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Bhattacharya A, Chauhan P, Singh SP, Narayan S, Bajpai RK, Dwivedi A, Mishra A. Bacillus tequilensis influences metabolite production in tomato and restores soil microbial diversity during Fusarium oxysporum infection. Plant Biol (Stuttg) 2024. [PMID: 38682466 DOI: 10.1111/plb.13647] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/08/2024] [Indexed: 05/01/2024]
Abstract
This study evaluates cellular damage, metabolite profiling, and defence-related gene expression in tomato plants and soil microflora during Fusarium wilt disease after treatment with B. tequilensis PBE-1. Histochemical analysis showed that PBE-1 was the primary line of defence through lignin deposition and reduced cell damage. GC-MS revealed that PBE-1 treatment ameliorated stress caused by F. oxysporum infection. PBE-1 also improved transpiration, photosynthesis, and stomatal conductance in tomato. qRT-PCR suggested that the defence-related genes FLS2, SERK, NOS, WRKYT, NHO, SAUR, and MYC2, which spread infection, were highly upregulated during F. oxysporum infection, but either downregulated or expressed normally in PBE-1 + P treated plants. This indicates that the plant not only perceives the bio-control agent as a non-pathogen entity but its presence in normal metabolism and gene expression within the host plant is maintained. The study further corroborated findings that application of PBE-1 does not cause ecological disturbances in the rhizosphere. Activity of soil microflora across four treatments, measured by Average Well Colour Development (AWCD), showed continuous increases from weeks 1 to 4 post-pathogen infection, with distinct substrate usage patterns like tannic and fumaric acids impacting microbial energy source utilization and diversity. Principal Component Analysis (PCA) and diversity indices like McIntosh, Shannon, and Simpson further illustrated significant microbial community shifts over the study period. In conclusion, our findings demonstrate that B. tequilensis PBE-1 is an ideal bio-agent for field application during Fusarium wilt disease management in tomato.
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Affiliation(s)
- A Bhattacharya
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - P Chauhan
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- School of Sciences, P P Savani University, Surat, Gujarat, India
| | - S P Singh
- Pharmacognosy Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - S Narayan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Plant Physiology Laboratory, CSIR-National Botanical Research Institute, Lucknow, India
| | - R K Bajpai
- Ex Director Research Services, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - A Dwivedi
- Photobiology Division, CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - A Mishra
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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2
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Oshternian SR, Loipfinger S, Bhattacharya A, Fehrmann RSN. Exploring combinations of dimensionality reduction, transfer learning, and regularization methods for predicting binary phenotypes with transcriptomic data. BMC Bioinformatics 2024; 25:167. [PMID: 38671342 PMCID: PMC11046904 DOI: 10.1186/s12859-024-05795-6] [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: 09/29/2023] [Accepted: 04/22/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Numerous transcriptomic-based models have been developed to predict or understand the fundamental mechanisms driving biological phenotypes. However, few models have successfully transitioned into clinical practice due to challenges associated with generalizability and interpretability. To address these issues, researchers have turned to dimensionality reduction methods and have begun implementing transfer learning approaches. METHODS In this study, we aimed to determine the optimal combination of dimensionality reduction and regularization methods for predictive modeling. We applied seven dimensionality reduction methods to various datasets, including two supervised methods (linear optimal low-rank projection and low-rank canonical correlation analysis), two unsupervised methods [principal component analysis and consensus independent component analysis (c-ICA)], and three methods [autoencoder (AE), adversarial variational autoencoder, and c-ICA] within a transfer learning framework, trained on > 140,000 transcriptomic profiles. To assess the performance of the different combinations, we used a cross-validation setup encapsulated within a permutation testing framework, analyzing 30 different transcriptomic datasets with binary phenotypes. Furthermore, we included datasets with small sample sizes and phenotypes of varying degrees of predictability, and we employed independent datasets for validation. RESULTS Our findings revealed that regularized models without dimensionality reduction achieved the highest predictive performance, challenging the necessity of dimensionality reduction when the primary goal is to achieve optimal predictive performance. However, models using AE and c-ICA with transfer learning for dimensionality reduction showed comparable performance, with enhanced interpretability and robustness of predictors, compared to models using non-dimensionality-reduced data. CONCLUSION These findings offer valuable insights into the optimal combination of strategies for enhancing the predictive performance, interpretability, and generalizability of transcriptomic-based models.
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Affiliation(s)
- S R Oshternian
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands
| | - S Loipfinger
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands
| | - A Bhattacharya
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands
| | - R S N Fehrmann
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
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Butail S, Bhattacharya A, Porfiri M. Estimating hidden relationships in dynamical systems: Discovering drivers of infection rates of COVID-19. Chaos 2024; 34:033117. [PMID: 38457848 DOI: 10.1063/5.0156338] [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] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 02/12/2024] [Indexed: 03/10/2024]
Abstract
Discovering causal influences among internal variables is a fundamental goal of complex systems research. This paper presents a framework for uncovering hidden relationships from limited time-series data by combining methods from nonlinear estimation and information theory. The approach is based on two sequential steps: first, we reconstruct a more complete state of the underlying dynamical system, and second, we calculate mutual information between pairs of internal state variables to detail causal dependencies. Equipped with time-series data related to the spread of COVID-19 from the past three years, we apply this approach to identify the drivers of falling and rising infections during the three main waves of infection in the Chicago metropolitan region. The unscented Kalman filter nonlinear estimation algorithm is implemented on an established epidemiological model of COVID-19, which we refine to include isolation, masking, loss of immunity, and stochastic transition rates. Through the systematic study of mutual information between infection rate and various stochastic parameters, we find that increased mobility, decreased mask use, and loss of immunity post sickness played a key role in rising infections, while falling infections were controlled by masking and isolation.
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Affiliation(s)
- S Butail
- Department of Mechanical Engineering, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - A Bhattacharya
- Department of Mechanical Engineering, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - M Porfiri
- Center for Urban Science and Progress, Department of Mechanical and Aerospace Engineering, and Department of Biomedical Engineering, Tandon School of Engineering, New York University, Brooklyn, New York 11201, USA
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Bhattacharya A, Bhattacharya S, Mishra R. Current status of research in rare genetic disorders and drug discovery in India. J Biosci 2024; 49:39. [PMID: 38384247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
The major health agenda of India so far has prioritized infectious diseases and public health. Given the socioeconomic conditions and poverty, a large fraction of the Indian population is exposed to infections from different pathogens, most notably enteric, parasitic, mycobacterial, and viral. In recent years, however, there has been a decline in the spread of these diseases with better surveillance, availability of therapy, improvement of socioeconomic conditions, and education. It is now being realized that non-communicable diseases are reaching epidemic proportions in India and there is a greater emphasis on the diagnosis and management of these diseases. The proportion of deaths due to non-communicable diseases has gone up substantially and was found to be about 61.8% of all deaths in 2016 (https://www.wbhealth.gov.in/NCD/).
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Mazumder M, Kumar S, Kumar D, Bhattacharya A, Gourinath S. Machine learning-based modulation of Ca 2+-binding affinity in EF-hand proteins and comparative structural insights into site-specific cooperative binding. Int J Biol Macromol 2023; 248:125866. [PMID: 37473887 DOI: 10.1016/j.ijbiomac.2023.125866] [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: 01/20/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 07/22/2023]
Abstract
Ca2+-binding proteins are present in almost all living organisms and different types display different levels of binding affinities for the cation. Here, we report two new scoring schemes enabling the user to estimate and manipulate the calcium binding affinities in EF hand containing proteins. To validate this, we designed a unique EF-hand loop capable of binding calcium with high affinity by altering five residues. The N-terminal domain of Entamoeba histolytica calcium-binding protein1 (NtEhCaBP1) is used for site-directed mutagenesis to incorporate the designed loop sequence into the second EF-hand motif of this protein, referred as Nt-EhCaBP1-EF2 mutant. The binding isotherms calculated using ITC calorimetry showed that Nt-EhCaBP1-EF2 mutant site binds Ca2+ with higher affinity than Wt-Nt-EhCaBP1, by ∼600 times. The crystal structure of the mutant displayed more compact Ca2+-coordination spheres in both of its EF loops than the structure of the wildtype protein. The compact coordination sphere of EF-2 causes the bend in the helix-3, which leads to the formation of unexpected hexamer of NtEhCaBP1-EF2 mutant structure. Further dynamic correlation analysis revealed that the mutation in the second EF loop changed the entire residue network of the monomer, resulting in stronger coordination of Ca2+ even in another EF-hand loop.
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Affiliation(s)
- Mohit Mazumder
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Pine Biotech, 1441 Canal Street, New Orleans, LA 70112, USA
| | - Sanjeev Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, Nashville, TN 37232-0146, USA
| | - Devbrat Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
| | - S Gourinath
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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Oosting SF, van der Veldt AAM, Fehrmann RSN, Bhattacharya A, van Binnendijk RS, GeurtsvanKessel CH, Dingemans AMC, Smit EF, Hiltermann TJN, den Hartog G, Jalving M, Westphal TT, de Wilt F, Ernst SM, Boerma A, van Zijl L, Rimmelzwaan GF, Kvistborg P, van Els CACM, Rots NY, van Baarle D, Haanen JBAG, de Vries EGE. Factors associated with long-term antibody response after COVID-19 vaccination in patients treated with systemic treatment for solid tumors. ESMO Open 2023; 8:101599. [PMID: 37450950 PMCID: PMC10284446 DOI: 10.1016/j.esmoop.2023.101599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 06/11/2023] [Indexed: 07/18/2023] Open
Affiliation(s)
- S F Oosting
- Department of Medical Oncology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - A A M van der Veldt
- Department of Medical Oncology, Erasmus Medical Centre, Rotterdam, the Netherlands; Department of Radiology & Nuclear Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands.
