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Basu M. The great smog of Delhi. Lung India 2019. [DOI: 10.4103/0970-2113.257709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Lenka SS, Paichha M, Basu M, Samanta M. LrHMGB1 Shares Structural Similarities with Human HMGB1, and Its Expression Is Induced in Bacterial Infection, Antiviral Vaccination, and Pathogen-Associated Molecular Patterns Stimulation. DNA Cell Biol 2018; 37:708-723. [DOI: 10.1089/dna.2018.4221] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Kobie J, Basu M, Piepenbrink M, Francois C, Roche F, Fucile C, Rosenberg A, Liesveld J, Keefer M. Induction and relationship of HIV Envelope-specific B cells in the peripheral blood and bone marrow following vaccination in humans. THE JOURNAL OF IMMUNOLOGY 2018. [DOI: 10.4049/jimmunol.200.supp.125.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Induction of long-lived plasma cells producing protective HIV-1 Envelope (Env)-specific antibody (Ab) is a primary goal of HIV vaccine strategies. However, vaccine-induced Env-specific human plasma cells have not yet been identified. In an effort to do so, samples were obtained from HVTN 105, a phase I trial in which participants were immunized with the same bivalent gp120 protein, AIDSVAX B/E, as used in RV144, although combined with a DNA immunogen (instead of ALVAC-HIV) in various prime/boost strategies. Participants who received a boosting regimen that included AIDSVAX B/E had robust peripheral blood plasmablast responses as measured by Env-specific ELISpot (n=21) and flow cytometry (n=20). The Env-specific immunoglobulin repertoire of the plasmablasts, assessed by monoclonal Ab generation (>110 mAbs total from 15 participants), was dominated by VH1 gene usage (~60%, VH1-2>VH1-46>VH1-24), and had modest mutation from germline (~5%). Ongoing epitope mapping has indicated V3 is a dominant target; however other regions including V1/V2 and C1/C5 were also targeted. The majority of the mAbs are high avidity, and a subset can mediate Ab-dependent cellular phagocytosis; additional functional analysis is ongoing. Bone marrow was evaluated ~7 months after immunization (n=3), and although ELISpot of CD138+ plasma cells could readily detect influenza specific IgG Ab secreting cells (ASCs), Env-specific IgG ASCs were not convincingly detected by ELISpot. However, when using VH deep sequencing of the bone marrow (n=4), multiple members of plasmablast-derived mAb clonal lineages were detected. Our results indicate that HIV-1 Env-specific B cells are present in human bone marrow after vaccination, but may persist at very low frequency.
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Nogales A, Piepenbrink MS, Wang J, Ortega S, Basu M, Fucile CF, Treanor JJ, Rosenberg AF, Zand MS, Keefer MC, Martinez-Sobrido L, Kobie JJ. A Highly Potent and Broadly Neutralizing H1 Influenza-Specific Human Monoclonal Antibody. Sci Rep 2018. [PMID: 29531320 PMCID: PMC5847613 DOI: 10.1038/s41598-018-22307-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Influenza’s propensity for antigenic drift and shift, and to elicit predominantly strain specific antibodies (Abs) leaves humanity susceptible to waves of new strains with pandemic potential for which limited or no immunity may exist. Subsequently new clinical interventions are needed. To identify hemagglutinin (HA) epitopes that if targeted may confer universally protective humoral immunity, we examined plasmablasts from a subject that was immunized with the seasonal influenza inactivated vaccine, and isolated a human monoclonal Ab (mAb), KPF1. KPF1 has broad and potent neutralizing activity against H1 influenza viruses, and recognized 83% of all H1 isolates tested, including the pandemic 1918 H1. Prophylactically, KPF1 treatment resulted in 100% survival of mice from lethal challenge with multiple H1 influenza strains and when given as late as 72 h after challenge with A/California/04/2009 H1N1, resulted in 80% survival. KPF1 recognizes a novel epitope in the HA globular head, which includes a highly conserved amino acid, between the Ca and Cb antigenic sites. Although recent HA stalk-specific mAbs have broader reactivity, their potency is substantially limited, suggesting that cocktails of broadly reactive and highly potent HA globular head-specific mAbs, like KPF1, may have greater clinical feasibility for the treatment of influenza infections.
