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Purohit P, Barik D, Agasti S, Panda M, Meher BR. Evaluation of the inhibitory potency of anti-dengue phytocompounds against DENV-2 NS2B-NS3 protease: virtual screening, ADMET profiling and molecular dynamics simulation investigations. J Biomol Struct Dyn 2024; 42:2990-3009. [PMID: 37194462 DOI: 10.1080/07391102.2023.2212798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/28/2023] [Indexed: 05/18/2023]
Abstract
Dengue fever has been a worldwide concern, with 50-100 million new infections each year mainly due to five different serotypes of the Dengue virus (DENV). Designing a perfect anti-dengue agent that can inhibit all the serotypes by distinguishing antigenic differences is quite difficult. Previous anti-dengue researches have included chemical compounds screening against DENV enzymes. The ongoing analysis is meant for investigation of the plant-based compounds as antagonistic to DENV-2 focusing on the specific NS2B-NS3Pro target, a trypsin like serine protease that cuts the DENV polyprotein into separate proteins crucial for viral reproduction. Initially, a virtual library of more than 130 phytocompounds was prepared from previously published reports of plants with anti-dengue properties, which were then virtually screened and shortlisted against the WT, H51N and S135A mutant of DENV-2 NS2B-NS3Pro. The three top-most compounds were viewed as Gallocatechin (GAL), Flavokawain-C (FLV), and Isorhamnetin (ISO) showing docking scores of -5.8, -5.7, -5.7 kcal/mol for WT, -7.5, -6.8, -7.6 kcal/mol for the H51N, and -6.9, -6.5, -6.1 kcal/mol for the S135A mutant protease, respectively. 100 ns long MD simulations and MM-GBSA based free energy calculations were performed on the NS2B-NS3Pro complexes to witness the relative binding affinity of the compounds and favourable molecular interactions network. A comprehensive analysis of the study reveals some promising outcomes with ISO as the topmost compound with favourable pharmacokinetic properties for the WT and mutants (H51N and S135A) as well, suggesting as a novel anti-NS2B-NS3Pro agent with better adapting characters in both the mutants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Debashis Barik
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Sidhartha Agasti
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
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Das D, Sahu SN, Panda PK, Panda M. Oro-Pharyngeal Candidiasis in Two Dengue Patients. Cureus 2024; 16:e52627. [PMID: 38374848 PMCID: PMC10876100 DOI: 10.7759/cureus.52627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2024] [Indexed: 02/21/2024] Open
Abstract
Dengue, a prevalent arboviral disease, has witnessed a resurgence in India, with outbreaks frequently reported. However, dengue-associated oral (oro-pharyngeal) candidiasis (DAOC) was never reported. We present two severe dengue cases with oral/oro-pharyngeal pseudomembranous candidiasis. Case 1 of a young man without any comorbidities or abuse or immunosuppression presented with fever, headache, altered sensorium, throat pain on recovery, and laboratory reports confirmed dengue with leukopenia, thrombocytopenia, and severe hepatic involvement with oro-pharyngeal candidiasis. Similarly, case 2 of a middle-aged man with a history of smoking and diabetes presented with fever, gum bleeding, and throat pain, later confirmed to be dengue NS1 positive with thrombocytopenia, and mild-moderate hepatic involvement along with oral-oro-pharyngeal candidiasis. Both cases showed improvement with conservative management and oral nystatin suspension. These cases prompt consideration of superadded candida infections in dengue patients, emphasizing the need for further study and clinical vigilance.
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Affiliation(s)
- Drupad Das
- Internal Medicine, All India Institute of Medical Sciences, Rishikesh, Rishikesh, IND
| | - Shiv N Sahu
- Internal Medicine, All India Institute of Medical Sciences, Rishikesh, Rishikesh, IND
| | - Prasan K Panda
- Internal Medicine, All India Institute of Medical Sciences, Rishikesh, Rishikesh, IND
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Purohit P, Panda M, Muya JT, Bandyopadhyay P, Meher BR. Theoretical insights into the binding interaction of Nirmatrelvir with SARS-CoV-2 Mpro mutants (C145A and C145S): MD simulations and binding free-energy calculation to understand drug resistance. J Biomol Struct Dyn 2023:1-20. [PMID: 37599474 DOI: 10.1080/07391102.2023.2248519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
Abstract
Mpro, the main protease and a crucial enzyme in SARS-CoV-2 is the most fascinating molecular target for pharmacological treatment and is also liable for viral protein maturation. For antiviral therapy, no drugs have been approved clinically to date. Targeting the Mpro with a compound having inhibitory properties against it can hinder viral replication. The therapeutic potential of the antiviral compound Nirmatrelvir (NMV) against SARS-CoV-2 Mpro was investigated using a systematic approach of molecular docking, MD simulations, and binding free energy calculation based on the MM-GBSA method. NMV, a covalent inhibitor with a recently revealed chemical structure, is a promising oral antiviral clinical candidate with significant in vitro anti-SARS-CoV-2 action in third-phase clinical trials. To explore the therapeutic ability and possible drug resistance, the Mpro system was studied for WT and two of its primary mutants (C145A & C145S). The protein-ligand (Mpro/NMV) complexes were further examined through long MD simulations to check the possible drug resistance in the mutants. To understand the binding affinity, the MM-GBSA method was applied to the Mpro/NMV complexes. Moreover, PCA analysis confirms the detachment of the linker region from the major domains in C145S and C145A mutants allowing for conformational alterations in the active-site region. Based on the predicted biological activities and binding affinities of NMV to WT and mutant (C145A & C145S) Mpro, it can be stipulated that NMV may have conventional potency to act as an anti-viral agent against WT Mpro, while the catalytic-dyad mutations may show substantial mutation-induced drug resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Jules Tshishimbi Muya
- Faculte of Science, Research Centre for Theoretical Chemistry and Physics in Central Africa, University of Kinshasa, Kinshasa, Congo
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
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Murmu LK, Panda M, Meher BR, Purohit P, Behera J, Barik TK. Molecular surveillance of Kelch-13 gene in Plasmodium falciparum field isolates from Mayurbhanj District, Odisha, India, and in silico artemisinin-Kelch-13 protein interaction study. Parasitol Res 2023; 122:717-727. [PMID: 36729138 DOI: 10.1007/s00436-023-07784-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 01/15/2023] [Indexed: 02/03/2023]
Abstract
The global malaria control and elimination program faces major threats due to the emergence and transmission of the anti-malarial drug-resistant strain of Plasmodium falciparum. Monitoring of artemisinin (ART) resistance marker Kelch-13 in the malaria-endemic region is essential in mitigating the disease's morbidity and mortality. The current study aimed to generate baseline information for further surveillance in the future. The current research was designed and conducted from July 2019 to June 2021 to monitor Pfkelch13 mutation at the molecular level in the eastern region of India. We also conducted an in silico study to understand the drug-protein interactions between ART and the protein crystal of PfKelch13 (KELCH) with PDB id:4ZGC. The kelch-13 gene was amplified by nested polymerase chain reaction (PCR) and sequenced through the Sanger sequencing method. Reference 3D7 clone (PF3D7_1343700) was used to align and probe all the sequences. The sequence analysis showed the absence of validated or associated mutation in the Kelch-13 propeller domain. The absence of natural selection in drug resistance was confirmed by the Tajima test. Further, in silico interaction studies between the drug ART and the Kelch propeller domain of P. falciparum were evaluated by structure predictions, molecular docking, molecular dynamics (MD) simulations, and estimations of binding free energies for the KELCH-ART complex. The results were compared with the apoprotein (KELCH-APO). The study confirmed the favorable binding of ART with the Kelch-13 propeller domain.
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Affiliation(s)
- Laxman Kumar Murmu
- P.G. Department of Zoology, Berhampur University, Berhampur, Odisha, 760007, India
| | - Madhusmita Panda
- Computational Biology & Bioinformatics Laboratory, P.G. Dept. of Botany, Berhampur University, Berhampur, Odisha, 760007, India
| | - Biswa Ranjan Meher
- Computational Biology & Bioinformatics Laboratory, P.G. Dept. of Botany, Berhampur University, Berhampur, Odisha, 760007, India
| | - Prasant Purohit
- Multi-Disciplinary Research Unit, M.K.C.G Medical College, Berhampur, Odisha, India
| | - Jayantiprava Behera
- Department of Pharmacology, M.K.C.G Medical College, Berhampur, Odisha, India
| | - Tapan Kumar Barik
- P.G. Department of Zoology, Berhampur University, Berhampur, Odisha, 760007, India.