| | - R S N Fehrmann
- Department of Medical Oncology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - A Bhattacharya
- Department of Medical Oncology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - R S van Binnendijk
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - C H GeurtsvanKessel
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - A-M C Dingemans
- Department of Respiratory Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - E F Smit
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - T J N Hiltermann
- Department of Pulmonary Diseases, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - G den Hartog
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - M Jalving
- Department of Medical Oncology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - T T Westphal
- The Netherlands Comprehensive Cancer Organization, Utrecht, the Netherlands
| | - F de Wilt
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - S M Ernst
- Department of Respiratory Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - A Boerma
- Department of Medical Microbiology and Infection Prevention University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - L van Zijl
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - G F Rimmelzwaan
- Research Centre for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - P Kvistborg
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - C A C M van Els
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - N Y Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D van Baarle
- Department of Medical Microbiology and Infection Prevention University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - J B A G Haanen
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - E G E de Vries
- Department of Medical Oncology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
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7
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de Waard J, Bhattacharya A, de Boer MT, van Hemel BM, Esajas MD, Vermeulen KM, de Bock GH, Schuuring E, Wisman GBA. Identification of a methylation panel as an alternative triage to detect CIN3+ in hrHPV-positive self-samples from the population-based cervical cancer screening programme. Clin Epigenetics 2023; 15:103. [PMID: 37322534 PMCID: PMC10273737 DOI: 10.1186/s13148-023-01517-6] [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: 04/12/2023] [Accepted: 06/03/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND The Dutch population-based cervical cancer screening programme (PBS) consists of primary high-risk human papilloma virus (hrHPV) testing with cytology as triage test. In addition to cervical scraping by a general practitioner (GP), women are offered self-sampling to increase participation. Because cytological examination on self-sampled material is not feasible, collection of cervical samples from hrHPV-positive women by a GP is required. This study aims to design a methylation marker panel to detect CIN3 or worse (CIN3+) in hrHPV-positive self-samples from the Dutch PBS as an alternative triage test for cytology. METHODS Fifteen individual host DNA methylation markers with high sensitivity and specificity for CIN3+ were selected from literature and analysed using quantitative methylation-specific PCR (QMSP) on DNA from hrHPV-positive self-samples from 208 women with CIN2 or less (< CIN2) and 96 women with CIN3+. Diagnostic performance was determined by area under the curve (AUC) of receiver operating characteristic (ROC) analysis. Self-samples were divided into a train and test set. Hierarchical clustering analysis to identify input methylation markers, followed by model-based recursive partitioning and robustness analysis to construct a predictive model, was applied to design the best marker panel. RESULTS QMSP analysis of the 15 individual methylation markers showed discriminative DNA methylation levels between < CIN2 and CIN3+ for all markers (p < 0.05). The diagnostic performance analysis for CIN3+ showed an AUC of ≥ 0.7 (p < 0.001) for nine markers. Hierarchical clustering analysis resulted in seven clusters with methylation markers with similar methylation patterns (Spearman correlation> 0.5). Decision tree modeling revealed the best and most robust panel to contain ANKRD18CP, LHX8 and EPB41L3 with an AUC of 0.83 in the training set and 0.84 in the test set. Sensitivity to detect CIN3+ was 82% in the training set and 84% in the test set, with a specificity of 74% and 71%, respectively. Furthermore, all cancer cases (n = 5) were identified. CONCLUSION The combination of ANKRD18CP, LHX8 and EPB41L3 revealed good diagnostic performance in real-life self-sampled material. This panel shows clinical applicability to replace cytology in women using self-sampling in the Dutch PBS programme and avoids the extra GP visit after a hrHPV-positive self-sampling test.
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Affiliation(s)
- J de Waard
- Department of Gynaecologic Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, PO-Box 30001, 9700 RB, Groningen, The Netherlands
| | - A Bhattacharya
- Department of Medical Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M T de Boer
- Department of Gynaecologic Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, PO-Box 30001, 9700 RB, Groningen, The Netherlands
| | - B M van Hemel
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M D Esajas
- Department of Obstetrics and Gynaecology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - K M Vermeulen
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - G H de Bock
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - E Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - G B A Wisman
- Department of Gynaecologic Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, PO-Box 30001, 9700 RB, Groningen, The Netherlands.
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Schulte PA, Jacklitsch BL, Bhattacharya A, Chun H, Edwards N, Elliott KC, Flynn MA, Guerin R, Hodson L, Lincoln JM, MacMahon KL, Pendergrass S, Siven J, Vietas J. Updated assessment of occupational safety and health hazards of climate change. J Occup Environ Hyg 2023; 20:183-206. [PMID: 37104117 PMCID: PMC10443088 DOI: 10.1080/15459624.2023.2205468] [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] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Workers, particularly outdoor workers, are among the populations most disproportionately affected by climate-related hazards. However, scientific research and control actions to comprehensively address these hazards are notably absent. To assess this absence, a seven-category framework was developed in 2009 to characterize the scientific literature published from 1988-2008. Using this framework, a second assessment examined the literature published through 2014, and the current one examines literature from 2014-2021. The objectives were to present literature that updates the framework and related topics and increases awareness of the role of climate change in occupational safety and health. In general, there is substantial literature on worker hazards related to ambient temperatures, biological hazards, and extreme weather but less on air pollution, ultraviolet radiation, industrial transitions, and the built environment. There is growing literature on mental health and health equity issues related to climate change, but much more research is needed. The socioeconomic impacts of climate change also require more research. This study illustrates that workers are experiencing increased morbidity and mortality related to climate change. In all areas of climate-related worker risk, including geoengineering, research is needed on the causality and prevalence of hazards, along with surveillance to identify, and interventions for hazard prevention and control.
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Affiliation(s)
- P. A. Schulte
- Advanced Technologies and Laboratories International, Inc, Cincinnati, Ohio
| | - B. L. Jacklitsch
- Centers for Disease Control and Prevention (CDC), National Institute for Occupational Safety and Health (NIOSH), Cincinnati, Ohio
| | - A. Bhattacharya
- Centers for Disease Control and Prevention (CDC), National Institute for Occupational Safety and Health (NIOSH), Cincinnati, Ohio
| | - H. Chun
- Centers for Disease Control and Prevention (CDC), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Atlanta, Georgia
| | - N. Edwards
- Centers for Disease Control and Prevention (CDC), National Institute for Occupational Safety and Health (NIOSH), Morgantown, West Virginia
| | - K. C. Elliott
- Centers for Disease Control and Prevention (CDC), National Institute for Occupational Safety and Health (NIOSH), Anchorage, Alaska
| | - M. A. Flynn
- Centers for Disease Control and Prevention (CDC), National Institute for Occupational Safety and Health (NIOSH), Cincinnati, Ohio
| | - R. Guerin
- Centers for Disease Control and Prevention (CDC), National Institute for Occupational Safety and Health (NIOSH), Cincinnati, Ohio
| | - L. Hodson
- Centers for Disease Control and Prevention (CDC), National Institute for Occupational Safety and Health (NIOSH) (retired), Cincinnati, Ohio
| | - J. M. Lincoln
- Centers for Disease Control and Prevention (CDC), National Institute for Occupational Safety and Health (NIOSH), Cincinnati, Ohio
| | - K. L. MacMahon
- Centers for Disease Control and Prevention (CDC), National Institute for Occupational Safety and Health (NIOSH), Cincinnati, Ohio
| | - S. Pendergrass
- Centers for Disease Control and Prevention (CDC), National Institute for Occupational Safety and Health (NIOSH) (retired), Cincinnati, Ohio
| | - J. Siven
- Centers for Disease Control and Prevention (CDC), National Institute for Occupational Safety and Health (NIOSH), Cincinnati, Ohio
| | - J. Vietas
- Centers for Disease Control and Prevention (CDC), National Institute for Occupational Safety and Health (NIOSH), Cincinnati, Ohio
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van der Veldt AAM, Oosting SF, Fehrmann RSN, GeurtsvanKessel CH, van Binnendijk RS, Dingemans AMC, Smit EF, Hiltermann TJN, Hartog GD, Jalving M, Westphal TT, Bhattacharya A, de Wilt F, Ernst SM, Boerma A, van Zijl L, Rimmelzwaan GF, Kvistborg P, van Els CACM, Rots NY, van Baarle D, Haanen JBAG, de Vries EGE. One-year data on immunogenicity and breakthrough infections in patients with solid tumors vaccinated against COVID-19 during systemic cancer treatment. ESMO Open 2023; 8:100785. [PMID: 36764094 PMCID: PMC9829609 DOI: 10.1016/j.esmoop.2023.100785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Affiliation(s)
- A A M van der Veldt
- Department of Medical Oncology, Erasmus Medical Centre, Rotterdam, Netherlands; Radiology & Nuclear Medicine, Erasmus Medical Centre, Rotterdam, Netherlands.
| | - S F Oosting
- Department of Medical Oncology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - R S N Fehrmann
- Department of Medical Oncology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | | | - R S van Binnendijk
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - A-M C Dingemans
- Department of Respiratory Medicine Erasmus Medical Centre, Rotterdam, Netherlands
| | - E F Smit
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - T J N Hiltermann
- Department of Pulmonary Diseases, University Medical Centre Groningen, Amsterdam, Netherlands
| | - G den Hartog
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - M Jalving
- Department of Medical Oncology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - T T Westphal
- Comprehensive Cancer Organization the Netherlands, Utrecht, Netherlands
| | - A Bhattacharya
- Department of Medical Oncology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - F de Wilt
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, Netherlands
| | - S M Ernst
- Department of Respiratory Medicine Erasmus Medical Centre, Rotterdam, Netherlands
| | - A Boerma
- Department of Medical Microbiology and Infection Prevention, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - L van Zijl
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - G F Rimmelzwaan
- Research Centre for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - P Kvistborg
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - C A C M van Els
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands; Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - N Y Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - D van Baarle
- Department of Medical Microbiology and Infection Prevention, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - J B A G Haanen
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - E G E de Vries
- Department of Medical Oncology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
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Bhattacharya A, Maitra D. A comparative analysis between vertical rectus abdominis myocutaneous (VRAM) flap and transverse rectus abdominis myocutaneous (TRAM) flap as options for post-mastectomy chest wall reconstruction. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)01400-9] [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: 11/19/2022]
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Singh SS, Mansuri MS, Naiyer S, Kaur D, Agrahari M, Srinivasan S, Jhingan GD, Bhattacharya A, Bhattacharya S. Multi-omics analysis to characterize molecular adaptation of Entamoeba histolytica during serum stress. Proteomics 2022; 22:e2200148. [PMID: 36066285 DOI: 10.1002/pmic.202200148] [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: 04/11/2022] [Revised: 08/07/2022] [Accepted: 08/19/2022] [Indexed: 12/29/2022]
Abstract
Entamoeba histolytica is responsible for dysentery and extraintestinal disease in humans. To establish successful infection, it must generate adaptive response against stress due to host defense mechanisms. We have developed a robust proteomics workflow by combining miniaturized sample preparation, low flow-rate chromatography, and ultra-high sensitivity mass spectrometry, achieving increased proteome coverage, and further integrated proteomics and RNA-seq data to decipher regulation at translational and transcriptional levels. Label-free quantitative proteomics led to identification of 2344 proteins, an improvement over the maximum number identified in E. histolytica proteomic studies. In serum-starved cells, 127 proteins were differentially abundant and were associated with functions including antioxidant activity, cytoskeleton, translation, catalysis, and transport. The virulence factor, Gal/GalNAc-inhibitable lectin subunits, was significantly altered. Integration of transcriptomic and proteomic data revealed that only 30% genes were coordinately regulated at both transcriptional and translational levels. Some highly expressed transcripts did not change in protein abundance. Conversely, genes with no transcriptional change showed enhanced protein abundance, indicating post-transcriptional regulation. This multi-omics approach enables more refined gene expression analysis to understand the adaptive response of E. histolytica during growth stress.
