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Mol N, Priya A, Singh AK, Mago P, Shalimar, Ray AK. "Unravelling the impacts of climatic heat events on cardiovascular health in animal models". Environ Res 2024; 248:118315. [PMID: 38301760 DOI: 10.1016/j.envres.2024.118315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/03/2024]
Abstract
Climate change has led to an increase in high ambient temperatures, causing extreme heat events worldwide. According to the World Meteorological Organization (WMO), July 2023 marked a historic milestone as the Earth reached its hottest recorded temperature, precisely hitting the critical threshold of 1.5 °C set by the Paris Agreement. This distressing development led to a stark warning from the United Nations, signaling the dawn of what they call "an era of global boiling". The increasing global temperatures can result in high heat stress which leads to various physiological and biochemical alterations in the human body. Given that cardiovascular diseases (CVDs) are a leading cause of morbidity and mortality globally, heat events exacerbate this public health issue. While clinical and in-vitro studies have suggested a range of pathophysiological and biochemical mechanisms underlying the body's response to heat stress, the complex nature of organ-system level interactions makes precise investigation challenging. To address this knowledge gap effectively, the use of animal models exposed to acute or chronic heat stress can be invaluable. These models can closely replicate the multifaceted effects observed in humans during heat stress conditions. Despite extensive independent reviews, limited focus has been shed on the high heat-induced cardiovascular complications and their mechanisms, particularly utilizing animal models. Therefore, in this comprehensive review, we highlight the crucial biomarkers altered during heat stress, contributing significantly to various CVDs. We explore potential mechanisms underlying heat-induced cardiovascular dysfunction and damage, delving into various animal models. While traditional rodent models are commonly employed, we also examine less conventional models, including ruminants, broilers, canines, and primates. Furthermore, we delve into various potential therapeutic approaches and preventive measures. These insights hold significant promise for the development of more effective clinical interventions against the effects of heat stress on the human cardiovascular system.
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Affiliation(s)
- Nidhi Mol
- Department of Environmental Studies, University of Delhi, New Delhi, India
| | - Anjali Priya
- Department of Environmental Studies, University of Delhi, New Delhi, India
| | - Alok Kumar Singh
- Department of Zoology, Ramjas College, University of Delhi, New Delhi, India
| | - Payal Mago
- Shaheed Rajguru College of Applied Sciences for Women, University of Delhi, New Delhi, India; Campus of Open Learning, University of Delhi, New Delhi, India
| | - Shalimar
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Ashwini Kumar Ray
- Department of Environmental Studies, University of Delhi, New Delhi, India.
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2
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Ray AK, Priya A, Malik MZ, Thanaraj TA, Singh AK, Mago P, Ghosh C, Shalimar, Tandon R, Chaturvedi R. A bioinformatics approach to elucidate conserved genes and pathways in C. elegans as an animal model for cardiovascular research. Sci Rep 2024; 14:7471. [PMID: 38553458 PMCID: PMC10980734 DOI: 10.1038/s41598-024-56562-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Abstract
Cardiovascular disease (CVD) is a collective term for disorders of the heart and blood vessels. The molecular events and biochemical pathways associated with CVD are difficult to study in clinical settings on patients and in vitro conditions. Animal models play a pivotal and indispensable role in CVD research. Caenorhabditis elegans, a nematode species, has emerged as a prominent experimental organism widely utilized in various biomedical research fields. However, the specific number of CVD-related genes and pathways within the C. elegans genome remains undisclosed to date, limiting its in-depth utilization for investigations. In the present study, we conducted a comprehensive analysis of genes and pathways related to CVD within the genomes of humans and C. elegans through a systematic bioinformatic approach. A total of 1113 genes in C. elegans orthologous to the most significant CVD-related genes in humans were identified, and the GO terms and pathways were compared to study the pathways that are conserved between the two species. In order to infer the functions of CVD-related orthologous genes in C. elegans, a PPI network was constructed. Orthologous gene PPI network analysis results reveal the hubs and important KRs: pmk-1, daf-21, gpb-1, crh-1, enpl-1, eef-1G, acdh-8, hif-1, pmk-2, and aha-1 in C. elegans. Modules were identified for determining the role of the orthologous genes at various levels in the created network. We also identified 9 commonly enriched pathways between humans and C. elegans linked with CVDs that include autophagy (animal), the ErbB signaling pathway, the FoxO signaling pathway, the MAPK signaling pathway, ABC transporters, the biosynthesis of unsaturated fatty acids, fatty acid metabolism, glutathione metabolism, and metabolic pathways. This study provides the first systematic genomic approach to explore the CVD-associated genes and pathways that are present in C. elegans, supporting the use of C. elegans as a prominent animal model organism for cardiovascular diseases.
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Affiliation(s)
- Ashwini Kumar Ray
- Department of Environmental Studies, University of Delhi, New Delhi, India.
| | - Anjali Priya
- Department of Environmental Studies, University of Delhi, New Delhi, India
| | - Md Zubbair Malik
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait.
| | | | - Alok Kumar Singh
- Department of Zoology, Ramjas College, University of Delhi, New Delhi, India
| | - Payal Mago
- Shaheed Rajguru College of Applied Science for Women, University of Delhi, New Delhi, India
- Campus of Open Learning, University of Delhi, New Delhi, India
| | - Chirashree Ghosh
- Department of Environmental Studies, University of Delhi, New Delhi, India
| | - Shalimar
- Department of Gastroenterology, All India Institute of Medical Science, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Priya A, Dashti M, Thanaraj TA, Irshad M, Singh V, Tandon R, Mehrotra R, Singh AK, Mago P, Singh V, Malik MZ, Ray AK. Identification of potential regulatory mechanisms and therapeutic targets for lung cancer. J Biomol Struct Dyn 2024:1-18. [PMID: 38319037 DOI: 10.1080/07391102.2024.2310208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024]
Abstract
Lung cancer poses a significant health threat globally, especially in regions like India, with 5-year survival rates remain alarmingly low. Our study aimed to uncover key markers for effective treatment and early detection. We identified specific genes related to lung cancer using the BioXpress database and delved into their roles through DAVID enrichment analysis. By employing network theory, we explored the intricate interactions within lung cancer networks, identifying ASPM and MKI67 as crucial regulator genes. Predictions of microRNA and transcription factor interactions provided additional insights. Examining gene expression patterns using GEPIA and KM Plotter revealed the clinical relevance of these key genes. In our pursuit of targeted therapies, Drug Bank pointed to methotrexate as a potential drug for the identified key regulator genes. Confirming this, molecular docking studies through Swiss Dock showed promising binding interactions. To ensure stability, we conducted molecular dynamics simulations using the AMBER 16 suite. In summary, our study pinpoints ASPM and MKI67 as vital regulators in lung cancer networks. The identification of hub genes and functional pathways enhances our understanding of molecular processes, offering potential therapeutic targets. Importantly, methotrexate emerged as a promising drug candidate, supported by robust docking and simulation studies. These findings lay a solid foundation for further experimental validations and hold promise for advancing personalized therapeutic strategies in lung cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anjali Priya
- Department of Environmental Studies, University of Delhi, New Delhi, India
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | | | | | | | - Virendra Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rekha Mehrotra
- Department of Microbiology, Shaheed Rajguru College of Applied Sciences for Women, University of Delhi, New Delhi, India
| | - Alok Kumar Singh
- Department of Zoology, Ramjas College, University of Delhi, New Delhi, India
| | - Payal Mago
- Department of Botany, Shri Aurobindo College, University of Delhi, New Delhi, India to Campus Of Open Learning, University of Delhi, New Delhi, India
- Shaheed Rajguru College of Applied Sciences for Women, University of Delhi, New Delhi, India
| | - Vishal Singh
- Delhi School of Public Health, Institution of Eminence, University of Delhi, New Delhi, India
| | | | - Ashwini Kumar Ray
- Department of Environmental Studies, University of Delhi, New Delhi, India
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Ray AK, Priya A, Malik MZ, Thanaraj TA, Singh AK, Mago P, Ghosh C, Shalimar, Tandon R, Chaturvedi R. Conserved Cardiovascular Network: Bioinformatics Insights into Genes and Pathways for Establishing Caenorhabditis elegans as an Animal Model for Cardiovascular Diseases. bioRxiv 2024:2023.12.24.573256. [PMID: 38234826 PMCID: PMC10793405 DOI: 10.1101/2023.12.24.573256] [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: 01/19/2024]
Abstract
Cardiovascular disease (CVD) is a collective term for disorders of the heart and blood vessels. The molecular events and biochemical pathways associated with CVD are difficult to study in clinical settings on patients and in vitro conditions. Animal models play a pivotal and indispensable role in cardiovascular disease (CVD) research. Caenorhabditis elegans , a nematode species, has emerged as a prominent experimental organism widely utilised in various biomedical research fields. However, the specific number of CVD-related genes and pathways within the C. elegans genome remains undisclosed to date, limiting its in-depth utilisation for investigations. In the present study, we conducted a comprehensive analysis of genes and pathways related to CVD within the genomes of humans and C. elegans through a systematic bioinformatic approach. A total of 1113 genes in C. elegans orthologous to the most significant CVD-related genes in humans were identified, and the GO terms and pathways were compared to study the pathways that are conserved between the two species. In order to infer the functions of CVD-related orthologous genes in C. elegans, a PPI network was constructed. Orthologous gene PPI network analysis results reveal the hubs and important KRs: pmk-1, daf-21, gpb-1, crh-1, enpl-1, eef-1G, acdh-8, hif-1, pmk-2, and aha-1 in C. elegans. Modules were identified for determining the role of the orthologous genes at various levels in the created network. We also identified 9 commonly enriched pathways between humans and C. elegans linked with CVDs that include autophagy (animal), the ErbB signalling pathway, the FoxO signalling pathway, the MAPK signalling pathway, ABC transporters, the biosynthesis of unsaturated fatty acids, fatty acid metabolism, glutathione metabolism, and metabolic pathways. This study provides the first systematic genomic approach to explore the CVD-associated genes and pathways that are present in C. elegans, supporting the use of C. elegans as a prominent animal model organism for cardiovascular diseases.
