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Kugalingam N, De Silva D, Abeysekera H, Nanayakkara S, Tirimanne S, Ranaweera D, Suravajhala P, Chandrasekharan V. RB1 screening of retinoblastoma patients in Sri Lanka using targeted next generation sequencing (NGS) and gene ratio analysis copy enumeration PCR (GRACE-PCR). BMC Med Genomics 2023; 16:279. [PMID: 37932687 PMCID: PMC10626775 DOI: 10.1186/s12920-023-01721-6] [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: 05/16/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Retinoblastoma (RB) a tumour affecting those under 5 years, has a prevalence of 1 in 20,000, with around twenty new diagnoses per year in Sri Lanka. Unilateral and bilateral RB presents around 24 and 15 months respectively. Approximately 10% are familial. Systematic genetic testing for germline pathogenic variants of RB1, the only gene associated with an inherited risk of RB, is unavailable in Sri Lanka. Genetic testing optimizes management of affected children and at-risk siblings. This study aimed to develop accessible genetic testing to identify children with a germline pathogenic variant of RB1 in Sri Lanka. METHODS Targeted next generation sequencing (NGS) for detecting pathogenic sequence variants and Gene Ratio Analysis Copy Enumeration PCR (GRACE-PCR) for detecting RB1 copy number variations (CNVs) were performed for 49 consecutive RB patients treated between 2016 and 2020 at the designated RB care unit, Lady Ridgway hospital, Colombo. Patients (bilateral RB (n = 18; 37%), unilateral n = 31) were recruited following ethical clearance and informed consent. RESULTS There were 26 (53%) females. Mean age at diagnosis was 18 months. Thirty-five patients (71%) had undergone enucleation. Germline pathogenic variants of RB1 identified in 22/49 (45%) patients including 18 (37%; 12 bilateral and 6 unilateral) detected by targeted NGS (2 missense, 7 stop gained, 1 splice donor, 8 frameshift variants). Six were previously undescribed, likely pathogenic frameshift variants. Four bilateral RB patients had GRACE-PCR detected CNVs including one whole RB1, two intragenic deletions (exon 12/13; exon 11 and 23) and a partial duplication of exon 27. The only familial case (affected mother and child) shared the duplication. Only 2 of 4 CNVs and 10 of 18 pathogenic variants were confirmed by whole exome sequencing and Sanger sequencing respectively, due to funding limitations. CONCLUSIONS The study identified pathogenic or likely pathogenic germline RB1 sequence variants and copy number variants in 16/18 (89%) bilateral and 6/31(19%) unilateral cases, which is comparable to worldwide data (10-15% unilateral, 80-85% bilateral). Targeted NGS combined with GRACE-PCR significantly reduce the cost of RB1 testing in Sri Lanka, and may widen access for genetic diagnosis of RB patients in other low and middle income countries.
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Affiliation(s)
- Nirosha Kugalingam
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka.
| | - Deepthi De Silva
- Department of Physiology, Faculty of Medicine, University of Kelaniya, Kelaniya, Sri Lanka
| | | | | | - Shamala Tirimanne
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | - Dinali Ranaweera
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
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Ekanayake A, Madegedara D, Chandrasekharan V, Magana-Arachchi D. Respiratory Bacterial Microbiota and Individual Bacterial Variability in Lung Cancer and Bronchiectasis Patients. Indian J Microbiol 2019; 60:196-205. [PMID: 32255852 DOI: 10.1007/s12088-019-00850-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 12/06/2019] [Indexed: 12/01/2022] Open
Abstract
Respiratory bacterial microbiota plays a key role in human health. Lung cancer microbiome is a significant yet an understudied area while bronchiectasis microbiome is often studied. We assessed the bacterial microbiota in the upper and lower respiratory tract of the patients with lung cancer and bronchiectasis against a healthy group and their variations in individuality. 16S rRNA gene based metagenomic sequencing was used to detect entire bacterial community along with conventional aerobic bacterial culturing. In comparison to healthy, increased bacterial diversity was observed in diseased population. Abundance of more than 1% was considered and bacteria were identified in 97% similarity. Only lung cancer patients exhibited bacteria specific to the disease: Corynebacterium tuberculostearicum and Keratinibaculum paraultunense. However, Enterococcus faecalis and Delftia tsuruhatensis were also observed limited to lung cancer and bronchiectasis respectively, in less than 1% but supported with bacterial culturing. In conclusion the disease condition and intra-group variability should be considered in future with larger cohorts to understand individual patient variability highlighting the social habits and gender of the individual.
