
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Kumar S, Lomash A, Faruq M, Siddiqui O, Kumar S, Kapoor S, Suravajhala P, Polipalli SK. Amplicon-Based Nanopore Sequencing of Patients Infected by the SARS-CoV-2 Omicron (B.1.1.529) Variant in India. Adv Exp Med Biol 2023; 1412:271-283. [PMID: 37378773 DOI: 10.1007/978-3-031-28012-2_15] [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] [Indexed: 06/29/2023]
Abstract
We report the sequencing of SARS-CoV-2 Omicron variants from 75 patients, using nanopore long-read sequencing chemistry. These data show a range of mutations in spike glycoprotein that are both unique and common to other populations.
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Affiliation(s)
- Somesh Kumar
- Genome Sequencing Laboratory, Lok Nayak Hospital, New Delhi, Delhi, India
| | - Avinash Lomash
- Genome Sequencing Laboratory, Lok Nayak Hospital, New Delhi, Delhi, India
| | - Mohammed Faruq
- Genomic & Molecular Medicine Division, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
| | - Oves Siddiqui
- Department of Microbiology, Maulana Azad Medical College, New Delhi, India
| | - Suresh Kumar
- Genome Sequencing Laboratory, Lok Nayak Hospital, New Delhi, Delhi, India
| | - Seema Kapoor
- Genome Sequencing Laboratory, Lok Nayak Hospital, New Delhi, Delhi, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, India.
- Amrita School of Biotechnology, Amrita Vishwavidyapeetham, Clappana, Kerala, India.
| | - Sunil K Polipalli
- Genome Sequencing Laboratory, Lok Nayak Hospital, New Delhi, Delhi, India
- Bioclues.org, Hyderabad, India
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16
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Rao RSP, Ghate SD, Shastry RP, Kurthkoti K, Suravajhala P, Patil P, Shetty P. Prevalence and heterogeneity of antibiotic resistance genes in Orientia tsutsugamushi and other rickettsial genomes. Microb Pathog 2023; 174:105953. [PMID: 36529286 DOI: 10.1016/j.micpath.2022.105953] [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: 10/22/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/16/2022]
Abstract
Despite a million infections every year and an estimated one billion people at risk, scrub typhus is regarded as a neglected tropical disease. The causative bacterium Orientia tsutsugamushi, a member of rickettsiae, seems to be intrinsically resistant to several classes of antibiotics. The emergence of antibiotic-resistant scrub typhus is likely to become a global public health concern. Yet, it is unknown as to how common antibiotic resistance genes are in O. tsutsugamushi, and how variable these loci are among the genomes of rickettsiae. By using the comprehensive antibiotic resistance database, we explored 79 complete genomes from 24 species of rickettsiae for antibiotic resistance loci. There were 244 unique antibiotic resistance genes in rickettsiae. Both the total and unique antibiotic resistance genes in O. tsutsugamushi were significantly less compared to other members of rickettsiae. However, antibiotic resistance genes in O. tsutsugamushi genomes were more unique and highly variable. Many genes such as resistant variants of evgS, and vanS A/G were present in numerous copies. These results will have important implications in the context of antibiotic-resistant scrub typhus.
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Affiliation(s)
- R Shyama Prasad Rao
- Center for Bioinformatics, NITTE deemed to be University, Mangaluru, 575018, India.
| | - Sudeep D Ghate
- Center for Bioinformatics, NITTE deemed to be University, Mangaluru, 575018, India
| | - Rajesh P Shastry
- Division of Microbiology and Biotechnology, Yenepoya Research Center, Yenepoya deemed to be University, Mangaluru, 575018, India
| | - Krishna Kurthkoti
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana PO, 690525, Kerala, India
| | - Prakash Patil
- Central Research Laboratory, KS Hegde Medical Academy (KSHEMA), NITTE deemed to be University, Mangaluru, 575018, India
| | - Praveenkumar Shetty
- Central Research Laboratory, KS Hegde Medical Academy (KSHEMA), NITTE deemed to be University, Mangaluru, 575018, India; Department of Biochemistry, KS Hegde Medical Academy (KSHEMA), NITTE deemed to be University, Mangaluru, 575018, India
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17
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Najeeb N, Murukan AB, Renjitha A, Jayaram M, Jabbar AA, Haridasan H, Prijikumar A, Baiju S, Nixon AA, Krishnan PA, Rodriguez S, Kumar S, Polipalli SK, Singh KK, Nair BG, Ghate SD, Rao RSP, Kishor PBK, Aloor A, Suravajhala R, Chaubey G, Suravajhala P. Inferring Recombination Events in SARS-CoV-2 Variants In Silico. Adv Exp Med Biol 2023; 1412:253-270. [PMID: 37378772 DOI: 10.1007/978-3-031-28012-2_14] [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] [Indexed: 06/29/2023]
Abstract
Over the last 34 months, at least 10 severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) distinct variants have evolved. Among these, some were more infectious while others were not. These variants may serve as candidates for identification of the signature sequences linked to infectivity and viral transgressions. Based on our previous hijacking and transgression hypothesis, we aimed to investigate whether SARS-CoV-2 sequences associated with infectivity and trespassing of long noncoding RNAs (lncRNAs) provide a possible recombination mechanism to drive the formation of new variants. This work involved a sequence and structure-based approach to screen SARS-CoV-2 variants in silico, taking into account effects of glycosylation and links to known lncRNAs. Taken together, the findings suggest that transgressions involving lncRNAs may be linked with changes in SARS-CoV-2-host interactions driven by glycosylation events.
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Affiliation(s)
- Nihal Najeeb
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Aparna B Murukan
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Anagha Renjitha
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Malavika Jayaram
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Ayisha A Jabbar
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Haripriya Haridasan
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Akshara Prijikumar
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Sneha Baiju
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Adrial Ann Nixon
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | | | - Sunu Rodriguez
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Somesh Kumar
- Genome Sequencing Lab, Lok Nayak Hospital, Delhi, India
| | | | - Keshav K Singh
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Kaul Genetics Building, Birmingham, AL, USA
| | - Bipin G Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Sudeep D Ghate
- Center for Bioinformatics, NITTE University, Mangaluru, India
| | | | | | - Arya Aloor
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Renuka Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India.
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18
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Manoj G, Anjali K, Presannan A, Melethadathil N, Suravajhala R, Suravajhala P. Epigenetics, genomics imprinting and non-coding RNAs. Progress in Molecular Biology and Translational Science 2023; 197:93-104. [PMID: 37019598 DOI: 10.1016/bs.pmbts.2023.02.001] [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] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Epigenetic traits are heritable phenotypes caused by alterations in chromosomes rather than DNA sequences. The actual epigenetic expression of the somatic cells of a species is identical, however, they may show distinct subtleties in various cell types in which they may be affected. Several recent studies demonstrated that the epigenetic system plays a very important role in regulating all biological natural processes in the body from birth to death. We outline the essential elements of epigenetics, genomic imprinting, and non-coding RNAs in this mini-review.
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Affiliation(s)
- Gautham Manoj
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Krishna Anjali
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Anandhu Presannan
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | | | - Renuka Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India.
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19
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Singh T, Malik G, Someshwar S, Le HTT, Polavarapu R, Chavali LN, Melethadathil N, Sundararajan VS, Valadi J, Kavi Kishor PB, Suravajhala P. Machine Learning Heuristics on Gingivobuccal Cancer Gene Datasets Reveals Key Candidate Attributes for Prognosis. Genes (Basel) 2022; 13:genes13122379. [PMID: 36553647 PMCID: PMC9777687 DOI: 10.3390/genes13122379] [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: 10/22/2022] [Revised: 11/28/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Delayed cancer detection is one of the common causes of poor prognosis in the case of many cancers, including cancers of the oral cavity. Despite the improvement and development of new and efficient gene therapy treatments, very little has been carried out to algorithmically assess the impedance of these carcinomas. In this work, from attributes or NCBI's oral cancer datasets, viz. (i) name, (ii) gene(s), (iii) protein change, (iv) condition(s), clinical significance (last reviewed). We sought to train the number of instances emerging from them. Further, we attempt to annotate viable attributes in oral cancer gene datasets for the identification of gingivobuccal cancer (GBC). We further apply supervised and unsupervised machine learning methods to the gene datasets, revealing key candidate attributes for GBC prognosis. Our work highlights the importance of automated identification of key genes responsible for GBC that could perhaps be easily replicated in other forms of oral cancer detection.
