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Priya GB, Agrawal RK, Milton AAP, Mishra M, Mendiratta SK, Singh BR, Kumar D, Gandham RK, Dubal ZB, Rajkhowa S, Luke A, Patil G. Rapid and visual detection of Shiga-toxigenic Escherichia coli (STEC) in carabeef meat harnessing loop-mediated isothermal amplification (LAMP). Braz J Microbiol 2024:10.1007/s42770-024-01335-9. [PMID: 38639846 DOI: 10.1007/s42770-024-01335-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Shiga toxigenic E. coli are important foodborne zoonotic pathogens. The present study was envisaged to standardize loop-mediated isothermal amplification assays targeting stx1 and stx2 genes for rapid and visual detection of STEC and compare its sensitivity with PCR. The study also assessed the effect of short enrichment on the detection limit of LAMP and PCR. The developed LAMP assays were found to be highly specific. Analytical sensitivity of LAMP was 94 fg/µLand 25.8 fg/µL for stx-1 and stx-2 while LOD of 5 CFU/g of carabeef was measured after 6-12 h enrichment. The study highlights the importance of short (6-12 h) enrichment for improving the sensitivity of LAMP. The entire detection protocol could be performed within 9 h yielding results on the same day. The developed LAMP assays proved to be a handy and cost-effective alternative for screening STEC contamination in meat.
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Affiliation(s)
- Govindarajan Bhuvana Priya
- College of Agriculture, Central Agricultural University, Imphal, Manipur, India
- Division of Bacteriology & Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Ravi Kant Agrawal
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India.
| | | | - Madhu Mishra
- Division of Bacteriology & Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sanjod Kumar Mendiratta
- Division of Livestock Products Technology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Bhoj Raj Singh
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Deepak Kumar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Zunjar Baburao Dubal
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | | | - Ashish Luke
- Division of Livestock Products Technology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Girish Patil
- ICAR-NRC on Meat, Post Box 19, Boduppal Post, Chengicherla, Hyderabad, 500092, India
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2
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Kumar SL, Mohanty A, Kumari A, Etikuppam AK, Kumar S R, Athar M, Kumar P K, Beniwal R, Potula MM, Gandham RK, Rao HBDP. Balanced spatiotemporal arrangements of histone H3 and H4 posttranslational modifications are necessary for meiotic prophase I chromosome organization. J Cell Physiol 2024; 239:e31201. [PMID: 38284481 DOI: 10.1002/jcp.31201] [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: 09/15/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/30/2024]
Abstract
Dynamic nuclear architecture and chromatin organizations are the key features of the mid-prophase I in mammalian meiosis. The chromatin undergoes major changes, including meiosis-specific spatiotemporal arrangements and remodeling, the establishment of chromatin loop-axis structure, pairing, and crossing over between homologous chromosomes, any deficiencies in these events may induce genome instability, subsequently leading to failure to produce gametes and infertility. Despite the significance of chromatin structure, little is known about the location of chromatin marks and the necessity of their balance during meiosis prophase I. Here, we show a thorough cytological study of the surface-spread meiotic chromosomes of mouse spermatocytes for H3K9,14,18,23,27,36, H4K12,16 acetylation, and H3K4,9,27,36 methylation. Active acetylation and methylation marks on H3 and H4, such as H3K9ac, H3K14ac, H3K18ac, H3K36ac, H3K56ac, H4K12ac, H4K16ac, and H3K36me3 exhibited pan-nuclear localization away from heterochromatin. In comparison, repressive marks like H3K9me3 and H3K27me3 are localized to heterochromatin. Further, taking advantage of the delivery of small-molecule chemical inhibitors methotrexate (heterochromatin enhancer), heterochromatin inhibitor, anacardic acid (histone acetyltransferase inhibitor), trichostatin A (histone deacetylase inhibitor), IOX1 (JmjC demethylases inhibitor), and AZ505 (methyltransferase inhibitor) in seminiferous tubules through the rete testis route, revealed that alteration in histone modifications enhanced the centromere mislocalization, chromosome breakage, altered meiotic recombination and reduced sperm count. Specifically, IOX1 and AZ505 treatment shows severe meiotic phenotypes, including altering chromosome axis length and chromatin loop size via transcriptional regulation of meiosis-specific genes. Our findings highlight the importance of balanced chromatin modifications in meiotic prophase I chromosome organization and instability.
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Affiliation(s)
- S Lava Kumar
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
- Graduate Studies, Regional Center for Biotechnology, Faridabad, Haryana, India
| | - Aradhana Mohanty
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
- Graduate Studies, Regional Center for Biotechnology, Faridabad, Haryana, India
| | - Anjali Kumari
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
- Graduate Studies, Regional Center for Biotechnology, Faridabad, Haryana, India
| | - Ajith Kumar Etikuppam
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
- Graduate Studies, Regional Center for Biotechnology, Faridabad, Haryana, India
| | - Ranjith Kumar S
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
| | - Mohd Athar
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
- Graduate Studies, Regional Center for Biotechnology, Faridabad, Haryana, India
| | - Kiran Kumar P
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
| | - Rohit Beniwal
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
- Graduate Studies, Regional Center for Biotechnology, Faridabad, Haryana, India
| | | | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-IVRI, Izatnagar, Bareilly, Uttar Pradesh, India
| | - H B D Prasada Rao
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
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Nabi Khan RI, Praharaj MR, Malla WA, Hosamani N, Saxena S, Mishra B, Rajak KK, Dhanavelu M, Tiwari AK, Sajjanar B, Gandham RK, Mishra B. Changes in m 6A RNA methylation of goat lung following PPRV infection. Heliyon 2023; 9:e19358. [PMID: 37681172 PMCID: PMC10480600 DOI: 10.1016/j.heliyon.2023.e19358] [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: 04/12/2023] [Revised: 08/12/2023] [Accepted: 08/20/2023] [Indexed: 09/09/2023] Open
Abstract
Peste des petits ruminants (PPR) is an acute, highly contagious viral disease of goats and sheep, caused by the Peste des petits ruminants virus (PPRV). Earlier studies suggest the involvement of diverse regulatory mechanisms in PPRV infection. Methylation at N6 of Adenosine called m6A is a type RNA modification that influences various physiological and pathological phenomena. As the lung tissue represents the primary target organ of PPRV, the present study explored the m6A changes and their functional significance in PPRV disease pathogenesis. m6A-seq analysis revealed 1289 m6A peaks to be significantly altered in PPRV infected lung in comparison to normal lung, out of which 975 m6A peaks were hypomethylated and 314 peaks were hypermethylated. Importantly, hypomethylated genes were enriched in Interleukin-4 and Interleukin-13 signaling and various processes associated with extracellular matrix organization. Further, of the 843 differentially m6A-containing cellular transcripts, 282 transcripts were also found to be differentially expressed. Functional analysis revealed that these 282 transcripts are significantly enriched in signaling by Interleukins, extracellular matrix organization, cytokine signaling in the immune system, signaling by receptor tyrosine kinases, and Toll-like Receptor Cascades. We also found m6A reader HNRNPC and the core component of methyltransferase complex METTL14 to be highly upregulated than the m6A readers - HNRNPA2B1 and YTHDF1 at the transcriptome level. These findings suggest that alteration in the m6A landscape following PPRV is implicated in diverse processes including Interleukin signaling.
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Affiliation(s)
- Raja Ishaq Nabi Khan
- Division of Veterinary Biotechnology, ICAR – Indian Veterinary Research Institute, Izatnagar Bareilly, 243122, U.P., India
- Center for Advanced Biotechnology and Medicine, Rutgers University, 08854-8021, New Jersey, USA
| | - Manas Ranjan Praharaj
- DBT- National Institute of Animal Biotechnology, Hyderabad, 500032, Telangana, India
- DBT-Regional Centre for Biotechnology (RCB), Faridabad 121001, Haryana, India
| | - Waseem Akram Malla
- Division of Veterinary Biotechnology, ICAR – Indian Veterinary Research Institute, Izatnagar Bareilly, 243122, U.P., India
| | - Neelima Hosamani
- DBT- National Institute of Animal Biotechnology, Hyderabad, 500032, Telangana, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, ICAR – Indian Veterinary Research Institute, Izatnagar Bareilly, 243122, U.P., India
| | - Bina Mishra
- Division of Biological Products, ICAR – Indian Veterinary Research Institute, Izatnagar Bareilly, 243122, U.P., India
- ICAR – National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Kaushal Kishor Rajak
- Division of Biological Products, ICAR – Indian Veterinary Research Institute, Izatnagar Bareilly, 243122, U.P., India
| | | | - Ashok Kumar Tiwari
- ICAR – Central Avian Research Institute, Izatnagar Bareilly, 243122, U.P., India
| | - Basavaraj Sajjanar
- Division of Veterinary Biotechnology, ICAR – Indian Veterinary Research Institute, Izatnagar Bareilly, 243122, U.P., India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR – Indian Veterinary Research Institute, Izatnagar Bareilly, 243122, U.P., India
- ICAR – National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - B.P. Mishra
- Division of Veterinary Biotechnology, ICAR – Indian Veterinary Research Institute, Izatnagar Bareilly, 243122, U.P., India
- ICAR – National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
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4
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Sajjanar B, Aalam MT, Khan O, Tanuj GN, Sahoo AP, Manjunathareddy GB, Gandham RK, Dhara SK, Gupta PK, Mishra BP, Dutt T, Singh G. Genome-wide expression analysis reveals different heat shock responses in indigenous (Bos indicus) and crossbred (Bos indicus X Bos taurus) cattle. Genes Environ 2023; 45:17. [PMID: 37127630 PMCID: PMC10152620 DOI: 10.1186/s41021-023-00271-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 04/03/2023] [Indexed: 05/03/2023] Open
Abstract
Environmental heat stress in dairy cattle leads to poor health, reduced milk production and decreased reproductive efficiency. Multiple genes interact and coordinate the response to overcome the impact of heat stress. The present study identified heat shock regulated genes in the peripheral blood mononuclear cells (PBMC). Genome-wide expression patterns for cellular stress response were compared between two genetically distinct groups of cattle viz., Hariana (B. indicus) and Vrindavani (B. indicus X B. taurus). In addition to major heat shock response genes, oxidative stress and immune response genes were also found to be affected by heat stress. Heat shock proteins such as HSPH1, HSPB8, FKB4, DNAJ4 and SERPINH1 were up-regulated at higher fold change in Vrindavani compared to Hariana cattle. The oxidative stress response genes (HMOX1, BNIP3, RHOB and VEGFA) and immune response genes (FSOB, GADD45B and JUN) were up-regulated in Vrindavani whereas the same were down-regulated in Hariana cattle. The enrichment analysis of dysregulated genes revealed the biological functions and signaling pathways that were affected by heat stress. Overall, these results show distinct cellular responses to heat stress in two different genetic groups of cattle. This also highlight the long-term adaptation of B. indicus (Hariana) to tropical climate as compared to the crossbred (Vrindavani) with mixed genetic makeup (B. indicus X B. taurus).
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Affiliation(s)
- Basavaraj Sajjanar
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India.
| | - Mohd Tanzeel Aalam
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Owais Khan
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Gunturu Narasimha Tanuj
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Aditya Prasad Sahoo
- ICAR- Directorate of Foot and Mouth Disease, Bhubaneswar, 752050, Odisha, India
| | | | - Ravi Kumar Gandham
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Sujoy K Dhara
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Praveen K Gupta
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Bishnu Prasad Mishra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Triveni Dutt
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Gyanendra Singh
- Physiology and Climatology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India.
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Topno NA, Kesarwani V, Kushwaha SK, Azam S, Kadivella M, Gandham RK, Majumdar SS. Non-Synonymous Variants in Fat QTL Genes among High- and Low-Milk-Yielding Indigenous Breeds. Animals (Basel) 2023; 13:ani13050884. [PMID: 36899741 PMCID: PMC10000039 DOI: 10.3390/ani13050884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/17/2022] [Accepted: 12/25/2022] [Indexed: 03/06/2023] Open
Abstract
The effect of breed on milk components-fat, protein, lactose, and water-has been observed to be significant. As fat is one of the major price-determining factors for milk, exploring the variations in fat QTLs across breeds would shed light on the variable fat content in their milk. Here, on whole-genome sequencing, 25 differentially expressed hub or bottleneck fat QTLs were explored for variations across indigenous breeds. Out of these, 20 genes were identified as having nonsynonymous substitutions. A fixed SNP pattern in high-milk-yielding breeds in comparison to low-milk-yielding breeds was identified in the genes GHR, TLR4, LPIN1, CACNA1C, ZBTB16, ITGA1, ANK1, and NTG5E and, vice versa, in the genes MFGE8, FGF2, TLR4, LPIN1, NUP98, PTK2, ZTB16, DDIT3, and NT5E. The identified SNPs were ratified by pyrosequencing to prove that key differences exist in fat QTLs between the high- and low-milk-yielding breeds.
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Affiliation(s)
- Neelam A. Topno
- DBT—National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India
- RCB—Regional Centre of Biotechnology, Delhi 121001, India
| | - Veerbhan Kesarwani
- DBT—National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India
| | | | - Sarwar Azam
- DBT—National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India
| | - Mohammad Kadivella
- DBT—National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India
| | - Ravi Kumar Gandham
- ICAR—Indian Veterinary Research Institute, Bareilly 243122, India
- Correspondence: (R.K.G.); (S.S.M.)
| | - Subeer S. Majumdar
- DBT—National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India
- Correspondence: (R.K.G.); (S.S.M.)