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Affiliation(s)
- Anuradha Ekanayake
- 1Molecular Microbiology and Human Diseases, National Institute of Fundamental Studies, Kandy, 20000 Sri Lanka
| | | | | | - Dhammika Magana-Arachchi
- 1Molecular Microbiology and Human Diseases, National Institute of Fundamental Studies, Kandy, 20000 Sri Lanka
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Branavan U, Muneeswaran K, Wijesundera S, Jayakody S, Chandrasekharan V, Wijeyaratne C. Identification of selected genetic polymorphisms in polycystic ovary syndrome in Sri Lankan women using low cost genotyping techniques. PLoS One 2018; 13:e0209830. [PMID: 30596735 PMCID: PMC6312267 DOI: 10.1371/journal.pone.0209830] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 08/10/2018] [Accepted: 12/12/2018] [Indexed: 12/14/2022] Open
Abstract
Background Polycystic ovary syndrome (PCOS), the commonest endocrine disorder affecting young women, appears to be a multigenic trait with contributing genes being unclear. Hence, analysis of polymorphisms in multiple candidate genes is required. Currently available genotyping methods are expensive, time-consuming with limited analytical sensitivity. Aim (i) Develop and validate high resolution melting (HRM) assay and allele-specific real-time quantitative PCR (AS-qPCR) for genotyping selected SNPs associated with PCOS. (ii) Identify selected SNPs and their association with a Sri Lankan cohort of well-characterized PCOS. Methods DNA was extracted from women with well-characterized PCOS from adolescence (n = 55) and ethnically matched controls (n = 110). FTO (Fat mass and obesity associated gene; rs9939609), FSHB (Follicle stimulating hormone beta subunit; rs6169), FSHR (Follicle stimulating hormone receptor; rs6165/rs6166), and INSR (Insulin receptor; rs1799817) genes were genotyped using HRM assay. GnRH1 (Gonadotropin releasing hormone; rs6185), LHB (Luteinizing hormone beta subunit; rs1800447/rs34349826) and LHCGR (Luteinizing hormone/choriogonadotropin receptor; rs2293275) genes were genotyped using AS-qPCR method. Genotyping results were validated using Sanger sequencing. Results A significant association was observed within FTO gene polymorphism (rs9939609) and PCOS. Genotype frequency of FTO gene (rs9939609)—cases versus controls were TT-36.4% vs.65.4% (p<0.05), AT-23.6% vs.20.9%, AA-40% vs.13.6% (p<0.05). Genotype frequencies of the SNPs GnRH1 (rs6185), FSHB (rs6169), FSHR (rs6165 & rs6166), LHB (rs1800447 & rs34349826), LHCGR (rs2293275) and INSR (rs1799817) were not significantly different between cases and controls (p>0.05). Only the mutant alleles were observed for LHB rs1800447 and rs34349826 SNPs in both groups. The HRM and AS-qPCR assay results had 100% concordance with sequencing results. Conclusions FTO gene rs9939609 polymorphism is significantly more prevalent among Sri Lankan PCOS subjects while the other selected SNPs of HPG axis genes and INSR gene showed no association. HRM and AS-qPCR assays provide a reliable, fast and user-friendly genotyping method facilitating wider implication in clinical practice.