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Affiliation(s)
| | - Girik Malik
- Bioclues.org, Hyderabad 500072, India
- Khoury College of Computer Sciences, Northeastern University, Boston, MA 02115, USA
| | | | - Hien Thi Thu Le
- Molecular Signaling Lab, Faculty of Medicine & Health Technology, Tampere University, 33100 Tampere, Finland
| | - Rathnagiri Polavarapu
- Amity Institute of Microbial Technology, Amity University, SP-1 Kant Kalwar, NH11C, RIICO Industrial Area, Rajasthan 303002, India
| | | | | | | | - Jayaraman Valadi
- Bioclues.org, Hyderabad 500072, India
- Department of Computer Science, FLAME University, Pune 412115, India
| | - P. B. Kavi Kishor
- MNR Foundation for Research & Innovation, MNR Medical College and Hospital, Fasalwadi, Sangareddy, Hyderabad 502294, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana 690525, India
- Correspondence:
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20
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Anil Kumar S, Kaniganti S, Hima Kumari P, Sudhakar Reddy P, Suravajhala P, P S, Kishor PBK. Functional and biotechnological cues of potassium homeostasis for stress tolerance and plant development. Biotechnol Genet Eng Rev 2022:1-44. [PMID: 36469501 DOI: 10.1080/02648725.2022.2143317] [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: 06/03/2022] [Revised: 09/22/2022] [Accepted: 10/29/2022] [Indexed: 12/12/2022]
Abstract
Potassium (K+) is indispensable for the regulation of a plethora of functions like plant metabolism, growth, development, and abiotic stress responses. K+ is associated with protein synthesis and entangled in the activation of scores of enzymes, stomatal regulation, and photosynthesis. It has multiple transporters and channels that assist in the uptake, efflux, transport within the cell as well as from soil to different tissues, and the grain filling sites. While it is implicated in ion homeostasis during salt stress, it acts as a modulator of stomatal movements during water deficit conditions. K+ is reported to abate the effects of chilling and photooxidative stresses. K+ has been found to ameliorate effectively the co-occurrence of drought and high-temperature stresses. Nutrient deficiency of K+ makes leaves necrotic, leads to diminished photosynthesis, and decreased assimilate utilization highlighting the role it plays in photosynthesis. Notably, K+ is associated with the detoxification of reactive oxygen species (ROS) when plants are exposed to diverse abiotic stress conditions. It is irrefutable now that K+ reduces the activity of NADPH oxidases and at the same time maintains electron transport activity, which helps in mitigating the oxidative stress. K+ as a macronutrient in plant growth, the role of K+ during abiotic stress and the protein phosphatases involved in K+ transport have been reviewed. This review presents a holistic view of the biological functions of K+, its uptake, translocation, signaling, and the critical roles it plays under abiotic stress conditions, plant growth, and development that are being unraveled in recent times.
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Affiliation(s)
- S Anil Kumar
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research Deemed to be University, Guntur, Andhra Pradesh, India
| | - Sirisha Kaniganti
- Crop transformation Laboratory, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | | | - P Sudhakar Reddy
- Crop transformation Laboratory, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | | | - Suprasanna P
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research Deemed to be University, Guntur, Andhra Pradesh, India
- Amity Institute of Biotechnology, Amity University Mumbai, Bhatan, Mumbai, India
| | - P B Kavi Kishor
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research Deemed to be University, Guntur, Andhra Pradesh, India
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Srivastava U, Tripathi AK, Kaur J, Devi S, Verma S, Singh V, Das D, Singh PP, Mishra RK, Kumar NA, Mishra VN, Kumar P, Rai V, Tamang R, Suravajhala P, Pandey R, Chaubey G. Vaccine hesitancy for coronavirus SARS-CoV-2 in Varanasi India. Front Public Health 2022; 10:892584. [PMID: 36276375 PMCID: PMC9581394 DOI: 10.3389/fpubh.2022.892584] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 09/09/2022] [Indexed: 01/22/2023] Open
Abstract
With the rollout of the world's largest vaccine drive for SARS-CoV-2 by the Government of India on January 16 2021, India had targeted to vaccinate its entire population by the end of 2021. Struggling with vaccine procurement and production earlier, India overcome these hurdles, but the Indian population still did not seem to be mobilizing swiftly toward vaccination centers. The severe second wave has slowed the vaccination pace and was also one of the major contributing factors to vaccine hesitancy. To understand the nature of vaccine hesitancy and its underlying factors, we conducted extensive online and offline surveys in Varanasi and adjoining regions using structured questions. Most respondents were students (0.633). However, respondents from other occupations, such as government officials (0.10), have also participated in the study. Interestingly, most people (0.75) relied on fake news and did not take COVID-19 seriously. Most importantly, we noticed that a substantial proportion of respondents (relative frequency 0.151; mean age 24.8 years) reported that they were still not interested in vaccination. We observed a significant association between vaccine hesitancy and socioeconomic status (χ2 = 307.6, p < 0.001). However, we failed to detect any association between vaccine hesitancy and gender (χ2 = 0.007, p > 0.5). People who have neither been vaccinated nor have ever been infected may become the medium for spreading the virus and creating new variants, which may lead to the vaccine-resistant variant. We expect this extensive survey to help the Government upgrade their vaccination policies for COVID-19 in North India.
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Affiliation(s)
- Utkarsh Srivastava
- Anthropology Division, Department of Sociology, Faculty of Social Sciences, Banaras Hindu University, Varanasi, India
| | - Avanish Kumar Tripathi
- Anthropology Division, Department of Sociology, Faculty of Social Sciences, Banaras Hindu University, Varanasi, India
| | - Jagjeet Kaur
- Anthropology Division, Department of Sociology, Faculty of Social Sciences, Banaras Hindu University, Varanasi, India
| | - Sabita Devi
- Anthropology Division, Department of Sociology, Faculty of Social Sciences, Banaras Hindu University, Varanasi, India
| | - Shipra Verma
- Anthropology Division, Department of Sociology, Faculty of Social Sciences, Banaras Hindu University, Varanasi, India
| | - Vanya Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Debashruti Das
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Prajjval Pratap Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Rahul Kumar Mishra
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Nikhil A. Kumar
- Department of Neurology, Institute of Medical Science, Banaras Hindu University, Varanasi, India
| | - Vijaya Nath Mishra
- Department of Neurology, Institute of Medical Science, Banaras Hindu University, Varanasi, India
| | - Pradeep Kumar
- Department of Biotechnology, VBS Purvanchal University, Jaunpur, India
| | - Vandana Rai
- Department of Biotechnology, VBS Purvanchal University, Jaunpur, India
| | - Rakesh Tamang
- Department of Zoology, University of Calcutta, Kolkata, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Rakesh Pandey
- Department of Psychology, Faculty of Social Sciences, Banaras Hindu University, Varanasi, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
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22
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Valadi J, Sundararajan VS, Bandapalli OR, Benso A, Suravajhala P. Editorial: Integrated systems genomic approaches for characterizing uncharacterized proteins. Front Genet 2022; 13:1000825. [PMID: 36176288 PMCID: PMC9513579 DOI: 10.3389/fgene.2022.1000825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/22/2022] [Indexed: 12/02/2022] Open
Affiliation(s)
- Jayaraman Valadi
- Department of Computer Science, Vidyashilp University, Maharastra, India
- Bioclues.org, Hyderabad, India
- Department of Computer Science, FLAME University, Pune, India
- *Correspondence: Jayaraman Valadi, ; Prashanth Suravajhala,
| | | | | | - Alfredo Benso
- PolitoBIOMed Lab—Biomedical Engineering Lab, Turin, Italy
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham University, Kollam, Kerala, India
- *Correspondence: Jayaraman Valadi, ; Prashanth Suravajhala,
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23
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Suravajhala P, Goltsov A. Three Grand Challenges in High Throughput Omics Technologies. Biomolecules 2022; 12:biom12091238. [PMID: 36139077 PMCID: PMC9496467 DOI: 10.3390/biom12091238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwavidyapeetham, Amritapuri, Clappana, Kerala 690525, India
- Bioclues.org, Hyderabad 500072, India
- Correspondence:
| | - Alexey Goltsov
- Biocybernetics Systems and Technologies Division, Institute for Artificial intelligence, MIREA–Russian Technological University, 119454 Moscow, Russia
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24
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Oyelami FO, Usman T, Suravajhala P, Ali N, Do DN. Emerging Roles of Noncoding RNAs in Bovine Mastitis Diseases. Pathogens 2022; 11:pathogens11091009. [PMID: 36145441 PMCID: PMC9501195 DOI: 10.3390/pathogens11091009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 06/05/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are an abundant class of RNA with varying nucleotide lengths. They have been shown to have great potential in eutherians/human disease diagnosis and treatments and are now gaining more importance for the improvement of diseases in livestock. To date, thousands of ncRNAs have been discovered in the bovine genome and the continuous advancement in deep sequencing technologies and various bioinformatics tools has enabled the elucidation of their roles in bovine health. Among farm animals' diseases, mastitis, a common inflammatory disease in cattle, has caused devastating economic losses to dairy farmers over the last few decades. Here, we summarize the biology of bovine mastitis and comprehensively discuss the roles of ncRNAs in different types of mastitis infection. Based on our findings and relevant literature, we highlighted various evidence of ncRNA roles in mastitis. Different approaches (in vivo versus in vitro) for exploring ncRNA roles in mastitis are emphasized. More particularly, the potential applications of emerging genome editing technologies, as well as integrated omics platforms for ncRNA studies and implications for mastitis are presented.