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Gupta J, Malik MZ, Chaturvedi M, Mishra M, Mishra SK, Grover A, Ray AK, Chaturvedi R. SARS CoV-2 spike protein variants exploit DC-SIGN/DC-SIGNR receptor for evolution and severity: an in-silico insight. Virusdisease 2023:1-19. [PMID: 37363363 PMCID: PMC10206574 DOI: 10.1007/s13337-023-00820-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/10/2023] [Indexed: 06/28/2023] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is related with the COVID-19 pandemic. Recent spike protein variations have had an effect on the transmission of the virus. In addition to ACE-2, spike proteins can employ DC-SIGN and its analogous receptor, DC-SIGNR, for host evasion. Spike variations in the DC-SIGN interaction region and role of DC-SIGN in immune evasion have not been well defined. To understand the spike protein variations and their binding mode, phylogenetic analysis of the complete GISAID (Global Initiative for Sharing Avian Influenza Data) data of the SARS-CoV-2 spike protein was considered. In addition, an in silico knockout network evaluation of the SARS-CoV-2 single-cell transcriptome was conducted to determine the key role of DC-SIGN/R in immunological dysregulation. Within the DC-SIGN-interacting region of the SARS-CoV spike protein, the spike protein of SARS-CoV-2 displayed remarkable similarity to the SARS-CoV spike protein. Surprisingly, the phylogenetic analysis revealed that the SARS-CoV-2's spike exhibited significantly diverse variants in the DC-SIGN interaction domain, which altered the frequency of these variants. The variation within the DC-SIGN-interacting domain of spike proteins affected the binding of a limited number of variants with DC-SIGN and DC-SIGNR and affected their evolution. MMGBSA binding free energies evaluation differed for variants from those of the wild type, suggesting the influence of substitution mutations on the interaction pattern. In silico knockout network analysis of the single-cell transcriptome of Bronchoalveolar Lavage and peripheral blood mononuclear cells revealed that SARS-CoV-2 altered DC-SIGN/R signaling. Early surveillance of diverse SARS-CoV-2 strains could preclude a worsening of the pandemic and facilitate the development of an optimum vaccine against variations. The spike Receptor Binding Domain genetic variants are thought to boost SARS CoV-2 immune evasion, resulting in its higher longevity. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00820-3.
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Affiliation(s)
- Jyoti Gupta
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Md. Zubbair Malik
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, 15462 Kuwait
| | - Maya Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Mohit Mishra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Surbhi Kriti Mishra
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Ashwini Kumar Ray
- Department of Environmental Studies, University of Delhi, New Delhi, 11007 India
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
- Special Center for Systems Medicine, Jawaharlal Nehru University, New Delhi, 110067 India
- Nanofludiks Research Pvt. Ltd., JNU-Atal Incubation Center, Jawaharlal Nehru University, New Delhi, 110067 India
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6
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Bhattacharyya N, Gupta S, Sharma S, Soni A, Bagabir SA, Bhattacharyya M, Mukherjee A, Almalki AH, Alkhanani MF, Haque S, Ray AK, Malik MZ. CDK1 and HSP90AA1 Appear as the Novel Regulatory Genes in Non-Small Cell Lung Cancer: A Bioinformatics Approach. J Pers Med 2022; 12:jpm12030393. [PMID: 35330393 PMCID: PMC8955443 DOI: 10.3390/jpm12030393] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/08/2022] [Accepted: 01/26/2022] [Indexed: 02/05/2023] Open
Abstract
Lung cancer is one of the most invasive cancers affecting over a million of the population. Non-small cell lung cancer (NSCLC) constitutes up to 85% of all lung cancer cases, and therefore, it is essential to identify predictive biomarkers of NSCLC for therapeutic purposes. Here we use a network theoretical approach to investigate the complex behavior of the NSCLC gene-regulatory interactions. We have used eight NSCLC microarray datasets GSE19188, GSE118370, GSE10072, GSE101929, GSE7670, GSE33532, GSE31547, and GSE31210 and meta-analyzed them to find differentially expressed genes (DEGs) and further constructed a protein–protein interaction (PPI) network. We analyzed its topological properties and identified significant modules of the PPI network using cytoscape network analyzer and MCODE plug-in. From the PPI network, top ten genes of each of the six topological properties like closeness centrality, maximal clique centrality (MCC), Maximum Neighborhood Component (MNC), radiality, EPC (Edge Percolated Component) and bottleneck were considered for key regulator identification. We further compared them with top ten hub genes (those with the highest degrees) to find key regulator (KR) genes. We found that two genes, CDK1 and HSP90AA1, were common in the analysis suggesting a significant regulatory role of CDK1 and HSP90AA1 in non-small cell lung cancer. Our study using a network theoretical approach, as a summary, suggests CDK1 and HSP90AA1 as key regulator genes in complex NSCLC network.
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Affiliation(s)
| | - Samriddhi Gupta
- Department of Biochemistry, University of Hyderabad, Hyderabad 500046, India;
| | - Shubham Sharma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (S.S.); (A.S.)
| | - Aman Soni
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (S.S.); (A.S.)
| | - Sali Abubaker Bagabir
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia;
| | - Malini Bhattacharyya
- Department of Environmental Plant Biology, Hemvati Nandan Bahuguna, Garhwal Central University, Srinagar 246174, India;
| | - Atreyee Mukherjee
- Department of Life Sciences, Presidency University, Kolkata 700073, India;
| | - Atiah H. Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif 21944, Saudi Arabia;
- Addiction and Neuroscience Research Unit, College of Pharmacy, Taif University, Taif 21944, Saudi Arabia
| | - Mustfa F. Alkhanani
- Emergency Service Department, College of Applied Sciences, Al Maarefa University, Riyadh 11597, Saudi Arabia;
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
- Faculty of Medicine, Bursa Uludağ University, Görükle Campus, Bursa 16059, Turkey
| | - Ashwini Kumar Ray
- Department of Environmental Studies, University Delhi, New Delhi 110007, India
- Correspondence: (A.K.R.); (M.Z.M.)
| | - Md. Zubbair Malik
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (S.S.); (A.S.)
- Correspondence: (A.K.R.); (M.Z.M.)
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7
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Ray AK, Luis PB, Mishra SK, Barry DP, Asim M, Pandey A, Chaturvedi M, Gupta J, Gupta S, Mahant S, Das R, Kumar P, Shalimar, Wilson KT, Schneider C, Chaturvedi R. Curcumin Oxidation Is Required for Inhibition of Helicobacter pylori Growth, Translocation and Phosphorylation of Cag A. Front Cell Infect Microbiol 2022; 11:765842. [PMID: 35004346 PMCID: PMC8740292 DOI: 10.3389/fcimb.2021.765842] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/02/2021] [Indexed: 01/22/2023] Open
Abstract
Curcumin is a potential natural remedy for preventing Helicobacter pylori-associated gastric inflammation and cancer. Here, we analyzed the effect of a phospholipid formulation of curcumin on H. pylori growth, translocation and phosphorylation of the virulence factor CagA and host protein kinase Src in vitro and in an in vivo mouse model of H. pylori infection. Growth of H. pylori was inhibited dose-dependently by curcumin in vitro. H. pylori was unable to metabolically reduce curcumin, whereas two enterobacteria, E. coli and Citrobacter rodentium, which efficiently reduced curcumin to the tetra- and hexahydro metabolites, evaded growth inhibition. Oxidative metabolism of curcumin was required for the growth inhibition of H. pylori and the translocation and phosphorylation of CagA and cSrc, since acetal- and diacetal-curcumin that do not undergo oxidative transformation were ineffective. Curcumin attenuated mRNA expression of the H. pylori virulence genes cagE and cagF in a dose-dependent manner and inhibited translocation and phosphorylation of CagA in gastric epithelial cells. H. pylori strains isolated from dietary curcumin-treated mice showed attenuated ability to induce cSrc phosphorylation and the mRNA expression of the gene encoding for IL-8, suggesting long-lasting effects of curcumin on the virulence of H. pylori. Our work provides mechanistic evidence that encourages testing of curcumin as a dietary approach to inhibit the virulence of CagA.