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6
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Khan O, Tanuj GN, Choravada DR, Rajak KK, Chandra Sekar S, Lingaraju MC, Dhara SK, Gupta PK, Mishra BP, Dutt T, Gandham RK, Sajjanar B. N 6-Methyladenosine RNA Modification in Host Cells Regulates Peste des Petits Ruminants Virus Replication. Microbiol Spectr 2023; 11:e0266622. [PMID: 36786625 PMCID: PMC10101086 DOI: 10.1128/spectrum.02666-22] [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: 07/20/2022] [Accepted: 12/09/2022] [Indexed: 02/15/2023] Open
Abstract
N6-methyladenosine (m6A) modification is a major RNA epigenetic regulatory mechanism. The dynamics of m6A levels in viral genomic RNA and their mRNAs have been shown to have either pro- or antiviral functions, and therefore, m6A modifications influence virus-host interactions. Currently, no reports are available on the effect of m6A modifications in the genome of Peste des petits ruminants virus (PPRV). In the present study, we took PPRV as a model for nonsegmented negative-sense single-stranded RNA viruses and elucidate the role of m6A modification on viral replication. We detected m6A-modified sites in the mRNA of the virus and host cells, as well as the PPRV RNA genome. Further, it was found that the level of m6A modification in host cells alters the viral gene expression. Knockdown of the METTL3 and FTO genes (encoding the m6A RNA modification writer and eraser proteins, respectively) results in alterations of the levels of m6A RNA modifications in the host cells. Experiments using these genetically modified clones of host cells infected with PPRV revealed that both higher and lower m6A RNA modification in the host cells negatively affect PPRV replication. We found that m6A-modified viral transcripts had better stability and translation efficiency compared to the unmodified mRNA. Altogether, from these data, we conclude that the m6A modification of RNA regulates PPRV replication. These findings contribute toward a way forward for developing novel antiviral strategies against PPRV by modulating the dynamics of host m6A RNA modification. IMPORTANCE Peste des petits ruminants virus (PPRV) causes a severe disease in sheep and goats. PPRV infection is a major problem, causing significant economic losses to small ruminant farmers in regions of endemicity. N6-methyladenosine (m6A) is an important RNA modification involved in various functions, including virus-host interactions. In the present study, we used stable clones of Vero cells, having knocked down the genes encoding proteins involved in dynamic changes of the levels of m6A modification. We also used small-molecule compounds that interfere with m6A methylation. This resulted in a platform of host cells with various degrees of m6A RNA modification. The host cells with these different microenvironments were useful for studying the effect of m6A RNA modification on the expression of viral genes and viral replication. The results pinpoint the level of m6A modifications that facilitate the maximum replication of PPRV. These findings will be useful in increasing the virus titers in cultured cells needed for the economical development of the vaccine. Furthermore, the findings have guiding significance for the development of novel antiviral strategies for limiting PPRV replication in infected animals.
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Affiliation(s)
- Owais Khan
- Veterinary Biotechnology Division, ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly, Uttar Pradesh, India
| | - Gunturu Narasimha Tanuj
- Veterinary Biotechnology Division, ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly, Uttar Pradesh, India
| | - Divyaprakash R. Choravada
- Veterinary Biotechnology Division, ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly, Uttar Pradesh, India
| | - Kaushal Kishore Rajak
- Biological Products Division, ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly, Uttar Pradesh, India
| | - S Chandra Sekar
- Division of Virology, ICAR—Indian Veterinary Research Institute, Mukteshwar, Uttarakhand, India
| | - Madhu Cholenahalli Lingaraju
- Pharmacology and Toxicology Division, ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly, Uttar Pradesh, India
| | - Sujoy K. Dhara
- Veterinary Biotechnology Division, ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly, Uttar Pradesh, India
| | - Praveen K. Gupta
- Veterinary Biotechnology Division, ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly, Uttar Pradesh, India
| | | | - Triveni Dutt
- Veterinary Biotechnology Division, ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly, Uttar Pradesh, India
| | - Ravi Kumar Gandham
- Veterinary Biotechnology Division, ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly, Uttar Pradesh, India
| | - Basavaraj Sajjanar
- Veterinary Biotechnology Division, ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly, Uttar Pradesh, India
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Mote AB, Mehta D, Kumar MS, Gupta M, Hussain M, Patel SM, Gandham RK, Dhanze H. Genotypic characterization of Japanese encephalitis virus circulating in swine population of India: Genotype-III still in dominance. Virus Genes 2023; 59:67-78. [PMID: 36357764 DOI: 10.1007/s11262-022-01953-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/29/2022] [Indexed: 11/12/2022]
Abstract
Swine is considered as a suitable sentinel to predict Japanese encephalitis virus (JEV) outbreaks in humans. The present study was undertaken to determine the circulating genotypes of JEV in swine population of India. A total of 702 swine serum samples from four states of western, northern, northern-temperate, and north-eastern zones of India were screened by real-time RT-PCR targeting envelope gene of JEV, which showed positivity of 35.33%. The viral copy number ranged from 3 copies to 6.3 × 104 copies/reaction. Subsequently, the capsid/prM structural gene region of JEV positive samples was amplified by nested RT-PCR, sequenced, and genetically characterized. The phylogenetic analysis of the partial sequences of the capsid gene of 42 JEV positive samples showed that they all belonged to genotype-III (G-III) of JEV. Notably, JEV positive swine samples showed high nucleotide identity with human isolates from China and Nepal which explains the probable spillover of infection between neighboring countries probably by migratory birds. The novel mutations were observed in JEV positive sample B8 at C54 position (Phe → Ser), and JEV positive sample K50 at C62 (Thr → Ala) and C65 (Leu → Pro) positions which were absent from other JEV isolates reported till now. The mutation at the C66 position (Leu → Ser) observed in live attenuated vaccine SA14-14-2 strain was not found in JEV positive samples of our study. The detection of the G-III JE virus from climatically diverse states of India reinforces the need to continue the ongoing human vaccination program in India by extending vaccine coverage in temperate states.
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Affiliation(s)
- Akash Balasaheb Mote
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Deepa Mehta
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - M Suman Kumar
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Megha Gupta
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Mir Hussain
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Sagar M Patel
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Ravi Kumar Gandham
- Division of Animal Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Himani Dhanze
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India.
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8
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Roberts A, Prakashan D, Dhanze H, Gandham RK, Gandhi S, Sharma GT. Immuno-chromatic probe based lateral flow assay for point-of-care detection of Japanese encephalitis virus NS1 protein biomarker in clinical samples using a smartphone-based approach. Nanoscale Adv 2022; 4:3966-3977. [PMID: 36133331 PMCID: PMC9470087 DOI: 10.1039/d2na00463a] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/08/2022] [Indexed: 05/08/2023]
Abstract
Lateral flow assays (LFAs) are one of the most economical, point-of-care (PoC) diagnostic assays that exploit the colorimetric properties of gold nanoparticles (AuNPs). Up to the best of our knowledge, no rapid antigen-based LFA exists for Japanese Encephalitis Virus (JEV) detection. Herein, we have reported a novel portable sandwich-type LFA for on-site detection of the non-structural 1 (NS1) secretory protein of JEV. In-house JEV NS1 antibodies (Abs) were generated and labelled with AuNPs as immunoprobes. A glass fibre membrane conjugate pad was soaked with AuNPs-Ab solution, while the JEV NS1 Ab and anti-rabbit IgG 2° Ab were coated as the test and control lines, respectively, on a nitrocellulose (NC) membrane. Different layers of the LFA were fabricated and various parameters were standardised for optimum colour intensity development. JEV negative serum samples spiked with JEV NS1 Ags (linear range - 1 pg ml-1 to 1 μg ml-1) were applied onto the sample pad and the intensity of the red colour developed on the test line increased with increasing concentration of Ag. The visual limit of detection (LOD) determined from the LFA was 10 pg ml-1, which corresponded to the LOD determined by the graphical data obtained from ImageJ software and the Colorimeter smartphone application. Furthermore, the colorimetric based immunosensor showed minimal non-specific detection of other closely related flaviviral NS1 Ags in the spiked serum, provided a rapid result within 10 min, showed storage stability up to a month at 4 °C, successfully detected the JEV NS1 protein in clinically infected pig serum samples, and hence, may be developed into a PoC screening diagnostic kit for JEV.
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Affiliation(s)
- Akanksha Roberts
- DBT-National Institute of Animal Biotechnology (NIAB) Hyderabad-500032 Telangana India +91-040-23120127
- DBT-Regional Centre for Biotechnology (RCB) Faridabad-121001 Haryana India
| | - Drishya Prakashan
- DBT-National Institute of Animal Biotechnology (NIAB) Hyderabad-500032 Telangana India +91-040-23120127
- DBT-Regional Centre for Biotechnology (RCB) Faridabad-121001 Haryana India
| | - Himani Dhanze
- ICAR-Indian Veterinary Research Institute (IVRI) Bareilly-243122 Uttar Pradesh India
| | - Ravi Kumar Gandham
- ICAR-Indian Veterinary Research Institute (IVRI) Bareilly-243122 Uttar Pradesh India
| | - Sonu Gandhi
- DBT-National Institute of Animal Biotechnology (NIAB) Hyderabad-500032 Telangana India +91-040-23120127
- DBT-Regional Centre for Biotechnology (RCB) Faridabad-121001 Haryana India
| | - G Taru Sharma
- DBT-National Institute of Animal Biotechnology (NIAB) Hyderabad-500032 Telangana India +91-040-23120127
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9
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Sonowal J, Patel CL, Gandham RK, Khan RIN, Praharaj MR, Malla WA, Dev K, Barkathullah N, Bharali K, Dubey A, Singh N, Mishra BP, Mishra B. Temporal dysregulation of genes in Lamb testis cell during sheeppox virus infection. Lett Appl Microbiol 2022; 75:1628-1638. [PMID: 36067038 DOI: 10.1111/lam.13830] [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: 05/03/2022] [Revised: 07/15/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022]
Abstract
The present study was aimed to elucidate the host-virus interactions using RNA-Seq analysis at 1h and 8h of post-infection of SPPV in LTC. The differentially expressed genes (DEGs) and the underlying mechanisms linked to the host immune responses were obtained. The protein-protein interaction (PPI) network analysis and Ingenuity pathway analysis (IPA) illustrated the interaction between the DEGs and their involvement in cell signalling responses. Highly connected hubs viz. AURKA, CHEK1, CCNB2, CDC6, and MAPK14 were identified through PPI network analysis. IPA analysis showed that IL-6 and ERK5 mediated signalling pathways were highly enriched at both time points. The TP53 gene was identified to be the leading upstream regulator that directly responded to SPPV infection, resulting in downregulation at both time points. The study provides an overview of how the lamb testis genes and their underlying mechanisms link to growth and immune response during SPPV infection.
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Affiliation(s)
- Joyshikh Sonowal
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Chhabi Lal Patel
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Ravi Kumar Gandham
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | | | | | - Waseem Akram Malla
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Kapil Dev
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - N Barkathullah
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Krishna Bharali
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Amitesh Dubey
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Neha Singh
- Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - B P Mishra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Bina Mishra
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
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10
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Masroor S, Aalam MT, Khan O, Tanuj GN, Gandham RK, Dhara SK, Gupta PK, Mishra BP, Dutt T, Singh G, Sajjanar BK. Effect of acute heat shock on stress gene expression and DNA methylation in zebu (Bos indicus) and crossbred (Bos indicus × Bos taurus) dairy cattle. Int J Biometeorol 2022; 66:1797-1809. [PMID: 35796826 DOI: 10.1007/s00484-022-02320-3] [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] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/15/2022] [Accepted: 06/21/2022] [Indexed: 05/19/2023]
Abstract
Environmental temperature is one of the major factors to affect health and productivity of dairy cattle. Gene expression networks within the cells and tissues coordinate stress response, metabolism, and milk production in dairy cattle. Epigenetic DNA methylations were found to mediate the effect of environment by regulating gene expression patterns. In the present study, we compared three Indian native zebu cattle, Bos indicus (Sahiwal, Tharparkar, and Hariana) and one crossbred Bos indicus × Bos taurus (Vrindavani) for stress gene expression and differences in the DNA methylation patterns. The results indicated acute heat shock to cultured PBMC affected their proliferation, stress gene expression, and DNA methylation. Interestingly, expressions of HSP70, HSP90, and STIP1 were found more pronounced in zebu cattle than the crossbred cattle. However, no significant changes were observed in global DNA methylation due to acute heat shock, even though variations were observed in the expression patterns of DNA methyltransferases (DNMT1, DNMT3a) and demethylases (TET1, TET2, and TET3) genes. The treatment 5-AzaC (5-azacitidine) that inhibit DNA methylation in proliferating PBMC caused significant increase in heat shock-induced HSP70 and STIP1 expression indicating that hypomethylation facilitated stress gene expression. Further targeted analysis DNA methylation in the promoter regions revealed no significant differences for HSP70, HSP90, and STIP1. However, there was a significant hypomethylation for BDNF in both zebu and crossbred cattle. Similarly, NR3C1 promoter region showed hypomethylation alone in crossbred cattle. Overall, the results indicated that tropically adapted zebu cattle had comparatively higher expression of stress genes than the crossbred cattle. Furthermore, DNA methylation may play a role in regulating expression of certain genes involved in stress response pathways.
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Affiliation(s)
- Sana Masroor
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Mohd Tanzeel Aalam
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Owais Khan
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Gunturu Narasimha Tanuj
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Ravi Kumar Gandham
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Sujoy K Dhara
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Praveen K Gupta
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Bishnu Prasad Mishra
- ICAR-National Bureau of Animal Genetic Resources, Haryana, Karnal, 132001, India
| | - Triveni Dutt
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Gynendra Singh
- Physiology and Climatology Division, ICAR-Indian Veterinary Research Institute, Izatnagar Bareilly, 243122, Uttar Pradesh, India
| | - Basavaraj K Sajjanar
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India.