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Banerjee R, Patel B, Basu M, Lenka SS, Paicha M, Samanta M, Das S. Molecular cloning, characterization and expression of immunoglobulin D on pathogen challenge and pathogen associated molecular patterns stimulation in freshwater carp, Catla catla. Microbiol Immunol 2017; 61:452-458. [DOI: 10.1111/1348-0421.12534] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/31/2017] [Indexed: 11/27/2022]
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Kobie J, Sarkar S, Piepenbrink M, Basu M, Keefer M, Thakar J, Hessell AJ, Haigwood NL. IL-33 enhances the induction, durability, and breadth of the antibody response to a DNA/protein-based HIV Env vaccine. THE JOURNAL OF IMMUNOLOGY 2017. [DOI: 10.4049/jimmunol.198.supp.225.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Induction of a sustained and broad antibody (Ab) response is a major goal in developing a protective HIV vaccine. DNA is an attractive priming strategy when combined with protein or viral vector boosting; however, DNA priming alone fails to induce a substantial Ab response, limiting its potential as a stand-alone immunogen. Using the VC10014 DNA/protein vaccine consisting of gp160 plasmids and gp140 proteins derived from an HIV clade B infected subject who developed broadly neutralizing serum Abs, and which has been previously shown to induce Tier 2 heterologous neutralizing Abs in rhesus macaques, we screened a panel of factors in C57BL/6 mice for their ability to enhance the Env-specific Ab response. IL-33, an alarmin, emerged as the lead candidate. The addition of recombinant IL-33 during the gp160 DNA priming phase dramatically changed the kinetics of the Ab response, inducing serum gp120-specific IgG (>1:12,500 titer) after a single DNA immunization, which was not detectable in mice that did not receive IL-33 (p<0.0001). Then following boosting with DNA/protein coimmunization in Alum, gp120-specific IgG levels were extraordinarily durable, remaining stable even at 6 weeks after final immunization compared to mice not receiving IL-33 (p<0.0001), in which they rapidly declined. IL-33 also increased the cross-clade breadth and avidity of the serum gp120-specific IgG response. Analysis of the Env-specific B cell immunoglobulin repertoire and the IL-33 mechanism of action is ongoing. These results demonstrate the profound effect that priming conditions can have on the quality of the Env-specific antibody response.
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Patel B, Banerjee R, Basu M, Lenka S, Samanta M, Das S. Molecular cloning of IgZ heavy chain isotype in Catla catla and comparative expression profile of IgZ and IgM following pathogenic infection. Microbiol Immunol 2017; 60:561-7. [PMID: 27301776 DOI: 10.1111/1348-0421.12399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 05/27/2016] [Accepted: 06/07/2016] [Indexed: 11/28/2022]
Abstract
Immunoglobulins serve as a crucial arm of the adaptive immune system against detrimental pathogenic threats in teleosts. However, whether the novel Ig isotype IgZ is present in the Indian major carp, Catla catla, has not yet been elucidated. The present study reports the presence of IgZ ortholog in C. catla (CcIgZ) and further demonstrates its comparative tissue specific expression with IgM (CcIgM) in response to bacterial and parasitic stimulation. The putative 139 amino acid sequence of IgZ heavy chain cDNA of C. catla showed homology with IgZ constant domains of other teleosts. Phylogenetic analysis of the predicted IgZ transcript sequence clustered with previously identified IgZ heavy chain sequences of Cyprinidae family members. The inductive expression profiles of IgZ and IgM genes were evaluated in immunologically relevant tissues at 24, 48 and 72 hr post infection with Aeromonas hydrophila, Streptococcus uberis and Argulus sp. Both CcIgZ and CcIgM were expressed most strongly in the kidneys of healthy fish. Basal expression of CcIgM transcript was higher than that of CcIgZ in all the examined tissues. Stimulation with bacteria triggered significant increase of IgZ in the intestine (P < 0.001) and spleen (P < 0.01), whereas IgM was relatively up-regulated in blood (P < 0.001) after stimulation with each of the three pathogens assessed. The study is the first to report identification of IgZ in C. catla. Further, it provides insights into the differential expression profiles of IgZ and IgM isotypes against various pathogenic infection in C. catla, which may facilitate better prophylaxis again such infections.