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Affiliation(s)
- Ashwini Kumar Ray
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Department of Microbiology, Saheed Rajguru College of Applied Sciences for Women, University of Delhi, New Delhi, India.,Department of Environmental Studies, University of Delhi, New Delhi, India
| | - Paula B Luis
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | | | - Daniel P Barry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Mohammad Asim
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Achyut Pandey
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Maya Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Jyoti Gupta
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Shilpi Gupta
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Shweta Mahant
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Rajashree Das
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Pramod Kumar
- Department of Chemistry, Sri Aurobindo College, University of Delhi, New Delhi, India
| | - Shalimar
- Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences, New Delhi, India
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, United States.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, United States
| | - Claus Schneider
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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8
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Chakraborty U, Biswas P, Chandra A, Pal J, Ray AK. Chik sign: post-chikungunya hyperpigmentation. QJM 2021; 114:137-138. [PMID: 33367777 DOI: 10.1093/qjmed/hcaa329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- U Chakraborty
- Department of Internal Medicine, R.G.Kar Medical College and Hospital, Room No-11, Main Boy's hostel (Inside RG Kar Medical College Campus), 1, Khudiram Bose Sarani, Kolkata 700004, India
| | - P Biswas
- Department of Internal Medicine, R.G.Kar Medical College and Hospital, Room No-6, Girl's hostel (Inside RG Kar Medical College Campus), 1, Khudiram Bose Sarani, Kolkata 700004, India
| | - A Chandra
- Department of Internal Medicine, R.G.Kar Medical College and Hospital, Quarter No-1, Doctor's Quarter (Inside RG Kar Medical College Campus), 1, Khudiram Bose Sarani, Kolkata 700004, India
| | - J Pal
- Department of Internal Medicine, R.G.Kar Medical College and Hospital, 37a, Panpara 1st lane, Talpukur, North 24-parganas, Kolkata 700123, India
| | - A K Ray
- Department of Internal Medicine, R.G Kar Medical College and Hospital, Room No 23, Main Boy's hostel (Inside RG Kar Medical College Campus), 1, Khudiram Bose Sarani, Kolkata 700004, India
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9
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Grover R, Burse SA, Shankrit S, Aggarwal A, Kirty K, Narta K, Srivastav R, Ray AK, Malik G, Vats A, Motiani RK, Thukral L, Roy SS, Bhattacharya S, Sharma R, Natarajan K, Mukerji M, Pandey R, Gokhale RS, Natarajan VT. Myg1 exonuclease couples the nuclear and mitochondrial translational programs through RNA processing. Nucleic Acids Res 2019; 47:5852-5866. [PMID: 31081026 PMCID: PMC6582341 DOI: 10.1093/nar/gkz371] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 04/12/2019] [Accepted: 04/30/2019] [Indexed: 01/25/2023] Open
Abstract
Semi-autonomous functioning of mitochondria in eukaryotic cell necessitates coordination with nucleus. Several RNA species fine-tune mitochondrial processes by synchronizing with the nuclear program, however the involved components remain enigmatic. In this study, we identify a widely conserved dually localized protein Myg1, and establish its role as a 3′-5′ RNA exonuclease. We employ mouse melanoma cells, and knockout of the Myg1 ortholog in Saccharomyces cerevisiae with complementation using human Myg1 to decipher the conserved role of Myg1 in selective RNA processing. Localization of Myg1 to nucleolus and mitochondrial matrix was studied through imaging and confirmed by sub-cellular fractionation studies. We developed Silexoseqencing, a methodology to map the RNAse trail at single-nucleotide resolution, and identified in situ cleavage by Myg1 on specific transcripts in the two organelles. In nucleolus, Myg1 processes pre-ribosomal RNA involved in ribosome assembly and alters cytoplasmic translation. In mitochondrial matrix, Myg1 processes 3′-termini of the mito-ribosomal and messenger RNAs and controls translation of mitochondrial proteins. We provide a molecular link to the possible involvement of Myg1 in chronic depigmenting disorder vitiligo. Our study identifies a key component involved in regulating spatially segregated organellar RNA processing and establishes the evolutionarily conserved ribonuclease as a coordinator of nucleo-mitochondrial crosstalk.
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Affiliation(s)
- Ritika Grover
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Shaunak A Burse
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Shambhavi Shankrit
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Ayush Aggarwal
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Kritika Kirty
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Kiran Narta
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajpal Srivastav
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Ashwini Kumar Ray
- School of environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Garima Malik
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Archana Vats
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajender K Motiani
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Soumya Sinha Roy
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Sudha Bhattacharya
- School of environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Sharma
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | | | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajesh S Gokhale
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Vivek T Natarajan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
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10
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Singh SS, Naiyer S, Bharadwaj R, Kumar A, Singh YP, Ray AK, Subbarao N, Bhattacharya A, Bhattacharya S. Correction: Stress-induced nuclear depletion of Entamoeba histolytica 3'-5' exoribonuclease EhRrp6 and its role in growth and erythrophagocytosis. J Biol Chem 2018; 293:19510. [PMID: 30552115 DOI: 10.1074/jbc.aac118.006754] [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: 11/06/2022] Open
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11
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Singh SS, Naiyer S, Bharadwaj R, Kumar A, Singh YP, Ray AK, Subbarao N, Bhattacharya A, Bhattacharya S. Stress-induced nuclear depletion of Entamoeba histolytica 3'-5' exoribonuclease EhRrp6 and its role in growth and erythrophagocytosis. J Biol Chem 2018; 293:16242-16260. [PMID: 30171071 DOI: 10.1074/jbc.ra118.004632] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/10/2018] [Indexed: 01/24/2023] Open
Abstract
The 3'-5' exoribonuclease Rrp6 is a key enzyme in RNA homeostasis involved in processing and degradation of many stable RNA precursors, aberrant transcripts, and noncoding RNAs. We previously have shown that in the protozoan parasite Entamoeba histolytica, the 5'-external transcribed spacer fragment of pre-rRNA accumulates under serum starvation-induced growth stress. This fragment is a known target of degradation by Rrp6. Here, we computationally and biochemically characterized EhRrp6 and found that it contains the catalytically important EXO and HRDC domains and exhibits exoribonuclease activity with both unstructured and structured RNA substrates, which required the conserved DEDD-Y catalytic-site residues. It lacked the N-terminal PMC2NT domain for binding of the cofactor Rrp47, but could functionally complement the growth defect of a yeast rrp6 mutant. Of note, no Rrp47 homologue was detected in E. histolytica Immunolocalization studies revealed that EhRrp6 is present both in the nucleus and cytosol of normal E. histolytica cells. However, growth stress induced its complete loss from the nuclei, reversed by proteasome inhibitors. EhRrp6-depleted E. histolytica cells were severely growth restricted, and EhRrp6 overexpression protected the cells against stress, suggesting that EhRrp6 functions as a stress sensor. Importantly EhRrp6 depletion reduced erythrophagocytosis, an important virulence determinant of E. histolytica This reduction was due to a specific decrease in transcript levels of some phagocytosis-related genes (Ehcabp3 and Ehrho1), whereas expression of other genes (Ehcabp1, Ehcabp6, Ehc2pk, and Eharp2/3) was unaffected. This is the first report of the role of Rrp6 in cell growth and stress responses in a protozoan parasite.
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Affiliation(s)
| | | | - Ravi Bharadwaj
- the School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Amarjeet Kumar
- the School of Computational and Integrative Sciences, and
| | | | | | - Naidu Subbarao
- the School of Computational and Integrative Sciences, and
| | - Alok Bhattacharya
- the School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
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12
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Rajasekharan SK, Ray AK, Ramesh S, Kannappan Mohanvel S. Species-specific detection of Candida tropicalis using evolutionary conserved intein DNA sequences. Lett Appl Microbiol 2018; 66:378-383. [PMID: 29427451 DOI: 10.1111/lam.12861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/04/2018] [Accepted: 02/04/2018] [Indexed: 01/05/2023]
Abstract
Inteins (internal proteins) are self-splicing transportable genetic elements present in conserved regions of housekeeping genes. The study highlights the importance of intein as a potential diagnostic marker for species-specific identification of Candida tropicalis, a rapidly emerging opportunistic human pathogen. Initial steps of primer validation, sequence alignment, phylogenetic tree analysis, gel electrophoresis and real-time polymerase chain reaction (PCR) assays were performed to confirm the specificity of the designed primers. The primers were selective for C. tropicalis with 100% inclusivity and showed no cross-species or cross-genera matches. The established technique is a prototype for developing multifaceted PCR assays and for point-of-care testing in near future. SIGNIFICANCE AND IMPACT OF THE STUDY Development of molecular markers for specific detection of microbial pathogens using real-time polymerase chain reaction (PCR) is an appealing and challenging technique. A real-time PCR is an emerging technology frequently used to detect the aetiologic agents. In recent times, designing species-specific primers for pathogen detection is gaining momentum. The method offers rapid, accurate and cost-effective strategy to identify the target, thus providing sufficient time to instigate appropriate chemotherapy. The study highlights the use of intein DNA sequence as molecular markers for species-specific identification of Candida tropicalis. The study also offers a prototype model for developing multifaceted PCR assays using intein DNA sequences, and provides a developmental starting point for point-of-care testing in near future.
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Affiliation(s)
- S K Rajasekharan
- Centre for Research and Development, PRIST University, Thanjavur, India.,School of Chemical Engineering, Yeungnam University, Gyeongsan, Republic of Korea
| | - A K Ray
- Central Institute of Brackishwater Aquaculture-ICAR, Chennai, India
| | - S Ramesh
- Centre for Research and Development, PRIST University, Thanjavur, India
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13
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Ray AK, Naiyer S, Singh SS, Bhattacharya A, Bhattacharya S. Application of SHAPE reveals in vivo RNA folding under normal and growth-stressed conditions in the human parasite Entamoeba histolytica. Mol Biochem Parasitol 2017; 219:42-51. [PMID: 29175581 DOI: 10.1016/j.molbiopara.2017.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/30/2022]
Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a versatile sequence independent method to probe RNA structure in vivo and in vitro. It has so far been tried mainly with model organisms. We show that cells of Entamoeba histolytica, a protozoan parasite of humans are hyper-sensitive to the in vivo SHAPE reagent, NAI, and show rapid loss of viability and RNA integrity. We optimized treatment conditions with 5.8S rRNA and Eh_U3 snoRNA to obtain NAI-modification while retaining RNA integrity. The modification patterns were highly reproducible. The in vivo folding was different from in vitro and correlated well with known interactions of 5.8S rRNA with proteins in vivo. The Eh_U3 snoRNA also showed many differences in its in vivo versus in vitro folding, which correlated with conserved interactions of this RNA with 18S rRNA and 5'-ETS. Further, Eh_U3 snoRNA obtained from serum-starved cells showed an open 3'-hinge structure, indicating disruption of 5'-ETS interaction. This could contribute to the observed slow processing of pre-rRNA in starved cells. Our work shows the applicability of SHAPE to study in vivo RNA folding in a parasite and will encourage the use of this reagent for RNA structure analysis in other such organisms.