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Affiliation(s)
- Umayal Branavan
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Kajan Muneeswaran
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
- Department of Psychiatry, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Sulochana Wijesundera
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Surangi Jayakody
- Department of Community Medicine, Faculty of Medical Sciences, University of Sri Jayawardanapura, Nugegoda, Sri Lanka
| | | | - Chandrika Wijeyaratne
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
- * E-mail: ,
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Abayasekara LM, Perera J, Chandrasekharan V, Gnanam VS, Udunuwara NA, Liyanage DS, Bulathsinhala NE, Adikary S, Aluthmuhandiram JVS, Thanaseelan CS, Tharmakulasingam DP, Karunakaran T, Ilango J. Detection of bacterial pathogens from clinical specimens using conventional microbial culture and 16S metagenomics: a comparative study. BMC Infect Dis 2017; 17:631. [PMID: 28927397 PMCID: PMC5606128 DOI: 10.1186/s12879-017-2727-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [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: 05/30/2017] [Accepted: 09/12/2017] [Indexed: 12/27/2022] Open
Abstract
Background Infectious disease is the leading cause of death worldwide, and diagnosis of polymicrobial and fungal infections is increasingly challenging in the clinical setting. Conventionally, molecular detection is still the best method of species identification in clinical samples. However, the limitations of Sanger sequencing make diagnosis of polymicrobial infections one of the biggest hurdles in treatment. The development of massively parallel sequencing or next generation sequencing (NGS) has revolutionized the field of metagenomics, with wide application of the technology in identification of microbial communities in environmental sources, human gut and others. However, to date there has been no commercial application of this technology in infectious disease diagnostic settings. Methods Credence Genomics Rapid Infection Detection™ test, is a molecular based diagnostic test that uses next generation sequencing of bacterial 16S rRNA gene and fungal ITS1 gene region to provide accurate identification of species within a clinical sample. Here we present a study comparing 16S and ITS1 metagenomic identification against conventional culture for clinical samples. Using culture results as gold standard, a comparison was conducted using patient specimens from a clinical microbiology lab. Results Metagenomics based results show a 91.8% concordance rate for culture positive specimens and 52.8% concordance rate with culture negative samples. 10.3% of specimens were also positive for fungal species which was not investigated by culture. Specificity and sensitivity for metagenomics analysis is 91.8 and 52.7% respectively. Conclusion 16S based metagenomic identification of bacterial species within a clinical specimen is on par with conventional culture based techniques and when coupled with clinical information can lead to an accurate diagnostic tool for infectious disease diagnosis. Electronic supplementary material The online version of this article (10.1186/s12879-017-2727-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jennifer Perera
- Dean and Chair Professor of Microbiology, Faculty of Medicine, University of Colombo, P.O. box 271, Colombo, Sri Lanka.,Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Vishvanath Chandrasekharan
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka.,Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Vaz S Gnanam
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Nisala A Udunuwara
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Dileepa S Liyanage
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | | | - Subhashanie Adikary
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | | | | | | | - Tharaga Karunakaran
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Janahan Ilango
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
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Yadav UN, Chandrasekharan V, Guddattu V, Gruiskens J. Mixed method approach for determining factors associated with late presentation to HIV/AIDS care in southern India. J Postgrad Med 2016; 62:173-7. [PMID: 27241809 PMCID: PMC4970344 DOI: 10.4103/0022-3859.183169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background: Early diagnosis and treatment of human Immunodeficiency virus (HIV) is not only beneficial for the people living with HIV/acquired immunodeficiency syndrome (AIDS) (PLHA) but for the public and society as well. The study was aimed to identify the factors associated with late presentation to HIV/AIDS care. Materials and Methods: A facility-based unmatched case-control (1:1) study along with in-depth qualitative assessment was conducted at an ART Plus center at a district hospital, Udupi, southern India. A sample of 320 HIV patients (160 cases and 160 controls) was selected randomly between February and July 2014. Information regarding the patients were collected using an interviewer-administered semi-structured questionnaire. The qualitative component was assessed by in-depth interviews of 4 health professionals and 12 HIV-positive patients who were late for HIV care. The quantitative data were analyzed using Statistical Package for the Social Sciences (SPSS) version 15.0. The technique of thematic analysis was adopted for the analysis of qualitative data. Results: HIV-positive individuals who lived with families [odds ratio (OR) = 5.11], the patients having non-AIDS comorbidities [OR= 2.19, 95% confidence interval (CI): 1.09-4.40], the patients who perceived fear of losing family [OR = 5.00, 95% CI: 2.17-11.49], the patients who perceived fear that their status will be ruined in the community [OR= 2.00, 95% CI: 1.01-3.97], the patients who perceived fear of side effects of ART medications [OR = 4.3, 95% CI: 2.65-11.33], the patients who perceived fear of losing confidentiality [OR = 4.94, 95% CI: 2.54-9.59], the patients those who lack information available on government services [OR = 4.12, 95% CI: 2.127-8.005], and the patients who consumed alcohol [OR= 3.52, 95% CI: 1.83-6.77] were found to be independently associated with the late presentation to HIV/AIDS care after adjusting for all known confounders in a multivariable analysis. The qualitative summary showed that the perceived HIV stigma, inadequate health education, lack of awareness on available government services, psychological problems, alcohol use, asymptomatic conditions, and financial problems are major barriers to access care early for the late presenters. Conclusion: The identified factors can be utilized for the formulation of policies and interventions by promoting early diagnoses and addressing special concerns such as stigma, disclosure, health education, and awareness.