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11
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Sonowal J, Lal Patel C, Dev K, Singh R, Barkathullah N, Akram Malla W, Kumar Gandham R, Kant Agarwal R, Kumar D, Saxena S, Kalaiselvan E, Dubey A, Bharali K, Ishaq Nabi Khan R, Mishra BP, Mishra B. Selection and validation of suitable reference gene for qPCR gene expression analysis in lamb testis cells under Sheep pox virus infection. Gene 2022; 831:146561. [PMID: 35561845 DOI: 10.1016/j.gene.2022.146561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/01/2022] [Accepted: 05/06/2022] [Indexed: 11/30/2022]
Abstract
Virus infection alters host gene expression, therefore ideal and stable reference housekeeping genes are required to normalise the expression of other expressed host genes in quantitative real-time PCR (qRT-PCR). The suitable reference gene may vary in response to different viral infections in different hosts or cells. In the present study, we cultured primary lamb testis cells (LTC) and assessed the expression stability of seven widely used housekeeping genes (B2M, HMBS, HPRT1, HSP-90, POLR2A, 18s_RNA, GAPDH) as reference genes in Sheeppox virus (SPPV) infected and control (uninfected-0h) LTC at 0.5h, 4.0h, 8.0h, and 12.0h post-infection) using NormFinder, Bestkeeper, geNorm, and the comparative ΔCT method in RefFinder based on their expression levels. Analysis revealed that HSP90, 18s_RNA, HPRT, POLR2A, and B2M were the most stable genes from the panel in the individual analysis group in 0h, 0.5h, 4.0h, 8.0h, and 12.0h, respectively. Furthermore, B2M was shown to be the most stable reference gene in the combined control with the respective and overall infected groups, except the control group of 4.0hpi of SPPV infection. In this study, we selected the most suitable reference genes in LTC for particular time points of SPPV infection. The identified most suitable housekeeping gene can be used during normalization of expression of other targeted genes at aspecific time point of SPPV infection.
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Affiliation(s)
- Joyshikh Sonowal
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Chhabi Lal Patel
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India.
| | - Kapil Dev
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Rohit Singh
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - N Barkathullah
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Waseem Akram Malla
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Ravi Kumar Gandham
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Ravi Kant Agarwal
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Deepak Kumar
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Shikha Saxena
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - E Kalaiselvan
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Amitesh Dubey
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Krishna Bharali
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | | | - B P Mishra
- ICAR- National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Bina Mishra
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India.
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12
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Praharaj MR, Garg P, Kesarwani V, Topno NA, Khan RIN, Sharma S, Panigrahi M, Mishra BP, Mishra B, Kumar GS, Gandham RK, Singh RK, Majumdar S, Mohapatra T. SARS-CoV-2 Spike Glycoprotein and ACE2 Interaction Reveals Modulation of Viral Entry in Wild and Domestic Animals. Front Med (Lausanne) 2022; 8:775572. [PMID: 35360445 PMCID: PMC8962831 DOI: 10.3389/fmed.2021.775572] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/30/2021] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a viral pathogen causing life-threatening diseases in humans. Interaction between the spike protein of SARS-CoV-2 and angiotensin-converting enzyme 2 (ACE2) is a potential factor in the infectivity of a host. In this study, the interaction of SARS-CoV-2 spike protein with its receptor, ACE2, in different hosts was evaluated to predict the probability of viral entry. Phylogeny and alignment comparison of the ACE2 sequences did not lead to any meaningful conclusion on viral entry in different hosts. The binding ability between ACE2 and the spike protein was assessed to delineate several spike binding parameters of ACE2. A significant difference between the known infected and uninfected species was observed for six parameters. However, these parameters did not specifically categorize the Orders into infected or uninfected. Finally, a logistic regression model constructed using spike binding parameters of ACE2, revealed that in the mammalian class, most of the species of Carnivores, Artiodactyls, Perissodactyls, Pholidota, and Primates had a high probability of viral entry. However, among the Proboscidea, African elephants had a low probability of viral entry. Among rodents, hamsters were highly probable for viral entry with rats and mice having a medium to low probability. Rabbits have a high probability of viral entry. In Birds, ducks have a very low probability, while chickens seemed to have medium probability and turkey showed the highest probability of viral entry. The findings prompt us to closely follow certain species of animals for determining pathogenic insult by SARS-CoV-2 and for determining their ability to act as a carrier and/or disseminator.
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Affiliation(s)
| | - Priyanka Garg
- National Institute of Animal Biotechnology, Hyderabad, India
| | - Veerbhan Kesarwani
- National Institute of Animal Biotechnology, Hyderabad, India
- Hap Biosolutions Pvt. Ltd., Bhopal, India
| | - Neelam A. Topno
- National Institute of Animal Biotechnology, Hyderabad, India
| | | | - Shailesh Sharma
- National Institute of Animal Biotechnology, Hyderabad, India
| | | | - B. P. Mishra
- ICAR-National Bureau of Animal Genetic Resources, Haryana, India
| | - Bina Mishra
- ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - G. Sai Kumar
- ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Ravi Kumar Gandham
- ICAR-Indian Veterinary Research Institute, Izatnagar, India
- *Correspondence: Ravi Kumar Gandham
| | - Raj Kumar Singh
- ICAR-Indian Veterinary Research Institute, Izatnagar, India
- Raj Kumar Singh
| | - Subeer Majumdar
- National Institute of Animal Biotechnology, Hyderabad, India
- Subeer Majumdar
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13
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Kumar A, Kumar Gaur G, Panigrahi M, V N MA, Priya B, Gupta JP, Gandham RK. Comparative gene expression profile in circulating PBMCs of Bos indicus and crossbred cattle to understand disease tolerance mechanism. Anim Biotechnol 2022:1-9. [PMID: 35244514 DOI: 10.1080/10495398.2022.2043883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The present investigation was performed to compare the global gene expression profile in peripheral blood mononuclear cells (PBMCs) of Bos indicus and crossbred (Bos taurus × B. indicus) cattle. Previously, several studies revealed the disease tolerance potential of B. indicus cattle but underlying genetic mechanism is still not fully explored. The PBMCs model was used for this investigation as it plays crucial role in the immune system regulation. Transcriptomic analysis revealed total 6767 significantly differentially expressed transcripts (fold change (absolute) >2.0, p < .05). In addition, 4149 transcripts were upregulated, 2618 transcripts were downregulated and fold change (absolute) of differentially expressed transcript varied from -223.32 to 213.63. Functional annotation analysis of differentially expressed genes confirmed their role in various molecular pathways viz. innate immune response, antigen processing and presentation, MHC protein complex, defense response to bacterium, regulation of immune response, positive regulation of JAK-STAT cascade, cytoskeletal protein binding, etc. Protein-protein interaction network analysis provided understanding of inter-relationship of immune genes with differentially expressed genes. In conclusion, this study could provide comprehensive information about the dysregulated genes and biological pathways in PBMCs which might be responsible for disease tolerance in B. indicus cattle.
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Affiliation(s)
- Amod Kumar
- ICAR - National Bureau of Animal Genetic Resources (NBAGR), Karnal, India
| | | | | | | | - Bhuvana Priya
- ICAR - Indian Veterinary Research Institute, Bareilly, India
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14
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Pandey A, Malla WA, Sahu AR, Wani SA, Khan RIN, Saxena S, Ramteke PW, Praharaj MR, Kumar A, Rajak KK, Mishra B, Muthuchelvan D, Sajjanar B, Mishra BP, Singh RK, Gandham RK. Differential expression of long non-coding RNAs under Peste des petits ruminants virus (PPRV) infection in goats. Virulence 2022; 13:310-322. [PMID: 35129076 PMCID: PMC8824212 DOI: 10.1080/21505594.2022.2026564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Peste des petits ruminants (PPR) characterized by fever, sore mouth, conjunctivitis, gastroenteritis, and pneumonia, is an acute, highly contagious viral disease of sheep and goats. The role of long non-coding RNAs (lncRNAs) in PPRV infection has not been explored to date. In this study, the transcriptome profiles of virulent Peste des petits ruminants virus (PPRV) infected goat tissues – lung and spleen were analyzed to identify the role of lncRNAs in PPRV infection. A total of 13,928 lncRNA transcripts were identified, out of which 170 were known lncRNAs. Intergenic lncRNAs (7625) formed the major chunk of the novel lncRNA transcripts. Differential expression analysis revealed that 15 lncRNAs (11 downregulated and 4 upregulated) in the PPRV infected spleen samples and 16 lncRNAs (13 downregulated and 3 upregulated) in PPRV infected lung samples were differentially expressed as compared to control. The differentially expressed lncRNAs (DElncRNAs) possibly regulate various immunological processes related to natural killer cell activation, antigen processing and presentation, and B cell activity, by regulating the expression of mRNAs through the cis- or trans-regulatory mechanism. Functional enrichment analysis of differentially expressed mRNAs (DEmRNAs) revealed enrichment of immune pathways and biological processes in concordance with the pathways in which correlated lncRNA-neighboring genes were enriched. The results suggest that a coordinated immune response is raised in both lung and spleen tissues of the goat through mRNA-lncRNA crosstalk.
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Affiliation(s)
- Aruna Pandey
- Division of Veterinary Biotechnology, ICAR-IVRI, Bareilly, India
| | | | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, ICAR-IVRI, Bareilly, India
| | - Sajad Ahmad Wani
- Division of Veterinary Biotechnology, ICAR-IVRI, Bareilly, India
| | | | - Shikha Saxena
- Division of Veterinary Biotechnology, ICAR-IVRI, Bareilly, India
| | - P W Ramteke
- Department of Biological Sciences, SHUATS, Allahabad, India
| | - Manas Ranjan Praharaj
- Genomics and Bioinformatics, National Institute of Animal Biotechnology, Hyderabad, India
| | - Amit Kumar
- Division of Animal Genetics and Breeding, ICAR-IVRI, Bareilly, India
| | | | - Bina Mishra
- Division of Biological Products, ICAR-IVRI, Bareilly, India
| | | | | | | | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-IVRI, Bareilly, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-IVRI, Bareilly, India.,Genomics and Bioinformatics, National Institute of Animal Biotechnology, Hyderabad, India
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15
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Khan RIN, Sahu AR, Malla WA, Praharaj MR, Hosamani N, Kumar S, Gupta S, Sharma S, Saxena A, Varshney A, Singh P, Verma V, Kumar P, Singh G, Pandey A, Saxena S, Gandham RK, Tiwari AK. Systems biology under heat stress in Indian cattle. Gene 2021; 805:145908. [PMID: 34411649 DOI: 10.1016/j.gene.2021.145908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 11/26/2022]
Abstract
Transcriptome profiling of Vrindavani and Tharparkar cattle (n = 5 each) revealed that more numbers of genes were dysregulated in Vrindavani than in Tharparkar. A contrast in gene expression was observed with 18.9 % of upregulated genes in Vrindavani downregulated in Tharparkar and 17.8% upregulated genes in Tharparkar downregulated in Vrindavani. Functional annotation of genes differentially expressed in Tharparkar and Vrindavani revealed that the systems biology in Tharparkar is moving towards counteracting the effects due to heat stress. Unlike Vrindavani, Tharparkar is not only endowed with higher expression of the scavengers (UBE2G1, UBE2S, and UBE2H) of misfolded proteins but also with protectors (VCP, Serp1, and CALR) of naïve unfolded proteins. Further, higher expression of the antioxidants in Tharparkar enables it to cope up with higher levels of free radicals generated as a result of heat stress. In this study, we found relevant genes dysregulated in Tharparkar in the direction that can counter heat stress.
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Affiliation(s)
- Raja Ishaq Nabi Khan
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Waseem Akram Malla
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Manas Ranjan Praharaj
- Computational Biology and Genomics, National Institute of Animal Biotechnology, Hyderabad, India
| | - Neelima Hosamani
- Computational Biology and Genomics, National Institute of Animal Biotechnology, Hyderabad, India
| | - Shakti Kumar
- Computational Biology and Genomics, National Institute of Animal Biotechnology, Hyderabad, India
| | - Smita Gupta
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Shweta Sharma
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Archana Saxena
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Anshul Varshney
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Pragya Singh
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Vinay Verma
- Division of Physiology and Climatology, Indian Veterinary Research Institute, Bareilly, India
| | - Puneet Kumar
- Division of Physiology and Climatology, Indian Veterinary Research Institute, Bareilly, India
| | - Gyanendra Singh
- Division of Physiology and Climatology, Indian Veterinary Research Institute, Bareilly, India
| | - Aruna Pandey
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Ravi Kumar Gandham
- Computational Biology and Genomics, National Institute of Animal Biotechnology, Hyderabad, India.
| | - Ashok Kumar Tiwari
- Division of Biological Standardization, Indian Veterinary Research Institute, Bareilly, India.
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16
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Wani SA, Sahu AR, Khan RIN, Praharaj MR, Saxena S, Rajak KK, Muthuchelvan D, Sahoo A, Mishra B, Singh RK, Mishra BP, Gandham RK. Proteome Modulation in Peripheral Blood Mononuclear Cells of Peste des Petits Ruminants Vaccinated Goats and Sheep. Front Vet Sci 2021; 8:670968. [PMID: 34631844 PMCID: PMC8493254 DOI: 10.3389/fvets.2021.670968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/31/2021] [Indexed: 12/03/2022] Open
Abstract
In the present study, healthy goats and sheep (n = 5) that were confirmed negative for peste des petits ruminants virus (PPRV) antibodies by monoclonal antibody-based competitive ELISA and by serum neutralization test and for PPRV antigen by s-ELISA were vaccinated with Sungri/96. A quantitative study was carried out to compare the proteome of peripheral blood mononuclear cells (PBMCs) of vaccinated goat and sheep [5 days post-vaccination (dpv) and 14 dpv] vs. unvaccinated (0 day) to divulge the alteration in protein expression following vaccination. A total of 232 and 915 proteins were differentially expressed at 5 and 14 dpv, respectively, in goats. Similarly, 167 and 207 proteins were differentially expressed at 5 and 14 dpv, respectively, in sheep. Network generated by Ingenuity Pathway Analysis was “infectious diseases, antimicrobial response, and inflammatory response,” which includes the highest number of focus molecules. The bio functions, cell-mediated immune response, and humoral immune response were highly enriched in goats at 5 dpv and at 14 dpv. At the molecular level, the immune response produced by the PPRV vaccine virus in goats is effectively coordinated and stronger than that in sheep, though the vaccine provides protection from virulent virus challenge in both. The altered expression of certain PBMC proteins especially ISG15 and IRF7 induces marked changes in cellular signaling pathways to coordinate host immune responses.