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Musters AH, Broderick C, Prieto‐Merino D, Chiricozzi A, Damiani G, Peris K, Dhar S, De A, Freeman E, Arents BWM, Burton T, Bosma AL, Chi C, Fletcher G, Drucker AM, Kabashima K, de Monchy EF, Panda M, Wall D, Vestergaard C, Mahé E, Bonzano L, Kattach L, Napolitano M, Ordoñez‐Rubiano MF, Haufe E, Patruno C, Irvine AD, Spuls PI, Flohr C. The effects of systemic immunomodulatory treatments on COVID-19 outcomes in patients with atopic dermatitis: Results from the global SECURE-AD registry. J Eur Acad Dermatol Venereol 2022; 37:365-381. [PMID: 36169355 PMCID: PMC9537876 DOI: 10.1111/jdv.18613] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 08/17/2022] [Indexed: 01/18/2023]
Abstract
BACKGROUND Limited data are available on the effects of systemic immunomodulatory treatments on COVID-19 outcomes in patients with atopic dermatitis (AD). OBJECTIVE To investigate COVID-19 outcomes in patients with AD treated with or without systemic immunomodulatory treatments, using a global registry platform. METHODS Clinicians were encouraged to report cases of COVID-19 in their patients with AD in the Surveillance Epidemiology of Coronavirus Under Research Exclusion for Atopic Dermatitis (SECURE-AD) registry. Data entered from 1 April 2020 to 31 October 2021 were analysed using multivariable logistic regression. The primary outcome was hospitalization from COVID-19, according to AD treatment groups. RESULTS 442 AD patients (mean age 35.9 years, 51.8% male) from 27 countries with strongly suspected or confirmed COVID-19 were included in analyses. 428 (96.8%) patients were treated with a single systemic therapy (n = 297 [67.2%]) or topical therapy only (n = 131 [29.6%]). Most patients treated with systemic therapies received dupilumab (n = 216). Fourteen patients (3.2%) received a combination of systemic therapies. Twenty-six patients (5.9%) were hospitalized. No deaths were reported. Patients treated with topical treatments had significantly higher odds of hospitalization, compared with those treated with dupilumab monotherapy (odds ratio (OR) 4.65 [95%CI 1.71-14.78]), including after adjustment for confounding variables (adjusted OR (aOR) 4.99 [95%CI 1.4-20.84]). Combination systemic therapy which did not include systemic corticosteroids was associated with increased odds of hospitalization, compared with single agent non-steroidal immunosuppressive systemic treatment (OR 8.09 [95%CI 0.4-59.96], aOR 37.57 [95%CI 1.05-871.11]). Hospitalization was most likely in patients treated with combination systemic therapy which included systemic corticosteroids (OR 40.43 [95%CI 8.16-207.49], aOR 45.75 [95%CI 4.54-616.22]). CONCLUSIONS Overall, the risk of COVID-19 complications appears low in patients with AD, even when treated with systemic immunomodulatory agents. Dupilumab monotherapy was associated with lower hospitalization than other therapies. Combination systemic treatment, particularly combinations including systemic corticosteroids, was associated with the highest risk of severe COVID-19.
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Affiliation(s)
- A. H. Musters
- Department of Dermatology, Amsterdam UMC, location Academic Medical CenterUniversity of Amsterdam, Amsterdam Public Health, Infection and ImmunityThe Netherlands
| | - C. Broderick
- Unit for Population‐Based Dermatology Research, Guy’s and St Thomas’ NHS Foundation Trust and King’s College LondonLondonUK
| | - D. Prieto‐Merino
- Faculty of Epidemiology & Population Health, London School of Hygiene & Tropical MedicineLondonUK
| | - A. Chiricozzi
- Dermatologia, Fondazione Policlinico Universitario A. Gemelli IRCCSRomeItaly,Dermatologia, Università Cattolica del Sacro CuoreRomeItaly
| | - G. Damiani
- Clinical Dermatology, IRCCS Istituto Ortopedico Galeazzi, 20161MilanItaly,Department of Biomedical, Surgical and Dental SciencesUniversity of MilanMilanItaly,PhD Degree Program in Pharmacological Sciences, Department of Pharmaceutical and Pharmacological SciencesUniversity of PaduaPaduaItaly
| | - K. Peris
- Dermatologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro CuoreRomeItaly,UOC di Dermatologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli ‐ IRCCSRomeItaly
| | - S. Dhar
- Department of Pediatric DermatologyInstitute of Child HealthKolkataIndia
| | - A. De
- Department of DermatologyCalcutta National Medical CollegeKolkataIndia
| | - E. Freeman
- Department of Dermatology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA,Medical Practice Evaluation CenterMongan Institute, Massachusetts General Hospital, Harvard Medical SchoolBostonMAUSA
| | - B. W. M. Arents
- Dutch Association for People with Atopic Dermatitis (VMCE), NijkerkThe Netherlands
| | - T. Burton
- Patient Representative (independent), NottinghamUnited Kingdom
| | - A. L. Bosma
- Department of Dermatology, Amsterdam UMC, location Academic Medical CenterUniversity of Amsterdam, Amsterdam Public Health, Infection and ImmunityThe Netherlands
| | - C.‐C. Chi
- Department of Dermatology, Chang Gung Memorial Hospital, LinkouTaoyuanTaiwan,College of MedicineChang Gung UniversityTaoyuanTaiwan
| | - G. Fletcher
- National and International Skin Registry Solutions (NISR), Charles Institute of DermatologyUniversity College DublinDublinIreland
| | - A. M. Drucker
- Department of MedicineUniversity of Toronto, Toronto, Canada; Women's College Research Institute, Women's College HospitalTorontoCanada
| | - K. Kabashima
- Department of DermatologyKyoto University Graduate School of MedicineKyotoJapan,Singapore Immunology Network (SIgN) and Skin Research Institute of Singapore (SRIS), Agency for Science, Technology and Research (A*STAR), BiopolisSingapore
| | - E. F. de Monchy
- Department of Dermatology, Amsterdam UMC, location Academic Medical CenterUniversity of Amsterdam, Amsterdam Public Health, Infection and ImmunityThe Netherlands
| | - M. Panda
- Department of DVLInstitute of Medical Sciences and SUM HospitalBhubaneswarOdishaIndia
| | - D. Wall
- National and International Skin Registry Solutions (NISR), Charles Institute of DermatologyUniversity College DublinDublinIreland,Hair Restoration BlackrockDublinIreland
| | - C. Vestergaard
- Department of DermatologyAarhus University HospitalAarhusDenmark
| | - E. Mahé
- Service de Dermatologie et Médecine VasculaireCentre Hospitalier Victor Dupouy, 69 rue du Lieutenant‐Colonel Prud'honArgenteuilCedexFrance
| | - L. Bonzano
- Dermatology Unit, Azienda USL‐IRCCS di Reggio EmiliaReggio EmiliaItaly
| | - L. Kattach
- Guy's & St. Thomas' Hospitals NHS Foundation Trust
| | - M. Napolitano
- Department of Medicine and Health Sciences Vincenzo TiberioUniversity of MoliseCampobassoItaly
| | | | - E. Haufe
- Center for Evidence‐based Health Care (ZEGV), Medical Faculty Carl Gustav Carus, TU DresdenDresdenGermany
| | - C. Patruno
- Dermatology and Venereology, Department of Health SciencesUniversity Magna Graecia of CatanzaroItaly
| | | | - P. I. Spuls
- Department of Dermatology, Amsterdam UMC, location Academic Medical CenterUniversity of Amsterdam, Amsterdam Public Health, Infection and ImmunityThe Netherlands
| | - C. Flohr
- Unit for Population‐Based Dermatology Research, Guy’s and St Thomas’ NHS Foundation Trust and King’s College LondonLondonUK
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Panda M, Purohit P, Meher BR. Structure-based virtual screening, ADMET profiling, and molecular dynamics simulation studies on HIV-1 protease for identification of active phytocompounds as potential anti-HIV agents. Molecular Simulation 2022. [DOI: 10.1080/08927022.2022.2060968] [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] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
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Joshi S, Jakathamani S, Panda M, Annalakshmi O, Mathiyarasu R, Venkata Srinivas C, Venkatesan R, Venkatraman B. A systematic quartz extraction method for retrospective dosimetry and dating. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Lele N, Kripa MK, Panda M, Das SK, Nivas AH, Divakaran N, Naik-Gaonkar S, Sawant A, Pattnaik AK, Samal RN, Thangaradjou T, Saravanakumar A, Rodrigues BF, Murthy TVR. Seasonal variation in photosynthetic rates and satellite-based GPP estimation over mangrove forest. Environ Monit Assess 2021; 193:61. [PMID: 33443643 DOI: 10.1007/s10661-021-08846-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
In view of increasing anthropogenic influences and global changes, quantification of carbon assimilation through photosynthesis has gained tremendous significance. Precise estimation of Gross Primary Productivity (GPP) is essential for several ecosystem models and is typically done using coarser scale satellite data. The mangrove ecosystem, which offers significant protection to the coastal environment, is one of the critical habitats from a global change point of view. Light use efficiency (LUE) was measured using diurnal in situ photosynthetic rate observations for 13 dominant mangrove species for 3 seasons at each of the three mangrove dominant test-sites situated along the east and west coast of India. Variations in photosynthetic rates among these species were studied for 3 seasons that indicated varying responses of mangrove ecosystem at each site. Among all species, Rhizophora mucronata and Sonneratia apetala indicated higher values at two of the test-sites. IRS Resourcesat-2 LISS-IV datasets were used for the estimation of GPP. Mean GPP for all the sites varied from 1.2 to 7.7 g C m-2 day-1 with maximum value of 14.4 g C m-2 day-1. Mean values of GPP varied across the sites, based on its maximum LUE values and available photosynthetically active radiation (PAR). The results provide GPP values at much better spatial resolution for a threatened habitat like mangroves that typically survive in a narrow habitat along the coasts.
