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Sapey E, Crowley LE, Edgar RG, Griffiths D, Samanta S, Crisford H, Bolton CE, Hurst JR, Stockley RA. Cardiovascular disease in Alpha 1 antitrypsin deficiency: an observational study assessing the role of neutrophil proteinase activity and the suitability of validated screening tools. Orphanet J Rare Dis 2024; 19:130. [PMID: 38515138 PMCID: PMC10956254 DOI: 10.1186/s13023-024-03124-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 03/03/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Alpha 1 Antitrypsin Deficiency (AATD) is a rare, inherited lung disease which shares features with Chronic Obstructive Pulmonary Disease (COPD) but has a greater burden of proteinase related tissue damage. These proteinases are associated with cardiovascular disease (CVD) in the general population. It is unclear whether patients with AATD have a greater risk of CVD compared to usual COPD, how best to screen for this, and whether neutrophil proteinases are implicated in AATD-associated CVD. This study had three aims. To compare CVD risk in never-augmented AATD patients to non-AATD COPD and healthy controls (HC). To assess relationships between CVD risk and lung physiology. To determine if neutrophil proteinase activity was associated with CVD risk in AATD. Cardiovascular risk was assessed by QRISK2® score and aortic stiffness measurements using carotid-femoral (aortic) pulse wave velocity (aPWV). Medical history, computed tomography scans and post-bronchodilator lung function parameters were reviewed. Systemic proteinase 3 activity was measured. Patients were followed for 4 years, to assess CVD development. RESULTS 228 patients with AATD, 50 with non-AATD COPD and 51 healthy controls were recruited. In all COPD and HC participants, QRISK2® and aPWV gave concordant results (with both measures either high or in the normal range). This was not the case in AATD. Once aPWV was adjusted for age and smoking history, aPWV was highest and QRISK2® lowest in AATD patients compared to the COPD or HC participants. Higher aPWV was associated with impairments in lung physiology, the presence of emphysema on CT scan and proteinase 3 activity following adjustment for age, smoking status and traditional CVD risk factors (using QRISK2® scores) in AATD. There were no such relationships with QRISK2® in AATD. AATD patients with confirmed CVD at four-year follow up had a higher aPWV but not QRISK2® at baseline assessment. CONCLUSION aPWV measured CVD risk is elevated in AATD. This risk is not captured by QRISK2®. There is a relationship between aPWV, lung disease and proteinase-3 activity. Proteinase-driven breakdown of elastin fibres in large arteries and lungs is a putative mechanism and forms a potential therapeutic target for CVD in AATD.
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Affiliation(s)
- E Sapey
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, B15 2GW, UK
- University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham, West Midlands, UK
| | - L E Crowley
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, B15 2GW, UK.
- University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham, West Midlands, UK.
| | - R G Edgar
- Institute of Applied Health, University of Birmingham, Birmingham, West Midlands, UK
| | - D Griffiths
- University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham, West Midlands, UK
| | - S Samanta
- UCL Respiratory, University College London, London, UK
| | - H Crisford
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, B15 2GW, UK
| | - C E Bolton
- NIHR Nottingham BRC Respiratory Theme, School of Medicine, University of Nottingham, City Hospital NUH Trust, Nottingham, UK
| | - J R Hurst
- UCL Respiratory, University College London, London, UK
| | - R A Stockley
- University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham, West Midlands, UK
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Gogoi P, Das SK, Jana C, Das BK, Saha A, Ramteke K, Jaiswar AK, Samanta S, Roshith CM. Assessing the trophic status of a tropical microtidal estuary applying TRIX and Random Forest - A combined approach. Mar Pollut Bull 2024; 200:116126. [PMID: 38330813 DOI: 10.1016/j.marpolbul.2024.116126] [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: 01/02/2024] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
The present study assessed the trophic status of a medium-sized microtidal estuary, Rushikulya, India using a combination of mutimetric trophic indices (TRIX, TRBIX) and a machine learning approach (Random Forest). A total of 108 samples were considered to build a predictive model for chlorophyll a (Chl a) and 17 response water variables by observing two annual periods (2021-2023) at six sampling sites. Mean values of TRIX (5.04 ± 0.72) and TRBIX (0.17 ± 0.08) reflected that the estuary has a moderate degree of eutrophication with 'good' water quality and 'biomass saturated'. However, the threshold of TRIX represents a transition state from 'moderate' to 'high' eutrophic. Random Forest model reflected that no apparent association between Chl a and water turbidity above 30 NTU and eutrophication in the estuary fluctuated mainly due to PO43--P along with electrical conductivity. Linear statistical correlations showed high correlation between Chl a and conductivity and a negative correlation between Chl a and dissolved oxygen, unlike PO43--P.
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Affiliation(s)
- Pranab Gogoi
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, India
| | - Sanjoy Kumar Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, India
| | - Chayna Jana
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, India
| | - Basanta Kumar Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, India.
| | - Ajoy Saha
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, India
| | - Karankumar Ramteke
- ICAR-Central Institute of Fisheries Education, Versova, Mumbai 400061, Maharastra, India
| | - A K Jaiswar
- ICAR-Central Institute of Fisheries Education, Versova, Mumbai 400061, Maharastra, India
| | - S Samanta
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, India
| | - C M Roshith
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, India
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Sahoo S, Saha A, Vijaykumar ME, Khan MF, Samanta S, Mol SS, Das BK. Assessment of water quality of Netravathi-Gurupur estuary, India through chemometric approach for fisheries sustainability. Mar Pollut Bull 2024; 200:116043. [PMID: 38278014 DOI: 10.1016/j.marpolbul.2024.116043] [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: 08/29/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/28/2024]
Abstract
The present study aimed to assess the water quality dynamics (physicochemical properties, nutrient and chlorophyll-a) in the Netravathi-Gurupur estuary, India across the space and seasons and to simplify the complex water quality dataset through a chemometric approach. The results indicated that pH, EC, temperature, alkalinity, salinity, TDS, hardness, chloride and intense mixing of suspended solids, driven by the semidiurnal tides, are the major factors affecting water quality. Spatial heterogeneity and monsoon have profound impact on nutrient distribution revealing the following values (mg l-1): phosphate-P (0.015-0.105), nitrate-N (0.016-0.094), nitrite-N (0.001-0.012), and silicate (1.83-14.50). The estuary was evaluated for suitability for brackish water fisheries. The results indicated fair water quality during pre- and post-monsoon but marginal quality in monsoon, primarily due to dilution associated with reduced salinity. The outcome of this study can be suitably utilized for the sustainable development of estuaries and their feasibility for brackish water fisheries.
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Affiliation(s)
- Sonalika Sahoo
- Regional Centre of ICAR-Central Inland Fisheries Research Institute, Bangalore 560 089, India
| | - Ajoy Saha
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India.
| | - M E Vijaykumar
- Regional Centre of ICAR-Central Inland Fisheries Research Institute, Bangalore 560 089, India
| | - M Feroz Khan
- Regional Centre of ICAR-Central Inland Fisheries Research Institute, Bangalore 560 089, India
| | - S Samanta
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India
| | - Sibina S Mol
- Regional Centre of ICAR-Central Inland Fisheries Research Institute, Bangalore 560 089, India
| | - B K Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India
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Sk MF, Samanta S, Poddar S, Kar P. Microsecond dynamics of H10N7 influenza neuraminidase reveals the plasticity of loop regions and drug resistance due to the R292K mutation. J Comput Chem 2024; 45:247-263. [PMID: 37787086 DOI: 10.1002/jcc.27234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/12/2023] [Accepted: 09/14/2023] [Indexed: 10/04/2023]
Abstract
At the beginning of the last century, multiple pandemics caused by influenza (flu) viruses severely impacted public health. Despite the development of vaccinations and antiviral medications to prevent and control impending flu outbreaks, unforeseen novel strains and continuously evolving old strains continue to represent a serious threat to human life. Therefore, the recently identified H10N7, for which not much data is available for rational structure-based drug design, needs to be further explored. Here, we investigated the structural dynamics of neuraminidase N7 upon binding of inhibitors, and the drug resistance mechanisms against the oseltamivir (OTV) and laninamivir (LNV) antivirals due to the crucial R292K mutation on the N7 using the computational microscope, molecular dynamics (MD) simulations. In this study, each system underwent long 2 × 1 μs MD simulations to answer the conformational changes and drug resistance mechanisms. These long time-scale dynamics simulations and free energy landscapes demonstrated that the mutant systems showed a high degree of conformational variation compared to their wildtype (WT) counterparts, and the LNV-bound mutant exhibited an extended 150-loop conformation. Further, the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculation and MM/GBSA free energy decomposition were used to characterize the binding of OTV and LNV with WT, and R292K mutated N7, revealing the R292K mutation as drug-resistant, facilitated by a decline in binding interaction and a reduction in the dehydration penalty. Due to the broader binding pocket cavity of the smaller K292 mutant residue relative to the wildtype, the drug carboxylate to K292 hydrogen bonding was lost, and the area surrounding the K292 residue was more accessible to water molecules. This implies that drug resistance could be reduced by strengthening the hydrogen bond contacts between N7 inhibitors and altered N7, creating inhibitors that can form a hydrogen bond to the mutant K292, or preserving the closed cavity conformations.
