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John DV, Sreenivas N, Deora H, Purushottam M, Debnath M, Mahadevan A, Patil SA. Cerebrospinal fluid inflammatory cytokine profiles of patients with neurotropic parasitic infections. Trop Biomed 2023; 40:406-415. [PMID: 38308827 DOI: 10.47665/tb.40.4.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Abstract
The pathogenesis of chronic parasitic central nervous system (CNS) infections, including granulomatous amoebic meningoencephalitis (GAE), cerebral toxoplasmosis (CT), and neurocysticercosis (NCC), is primarily due to an inflammatory host reaction to the parasite. Inflammatory cytokines produced by invading T cells, monocytes, and CNS resident cells lead to neuroinflammation which underlie the immunopathology of these infections. Immune molecules, especially cytokines, can therefore emerge as potential biomarker(s) of CNS parasitic infections. In this study, cerebral spinal fluid (CSF) samples from suspected patients with parasitic infections were screened for pathogenic free-living amoebae by culture (n=2506) and PCR (n=275). Six proinflammatory cytokines in smear and culture-negative CSF samples from patients with GAE (n = 2), NCC (n = 7), and CT (n = 23) as well as control (n = 7) patients were measured using the Multiplex Suspension assay. None of the CSF samples tested was positive for neurotropic free-living amoebae by culture and only two samples showed Acanthamoeba 18S rRNA by PCR. Of the six cytokines measured, only IL-6 and IL-8 were significantly increased in all three infection groups compared to the control group. In addition, TNFa levels were higher in the GAE and NCC groups and IL-17 in the GAE group compared to controls. The levels of IL-1b and IFNg were very low in all the infection groups and the control group. There was a correlation between CSF cellularity and increased levels of IL-6, IL-8, and TNFa in 11 patients. Thus, quantifying inflammatory cytokine levels in CSF might help with understanding the level of neuroinflammation in patients with neurotropic parasitic diseases. Further studies with clinico-microbiological correlation in the form of reduction of cytokine levels with treatment and the correlation with neurological deficits are needed.
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Affiliation(s)
- D V John
- Department of Neuromicrobiology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - N Sreenivas
- Department of Human Genetics, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - H Deora
- Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - M Purushottam
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - M Debnath
- Department of Human Genetics, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - A Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - S A Patil
- Department of Neuromicrobiology, National Institute of Mental Health and Neurosciences, Bangalore, India
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2
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Khanam R, Nayak AK, Kulsum PGPS, Mandal J, Shahid M, Tripathy R, Bhattacharyya P, Selvam P, Munda S, Manickam S, Debnath M, Bandaru RG. Silica sources for arsenic mitigation in rice: machine learning-based predictive modeling and risk assessment. Environ Sci Pollut Res Int 2023; 30:113660-113673. [PMID: 37851247 DOI: 10.1007/s11356-023-30339-5] [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: 05/08/2023] [Accepted: 10/04/2023] [Indexed: 10/19/2023]
Abstract
Arsenic (As) is a well-known human carcinogen, and the consumption of rice is the main pathway for the South Asian people. The study evaluated the impact of the amendments involving CaSiO3, SiO2 nanoparticles, silica solubilizing bacteria (SSB), and rice straw compost (RSC) on mitigation of As toxicity in rice. The translocation of As from soil to cooked rice was tracked, and the results showed that RSC and its combination with SSB were the most effective in reducing As loading in rice grain by 53.2%. To determine the risk of dietary exposure to As, the average daily intake (ADI), hazard quotient (HQ), and incremental lifetime cancer risk (ILCR) were computed. The study observed that the ADI was reduced to one-third (0.24 μg kg-1bw) under RSC+SSB treatments compared to the control. An effective prediction model was established using random forest model and described the accumulation of As by rice grains depend on bioavailable As, P, and Fe which explained 48.5, 5.07%, and 2.6% of the variation in the grain As, respectively. The model anticipates that to produce As benign rice grain, soil should have P and Fe concentration more than 30 mg kg-1 and 12 mg kg-1, respectively if soil As surpasses 2.5 mg kg-1.
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Affiliation(s)
- Rubina Khanam
- ICAR-Crop Production Division, National Rice Research Institute, 753006, Cuttack, Odisha, India
| | - Amaresh Kumar Nayak
- ICAR-Crop Production Division, National Rice Research Institute, 753006, Cuttack, Odisha, India.
| | | | - Jajati Mandal
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Mohammad Shahid
- ICAR-Crop Production Division, National Rice Research Institute, 753006, Cuttack, Odisha, India
| | - Rahul Tripathy
- ICAR-Crop Production Division, National Rice Research Institute, 753006, Cuttack, Odisha, India
| | - Pratap Bhattacharyya
- ICAR-Crop Production Division, National Rice Research Institute, 753006, Cuttack, Odisha, India
| | - Panneer Selvam
- ICAR-Crop Production Division, National Rice Research Institute, 753006, Cuttack, Odisha, India
| | - Sushmita Munda
- ICAR-Crop Production Division, National Rice Research Institute, 753006, Cuttack, Odisha, India
| | - Sivashankari Manickam
- ICAR-Crop Production Division, National Rice Research Institute, 753006, Cuttack, Odisha, India
| | - Manish Debnath
- ICAR-Crop Production Division, National Rice Research Institute, 753006, Cuttack, Odisha, India
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NOBI F, Debnath M, Mahjabin S, Biswas T, Ashraf I, Azad S, Ahmad M, Mobashwera B, Akhtar M, Emon R, Chowdhury M, Islam M, Miah M. WCN23-0334 VITAMIN D LEVEL IN SLE PATIENTS WITH OR WITHOUT RENAL INVOLVEMENT AND IT’S RELATIONSHIP WITH DISEASE ACTIVITY (SLEDAI SCORE). Kidney Int Rep 2023. [DOI: 10.1016/j.ekir.2023.02.138] [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: 03/22/2023] Open
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Debnath M, Dey S, Bandyopadhyay A, Datta G. Effect of dietary modification and intense training on body composition and lipid profile of young male footballers. Sci Sports 2023. [DOI: 10.1016/j.scispo.2021.08.012] [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: 02/13/2023]
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Paul R, Dutta D, Das T, Debnath M, Dash J. G4 Sensing Pyridyl-Thiazole Polyamide Represses c-KIT Expression in Leukemia Cells. Chemistry 2021; 27:8590-8599. [PMID: 33851760 DOI: 10.1002/chem.202100907] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 12/27/2022]
Abstract
Specific sensing and functional tuning of nucleic acid secondary structures remain less explored to date. Herein, we report a thiazole polyamide TPW that binds specifically to c-KIT1 G-quadruplex (G4) with sub-micromolar affinity and ∼1 : 1 stoichiometry and represses c-KIT proto-oncogene expression. TPW shows up to 10-fold increase in fluorescence upon binding with c-KIT1 G4, but shows weak or no quantifiable binding to other G4s and ds26 DNA. TPW can increase the number of G4-specific antibody (BG4) foci and mark G4 structures in cancer cells. Cell-based assays reveal that TPW can efficiently repress c-KIT expression in leukemia cells via a G4-dependent process. Thus, the polyamide can serve as a promising probe for G-quadruplex recognition with the ability to specifically alter c-KIT oncogene expression.