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Affiliation(s)
- Ashwini Kumar Ray
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sarah Naiyer
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.
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14
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Henseler H, Khambay B, Ju X, Ayoub A, Ray AK. [Landmark-based statistical procrustes analysis in the examination of breast shape and symmetry]. HANDCHIR MIKROCHIR P 2015; 46:342-9. [PMID: 25564948 DOI: 10.1055/s-0034-1395578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
AIM The aim of this presentation is the explanation of a mathematical analysis of a landmark-based procrustes calculation. The various components of breast symmetry and their impact on breast reconstruction have been examined. METHOD In an objective breast shape analysis asymmetries are quantified as a measure of the difference between a 3D landmark configuration of a breast and its mirror image. 10 landmarks, 4 on each side and 2 for a definition of the midline were defined. For each landmark the 3D coordinates were calculated statistically with the help of the software Programme R. Over a midline from the jugulum to the manubrium sterni, a mirror image of the breast was constructed. The data for the breast to be reconstructed and the non-operated breast from 44 patients were investigated. The statistical differences of the Procrustes analysis were used for an asymmetry score and the proportions of the individual components were calculated. These included size, location and orientation of the breast as well as the individual inherent morphological surface form data of the breast. RESULTS All 44 patients exhibited breast asymmetries and the mean asymmetry score amounted to 0.52. A calculation of the proportions of the individual components making up the asymmetry score revealed that morphological surface data made the largest contribution to the asymmetry score, closely followed by location, i. e., positioning of the breast on the thoracic wall. In contrast, the size of the breast and its orientation were of lesser relevance. CONCLUSION When considering breast symmetry in plastic surgery, the form plays a more important role than the size as objectively calculated by the statistical procrustes analysis. Almost equally important as the form is the positioning of the breast on the thoracic wall which contributes significantly more to total breast symmetry than axial displacements.
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Affiliation(s)
- H Henseler
- Medizinische Hochschule Hannover, Plastische, Hand- und Wiederherstellungschirurgie, Hannover
| | - B Khambay
- Faculty of Dentistry, Pediatric Dentistry and Orthodontics, Hong Kong, Hong Kong
| | - X Ju
- Glasgow University MVLS College, Dental Hospital and School, Glasgow, United Kingdom
| | - A Ayoub
- Glasgow University MVLS College, Dental Hospital and School, Glasgow, United Kingdom
| | - A K Ray
- Glasgow Royal Infirmary, Canniesburn Plastic Surgery Unit, Glasgow, United Kingdom
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15
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Jati A, Singh G, Koley S, Konar A, Ray AK, Chakraborty C. A novel segmentation approach for noisy medical images using intuitionistic fuzzy divergence with neighbourhood-based membership function. J Microsc 2014; 257:187-200. [PMID: 25458042 DOI: 10.1111/jmi.12200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 10/24/2014] [Indexed: 11/26/2022]
Abstract
Medical image segmentation demands higher segmentation accuracy especially when the images are affected by noise. This paper proposes a novel technique to segment medical images efficiently using an intuitionistic fuzzy divergence-based thresholding. A neighbourhood-based membership function is defined here. The intuitionistic fuzzy divergence-based image thresholding technique using the neighbourhood-based membership functions yield lesser degradation of segmentation performance in noisy environment. Its ability in handling noisy images has been validated. The algorithm is independent of any parameter selection. Moreover, it provides robustness to both additive and multiplicative noise. The proposed scheme has been applied on three types of medical image datasets in order to establish its novelty and generality. The performance of the proposed algorithm has been compared with other standard algorithms viz. Otsu's method, fuzzy C-means clustering, and fuzzy divergence-based thresholding with respect to (1) noise-free images and (2) ground truth images labelled by experts/clinicians. Experiments show that the proposed methodology is effective, more accurate and efficient for segmenting noisy images.
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Affiliation(s)
- A Jati
- Department of Electronics & Telecommunication Engineering, Jadavpur University, Kolkata, India
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16
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Crapulli F, Santoro D, Sasges MR, Ray AK. Mechanistic modeling of vacuum UV advanced oxidation process in an annular photoreactor. Water Res 2014; 64:209-225. [PMID: 25064486 DOI: 10.1016/j.watres.2014.06.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [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: 02/05/2014] [Revised: 06/29/2014] [Accepted: 06/30/2014] [Indexed: 05/28/2023]
Abstract
A novel mechanistic model that describes the vacuum UV advanced oxidation process in an annular photoreactor initiated by 172 nm and 185 nm (in combination with 253.7 nm, with and without exogenous H2O2) is presented in this paper. The model was developed from first principles by incorporating the vacuum UV-AOP kinetics into the theoretical framework of in-series continuous flow stirred tank reactors. After conducting a sensitivity analysis, model predictions were compared against experiments conducted under a variety of conditions: (a) photo-induced formation of hydrogen peroxide by water photolysis at 172 nm (for both air- and oxygen-saturated conditions); (b) photo-induced formation of hydrogen peroxide by water photolysis at 185 + 253.7 nm (in the presence of formic acid, with and without the initial addition of hydrogen peroxide); (c) direct photolysis of hydrogen peroxide by 253.7 nm; (d) degradation of formic acid by 185 + 253.7 nm (with and without initial addition of hydrogen peroxide); and (e) degradation of formic acid by 253.7 nm (with the addition of exogenous hydrogen peroxide). In all cases, the model was able to accurately predict the time-dependent profiles of hydrogen peroxide and formic acid concentrations. Two newly recognized aspects associated with water photolysis were identified through the use of the validated model. Firstly, unlike the 185 nm and 253.7 nm cases, water photolysis by the 172 nm wavelength revealed a depth of photoactive water layer an order of magnitude greater (∼230-390 μm, depending on the specific operating conditions) than the 1-log photon penetration layer (∼18 μm). To further investigate this potentially very important finding, a computational fluid dynamics model was set up to assess the role of transport mechanisms and species distributions within the photoreactor annulus. The model confirmed that short-lived hydroxyl radicals were present at a radial distance far beyond the ∼18 μm photon penetration layer. Secondly, kinetic simulations showed that the higher penetration depth of hydroxyl radicals was not caused by diffusive or convective transport phenomena but rather the effect of non-linear behavior of the complex reaction kinetics involved in the process.
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Affiliation(s)
- F Crapulli
- Western University, 1151 Richmond St., London, ON N6A 3K7, Canada.
| | - D Santoro
- Western University, 1151 Richmond St., London, ON N6A 3K7, Canada; Trojan Technologies, 3020 Gore Rd., London, ON N5V 4T7, Canada
| | - M R Sasges
- Trojan Technologies, 3020 Gore Rd., London, ON N5V 4T7, Canada
| | - A K Ray
- Western University, 1151 Richmond St., London, ON N6A 3K7, Canada
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17
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Srivastava A, Ahamad J, Ray AK, Kaur D, Bhattacharya A, Bhattacharya S. Analysis of U3 snoRNA and small subunit processome components in the parasitic protist Entamoeba histolytica. Mol Biochem Parasitol 2014; 193:82-92. [PMID: 24631428 DOI: 10.1016/j.molbiopara.2014.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 02/27/2014] [Accepted: 03/01/2014] [Indexed: 10/25/2022]
Abstract
In the early branching parasitic protist Entamoeba histolytica, pre-rRNA synthesis continues when cells are subjected to growth stress, but processing slows down and unprocessed pre-rRNA accumulates. To gain insight into the regulatory mechanisms leading to accumulation, it is necessary to define the pre-rRNA processing machinery in E. histolytica. We searched the E. histolytica genome sequence for homologs of the SSU processome, which contains the U3snoRNA, and 72 proteins in yeast. We could identify 57 of the proteins with high confidence. Of the rest, 6 were absent in human, and 4 were non-essential in yeast. The remaining 5 were absent in other parasite genomes as well. Analysis of U3snoRNA showed that the E. histolytica U3snoRNA adopted the same conserved secondary structure as seen in yeast and human. The predicted structure was verified by chemical modification followed by primer extension (SHAPE). Further we showed that the predicted interactions of Eh_U3snoRNA boxes A and A' with pre-18S rRNA were highly conserved both in position and sequence. The predicted interactions of 5'-hinge and 3'-hinge sequences of Eh_U3 snoRNA with the 5'-ETS sequences were conserved in position but not in sequence. Transcription of selected genes of SSU processome was tested by northern analysis, and transcripts of predicted sizes were obtained. During serum starvation, when unprocessed pre-RNA accumulated, the transcript levels of some of these genes declined. This is the first report on pre-rRNA processing machinery in E. histolytica, and shows that the components are well conserved with respect to yeast and human.
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Affiliation(s)
- Ankita Srivastava
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Jamaluddin Ahamad
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Ashwini Kumar Ray
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Devinder Kaur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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18
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Banerjee G, Ray AK, Askarian F, Ringø E. Characterisation and identification of enzyme-producing autochthonous bacteria from the gastrointestinal tract of two Indian air-breathing fish. Benef Microbes 2014; 4:277-84. [PMID: 23685371 DOI: 10.3920/bm2012.0051] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Characterisation and identification of autochthonous enzyme-producing bacteria isolated from the proximal intestine and distal intestine of two species of Indian air-breathing fish, murrel (Channa punctatus) and stinging catfish (Heteropneustes fossilis), were investigated using conventional culture technique. Population levels of proteolytic strains were highest in the digestive tract of stinging catfish. In both species, the viable counts of amylase-producing bacteria were somewhat higher than cellulase-producing bacteria. Among the gut bacteria isolated, 8 strains (4 from murrel and 4 from stinging catfish) were selected as potent enzyme-producers on the basis of quantitative enzyme assays. All these strains were Gram-positive rods, but only four isolates (CPF4, CPH6, CPH7 and HFH4) were capable of forming endospores. The tested bacteria grew in wide range of temperatures and pH. The strains were further identified by 16S rRNA gene sequence analysis. Two strains, CPF3 (isolated from murrel) and HFH4 (isolated from stinging catfish) showed high similarity to Bacillus sp., strain HFH7 (isolated from the stinging catfish) was most closely related to Bacillus subtilis, while five strains belonged to Bacillus licheniformis. Based on the results of the present study, we suggest that incorporation of autochthonous enzyme-producing bacteria in aquafeeds merits further investigations.