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Affiliation(s)
- Favour Oluwapelumi Oyelami
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Tahir Usman
- College of Veterinary Sciences & Animal Husbandry, Abdul Wali Khan University, Mardan 23200, KP, Pakistan
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana 690525, Kerala, India
| | - Nawab Ali
- Department of Zoology, Abdul Wali Khan University, Mardan 23200, KP, Pakistan
| | - Duy N. Do
- Faculty of Veterinary Medicine, Viet Nam National University of Agriculture, Hanoi 100000, Vietnam
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
- Correspondence: ; Tel.: +1-9029578789
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25
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Abbasi BA, Dharan A, Mishra A, Saraf D, Ahamad I, Suravajhala P, Valadi J. In Silico Characterization of Uncharacterized Proteins From Multiple Strains of Clostridium Difficile. Front Genet 2022; 13:878012. [PMID: 36035185 PMCID: PMC9403866 DOI: 10.3389/fgene.2022.878012] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 02/17/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
Clostridium difficile (C. difficile) is a multi-strain, spore-forming, Gram-positive, opportunistic enteropathogen bacteria, majorly associated with nosocomial infections, resulting in severe diarrhoea and colon inflammation. Several antibiotics including penicillin, tetracycline, and clindamycin have been employed to control C. difficile infection, but studies have suggested that injudicious use of antibiotics has led to the development of resistance in C. difficile strains. However, many proteins from its genome are still considered uncharacterized proteins that might serve crucial functions and assist in the biological understanding of the organism. In this study, we aimed to annotate and characterise the 6 C. difficile strains using in silico approaches. We first analysed the complete genome of 6 C. difficile strains using standardised approaches and analysed hypothetical proteins (HPs) employing various bioinformatics approaches coalescing, including identifying contigs, coding sequences, phage sequences, CRISPR-Cas9 systems, antimicrobial resistance determination, membrane helices, instability index, secretory nature, conserved domain, and vaccine target properties like comparative homology analysis, allergenicity, antigenicity determination along with structure prediction and binding-site analysis. This study provides crucial supporting information about the functional characterization of the HPs involved in the pathophysiology of the disease. Moreover, this information also aims to assist in mechanisms associated with bacterial pathogenesis and further design candidate inhibitors and bona fide pharmaceutical targets.
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Affiliation(s)
| | | | | | | | | | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, India
- *Correspondence: Prashanth Suravajhala, ; Jayaraman Valadi,
| | - Jayaraman Valadi
- Bioclues.org, Hyderabad, India
- School of Computational and Data Sciences, Vidyashilp University, Bengaluru, India
- Department of Computer Science, FLAME University, Pune, India
- *Correspondence: Prashanth Suravajhala, ; Jayaraman Valadi,
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26
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Shanthappa PM, Suravajhala R, Suravajhala P, Kumar G, Melethadathil N. In silico based multi-epitope vaccine design against norovirus. J Biomol Struct Dyn 2022:1-11. [PMID: 35916029 DOI: 10.1080/07391102.2022.2105400] [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] [Indexed: 10/16/2022]
Abstract
Norovirus (NoV) belongs to the Calciviridae family that causes diarrhoea, vomiting, and stomach pain in people who have acute gastroenteritis (AGE). Identifying multi-epitope dependent vaccines for single stranded positive sense viruses such as NoV has been a long due. Although efforts have been in place to look into the candidate epitopes, understanding molecular mimicry and finding new epitopes for inducing immune responses against the T/B-cells which play an important role for the cell-mediated and humoral immunity was not dealt with in great detail. The current study focuses on identifying new epitopes from various databases that were filtered for antigenicity, allergenicity, and toxicity. The adjuvant β-defensin along with different linkers were used for vaccine construction. Further, the binding relationship between the vaccine construct and toll-like immune receptor (TLR3) complex was determined using a molecular docking analysis, followed by molecular dynamics simulation of 100 ns. The vaccine candidate developed expresses good solubility with a score of 0.530, Z-score of -4.39 and molecular docking score of -140.4 ± 12.1. The MD trajectories reveal that there is a stability between TLR3 and the developed vaccine candidate with an average of 0.91 nm RMSD value and also the system highest occupancy H-bond formed between GLU127 of TLR3 and TYR10 of vaccine candidate (61.55%). Four more H-bonds exist with an occupancy of more than 32% between TLR3 and the vaccine candidates which makes it stable. Thus, the multi-epitope based vaccine developed in the present study forms the basis for further experimental investigations to develop a potentially good vaccine against NoV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pallavi M Shanthappa
- Department Computer Science, Amrita School of Arts and Sciences, Mysuru, Amrita Vishwa Vidyapeetham, India
| | | | | | - Geetha Kumar
- School of Biotechnology, Amritapuri, Amrita Vishwa Vidyapeetham, India
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27
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Rout M, Kour B, Vuree S, Lulu SS, Medicherla KM, Suravajhala P. Diabetes mellitus susceptibility with varied diseased phenotypes and its comparison with phenome interactome networks. World J Clin Cases 2022; 10:5957-5964. [PMID: 35949812 PMCID: PMC9254192 DOI: 10.12998/wjcc.v10.i18.5957] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/02/2022] [Accepted: 04/22/2022] [Indexed: 02/06/2023] Open
Abstract
An emerging area of interest in understanding disease phenotypes is systems genomics. Complex diseases such as diabetes have played an important role towards understanding the susceptible genes and mutations. A wide number of methods have been employed and strategies such as polygenic risk score and allele frequencies have been useful, but understanding the candidate genes harboring those mutations is an unmet goal. In this perspective, using systems genomic approaches, we highlight the application of phenome-interactome networks in diabetes and provide deep insights. LINC01128, which we previously described as candidate for diabetes, is shown as an example to discuss the approach.
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Affiliation(s)
- Madhusmita Rout
- Department of Pediatrics, University of Oklahoma Health Sciences Centre, Oklahoma City, OK 73104, United States
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, Rajasthan, India
| | - Bhumandeep Kour
- Department of Biotechnology, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Sugunakar Vuree
- Department of Biotechnology, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Sajitha S Lulu
- Department of Biotechnology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, Rajasthan, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Vallikavu PO, Amritapuri, Clappana, Kollam 690525, Kerala, India
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28
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Kavi Kishor PB, Suravajhala P, Rathnagiri P, Sreenivasulu N. Intriguing Role of Proline in Redox Potential Conferring High Temperature Stress Tolerance. Front Plant Sci 2022; 13:867531. [PMID: 35795343 PMCID: PMC9252438 DOI: 10.3389/fpls.2022.867531] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/21/2022] [Indexed: 05/24/2023]
Abstract
Proline is a proteinogenic amino acid synthesized from glutamate and ornithine. Pyrroline-5-carboxylate synthetase and pyrroline-5-carboxylate reductase are the two key enzymes involved in proline synthesis from glutamate. On the other hand, ornithine-δ-aminotransferase converts ornithine to pyrroline 5-carboxylate (P5C), an intermediate in the synthesis of proline as well as glutamate. Both proline dehydrogenase and P5C dehydrogenase convert proline back to glutamate. Proline accumulation is widespread in response to environmental challenges such as high temperatures, and it is known to defend plants against unpropitious situations promoting plant growth and flowering. While proline accumulation is positively correlated with heat stress tolerance in some crops, it has detrimental consequences in others. Although it has been established that proline is a key osmolyte, its exact physiological function during heat stress and plant ontogeny remains unknown. Emerging evidence pointed out its role as an overriding molecule in alleviating high temperature stress (HTS) by quenching singlet oxygen and superoxide radicals. Proline cycle acts as a shuttle and the redox couple (NAD+/NADH, NADP+/NADPH) appears to be highly crucial for energy transfer among different cellular compartments during plant development, exposure to HTS conditions and also during the recovery of stress. In this review, the progress made in recent years regarding its involvement in heat stress tolerance is highlighted.