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Affiliation(s)
- Shashi Shekhar Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Center for RNA Science and Therapeutics, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mohammad Shahid Mansuri
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sarah Naiyer
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Department of Immunology and Microbiology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Devinder Kaur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Central University of Punjab, Bathinda, Punjab, India
| | - Mridula Agrahari
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Vproteomics, Valerian Chem Private Limited, New Delhi, India
| | | | | | - Alok Bhattacharya
- Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, India
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12
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Sohn SY, Russell CD, Jamjoom AAB, Poon MT, Lawson McLean A, Ahmed AI, Abdulla MAH, Alalade A, Bailey M, Basu S, Baudracco I, Bayston R, Bhattacharya A, Bodkin P, Boissaud-Cooke M, Bojanic S, Brennan PM, Bulters DO, Buxton N, Chari A, Corns R, Coulter C, Coulter I, Critchley G, Dando A, Dardis R, Duddy J, Dyson E, Edwards R, Garnett M, Gatcher S, Georges H, Glancz LJ, Gray WP, Hallet J, Harte J, Haylock-Vize P, Hutchinson PJ, Humphreys H, Jenkinson MD, Joannides AJ, Kandasamy J, Kitchen J, Kolias AG, Loan JJM, Ma R, Madder H, Mallucci CL, Manning A, Mcelligott S, Mukerji N, Narayanamurthy H, O’Brien D, Okasha M, Papadopoulos M, Phan V, Phang I, Poots J, Rajaraman C, Roach J, Ross N, Sharouf F, Shastin D, Simms N, Steele L, Solth A, Tajsic T, Talibi S, Thanabalasundaram G, Vintu M, Wan Y, Wang D, Watkins L, Whitehouse K, Whitfield PC, Williams A, Zaben M. Comparison of suspected and confirmed internal EVD-related infections: a prospective multi-centre U.K. observational study. Open Forum Infect Dis 2022; 9:ofac480. [PMID: 36267249 PMCID: PMC9578167 DOI: 10.1093/ofid/ofac480] [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] [Received: 06/22/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Background Diagnosis of internal external ventricular drain (EVD)-related infections (iERI) is an area of diagnostic difficulty. Empiric treatment is often initiated on clinical suspicion. There is limited guidance around antimicrobial management of confirmed versus suspected iERI. Methods Data on patients requiring EVD insertion were collected from 21 neurosurgical units in the United Kingdom from 2014 to 2015. Confirmed iERI was defined as clinical suspicion of infection with positive cerebrospinal fluid (CSF) culture and/or Gram stain. Cerebrospinal fluid, blood, and clinical parameters and antimicrobial management were compared between the 2 groups. Mortality and Modified Rankin Scores were compared at 30 days post-EVD insertion. Results Internal EVD-related infection was suspected after 46 of 495 EVD insertions (9.3%), more common after an emergency insertion. Twenty-six of 46 were confirmed iERIs, mostly due to Staphylococci (16 of 26). When confirmed and suspected infections were compared, there were no differences in CSF white cell counts or glucose concentrations, nor peripheral blood white cell counts or C-reactive protein concentrations. The incidence of fever, meningism, and seizures was also similar, although altered consciousness was more common in people with confirmed iERI. Broad-spectrum antimicrobial usage was prevalent in both groups with no difference in median duration of therapy (10 days [interquartile range {IQR}, 7–24.5] for confirmed cases and 9.5 days [IQR, 5.75–14] for suspected, P = 0.3). Despite comparable baseline characteristics, suspected iERI was associated with lower mortality and better neurological outcomes. Conclusions Suspected iERI could represent sterile inflammation or lower bacterial load leading to false-negative cultures. There is a need for improved microbiology diagnostics and biomarkers of bacterial infection to permit accurate discrimination and improve antimicrobial stewardship.
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Affiliation(s)
- Sei Yon Sohn
- Division of Anaesthesia, University of Cambridge , Cambridge , U.K
| | - Clark D Russell
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute , Edinburgh , U.K
| | - Aimun AB Jamjoom
- Department of Clinical Neuroscience, Royal Infirmary of Edinburgh , Edinburgh , U.K
| | - Michael T Poon
- Department of Clinical Neuroscience, Royal Infirmary of Edinburgh , Edinburgh , U.K
| | - Aaron Lawson McLean
- Department of Neurosurgery, Jena University Hospital – Friedrich Schiller University Jena , Jena , Germany
| | - Aminul I Ahmed
- Wolfson CARD, King’s College London and Department of Neurosurgery, King’s College Hospital , London , U.K
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13
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Saxena M, Singh PS, Bhattacharya A. Composite Membranes Prepared by Polyvinyl Alcohol-Maleic Acid onto Polysulfone: Separation Performance of Tea Polyphenol. Macromol Res 2022. [DOI: 10.1007/s13233-022-0064-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Awasthi K, Bhattacharya S, Bhattacharya A. Tissue-specific isoform expression of GNE gene in human tissues. J Muscle Res Cell Motil 2022; 43:49-61. [PMID: 35524895 DOI: 10.1007/s10974-022-09618-0] [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: 08/03/2021] [Accepted: 04/11/2022] [Indexed: 11/28/2022]
Abstract
Mutations in the sialic acid biosynthesis enzyme GNE lead to a late-onset, debilitating neuromuscular disorder, GNE myopathy, characterized by progressive skeletal muscle weakness. The mechanisms responsible for skeletal muscle specificity, late-onset, and disease progression are unknown. Our main aim is to understand the reason for skeletal muscle-specific phenotype. To answer this question, we have analyzed the expression profile of the GNE gene and its multiple mRNA variants in different human tissues. A combinatorial approach encompassing bioinformatics tools and molecular biology techniques was used. NCBI, Ensembl, and GTEx were used for data mining. The expression analysis of GNE and its variants was performed with cDNA tissue panel using PCR and targeted RNA-seq. Among nine different GNE isoforms reported in this study, transcript variants 1, X1, and X2 were not tissue specific. Transcript variants 1, 6, X1, and X2, were found in skeletal muscles suggesting their possible role in GNE myopathy. In the current study, we present new data about GNE expression patterns in human tissues. Our results suggest that there may be a link between tissue-specific pathology and isoform pattern in skeletal muscles, which could provide clues for the development of new treatment strategies for GNE myopathy.
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Affiliation(s)
- Kapila Awasthi
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sudha Bhattacharya
- Ashoka University, Plot No. 2, Rajiv Gandhi Education City, P.O.Rai, Sonepat, Haryana, 131029, India
| | - Alok Bhattacharya
- Ashoka University, Plot No. 2, Rajiv Gandhi Education City, P.O.Rai, Sonepat, Haryana, 131029, India.
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15
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Ochatt S, Alan AR, Bhattacharya A, Hano C, Kiselev KV, Marconi PL, Otoni WC, Park SY, Tang KX, Weathers PJ. Secondary metabolites: a boon from plants, the best chemist in nature: preface from the editors. Plant Cell Tissue Organ Cult 2022; 149:1-6. [PMID: 35369037 PMCID: PMC8959786 DOI: 10.1007/s11240-022-02289-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- S. Ochatt
- Agroécologie, InstitutAgro Dijon, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - A. R. Alan
- Pamukkale University, Kinikli/Denizli, 20017 Pamukkale, Turkey
| | - A. Bhattacharya
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061 India
| | - C. Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE USC1328, Université d’Orléans, Eure & Loir Campus, Chartres, France
| | - K. V. Kiselev
- Institute of Biology and Soil Science, Department Biotechnology, Far East Branch of Russian Academy of Sciences, Vladivostok, 690034 Russia
| | - P. L. Marconi
- Faculty Biology- CEBBAD. Laboratory of Environmental Biotechnology, Maimónides University -CONICET, Ciudad de Buenos Aires, 1405 Argentina
| | - W. C. Otoni
- Plant Biology Department/BIOAGRO, Federal University of Viçosa, University Campus, Viçosa, MG 36570-900 Brazil
| | - S. Y. Park
- Department of Horticultural Sciences, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | - K. X. Tang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - P. J. Weathers
- Worcester Polytechnic Institute, Worcester, MA 01609 USA
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16
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Kaur D, Agrahari M, Bhattacharya A, Bhattacharya S. The non-LTR retrotransposons of Entamoeba histolytica: genomic organization and biology. Mol Genet Genomics 2022; 297:1-18. [PMID: 34999963 DOI: 10.1007/s00438-021-01843-5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/26/2021] [Indexed: 11/24/2022]
Abstract
Genome sequence analysis of Entamoeba species revealed various classes of transposable elements. While E. histolytica and E. dispar are rich in non-long terminal repeat (LTR) retrotransposons, E. invadens contains predominantly DNA transposons. Non-LTR retrotransposons of E. histolytica constitute three families of long interspersed nuclear elements (LINEs), and their short, nonautonomous partners, SINEs. They occupy ~ 11% of the genome. The EhLINE1/EhSINE1 family is the most abundant and best studied. EhLINE1 is 4.8 kb, with two ORFs that encode functions needed for retrotransposition. ORF1 codes for the nucleic acid-binding protein, and ORF2 has domains for reverse transcriptase (RT) and endonuclease (EN). Most copies of EhLINEs lack complete ORFs. ORF1p is expressed constitutively, but ORF2p is not detected. Retrotransposition could be demonstrated upon ectopic over expression of ORF2p, showing that retrotransposition machinery is functional. The newly retrotransposed sequences showed a high degree of recombination. In transcriptomic analysis, RNA-Seq reads were mapped to individual EhLINE1 copies. Although full-length copies were transcribed, no full-length 4.8 kb transcripts were seen. Rather, sense transcripts mapped to ORF1, RT and EN domains. Intriguingly, there was strong antisense transcription almost exclusively from the RT domain. These unique features of EhLINE1 could serve to attenuate retrotransposition in E. histolytica.
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Nagasaka M, Goto K, Gomez J, Hida T, Shu C, Lee C, Park K, Cho B, Lee J, Ou S, Bestvina C, Natale R, Haddish-Berhane N, Bhattacharya A, Verheijen R, Agrawal T, Knoblauch R, Govindan R. P50.04 Amivantamab in Combination With Chemotherapy in Patients With Advanced Non-Small Cell Lung Cancer (NSCLC). J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.532] [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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18
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Leeuwenburgh VC, Urzúa-Traslaviña CG, Bhattacharya A, Walvoort MTC, Jalving M, de Jong S, Fehrmann RSN. Robust metabolic transcriptional components in 34,494 patient-derived cancer-related samples and cell lines. Cancer Metab 2021; 9:35. [PMID: 34565468 PMCID: PMC8474886 DOI: 10.1186/s40170-021-00272-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/09/2021] [Indexed: 12/25/2022] Open
Abstract
Background Patient-derived bulk expression profiles of cancers can provide insight into the transcriptional changes that underlie reprogrammed metabolism in cancer. These profiles represent the average expression pattern of all heterogeneous tumor and non-tumor cells present in biopsies of tumor lesions. Hence, subtle transcriptional footprints of metabolic processes can be concealed by other biological processes and experimental artifacts. However, consensus independent component analyses (c-ICA) can capture statistically independent transcriptional footprints of both subtle and more pronounced metabolic processes. Methods We performed c-ICA with 34,494 bulk expression profiles of patient-derived tumor biopsies, non-cancer tissues, and cell lines. Gene set enrichment analysis with 608 gene sets that describe metabolic processes was performed to identify the transcriptional components enriched for metabolic processes (mTCs). The activity of these mTCs was determined in all samples to create a metabolic transcriptional landscape. Results A set of 555 mTCs was identified of which many were robust across different datasets, platforms, and patient-derived tissues and cell lines. We demonstrate how the metabolic transcriptional landscape defined by the activity of these mTCs in samples can be used to explore the associations between the metabolic transcriptome and drug sensitivities, patient outcomes, and the composition of the immune tumor microenvironment. Conclusions To facilitate the use of our transcriptional metabolic landscape, we have provided access to all data via a web portal (www.themetaboliclandscapeofcancer.com). We believe this resource will contribute to the formulation of new hypotheses on how to metabolically engage the tumor or its (immune) microenvironment. Supplementary Information The online version contains supplementary material available at 10.1186/s40170-021-00272-7.