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Affiliation(s)
- U N Yadav
- Department of Public Health, Manipal University, Manipal, Karnataka, India
| | - V Chandrasekharan
- Department of Public Health, Manipal University, Manipal, Karnataka, India
| | - V Guddattu
- Department of Statistics, Manipal University, Manipal, Karnataka, India
| | - Jrjh Gruiskens
- CAPHRI School of Public Health and Preventive Medicine, Maastricht University, Netherlands
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Ranasinghe S, Wickremasinghe R, Hulangamuwa S, Sirimanna G, Opathella N, Maingon RDC, Chandrasekharan V. Polymerase chain reaction detection of Leishmania DNA in skin biopsy samples in Sri Lanka where the causative agent of cutaneous leishmaniasis is Leishmania donovani. Mem Inst Oswaldo Cruz 2015; 110:1017-23. [PMID: 26676321 PMCID: PMC4708022 DOI: 10.1590/0074-02760150286] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/06/2015] [Indexed: 11/22/2022] Open
Abstract
Leishmania donovani is the known causative agent of both cutaneous
(CL) and visceral leishmaniasis in Sri Lanka. CL is considered to be under-reported
partly due to relatively poor sensitivity and specificity of microscopic diagnosis.
We compared robustness of three previously described polymerase chain reaction (PCR)
based methods to detectLeishmania DNA in 38 punch biopsy samples
from patients presented with suspected lesions in 2010. Both,
Leishmaniagenus-specific JW11/JW12 KDNA and LITSR/L5.8S internal
transcribed spacer (ITS)1 PCR assays detected 92% (35/38) of the samples whereas a
KDNA assay specific forL. donovani (LdF/LdR) detected only 71%
(27/38) of samples. All positive samples showed a L. donovani
banding pattern upon HaeIII ITS1 PCR-restriction fragment length polymorphism
analysis. PCR assay specificity was evaluated in samples containing
Mycobacterium tuberculosis, Mycobacterium
leprae, and human DNA, and there was no cross-amplification in JW11/JW12
and LITSR/L5.8S PCR assays. The LdF/LdR PCR assay did not amplify M.
leprae or human DNA although 500 bp and 700 bp bands were observed in
M. tuberculosis samples. In conclusion, it was successfully shown
in this study that it is possible to diagnose Sri Lankan CL with high accuracy, to
genus and species identification, using Leishmania DNA PCR
assays.
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Affiliation(s)
- Shalindra Ranasinghe
- Department of Parasitology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Renu Wickremasinghe
- Department of Parasitology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | | | - Ganga Sirimanna
- Dermatology Unit, National Hospital of Sri Lanka, Colombo, Sri Lanka
| | | | - Rhaiza D C Maingon
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire, UK
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Ranasinghe S, Zhang WW, Wickremasinghe R, Abeygunasekera P, Chandrasekharan V, Athauda S, Mendis S, Hulangamuwa S, Matlashewski G, Pratlong F. Leishmania donovani zymodeme MON-37 isolated from an autochthonous visceral leishmaniasis patient in Sri Lanka. Pathog Glob Health 2013; 106:421-4. [PMID: 23265615 DOI: 10.1179/2047773212y.0000000054] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Although the strain causing cutaneous leishmaniasis (CL) in Sri Lanka was first identified in 2003, the strain causing visceral leishmaniasis (VL) has not yet been identified. We report the first isoenzyme typing of a strain causing VL in Sri Lanka at an early stage of emergence of VL in the country. The parasite was isolated from a 57-year-old civil soldier who had been in the jungle in the Vavuniya district in the Northern Province of Sri Lanka for a period of nearly 6 months immediately before the onset of symptoms. Multilocus enzyme electrophoresis (MLEE) revealed that the strain is Leishmania donovani zymodeme MON-37, the zymodeme which was previously identified from the CL patients in the country. The MLEE analysis was confirmed by sequencing the gene encoding the 6-phosphogluconate dehydrogenase isoenzyme. This is an instance of the same Leishmania zymodeme associated with both dermotropism and viscerotropism in the same geographic region. Further investigations into the genetic structure and identification of virulence factors in the parasite and immune factors in the host are required to understand the factors responsible for different tropism shown by the same zymodeme MON-37 L. donovani from Sri Lanka.