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Affiliation(s)
- N Lele
- Agriculture and Land Ecosystem Division (AED-BPSG-EPSA), Space Applications Centre (ISRO), Ahmedabad, Gujarat, India.
| | - M K Kripa
- Agriculture and Land Ecosystem Division (AED-BPSG-EPSA), Space Applications Centre (ISRO), Ahmedabad, Gujarat, India
| | - M Panda
- Chilika Development Authority, Bhubaneshwar, Odisha, India
| | - S K Das
- Chilika Development Authority, Bhubaneshwar, Odisha, India
| | - A Hari Nivas
- Centre of Advanced Study in Marine Biology, Annamalai University, Parangipettai, Tamil Nadu, India
| | - N Divakaran
- Centre of Advanced Study in Marine Biology, Annamalai University, Parangipettai, Tamil Nadu, India
| | | | - A Sawant
- Botany Department, Goa University, Taleigao, Goa, India
| | - A K Pattnaik
- Chilika Development Authority, Bhubaneshwar, Odisha, India
| | - R N Samal
- Chilika Development Authority, Bhubaneshwar, Odisha, India
| | - T Thangaradjou
- Centre of Advanced Study in Marine Biology, Annamalai University, Parangipettai, Tamil Nadu, India
| | - A Saravanakumar
- Centre of Advanced Study in Marine Biology, Annamalai University, Parangipettai, Tamil Nadu, India
| | - B F Rodrigues
- Botany Department, Goa University, Taleigao, Goa, India
| | - T V R Murthy
- Agriculture and Land Ecosystem Division (AED-BPSG-EPSA), Space Applications Centre (ISRO), Ahmedabad, Gujarat, India
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Agarwal A, Hassanandani T, Das A, Panda M, Chakravorty S. 'Mask tinea': tinea faciei possibly potentiated by prolonged mask usage during the COVID-19 pandemic. Clin Exp Dermatol 2020; 46:190-193. [PMID: 33098693 PMCID: PMC9213933 DOI: 10.1111/ced.14491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 08/27/2020] [Revised: 10/16/2020] [Accepted: 10/20/2020] [Indexed: 11/26/2022]
Affiliation(s)
- A Agarwal
- Department of Dermatology, IMS & SUM Hospital, Bhubaneshwar, India
| | - T Hassanandani
- Department of Dermatology, IMS & SUM Hospital, Bhubaneshwar, India
| | - A Das
- Department of Dermatology, KPC Medical College and Hospital, Kolkata, India
| | - M Panda
- Department of Dermatology, IMS & SUM Hospital, Bhubaneshwar, India
| | - S Chakravorty
- Department of Microbiology, Bhagirathi Neotia Woman and Child Care Centre, Kolkata, India
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10
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Rai AK, Panda M, Das AK, Rahman T, Das R, Das K, Sarma A, Kataki AC, Chattopadhyay I. Dysbiosis of salivary microbiome and cytokines influence oral squamous cell carcinoma through inflammation. Arch Microbiol 2020; 203:137-152. [PMID: 32783067 DOI: 10.1007/s00203-020-02011-w] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/23/2020] [Accepted: 08/03/2020] [Indexed: 01/10/2023]
Abstract
Advanced combinatorial treatments of surgery, chemotherapy, and radiotherapy do not have any effect on the enhancement of a 5-year survival rate of oral squamous cell carcinoma (OSCC). The discovery of early diagnostic non-invasive biomarkers is required to improve the survival rate of OSCC patients. Recently, it has been reported that oral microbiome has a significant contribution to the development of OSCC. Oral microbiome induces inflammatory response through the production of cytokines and chemokines that enhances tumor cell proliferation and survival. The study aims to develop saliva-based oral microbiome and cytokine biomarker panel that screen OSCC patients based on the level of the microbiome and cytokine differences. We compared the oral microbiome signatures and cytokine level in the saliva of OSCC patients and healthy individuals by 16S rRNA gene sequencing targeting the V3/V4 region using the MiSeq platform and cytokine assay, respectively. The higher abundance of Prevotella melaninogenica, Fusobacterium sp., Veillonella parvula, Porphyromonas endodontalis, Prevotella pallens, Dialister, Streptococcus anginosus, Prevotella nigrescens, Campylobacter ureolyticus, Prevotella nanceiensis, Peptostreptococcus anaerobius and significant elevation of IL-8, IL-6, TNF-α, GM-CSF, and IFN-γ in the saliva of patients having OSCC. Oncobacteria such as S. anginosus, V. parvula, P. endodontalis, and P. anaerobius may contribute to the development of OSCC by increasing inflammation via increased expression of inflammatory cytokines such as IL-6, IL-8, TNF-α, IFN-γ, and GM-CSF. These oncobacteria and cytokines panels could potentially be used as a non-invasive biomarker in clinical practice for more efficient screening and early detection of OSCC patients.
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Affiliation(s)
- Avdhesh Kumar Rai
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 16, India
| | - Madhusmita Panda
- Department of Life Sciences, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India
| | - Ashok Kumar Das
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 16, India
| | - Tashnin Rahman
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 16, India
| | - Rajjyoti Das
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 16, India
| | - Kishore Das
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 16, India
| | - Anupam Sarma
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 16, India
| | - Amal Ch Kataki
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 16, India
| | - Indranil Chattopadhyay
- Department of Life Sciences, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India.
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Abstract
Despite advancement in cancer treatment, oral cancer has a poor prognosis and is often detected at late stage. To overcome these challenges, investigators should search for early diagnostic and prognostic biomarkers. More than 700 bacterial species reside in the oral cavity. The oral microbiome population varies by saliva and different habitats of oral cavity. Tobacco, alcohol, and betel nut, which are causative factors of oral cancer, may alter the oral microbiome composition. Both pathogenic and commensal strains of bacteria have significantly contributed to oral cancer. Numerous bacterial species in the oral cavity are involved in chronic inflammation that lead to development of oral carcinogenesis. Bacterial products and its metabolic by-products may induce permanent genetic alterations in epithelial cells of the host that drive proliferation and/or survival of epithelial cells. Porphyromonas gingivalis and Fusobacterium nucleatum induce production of inflammatory cytokines, cell proliferation, and inhibition of apoptosis, cellular invasion, and migration thorough host cell genomic alterations. Recent advancement in metagenomic technologies may be useful in identifying oral cancer-related microbiome, their genomes, virulence properties, and their interaction with host immunity. It is very important to address which bacterial species is responsible for driving oral carcinogenesis. Alteration in the oral commensal microbial communities have potential application as a diagnostic tool to predict oral squamous cell carcinoma. Clinicians should be aware that the protective properties of the resident microflora are beneficial to define treatment strategies. To develop highly precise and effective therapeutic approaches, identification of specific oral microbiomes may be required. In this review, we narrate the role of microbiome in the progression of oral cancer and its role as an early diagnostic and prognostic biomarker for oral cancer.