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Affiliation(s)
- G Banerjee
- Fisheries Laboratory, Department of Zoology, Visva-Bharati University, Santiniketan 731 235, West Bengal, India
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19
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Pal C, Sharma AK, Cammidge AN, Cook MJ, Ray AK. Octaoctyl-substituted lutetium bisphthalocyanine for NADH biosensing. J Phys Chem B 2013; 117:15033-40. [PMID: 24205933 DOI: 10.1021/jp4078568] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cyclic voltammetric and Raman and UV-vis spectroscopic measurements were performed on thin films of nonperipherally substituted bis[1,4,8,11,15,18,22,25-octakis(octyl)phthalocyaninato] lutetium(III) (R16LuPc2). Voltammograms exhibit one-electron quasi-reversible redox processes in 1.5 M LiClO4 aqueous solutions. The red-shift of the Q-band of R16LuPc2 in the UV-visible absorption spectra upon oxidation is attributed to the shortening of the inter-ring distance between the two phthalocyanine moieties. This observation is also consistent with the shift in the redox-sensitive vibrational modes in the Raman spectra due to the localization of the positive charge on phthalocyanine moieties. Neutralization of the oxidized R16LuPc2(+) film by dihydronicotinamide adenine dinucleotide (NADH) using different concentrations varying from 0.05 to 1 mM has been studied by UV-vis absorption and Raman spectroscopies. The reduction processes for a three month old film were found to be slower than those for freshly prepared films and showed a dependence upon NADH concentration. The data provide a basis for application of R16LuPc2 as a sensor for NADH.
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Affiliation(s)
- C Pal
- The Wolfson Centre for Materials Processing, Brunel University , Uxbridge, Middlesex UB8 3PH, U.K
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20
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Das DK, Chakraborty C, Mitra B, Maiti AK, Ray AK. Quantitative microscopy approach for shape-based erythrocytes characterization in anaemia. J Microsc 2012; 249:136-49. [PMID: 23252834 DOI: 10.1111/jmi.12002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anaemia is one of the most common diseases in the world population. Primarily anaemia is identified based on haemoglobin level; and then microscopically examination of peripheral blood smear is required for characterizing and confirmation of anaemic stages. In conventional approach, experts visually characterize abnormality present in the erythrocytes under light microscope, and this evaluation process is subjective in nature and error prone. In this study, we have proposed a methodology using machine learning techniques for characterizing erythrocytes in anaemia associated with anaemia using microscopic images of peripheral blood smears. First, peripheral blood smear images are preprocessed based on grey world assumption technique and geometric mean filter for reducing unevenness of background illumination and noise reduction. Then erythrocyte cells are segmented using marker-controlled watershed segmentation technique. The erythrocytes in anaemia, such as, tear drop, echinocyte, acanthocyte, elliptocyte, sickle cells and normal erythrocytes cells have been characterized and classified based on their morphological changes. Optimal subset of features, ranked by information gain measure provides highest classification performance using logistic regression classifier in comparison with other standard classifiers.
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Affiliation(s)
- D K Das
- School of Medical Science and Technology, IIT Kharagpur, India
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Abstract
The principles of attenuation of the light intensity due to multiple reflections are realised in a planar silicon oxide (SiO(2))silicon nitride (Si(3)N(4)) waveguiding structure for the purpose of developing optical biosensors with improved sensitivity. The analysis of the experimental data shows that the large difference in refractive indices of core and cladding layers gives rise to an increase in sensitivity by a factor of 3 over previously reported structures. Composite polyelectrolyte self-assembled thin films containing cyclo-tetra-chromotropylene as an indicator and enzymes glucose oxidase or urease were employed in the superstrate as a sensing membrane. Individual enzyme reactions as well as their inhibition by pesticides were studied by monitoring the intensity of light output from the planar waveguide. The results were compatible with those obtained by conventional ultraviolet-visible absorption spectroscopy. The instrument detection limit for Imidacloprid pesticide was found to be as low as 10 ppb in concentration.
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Affiliation(s)
- A V Nabok
- Sheffield Hallam University, Nanotechnology Laboratories, School of Engineering, Sheffield, UK
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22
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Abstract
An 11-year-old girl with rapidly enlarging bilateral breast lumps is reported. It was diagnosed as a case of juvenile fibroadenoma following fine needle aspiration cytology and confirmed on histopathological examination of the excised specimens.
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Pal C, Cammidge AN, Cook MJ, Sosa-Sanchez JL, Sharma AK, Ray AK. In situ chemichromic studies of interactions between a lutetium bis-octaalkyl-substituted phthalocyanine and selected biological cofactors. J R Soc Interface 2011; 9:183-9. [PMID: 21676969 DOI: 10.1098/rsif.2010.0726] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Spin-coated films, approximately 100 nm thick, of a newly synthesized bis[octakis(octyl)phthalocyaninato] lutetium(III) complex on ultrasonically cleaned glass substrates exhibit pronounced chemichromic behaviour with potential application in healthcare. In situ kinetic optical absorption spectroscopic measurements show that the phthalocyanine Q-band is red shifted by 60 nm upon oxidation arising from exposure to bromine vapour. Recovery to the original state is achieved by the treatment of the oxidized films with nicotinamide adenine dinucleotide and l-ascorbic acid (vitamin C) in an aqueous solution containing 1.5 M lithium perchlorate. The neutralization process is found to be governed by first-order kinetics. The linear increase of the reduction rate with increasing concentration of cofactors provides a basis for calibration of analyte concentrations ranging from 3.5 mM down to 0.03 mM.
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Affiliation(s)
- C Pal
- The Wolfson Centre for Materials Processing, Brunel University, Uxbridge, Middlesex UB8 3PH, UK
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24
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Banavath HN, Bhardwaj NK, Ray AK. A comparative study of the effect of refining on charge of various pulps. Bioresour Technol 2011; 102:4544-4551. [PMID: 21262570 DOI: 10.1016/j.biortech.2010.12.109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 12/28/2010] [Accepted: 12/30/2010] [Indexed: 05/30/2023]
Abstract
This work studied the influence of refining on various pulp properties such as freeness, specific surface area, specific volume, water retention value, surface charge, total charge and tensile index of five different pulps. At a freeness level the wheat straw pulp exhibited higher surface charge and total charge compared to other pulps. The specific surface area, specific volume and water retention value of the pulps increased with increased refining. The total fibre charge as determined by conductometric titrations was not affected by refining. However, the surface charge as determined by titrations with poly-DADMAC increased with refining. The increases in specific surface area of pulps by refining resulted in a higher fibre surface charge and also better fibre-fibre bonding. The linear regression models developed using experimental data were found to be accurate. The comparison of model predicted data and the experimental data showed an excellent agreement between them.
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Affiliation(s)
- Hussen Naik Banavath
- Department of Paper Technology, Saharanpur Campus, Indian Institute of Technology Roorkee, Saharanpur 247001, Uttar Pradesh, India.
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Abstract
Surface plasmon resonance imaging (SPRI) is a useful tool for the study of surface biomolecular interactions allowing for label-free detection and elegant instrumentation. SPRI imaging system is described in this review with an emphasis on recent applications with examples of different biological interactions and high throughput analysis. Signal amplification in SPRI using nanoparticle and waveguide-based optical coupling is introduced. Finally the detection sensitivity of the SPRI system is examined in terms of other competitive methods.
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Affiliation(s)
- S Paul
- Queen Mary, University of London, School of Engineering and Materials Science, London, UK
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Solanki GK, Amin A, Padhiyar A, Ray AK, Oza AT. Polaron hopping in some biomolecular solids and their charge transfer complexes. Indian J Biochem Biophys 2008; 45:421-429. [PMID: 19239130] [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: 05/27/2023]
Abstract
The solid state spectroscopy of charge transfer complexes of biomolecules such as fatty acids, tripalmitin, lysozyme. folic acid, beta-carotene, cytochrome c, valinomycin and gramicidin has been carried out. The absorption coefficient is related with electronic conductivity. A half-power beta density is found common among these macromolecular solids, indicating photon-induced polaron hopping or hopping of a charge carrier between two branches of a polariton. Band gap vs full width at half-maximum of the mid-IR peak also reveals a linear relation.
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Affiliation(s)
- G K Solanki
- Department of Physics, Sardar Patel University, Vallabh Vidyanagar, -388 120, Gujarat, India
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27
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Basova T, Jushina I, Gürek AG, Ahsen V, Ray AK. Use of the electrochromic behaviour of lanthanide phthalocyanine films for nicotinamide adenine dinucleotide detection. J R Soc Interface 2008; 5:801-6. [PMID: 17971319 DOI: 10.1098/rsif.2007.1241] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Electrochromic properties of spun films of bis[octakis(hexylthio)phthalocyaninato] dysprosium(III) were investigated for determining nicotinamide adenine dinucleotide hydride (NADH) in water solutions. A spin-coated film deposited on indium tin oxide electrode displays only one redox couple (at E1/2=0.78V). The films of [(C6H13S)8Pc]2Dy were modified chemically or electrochemically for the detection of reduced NADH in water solution. The modified film in the oxidized ([(C6H13S)8Pc]2Dy)+ form is believed to be reduced to its neutral form on interaction with NADH.