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Affiliation(s)
- P. B. Kavi Kishor
- Department of Biotechnology, Vignan’s Foundation for Science, Technology & Research (Deemed to Be University), Guntur, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham University, Kerala, India
| | - P. Rathnagiri
- Department of Biotechnology, Vignan’s Foundation for Science, Technology & Research (Deemed to Be University), Guntur, India
| | - Nese Sreenivasulu
- Consumer-Driven Grain Quality and Nutrition Research Unit, International Rice Research Institute, Los Banos, Philippines
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29
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Khan AM, Ranganathan S, Suravajhala P. Editorial: Bioinformatics and the Translation of Data-Driven Discoveries. Front Genet 2022; 13:902940. [PMID: 35620463 PMCID: PMC9127959 DOI: 10.3389/fgene.2022.902940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Asif M Khan
- School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia.,Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul, Turkey.,APBioNET.org, Singapore, Singapore
| | - Shoba Ranganathan
- APBioNET.org, Singapore, Singapore.,Applied BioSciences, Macquarie University, Sydney, NSW, Australia
| | - Prashanth Suravajhala
- APBioNET.org, Singapore, Singapore.,Bioclues.org, Hyderabad, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham University, Kollam, India
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30
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Parihar J, Parihar SP, Suravajhala P, Bagaria A. Spatial Metagenomic Analysis in Understanding the Microbial Diversity of Thar Desert. Biology 2022; 11:biology11030461. [PMID: 35336834 PMCID: PMC8945486 DOI: 10.3390/biology11030461] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary We present a systematic investigation of the distribution of microbial communities in arid and semi-arid regions of Thar Desert Rajasthan, India. Their responses in multiple environmental stresses, including surface soil, surface water and underground water were evaluated. We further assess the biotechnological potential of native microorganisms and discover functional species with results providing a detailed understanding of the abundance of microbial communities in these regions, associated with various stress-related biogeochemical and biotechnological processes. We hope our work will facilitate the development of effective future strategies for the use of extremophiles in complex environments. Abstract The arid and semi-arid regions of Rajasthan are one of the most extreme biomes of India, possessing diverse microbial communities that exhibit immense biotechnological potential for industries. Herein, we sampled study sites from arid and semi-arid regions of Thar Desert, Rajasthan, India and subjected them to chemical, physical and metagenomics analysis. The microbial diversity was studied using V3–V4 amplicon sequencing of 16S rRNA gene by Illumina MiSeq. Our metagenomic analyses revealed that the sampled sites consist mainly of Proteobacteria (19–31%) followed by unclassified bacteria (5–21%), Actinobacteria (3–25%), Planctomycetes (5–13%), Chloroflexi (2–14%), Bacteroidetes (3–12%), Firmicutes (3–7%), Acidobacteria (1–4%) and Patescibacteria (1–4%). We have found Proteobacteria in abundance which is associated with a range of activities involved in biogeochemical cycles such as carbon, nitrogen, and sulphur. Our study is perhaps the first of its kind to explore soil bacteria from arid and semi-arid regions of Rajasthan, India. We believe that the new microbial candidates found can be further explored for various industrial and biotechnological applications.
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Affiliation(s)
- Jagdish Parihar
- Department of Physics, Manipal University Jaipur, Jaipur 303007, India
| | - Suraj P Parihar
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
| | - Prashanth Suravajhala
- Bioclues.org, Vivekananda Nagar, Kukatpally, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita Vishwavidyapeetham, Amritapuri Campus, Clappana P.O., Kollam 690525, India
| | - Ashima Bagaria
- Department of Physics, Manipal University Jaipur, Jaipur 303007, India
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31
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Shaji SK, Drishya G, Sunilkumar D, Suravajhala P, Kumar GB, Nair BG. Systematic understanding of anti-tumor mechanisms of Tamarixetin through network and experimental analyses. Sci Rep 2022; 12:3966. [PMID: 35273218 PMCID: PMC8913656 DOI: 10.1038/s41598-022-07087-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 09/16/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022] Open
Abstract
Tamarixetin, a flavonoid derived from Quercetin, was shown to possess anti-cancer properties in various types of cancer. However, the mechanism of action of this compound is not well understood. Observations from reverse docking and network pharmacology analysis, were validated by cell based studies to analyse the chemotherapeutic potential and elucidate the molecular mechanism of action of Tamarixetin in breast cancer. In silico analysis using reverse docking and PPI analysis clearly indicated that out of 35 proteins targeted by Tamarixetin, the top 3 hub genes, namely, AKT1, ESR1 and HSP90AA1, were upregulated in breast tumor tissues and more importantly showed strong negative correlation to breast cancer patient survival. Furthermore, the KEGG pathway analysis showed enrichment of target proteins of Tamarixetin in 33 pathways which are mainly involved in neoplastic signalling. In vitro cell-based studies demonstrated that Tamarixetin could inhibit cell proliferation, induce ROS and reduce mitochondrial membrane potential, leading to cell death. Tamarixetin induced cell cycle arrest at G2/M phase and inhibited the migration as well as the invasion of breast cancer cells. Taken together, the combination of in silico and in vitro approaches used in the present study clearly provides evidence for the chemotherapeutic potential of Tamarixetin in breast cancer.
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Affiliation(s)
- Sanu K Shaji
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana P.O, Kollam, Kerala, 690525, India
| | - G Drishya
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana P.O, Kollam, Kerala, 690525, India
| | - Damu Sunilkumar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana P.O, Kollam, Kerala, 690525, India
| | - Prashanth Suravajhala
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana P.O, Kollam, Kerala, 690525, India
| | - Geetha B Kumar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana P.O, Kollam, Kerala, 690525, India.
| | - Bipin G Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana P.O, Kollam, Kerala, 690525, India.
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Pathirana S, Elvitigala D, Nanayakkara C, Suravajhala P, Rajapakse S, Hettiarachchi G, Chandrasekharan N. Identification and in-silico analysis of a novel restriction enzyme coding gene from Pseudomonas anguilliseptica. Gene Reports 2022. [DOI: 10.1016/j.genrep.2021.101487] [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: 10/19/2022]
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Singh PP, Suravajhala P, Basu Mallick C, Tamang R, Rai AK, Machha P, Singh R, Pathak A, Mishra VN, Shrivastava P, Singh KK, Thangaraj K, Chaubey G. COVID-19: Impact on linguistic and genetic isolates of India. Genes Immun 2022; 23:47-50. [PMID: 34635809 PMCID: PMC8504558 DOI: 10.1038/s41435-021-00150-8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 11/24/2022]
Abstract
The rapid expansion of coronavirus SARS-CoV-2 has impacted various ethnic groups all over the world. The burden of infectious diseases including COVID-19 are generally reported to be higher for the Indigenous people. The historical knowledge have also suggested that the indigenous populations suffer more than the general populations in the pandemic. Recently, it has been reported that the indigenous groups of Brazil have been massively affected by COVID-19. Series of studies have shown that many of the indigenous communities reached at the verge of extinction due to this pandemic. Importantly, South Asia also has several indigenous and smaller communities, that are living in isolation. Till date, despite the two consecutive waves in India, there is no report on the impact of COVID-19 for indigenous tribes. Since smaller populations experiencing drift may have greater risk of such pandemic, we have analysed Runs of Homozygosity (ROH) among South Asian populations and identified several populations with longer homozygous segments. The longer runs of homozygosity at certain genomic regions may increases the susceptibility for COVID-19. Thus, we suggest extreme careful management of this pandemic among isolated populations of South Asia.