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Samanta M, Basu M, Swain B, Paichha M, Lenka SS, Das S, Jayasankar P, Maiti NK. Molecular cloning and characterization of LrTLR4, analysis of its inductive expression and associated down-stream signaling molecules following lipopolysaccharide stimulation and Gram-negative bacterial infection. FISH & SHELLFISH IMMUNOLOGY 2017; 60:164-176. [PMID: 27838566 DOI: 10.1016/j.fsi.2016.11.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/31/2016] [Accepted: 11/08/2016] [Indexed: 06/06/2023]
Abstract
Toll-like receptors (TLRs) play key roles in innate immunity from lower to higher vertebrates. Among various TLR types, TLR4 was reported to recognize LPS in higher vertebrates resulting in the activation of down-stream signaling pathway. Except in some teleosts, function of TLR4 in most fish species including rohu (Labeo rohita) a commercially important fish species in the South-East Asian countries remained unknown. To investigate it, full-length cDNA of Labeo rohita TLR4 (LrTLR4) was cloned, and it consisted of 2729 bp, with a single ORF of 2469 bp encoding a polypeptide of 822 aa with a predicted molecular mass of 94.753 kDa. Structurally, LrTLR4 consisted of 25 LRRs (leucine rich repeat regions), one TM (trans-membrane) domain and one TIR (Toll/interleukin-1 receptor) domain, and was similar to higher vertebrate's TLR4. Phylogenetically, LrTLR4 exhibited highest (85%) identity with the common carp TLR4b amino acids sequence, and formed a separate subgroup in the phylogenetic tree. LrTLR4 was widely expressed in all tested organs/tissues, and amidst the tissues highest expression was detected in blood and the lowest in eye. In response to LPS-stimulation, LrTLR4 was induced with the activation of MyD88-dependent and TRIF-dependent signaling pathway resulting in pro-inflammatory cytokines (interleukin 6 and 8) and type I IFN gene expression. Infection of rohu with a Gram-negative fish pathogen (Aeromonas hydrophila), also activated LrTLR4. Together, these findings suggest the important role of TLR4 in LPS sensing and augmentation of innate immunity against Gram-negative bacterial infection in fish.
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Basu M, Lenka SS, Paichha M, Swain B, Patel B, Banerjee R, Jayasankar P, Das S, Samanta M. Immunoglobulin (Ig) D in Labeo rohita is widely expressed and differentially modulated in viral, bacterial and parasitic antigenic challenges. Vet Immunol Immunopathol 2016; 179:77-84. [DOI: 10.1016/j.vetimm.2016.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/20/2016] [Accepted: 08/08/2016] [Indexed: 11/29/2022]
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Chandramouleeswaran S, Ramkumar J, Basu M. Insight of solvent extraction process: Reassessment of trace level determinations. Anal Chim Acta 2016; 938:123-8. [PMID: 27619094 DOI: 10.1016/j.aca.2016.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/05/2016] [Accepted: 08/08/2016] [Indexed: 11/27/2022]
Abstract
Solvent extraction is hoary yet modern technique with great scope of research due to the various intriguing phenomena in the system. Tri-n-butyl phosphate (TBP) is a well known extractant which has been extensively used for separation of uranium matrix prior to elemental profiling. In this paper, one of the impurities namely Fe is being considered as it posed a challenge to the separation due to its co-extraction with TBP along with uranium. In these studies, for the first time, the existence of cation-cation inner sphere complexes between the UO2(2+)and Fe(3+) ions in both aqueous and organic phases have been establisted in addition to the selective separation of iron from uranium sample matrix using only TBP. The data from both spectrophotometric and thermophysical studies corroborated one another confirming the presence of cation-cation interactions (CCIs). The developed solvent extraction with only TBP showed almost no interferences on the iron extraction from matrix uranium and other co-ions like aluminum and copper. This has been the first time application of pure TBP for selective removal of iron from uranium samples. The procedure possessed excellent reproducibility and robustness.
