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Sheth H, Nair A, Bhavsar R, Kamate M, Gowda VK, Bavdekar A, Kadam S, Nampoothiri S, Panigrahi I, Kaur A, Shah S, Mehta S, Jagadeesan S, Suresh I, Kapoor S, Bajaj S, Devi RR, Prajapati A, Godbole K, Patel H, Luhar Z, Shah RC, Iyer A, Bijarnia S, Puri R, Muranjan M, Shah A, Magar S, Gupta N, Tayade N, Gandhi A, Sowani A, Kale S, Jalan A, Solanki D, Dalal A, Mane S, Prabha CR, Sheth F, Joshi CG, Joshi M, Sheth J. Development, validation and application of single molecule molecular inversion probe based novel integrated genetic screening method for 29 common lysosomal storage disorders in India. Hum Genomics 2024; 18:46. [PMID: 38730490 PMCID: PMC11088154 DOI: 10.1186/s40246-024-00613-9] [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: 03/05/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Current clinical diagnosis pathway for lysosomal storage disorders (LSDs) involves sequential biochemical enzymatic tests followed by DNA sequencing, which is iterative, has low diagnostic yield and is costly due to overlapping clinical presentations. Here, we describe a novel low-cost and high-throughput sequencing assay using single-molecule molecular inversion probes (smMIPs) to screen for causative single nucleotide variants (SNVs) and copy number variants (CNVs) in genes associated with 29 common LSDs in India. RESULTS 903 smMIPs were designed to target exon and exon-intron boundaries of targeted genes (n = 23; 53.7 kb of the human genome) and were equimolarly pooled to create a sequencing library. After extensive validation in a cohort of 50 patients, we screened 300 patients with either biochemical diagnosis (n = 187) or clinical suspicion (n = 113) of LSDs. A diagnostic yield of 83.4% was observed in patients with prior biochemical diagnosis of LSD. Furthermore, diagnostic yield of 73.9% (n = 54/73) was observed in patients with high clinical suspicion of LSD in contrast with 2.4% (n = 1/40) in patients with low clinical suspicion of LSD. In addition to detecting SNVs, the assay could detect single and multi-exon copy number variants with high confidence. Critically, Niemann-Pick disease type C and neuronal ceroid lipofuscinosis-6 diseases for which biochemical testing is unavailable, could be diagnosed using our assay. Lastly, we observed a non-inferior performance of the assay in DNA extracted from dried blood spots in comparison with whole blood. CONCLUSION We developed a flexible and scalable assay to reliably detect genetic causes of 29 common LSDs in India. The assay consolidates the detection of multiple variant types in multiple sample types while having improved diagnostic yield at same or lower cost compared to current clinical paradigm.
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Affiliation(s)
- Harsh Sheth
- FRIGE Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, India, 380015.
| | - Aadhira Nair
- FRIGE Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, India, 380015
| | - Riddhi Bhavsar
- FRIGE Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, India, 380015
| | - Mahesh Kamate
- KLES Prabhakar Kore Hospital, Belgaum, Karnataka, India
| | - Vykuntaraju K Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | | | - Sandeep Kadam
- Department of Pediatrics, K.E.M Hospital, Pune, India
| | | | - Inusha Panigrahi
- Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Anupriya Kaur
- Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Siddharth Shah
- Royal Institute of Child Neurosciences, Vastrapur, Ahmedabad, India
| | - Sanjeev Mehta
- Royal Institute of Child Neurosciences, Vastrapur, Ahmedabad, India
| | - Sujatha Jagadeesan
- Department of Clinical Genetics and Genetic Counselling, Mediscan Systems, Chennai, India
| | - Indrani Suresh
- Department of Clinical Genetics and Genetic Counselling, Mediscan Systems, Chennai, India
| | - Seema Kapoor
- Division of Genetics and Metabolism Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Shruti Bajaj
- The Purple Gene Clinic, Simplex Khushaangan, SV Road, Malad West, Mumbai, India
| | | | | | - Koumudi Godbole
- Deenanath Mangeshkar Hospital &Amp; Research Centre, Pune, India
| | - Harsh Patel
- Zydus Hospital & Healthcare Research Pvt Ltd, Ahmedabad, India
| | | | - Raju C Shah
- Ankur Institute of Child Health, Ahmedabad, India
| | | | - Sunita Bijarnia
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Mamta Muranjan
- Department of Paediatrics, KEM Hospital, Parel, Mumbai, India
| | - Ami Shah
- BJ Wadia Hospital for Children, Parel, Mumbai, India
| | | | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Naresh Tayade
- Department of Pediatrics, Dr. Panjabrao Deshmukh Memorial Medical College, Amravati, India
| | | | - Ajit Sowani
- Zydus Hospital & Healthcare Research Pvt Ltd, Ahmedabad, India
| | - Shrutikaa Kale
- FRIGE Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, India, 380015
| | | | - Dhaval Solanki
- Mantra Child Neurology and Epilepsy Hospital, Bhavnagar, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Shrikant Mane
- Department of Genetics, Yale School of Medicine, Yale Center for Genome Analysis, West Haven, CT, USA
| | - C Ratna Prabha
- Department of Biochemistry, Faculty of Science, The M. S. University of Baroda, Vadodara, India
| | - Frenny Sheth
- FRIGE Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, India, 380015
| | | | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Jayesh Sheth
- FRIGE Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, India, 380015.
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Bhardwaj L, Kumar D, Singh UP, Joshi CG, Dubey SK. Herbicide application impacted soil microbial community composition and biochemical properties in a flooded rice field. Sci Total Environ 2024; 914:169911. [PMID: 38185156 DOI: 10.1016/j.scitotenv.2024.169911] [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] [Received: 10/08/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
Herbicide application is a common practice in intensive agriculture. However, accumulating herbicide residues in the ecosystem affects important soil attributes. The effect of two herbicides, pendimethalin and pretilachlor, on soil biochemical properties and microbial community composition was studied in a transplanted paddy field. Results reveal a gradual decline in herbicide residue up to 60 days after application. Changes in soil microbiological and biochemical properties (microbial biomass, enzymes, respiration, etc.) showed an inconsistent pattern across the treatments. Quantitative polymerase chain reaction analysis showed the archaeal, bacterial and fungal populations to be of higher order in control soil compared to the treated one. Amplicon sequencing (16S rRNA and ITS genes) exhibited that besides the unclassified genera, ammonia-oxidizing Crenarchaeota and the group represented by Candidatus Nitrososphaera were dominant in both the control and treated samples. Other archaeal genera viz. Methanosarcina and Bathyarchaeia showed a slight decrease in relative abundance of control (0.5 %) compared to the treated soil (0.7 %). Irrespective of treatments, the majority of bacterial genera comprised unclassified and uncultured species, accounting for >64-75 % in the control group and over 78.29 % in the treated samples. Members of Vicinamibacteraceae, Bacillus and Bryobacter were dominant in control samples. Dominant fungal genera belonging to unclassified groups comprised Curvularia, Aspergillus, and Emericellopsis in the control group, whereas Paraphysoderma and Emericellopsis in the herbicide-treated groups. Inconsistent response of soil properties and microbial community composition is evident from the present study, suggesting that the recommended dose of herbicides might not result in any significant change in microbial community composition. The findings of this investigation will help in the formulation of a framework for risk assessment and maintaining sustainable rice cultivation in herbicide- amended soils.
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Affiliation(s)
- Laliteshwari Bhardwaj
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre, Government of Gujarat, Gandhinagar, Gujarat 382011, India
| | - Udai P Singh
- Department of Agronomy, Institute of Agriculture Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre, Government of Gujarat, Gandhinagar, Gujarat 382011, India
| | - Suresh Kumar Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
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Shukla N, Harshini V, Raval I, Patel AK, Joshi CG. lncRNA-miRNA-mRNA network in kidney transcriptome of Labeo rohita under hypersaline environment. Sci Data 2024; 11:226. [PMID: 38388642 PMCID: PMC10883911 DOI: 10.1038/s41597-024-03056-y] [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: 09/26/2023] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
The present study describes the kidney transcriptome of Labeo rohita, a freshwater fish, exposed to gradually increased salinity concentrations (2, 4, 6 and 8ppt). A total of 10.25 Gbps data was generated, and a suite of bioinformatics tools, including FEELnc, CPC2 and BLASTn were employed for identification of long non-coding RNAs (lncRNAs) and micro RNAs (miRNAs). Our analysis revealed a total of 170, 118, 99, and 269 differentially expressed lncRNA and 120, 118, 99, and 124 differentially expressed miRNAs in 2, 4, 6 and 8 ppt treatment groups respectively. Two competing endogenous RNA (ceRNA) networks were constructed i.e. A* ceRNA network with up-regulated lncRNAs and mRNAs, down-regulated miRNAs; and B* ceRNA network vice versa. 2ppt group had 131 and 83 lncRNA-miRNA-mRNA pairs in A* and B* networks, respectively. 4ppt group featured 163 pairs in A* network and 191 in B* network, while the 6ppt had 103 and 105 pairs. 8ppt group included 192 and 174 pairs. These networks illuminate the intricate RNA interactions in freshwater fish to varying salinity conditions.
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Affiliation(s)
- Nitin Shukla
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, Gujarat, India
| | - Vemula Harshini
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, Gujarat, India
| | - Ishan Raval
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, Gujarat, India
| | - Amrutlal K Patel
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, Gujarat, India.
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, Gujarat, India.
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Maurya S, Arya CK, Parmar N, Sathyanarayanan N, Joshi CG, Ramanathan G. Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF. Arch Microbiol 2023; 206:6. [PMID: 38015256 DOI: 10.1007/s00203-023-03729-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P. DMF) that was isolated from a domestic wastewater treatment plant in Kanpur, India (26.4287 °N, 80.3891 °E) based on its ability to degrade a recalcitrant organic solvent N, N-dimethylformamide (DMF). The results reveal a genome size of 4,202,269 base pairs (bp) with a G + C content of 67.9%. The assembled genome comprises 4141 coding sequences (CDS), 46 RNA sequences, and 2 CRISPRs. Interestingly, catabolic operons related to the conventional marine-based methylated amines (MAs) degradation pathway were functionally annotated within the genome of an obligated aerobic heterotroph that is P. DMF. The genomic data-based characterization presented here for the novel heterotroph P. DMF aims to improve the understanding of the phenotypic gene products, enzymes, and pathways involved with greater emphasis on facultative methylotrophic motility-based latent pathogenicity.
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Affiliation(s)
- Shiwangi Maurya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Chetan Kumar Arya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Nidhi Parmar
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Nitish Sathyanarayanan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, 560065, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Gurunath Ramanathan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
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Jhala D, Nathani N, Joshi M, Patel A, Joshi CG. Oncolytic Activity of Canine Distemper Virus in Human Ductal Breast Carcinoma Cells. Oncol Res Treat 2023; 47:10-17. [PMID: 38008084 DOI: 10.1159/000535418] [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: 09/20/2023] [Accepted: 11/17/2023] [Indexed: 11/28/2023]
Abstract
INTRODUCTION Oncolytic virotherapy is a novel strategy for cancer treatment in humans and companion animals. Canine distemper virus (CDV) is known to induce apoptosis in tumor cells, thus serving as a potential candidate for oncolytic therapy. However, the mechanism of viral oncolytic activity is less studied and varies depending on the type of cancer and cell lines. METHODS In the present study, the susceptibility of the MCF-7 cell line to CDV infection was assessed using the CDV strain, which was confirmed previously through sequence analysis in the Vero cell line. The impact of CDV infection on cell proliferation and apoptosis was studied by evaluating the expression of four target genes including the myeloid cell leukemia 1 (MCL-1), phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1), transcription factor (SP1), and DNA (cytosine-5)-methyltransferase 3A (DNMT3A). RESULTS CDV replication in the cells induced cytopathic effect and decreased in the cell proliferation rates compared to the uninfected control. MCL-1, SP1, and PIK3R1 gene expression was down-regulated, while the expression of DNMT3A was up-regulated 3 days post-infection. The expression levels of the target genes suggest that CDV may be inducing the intrinsic apoptotic pathway in the cancer cell line. CONCLUSION Overall, the results strongly propose CDV strain as a potential candidate for cancer therapy after detailed studies.