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Affiliation(s)
- Raj Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Debasish Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Tania Das
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Manish Debnath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
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6
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Sarangi A, Das BS, Patnaik G, Sarkar S, Debnath M, Mohan M, Bhattacharya D. Potent anti-mycobacterial and immunomodulatory activity of some bioactive molecules of Indian ethnomedicinal plants that have the potential to enter in TB management. J Appl Microbiol 2021; 131:1578-1599. [PMID: 33772980 DOI: 10.1111/jam.15088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 03/01/2021] [Accepted: 03/23/2021] [Indexed: 11/26/2022]
Abstract
Tuberculosis (TB) is one of the deadliest infectious diseases of human civilization. Approximately one-third of global population is latently infected with the TB pathogen Mycobacterium tuberculosis (M.tb). The discovery of anti-TB antibiotics leads to decline in death rate of TB. However, the evolution of antibiotic-resistant M.tb-strain and the resurgence of different immune-compromised diseases re-escalated the death rate of TB. WHO has already cautioned about the chances of pandemic situation in TB endemic countries until the discovery of new anti-tubercular drugs, that is, the need of the hour. Analysing the pathogenesis of TB, it was found that M.tb evades the host by altering the balance of immune response and affects either by killing the cells or by creating inflammation. In the pre-antibiotic era, traditional medicines were only therapeutic measures for different infectious diseases including tuberculosis. The ancient literatures of India or ample Indian traditional knowledge and ethnomedicinal practices are evidence for the treatment of TB using different indigenous plants. However, in the light of modern scientific approach, anti-TB effects of those plants and their bioactive molecules were not established thoroughly. In this review, focus has been given on five bioactive molecules of different traditionally used Indian ethnomedicinal plants for treatment of TB or TB-like symptom. These compounds are also validated with proper identification and their mode of action with modern scientific approaches. The effectiveness of these molecules for sensitive or drug-resistant TB pathogen in clinical or preclinical studies was also evaluated. Thus, our specific aim is to highlight such scientifically validated bioactive compounds having anti-mycobacterial and immunomodulatory activity for future use as medicine or adjunct-therapeutic molecule for TB management.
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Affiliation(s)
- A Sarangi
- Centre for Biotechnology, School of Pharmaceutical Sciences, SOA Deemed to be University, Bhubaneswar, Odisha, India
| | - B S Das
- Centre for Biotechnology, School of Pharmaceutical Sciences, SOA Deemed to be University, Bhubaneswar, Odisha, India
| | - G Patnaik
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - S Sarkar
- Barsal High School, Rampurhat, West Bengal, India
| | - M Debnath
- Panskura Banamali College (Autonomous), Vidyasagar University, Panskura, West Bengal, India
| | - M Mohan
- ICMR-National Institute of Malarial Research (NIMR), New Delhi, India
| | - D Bhattacharya
- Centre for Biotechnology, School of Pharmaceutical Sciences, SOA Deemed to be University, Bhubaneswar, Odisha, India
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7
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Al-makdase L, Ioannou P, Tew ZY, Khan M, Debnath M, Ogunrinde I, Shields L. 5 Improving Diagnosis and Management of Urinary Tract Infections for Elderly Patients. Age Ageing 2020. [DOI: 10.1093/ageing/afz183.05] [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: 11/14/2022] Open
Abstract
Abstract
Introduction
Diagnosis of urinary tract infection (UTI) in the elderly population is challenging as they commonly present with atypical signs and symptoms. Prevalence of asymptomatic bacteriuria in the elderly population is high. Hence, urine dipstick and urine culture are no longer diagnostic tests. UTI is over-diagnosed and overtreated in the elderly, resulting in poor antimicrobial stewardship. This project was carried out to assess and improve the current practices in the diagnosis and treatment of UTI in the Department of Medicine of the Elderly.
Methods
We reviewed current Scottish Intercollegiate Guidelines Network (SIGN) and National Institute for health and Care Excellence (NICE) guidelines on management of UTI and defined indications for performing urine dipstick and sending urine culture. We then collected and assessed data on all urine dipsticks performed, urine cultures sent, and use of antibiotics in treating UTI and asymptomatic bacteriuria in three Medicine of the Elderly wards in Aberdeen Royal Infirmary.
We carried out intervention by means of presenting and discussing findings of Plan-Do-Study-Act (PDSA) cycles in departmental multi-disciplinary Quality Improvement (QI) meetings followed by educational sessions.
Results
Our baseline data showed 77% of urine dipsticks were performed without clinical indication and 18% of patients had urine cultures sent without clinical indication. After presenting our initial findings and carrying out an educational intervention session, 25% of patients had urine dipstick done without clinical indication, and 0% of patients had urine cultures sent without clinical indication. However, over the course of four subsequent PDSA cycles, practices in investigation of UTI fluctuated but were overall consistently better than the initial practice with further interventions. In all PDSA cycles, no patients were treated for asymptomatic bacteriuria.
Conclusions
Multidisciplinary team involvement in discussion of this QI project findings and educational sessions proved to be an effective form of intervention for improving current practice.
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Affiliation(s)
- L Al-makdase
- Department of Medicine for the Elderly, Aberdeen Royal Infirmary, Aberdeen
| | - P Ioannou
- Department of Medicine for the Elderly, Aberdeen Royal Infirmary, Aberdeen
| | - Z Y Tew
- Department of Medicine for the Elderly, Aberdeen Royal Infirmary, Aberdeen
| | - M Khan
- Department of Medicine for the Elderly, Aberdeen Royal Infirmary, Aberdeen
| | - M Debnath
- Department of Medicine for the Elderly, Aberdeen Royal Infirmary, Aberdeen
| | - I Ogunrinde
- Department of Medicine for the Elderly, Aberdeen Royal Infirmary, Aberdeen
| | - L Shields
- Department of Medicine for the Elderly, Aberdeen Royal Infirmary, Aberdeen
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8
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Paul R, Das T, Debnath M, Chauhan A, Dash J. G-Quadruplex-Binding Small Molecule Induces Synthetic Lethality in Breast Cancer Cells by Inhibiting c-MYC and BCL2 Expression. Chembiochem 2019; 21:963-970. [PMID: 31621996 DOI: 10.1002/cbic.201900534] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Indexed: 12/21/2022]
Abstract
Herein, a prolinamide-derived peptidomimetic that preferentially binds to c-MYC and BCL2 G-quadruplexes present in the promoter regions of apoptosis-related genes (c-MYC and BCL2) over other DNA quadruplexes are described. Biological assays, such as real-time quantitative reverse transcription, western blot, dual luciferase, and small interfering RNA knockdown assays, indicate that the ligand triggers a synthetic lethal interaction by simultaneously inhibiting the expression of c-MYC and BCL2 genes through their promoter G-quadruplexes. The ligand shows antiproliferative activity in MCF-7 cells that overexpress both MYC and BCL2 genes, in comparison to cells that overexpress either of the two. Moreover, the ligand induces S-phase cell-cycle arrest, DNA damage, and apoptosis in MCF-7 cells.
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Affiliation(s)
- Rakesh Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Tania Das
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Manish Debnath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Ajay Chauhan
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
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Konhar R, Debnath M, Vishwakarma S, Bhattacharjee A, Sundar D, Tandon P, Dash D, Biswal DK. The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from north-east India and its comparison with related Dendrobium species. PeerJ 2019; 7:e7756. [PMID: 31695964 PMCID: PMC6830405 DOI: 10.7717/peerj.7756] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 08/26/2019] [Indexed: 11/21/2022] Open
Abstract
The medicinal orchid genus Dendrobium belonging to the Orchidaceae family is a huge genus comprising about 800-1,500 species. To better illustrate the species status in the genus Dendrobium, a comparative analysis of 33 available chloroplast genomes retrieved from NCBI RefSeq database was compared with that of the first complete chloroplast genome of D. nobile from north-east India based on next-generation sequencing methods (Illumina HiSeq 2500-PE150). Our results provide comparative chloroplast genomic information for taxonomical identification, alignment-free phylogenomic inference and other statistical features of Dendrobium plastomes, which can also provide valuable information on their mutational events and sequence divergence.