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Affiliation(s)
- Prajjval Pratap Singh
- grid.411507.60000 0001 2287 8816Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005 India
| | - Prashanth Suravajhala
- grid.469354.90000 0004 0610 6228Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research Statue Circle, Jaipur, Rajasthan India ,grid.411370.00000 0000 9081 2061Amrita School of Biotechnology, Amrita University Kerala India, Vallikavu, 690525 India
| | - Chandana Basu Mallick
- grid.411507.60000 0001 2287 8816Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - Rakesh Tamang
- grid.59056.3f0000 0001 0664 9773Department of Zoology, University of Calcutta, Kolkata, 700019 India
| | - Ashutosh Kumar Rai
- grid.411975.f0000 0004 0607 035XDepartment of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Pratheusa Machha
- grid.417634.30000 0004 0496 8123CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002 India
| | - Royana Singh
- grid.411507.60000 0001 2287 8816Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Abhishek Pathak
- grid.411507.60000 0001 2287 8816Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Vijay Nath Mishra
- grid.411507.60000 0001 2287 8816Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Pankaj Shrivastava
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Government of MP, Sagar, India
| | - Keshav K. Singh
- grid.265892.20000000106344187Department of Genetics, School of Medicine, University of Alabama at Birmingham, Kaul Genetics Building, Birmingham, AL USA
| | - Kumarasamy Thangaraj
- grid.417634.30000 0004 0496 8123CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007 India ,grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, 500039 India
| | - Gyaneshwer Chaubey
- grid.411507.60000 0001 2287 8816Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005 India
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Rajagopal S, Gupta A, Parveen R, Shukla N, Bhattacharya S, Naravula J, Kumar S A, Mathur P, Simlot A, Mehta S, Bihari C, Mehta S, Mishra AK, Nair BG, Medicherla KM, Reddy GB, Sreenivasulu N, Kishor PK, Suravajhala P. Vitamin K in human health and metabolism: A nutri-genomics review. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2021.12.012] [Citation(s) in RCA: 1] [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: 12/31/2022]
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Bernardino RMM, Leão R, Henrique R, Pinheiro LC, Kumar P, Suravajhala P, Beck HC, Carvalho AS, Matthiesen R. Extracellular Vesicle Proteome in Prostate Cancer: A Comparative Analysis of Mass Spectrometry Studies. Int J Mol Sci 2021; 22:ijms222413605. [PMID: 34948404 PMCID: PMC8707426 DOI: 10.3390/ijms222413605] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/15/2021] [Accepted: 12/15/2021] [Indexed: 12/24/2022] Open
Abstract
Molecular diagnostics based on discovery research holds the promise of improving screening methods for prostate cancer (PCa). Furthermore, the congregated information prompts the question whether the urinary extracellular vesicles (uEV) proteome has been thoroughly explored, especially at the proteome level. In fact, most extracellular vesicles (EV) based biomarker studies have mainly targeted plasma or serum. Therefore, in this study, we aim to inquire about possible strategies for urinary biomarker discovery particularly focused on the proteome of urine EVs. Proteomics data deposited in the PRIDE archive were reanalyzed to target identifications of potential PCa markers. Network analysis of the markers proposed by different prostate cancer studies revealed moderate overlap. The recent throughput improvements in mass spectrometry together with the network analysis performed in this study, suggest that a larger standardized cohort may provide potential biomarkers that are able to fully characterize the heterogeneity of PCa. According to our analysis PCa studies based on urinary EV proteome presents higher protein coverage compared to plasma, plasma EV, and voided urine proteome. This together with a direct interaction of the prostate gland and urethra makes uEVs an attractive option for protein biomarker studies. In addition, urinary proteome based PCa studies must also evaluate samples from bladder and renal cancers to assess specificity for PCa.
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Affiliation(s)
- Rui Miguel Marques Bernardino
- Computational and Experimental Biology Group, Chronic Diseases Research Centre (CEDOC), NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal;
- Urology Department, Centro Hospitalar e Universitário de Lisboa Central, 1169-050 Lisbon, Portugal;
- Correspondence: (R.M.M.B.); (R.M.); Tel.: +351-939218696 (R.M.M.B. & R.M.)
| | - Ricardo Leão
- Faculty of Medicine, University of Coimbra, 3000-370 Coimbra, Portugal;
| | - Rui Henrique
- Pathology Department, Instituto Português de Oncologia, 4200-072 Porto, Portugal;
| | - Luis Campos Pinheiro
- Urology Department, Centro Hospitalar e Universitário de Lisboa Central, 1169-050 Lisbon, Portugal;
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
- Somaiya Institute of Research and Consultancy (SIRAC), Somaiya Vidyavihar University (SVU), Vidyavihar, Mumbai 400077, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri Campus, Clappana P.O., Kollam 690525, India;
| | - Hans Christian Beck
- Centre for Clinical Proteomics, Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, 5000 Odense, Denmark;
| | - Ana Sofia Carvalho
- Computational and Experimental Biology Group, Chronic Diseases Research Centre (CEDOC), NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal;
| | - Rune Matthiesen
- Computational and Experimental Biology Group, Chronic Diseases Research Centre (CEDOC), NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal;
- Correspondence: (R.M.M.B.); (R.M.); Tel.: +351-939218696 (R.M.M.B. & R.M.)
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Bhargava H, Sharma A, Suravajhala P. Chemogenomic Approaches for Revealing Drug Target Interactions in
Drug Discovery. Curr Genomics 2021; 22:328-338. [PMID: 35283667 PMCID: PMC8844939 DOI: 10.2174/1389202922666210920125800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/24/2020] [Revised: 05/30/2021] [Accepted: 06/25/2021] [Indexed: 11/26/2022] Open
Abstract
The drug discovery process has been a crucial and cost-intensive process. This cost is not only monetary but also involves risks, time, and labour that are incurred while introducing a drug in the market. In order to reduce this cost and the risks associated with the drugs that may result in severe side effects, the in silico methods have gained popularity in recent years. These methods have had a significant impact on not only drug discovery but also the related areas such as drug repositioning, drug-target interaction prediction, drug side effect prediction, personalised medicine, etc. Amongst these research areas predicting interactions between drugs and targets forms the basis for drug discovery. The availability of big data in the form of bioinformatics, genetic databases, along with computational methods, have further supported data-driven decision-making. The results obtained through these methods may be further validated using in vitro or in vivo experiments. This validation step can further justify the predictions resulting from in silico approaches, further increasing the accuracy of the overall result in subsequent stages. A variety of approaches are used in predicting drug-target interactions, including ligand-based, molecular docking based and chemogenomic-based approaches. This paper discusses the chemogenomic methods, considering drug target interaction as a classification problem on whether or not an interaction between a particular drug and target would serve as a basis for understanding drug discovery/drug repositioning. We present the advantages and disadvantages associated with their application.
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Affiliation(s)
- Harshita Bhargava
- Department of Computer Science & IT, IIS (Deemed to be University), Jaipur,India
| | - Amita Sharma
- Department of Computer Science & IT, IIS (Deemed to be University), Jaipur,India
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Kaur A, Chopra M, Bhushan M, Gupta S, Kumari P H, Sivagurunathan N, Shukla N, Rajagopal S, Bhalothia P, Sharma P, Naravula J, Suravajhala R, Gupta A, Abbasi BA, Goswami P, Singh H, Narang R, Polavarapu R, Medicherla KM, Valadi J, Kumar S A, Chaubey G, Singh KK, Bandapalli OR, Kavi Kishor PB, Suravajhala P. The Omic Insights on Unfolding Saga of COVID-19. Front Immunol 2021; 12:724914. [PMID: 34745097 PMCID: PMC8564481 DOI: 10.3389/fimmu.2021.724914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
The year 2019 has seen an emergence of the novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease of 2019 (COVID-19). Since the onset of the pandemic, biological and interdisciplinary research is being carried out across the world at a rapid pace to beat the pandemic. There is an increased need to comprehensively understand various aspects of the virus from detection to treatment options including drugs and vaccines for effective global management of the disease. In this review, we summarize the salient findings pertaining to SARS-CoV-2 biology, including symptoms, hosts, epidemiology, SARS-CoV-2 genome, and its emerging variants, viral diagnostics, host-pathogen interactions, alternative antiviral strategies and application of machine learning heuristics and artificial intelligence for effective management of COVID-19 and future pandemics.
