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Albrecht C, Rajaram N, Broche J, Bashtrykov P, Jeltsch A. Locus-Specific and Stable DNA Demethylation at the H19/ IGF2 ICR1 by Epigenome Editing Using a dCas9-SunTag System and the Catalytic Domain of TET1. Genes (Basel) 2024; 15:80. [PMID: 38254969 PMCID: PMC10815749 DOI: 10.3390/genes15010080] [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: 12/19/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
DNA methylation is critically involved in the regulation of chromatin states and cell-type-specific gene expression. The exclusive expression of imprinted genes from either the maternal or the paternal allele is regulated by allele-specific DNA methylation at imprinting control regions (ICRs). Aberrant DNA hyper- or hypomethylation at the ICR1 of the H19/IGF2 imprinting locus is characteristic for the imprinting disorders Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS), respectively. In this paper, we performed epigenome editing to induce targeted DNA demethylation at ICR1 in HEK293 cells using dCas9-SunTag and the catalytic domain of TET1. 5-methylcytosine (5mC) levels at the target locus were reduced up to 90% and, 27 days after transient transfection, >60% demethylation was still observed. Consistent with the stable demethylation of CTCF-binding sites within the ICR1, the occupancy of the DNA methylation-sensitive insulator CTCF protein increased by >2-fold throughout the 27 days. Additionally, the H19 expression was increased by 2-fold stably, while IGF2 was repressed though only transiently. Our data illustrate the ability of epigenome editing to implement long-term changes in DNA methylation at imprinting control regions after a single transient treatment, potentially paving the way for therapeutic epigenome editing approaches in the treatment of imprinting disorders.
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Affiliation(s)
- Claudia Albrecht
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Nivethika Rajaram
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Julian Broche
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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Kouroukli AG, Rajaram N, Bashtrykov P, Kretzmer H, Siebert R, Jeltsch A, Bens S. Targeting oncogenic TERT promoter variants by allele-specific epigenome editing. Clin Epigenetics 2023; 15:183. [PMID: 37993930 PMCID: PMC10666398 DOI: 10.1186/s13148-023-01599-2] [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: 08/24/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Activation of dominant oncogenes by small or structural genomic alterations is a common driver mechanism in many cancers. Silencing of such dominantly activated oncogenic alleles, thus, is a promising strategy to treat cancer. Recently, allele-specific epigenome editing (ASEE) has been described as a means to reduce transcription of genes in an allele-specific manner. In cancer, specificity to an oncogenic allele can be reached by either targeting directly a pathogenic single-nucleotide variant or a polymorphic single-nucleotide variant linked to the oncogenic allele. To investigate the potential of ASEE in cancer, we here explored this approach by targeting variants at the TERT promoter region. The TERT promoter region has been described as one of the most frequently mutated non-coding cancer drivers. RESULTS Sequencing of the TERT promoter in cancer cell lines showed 53% (41/77) to contain at least one heterozygous sequence variant allowing allele distinction. We chose the hepatoblastoma cell line Hep-G2 and the lung cancer cell line A-549 for this proof-of-principle study, as they contained two different kinds of variants, namely the activating mutation C228T in the TERT core promoter and the common SNP rs2853669 in the THOR region, respectively. These variants were targeted in an allele-specific manner using sgRNA-guided dCas9-DNMT3A-3L complexes. In both cell lines, we successfully introduced DNA methylation specifically to the on-target allele of the TERT promoter with limited background methylation on the off-target allele or an off-target locus (VEGFA), respectively. We observed a maximum CpG methylation gain of 39% and 76% on the target allele when targeting the activating mutation and the common SNP, respectively. The epigenome editing translated into reduced TERT RNA expression in Hep-G2. CONCLUSIONS We applied an ASEE-mediated approach to silence TERT allele specifically. Our results show that the concept of dominant oncogene inactivation by allele-specific epigenome editing can be successfully translated into cancer models. This new strategy may have important advantages in comparison with existing therapeutic approaches, e.g., targeting telomerase, especially with regard to reducing adverse side effects.