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Affiliation(s)
- Ruchishree Konhar
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
- Informatics and Big Data, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Manish Debnath
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Santosh Vishwakarma
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Atanu Bhattacharjee
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Pramod Tandon
- Biotech Park, Kursi road, Lucknow, Uttar Pradesh, India
| | - Debasis Dash
- Informatics and Big Data, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
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Chatterjee D, Nayak AK, Vijayakumar S, Debnath M, Chatterjee S, Swain CK, Bihari P, Mohanty S, Tripathi R, Shahid M, Kumar A, Pathak H. Water vapor flux in tropical lowland rice. Environ Monit Assess 2019; 191:550. [PMID: 31396767 DOI: 10.1007/s10661-019-7709-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
A field experiment was conducted at Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India in the dry seasons of 2015 and 2016 to assess the water vapor flux (FH2O) and its relationship with other climatic variables. The FH2O and climatic variables were measured by an eddy covariance system and a micrometeorological observatory. Daily mean FH2O during the dry seasons of 2015 and 2016 were 0.009-0.092 g m-2 s-1 and 0.014-0.101 g m-2 s-1, respectively. Seasonal average FH2O was 14.6% higher in 2016 than that in 2015. Diurnal variation for FH2O showed a bell-shaped curve with its peak at 13:30-14:00 Indian Standard Time (IST) in both the years. Carbon dioxide flux was found higher with rise in FH2O. This relationship was stronger at higher vapor pressure deficit (VPD) (20 ≤ VPD ≤ 40 and VPD > 40 hPa). The FH2O showed significant positive correlation with latent heat flux, net radiation flux, photosynthatically active radiation, air, water and soil temperatures, shortwave down and upwell radiations, maximum and minimum temperatures, evaporation, and relative humidity in both the years. Principal component analysis showed that FH2O was very close to latent heat flux in both the years (Pearson correlation coefficient close to 1). The two-dimensional observation map of the principal component F1 and F2 showed the observations taken during the vegetative stage and panicle initiation stage, and flowering stage and maturity stage were closer to each other. It can be concluded that the most important climatic variables controlling the FH2O were latent heat of vaporization, net radiation, air temperature, soil temperatures, and water temperature.
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Affiliation(s)
- Dibyendu Chatterjee
- Division of Crop Production, National Rice Research Institute, -753006, Cuttack, Odisha, India
| | - Amaresh Kumar Nayak
- Division of Crop Production, National Rice Research Institute, -753006, Cuttack, Odisha, India.
| | - S Vijayakumar
- Division of Crop Production, National Rice Research Institute, -753006, Cuttack, Odisha, India
| | - Manish Debnath
- Division of Crop Production, National Rice Research Institute, -753006, Cuttack, Odisha, India
| | - Sumanta Chatterjee
- Division of Crop Production, National Rice Research Institute, -753006, Cuttack, Odisha, India
| | - Chinmaya Kumar Swain
- Division of Crop Production, National Rice Research Institute, -753006, Cuttack, Odisha, India
| | - Priyanka Bihari
- Division of Crop Production, National Rice Research Institute, -753006, Cuttack, Odisha, India
| | - S Mohanty
- Division of Crop Production, National Rice Research Institute, -753006, Cuttack, Odisha, India
| | - Rahul Tripathi
- Division of Crop Production, National Rice Research Institute, -753006, Cuttack, Odisha, India
| | - Mohammad Shahid
- Division of Crop Production, National Rice Research Institute, -753006, Cuttack, Odisha, India
| | - Anjani Kumar
- Division of Crop Production, National Rice Research Institute, -753006, Cuttack, Odisha, India
| | - H Pathak
- Division of Crop Production, National Rice Research Institute, -753006, Cuttack, Odisha, India
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Dutta D, Debnath M, Müller D, Paul R, Das T, Bessi I, Schwalbe H, Dash J. Cell penetrating thiazole peptides inhibit c-MYC expression via site-specific targeting of c-MYC G-quadruplex. Nucleic Acids Res 2019; 46:5355-5365. [PMID: 29762718 PMCID: PMC6009605 DOI: 10.1093/nar/gky385] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 05/02/2018] [Indexed: 02/03/2023] Open
Abstract
The structural differences among different G-quadruplexes provide an opportunity for site-specific targeting of a particular G-quadruplex structure. However, majority of G-quadruplex ligands described thus far show little selectivity among different G-quadruplexes. In this work, we delineate the design and synthesis of a crescent-shaped thiazole peptide that preferentially stabilizes c-MYC quadruplex over other promoter G-quadruplexes and inhibits c-MYC oncogene expression. Biophysical analysis such as Förster resonance energy transfer (FRET) melting and fluorescence spectroscopy show that the thiazole peptide TH3 can selectively interact with the c-MYC G-quadruplex over other investigated G-quadruplexes and duplex DNA. NMR spectroscopy reveals that peptide TH3 binds to the terminal G-quartets and capping regions present in the 5′- and 3′-ends of c-MYC G-quadruplex with a 2:1 stoichiometry; whereas structurally related distamycin A is reported to interact with quadruplex structures via groove binding and end stacking modes with 4:1 stoichiometry. Importantly, qRT-PCR, western blot and dual luciferase reporter assay show that TH3 downregulates c-MYC expression by stabilizing the c-MYC G-quadruplex in cancer cells. Moreover, TH3 localizes within the nucleus of cancer cells and exhibits antiproliferative activities by inducing S phase cell cycle arrest and apoptosis.
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Affiliation(s)
- Debasish Dutta
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Manish Debnath
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Diana Müller
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Rakesh Paul
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Tania Das
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Jyotirmayee Dash
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
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12
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Affiliation(s)
- Manish Debnath
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
| | - Khushnood Fatma
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
| | - Jyotirmayee Dash
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
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13
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Debnath M, Fatma K, Dash J. Chemical Regulation of DNA i-Motifs for Nanobiotechnology and Therapeutics. Angew Chem Int Ed Engl 2019; 58:2942-2957. [PMID: 30600876 DOI: 10.1002/anie.201813288] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [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: 11/21/2018] [Revised: 12/27/2018] [Indexed: 12/20/2022]
Abstract
DNA sequences rich in cytosine have the propensity, under acidic pH, to fold into four-stranded intercalated DNA structures called i-motifs. Recent studies have provided significant breakthroughs that demonstrate how chemists can manipulate these structures for nanobiotechnology and therapeutics. The first section of this Minireview discusses the development of advanced functional nanostructures by synthetic conjugation of i-motifs with organic scaffolds and metal nanoparticles and their role in therapeutics. The second section highlights the therapeutic targeting of i-motifs with chemical scaffolds and their significance in biology. For this, first we shed light on the long-lasting debate regarding the stability of i-motifs under physiological conditions. Next, we present a comparative analysis of recently reported small molecules for specifically targeting i-motifs over other abundant DNA structures and modulating their function in cellular systems. These advances provide new insights into i-motif-targeted regulation of gene expression, telomere maintenance, and therapeutic applications.
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Affiliation(s)
- Manish Debnath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
| | - Khushnood Fatma
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
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14
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Biswal DK, Debnath M, Konhar R, Yanthan S, Tandon P. Phylogeny and Biogeography of Carnivorous Plant Family Nepenthaceae With Reference to the Indian Pitcher Plant Nepenthes Khasiana Reveals an Indian Subcontinent Origin of Nepenthes Colonization in South East Asia During the Miocene Epoch. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00108] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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15
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Debnath S, Mukherjee A, Karan S, Debnath M, Chatterjee TK. Induction of apoptosis, anti-proliferation, tumor-angiogenic suppression and down-regulation of Dalton’s Ascitic Lymphoma (DAL) induced tumorigenesis by poly- l -lysine: A mechanistic study. Biomed Pharmacother 2018; 102:1064-1076. [DOI: 10.1016/j.biopha.2018.03.076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 02/09/2023] Open
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16
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Abstract
Herein, we report a carbazole (Cz) ligand that displays distinct turn-on fluorescence signals upon interaction with human telomeric G-quadruplex ( h-TELO) and nuclease enzymes. Interestingly, Cz selectively binds and stabilizes the mixed hybrid topology of h-TELO G-quadruplex that withstands digestion by exonucleases and nuclease S1. The distinct fluorescence signatures of Cz-stabilized h-TELO with nucleases are used to design conceptually novel DNA devices for selectively detecting the enzymatic activity of DNase I as well as performing logic operations. An INHIBIT logic gate is constructed using h-TELO and DNase I as the inputs while the inputs of h-TELO and nuclease S1 form a YES logic gate. Furthermore, a two-input two-output reusable logic device with "multireset" function is developed by using h-TELO and DNase I as inputs. On the basis of this platform, combinatorial logic systems (INHIBIT-INHIBIT and NOR-OR) have been successfully installed using different combinations of nucleases as inputs. Moreover, this new strategy of using a synthetic dual emissive probe and enzyme/DNA inputs for constructing reusable logic device may find important applications in biological computing and information processing.