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Affiliation(s)
- Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Sunanda Samanta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Sayan Poddar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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Sk MF, Samanta S, Poddar S, Kar P. Deciphering the molecular choreography of Janus kinase 2 inhibition via Gaussian accelerated molecular dynamics simulations: a dynamic odyssey. J Comput Aided Mol Des 2024; 38:8. [PMID: 38324213 DOI: 10.1007/s10822-023-00548-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/24/2023] [Indexed: 02/08/2024]
Abstract
The Janus kinases (JAK) are crucial targets in drug development for several diseases. However, accounting for the impact of possible structural rearrangements on the binding of different kinase inhibitors is complicated by the extensive conformational variability of their catalytic kinase domain (KD). The dynamic KD contains mainly four prominent mobile structural motifs: the phosphate-binding loop (P-loop), the αC-helix within the N-lobe, the Asp-Phe-Gly (DFG) motif, and the activation loop (A-loop) within the C-lobe. These distinct structural orientations imply a complex signal transmission path for regulating the A-loop's flexibility and conformational preference for optimal JAK function. Nevertheless, the precise dynamical features of the JAK induced by different types of inhibitors still remain elusive. We performed comparative, microsecond-long, Gaussian accelerated molecular dynamics simulations in triplicate of three phosphorylated JAK2 systems: the KD alone, type-I ATP-competitive inhibitor (CI) bound KD in the catalytically active DFG-in conformation, and the type-II inhibitor (AI) bound KD in the catalytically inactive DFG-out conformation. Our results indicate significant conformational variations observed in the A-loop and αC helix motions upon inhibitor binding. Our studies also reveal that the DFG-out inactive conformation is characterized by the closed A-loop rearrangement, open catalytic cleft of N and C-lobe, the outward movement of the αC helix, and open P-loop states. Moreover, the outward positioning of the αC helix impacts the hallmark salt bridge formation between Lys882 and Glu898 in an inactive conformation. Finally, we compared their ligand binding poses and free energy by the MM/PBSA approach. The free energy calculations suggested that the AI's binding affinity is higher than CI against JAK2 due to an increased favorable contribution from the total non-polar interactions and the involvement of the αC helix. Overall, our study provides the structural and energetic insights crucial for developing more promising type I/II JAK2 inhibitors for treating JAK-related diseases.
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Affiliation(s)
- Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, MP, 453552, India
- Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, NIH Resource for Macromolecular Modeling and Visualization, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sunanda Samanta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, MP, 453552, India
| | - Sayan Poddar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, MP, 453552, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, MP, 453552, India.
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Saha A, Das BK, Sarkar DJ, Samanta S, Vijaykumar ME, Khan MF, Kayal T, Jana C, Kumar V, Gogoi P, Chowdhury AR. Trace metals and pesticides in water-sediment and associated pollution load indicators of Netravathi-Gurupur estuary, India: Implications on coastal pollution. Mar Pollut Bull 2024; 199:115950. [PMID: 38183833 DOI: 10.1016/j.marpolbul.2023.115950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/15/2023] [Accepted: 12/15/2023] [Indexed: 01/08/2024]
Abstract
Various environmental indicators were used to evaluate the water and sediment quality of the Netravathi-Gurupur estuary, India, for trace metals and pesticide pollution. The descended order of studied metal concentrations (μg/L) in the water was Fe (592.71) > Mn (98.35) > Zn (54.69) > Cu (6.64) > Cd (3.24) > Pb (2.38) > Cr (0.82) and in sediment (mg/kg) was Fe (11,396.53) > Mn (100.61) > Cr (75.41) > Zn (20.04) > Cu (12.77) > Pb (3.46) > Cd (0.02). However, pesticide residues were not detected in this estuarine environment. The various metal indexes categorised the water as uncontaminated, whereas contamination factor, enrichment factor, geo-accumulation index, degree of contamination and pollution load index indicated low to moderate sediment contamination. Multivariate statistics showed that the dominance of natural sources of trace metals with little anthropogenic impact. Improvement in water/sediment quality during the study period might be due to COVID-19 imposed lockdown.
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Affiliation(s)
- Ajoy Saha
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India.
| | - B K Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India
| | - D J Sarkar
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India
| | - S Samanta
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India
| | - M E Vijaykumar
- Regional Centre of ICAR-Central Inland Fisheries Research Institute, Bangalore 560 089, India
| | - M Feroz Khan
- Regional Centre of ICAR-Central Inland Fisheries Research Institute, Bangalore 560 089, India
| | - Tania Kayal
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India
| | - Chayna Jana
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India
| | - Vikas Kumar
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India
| | - Pranab Gogoi
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India
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Liu C, Zhang Y, Li P, Jia H, Ju H, Zhang J, Ferreira da Silva-Júnior E, Samanta S, Kar P, Huang B, Liu X, Zhan P. Development of chalcone-like derivatives and their biological and mechanistic investigations as novel influenza nuclear export inhibitors. Eur J Med Chem 2023; 261:115845. [PMID: 37804770 DOI: 10.1016/j.ejmech.2023.115845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/09/2023]
Abstract
Concerning the emergence of resistance to current anti-influenza drugs, our previous phenotypic-based screening study identified the compound A9 as a promising lead compound. This chalcone analog, containing a 2,6-dimethoxyphenyl moiety, exhibited significant inhibitory activity against oseltamivir-resistant strains (H1N1 pdm09), with an EC50 value of 1.34 μM. However, it also displayed notable cytotoxicity, with a CC50 value of 41.46 μM. Therefore, compound A9 was selected as a prototype structure for further structural optimization in this study. Initially, it was confirmed that the substituting the α,β-unsaturated ketone with pent-1,4-diene-3-one as a linker group significantly reduced the cytotoxicity of the final compounds. Subsequently, the penta-1,4-dien-3-one group was utilized as a privileged fragment for further structural optimization. Following two subsequent rounds of optimizations, we identified compound IIB-2, which contains a 2,6-dimethoxyphenyl- and 1,4-pentadiene-3-one moieties. This compound exhibited inhibitory effects on oseltamivir-resistant strains comparable to its precursor (compound A9), while demonstrating reduced toxicity (CC50 > 100 μM). Furthermore, we investigated its mechanism of action against anti-influenza virus through immunofluorescence, Western blot, and surface plasmon resonance (SPR) experiments. The results revealed that compound IIB-2 can impede virus proliferation by blocking the export of influenza virus nucleoprotein. Thusly, our findings further emphasize influenza nuclear export as a viable target for designing novel chalcone-like derivatives with potential inhibitory properties that could be explored in future lead optimization studies.
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Affiliation(s)
- Chuanfeng Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China; Suzhou Research Institute of Shandong University, Room607, Building B of NUSP, NO.388 Ruoshui Road, SIP, Suzhou, Jiangsu, 215123, PR China
| | - Ying Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Ping Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China; Innovation Research Institute of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Huinan Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Han Ju
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Jiwei Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Edeildo Ferreira da Silva-Júnior
- Research Group of Biological and Molecular Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões Campus, 57072-970, Alagoas, Maceió, Brazil
| | - Sunanda Samanta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore, 453552, Madhya Pradesh, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore, 453552, Madhya Pradesh, India.