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Affiliation(s)
- V C Leeuwenburgh
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands
| | - C G Urzúa-Traslaviña
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - A Bhattacharya
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - M T C Walvoort
- Department of Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands
| | - M Jalving
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - S de Jong
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - R S N Fehrmann
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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Bharadwaj R, Bhattacharya A, Somlata. Coordinated activity of amoebic formin and profilin are essential for phagocytosis. Mol Microbiol 2021; 116:974-995. [PMID: 34278607 DOI: 10.1111/mmi.14787] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 10/24/2022]
Abstract
For the protist parasite Entamoeba histolytica, endocytic processes, such as phagocytosis, are essential for its survival in the human gut. The actin cytoskeleton is involved in the formation of pseudopods and phagosomal vesicles by incorporating a number of actin-binding and modulating proteins along with actin in a temporal manner. The actin dynamics, which comprises polymerization, branching, and depolymerization is very tightly regulated and takes place directionally at the sites of initiation of phagocytosis. Formin and profilin are two actin-binding proteins that are known to regulate actin cytoskeleton dynamics and thereby, endocytic processes. In this article, we report the participation of formin and profilin in E. histolytica phagocytosis and propose that these two proteins interact with each other and their sequential recruitment at the site is required for the successful completion of phagocytosis. The evidence is based on detailed microscopic, live imaging, interaction studies, and expression downregulation. The cells downregulated for expression of formin show absence of profilin at the site of phagocytosis, whereas downregulation of profilin does not affect formin localization.
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Affiliation(s)
- Ravi Bharadwaj
- Department of Medicine, UMass Medical School, Worcester, MA, USA
| | | | - Somlata
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi, India
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20
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Agrawal T, Artis E, Xie J, Bhattacharya A, Haddish-Berhane N, Gopen T, Curtin J, Karkera J, Roshak A, Knoblauch R, Patel K. P76.74 PAPILLON: Randomized Phase 3 Study of Amivantamab Plus Chemotherapy vs Chemotherapy Alone in EGFR Exon20ins NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.1131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Barman C, Rath P, Bhattacharya A. A Non-Fourier Bioheat Transfer Model for Cryosurgery of Tumor Tissue with Minimum Collateral Damage. Comput Methods Programs Biomed 2021; 200:105857. [PMID: 33280936 DOI: 10.1016/j.cmpb.2020.105857] [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: 09/04/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND OBJECTIVES Incorporation of non-Fourier heat conduction while studying heat transfer phenomena in biological materials has emerged has an important approach as it predicts better and more realistic results than Fourier based models. In this article we have proposed a non-Fourier computational model and applied the same to simulate cryosurgery of lung tumor and attempted minimization of freezing damage of healthy lung tissue using pulsed laser irradiation. METHODS A non-Fourier bioheat transfer model for phase change in biological tissues is solved via a Fourier heat conduction based solution approach. A unified model is proposed combining all variants of bioheat models: Fourier's heat conduction based Pennes' bioheat model, hyperbolic heat conduction model and dual phase lag model. The proposed model takes into account the different thermophysical properties of frozen and unfrozen regions. In order to mimic the actual biotransport process, the blood perfusion and metabolic heat generation are switched off in the frozen region. Implicit source based enthalpy method is used to model phase change process. A new iterative enthalpy update equation is developed for capturing evolution of freezing front implicitly. Finite Volume based numerical discretization technique is used to discretize the governing PDE. The resulting discrete algebraic equation set is solved implicitly by Tri-diagonal Matrix Algorithm. The proposed model is verified with existing results from the literature. RESULTS For Fourier heat conduction, freezing time of 99.99% of tumor is 1247s, which increases to 1267s for τq= 5s (τT= 0s) and again reduces to 1255s for τq= 5s and τT= 3s. τq and τT are phase lag parameters for non-Fourier heat conduction. For τq= 5s and τT= 0.05s, the freezing damage of healthy tissue decreases by 23.76% when pulsed laser irradiation (Io = 106 W/m2) is used to warm the neighboring healthy tissue. CONCLUSIONS So non-Fourier bioheat transport models are better and more accurate in predicting temperature history, freezing time and freezing front propagation as compared to Fourier based models. Pulsed laser irradiation can prove to be a very efficient technique in minimizing collateral damage during cryosurgery.
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Affiliation(s)
- C Barman
- Heat Transfer Laboratory, School of Mechanical Sciences, Indian Institute of Technology, Bhubaneswar, Odisha, India, 752050
| | - P Rath
- Heat Transfer Laboratory, School of Mechanical Sciences, Indian Institute of Technology, Bhubaneswar, Odisha, India, 752050.
| | - A Bhattacharya
- Heat Transfer Laboratory, School of Mechanical Sciences, Indian Institute of Technology, Bhubaneswar, Odisha, India, 752050
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22
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Kaur D, Agrahari M, Singh SS, Mandal PK, Bhattacharya A, Bhattacharya S. Transcriptomic analysis of Entamoeba histolytica reveals domain-specific sense strand expression of LINE-encoded ORFs with massive antisense expression of RT domain. Plasmid 2021; 114:102560. [PMID: 33482228 DOI: 10.1016/j.plasmid.2021.102560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 09/21/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 11/29/2022]
Abstract
LINEs are retrotransposable elements found in diverse organisms. Their activity is kept in check by several mechanisms, including transcriptional silencing. Here we have analyzed the transcription status of LINE1 copies in the early-branching parasitic protist Entamoeba histolytica. Full-length EhLINE1 encodes ORF1, and ORF2 with reverse transcriptase (RT) and endonuclease (EN) domains. RNA-Seq analysis of EhLINE1 copies (both truncated and full-length) showed unique features. Firstly, although 20/41 transcribed copies were full-length, we failed to detect any full-length transcripts. Rather, sense-strand transcripts mapped to the functional domains- ORF1, RT and EN. Secondly, there was strong antisense transcription specifically from RT domain. No antisense transcripts were seen from ORF1. Antisense RT transcripts did not encode known functional peptides. They could possibly be involved in attenuating translation of RT domain, as we failed to detect ORF2p, whereas ORF1p was detectable. Lack of full-length transcripts and strong antisense RT expression may serve to limit EhLINE1 retrotransposition.
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Affiliation(s)
- Devinder Kaur
- School of Environmental Sciences, Jawaharlal Nehru University, India
| | - Mridula Agrahari
- School of Environmental Sciences, Jawaharlal Nehru University, India
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Naik K, Janal MN, Chen J, Bandary D, Brar B, Zhang S, Dolan JC, Schmidt BL, Albertson DG, Bhattacharya A. The Histopathology of Oral Cancer Pain in a Mouse Model and a Human Cohort. J Dent Res 2020; 100:194-200. [PMID: 33030108 DOI: 10.1177/0022034520961020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Oral cancer patients often have severe, chronic, and mechanically induced pain at the site of the primary cancer. Oral cancer pain is initiated and maintained in the cancer microenvironment and attributed to release of mediators that sensitize primary sensory nerves. This study was designed to investigate the histopathology associated with painful oral cancers in a preclinical model. The relationship of pain scores with pathologic variables was also investigated in a cohort of 72 oral cancer patients. Wild-type mice were exposed to the carcinogen, 4-nitroquinoline 1-oxide (4NQO). Nociceptive (pain) behavior was measured with the dolognawmeter, an operant device and assay for measuring functional and mechanical allodynia. Lesions developed on the tongues and esophagi of the 4NQO-treated animals and included hyperkeratoses, papillomas, dysplasias, and cancers. Papillomas included lesions with benign and dysplastic pathological features. Two histologic subtypes of squamous cell carcinomas (SCCs) were identified-SCCs with exophytic and invasive components associated with papillary lesions (pSCCs) and invasive SCCs without exophytic histology (iSCCs). Only the pSCC subtype of tongue cancer was associated with nociceptive behavior. Increased tumor size was associated with greater nociceptive behavior in the mouse model and more pain experienced by oral cancer patients. In addition, depth of invasion was associated with patient-reported pain. The pSCC histology identifies 4NQO-induced tongue cancers that are expected to be enriched for expression and release of nociceptive mediators.
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Affiliation(s)
- K Naik
- Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, NY, USA
| | - M N Janal
- Department of Epidemiology and Health Promotion, New York University College of Dentistry, New York, NY, USA
| | - J Chen
- New York University College of Dentistry, New York, NY, USA
| | - D Bandary
- New York University College of Dentistry, New York, NY, USA
| | - B Brar
- New York University College of Dentistry, New York, NY, USA
| | - S Zhang
- New York University College of Dentistry, New York, NY, USA
| | - J C Dolan
- Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, NY, USA
| | - B L Schmidt
- Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, NY, USA
| | - D G Albertson
- Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, NY, USA
| | - A Bhattacharya
- Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, NY, USA
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Awasthi K, Srivastava A, Bhattacharya S, Bhattacharya A. Tissue specific expression of sialic acid metabolic pathway: role in GNE myopathy. J Muscle Res Cell Motil 2020; 42:99-116. [PMID: 33029681 DOI: 10.1007/s10974-020-09590-7] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022]
Abstract
GNE myopathy is an adult-onset degenerative muscle disease that leads to extreme disability in patients. Biallelic mutations in the rate-limiting enzyme UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine-kinase (GNE) of sialic acid (SA) biosynthetic pathway, was shown to be the cause of this disease. Other genetic disorders with muscle pathology where defects in glycosylation are known. It is yet not clear why a defect in SA biosynthesis and glycosylation affect muscle cells selectively even though they are ubiquitously present in all tissues. Here we have comprehensively examined the complete SA metabolic pathway involving biosynthesis, sialylation, salvage, and catabolism. To understand the reason for tissue-specific phenotype caused by mutations in genes of this pathway, we analysed the expression of different SA pathway genes in various tissues, during the muscle tissue development and in muscle tissues from GNE myopathy patients (p.Met743Thr) using publicly available databases. We have also analysed gene co-expression networks with GNE in different tissues as well as gene interactions that are unique to muscle tissues only. The results do show a few muscle specific interactions involving ANLN, MYO16 and PRAMEF25 that could be involved in specific phenotype. Overall, our results suggest that SA biosynthetic and catabolic genes are expressed at a very low level in skeletal muscles that also display a unique gene interaction network.
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Affiliation(s)
- Kapila Awasthi
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Srivastava
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Amity Education Valley, Gurgaon, India.,Institute of Bioinformatics and Computational Biology, Visakhapatnam, Andhra Pradesh, India
| | - Sudha Bhattacharya
- Ashoka University, Plot No. 2, Rajiv Gandhi Education City, P.O.Rai, Sonepat, Haryana, 131029, India
| | - Alok Bhattacharya
- Ashoka University, Plot No. 2, Rajiv Gandhi Education City, P.O.Rai, Sonepat, Haryana, 131029, India.