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Affiliation(s)
- Dhwani Jhala
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India,
| | - Neelam Nathani
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
- School of Applied Sciences and Technology (SAST-GTU), Gujarat Technological University, Ahmedabad, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Amrutlal Patel
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
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Sangavi R, Muthumanickam S, Malligarjunan N, Jothi R, Boomi P, Arivudainambi S, Raman M, Joshi CG, Pandian SK, Gowrishankar S. In silico analysis unravels the promising anticariogenic efficacy of fatty acids against dental caries causing Streptococcus mutans. J Biomol Struct Dyn 2023:1-16. [PMID: 37993988 DOI: 10.1080/07391102.2023.2283155] [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: 04/02/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023]
Abstract
Globally, dental caries is a prevalent oral disease caused by cariogenic bacteria, primarily Streptococcus mutans. It establishes caries either through sucrose-dependent (via glycosyltransferases) or through sucrose-independent (via surface adhesins Antigen I/II) mechanism. Sortase A (srtA) attaches virulence-associated adhesins to host tissues. Because of their importance in the formation of caries, targeting these proteins is decisive in the development of new anticariogenic drugs. High-throughput virtual screening with LIPID MAPS -a fatty acid database was performed. The selected protein-ligand complexes were subjected to molecular dynamics simulation (MDs). The Binding Free Energy of complexes was predicted using MM/PBSA. Further, the drug-likeness and pharmacokinetic properties of ligands were also analyzed. Out of 46,200 FAs scrutinized virtually against the three protein targets (viz., GtfC, Ag I/II and srtA), top 5 FAs for each protein were identified as the best hit based on interaction energies viz., hydrogen bond numbers and hydrophobic interaction. Further, two common FAs (LMFA01050418 and LMFA01040045) that showed high binding affinity against Ag I/II and srtA were selected for MDs analysis. A 100ns MDs unveiled a stable conformation. Results of Rg signified that FAs does not induce significant structural & conformational changes. SASA indicated that the complexes maintain higher thermodynamic stability during MDs. The predicted binding free energy (MM/PBSA) of complexes elucidated their stable binding interaction. ADME analysis suggested the FAs are biologically feasible as therapeutic candidates. Overall, the presented in silico data is the first of its kind in delineating FAs as promising anticaries agents of future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravichellam Sangavi
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, India
| | - Sankar Muthumanickam
- Department of Bioinformatics, Science Campus, Alagappa University, Karaikudi, India
| | | | - Ravi Jothi
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, India
| | - Pandi Boomi
- Department of Bioinformatics, Science Campus, Alagappa University, Karaikudi, India
| | - Seenichamy Arivudainambi
- Department of Science & Technology, Gujarat Biotechnology Research Centre (GBRC), Government of Gujarat, Gandhinagar, India
| | - Muthusamy Raman
- Department of Microbiology, Centre for Infectious Diseases, Saveetha Dental University, Chennai, India
| | - Chaitanya G Joshi
- Department of Science & Technology, Gujarat Biotechnology Research Centre (GBRC), Government of Gujarat, Gandhinagar, India
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Dharajiya DT, Shukla N, Pandya M, Joshi M, Patel AK, Joshi CG. Resistant cumin cultivar, GC-4 counters Fusarium oxysporum f. sp. cumini infection through up-regulation of steroid biosynthesis, limonene and pinene degradation and butanoate metabolism pathways. Front Plant Sci 2023; 14:1204828. [PMID: 37915505 PMCID: PMC10616826 DOI: 10.3389/fpls.2023.1204828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/21/2023] [Indexed: 11/03/2023]
Abstract
Cumin (Cuminum cyminum L.), an important spice crop belonging to the Apiaceae family is infected by Fusarium oxysporum f. sp. cumini (Foc) to cause wilt disease, one of the most devastating diseases of cumin adversely affects its production. As immune responses of cumin plants against the infection of Foc are not well studied, this research aimed to identify the genes and pathways involved in responses of cumin (cv. GC-2, GC-3, GC-4, and GC-5) to the wilt pathogen. Differential gene expression analysis revealed a total of 2048, 1576, 1987, and 1174 differentially expressed genes (DEGs) in GC-2, GC-3, GC-4, and GC-5, respectively. In the resistant cultivar GC-4 (resistant against Foc), several important transcripts were identified. These included receptors, transcription factors, reactive oxygen species (ROS) generating and scavenging enzymes, non-enzymatic compounds, calcium ion (Ca2+) transporters and receptors, R-proteins, and PR-proteins. The expression of these genes is believed to play crucial roles in conferring resistance against Foc. Gene ontology (GO) analysis of the up-regulated DEGs showed significant enrichment of 19, 91, 227, and 55 biological processes in GC-2, GC-3, GC-4, and GC-5, respectively. Notably, the resistant cultivar GC-4 exhibited enrichment in key GO terms such as 'secondary metabolic process', 'response to reactive oxygen species', 'phenylpropanoid metabolic process', and 'hormone-mediated signaling pathway'. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the enrichment of 28, 57, 65, and 30 pathways in GC-2, GC-3, GC-4, and GC-5, respectively, focusing on the up-regulated DEGs. The cultivar GC-4 showed enrichment in pathways related to steroid biosynthesis, starch and sucrose metabolism, fatty acid biosynthesis, butanoate metabolism, limonene and pinene degradation, and carotenoid biosynthesis. The activation or up-regulation of various genes and pathways associated with stress resistance demonstrated that the resistant cultivar GC-4 displayed enhanced defense mechanisms against Foc. These findings provide valuable insights into the defense responses of cumin that could contribute to the development of cumin cultivars with improved resistance against Foc.
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Affiliation(s)
| | | | | | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, Gujarat, India
| | - Amrutlal K. Patel
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, Gujarat, India
| | - Chaitanya G. Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, Gujarat, India
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Shukla N, Vemula H, Raval I, Kumar S, Shrivastava V, Chaudhari A, Patel AK, Joshi CG. Integrative miRNA-mRNA network analysis to identify crucial pathways of salinity adaptation in brain transcriptome of Labeo rohita. Front Genet 2023; 14:1209843. [PMID: 37719712 PMCID: PMC10500595 DOI: 10.3389/fgene.2023.1209843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/17/2023] [Indexed: 09/19/2023] Open
Abstract
Introduction: Brain being the master regulator of the physiology of animal, the current study focuses on the gene expression pattern of the brain tissue with special emphasis on regulation of growth, developmental process of an organism and cellular adaptation of Labeo rohita against unfavourable environmental conditions. Methods: RNA-seq study was performed on collected brain samples at 8ppt salt concentration and analyzed for differential gene expression, functional annotation and miRNA-mRNA regulatory network. Results: We found that 2450 genes were having significant differential up and down regulation. The study identified 20 hub genes based on maximal clique centrality algorithm. These hub genes were mainly involved in various signaling pathways, energy metabolism and ion transportation. Further, 326 up and 1214 down regulated genes were found to be targeted by 7 differentially expressed miRNAs i.e., oni-miR-10712, oni-miR-10736, ssa-miR-221-3p, ssa-miR-130d-1-5p, ssa-miR-144-5p and oni-miR-10628. Gene ontology analysis of these differentially expressed genes led to the finding that these genes were involved in signal transduction i.e., calcium, FOXO, PI3K-AKT, TGF-β, Wnt and p53 signalling pathways. Differentially expressed genes were also involved in regulation of immune response, environmental adaptation i.e., neuroactive ligand-receptor interaction, ECM-receptor interaction, cell adhesion molecules and circadian entrainment, osmoregulation and energy metabolism, which are critical for salinity adaptation. Discussion: The findings of whole transcriptomic study on brain deciphered the miRNA-mRNA interaction patterns and pathways associated with salinity adaptation of L. rohita.
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Affiliation(s)
- Nitin Shukla
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Harshini Vemula
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Ishan Raval
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Sujit Kumar
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Gandhinagar, Gujarat, India
| | - Vivek Shrivastava
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Gandhinagar, Gujarat, India
| | - Aparna Chaudhari
- Central Institute of Fisheries Education, Mumbai, Maharashtra, India
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Harshini V, Shukla N, Raval I, Kumar S, Shrivastava V, Chaudhari A, Patel AK, Joshi CG. Interplay of gene expression and regulators under salinity stress in gill of Labeo rohita. BMC Genomics 2023; 24:336. [PMID: 37337199 DOI: 10.1186/s12864-023-09426-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Labeo rohita is the most preferred freshwater carp species in India. The concern of increasing salinity concentration in freshwater bodies due to climate change may greatly impact the aquatic environment. Gills are one of the important osmoregulatory organs and have direct contact with external environment. Hence, the current study is conducted to understand the gill transcriptomic response of L. rohita under hypersalinity environment. RESULTS Comprehensive analysis of differentially expressed long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and mRNAs was performed in gills of L. rohita treated with 2, 4, 6 and 8ppt salinity concentrations. Networks of lncRNA-miRNA-mRNA revealed involvement of 20, 33, 52 and 61 differentially expressed lncRNAs, 11, 13, 26 and 21 differentially expressed miRNAs in 2, 4, 6 and 8ppt groups between control and treatment respectively. These lncRNA-miRNA pairs were regulating 87, 214, 499 and 435 differentially expressed mRNAs (DE mRNAs) in 2, 4, 6 and 8ppt treatments respectively. Functional analysis of these genes showed enrichment in pathways related to ion transportation and osmolyte production to cope with induced osmotic pressure due to high salt concentration. Pathways related to signal transduction (MAPK, FOXO and phosphatidylinositol signaling), and environmental information processing were also upregulated under hypersalinity. Energy metabolism and innate immune response pathways also appear to be regulated. Protein turnover was high at 8ppt as evidenced by enrichment of the proteasome and aminoacyl tRNA synthesis pathways, along with other enriched KEGG terms such as apoptosis, cellular senescence and cell cycle. CONCLUSION Altogether, the RNA-seq analysis provided valuable insights into competitive endogenous (lncRNA-miRNA-mRNA) regulatory network of L. rohita under salinity stress. L. rohita is adapting to the salinity stress by means of upregulating protein turnover, osmolyte production and removing the damaged cells using apoptotic pathway and regulating the cell growth and hence diverting the essential energy for coping with salinity stress.
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Affiliation(s)
- Vemula Harshini
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, 382010, Gujarat, India
| | - Nitin Shukla
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, 382010, Gujarat, India
| | - Ishan Raval
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, 382010, Gujarat, India
| | - Sujit Kumar
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Himmatnagar, 383010, Gujarat, India
| | - Vivek Shrivastava
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Himmatnagar, 383010, Gujarat, India
| | - Aparna Chaudhari
- Central Institute of Fisheries Education, Mumbai, 400061, Maharashtra, India
| | - Amrutlal K Patel
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, 382010, Gujarat, India.
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, 382010, Gujarat, India.
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10
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Tripathi A, Kumar D, Chavda P, Rathore DS, Pandit R, Blake D, Tomley F, Joshi M, Joshi CG, Dubey SK. Resistome profiling reveals transmission dynamics of antimicrobial resistance genes from poultry litter to soil and plant. Environ Pollut 2023; 327:121517. [PMID: 36990341 DOI: 10.1016/j.envpol.2023.121517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/26/2023] [Accepted: 03/25/2023] [Indexed: 06/19/2023]
Abstract
Poultry farming is a major livelihood in South and Southeast Asian economies where it is undergoing rapid intensification to meet the growing human demand for dietary protein. Intensification of poultry production systems is commonly supported by increased antimicrobial drug use, risking greater selection and dissemination of antimicrobial resistance genes (ARGs). Transmission of ARGs through food chains is an emerging threat. Here, we investigated transmission of ARGs from chicken (broiler and layer) litter to soil and Sorghum bicolor (L.) Moench plants based on field and pot experiments. The results demonstrate ARGs transmission from poultry litter to plant systems under field as well as experimental pot conditions. The most common ARGs could be tracked for transmission from litter to soil to plants were identified as detected were cmx, ErmX, ErmF, lnuB, TEM-98 and TEM-99, while common microorganisms included Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Pseudomonas aeruginosa, and Vibrio cholerae. Using next generation sequencing and digital PCR assays we detected ARGs transmitted from poultry litter in both the roots and stems of S. bicolor (L.) Moench plants. Poultry litter is frequently used as a fertiliser because of its high nitrogen content; our studies show that ARGs can transmit from litter to plants and illustrates the risks posed to the environment by antimicrobial treatment of poultry. This knowledge is useful for formulating intervention strategies that can reduce or prevent ARGs transmission from one value chain to another, improving understanding of impacts on human and environmental health. The research outcome will help in further understanding the transmission and risks posed by ARGs from poultry to environmental and human/animal health.
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Affiliation(s)
- Animesh Tripathi
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Priyank Chavda
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Dalip Singh Rathore
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Damer Blake
- Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, UK
| | - Fiona Tomley
- Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, UK
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Suresh Kumar Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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11
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Gohil P, Nanavati B, Patel K, Suthar V, Joshi M, Patil DB, Joshi CG. Assessing the efficacy of probiotics in augmenting bovine reproductive health: an integrated in vitro, in silico, and in vivo study. Front Microbiol 2023; 14:1137611. [PMID: 37275132 PMCID: PMC10232901 DOI: 10.3389/fmicb.2023.1137611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
The aim of this study was to isolate and characterize bovine-vaginal probiotics genotypically and phenotypically using in silico and evaluate their in vivo performance in buffaloes with endometritis. For the in vitro isolation and characterization, vaginal swabs were collected from 34 cows and 17 buffaloes, and 709 primary bacterial isolates with probiotic activity were obtained using MRS agar media. Two isolates Lactiplantibacillus plantarum KUGBRC (LPKUGBRC) and Pediococcus pentosaceus GBRCKU (PPGBRCKU) demonstrated optimum in vitro probiotic activities as compared to Lacticaseibacillus rhamnosus GG including, acid production, secretion of fatty acids and exopolysaccharide, cell surface hydrophobicity, self-aggregating and co-aggregating capacity with pathogens, anti-microbial activity and bacteriocin-like compounds against pathogens Escherichia coli and Staphylococcus aureus in cell-free supernatant and absence of hemolytic activity. Their phenotypic capacity was confirmed by analyzing the whole genome sequencing data and identifying genes and pathways associated with probiotic properties. These probiotic isolates have shown no virulence genes were discovered in their genomic study. In vivo study of 92 buffaloes suffering from clinical endometritis with purulent cervico-vaginal mucus (CVM) were randomly allocated 40 × 108 CFU/ml LPKUGBRC and PPGBRCKU and 40 ml Normal saline. The LPKUGBRC reduced the duration between administration of probiotic to induction of healthy estrus significantly. However, no effect was observed on pregnancy rate. These results suggest that LPKUGBRC and PPGBRCKU probiotic bacteria demonstrate probiotic efficiency and adaptability. Further sourced from the same niche as the targeted infection, they offer a distinct advantage in targeting the specific microbial population associated with endometritis. The findings of this study highlight the potential of LPKUGBRC and PPGBRCKU probiotics in treating endometritis and suggest further exploration of their clinical applications.