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Basu M, Choudhury S, Sharma J, Hassan P. Equilibrium and dynamic interfacial behavior of tetra (2-ethyl hexyl) diglycolamide (TEHDGA) - TritonX-100 mixtures. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.06.070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Patel B, Kumar P, Banerjee R, Basu M, Pal A, Samanta M, Das S. Lactobacillus acidophilus attenuates Aeromonas hydrophila induced cytotoxicity in catla thymus macrophages by modulating oxidative stress and inflammation. Mol Immunol 2016; 75:69-83. [PMID: 27262084 DOI: 10.1016/j.molimm.2016.05.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/16/2016] [Accepted: 05/16/2016] [Indexed: 01/16/2023]
Abstract
The pathogenesis of Aeromonas hydrophila, a potent fish pathogen, is attributed to its ability to cause motile aeromonad septicaemia leading to apoptosis in a myriad of fish species, including freshwater carp Catla catla. However, the underlying mechanism of antagonistic activity of probiotics against A. hydrophila induced apoptosis is not elucidated due to lack of appropriate in-vitro models. This study reported that the exposure of catla thymus macrophages (CTM) to A. hydrophila markedly induced cellular injuries as evidenced by elevated levels of reactive oxygen species (ROS), reactive nitrogen species (RNS), increased apoptosis, DNA damage and decreased cellular viability. Flow cytometry analysis and Annexin-V/propidium iodide assay further confirmed increased ROS positive cells leading to cell death after infection. The quantitative real-time PCR analysis, also revealed upregulation of inducible nitric-oxide synthase (iNOS), pro-inflammatory cytokine (TNFα), cyclooxygenase2 (COX-2) and downregulation of anti-inflammatory cytokine (IL-10). Pretreatment of cells with probiotic, Lactobacillus acidophilus attenuated A. hydrophila induced apoptosis as evident from the decrease in the levels of ROS, RNS and DNA damage. Significant increase (P≤0.05) in expression of TNFα and IL-10 and decrease in iNOS and COX-2 was observed on probiotic stimulation. In-vivo study using catla fingerlings confirmed similar pattern of ROS, iNOS, NO production and cytokine expression in thymus. This study provides a comprehensive insight into the mechanistic basis of L. acidophilus induced macrophage mediated inflammatory response against A. hydrophila in CTM cells. Further, it speculates the possibility of using cost-effective in-vitro models for screening probiotic candidates of therapeutic potential in aquaculture industry.
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Basu M, Paichha M, Swain B, Lenka SS, Singh S, Chakrabarti R, Samanta M. Modulation of TLR2, TLR4, TLR5, NOD1 and NOD2 receptor gene expressions and their downstream signaling molecules following thermal stress in the Indian major carp catla (Catla catla). 3 Biotech 2015; 5:1021-1030. [PMID: 28324409 PMCID: PMC4624144 DOI: 10.1007/s13205-015-0306-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/27/2015] [Indexed: 12/13/2022] Open
Abstract
Toll-like receptors (TLRs) and nucleotide binding and oligomerization domain (NOD) receptors are pattern recognition receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs) and play crucial role in innate immunity. In addition to PAMPs, PRRs recognize endogenous molecules released from damaged tissue or dead cells [damage-associated molecular patterns (DAMPs)] and activate signaling cascades to induce inflammatory processes. In the aquatic environment, large variation in seasonal and diurnal water temperature causes heat and cold stresses in fish, resulting in tissue injury and mortality of fish. In the Indian subcontinent, catla (Catla catla) is an economically important freshwater fish species and is prone to thermal stresses. To investigate the response of pattern recognition receptors in thermal stress, we analyzed TLRs (TLR2, TLR4 and TLR5) and NOD (NOD1 and NOD2) receptors gene expression in catla following heat and cold stress. Analysis of tissue samples (gill, liver, kidney and blood) of the thermal stressed and control fish by quantitative real-time PCR (qRT-PCR) assay revealed significant (p < 0.05) induction of TLR2, TLR4 and NOD2 gene expression in majority of the tested tissues of the treated fish as compared to the control. The expression of TLR5 and NOD1 gene was also induced in the heat and cold stressed fish, but mostly restricted in the blood. The downstream signaling molecule of TLR and NOD signaling pathway viz., MyD88 (myeloid differentiation primary response gene 88) and RICK (receptor interacting serine-threonine protein kinase-2) was also induced in the thermal stressed fish suggesting the engagement of TLR and NOD signaling pathway during thermal stress.
