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Pustam A, Jayaraman J, Ramsubhag A. Whole genome sequencing reveals complex resistome features of Klebsiella pneumoniae isolated from patients at major hospitals in Trinidad, West Indies. J Glob Antimicrob Resist 2024; 37:141-149. [PMID: 38608934 DOI: 10.1016/j.jgar.2024.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/17/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
OBJECTIVES Antibiotic-resistant Klebsiella pneumoniae is a human pathogen of major global concern due to its ability to cause multiple severe diseases that are often difficult to treat therapeutically. This study aimed to investigate the resistome of local clinical K. pneumoniae isolates. METHODS Herein, we used a whole genome sequencing approach and bioinformatics tools to reconstruct the resistome of 10 clinical K. pneumoniae isolates and one clinical isolate of the closely related Klebsiella quasipneumoniae obtained from patients from three major hospitals in Trinidad, West Indies. RESULTS The results of the study revealed the presence of a complex antibiotic-resistant armoury among the local isolates with multiple resistance mechanisms involving (i) inactivation of antibiotics, (ii) efflux pumps, (iii) antibiotic target alteration, protection, and replacement against antibiotics, and (iv) altered porin protein that reduced the permeability to antibiotics. Several resistance genes such as blaCTX-M-15, blaTEM-1B, blaSHV-28, blaKPC-2, oqxA, sul1, tetD, aac(6')-Ib-cr5, aph(6)-Id, and fosA6, which are known to confer resistance to antibiotics used to treat K. pneumoniae infections. In most cases, the resistance genes were flanked by mobile elements, including insertion sequences and transposons, which facilitate the spread of these genetic features among related organisms. CONCLUSION This is the first comprehensive study to thoroughly investigate the resistome of clinical K. pneumoniae isolates and K. quasipneumoniae from Trinidad, West Indies. These findings suggest that monitoring K. pneumoniae and its genome-wide antibiotic resistance features in clinical strains would be of critical importance for guiding antibiotic stewardship programs and improving regional disease management systems for this pathogen.
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Affiliation(s)
- Aarti Pustam
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago.
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Ramnarine SDBJ, Jayaraman J, Ramsubhag A. Crucifer Lesion-Associated Xanthomonas Strains Show Multi-Resistance to Heavy Metals and Antibiotics. Curr Microbiol 2024; 81:136. [PMID: 38598029 DOI: 10.1007/s00284-024-03646-4] [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: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 04/11/2024]
Abstract
Copper resistance in phytopathogens is a major challenge to crop production globally and is known to be driven by excessive use of copper-based pesticides. However, recent studies have shown co-selection of multiple heavy metal and antibiotic resistance genes in bacteria exposed to heavy metal and xenobiotics, which may impact the epidemiology of plant, animal, and human diseases. In this study, multi-resistance to heavy metals and antibiotics were evaluated in local Xanthomonas campestris pv. campestris (Xcc) and co-isolated Xanthomonas melonis (Xmel) strains from infected crucifer plants in Trinidad. Resistance to cobalt, cadmium, zinc, copper, and arsenic (V) was observed in both Xanthomonas species up to 25 mM. Heavy metal resistance (HMR) genes were found on a small plasmid-derived locus with ~ 90% similarity to a Stenotrophomonas spp. chromosomal locus and a X. perforans pLH3.1 plasmid. The co-occurrence of mobile elements in these regions implies their organization on a composite transposon-like structure. HMR genes in Xcc strains showed the lowest similarity to references, and the cus and ars operons appear to be unique among Xanthomonads. Overall, the similarity of HMR genes to Stenotrophomonas sp. chromosomal genomes suggest their origin in this genus or a related organism and subsequent spread through lateral gene transfer events. Further resistome characterization revealed the presence of small multidrug resistance (SMR), multidrug resistance (MDR) efflux pumps, and bla (Xcc) genes for broad biocide resistance in both species. Concurrently, resistance to antibiotics (streptomycin, kanamycin, tetracycline, chloramphenicol, and ampicillin) up to 1000 µg/mL was confirmed.
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Affiliation(s)
- Stephen D B Jr Ramnarine
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine, Trinidad and Tobago.