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Affiliation(s)
- Sajad Ahmad Wani
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India.,College of Pharmacy, Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH, United States
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - Raja Ishaq Nabi Khan
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - Manas Ranjan Praharaj
- Systems Biology Lab, Department of Biotechnology -National Institute of Animal Biotechnology, Hyderabad, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - Kaushal Kishor Rajak
- Division of Biological Products, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - Dhanavelu Muthuchelvan
- Division of Virology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Mukteswar, India
| | - Aditya Sahoo
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - Bina Mishra
- Division of Biological Products, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - R K Singh
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - Bishnu Prasad Mishra
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India.,Systems Biology Lab, Department of Biotechnology -National Institute of Animal Biotechnology, Hyderabad, India
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17
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Priya GB, Agrawal RK, Milton AAP, Mendiratta SK, Singh BR, Kumar D, Mishra M, Gandham RK. Isothermal amplification assay for visual on-site detection of Staphylococcus aureus in Chevon. FOOD BIOTECHNOL 2021. [DOI: 10.1080/08905436.2021.1941078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Govindarajan Bhuvana Priya
- Division of Bacteriology & Mycology, ICAR-Indian Veterinary Research Institute, Bareilly, India
- College of Agriculture, Central Agriculture University (Imphal), Imphal, India
| | - Ravi Kant Agrawal
- Division of Livestock Products Technology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | | | - Sanjod Kumar Mendiratta
- Division of Livestock Products Technology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Bhoj Raj Singh
- Division of Veterinary Epidemiology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Deepak Kumar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Madhu Mishra
- Division of Bacteriology & Mycology, ICAR-Indian Veterinary Research Institute, Bareilly, India
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Vanamamalai VK, Garg P, Kolluri G, Gandham RK, Jali I, Sharma S. Transcriptomic analysis to infer key molecular players involved during host response to NDV challenge in Gallus gallus (Leghorn & Fayoumi). Sci Rep 2021; 11:8486. [PMID: 33875770 PMCID: PMC8055681 DOI: 10.1038/s41598-021-88029-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are the transcripts of length longer than 200 nucleotides. They are involved in the regulation of various biological activities. Leghorn and Fayoumi breeds of Gallus gallus were known to be having differential resistance against Newcastle Disease Virus (NDV) infection. Differentially expressed genes which were thought to be involved in this pattern of resistance were already studied. Here we report the analysis of the transcriptomic data of Harderian gland of Gallus gallus for studying the lncRNAs involved in regulation of these genes. Using bioinformatics approaches, a total of 37,411 lncRNAs were extracted and 359 lncRNAs were differentially expressing. Functional annotation using co-expression analysis revealed the involvement of lncRNAs in the regulation of various pathways. We also identified 1232 quantitative trait loci (QTLs) associated with the genes interacting with lncRNA. Additionally, we identified the role of lncRNAs as putative micro RNA precursors, and the interaction of differentially expressed Genes with transcription factors and micro RNAs. Our study revealed the role of lncRNAs during host response against NDV infection which would facilitate future experiments in unravelling regulatory mechanisms of development in the genetic improvement of the susceptible breeds of Gallus gallus.
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Affiliation(s)
- Venkata Krishna Vanamamalai
- National Institute of Animal Biotechnology (NIAB), Opposite Journalist Colony, Near Gowlidoddi Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Priyanka Garg
- National Institute of Animal Biotechnology (NIAB), Opposite Journalist Colony, Near Gowlidoddi Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Gautham Kolluri
- ICAR-Central Avian Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Ravi Kumar Gandham
- National Institute of Animal Biotechnology (NIAB), Opposite Journalist Colony, Near Gowlidoddi Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Itishree Jali
- National Institute of Animal Biotechnology (NIAB), Opposite Journalist Colony, Near Gowlidoddi Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Shailesh Sharma
- National Institute of Animal Biotechnology (NIAB), Opposite Journalist Colony, Near Gowlidoddi Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India.
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Nagalingam M, Basheer TJ, Balamurugan V, Shome R, Kumari SS, Reddy GBM, Shome BR, Rahman H, Roy P, Kingston JJ, Gandham RK. Comparative evaluation of the immunodominant proteins of Brucella abortus for the diagnosis of cattle brucellosis. Vet World 2021; 14:803-812. [PMID: 33935431 PMCID: PMC8076471 DOI: 10.14202/vetworld.2021.803-812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 02/15/2021] [Indexed: 11/20/2022] Open
Abstract
Background and Aim: The present serodiagnosis of brucellosis in livestock is based on the whole cell or smooth lipopolysaccharide of the Brucella organism in which specificity is hampered by the cross-reactivity, especially with the antibodies against Yersinia enterocolitica O:9 organism. The problem can be addressed by screening for better immunodominant antigens. Hence, the present study was undertaken to screen protein antigens of Brucella abortus for their diagnostic potential in cattle brucellosis. Materials and Methods: Protein antigens of B. abortus (n=10) non-reactive to antibodies against Y. enterocolitica O:9 were selected, expressed in Escherichia coli, assessed the reactivity of expressed recombinant proteins by Western blot, standardized indirect-enzyme-linked immunosorbent assay (ELISA) for detecting Brucella antibodies in cattle serum, and comparative evaluation was done. Results: All the selected protein antigens were expressed and in the Western blot with Brucella antibodies positive cattle serum, six recombinant (Brucella protein 26 [BP26], Cu-Zn Superoxide dismutase [SodC], B. abortus I-1885, Serine protease, Bacterioferritin, and Brucella Lumazine Synthase [BLS]) proteins showed reaction whereas none of the proteins showed reactivity with Brucella negative cattle serum. ELISA has been done using known Brucella positive and negative cattle sera samples (n=113 each) in which the performance of recombinant proteins in diagnosing brucellosis was in the order of BP26 > BLS > SodC followed by rest of the proteins. BP26 based ELISA was found to be better with area under the curve as 0.953, and diagnostic sensitivity, diagnostic specificity, and Youden’s index of 90.27%, 95.58%, and 0.8584, respectively, with the excellent agreement (k=0.85). Conclusion: BP26 could be a potential diagnostic antigen among the immunodominant proteins of B. abortus in ruling out Y. enterocolitica O:9 infection while diagnosing brucellosis in cattle herds.
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Affiliation(s)
- Mohandoss Nagalingam
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Thaslim J Basheer
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | | | - Rajeswari Shome
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - S Sowjanya Kumari
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - G B Manjunatha Reddy
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Bibek Ranjan Shome
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Habibur Rahman
- International Livestock Research Institute, New Delhi, India
| | - Parimal Roy
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | | | - R K Gandham
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
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20
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Rao PL, Gandham RK, Subbiah M. Publisher Correction: Molecular evolution and genetic variations of V and W proteins derived by RNA editing in Avian Paramyxoviruses. Sci Rep 2020; 10:16711. [PMID: 33009419 PMCID: PMC7532195 DOI: 10.1038/s41598-020-70782-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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21
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Trivedi JK, Mahapatra RP, Gandham RK, Ramakrishna GV, Satapathy SK, Mohanty SK, Suresh A. Ebstein's anomaly presenting with the acute coronary syndrome-a rare combination. Indian J Thorac Cardiovasc Surg 2020; 36:56-59. [PMID: 33061095 DOI: 10.1007/s12055-019-00840-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 11/30/2022] Open
Abstract
Ebstein's anomaly is a relatively rare congenital heart disorder characterised by downward displacement of septal and posterior leaflets of the tricuspid valve into the right ventricle cavity. The usual presenting symptoms are cyanosis, right-sided heart failure and arrhythmia. Progressive heart failure or tachyarrhythmia may worsen cyanosis. The acute coronary syndrome is rarely reported in Ebstein's anomaly. We report a patient of undiagnosed Ebstein's anomaly who was apparently asymptomatic but presented with the acute coronary syndrome. This case report deals with a rare combination of congenital heart disease (Ebstein's anomaly) and coronary artery disease. Ebstein's anomaly (EA) has a prevalence of 1% of all congenital heart diseases, and little evidence is reported in the literature where EA along with coronary artery disease (CAD) exists in individuals less than 45 years old. Therefore, this case report brings attention to the rarity of those pathologies, which individually are already considered rare. And in this case, the association turns this diagnosis exceptional and highlights the complexity of the treatment.
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Affiliation(s)
- Jaideep Kumar Trivedi
- Department of CT Surgery, Apollo Hospitals, Health City, Arilova, Vishakhapatnam, Andhra Pradesh PIN-530040 India
| | - Rudra Pratap Mahapatra
- Department of CT Surgery, Apollo Hospitals, Health City, Arilova, Vishakhapatnam, Andhra Pradesh PIN-530040 India
| | - Ravi Kumar Gandham
- Department of CT Surgery, Apollo Hospitals, Health City, Arilova, Vishakhapatnam, Andhra Pradesh PIN-530040 India
| | | | - Sunil Kumar Satapathy
- Department of CT Surgery, Apollo Hospitals, Health City, Arilova, Vishakhapatnam, Andhra Pradesh PIN-530040 India
| | - Sujit Kumar Mohanty
- Department of CT Surgery, Apollo Hospitals, Health City, Arilova, Vishakhapatnam, Andhra Pradesh PIN-530040 India
| | - Allamsetty Suresh
- Department of CT Surgery, Apollo Hospitals, Health City, Arilova, Vishakhapatnam, Andhra Pradesh PIN-530040 India
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22
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Roberts A, Chauhan N, Islam S, Mahari S, Ghawri B, Gandham RK, Majumdar SS, Ghosh A, Gandhi S. Graphene functionalized field-effect transistors for ultrasensitive detection of Japanese encephalitis and Avian influenza virus. Sci Rep 2020; 10:14546. [PMID: 32884083 PMCID: PMC7471952 DOI: 10.1038/s41598-020-71591-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/18/2020] [Indexed: 01/21/2023] Open
Abstract
Graphene, a two-dimensional nanomaterial, has gained immense interest in biosensing applications due to its large surface-to-volume ratio, and excellent electrical properties. Herein, a compact and user-friendly graphene field effect transistor (GraFET) based ultrasensitive biosensor has been developed for detecting Japanese Encephalitis Virus (JEV) and Avian Influenza Virus (AIV). The novel sensing platform comprised of carboxy functionalized graphene on Si/SiO2 substrate for covalent immobilization of monoclonal antibodies of JEV and AIV. The bioconjugation and fabrication process of GraFET was characterized by various biophysical techniques such as Ultraviolet-Visible (UV-Vis), Raman, Fourier-Transform Infrared (FT-IR) spectroscopy, optical microscopy, Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). The change in the resistance due to antigen-antibody interaction was monitored in real time to evaluate the electrical response of the sensors. The sensors were tested in the range of 1 fM to 1 μM for both JEV and AIV antigens, and showed a limit of detection (LOD) upto 1 fM and 10 fM for JEV and AIV respectively under optimised conditions. Along with ease of fabrication, the GraFET devices were highly sensitive, specific, reproducible, and capable of detecting ultralow levels of JEV and AIV antigen. Moreover, these devices can be easily integrated into miniaturized FET-based real-time sensors for the rapid, cost-effective, and early Point of Care (PoC) diagnosis of JEV and AIV.
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Affiliation(s)
- Akanksha Roberts
- DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, 500032, India
| | - Neha Chauhan
- Department of Physics, Indian Institute of Science (IISc), Bangalore, 560012, India
| | - Saurav Islam
- Department of Physics, Indian Institute of Science (IISc), Bangalore, 560012, India
| | - Subhasis Mahari
- DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, 500032, India
| | - Bhaskar Ghawri
- Department of Physics, Indian Institute of Science (IISc), Bangalore, 560012, India
| | - Ravi Kumar Gandham
- DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, 500032, India
| | - S S Majumdar
- DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, 500032, India
| | - Arindam Ghosh
- Department of Physics, Indian Institute of Science (IISc), Bangalore, 560012, India
- Center for Nanoscience and Engineering, Indian Institute of Science (IISc), Bangalore, 560012, India
| | - Sonu Gandhi
- DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, 500032, India.
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23
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Sah V, Kumar A, Dhar P, Upmanyu V, Tiwari AK, Wani SA, Sahu AR, Kumar A, Badasara SK, Pandey A, Saxena S, Rai A, Mishra BP, Singh RK, Gandham RK. Signature of genome wide gene expression in classical swine fever virus infected macrophages and PBMCs of indigenous vis-a-vis crossbred pigs. Gene 2020; 731:144356. [PMID: 31935504 DOI: 10.1016/j.gene.2020.144356] [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: 08/28/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 01/07/2023]
Abstract
The genetic basis of differential host immune response vis-à-vis transcriptome profile was explored in PBMCs of indigenous (Ghurrah) and crossbred pigs after classical swine fever vaccination and in monocyte derived macrophages (MDMs) challenged with virulent classical swine fever (CSF) virus. The humoral immune response (E2 antibody) was higher (74.87%) in crossbred than indigenous pigs (58.20%) at 21st days post vaccination (21dpv). The rate of reduction of ratio of CD4+/CD8+ was higher in crossbred pigs than indigenous pigs at 7th days post vaccination (7dpv). The immune genes IFIT1, IFIT5, RELA, NFKB2, TNF and LAT2 were up regulated at 7dpv in RNA seq data set and was in concordance during qRT-PCR validation. The Laminin Subunit Beta 1 (LAMB1) was significantly (p ≤ 0.05) down-regulated in MDMs of indigenous pigs and consequently a significantly (p ≤ 0.01) higher copy number of virulent CSF virus was evidenced in macrophages of crossbred pigs than indigenous pigs. Activation of LXR:RXR pathway at 60 h post infection (60hpi) in MDMs of indigenous versus crossbred pigs inhibited nuclear translocation of NF-κB, resulted into transrepression of proinflammatory genes. But it helped in maintenance of HDL level by lowering down cholesterol/LDL level in MDMs of indigenous pigs. The key immune genes (TLR2, TLR4, IL10, IL8, CD86, CD54, CASP1) of TREM1 signaling pathway were upregulated at 7dpv in PBMCs but those genes were downregulated at 60hpi in MDMs indigenous pigs. Using qRT-PCR, the validation of differentially expressed, immunologically important genes (LAMB1, OAS1, TLR 4, TLR8 and CD86) in MDMs revealed that expression of these genes were in concordance with RNA-seq data.