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Basu M, Paichha M, Lenka SS, Chakrabarty R, Samanta M. Hypoxic stress: impact on the modulation of TLR2, TLR4, NOD1 and NOD2 receptor and their down-stream signalling genes expression in catla (Catla catla). Mol Biol Rep 2015; 43:1-9. [DOI: 10.1007/s11033-015-3932-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/13/2015] [Indexed: 01/06/2023]
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Das A, Basu M. A Case of Hereditary Pancreatitis Presenting as Recurrent Abdominal Pain in a 11 Year Old Girl. JOURNAL OF NEPAL PAEDIATRIC SOCIETY 2015. [DOI: 10.3126/jnps.v35i1.10479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recurrent abdominal pain is a common problem among children. Since its first description by John Apley in 1958, the condition has remained poorly understood with a multitude of factors being implicated in causation. The symptoms tend to be vague and investigations seldom show organic disease. But the importance to evaluate each child with recurrent abdominal pain should be considered important nevertheless, particularly, in protracted cases. Here, we present a case who presented with history of recurrent abdominal pain for several years before being diagnosed as a case of hereditary pancreatitis. This stresses the importance of evaluating each case with a detailed and complete history, physical examination and selected investigations.J Nepal Paediatr Soc 2015;35(1):57-58
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Swain B, Basu M, Lenka SS, Das S, Jayasankar P, Samanta M. Characterization and Inductive Expression Analysis of Interferon Gamma-Related Gene in the Indian Major Carp, Rohu (Labeo rohita). DNA Cell Biol 2015; 34:367-78. [PMID: 25756860 DOI: 10.1089/dna.2014.2656] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Interferon gamma (IFN-γ) is one of the key cytokines that plays a major role against viral and intracellular bacterial infection. In addition to the IFN-γ gene, teleost fish possess a second copy known as IFN-γ-related (IFN-γrel) gene. This report describes structural and functional properties of IFN-γrel gene in the Indian major carp, rohu (Labeo rohita), a commercially important freshwater fish species in the Indian subcontinent. The rohu IFN-γrel gene consisted of four exons with three intervening introns and phylogenetically closely related to grass carp. The full-length IFN-γrel cDNA comprised 927 bp nucleotides with a single open reading frame of 504 bp, encoding 167 amino acids (aa) polypeptide with a signal peptide of 24 aa. The mature rohu IFN-γrel protein was 143 aa with a predicted molecular weight of 16.85 kDa. Basal expression analysis of IFN-γrel showed its wide range of expression in all examined tissues: The highest was in the skin and the lowest was in the liver. In response to LPS, poly I:C, iE-DAP, muramyl dipeptide stimulations, and bacterial infections, IFN-γrel gene expression was significantly (p<0.05) induced in treated fish tissues as compared with their control. The IFN-γrel was expressed as recombinant protein (rIFN-γrel) and confirmed through western blot. Stimulation of peripheral blood leukocytes with rIFN-γrel protein resulted in the activation of IFN-γ receptor and marked induction of inducible nitric oxide synthase gene expression. These results together may suggest the important role of IFN-γrel as an antimicrobial cytokine in fish.
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Soni S, Agrawal P, Kumar N, Mittal G, Nishad DK, Chaudhury NK, Bhatnagar A, Basu M, Chhillar N. Salivary biochemical markers as potential acute toxicity parameters for acute radiation injury: A study on small experimental animals. Hum Exp Toxicol 2015; 35:221-8. [PMID: 25813962 DOI: 10.1177/0960327115579433] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Researchers have been evaluating several biodosimetric/screening approaches to assess acute radiation injury, related to mass causality. Keeping in mind this background, we hypothesized that effect of whole-body irradiation in single fraction in graded doses can affect the secretion of various salivary components that could be used as acute radiation injury/toxicity marker, which can be used in screening of large population at the time of nuclear accidents/disaster. Thirty Sprague Dawley rats treated with whole-body cobalt-60 gamma irradiation of dose 1-5 Gy (dose rate: 0.95 Gy/min) were included in this study. Whole mixed saliva was collected from all animals before and after radiation up to 72 h postradiation. Saliva was analyzed for electrolytes, total protein, urea, and amylase. Intragroup comparison of salivary parameters at different radiation doses showed significant differences. Potassium was significantly increased as the dose increased from 1 Gy to 5 Gy (p < 0.01) with effect size of difference (r > 0.5). Sodium was significantly altered after 3-5 Gy (p < 0.01, r > 0.5), except 1 and 2 Gy, whereas changes in sodium level were nonsignificant (p > 0.5). Urea, total protein, and amylase levels were also significantly increased as the radiation dose increased (p < 0.01) with large effect size of difference (r > 0.5). This study suggests that salivary parameters were sensitive toward radiation even at low radiation dose which can be used as a predictor of radiation injury.