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Affiliation(s)
- Alexandra G Kouroukli
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Nivethika Rajaram
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Pavel Bashtrykov
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Helene Kretzmer
- Computational Genomics, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Susanne Bens
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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Rajaram N, Kouroukli AG, Bens S, Bashtrykov P, Jeltsch A. Development of super-specific epigenome editing by targeted allele-specific DNA methylation. Epigenetics Chromatin 2023; 16:41. [PMID: 37864244 PMCID: PMC10589950 DOI: 10.1186/s13072-023-00515-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 07/05/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Epigenome editing refers to the targeted reprogramming of genomic loci using an EpiEditor which may consist of an sgRNA/dCas9 complex that recruits DNMT3A/3L to the target locus. Methylation of the locus can lead to a modulation of gene expression. Allele-specific DNA methylation (ASM) refers to the targeted methylation delivery only to one allele of a locus. In the context of diseases caused by a dominant mutation, the selective DNA methylation of the mutant allele could be used to repress its expression but retain the functionality of the normal gene. RESULTS To set up allele-specific targeted DNA methylation, target regions were selected from hypomethylated CGIs bearing a heterozygous SNP in their promoters in the HEK293 cell line. We aimed at delivering maximum DNA methylation with highest allelic specificity in the targeted regions. Placing SNPs in the PAM or seed regions of the sgRNA, we designed 24 different sgRNAs targeting single alleles in 14 different gene loci. We achieved efficient ASM in multiple cases, such as ISG15, MSH6, GPD1L, MRPL52, PDE8A, NARF, DAP3, and GSPT1, which in best cases led to five to tenfold stronger average DNA methylation at the on-target allele and absolute differences in the DNA methylation gain at on- and off-target alleles of > 50%. In general, loci with the allele discriminatory SNP positioned in the PAM region showed higher success rate of ASM and better specificity. Highest DNA methylation was observed on day 3 after transfection followed by a gradual decline. In selected cases, ASM was stable up to 11 days in HEK293 cells and it led up to a 3.6-fold change in allelic expression ratios. CONCLUSIONS We successfully delivered ASM at multiple genomic loci with high specificity, efficiency and stability. This form of super-specific epigenome editing could find applications in the treatment of diseases caused by dominant mutations, because it allows silencing of the mutant allele without repression of the expression of the normal allele thereby minimizing potential side-effects of the treatment.
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Affiliation(s)
- Nivethika Rajaram
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Alexandra G Kouroukli
- Institute of Human Genetics, University of Ulm and Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Susanne Bens
- Institute of Human Genetics, University of Ulm and Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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Kouroukli AG, Fischer A, Kretzmer H, Chteinberg E, Rajaram N, Glaser S, Kolarova J, Bashtrykov P, Mathas S, Drexler HG, Ohno H, Ammerpohl O, Jeltsch A, Siebert R, Bens S. The DNA methylation status of the TERT promoter differs between subtypes of mature B-cell lymphomas. Blood Cancer J 2023; 13:98. [PMID: 37365157 DOI: 10.1038/s41408-023-00872-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/24/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Affiliation(s)
- Alexandra G Kouroukli
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Anja Fischer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Helene Kretzmer
- Computational Genomics, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Emil Chteinberg
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Nivethika Rajaram
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Selina Glaser
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Julia Kolarova
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Stephan Mathas
- Charité - Universitätsmedizin Berlin, Hematology, Oncology and Tumor Immunology, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Group Biology of Malignant Lymphomas, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a cooperation between the MDC and the Charité, Berlin, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, D-38124, Braunschweig, Germany
| | - Hitoshi Ohno
- Tenri Institute of Medical Research, Tenri Hospital, Tenri, Nara, Japan
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany
| | - Susanne Bens
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89091, Ulm, Germany.
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Bashtrykov P, Rajaram N, Jeltsch A. Efficient Targeted DNA Methylation with dCas9-Coupled DNMT3A-DNMT3L Methyltransferase. Methods Mol Biol 2023; 2577:177-188. [PMID: 36173573 DOI: 10.1007/978-1-0716-2724-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Epigenome editing is a powerful approach for the establishment of a chromatin environment with desired properties at a selected genomic locus, which is used to influence the transcription of target genes and to study properties and functions of gene regulatory elements. Targeted DNA methylation is one of the most often used types of epigenome editing, which typically aims for gene silencing by methylation of gene promoters. Here, we describe the design principles of EpiEditors for targeted DNA methylation and provide step-by-step guidelines for the realization of this approach. We focus on the dCas9 protein as the state-of-the-art DNA targeting module fused to 10×SunTag as the most frequently used system for editing enhancement. Further, we discuss different flavors of DNA methyltransferase modules used for this purpose including the most specific variants developed recently. Finally, we explain the principles of gRNA selection, outline the setup of the cell culture experiments, and briefly introduce the available options for the downstream DNA methylation data analysis.
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Affiliation(s)
- Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany.
| | - Nivethika Rajaram
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany.