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Affiliation(s)
- Vaishali Sah
- Animal Genetics, ICAR-IVRI, Izatnagar, Bareilly, India
| | - Amit Kumar
- Animal Genetics, ICAR-IVRI, Izatnagar, Bareilly, India.
| | - P Dhar
- Standardization Division, ICAR-IVRI, Izatnagar, Bareilly, India
| | - V Upmanyu
- Standardization Division, ICAR-IVRI, Izatnagar, Bareilly, India
| | - A K Tiwari
- Standardization Division, ICAR-IVRI, Izatnagar, Bareilly, India
| | | | - A R Sahu
- Animal Biotechnology, ICAR-IVRI, Izatnagar, Bareilly, India
| | - Ajay Kumar
- Animal Biochemistry, ICAR-IVRI, Izatnagar, Bareilly, India
| | - S K Badasara
- Immunology, ICAR-IVRI, Izatnagar, Bareilly, India
| | - Aruna Pandey
- Animal Biotechnology, ICAR-IVRI, Izatnagar, Bareilly, India
| | - Shikha Saxena
- Animal Genetics, ICAR-IVRI, Izatnagar, Bareilly, India
| | - Anil Rai
- Centre for Bioinformatics, ICAR-IASRI, Pusa, New Delhi, India
| | - B P Mishra
- Animal Biotechnology, ICAR-IVRI, Izatnagar, Bareilly, India
| | - R K Singh
- Animal Biotechnology, ICAR-IVRI, Izatnagar, Bareilly, India
| | - Ravi Kumar Gandham
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India.
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24
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Solanki KS, Gandham RK, Thomas P, Chaudhuri P. Transcriptome analysis of Brucella abortus S19∆ per immunized mouse spleen revealed activation of MHC-I and MHC-II pathways. Access Microbiol 2019; 2:acmi000082. [PMID: 33062939 PMCID: PMC7525051 DOI: 10.1099/acmi.0.000082] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/23/2019] [Indexed: 12/24/2022] Open
Abstract
The mouse (Mus musculus) has been extensively used for studying brucellosis, regarding pathogenesis, immunity and the evaluation of vaccines and therapeutics. In this work, RNA-seq was applied to explore the immunological potential of a live Brucella abortus S19∆per, a perosamine synthetase gene mutant of B. abortus S19. Comparison of transcriptome data was carried out for identifying differentially expressed genes among PBS (control) and B. abortus S19∆per immunized mice at 15 days post-immunization. Functional analysis revealed 545 significant differentially expressed genes related to mouse immunity. Specific activation of MHC-I and MHC-II antigen-processing pathways were identified as the highly enriched pathways based on Kyoto Encyclopedia of Genes and Genomes annotation. Other major immune response pathways regulated within the host were NF-kappa B signalling, chemokine signalling, T-cell receptor pathway, apoptosis, TNF signalling and nucleotide-binding oligomerization domain-like receptor signalling. These data provided new insights into the molecular mechanisms of B. abortus S19∆per-induced immune response in mice spleen that might facilitate the development of a highly immunogenic vaccine against brucellosis.
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Affiliation(s)
- Khushal Singh Solanki
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India.,National Institute of Animal Biotechnology, Opp. Journalist Colony, Near Gowlidoddy Extended, Q City Road, Gachibowli, Hyderabad, Telangana 500032, India
| | - Prasad Thomas
- Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Pallab Chaudhuri
- Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
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25
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Pesingi PV, Singh BR, Pesingi PK, Bhardwaj M, Singh SV, Kumawat M, Sinha DK, Gandham RK. MexAB-OprM Efflux Pump of Pseudomonas aeruginosa Offers Resistance to Carvacrol: A Herbal Antimicrobial Agent. Front Microbiol 2019; 10:2664. [PMID: 31803171 PMCID: PMC6877666 DOI: 10.3389/fmicb.2019.02664] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 11/01/2019] [Indexed: 11/13/2022] Open
Abstract
Carvacrol is a herbal antimicrobial agent with in vitro activity against several bacterial pathogens. However, multidrug resistant strains of Pseudomonas aeruginosa are resistant to herbal antimicrobial compounds including carvacrol. Resistance of P. aeruginosa to carvacrol is not well studied. This study was aimed to identify the gene(s) associated with carvacrol resistance, thus to understand its mechanisms in P. aeruginosa. A herbal drug resistant strain was isolated from a hospital environment. Carvacrol sensitive mutant was generated using transposon mutagenesis. The inactivated gene in the mutant was identified as mexA, which is part of the mexAB-oprM operon. Inactivation of the mexA gene resulted in a >31-fold reduction in MIC of carvacrol, whereas a >80-fold reduction was observed in the presence of drug efflux inhibitor phenylalanine-arginine β-naphthylamide (PAβN). The parental herbal-resistant strain was completely killed within 3 h of incubation in the presence of carvacrol and PAβN. The mexA inactivation did not affect the resistance to other herbal compounds used. The results demonstrate that resistance to carvacrol in P. aeruginosa is mediated by the MexAB-OprM efflux pump.
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Affiliation(s)
| | - Bhoj Raj Singh
- Division of Epidemiology, Indian Veterinary Research Institute, Bareilly, India
| | - Pavan Kumar Pesingi
- Veterinary Public Health Division, Indian Veterinary Research Institute, Bareilly, India
| | - Monika Bhardwaj
- Bacteriology & Mycology Division, Indian Veterinary Research Institute, Bareilly, India
| | - Shiv Varan Singh
- Bacteriology & Mycology Division, Indian Veterinary Research Institute, Bareilly, India
| | - Manoj Kumawat
- Division of Biochemistry, Indian Veterinary Research Institute, Bareilly, India
| | | | - Ravi Kumar Gandham
- Division of Animal Biotechnology, Indian Veterinary Research Institute, Bareilly, India
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26
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Wani SA, Sahu AR, Khan RIN, Pandey A, Saxena S, Hosamani N, Malla WA, Chaudhary D, Kanchan S, Sah V, Rajak KK, Muthuchelvan D, Mishra B, Tiwari AK, Sahoo AP, Sajjanar B, Singh YP, Gandham RK, Mishra BP, Singh RK. Contrasting Gene Expression Profiles of Monocytes and Lymphocytes From Peste-Des-Petits-Ruminants Virus Infected Goats. Front Immunol 2019; 10:1463. [PMID: 31333643 PMCID: PMC6624447 DOI: 10.3389/fimmu.2019.01463] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 01/31/2019] [Accepted: 06/10/2019] [Indexed: 01/06/2023] Open
Abstract
In this study, transcriptome analysis of PPRV infected PBMC subsets-T helper cells, T cytotoxic cells, monocytes, and B lymphocytes was done to delineate their role in host response. PPRV was found to infect lymphocytes and not monocytes. The established receptor for PPRV-SLAM was found downregulated in lymphocytes and non-differentially expressed in monocytes. A profound deviation in the global gene expression profile with a large number of unique upregulated genes (851) and downregulated genes (605) was observed in monocytes in comparison to lymphocytes. ISGs-ISG15, Mx1, Mx2, RSAD2, IFIT3, and IFIT5 that play a role in antiviral response and the genes for viral sensors-MDA5, LGP2, and RIG1, were found to be upregulated in lymphocytes and downregulated in monocytes. The transcription factors-IRF-7 and STAT-1 that regulate expression of most of the ISGs were found activated in lymphocytes and not in monocytes. Interferon signaling pathway and RIG1 like receptor signaling pathway were found activated in lymphocytes and not in monocytes. This contrast in gene expression profiles and signaling pathways indicated the predominant role of lymphocytes in generating the antiviral response against PPRV in goats, thus, giving us new insights into host response to PPRV.
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Affiliation(s)
- Sajad Ahmad Wani
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH, United States
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,Genomics and Computational Biology, DBT-National Institute of Animal Biotechnology, Hyderabad, India
| | - Raja Ishaq Nabi Khan
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Aruna Pandey
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Neelima Hosamani
- Genomics and Computational Biology, DBT-National Institute of Animal Biotechnology, Hyderabad, India
| | - Waseem Akram Malla
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Dheeraj Chaudhary
- Division of Virology, ICAR-Indian Veterinary Research Institute (IVRI), Mukteswar, India
| | - Sonam Kanchan
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Vaishali Sah
- Division of Animal Genetics and Breeding, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Kaushal Kishor Rajak
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - D Muthuchelvan
- Division of Virology, ICAR-Indian Veterinary Research Institute (IVRI), Mukteswar, India
| | - Bina Mishra
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Ashok Kumar Tiwari
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Aditya P Sahoo
- ICAR- Directorate of Foot and Mouth Disease, Mukteswar, India
| | - Basavaraj Sajjanar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Yash Pal Singh
- ARIS Cell, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,Genomics and Computational Biology, DBT-National Institute of Animal Biotechnology, Hyderabad, India
| | - Bishnu Prasad Mishra
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
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27
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Sailo L, Kumar A, Sah V, Chaudhary R, Upmanyu V, Tiwari AK, Kumar A, Pandey A, Saxena S, Singh A, Wani SA, Gandham RK, Rai A, Mishra BP, Singh RK. Genome-wide integrated analysis of miRNA and mRNA expression profiles to identify differentially expressed miR-22-5p and miR-27b-5p in response to classical swine fever vaccine virus. Funct Integr Genomics 2019; 19:901-918. [PMID: 31134483 DOI: 10.1007/s10142-019-00689-w] [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: 12/18/2018] [Revised: 04/29/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022]
Abstract
The present study was conducted to identify the differentially expressed miRNAs (DE miRNAs) in the peripheral blood mononuclear cells of crossbred pigs in response to CSF vaccination on 7 and 21 days of post vaccination as compared to unvaccinated control (0 dpv). Simultaneously, set of miRNA was predicted using mRNA seq data at same time point. The proportion of CD4-CD8+ and CD4+CD8+ increased after vaccination, and the mean percentage inhibition was 86.89% at 21 dpv. It was observed that 22 miRNAs were commonly expressed on both the time points. Out of predicted DE miRNAs, it was found that 40 and 35 DE miRNAs were common, obtained from miRNA seq analysis and predicted using mRNA seq data on 7 dpv versus 0 dpv and 21 dpv versus 0 dpv respectively. Two DE miRNAs, ssc-miR-22-5p and ssc-miR-27b-5p, were selected based on their log2 fold change and functions of their target genes in immune process/pathway of viral infections. The validations of DE miRNAs using qRT-PCR were in concordance with miRNA seq analysis. Two set of target genes, CD40 and SWAP70 (target gene of ssc-miR-22-5p) and TLR4 and Lyn (target gene of ssc-miR-27b-5p), were validated and were in concordance with results of RNA seq analysis at a particular time point (except TLR4). The first report of genome-wide identification of differentially expressed miRNA in response to live attenuated vaccine virus of classical swine fever revealed miR-22-5p and miR-27b-5p were differentially expressed at 7 dpv and 21 dpv.
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Affiliation(s)
- Lalrengpuii Sailo
- Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, 143122, India
| | - Amit Kumar
- Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, 143122, India.
| | - Vaishali Sah
- Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, 143122, India
| | - Rajni Chaudhary
- Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, 143122, India
| | - Vikramaditya Upmanyu
- Standardization Division, Indian Veterinary Research Institute, Izatnagar, Bareilly, 143122, India
| | - A K Tiwari
- Standardization Division, Indian Veterinary Research Institute, Izatnagar, Bareilly, 143122, India
| | - Ajay Kumar
- Animal Biochemistry, Indian Veterinary Research Institute, Izatnagar, Bareilly, 143122, India
| | - Aruna Pandey
- Animal Biochemistry, Indian Veterinary Research Institute, Izatnagar, Bareilly, 143122, India
| | - Shikha Saxena
- Animal Biochemistry, Indian Veterinary Research Institute, Izatnagar, Bareilly, 143122, India
| | - Akansha Singh
- Animal Genetics and Breeding, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | | | - Ravi Kumar Gandham
- Animal Biotechnology, National Institute of Animal Biotechnology, Hyderabad, Telangana, 500032, India.
| | - Anil Rai
- Head Centre for Bioinformatics, IASRI, New Delhi, 110012, India
| | - B P Mishra
- Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 143122, India
| | - R K Singh
- Animal Biochemistry, Indian Veterinary Research Institute, Izatnagar, Bareilly, 143122, India
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Bhatt M, Rajak KK, Chakravarti S, Yadav AK, Kumar A, Gupta V, Chander V, Mathesh K, Chandramohan S, Sharma AK, Mahendran K, Sankar M, Muthuchelvan D, Gandham RK, Baig M, Singh RP, Singh RK. Phylogenetic analysis of haemagglutinin gene deciphering a new genetically distinct lineage of canine distemper virus circulating among domestic dogs in India. Transbound Emerg Dis 2019; 66:1252-1267. [PMID: 30725534 DOI: 10.1111/tbed.13142] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 11/24/2018] [Revised: 01/02/2019] [Accepted: 01/26/2019] [Indexed: 11/30/2022]
Abstract
Canine distemper (CD) is one of the highly contagious and invariably fatal viral diseases of dogs and other carnivores. Despite the widespread use of modified live vaccines to control CD, the prevalence of disease has increased at an alarming rate in recent years. Although a number of factors may be ascribed for vaccine failure, antigenic differences among the vaccine and wild-type strains have gained the interest of researchers. Considering the high genetic variability of haemagglutinin gene (H gene) and its role in eliciting the immune response to canine distemper virus (CDV), we have generated nine full-length CDV H gene sequences from infected dogs including three vaccinated cases. Bayesian analysis was performed using 102 full-length H gene nucleotide sequences over a time frame of 76 years (1940-2016) from 18 countries. The time to the most recent common ancestor (tMRCA) of CDV was estimated to be 1696 AD. Phylogenetic reconstruction clustered Indian wild-type viruses into a distinct monophyletic group clearly separated from the previously established CDV lineages. This signifies the presence of a novel genetic variant (proposed as "Lineage India-1/Asia-5") circulating among dog population in India. To investigate the importance of substitutions at amino acid residues 530 and 549 of CDV H protein in determining the host switches from canid to non-canid hosts, we analysed 125 H gene sequences including nine sequences generated in this study. Selection pressure analysis and analysis of amino acid sequences revealed a trend towards adaptation of 549H variants in non-canid hosts although no role of G/E530R/D/N substitution could be identified. This is the first comprehensive study about the nature and ecology of CDV circulating among dog population in India. Outbreaks in vaccinated animals as observed in this study have raised a concern towards the effectiveness of current vaccine strains warranting detailed investigation.