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Affiliation(s)
- Indranil Chattopadhyay
- 1 Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Mukesh Verma
- 2 Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Madhusmita Panda
- 1 Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
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Panda M, Rao MEB, Patra CN, Panda J, Panigrahi KC, Patro G. Formulation and development of floating multiple-unit minitablets of Nimodipine without using a gas-generating agent: in vitro and in vivo characterization. Futur J Pharm Sci 2020. [DOI: 10.1186/s43094-020-0021-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
Background
Floating drug delivery systems have been reported for different active pharmaceutical ingredients as single-unit tablets with gas-generating agents. In this present research, the formulation of floating multiple-unit minitablets of Nimodipine without using gas-generating agent was attempted with an objective of increased residence time, sustain-release and improved oral bioavailability. Solid dispersion with different ratios (1:0.5, 1:1, 1:1.5, 1:2, 1:2.5) of drug with the lipophilic carrier such as Compritol ATO 888, Gelucire 43/01, G39/01 and Precirol ATO 05 was formulated using melt granulation technique. The adsorbent Sylysia 350 to lipophilic carrier is maintained at 1:1. The granules were compressed into minitablets weighing 15 mg and were filled into a ‘0’ size capsule.
Results
Differential scanning calorimetry study justified no interaction of the drug with excipients. The formulations which exhibited desirable flow property, floating lag time less than 1 min and floating time of 12 h were further characterized for various post-compression parameters. The optimized single-dose (capsule) of floating multiple-unit minitablets of Nimodipine consisting of 60 mg of drug, 120 mg of G43/01 and 120 mg of Sylysia 350 showed an average of floating lag time within 24.48 s, floating time of 14.32 h and sustained-release up to 12 h. Pharmacokinetic study of the optimized formulation (F9) showed nearly 2.5 times increase in area under the curve with increased residence time in comparison to aqueous suspension of Nimodipine. The stability study revealed no significant change in various parameters before and after storage.
Conclusion
Hence, gelucire 43/01-based multiple-unit minitablets of Nimodipine can be considered a promising approach for sustaining the drug release with gastric retention for 12 h without using gas-generating agent.
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Mishra P, Ravi P, Gaikwad M, Tirpude A, Panda M. Morphological variations of biceps brachii muscle in eastern indian population: A cadaveric study. Natl J Clin Anat 2020. [DOI: 10.1055/s-0040-1708923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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14
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Panda M, Rai AK, Rahman T, Das A, Das R, Sarma A, Kataki AC, Chattopadhyay I. Alterations of salivary microbial community associated with oropharyngeal and hypopharyngeal squamous cell carcinoma patients. Arch Microbiol 2019; 202:785-805. [PMID: 31832691 DOI: 10.1007/s00203-019-01790-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 09/03/2019] [Revised: 11/20/2019] [Accepted: 12/03/2019] [Indexed: 02/06/2023]
Abstract
The highest number (35.1% of global incident cases) of new oropharyngeal (OP) and hypopharyngeal (HP) cancer cases was reported in South-Central Asia. The highest incidence of HP cancer in India was reported in East Khasi Hills District of Meghalaya, Aizawl District of Mizoram, and Kamrup Urban District of Assam. HP and OP cancer showed the highest mortality rate, worst prognoses and the highest rate of nodal metastases and distant metastases. Thus, research is required to detect specific biomarkers for early prevention and diagnosis for these cancers. Oral microbiome signatures in saliva are considered as a potential diagnostic biomarker for OP and HP cancer. Bacterial profile alterations in OP and HP cancer have not been reported in India population, to establish the association of oral bacteria in the progression of OP and HP cancer; we studied bacterial communities in saliva of eight OP and seven HP cancer patients as compared to healthy controls using 16S rRNA V3-V4 region sequencing. The higher abundance of Haemophilus parainfluenzae, Haemophilus influenzae and Prevotella copri and lower abundance of Rothia mucilaginosa, Aggregatibacter segnis, Veillonella dispar, Prevotella nanceiensis, Rothia aeria, Capnocytophaga ochracea, Neisseria bacilliformis, Prevotella nigrescens and Selenomonas noxia in saliva of OP and HP cancer patients may be considered as a non-invasive diagnostic biomarker for OP and HP cancer patients. Streptococcus anginosus may be considered as a non-invasive diagnostic biomarker for OP cancer patients only. Therefore, evaluation of salivary microbial biomarkers may be informative to understand the pathobiology and carcinogenesis of OP and HP cancer.
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Affiliation(s)
- Madhusmita Panda
- Department of Life Sciences, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610005, India
| | - Avdhesh Kumar Rai
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 781016, India
| | - Tashnin Rahman
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 781016, India
| | - Ashok Das
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 781016, India
| | - Rajjyoti Das
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 781016, India
| | - Anupam Sarma
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 781016, India
| | - Amal Ch Kataki
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 781016, India
| | - Indranil Chattopadhyay
- Department of Life Sciences, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610005, India.
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Rathore SK, Dwibedi B, Pati SS, Panda S, Panda M, Sabat J, Kar SK. An Investigation on the Coinfection of Measles and HSV-1 in Hospitalized Acute Encephalitis Syndrome Patients in Eastern India. Neurol India 2019; 67:1358-1359. [PMID: 31744976 DOI: 10.4103/0028-3886.271247] [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: 11/04/2022]
Abstract
Acute encephalitis syndrome (AES) is a clinical condition that occurs due to infectious and noninfectious agents- however, viruses are considered to be the dominant pathogen. agents- however, viruses are considered to be the dominant pathogen. In this study, suspected AES cases were enrolled and tested for viral etiology through serology and polymerase chain reaction (PCR)/reverse transcriptase PCR from August 2012-July 2013. During this period, 820 cases were investigated and 96 cases were diagnosed to have a viral etiology whereas 20 patients had IgM antibodies for measles in serum and HSV-1 DNA in cerebrospinal fluid. All 20 of the patients were children below 14 years of age. The median hospital stay was 15 days (IQR: 14.2-17 days) and median GCS score was 7(IQR: 6-8) and were significantly different with patients with co-infections when comapred with patients having HSV-1 infection only. It may be suspected that the measles infection may have a role in the pathogenesis and thus an impact on the prognosis of the AES when present with HSV-1.
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Affiliation(s)
- S K Rathore
- Virology Division, ICMR-RMRC; Department of Biotechnology, School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
| | - B Dwibedi
- Virology Division, ICMR-RMRC; Department of Pediatrics, AIIMS, Bhubaneswar, Odisha, India
| | - S S Pati
- Virology Division, ICMR-RMRC, Bhubaneswar, Odisha, India
| | - S Panda
- Virology Division, ICMR-RMRC, Bhubaneswar, Odisha, India
| | - M Panda
- Department of Microbiology, Apollo Hospital, Bhubaneswar, Odisha, India
| | - J Sabat
- Virology Division, ICMR-RMRC, Bhubaneswar, Odisha, India
| | - S K Kar
- IMS and SUM Hospital, Director, Medical Research and Life Sciences, Bhubaneswar, Odisha, India
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16
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Sabat J, Subhadra S, Thakur B, Panda M, Panda S, Pati SS, Ho LM, Dixit S, Rathore SK, Kar SK, Dwibedi B. Molecular and phylogenetic analysis of the dengue strains circulating in Odisha, India. Virusdisease 2019; 30:380-386. [PMID: 31803805 DOI: 10.1007/s13337-019-00544-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 02/02/2023] Open
Abstract
Dengue has emerged as a major public health challenge in terms of both changing clinical pattern and epidemiological features. The state of Odisha reported first dengue epidemic in the year 2010 and this continued each year in epidemic form during post monsoon period gradually becoming an endemic phenomenon. Present study depicts the changing epidemiological and clinical pattern of dengue with reference to its serotypes and genotypes. The study included 5320 suspected dengue cases from different health facilities of the state during 2010-2017. Dengue NS1 antigen and IgM antibody was done through ELISA. Serotyping was done through RTPCR by amplifying a part of core-pre-membrane gene (CprM) followed by sequencing and phylogenetic analysis. Dengue IgM antibody in 17.7% cases and NS1 antigen in 53.20% cases was detected. Dengue serotype 2 (DEN-2) was the only serotype detected in 2010 and 2011 where as all four serotypes 1, 2, 3, 4 were detected in 2012-2017, DEN-2 being dominant but in 2017 DEN-3 was found to be dominant. Phylogenetic analysis revealed genotype IV of DEN-2 and genotype III of DEN-1 and DEN-3 circulating in this region. In 6 cases involvement of DEN-2 in clinically evident encephalitis cases is an important observation in this region and needs public health attention. High prevalence of dengue was observed without any previous reported outbreaks in the state with increased number of cases from 2010 to 2012 affecting both urban and rural areas. High incidence in 2012 was due to co-circulation of more than one serotype which continued in the following years. Severity in some cases was associated with mixed infection but in most cases it was mild indicating the endemic nature of the virus in most parts of Odisha.