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Abstract
Background 3D printers emit potentially hazardous ultrafine particles and volatile organic compounds. Workers using 3D printing technologies may be at risk of respiratory illness from occupational exposure. Aims To assess whether 3D printing is associated with health effects in occupational users. Methods This was a preliminary survey. Workers in 17 companies using 3D printing, including commercial prototyping businesses, educational institutions and public libraries, in the Greater Toronto Area, Canada, were asked to complete survey questionnaires concerning demographic, occupational and health information. Associations between self-reported health history variables and occupational characteristics were examined by chi-square and Fisher's exact tests. Results Among 46 surveyed workers, 27 (59% of participants) reported having respiratory symptoms at least once per week in the past year. Working more than 40 h per week with 3D printers was significantly associated with having been given a respiratory-related diagnosis (asthma or allergic rhinitis) (P < 0.05). We observed a wide variation in occupational hygiene practices in the 17 printing workplaces that we surveyed. Conclusions Our finding of frequently reported respiratory symptoms suggests a need for additional studies on exposed workers in this field.
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Affiliation(s)
- F L Chan
- Division of Occupational Medicine, St. Michael's Hospital, Toronto, Ontario, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - R House
- Division of Occupational Medicine, St. Michael's Hospital, Toronto, Ontario, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - I Kudla
- Division of Occupational Medicine, St. Michael's Hospital, Toronto, Ontario, Canada
| | - J C Lipszyc
- Division of Occupational Medicine, St. Michael's Hospital, Toronto, Ontario, Canada
| | - N Rajaram
- Division of Occupational Medicine, St. Michael's Hospital, Toronto, Ontario, Canada
| | - S M Tarlo
- Division of Occupational Medicine, St. Michael's Hospital, Toronto, Ontario, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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Lim Z, Rajaram N, Song C, Kaur R, Taib NM, Muhamad M, Ong W, Schouwenburg M, See M, Teo SH, Saunders C, Yip C. Patient-Reported Outcome Measures Among Breast Cancer Survivors in Malaysia: A Comparative Study With Patients From High-Income Countries. J Glob Oncol 2018. [DOI: 10.1200/jgo.18.75100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Patient-reported outcome measures (PROMs) are essential for identifying how patients perceive the outcomes of their cancer treatment, and is the ultimate success of cancer care. Although a growing number of studies have focused on PROMs in high income countries (HICs), outcomes relevant to patients in developing countries are less understood. Furthermore, the lack of standardization in PROMs makes it difficult to interpret these data for research or quality monitoring. Aim: In this study, we compared the results of PROM measures between patients in Malaysia, a middle income country, and those in HICs, using standard PROMs questionnaires. We also explored the differences in perceived importance of patient reported outcomes within the multiracial Malaysian cohort. Methods: Breast cancer patients (n=1063) were recruited in hospitals serving suburban areas of Malaysia. Of these, 969 patients were eligible for analysis. The surveys were conducted through face-to-face interviews (68%) or were self-administered (30%). An outcome was considered important if it was scored between 7-9 on a 9-point Likert scale. We compared PROMs scores between Malaysian patients and data previously collected from patients in HICs using logistic regression models, adjusting for demographic and clinical characteristics. A two-step cluster analysis was conducted to explore differences in the perceived importance of PROMs between clusters of Malaysian patients. Results: Compared with 1777 patients from HICs, Malaysian patients were less likely to rate overall and recurrence free survival, as well as emotional, cognitive, social and sexual functioning as very important outcomes. Interestingly, more Malaysian women reported that pain (50% vs. 39%), breast symptoms (51% vs. 35%), and major complications (60% vs. 44%) were very important outcomes ( P < 0.001). Compared with young, married Malaysian women, the cluster of older married women (mean age of 57 vs. 52), who were less likely to have received breast reconstructive surgery (8.6% vs. 16.8%), was more likely to rate sexual functioning (32.8% vs. 25.0%, P = 0.036), body image (63.9% vs. 42.4%, P < 0.001), and satisfaction with the breast (50.7% vs. 37.0%, P = 0.011) as very important outcomes. Conclusion: The differences in breast cancer patient needs between and within populations should be considered carefully to better clinician-patient relationship, patient care and satisfaction and assess the outcomes of our cancer care. Future research is needed to find suitable targeted interventions to identify and address the diverse needs of breast cancer patients in low and middle income countries.