| | - Bing Huang
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
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Kashyap D, Koirala S, Roy R, Saini V, Varshney N, Bagde PH, Samanta S, Kar P, Jha HC. Computational insights into VacA toxin inhibition: harnessing FDA-approved antibiotics against Helicobacter pylori. J Biomol Struct Dyn 2023:1-13. [PMID: 37937550 DOI: 10.1080/07391102.2023.2278080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
Cancer is a condition in which a few of the body's cells grow beyond its control and spread to other outward regions. Globally, gastric cancer (GC) is third most common cause of cancer-related mortality and the fourth most common kind of cancer. Persistent infection of VacA-positive Helicobacter pylori (H. pylori) modulates cellular physiology and leads to GC. About ∼70% of H. pylori are positive for vacuolating cytotoxin-A (VacA), and it infects ∼80-90% of world populations. Herein, for first time, we repurposed FDA-approved gram-negative antibiotics, which are feasible alternatives to existing regimens and may be used in combinatorial treatment against VacA-positive H. pylori. Out of 110 FDA-approved antibiotics, we retrieved 92 structures, which were screened against the VacA protein. Moreover, we determined that the top eight hit antibiotics viz; cefpiramide, cefiderocol, eravacycline, doxycycline, ceftriaxone, enoxacin, tedizolid, and cefamandole show binding free energies of -9.1, -8.9, -8.1, -8.0, -7.9, -7.8, -7.8 and -7.8 Kcal/mol, respectively, with VacA protein. Finally, we performed 100 ns duplicate MD simulations on the top eight selected antibiotics showing strong VacA binding. Subsequently, five antibiotics, including cefiderocol, cefpiramide, doxycycline, enoxacin, and tedizolid show stable ligand protein distance and good binding affinity revealed by the MM-PBSA scheme. Among the five antibiotics cefiderocol act as the most potent inhibitor (-28.33 kcal/mol). Furthermore, we also identified the hotspot residue like Asn-506, Tyr-529, and Phe-483 which control the interaction. Concisely, we identified antibiotics that can be repurposed against VacA of H. pylori and explored their molecular mechanism of interaction with VacA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dharmendra Kashyap
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Suman Koirala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Rajarshi Roy
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Vaishali Saini
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Nidhi Varshney
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Pranit Hemant Bagde
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Sunanda Samanta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
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9
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Koirala S, Samanta S, Mahapatra S, Ursal KD, Poddar S, Kar P. Molecular level investigation for identifying potential inhibitors against thymidylate kinase of monkeypox through in silico approaches. J Biomol Struct Dyn 2023:1-14. [PMID: 37909473 DOI: 10.1080/07391102.2023.2274982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
The need for more advanced and effective monkeypox (Mpox) treatments has become evident with numerous Mpox virus (MPXV) outbreaks. Over the years, interest has increased in developing targeted medicines that are efficient, safe, and precise while avoiding adverse effects. Here, we screened 32409 compounds against thymidylate kinase (TMPK), an emerging target for Mpox treatment. We studied their pharmacological characteristics and analyzed those through all-atom molecular dynamics simulations followed by molecular mechanics Poisson Boltzmann surface area (MM-PBSA) based free energy calculations. According to our findings, the leads CID40777874 and CID28960001 had the highest binding affinities towards TMPK with ΔGbind of -8.04 and -5.58 kcal/mol, respectively, which outperformed our control drug cidofovir (ΔGbind = -2.92 kcal/mol) in terms of binding favourability. Additionally, we observed crucial TMPK dynamics brought on by ligand-binding and identified key residues such as Phe68 and Tyr101 as the critical points of the protein-ligand interaction. The DCCM analysis revealed the role of ligand binding in stabilizing TMPK's binding region, as indicated by residual correlation motions. Moreover, the PSN analysis revealed that the interaction with ligand induces changes in residual network properties, enhancing the stability of complexes. We successfully identified novel compounds that may serve as potential building blocks for constructing contemporary antivirals against MPXV and highlighted the molecular mechanisms underlying their binding with TMPK. Overall, our findings will play a significant role in advancing the development of new therapies against Mpox and facilitating a comprehensive understanding of their interaction patterns.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suman Koirala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Sunanda Samanta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Subhasmita Mahapatra
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Kapil Dattatray Ursal
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Sayan Poddar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
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Samanta S, Sk MF, Koirala S, Kar P. Exploring molecular interactions of potential inhibitors against the spleen tyrosine kinase implicated in autoimmune disorders via virtual screening and molecular dynamics simulations. SAR QSAR Environ Res 2023:1-29. [PMID: 37881946 DOI: 10.1080/1062936x.2023.2266364] [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] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/19/2023] [Indexed: 10/27/2023]
Abstract
The spleen tyrosine kinase (Syk) plays a pivotal role in immune cells' signal transduction mechanism. While fostamatinib, an FDA-approved Syk inhibitor, is currently used to treat immune thrombocytopenia, the search for improved Syk-targeted medications to treat autoimmune diseases is still underway. Herein, we screened 38,493 compounds against Syk and selected eight leads based on the docking score and ADMET properties, and performed 3× 200 ns long molecular dynamics simulations of the apo and Syk-ligand complexes. We considered R406, the active component of fostamatinib, as a control. The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations demonstrated the lead1 (Δ G b i n d = -30.35 kcal/mol) exhibited a similar binding free energy as the control (Δ G b i n d = -29.82 kcal/mol). The Syk stabilizing effect of lead1 was also indicated in its network features, sampling space, and residual correlation motion analysis. We further generated 100 structural analogues of lead1 using deep learning, and one of the analogues displayed a better binding free energy (Δ G b i n d = -47.58 kcal/mol) compared to the control or lead1, facilitated by more favourable van der Waals interactions and lesser binding-opposing net polar forces. This analogue may be further exploited to develop effective therapeutics against Syk-associated diseases after validation in vitro and in vivo.
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Affiliation(s)
- S Samanta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Madhya Pradesh, India
| | - M F Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Madhya Pradesh, India
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - S Koirala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Madhya Pradesh, India
| | - P Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Madhya Pradesh, India
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Megahed RJ, Samanta S, Patel M, Kesaria AZ, Wang K, Lewis GD. A Single Institution Experience of a Biweekly Head and Neck Contouring Peer Review. Int J Radiat Oncol Biol Phys 2023; 117:e416. [PMID: 37785373 DOI: 10.1016/j.ijrobp.2023.06.1566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Due to the complexity of head and neck radiotherapy, a single weekly chart rounds session is insufficient to review contours. A dedicated biweekly review of all head and neck contours (prior to treatment planning) that can fully assess images and targets can lead to better patient outcomes. A full review of all head and neck contours also increases the number of contours that resident physicians can observe. MATERIALS/METHODS In total, 38 consecutive patients treated between August 2022 and December 2022 were analyzed in a biweekly head and neck contouring peer review. Three head and neck faculty radiation oncologists and four resident physicians participated. An allotted 30-minute time was granted per review session. Changes were tracked and stratified by whether physician contours underwent no changes/minor changes/major changes. Other metrics including re-irradiation status and attendance were noted. RESULTS An average of 1.65 patients were discussed per review. Given the allotted time, on average this allowed for up to 18 minutes of discussion per patient. In contrast, our departmental chart rounds session is allotted 1 hour for 40+ patients to be discussed (1.5 minutes per patient). Overall, 10/38 patients underwent minor changes (26.3%) to contour structures and 1 patient underwent a major change (2.6%). Four patients (10.5%) were re-irradiation cases CONCLUSION: A dedicated biweekly half hour review session is both feasible and practical. Additional discussion of head and neck contours helps to implement improvements into a patient's treatment plan. Additional discussion and debate for primary and re-irradiation also increases the number of cases that a training resident physician can observe.
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Affiliation(s)
- R J Megahed
- Department of Radiation Oncology, UAMS Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR
| | - S Samanta
- Department of Radiation Oncology, UAMS Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR
| | - M Patel
- Department of Radiation Oncology, UAMS Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR
| | - A Z Kesaria
- Department of Radiation Oncology, UAMS Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR
| | - K Wang
- Department of Radiation Oncology, UAMS Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR
| | - G D Lewis
- Department of Radiation Oncology, UAMS Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR
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Samanta S, Kesaria AZ, Kalantari F, Mian M, Prior FW, Xia F, Lewis GD. Analysis of the Cancer Imaging Archive for Patterns of Locoregional Failure in Relation to the Mucous Membranes among Patients with Head and Neck Squamous Cell Carcinoma: Potential Organ at Risk that can be Spared? Int J Radiat Oncol Biol Phys 2023; 117:e622-e623. [PMID: 37785864 DOI: 10.1016/j.ijrobp.2023.06.2008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Radiation-induced oral mucositis (RIOM), a painful inflammation and ulceration of the mucous membranes (MM), occurs as a common and severe side effect of radiation treatment (RT) for head and neck cancers. It worsens significant quality of life leading to treatment interruption or cancellation. In RIOM, radiation injury of the MM basal epithelial cells may be one of the critical pathophysiological mechanisms. However, it is unclear if advanced radiation treatments could spare MM, without compromise on tumor control. The purpose of this study is to determine whether the MM that do not overlap with the prescription target volumes are a common site of locoregional recurrence in head and neck cancers. MATERIALS/METHODS A de-identified data collection of 215 head and neck cancer patients stored within The Cancer Imaging Archive was downloaded for analysis. Imaging series both before and after RT were downloaded, as well as RT structures and RT dosimetric data. Diagnostic CECT and/or PET/CT and/or MRI scans documenting the initial evidence of recurrence were co-registered with corresponding original planning CTs. Radiologically evident recurrent gross disease (rGTV) was manually contoured, as well as the MM (defined as an approximately 3mm thick wall of mucosa tissue lining the oral cavity and pharynx and excluding any overlap with the radiation prescription targets). Contoured MM structures were cross-referenced with the sites of recurrence by examining the overlap of the MM volumes with the rGTV volumes. RESULTS A total of 40 patients had documented evidence of recurrence; 38 of which had images available for analysis. Overall, 23 (60.5%) were oropharynx cancer. Of the 38 recurrences, 35 (92%) were locoregional: 23 with only local (60.5%) recurrences, 9 with only regional (23.7%) recurrences and 3 (7.9%) with both local and regional recurrences. One patient (2.6%) had distant recurrence, one patient had both regional and distant recurrences concomitantly, and one patient had local, regional and distant recurrences simultaneously. Overall, 30 patients (78.9%) had recurrences located exclusively within prescription PTV volumes/isodose lines. Four patients (10.5%) had recurrences located outside prescription PTV volumes/isodose lines, four patients (10.5%) had recurrences located both within and outside prescription PTV volumes/isodose lines (i.e., 2 sites of concomitant recurrence). Importantly, 0 patients (0%) had recurrences located in the contoured MM (excluding any overlap with the radiation prescription targets). CONCLUSION Based on this retrospective series, the MM (excluding the areas of overlap with radiation prescription targets) are a rare location of locoregional recurrence. Hence, sparing the MM using radiation advanced dosimetry techniques could be a reasonable approach to reducing the incidence/severity of radiation-induced oral mucositis, without compromising tumor control. However, this requires further prospective investigation.