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Affiliation(s)
- Arvinpreet Kaur
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Punjab, India
- Bioclues.org, Hyderabad, India
| | - Mehak Chopra
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Mahak Bhushan
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, India
| | - Sonal Gupta
- Bioclues.org, Hyderabad, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | | | - Narmadhaa Sivagurunathan
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Nidhi Shukla
- Bioclues.org, Hyderabad, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Shalini Rajagopal
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Purva Bhalothia
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Purnima Sharma
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Punjab, India
| | - Jalaja Naravula
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Renuka Suravajhala
- Bioclues.org, Hyderabad, India
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
| | - Ayam Gupta
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Bilal Ahmed Abbasi
- Functional Genomics Unit, Council of Scientific and Industrial Research- Institute of Genomics & Integrative Biology (CSIR-IGIB), Delhi, India
| | - Prittam Goswami
- Department of Biotechnology, Haldia Institute of Technology, West Bengal, India
| | - Harpreet Singh
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Punjab, India
- Bioclues.org, Hyderabad, India
| | - Rahul Narang
- Department of Microbiology, All India Institute of Medical Sciences, Bibinagar, Hyderabad, India
| | | | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Jayaraman Valadi
- Bioclues.org, Hyderabad, India
- Department of Computer Science, Flame University, Pune, India
| | - Anil Kumar S
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Benaras Hindu University, Varanasi, India
| | - Keshav K. Singh
- Department of Genetics, University of Alabama, Birmingham, AL, United States
| | - Obul Reddy Bandapalli
- Bioclues.org, Hyderabad, India
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Department of Applied Biology, Council of Scientific and Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, India
| | - Polavarapu Bilhan Kavi Kishor
- Bioclues.org, Hyderabad, India
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kerala, India
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Kavi Kishor PB, Anil Kumar S, Naravula J, Hima Kumari P, Kummari D, Guddimalli R, Edupuganti S, Karumanchi AR, Venkatachalam P, Suravajhala P, Polavarapu R. Improvement of small seed for big nutritional feed. Physiol Mol Biol Plants 2021; 27:2433-2446. [PMID: 34566283 PMCID: PMC8455807 DOI: 10.1007/s12298-021-01071-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/04/2021] [Accepted: 09/11/2021] [Indexed: 05/14/2023]
Abstract
Exploding global population, rapid urbanization, salinization of soils, decreasing arable land availability, groundwater resources, and dynamic climatic conditions pose impending damage to our food security by reducing the grain quality and quantity. This issue is further compounded in arid and semi-arid regions due to the shortage of irrigation water and erratic rainfalls. Millets are gluten (a family of proteins)-free and cultivated all over the globe for human consumption, fuel, feed, and fodder. They provide nutritional security for the under- and malnourished. With the deployment of strategies like foliar spray, traditional/marker-assisted breeding, identification of candidate genes for the translocation of important minerals, and genome-editing technologies, it is now tenable to biofortify important millets. Since the bioavailability of iron and zinc has been proven in human trials, the challenge is to make such grains accessible. This review encompasses nutritional benefits, progress made, challenges being encountered, and prospects of enriching millet crops with essential minerals.
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Affiliation(s)
- P. B. Kavi Kishor
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research, Vadlamudi, Guntur, Andhra Pradesh 522 213 India
| | - S. Anil Kumar
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research, Vadlamudi, Guntur, Andhra Pradesh 522 213 India
- Bioclues.Org, Hyderabad, India
| | - Jalaja Naravula
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research, Vadlamudi, Guntur, Andhra Pradesh 522 213 India
| | | | - Divya Kummari
- Department of Genetics, Osmania University, Hyderabad, Telangana, 500 007 India
| | | | - Sujatha Edupuganti
- Department of Botany, Osmania University, Hyderabad, Telangana, 500 007 India
| | - Appa Rao Karumanchi
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Andhra Pradesh, 522 508 India
| | | | - Prashanth Suravajhala
- Bioclues.Org, Hyderabad, India
- Amrita School of Biotechnology, Amrita University, Amritapuri, 690 525, Clappana, Kerala, India
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Shukla N, Prasad A, Kanga U, Suravajhala R, Nigam VK, Kishor PBK, Polavarapu R, Chaubey G, Singh KK, Suravajhala P. SARS-CoV-2 transgressing LncRNAs uncovers the known unknowns. Physiol Genomics 2021; 53:433-440. [PMID: 34492207 PMCID: PMC8562947 DOI: 10.1152/physiolgenomics.00075.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 12/21/2022] Open
Abstract
SARS-CoV-2 harbors many known unknown regions in the form of hypothetical open reading frames (ORFs). Although the mechanisms underlying the disease pathogenesis are not clearly understood, molecules such as long noncoding RNAs (lncRNAs) play a key regulatory role in the viral pathogenesis from endocytosis. We asked whether or not the lncRNAs in the host are associated with the viral proteins and argue that lncRNA-mRNAs molecules related to viral infection may regulate SARS-CoV-2 pathogenesis. Toward the end of the perspective, we provide challenges and insights into investigating these transgression pathways.
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Affiliation(s)
- Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
- Department of Chemistry, Manipal University Jaipur, Jaipur, India
| | - Anchita Prasad
- Department of Bioengineering, Birla Institute of Technology Mesra, Ranchi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, AIIMS, New Delhi, India
| | | | - Vinod Kumar Nigam
- Department of Bioengineering, Birla Institute of Technology Mesra, Ranchi, India
| | - P B Kavi Kishor
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research (VFSTR), Guntur, India
| | | | - Gyaneshwer Chaubey
- Cytogenetics Lab, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Keshav K Singh
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
- Bioclues Organization, Hyderabad, India
- Amrita School of Biotechnology, Amrita University, Amritapuri, Kerala, India
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Singh PP, Srivastava A, Sultana GNN, Khanam N, Pathak A, Suravajhala P, Singh R, Shrivastava P, van Driem G, Thangaraj K, Chaubey G. Publisher Correction: The major genetic risk factor for severe COVID‑19 does not show any association among South Asian populations. Sci Rep 2021; 11:16296. [PMID: 34354116 PMCID: PMC8342624 DOI: 10.1038/s41598-021-94864-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Prajjval Pratap Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Anshika Srivastava
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Gazi Nurun Nahar Sultana
- Centre for Advanced Research in Sciences (CARS), Genetic Engineering and Biotechnology Research Laboratory, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Nargis Khanam
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Abhishek Pathak
- Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research Statue Circle, Jaipur, Rajasthan, India
| | - Royana Singh
- Department of Anatomy, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Pankaj Shrivastava
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Government of MP, Sagar, India
| | - George van Driem
- Institut Für Sprachwissenschaft, Universität Bern, Länggassstrasse 49, 3012, Bern, Switzerland
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India. .,Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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Suravajhala R, Parashar A, Choudhir G, Kumar A, Malik B, Nagaraj VA, Padmanaban G, Polavarapu R, Suravajhala P, Kishor PBK. Molecular docking and dynamics studies of curcumin with COVID-19 proteins. ACTA ACUST UNITED AC 2021; 10:44. [PMID: 34131556 PMCID: PMC8192041 DOI: 10.1007/s13721-021-00312-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 02/01/2021] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 02/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is caused by a Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2), which is a positive-strand RNA virus. The SARS-CoV-2 genome and its association to SAR-CoV-1 vary from ca. 66 to 96% depending on the type of betacoronavirideae family members. With several drugs, viz. chloroquine, hydroxychloroquine, ivermectin, artemisinin, remdesivir, azithromycin considered for clinical trials, there has been an inherent need to find distinctive antiviral mechanisms of these drugs. Curcumin, a natural bioactive molecule has been shown to have therapeutic potential for various diseases, and its effect on COVID-19 is also currently being explored. In this study, we show the binding potential of curcumin targeted to a variety of SARS-CoV-2 proteins, viz. spike glycoproteins (PDB ID: 6VYB), nucleocapsid phosphoprotein (PDB ID: 6VYO), spike protein-ACE2 (PDB ID: 6M17) along with nsp10 (PDB ID: 6W4H) and RNA dependent RNA polymerase (PDB ID: 6M71) structures. Furthermore, representative docking complexes were validated using molecular dynamics simulations and mechanistic studies at 100 ns was carried on nucleocapsid and nsp10 proteins with curcumin complexes which resulted in stable and efficient binding energies and correlated with that of docked binding energies of the complexes. Both the docking and simulation studies indicate that curcumin has the potential as an antiviral against COVID-19.