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Affiliation(s)
- J Sabat
- 2ICMR- Regional Medical Research Centre, Bhubaneswar, Odisha 751023 India
| | - S Subhadra
- 2ICMR- Regional Medical Research Centre, Bhubaneswar, Odisha 751023 India
| | - B Thakur
- 2ICMR- Regional Medical Research Centre, Bhubaneswar, Odisha 751023 India
| | - M Panda
- 2ICMR- Regional Medical Research Centre, Bhubaneswar, Odisha 751023 India
| | - S Panda
- 2ICMR- Regional Medical Research Centre, Bhubaneswar, Odisha 751023 India
| | - S S Pati
- 2ICMR- Regional Medical Research Centre, Bhubaneswar, Odisha 751023 India
| | - L M Ho
- 2ICMR- Regional Medical Research Centre, Bhubaneswar, Odisha 751023 India
| | - S Dixit
- 2ICMR- Regional Medical Research Centre, Bhubaneswar, Odisha 751023 India
| | - S K Rathore
- 2ICMR- Regional Medical Research Centre, Bhubaneswar, Odisha 751023 India
| | - S K Kar
- 3Directorate of Medical research, IMS & SUM Hospital, S 'O' A University, Bhubaneswar, Odisha 751030 India
| | - B Dwibedi
- 1Department of Pediatrics, AIIMS, Bhubaneswar, Odisha 751019 India
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Kumar D, Panda M, Mohapatra C, Das R, Sarangi C, Biswal R, Gurudiwan R, Das C. Interhemispheric variations & sexual dimorphism of the length of the fissure of Rolando & Rolandic angle in brains of cadavers of eastern Odisha. J ANAT SOC INDIA 2018. [DOI: 10.1016/j.jasi.2018.06.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Panda M, Asmita, Kumar S, Mishra P, Sahu M, De S, Datta T, Kumar R. Effect of exogenous progesterone on cumulus characteristics of buffalo oocytes by allowing passage of more number of sperm through cumulus but not essentially fertilization. Asian Pac J Reprod 2018. [DOI: 10.4103/2305-0500.228017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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19
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Patra S, Bara D, Ray S, Panda M, Sarangi C, Das RK, Biswal R, Mohapatra C. A case of tibiofibular synostosis. J ANAT SOC INDIA 2017. [DOI: 10.1016/j.jasi.2017.08.370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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20
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Patra S, Bara D, Ray S, Panda M, Sarangi C, Rajashree Biswal RKD, Mohapatra C. Variations of anterior cerebral artery and anterior communicating artery in East Indian population. J ANAT SOC INDIA 2017. [DOI: 10.1016/j.jasi.2017.08.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Abstract
Purpose
The purpose of this paper is to examine the role of transformational leadership in psychological empowerment in Indian retail industry. This study also tries to examine whether organizational culture plays a mediating role in the relationships between transformational leadership and psychological empowerment.
Design/methodology/approach
A sample of 310 respondents was randomly selected from different Indian retail organizations for the study. Data collections were carried out using a set of standardized questionnaires. Raw data were analyzed using SPSS 20.0 and process plugin of Hayes for mediation analysis.
Findings
The empirical investigations of the study have shown that transformational leadership is positively related to psychological empowerment. The study also found partial mediation of organizational culture between transformational leadership and psychological empowerment.
Research limitations/implications
First of all, the sample size of the study is relatively small (n=310). The study is limited to the employees of eastern Indian retail organizations. Second, the common method bias is presumed to influence and inflate the relationships between the variables of the study as the data on all three variables were collected at the same point of time from respondents.
Practical implications
The road map presented in this paper may be helpful for the retail executives to diagnose organizational culture and leadership styles prevailing in the organization and their influence on psychological empowerment. The study may be helpful for retail managers to develop a desirable culture through the practice of transformational leadership that would enhance the empowerment process.
Originality/value
This paper adds value to the limited body of knowledge about the association among transformational leadership, psychological empowerment, and organizational culture. The findings presented in this paper would be beneficial for Indian researchers, OD experts and organization scientists in developing a culture of empowerment by the help of transformational leadership. Unique statistical tools have been used for mediation analysis.
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22
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Panda M, Panda N, Swain R, Panigrahi B, Behera P, Das B. Mineral Profiles and Metabolic Status of Animals in North Eastern Ghat Zone of Odisha. ANIM NUTR FEED TECHN 2017. [DOI: 10.5958/0974-181x.2017.00006.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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Panda D, Panda M. Non-Volatile Flash Memory Characteristics of Tetralayer Nickel-Germanide Nanocrystals Embedded Structure. J Nanosci Nanotechnol 2016; 16:1216-9. [PMID: 27398590 DOI: 10.1166/jnn.2016.11047] [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] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Formation of tetralayer memory structure having nickel-germanide nanocrystals using a Ge/Ni multilayers is proposed. X-ray diffraction study shows the NiGe (002) phase formation after proper annealing. Cross sectional HRTEM clearly shows the sharpness and the size (~4-6 nm) of the stacked nanocrystals embedded in the oxide matrix. A large anti-clockwise hysteresis memory win- dow of 13.4 Volt at ± 15 Volt is observed for the optimized samples. This large memory window indicates for the MLC applications. Frequency independent C-V curve confirms about the charge storage in the nanocrystals. A good charge retention and endurance characteristics are exhibited upto 125 °C for the nonvolatile memory application.
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25
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Panda M, Mangamma G, Krishnan R, Madapu KK, Krishna DNG, Dash S, Tyagi AK. Nano scale investigation of particulate contribution to diamond like carbon film by pulsed laser deposition. RSC Adv 2016. [DOI: 10.1039/c5ra21361d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Raman mapping and AFAM are useful tools to evaluate the relative stiffness of DLC films embedded with micro graphitic particulates.