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Affiliation(s)
- Z.Y. Lim
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | - N. Rajaram
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | - C.V. Song
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | - R. Kaur
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | | | - M. Muhamad
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | - W.L. Ong
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | | | - M.H. See
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | - S.-H. Teo
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | - C. Saunders
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | - C.H. Yip
- Cancer Research Malaysia, Subang Jaya, Malaysia
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Jaganathan M, Zainal N, Rajaram N, Hwang TS, Wahab MA. The Feasibility and Performance of the Patient Navigation Programme in Improving Breast Cancer Care in Malaysia. J Glob Oncol 2018. [DOI: 10.1200/jgo.18.59500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Breast cancer is the most common cancer in Malaysia and it is anticipated that incidence will increase by 49% from 2012 to 2025. Unfortunately, survival remains poor because of late presentation and poor adherence to evidence-based medicine. Barriers to early presentation include inadequate knowledge about the disease, financial issues, negative influence of relatives and perceived poor quality of care and services in state-run hospitals. Poor adherence to treatment is also a common struggle, and is further exacerbated by the use of traditional, alternative healing methods. While patient navigation (PN) programs have been shown to improve breast cancer outcomes in the US, its implementation and performance in low and middle income countries is not well studied. Aim: We sought to determine the impact of a PN program in reducing treatment delays and improving adherence to treatment and patient satisfaction, as well as to evaluate the barriers faced by women seeking breast cancer care in Malaysia. Methods: We established a nurse-led patient navigation center at a secondary government hospital in Klang. This clinical team involved the surgery, pathology, radiology and nursing departments and provided patient-centered care, including patient tracking and call reminder systems, family counseling, health education and decision aids. The community team involved a Patient Navigator Program Coordinator and a Community Navigator. We compared treatment delays and adherence to treatment between navigated patients and patients registered in the year prior to the PN program. We used Student t-tests and Pearson χ2 or Fisher's Exact tests to compare timeliness between navigated patients and patients registered in the year prior. Results: Of the 136 Malaysian women enrolled in the PNP in 2015, 48.9% were diagnosed with advanced disease (stage 3 or 4). Women with advance disease had a lower median monthly household income compared with women with early disease (USD $350 vs $540, P = 0.023). Women with advance disease were also less likely to have personal transportation to the hospital (36.4% vs 56.5%, P = 0.048). Compared with the year before PN, more navigated patients underwent mammography within 7 days of their first visit (96.4% vs 74.4%, P < 0.001) and received their diagnosis within 14 days of their first visit (80.0% vs 58.5%, P < 0.001). The proportion of women who met timeliness to treatment initiation was similar for navigated patients and patients in the year prior. The proportion of defaulters were marginally lesser among navigated patients compared with the year prior (4.4% vs 11.5%, P = 0.048). Conclusion: We found that integrating PN within a breast clinic of a middle income country is feasible, and in the long run, could improve outcomes for breast cancer patients. Long-term follow-up is needed to assess the impact of the PN program on improving treatment completion and survival.
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Affiliation(s)
- M. Jaganathan
- Cancer Research Malaysia, Breast Cancer Research Team, Subang Jaya, Malaysia
| | - N.H. Zainal
- Cancer Research Malaysia, Breast Cancer Research Team, Subang Jaya, Malaysia
| | - N. Rajaram
- Cancer Research Malaysia, Breast Cancer Research Team, Subang Jaya, Malaysia
| | - T. Soo Hwang
- Cancer Research Malaysia, Breast Cancer Research Team, Subang Jaya, Malaysia
| | - M.Y. Abdul Wahab
- Cancer Research Malaysia, Breast Cancer Research Team, Subang Jaya, Malaysia
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Abstract
Background Three-dimensional (3D) printing is being increasingly used in manufacturing and by small business entrepreneurs and home hobbyists. Exposure to airborne emissions during 3D printing raises the issue of whether there may be adverse health effects associated with these emissions. Aims We present a case of a worker who developed asthma while using 3D printers, which illustrates that respiratory problems may be associated with 3D printer emissions. Case report The patient was a 28-year-old self-employed businessman with a past history of asthma in childhood, which had resolved completely by the age of eight. He started using 10 fused deposition modelling 3D printers with acrylonitrile-butadiene-styrene filaments in a small work area of approximately 3000 cubic feet. Ten days later, he began to experience recurrent chest tightness, shortness of breath and coughing at work. After 3 months, his work environment was modified by reducing the number of printers, changing to polylactic acid filaments and using an air purifier with an high-efficiency particulate air filter and organic cartridge. His symptoms improved gradually, although he still needed periodic treatment with a salbutamol inhaler. While still symptomatic, a methacholine challenge indicated a provocation concentration causing a 20% fall in FEV1 (PC20) of 4 mg/ml, consistent with mild asthma. Eventually, his symptoms resolved completely and a second methacholine challenge after symptom resolution was normal (PC20 > 16 mg/ml). Conclusions This case indicates that workers may develop respiratory problems, including asthma when using 3D printers. Further investigation of the specific airborne emissions and health problems from 3D printing is warranted.