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Bhattacharya A, Lenka A, Thomas M, Yadav R, Pal PK. Kinematic analysis of handwriting in patients of Parkinson's disease using various machine learning algorithms. Parkinsonism Relat Disord 2020. [DOI: 10.1016/j.parkreldis.2020.06.337] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Glazer R, Gao S, Yuan H, Ranjit S, Lu J, Xiang H, Bhattacharya A, Brandish P, Levi M. Targeting immune tolerance and stromal fibrosis with an LXR agonist in a conditional transgenic model of mammary fibrosis. Eur J Cancer 2020. [DOI: 10.1016/s0959-8049(20)31117-5] [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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Kavanal AJ, Bhattacharya A, Sharma A, Shukla J, Chattopadhyay A, Vatsa R, Rana N, Kaur G, Mittal BR. THU0531 A PROSPECTIVE STUDY EVALUATING THE ROLE OF 68GA-RGD2 PET/CT ANGIOGENESIS IMAGING IN ASSESSING DISEASE ACTIVITY AND TREATMENT RESPONSE IN RHEUMATOID ARTHRITIS AND ITS COMPARISON WITH DAS28. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.3276] [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: 11/04/2022]
Abstract
Background:PET/CT imaging of synovial angiogenesis using68Ga-RGD (cyclic tripeptide agent targeting αvβ3integrin) to study disease activity in rheumatoid arthritis (RA) has been demonstrated earlier in a few patients. However, post treatment changes in disease activity on68Ga-RGD2PET/CT imaging have not been adequately assessed.Objectives:To compare the performance of68Ga-RGD2PET/CT with disease activity score (DAS) 28 in assessing disease activity and treatment response in RA.Methods:Thirty patients (24F, 6M) aged 43±12 years with clinically diagnosed RA were prospectively studied. After calculation of DAS28 by a rheumatologist, all 30 patients underwent68Ga-RGD2PET/CT scan. Of these, 27 patients underwent a second68Ga-RGD2PET/CT scan and clinical assessment after at least 3 months of treatment. Total body and regional images of the upper limbs were acquired and interpreted by two nuclear medicine physicians blinded to the clinical findings. Joints showing focally increased tracer uptake compared to the background were considered positive and joints showing uptake equal to or less than background were considered negative. Data of 30 patients were used for inter-observer and inter-modality agreement calculations. Changes in PET parameters and DAS28 were compared in 27 patients to assess treatment response.Results:Out of 1560 joints examined in the initial scan, 394 were positive on PET/CT compared to 348 on clinical evaluation. Inter-observer agreement between nuclear medicine physicians was excellent (Cohen’s kappa 0.92, p<0.05) and inter-modality agreement between PET and clinical examination was moderate (Cohen’s kappa 0.55, p<0.05). The DAS28 and SUVmax values (highest and average) of 27 patients showed significant reduction on follow-up compared to the initial evaluation. There was significant correlation between percentage change in DAS28 and percentage change in scan parameters like PET positive joint counts (0.689, p<0.001), average SUVmax (0.712, p<0.001) and highest SUVmax values (0.558, p=0.003) of scan-positive joints in 27 patients. Additional advantages of68Ga-RGD2PET/CT included objective assessment, whole body evaluation of all small and large joints, and greater reproducibility.Conclusion:68Ga-RGD2PET/CT is a promising tool for objective assessment of disease activity and treatment response in patients with RA.Table 1.Clinical and PET parameters of the patientsParameterInitial data (n=27)Mean (SD)/Median (IQR)Follow-up data (n=27)Mean (SD)/Median (IQR)TJC(28)10 (5-13)3 (2-4)SJC(28)6 (3-7)1 (0-2)ESR25 (20-41)24 (18-35)PtGA6.0 (5.0-6.0)3.0 (2.0-4.0)DAS28(3)5.14 (0.85)3.74 (0.88)DAS28(4)5.60 (0.90)3.80 (0.96)PET positive Joints12 (7-8)4 (2-9)aSUVmax2.08 (1.68-2.52)1.79 (1.00-2.06)hSUVmax3.45 (2.71-4.70)3.34 (1.95-4.25)TJC/SJC: tender/swollen joint counts; ESR: erythrocyte sedimentation rate; PtGA: patients global assessment scale; DAS: disease activity score; aSUVmax/hSUVmax: average/highest SUVmax (maximum standardized uptake value); SD: standard deviation; IQR: interquartile rangeFigure 1.68Ga-RGD2PET scan of a 26-year female RA patient on treatment.A.Initial scan shows increased tracer uptake in multiple joints of upper and lower limbs and tendon sheaths of hands and ankle region (arrows); DAS28 was 4.56 (moderate disease activity) and ESR 12 mm/1sthour.B. Follow-up scan after 4 months shows resolution of tracer activity in the previously involved joints with only a mild focus persisting in the left knee joint; DAS28 was 1.73 (clinical remission according to ARA) and ESR 08 mm/1sthour.Acknowledgments:This study was supported by Indian Council of Medical Research, New Delhi [grant no.3/2/June-2017/PG-Thesis-HRD (23)]Disclosure of Interests:None declared
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Purkait S, Bhattacharya A, Bag A, Chattopadhyay R. Evaluation of antibiofilm efficacy of essential oil components β‐caryophyllene, cinnamaldehyde and eugenol alone and in combination against biofilm formation and preformed biofilms of
Listeria monocytogenes
and
Salmonella typhimurium. Lett Appl Microbiol 2020; 71:195-202. [DOI: 10.1111/lam.13308] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 12/20/2022]
Affiliation(s)
- S. Purkait
- Agricultural and Ecological Research Unit Indian Statistical Institute Kolkata India
| | - A. Bhattacharya
- Agricultural and Ecological Research Unit Indian Statistical Institute Kolkata India
| | - A. Bag
- Agricultural and Ecological Research Unit Indian Statistical Institute Kolkata India
| | - R.R. Chattopadhyay
- Agricultural and Ecological Research Unit Indian Statistical Institute Kolkata India
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Abstract
Calcium signaling plays a key role in many essential processes in almost all eukaryotic systems. It is believed that it may also be an important signaling system of the protist parasite Entamoeba histolytica. Motility, adhesion, cytolysis, and phagocytosis/trogocytosis are important steps in invasion and pathogenesis of E. histolytica, and Ca2+ signaling is thought to be associated with these processes leading to tissue invasion. There are a large number of Ca2+-binding proteins (CaBPs) in E. histolytica, and a number of these proteins appear to be associated with different steps in pathogenesis. The genome encodes 27 EF-hand–containing CaBPs in addition to a number of other Ca2+-binding domain/motif-containing proteins, which suggest intricate calcium signaling network in this parasite. Unlike other eukaryotes, a typical calmodulin-like protein has not been seen in E. histolytica. Though none of the CaBPs display sequence similarity with a typical calmodulin, extensive structural similarity has been seen in spite of lack of significant functional overlap with that of typical calmodulins. One of the unique features observed in E. histolytica is the identification of CaBPs (EhCaBP1, EhCaBP3) that have the ability to directly bind actin and modulate actin dynamics. Direct interaction of CaBPs with actin has not been seen in any other system. Pseudopod formation and phagocytosis are some of the processes that require actin dynamics, and some of the amoebic CaBPs (EhC2Pk, EhCaBP1, EhCaBP3, EhCaBP5) participate in this process. None of these E. histolytica CaBPs have any homolog in organisms other than different species of Entamoeba, suggesting a novel Ca2+ signaling pathway that has evolved in this genus.
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Affiliation(s)
- Mrigya Babuta
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- Department of Biology, Ashoka University, Sonepat, Haryana, India
- * E-mail:
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Purkait S, Bhattacharya A, Bag A, Chattopadhyay RR. Synergistic antibacterial, antifungal and antioxidant efficacy of cinnamon and clove essential oils in combination. Arch Microbiol 2020; 202:1439-1448. [PMID: 32185411 DOI: 10.1007/s00203-020-01858-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [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: 01/15/2020] [Revised: 02/25/2020] [Accepted: 03/04/2020] [Indexed: 12/01/2022]
Abstract
The present investigation aimed to evaluate antibacterial, antifungal and antioxidant efficacy of essential oils of three commonly used spices (black pepper, cinnamon and clove) in combination along with chemical characterization and toxicity evaluation. Among the possible combinations tested, cinnamon/clove oil combination showed synergistic antibacterial activity against foodborne bacteria Staphylococcus aureus, Listeria monocytogenes, Salmonella typhimurium and Pseudomonas aeruginosa and synergistic antifungal activity against Aspergillus niger as well as synergistic antioxidant potential in DPPH radical scavenging model system. GC-HRMS analysis revealed that out of thirteen identified components from clove oil, eugenol was found to be the main constituent of the oil; whereas out of twenty one identified constituents from cinnamon oil, the main component was cinnamaldehyde. Cinnamon/clove oil combination did not show any cytotoxic potential at recommended dosage level (IC50 > 2000 µg/ml). The results provide evidence that cinnamon/clove oil combination might indeed be used as a potential source of safe and effective novel natural antibacterial, antifungal and antioxidant blend in the food and pharmaceutical industries. To the best of our knowledge, this is the first time a combination of essential oils has been tested as natural preservatives to prevent both microbial proliferation and oxidative deterioration at sufficiently low concentrations.
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Affiliation(s)
- S Purkait
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India.
| | - A Bhattacharya
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India
| | - A Bag
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India
| | - R R Chattopadhyay
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India
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Dey D, Jingar P, Agrawal S, Shrivastava V, Bhattacharya A, Manhas J, Garg B, Ansari MT, Mridha AR, Sreenivas V, Khurana A, Sen S. Symphytum officinale augments osteogenesis in human bone marrow-derived mesenchymal stem cells in vitro as they differentiate into osteoblasts. J Ethnopharmacol 2020; 248:112329. [PMID: 31672526 DOI: 10.1016/j.jep.2019.112329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 08/05/2019] [Revised: 10/11/2019] [Accepted: 10/19/2019] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Mesenchymal stem cells (MSCs) are multipotent stem cells possessing regenerative potential. Symphytum officinale (SO) is a medicinal plant and in homoeopathic literature, believed to accelerate bone healing. AIM OF THE STUDY This study aimed to determine if homoeopathic doses of SO could augment osteogenesis in MSCs as they differentiate into osteoblasts in vitro. MATERIALS AND METHODS Bone marrow samples were obtained from patients who underwent bone grafting procedures (n = 15). MSCs were isolated, expanded and characterized by flow cytometry (CD90, CD105). Cytotoxicity of SO was evaluated by MTT assay. Osteogenic differentiation was induced in MSCs with β-glycerophosphate, ascorbic acid and dexamethasone over 2 weeks. Different homoeopathic doses of SO (MT, 3C, 6C, 12C and 30C) were added to the basic differentiation medium (BDM) and efficiency of MSCs differentiating into osteoblasts were measured by evaluating expression of Osteocalcin using flow cytometry, and alkaline phosphatase activity using ELISA. Gene expression analyses for osteoblast markers (Runx-2, Osteopontin and Osteocalcin) were evaluated in differentiated osteoblasts using qPCR. RESULTS Flow cytometry (CD90, CD105) detected MSCs isolated from bone marrow (93-98%). MTT assay showed that the selected doses of SO did not induce any cytotoxicity in MSCs (24 hours). The efficiency of osteogenic differentiation (2 weeks) for different doses of Symphytum officinale was determined by flow cytometry (n = 10) for osteoblast marker, Osteocalcin, and most doses of Symphytum officinale enhanced osteogenesis. Interestingly, gene expression analysis for Runx-2 (n = 10), Osteopontin (n = 10), Osteocalcin (n = 10) and alkaline phosphatase activity (n = 8) also showed increased osteogenesis with the addition of Symphytum officinale to BDM, specially mother tincture. CONCLUSIONS Our findings suggest that homoeopathic dose (specially mother tincture) of Symphytum officinale has the potential to enhance osteogenesis.