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Affiliation(s)
- Purva Gohil
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Bhavya Nanavati
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Kajal Patel
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Vishal Suthar
- Directorate of Research, Kamdhenu University, Gandhinagar, Gujarat, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Deepak B. Patil
- Directorate of Research, Kamdhenu University, Gandhinagar, Gujarat, India
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12
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Kushwaha B, Nagpure NS, Srivastava S, Pandey M, Kumar R, Raizada S, Agarwal S, Singh M, Basheer VS, Kumar RG, Das P, Das SP, Patnaik S, Bit A, Srivastava SK, Vishwakarma AL, Joshi CG, Kumar D, Jena JK. Genome size estimation and its associations with body length, chromosome number and evolution in teleost fishes. Gene 2023; 864:147294. [PMID: 36858189 DOI: 10.1016/j.gene.2023.147294] [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: 09/29/2022] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 03/02/2023]
Abstract
Precise estimation of genome size (GS) is vital for various genomic studies, such as deciding genome sequencing depth, genome assembly, biodiversity documentation, evolution, genetic disorders studies, duplication events etc. Animal Genome Size Database provides GS of over 2050 fish species, which ranges from 0.35 pg in pufferfish (Tetraodon nigroviridis) to 132.83 pg in marbled lungfish (Protopterus aethiopicus). The GS of majority of the fishes inhabiting waters of Indian subcontinent are still missing. In present study, we estimated GS of 51 freshwater teleost (31 commercially important, 7 vulnerable and 13 ornamental species) that ranged from 0.58 pg in banded gourami (Trichogaster fasciata) to 1.92 pg in scribbled goby (Awaous grammepomus). Substantial variation in GS was observed within the same fish orders (0.64-1.45 pg in cypriniformes, 0.70-1.41 pg in siluriformes and 0.58-1.92 pg in perciformes). We examined the relationship between the GS, chromosome number and body length across all the fishes. Body length was found to be associated with GS, whereas no relationship was noticed between the GS and the chromosome number. The analysis using ancestral information revealed haploid chromosome number 25, 27 and 24 for the most recent common ancestor of cypriniformes, siluriformes and perciformes, respectively. The study led to generation of new records on GS of 43 fish species and revalidated records for 8 species. The finding is valuable resource for further research in the areas of fish genomics, molecular ecology and evolutionary conservation genetics.
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Affiliation(s)
- Basdeo Kushwaha
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India.
| | - Naresh S Nagpure
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India
| | - Shreya Srivastava
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India
| | - Manmohan Pandey
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India
| | - Ravindra Kumar
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India.
| | - Sudhir Raizada
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India
| | - Suyash Agarwal
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India
| | - Mahender Singh
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India
| | - Valaparamail S Basheer
- PMFGR Division, ICAR-National Bureau of Fish Genetic Resources, CMFRI Campus, Ernakulam North, P.O. Kochi, 682 018 Kerala, India
| | - Rahul G Kumar
- PMFGR Division, ICAR-National Bureau of Fish Genetic Resources, CMFRI Campus, Ernakulam North, P.O. Kochi, 682 018 Kerala, India
| | - Paramananda Das
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyanga, Bhubaneswar, 751 002 Odisha, India
| | - Sofia P Das
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyanga, Bhubaneswar, 751 002 Odisha, India
| | - Siddhi Patnaik
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyanga, Bhubaneswar, 751 002 Odisha, India
| | - Amrita Bit
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyanga, Bhubaneswar, 751 002 Odisha, India
| | - Satish Kumar Srivastava
- Experimental Field Centre, ICAR-Directorate of Coldwater Fisheries Research, Champawat, 262 523 Uttarakhand, India
| | - Achchhe L Vishwakarma
- Flow Cytometry Lab, SAIF Division, CSIR-Central Drug Research Institute, Lucknow, 226 031 Uttar Pradesh, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat 388 001, India
| | - Dinesh Kumar
- Centre for Agricultural Bio-informatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110 012, India
| | - Joy K Jena
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India
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13
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Srivastava S, Bombaywala S, Jakhesara SJ, Patil NV, Joshi CG, Purohit HJ, Dafale NA. Potential of camel rumen derived Bacillus subtilis and Bacillus velezensis strains for application in plant biomass hydrolysis. Mol Genet Genomics 2023; 298:361-374. [PMID: 36575347 DOI: 10.1007/s00438-022-01987-y] [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: 03/22/2022] [Accepted: 12/18/2022] [Indexed: 12/29/2022]
Abstract
Rumen inhabiting Bacillus species possesses a high genetic potential for plant biomass hydrolysis and conversion to value-added products. In view of the same, five camel rumen-derived Bacillus strains, namely B. subtilis CRN 1, B. velezensis CRN 2, B. subtilis CRN 7, B. subtilis CRN 11, and B. velezensis CRN 23 were initially assayed for diverse hydrolytic activities, followed by genome mining to unravel the potential applications. CRN 1 and CRN 7 showed the highest endoglucanase activity with 0.4 U/ml, while CRN 23 showed high β-xylosidase activity of 0.36 U/ml. The comprehensive genomic insights of strains resolve taxonomic identity, clusters of an orthologous gene, pan-genome dynamics, and metabolic features. Annotation of Carbohydrate active enzymes (CAZymes) reveals the presence of diverse glycoside hydrolases (GH) GH1, GH5, GH43, and GH30, which are solely responsible for the effective breakdown of complex bonds in plant polysaccharides. Further, protein modeling and ligand docking of annotated endoglucanases showed an affinity for cellotrioside, cellobioside, and β-glucoside. The finding indicates the flexibility of Bacillus-derived endoglucanase activity on diverse cellulosic substrates. The presence of the butyrate synthesis gene in the CRN 1 strain depicts its key role in the production of important short-chain fatty acids essential for healthy rumen development. Similarly, antimicrobial peptides such as bacilysin and non-ribosomal peptides (NRPS) synthesized by the Bacillus strains were also annotated in the genome. The findings clearly define the role of Bacillus sp. inside the camel rumen and its potential application in various plant biomass utilizing industry and animal health research sectors.
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Affiliation(s)
- Shweta Srivastava
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sakina Bombaywala
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Niteen V Patil
- National Research Centre on Camel, Indian Council for Agriculture Research, Bikaner, 334001, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
| | - Nishant A Dafale
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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14
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Waghela BN, Pandit RJ, Puvar A, Shah FD, Patel PS, Vora H, Sheth H, Tarapara B, Pandya S, Joshi CG, Joshi MN. Identification of novel exonic variants contributing to hereditary breast and ovarian cancer in west Indian population. Gene 2023; 852:147070. [PMID: 36427680 DOI: 10.1016/j.gene.2022.147070] [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: 05/25/2022] [Revised: 10/21/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
Breast and ovarian cancers are the most common cancer types in females worldwide and in India. Patients with these cancers require an early diagnosis which is essential for better prognosis, treatment and improved patient survival. Recently, the utilization of next-generation sequencing (NGS)-based screening has accelerated molecular diagnosis of various cancers. In the present study, we performed whole-exome sequencing (WES) of 30 patients who had a first or second-degree relative with breast or ovarian cancer and are tested negative for BRCA1/2 or other high and moderate-risk genes reported for HBOC. WES data from patients were analyzed and variants were called using bcftools. Functional annotation of variants and variant prioritization was performed by Exomiser. The clinical significance of variants was determined as per ACMG classification using Varsome tool. The functional analysis of genes was determined by STRING analysis and disease association was determined by open target tool. We found novel variants and gene candidates having significant association with HBOC conditions. The genes identified by exomiser (phenotype score > 0.75) are associated with various biological processes such as DNA integrity maintenance, transcription regulation, cell cycle regulation, and apoptosis. Our findings provide novel and prevalent gene variants associated with the HBOC condition in the West Indian population which could be further studied for early diagnosis and better prognosis of HBOC.
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Affiliation(s)
- Bhargav N Waghela
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, Gujarat 382011, India
| | - Ramesh J Pandit
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, Gujarat 382011, India
| | - Apurvasinh Puvar
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, Gujarat 382011, India
| | - Franky D Shah
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, Gujarat 380016, India
| | - Prabhudas S Patel
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, Gujarat 380016, India
| | - Hemangini Vora
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, Gujarat 380016, India
| | - Harsh Sheth
- Frige House, Jodhpur Gam Rd, Satellite, Ahmedabad, Gujarat 380015, India
| | - Bhoomi Tarapara
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, Gujarat 380016, India
| | - Shashank Pandya
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, Gujarat 380016, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, Gujarat 382011, India
| | - Madhvi N Joshi
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, Gujarat 382011, India.
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15
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Italiya JM, Patel MR, Golaviya AV, Patel SS, Thakkar BK, Jakhesara SJ, Joshi CG, Koringa PG. RNA-sequencing attest increased sperm motility in bovine spermatozoa treated with ethanolic extract of Putranjiva roxburghii. 3 Biotech 2023; 13:33. [PMID: 36619823 PMCID: PMC9810775 DOI: 10.1007/s13205-022-03452-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/24/2022] [Indexed: 01/05/2023] Open
Abstract
In the course of time, scientific communities have a growing interest in understanding ethano medicines. The Putranjiva roxburghii, a native plant of the Indian Subcontinent is described as a "Child amulet tree" in Ayurveda. Based on the fact that this herbal medicine has an indispensable component of integrative medicine, the present study was planned to assess the effect of ethanolic dried extract of Putranjiva seeds on the motility of X and Y-bearing bovine spermatozoa. The in-vitro effect of seed extract diluted in S-TALP medium on bull semen has been evaluated by Computer Assisted Semen Analysis (CASA) shows a marked increase in the motility of spermatozoa. Motile and non-motile spermatozoa have been separated by glass wool column from the control as well as treated group. The X and Y-bearing sperm quantification have been carried out by droplet digital polymerase chain reaction (ddPCR). The extract didn't exert any differential effect on the motility and viability of X and Y chromosome-bearing spermatozoa. The transcriptome profiling (RNA-Seq) identified 93 differentially expressed genes between the extract treated and control group. It unveils the up-regulation of CATSPER, AKAP3, SPAG, ADAM1B, ADAM2 and ADAM32 genes that are involved in increasing sperm motility. Transcriptome profile also unveil the expression of ZAR1, CYP17A1, APPL2, HOXB4 and SP9 genes involved with embryonic development processes in Putranjiva extract-treated motile spermatozoa. The results envisaged the medicinal value of Putranjiva herb on increased fertility due to combinatory effect like increased sperm motility and favourableness on embryogenesis. The study ruled out the possibility of herbs having any biased effect on the selection of either male or female-bearing spermatozoa in the bull. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03452-4.
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Affiliation(s)
- Jignesh M. Italiya
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat India
- Centre for Infectious Animal Diseases, Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Mayank R. Patel
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat India
| | - Akash V. Golaviya
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat India
| | - Shiven S. Patel
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat India
| | - Bhumi K. Thakkar
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat India
| | - Subhash J. Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat India
| | - Chaitanya G. Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat 382010 India
| | - Prakash G. Koringa
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat India
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16
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Khatoon M, Jakhesara SJ, Rank DN, Joshi CG, Kunjadiya AP. Exploration of rumen microbial and carbohydrate-active enzyme profiles in cattle fed coir a lignin-rich diet using a metagenomic approach. Gene 2022; 846:146868. [PMID: 36075329 DOI: 10.1016/j.gene.2022.146868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/26/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
Lignocellulosic biomass is a rich source of feed for cattle. Amongst them, coconut coir may be the potential source of feed supplements. To assess, the effect of various concentrations of coconut coir (0 %, 21 % and 40 %) as a feed supplement on the rumen microbiome of cattle (Kankrej breed), a metagenomic (16S rRNA gene amplicon and shotgun sequencing) study was performed. The Alpha diversity estimation from the amplicon study suggested that the group of cattle fed food without the coconut coir has a higher number of genera than the cattle fed with mixed ration. Within the liquid fraction, bacterial phyla Bacteroidetes were abundant followed by Firmicutes and Fibrobacteres, whereas the proportion of Tenericutes, TM7, SRI, Verrucomicrobia, Lentisphaerae, and Elusimicrobia had decreased with the rise in the coir concentration. While within the solid fractions, the proportion of Elusimicrobia increased, but the count of Bacteriodetes, Firmicutes, Fibrobacteres Tenericutes, TM7, SRI, Verrucomicrobia, and Lentisphaerae decreased with an increase in coir percentages. The results obtained from shotgun sequencing show similar results for bacterial diversity. The functions associated with carbohydrate metabolism were abundant in both the treatments as compared to the control. Functions related to glycoside hydrolases, glycosyltransferases and carbohydrate-binding modules were abundant in both the treatments as compared to control. Thus, the study indicates that the microbiome does alter after feeding coir as a supplement and may be used as feed for cattle.
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Affiliation(s)
- Munni Khatoon
- Department of Applied and Interdisciplinary Sciences, Sardar Patel University, Anand 388120, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388110, Gujarat, India
| | - D N Rank
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388110, Gujarat, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Center, Gandhinagar 382001, Gujarat, India
| | - Anju P Kunjadiya
- Department of Applied and Interdisciplinary Sciences, Sardar Patel University, Anand 388120, Gujarat, India.