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Affiliation(s)
- T Basova
- Institute of Inorganic Chemistry, Lavrentiev Prospect 3, Novosibirsk 630090, Russia.
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28
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Viano AM, Spence KE, Shanks MA, Scott MA, Redfearn RD, Carlson CW, Holm TA, Ray AK. Structural and chemical changes in ultra-high-molecular-weight polyethylene due to gamma radiation-induced crosslinking and annealing in air. Biomed Mater Eng 2007; 17:257-68. [PMID: 17851168] [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: 05/17/2023]
Abstract
Ultra-High-Molecular-Weight-Polyethylene (UHMWPE) is the material of choice for one of the articulating surfaces in many total joint replacements, notably hip and knee prostheses. The various methods used by the orthopaedic biomaterials industry to sterilize and anneal UHMWPE components, and the resulting oxidation and crosslinking, affect the mechanical wear resistance properties in ways still unknown at the microscopic and molecular levels. Transmission electron microscopy and chemical pyrolysis were used to quantify crosslinking induced by gamma irradiation and annealing in air. Changes in lamellar stacking and the amount of crosslinking suggest two types of crosslinking: relatively unstable crosslinks in the amorphous region initially resulting from gamma irradiation which are later replaced by more thermally stable crosslinks resulting from rearrangements at the annealing temperature. Lamellar mobility, the ability of crystalline lamellae to flow in the material, is enhanced during the transition from one type of bond to the other, and this appears to optimize near eight hours of annealing time. Results from decomposition and percent crystallinity measurements provide further support for this theory.
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Affiliation(s)
- A M Viano
- Department of Physics, Rhodes College, Memphis, TN 38112, USA.
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29
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Abstract
Trace metals (Fe, Mn, Cu, Co, Ni. Pb, Cd and Cr) analyses in particulate matter and sediments were carried out at 16 different stations in the Godavari mangrove ecosystem covering the three regions viz., Kakinada (KKD) bay, Goutami-Godavari estuary (GGE) and Coringa and Gaderu mangrove environments (CGME). Higher concentrations of trace metals in particulate matter and in sediments were noticed in the mangrove environment compared to the KKD bay and GGE region. The significant correlations observed between several couples of metals in different regions as well as between numbers of heavy metals (Fe, Mn, Zn) with Total Suspended Matter (TSM) in particulate organic matter could be an indication of the role of the complexation with organic matter in the distribution pattern of these metals. Further significant correlations between organic carbon (OC) and Cr, Co, Pb, Cu and Mn in sediments of all the three regions indicate that organic matter acts as a metal carrier. The values of Pollution Load Index (PLI) were low and varied between 0.34 and 0.68 in KKD bay, 0.47 and 0.49 in GGE and, from 0.62 to 1.03 in CGME area, which indicate that the estuarine ecosystem is not of pollution concern under the present scenario.
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Affiliation(s)
- A K Ray
- National Institute of Oceanography, Regional Centre, 176, Lawson's Bay Colony, Visakhapatnam-530 017, India
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30
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Vannemreddy P, Ray AK, Patnaik R, Patnaik S, Mohanty S, Sharma HS. Zinc protoporphyrin IX attenuates closed head injury-induced edema formation, blood-brain barrier disruption, and serotonin levels in the rat. Acta Neurochir Suppl 2006; 96:151-6. [PMID: 16671445 DOI: 10.1007/3-211-30714-1_34] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The role of heme oxygenase (HO) in closed head injury (CHI) was examined using a potent HO and guanylyl cyclase inhibitor, zinc protoporphyrin (Zn-PP) in the rat. Blood-brain barrier (BBB) permeability to Evans blue and radioiodine, edema formation, and plasma and brain levels of serotonin were measured in control, CHI, and Zn-PP-treated CHI rats. CHI was produced by an impact of 0.224 N on the right parietal bone by dropping 114.6 g weight from a height of 20 cm in anesthetized rats. This concussive injury resulted in edema formation and brain swelling 5 hours after insult that was most pronounced in the contralateral hemisphere. The whole brain was edematous and remained in a semi-fluid state. Microvascular permeability disturbances to protein tracers were prominent in both cerebral hemispheres and the underlying cerebral structures. Plasma and brain serotonin showed pronounced increases and correlated with edema formation. Pretreatment with Zn-PP (10 mg/ kg, i.p) 30 minutes before or after CHI attenuated edema formation, brain swelling, plasma and brain serotonin levels, and microvascular permeability at 5 hours. Brain edema, BBB permeability, and serotonin levels were not attenuated when the compound was administered 60 minutes post-CHI suggesting that HO is involved in cellular and molecular mechanisms of edema formation and BBB breakdown early after CHI.
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Affiliation(s)
- P Vannemreddy
- Laboratory of Neuroanatomy, Department of Medical Cell Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
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31
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Gapan R, Ray AK, Richardson TH, Hassan AK, Davis F. Pyroelectric and conduction properties of Z-type calix[4] acid Langmuir-Blodgett films. J Nanosci Nanotechnol 2005; 5:1910-4. [PMID: 16433430 DOI: 10.1166/jnn.2005.419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Non-centrosymmetric Z-type Langmuir-Blodgett (LB) films were prepared by transferring a calix[4] acid monolayer from a subphase of Millipore water (18 Momegacm(-1)) onto aluminised glass substrates. Electrical measurements were performed at room temperature on LB films with a sandwich structure comprising a 50 nm thick thermally evaporated aluminium film. A pyroelectric figure of merit of 2.23 microC m(-2)K(-1) is reported for this LB system. The low voltage value of conductivity is 1.82 x 10(-12) Sm(-1). The electrode-limited Schottky effect is responsible for the conduction mechanism at a relatively high field due to the dc bias and the barrier potential height is determined to be 1.72 eV. The ac conductance for both samples shows a typical power law dependence with a value of approximately 0.86 for the exponent.
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Affiliation(s)
- R Gapan
- University of Balikesir, Faculty of Science Department of Physics, Balikesir 10100, Turkey
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32
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Ramachandran S, Bairagi A, Ray AK. Improvement of nutritive value of grass pea (Lathyrus sativus) seed meal in the formulated diets for rohu, Labeo rohita (Hamilton) fingerlings after fermentation with a fish gut bacterium. Bioresour Technol 2005; 96:1465-72. [PMID: 15939274 DOI: 10.1016/j.biortech.2004.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2004] [Revised: 11/27/2004] [Accepted: 12/02/2004] [Indexed: 05/02/2023]
Abstract
Eight isonitrogenous (35% crude protein approximately) and isocaloric (4.0 kcalg(-1) approximately) diets were formulated incorporating raw and fermented grass pea (Lathyrus sativus) seed meal at 10%, 20%, 30% and 40% levels by weight into a fish meal based diet and fed to rohu, Labeo rohita, fingerlings for 80 days and fish performance was studied. A particular bacterial strain (Bacillus sp.) isolated from the intestine of adult common carp (Cyprinus carpio) reared in the wild having significant amylolytic, cellulolytic, lipolytic and proteolytic activities were used for fermentation of seed meal for 15 days at 37 degrees C. Fermentation of grass pea seed meal was effective in significantly reducing the crude fibre content and anti-nutritional factors, such as tannins, phytic acid and the neurotoxin, beta-ODAP and enhancing the available free amino acids and fatty acids. In terms of growth response, feed conversion ratio and protein efficiency ratio, 30% fermented grass pea seed meal incorporated diet resulted in significantly (P < 0.05) better performance of rohu fingerlings. In general, growth and feed utilization efficiencies of fish fed diets containing fermented seed meal were superior to those fed diets containing raw seed meal. The apparent protein digestibility (APD) values decreased with increasing levels of raw seed meal in the diets. The APD for raw seed meal was lower at all levels of inclusion in comparison to those for the fermented seed meals. The highest deposition of carcass protein was recorded in fish fed the diet containing 40% fermented seed meal. The results indicated that fermented grass pea seed meal can be incorporated in carp diets up to 30% level compared to 10% level of raw seed meal.
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Affiliation(s)
- S Ramachandran
- Fisheries Laboratory, Department of Zoology, Visva-Bharati University, Santiniketan, West Bengal, India
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33
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Abstract
Autosomal dominant EEC syndrome consists of ectrodactyly, ectodermal dysplasia, and cleft lip with or without cleft palate (CL/P). We investigated an EEC kindred with 10 affected persons in three generations in order to map the causative mutation in this family and to map modifier genes that contribute to the expression of facial clefting in the phenotype. DNA from 15 family members was genotyped for 388 genome screen markers. Analysis revealed maximal linkage between EEC and chromosome 3q27, which contains a known EEC gene - tumor protein 63 (TP63). Sequencing showed a CGT-->TGT missense mutation (R280C) in exon 7, previously reported to cause EEC in four families, and ectrodactyly alone (split hand-foot malformation) in one sporadic case and one large kindred. Analysis of the clefting phenotype in this EEC family demonstrated maximal linkage to two regions on chromosomes 4q and 14, which multiple studies have implicated in non-syndromic CL/P. In conclusion, this study demonstrates that the mutation of TP63 is the major (Mendelian) EEC gene in this kindred and suggests that additional minor modifying genes which predispose to non-syndromic CL/P could also contribute to the expression of the clefting component of the syndrome in this family.