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Affiliation(s)
- D Dey
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - P Jingar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - S Agrawal
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - V Shrivastava
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - A Bhattacharya
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - J Manhas
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - B Garg
- Department of Orthopaedics, All India Institute of Medical Sciences, New Delhi, India
| | - M T Ansari
- Department of Orthopaedics, All India Institute of Medical Sciences, New Delhi, India
| | - A R Mridha
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - V Sreenivas
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
| | - A Khurana
- Central Council for Research in Homoeopathy, New Delhi, India
| | - S Sen
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
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Affiliation(s)
- Alok Bhattacharya
- Department of Biology, Ashoka University, National Capital Region, Sonepat 131 029, Haryana, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
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Singh U, Mani A, James K, Rao MB, Bhattacharya A. Effects of Heat Exposure from Live-Burn Fire Training on Postural Stability of Firefighters. Ergon Int J 2019; 3. [PMID: 31815252 DOI: 10.23880/eoji-16000213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Firefighters perform physically intensive jobs in suboptimal environments, making it even more important for them to maintain good functional postural balance or stability. As part of their training, firefighters are required to perform physically demanding tasks under high stress and high heat environments. These demanding tasks lead to increased physical fatigue which can then result in poor performance and/or postural instability. The objectives of this study were to 1) investigate the effect of live-firefighting training-induced heat stress on static postural balance, and 2) investigate the association between commonly monitored physiological responses (core body temperature, heart rate, oxygen saturation and blood pressure) and measures of static postural balance. Twenty-six firefighters (mean ± SD: age 36.0 years ±5.2, weight 216 lbs. ± 34, BMI 29.7 ± 4.2) participated in live firefighting training while performing following tasks: search and rescue, hose advancement, and backup. Prior to heat exposure (PRE) and following each scenario (POST1, POST2, POST3), firefighters' postural balance was assessed with a wearable 3-D inertial sensor system quantifying time dependent changes in linear acceleration (LIN ACC) and angular velocity (AV) about three orthogonal axes [Anterior-Posterior (AP), Medial-Lateral (ML), and vertical (V)] during one foot balance tests for 30 seconds under eyes open and eyes closed conditions. The outcome variables from 3-D wearable sensors were used to create 3-D Phase-Plane based postural stability metrics. Physiological measurement of core body temperature (CBT) (measured with a radio pill) as well as perception of heat increased significantly during the live fire-training exercise. In addition, firefighters also perceived an increase in physical fatigue and respiratory distress. Angular combined stability parameters (ACSP), RMS angular velocity around ML axis were significantly correlated with CBT. In the multivariate analysis adjusted for the scenarios, height and weight of the firefighters, these measures of static postural balance were significantly associated with CBT. As per the model results, static postural balance, as indicated by ACSP, worsened with an increase in CBT. Future studies should place sensors at body extremities along with close to center of mass to capture the kinematic movements more comprehensively influencing postural balance.
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Affiliation(s)
- U Singh
- Dept of Internal Medicine, University of Cincinnati College of Medicine, USA
| | - A Mani
- Dept of Environmental Health, University of Cincinnati College of Medicine, USA
| | - K James
- Dept of Environmental Health, University of Cincinnati College of Medicine, USA
| | - M B Rao
- Dept of Environmental Health, University of Cincinnati College of Medicine, USA
| | - A Bhattacharya
- Dept of Environmental Health, University of Cincinnati College of Medicine, USA
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Abstract
Inherited neuromuscular diseases are a heterogeneous group of rare diseases for which the low general awareness leads to frequent misdiagnosis. Advances in DNA sequencing technologies are changing this situation, and it is apparent that these diseases are not as rare as previously thought. Knowledge of the pathogenic variants in patients is helping in research efforts to develop new therapies. Here we present a review of current knowledge in GNE myopathy, a rare neuromuscular disorder caused by mutations in the GNE gene that catalyzes the biosynthesis of sialic acid. The most common initial symptom is foot drop caused by anterior tibialis muscle weakness. There is a progressive wasting of distal skeletal muscles in the lower and upper extremities as well. The quadriceps is relatively spared, which is a distinguishing feature of this disease. The characteristic histological features include autophagic rimmed vacuoles with inclusion bodies. GNE variant analysis of Indian patients has revealed a founder mutation (p.Val727Met) common within the normal Indian populations, especially in the state of Gujurat. We discuss therapeutic options, including metabolite supplementation, pharmacological chaperones, and gene therapy. Initiatives that bring together patients, researchers, and physicians are necessary to improve knowledge and treatment for these rare disorders.
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Affiliation(s)
- Kapila Awasthi
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ranjana Arya
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- School of Life Sciences; World without GNE Myopathy, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- World without GNE Myopathy, Jawaharlal Nehru University; School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
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Kumar R, Mittal BR, Bhattacharya A, Vadi SK, Singh H, Bal A, Shukla J, Singh H, Sharma V, Sood A, Singh SK. Positron emission tomography/computed tomography guided percutaneous biopsies of Ga-68 avid lesions using an automated robotic arm. Diagn Interv Imaging 2019; 101:157-167. [PMID: 31722844 DOI: 10.1016/j.diii.2019.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/09/2019] [Accepted: 10/15/2019] [Indexed: 12/11/2022]
Abstract
PURPOSE The purpose of this prospective study was to evaluate the feasibility of positron emission tomography/computed tomography (PET/CT)-guided biopsy of Ga-68 avid lesions using an automated robotic arm and determine the diagnostic yield of this technique. MATERIAL AND METHODS Patients who underwent Ga-68 labelled tracers imaging followed by PET/CT-guided biopsies of tracer-avid lesions were prospectively included. Biopsies were performed using a dedicated automated-robotic-arm assisted PET/CT-guided biopsy device on the same-day of diagnostic PET/CT-imaging. The tissue samples were retrieved after confirming the position of needle-tip in the target lesion. Procedure-related complications and radiation exposure of the interventionist were recorded. Histopathological reports were reviewed for diagnostic yield. RESULTS A total of 25 patients (19 men, six women) with a mean age of 50.8±17.3 (SD) years (range: 17-83 years) were included. The biopsies were performed after PET/CT using Ga-68 DOTANOC (n=16) or Ga-68 PSMA (n=8) and Ga-68 chemokine-analogue (n=1). The biopsy samples were obtained from the liver (n=9), bone (n=8), lymph-nodes (n=3), lung (n=1), pancreas (n=1), anterior mediastinal lesion (n=1), peritoneal-deposit (n=1) and thigh-lesion (n=1). No immediate or delayed procedure-related complications were documented in any patient. PET/CT-guided molecular sampling was technically successful in all the patients. Histopathology revealed malignancies in all the biopsied specimens without the need for repeat sampling or further invasive-diagnostic workup, with a diagnostic yield of 100%. The estimated absorbed-radiation dose was 566.7μSv/year for the interventionist. CONCLUSION PET/CT-guided molecular biopsy using Ga-68 labelled radiotracers is feasible and can be performed safely and accurately with a high-diagnostic yield. It is helpful in accurately staging the disease when tracer-avid isolated distant lesion evident on imaging and highly practical in patients with previous inconclusive sampling.
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Affiliation(s)
- R Kumar
- Department of Nuclear Medicine and PET/CT, Post Graduate Institute of Medical Education and Research, 160012 Chandigarh, India
| | - B R Mittal
- Department of Nuclear Medicine and PET/CT, Post Graduate Institute of Medical Education and Research, 160012 Chandigarh, India.
| | - A Bhattacharya
- Department of Nuclear Medicine and PET/CT, Post Graduate Institute of Medical Education and Research, 160012 Chandigarh, India
| | - S K Vadi
- Department of Nuclear Medicine and PET/CT, Post Graduate Institute of Medical Education and Research, 160012 Chandigarh, India
| | - H Singh
- Department of Nuclear Medicine and PET/CT, Post Graduate Institute of Medical Education and Research, 160012 Chandigarh, India
| | - A Bal
- Department of Pathology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - J Shukla
- Department of Nuclear Medicine and PET/CT, Post Graduate Institute of Medical Education and Research, 160012 Chandigarh, India
| | - H Singh
- Department of Surgery, Post Graduate Institute of Medical Education and Research, 160012 Chandigarh, India
| | - V Sharma
- Department of Gastroenterology, Post Graduate Institute of Medical Education and Research, 160012 Chandigarh, India
| | - A Sood
- Department of Nuclear Medicine and PET/CT, Post Graduate Institute of Medical Education and Research, 160012 Chandigarh, India
| | - S K Singh
- Department of Urology, Post Graduate Institute of Medical Education and Research, 160012 Chandigarh, India
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Naiyer S, Bhattacharya A, Bhattacharya S. Advances in Entamoeba histolytica Biology Through Transcriptomic Analysis. Front Microbiol 2019; 10:1921. [PMID: 31481949 PMCID: PMC6710346 DOI: 10.3389/fmicb.2019.01921] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 05/15/2019] [Accepted: 08/05/2019] [Indexed: 12/13/2022] Open
Abstract
A large number of transcriptome-level studies in Entamoeba histolytica, the protozoan parasite that causes amoebiasis, have investigated gene expression patterns to help understand the pathology and biology of the organism. They have compared virulent and avirulent strains in lab culture and after tissue invasion, cells grown under different stress conditions, response to anti-amoebic drug treatments, and gene expression changes during the process of encystation. These studies have revealed interesting molecules/pathways that will help increase our mechanistic understanding of differentially expressed genes during growth perturbations and tissue invasion. Some of the important insights obtained from transcriptome studies include the observations that regulation of carbohydrate metabolism may be an important determinant for tissue invasion, while the novel up-regulated genes during encystation include phospholipase D, and meiotic genes, suggesting the possibility of meiosis during the process. Classification of genes according to expression levels showed that amongst the highly transcribed genes in cultured E. histolytica trophozoites were some virulence factors, raising the question of the role of these factors in normal parasite growth. Promoter motifs associated with differential gene expression and regulation were identified. Some of these motifs associated with high gene expression were located downstream of start codon, and were required for efficient transcription. The listing of E. histolytica genes according to transcript expression levels will help us determine the scale of post-transcriptional regulation, and the possible roles of predicted promoter motifs. The small RNA transcriptome is a valuable resource for detailed structural and functional analysis of these molecules and their regulatory roles. These studies provide new drug targets and enhance our understanding of gene regulation in E. histolytica.