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17
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Kumar D, Pandit R, Sharma S, Raval J, Patel Z, Joshi M, Joshi CG. Nasopharyngeal microbiome of COVID-19 patients revealed a distinct bacterial profile in deceased and recovered individuals. Microb Pathog 2022; 173:105829. [PMID: 36252893 PMCID: PMC9568276 DOI: 10.1016/j.micpath.2022.105829] [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: 08/11/2022] [Revised: 09/20/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
The bacterial co-infections in SARS-CoV-2 patients remained the least explored subject of clinical manifestations that may also determine the disease severity. Nasopharyngeal microbial community structure within SARS-CoV-2 infected patients could reveal interesting microbiome dynamics that may influence the disease outcomes. Here, in this research study, we analyzed distinct nasopharyngeal microbiome profile in the deceased (n = 48) and recovered (n = 29) COVID-19 patients and compared it with control SARS-CoV-2 negative individuals (control) (n = 33). The nasal microbiome composition of the three groups varies significantly (PERMANOVA, p-value <0.001), where deceased patients showed higher species richness compared to the recovered and control groups. Pathogenic genera, including Corynebacterium (LDA score 5.51), Staphylococcus, Serratia, Klebsiella and their corresponding species were determined as biomarkers (p-value <0.05, LDA cutoff 4.0) in the deceased COVID-19 patients. Ochrobactrum (LDA score 5.79), and Burkholderia (LDA 5.29), were found in the recovered group which harbors ordinal bacteria (p-value <0.05, LDA-4.0) as biomarkers. Similarly, Pseudomonas (LDA score 6.19), and several healthy nasal cavity commensals including Veillonella, and Porphyromonas, were biomarkers for the control individuals. Healthy commensal bacteria may trigger the immune response and alter the viral infection susceptibility and thus, may play important role and possible recovery that needs to be further explored. This research finding provide vital information and have significant implications for understanding the microbial diversity of COVID-19 patients. However, additional studies are needed to address the microbiome-based therapeutics and diagnostics interventions.
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Affiliation(s)
- Dinesh Kumar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, 6th Floor, MS Building, Gandhinagar, 382011, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, 6th Floor, MS Building, Gandhinagar, 382011, India
| | - Sonal Sharma
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, 6th Floor, MS Building, Gandhinagar, 382011, India
| | - Janvi Raval
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, 6th Floor, MS Building, Gandhinagar, 382011, India
| | - Zarna Patel
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, 6th Floor, MS Building, Gandhinagar, 382011, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, 6th Floor, MS Building, Gandhinagar, 382011, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, 6th Floor, MS Building, Gandhinagar, 382011, India.
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18
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Kumar D, Antiya SP, Patel SS, Pandit R, Joshi M, Mishra AK, Joshi CG, Patel AC. Surveillance and Molecular Characterization of SARS-CoV-2 Infection in Non-Human Hosts in Gujarat, India. Int J Environ Res Public Health 2022; 19:14391. [PMID: 36361271 PMCID: PMC9657030 DOI: 10.3390/ijerph192114391] [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] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/26/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Since December 2019, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been spreading worldwide, triggering one of the most challenging pandemics in the human population. In light of the reporting of this virus in domestic and wild animals from several parts of the world, a systematic surveillance study was conceptualized to detect SARS-CoV-2 among species of veterinary importance. Nasal and/or rectal samples of 413 animals (dogs n= 195, cattle n = 64, horses n = 42, goats n = 41, buffaloes n = 39, sheep n = 19, cats n = 6, camels n = 6, and a monkey n = 1) were collected from different places in the Gujarat state of India. RNA was extracted from the samples and subjected to RT-qPCR-based quantification of the target sequences in viral nucleoprotein (N), spike (S), and ORF1ab genes. A total of 95 (23.79%) animals were found positive, comprised of n = 67 (34.35%) dogs, n= 15 (23.43%) cattle, and n = 13 (33.33%) buffaloes. Whole SARS-CoV-2 genome sequencing was done from one sample (ID-A4N, from a dog), where 32 mutations, including 29 single-nucleotide variations (SNV) and 2 deletions, were detected. Among them, nine mutations were located in the receptor binding domain of the spike (S) protein. The consequent changes in the amino acid sequence revealed T19R, G142D, E156-, F157-, A222V, L452R, T478K, D614G, and P681R mutations in the S protein and D63G, R203M, and D377Y in the N protein. The lineage assigned to this SARS-CoV-2 sequence is B.1.617.2. Thus, the present study highlights the transmission of SARS-CoV-2 infection from human to animals and suggests being watchful for zoonosis.
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Affiliation(s)
- Dinesh Kumar
- Gujarat Biotechnology Research Centre (GBRC), Sector-11, Gandhinagar 382011, Gujarat, India
| | - Sejalben P. Antiya
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Campus, Kamdhenu University, Gandhinagar 382010, Gujarat, India
| | - Sandipkumar S. Patel
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Campus, Kamdhenu University, Gandhinagar 382010, Gujarat, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Sector-11, Gandhinagar 382011, Gujarat, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Sector-11, Gandhinagar 382011, Gujarat, India
| | - Abhinava K. Mishra
- Molecular, Cellular and Developmental Biology Department, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Chaitanya G. Joshi
- Gujarat Biotechnology Research Centre (GBRC), Sector-11, Gandhinagar 382011, Gujarat, India
| | - Arunkumar C. Patel
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Campus, Kamdhenu University, Gandhinagar 382010, Gujarat, India
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Harshini V, Shukla N, Raval I, Kumar S, Shrivastava V, Patel AK, Joshi CG. Kidney transcriptome response to salinity adaptation in Labeo rohita. Front Physiol 2022; 13:991366. [PMID: 36311223 PMCID: PMC9606766 DOI: 10.3389/fphys.2022.991366] [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: 07/11/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
The increasing salinization of freshwater resources, owing to global warming, has caused concern to freshwater aquaculturists. In this regard, the present study is aimed at economically important freshwater fish, L. rohita (rohu) adapting to varying degrees of salinity concentrations. The RNA-seq analysis of kidney tissue samples of L. rohita maintained at 2, 4, 6, and 8 ppt salinity was performed, and differentially expressed genes involved in various pathways were studied. A total of 755, 834, 738, and 716 transcripts were downregulated and 660, 926, 576, and 908 transcripts were up-regulated in 2, 4, 6, and 8 ppt salinity treatment groups, respectively, with reference to the control. Gene ontology enrichment analysis categorized the differentially expressed genes into 69, 154, 92, and 157 numbers of biological processes with the p value < 0.05 for 2, 4, 6, and 8 ppt salinity groups, respectively, based on gene functions. The present study found 26 differentially expressed solute carrier family genes involved in ion transportation and glucose transportation which play a significant role in osmoregulation. In addition, the upregulation of inositol-3-phosphate synthase 1A (INO1) enzyme indicated the role of osmolytes in salinity acclimatization of L. rohita. Apart from this, the study has also found a significant number of genes involved in the pathways related to salinity adaptation including energy metabolism, calcium ion regulation, immune response, structural reorganization, and apoptosis. The kidney transcriptome analysis elucidates a step forward in understanding the osmoregulatory process in L. rohita and their adaptation to salinity changes.
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Affiliation(s)
- Vemula Harshini
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Nitin Shukla
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Ishan Raval
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Sujit Kumar
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Himmatnagar, Gujarat, India
| | - Vivek Shrivastava
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Himmatnagar, Gujarat, India
| | - Amrutlal K. Patel
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
- *Correspondence: Amrutlal K. Patel, ; Chaitanya G. Joshi,
| | - Chaitanya G. Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
- *Correspondence: Amrutlal K. Patel, ; Chaitanya G. Joshi,
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20
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Joshi M, Kumar M, Srivastava V, Kumar D, Rathore DS, Pandit R, Graham DW, Joshi CG. Genetic sequencing detected the SARS-CoV-2 delta variant in wastewater a month prior to the first COVID-19 case in Ahmedabad (India). Environ Pollut 2022; 310:119757. [PMID: 35853573 PMCID: PMC9287018 DOI: 10.1016/j.envpol.2022.119757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/22/2022] [Accepted: 07/08/2022] [Indexed: 05/23/2023]
Abstract
Wastewater-based genomic surveillance can identify a huge majority of variants shed by the infected individuals within a population, which goes beyond genomic surveillance based on clinical samples (i.e., symptomatic patients only). We analyzed four samples to detect key mutations in the SARS-CoV-2 genome and track circulating variants in Ahmedabad during the first wave (Sep/Nov 2020) and before the second wave (in Feb 2021) of COVID-19 in India. The analysis identified a total of 34 mutations in the spike protein across samples categorized into 23 types. The spike protein mutations were linked to the VOC-21APR-02; B.1.617.2 lineage (Delta variant) with 57% frequency in wastewater samples of Feb 2021. The key spike protein mutations were T19R, L452R, T478K, D614G, & P681R and deletions at 22029 (6 bp), 28248 (6 bp), & 28271 (1 bp). Interestingly, these mutations were not seen in the samples from Sep/Nov 2020 but did appear before the massive second wave of COVID-19 cases, which in India started in early April 2021. In fact, genetic traces of the Delta variant were found in samples of early Feb 2021, more than a month before the first clinically confirmed case of this in March 2021 in Ahmedabad, Gujarat. The present work describes the circulating of SARS-CoV-2 variants in Ahmedabad and confirms the consequential value of wastewater surveillance for the early detection of variants of concerns (VOCs). Such monitoring must be included as a major component of future health protection systems.
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Affiliation(s)
- Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat, 382 011, India
| | - Manish Kumar
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat, 382 355, India; Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand, 248007, India.
| | - Vaibhav Srivastava
- Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand, 248007, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat, 382 011, India
| | - Dalip Singh Rathore
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat, 382 011, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat, 382 011, India
| | - David W Graham
- Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat, 382 011, India.
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21
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Jakhesara, Tulsani NJ, Hinsu AT, Jyotsana B, Dafale NA, Patil NV, Purohit HJ, Joshi CG. Genome analysis and CAZy repertoire of a novel fungus Aspergillus sydowii C6d with lignocellulolytic ability isolated from camel rumen. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.06.004] [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: 11/03/2022] Open
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22
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Khatoon M, Patel SH, Pandit RJ, Jakhesara SJ, Rank D, Joshi CG, Kunjadiya AP. Rumen and fecal microbial profiles in cattle fed high lignin diets using metagenome analysis. Anaerobe 2022; 73:102508. [DOI: 10.1016/j.anaerobe.2021.102508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 12/30/2022]
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23
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Patel KM, Bhatt AD, Shah K, Waghela BN, Pandit RJ, Sheth H, Joshi CG, Joshi MN. Molecular Diagnosis of Muscular Dystrophy Patients in Western Indian Population: A Comprehensive Mutation Analysis Using Amplicon Sequencing. Front Genet 2021; 12:770350. [PMID: 34925456 PMCID: PMC8679082 DOI: 10.3389/fgene.2021.770350] [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: 09/03/2021] [Accepted: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
Muscular Dystrophies (MDs) are a group of inherited diseases and heterogeneous in nature. To date, 40 different genes have been reported for the occurrence and/or progression of MDs. This study was conducted to demonstrate the application of next-generation sequencing (NGS) in developing a time-saving and cost-effective diagnostic method to detect single nucleotide variants (SNVs) and copy number variants (CNVs) in a single test. A total of 123 cases clinically suspected of MD were enrolled in this study. Amplicon panel-based diagnosis was carried out for 102 (DMD/BMD) cases and the results were further screened using multiplex ligation-dependent probe amplification (MLPA). Whilst in the case of LGMD (N = 19) and UMD (N = 2), only NGS panel-based analysis was carried out. We identified the large deletions in 74.50% (76/102) of the cases screened with query DMD or BMD. Further, the large deletion in CAPN3 gene (N = 3) and known SNV mutations (N = 4) were identified in LGMD patients. Together, the total diagnosis rate for this amplicon panel was 70.73% (87/123) which demonstrated the utility of panel-based diagnosis for high throughput, affordable, and time-saving diagnostic strategy. Collectively, present study demonstrates that the panel based NGS sequencing could be superior over to MLPA.
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Affiliation(s)
- Komal M Patel
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Arpan D Bhatt
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Krati Shah
- ONE-Centre for Rheumatology and Genetics, Vadodara, India
| | - Bhargav N Waghela
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Ramesh J Pandit
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Harsh Sheth
- Foundation for Research in Genetics and Endocrinology (FRIGE), Ahmedabad, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Madhvi N Joshi
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
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24
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Nimavat J, Mootapally C, Nathani NM, Dave D, Kher MN, Mahajan MS, Joshi CG, Bhatt VD. Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. Front Genet 2021; 12:764927. [PMID: 34858480 PMCID: PMC8632030 DOI: 10.3389/fgene.2021.764927] [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: 08/26/2021] [Accepted: 10/18/2021] [Indexed: 11/24/2022] Open
Abstract
Humankind has suffered many pandemics in history including measles, SARS, MERS, Ebola, and recently the novel Coronavirus disease caused by SARS-CoV-2. As of September 2021, it has affected over 200 million people and caused over 4 million deaths. India is the second most affected country in the world. Up to this date, more than 38 Lakh viral genomes have been submitted to public repositories like GISAID and NCBI to analyze the virus phylogeny and mutations. Here, we analyzed 2349 genome sequences of SARS-CoV-2 submitted in GISAID by a single institute pertaining to infections from the Gujarat state to know their variants and phylogenetic distributions with a major focus on the spike protein. More than 93% of the genomes had one or more mutations in the spike glycoprotein. The D614G variant in spike protein is reported to have a very high frequency of >95% globally followed by the L452R and P681R, thus getting significant attention. The antigenic propensity of a small peptide of 29 residues from 597 to 625 of the spike protein variants having D614 and G614 showed that G614 has a little higher antigenic propensity. Thus, the D614G is the cause for higher viral antigenicity, however, it has not been reported to be effective to be causing more deaths.