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Affiliation(s)
- S Samanta
- Department of Radiation Oncology, UAMS Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR
| | - A Z Kesaria
- Department of Radiation Oncology, UAMS Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR
| | - F Kalantari
- University of Arkansas for Medical Sciences, Little Rock, AR
| | - M Mian
- University of Arkansas for Medical Sciences, Little Rock, AR
| | - F W Prior
- University of Arkansas for Medical Sciences, Little Rock, AR
| | - F Xia
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR
| | - G D Lewis
- Department of Radiation Oncology, UAMS Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR
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Koirala S, Roy R, Samanta S, Mahapatra S, Kar P. Plant derived active compounds of ayurvedic neurological formulation, Saraswatharishta as a potential dual leucine zipper kinase inhibitor: an in-silico study. J Biomol Struct Dyn 2023:1-14. [PMID: 37771163 DOI: 10.1080/07391102.2023.2260892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023]
Abstract
Recent findings have highlighted the essential role of dual leucine zipper kinase (DLK) in neuronal degeneration. Saraswatharishta (SWRT), an ayurvedic formulation utilized in traditional Indian medicine, has demonstrated effectiveness in addressing neurodegenerative diseases. Herein, we aim to delve into the atomistic details of the mode of action of phytochemicals present in SWRT against DLK. Our screening process encompassed over 500 distinct phytochemicals derived from the main ingredients of the SWRT formulation. Through a comparative analysis of docking scores and relative poses, we successfully identified four novel compounds, which underwent further investigation via 2 × 500 ns long molecular dynamics (MD) simulations. Among the top four compounds, CID16066851 sourced from the Acorus calamus displayed the most stable complex with DLK. The molecular mechanics Poisson - Boltzmann surface area (MM-PBSA) calculations highlighted the significance of electrostatic and van der Waals interactions in the binding recognition process. Additionally, we identified key residues, namely Phe192, Leu243, Val139, and Leu141, as hotspots that predominantly govern the DLK-inhibitor interaction. Notably, the leading compounds are sourced from the Acorus calamus, Syzygium aromaticum, Zingiber officinale, and Anethum sowa plants present in the SWRT formulation. Overall, the findings of our study hold promise for future drug development endeavors combating neurodegenerative conditions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suman Koirala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Rajarshi Roy
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Sunanda Samanta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Subhasmita Mahapatra
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
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Anandu S, Chaithra SN, Manjusha KM, Tiwari VK, Tewari AK, Tanuj GN, Samanta S, Sankar M. First report of molecular confirmation and phylogenetic analysis of ocular seteriasis in buffalo in India using 12S rRNA. J Helminthol 2023; 97:e70. [PMID: 37665112 DOI: 10.1017/s0022149x23000512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
An adult Indian buffalo (Bubalus bubalis) presented with corneal opacity, irritation, and excessive lacrimation from the left eye in the Referral Veterinary Polyclinic-Teaching Veterinary Clinical Complex (RVC-TVCC), Indian Veterinary Research Institute, Izatnagar. Clinical examination revealed a whitish thread-like worm in the left eye's anterior chamber. The worm was surgically removed from the eye with supportive nerve blocks. Light microscopy was used for parasite morphological identification, which provided insight into the worm as female Setaria sp. Genomic DNA was isolated, and polymerase chain reaction amplification of 12S rRNA was conducted for molecular confirmation of the parasite. The amplicon was sequenced and analysed by bioinformatics software. Sequence data showed an amplicon size of 243 bp. Phylogenetic analysis with reference data from the NCBI Genbank database revealed the worm was S. digitata, with a similarity of 99.17%. The common predilection site of S. digitata is in the peritoneal cavity of natural hosts like cattle and buffalo and is mostly non-pathogenic. The aberrant migration of the parasite larva to the brain and eye commonly occurs in goats, sheep, and horses, causing clinical conditions like cerebrospinal nematodiasis (lumbar paralysis) and ocular setariasis, respectively. Nevertheless, until now, there have been no reports of ocular setariasis in buffalo. This report is the first unusual occurrence of ocular setariasis in buffalo and its molecular confirmation and phylogenetic analysis using 12S rRNA.
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Affiliation(s)
- S Anandu
- Division of Parasitology, Indian Veterinary Research Institute, Uttar Pradesh, India
| | - S N Chaithra
- Division of Surgery, Indian Veterinary Research Institute, Uttar Pradesh, India
| | - K M Manjusha
- Division of Surgery, Indian Veterinary Research Institute, Uttar Pradesh, India
| | - V K Tiwari
- Division of Parasitology, Indian Veterinary Research Institute, Uttar Pradesh, India
| | - A K Tewari
- Division of Parasitology, Indian Veterinary Research Institute, Uttar Pradesh, India
| | - G N Tanuj
- Division of Animal Biotechnology, Indian Veterinary Research Institute, Uttar Pradesh, India
| | - S Samanta
- Division of Parasitology, Indian Veterinary Research Institute, Uttar Pradesh, India
| | - M Sankar
- Division of Parasitology, Indian Veterinary Research Institute, Uttar Pradesh, India
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Kashyap D, Koirala S, Saini V, Bagde PH, Samanta S, Kar P, Jha HC. Prediction of Rab5B inhibitors through integrative in silico techniques. Mol Divers 2023:10.1007/s11030-023-10693-9. [PMID: 37505376 DOI: 10.1007/s11030-023-10693-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023]
Abstract
Rab5B is a small monomeric G protein that regulates early endocytosis and controls signaling pathways related to cell growth, survival, and apoptosis. Dysregulation of Rab5B protein expression has been linked to the development of several cancers such as leukemia, lymphoma, kidney, prostate, ovarian, breast cancer, etc. Our research shows the first attempt to identify inhibitors that can target Rab5B GTPase. In this study, we performed molecular docking using Autodock Vina 1.5.6 and identified eight molecules with docking scores ranging from -9.8 to -10.6 kcal/mol. Thereafter, we examined the pharmacological characteristics of these compounds, and selected compounds were further analyzed for their conformational dynamics and thermodynamic stability using molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA)-based free energy calculations. Notably, our findings revealed that strychnine had the highest binding affinity to Rab5B followed by anonaine, helioxanthin, and taiwanin E, with a ΔGbind value of -21.43, -17.11, -15.11, and -14.09 kcal/mol respectively. The binding free energy calculations showed that Van der Waals interactions are the primary contributor to the binding between Rab5B and the inhibitor. The interaction between the inhibitor and Rab5B was shown to be controlled by certain hot spot residues, including Phe45, Tyr48, Ala64, and Ala30. Overall, we believe that these findings could facilitate the exploration and development of potential hits against Rab5B, subject to optimization and further research. Rab5B inhibitory binding affinity of natural plants active compounds.
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Affiliation(s)
- Dharmendra Kashyap
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Suman Koirala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Vaishali Saini
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Pranit Hemant Bagde
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Sunanda Samanta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India.
- Lab No. POD 1B 502, Computational Biophysics Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India.
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India.
- Lab No. POD 1B 602, Infection Bio-Engineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India.
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Abhiram S, Mondal T, Samanta S, Batabyal K, Joardar SN, Samanta I, Isore DP, Dey S. Occurrence of canine parvovirus type 2c in diarrhoeic faeces of dogs in Kolkata, India. Virusdisease 2023; 34:339-344. [PMID: 37408551 PMCID: PMC10317913 DOI: 10.1007/s13337-023-00817-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/19/2023] [Indexed: 07/07/2023] Open
Abstract
Canine parvovirus-2(CPV-2) causes a highly contagious disease of dogs characterised by acute hemorrhagic gastroenteritis, lethargy, vomiting, fever and usually bloody or mucoid diarrhoea. In the present study, 41 faecal samples collected from dogs exhibiting the signs of fever, vomition, bloody or mucoid diarrhoea in Kolkata, India were screened by haemagglutination test and PCR for detection of capsid protein coding VP2 gene. The viral genotype was detected by multiplex PCR and analysis of partial VP2 gene nucleotide sequences of selected PCR products with bioinformatics tool. Thirteen (31.71%) samples were found positive with HA titre ≥ 32 whereas 28 (68.29%) samples were positive by PCR of VP2 gene indicating higher sensitivity of PCR. Highest occurrence of CPV-2 was observed in the age group of 1-6 months (80.65%) and non-descript breeds with no history of vaccination (85%). Three samples were antigenic type CPV-2a, rest were CPV-2b/CPV 2c. Six CPV sequences were found to be highly similar to published CPV 2c sequences in BLAST analysis revealing a maximum identity of 99-100% with other CPV-2c strains and clustered together with CPV-2c strains of India and other countries in phylogenetic analysis. The present study highlights the need for continuous monitoring of samples to detect gradual changes in circulating CPV-2 genotypes in India.