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Affiliation(s)
- Sarah Naiyer
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
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Mehta R, Brahmbhatt H, Bhojani G, Mukherjee M, Bhattacharya A. Poly(piperizinamide) with copper ion composite membranes: Application for mitigation of Hexaconazole from water and combat microbial contamination. J Hazard Mater 2019; 376:102-111. [PMID: 31125940 DOI: 10.1016/j.jhazmat.2019.05.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 03/14/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Thin film Poly(piperazine-amide) composite membranes using sequential interfacial polymerization with tuning by Cu2+ have brought significant findings in it. The hydrophobicity is relatively enhanced for the copper containing membranes. The membrane in which copper solution is applied prior to piperizine (Memb-III) exhibits higher hydrophobicity where as membrane (Memb-II) in which copper solution is applied following piperizine, possesses higher roughness compared to other two. Filtration experiments in terms of salts, mono/disaccharides and hexaconazole indicate that modified membranes are of different behaviours according to their sequence of preparative methods. Memb-III has shown lower SO4=/Cl- selectivity compared to Memb-II (i.e. 3.92), though they are in different range. The unmodified membrane (Memb-I) exhibits SO4=/Cl- selectivity 3.23 is in the same scale of Memb-III (2.27). Memb-III exhibits higher hexaconazole separation (91.5%) compared to Memb-II (i.e. 53.9%). The flux decline follows the order: field water > tap water > deionized water. The copper incorporated membrane (Memb-II) has shown a low flux decline compared to Memb-III as well as Memb-I. The antibacterial properties towards E. Coli and Bacillus subtilis are well reflected. The copper containing membranes have promising antibacterial properties and follows the order Memb-II > Memb-III > Memb-I.
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Affiliation(s)
- Romil Mehta
- Membrane Science and Separation Technology Division, Bhavnagar, 364002 Gujarat, India
| | - H Brahmbhatt
- Analytical and Environmental Science Division and Centralized Instrument Facility, Council of Scientific & Industrial Research-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Bhavnagar, 364002 Gujarat, India
| | - Gopal Bhojani
- Membrane Science and Separation Technology Division, Bhavnagar, 364002 Gujarat, India
| | - M Mukherjee
- Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, W. Bengal, India
| | - A Bhattacharya
- Membrane Science and Separation Technology Division, Bhavnagar, 364002 Gujarat, India.
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Sharma S, Agarwal S, Bharadwaj R, Somlata, Bhattacharya S, Bhattacharya A. Novel regulatory roles of PtdIns(4,5)P2generating enzyme EhPIPKI in actin dynamics and phagocytosis ofEntamoeba histolytica. Cell Microbiol 2019; 21:e13087. [DOI: 10.1111/cmi.13087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/03/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Shalini Sharma
- School of Life SciencesJawaharlal Nehru University New Delhi India
| | - Shalini Agarwal
- School of Life SciencesJawaharlal Nehru University New Delhi India
| | - Ravi Bharadwaj
- School of MedicineUMASS Medical School Worcester Massachusetts USA
| | - Somlata
- Multidisciplinary Centre for Advance Research and StudiesJamia Milia Islamia New Delhi India
| | - Sudha Bhattacharya
- School of Environmental SciencesJawaharlal Nehru University New Delhi India
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Agarwal S, Anand G, Sharma S, Parimita Rath P, Gourinath S, Bhattacharya A. EhP3, a homolog of 14-3-3 family of protein participates in actin reorganization and phagocytosis in Entamoeba histolytica. PLoS Pathog 2019; 15:e1007789. [PMID: 31095644 PMCID: PMC6541287 DOI: 10.1371/journal.ppat.1007789] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 05/29/2019] [Accepted: 04/24/2019] [Indexed: 11/19/2022] Open
Abstract
The highly conserved proteins of the 14-3-3 family are universal adaptors known to regulate an enormous range of cellular processes in eukaryotes. However, their biological functions remain largely uncharacterized in pathogenic protists comprising of several 14-3-3 protein isoforms. In this study, we report the role of 14-3-3 in coordinating cytoskeletal dynamics during phagocytosis in a professional phagocytic protist Entamoeba histolytica, the etiological agent of human amebiasis. There are three isoforms of 14-3-3 protein in amoeba and here we have investigated Eh14-3-3 Protein 3 (EhP3). Live and fixed cell imaging studies revealed the presence of this protein throughout the parasite phagocytosis process, with high rate of accumulation at the phagocytic cups and closed phagosomes. Conditional suppression of EhP3 expression caused significant defects in phagocytosis accompanied by extensive diminution of F-actin at the site of cup formation. Downregulated cells also exhibited defective recruitment of an F-actin stabilizing protein, EhCoactosin at the phagocytic cups. In addition, mass spectrometry based analysis further revealed a large group of EhP3-associated proteins, many of these proteins are known to regulate cytoskeletal architecture in E histolytica. The dynamics of these proteins may also be controlled by EhP3. Taken together, our findings strongly suggest that EhP3 is a novel and a key regulatory element of actin dynamics and phagocytosis in E. histolytica. Phagocytosis of host cells is central to pathogenesis of protist parasite Entamoeba histolytica, the etiological agent of human amebiasis. It is a complex and multistep process that requires dynamic remodelling of the actin cytoskeleton by a large number of scaffolding, signaling and actin-binding proteins (ABPs). Although several parasite ligands such as EhC2PK, EhCaBP1, EhCaBP3, EhAK1, Arp2/3 complex and EhCoactosin that participate in the phagocytic machinery have been identified, the mechanistic insights to their regulation process remain largely elusive. We have in this study identified and characterized the important role of scaffolding protein EhP3 in modulating cytoskeletal dynamics and regulating phagocytosis in E. histolytica. Expression knockdown, imaging and interaction studies suggest that EhP3 function as an adaptor molecule that controls the localization of an F-actin stabilizing protein EhCoactosin and thus the dynamics of F-actin rearrangement during phagocytosis. EhP3 also interact with other actin dynamics regulating proteins that may in coordination regulate cytoskeletal dynamics and thereby phagocytosis in Entamoeba.
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Affiliation(s)
- Shalini Agarwal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail:
| | - Gaurav Anand
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Shalini Sharma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | | | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- Ashoka University, P.O. Rai, Sonepat, Haryana, India
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Sharma S, Bhattacharya S, Bhattacharya A. PtdIns(4,5)P 2 is generated by a novel phosphatidylinositol 4-phosphate 5-kinase in the protist parasite Entamoeba histolytica. FEBS J 2019; 286:2216-2234. [PMID: 30843363 DOI: 10.1111/febs.14804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 11/04/2018] [Revised: 02/03/2019] [Accepted: 03/05/2019] [Indexed: 01/02/2023]
Abstract
Entamoeba histolytica is an intestinal protist parasite that causes amoebiasis, a major source of morbidity and mortality in developing countries. Phosphoinositides are involved in signalling systems that have a role in invasion and pathogenesis of this parasite. Phosphatidylinositol 4-phosphate 5-kinase (PIP5K) catalyses the generation of phosphatidylinositol(4,5)bisphosphate (PtdIns(4,5)P2 ), a key species of phosphoinositide that regulates various cellular processes. However, phosphatidylinositol phosphate kinase (PIPK) family of enzymes have not been characterized in E. histolytica. Here, we report the identification and characterization of type I PIPK (EhPIPKI) of E. histolytica. Computational analysis revealed homologs of type I and III PIPK family in E. histolytica and the absence of type II PIPK. In spite of low overall sequence identity, the kinase domain was found to be highly conserved. Interestingly, a unique insertion of a tandem repeat motif was observed in EhPIPKI distinguishing it from existing PIPKs of other organisms. Substrate profiling showed that EhPIPKI could phosphorylate at third and fifth hydroxyl positions of phosphatidylinositols, though the predominant substrate was phosphatidylinositol 4-phosphate (PtdIns(4)P). Furthermore, EhPIPKI underwent intracellular cleavage close to the amino-terminal, generating two distinct fragments Nter-EhPIPKI (27p) and Cter-EhPIPKI (47p). Immunofluorescence and cellular fractionation revealed that the full-length EhPIPKI and the Cter-EhPIPKI containing carboxyl-terminal activation loop were present in the plasma membrane while the Nter-EhPIPKI was observed in the cytosolic region. In conclusion, E. histolytica has a single EhPIPKI gene that displays novel properties of post-translational processing, the presence of a repeat domain and substrate specificity not observed in any PIPK enzyme so far.
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Affiliation(s)
- Shalini Sharma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Naiyer S, Kaur D, Ahamad J, Singh SS, Singh YP, Thakur V, Bhattacharya A, Bhattacharya S. Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica. BMC Genomics 2019; 20:206. [PMID: 30866809 PMCID: PMC6416950 DOI: 10.1186/s12864-019-5570-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 11/30/2018] [Accepted: 02/27/2019] [Indexed: 11/16/2022] Open
Abstract
Background Promoter motifs in Entamoeba histolytica were earlier analysed using microarray data with lower dynamic range of gene expression. Additionally, previous transcriptomic studies did not provide information on the nature of highly transcribed genes, and downstream promoter motifs important for gene expression. To address these issues we generated RNA-Seq data and identified the high and low expressing genes, especially with respect to virulence potential. We analysed sequences both upstream and downstream of start site for important motifs. Results We used RNA-Seq data to classify genes according to expression levels, which ranged six orders of magnitude. Data were validated by reporter gene expression. Virulence-related genes (except AIG1) were amongst the highly expressed, while some kinases and BspA family genes were poorly expressed. We looked for conserved motifs in sequences upstream and downstream of the initiation codon. Following enrichment by AME we found seven motifs significantly enriched in high expression- and three in low expression-classes. Two of these motifs (M4 and M6) were located downstream of AUG, were exclusively enriched in high expression class, and were mostly found in ribosomal protein, and translation-related genes. Motif deletion resulted in drastic down regulation of reporter gene expression, showing functional relevance. Distribution of core promoter motifs (TATA, GAAC, and Inr) in all genes revealed that genes with downstream motifs were not preferentially associated with TATA-less promoters. We looked at gene expression changes in cells subjected to growth stress by serum starvation, and experimentally validated the data. Genes showing maximum up regulation belonged to the low or medium expression class, and included genes in signalling pathways, lipid metabolism, DNA repair, Myb transcription factors, BspA, and heat shock. Genes showing maximum down regulation belonged to the high or medium expression class. They included genes for signalling factors, actin, Ariel family, and ribosome biogenesis factors. Conclusion Our analysis has added important new information about the E. histolytica transcriptome. We report for the first time two downstream motifs required for gene expression, which could be used for over expression of E. histolytica genes. Most of the virulence-related genes in this parasite are highly expressed in culture. Electronic supplementary material The online version of this article (10.1186/s12864-019-5570-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah Naiyer
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Devinder Kaur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Jamaluddin Ahamad
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | | | - Vivek Thakur
- Centre for Systems Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.
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Abstract
The protist parasite Entamoeba histolytica causes amoebiasis, a major public health problem in developing countries. Only a small fraction of patients infected with the parasite display invasive disease involving colon or extra intestinal tissues such as liver. E. histolytica exists as two distinct forms, cysts, the infective form, and trophozoites, that are responsible for disease pathology. The latter multiply in the large intestine occasionally causing disease. The large intestine in humans is populated by a number of different bacterial communities and amoebic cells grow in their midst using some as food material. Several studies have shown relationship between bacteria and E. histolytica growth and virulence. However, an understanding of this relationship in human gut environment is not clear. We have investigated the possibility that there may be specific interaction of amoeba with different bacteria present in the gut environment by using a metagenomic pipe line. This was done by incubating bacteria isolated from human fecal material with E. histolytica and then identifying the bacterial population isolated from amoebic cells using a rRNA based metagenomic approach. Our results show that the parasite prefers a few bacterial species. One of these species is Lactobacillus ruminus which has never shown to be associated with E. histolytica.