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Affiliation(s)
- Manish Debnath
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Rakesh Paul
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Deepanjan Panda
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Jyotirmayee Dash
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
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17
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Debnath M, Ghosh S, Chauhan A, Paul R, Bhattacharyya K, Dash J. Preferential targeting of i-motifs and G-quadruplexes by small molecules. Chem Sci 2017; 8:7448-7456. [PMID: 29163897 PMCID: PMC5674183 DOI: 10.1039/c7sc02693e] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/07/2017] [Indexed: 01/01/2023] Open
Abstract
i-Motifs and G-quadruplexes are dynamic nucleic acid secondary structures, which are believed to play key roles in gene expression. We herein report two peptidomimetic ligands (PBP1 and PBP2) that selectively target i-motifs and G-quadruplexes over double-stranded DNA. These peptidomimetics, regioisomeric with respect to the position of triazole/prolinamide motifs, have been synthesized using a modular method involving Cu(i)-catalyzed azide and alkyne cycloaddition. The para-isomer, PBP1 exhibits high selectivity for i-motifs while the meta-isomer PBP2 binds selectively to G-quadruplex structures. Interestingly, these ligands have the ability to induce G-quadruplex or i-motif structures from the unstructured single-stranded DNA conformations, as observed using single molecule Förster resonance energy transfer (smFRET) studies. The quantitative real-time polymerase chain reaction (qRT-PCR), western blot, and dual-luciferase assays indicate that PBP1 upregulates and PBP2 downregulates BCL-2 gene expression in cancer cells.
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Affiliation(s)
- Manish Debnath
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Shirsendu Ghosh
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India
| | - Ajay Chauhan
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Rakesh Paul
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Kankan Bhattacharyya
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India
| | - Jyotirmayee Dash
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
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18
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Debnath M, Das S, Bera N, Nayak C, Chaudhuri T. Association of HLA Class-I Antigens with Delusional Disorder. INT J HUM GENET 2017. [DOI: 10.1080/09723757.2003.11885849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- M. Debnath
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Siliguri 734 430, West Bengal, India
| | - S.K. Das
- Department of Psychiatry, North Bengal Medical College and Hospital, Siliguri, West Bengal, India
| | - N.K. Bera
- Department of Psychiatry, North Bengal Medical College and Hospital, Siliguri, West Bengal, India
| | - C.R. Nayak
- Computer Centre, University of North Bengal, Siliguri, West Bengal, India
| | - T.K. Chaudhuri
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Siliguri 734 430, West Bengal, India
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19
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Debnath S, Karan S, Debnath M, Dash J, Chatterjee TK. Poly-L-Lysine Inhibits Tumor Angiogenesis and Induces Apoptosis in Ehrlich Ascites Carcinoma and in Sarcoma S-180 Tumor. Asian Pac J Cancer Prev 2017; 18:2255-2268. [PMID: 28843265 PMCID: PMC5697490 DOI: 10.22034/apjcp.2017.18.8.2255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Background: This study focuses on the role of Poly-L-lysine (PLL), an essential amino acid, on molecular changes of tumor angiogenesis suppression, pro-apoptotic and anti-apoptotic gene expression after treatment on Ehrlich ascites carcinoma (EAC) and solid sarcoma-180 tumor cells bearing mice. Materials and Methods: The cell viability was carried out using MTT assay. The antitumor activity was evaluated by treatment with PLL at 20 and 40mg/kg/b.w doses for 14 days in EAC ascites tumor and 21 days for Sarcoma-180 solid tumor model. Several tumor evaluation studies, haematological and biochemical parameters were estimated. Importantly, the tumor cell apoptosis was assessed using microscopic observations, DNA fragmentation assay, Flow cytometric analysis, cell-cycle and electron-microscopic study, following which, the expression of several signal proteins related to pro-apoptosis, anti-apoptosis and tumor angiogenesis were quantified using western blotting and immunohistochemistry study. Results: Precisely, PLL had cytotoxic effect on K562; A549; U937 and B16F10 cancer cells. Significant decreases in liquid and solid tumors and increased life span of treated mice were observed (P<0.05). Typical morphological changes, apoptosis bleb phenomenon and sub-G1 cell cycle arrests revealed that PLL promoted apoptotic cell death. Western blot and immunohistochemistry confirms, PLL activated apoptotic signalling cascades through down regulation of Bcl-2 and CD31 protein and up-regulation of Bax and p53 proteins. The anti-angiogenic effects were also accompanied with decreased VEGF expression and reduced peritoneal-angiogenesis and microvessel density. Conclusions: The antitumor and antitumor-angiogenic activity of PLL was confirmed from all the results via up and down regulation of relevant signal proteins reported in this publication.
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Affiliation(s)
- Souvik Debnath
- Pharmacology Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Jadavpur, India.
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20
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Debnath M, Santoni C, Leonardi S, Iungo GV. Towards reduced order modelling for predicting the dynamics of coherent vorticity structures within wind turbine wakes. Philos Trans A Math Phys Eng Sci 2017; 375:rsta.2016.0108. [PMID: 28265029 DOI: 10.1098/rsta.2016.0108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/14/2016] [Indexed: 06/06/2023]
Abstract
The dynamics of the velocity field resulting from the interaction between the atmospheric boundary layer and a wind turbine array can affect significantly the performance of a wind power plant and the durability of wind turbines. In this work, dynamics in wind turbine wakes and instabilities of helicoidal tip vortices are detected and characterized through modal decomposition techniques. The dataset under examination consists of snapshots of the velocity field obtained from large-eddy simulations (LES) of an isolated wind turbine, for which aerodynamic forcing exerted by the turbine blades on the atmospheric boundary layer is mimicked through the actuator line model. Particular attention is paid to the interaction between the downstream evolution of the helicoidal tip vortices and the alternate vortex shedding from the turbine tower. The LES dataset is interrogated through different modal decomposition techniques, such as proper orthogonal decomposition and dynamic mode decomposition. The dominant wake dynamics are selected for the formulation of a reduced order model, which consists in a linear time-marching algorithm where temporal evolution of flow dynamics is obtained from the previous temporal realization multiplied by a time-invariant operator.This article is part of the themed issue 'Wind energy in complex terrains'.
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Affiliation(s)
- M Debnath
- Wind Fluids and Experiments (WindFluX) Laboratory, The University of Texas at Dallas, Richardson, TX, USA
| | - C Santoni
- CFD Laboratory, Mechanical Engineering Department, The University of Texas at Dallas, Richardson, TX, USA
| | - S Leonardi
- CFD Laboratory, Mechanical Engineering Department, The University of Texas at Dallas, Richardson, TX, USA
| | - G V Iungo
- Wind Fluids and Experiments (WindFluX) Laboratory, The University of Texas at Dallas, Richardson, TX, USA
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21
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Chhabra H, Shivakumar V, Subbanna M, Bose A, Agrawal M, Sreeraj V, Kalmady S, Narayanaswamy J, Debnath M, Venkatasubramanian G. Influence of COMT and NRG-1 gene polymorphisms on the effect of tDCS on Auditory Verbal Hallucinations in Schizophrenia. Brain Stimul 2017. [DOI: 10.1016/j.brs.2017.01.215] [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] Open
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22
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Konhar R, Debnath M, Marbaniang JV, Biswal DK, Tandon P. Age estimation for the genus Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) and phylogeographic inference from ancestral area reconstruction. J Bioinform Comput Biol 2017; 14:1660001. [DOI: 10.1142/s0219720016600015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and biogeographers. One such family belonging to angiosperms is Orchidaceae with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and biogeographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are distinctly distributed in tropical to temperate regions. Much is not known about correlations among the level of CAM activity (one of the photosynthetic pathways often regarded as an adaptation to water stress in land plants), habitat, life forms, and phylogenetic relationships of orchids from an evolutionary perspective. A relatively well-resolved and highly supported phylogeny for Cymbidium orchids is reconstructed based on sequence analysis of ITS2 and matK regions from the chloroplast DNA available in public repositories viz. GenBank at NCBI. This study examines a genus level analysis by integrating different molecular matrices to existing fossil data on orchids in a molecular Bayesian relaxed clock employed in BEAST and assessed divergence times for the genus Cymbidium with a focus on evolutionary history of photosynthetic characters. Our study has enabled age estimations (45Ma) as well as ancestral area reconstruction for the genus Cymbidium using BEAST by addition of previously analyzed two internal calibration points.