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Affiliation(s)
- Shalindra Ranasinghe
- Department of Parasitology, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka.
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Brahms J, Pilet J, Damany H, Chandrasekharan V. Application of a new modulation method for linear dichroism studies of oriented biopolymers in the vacuum ultraviolet. Proc Natl Acad Sci U S A 2010; 60:1130-7. [PMID: 16591671 PMCID: PMC224891 DOI: 10.1073/pnas.60.4.1130] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- J Brahms
- CENTRE DE BIOPHYSIQUE MOLECULAIRE (ORLEANS) AND LABORATOIRE DES HAUTES PRESSIONS (BELLEVUE), CENTRE NATIONAL DE RECHERCHE SCIENTIFIQUE, FRANCE
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Magana-Arachchi D, Perera J, Gamage S, Chandrasekharan V. Low cost in-house PCR for the routine diagnosis of extra-pulmonary tuberculosis. Int J Tuberc Lung Dis 2008; 12:275-280. [PMID: 18284832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
SETTING Conventional methods for the identification of mycobacteria are slow and labour intensive. DNA amplification methods offer rapid sensitive and specific diagnosis. OBJECTIVE To determine the feasibility of an in-house polymerase chain reaction (PCR) method to detect Mycobacterium tuberculosis in clinical samples. DESIGN The present study focused mainly on diagnosing extra-pulmonary tuberculosis (EPTB) using an in-house PCR method in 465 clinical samples. This study also compared the efficacy of a standard phenol-chloroform (PC) extraction procedure and the guanidine thiocyanate with diatomaceous silica (GTCS) method of DNA extraction and purification. A subsample of patients was used for the validation of results based on the final diagnosis. RESULTS Among 373 patients with suspected EPTB, 75 specimens were positive by PCR, four by microscopy and six by culture. Of the 25 PCR-positive patients, 95% had a final diagnosis of TB. Globally, the GTCS method was found to be superior to the PC method for DNA extraction and removal of inhibitors from clinical specimens. CONCLUSION The DNA amplification method was found to be significantly more sensitive and rapid compared to culture and microscopy for a reliable final diagnosis of EPTB.
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Affiliation(s)
- D Magana-Arachchi
- Department of Microbiology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
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Karunaweera N, Wanasekara D, Chandrasekharan V, Mendis K, Carter R. Plasmodium vivax: paroxysm-associated lipids mediate leukocyte aggregation. Malar J 2007; 6:62. [PMID: 17517147 PMCID: PMC1891311 DOI: 10.1186/1475-2875-6-62] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Accepted: 05/22/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Paroxysms are recurrent febrile episodes, characteristic of Plasmodium vivax infections, which coincide with the rupture of schizont-infected erythrocytes in the patients' circulation. The present study describes the formation of prominent aggregates of leukocytes in vitro in the presence of parasite and host factors released during paroxysms. METHODS Whole blood cells from uninfected malaria-naïve donors were incubated with plasma taken during a paroxysm or normal human plasma as a control and cell smears were observed under the microscope for the presence of leukocyte aggregates. Plasma factors involved in mediating the leukocyte aggregation were identified using immune depletion and reconstitution experiments. Furthermore, biochemical characterization was carried out to determine the chemical nature of the active moieties in plasma present during paroxysms. RESULTS Leukocyte aggregates were seen exclusively when cells were incubated in plasma collected during a paroxysm. Immune depletion and reconstitution experiments revealed that the host cytokines TNF-alpha, GM-CSF, IL-6 and IL-10 and two lipid fractions of paroxysm plasma comprise the necessary and sufficient mediators of this phenomenon. The two lipid components of the paroxysm plasmas speculated to be of putative parasite origin, were a phospholipid-containing fraction and another containing cholesterol and triglycerides. The phospholipid fraction was dependent upon the presence of cytokines for its activity unlike the cholesterol/triglyceride-containing fraction which in the absence of added cytokines was much more active than the phospholipids fraction. The biological activity of the paroxysm plasmas from non-immune patients who presented with acute P. vivax infections was neutralized by immune sera raised against schizont extracts of either P. vivax or Plasmodium falciparum. However, immune sera against P. vivax were more effective than that against P. falciparum indicating that the parasite activity involved may be antigenically at least partially parasite species-specific. CONCLUSION Leukocyte aggregation was identified as associated with paroxysms in P. vivax infections. This phenomenon is mediated by plasma factors including host-derived cytokines and lipids of putative parasite origin. The characteristics of the phospholipid fraction in paroxysm plasma are congruent with those of the parasite-derived, TNF-inducing GPI moieties described by others. The more active cholesterol/triglyceride(s), however, represent a novel malarial toxin, which is a new class of biologically active lipid associated with the paroxysm of P. vivax malaria.