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MESH Headings
- Abnormalities, Multiple/genetics
- Chromosome Mapping
- Chromosomes, Human, Pair 14/genetics
- Chromosomes, Human, Pair 3/genetics
- Chromosomes, Human, Pair 4/genetics
- Cleft Lip/genetics
- DNA Mutational Analysis
- Ectodermal Dysplasia/genetics
- Genes, Dominant
- Genotype
- Humans
- Lod Score
- Mutation, Missense/genetics
- Pedigree
- Sequence Analysis, DNA
- Syndrome
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Affiliation(s)
- A K Ray
- Department of Anthropology, University of Toronto, Toronto, Canada
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Samanta N, Saha K, Srivastava V, Ray AK, Patra R, Saha Basu K. Urogenital anomalies associated with anorectal malformation. J Indian Assoc Pediatr Surg 2005. [DOI: 10.4103/0971-9261.16076] [Citation(s) in RCA: 5] [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: 11/04/2022] Open
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Abstract
A pair of female thoraco-omphalopagus twins, with two pairs of lungs, common diaphragm and separate pleural cavities was separated at the age of 5(1/2) months after a parasitic relationship had developed between them. Before separation both the babies developed recurrent respiratory tract infection and frequent diarrhea. They were treated with medical therapy and made fit for anesthesia. The combined weight of the twins was 4(1/2) kg at birth and the combined weight at the time of separation was 9(1/2) kg. One baby was smaller in growth compared to the other baby. The closure of anterior abdominal wall was difficult in both babies. However, we could close it without use of any biodegradable patches or tissue expander. Both the babies survived and are doing well after 3 months of separation.
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Affiliation(s)
- A K Ray
- Department of Pediatric Surgery, Calcutta Medical College, Kolkata, India.
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36
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Ray AK, Singhania AK, Mukherjee S. Post PSRRP anorectol manometry--experience of 115 cases of imperforate anus. J Indian Med Assoc 2004; 102:253-5. [PMID: 15636027] [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: 05/01/2023]
Abstract
The conventional treatment of high and intemiediate anomalies of anorectal malformations is proximal pelvic colostomy in neonate (day 1) followed by PSARP (postsagittal anorectoplasty) by the age of 4-6 months and closure of colostomy when adequate dilatation of neo-anus has been performed using Nol 2 or 13 Hegar's dilator or No4 St Mark's anal dilator, It is usually done 3 months after the PSARP operation (anorectal pull through), ie, around 9 months. So the child born without anus in the perineum should be able to pass stool via his or her neo-anus by the age of 9 months and they should ideally be penneally continent. The present study, between August 1993 and December 1999, on the anorectal continence evaluation by doing anorectal manometry was carried out in 115 babies who underwent PSARP operation and subsequent closure of the colostomy. The study showed intermediate anomalies dominated the picture in both males and females (103 babies belonging to intermediate anomalies and 12 babies having high anomalies). In all these children the results of continence have been studied both clinically (Kiesewetter criteria) and by anorectal manometry.
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Affiliation(s)
- A K Ray
- Department of Paediatric Surgery, Medical College, Kolkata 700073
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37
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Brown IM, Wilson CR, Doughty JC, George WD, Cooke TG, Weiler-Mithoft EM, Scott JR, Ray AK. The future of breast surgery: a new sub-speciality of oncoplastic breast surgeons? Breast 2004; 13:82. [PMID: 14759724 DOI: 10.1016/j.breast.2003.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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38
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Affiliation(s)
- P K Sarkar
- Department of Biology, Rutgers University, Camden, New Jersey 08102, USA.
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39
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Bairagi A, Sarkar Ghosh K, Sen SK, Ray AK. Duckweed (Lemna polyrhiza) leaf meal as a source of feedstuff in formulated diets for rohu (Labeo rohita Ham.) fingerlings after fermentation with a fish intestinal bacterium. Bioresour Technol 2002; 85:17-24. [PMID: 12146637 DOI: 10.1016/s0960-8524(02)00067-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Eight isonitrogenous (35% crude protein approximately) and isocaloric (4.2 kcal g(-1) approximately) diets were formulated including raw and fermented duckweed (Lemna polyrhiza) leaf meal at 10%, 20%, 30% and 40% levels. A particular bacterial strain (Bacillus sp.) isolated from carp (Cyprinus carpio) intestine and having extracellular amylolytic, cellulolytic, proteolytic and lipolytic activities was used for leaf meal fermentation for 15 days at 37 degrees C. The fibre content of leaf meal reduced from 11.0% to 7.5% and the antinutritional factors, tannin and phytic acid, were reduced from 1.0% to 0.02% and 1.23% to 0.09%, respectively after fermentation. However, the available reducing sugars, free amino acids and fatty acids increased in the fermented leaf meal. The response of rohu, Labeo rohita, fingerlings fed the experimental diets for 80 days was compared with fish fed a fish meal based reference diet. On the basis of growth response, food conversion ratio and protein efficiency ratio, 30% fermented Lemna leaf meal incorporated in the diet resulted in the best performance of rohu fingerlings. In general, growth and feed utilization efficiencies of fish fed fermented leaf meal containing diets were superior to those fed diets containing raw leaf meal. The apparent protein digestibility (APD) decreased with increasing levels of leaf meal irrespective of treatment. The APD for raw leaf meal was lower at all levels of inclusion in comparison to those for the fermented meals. The highest carcass protein and lipid deposition was recorded in fish fed the diet containing 30% fermented leaf meal. The results showed that fermented Lemna leaf meal can be incorporated into carp diets up to 30% level compared to 10% level of raw meal.
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Affiliation(s)
- A Bairagi
- Department of Zoology, Visva-Bharati University, West Bengal, India
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40
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Bhattacharyya M, Ray AK. A case of primary mucus secreting adenocarcinoma of the appendix. J Indian Med Assoc 2001; 99:648, 650. [PMID: 12022210] [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: 02/25/2023]
Abstract
Primary mucus secreting adenocarcinoma of the appendix is a rare finding, one in 2500 cases of intestinal malignancies. This is a report of a young man with vague abdominal symptoms for about two years followed by appendicitis. Interval appendectomy revealed a neoplasm of the appendix. Histopathology confirmed the diagnosis of mucus secreting adenocarcinoma and right hemicolectomy was done.
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41
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Keshan B, Ray AK. Effect of estradiol-17beta on cell area, lumen area and trehalase activity of posterior silk gland of Bombyx mori L. Indian J Exp Biol 2001; 39:1096-102. [PMID: 11906100] [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: 02/24/2023]
Abstract
Estradiol-17beta (E2) at the dose of 1 microg/g caused an increase in cell area, lumen area and the total (cell + lumen) area of posterior silk gland (PSG) in Bombyx mori indicating that exogenously applied estradiol-17beta has a regulatory influence on silk gland activity. A dose-dependent variation in trehalase activity of PSG was found on the 5th day after topical administration of estradiol on 1st and 2nd day of the fifth larval instar. Of all the doses of E2 used, 1 microg/g dose had maximum stimulatory effect on trehalase activity. Co-administration of each of a specific receptor antagonist for estradiol, the ICI-182780 and a protein biosynthetic blocker, cycloheximide with E2 suppressed the E2-induced increase in silk gland activity. The results suggest some specific metabolic action of E2 on silk gland and offer a promising way for future investigations regarding the physiological significance of vertebrate steroids in insects.
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Affiliation(s)
- B Keshan
- Department of Animal Physiology, Bose Institute, Calcutta, India.
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Shirshov YM, Snopok BA, Samoylov AV, Kiyanovskij AP, Venger EF, Nabok AV, Ray AK. Analysis of the response of planar polarization interferometer to molecular layer formation: fibrinogen adsorption on silicon nitride surface. Biosens Bioelectron 2001; 16:381-90. [PMID: 11672652 DOI: 10.1016/s0956-5663(01)00148-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [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: 11/25/2022]
Abstract
The most sensitive optical method of interferometry was exploited for determination of changes in the refractive index following the adsorption of biological molecules onto the solid surface. Instead of having two waveguiding arms (the main and the reference) in traditional Mach-Zhender interferometer, two ortogonal TM and TE modes propagating through the SiO(2)-Si(3)N(4)-SiO(2) waveguide structure were employed in planar polarization interferometer (PPI). Multiperiodic PPI response was, therefore, formed due to the phase shift between TM and TE modes. A matrix simulation procedure was developed in order to investigate the influence of both the refractive index and molecular layer thickness on the PPI response. Nonspecifical binding of fibrinogen to silicon nitride surface was studied as a model object for PPI testing. The results obtained are in good agreement with the known information about fibrinogen adsorption on the different surfaces. An attempt to introduce the concept of 'surface molecular concentration and molecular polariziability' instead of 'molecular layer thickness and refractivity' was undertaken.
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Affiliation(s)
- Y M Shirshov
- Department of Functional Optoelectronics, Institute of Semiconductor Physics, National Academy of Sciences, 252028 Kiev, Ukraine
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43
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Starodub NF, Nabok AV, Starodub VM, Ray AK, Hassan AK. Immobilization of biocomponents for immune optical sensors. Ukr Biokhim Zh (1999) 2001; 73:55-64. [PMID: 12035530] [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: 02/25/2023]
Abstract
Immobilisation of both human immunoglobulin(IgG) and antiimmunoglobulin (anti-IgG) was performed by means of polyelectrolyte self-assembly. This technique was compared with direct immobilisation of the immune components on bare gold and their covalent binding via glutaraldehyde as a bifunctional reagent. Additionally, the immune components were properly oriented during their immobilisation by using a predeposited layer of the protein A. Methods of the surface plasmon resonance (SPR) and planar interferometry were employed for monitoring the immobilisation as well as specific immune reaction. It was shown that in case of the use of polyelectrolyte self-assembly it is possible to achieve the sensitivity of the analysis up to 30 ng/ml for SPR and up to 1 ng/ml for planar interferometer based immune sensors.
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Affiliation(s)
- N F Starodub
- Palladin Institute of Biochemistry, NAS of Ukraine, Department of Sensory and Regulatory Systems.