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Affiliation(s)
- Jay Nimavat
- Department of Pharmaceutical Sciences, Saurashtra University, Rajkot, India
| | - Chandrashekar Mootapally
- School of Applied Sciences and Technology (GTU-SAST), Gujarat Technological University, Ahmedabad, India
| | - Neelam M Nathani
- School of Applied Sciences and Technology (GTU-SAST), Gujarat Technological University, Ahmedabad, India
| | - Devyani Dave
- Department of Pharmaceutical Sciences, Saurashtra University, Rajkot, India
| | | | - Mayur S Mahajan
- Atal Incubation Centre, Gujarat Technological University, Ahmedabad, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Gandhinagar, India
| | - Vaibhav D Bhatt
- School of Applied Sciences and Technology (GTU-SAST), Gujarat Technological University, Ahmedabad, India.,Atal Incubation Centre, Gujarat Technological University, Ahmedabad, India
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25
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Thakor JM, Parmar G, Mistry KN, Gang S, Rank DN, Joshi CG. Mutational landscape of TRPC6, WT1, LMX1B, APOL1, PTPRO, PMM2, LAMB2 and WT1 genes associated with Steroid resistant nephrotic syndrome. Mol Biol Rep 2021; 48:7193-7201. [PMID: 34546508 DOI: 10.1007/s11033-021-06711-4] [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: 07/24/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Nephrotic syndrome appears as a group of symptoms like proteinuria, edema and hyperlipidemia. Identification of monogenic forms revealed the physiology and pathogenesis of the SRNS. METHODS AND RESULTS We performed Illumina panel sequencing of seven genes in 90 Indian patients to determine the role of these genetic mutations in nephrotic syndrome prognosis. Samtool was used for variants calling, and SnpEff and Snpsift did variants annotation. Clinical significance and variant classification were performed by the ClinVar database. In SSNS and SRNS patients, we found 0.78% pathogenic and 3.41% likely pathogenic mutations. Pathogenic mutations were found in LAMB2, LMX1B and WT1 genes, while likely pathogenic mutations were found in (6/13) LAMB2, (2/13) LMX1B, (2/13) TRPC6, (2/13) PTPRO and (1/13) PMM2 genes. Approximately 46% likely pathogenic mutations were contributed to the LAMB2 gene in SSNS and SRNS patients. We also detect 30 VUS (variants of uncertain significance), which were found (17/30) pathogenic and (13/30) likely pathogenic by different prediction tools. CONCLUSIONS Multigene panels were used for genetic screening of heterogeneous disorders like nephrotic syndrome in the Indian population. We found pathogenic, likely pathogenic and certain VUS, which were responsible for the pathogenesis of the disease. Therefore, mutational analysis of SSNS and SRNS is necessary to avoid adverse effects of corticosteroids, modify the intensity of immunosuppressing agents, and prevent the disease's progression.
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Affiliation(s)
- Jinal M Thakor
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, ADIT Campus, New Vallabh Vidyanagar, 388121, Anand, Gujarat, India
| | - Glory Parmar
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, ADIT Campus, New Vallabh Vidyanagar, 388121, Anand, Gujarat, India
| | - Kinnari N Mistry
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, ADIT Campus, New Vallabh Vidyanagar, 388121, Anand, Gujarat, India.
| | - Sishir Gang
- Muljibhai Patel Urological Hospital, Dr. V.V. Desai Road, Nadiad, 387001, Gujarat, India
| | - Dharamshibhai N Rank
- Department of Animal Breeding and Genetics, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, 388110, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, 388110, Gujarat, India
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26
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Tulsani NJ, Mishra P, Jakhesara SJ, Srivastava S, Jyotsana B, Dafale NA, Patil NV, Purohit HJ, Joshi CG. Isolation, purification and characterization of a novel esterase from camel rumen metagenome. Protein Expr Purif 2021; 187:105941. [PMID: 34273540 DOI: 10.1016/j.pep.2021.105941] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Bacterial esterases are gaining the importance in pharmaceuticals and agrochemical industries due to their excellent biocatalytic properties and a wide range of applications. In the present study, a novel gene encoding an esterase (designated as Est-CR) was identified from shotgun metagenomic sequencing data of camel rumen (Camelus dromedarius) liquor. The open reading frame consisted of 1,224bp, which showed 84.03% sequence identity to Bacteroidales bacterium, corresponding to a protein of 407 amino acids and has a catalytic domain belonging to an esterase. Est-CR belonged to family V with GLSMG domain. The purified enzyme with a molecular mass of 62.64 kDa was checked on SDS-PAGE, and its expression was confirmed by western blotting. The enzyme was active and stable over a broad range of temperature (35-65 °C), displayed the maximum activity at 50 °C and pH 7.0. Individually all metal ions inhibited the enzyme activity, while in combination, K2+, Ca2+, Mg2+ and Mn2+ metal ions enhanced the enzyme activity. The detergents strongly inhibited the activity, while EDTA (10 mM) increased the activity of the Est-CR enzyme. The enzyme showed specificity to short-chain substrates and displayed an optimum activity against butyrate ester. This novel enzyme might serve as a promising candidate to meet some harsh industrial processes enzymatic needs.
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Affiliation(s)
- Nilam J Tulsani
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Priyaranjan Mishra
- Department of Animal Genetic and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India.
| | - Shweta Srivastava
- Environmental Genomic Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020, India
| | - Basanti Jyotsana
- ICAR-National Research Centre on Camel (NRCC) Jorbeer, Bikaner, Rajasthan, 334001, India
| | - Nishant A Dafale
- Environmental Genomic Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020, India
| | - Niteen V Patil
- ICAR-Central Arid Zone Research Institute, Jodhpur, Rajasthan, 342003, India
| | - Hemant J Purohit
- Environmental Genomic Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India; Gujarat Biotechnology Research Canter, MS Building, Block B & D, 6th Floor, GH Road, Sector-11, Gandhinagar, Gujarat, 382001, India
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27
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Thakor PB, Hinsu AT, Bhatia DR, Shah TM, Nayee N, Sudhakar A, Rank DN, Joshi CG. High-throughput genotype-based population structure analysis of selected buffalo breeds. Transl Anim Sci 2021; 5:txab033. [PMID: 33981962 PMCID: PMC8103726 DOI: 10.1093/tas/txab033] [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: 06/15/2020] [Accepted: 05/01/2021] [Indexed: 11/29/2022] Open
Abstract
India is considered as the home tract of some of the best buffalo breeds. However, the genetic structure of the Indian river buffalo is poorly understood. Hence, there is a need to characterize the populations and understand the genetic structure of various buffalo breeds for selection and to design breeding strategies. In this study, we have analyzed genetic variability and population structure of seven buffalo breeds from their respective geographical regions using Axiom Buffalo Genotyping Array. Diversity, as measured by expected heterozygosity, ranged from 0.364 in Surti to 0.384 in Murrah breed, and pair-wise FST values revealed the lowest genetic distance between Murrah and Nili-Ravi (0.0022), while the highest between Surti and Pandharpuri (0.030). Principal component analysis and structure analysis unveiled the differentiation of Surti, Pandharpuri, and Jaffarabadi in first two principal components and at K = 4, respectively, while remaining breeds were grouped together as a separate single cluster and admixed. Murrah and Mehsana showed early linkage disequilibrium (LD) decay, while Surti breed showed late decay. In LD blocks to quantitative trait locis (QTLs) concordance analysis, 4.65% of concordance was observed with 873 LD blocks overlapped with 2,330 QTLs. Overall, total 4,090 markers were identified from all LD blocks for six types of traits. Results of this study indicated that these single-nucleotide polymorphism (SNP) markers could differentiate phenotypically distinct breeds like Surti, Pandharpuri, and Jaffarabadi but not others. So, there is a need to develop SNP chip based on SNP markers identified by sequence information of local breeds.
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Affiliation(s)
- Prakash B Thakor
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Ankit T Hinsu
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Dhruv R Bhatia
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Tejas M Shah
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Nilesh Nayee
- National Dairy Development Board, Anand 388001, India
| | - A Sudhakar
- National Dairy Development Board, Anand 388001, India
| | - Dharamshibhai N Rank
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India.,Gujarat Biotechnology Research Centre, Gandhinagar 382017, India
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28
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Kumar M, Joshi M, Patel AK, Joshi CG. Unravelling the early warning capability of wastewater surveillance for COVID-19: A temporal study on SARS-CoV-2 RNA detection and need for the escalation. Environ Res 2021; 196:110946. [PMID: 33662347 PMCID: PMC7921726 DOI: 10.1016/j.envres.2021.110946] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/02/2021] [Accepted: 02/25/2021] [Indexed: 05/04/2023]
Abstract
Wastewater-based Epidemiological (WBE) surveillance offers a promising approach to assess the pandemic situation covering pre-symptomatic and asymptomatic cases in highly populated area under limited clinical tests. In the present study, we analyzed SARS-CoV-2 RNA in the influent wastewater samples (n = 43) from four wastewater treatment plants (WWTPs) in Gandhinagar, India, during August 7th to September 30th, 2020. A total of 40 samples out of 43 were found positive i.e. having at least two genes of SARS-CoV-2. The average Ct values for S, N, and ORF 1 ab genes were 32.66, 33.03, and 33.95, respectively. Monthly variation depicted a substantial rise in the average copies of N (~120%) and ORF 1 ab (~38%) genes in the month of September as compared to August, while S-gene copies declined by 58% in September 2020. The SARS-CoV-2 genome concentration was higher in the month of September (~924.5 copies/L) than August (~897.5 copies/L), corresponding to a ~2.2-fold rise in the number of confirmed cases during the study period. Further, the percentage change in genome concentration level on a particular date was found in the lead of 1-2 weeks of time with respect to the official confirmed cases registered based on clinical tests on a temporal scale. The results profoundly unravel the potential of WBE surveillance to predict the fluctuation of COVID-19 cases to provide an early warning. Our study explicitly suggests that it is the need of hour that the wastewater surveillance must be included as an integral part of COVID-19 pandemic monitoring which can not only help the water authorities to identify the hotspots within a city but can provide up to 2 weeks of time lead for better tuning the management interventions.
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Affiliation(s)
- Manish Kumar
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat, 382 355, India; Kiran C Patel Centre for Sustainable Development, Indian Institute of Technology Gandhinagar, Gujarat, India.
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat, 382 011, India
| | - Arbind Kumar Patel
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat, 382 355, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat, 382 011, India
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Hinsu AT, Tulsani NJ, Panchal KJ, Pandit RJ, Jyotsana B, Dafale NA, Patil NV, Purohit HJ, Joshi CG, Jakhesara SJ. Characterizing rumen microbiota and CAZyme profile of Indian dromedary camel (Camelus dromedarius) in response to different roughages. Sci Rep 2021; 11:9400. [PMID: 33931716 PMCID: PMC8087840 DOI: 10.1038/s41598-021-88943-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 12/10/2020] [Accepted: 04/12/2021] [Indexed: 02/07/2023] Open
Abstract
In dromedary camels, which are pseudo-ruminants, rumen or C1 section of stomach is the main compartment involved in fiber degradation, as in true ruminants. However, as camels are adapted to the harsh and scarce grazing conditions of desert, their ruminal microbiota makes an interesting target of study. The present study was undertaken to generate the rumen microbial profile of Indian camel using 16S rRNA amplicon and shotgun metagenomics. The camels were fed three diets differing in the source of roughage. The comparative metagenomic analysis revealed greater proportions of significant differences between two fractions of rumen content followed by diet associated differences. Significant differences were also observed in the rumen microbiota collected at different time-points of the feeding trial. However, fraction related differences were more highlighted as compared to diet dependent changes in microbial profile from shotgun metagenomics data. Further, 16 genera were identified as part of the core rumen microbiome of Indian camels. Moreover, glycoside hydrolases were observed to be the most abundant among all Carbohydrate-Active enzymes and were dominated by GH2, GH3, GH13 and GH43. In all, this study describes the camel rumen microbiota under different dietary conditions with focus on taxonomic, functional, and Carbohydrate-Active enzymes profiles.
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Affiliation(s)
- Ankit T Hinsu
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India
| | - Nilam J Tulsani
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India
| | - Ketankumar J Panchal
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India
| | - Ramesh J Pandit
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India
| | | | - Nishant A Dafale
- ICAR-Central Arid Zone Research Institute, Jodhpur, 342003, India
| | - Niteen V Patil
- ICAR-National Research Centre On Camel, Bikaner, 334001, India.,ICAR-Central Arid Zone Research Institute, Jodhpur, 342003, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India.,Gujarat Biotechnology Research Centre, Gandhinagar, 382010, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India.