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Affiliation(s)
- S. Abhiram
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences (WBUAFS) , Belgachia, Kolkata, 700037 India
| | - T. Mondal
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences (WBUAFS) , Belgachia, Kolkata, 700037 India
| | - S. Samanta
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences (WBUAFS) , Belgachia, Kolkata, 700037 India
| | - K. Batabyal
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences (WBUAFS) , Belgachia, Kolkata, 700037 India
| | - S. N. Joardar
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences (WBUAFS) , Belgachia, Kolkata, 700037 India
| | - I. Samanta
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences (WBUAFS) , Belgachia, Kolkata, 700037 India
| | - D. P. Isore
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences (WBUAFS) , Belgachia, Kolkata, 700037 India
| | - S. Dey
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences (WBUAFS) , Belgachia, Kolkata, 700037 India
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Yashica KA, Samanta S, Balaji R, Jawalagatti V, Silamparasan M, Anandu S, Rialch A, Gupta SC, Tewari AK. Molecular characterization and serodiagnostic evaluation of the Echinococcus ortleppi recombinant glutaredoxin 1 protein for cystic echinococcosis in buffalo (Bubalus bubalis). Vet Parasitol 2023; 319:109941. [PMID: 37156090 DOI: 10.1016/j.vetpar.2023.109941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/22/2023] [Accepted: 04/30/2023] [Indexed: 05/10/2023]
Abstract
Cystic echinococcosis (CE), caused by the metacestode of Echinococcus granulosus sensu lato (s.l.), adversely affects the physiology of the vital organs in which they grow. Condemnation of meat causes substantial economic loss to the livestock industry. Conventionally the infection is detected by necropsy as serological diagnosis of the infection in livestock is ambiguous. Identification of specific diagnostic antigens would be a substitute for the cyst fluid antigens which lack adequate diagnostic sensitivity and specificity. BLAST analysis supported by the negligible pairwise nucleotide distance of the 389 nt COX1, 489 nt NAD1, and 425 nt ITS1 with the related sequences of E. ortleppi ascertained the association of E. ortleppi with CE in buffaloes. Given the extensive distribution of glutaredoxin 1 in every developmental stage of Echinococcus granulosus s.l that makes it an ideal serodiagnostic antigen for CE, we expressed the 14 kDa E. ortleppi glutaredoxin 1 (rEoGrx1) protein in E. coli BL21 (DE3) and tested a total of 225 sera samples, including 126 sera samples from the necropsy-positive buffalo, by the rEoGrx1 IgG-ELISA. The ELISA could detect a total of 82/126 sera samples as positive. The diagnostic sensitivity and specificity of the rEoGrx1 IgG-ELISA were 65.1 % and 51.5 %, respectively. The protein showed serological cross-reaction against Fasciola gigantica, Toxoplasma gondii, and Sarcocystis sp. The in silico bioinformatics analysis of the E. ortleppi, F. gigantica, and T. gondii glutaredoxin sequences revealed fully conserved amino acids at positions 11 and 21, the substitution of conserved amino acids at positions 14 and 6, and semi-conserved substitutions at positions 3 and 4, respectively. The findings partly explain the molecular basis of the serological cross-reactivity of the protein.
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Affiliation(s)
- K A Yashica
- Division of Parasitology, ICAR, Indian Veterinary Research Institute, Izatnagar 243122, Uttar Pradesh, India
| | - S Samanta
- Division of Parasitology, ICAR, Indian Veterinary Research Institute, Izatnagar 243122, Uttar Pradesh, India
| | - R Balaji
- Division of Parasitology, ICAR, Indian Veterinary Research Institute, Izatnagar 243122, Uttar Pradesh, India
| | - V Jawalagatti
- Division of Parasitology, ICAR, Indian Veterinary Research Institute, Izatnagar 243122, Uttar Pradesh, India
| | - M Silamparasan
- Division of Parasitology, ICAR, Indian Veterinary Research Institute, Izatnagar 243122, Uttar Pradesh, India
| | - S Anandu
- Division of Parasitology, ICAR, Indian Veterinary Research Institute, Izatnagar 243122, Uttar Pradesh, India
| | - A Rialch
- ICAR, Indian Veterinary Research Institute, Regional Station, Palampur 176061, Himachal Pradesh, India
| | - S C Gupta
- Division of Parasitology, ICAR, Indian Veterinary Research Institute, Izatnagar 243122, Uttar Pradesh, India
| | - Anup Kumar Tewari
- Division of Parasitology, ICAR, Indian Veterinary Research Institute, Izatnagar 243122, Uttar Pradesh, India; ICAR, Indian Veterinary Research Institute, Regional Station, Palampur 176061, Himachal Pradesh, India.
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Saha A, Vijaykumar ME, Das BK, Samanta S, Khan MF, Kayal T, Jana C, Chowdhury AR. Geochemical distribution and forms of phosphorus in the surface sediment of Netravathi-Gurupur estuary, southwestern coast of India. Mar Pollut Bull 2023; 187:114543. [PMID: 36640498 DOI: 10.1016/j.marpolbul.2022.114543] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Estuaries are the most productive transition ecosystem and phosphorus (P) plays an important role in these ecosystems. Therefore, in the present study, sequential extraction method was used to determine the abundance of five sediment P fractions (calcium (Ca-P), Iron (FeP), aluminum (AlP), exchangeable (Ex-P) and organic (OrgP) bound P) in Netravathi-Gurupur estuary, India. Total phosphorus (TP) content varied from 435-810 mg/kg (non-monsoon) and 258-699 mg/kg (monsoon). Inorganic P was dominant part. Different P fractions followed similar order (Fe-P > Ca-P > Al-P > Org-P > Ex-P) with respect to seasons. FeP was dominant fraction, indicating probable anthropogenic stress. Sediment may act as source of P as bioavailable P constituted 40-69.2 % of TP. Molar ratio of OC to Org-P in sediment indicated terrestrial sources of organic matter. However, the estimated phosphorus pollution index were lower than one except a few cases indicating less ecological risk with respect to sedimentary TP load.
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Affiliation(s)
- Ajoy Saha
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India.
| | - M E Vijaykumar
- Regional Centre of ICAR-Central Inland Fisheries Research Institute, Bangalore 560 089, India
| | - B K Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India
| | - S Samanta
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India
| | - M Feroz Khan
- Regional Centre of ICAR-Central Inland Fisheries Research Institute, Bangalore 560 089, India
| | - Tania Kayal
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India
| | - Chayna Jana
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, India
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Samanta S, Chaudhuri AG. Guanylin and uroguanylin: a promising nexus in intestinal electrolyte and fluid homeostasis. J Physiol Pharmacol 2021; 72. [PMID: 35158329 DOI: 10.26402/jpp.2021.5.02] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/30/2021] [Indexed: 06/14/2023]
Abstract
Intestinal guanyl peptides like guanylin and uroguanylin are the potent regulators of fluid-ion homeostasis. They are secreted from various cells of the intestinal mucosa, including enterochromaffin cells, epithelial cells, goblet cells, Paneth cells and others. These peptide hormones serve as ligands for receptor guanylyl cyclase-C (GC-C), which produces intracellular cyclic guanosine monophosphate (cGMP) and activates protein kinase G II (PKGII). cGMP/PKGII activates cystic fibrosis transmembrane conductance regulator for anion transport to the intestinal lumen, inhibits Na+/H+ exchanger that restricts H+ secretion and Na+ absorption, resulting in the retention of luminal fluid. These functions maintain intestinal pH, prevents hypernatremia and unwanted hypervolemic shock. Additionally, fluid balance in the intestine preserves the hydrated state of the colonic mucus that influences the growth of the commensal microorganisms and bowel clearance. Moreover, GC-C/cGMP signaling is involved in the regulation of intestinal barrier integrity, epithelial cell renewal, cell cycle, DNA damage repair, inflammatory responses, epithelial-mesenchymal transition and cancer progression. Impairment of GC-C activation causes functional gastrointestinal disorders, inflammatory bowel disease, visceral pain and colorectal cancer, suggesting that oral supplementation of guanyl peptide analogs (linaclotide, plecanatide) may prove useful for the treatment of these diseases.
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Affiliation(s)
- S Samanta
- Department of Physiology, Midnapore College, Midnapore, West Bengal, India.
| | - A G Chaudhuri
- Department of Physiology, Vidyasagar College, Kolkata, West Bengal, India.