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Affiliation(s)
- Madhusmita Panda
- Materials Science Group
- Indira Gandhi Centre for Atomic Research
- India
| | - G. Mangamma
- Materials Science Group
- Indira Gandhi Centre for Atomic Research
- India
| | - R. Krishnan
- Materials Science Group
- Indira Gandhi Centre for Atomic Research
- India
| | - Kishore K. Madapu
- Materials Science Group
- Indira Gandhi Centre for Atomic Research
- India
| | | | - S. Dash
- Materials Science Group
- Indira Gandhi Centre for Atomic Research
- India
| | - A. K. Tyagi
- Materials Science Group
- Indira Gandhi Centre for Atomic Research
- India
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26
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Patra S, Mohapatra C, Sarangi C, Biswal R, Panda M, Pradhan S, Bara D, Nayak S. Incidence of accessory mandibular foramen and its clinical significance. J ANAT SOC INDIA 2015. [DOI: 10.1016/j.jasi.2015.07.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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27
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Rath S, Panda M, Sahu MC, Padhy RN. Bayesian analysis of two diagnostic methods for paediatric ringworm infections in a teaching hospital. J Mycol Med 2015; 25:191-9. [PMID: 26271198 DOI: 10.1016/j.mycmed.2015.06.065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 04/04/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 11/30/2022]
Abstract
Quantitatively, conventional methods of diagnosis of tinea capitis or paediatric ringworm, microscopic and culture tests were evaluated with Bayes rule. This analysis would help in quantifying the pervasive errors in each diagnostic method, particularly the microscopic method, as a long-term treatment would be involved to eradicate the infection by the use of a particular antifungal chemotherapy. Secondly, the analysis of clinical data would help in obtaining digitally the fallible standard of the microscopic test method, as the culture test method is taken as gold standard. Test results of 51 paediatric patients were of 4 categories: 21 samples were true positive (both tests positive), and 13 were true negative; the rest samples comprised both 14 false positive (microscopic test positivity with culture test negativity) and 3 false negative (microscopic test negativity with culture test positivity) samples. The prevalence of tinea infection was 47.01% in the population of 51 children. The microscopic test of a sample was efficient by 87.5%, in arriving at a positive result on diagnosis, when its culture test was positive; and, this test was efficient by 76.4%, in arriving at a negative result, when its culture test was negative. But, the post-test probability value of a sample with both microscopic and culture tests would be correct in distinguishing a sample from a sick or a healthy child with a chance of 71.5%. However, since the sensitivity of the analysis is 87.5%, the microscopic test positivity would be easier to detect in the presence of infection. In conclusion, it could be stated that Trychophyton rubrum was the most prevalent species; sensitivity and specificity of treating the infection, by antifungal therapy before ascertaining by the culture method remain as 0.8751 and 0.7642, respectively. A correct/coveted diagnostic method of fungal infection would be could be achieved by modern molecular methods (matrix-assisted laser desorption ionisation-time of flight mass spectrometry or fluorescence in situ hybridization or enzyme-linked immunosorbent assay [ELISA] or restriction fragment length polymorphism or DNA/RNA probes of known fungal taxa) in advanced laboratories.
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Affiliation(s)
- S Rath
- Central Research Laboratory, Institute of Medical Sciences & Sum Hospital, Siksha 'O' Anusandhan University, Bhubaneswar 751003, Odisha, India
| | - M Panda
- Department of Skin and VD, Institute of Medical Sciences & Sum Hospital, Siksha 'O' Anusandhan University, Kalinga Nagar, Bhubaneswar 751003, Odisha, India
| | - M C Sahu
- Central Research Laboratory, Institute of Medical Sciences & Sum Hospital, Siksha 'O' Anusandhan University, Bhubaneswar 751003, Odisha, India
| | - R N Padhy
- Central Research Laboratory, Institute of Medical Sciences & Sum Hospital, Siksha 'O' Anusandhan University, Bhubaneswar 751003, Odisha, India.
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Abstract
Neonatal care practices have been shown to vary across tribal communities. This cross-sectional study was conducted in tribal block in Nabarangpur district of Odisha, India, to measure perinatal and antenatal practices by qualitative inquiries of 55 mothers who had babies aged <60 days and from 11 traditional birth attendants. Reasons for home deliveries were cited as easy availability of traditional birth attendants and family preferences. Application of indigenously made substances on umbilical stump and skin of the baby, bathing baby immediately after birth, late initiation of breast-feeding and 'Budu practices' were common. Cultural issues, decision of family members and traditional beliefs still play a crucial role in shaping neonatal care practice in tribal communities. Awareness on child care, ethnographic understanding of health-seeking behavior of tribal community and mobilization of community by health workers can be useful in improving health status of mothers and newborn babies in tribal population.
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Affiliation(s)
- Sanghamitra Pati
- Academics Indian Institute of Public Health- Bhubaneswar, Public Health Foundation of India, Patia, Bhubaneswar 751024, Odisha, India
| | - Abhimanyu S Chauhan
- Research International Clinical Epidemiology Network, New Delhi 110020, India
| | - Madhusmita Panda
- Programme RCH Division, UNICEF-Odisha, Mayurbhanj, Odisha 757043, India
| | - Subhashish Swain
- Academics Indian Institute of Public Health- Bhubaneswar, Public Health Foundation of India, Patia, Bhubaneswar 751024, Odisha, India
| | - Mohammad A Hussain
- Division of Epidemiology & Biostatistics, School of Population Health, The University of Queensland Herston, Brisbane 4006, Australia
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Pratheepa M, Jalali SK, Arokiaraj RS, Venkatesan T, Nagesh M, Panda M, Pattar S. Insect barcode information system. Bioinformation 2014; 10:98-100. [PMID: 24616562 PMCID: PMC3937583 DOI: 10.6026/97320630010098] [Citation(s) in RCA: 3] [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: 12/28/2013] [Accepted: 01/15/2014] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED Insect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects. IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client- server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBIn allows the registered users to input new information, search and view information related to DNA barcode of agriculturally important insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn. AVAILABILITY http://www.nabg-nbaii.res.in/barcode.
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Affiliation(s)
- Maria Pratheepa
- National Bureau of Agriculturally Important Insects, Post Bag No. 2491, H.A. Farm Post, Hebbal, Bellary Road, Bangalore – 560 024, Karnataka, India
| | - Sushil Kumar Jalali
- National Bureau of Agriculturally Important Insects, Post Bag No. 2491, H.A. Farm Post, Hebbal, Bellary Road, Bangalore – 560 024, Karnataka, India
| | - Robinson Silvester Arokiaraj
- National Bureau of Agriculturally Important Insects, Post Bag No. 2491, H.A. Farm Post, Hebbal, Bellary Road, Bangalore – 560 024, Karnataka, India
| | - Thiruvengadam Venkatesan
- National Bureau of Agriculturally Important Insects, Post Bag No. 2491, H.A. Farm Post, Hebbal, Bellary Road, Bangalore – 560 024, Karnataka, India
| | - Mandadi Nagesh
- National Bureau of Agriculturally Important Insects, Post Bag No. 2491, H.A. Farm Post, Hebbal, Bellary Road, Bangalore – 560 024, Karnataka, India
| | - Madhusmita Panda
- National Bureau of Agriculturally Important Insects, Post Bag No. 2491, H.A. Farm Post, Hebbal, Bellary Road, Bangalore – 560 024, Karnataka, India
| | - Sharath Pattar
- National Bureau of Agriculturally Important Insects, Post Bag No. 2491, H.A. Farm Post, Hebbal, Bellary Road, Bangalore – 560 024, Karnataka, India
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Abstract
The role of steroids in treatment of postinfectious glomerulonephritis (PIGN) has been controversial. The reason for such controversy is the risk of infection relapse associated with steroid therapy. Steroids may have a place in the treatment of resistant cases where renal function does not improve despite aggressive antibiotic therapy as well as in patients with crescentic form of PIGN. We report a case of a 39 year-old Caucasian man who was diagnosed with methicillin-resistant Staphylococcus aureus (MRSA) bacteremia resulting in acute IgA dominant PIGN that failed to respond to antibiotic treatment alone, but responded significantly to steroids in addition to antibiotics. This anecdotal experience suggests that steroids could be considered in conjunction with antibiotic therapy for the treatment of refractory cases of PIGN or crescentic form of PIGN. More studies with long-term follow-up of patients treated with steroids in addition to antimicrobial agents are required to quantify the risk of infection relapse with steroid therapy.
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Affiliation(s)
- A S Kapadia
- Department of Medicine, University of Tennessee College of Medicine, Chattanooga, USA
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31
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Abstract
Removal of hexavalent chromium ions from an aqueous solution by crude tamarind (Tamarindus indica) fruit shell was examined in a rotating packed bed contactor by continuously recirculating a given volume of solution through the bed. Reduction of Cr(VI) to Cr(III) within the biosorbent appeared to be the removal mechanism. Depletion rate of Cr(VI) from, and release of reduced Cr(III) ions into the aqueous phase, was influenced by mass transfer resistance besides pH and packing depth. A mathematical model considering the reduction reaction to be irreversible and incorporating intraparticle and external phase mass transfer resistances represented the experimental data adequately. The study indicated that the limitations of fixed bed contactor operating under terrestrial gravity in intensifying mass transfer rates for this system can be overcome with rotating packed bed due to liquid flow under centrifugal acceleration.