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Kumar M, Kuroda K, Patel AK, Patel N, Bhattacharya P, Joshi M, Joshi CG. Decay of SARS-CoV-2 RNA along the wastewater treatment outfitted with Upflow Anaerobic Sludge Blanket (UASB) system evaluated through two sample concentration techniques. Sci Total Environ 2021; 754:142329. [PMID: 33254951 PMCID: PMC7490623 DOI: 10.1016/j.scitotenv.2020.142329] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 05/18/2023]
Abstract
For the first time, we present, i) an account of decay in the genetic material loading of SARS-CoV-2 during Upflow Anaerobic Sludge Blanket (UASB) treatment of wastewater, and ii) comparative evaluation of polyethylene glycol (PEG), and ultrafiltration as virus concentration methods from wastewater for the quantification of SARS-CoV-2 genes. The objectives were achieved through tracking of SARS-CoV-2 genetic loadings i.e. ORF1ab, N and S protein genes on 8th and 27th May 2020 along the wastewater treatment plant (106000 m3 million liters per day) equipped with UASB system in Ahmedabad, India. PEG method performed better in removing materials inhibiting RT-qPCR for SARS-CoV-2 gene detection from the samples, as evident from constant and lower CT values of control (MS2). Using the PEG method, we found a reduction >1.3 log10 reduction in SARS-CoV-2 RNA abundance during UASB treatment, and the RNA was not detected at all in the final effluent. The study implies that i) conventional wastewater treatment systems is effective in SARS-CoV-2 RNA removal, and ii) UASB system significantly reduces SARS-CoV-2 genetic loadings. Finally, PEG method is recommended for better sensitivity and inhibition removal during SARS-CoV-2 RNA quantification in wastewater.
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Affiliation(s)
- Manish Kumar
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat 382 355, India; Kiran C Patel Centre for Sustainable Development, Indian Institute of Technology Gandhinagar, Gujarat, India.
| | - Keisuke Kuroda
- Department of Environmental and Civil Engineering, Toyama Prefectural University, Toyama, 9390398, Japan
| | - Arbind Kumar Patel
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat 382 355, India
| | - Nidhi Patel
- Gujarat Biotechnology Research Centre (GBRC), Sector-11, Gandhinagar, Gujarat 382 011, India
| | - Prosun Bhattacharya
- Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 42, SE-11428 Stockholm, Sweden
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Sector-11, Gandhinagar, Gujarat 382 011, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Sector-11, Gandhinagar, Gujarat 382 011, India
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Kadri MSN, Patel KM, Bhargava PA, Shah FD, Badgujar NV, Tarapara BV, Patel PS, Shaikh MI, Shah K, Patel A, Pandya S, Vora H, Joshi CG, Joshi MN. Mutational Landscape for Indian Hereditary Breast and Ovarian Cancer Cohort Suggests Need for Identifying Population Specific Genes and Biomarkers for Screening. Front Oncol 2021; 10:568786. [PMID: 33552952 PMCID: PMC7859489 DOI: 10.3389/fonc.2020.568786] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 06/24/2020] [Accepted: 12/02/2020] [Indexed: 12/29/2022] Open
Abstract
Background Breast and ovarian cancers are the most prevalent cancers and one of the leading causes of death in Indian women. The healthcare burden of breast and ovarian cancers and the rise in mortality rate are worrying and stress the need for early detection and treatment. Methods We performed amplicon sequencing of 144 cases who had breast/ovarian cancer disease (total 137 cases are patients and seven are tested for BRCA1/2 carrier) Using our custom designed gene panel consisting of 14 genes, that are associated with high to moderate risk of breast and ovarian cancers. Variants were called using Torrent Variant Caller and were annotated using ThermoFisher's Ion Reporter software. Classification of variants and their clinical significance were identified by searching the variants against ClinVar database. Results From a total of 144 cases, we were able to detect 42 pathogenic mutations in [40/144] cases. Majority of pathogenic mutations (30/41) were detected in BRCA1 gene, while (7/41) pathogenic mutations were detected in BRCA2 gene, whereas, (2/41) pathogenic mutations were detected in TP53 gene and BRIP1, PALB2, and ATM genes respectively. So, BRCA genes contributed 88.09% of pathogenic mutations, whereas non-BRCA genes contributed 11.91% of pathogenic mutations. We were also able to detect 25 VUS which were predicted to be damaging by in silico prediction tools. Conclusion Early detection of cancers in the Indian population can be done by genetic screening using customized multi-gene panels. Indications of our findings show that in the Indian population, apart from the common BRCA genes, there are other genes that are also responsible for the disease. High frequency mutations detected in the study and variants of uncertain significance predicted to be damaging by in silico pathogenicity prediction tools can be potential biomarkers of hereditary breast and ovarian cancer in Indian HBOC patients.
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Affiliation(s)
- Mohammed Shaad N Kadri
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Komal M Patel
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Poonam A Bhargava
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Franky D Shah
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, India
| | - Nutan V Badgujar
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, India
| | | | | | - Mohammed Inayatullah Shaikh
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Krati Shah
- Clinical Genetics, ONE-Centre for Rheumatology and Genetics, Vadodara, India
| | - Apurva Patel
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, India
| | - Shashank Pandya
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, India
| | - Hemangini Vora
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Madhvi N Joshi
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
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Kushwaha B, Pandey M, Das P, Joshi CG, Nagpure NS, Kumar R, Kumar D, Agarwal S, Srivastava S, Singh M, Sahoo L, Jayasankar P, Meher PK, Shah TM, Hinsu AT, Patel N, Koringa PG, Das SP, Patnaik S, Bit A, Iquebal MA, Jaiswal S, Jena J. The genome of walking catfish Clarias magur (Hamilton, 1822) unveils the genetic basis that may have facilitated the development of environmental and terrestrial adaptation systems in air-breathing catfishes. DNA Res 2021; 28:6070145. [PMID: 33416875 PMCID: PMC7934567 DOI: 10.1093/dnares/dsaa031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 08/14/2020] [Accepted: 12/21/2020] [Indexed: 11/14/2022] Open
Abstract
The walking catfish Clarias magur (Hamilton, 1822) (magur) is an important catfish species inhabiting the Indian subcontinent. It is considered as a highly nutritious food fish and has the capability to walk to some distance, and survive a considerable period without water. Assembly, scaffolding and several rounds of iterations resulted in 3,484 scaffolds covering ∼94% of estimated genome with 9.88 Mb largest scaffold, and N50 1.31 Mb. The genome possessed 23,748 predicted protein encoding genes with annotation of 19,279 orthologous genes. A total of 166 orthologous groups represented by 222 genes were found to be unique for this species. The Computational Analysis of gene Family Evolution (CAFE) analysis revealed expansion of 207 gene families and 100 gene families have rapidly evolved. Genes specific to important environmental and terrestrial adaptation, viz. urea cycle, vision, locomotion, olfactory and vomeronasal receptors, immune system, anti-microbial properties, mucus, thermoregulation, osmoregulation, air-breathing, detoxification, etc. were identified and critically analysed. The analysis clearly indicated that C. magur genome possessed several unique and duplicate genes similar to that of terrestrial or amphibians’ counterparts in comparison to other teleostean species. The genome information will be useful in conservation genetics, not only for this species but will also be very helpful in such studies in other catfishes.
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Affiliation(s)
- Basdeo Kushwaha
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Manmohan Pandey
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Naresh S Nagpure
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Ravindra Kumar
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Suyash Agarwal
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Shreya Srivastava
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Mahender Singh
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Pallipuram Jayasankar
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Prem K Meher
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Tejas M Shah
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Ankit T Hinsu
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Namrata Patel
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Sofia P Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Siddhi Patnaik
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Amrita Bit
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Mir A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Joykrushna Jena
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
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Kumar M, Patel AK, Shah AV, Raval J, Rajpara N, Joshi M, Joshi CG. First proof of the capability of wastewater surveillance for COVID-19 in India through detection of genetic material of SARS-CoV-2. Sci Total Environ 2020; 746:141326. [PMID: 32768790 PMCID: PMC7386605 DOI: 10.1016/j.scitotenv.2020.141326] [Citation(s) in RCA: 297] [Impact Index Per Article: 74.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 04/14/2023]
Abstract
We made the first ever successful effort in India to detect the genetic material of SARS-CoV-2 viruses to understand the capability and application of wastewater-based epidemiology (WBE) surveillance in India. Sampling was carried out on 8 and 27 May 2020 at the Old Pirana Waste Water Treatment Plant (WWTP) at Ahmedabad, Gujarat that receives effluent from Civil Hospital treating COVID-19 patients. All three, i.e. ORF1ab, N and S genes of SARS-CoV-2, were found in the influent with no genes detected in effluent collected on 8 and 27 May 2020. Increase in SARS-CoV-2 genetic loading in the wastewater between 8 and 27 May 2020 samples concurred with corresponding increase in the number of active COVID-19 patients in the city. The number of gene copies was comparable to that reported in untreated wastewaters of Australia, China and Turkey and lower than that of the USA, France and Spain. However, temporal changes in SARS-CoV-2 RNA concentrations need to be substantiated further from the perspectives of daily and short-term changes of SARS-CoV-2 in wastewater through long-term monitoring. The study results SARS-CoV-2 will assist concerned authorities and policymakers to formulate and/or upgrade COVID-19 surveillance to have a more explicit picture of the pandemic curve. While infectivity of SARS-CoV-2 through the excreted viral genetic material in the aquatic environment is still being debated, the presence and detection of genes in wastewater systems makes a strong case for the environmental surveillance of the COVID-19 pandemic.
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Affiliation(s)
- Manish Kumar
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat 382 355, India; Kiran C Patel Centre for Sustainable Development, Indian Institute of Technology Gandhinagar, Gujarat, India.
| | - Arbind Kumar Patel
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat 382 355, India
| | - Anil V Shah
- Gujarat Pollution Control Board (GPCB), Paryavaran Bhavan, Gandhinagar, Gujarat 382 010, India
| | - Janvi Raval
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat 382 011, India
| | - Neha Rajpara
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat 382 011, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat 382 011, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat 382 011, India
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Kumar M, Patel AK, Shah AV, Raval J, Rajpara N, Joshi M, Joshi CG. First proof of the capability of wastewater surveillance for COVID-19 in India through detection of genetic material of SARS-CoV-2. Sci Total Environ 2020. [PMID: 32768790 DOI: 10.1101/2020.06.16.20133215] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We made the first ever successful effort in India to detect the genetic material of SARS-CoV-2 viruses to understand the capability and application of wastewater-based epidemiology (WBE) surveillance in India. Sampling was carried out on 8 and 27 May 2020 at the Old Pirana Waste Water Treatment Plant (WWTP) at Ahmedabad, Gujarat that receives effluent from Civil Hospital treating COVID-19 patients. All three, i.e. ORF1ab, N and S genes of SARS-CoV-2, were found in the influent with no genes detected in effluent collected on 8 and 27 May 2020. Increase in SARS-CoV-2 genetic loading in the wastewater between 8 and 27 May 2020 samples concurred with corresponding increase in the number of active COVID-19 patients in the city. The number of gene copies was comparable to that reported in untreated wastewaters of Australia, China and Turkey and lower than that of the USA, France and Spain. However, temporal changes in SARS-CoV-2 RNA concentrations need to be substantiated further from the perspectives of daily and short-term changes of SARS-CoV-2 in wastewater through long-term monitoring. The study results SARS-CoV-2 will assist concerned authorities and policymakers to formulate and/or upgrade COVID-19 surveillance to have a more explicit picture of the pandemic curve. While infectivity of SARS-CoV-2 through the excreted viral genetic material in the aquatic environment is still being debated, the presence and detection of genes in wastewater systems makes a strong case for the environmental surveillance of the COVID-19 pandemic.
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Affiliation(s)
- Manish Kumar
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat 382 355, India; Kiran C Patel Centre for Sustainable Development, Indian Institute of Technology Gandhinagar, Gujarat, India.
| | - Arbind Kumar Patel
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat 382 355, India
| | - Anil V Shah
- Gujarat Pollution Control Board (GPCB), Paryavaran Bhavan, Gandhinagar, Gujarat 382 010, India
| | - Janvi Raval
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat 382 011, India
| | - Neha Rajpara
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat 382 011, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat 382 011, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat 382 011, India
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Menon DV, Bhaskar S, Sheshadri P, Joshi CG, Patel D, Kumar A. Positioning canine induced pluripotent stem cells (iPSCs) in the reprogramming landscape of naïve or primed state in comparison to mouse and human iPSCs. Life Sci 2020; 264:118701. [PMID: 33130086 DOI: 10.1016/j.lfs.2020.118701] [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: 03/09/2020] [Revised: 10/25/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022]
Abstract
AIMS Deriving canine-induced pluripotent stem cells (ciPSCs) have paved the way for developing novel cell-based disease models and transplantation therapies in the dog. Though ciPSCs have been derived in the presence of Leukemia inhibitory factor (LIF) as well in the presence of basic fibroblast growth factor (bFGF), the positioning of ciPSCs in the naïve or the primed state of pluripotency remains elusive. This study aims to understand whether canine iPSCs belong to naïve or prime state in comparison to mouse (m) iPSCs and human (h) iPSCs. MAIN METHODS In the present study, we derived ciPSCs in presence of LIF and compared their state of pluripotency with that of miPSCs and hiPSCs by culturing them in the presence of LIF, bFGF, and LIF + bFGF. Gene expression level at transcript level was performed by RT-PCR and qRT-PCR and at the protein level was analysed by immunofluorescence. We also attempted to understand the pluripotency state using lipid body analysis by bodipy staining and blue fluorescence emission. KEY FINDINGS In contrast to miPSCs, the naïve pluripotent stem cells, ciPSCs showed the expression of FGF5 similar to that of primed pluripotent stem cell, hiPSCs. Compared to miPSCs, ciPSCs cultured in presence of LIF showed enhanced expression of primed pluripotent marker FGF5, similar to hiPSCs cultured in presence of bFGF. Upon culturing in hiPSC culture condition, ciPSCs showed enhanced expression of core pluripotency genes compared to miPSCs cultured in similar condition. However, ciPSCs expressed naïve pluripotent marker SSEA1 similar to miPSCs and lacked the expression of primed state marker SSEA4 unlike hiPSCs. Interestingly, for the first time, we demonstrate the ciPSC pluripotency using lipid body analysis wherein ciPSCs showed enhanced bodipy staining and blue fluorescence emission, reflecting the primed state of pluripotency. ciPSCs expressed higher levels of fatty acid synthase (FASN), the enzyme involved in the synthesis of palmitate, similar to that of hiPSCs and higher than that of miPSCs. As ciPSCs exhibit characteristic properties of both naïve and primed pluripotent state, it probably represents a unique intermediary state of pluripotency that is distinct from that of mice and human pluripotent stem cells. SIGNIFICANCE Elucidating the pluripotent state of ciPSCs assists in better understanding of the reprogramming events and development in different species. The study would provide a footprint of species-specific differences involved in reprogramming and the potential implication of iPSCs as a tool to analyse evolution.