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Samanta S, Banerjee A, Roychoudhury A. Melatonin application differentially modulates the enzymes associated with antioxidative machinery and ascorbate-glutathione cycle during arsenate exposure in indica rice varieties. Plant Biol (Stuttg) 2021; 23 Suppl 1:193-201. [PMID: 32920948 DOI: 10.1111/plb.13181] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 08/04/2020] [Accepted: 09/02/2020] [Indexed: 05/03/2023]
Abstract
Arsenic (As) contamination and accumulation in rice is a serious concern causing severe oxidative damage. Melatonin acts as a protective agent in plant defence against multiple abiotic stresses. The mechanism of antioxidant function of melatonin during As stress in rice genotypes is less studied. In this study, hydroponically-grown As-susceptible (Khitish) and As-tolerant (Muktashri) rice cultivars, subjected to 150 µm arsenate stress, were supplemented with exogenously applied melatonin (20 µm) to examine the plant defence mechanism. Melatonin (Mel) increased root and shoot length, fresh and dry weight, chlorophyll a and b content and activated reducing power and free radical scavenging capacity in both rice cultivars. The role of Mel in the sensitive variety appeared to be more prominent with respect to reduced water saturation deficit by reducing endogenous As and H2 O2 accumulation, and enhancing overall antioxidant capacity by imposing reduced requirement of catalase for ROS detoxification, and restoring As-inhibited activity of glutathione-S-transferase, glutathione peroxidase and dehydroascorbate reductase. In contrast, melatonin treatment in the tolerant cultivar required reduced involvement of ascorbate peroxidase to deal with As toxicity, and complemented the stress-mediated inhibition of guaiacol peroxidase activity. Isozyme profiling also established extensive varietal differences with regard to induction of new isoform(s) by Mel during As treatment. This study provides clear insights into mechanistic details of the regulation of antioxidative enzymes by melatonin in contrasting rice genotypes, which may prove helpful in generating As tolerance in susceptible rice varieties grown in marginalized soils, thereby improving crop yield and productivity.
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Affiliation(s)
- S Samanta
- Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, West Bengal, India
| | - A Banerjee
- Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, West Bengal, India
| | - A Roychoudhury
- Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, West Bengal, India
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Samanta S, Kumar V, Nag SK, Raman RK, Saha K, Bandyopadhyay S, Mohanty BP, Das BK. Metal contaminations in sediment and associated ecological risk assessment of river Mahanadi, India. Environ Monit Assess 2021; 192:810. [PMID: 33443675 DOI: 10.1007/s10661-020-08708-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 10/25/2020] [Indexed: 06/12/2023]
Abstract
Mahanadi is one of the major rivers of peninsular India. Like other Indian rivers, it is contaminated with sewages, industrial discharges, and agricultural runoff. Thus, necessity was felt to monitor its pollution status. Present work was part of that program and aimed to assess the sediment contamination due to the trace metals Cd, Cr, Cu, Mn, Pb, and Zn during 2012-2015. Sediment pollution status and ecological risks were evaluated calculating contamination factor (CF), geo-accumulation (Igeo), pollution load index (PLI), potential ecological risk (EiR), etc. The recorded metal concentrations were Cd BDL of flame mode of AAS; Cr BDL - 73.9; Cu BDL - 44.4; Mn 37.2 - 1887.0; Pb BDL - 29.5; and Zn BDL - 92.5 mg kg-1. As per US EPA guidelines, Cr concentrations at many locations were in the moderately polluted range. Igeo, CF, mCd, PLI, and EiR indicated low pollution levels and low ecological risks due to the trace metals assessed. The sediment quality guidelines (SQGs) indicated that Cr and Cu concentrations exceeded (16% sample) the threshold effect concentrations and may occasionally exhibit adverse biological effects. The association of sediment organic matter, conductivity and content of Cu, and their grouping in component 1 of PCA revealed that the anthropogenic input was dominant and so also the component 2 where Cr exhibited moderately good correlation with organic matter. Cluster analysis of the sampling sites based on pollution status yielded 3 groups: relatively uncontaminated (S3, S4), low to moderately contaminated (S2), and moderately contaminated (S1, S5, S6) stretches.
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Affiliation(s)
- S Samanta
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India.
| | - Vikas Kumar
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India
| | - S K Nag
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India
| | - R K Raman
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India
| | - K Saha
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India
| | - S Bandyopadhyay
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India
| | - B P Mohanty
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India
| | - B K Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India
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Pollock A, Becker S, Lamichhane N, Guerrero M, Samanta S, Zhang B, Zakhary M, McAvoy S, Nichols E. Accelerated Partial Breast Irradiation (APBI): A Comparison Between a Breast-Specific Radiosurgery Device and Volumetric Modulated Arc Therapy (VMAT). Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Samanta S, Damron P, Poirier Y, Mao S, Lamichhane N, Dahiya S, Yared J, Rapoport A, Hardy N, Molitoris J, Kaiser A, Yi B, Mohindra P. Dose To Lungs And Kidneys During Total Body Irradiation: Are We Delivering The Expected Dose? Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Nandi S, Mukherjee G, Chen QB, Frauendorf S, Banik R, Bhattacharya S, Dar S, Bhattacharyya S, Bhattacharya C, Chatterjee S, Das S, Samanta S, Raut R, Ghugre SS, Rajbanshi S, Ali S, Pai H, Asgar MA, Das Gupta S, Chowdhury P, Goswami A. First Observation of Multiple Transverse Wobbling Bands of Different Kinds in ^{183}Au. Phys Rev Lett 2020; 125:132501. [PMID: 33034500 DOI: 10.1103/physrevlett.125.132501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/17/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
We report the first observation of two wobbling bands in ^{183}Au, both of which were interpreted as the transverse wobbling (TW) band but with different behavior of their wobbling energies as a function of spin. It increases (decreases) with spin for the positive (negative) parity configuration. The crucial evidence for the wobbling nature of the bands, dominance of the E2 component in the ΔI=1 transitions between the partner bands, is provided by the simultaneous measurements of directional correlation from the oriented states ratio and the linear polarization of the γ rays. Particle rotor model calculations with triaxial deformation reproduce the experimental data well. A value of spin, I_{m}, has been determined for the observed TW bands below which the wobbling energy increases and above which it decreases with spin. The nucleus ^{183}Au is, so far, the only nucleus in which both the increasing and the decreasing parts are observed and thus gives the experimental evidence of the complete transverse wobbling phenomenon.
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Affiliation(s)
- S Nandi
- Variable Energy Cyclotron Centre, 1/AF, Bidhan Nagar, Kolkata 700064, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - G Mukherjee
- Variable Energy Cyclotron Centre, 1/AF, Bidhan Nagar, Kolkata 700064, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Q B Chen
- Physik-Department, Technische Universität München, D-85747 Garching, Germany
| | - S Frauendorf
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - R Banik
- Variable Energy Cyclotron Centre, 1/AF, Bidhan Nagar, Kolkata 700064, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Soumik Bhattacharya
- Variable Energy Cyclotron Centre, 1/AF, Bidhan Nagar, Kolkata 700064, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Shabir Dar
- Variable Energy Cyclotron Centre, 1/AF, Bidhan Nagar, Kolkata 700064, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - S Bhattacharyya
- Variable Energy Cyclotron Centre, 1/AF, Bidhan Nagar, Kolkata 700064, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - C Bhattacharya
- Variable Energy Cyclotron Centre, 1/AF, Bidhan Nagar, Kolkata 700064, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - S Chatterjee
- UGC-DAE CSR, Kolkata Centre, Kolkata 700098, India
| | - S Das
- UGC-DAE CSR, Kolkata Centre, Kolkata 700098, India
| | - S Samanta
- UGC-DAE CSR, Kolkata Centre, Kolkata 700098, India
| | - R Raut
- UGC-DAE CSR, Kolkata Centre, Kolkata 700098, India
| | - S S Ghugre
- UGC-DAE CSR, Kolkata Centre, Kolkata 700098, India
| | - S Rajbanshi
- Department of Physics, Presidency University, Kolkata 700043, India
| | - Sajad Ali
- Government General Degree College at Pedong, Kalimpong 734311, India
| | - H Pai
- Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Md A Asgar
- Department of Physics, Prabhat Kumar College, Contai 721404, India
| | - S Das Gupta
- Victoria Institution (College), Kolkata 700009, India
| | - P Chowdhury
- University of Massachusetts Lowell, Lowell, Massachusetts 01854, USA
| | - A Goswami
- Saha Institute of Nuclear Physics, Kolkata 700064, India
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Banik R, Bhattacharyya S, Biswas S, Bhattacharya S, Mukherjee G, Rajbanshi S, Dar S, Nandi S, Ali R, Chatterjee S, Das S, Das Gupta S, Ghugre SS, Goswami A, Mondal D, Mukhopadhyay S, Pai H, Pal S, Pandit D, Raut R, Ray P, Samanta S. Exploring the structure of Xe isotopes in A ~ 130 region: Single particle and collective excitations. EPJ Web Conf 2020. [DOI: 10.1051/epjconf/202023204001] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
High and medium spin structures of 130,131Xe have been studied using α-induced fusion-evaporation reaction and the Indian National Gamma Array (INGA) coupled with a digital data acquisition system. Various new band structures and near yrast levels of 131Xe have been established. The multipolarities of the observed transitions have been assigned on the basis of the DCO ratios and the polarization asymmetry measurements. Band structures based on 1-quasi-particle (qp), 3-qp configurations have been observed. A new Magnetic Rotational (MR) band based on 5-qp configuration has also been established in 131Xe. The MR band has been interpreted in terms of shears mechanism with principal axis cranking (SPAC) calculations. Shell Model calculations are carried out to describe the non yrast states of 131Xe above the 11/2− isomer. New excited states have also been identified in 130Xe, produced in the same reaction.