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Affiliation(s)
- Renuka Suravajhala
- Department of Chemistry, Manipal University Jaipur, Jaipur, 303 007 Rajasthan India
- Bioclues.org, Hyderabad, India
| | - Abhinav Parashar
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research (Deemed To Be University), Vadlamudi, Guntur, 522 213 Andhra Pradesh India
| | - Gourav Choudhir
- Centre for Rural Development and Technology, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, 110 016 India
| | - Anuj Kumar
- Bioinformatics Laboratory, Uttarakhand Council for Biotechnology (UCB), Biotech Bhawan, Haldi, U.S. Nagar, Pantnagar, 263 145 Uttarakhand India
| | - Babita Malik
- Department of Chemistry, Manipal University Jaipur, Jaipur, 303 007 Rajasthan India
| | | | | | | | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, 320 001 Rajasthan India
- Bioclues.org, Hyderabad, India
| | - P. B. Kavi Kishor
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research (Deemed To Be University), Vadlamudi, Guntur, 522 213 Andhra Pradesh India
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Choudhary C, Sharma S, Meghwanshi KK, Patel S, Mehta P, Shukla N, Do DN, Rajpurohit S, Suravajhala P, Shukla JN. Long Non-Coding RNAs in Insects. Animals (Basel) 2021; 11:1118. [PMID: 33919662 PMCID: PMC8069800 DOI: 10.3390/ani11041118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 03/04/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 12/27/2022] Open
Abstract
Only a small subset of all the transcribed RNAs are used as a template for protein translation, whereas RNA molecules that are not translated play a very important role as regulatory non-coding RNAs (ncRNAs). Besides traditionally known RNAs (ribosomal and transfer RNAs), ncRNAs also include small non-coding RNAs (sncRNAs) and long non-coding RNAs (lncRNAs). The lncRNAs, which were initially thought to be junk, have gained a great deal attention because of their regulatory roles in diverse biological processes in animals and plants. Insects are the most abundant and diverse group of animals on this planet. Recent studies have demonstrated the role of lncRNAs in almost all aspects of insect development, reproduction, and genetic plasticity. In this review, we describe the function and molecular mechanisms of the mode of action of different insect lncRNAs discovered up to date.
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Affiliation(s)
- Chhavi Choudhary
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
| | - Shivasmi Sharma
- Department of Biotechnology, Amity University Jaipur, Jaipur 303002, India; (S.S.); (S.P.)
| | - Keshav Kumar Meghwanshi
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
| | - Smit Patel
- Department of Biotechnology, Amity University Jaipur, Jaipur 303002, India; (S.S.); (S.P.)
| | - Prachi Mehta
- Division of Biological & Life Sciences, School of Arts and Sciences, Ahmedabad University, Gujarat 380009, India; (P.M.); (S.R.)
| | - Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, India;
| | - Duy Ngoc Do
- Institute of Research and Development, Duy Tan University, Danang 550000, Vietnam;
| | - Subhash Rajpurohit
- Division of Biological & Life Sciences, School of Arts and Sciences, Ahmedabad University, Gujarat 380009, India; (P.M.); (S.R.)
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, India;
- Bioclues.org, Vivekananda Nagar, Kukatpally, Hyderabad, Telangana 500072, India
| | - Jayendra Nath Shukla
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
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Shukla NI, Siva N, Sivakumar M, Parveen R, Mishra A, Shah A, Medicherla K, Suravajhala P. Extraction of DNA and RNA from Formalin-fixed Paraffin-embedded Tissue Specimens. Bio Protoc 2021. [DOI: 10.21769/bioprotoc.4095] [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: 11/02/2022] Open
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44
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Prasad A, Bhargava H, Gupta A, Shukla N, Rajagopal S, Gupta S, Sharma A, Valadi J, Nigam V, Suravajhala P. Next Generation Sequencing. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_14] [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: 11/24/2022] Open
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Abstract
Deciphering RNA-protein interactions are important to study principal biological mechanisms including transcription and translation regulation, gene silencing, among others. Predicting RNA molecule interaction with the target protein could allow us to understand important cellular processes and design novel treatment therapies for various diseases. As non-coding RNAs do not have coding potential our knowledge about their functions is still limited. Therefore, RNA-binding proteins of non-coding RNAs regulating functions, viz. including cellular maturation, nuclear export and stability may play a very important role. Keeping in view of the need for refined methods to understand protein-RNA interactions, we have attempted a docking model to infer binding sites between lncRNA NONHSAT02007 and protein KIF13A for a rare disease phenotype that we are studying in our lab.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Renuka Suravajhala
- Department of Chemistry, School of Basic Science, Manipal University, Manipal, India
| | - Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, India.,Department of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Narayan Kumar
- Department of Biotechnology and Bioinformatics, NIIT University, Neemrana, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, India.,Bioclues.org, India
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46
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Malik G, Agarwal T, Raj U, Sundararajan VS, Bandapalli OR, Suravajhala P. Hypothetical Proteins as Predecessors of Long Non-coding RNAs. Curr Genomics 2020; 21:531-535. [PMID: 33214769 PMCID: PMC7604745 DOI: 10.2174/1389202921999200611155418] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/28/2020] [Accepted: 05/16/2020] [Indexed: 02/07/2023] Open
Abstract
Hypothetical Proteins [HP] are the transcripts predicted to be expressed in an organism, but no evidence of it exists in gene banks. On the other hand, long non-coding RNAs [lncRNAs] are the transcripts that might be present in the 5’ UTR or intergenic regions of the genes whose lengths are above 200 bases. With the known unknown [KU] regions in the genomes rapidly existing in gene banks, there is a need to understand the role of open reading frames in the context of annotation. In this commentary, we emphasize that HPs could indeed be the predecessors of lncRNAs.
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Affiliation(s)
- Girik Malik
- 1Khoury College of Computer Sciences, Northeastern University, 360 Huntington Ave., Boston, MA02115, USA; 2Bioclues.org, Kukatpally, Hyderabad, 500072, India; 3Labrynthe Pvt. Ltd., New Delhi, India; 4NIIT University, NH8, Delhi- Jaipur Highway, District Alwar, Neemrana, Rajasthan 301705, India; 5Hopp Children's Cancer Center [KiTZ], Heidelberg, Germany; 6Division of Pediatric Neuro Oncology, German Cancer Research Center [DKFZ], German Cancer Consortium [DKTK], Heidelberg, Germany; 7Heidelberg University, Medical Faculty, Heidelberg, Germany; 8Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur302021, RJ, India
| | - Tanu Agarwal
- 1Khoury College of Computer Sciences, Northeastern University, 360 Huntington Ave., Boston, MA02115, USA; 2Bioclues.org, Kukatpally, Hyderabad, 500072, India; 3Labrynthe Pvt. Ltd., New Delhi, India; 4NIIT University, NH8, Delhi- Jaipur Highway, District Alwar, Neemrana, Rajasthan 301705, India; 5Hopp Children's Cancer Center [KiTZ], Heidelberg, Germany; 6Division of Pediatric Neuro Oncology, German Cancer Research Center [DKFZ], German Cancer Consortium [DKTK], Heidelberg, Germany; 7Heidelberg University, Medical Faculty, Heidelberg, Germany; 8Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur302021, RJ, India
| | - Utkarsh Raj
- 1Khoury College of Computer Sciences, Northeastern University, 360 Huntington Ave., Boston, MA02115, USA; 2Bioclues.org, Kukatpally, Hyderabad, 500072, India; 3Labrynthe Pvt. Ltd., New Delhi, India; 4NIIT University, NH8, Delhi- Jaipur Highway, District Alwar, Neemrana, Rajasthan 301705, India; 5Hopp Children's Cancer Center [KiTZ], Heidelberg, Germany; 6Division of Pediatric Neuro Oncology, German Cancer Research Center [DKFZ], German Cancer Consortium [DKTK], Heidelberg, Germany; 7Heidelberg University, Medical Faculty, Heidelberg, Germany; 8Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur302021, RJ, India
| | - Vijayaraghava Seshadri Sundararajan
- 1Khoury College of Computer Sciences, Northeastern University, 360 Huntington Ave., Boston, MA02115, USA; 2Bioclues.org, Kukatpally, Hyderabad, 500072, India; 3Labrynthe Pvt. Ltd., New Delhi, India; 4NIIT University, NH8, Delhi- Jaipur Highway, District Alwar, Neemrana, Rajasthan 301705, India; 5Hopp Children's Cancer Center [KiTZ], Heidelberg, Germany; 6Division of Pediatric Neuro Oncology, German Cancer Research Center [DKFZ], German Cancer Consortium [DKTK], Heidelberg, Germany; 7Heidelberg University, Medical Faculty, Heidelberg, Germany; 8Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur302021, RJ, India
| | - Obul Reddy Bandapalli