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Affiliation(s)
- R House
- Division of Occupational Medicine, Department of Medicine, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - N Rajaram
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - S M Tarlo
- Division of Occupational Medicine, Department of Medicine, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Medicine, University Health Network, Toronto, Ontario, Canada
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Abstract
While some migration research looks at how time influences individual migration trajectories, little attention has been paid to the ways in which temporal considerations influence migration and development. We propose the idea of “organizational time” and argue that bringing time into sharper focus calls into question how the categories of migration and return affect organizational change; reveals how the career stage at which migrants leave affects their ability to influence organizational change when they return, and shows how the role of senders and receivers of social remittances shifts over time. We draw on research on the impact of return migration and social remittances on institutional capacity building and policymaking in the health sectors in Gujarat, India to make these arguments.
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Govindaraju G, Jabeena CA, Sethumadhavan DV, Rajaram N, Rajavelu A. DNA methyltransferase homologue TRDMT1 in Plasmodium falciparum specifically methylates endogenous aspartic acid tRNA. Biochim Biophys Acta Gene Regul Mech 2017; 1860:1047-1057. [PMID: 28847733 DOI: 10.1016/j.bbagrm.2017.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/17/2017] [Accepted: 08/21/2017] [Indexed: 11/28/2022]
Abstract
In eukaryotes, cytosine methylation regulates diverse biological processes such as gene expression, development and maintenance of genomic integrity. However, cytosine methylation and its functions in pathogenic apicomplexan protozoans remain enigmatic. To address this, here we investigated the presence of cytosine methylation in the nucleic acids of the protozoan Plasmodium falciparum. Interestingly, P. falciparum has TRDMT1, a conserved homologue of DNA methyltransferase DNMT2. However, we found that TRDMT1 did not methylate DNA, in vitro. We demonstrate that TRDMT1 methylates cytosine in the endogenous aspartic acid tRNA of P. falciparum. Through RNA bisulfite sequencing, we mapped the position of 5-methyl cytosine in aspartic acid tRNA and found methylation only at C38 position. P. falciparum proteome has significantly higher aspartic acid content and a higher proportion of proteins with poly aspartic acid repeats than other apicomplexan pathogenic protozoans. Proteins with such repeats are functionally important, with significant roles in host-pathogen interactions. Therefore, TRDMT1 mediated C38 methylation of aspartic acid tRNA might play a critical role by translational regulation of important proteins and modulate the pathogenicity of the malarial parasite.
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Affiliation(s)
- Gayathri Govindaraju
- Department of Tropical Disease Biology Group, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695 014, India
| | - C A Jabeena
- Department of Tropical Disease Biology Group, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695 014, India
| | | | - Nivethika Rajaram
- Department of Tropical Disease Biology Group, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695 014, India
| | - Arumugam Rajavelu
- Department of Tropical Disease Biology Group, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695 014, India.
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Bose K, Kamaraj M, Rajaram N, Balaji P, Babu PK, Rafeeque K, Kannan S. An unusual presentation of intramedullary spinal tumour. J Assoc Physicians India 1998; 46:968-9. [PMID: 11229227] [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] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- K Bose
- Dept of Medicine, Govt Rajaji Hospital, Madurai-625 020
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Diebold RJ, Rajaram N, Leonard DA, Kerppola TK. Molecular basis of cooperative DNA bending and oriented heterodimer binding in the NFAT1-Fos-Jun-ARRE2 complex. Proc Natl Acad Sci U S A 1998; 95:7915-20. [PMID: 9653115 PMCID: PMC20904 DOI: 10.1073/pnas.95.14.7915] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Cooperative DNA binding by transcription factors that bind to separate recognition sites is likely to require bending of intervening sequences and the appropriate orientation of transcription factor binding. We investigated DNA bending in complexes formed by the basic region-leucine zipper domains of Fos and Jun with the DNA binding region of nuclear factor of activated T cells 1 (NFAT1) at composite regulatory elements using gel electrophoretic phasing analysis. The NFAT1-Fos-Jun complex induced a bend at the ARRE2 site that was distinct from the sum of the bends induced by NFAT1 and Fos-Jun separately. We designate this difference DNA bending cooperativity. The bending cooperativity was directed toward the interaction interface between Fos-Jun and NFAT1. We also examined the influence of NFAT1 on the orientation of Fos-Jun heterodimer binding using a novel fluorescence resonance energy transfer assay. The interaction with NFAT1 could reverse the orientation of Fos-Jun heterodimer binding to the ARRE2 site. The principal determinants of both cooperative DNA bending and oriented heterodimer binding were localized to three amino acid residues at the amino-terminal ends of the leucine zippers of Fos and Jun. Consequently, interactions between transcription factors can remodel promoters by altering DNA bending and the orientation of heterodimer binding.