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Affiliation(s)
- Dhanya V Menon
- Manipal Institute of Regenerative Medicine (MIRM), Manipal Academy of Higher Education, Bangalore, India; P.D.Patel Institute of Applied Sciences, Charusat University, Changa, Gujarat, India
| | - Smitha Bhaskar
- Manipal Institute of Regenerative Medicine (MIRM), Manipal Academy of Higher Education, Bangalore, India
| | - Preethi Sheshadri
- Manipal Institute of Regenerative Medicine (MIRM), Manipal Academy of Higher Education, Bangalore, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Gandhinagar, Gujarat, India
| | - Darshan Patel
- P.D.Patel Institute of Applied Sciences, Charusat University, Changa, Gujarat, India
| | - Anujith Kumar
- Manipal Institute of Regenerative Medicine (MIRM), Manipal Academy of Higher Education, Bangalore, India.
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Agarwal D, Gireesh-Babu P, Pavan-Kumar A, Koringa P, Joshi CG, Chaudhari A. Transcriptome analysis of Clarias magur brain and gonads suggests neuro-endocrine inhibition of milt release from captive GnRH-induced males. Genomics 2020; 112:4041-4052. [PMID: 32650102 DOI: 10.1016/j.ygeno.2020.07.012] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/18/2020] [Accepted: 07/03/2020] [Indexed: 10/24/2022]
Abstract
Transcriptome analysis of Clarias magur brain and gonads at preparatory, mature, 6 and 16 h post-GnRH injection (hpi) stages yielded 9.5 GB data with 39,738 contigs. Sequences of 45 reproductive genes were identified for the first time in C. magur along with unique and differentially expressed genes. The expression of 20 genes was validated by qRT-PCR. Upregulation of Cyp11A1, Cyp17A1 and FTZF1 genes in the 16hpi testis accompanied by the 17β-HSD3 expression indicates testosterone (T) synthesis in response to LH surge, while reduced expression of CYP11B1 suggests a high T: 11-KT ratio. It is evident by the gene expression analysis that the inhibitory neurotransmitter GABA, altered T: 11-KT, increased testicular bile acids, and oxytocin-like neuropeptide in the male brain, appear to be involved in arresting the pulsatile motion of testicular smooth muscles. The work generates important leads for an effective induced breeding strategy for silurid catfish.
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Affiliation(s)
- Deepak Agarwal
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - P Gireesh-Babu
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - A Pavan-Kumar
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Prakash Koringa
- Animal Biotechnology Department, Anand Agricultural University, Anand, India
| | - C G Joshi
- Animal Biotechnology Department, Anand Agricultural University, Anand, India
| | - Aparna Chaudhari
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Mumbai, India.
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Hinsu AT, Patel AB, Pandit RJ, Thakkar JR, Shah RK, Jakhesara SJ, Koringa PG, Joshi CG. MetaRNAseq analysis of surti buffalo rumen content reveals that transcriptionally active microorganisms need not be abundant. Mol Biol Rep 2020; 47:5101-5114. [PMID: 32557173 DOI: 10.1007/s11033-020-05581-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 03/26/2020] [Accepted: 06/10/2020] [Indexed: 11/26/2022]
Abstract
The present study describes rumen microbiota composition and their functional profiles in Indian Surti buffaloes by metagenomic (MG) and metatranscriptomic (MT) approaches. The study compares samples from buffaloes fed three different proportion of roughages; green and dry type of roughage; and different rumen liquor fractions. Irrespective of sample, Bacteroidetes and Firmicutes were the most predominant bacterial phyla, followed by Proteobacteria, Fibrobacteres and Actinobacteria while, Prevotella, Bacteroides, Ruminococcus and Clostridium were the most abundant genera. Different proportions of taxa were observed in both MG and MT approaches indicating the differences in organisms present and organisms active in the rumen. Higher proportions of fungal taxa were observed in MT while important organisms like Fibrobacter and Butyrivibrio and abundant organisms like Bacteroides and Prevotella were underrepresented in MT data. Functionally, higher proportions of genes involved in Carbohydrate metabolism, Amino acid metabolism and Translation were observed in both data. Genes involved in Metabolism were observed to be underrepresented in MT data while, those involved in Genetic information processing were overrepresented in MT data. Further, genes involved in Carbohydrate metabolism were overexpressed compared to genes involved in Amino acid metabolism in MT data compared to MG data which had higher proportion of genes involved in Amino acid metabolism than Carbohydrate metabolism. In all significant differences were observed between both approaches, different fractions of rumen liquor (liquid and solid) and different proportions of roughage in diet.
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Affiliation(s)
- Ankit T Hinsu
- Department of Animal Genetics & Breeding, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Avani B Patel
- Department of Animal Genetics & Breeding, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Ramesh J Pandit
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Jalpa R Thakkar
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Ravi K Shah
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India.
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Kala A, Kamra DN, Agarwal N, Chaudhary LC, Joshi CG. Insights into Metatranscriptome, and CAZymes of Buffalo Rumen Supplemented with Blend of Essential Oils. Indian J Microbiol 2020; 60:485-493. [PMID: 33087998 DOI: 10.1007/s12088-020-00894-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/02/2020] [Indexed: 11/30/2022] Open
Abstract
The aim of this study was to investigate the rumen microbial diversity and functionality in buffaloes fed with a blend of essential oils (BEO) using LSD switch over design. The BEO consisting of blend of Trachyspermum copticum (Ajwain) oil, Cymbopogon citratus (lemon grass) oil and Syzygium aromaticum (clove bud) oleoresin mixed in equal proportion, was fed at the rate of 0, 0.75 and 1.5 ml/100 kg of body weight in 0 (control), 0.75 and 1.5 groups, respectively. The metatranscriptomic libraries of the rumen microbiome were represented by 7 domains, 84 phyla, 64 archeal genera and 663 bacterial genera with Bacteroidetes and Firmicutes constituting 80% of phyla abundance irrespective of feeding regime. Methanogenic archaea was represented by 22 phyla with Methanobrevibacter as the major genus. BEO feeding reduced the abundance of Methanococcus and Thermoplasma (P < 0.05) at all levels. The results revealed that the feeding of BEO shifted the archeal and bacterial population at very low magnitude. The study explored the vast diversity of buffalo rumen bacteria and archaea, and the diverse wealth of rumen enzymes (CAZymes), which revealed that a major part of CAZymes comes from the less known rumen microbes indicating alternative paths of fiber degradation along with the very well known ones.
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Affiliation(s)
- Anju Kala
- Animal Nutrition Division, Indian Veterinary Research Institute, Izatnagar, UP 243122 India
| | - D N Kamra
- Animal Nutrition Division, Indian Veterinary Research Institute, Izatnagar, UP 243122 India
| | - N Agarwal
- Animal Nutrition Division, Indian Veterinary Research Institute, Izatnagar, UP 243122 India
| | - L C Chaudhary
- Animal Nutrition Division, Indian Veterinary Research Institute, Izatnagar, UP 243122 India
| | - C G Joshi
- Department of Biotechnology, College of Veterinary Science, Anand Agricultural University, Anand, Gujarat India
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Mishra P, Tulsani NJ, Jakhesara SJ, Dafale NA, Patil NV, Purohit HJ, Koringa PG, Joshi CG. Exploring the eukaryotic diversity in rumen of Indian camel (Camelus dromedarius) using 18S rRNA amplicon sequencing. Arch Microbiol 2020; 202:1861-1872. [PMID: 32448959 DOI: 10.1007/s00203-020-01897-w] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 04/13/2020] [Accepted: 05/11/2020] [Indexed: 12/18/2022]
Abstract
In addition to a wide variety of anaerobic and facultative anaerobic bacteria, camel rumen also harbors a diverse of eukaryotic organisms. In the present study, the eukaryotic communities of camel rumen were characterized using 18S rRNA amplicon sequencing. Metagenomic DNA was isolated from rumen samples of fourteen adult Bikaneri and Kachchhi breeds of camel fed different diets containing Jowar, Bajra, Maize, and Guar. Illumina sequencing generated 27,161,904 number of reads corresponding to 1543 total operational taxonomic units (OTUs). Taxonomic classification of community metagenome sequences from all the samples revealed the presence of 92 genera belonging to 16 different divisions, out of which Ciliophora (73%), Fungi (13%) and Streptophyta (9%) were found to be the most dominant. Notably, the abundance of Ciliophora was significantly higher in the case of Guar feed, while Fungi was significantly higher in the case of Maize feed, indicating the influence of cellulose and hemicellulose content of feedstuff on the composition of eukaryotes. The results suggest that the camel rumen eukaryotes are highly dynamic and depend on the type of diet given to the animal. Pearson's correlation analysis suggested the ciliate protozoa and fungi were negatively correlated with each other. To the best of our knowledge, this is first systematic study to characterize camel rumen eukaryotes, which has provided newer information regarding eukaryotic diversity patterns amongst camel fed on different diets.
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Affiliation(s)
- Priyaranjan Mishra
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Nilam J Tulsani
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India.
| | - Nishant A Dafale
- Environmental Genomic Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020, India
| | - Niteen V Patil
- ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh, 334001, India
| | - Hemant J Purohit
- Environmental Genomic Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Center, MS Building, Block B & D, 6th Floor, GH Road, Sector-11, Gujarat, Gandhinagar, 382001, India
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Das P, Sahoo L, Das SP, Bit A, Joshi CG, Kushwaha B, Kumar D, Shah TM, Hinsu AT, Patel N, Patnaik S, Agarwal S, Pandey M, Srivastava S, Meher PK, Jayasankar P, Koringa PG, Nagpure NS, Kumar R, Singh M, Iquebal MA, Jaiswal S, Kumar N, Raza M, Das Mahapatra K, Jena J. De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita. Front Genet 2020; 11:386. [PMID: 32373166 PMCID: PMC7186481 DOI: 10.3389/fgene.2020.00386] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 10/25/2019] [Accepted: 03/27/2020] [Indexed: 11/24/2022] Open
Affiliation(s)
- Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Sofia P Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Amrita Bit
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India
| | - Basdeo Kushwaha
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Dinesh Kumar
- Center for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Tejas M Shah
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India
| | - Ankit T Hinsu
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India
| | - Namrata Patel
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India
| | - Siddhi Patnaik
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Suyash Agarwal
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Manmohan Pandey
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Shreya Srivastava
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Prem Kumar Meher
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Pallipuram Jayasankar
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India
| | - Naresh S Nagpure
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Ravindra Kumar
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Mahender Singh
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Mir Asif Iquebal
- Center for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Center for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Neeraj Kumar
- Center for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mustafa Raza
- Center for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Kanta Das Mahapatra
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Joykrushna Jena
- Division of Fisheries, Krishi Anusandhan Bhawan - II, New Delhi, India
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Puvar AC, Nathani NM, Shaikh I, Bhatt AD, Bhargava P, Joshi CG, Joshi MN. Bacterial line of defense in Dirinaria lichen from two different ecosystems: First genomic insights of its mycobiont Dirinaria sp. GBRC AP01. Microbiol Res 2019; 233:126407. [PMID: 31945518 DOI: 10.1016/j.micres.2019.126407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/09/2019] [Accepted: 12/27/2019] [Indexed: 11/30/2022]
Abstract
Lichens have been widely studied for their symbiotic properties and for the secondary metabolites production by its fungal symbiont. Recent molecular studies have confirmed coexistence of bacteria along with the fungal and algal symbionts. Direct nucleic acid study by -omics approaches is providing better insights into their structural and functional dynamics. However, genomic analysis of individual members of lichen is difficult by the conventional approach. Hence, genome assembly from metagenome data needs standardization in the eukaryotic system like lichens. The present study aimed at metagenomic characterization of rock associated lichen Dirinaria collected from Kutch and Dang regions of Gujarat, followed by genome reconstruction and annotation of the mycobiont Dirinaria. The regions considered in the study are eco-geographically highly variant. The results revealed higher alpha diversity in the dry region Kutch as compared to the tropical forest associated lichen from Dang. Ascomycota was the most abundant eukaryote while Proteobacteria dominated the bacterial population. There were 23 genera observed only in the Kutch lichen (KL) and one genus viz., Candidatus Vecturithrix unique to the Dang lichen (DL). The exclusive bacterial genera in the Kutch mostly belonged to groups reported for stress tolerance and earlier isolated from lithobionts of extreme niches. The assembled data of KL & DL were further used for genome reconstruction of Dirinaria sp. using GC and tetra-pentamer parameters and reassembly that resulted into a final draft genome of 31.7 Mb and 9556 predicted genes. Twenty-eight biosynthesis gene clusters were predicted that included genes for polyketide, indole and terpene synthesis. Association analysis of bacteria and mycobiont revealed 8 pathways specific to bacteria with implications in lichen symbiosis and environment interaction. The study provides the first draft genome of the entire fungal Dirinaria genus and provides insights into the Dirinaria lichen metagenome from Gujarat region.