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Affiliation(s)
- M Panda
- Department of Chemical Engineering, Jadavpur University , Kolkata 700032, India
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Singh V, Bhattarai N, Panda M. Iron deficiency in a male with multiple myeloma. Case Reports 2010; 2010:2010/dec15_1/bcr0420102956. [DOI: 10.1136/bcr.04.2010.2956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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33
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Panda M, Thakur AK, Srinivas V. Thermal effects on the percolation behavior of polyvinylidene fluoride/nickel composites. J Appl Polym Sci 2010. [DOI: 10.1002/app.31223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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34
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Kibadi K, Mputu-Yamba JB, Mokassa B, Panda M, Muyembe-Tamfum JJ. [Relapse after surgical treatment of mycobacterium ulcerans infection (buruli ulcer): study of risk factors in 84 patients in the Democratic Republic of the Congo]. Med Trop (Mars) 2009; 69:471-474. [PMID: 20025176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
OBJECTIVE To identify risk factors for relapse after exclusively surgical treatment of Mycobacterium ulcerans infection (Buruli ulcer). METHODS Study was carried out in 102 patients treated exclusively by surgery for Buruli ulcer at various care facilities in the Congo from January 1, 2000 to January 1, 2005. RESULTS Outcomes included relapse in 22 patients (21.5%), cure in 62 (60.7%), and unknown in 18 (17.6%). Statistical analysis identified the following variables as independent risk factors for relapse after exclusively surgical treatment: incomplete surgical excision (OR = 91.83; P = 0.0000; IC to 95%), age under 16 years (OR = 14.80; P = 0.0000; IC to 95%) and pre-ulcerative Buruli lesions (edema and plaque) (OR = 3.18; P = 0.0215; IC to 95%). CONCLUSION Quality of excision, patient age, and clinical form of lesion are the main predictors of relapse after isolated surgical treatment of Buruli ulcer.
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Affiliation(s)
- K Kibadi
- Département de Chirurgie, Faculté de Médecine, Université de Kinshasa, République Démocratique du Congo.
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35
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Sinan M, Panda M, Ghosh A, Dhara K, Fanwick PE, Chattopadhyay DJ, Goswami S. Mild Synthesis of a Family of Planar Triazinium Cations via Proton-Assisted Cyclization of Pyridyl Containing Azo Compounds and Studies on DNA Intercalation. J Am Chem Soc 2008; 130:5185-93. [DOI: 10.1021/ja710211u] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Sinan
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700 032, India, Department of Bio-Chemistry, University of Calcutta, Kolkata 700 019, India, and Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - M. Panda
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700 032, India, Department of Bio-Chemistry, University of Calcutta, Kolkata 700 019, India, and Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - A. Ghosh
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700 032, India, Department of Bio-Chemistry, University of Calcutta, Kolkata 700 019, India, and Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - K. Dhara
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700 032, India, Department of Bio-Chemistry, University of Calcutta, Kolkata 700 019, India, and Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - P. E. Fanwick
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700 032, India, Department of Bio-Chemistry, University of Calcutta, Kolkata 700 019, India, and Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - D. J. Chattopadhyay
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700 032, India, Department of Bio-Chemistry, University of Calcutta, Kolkata 700 019, India, and Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - S. Goswami
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700 032, India, Department of Bio-Chemistry, University of Calcutta, Kolkata 700 019, India, and Department of Chemistry, Purdue University, West Lafayette, Indiana
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Panda M, Kar K. HIV, hepatitis B and C infection status of the blood donors in a blood bank of a tertiary health care centre of Orissa. Indian J Public Health 2008; 52:43-44. [PMID: 18700722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
A record based retrospective study was conducted at the blood bank of SCB Medical College, Cuttack. All the donors who had donated blood from June to December 2005 were considered. 91.7%of the donors were males and majority belonged to 21-30 years age group. 1.98% of the donors were positive for hepatitis C, 1.13% for hepatitis B and 0.35% for HIV. For HBV infection, majority belonged to 31-40 years age group. But for HCV and HIV infection more were in the 21-30 year age group. Significantly more number of exchange donors was positive for HBV and HCV in comparison to voluntary donors in blood bank and camp. No voluntary donors from the camp were HIV positive.
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Affiliation(s)
- M Panda
- SCB Medical College, Cuttack.
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37
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Simpson E, Panda M, Enzenauer R. 321 EVIDENCE-BASED ADVERTISING IN RHEUMATOLOGY. J Investig Med 2006. [DOI: 10.2310/6650.2005.x0008.320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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38
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Mannepalli S, Manthabala T, Panda M, Moffitt B. 355 DETERMINANTS OF ORDERING SERUM PROLACTIN AND ITS UTILITY IN PATIENTS WITH SEIZURES AND PSEUDOSEIZURES. J Investig Med 2006. [DOI: 10.2310/6650.2005.x0008.354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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39
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Mannepalli S, Manthabala T, Panda M, Moffitt B. 109 DETERMINANTS OF ORDERING SERUM PROLACTIN AND ITS UTILITY IN PATIENTS WITH SEIZURES AND PSEUDOSEIZURES. J Investig Med 2006. [DOI: 10.2310/6650.2005.x0008.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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40
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Jáchymová M, Martásek P, Panda S, Roman LJ, Panda M, Shea TM, Ishimura Y, Kim JJP, Masters BSS. Recruitment of governing elements for electron transfer in the nitric oxide synthase family. Proc Natl Acad Sci U S A 2005; 102:15833-8. [PMID: 16249336 PMCID: PMC1276075 DOI: 10.1073/pnas.0506522102] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
At least three building blocks are responsible for the molecular basis of the modulation of electron transfer in nitric oxide synthase (NOS) isoforms: the calmodulin-binding sequence, the C-terminal extension, and the autoregulatory loop in the reductase domain. We have attempted to impart the control conferred by the C termini of NOS to cytochrome P450 oxidoreductase (CYPOR), which contains none of these regulatory elements. The effect of these C termini on the properties of CYPOR sheds light on the possible evolutionary origin of NOS and addresses the recruitment of new peptides on the development of new functions for CYPOR. The C termini of NOSs modulate flavoprotein-mediated electron transfer to various electron acceptors. The reduction of the artificial electron acceptors cytochrome c, 2,6-dichlorophenolindophenol, and ferricyanide was inhibited by the addition of any of these C termini to CYPOR, whereas the reduction of molecular O(2) was increased. This suggests a shift in the rate-limiting step, indicating that the NOS C termini interrupt electron flux between flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) and/or the electron acceptors. The modulation of CYPOR by the addition of the NOS C termini is also supported by flavin reoxidation and fluorescence-quenching studies and antibody recognition of the C-terminal extension. These experiments support the origin of the NOS enzymes from modules consisting of a heme domain and CYPOR or ferredoxin-NADP(+) reductase- and flavodoxin-like subdomains that constitute CYPOR, followed by further recruitment of smaller modulating elements into the flavin-binding domains.