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Affiliation(s)
- M Bhatt
- Division of Biological Products, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, India.,Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, India
| | - K K Rajak
- Division of Biological Products, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, India
| | - S Chakravarti
- Division of Biological Products, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, India
| | - A K Yadav
- Division of Biological Products, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, India.,ICAR-National Research Centre on Pig, Rani, Guwahati, India
| | - A Kumar
- Division of Biological Products, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, India
| | - V Gupta
- CADRAD, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, India
| | - V Chander
- CADRAD, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, India
| | - K Mathesh
- Centre for wildlife, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, India
| | - S Chandramohan
- Centre for wildlife, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, India
| | - A K Sharma
- Centre for wildlife, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, India
| | - K Mahendran
- Referral Veterinary Polyclinic, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, India
| | - M Sankar
- TAH Division, ICAR-Indian Veterinary Research Institute (IVRI), Mukteswar, Nainital, India
| | - D Muthuchelvan
- Division of Virology, ICAR-Indian Veterinary Research Institute (IVRI), Mukteswar, Nainital, India
| | - R K Gandham
- National Institute of Animal Biotechnology, Hyderabad, India
| | - M Baig
- Department of Zoology, Goverment Vidarbha Institute of Science & Humanities, Amravati, India
| | - R P Singh
- Division of Biological Products, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, India
| | - R K Singh
- ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, India
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Pandit AA, Gandham RK, Mukhopadhyay CS, Verma R, Sethi RS. Transcriptome analysis reveals the role of the PCP pathway in fipronil and endotoxin-induced lung damage. Respir Res 2019; 20:24. [PMID: 30709343 PMCID: PMC6359862 DOI: 10.1186/s12931-019-0986-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/16/2019] [Indexed: 12/21/2022] Open
Affiliation(s)
- Arif Ahmad Pandit
- Department of Animal Biotechnology, School of Animal Biotechnology, Guru Angad Dev Veterinary and Animals Sciences University, Ludhiana, Punjab, 141004, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University], Izatnagar, Bareilly, UP, India. National Institute of Animal Biotechnology, Hyderabad, India
| | - C S Mukhopadhyay
- Department of Animal Biotechnology, School of Animal Biotechnology, Guru Angad Dev Veterinary and Animals Sciences University, Ludhiana, Punjab, 141004, India
| | - Ramneek Verma
- Department of Animal Biotechnology, School of Animal Biotechnology, Guru Angad Dev Veterinary and Animals Sciences University, Ludhiana, Punjab, 141004, India
| | - R S Sethi
- Department of Animal Biotechnology, School of Animal Biotechnology, Guru Angad Dev Veterinary and Animals Sciences University, Ludhiana, Punjab, 141004, India.
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30
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Hussain S, Saxena S, Shrivastava S, Mohanty AK, Kumar S, Singh RJ, Kumar A, Wani SA, Gandham RK, Kumar N, Sharma AK, Tiwari AK, Singh RK. Gene expression profiling of spontaneously occurring canine mammary tumours: Insight into gene networks and pathways linked to cancer pathogenesis. PLoS One 2018; 13:e0208656. [PMID: 30517191 PMCID: PMC6281268 DOI: 10.1371/journal.pone.0208656] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/20/2018] [Indexed: 11/24/2022] Open
Abstract
Spontaneously occurring canine mammary tumours (CMTs) are the most common neoplasms of unspayed female dogs leading to thrice higher mortality rates than human breast cancer. These are also attractive models for human breast cancer studies owing to clinical and molecular similarities. Thus, they are important candidates for biomarker studies and understanding cancer pathobiology. The study was designed to explore underlying molecular networks and pathways in CMTs for deciphering new prognostic factors and therapeutic targets. To gain an insight into various pathways and networks associated with the development and pathogenesis of CMTs, comparative cDNA microarray expression profiling was performed using CMT tissues and healthy mammary gland tissues. Upon analysis, 1700 and 1287 differentially expressed genes (DEGs, P ≤ 0.05) were identified in malignant and benign tissues, respectively. DEGs identified from microarray analysis were further annotated using the Ingenuity Systems Pathway Analysis (IPA) tool for detection of deregulated canonical pathways, upstream regulators, and networks associated with malignant, as well as, benign disease. Top scoring key networks in benign and malignant mammary tumours were having central nodes of VEGF and BUB1B, respectively. Cyclins & cell cycle regulation and TREM1 signalling were amongst the top activated canonical pathways in CMTs. Other cancer related significant pathways like apoptosis signalling, dendritic cell maturation, DNA recombination and repair, Wnt/β-catenin signalling, etc. were also found to be altered. Furthermore, seven proteins (ANXA2, APOCII, CDK6, GATC, GDI2, GNAQ and MYH9) highly up-regulated in malignant tissues were identified by two-dimensional gel electrophoresis (2DE) and MALDI-TOF PMF studies which were in concordance with microarray data. Thus, the study has uncovered ample number of candidate genes associated with CMTs which need to be further validated as therapeutic targets and prognostic markers.
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Affiliation(s)
- Shahid Hussain
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University], Izatnagar, Bareilly, UP, India
| | - Sonal Saxena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University], Izatnagar, Bareilly, UP, India
- * E-mail: (SON); (SAM); (RKS)
| | - Sameer Shrivastava
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University], Izatnagar, Bareilly, UP, India
- * E-mail: (SON); (SAM); (RKS)
| | - Ashok Kumar Mohanty
- Animal Biotechnology Division, ICAR-National Dairy Research Institute [Deemed University], Karnal, Haryana, India
| | - Sudarshan Kumar
- Animal Biotechnology Division, ICAR-National Dairy Research Institute [Deemed University], Karnal, Haryana, India
| | - Rajkumar James Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University], Izatnagar, Bareilly, UP, India
| | - Abhinav Kumar
- Department of Computer Science and Engineering, Indian Institute of Technology (IIT) BHU, Varanasi, India
| | | | - Ravi Kumar Gandham
- National Institute of Animal Biotechnology, Miyapur, Hyderabad, Telangana, India
| | - Naveen Kumar
- Division of Veterinary Surgery, ICAR-Indian Veterinary Research Institute [Deemed University], Izatnagar, Bareilly, UP, India
| | - Anil Kumar Sharma
- Division of Veterinary Pathology, ICAR-Indian Veterinary Research Institute [Deemed University], Izatnagar, Bareilly, UP, India
| | - Ashok Kumar Tiwari
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University], Izatnagar, Bareilly, UP, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute [Deemed University], Izatnagar, Bareilly, UP, India
- * E-mail: (SON); (SAM); (RKS)
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31
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Khanduri A, Sahu AR, Wani SA, Khan RIN, Pandey A, Saxena S, Malla WA, Mondal P, Rajak KK, Muthuchelvan D, Mishra B, Sahoo AP, Singh YP, Singh RK, Gandham RK, Mishra BP. Dysregulated miRNAome and Proteome of PPRV Infected Goat PBMCs Reveal a Coordinated Immune Response. Front Immunol 2018; 9:2631. [PMID: 30524425 PMCID: PMC6262310 DOI: 10.3389/fimmu.2018.02631] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 10/25/2018] [Indexed: 12/11/2022] Open
Abstract
In this study, the miRNAome and proteome of virulent Peste des petits ruminants virus (PPRV) infected goat peripheral blood mononuclear cells (PBMCs) were analyzed. The identified differentially expressed miRNAs (DEmiRNAs) were found to govern genes that modulate immune response based on the proteome data. The top 10 significantly enriched immune response processes were found to be governed by 98 genes. The top 10 DEmiRNAs governing these 98 genes were identified based on the number of genes governed by them. Out of these 10 DEmiRNAs, 7 were upregulated, and 3 were downregulated. These include miR-664, miR-2311, miR-2897, miR-484, miR-2440, miR-3533, miR-574, miR-210, miR-21-5p, and miR-30. miR-664 and miR-484 with proviral and antiviral activities, respectively, were upregulated in PPRV infected PBMCs. miR-210 that inhibits apoptosis was downregulated. miR-21-5p that decreases the sensitivity of cells to the antiviral activity of IFNs and miR-30b that inhibits antigen processing and presentation by primary macrophages were downregulated, indicative of a strong host response to PPRV infection. miR-21-5p was found to be inhibited on IPA upstream regulatory analysis of RNA-sequencing data. This miRNA that was also highly downregulated and was found to govern 16 immune response genes in the proteome data was selected for functional validation vis-a-vis TGFBR2 (TGF-beta receptor type-2). TGFBR2 that regulates cell differentiation and is involved in several immune response pathways was found to be governed by most of the identified immune modulating DEmiRNAs. The decreased luciferase activity in Dual Luciferase Reporter Assay indicated specific binding of miR-21-5p and miR-484 to their target thus establishing specific binding of the miRNAs to their targets.This is the first report on the miRNAome and proteome of virulent PPRV infected goat PBMCs.
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Affiliation(s)
- Alok Khanduri
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,DBT-National Institute of Animal Biotechnology, Hyderabad, India
| | - Sajad Ahmad Wani
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,The Ohio State University, Columbus, Ohio, OH, United States
| | - Raja Ishaq Nabi Khan
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Aruna Pandey
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Waseem Akram Malla
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Piyali Mondal
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Kaushal Kishor Rajak
- Division of Biological Products, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - D Muthuchelvan
- Division of Virology, ICAR-Indian Veterinary Research Institute (IVRI), Mukteswar, India
| | - Bina Mishra
- Division of Biological Products, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Aditya P Sahoo
- ICAR- Directorate of Foot and Mouth Disease, Mukteswar, India
| | - Yash Pal Singh
- ARIS Cell, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,DBT-National Institute of Animal Biotechnology, Hyderabad, India
| | - Bishnu Prasad Mishra
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
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32
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Mishra B, Mondal P, Patel CL, Zafir I, Gangwar R, Singh N, Sonowal J, Bisht D, Sahu AR, Baig M, Sajjanar B, Singh RK, Gandham RK. VARV B22R homologue as phylogenetic marker gene for Capripoxvirus classification and divergence time dating. Virus Genes 2018; 55:51-59. [PMID: 30446925 DOI: 10.1007/s11262-018-1613-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 11/07/2018] [Indexed: 10/27/2022]
Abstract
Sheeppox disease is associated with significant losses in sheep production world over. The sheep pox virus, the goatpox virus, and the lumpy skin disease virus cannot be distinguished by conventional serological tests. Identification of these pathogens needs molecular methods. In this study, seven genes viz. EEV maturation protein-F12L, Virion protein-D3R, RNA polymerase subunit-A5R, Virion core protein-A10L, EEV glycoprotein-A33R, VARV B22R homologue, and Kelch like protein-A55R that cover the start, middle, and end of the genome were selected. These genes were amplified from Roumanian-Fanar vaccine strain and Jaipur virulent strain, cloned, and sequenced. On analysis with the available database sequences, VARV B22R homologue was identified as a marker for phylogenetic reconstruction for classifying the sheeppox viruses of the ungulates. Further, divergence time dating with VARV B22R gene accurately predicted the sheeppox disease outbreak involving Jaipur virulent strain.
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Affiliation(s)
- Bina Mishra
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India.
| | - Piyali Mondal
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - C L Patel
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Insha Zafir
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Rachna Gangwar
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Neha Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Joyshikh Sonowal
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Deepanker Bisht
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Mumtaz Baig
- Department of Zoology, Laboratory of Molecular and Conservation Genetics (LMCG), Govt. Vidarbha Institute of Science & Humanities, Amravati, Maharastra, 444604, India
| | - Basavaraj Sajjanar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - R K Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India.,National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi Gachibowli, Hyderabad, Telangana, 500 032, India
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Singh DK, Kumar B, Shrinet G, Singh RP, Das A, Mantur BG, Pandey A, Mondal P, Sajjanar BK, Doimari S, Singh V, Kumari R, Tiwari AK, Gandham RK. Draft genome sequence of field isolate Brucella melitensis strain 2007BM/1 from India. J Glob Antimicrob Resist 2018; 13:152-153. [PMID: 29684575 DOI: 10.1016/j.jgar.2018.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 02/22/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES Brucellosis is among one of the most widespread important global zoonotic diseases that is endemic in many parts of India. Brucella melitensis is supposed to be the most pathogenic species for humans. Here we report the draft genome sequence of B. melitensis strain 2007BM/1 isolated from a human in India. METHODS Genomic DNA was extracted from Brucella culture and was sequenced using an Illumina MiSeq platform. The generated reads were assembled using three de novo assemblers and the draft genome was annotated. RESULTS This monoisolate, with a genome length of 3268756bp, was found to be resistant to azithromycin and trimethoprim/sulfamethoxazole but susceptible to tetracycline, ofloxacin, rifampicin, ciprofloxacin and doxycycline. The presence of virulence genes in the strain was identified. CONCLUSIONS The results obtained will help in understanding drug resistance mechanisms and virulence factors in highly zoonotic B. melitensis and suggest the need for judicious use of antibiotics in livestock health and management practices.