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Affiliation(s)
- R J Diebold
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109-0650, USA
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15
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Abstract
Interactions among transcription factors that bind to separate promoter elements depend on distortion of DNA structure and the appropriate orientation of transcription factor binding to allow juxtaposition of complementary structural motifs. We show that Fos and Jun induce distinct DNA bends at different binding sites, and that heterodimers bind to AP-1 sites in a preferred orientation. Sequences on each side of the consensus AP-1 recognition element have independent effects on DNA bending. A single base pair substitution outside the sequences contacted in the X-ray crystal structure alters DNA bending. Substitution of sequences flanking the AP-1 site has converse effects on DNA bending in opposite directions, suggesting that the extent of DNA bending by Fos and Jun is determined in part by the anisotropic bendability of sequences flanking the AP-1 site. DNA bending by Fos and Jun, and the orientation of heterodimer binding are interrelated. Reversal of the orientation of heterodimer binding causes a shift in the direction of DNA bending. The preferred orientation of heterodimer binding is determined both by contacts between a conserved arginine in the basic region of Fos and the central asymmetric guanine as well as the structure of sequences flanking the AP-1 site. Consequently, the structural adaptability of the Fos-Jun-AP1 complex may contribute to its functional versatility at different promoters.
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Affiliation(s)
- N Rajaram
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor 48109-0650, USA
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Leonard DA, Rajaram N, Kerppola TK. Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun. Proc Natl Acad Sci U S A 1997; 94:4913-8. [PMID: 9144164 PMCID: PMC24605 DOI: 10.1073/pnas.94.10.4913] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Interactions among transcription factors that bind to separate sequence elements require bending of the intervening DNA and juxtaposition of interacting molecular surfaces in an appropriate orientation. Here, we examine the effects of single amino acid substitutions adjacent to the basic regions of Fos and Jun as well as changes in sequences flanking the AP-1 site on DNA bending. Substitution of charged amino acid residues at positions adjacent to the basic DNA-binding domains of Fos and Jun altered DNA bending. The change in DNA bending was directly proportional to the change in net charge for all heterodimeric combinations between these proteins. Fos and Jun induced distinct DNA bends at different binding sites. Exchange of a single base pair outside of the region contacted in the x-ray crystal structure altered DNA bending. Substitution of base pairs flanking the AP-1 site had converse effects on the opposite directions of DNA bending induced by homodimers and heterodimers. These results suggest that Fos and Jun induce DNA bending in part through electrostatic interactions between amino acid residues adjacent to the basic region and base pairs flanking the AP-1 site. DNA bending by Fos and Jun at inverted binding sites indicated that heterodimers bind to the AP-1 site in a preferred orientation. Mutation of a conserved arginine within the basic regions of Fos and transversion of the central C:G base pair in the AP-1 site to G:C had complementary effects on the orientation of heterodimer binding and DNA bending. The conformational variability of the Fos-Jun-AP-1 complex may contribute to its functional versatility at different promoters.
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Affiliation(s)
- D A Leonard
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109-0650, USA
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Mongini PK, Blessinger CA, Chiorazzi N, Rajaram N, Rudich SM. A monovalent C mu 4-specific ligand enhances the activation of human B cells by membrane IgM cross-linking ligands. Int Immunol 1995; 7:317-30. [PMID: 7734425 DOI: 10.1093/intimm/7.2.317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The ligand-receptor binding requirements for achieving full B cell activation through the membrane immunoglobulin (mIg) signaling pathway are relatively demanding, and mIg-antigen engagements which fall below these critical thresholds cause, at most, only the partial activation of B cells. In an effort to resolve new means of enhancing the efficacy of mIgM-mediated signal transduction, as well as to further understand the process by which mIgM-mediated signals are initiated, we have explored the mechanism for a previously reported synergy between certain mixtures of murine anti-IgM mAbs in eliciting human B cell DNA synthesis. We here report that striking synergy occurs when any of several relatively high affinity mAbs specific for diverse domains of mIgM are combined in culture with the relatively low affinity C mu 4-specific ligand, mAb IG6. Although B cell activation was dependent upon the bivalency, and hence mIgM cross-linking potential, of the high affinity ligand, low affinity mAb IG6 could enhance the activation process when present as a monovalent Fab' fragment. This did not appear due to F(ab')2 contamination or Fab' aggregation, since IG6 Fab' preparations were notably compromised in several other functions requiring ligand bivalency. Pulsing studies revealed that the C mu 4-specific ligand exhibits its functional effects only when stimulatory mIgM receptor cross-links are being formed by bivalent ligands, and that IG6 Fab' enhancement is most notable during the later interval of the prolonged mIgM signaling process that leads to S phase entry. A unique region of the membrane-proximal IgM domain may be important for Fab'-mediated enhancement, since Fab' fragments that bind with higher affinities to distinct sites on C mu 4 were not as effective at mediating this phenomenon. Several possibilities for the adjuvant effects of this C mu 4-specific Fab' on B cell responses triggered by mIgM crosslinking ligands are discussed, including the possibility that IG6 Fab' influences the potential for mIgM dimer formation or interactions of mIgM with other signal-transducing molecules.