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Affiliation(s)
- Nadira Karunaweera
- Malaria Research Unit, Department of Parasitology, Faculty of Medicine, University of Colombo,, P.O. Box 271, Kynsey Road, Colombo 08, Sri Lanka
| | - Deepani Wanasekara
- Malaria Research Unit, Department of Parasitology, Faculty of Medicine, University of Colombo,, P.O. Box 271, Kynsey Road, Colombo 08, Sri Lanka
| | | | - Kamini Mendis
- Malaria Research Unit, Department of Parasitology, Faculty of Medicine, University of Colombo,, P.O. Box 271, Kynsey Road, Colombo 08, Sri Lanka
| | - Richard Carter
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Affiliation(s)
- K. Kobashi
- a Laboratoire des Interactions Moléculaires et des Hautes Pressions, CNRS, Centre Universitaire Paris Nord , 93430 , Villetaneuse , France
- b Department of Chemistry , Faculty of Science, Kyoto University , Kyoto , Japan , 606
| | - V. Chandrasekharan
- a Laboratoire des Interactions Moléculaires et des Hautes Pressions, CNRS, Centre Universitaire Paris Nord , 93430 , Villetaneuse , France
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Affiliation(s)
- M.M. Thiéry
- a Laboratoire des Interactions Moléculaires et des Hautes Pressions, C.N.R.S., Centre Universitaire Paris-Nord , 93430 , Villetaneuse , France
| | - D. Fabre
- a Laboratoire des Interactions Moléculaires et des Hautes Pressions, C.N.R.S., Centre Universitaire Paris-Nord , 93430 , Villetaneuse , France
| | - V. Chandrasekharan
- a Laboratoire des Interactions Moléculaires et des Hautes Pressions, C.N.R.S., Centre Universitaire Paris-Nord , 93430 , Villetaneuse , France
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Chandrasekharan V, Kapoor SG, DeVor RE. A Mechanistic Approach to Predicting the Cutting Forces in Drilling: With Application to Fiber-Reinforced Composite Materials. ACTA ACUST UNITED AC 1995. [DOI: 10.1115/1.2803534] [Citation(s) in RCA: 103] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In this paper models are developed to predict the thrust and torque forces at the different regions of cutting on a drill. The mechanistic approach adopted to develop these models exploits the geometry of the process, which is independent of the workpiece material. The models are calibrated to a particular material using the well-established relationships between chip load and cutting forces, modified to take advantage of the characteristics of the drill point geometry. The models are validated independently for the cutting lips and the chisel edge for drilling both metals and fiber-reinforced composite materials for a wide range of machining conditions and drill geometry. While the cutting-lips model predictions agree well with the experimental data for both materials, only the chisel-edge model proposed for metals agrees well with the experimental data.