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Affiliation(s)
- Apurvasinh C Puvar
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, 382011, Gujarat, India; Hemchandracharya North Gujarat University (HNGU), Patan, Gujarat, India
| | - Neelam M Nathani
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, 382011, Gujarat, India
| | - Inayatullah Shaikh
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, 382011, Gujarat, India
| | - Arpan D Bhatt
- Hemchandracharya North Gujarat University (HNGU), Patan, Gujarat, India
| | - Poonam Bhargava
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, 382011, Gujarat, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, 382011, Gujarat, India
| | - Madhvi N Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, 382011, Gujarat, India.
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Shaikh I, Ansari A, Ayachit G, Gandhi M, Sharma P, Bhairappanavar S, Joshi CG, Das J. Differential gene expression analysis of HNSCC tumors deciphered tobacco dependent and independent molecular signatures. Oncotarget 2019; 10:6168-6183. [PMID: 31692905 PMCID: PMC6817442 DOI: 10.18632/oncotarget.27249] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 06/14/2019] [Accepted: 09/16/2019] [Indexed: 12/15/2022] Open
Abstract
Head and neck cancer is the sixth most common cancer worldwide, with tobacco as the leading cause. However, it is increasing in non-tobacco users also, hence limiting our understanding of its underlying molecular mechanisms. RNA-seq analysis of cancers has proven as effective tool in understanding disease etiology. In the present study, RNA-Seq of 86 matched Tumor/Normal pairs, of tobacco smoking (TOB) and non-smokers (N-TOB) HNSCC samples analyzed, followed by validation on 375 similar datasets. Total 2194 and 2073 differentially expressed genes were identified in TOB and N-TOB tumors, respectively. GO analysis found muscle contraction as the most enriched biological process in both TOB and N-TOB tumors. Pathway analysis identified muscle contraction and salivary secretion pathways enriched in both categories, whereas calcium signaling and neuroactive ligand-receptor pathway was more enriched in TOB and N-TOB tumors respectively. Network analysis identified muscle development related genes as hub node i. e. ACTN2, MYL2 and TTN in both TOB and N-TOB tumors, whereas EGFR and MYH6, depicts specific role in TOB and N-TOB tumors. Additionally, we found enriched gene networks possibly be regulated by tumor suppressor miRNAs such as hsa-miR-29/a/b/c, hsa-miR-26b-5p etc., suggestive to be key riboswitches in regulatory cascade of HNSCC. Interestingly, three genes PKLR, CST1 and C17orf77 found to show opposite regulation in each category, hence suggested to be key genes in separating TOB from N-TOB tumors. Our investigation identified key genes involved in important pathways implicated in tobacco dependent and independent carcinogenesis hence may help in designing precise HNSCC diagnostics and therapeutics strategies.
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Affiliation(s)
- Inayatullah Shaikh
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Afzal Ansari
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Garima Ayachit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Monika Gandhi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Priyanka Sharma
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Shivarudrappa Bhairappanavar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Jayashankar Das
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
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Raval NP, Shah TM, George LB, Joshi CG. Effect of the pH in the enrichment of X or Y sex chromosome-bearing sperm in bovine. Vet World 2019; 12:1299-1303. [PMID: 31641311 PMCID: PMC6755399 DOI: 10.14202/vetworld.2019.1299-1303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 04/27/2019] [Accepted: 07/05/2019] [Indexed: 12/26/2022] Open
Abstract
Background and Aim: Studies have shown that the pH of the vagina during the course of fertilization may influence the migration of X- and Y-bearing spermatozoa and thus leading to skewness in the sex of the offspring. Hence, this study was carried out to check the effect of the pH in the enrichment of X or Y sex chromosome-bearing sperm in bovine (Bos indicus). Materials and Methods: To check the effect of pH in the enrichment of X or Y sex chromosome-bearing sperm in bovine, we used buffers of various pH ranging from 5.5 to 9.0 for swim-up procedure of sperm sample and collected upper and bottom fraction from the same buffer and checked the abundance of X- and Y-bearing spermatozoa by droplet digital polymerase chain reaction using X- and Y-chromosome-specific DNA probe. Results: The abundance of X- and Y-bearing spermatozoa was not differed significantly in either of the fraction collected. Conclusion: Thus, it appears to be unlikely that an immediate impact of pH on sperm can be a solitary impact on the sex of offspring in bovine.
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Affiliation(s)
- Nidhi P Raval
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India.,Department of Zoology, Biomedical Technology and Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Tejas M Shah
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - Linz-Buoy George
- Department of Zoology, Biomedical Technology and Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre, Block B and D, 6 Floor, MS Building, Sector - 11, Gandhinagar, Gujarat, India
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Sabara PH, Jakhesara SJ, Panchal KJ, Joshi CG, Koringa PG. Transcriptomic analysis to affirm the regulatory role of long non-coding RNA in horn cancer of Indian zebu cattle breed Kankrej (Bos indicus). Funct Integr Genomics 2019; 20:75-87. [PMID: 31368028 DOI: 10.1007/s10142-019-00700-4] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/15/2019] [Accepted: 07/01/2019] [Indexed: 01/08/2023]
Abstract
Long non-coding RNA (lncRNA) was previously considered as a non-functional transcript, which now established as part of regulatory elements of biological events such as chromosome structure, remodeling, and regulation of gene expression. The study presented here showed the role of lncRNA through differential expression analysis on cancer-related coding genes in horn squamous cell carcinoma of Indian zebu cattle. A total of 10,360 candidate lncRNAs were identified and further analyzed for its coding potential ability using three tools (CPC, CPAT, and PLEK) that provide 8862 common lncRNAs. Pfam analysis of these common lncRNAs gave 8612 potential candidates for lncRNA differential expression analysis. Differential expression analysis showed a total of 59 significantly differentially expressed genes and 19 lncRNAs. Pearson's correlation analysis was used to identify co-expressed mRNA-lncRNAs to established relation of the regulatory role of lncRNAs in horn cancer. We established a positive relation of seven upregulated (XLOC_000016, XLOC_002198, XLOC_002851, XLOC_ 007383, XLOC_010701, XLOC_010272, and XLOC_011517) and one downregulated (XLOC_011302) lncRNAs with eleven genes that are related to keratin family protein, keratin-associated protein family, cornifelin, corneodesmosin, serpin family protein, and metallothionein that have well-established role in squamous cell carcinoma through cellular communication, cell growth, cell invasion, and cell migration. These biological events were found to be related to the MAPK pathway of cell cycle regulation indicating the role of lncRNAs in manipulating cell cycle regulation during horn squamous cell carcinomas that will be useful in identifying molecular portraits related to the development of horn cancer.
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Affiliation(s)
- Pritesh H Sabara
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Ketankumar J Panchal
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India.
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Hinsu AT, Pandit RJ, Patel SH, Psifidi A, Tomley FM, Das SK, Blake DP, Joshi CG. Genome reconstruction of a novel carbohydrate digesting bacterium from the chicken caecal microflora. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Bhatt A, Purani C, Bhargava P, Patel K, Agarbattiwala T, Puvar A, Shah K, Joshi CG, Dhamecha N, Prabhakar M, Joshi M. Whole exome sequencing reveals novel LEPR frameshift mutation in severely obese children from Western India. Mol Genet Genomic Med 2019; 7:e00692. [PMID: 31070016 PMCID: PMC6625100 DOI: 10.1002/mgg3.692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 11/19/2018] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 01/27/2023] Open
Abstract
Background Obesity, especially early onset of obesity is a serious health concern in both developed and developing countries. This is further associated with serious comorbidities like a fatty liver disease, cardiovascular diseases, type‐2 diabetes, obstructive sleep apnea, renal complications and respiratory problems. Many times early onset of obesity is linked with heritable monogenic, polygenic and syndromic forms. Globally, studies on roles of genes involved in early onset of obesity are limited. Methods Here in this study, a consanguineous family of Western Indian origin having four siblings, one unaffected and three affected with severe early onset of obesity was enrolled. Affected siblings also displayed comorbidities like mild to moderate obstructive sleep apnea, raised Renal Resistance Index, oliguria, and severe anemia. Whole Exome Sequencing (WES) of Trio with one affected and unaffected sibling was done. Data analysis was performed to check pathogenic mutation segregation in unaffected parents with affected and unaffected sibling. Results WES of trio identified novel frameshift mutation in the LEPR gene resulting in truncated leptin receptor (LEPR). The same mutation was confirmed in other affected siblings and two siblings of distant relatives by Sanger sequencing. The possible effects of truncating mutation in LEPR function by in silico analysis were also studied. Conclusion Understanding genetic basis of obesity might provide a clue for better management and treatment in times to come. This work demonstrates identification of novel mutation in LEPR gene resulting into early onset of obesity. Discovery of novel, population‐specific genomics markers will help population screening programs in creating base for possible therapeutic applications and prevention of this disease for next generations.
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Affiliation(s)
- Arpan Bhatt
- Department of Biotechnology, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | | | - Poonam Bhargava
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Komal Patel
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | | | - Apurvasinh Puvar
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Krati Shah
- ONE-Centre for Rheumatology and Genetics, Vadodara, Gujarat, India
| | | | | | | | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
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Menon DV, Patel D, Joshi CG, Kumar A. The road less travelled: The efficacy of canine pluripotent stem cells. Exp Cell Res 2019; 377:94-102. [DOI: 10.1016/j.yexcr.2019.01.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/20/2019] [Accepted: 01/22/2019] [Indexed: 12/28/2022]
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Raval NP, Shah TM, George LB, Joshi CG. Insight into bovine (Bos indicus) spermatozoal whole transcriptome profile. Theriogenology 2019; 129:8-13. [PMID: 30784792 DOI: 10.1016/j.theriogenology.2019.01.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 08/13/2018] [Revised: 12/25/2018] [Accepted: 01/31/2019] [Indexed: 01/26/2023]
Abstract
Mature spermatozoa harbor both coding and non-coding type of RNAs which regulates spermatogenesis, fertilization and early development. Characterization of bovine sperm transcriptome can provide more insight into the molecular mechanisms involved in these processes. Here, we have analyzed whole transcriptome profile of Bos indicus spermatozoa to access the global RNA expression. RNA-Seq analysis identified 14,306 genes expressed with FPKM >0, while 405 genes expressed when threshold increased to FPKM >5. Functional annotations showed that sperm transcripts were associated with molecular processes (translation, ribosomal small and large subunit assembly) and cellular components (cytosolic small and large ribosomal subunit and membranes) related to known sperm functions at fertilization and spermatogenesis. The RNA-Seq data was validated using droplet digital PCR where both highly abundant gene viz. RN7SL1 and less abundant gene viz. ZFP280B were validated. This study may provide future directions in reproductive biology of Bos indicus.
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Affiliation(s)
- Nidhi P Raval
- Department of Zoology, Biomedical Technology and Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Tejas M Shah
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Linz-Buoy George
- Department of Zoology, Biomedical Technology and Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India.
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Bhatt AD, Shah K, Puvar A, Joshi CG, Joshi M. A Case of Limb Girdle Muscular Dystrophy Type 2A from India: Copy Number Variation Analysis using Targeted Amplicon Sequencing. J Clin Diagn Res 2019. [DOI: 10.7860/jcdr/2019/40923.12812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Agarwal D, Gireesh-Babu P, Pavan-Kumar A, Koringa P, Joshi CG, Gora A, Bhat IA, Chaudhari A. Molecular characterization and expression profiling of 17-beta-hydroxysteroid dehydrogenase 2 and spermatogenesis associated protein 2 genes in endangered catfish, Clarias magur (Hamilton, 1822). Anim Biotechnol 2018; 31:93-106. [PMID: 30570357 DOI: 10.1080/10495398.2018.1545663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The 17-beta-hydroxysteroid dehydrogenase 2 (17β-HSD2) enzyme regulates steroid levels by the inactivation of estrogen and androgens. Spermatogenesis associated protein 2 (SPATA2) plays a vital role in spermatogenesis in vertebrates including fish. We report cloning and characterization of full cds of 17β-HSD2 and SPATA2 genes in Clarias magur. The full-length cDNA sequences of 17β-HSD2 and SPATA2 were 1187 bp (ORF 1125 bp) and 1806 bp (ORF 1524 bp) encoding 375 and 508 amino acids, respectively. Signal peptide analysis revealed SPATA2 is nonsecretory, while 17β-HSD2 is a secretory protein. Hydropathy profiles showed both proteins are hydrophilic in nature. Tissue distribution of both the genes revealed high mRNA level of SPATA2 in all tissues examined indicating its wide range of expression. 17β-HSD2 indicated higher expression in preparatory phase compared to spawning phase in ovary while it was opposite in case of testis. SPATA2 showed significantly higher expression in preparatory phase compared to spawning phase in both ovary and testis. Administration of OvatideTM (GnRH analog) resulted in upregulation of SPATA2 expression at 6 and 16 h post-injection while 17β-HSD2 showed upregulation only at 6 h post-injection. To the best of our knowledge, this is a first report on characterization of 17β-HSD2 and SPATA2 full-length cDNA in catfish.
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Affiliation(s)
- Deepak Agarwal
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - Pathakota Gireesh-Babu
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - Annam Pavan-Kumar
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - Prakash Koringa
- Animal Biotechnology Department, College of veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - Chaitanya G Joshi
- Animal Biotechnology Department, College of veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - Adnan Gora
- Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | - Irfan Ahmad Bhat
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - Aparna Chaudhari
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
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