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Snider J, Molitoris J, Rice S, DeCesaris C, Kowalski E, Siddiqui O, Samanta S, Rodrigues D, Sharma A, Smith V, Guerrero M, Chen S, Vujaskovic Z. Concurrent Superficial Thermal Therapy and Pencil Beam Scanning Proton Therapy: Initial Clinical Experience and Safety Profile. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Samanta S, Suresh S, Senthilnath J, Sundararajan N. A new Neuro-Fuzzy Inference System with Dynamic Neurons (NFIS-DN) for system identification and time series forecasting. Appl Soft Comput 2019. [DOI: 10.1016/j.asoc.2019.105567] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Samanta S, Rice S, Siddiqui O, DeCesaris C, Kowalski E, Rodrigues D, Molitoris J, Vujaskovic Z, Snider J, Nichols E. Concurrent External Thermal Therapy and Pencil Beam Scanning Proton Therapy or Photon/Electron Therapy for Recurrent Breast Cancer: Early Outcomes and Toxicity. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.2368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pandit A, Ekka A, Das BK, Samanta S, Chakraborty L, Raman RK. Fishers’ Livelihood Diversification in Bhagirathi–Hooghly Stretch of Ganga River in India. CURR SCI INDIA 2019. [DOI: 10.18520/cs/v116/i10/1748-1752] [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: 11/15/2022]
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Chaudhary N, Singh A, Aswal D, Jha P, Samanta S, Chauhan A, Debnath A, Acharya S, Shah K, Muthe K, Gadkari S. Electron beam induced modifications of polyaniline silver nano-composite films: Electrical conductivity and H2S gas sensing studies. Radiat Phys Chem Oxf Engl 1993 2018. [DOI: 10.1016/j.radphyschem.2018.09.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Samanta S, Creed M, Anvari A, Mahmood J, Kingsbury T, Sawant A. Novel Strategy to Develop Orthotopic Prostate Tumor using Androgen Dependent LNCaP Transduced with miR133b. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Mahmood J, Alexander A, Samanta S, Soman S, Shukla H, Davila E, Carrier F, Jackson I, Vujaskovic Z. Radiation Therapy in Combination with Hyperthermia and Immunotherapy Inhibit Pancreatic Tumor Growth and Modulate Tumor Microenvironment in Mice. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Samanta S, Modiri A, Rozario T, Yu J, Yan Y, Timmerman R, Sawant A. Virtual Bronchoscopy-Guided Dose Response Modeling of Airways to Mitigate Radiation-Induced Airway Injury in Lung SAbR. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.06.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Mease P, van der Heijde D, Ritchlin C, Cuchacovich R, Shuler C, Lin CY, Vangerow H, Samanta S, Lee C, Gladman D, Augendre-Ferrante B. Étude de phase 3 de l’ixékizumab versus adalimumab et placebo chez des patients atteints de rhumatisme psoriasique naïfs de DMARDS biologiques. Ann Dermatol Venereol 2016. [DOI: 10.1016/j.annder.2016.09.647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Hall C, Samanta S, Verma N, Gooptu B, Hurst JR. P136 Relationship between progression of lung disease in alpha-1 antitrypsin deficiency and cardiovascular risk. Thorax 2016. [DOI: 10.1136/thoraxjnl-2016-209333.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Coates L, Gottlieb A, Shuler C, Lin CY, Samanta S, Moriarty S, Lee C, Mease P. THU0441 Effect of Concomitant Conventional Disease-Modifying Antirheumatic Drugs (cDMARDs) on The Efficacy and Safety of Ixekizumab in Biologic Dmard-Naive Patients with Active Psoriatic Arthritis. Ann Rheum Dis 2016. [DOI: 10.1136/annrheumdis-2016-eular.1399] [Citation(s) in RCA: 2] [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]
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Cosman F, Gilchrist N, McClung M, Foldes J, de Villiers T, Santora A, Leung A, Samanta S, Heyden N, McGinnis JP, Rosenberg E, Denker AE. A phase 2 study of MK-5442, a calcium-sensing receptor antagonist, in postmenopausal women with osteoporosis after long-term use of oral bisphosphonates. Osteoporos Int 2016; 27:377-86. [PMID: 26556736 DOI: 10.1007/s00198-015-3392-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 10/28/2015] [Indexed: 01/05/2023]
Abstract
UNLABELLED In women with osteoporosis treated with alendronate for >12 months and oral bisphosphonates for >3 of the last 4 years, switching to MK-5442, a calcium receptor antagonist, stimulated endogenous parathyroid hormone (PTH) secretion and increased bone turnover marker levels, but produced a decline in bone mineral density (BMD) at all sites. INTRODUCTION This study assessed the effects of switching from long-term oral bisphosphonate therapy to the calcium-sensing receptor antagonist MK-5442 on BMD and bone turnover markers (BTMs) in post-menopausal women with osteoporosis. METHODS This randomized, active and placebo-controlled, dose-ranging study enrolled 526 postmenopausal women, who had taken alendronate (ALN) for ≥12 months preceding the trial and any oral bisphosphonate for ≥3 of the preceding 4 years and had spine or hip BMD T-scores ≤-2.5 or ≤-1.5 with ≥1 prior fragility fracture. Women were randomized to continue ALN 70 mg weekly or switch to MK-5442 (5, 7.5, 10, or 15 mg daily) or placebo. RESULTS Switching from ALN to MK-5442 produced a dose-dependent parathyroid hormone (PTH) pulse of threefold to sixfold above baseline at 1 h, with PTH levels that remained twofold to threefold above baseline at 4 h and returned to baseline by 24 h. Switching to MK-5442 or placebo increased BTM levels compared to baseline within 3 months and MK-5442 10 mg increased BTM levels compared to placebo by 6 months. With all MK-5442 doses and placebo, spine and hip BMD declined from baseline, and at 12 months, BMD levels were below those who continued ALN (all groups P < 0.05 vs ALN). There was also a dose-dependent increase in the incidence of hypercalcemia with MK-5442. CONCLUSION Switching from ALN to MK-5442 resulted in a pulsatile increase in PTH and increases in BTMs, but a decline in BMD compared with continued ALN. MK-5442 is not a viable option for the treatment of osteoporosis.
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Affiliation(s)
- F Cosman
- Helen Hayes Hospital, West Haverstraw, NY, USA.
- Department of Medicine, Columbia University, New York, NY, USA.
| | - N Gilchrist
- CGM Research Trust, The Princess Margaret Hospital Christchurch, Christchurch, New Zealand
| | - M McClung
- Oregon Osteoporosis Center, Portland, OR, USA
| | - J Foldes
- Department of Orthopaedics, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - T de Villiers
- Mediclinic Panorama, Cape Town, South Africa
- Department of Obstetrics and Gynaecology, Faculty of Health, Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - A Santora
- Merck & Co, Inc., Kenilworth, NJ, USA
| | - A Leung
- Merck & Co, Inc., Kenilworth, NJ, USA
| | - S Samanta
- Merck & Co, Inc., Kenilworth, NJ, USA
| | - N Heyden
- Merck & Co, Inc., Kenilworth, NJ, USA
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Kulshrestha N, Srivastava D, Ghatak T, Yadav MS, Samanta S. An unusual case of recurrent urinary tract infection. Indian J Nephrol 2015; 25:392-3. [PMID: 26664226 PMCID: PMC4663788 DOI: 10.4103/0971-4065.161027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- N Kulshrestha
- Department of Microbiology, KGMU, Lucknow, Uttar Pradesh, India
| | - D Srivastava
- Department of Anesthesia and Critical Care, IIMS and R, Lucknow, Uttar Pradesh, India
| | - T Ghatak
- Department of Anesthesia and Critical Care, IIMS and R, Lucknow, Uttar Pradesh, India
| | - M S Yadav
- Department of Urology, KGMU, Lucknow, Uttar Pradesh, India
| | - S Samanta
- Department of Critical Care Medicine, SGPGIMS, Lucknow, Uttar Pradesh, India
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Samanta S, Saleh AD, Gooptu B, Marshall A, Thorburn D, Lomas DA, Hurst JR. S97 Severity of lung but not liver disease impacts cardiovascular risk in alpha-1 antitrypsin deficiency: Abstract S97 Table 1. Thorax 2015. [DOI: 10.1136/thoraxjnl-2015-207770.103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Ghatak T, Samanta S, Baronia AK. Cryptosporidial diarrhea in a patient of all-trans-retinoic-acid syndrome treated successfully with azithromycin. Indian J Cancer 2015; 50:296. [PMID: 24369198 DOI: 10.4103/0019-509x.123592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- T Ghatak
- Department of Critical Care Medicine, SGPGIMS, Lucknow, Uttar Pradesh, India
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Samanta S, Sun H, Goel HL, Pursell B, Chang C, Khan A, Greiner DL, Cao S, Lim E, Shultz LD, Mercurio AM. IMP3 promotes stem-like properties in triple-negative breast cancer by regulating SLUG. Oncogene 2015; 35:1111-21. [PMID: 25982283 DOI: 10.1038/onc.2015.164] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/19/2015] [Accepted: 03/23/2015] [Indexed: 12/20/2022]
Abstract
IMP3 (insulin-like growth factor-2 mRNA binding protein 3) is an oncofetal protein whose expression is prognostic for poor outcome in several cancers. Although IMP3 is expressed preferentially in triple-negative breast cancer (TNBC), its function is poorly understood. We observed that IMP3 expression is significantly higher in tumor initiating than in non-tumor initiating breast cancer cells and we demonstrate that IMP3 contributes to self-renewal and tumor initiation, properties associated with cancer stem cells (CSCs). The mechanism by which IMP3 contributes to this phenotype involves its ability to induce the stem cell factor SOX2. IMP3 does not interact with SOX2 mRNA significantly or regulate SOX2 expression directly. We discovered that IMP3 binds avidly to SNAI2 (SLUG) mRNA and regulates its expression by binding to the 5' UTR. This finding is significant because SLUG has been implicated in breast CSCs and TNBC. Moreover, we show that SOX2 is a transcriptional target of SLUG. These data establish a novel mechanism of breast tumor initiation involving IMP3 and they provide a rationale for its association with aggressive disease and poor outcome.