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Affiliation(s)
- Ruchishree Konhar
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Manish Debnath
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
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23
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Chauhan A, Paul R, Debnath M, Bessi I, Mandal S, Schwalbe H, Dash J. Synthesis of Fluorescent Binaphthyl Amines That Bind c-MYC G-Quadruplex DNA and Repress c-MYC Expression. J Med Chem 2016; 59:7275-81. [PMID: 27442915 DOI: 10.1021/acs.jmedchem.6b00328] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Two novel binaphthyl amines have been designed and synthesized using Buchwald amination and oxidative homocoupling as key steps. The binaphthyl amine containing two triazole rings shows higher affinity for c-MYC G-quadruplex, exhibits fluorescence "turn-on" response with c-MYC, and stains the nucleus in cells. The triazolyl binaphthyl amine shows cytotoxicity for cancer cells by inducing G2/M phase cell cycle arrest and apoptosis. Moreover, both ligands can downregulate c-MYC expression at transcriptional and translational levels.
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Affiliation(s)
- Ajay Chauhan
- Department of Chemical Sciences, Indian Institute of Science Education and Research , Mohanpur, West Bengal 741252, India
| | - Rakesh Paul
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
| | - Manish Debnath
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt , Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Samir Mandal
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt , Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Jyotirmayee Dash
- Department of Chemical Sciences, Indian Institute of Science Education and Research , Mohanpur, West Bengal 741252, India.,Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
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24
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Biswal DK, Debnath M, Kharumnuid G, Thongnibah W, Tandon V. Northeast India Helminth Parasite Information Database (NEIHPID): Knowledge Base for Helminth Parasites. PLoS One 2016; 11:e0157459. [PMID: 27285615 PMCID: PMC4902196 DOI: 10.1371/journal.pone.0157459] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 05/31/2016] [Indexed: 11/19/2022] Open
Abstract
Most metazoan parasites that invade vertebrate hosts belong to three phyla: Platyhelminthes, Nematoda and Acanthocephala. Many of the parasitic members of these phyla are collectively known as helminths and are causative agents of many debilitating, deforming and lethal diseases of humans and animals. The North-East India Helminth Parasite Information Database (NEIHPID) project aimed to document and characterise the spectrum of helminth parasites in the north-eastern region of India, providing host, geographical distribution, diagnostic characters and image data. The morphology-based taxonomic data are supplemented with information on DNA sequences of nuclear, ribosomal and mitochondrial gene marker regions that aid in parasite identification. In addition, the database contains raw next generation sequencing (NGS) data for 3 foodborne trematode parasites, with more to follow. The database will also provide study material for students interested in parasite biology. Users can search the database at various taxonomic levels (phylum, class, order, superfamily, family, genus, and species), or by host, habitat and geographical location. Specimen collection locations are noted as co-ordinates in a MySQL database and can be viewed on Google maps, using Google Maps JavaScript API v3. The NEIHPID database has been made freely available at http://nepiac.nehu.ac.in/index.php.
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Affiliation(s)
| | - Manish Debnath
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | | | - Welfrank Thongnibah
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Veena Tandon
- Department of Zoology, North-Eastern Hill University, Shillong, Meghalaya, India
- Biotech Park, Lucknow, Uttar Pradesh, India
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25
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Debnath M, Ghosh S, Panda D, Bessi I, Schwalbe H, Bhattacharyya K, Dash J. Small molecule regulated dynamic structural changes of human G-quadruplexes. Chem Sci 2016; 7:3279-3285. [PMID: 29997820 PMCID: PMC6006475 DOI: 10.1039/c6sc00057f] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/02/2016] [Indexed: 01/26/2023] Open
Abstract
A carbazole derivative (BTC) regulates the dynamics of unstructured human c-MYC and h-TELO sequences by folding them into compact quadruplex structures.
The changes in structure and dynamics of oncogenic (c-MYC) and telomeric (h-TELO) G-rich DNA sequences due to the binding of a novel carbazole derivative (BTC) are elucidated using single-molecule Förster resonance energy transfer (sm-FRET), fluorescence correlation spectroscopy (FCS) and NMR spectroscopy. In contrast to the previous reports on the binding of ligands to pre-folded G-quadruplexes, this work illustrates how ligand binding changes the conformational equilibria of both unstructured G-rich DNA sequences and K+-folded G-quadruplexes. The results demonstrate that K+ free c-MYC and h-TELO exist as unfolded and partially folded conformations. The binding of BTC shifts the equilibria of both investigated DNA sequences towards the folded G-quadruplex structure, increases the diffusion coefficients and induces faster end-to-end contact formation. BTC recognizes a minor conformation of the c-MYC quadruplex and the two-tetrad basket conformations of the h-TELO quadruplex.
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Affiliation(s)
- Manish Debnath
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Shirsendu Ghosh
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India
| | - Deepanjan Panda
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology , Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ) , Max-von-Laue Strasse 7 , 60438 , Frankfurt am Main , Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology , Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ) , Max-von-Laue Strasse 7 , 60438 , Frankfurt am Main , Germany
| | - Kankan Bhattacharyya
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India
| | - Jyotirmayee Dash
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
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26
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Abstract
Herein we report the design, synthesis, biophysical and biological evaluation of triazole containing prolinamide derivatives as selectivec-MYCG-quadruplex binding ligands.
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Affiliation(s)
- Ajay Chauhan
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Sushovan Paladhi
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
- Department of Organic Chemistry
| | - Manish Debnath
- Department of Organic Chemistry
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Jyotirmayee Dash
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
- Department of Organic Chemistry
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27
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Biswal DK, Konhar R, Debnath M, Tandon V. Complete mitochondrial genome annotation of the giant intestinal fluke, Fasciolopsis buski (Indian isolate) as revealed by ion torrent and illuminanext-generation sequencing. Mitochondrial DNA B Resour 2016; 1:693-695. [PMID: 34395880 PMCID: PMC7875049 DOI: 10.1080/23802359.2016.1222249] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The complete mitogenome sequences of the intestinal fluke Fasciolopsis buski are presented for the first time in this study. It is 14,119 bp long and is thus the shortest trematode mitochondrial genome sequenced to date. The F. buski mtDNA genome has a close resemblance with F. hepatica and has a similar gene order tallying with that of other trematodes. The overall base composition of F. buski mitogenome is 17.89% for A, 9.16% for C, 27.59% for G and 45.36% for T, and has a GC content of 36.75%. The assembled mitogenome (GenBank accession number KX449331) consists of 12 protein-coding genes (PCGs), 22 transfer RNAs and two ribosomal RNA genes. The mtDNA for the intestinal fluke reported herein would help investigate Fasciolidae taxonomy and systematics with the aid of mtDNA NGS data.