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Affiliation(s)
- D K Singh
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izzatnagar, Bareilly 243122, Uttar Pradesh, India.
| | - Bablu Kumar
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izzatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Garima Shrinet
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izzatnagar, Bareilly 243122, Uttar Pradesh, India
| | - R P Singh
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izzatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Aparajita Das
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izzatnagar, Bareilly 243122, Uttar Pradesh, India
| | - B G Mantur
- Department of Microbiology, Belgaum Institute of Medical Sciences, District Hospital Campus, Belgaum 590 001, Karnataka, India
| | - Aruna Pandey
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izzatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Piyali Mondal
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izzatnagar, Bareilly 243122, Uttar Pradesh, India
| | - B K Sajjanar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izzatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Soni Doimari
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izzatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Vijayata Singh
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izzatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Reena Kumari
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izzatnagar, Bareilly 243122, Uttar Pradesh, India
| | - A K Tiwari
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izzatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izzatnagar, Bareilly 243122, Uttar Pradesh, India
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Praharaj MR, Sahoo AP, Chauhan TKS, Gandham RK, Saxena S, Agarwal RK, Dhama K, Mishra B, Marriappan AK, Tiwari AK, Goswami PP, Mishra BP, Kumar D. In vitro study on role of σB protein in avian reovirus pathogenesis. Oncotarget 2018; 9:19569-19583. [PMID: 29731966 PMCID: PMC5929409 DOI: 10.18632/oncotarget.24668] [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: 12/26/2017] [Accepted: 02/23/2018] [Indexed: 11/25/2022] Open
Abstract
Avian reoviruses, members of Orthoreovirus genus was known to cause diseases like tenosynovitis, runting-stunting syndrome in chickens. Among eight structural proteins, the proteins of S-class are mainly associated with viral arthritis but the significance of σB protein in arthritis is not established till date. In this infection pathological condition together with infection of joints often leads to arthritis because joints consists of cartilage which forms lubricating surface between two bones, and has limited metabolic, replicative and repair capacity. To establish the role of σB protein in arthritis, an in-vitro microarray study was conducted consisting four groups viz. virus infected and control; pDsRed-Express-N1-σB and empty pDs-Red transfected, CEF cells. With cut-off value as FC ≥2, p value <0.05, 6709 and 4026 numbers of DEGs in virus and σB, respectively were identified. The Ingenuity Pathway Analysis gave an idea about the involvement of σB protein in "osteoarthritis pathway", which was activated with z-score with 3.151. The pathway "Role of IL-17A in arthritis pathway" was also enriched with -log (p-value) 1.64. Among total 122 genes involved in osteoarthritis pathway, 28 upregulated and 11 downregulated DEGs were common to both virus and σB treated cells. Moreover, 14 upregulated and 7 downregulated were unique in σB transfected cells. Using qRT-PCR for IL-1B, BMP2, SMAD1, SPP1 genes, the microarray data was validated. We concluded that during ARV infection σB protein, if not fully partially leads to molecular alteration of various genes of host orchestrating the different molecular pattern in joints, leading to tenosynovitis syndrome.
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Affiliation(s)
- Manas R Praharaj
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Aditya P Sahoo
- ICAR- Directorate on Foot and Mouth Disease, Mukteshwar, Nainital, Uttarakhand, India
| | - Tapan K S Chauhan
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Ravi K Agarwal
- Division of Livestock Product Technology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Kuldeep Dhama
- Avian Disease Section, Division of Pathology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Bina Mishra
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Asok K Marriappan
- Avian Disease Section, Division of Pathology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Ashok K Tiwari
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Puroshottam Prasad Goswami
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Bishnu Prasad Mishra
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Deepak Kumar
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
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Sethi RS, Pandit AA, Gandham RK, Verma R, Singh B. Upregulation Of Eicosanoid Signalling In Lung Following Fipronil And Endotoxin Interaction. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.521.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ram Saran Sethi
- School of Animal BiotechnologyGuru Angad Dev Vety and Animal Sciences UniversityLudhianaIndia
| | - Arif Ahmad Pandit
- School of Animal BiotechnologyGuru Angad Dev Vety and Animal Sciences UniversityLudhianaIndia
| | | | - Ramneek Verma
- School of Animal BiotechnologyGuru Angad Dev Vety and Animal Sciences UniversityLudhianaIndia
| | - Baljit Singh
- Faculty of Veterinary MedicineUniversity of CalgaryCalgaryABCanada
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Chaudhari RK, Mahla AS, Singh AK, Singh SK, Pawde AM, Gandham RK, Singh G, Sarkar M, Kumar H, Krishnaswamy N. Effect of dietary n-3 polyunsaturated fatty acid rich fish oil on the endometrial prostaglandin production in the doe ( Capra hircus ). Prostaglandins Other Lipid Mediat 2018; 135:27-35. [DOI: 10.1016/j.prostaglandins.2018.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 01/24/2018] [Accepted: 02/05/2018] [Indexed: 12/22/2022]
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Wani SA, Sahu AR, Saxena S, Rajak KK, Saminathan M, Sahoo AP, Kanchan S, Pandey A, Mishra B, Muthuchelvan D, Tiwari AK, Mishra BP, Singh RK, Gandham RK. Expression kinetics of ISG15, IRF3, IFNγ, IL10, IL2 and IL4 genes vis-a-vis virus shedding, tissue tropism and antibody dynamics in PPRV vaccinated, challenged, infected sheep and goats. Microb Pathog 2018; 117:206-218. [PMID: 29476787 DOI: 10.1016/j.micpath.2018.02.027] [Citation(s) in RCA: 20] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/18/2018] [Accepted: 02/12/2018] [Indexed: 11/16/2022]
Abstract
Here, we studied the in vivo expression of Th1 (IL2 and IFN gamma) and Th2 (IL4 and IL10) - cytokines and antiviral molecules - IRF3 and ISG15 in peripheral blood mononuclear cells in relation to antigen and antibody dynamics under Peste des petits ruminants virus (PPRV) vaccination, infection and challenge in both sheep and goats. Vaccinated goats were seropositive by 9 days post vaccination (dpv) while in sheep idiosyncratic response was observed between 9 and 14 dpv for different animals. Expression of PPRV N gene was not detected in PBMCs of vaccinated and vaccinated challenged groups of both species, but was detected in unvaccinated infected PBMCs at 9 and 14 days post infection. The higher viral load at 9 dpi coincided with the peak clinical signs of the disease. The peak in viral replication at 9 dpi correlated with significant expression of antiviral molecules IRF3, ISG15 and IFN gamma in both the species. With the progression of disease, the decrease in N gene expression also correlated with the decrease in expression of IRF3, ISG15 and IFN gamma. In the unvaccinated infected animals ISG15, IRF3, IFN gamma and IL10 expression was higher than vaccinated animals. The IFN gamma expression predominated over IL4 in both vaccinated and infected animals with the infected exhibiting a stronger Th1 response. The persistent upregulation of this antiviral molecular signature - ISG15 and IRF3 even after 2 weeks post vaccination, presumably reflects the ongoing stimulation of innate immune cells.
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Affiliation(s)
- Sajad Ahmad Wani
- Division of Veterinary Biotechnology, ICAR-IVRI, Izatnagar, Bareilly, UP, 243122, India
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, ICAR-IVRI, Izatnagar, Bareilly, UP, 243122, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, ICAR-IVRI, Izatnagar, Bareilly, UP, 243122, India
| | - Kaushal Kishor Rajak
- Division of Biological Products, ICAR-IVRI, Izatnagar, Bareilly, UP, 243122, India
| | - M Saminathan
- Division of Veterinary Pathology, ICAR-IVRI, Izatnagar, Bareilly, UP, 243122, India
| | - Aditya Prasad Sahoo
- Division of Veterinary Biotechnology, ICAR-IVRI, Izatnagar, Bareilly, UP, 243122, India
| | - Sonam Kanchan
- Division of Veterinary Biotechnology, ICAR-IVRI, Izatnagar, Bareilly, UP, 243122, India
| | - Aruna Pandey
- Division of Veterinary Biotechnology, ICAR-IVRI, Izatnagar, Bareilly, UP, 243122, India
| | - Bina Mishra
- Division of Biological Products, ICAR-IVRI, Izatnagar, Bareilly, UP, 243122, India
| | - D Muthuchelvan
- Division of Virology, ICAR-IVRI, Mukteshwar Campus, Nainital, 263138, India
| | - Ashok Kumar Tiwari
- Division of Biological Standardization, ICAR-IVRI, Izatnagar, Bareilly, UP, 243122, India
| | - Bishnu Prasad Mishra
- Division of Veterinary Biotechnology, ICAR-IVRI, Izatnagar, Bareilly, UP, 243122, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-IVRI, Izatnagar, Bareilly, UP, 243122, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-IVRI, Izatnagar, Bareilly, UP, 243122, India.
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Priya GB, Nagaleekar VK, Milton AAP, Saminathan M, Kumar A, Sahoo AR, Wani SA, Kumar A, Gupta SK, Sahoo AP, Tiwari AK, Agarwal RK, Gandham RK. Genome wide host gene expression analysis in mice experimentally infected with Pasteurella multocida. PLoS One 2017; 12:e0179420. [PMID: 28704394 PMCID: PMC5509158 DOI: 10.1371/journal.pone.0179420] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 05/30/2017] [Indexed: 12/25/2022] Open
Abstract
Pasteurella multocida causes acute septicemic and respiratory diseases, including haemorrhagic septicaemia, in cattle and buffalo with case fatality of 100%. In the present study, mice were infected with P. multocida (1.6 × 103 cfu, intraperitoneal) to evaluate host gene expression profile at early and late stages of infection using high throughput microarray transcriptome analyses. Several differentially expressed genes (DEGs) at both the time points were identified in P.multocida infected spleen, liver and lungs. Functional annotation of these DEGs showed enrichment of key pathways such as TLR, NF-κB, MAPK, TNF, JAK-STAT and NOD like receptor signaling pathways. Several DEGs overlapped across different KEGG pathways indicating a crosstalk between them. The predicted protein—protein interaction among these DEGs suggested, that the recognition of P. multocida LPS or outer membrane components by TLR4 and CD14, results in intracellular signaling via MyD88, IRAKs and/or TRAF6 leading to activation of NFκB and MAPK pathways and associated cytokines.
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Affiliation(s)
- G. Bhuvana Priya
- Division of Bacteriology & Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Viswas Konasagara Nagaleekar
- Division of Bacteriology & Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
- * E-mail: (RKG); (VKN); (RKA)
| | - A. Arun Prince Milton
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - M. Saminathan
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Amod Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Amit Ranjan Sahoo
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sajad Ahmad Wani
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Amit Kumar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - S. K. Gupta
- Division of Livestock and Fishery Management, ICAR Research Complex for Eastern Region (ICAR-RCER), Patna, Bihar, India
| | - Aditya P. Sahoo
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - A. K. Tiwari
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - R. K. Agarwal
- Division of Bacteriology & Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
- * E-mail: (RKG); (VKN); (RKA)
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
- * E-mail: (RKG); (VKN); (RKA)
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Singh A, Prasad M, Mishra B, Manjunath S, Sahu AR, Bhuvana Priya G, Wani SA, Sahoo AP, Kumar A, Balodi S, Deora A, Saxena S, Gandham RK. Transcriptome analysis reveals common differential and global gene expression profiles in bluetongue virus serotype 16 (BTV-16) infected peripheral blood mononuclear cells (PBMCs) in sheep and goats. Genom Data 2016; 11:62-72. [PMID: 28003963 PMCID: PMC5157708 DOI: 10.1016/j.gdata.2016.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 11/30/2016] [Accepted: 12/07/2016] [Indexed: 11/29/2022]
Abstract
Bluetongue is an economically important infectious, arthropod borne viral disease of domestic and wild ruminants, caused by Bluetongue virus (BTV). Sheep are considered the most susceptible hosts, while cattle, buffalo and goats serve as reservoirs. The viral pathogenesis of BTV resulting in presence or absence of clinical disease among different hosts is not clearly understood. In the present study, transcriptome of sheep and goats peripheral blood mononuclear cells infected with BTV-16 was explored. The differentially expressed genes (DEGs) identified were found to be significantly enriched for immune system processes - NFκB signaling, MAPK signaling, Ras signaling, NOD signaling, RIG signaling, TNF signaling, TLR signaling, JAK-STAT signaling and VEGF signaling pathways. Greater numbers of DEGs were found to be involved in immune system processes in goats than in sheep. Interestingly, the DEHC (differentially expressed highly connected) gene network was found to be dense in goats than in sheep. Majority of the DEHC genes in the network were upregulated in goats but down-regulated in sheep. The network of differentially expressed immune genes with the other genes further confirmed these findings. Interferon stimulated genes - IFIT1 (ISG56), IFIT2 (ISG54) and IFIT3 (ISG60) responsible for antiviral state in the host were found to be upregulated in both the species. STAT2 was the TF commonly identified to co-regulate the DEGs, with its network showing genes that are downregulated in sheep but upregulated in goats. The genes dysregulated and the networks perturbed in the present study indicate host variability with a positive shift in immune response to BTV in goats than in sheep.