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Jena C, Basu M, Panigrahi CK. Differential evolution with Gaussian mutation for combined heat and power economic dispatch. Soft comput 2014. [DOI: 10.1007/s00500-014-1531-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bej A, Sahoo BR, Swain B, Basu M, Jayasankar P, Samanta M. LRRsearch: An asynchronous server-based application for the prediction of leucine-rich repeat motifs and an integrative database of NOD-like receptors. Comput Biol Med 2014; 53:164-70. [PMID: 25150822 DOI: 10.1016/j.compbiomed.2014.07.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 01/01/2023]
Abstract
The leucine-rich repeat (LRR) motifs of the nucleotide-binding oligomerization domain like receptors (NLRs) play key roles in recognizing and binding various pathogen associated molecular patterns (PAMPs) resulting in the activation of downstream signaling and innate immunity. Therefore, identification of LRR motifs is very important to study ligand-receptor interaction. To date, available resources pose restrictions including both false negative and false positive prediction of LRR motifs from the primary protein sequence as their algorithms are relied either only on sequence based comparison or alignment techniques or are over biased for a particular LRR containing protein family. Therefore, to minimize the error (≤5%) and to identify a maximum number of LRR motifs in the wide range of proteins, we have developed "LRRsearch" web-server using position specific scoring matrix (PSSM) of 11 residue LRR-HCS (highly conserved segment) which are frequently observed motifs in the most divergent classes of LRR containing proteins. A data library of 421 proteins, distributed among five known NLR families has also been integrated with the "LRRsearch" for the rich user experience. The access to the "LRRsearch" program is freely available at http://www.lrrsearch.com/.
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Samanta M, Swain B, Basu M, Mahapatra G, Sahoo BR, Paichha M, Lenka SS, Jayasankar P. Toll-like receptor 22 in Labeo rohita: molecular cloning, characterization, 3D modeling, and expression analysis following ligands stimulation and bacterial infection. Appl Biochem Biotechnol 2014; 174:309-27. [PMID: 25064133 DOI: 10.1007/s12010-014-1058-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/14/2014] [Indexed: 10/25/2022]
Abstract
Toll-like receptors (TLRs) are a class of innate immune receptors that sense pathogens or their molecular signatures and activate signaling cascades to induce a quick and non-specific immune response in the host. Among various types of TLRs, TLR22 is exclusively present in teleosts and amphibians and is expected to play the distinctive role in innate immunity. This report describes molecular cloning, three-dimensional (3D) modeling, and expression analysis of TLR22 in rohu (Labeo rohita), the most commercially important freshwater fish species in the Indian subcontinent. The open reading frame (ORF) of rohu TLR22 (LrTLR22) comprised of 2,838 nucleotides (nt), encoding 946 amino acid (aa) residues with the molecular mass of ∼ 107.6 kDa. The secondary structure of deduced LrTLR22 exhibited the presence of signal peptide (1-22 aa), 18 leucine-rich repeat (LRR) regions (79-736 aa), and TIR domain (792-935 aa). The 3D model of LrTLR22-LRR regions together elucidated the horse-shoe-shaped structure having parallel β-strands at the concave surface and few α-helices at the convex surface. The TIR domain structure revealed alternate presence of five α-helices and β-sheets. Phylogenetically, LrTLR22 was closely related to common carp and exhibited significant similarity (92.2 %) and identity (86.1 %) in their amino acids. In rohu, TLR22 was constitutively expressed in all embryonic developmental stages, and tissue-specific analysis illustrated its expression in all examined tissues, highest was in liver and lowest in brain. In vivo modulation of TLR22 gene expression was analyzed by quantitative real-time PCR (qRT-PCR) assay following stimulation with lipopolysaccharide (LPS), synthetic double stranded RNA (polyinosinic-polycytidylic acid), and bacterial (Aeromonas hydrophila) RNA. Among these ligands, bacterial RNA most significantly (p < 0.05) induced TLR22 gene expression in most of the tested tissues. In A. hydrophila infection, induction of TLR22 gene expression was also observed in majority of the tested tissues. Together, these data suggested that in addition to sensing other microbial signatures, TLR22 can recognize bacterial RNA and may play the important role in augmenting innate immunity in fish.