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Affiliation(s)
| | - Ruchishree Konhar
- Bioinformatics Centre, North Eastern Hill University, Shillong, India
| | - Manish Debnath
- Bioinformatics Centre, North Eastern Hill University, Shillong, India
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28
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Oliveira J, Debnath M, Etain B, Bennabi M, Hamdani N, Lajnef M, Bengoufa D, Fortier C, Boukouaci W, Bellivier F, Kahn JP, Henry C, Charron D, Krishnamoorthy R, Leboyer M, Tamouza R. Violent suicidal behaviour in bipolar disorder is associated with nitric oxide synthase 3 gene polymorphism. Acta Psychiatr Scand 2015; 132:218-25. [PMID: 25939888 DOI: 10.1111/acps.12433] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/15/2015] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Given the importance of nitric oxide system in oxidative stress, inflammation, neurotransmission and cerebrovascular tone regulation, we postulated its potential dysfunction in bipolar disorder (BD) and suicide. By simultaneously analysing variants of three isoforms of nitric oxide synthase (NOS) genes, we explored interindividual genetic liability to suicidal behaviour in BD. METHOD A total of 536 patients with BD (DSM-IV) and 160 healthy controls were genotyped for functionally relevant NOS1, NOS2 and NOS3 polymorphisms. History of suicidal behaviour and violent suicide attempt was documented for 511 patients with BD. Chi-squared test was used to perform genetic association analyses and logistic regression to test for gene-gene interactions. RESULTS NOS3 rs1799983 T homozygous state was associated with violent suicide attempts (26.4% vs. 10.8%, in patients and controls, P = 0.002, corrected P (Pc) = 0.004, OR: 2.96, 95% CI = 1.33-6.34), and this association was restricted to the early-onset BD subgroup (37.9% vs. 10.8%, in early-onset BD and controls, P = 0.0003, Pc = 0.0006 OR: 5.05, 95% CI: 1.95-12.45), while we found no association with BD per se and no gene-gene interactions. CONCLUSION Our results bring further evidence for the potential involvement of endothelial NOS gene variants in susceptibility to suicidal behaviour. Future exploration of this pathway on larger cohort of suicidal behaviour is warranted.
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Affiliation(s)
- J Oliveira
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France
| | - M Debnath
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France
| | - B Etain
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - M Bennabi
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France
| | - N Hamdani
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - M Lajnef
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France
| | - D Bengoufa
- Laboratoire Jean Dausset and LabEx Transplantex, Hôpital Saint Louis, Paris, France
| | - C Fortier
- Laboratoire Jean Dausset and LabEx Transplantex, Hôpital Saint Louis, Paris, France
| | - W Boukouaci
- INSERM, U1160, Hôpital Saint Louis, Paris, France
| | - F Bellivier
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - J-P Kahn
- Fondation FondaMental, Créteil, France.,Service de Psychiatrie et Psychologie Clinique, CHU de Nancy, Hôpitaux de Brabois, Vandoeuvre Les Nancy, France
| | - C Henry
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - D Charron
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France.,Laboratoire Jean Dausset and LabEx Transplantex, Hôpital Saint Louis, Paris, France.,Sorbonne Paris-Cité, Université Paris Diderot, Paris, France
| | | | - M Leboyer
- Fondation FondaMental, Créteil, France.,INSERM, U955, Psychopathologie et Génétique des maladies psychiatriques, Créteil, France.,Faculté de Médecine, Université Paris-Est, Créteil, France.,AP-HP, Pôle de Psychiatrie et d'Addictologie des Hôpitaux Universitaires Henri Mondor, Créteil, France
| | - R Tamouza
- INSERM, U1160, Hôpital Saint Louis, Paris, France.,Fondation FondaMental, Créteil, France.,Laboratoire Jean Dausset and LabEx Transplantex, Hôpital Saint Louis, Paris, France.,Sorbonne Paris-Cité, Université Paris Diderot, Paris, France
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Panda D, Debnath M, Mandal S, Bessi I, Schwalbe H, Dash J. A Nucleus-Imaging Probe That Selectively Stabilizes a Minor Conformation of c-MYC G-quadruplex and Down-regulates c-MYC Transcription in Human Cancer Cells. Sci Rep 2015; 5:13183. [PMID: 26286633 PMCID: PMC4541407 DOI: 10.1038/srep13183] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/17/2015] [Indexed: 12/27/2022] Open
Abstract
The c-MYC proto-oncogene is a regulator of fundamental cellular processes such as cell cycle progression and apoptosis. The development of novel c-MYC inhibitors that can act by targeting the c-MYC DNA G-quadruplex at the level of transcription would provide potential insight into structure-based design of small molecules and lead to a promising arena for cancer therapy. Herein we report our finding that two simple bis-triazolylcarbazole derivatives can inhibit c-MYC transcription, possibly by stabilizing the c-MYC G-quadruplex. These compounds are prepared using a facile and modular approach based on Cu(I) catalysed azide and alkyne cycloaddition. A carbazole ligand with carboxamide side chains is found to be microenvironment-sensitive and highly selective for "turn-on" detection of c-MYC quadruplex over duplex DNA. This fluorescent probe is applicable to visualize the cellular nucleus in living cells. Interestingly, the ligand binds to c-MYC in an asymmetric fashion and selects the minor-populated conformer via conformational selection.
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Affiliation(s)
- Deepanjan Panda
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Manish Debnath
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Samir Mandal
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt and Centre for Biomolecular, Magnetic Resonance, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt and Centre for Biomolecular, Magnetic Resonance, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Jyotirmayee Dash
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
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30
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Rajasekaran A, Shivakumar V, Kalmady SV, Narayanaswamy JC, Venugopal D, Amaresha AC, Venkatasubramanian G, Debnath M. Soluble human leukocyte antigen (sHLA)-G levels may predict early onset of schizophrenia in male patients. ACTA ACUST UNITED AC 2015; 86:36-7. [DOI: 10.1111/tan.12589] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 11/28/2022]
Affiliation(s)
- A. Rajasekaran
- Department of Human Genetics; National Institute of Mental Health and Neurosciences; Bangalore India
- Translational Psychiatry Laboratory; Neurobiology Research Centre, National Institute of Mental Health and Neurosciences; Bangalore India
| | - V. Shivakumar
- Translational Psychiatry Laboratory; Neurobiology Research Centre, National Institute of Mental Health and Neurosciences; Bangalore India
- Department of Psychiatry; National Institute of Mental Health and Neurosciences; Bangalore India
| | - S. V. Kalmady
- Translational Psychiatry Laboratory; Neurobiology Research Centre, National Institute of Mental Health and Neurosciences; Bangalore India
- Department of Psychiatry; National Institute of Mental Health and Neurosciences; Bangalore India
| | - J. C. Narayanaswamy
- Translational Psychiatry Laboratory; Neurobiology Research Centre, National Institute of Mental Health and Neurosciences; Bangalore India
- Department of Psychiatry; National Institute of Mental Health and Neurosciences; Bangalore India
| | - D. Venugopal
- Department of Human Genetics; National Institute of Mental Health and Neurosciences; Bangalore India
- Translational Psychiatry Laboratory; Neurobiology Research Centre, National Institute of Mental Health and Neurosciences; Bangalore India
| | - A. C. Amaresha
- Translational Psychiatry Laboratory; Neurobiology Research Centre, National Institute of Mental Health and Neurosciences; Bangalore India
| | - G. Venkatasubramanian
- Translational Psychiatry Laboratory; Neurobiology Research Centre, National Institute of Mental Health and Neurosciences; Bangalore India
- Department of Psychiatry; National Institute of Mental Health and Neurosciences; Bangalore India
| | - M. Debnath
- Department of Human Genetics; National Institute of Mental Health and Neurosciences; Bangalore India
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31
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Das RN, Debnath M, Gaurav A, Dash J. Environment-Sensitive Probes Containing a 2,6-Diethynylpyridine Motif for Fluorescence Turn-On Detection and Induction of Nanoarchitectures of Human Telomeric Quadruplex. Chemistry 2014; 20:16688-93. [DOI: 10.1002/chem.201404795] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Indexed: 12/24/2022]