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44
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Abstract
Although estradiol-17beta (E2) is known to be a vertebrate sex steroid, its presence in insects, particularly in Bombyx mori, has recently created considerable sensation regarding its significance in insect life. The specificity of estradiol action on the posterior silk gland (PSG) of B. mori has been previously assessed by the use of ICI-182780 as a specific receptor antagonist for estradiol. The present study provides evidence for systematic changes in the titer of estradiol-17beta in B. mori and its specific binding sites in the posterior silk gland according to the physiological age of fifth instar larvae. The changes in the estradiol level in the PSG after E2 treatment have also been determined to assess whether the administered estradiol has been taken up by the silk gland cells and whether the effect of exogenously administered E2 on the PSG is direct. The correlation in the profile of E2 binding sites with the endogenous estradiol level of PSG on different days of fifth instar larvae suggests that the level of binding sites in the PSG is regulated by the estradiol titer and that E2 may have some biological function in B. mori. Scatchard analysis of E2 binding sites in the PSG on 9th day of fifth instar larvae reveals that it consists of only one type of binding component. The dissociation constant (Kd) and maximum binding capacity (Bmax) of this putative E2 receptor have been found to be 8.98 +/- 0.744 nM and 55.8 +/- 5.53 fmol/mg cytosolic protein, respectively. The study thus indicates an involvement of the putative receptor in E2-mediated action on the silk gland of B. mori and paves a pathway for further evaluation of the physiological relevance of the presence of vertebrate steroids in insects.
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Affiliation(s)
- B Keshan
- Department of Animal Physiology, Bose Institute, Calcutta, India
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45
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Abstract
The enzyme ethoxyresorufin-o-deethylase (EROD) of the cytochrome P4501A family (CYP1A) in fish liver is increasingly being used as a molecular marker for qualitative and quantitative estimation of aquatic pollution throughout the world. The regulation and expression of this enzyme protein is very important from the toxicological point of view. The regulation of gene expression for this enzyme is mediated by the aromatic hydrocarbon receptor. In addition, cellular glutathione status influences expression of CYP1A. In this study, we explored the relationships among glutathione, EROD, and copper in cultured hepatocytes from Indian catfish. EROD activity in cultured hepatocytes was induced by carbofuran (CF), a widely used agricultural pesticide, and by beta-napthoflavone (BNF), a known inducer of CYP1A. Addition of copper into the culture media of hepatocytes inhibited EROD activity significantly. The activity of EROD elevated by CF and BNF was inhibited in hepatocytes pretreated with CF and BNF exposed to CuSO4. This effect was reflected in the glutathione status of the cells. The level of glutathione was increased by 3.4 and 3.0 times in hepatocytes treated with CF and BNF, respectively. These levels were inhibited in hepatocytes exposed to CuSO(4). Thus, copper interactions with glutathione may play a role in regulating EROD in hepatocytes.
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Affiliation(s)
- M C Ghosh
- Department of Animal Physiology, Bose Institute, P-1/12 CIT Scheme VII M, Calcutta, 7009 054, India
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46
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Tu H, Ray AK. Analysis of time-dependent scattering spectra for studying processes associated with microdroplets. Appl Opt 2001; 40:2522-2534. [PMID: 18357266 DOI: 10.1364/ao.40.002522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Techniques are presented for analysis of time-dependent scattering spectra from single droplets undergoing physical changes. Times of appearance of resonances in experimental spectra are aligned with theoretical resonances, and the size and refractive index of a droplet as functions of time are determined from the minimum errors in alignment between observed and theoretical resonances. The techniques have been applied to time-dependent elastic scattering spectra obtained from single droplets evaporating under quasi-steady conditions and during unsteady growth. The results of quasi-steady evaporation data show that size and refractive index can be determined with relative errors of 1 x 10(-4). The quasi-steady evaporation data of a droplet are used to identify the resonances observed during the unsteady growth of the same droplet, and the size and refractive index at each resonance are calculated from the identity of the resonance.
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47
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Abstract
Despite the recently emerging notion of thyroid-hormone involvement in neurotransmission in the adult mammalian brain, adequate evidence for a cellular basis of the process is still lacking. The present study indicates the involvement of thyroid hormones in cholinergic system of the adult rat cerebral cortex. Administration of L-triiodothyronine (T3, 0.025 to 4 microg/g) in single doses increased the synaptosomal acetylcholinesterase (AchE) and Mg2+-ATPase activity maximally at 24 hours in a dose-dependent way. Propylthiouracil (PTU)-treated hypothyroid rats showed a significant increase in AchE and Mg2+-ATPase activity compared to euthyroid rats. T3-treatment on hypothyroid rats decreased AchE activity in synaptosomes compared to the hypothyroid synaptosomal values. Mg2+-ATPase activity found in (PTU + T3)-treated group and T3-treated group remained high. These results predict that T3 stimulates acetylcholine (Ach) metabolism by increasing AchE activity as well as uptake of the released Ach through an increase in synaptosomal Mg2+-ATPase activity. This indicates a positive impact of T3 on the cholinergic system in the adult mammalian brain.
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Affiliation(s)
- P K Sarkar
- Department of Biology, Rutgers University, Camden, New Jersey 08102, USA.
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Maitra SK, Ray AK. Role of light in the mediation of acute effects of a single afternoon melatonin injection on steroidogenic activity of testis in the rat. J Biosci 2000; 25:253-6. [PMID: 11022226 DOI: 10.1007/bf02703932] [Citation(s) in RCA: 12] [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: 10/22/2022]
Abstract
Young adult male rats, maintained either in an LD 12 : 12 or in continuous illumination (LL) for one week, were given a single injection of 25 microg melatonin/100 g body wt or ethanolic-saline (control) at 17.00 h. Animals from each group were sacrificed at 11.00 h on the following day. The activity of two important steroidogenic enzymes, 17 beta-hydroxysteroid dehydrogenase (17 beta-HSD) and delta(5)-3 beta-hydroxysteroid dehydrogenase (delta(5)-3 beta-HSD), and serum concentrations of testosterone, were measured following highly specific and sensitive spectrophotometric techniques and RIA, respectively. A significant decrease in the activity of both the steroidogenic enzymes was noted in the testes of melatonin-treated rats maintained under normal light-dark schedules, but this response was found to be lacking in the LL rats. However, no significant changes in the level of serum testosterone were noted in either group of melatonin-treated rats from the values in respective groups of ethanolic saline-administered LD and LL rats. Exposure of ethanolic saline-injected rats to continuous light also did not cause any change in the steroidogenic activity of the testis from those in LD rats. The study indicates that continuous light as such does not affect the endocrine function of testis but abolishes suppressive effects of melatonin on the steroidogenic activity of the testis in rat.
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Affiliation(s)
- S K Maitra
- Department of Zoology,University of Burdwan, Burdwan 713 104, India.
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Abstract
Carbofuran is a nematicide used in agricultural fields throughout the world. Indiscriminate use of this pesticide poses severe detrimental effects on our ecosystem. We have shown that it induces the CYP1A (cytochrome P4501A) monooxygenase enzyme system in cultured hepatocytes from Indian catfish, Heteropneustes fossilis (Bloch). We have quantified this induction by measuring the activity of the enzyme 7-ethoxyresorufin-O-deethylase (EROD), synthesized from CYP1A1 gene. The induction followed a dose-dependent relationship with carbofuran. The dose-dependent curve of EROD using carbofuran was very much similar with beta-napthoflavone, which is a known inducer of CYP1A1. Coexposure of these compounds to the culture media showed a synergistic effect on the enzyme activity. A blocker of aromatic hydrocarbon receptor, alpha-napthoflavone, blocked carbofuran-induced EROD activity in a dose-dependent manner. All these findings suggest that metabolism of carbofuran might be mediated by the CYP1A monooxygenase system through binding of the aromatic hydrocarbon receptor. We have also studied the superinduction phenomenon, which is a typical characteristic of the CYP1A gene in our system.
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Affiliation(s)
- M C Ghosh
- Department of Animal Physiology, Bose Institute, Calcutta, India
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Abstract
Although estrogen is well known as a vertebrate sex steroid, its presence in insects, including Bombyx mori, raises questions about its precise role in the physiology of insects. It was reported earlier that estradiol-17beta (E(2)) exerts a specific effect on silk-gland function in B. mori and that it may act in a nuclear-mediated way. To evaluate further the effect of E(2) on cocoon characters, larval growth and development, 1µg/g of E(2) was applied topically to the first and second day of fifth instar larvae. This resulted in a significant enhancement of cocoon characters, such as cocoon shell weight, silk filament length per cocoon, denier per filament and reelability of the cocoons, without any adverse effect on fecundity and hatchability. In the present study, E(2) levels in the haemolymph were quantified on different days of the fifth instar larvae and age-dependent changes in the endogenous E(2) titre have been demonstrated. These age-dependent variations in E(2) content coincide with physiological events occurring during the fifth instar. Such observations exclude the possibility of a dietary origin for E(2), as a sudden and sharp rise of the E(2) level in the haemolymph was observed on the 10th day of the fifth instar, preceded by a small increase on the ninth day after an eight-day feeding period. The increased level of estradiol in the haemolymph of larvae treated topically with E(2) indicates effective penetration of this hormone through the larval cuticle. Moreover, similar patterns of alteration of E(2) levels on different days of the fifth instar in both control and treated groups suggests the existence of some internal metabolic pathway in the silkworm body to regulate the hormone titre. Thus, the present investigation offers a system for investigating the unique function of E(2) in B. mori and offers potential for improvement of silk production.
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Affiliation(s)
- B Keshan
- Department of Animal Physiology, Bose Institute, P-1/12 CIT Scheme VII - M, Calcutta, India
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