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Affiliation(s)
- P K Mongini
- Department of Rheumatology and Molecular Medicine, Hospital for Joint Diseases, New York, NY 10003, USA
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Rajaram N, Damle RN, Advani SH, Gangal SG. T cell responses in Hodgkin's disease: frequency distribution of IL-2 producing cells and quantitation of IL-2 produced per cell. Indian J Biochem Biophys 1994; 31:221-5. [PMID: 8002002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
T cell dysfunction in Hodgkin's disease (HD) is well documented. Since interleukin-2 (IL-2) plays a pivotal role in T cell proliferation, we have investigated frequency distribution of IL-2 producing phytohaemagglutinin (PHA)-stimulated lymphocytes from HD patients compared to that of healthy donors using two limiting dilution (LD) culture systems in which autologous peripheral blood lymphocytes (PBL) and Epstein Barr Virus transformed allogeneic B lymphoblastoid cell lines (EBV-LCL) have been used as feeders. The latter provided better conditions for IL-2 production by single cells, as evident from the enhanced frequencies obtained (For healthy donors: 1/67 +/- 1545.5 using EBV-LCL and 1/1123 +/- 1.7438 using autologous PBL as feeders). The data showed significantly reduced frequency of IL-2 producing cells as well as reduced quantity of IL-2 produced per cell in HD even after using/EBV-LCL as feeders, the amount of IL-2 produced per activated responder cell in HD patients being 0.825-1.3 pg/well (p < 0.001) as compared to 1.48-2.43 pg/well in healthy donors. Thus, the EBV-LCL feeders did provide better culture conditions for estimating frequencies of functional T cells. However these cell lines were unable to restore in vitro the abnormalities in functional properties of T cells in HD.
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Affiliation(s)
- N Rajaram
- Immunology Division, Cancer Research Institute, Bombay, India
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Rajaram N, Janardhanan K. Studies on the underexploited tree pulses, Acacia catechu willd., Parkinsonia aculeata L. and Prosopis chilensis (molina) stunz: Chemical composition and antinutritional factors. Food Chem 1991. [DOI: 10.1016/0308-8146(91)90069-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
We report the natural killer (NK) and lymphokine activated killer (LAK) cell activities in peripheral blood lymphocytes (PBL) from untreated patients with Hodgkin's disease (HD) and from healthy donors. The frequency of LAK cell precursors was also studied using limiting dilution analysis (LDA). About 75% of the HD patients had normal NK activity. There was a higher percentage of low NK responders (mean percent NK activity of healthy donors--2 SD) in patients with lymphocyte depletion histologic grade of the disease and those who were in clinical stage IV, suggesting a correlation of decrease in NK activity with poor prognosis. We found efficient LAK activity against the NK-sensitive K562 cells and NK-resistant VIP (melanoma) and T-24 (bladder carcinoma) tumour targets in both low and normal NK responder HD patients, irrespective of the histopathological grade and clinical stage of the disease. In concordance with their good LAK cell activity, HD patients showed a frequency distribution of LAK cell progenitors in the PBL comparable to that of healthy donors.