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Affiliation(s)
- Anjali Singh
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP-243122, India; Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary & Animal Sciences, Hisar, India
| | - Minakshi Prasad
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary & Animal Sciences, Hisar, India
| | - Bina Mishra
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP-243122
| | - Siddappa Manjunath
- Oomens Lab, Division of Veterinary Pathobiology, CVHS, OSU, Stillwater, OK, USA
| | - Amit Ranjan Sahu
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP-243122, India
| | - G Bhuvana Priya
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP-243122, India; Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly UP-243122, India
| | - Sajad Ahmad Wani
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP-243122, India
| | - Aditya Prasad Sahoo
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP-243122, India; Molecular Biology Lab, Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP-243122, India
| | - Amit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP-243122, India
| | - Shweta Balodi
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary & Animal Sciences, Hisar, India
| | - Anupama Deora
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary & Animal Sciences, Hisar, India
| | - Shikha Saxena
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP-243122, India
| | - Ravi Kumar Gandham
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP-243122, India
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Wani SA, Sahu AR, Saxena S, Hussain S, Pandey A, Kanchan S, Sahoo AP, Mishra B, Tiwari AK, Mishra BP, Gandham RK, Singh RK. Systems biology approach: Panacea for unravelling host-virus interactions and dynamics of vaccine induced immune response. Gene Rep 2016; 5:23-29. [PMID: 32289096 PMCID: PMC7104209 DOI: 10.1016/j.genrep.2016.08.002] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/24/2016] [Accepted: 08/01/2016] [Indexed: 12/18/2022]
Abstract
Systems biology is an interdisciplinary research field in life sciences, which involves a comprehensive and quantitative analysis of the interactions between all of the components of biological systems over time. For the past 50 years the discipline of virology has overly focused on the pathogen itself. However, we now know that the host response is equally or more important in defining the eventual pathological outcome of infection. Systems biology has in recent years been increasingly recognised for its importance to infectious disease research. Host-virus interactions can be better understood by taking into account the dynamical molecular networks that constitute a biological system. To decipher the pathobiological mechanisms of any disease requires a deep knowledge of how multiple and concurrent signal-transduction pathways operate and are deregulated. Hence the intricacies of signalling pathways can be dissected only by system level approaches. Deciphering the host virus interactions through system biology approach reviewed High throughput techniques to understand the host pathogen interactions examined Shift from virus-centric perspective to spectrum of virus-host interactions Modeling of host-virus cross talk
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Affiliation(s)
- Sajad Ahmad Wani
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Shahid Hussain
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Aruna Pandey
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Sonam Kanchan
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Aditya Prasad Sahoo
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Bina Mishra
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Ashok Kumar Tiwari
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Bishnu Prasad Mishra
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
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Kumar A, Gaur GK, Gandham RK, Panigrahi M, Ghosh S, Saravanan BC, Bhushan B, Tiwari AK, Sulabh S, Priya B, V N MA, Gupta JP, Wani SA, Sahu AR, Sahoo AP. Global gene expression profile of peripheral blood mononuclear cells challenged with Theileria annulata in crossbred and indigenous cattle. Infect Genet Evol 2016; 47:9-18. [PMID: 27840256 DOI: 10.1016/j.meegid.2016.11.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 09/06/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 12/28/2022]
Abstract
Bovine tropical theileriosis is an important haemoprotozoan disease associated with high rates of morbidity and mortality particularly in exotic and crossbred cattle. It is one of the major constraints of the livestock development programmes in India and Southeast Asia. Indigenous cattle (Bos indicus) are reported to be comparatively less affected than exotic and crossbred cattle. However, genetic basis of resistance to tropical theileriosis in indigenous cattle is not well documented. Recent studies incited an idea that differentially expressed genes in exotic and indigenous cattle play significant role in breed specific resistance to tropical theileriosis. The present study was designed to determine the global gene expression profile in peripheral blood mononuclear cells derived from indigenous (Tharparkar) and cross-bred cattle following in vitro infection of T. annulata (Parbhani strain). Two separate microarray experiments were carried out each for cross-bred and Tharparkar cattle. The cross-bred cattle showed 1082 differentially expressed genes (DEGs). Out of total DEGs, 597 genes were down-regulated and 485 were up-regulated. Their fold change varied from 2283.93 to -4816.02. Tharparkar cattle showed 875 differentially expressed genes including 451 down-regulated and 424 up-regulated. The fold change varied from 94.93 to -19.20. A subset of genes was validated by qRT-PCR and results were correlated well with microarray data indicating that microarray results provided an accurate report of transcript level. Functional annotation study of DEGs confirmed their involvement in various pathways including response to oxidative stress, immune system regulation, cell proliferation, cytoskeletal changes, kinases activity and apoptosis. Gene network analysis of these DEGs plays an important role to understand the interaction among genes. It is therefore, hypothesized that the different susceptibility to tropical theileriosis exhibited by indigenous and crossbred cattle is due to breed-specific differences in the dealing of infected cells with other immune cells, which ultimately influence the immune response responded against T. annulata infection.
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Affiliation(s)
- Amod Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Gyanendra Kumar Gaur
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Shrikant Ghosh
- Division of Parasitology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - B C Saravanan
- Division of Parasitology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Ashok Kumar Tiwari
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sourabh Sulabh
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bhuvana Priya
- Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Muhasin Asaf V N
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Jay Prakash Gupta
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sajad Ahmad Wani
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Aditya Prasad Sahoo
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Rajmani RS, Gupta SK, Singh PK, Gandham RK, Sahoo AP, Chaturvedi U, Tiwari AK. HN protein of Newcastle disease virus sensitizes HeLa cells to TNF-α-induced apoptosis by downregulating NF-κB expression. Arch Virol 2016; 161:2395-405. [PMID: 27294845 DOI: 10.1007/s00705-016-2923-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/02/2016] [Indexed: 12/11/2022]
Abstract
Hemagglutinin neuraminidase (HN) is a membrane protein of Newcastle disease virus (NDV) with the ability to induce apoptosis in many transformed cell lines. TNF-α is a multi-factorial protein that regulates cell survival, differentiation and apoptosis. In a previous study, we reported that HN protein induces apoptosis by downregulating NF-κB expression. Further, we speculated that downregulation of NF-κB expression might sensitize HeLa cells to TNF-α-mediated apoptosis. Therefore, the present study was undertaken to investigate if HN protein could sensitize HeLa cells to TNF-α and to examine the apoptotic potential of the HN protein and TNF-α in combination. The results revealed that the pro-apoptotic effects were more pronounced with the combination of HN and TNF-α than with HN or TNF-α alone, which indicates that the HN protein indeed sensitized the HeLa cells to TNF-α-induced cell death. The results of the study provide a mechanistic insight into the apoptotic action of HN protein along with TNF-α, which could be valuable in treating tumor types that are naturally resistant to TNF-α.
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Affiliation(s)
- R S Rajmani
- Molecular Biology Lab, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, India.,Centre for Infectious Disease Research, IISc, Bangalore, 560012, India
| | - Shishir Kumar Gupta
- Molecular Biology Lab, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, India
| | - Prafull Kumar Singh
- Molecular Biology Lab, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, India
| | - Ravi Kumar Gandham
- Molecular Biology Lab, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, India
| | - A P Sahoo
- Molecular Biology Lab, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, India
| | - Uttara Chaturvedi
- Molecular Biology Lab, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, India
| | - Ashok K Tiwari
- Molecular Biology Lab, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, India.
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Gupta SK, Tiwari AK, Gandham RK, Sahoo AP. Combined administration of the apoptin gene and poly (I:C) induces potent anti-tumor immune response and inhibits growth of mouse mammary tumors. Int Immunopharmacol 2016; 35:163-173. [PMID: 27064544 DOI: 10.1016/j.intimp.2016.03.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/25/2016] [Accepted: 03/28/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Many viral proteins exhibit selective cytotoxicity for tumor cells without affecting the normal diploid cells. The apoptin protein of chicken infectious anemia virus is one of such proteins, which has been shown to kill tumor cells specifically. However, an effective cancer treatment strategy also requires assistance from the immune system. Recently, poly (I:C) has been shown to be an effective cancer vaccine adjuvant. AIM In this study, we assessed the anti-tumor potential of apoptin gene transfer alone and in combination with poly (I:C) in a 4T1 mouse mammary tumor model. METHODS 4T1 cells were used to induce mammary tumor in Balb/c mice. Mice bearing tumors were divided into 6 groups, and each group received six intratumoral injections during a period of one month. After the last immunization, the animals were sacrificed, and peripheral blood, spleen, lungs, liver, heart, kidney and tumor tissues were collected for immunological, molecular and pathological analysis. RESULTS We report that intratumoral administration of apoptin plasmid along with poly (I:C) not only significantly inhibited the growth of mammary tumor, but also induced a potent anti-tumor immune response as indicated by the increase in blood CD4+, CD8+ cells and infiltration of immune cells in the tumor tissue. Further, blood serum analysis of the cytokines revealed increased secretion of Th1 cytokines (IFN-γ and IL-2). CONCLUSIONS The results of our study demonstrate that the inclusion of poly (I:C) significantly enhanced the anti-tumor activity of apoptin mainly by inducing a potent anti-tumor immune response. Therefore, we report the use of apoptin and poly (I:C) combination as a novel and powerful strategy for cancer immunotherapy.
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Affiliation(s)
- Shishir Kumar Gupta
- Molecular Biology Laboratory, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 UP, India.
| | - Ashok K Tiwari
- Molecular Biology Laboratory, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 UP, India.
| | - Ravi Kumar Gandham
- Molecular Biology Laboratory, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 UP, India
| | - A P Sahoo
- Molecular Biology Laboratory, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 UP, India
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Gupta SK, Sahoo AP, Rosh N, Gandham RK, Saxena L, Singh AK, Harish DR, Tiwari AK. Canine parvovirus NS1 induced apoptosis involves mitochondria, accumulation of reactive oxygen species and activation of caspases. Virus Res 2015; 213:46-61. [PMID: 26555166 DOI: 10.1016/j.virusres.2015.10.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 08/10/2015] [Revised: 10/08/2015] [Accepted: 10/14/2015] [Indexed: 12/27/2022]
Abstract
The non-structural protein (NS1) of parvoviruses plays an important role in viral replication and is thought to be responsible for inducing cell death. However, the detailed mechanism and the pathways involved in canine parvovirus type 2 NS1 (CPV2.NS1) induced apoptosis are not yet known. In the present study, we report that expression of CPV2.NS1 in HeLa cells arrests cells in G1 phase of the cell cycle and the apoptosis is mitochondria mediated as indicated by mitochondrial depolarization, release of cytochrome-c and activation of caspase 9. Treatment of cells with caspase 9 inhibitor Z-LEHD-FMK reduced the induction of apoptosis significantly. We also report that expression of CPV2.NS1 causes accumulation of reactive oxygen species (ROS) and treatment with an antioxidant reduces the ROS levels and the extent of apoptosis. Our results provide an insight into the mechanism of CPV2.NS1 induced apoptosis, which might prove valuable in developing NS1 protein as an oncolytic agent.
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Affiliation(s)
- Shishir Kumar Gupta
- Molecular Biology Laboratory, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar-243122, India.
| | - Aditya Prasad Sahoo
- Molecular Biology Laboratory, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar-243122, India
| | - Nighil Rosh
- Molecular Biology Laboratory, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar-243122, India
| | - Ravi Kumar Gandham
- Molecular Biology Laboratory, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar-243122, India
| | - Lovleen Saxena
- Molecular Biology Laboratory, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar-243122, India
| | - Arvind Kumar Singh
- Molecular Biology Laboratory, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar-243122, India
| | - D R Harish
- Molecular Biology Laboratory, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar-243122, India
| | - Ashok Kumar Tiwari
- Molecular Biology Laboratory, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar-243122, India.
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Kumar R, Kumar Pate S, Rami Reddy B, Bhatt M, Karthik K, Gandham RK, Singh Mali Y, Dhama K. Apoptosis and Other Alternate Mechanisms of Cell Death. ACTA ACUST UNITED AC 2015. [DOI: 10.3923/ajava.2015.646.668] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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46
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Rajmani RS, Gandham RK, Gupta SK, Sahoo AP, Singh PK, Kumar R, Saxena S, Chaturvedi U, Tiwari AK. HN Protein of Newcastle Disease Virus Induces Apoptosis Through SAPK/JNK Pathway. Appl Biochem Biotechnol 2015; 177:940-56. [DOI: 10.1007/s12010-015-1788-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 07/27/2015] [Indexed: 02/06/2023]
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47
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Rajmani RS, Gandham RK, Gupta SK, Sahoo AP, Singh PK, Saxena S, Kumar R, Chaturvedi U, Tiwari AK. Administration of IκB-kinase inhibitor PS1145 enhances apoptosis in DMBA-induced tumor in male Wistar rats. Cell Biol Int 2015; 39:1317-28. [DOI: 10.1002/cbin.10510] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/30/2015] [Indexed: 11/11/2022]
Affiliation(s)
- R. S. Rajmani
- Molecular Biology Laboratory; Indian Veterinary Research Institute; Izatnagar, Bareilly Uttar Pradesh India
| | - Ravi Kumar Gandham
- Molecular Biology Laboratory; Indian Veterinary Research Institute; Izatnagar, Bareilly Uttar Pradesh India
| | - Shishir Kumar Gupta
- Molecular Biology Laboratory; Indian Veterinary Research Institute; Izatnagar, Bareilly Uttar Pradesh India
| | - Aditya P. Sahoo
- Molecular Biology Laboratory; Indian Veterinary Research Institute; Izatnagar, Bareilly Uttar Pradesh India
| | - Prafull Kumar Singh
- Molecular Biology Laboratory; Indian Veterinary Research Institute; Izatnagar, Bareilly Uttar Pradesh India
| | - Shikha Saxena
- Molecular Biology Laboratory; Indian Veterinary Research Institute; Izatnagar, Bareilly Uttar Pradesh India
| | - Rajiv Kumar
- Molecular Biology Laboratory; Indian Veterinary Research Institute; Izatnagar, Bareilly Uttar Pradesh India
| | - Uttara Chaturvedi
- Molecular Biology Laboratory; Indian Veterinary Research Institute; Izatnagar, Bareilly Uttar Pradesh India
| | - Ashok K. Tiwari
- Molecular Biology Laboratory; Indian Veterinary Research Institute; Izatnagar, Bareilly Uttar Pradesh India
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48
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Gupta SK, Gandham RK, Sahoo AP, Tiwari AK. Viral genes as oncolytic agents for cancer therapy. Cell Mol Life Sci 2014; 72:1073-94. [PMID: 25408521 DOI: 10.1007/s00018-014-1782-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 10/29/2014] [Accepted: 11/13/2014] [Indexed: 12/20/2022]
Abstract
Many viruses have the ability to modulate the apoptosis, and to accomplish it; viruses encode proteins which specifically interact with the cellular signaling pathways. While some viruses encode proteins, which inhibit the apoptosis or death of the infected cells, there are viruses whose encoded proteins can kill the infected cells by multiple mechanisms, including apoptosis. A particular class of these viruses has specific gene(s) in their genomes which, upon ectopic expression, can kill the tumor cells selectively without affecting the normal cells. These genes and their encoded products have demonstrated great potential to be developed as novel anticancer therapeutic agents which can specifically target and kill the cancer cells leaving the normal cells unharmed. In this review, we will discuss about the viral genes having specific cancer cell killing properties, what is known about their functioning, signaling pathways and their therapeutic applications as anticancer agents.
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Affiliation(s)
- Shishir Kumar Gupta
- Molecular Biology Lab, Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, UP, India
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Das DP, Malik S, Rawool D, Das S, Shoukat S, Gandham RK, Saxena S, Singh R, Doijad SP, Barbuddhe S. Isolation of Coxiella burnetii from bovines with history of reproductive disorders in India and phylogenetic inference based on the partial sequencing of IS1111 element. Infection, Genetics and Evolution 2014; 22:67-71. [DOI: 10.1016/j.meegid.2013.12.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 11/29/2013] [Accepted: 12/16/2013] [Indexed: 10/25/2022]
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