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32
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Chauhan A, Paladhi S, Debnath M, Mandal S, Das RN, Bhowmik S, Dash J. A small molecule peptidomimetic that binds to c-KIT1 G-quadruplex and exhibits antiproliferative properties in cancer cells. Bioorg Med Chem 2014; 22:4422-9. [DOI: 10.1016/j.bmc.2014.05.060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/19/2014] [Accepted: 05/28/2014] [Indexed: 10/25/2022]
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33
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Sarkar K, Debnath M, Kundu P. Preparation of low toxic fluorescent chitosan-graft-polyethyleneimine copolymer for gene carrier. Carbohydr Polym 2013; 92:2048-57. [DOI: 10.1016/j.carbpol.2012.11.067] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 11/23/2012] [Accepted: 11/23/2012] [Indexed: 10/27/2022]
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34
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Biswal DK, Debnath M, Kumar S, Tandon P. Phylogenetic reconstruction in the order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding. BMC Bioinformatics 2012; 13 Suppl 17:S26. [PMID: 23282079 PMCID: PMC3521246 DOI: 10.1186/1471-2105-13-s17-s26] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Nymphaeales (waterlilly and relatives) lineage has diverged as the second branch of basal angiosperms and comprises of two families: Cabombaceae and Nymphaceae. The classification of Nymphaeales and phylogeny within the flowering plants are quite intriguing as several systems (Thorne system, Dahlgren system, Cronquist system, Takhtajan system and APG III system (Angiosperm Phylogeny Group III system) have attempted to redefine the Nymphaeales taxonomy. There have been also fossil records consisting especially of seeds, pollen, stems, leaves and flowers as early as the lower Cretaceous. Here we present an in silico study of the order Nymphaeales taking maturaseK (matK) and internal transcribed spacer (ITS2) as biomarkers for phylogeny reconstruction (using character-based methods and Bayesian approach) and identification of motifs for DNA barcoding. RESULTS The Maximum Likelihood (ML) and Bayesian approach yielded congruent fully resolved and well-supported trees using a concatenated (ITS2+ matK) supermatrix aligned dataset. The taxon sampling corroborates the monophyly of Cabombaceae. Nuphar emerges as a monophyletic clade in the family Nymphaeaceae while there are slight discrepancies in the monophyletic nature of the genera Nymphaea owing to Victoria-Euryale and Ondinea grouping in the same node of Nymphaeaceae. ITS2 secondary structures alignment corroborate the primary sequence analysis. Hydatellaceae emerged as a sister clade to Nymphaeaceae and had a basal lineage amongst the water lilly clades. Species from Cycas and Ginkgo were taken as outgroups and were rooted in the overall tree topology from various methods. CONCLUSIONS MatK genes are fast evolving highly variant regions of plant chloroplast DNA that can serve as potential biomarkers for DNA barcoding and also in generating primers for angiosperms with identification of unique motif regions. We have reported unique genus specific motif regions in the Order Nymphaeles from matK dataset which can be further validated for barcoding and designing of PCR primers. Our analysis using a novel approach of sequence-structure alignment and phylogenetic reconstruction using molecular morphometrics congrue with the current placement of Hydatellaceae within the early-divergent angiosperm order Nymphaeales. The results underscore the fact that more diverse genera, if not fully resolved to be monophyletic, should be represented by all major lineages.
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Affiliation(s)
- Devendra Kumar Biswal
- Bioinformatics Centre, North Eastern Hill University, Shillong 793022, Meghalaya, India
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35
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Gupta N, Gundampati RK, Debnath M. Optimization of media composition for D-amino acid oxidase production by Trigonopsis variabilis using biostatistical analysis. Indian J Biochem Biophys 2012; 49:272-278. [PMID: 23077789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
D-amino acid oxidase (DAAO) is biotechnologically relevant enzyme that is used in various food and pharmaceutical industries. DAAO from the yeast Trigonopsis variabilis is an important agent for use in commercial applications because of its high activity with cephalosporin C and is reasonable resistant to the oxidants O2 and H2O2 byproducts of reaction. In this study, response surface methodology (RSM) in shake flask culture was used to enhance the production of DAAO from T. variabilis by optimization of fermentation media composition. The effects of six factors (DL-alanine, glucose, pH, ZnSO4, (NH4)2SO4 and temperature) were evaluated on DAAO production. Results of Placket-Burman design showed that DL-alanine, pH, glucose and ZnSO4 were significant factors for DAAO production (P<0.05). The optimum values of media components as predicted by the central composite design were inducer (DL-alanine) concentration 3 g/L, pH 7.7, glucose 17 g/L and ZnSO4 34 mg/L. At these optimum values of media composition, maximum production of DAAO was 153 U/g yeast dry weight. Two-fold increase in DAAO production was achieved after optimization of the physical parameters by RSM.
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Affiliation(s)
- Neeraj Gupta
- School of Biochemical Engineering, Indian Institute of Technology, Banaras Hindu University, Varanasi 221005, India
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36
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Ikonomovic M, Price J, Abrahamson E, Mathis C, Paljug W, Debnath M, Shao L, Becker C, Hamilton R, Klunk W. Direct Correlations of [H-3]Flutemetamol Binding with [H-3]PiB Binding and Amyloid-beta Concentration and Plaque Load in [C-11]PiB Imaged Brains (S34.002). Neurology 2012. [DOI: 10.1212/wnl.78.1_meetingabstracts.s34.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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37
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Dolui AK, Debnath M. Antifeedant activity of plant extracts to an insect Helopeltis theivora. J Environ Biol 2010; 31:557-559. [PMID: 21387902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The different solvent extracts (viz Petroleum ether Ethyl acetate and Methanol) obtained from leaves and flowers of Heliotropium indicum and Spilanthes calva were screened for antifeedant activity against Helopeltis theivora. All the six different extracts showed antifeedant activity at four different concentrations. The methanolic extracts of leaves of Heliotropium indicum and Spilanthes calva exhibited significant activity at 4% concentration. The numbers of spots produced were only 18.67 and 22.67 respectively which are significantly less than the numberof spots produced in control (104.00 and 93.33 respectively). The treatment with methanolic extracts of flowers of both the plants significantly reduced the number of feeding spots to 22.33 and 23.67 respectively in comparison to the control values of 101.33. All the activities are dose dependent. The mean results with SEM (mean +/- SE) were statistically significant at 1% level (p<0.01) for three observations.
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Affiliation(s)
- A K Dolui
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh - 786 004, India
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38
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Abstract
The frequency of HLA-A and HLA-B locus alleles was studied by using polymerase chain reaction-based sequence-specific primer method in a very primitive and vanishing sub-Himalayan Indian Tribe, the Toto population of North Bengal. The Toto, a Mongoloid tribe with a population size of 1172 reside only in the Totopara of Jalpaiguri district of North Bengal. We studied 40 individuals and observed some high frequency alleles when compared to other Indian tribal, non-tribal, and major world populations. Particularly, the frequency of HLA-B14 was 32.5% in the Toto population, the highest known frequency reported in any population in the world. This indigenous tribal population may harbour novel HLA alleles and unique haplotypes which extensive HLA genotyping will help to reveal, and thus further our understanding of their genetic admixture and migration patterns.