- 1Khoury College of Computer Sciences, Northeastern University, 360 Huntington Ave., Boston, MA02115, USA; 2Bioclues.org, Kukatpally, Hyderabad, 500072, India; 3Labrynthe Pvt. Ltd., New Delhi, India; 4NIIT University, NH8, Delhi- Jaipur Highway, District Alwar, Neemrana, Rajasthan 301705, India; 5Hopp Children's Cancer Center [KiTZ], Heidelberg, Germany; 6Division of Pediatric Neuro Oncology, German Cancer Research Center [DKFZ], German Cancer Consortium [DKTK], Heidelberg, Germany; 7Heidelberg University, Medical Faculty, Heidelberg, Germany; 8Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur302021, RJ, India
| | - Prashanth Suravajhala
- 1Khoury College of Computer Sciences, Northeastern University, 360 Huntington Ave., Boston, MA02115, USA; 2Bioclues.org, Kukatpally, Hyderabad, 500072, India; 3Labrynthe Pvt. Ltd., New Delhi, India; 4NIIT University, NH8, Delhi- Jaipur Highway, District Alwar, Neemrana, Rajasthan 301705, India; 5Hopp Children's Cancer Center [KiTZ], Heidelberg, Germany; 6Division of Pediatric Neuro Oncology, German Cancer Research Center [DKFZ], German Cancer Consortium [DKTK], Heidelberg, Germany; 7Heidelberg University, Medical Faculty, Heidelberg, Germany; 8Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur302021, RJ, India
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Gupta A, Shukla N, Nehra M, Gupta S, Malik B, Mishra AK, Vijay M, Batra J, Lohiya NK, Sharma D, Suravajhala P. A Pilot Study on the Whole Exome Sequencing of Prostate Cancer in the Indian Phenotype Reveals Distinct Polymorphisms. Front Genet 2020; 11:874. [PMID: 33193569 PMCID: PMC7477354 DOI: 10.3389/fgene.2020.00874] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 03/20/2020] [Accepted: 07/16/2020] [Indexed: 12/18/2022] Open
Abstract
Prostate cancer (PCa) is the third most common cancer among men in India, and no next-generation sequencing (NGS) studies have been attempted earlier. Recent advances in NGS have heralded the discovery of biomarkers from Caucasian/European and Chinese ancestry, but not much is known about the Indian phenotype/variant of PCa. In a pilot study using the whole exome sequencing of benign/PCa patients, we identified characteristic mutations specific to the Indian sub-population. We observed a large number of mutations in DNA repair genes, viz. helicases, TP53, and BRCA besides the variants of unknown significance with a possibly damaging rare variant (rs730881069/chr19:55154172C/TR136Q) in the TNNI3 gene that has been previously reported as a semi-conservative amino acid substitution. Our pilot study attempts to bring an understanding of PCa prognosis and recurrence for the Indian phenotype.
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Affiliation(s)
- Ayam Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India.,Vignan's Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India.,Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
| | - Mamta Nehra
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Babita Malik
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
| | | | | | - Jyotsna Batra
- Australian Prostate Cancer Research Centre, Queensland Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, QLD, Australia
| | | | | | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
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48
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Singh KK, Chaubey G, Chen JY, Suravajhala P. Decoding SARS-CoV-2 hijacking of host mitochondria in COVID-19 pathogenesis. Am J Physiol Cell Physiol 2020; 319:C258-C267. [PMID: 32510973 PMCID: PMC7381712 DOI: 10.1152/ajpcell.00224.2020] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [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: 05/19/2020] [Revised: 06/03/2020] [Accepted: 06/06/2020] [Indexed: 12/21/2022]
Abstract
Because of the ongoing pandemic around the world, the mechanisms underlying the SARS-CoV-2-induced COVID-19 are subject to intense investigation. Based on available data for the SARS-CoV-1 virus, we suggest how CoV-2 localization of RNA transcripts in mitochondria hijacks the host cell's mitochondrial function to viral advantage. Besides viral RNA transcripts, RNA also localizes to mitochondria. SARS-CoV-2 may manipulate mitochondrial function indirectly, first by ACE2 regulation of mitochondrial function, and once it enters the host cell, open-reading frames (ORFs) such as ORF-9b can directly manipulate mitochondrial function to evade host cell immunity and facilitate virus replication and COVID-19 disease. Manipulations of host mitochondria by viral ORFs can release mitochondrial DNA (mtDNA) in the cytoplasm and activate mtDNA-induced inflammasome and suppress innate and adaptive immunity. We argue that a decline in ACE2 function in aged individuals, coupled with the age-associated decline in mitochondrial functions resulting in chronic metabolic disorders like diabetes or cancer, may make the host more vulnerable to infection and health complications to mortality. These observations suggest that distinct localization of viral RNA and proteins in mitochondria must play essential roles in SARS-CoV-2 pathogenesis. Understanding the mechanisms underlying virus communication with host mitochondria may provide critical insights into COVID-19 pathologies. An investigation into the SARS-CoV-2 hijacking of mitochondria should lead to novel approaches to prevent and treat COVID-19.
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Affiliation(s)
- Keshav K Singh
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Kaul Genetics Building, Birmingham, Alabama
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Jake Y Chen
- Department of Genetics, Computer Science, and Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research Statue Circle, Jaipur, Rajasthan, India
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49
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Abstract
Because of the ongoing pandemic around the world, the mechanisms underlying the SARS-CoV-2-induced COVID-19 are subject to intense investigation. Based on available data for the SARS-CoV-1 virus, we suggest how CoV-2 localization of RNA transcripts in mitochondria hijacks the host cell's mitochondrial function to viral advantage. Besides viral RNA transcripts, RNA also localizes to mitochondria. SARS-CoV-2 may manipulate mitochondrial function indirectly, first by ACE2 regulation of mitochondrial function, and once it enters the host cell, open-reading frames (ORFs) such as ORF-9b can directly manipulate mitochondrial function to evade host cell immunity and facilitate virus replication and COVID-19 disease. Manipulations of host mitochondria by viral ORFs can release mitochondrial DNA (mtDNA) in the cytoplasm and activate mtDNA-induced inflammasome and suppress innate and adaptive immunity. We argue that a decline in ACE2 function in aged individuals, coupled with the age-associated decline in mitochondrial functions resulting in chronic metabolic disorders like diabetes or cancer, may make the host more vulnerable to infection and health complications to mortality. These observations suggest that distinct localization of viral RNA and proteins in mitochondria must play essential roles in SARS-CoV-2 pathogenesis. Understanding the mechanisms underlying virus communication with host mitochondria may provide critical insights into COVID-19 pathologies. An investigation into the SARS-CoV-2 hijacking of mitochondria should lead to novel approaches to prevent and treat COVID-19.
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Affiliation(s)
- Keshav K Singh
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Kaul Genetics Building, Birmingham, Alabama
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Jake Y Chen
- Department of Genetics, Computer Science, and Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research Statue Circle, Jaipur, Rajasthan, India
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50
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Shukla N, Siva N, Malik B, Suravajhala P. Current Challenges and Implications of Proteogenomic Approaches in Prostate Cancer. Curr Top Med Chem 2020; 20:1968-1980. [PMID: 32703135 DOI: 10.2174/1568026620666200722112450] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/30/2020] [Accepted: 06/29/2020] [Indexed: 12/16/2022]
Abstract
In the recent past, next-generation sequencing (NGS) approaches have heralded the omics era. With NGS data burgeoning, there arose a need to disseminate the omic data better. Proteogenomics has been vividly used for characterising the functions of candidate genes and is applied in ascertaining various diseased phenotypes, including cancers. However, not much is known about the role and application of proteogenomics, especially Prostate Cancer (PCa). In this review, we outline the need for proteogenomic approaches, their applications and their role in PCa.
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Affiliation(s)
- Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur 302001, RJ, India.,Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
| | - Narmadhaa Siva
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur 302001, RJ, India
| | - Babita Malik
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur 302001, RJ, India
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