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Basu M, Postlethwaite C, Cheema K, Duckett J. The effect of age on pressure flow parameters in women with lower urinary tract symptoms. J OBSTET GYNAECOL 2014; 33:873-6. [PMID: 24219733 DOI: 10.3109/01443615.2013.820265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This study aimed to evaluate changes in voiding with age in women with different urodynamic diagnoses. Correlation was used to analyse the association between age and voiding parameters (maximum flow rate, voided volume, flow rate centile and maximum detrusor pressure - PdetMax) in 896 datasets. Multivariate analysis was used to analyse the data further by age group and diagnosis - urodynamic stress incontinence (USI); detrusor overactivity (DO); mixed USI and DO; no urodynamic abnormality. Results showed that diagnosis accounts for a significant amount of variation in all four of the dependent variables Age group shows a significant effect on voiding volume but does not show significant effects on any other variable studied. There is no significant interaction term in any of the analyses, meaning that age and diagnosis do not appear to function together, e.g. age does not relate to flow rate centile, maximum flow rate or PdetQMax. It was concluded that the data suggest that there is no significant change in voiding function related to age. In the elderly, the main alteration in voiding is due to a higher prevalence of DO.
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Basu M, Das P, Dhar G, Datta S, Chattopaddhyay S, Bagchi S, Pal R. Pattern and Determinants of Overweight and Obesity Among Future Physicians. Nepal J Epidemiol 2014. [DOI: 10.3126/nje.v4i1.10134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background Overweight including obesity is a leading cause of present day morbidity and kills more people than underweight. Keeping this background in mind this study had been conducted to establish the pattern of overweight and obesity in the midst of undergraduate medical group and to find out the association of overweight (plump) and obesity with probable hazardous factors. Materials and Methods This descriptive observational study had been conducted among undergraduate medical group for the duration of May to June 2011. Simple random sampling was adopted to select the students under study. A pretested, predesigned self-administered questionnaire was utilized for data collection. Body Mass Index (BMI) was assessed through weight and height and acted as forecaster of heavy figure and or obesity. Overweight and or obesity were analyzed to see the association with certain socio-demographic variables, dietary habits, family history of overweight and or obesity, life style issues, computer use etc. After collection of data, these were analyzed using tabulation, proportion and Chi square through Epi-Info software. Results The study subjects were young adults. The general pattern of overweight (plump) and obesity was 18.0 percent and 4.0 percent respectively. Overweight and or obesity was found significantly high among male students, fast food and soft drinks takers, low takers of fruits and vegetables, alcohol consumers, students with lack of exercise and family history of obesity. Overweight and obesity were not found associated with type of diet (vegetarian or non-vegetarian) and smoking. Conclusion Presence of probable associated factors with regard to overweight (plump) and obesity exists amid medical undergraduate pupils.DOI: http://dx.doi.org/10.3126/nje.v4i1.10134 Nepal Journal of Epidemiology 2014;4 (1): 323-329
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Das P, Basu M, Chowdhury K, Mallik S, Dhar G, Biswas A. Observational assessment and correlates to blood pressure of future physicians of Bengal. Niger J Clin Pract 2013; 16:433-8. [PMID: 23974734 DOI: 10.4103/1119-3077.116884] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Hypertension is a modern day epidemic and growing public health problem. A sizable proportion of world populations suffer from prehypertension or hypertension. OBJECTIVES The present study was carried out to detect the prevalence of undiagnosed hypertension among undergraduate medical students and to identify the associated risk factors. MATERIALS AND METHODS The study was observational in nature and was done in medical colleges of Bengal. Study tool was a predesigned, pretested, validated, and semi-structured questionnaire containing both open-ended and close-ended questions. Data were collected through self-administration, clinical, and anthropometric examination. The data were then tabulated, analyzed and interpretation was done by using percentage and Chi-square test. RESULTS Most of the students (63%) were young adults, predominantly males (67%) and day scholars (71%). Almost one-third of them either suffered from hypertension or at risk of hypertension. Hypertension was found higher among male students. Family history of hypertension or diabetes mellitus was not associated with hypertension. Vegetarian or nonvegetarian diet or extra-salt consumption was also not associated with hypertension. Smoking was shown positively associated with hypertension but alcohol consumption was not. Higher per capita monthly income and overweight or obesity were shown positively associated with hypertension. CONCLUSION The overall prevalence of hypertension in this study was 13% and there were positive association of hypertension with multiple socio-demographic factors like age, sex, type of family, per capita monthly income, residence, BMI, smoking, etc.