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Affiliation(s)
- M Debnath
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Siliguri, West Bengal, India
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39
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Debnath M, Chaudhuri TK. The role of HLA-G in cytokine homeostasis during early pregnancy complicated with maternal infections: a novel etiopathological approach to the neurodevelopmental understanding of schizophrenia. Med Hypotheses 2005; 66:286-93. [PMID: 16183209 DOI: 10.1016/j.mehy.2005.06.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [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: 06/08/2005] [Revised: 06/17/2005] [Accepted: 06/21/2005] [Indexed: 10/25/2022]
Abstract
Schizophrenia is perhaps the most enigmatic and tragic psychotic disorder with remarkable mortality and morbidity. Schizophrenia is complex and clinically a heterogeneous disorder. The etiological basis of schizophrenia ranges from autoimmune to neurodevelopmental hypothesis in one hand and involvement of different major gene segment with susceptibility loci on the other. Recently, neurodevelopmental hypothesis gained much impetus over the other domain. To support the neurodevelopmental basis, a number of investigations have shown that maternal infections during pregnancy increases the risk of the offspring developing schizophrenia and other neurodevelopmental disorders. The pathological mechanisms underlying this phenomenon is largely unknown. Many have suggested the involvement of different immune markers and shown that cytokines generated in response to maternal infection alter early brain development through their inflammatory activity. However, these findings have escaped discussion on various important issues related to cytokine homeostasis which depends on a large number of immune parameters including non-classical HLA-G molecules. Infections during early stages of pregnancy may alter cytokine regulation by disturbing the whole uterine immune milieu. To elucidate this issue, authors have tried to correlate the possible relationships between maternal infections and aberration of immune networking at the feto-maternal interface and their subsequent influence on the structural and functional abnormalities of the developing brain. The authors hypothesize that there exists a counter regulatory interaction among proinflammatory cytokines like TNF-alpha, HLA-G molecules and different immune cells like NK cells. We emphasize that HLA-G molecules are the novel immune players which maintain the immune homeostasis during early pregnancy in a manner that it can protect developing fetus from maternal immune attack. However, maternal infections may lead to the disturbance of HLA-G expression which in turn may fail to maintain its otherwise inhibitory potential to down regulate the detrimental inflammatory cytokines. Investigation on such interaction may unravel novel molecular mechanisms of neurodevelopmental basis of schizophrenia. Testing of our proposed hypothesis on animal models and on in vitro derived extravillous trophoblast cell lines holds promise of great insights to usher a new dimension of schizophrenia research and for developing new therapeutic strategies for better treatment and to adopt genetic prediction in schizophrenia management paradigm.
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Affiliation(s)
- M Debnath
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Raja Rammohan PUR, Siliguri-734430, WB, India
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40
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Tulsawani RK, Debnath M, Pant SC, Kumar O, Prakash AO, Vijayaraghavan R, Bhattacharya R. Effect of sub-acute oral cyanide administration in rats: Protective efficacy of alpha-ketoglutarate and sodium thiosulfate. Chem Biol Interact 2005; 156:1-12. [PMID: 16154552 DOI: 10.1016/j.cbi.2005.05.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2005] [Revised: 05/03/2005] [Accepted: 05/03/2005] [Indexed: 11/15/2022]
Abstract
Chronic toxicity of cyanide in humans and animals has been previously described. Alpha-ketoglutarate (alpha-KG) and sodium thiosulfate (STS) are known to confer remarkable protection against acute cyanide poisoning in rodents. Their efficacy against sub-acute or chronic cyanide exposure is not known. The objective of the present study was to assess the sub-acute toxicity of potassium cyanide (KCN) in female rats following oral administration of 7.0 mg/kg (0.5 LD50) for 14 d. The effect of alpha-KG (oral; 1.0 g/kg) and/or STS (intraperitoneal, 1.0 g/kg) on cyanide toxicity was also evaluated. Various hematological and biochemical indices were determined after 7 d of treatment and additional parameters like organ-body weight index (OBI) and histology of brain, heart, lung, liver, kidney and spleen were performed after 14 and 21 d (recovery group) of cyanide exposure. Sub-acute exposure of KCN did not produce any significant change in body weight of the animals, OBI, hematology and the levels of blood urea, creatinine, aspartate aminotransferase, triiodothyronine (T3) and tetraiodothyronine (T4). The levels of temporal glutathione disulfide (GSSG) and hepatic malondialdehyde (MDA), reduced glutathione (GSH) and GSSG were unaffected. However, in KCN treated animals elevated levels of blood glucose and reduced levels of alanine aminotransferase were observed. Activities of cytochrome c oxidase in the brain and rhodanese in the liver were diminished. Reduced levels of GSH and enhanced levels of MDA in brain were observed. Increased levels of blood thiocyanate were observed in all the treatments of KCN. Additionally, KCN also produced various histological changes in the brain, heart, liver and kidney. Although, treatment of alpha-KG and STS alone significantly blunted the toxicity of KCN, concomitant use of both interventions afforded to maximum protection. This study indicates a promising role of alpha-KG and STS for the treatment of prolonged cyanide exposures.
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Affiliation(s)
- R K Tulsawani
- Division of Pharmacology and Toxicology, Defense Research and Development Establishment, Jhansi Road, Gwalior 474 002 (MP), India
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41
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Gupta MR, Sarkar S, Ghosh S, Debnath M, Khan M. Effect of nonadiabaticity of dust charge variation on dust acoustic waves: generation of dust acoustic shock waves. Phys Rev E Stat Nonlin Soft Matter Phys 2001; 63:046406. [PMID: 11308955 DOI: 10.1103/physreve.63.046406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2000] [Revised: 10/02/2000] [Indexed: 05/23/2023]
Abstract
The effect of nonadiabaticity of dust charge variation arising due to small nonzero values of tau(ch)/tau(d) has been studied where tau(ch) and tau(d) are the dust charging and dust hydrodynamical time scales on the nonlinear propagation of dust acoustic waves. Analytical investigation shows that the propagation of a small amplitude wave is governed by a Korteweg-de Vries (KdV) Burger equation. Notwithstanding the soliton decay, the "soliton mass" is conserved, but the dissipative term leads to the development of a noise tail. Nonadiabaticity generated dissipative effect causes the generation of a dust acoustic shock wave having oscillatory behavior on the downstream side. Numerical investigations reveal that the propagation of a large amplitude dust acoustic shock wave with dust density enhancement may occur only for Mach numbers lying between a minimum and a maximum value whose dependence on the dusty plasma parameters is presented.
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Affiliation(s)
- M R Gupta
- Centre For Plasma Studies, Faculty of Science Jadavpur University, Calcutta 700 032, India
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42
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Debnath M, Das SK, Ghosh P, Mandal BB, Chaudhuri TK. Role of hla class-I antigens in delusional disorder. Indian J Psychiatry 2000; 42:275-9. [PMID: 21407957 PMCID: PMC2958352] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The investigation was conducted to find out whether there is any association between delusional disorder and HLA antigens. The sample comprised 50 patients with delusional disorder and 282 control samples collected from normal controls. Statistical analysis revealed that the frequency of A3 antigen of the locus A are significantly higher. In case of HLA - B locus significantly higher frequency of B5 and B21 antigens have also been observed. The present study shows that there may be some association of HLA class-1 antigens with delusional disorder.
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Affiliation(s)
- M Debnath
- MONOJIT DEBNATH, Junior Research Fellow, Cellular Immunology Lab , Deptt. of Zoology, North Bengal University, Siliguri, West Bengal
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Bhattacharya S, Gupta VS, Prabhune AA, SivaRaman H, Debnath M, Ranjekar PK. Studies of operational variables in batch mode for genetically engineered Escherichia coli cells containing penicillin acylase. Enzyme Microb Technol 1993; 15:1070-3. [PMID: 7764296 DOI: 10.1016/0141-0229(93)90057-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A recombinant Escherichia coli was constructed by cloning the penicillin acylase gene from E. coli ATCC 11105. The cloning was carried out using a recombinant plasmid pUSAD2 harboring the pac gene. The recombinant E. coli DH 5 cells were used as a biocatalyst and were studied in a batch reactor for determination of optimum value for some of the process parameters, such as effect of pH, temperature, substrate concentration, kLa and effect of carbon and nitrogen source on penicillin acylase production. These values were then compared with the values obtained with the standard parent strain. Whereas the cloned pac gene was found to produce higher levels of penicillin acylase constitutively, the process parameters remained about the same for both the parent and the recombinant.
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Affiliation(s)
- S Bhattacharya
- Biochemical Sciences Division, National Chemical Laboratory, Pune, India
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44
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Debnath M. Nonstationary behavior, super-, subharmonic, and combination resonances in a periodically forced damped anharmonic oscillator. Phys Rev A 1992; 45:3571-3579. [PMID: 9907405 DOI: 10.1103/physreva.45.3571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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45
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Debnath M, Chowdhury AR. Period doubling and hysteresis in a periodically forced, damped anharmonic oscillator. Phys Rev A 1991; 44:1049-1060. [PMID: 9906055 DOI: 10.1103/physreva.44.1049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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