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Affiliation(s)
- N Rajaram
- Immunology Division, Cancer Research Institute, Parel, Bombay, India
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Tatake RJ, Rajaram N, Damle RN, Balsara B, Bhisey AN, Gangal SG. Establishment and characterization of four new squamous cell carcinoma cell lines derived from oral tumors. J Cancer Res Clin Oncol 1990; 116:179-86. [PMID: 1691185 DOI: 10.1007/bf01612674] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Four cell lines were established from squamous cell carcinomas (SCC) of the oral cavity. Cell lines AW 13516 and AW 8507 were derived from poorly differentiated SCC and epidermoid carcinoma of the tongue respectively. Cell line AW 10498 was derived from moderately differentiated SCC of the lower alveolus, and AW 9803 grew from a well-differentiated SCC of a retromolar trigone. The cultures showed typical epithelial cell morphology, numerous mitotic figures, occasional multinucleated giant cells, individual cell diskeratosis and nuclear and nucleolar abnormalities. The cell lines AW 13516 and AW 8507 were fast growers with a doubling time of 35.5 h and 31.9 h, respectively, which was independent of the initial seeding density. Cell lines AW 10498 (doubling time 52.2 h) and AW 9803 (doubling time 66 h) showed slower growth and had shorter doubling times at higher seeding densities. The presence of cytokeratins was detected in all the four cell lines by using polyclonal antikeratin antisera in indirect immunofluorescence and in Western blotting. None of the cell lines expressed major histocompatibility complex (MHC) class II antigens. MHC class I antigens were expressed by three cell lines but not by AW 9803. Flow cytometric analysis of DNA content and chromosomal studies suggested the presence of polyploidy and aneuploidy in all the four cell lines. Ultrastructural studies revealed typical epithelial cell features, such as the presence of desmosomes, tonofilaments and keratin bundles.
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Affiliation(s)
- R J Tatake
- Immunology Division, Tata Memorial Centre, Bombay, India
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Rajaram N, Tatake RJ, Advani SH, Naik SL, Gangal SG. Natural killer and lymphokine-activated killer cell functions in chronic myeloid leukemia. Cancer Immunol Immunother 1990; 31:44-8. [PMID: 2306755 PMCID: PMC11038834 DOI: 10.1007/bf01742494] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/1989] [Accepted: 09/26/1989] [Indexed: 12/31/2022]
Abstract
The natural killer (NK) and lymphokine-activated killer (LAK) cell activities of peripheral blood lymphocytes from chronic myeloid leukemia (CML) patients in remission and from healthy donors have been studied. Regression analysis to compare both cytotoxic responses in individual donors and the frequency of LAK cell precursors was also carried out. About 42% of CML patients in remission showed low NK activity (less than the mean percentage NK activity of healthy donors--2 SD) and were categorised as low NK responders. The stage of remission or the drugs used to bring about remission did not influence the NK status. The LAK activity of low NK as well as normal NK responder CML patients was significantly low against the NK-sensitive K562 cell line and the NK-resistant VIP (melanoma) and T-24 (bladder carcinoma) tumor targets, as assessed by linear regression analysis. Allogeneic leukemic cells were more resistant to killing, especially by patients' LAK cells. The frequency analysis of LAK cell precursors revealed a significant reduction in the LAK cell progenitor frequency in CML patients in remission.
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Affiliation(s)
- N Rajaram
- Immunology Division, Tata Memorial Centre, Bombay, India
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Ramu G, Pandian TD, Rajaram N, Sithambaram M, Bharati R. A sample survey of leprosy in the ELEP Leprosy Control Project, Dharmapuri, Tamil Nadu. Indian J Lepr 1985; 57:575-87. [PMID: 3831095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A sample survey of the Dharmapuri Leprosy Control Project was undertaken in 1983; a population of 60855 was enumerated out of which 51205 was examined. The sampling procedure which was followed consisted of stratifying the sub-centres according to prevalence and classifying the villages by the size of the population. Villages were selected by random allocation. 10 leprosy inspectors participated in the survey examining 626 to 774 persons per day. 859 active cases were detected giving a prevalence of 16.77 per thousand. The child prevalence was 6.19 per thousand. The number of lepromatous and BL cases detected were 70 giving an infectivity rate of 8.15%. The prevalence of leprosy as found in the last survey conducted in the different areas in the project approximate to those of the sample survey. Therefore it could be said that the prevalence has decreased in this project from 19.94 per thousand as observed in the first survey. The child prevalence has likewise decreased from 9.40 to 4.09 in the project.
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Kuppusami J, Lakshmanan AS, Lakshminarayanan R, Rajaram N, Suryanarayana CV. A Study of Concentrated Solutions of Mixed Electrolytes. Ultrasonic Velocities and Viscosities of Mixtures of Aqueous Solutions of Potassium and Sodium Chlorides at High Concentrations. BCSJ 1965. [DOI: 10.1246/bcsj.38.1610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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