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Affiliation(s)
- M Jáchymová
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
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41
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Katrapati P, Panda M. 163 ACCURACY OF SELF-AUDITS IN AN OUTPATIENT RESIDENT CLINIC:. J Investig Med 2005. [DOI: 10.2310/6650.2005.00006.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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42
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Katrapati P, Panda M. 241 ACCURACY AND USEFULNESS OF SELF-AUDITS IN AN OUTPATIENT RESIDENT CLINIC:. J Investig Med 2005. [DOI: 10.2310/6650.2005.00006.240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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43
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Perry B, Panda M, Okosun IS. 127 EXPLORING NEW MEANINGS FOR AN OLD SYMBOL: PATIENTS' ATTITUDES AND PERCEPTIONS OF MALE AND FEMALE PHYSICIANS DRESSED WITH AND WITHOUT TRADITIONAL WHITE COATS. J Investig Med 2004. [DOI: 10.1136/jim-52-suppl1-680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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44
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Jones RC, Panda M, Desbiens N. 264 DO INTERNAL MEDICINE RESIDENTS ACCURATELY ASSESS THEIR MEDICAL KNOWLEDGE? J Investig Med 2004. [DOI: 10.1136/jim-52-suppl1-817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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45
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Panda M, Ball T, Desbiens N. 258 GRADUATES' PERCERPTIONS OF THE VALUE OF AN “EDUCATION FOR LIFE” REQUIREMENT IN AN INTERNAL MEDICINE RESIDENCY PROGRAM. J Investig Med 2004. [DOI: 10.1136/jim-52-suppl1-811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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46
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Sudha R, Panda M, Chandrasekhar J, Balaram P. Structural effects on the formation of proton and alkali metal ion adducts of apolar, neutral peptides: electrospray ionization mass spectrometry and Ab initio theoretical studies. Chemistry 2002; 8:4980-91. [PMID: 12487135 DOI: 10.1002/1521-3765(20021104)8:21<4980::aid-chem4980>3.0.co;2-m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Apolar, neutral peptides have been shown to ionize extremely well under the conditions used for electrospray ionization mass spectrometry (ESIMS). Peptides for which the conformations have been independently determined in solution and in crystals have been examined by ESIMS. Studies of peptide helices ranging from 7 to 18 residues reveal that shorter helices yield exclusively singly charged ions, while in larger helices multiply charged species are detectable. Multiple sites for protonation/metallation are introduced in the helix by proline insertion or by changing the chirality in the residue. The preferred site of cation binding to helices may be the C-terminus end, where three free CO groups are available for chelation. Ab initio and DFT calculations at several levels have been carried out for the binding of H+, Li+, Na+, and K+ to CHO-(Gly)3)-OMe. The results reveal that metallation in helices is favoured by chelation to carbonyl groups at the C-terminus, while protonation involved two carbonyl groups and thus favour a 10-membered cyclic hydrogen-bonded structure. In -strands, metallation/protonation occurs at isolated carbonyl groups. Collision induced fragmentation of hydrophobic peptides under ESI conditions reveals that helix fragmentation occurs predominantly from the C-terminus, while in -hairpins cleavage occurs simultaneously at multiple sites.
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Affiliation(s)
- R Sudha
- Molecular Biophysics Unit, Department of Organic Chemistry, Indian Institute of Science, Bangalore, India
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Panda M, Smoot AL, Horowitz PM. The 4,4'-dipyridyl disulfide-induced formation of GroEL monomers is cooperative and leads to increased hydrophobic exposure. Biochemistry 2001; 40:10402-10. [PMID: 11513619 DOI: 10.1021/bi010831x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The molecular chaperone, GroEL, is completely disassembled into monomers by the addition of 4,4'-dipyridyl disulfide. The dissociation leads to monomers in a kinetically controlled process. The additions of functional ligands of GroEL such as Mg(2+) or adenine nucleotides produced differences in the observed rates, but at the end of the kinetics, the dissociation was complete. In addition to the information obtained from native gels, the fluorescent probe bis-ANS was utilized to follow the monomer formation. The results demonstrate that the formation of monomers was associated with the exposure of hydrophobic surfaces. This assessment was possible without the use of added chaotropes, such as urea, to dissociate GroEL. Dissociation kinetics were also followed by light scattering. The kinetics of dissociation of the 14mer are cooperative with respect to the concentration of 4,4'-DPDS. Thermodynamic parameters for the kinetic process gave a free energy of activation (DeltaG) of 19.3 +/- 1.2 kcal mol(-1), which was decomposed to an enthalpy of activation (DeltaH) of 19.30 +/- 1.2 kcal mol(-1) and an entropy of activation (DeltaS) of -8.2 +/- 3.9 cal mol(-1) K(-1). We conclude that the dissociation of GroEL observed in this investigation is an enthalpy-controlled process.
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Affiliation(s)
- M Panda
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900, USA
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Smoot AL, Panda M, Brazil BT, Buckle AM, Fersht AR, Horowitz PM. The binding of bis-ANS to the isolated GroEL apical domain fragment induces the formation of a folding intermediate with increased hydrophobic surface not observed in tetradecameric GroEL. Biochemistry 2001; 40:4484-92. [PMID: 11284705 DOI: 10.1021/bi001822b] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The extent of hydrophobic exposure upon bis-ANS binding to the functional apical domain fragment of GroEL, or minichaperone (residues 191-345), was investigated and compared with that of the GroEL tetradecamer. Although a total of seven molecules of bis-ANS bind cooperatively to this minichaperone, most of the hydrophobic sites were induced following initial binding of one to two molecules of probe. From the equilibrium and kinetics studies at low bis-ANS concentrations, it is evident that the native apical domain is converted to an intermediate conformation with increased hydrophobic surfaces. This intermediate binds additional bis-ANS molecules. Tyrosine fluorescence detected denaturation demonstrated that bis-ANS can destabilize the apical domain. The results from (i) bis-ANS titrations, (ii) urea denaturation studies in the presence and absence of bis-ANS, and (iii) intrinsic tyrosine fluorescence studies of the apical domain are consistent with a model in which bis-ANS binds tightly to the intermediate state, relatively weakly to the native state, and little to the denatured state. The results suggest that the conformational changes seen in apical domain fragments are not seen in the intact GroEL oligomer due to restrictions imposed by connections of the apical domain to the intermediate domain and suppression of movement due to quaternary structure.
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Affiliation(s)
- A L Smoot
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900, USA
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49
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Panda M, Ybarra J, Horowitz PM. High hydrostatic pressure can probe the effects of functionally related ligands on the quaternary structures of the chaperonins GroEL and GroES. J Biol Chem 2001; 276:6253-9. [PMID: 11085994 DOI: 10.1074/jbc.m009530200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We investigated the effects of high hydrostatic pressure in the range of 1--3 kilobars on tetradecameric GroEL, heptameric GroES, and the GroEL-GroES complex. Unlike GroEL monomers formed by urea dissociation, which can be reassembled back to the tetradecamer, the pressure-dissociated monomers do not reassemble readily. This indicates an alteration of their native structures, an example of conformational drift. Pressure versus time profiles and kinetics of the dissociation of both GroEL and GroES at fixed pressures were monitored by light scattering. Unlike GroEL, GroES monomers do reassociate readily. Reaction conditions were varied by adding ATP, Mg(2+), ADP, AMP-PNP, and KCl. At any individual pressure, the dissociation process is governed by both thermodynamics and kinetics. This leads to the decrease in the yield of monomers at lower pressures. In the presence of Mg(2+) and KCl, GroEL is stable up to 3 kilobars. The presence of either ATP or ADP but not AMP-PNP leads to GroEL dissociation at lower pressures. Interestingly, the GroEL-GroES complex is very stable in the range of 1--2.5 kilobars. However, the addition of ADP destabilizes the complex, which dissociates completely at 1.5 kilobars. The results are rationalized in terms of different degrees of cooperativity between individual monomers and heptameric rings in the GroEL tetradecamer. Such allosteric interactions leading to the alteration of quaternary structure of GroEL in the absence of chemical denaturants are important in understanding the mechanism of chaperonin-assisted protein folding by the GroEL-GroES system.
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Affiliation(s)
- M Panda
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229-3900, USA
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Abstract
Unfolded bovine rhodanese, a sulfurtransferase, does not regain full activity upon refolding due to the formation of aggregates and disulfide-linked misfolded states unless a large excess of reductant such as 200 mM beta-ME and 5 mg/ml detergent are present [Tandon and Horowitz (1990), J. Biol. Chem. 265, 5967]. Even then, refolding is incomplete. We have studied the unfolding and refolding of three rhodanese forms whose crystal structures are known: ES, containing the transferred sulfur as a persulfide; E, without the transferred sulfur, and carboxymethylated rhodanese (CMR), in which the active site was blocked by chemical modification. The X-ray structures of ES, E, and CMR are virtually the same, but their tertiary structures in solution differ somewhat as revealed by near-UV CD. Among these three, CMR is the only form of rhodanese that folds reversibly, requiring 1 mM DTT. A minimum three-state folding model of CMR (N<-->I<-->U) followed by fluorescence at 363 nm, (N<-->I) by fluorescence at 318 nm, and CD (I<-->U) is consistent with the presence of a thermodynamically stable molten globule intermediate in 5-6 M urea. We conclude that the active-site sulfhydryl group in the persulfide form is very reactive; therefore, its modification leads to the successful refolding of urea-denatured rhodanese even in the absence of a large excess of reductant and detergent. The requirement for DTT for complete reversibility of CMR suggests that oxidation among the three non-active-site SH groups can represent a minor trap for refolding through species that can be easily reduced.
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Affiliation(s)
- M Panda
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, 78229-3900, USA
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