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Affiliation(s)
- S Samanta
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - H Sun
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - H L Goel
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - B Pursell
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - C Chang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - A Khan
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - D L Greiner
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - S Cao
- Dana Farber Cancer Institute, Boston, MA, USA
| | - E Lim
- Dana Farber Cancer Institute, Boston, MA, USA
| | - L D Shultz
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - A M Mercurio
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
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Jensen S, Samanta S, Chakrabarti-Bell S, Regenauer-Lieb K, Siddique KHM, Wang S. Automated thresholding and analysis of microCT scanned bread dough. J Microsc 2014; 256:100-10. [PMID: 25142372 DOI: 10.1111/jmi.12163] [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: 11/04/2013] [Accepted: 07/11/2014] [Indexed: 11/26/2022]
Abstract
Computer aided x-ray microtomography is an increasingly popular method to investigate the structure of materials. Continuing improvements in the technique are resulting in increasingly larger data sets. The analysis of these data sets generally involves executing a static workflow for multiple samples and is generally performed manually by researchers. Executing these processes requires a significant time investment. A workflow which is able to automate the activities of the user would be useful. In this work, we have developed an automated workflow for the analysis of microtomography scanned bread dough data sets averaging 5 GB in size. Comparing the automated workflow with the manual workflow indicates a significant amount of the time spent (33% in the case of bread dough) on user interactions in manual method. Both workflows return similar results for porosity and pore frequency distribution. Finally, by implementing an automated workflow, users save the time which would be required to manually execute the workflow. This time can be spent on more productive tasks.
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Affiliation(s)
- S Jensen
- CSIRO, Animal, Food and Health Sciences, Kensington, WA, Australia; CSIRO Food Futures National Research Flagship, Canberra, ACT, Australia
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Chatterjee D, Gupta V, Sharma V, Sinha B, Samanta S. A reliable and cost effective approach for radiographic monitoring in nutritional rickets. Br J Radiol 2014; 87:20130648. [PMID: 24593231 DOI: 10.1259/bjr.20130648] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVE Radiological scoring is particularly useful in rickets, where pre-treatment radiographical findings can reflect the disease severity and can be used to monitor the improvement. However, there is only a single radiographic scoring system for rickets developed by Thacher and, to the best of our knowledge, no study has evaluated radiographic changes in rickets based on this scoring system apart from the one done by Thacher himself. The main objective of this study is to compare and analyse the pre-treatment and post-treatment radiographic parameters in nutritional rickets with the help of Thacher's scoring technique. METHODS 176 patients with nutritional rickets were given a single intramuscular injection of vitamin D (600 000 IU) along with oral calcium (50 mg kg(-1)) and vitamin D (400 IU per day) until radiological resolution and followed for 1 year. Pre- and post-treatment radiological parameters were compared and analysed statistically based on Thacher's scoring system. RESULTS Radiological resolution was complete by 6 months. Time for radiological resolution and initial radiological score were linearly associated on regression analysis. The distal ulna was the last to heal in most cases except when the initial score was 10, when distal femur was the last to heal. CONCLUSION Thacher's scoring system can effectively monitor nutritional rickets. The formula derived through linear regression has prognostic significance. ADVANCES IN KNOWLEDGE The distal femur is a better indicator in radiologically severe rickets and when resolution is delayed. Thacher's scoring is very useful for monitoring of rickets. The formula derived through linear regression can predict the expected time for radiological resolution.
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Affiliation(s)
- D Chatterjee
- Department of Orthopaedics, Vardhaman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
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Samanta S, Chowdhury T, Chattopadhyay J. Mathematical modeling of cascading migration in a tri-trophic food-chain system. J Biol Phys 2013; 39:469-87. [PMID: 23860921 DOI: 10.1007/s10867-013-9311-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 03/04/2013] [Indexed: 11/26/2022] Open
Abstract
Diel vertical migration is a behavioral antipredator defense that is shaped by a trade-off between higher predation risk in surface waters and reduced growth in deeper waters. The strength of migration of zooplankton increases with a rise in the abundance of predators and their exudates (kairomone). Recent studies span multiple trophic levels, which lead to the concept of coupled vertical migration. The migrations that occur at one trophic level can affect the vertical migration of the next lower trophic level, and so on, throughout the food chain. This is called cascading migration. In this paper, we introduce cascading migration in a well-known model (Hastings and Powell, Ecology 73:896-903, 1991). We represent the dynamics of the system as proposed by Hastings and Powell as a phytoplankton-zooplankton-fish (prey-middle predator-top predator) model where fish affect the migrations of zooplankton, which in turn affect the migrations of motile phytoplankton. The system under cascading migration enhances system stability and population coexistence. It is also observed that for a higher rate of cascading migration, the system shows chaotic behavior. We conclude that the observations of Hastings and Powell remain true if the cascading migration rate is high enough.
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Affiliation(s)
- S Samanta
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, India
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46
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Ghatak T, Samanta S. Accidental intra-arterial dexmedetomidine injection in postoperative ward. Anaesth Intensive Care 2013; 41:431. [PMID: 23659412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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47
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Samanta S, Samanta S, Haldar R. Guidewire fragmentation complicating hemodialysis catheter insertion. Indian J Nephrol 2013; 23:468-9. [PMID: 24339535 PMCID: PMC3841525 DOI: 10.4103/0971-4065.120354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Sudhakar N, Samanta S, Sahu S, Raina O, Gupta SC, Madhu D, Kumar A. Prevalence of Toxocara species eggs in soil samples of public health importance in and around Bareilly, Uttar Pradesh, India. Vet World 2013. [DOI: 10.5455/vetworld.2013.87-90] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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49
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Sahu S, Samanta S, Sudhakar N, Raina O, Gupta S, Goswami T, Madhu D, Kumar A. Characterization of somatic antigens of adult Toxocara canis by western blotting. Vet World 2013. [DOI: 10.5455/vetworld.2013.424-427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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50
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Sudhakar NR, Samanta S, Sahu S, Raina OK, Gupta SC, Goswami TK, Lokesh KM, Kumar A. Characterization of excretory-secretory antigens of adult Toxocara canis by western blotting. J Parasit Dis 2012; 38:166-9. [PMID: 24808645 DOI: 10.1007/s12639-012-0209-x] [Citation(s) in RCA: 5] [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: 10/02/2012] [Accepted: 11/11/2012] [Indexed: 11/24/2022] Open
Abstract
Toxocara canis is one of the most common helminth worm of dogs which continues to stimulate both public health concern alongside the higher scientific interest. It may cause visceral and ocular damage in humans especially in children. The identification of specific antigens of T. canis is important so as to develop better diagnostic techniques. Excretory-secretory (ES) antigens were prepared by culturing the adult T. canis worms in RPMI 1640 medium without serum supplementation followed by ammonium sulphate precipitation. These antigens were separated using sodium dodecyl sulphate-electrophoresis (SDS-PAGE). Recovered proteins ranged from 30 to 384 kDa. The specific reactivity of the T. canis excretory-secretory (TC-ES) proteins was checked by western blotting. The immuno-reactivity of the naturally infected dog sera with the TC-ES antigens showed five bands at 43, 57,105, 139 and 175 kDa. The immuno-reactivity of the hyper immune serum raised in rabbits against TC-ES antigens was observed with ten polypeptides of 21, 25, 30, 37, 45, 50, 57, 69, 77 and 105 kDa. Common antigens band were observed at 57 and 105 KDa. These antigens merit further evaluation as candidate for use in diagnosis of toxocariasis in humans and adult dogs.
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Affiliation(s)
- N R Sudhakar
- Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, 243122 India
| | - S Samanta
- Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, 243122 India
| | - Shivani Sahu
- Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, 243122 India
| | - O K Raina
- Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, 243122 India
| | - S C Gupta
- Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, 243122 India
| | - T K Goswami
- Immunology Section, Indian Veterinary Research Institute, Izatnagar, 243122 India
| | - K M Lokesh
- Division of Veterinary Public Health, Indian Veterinary Research Institute, Izatnagar, India
| | - Ashok Kumar
- Division of Veterinary Public Health, Indian Veterinary Research Institute, Izatnagar, India
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