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Affiliation(s)
- V. Chandrasekharan
- Department of Mechanical and Industrial Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - S. G. Kapoor
- Department of Mechanical and Industrial Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - R. E. DeVor
- Department of Mechanical and Industrial Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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Chergui M, Schwentner N, Chandrasekharan V. Fano profiles on multiphonon continua in electronic transitions of matrix-isolated NO. Phys Rev Lett 1991; 66:2499-2502. [PMID: 10043504 DOI: 10.1103/physrevlett.66.2499] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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18
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Garrabos Y, Chandrasekharan V, Echargui M, Marsault-Herail F. Density effect on the raman fermi resonance in the fluid phases of CO2. Chem Phys Lett 1989. [DOI: 10.1016/0009-2614(89)87591-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Alikhani ME, Silvi B, Perchard JP, Chandrasekharan V. Reinvestigation of the Raman spectra of dihydrogen trapped in rare gas solids. I. H2, HD, and D2 monomeric species. J Chem Phys 1989. [DOI: 10.1063/1.456475] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Etters RD, Chandrasekharan V, Uzan E, Kobashi K. High-pressure static and dynamic properties of the R3-barc phase of solid nitrogen. Phys Rev B Condens Matter 1986; 33:8615-8621. [PMID: 9938261 DOI: 10.1103/physrevb.33.8615] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Silvi B, Chandrasekharan V, Chergui M, Etters RD. Frequency shifts of vibrational and rotational states of dilute H2, D2, and HD impurities in solid Ar under pressure. Phys Rev B Condens Matter 1986; 33:2749-2756. [PMID: 9938615 DOI: 10.1103/physrevb.33.2749] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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24
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Chandrasekharan V, Uzan E. Librational zero point motion and Raman intensities in simple molecular crystals. Mol Phys 1985. [DOI: 10.1080/00268978500102431] [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: 10/24/2022]
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Etters RD, Flurchick K, Pan RP, Chandrasekharan V. Thermodynamic properties and phase transitions in CO2 molecular clusters. J Chem Phys 1981. [DOI: 10.1063/1.442091] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Chandrasekharan V, Thiéry MM, Walmsley SH. Comment on ’’Vibron and lattice frequency shifts in the Raman spectra of solid α‐N 2and γ‐N 2and librational force constants of diatomic molecular crystals’’. J Chem Phys 1979. [DOI: 10.1063/1.438802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Chandrasekharan V, Etters RD. On the contribution of intramolecular zero point energy to the equation of state of solid H2. J Chem Phys 1978. [DOI: 10.1063/1.435650] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Zumofen G, Dressler K, Thiéry MM, Chandrasekharan V. On the a priori calculation of the vibron band in the Raman spectrum of solid α‐N2. J Chem Phys 1977. [DOI: 10.1063/1.434782] [Citation(s) in RCA: 10] [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: 11/14/2022] Open
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Thiéry MM, Chandrasekharan V. Vibron and lattice frequency shifts in the Raman spectra of solid α‐N2 and γ‐N2 and librational force constants of diatomic molecular crystals. J Chem Phys 1977. [DOI: 10.1063/1.435306] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Chandrasekharan V, Farbre D, Thiery M, Uzan E, Donkersloot M, Walmsley S. Intermolecular potential energy functions and Gruneisen Parameters of simple molecular crystals. Chem Phys Lett 1974. [DOI: 10.1016/0009-2614(74)85416-3] [Citation(s) in RCA: 17] [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: 10/17/2022]
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Chandrasekharan V, Damany H. Rotating polarizer and phase detection applied to optical rotation measurements in the vacuum ultraviolet. Appl Opt 1969; 8:1506. [PMID: 20072464 DOI: 10.1364/ao.8.001506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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Chandrasekharan V, Damany H. Anomalous dispersion of birefringence of sapphire and magnesium fluoride in the vacuum ultraviolet. Appl Opt 1969; 8:671-675. [PMID: 20072279 DOI: 10.1364/ao.8.000671] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Previous measurements of the birefringence of sapphire and magnesium fluoride have been extended to their respective limits of transparency, revealing anomalous dispersion effects at short wavelengths, which are qualitatively discussed. Possible practical applications to Lyot filters and quarter-wave plates for Lyman-alpha are indicated.
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Chandrasekharan V, Damany H. Birefringence of sapphire, magnesium fluoride, and quartz in the vacuum ultraviolet, and retardation plates. Appl Opt 1968; 7:939-941. [PMID: 20068710 DOI: 10.1364/ao.7.000939] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Measurements of the birefringence of sapphire, magnesium fluoride, and synthetic quartz from 3000 A to 1500 A are reported and are followed by a discussion of the methods of achromatizing quarter-wave plates and of linearizing the path retardation of a multiwave plate against wavelength (equichromatic wave plates).
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Chandrasekharan V, Damany H. Dispersion of quartz in the vacuum ultraviolet from interference in a thin parallel plate. Appl Opt 1968; 7:687-688. [PMID: 20068659 DOI: 10.1364/ao.7.000687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Measurements of the ordinary and extraordinary refractive indices of synthetic quartz in the vacuum uv down to 1440 A are reported as deduced from the determination of the orders of interference fringes in a thin parallel plate.
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