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Affiliation(s)
- Lakshmi Rani Iyer
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Anil Kumar Verma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Jaishree Paul
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Singh SS, Naiyer S, Bharadwaj R, Kumar A, Singh YP, Ray AK, Subbarao N, Bhattacharya A, Bhattacharya S. Correction: Stress-induced nuclear depletion of Entamoeba histolytica 3'-5' exoribonuclease EhRrp6 and its role in growth and erythrophagocytosis. J Biol Chem 2018; 293:19510. [PMID: 30552115 DOI: 10.1074/jbc.aac118.006754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Mukhopadhyay S, Mehta R, Paidi MK, Mandal SK, Bhattacharya A. Development of Hg2+ colorimetric sensor using polymeric membrane. SEP SCI TECHNOL 2018. [DOI: 10.1080/01496395.2018.1547762] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Sarbartha Mukhopadhyay
- Marine Biotechnology and Phycology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific & Industrial Research (CSIR), Bhavnagar, Gujarat, India
| | - Romil Mehta
- Membrane Science and Separation Technology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific & Industrial Research (CSIR), Bhavnagar, Gujarat, India
| | - Murali Krishna Paidi
- Marine Biotechnology and Phycology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific & Industrial Research (CSIR), Bhavnagar, Gujarat, India
| | - Subir Kumar Mandal
- Marine Biotechnology and Phycology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific & Industrial Research (CSIR), Bhavnagar, Gujarat, India
| | - A. Bhattacharya
- Membrane Science and Separation Technology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific & Industrial Research (CSIR), Bhavnagar, Gujarat, India
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Camacho D, Lee Y, Lukens E, Bhattacharya A, Vargas L, Kimberly L. LIFE SATISFACTION AMONG MEXICAN ELDERS: FINDINGS FROM THE STUDY ON GLOBAL AGEING AND ADULT HEALTH WAVE 1. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.2413] [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: 11/12/2022] Open
Affiliation(s)
| | - Y Lee
- University of Alabama, Birmingham
| | - E Lukens
- Columbia University School of Social Work
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Camacho D, Lukens E, Lee Y, Bhattacharya A, Vargas L, Kimberly L. MEXICAN ELDERS AND SOCIAL ISOLATION: EXPLORING THE RELATIONSHIP WITH HEALTH, HEALTHCARE UTILIZATION AND VIOLENCE. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.2463] [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: 11/14/2022] Open
Affiliation(s)
| | - E Lukens
- Columbia University School of Social Work
| | - Y Lee
- University of Alabama, Birmingham
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Fan B, Bhattacharya A, Bandaru PR. Enhanced voltage generation through electrolyte flow on liquid-filled surfaces. Nat Commun 2018; 9:4050. [PMID: 30283012 PMCID: PMC6170469 DOI: 10.1038/s41467-018-06297-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 03/22/2018] [Accepted: 08/28/2018] [Indexed: 11/10/2022] Open
Abstract
The generation of electrical voltage through the flow of an electrolyte over a charged surface may be used for energy transduction. Here, we show that enhanced electrical potential differences (i.e., streaming potential) may be obtained through the flow of salt water on liquid-filled surfaces that are infiltrated with a lower dielectric constant liquid, such as oil, to harness electrolyte slip and associated surface charge. A record-high figure of merit, in terms of the voltage generated per unit applied pressure, of 0.043 mV Pa−1 is obtained through the use of the liquid-filled surfaces. In comparison with air-filled surfaces, the figure of merit associated with the liquid-filled surface increases by a factor of 1.4. These results lay the basis for innovative surface charge engineering methodology for the study of electrokinetic phenomena at the microscale, with possible application in new electrical power sources. Superhydrophobic surfaces are expected to increase streaming potential, but are hindered by the presence of air. Here the authors enhance streaming potential by flowing high-dielectric salt water over liquid-filled surfaces infiltrated with low-dielectric liquid, harnessing electric slip and surface charge.
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Affiliation(s)
- B Fan
- Department of Mechanical Engineering, University of California, San Diego, La Jolla, 92093-0411, CA, USA
| | - A Bhattacharya
- Department of Mechanical Engineering, University of California, San Diego, La Jolla, 92093-0411, CA, USA
| | - P R Bandaru
- Department of Mechanical Engineering, University of California, San Diego, La Jolla, 92093-0411, CA, USA. .,Program in Materials Science, University of California, San Diego, La Jolla, 92093-0411, CA, USA.
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Arora R, Rahman R, Joe W, Bakhshi S, Radhakrishnan V, Mahajan A, Chinnaswamy G, Bhattacharya A, Swami A, Manglani M, Seth R, Singh A, De S, MS L, Raj R, Borker A, Martiniuk A, Tsimicalis A. Families of Children Newly Diagnosed With Cancer Incur Significant Out-of-Pocket Expenditure for Treatment: Report of a Multi-Site Prospective Longitudinal Study From India (INPOG-ACC-16-01). J Glob Oncol 2018. [DOI: 10.1200/jgo.18.42400] [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: 11/20/2022] Open
Abstract
Background: Diagnosis of cancer in a child places considerable economic burden on families. The health expenditures are more catastrophic in resource limited countries like India where GDP spend on health is just over 1% and financing of treatment is usually out-of-pocket (OOP). Consequently parents may abandon their child's cancer treatment to ensure financial sustainability of the family. Research in this area is mostly from resource rich countries and OOP expenditure burden remains unknown in India. Aim: The objective of this study is to describe the OOP expenditure incurred by families of children (< 18 years age) with cancer being treated in India prior to and during cancer directed treatment. Methods: A prospective cost of illness study from a family household perspective was conducted in 14 centers (5 public, 5 private and 4 charitable trust sector) in 4 cities in India from 2016-2018. Baseline family demographic and socioeconomic data were collected followed by OOP expenditure incurred prior to start of treatment. For the duration of the child's treatment, a social worker contacted parents at regular intervals to record their expenditure on cancer directed treatment. Data collection was stopped when one of these happened - completion of treatment or death or progression/relapse or abandonment or transfer. Data were described descriptively and a univariate/multivariate analysis using logistic regression was done to detect factors associated with OOP expenditure. Results: 394 children (63% male, median age 5 years) with cancer (64% leukemia/lymphoma, 33% solid tumors, 3% CNS tumors) were enrolled from public (45%), charitable trust (28%) and private (27%) sector hospitals. They were symptomatic for a median duration of 6 weeks (range 0 to 104 weeks). 88% had no insurance and 73% were from families with monthly income of ≤ 10,000 rupees (≤ 159 US$). Mean OOP expenditure was Rs 209,500 (3325 US$) which is 195% of per capita income (1706 US$) of India. OOP expenditure from onset of symptoms to start of treatment was Rs 53,104 (843 US$) of which 77% was medical (15% laboratory tests, 11% medicines, 9% hospital bed costs) and 23% nonmedical (12% travel, 6% food, 3% lodging). OOP expenditure on cancer directed treatment was Rs 156,396 (2482 US$) of which 64% was medical (9% hospital bed costs, 9% supportive care drugs, 8% laboratory tests) and 36% nonmedical (19% food, 9% travel, 6% lodging). On univariate analysis age, gender, city, type of treatment facility, insurance, type of cancer, driving time and distance were significantly associated with OOP expenditure but only insurance and type of treatment facility were found significant on multivariate analysis. Conclusion: Families of children with cancer incur significant OOP expenditure prior to and during cancer directed treatment, which includes a significant portion on nonmedical expenses. Expenditure varied significantly by insurance and type of treatment facility.
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Affiliation(s)
- R. Arora
- Max Super Speciality Hospital, New Delhi, India
| | - R.U. Rahman
- Max Super Speciality Hospital, New Delhi, India
| | - W. Joe
- Max Super Speciality Hospital, New Delhi, India
| | - S. Bakhshi
- Max Super Speciality Hospital, New Delhi, India
| | | | - A. Mahajan
- Max Super Speciality Hospital, New Delhi, India
| | | | | | - A. Swami
- Max Super Speciality Hospital, New Delhi, India
| | - M. Manglani
- Max Super Speciality Hospital, New Delhi, India
| | - R. Seth
- Max Super Speciality Hospital, New Delhi, India
| | - A. Singh
- Max Super Speciality Hospital, New Delhi, India
| | - S. De
- Max Super Speciality Hospital, New Delhi, India
| | - L. MS
- Sri Ramachandra Medical College and Research Institute, Chennai, India
| | - R. Raj
- Apollo Speciality Cancer Hospital, Chennai, India
| | - A. Borker
- Asian Institute of Oncology, Mumbai, India
| | - A. Martiniuk
- The George Institute for Global Health, Sydney, Australia
- University of Sydney, Faculty of Medicine, Sydney, Australia
| | - A. Tsimicalis
- Ingram School of Nursing, McGill University, Montreal, Canada
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Deng A, Pattanaik S, Bhattacharya A, Yin J, Ross L, Liu C, Zhang J. Fish consumption is associated with a decreased risk of death among adults with diabetes: 18-year follow-up of a national cohort. Nutr Metab Cardiovasc Dis 2018; 28:1012-1020. [PMID: 30017435 DOI: 10.1016/j.numecd.2018.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 01/21/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND There is a paucity of studies examining the beneficial effects of fish consumption on cardiovascular diseases (CVDs) among adults with diabetes, who experience a substantially high risk of CVDs. METHODS AND RESULTS We analyzed the data of 1136 adults with diabetes mellitus aged 18 years and older who participated in the National Health and Nutrition Examination Survey, 1988-1994, and were followed up through December 31, 2010. We used Cox regression to estimate the adjusted hazard ratios (HRs) for the relative risk across the levels of fish consumption. A total of 698 deaths were recorded at the end of 11,465 person-years follow-up with a mortality rate of 60.88 per 1000 person-years. CVDs were listed as a contributing cause for 326 deaths, thus accounting for 46.4% of total deaths. Stroke-specific mortality rate among patients who ate fish less than once a week was more than twice as high as that among patients who ate fish more than twice a week, 6.23 vs. 2.36 per 1000 person-years, respectively. The corresponding CVD-specific rate was 34.38 vs. 22.99 per 1000 person-years, respectively. The adjusted HRs of death due to stroke were 1.00 (reference), 0.55 (95% confidence interval = 0.28-1.07), and 0.30 (0.11-0.80) among patients who ate fish <1, 1-2, and 2 + times a week, and the corresponding HRs of death due to CVDs were 1.00 (reference), 0.78 (0.60-1.02), and 0.69 (0.50-0.96), respectively. CONCLUSIONS A high consumption of fish was associated with a low risk of death due to CVDs, especially stroke, among adults with diabetes.
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Affiliation(s)
- A Deng
- Department of Epidemiology, Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA, 30460, USA
| | - S Pattanaik
- Department of Health Education and Community Health, Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA, 30460, USA
| | - A Bhattacharya
- Department of Epidemiology, Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA, 30460, USA
| | - J Yin
- Department of Biostatistics, Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA, 30460, USA
| | - L Ross
- The University of Alabama, Health Science, 461 Russell Hall, Box 870311, Tuscaloosa, AL, 35487, USA
| | - C Liu
- Department of Biostatistics, Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA, 30460, USA
| | - J Zhang
- Department of Epidemiology, Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA, 30460, USA.
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