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Maharana J, Swain B, Sahoo BR, Dikhit MR, Basu M, Mahapatra AS, Jayasankar P, Samanta M. Identification of MDP (muramyl dipeptide)-binding key domains in NOD2 (nucleotide-binding and oligomerization domain-2) receptor of Labeo rohita. FISH PHYSIOLOGY AND BIOCHEMISTRY 2013; 39:1007-1023. [PMID: 23255217 DOI: 10.1007/s10695-012-9758-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 12/06/2012] [Indexed: 06/01/2023]
Abstract
In lower eukaryotes-like fish, innate immunity contributed by various pattern recognition receptor (PRR) plays an essential role in protection against diseases. Nucleotide-binding and oligomerization domain (NOD)-2 is a cytoplasmic PRR that recognizes MDP (muramyl dipeptide) of the Gram positive and Gram negative bacteria as ligand and activates signalling to induce innate immunity. Hypothesizing a similar NOD2 signalling pathway of higher eukaryotes, the peripheral blood leucocytes (PBLs) of rohu (Labeo rohita) was stimulated with MDP. The data of quantitative real-time PCR (qRT-PCR) revealed MDP-mediated inductive expression of NOD2 and its down-stream molecule RICK/RIP2 (receptor-interacting serine-threonine protein kinase-2). This observation suggested the existence of MDP-binding sites in rohu NOD2 (rNOD2). To investigate it, 3D model of ligand-binding leucine-rich repeat (LRR) region of rNOD2 (rNOD2-LRR) was constructed following ab initio and threading approaches in I-TASSER web server. Structural refinement of the model was performed by energy minimization, and MD (molecular dynamics) simulation was performed in GROMACS (Groningen Machine for Chemical Simulations). The refined model of rNOD2-LRR was validated through SAVES, ProSA, ProQ, WHAT IF and MolProbity servers, and molecular docking with MDP was carried out in GOLD 4.1. The result of docking identified LRR3-7 comprising Lys820, Phe821, Asn822, Arg847, Gly849, Trp877, Trp901 and Trp931 as MDP-binding critical amino acids in rNOD2. This is the first study in fish to provide an insight into the 3D structure of NOD2-LRR region and its important motifs that are expected to be engaged in MDP binding and innate immunity.
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Basu M, Mukerji S, Doumouchtsis SK. Perineal trauma in women undergoing vaginal delivery following intra-uterine fetal demise: a case-control analysis. Int Urogynecol J 2013; 25:61-4. [PMID: 23818128 DOI: 10.1007/s00192-013-2148-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 05/28/2013] [Indexed: 11/26/2022]
Abstract
INTRODUCTION AND HYPOTHESIS This study aimed to evaluate any differences in the incidence of perineal trauma in women undergoing vaginal delivery following intrauterine fetal death (IUFD) versus live-births. This information would be of interest in evaluating the possible effect of fetal demise on the mechanism of labour in the second stage and thus may provide invaluable insights to contribute to our understanding of the impact of fetal tone on the mechanics of labour and delivery. METHODS 323 women who delivered vaginally following IUFD were matched with 1,000 women with a live-birth for age, parity, gestation and birth weight. Women undergoing assisted vaginal delivery and/or episiotomy were excluded. RESULTS Women with an IUFD had a significantly lower risk of perineal trauma overall (relative risk 0.16) as well as a lower risk of obstetric anal sphincter injury specifically (RR 0.12). CONCLUSIONS Women delivering vaginally after IUFD have a lower incidence of perineal trauma compared with women delivering a live infant. This may be due to differences in biomechanics following an IUFD.
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