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Ali R, Lezcano RD, Jayaraman J, Mohammed A, Carrington CVF, Daniel B, Lovin DD, Cunningham JM, Severson DW, Ramsubhag A. DNA Barcoding Analysis of Trinidad Haemagogus Mosquitoes Reveals Evidence for Putative New Species. Vector Borne Zoonotic Dis 2024; 24:237-244. [PMID: 38306182 DOI: 10.1089/vbz.2023.0031] [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: 02/04/2024] Open
Abstract
Background: Haemagogus janthinomys is a primary sylvan vector of yellow fever virus and the emerging Mayaro virus. However, despite its medical importance, there is a dearth of data on the molecular taxonomy of this mosquito species. Methods: In this study, DNA barcoding analysis was performed on 64 adult female mosquitoes from Trinidad morphologically identified as Hg. janthinomys. The mitochondrial cytochrome c oxidase I (COI) gene and ribosomal DNA internal transcribed spacer 2 (ITS2) region of the mosquitoes were PCR amplified and sequenced, and molecular phylogenies inferred. Results: The BLASTN analysis showed that only 20% (n = 13/66) of COI sequences had high similarity (>99% identity) to Hg. janthinomys and the remaining sequences had low similarity (<90% identity) to reference GenBank sequences. Phylogenetic analysis of COI sequences revealed the presence of four strongly supported groups, with one distinct clade that did not align with any reference sequences. Corresponding ITS2 sequences for samples in this distinct COI group clustered into three clades. Conclusions: These molecular findings suggest the existence of a putative new Haemagogus mosquito species and underscore the need for further, more in-depth investigations into the taxonomy and classification of the Haemagogus genus.
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Affiliation(s)
- Renee Ali
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies at St. Augustine, St. Augustine, Trinidad and Tobago
| | - Raul Diosany Lezcano
- Insect Vector Control Division, Ministry of Health, Cunupia, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies at St. Augustine, St. Augustine, Trinidad and Tobago
| | - Azad Mohammed
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies at St. Augustine, St. Augustine, Trinidad and Tobago
| | - Christine V F Carrington
- Department of Pre-Clinical Sciences, Faculty of Medical Sciences, The University of the West Indies at St. Augustine, St. Augustine, Trinidad and Tobago
| | - Brent Daniel
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies at St. Augustine, St. Augustine, Trinidad and Tobago
| | - Diane D Lovin
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Joanne M Cunningham
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - David W Severson
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies at St. Augustine, St. Augustine, Trinidad and Tobago
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, South Bend, Indiana, USA
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies at St. Augustine, St. Augustine, Trinidad and Tobago
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Ramnarine SDB, Ali O, Jayaraman J, Ramsubhag A. Early transcriptional changes of heavy metal resistance and multiple efflux genes in Xanthomonas campestris pv. campestris under copper and heavy metal ion stress. BMC Microbiol 2024; 24:81. [PMID: 38461228 PMCID: PMC10924375 DOI: 10.1186/s12866-024-03206-7] [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: 01/10/2023] [Accepted: 01/28/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Copper-induced gene expression in Xanthomonas campestris pv. campestris (Xcc) is typically evaluated using targeted approaches involving qPCR. The global response to copper stress in Xcc and resistance to metal induced damage is not well understood. However, homologs of heavy metal efflux genes from the related Stenotrophomonas genus are found in Xanthomonas which suggests that metal related efflux may also be present. METHODS AND RESULTS Gene expression in Xcc strain BrA1 exposed to 0.8 mM CuSO4.5H2O for 15 minutes was captured using RNA-seq analysis. Changes in expression was noted for genes related to general stress responses and oxidoreductases, biofilm formation, protein folding chaperones, heat-shock proteins, membrane lipid profile, multiple drug and efflux (MDR) transporters, and DNA repair were documented. At this timepoint only the cohL (copper homeostasis/tolerance) gene was upregulated as well as a chromosomal czcCBA efflux operon. An additional screen up to 4 hrs using qPCR was conducted using a wider range of heavy metals. Target genes included a cop-containing heavy metal resistance island and putative metal efflux genes. Several efflux pumps, including a copper resistance associated homolog from S. maltophilia, were upregulated under toxic copper stress. However, these pumps were also upregulated in response to other toxic heavy metals. Additionally, the temporal expression of the coh and cop operons was also observed, demonstrating co-expression of tolerance responses and later activation of part of the cop operon. CONCLUSIONS Overall, initial transcriptional responses focused on combating oxidative stress, mitigating protein damage and potentially increasing resistance to heavy metals and other biocides. A putative copper responsive efflux gene and others which might play a role in broader heavy metal resistance were also identified. Furthermore, the expression patterns of the cop operon in conjunction with other copper responsive genes allowed for a better understanding of the fate of copper ions in Xanthomonas. This work provides useful evidence for further evaluating MDR and other efflux pumps in metal-specific homeostasis and tolerance phenotypes in the Xanthomonas genus. Furthermore, non-canonical copper tolerance and resistance efflux pumps were potentially identified. These findings have implications for interpreting MIC differences among strains with homologous copLAB resistance genes, understanding survival under copper stress, and resistance in disease management.
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Affiliation(s)
- Stephen D B Ramnarine
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine campus, St. Augustine, Trinidad and Tobago, W. I
| | - Omar Ali
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine campus, St. Augustine, Trinidad and Tobago, W. I
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine campus, St. Augustine, Trinidad and Tobago, W. I
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine campus, St. Augustine, Trinidad and Tobago, W. I.
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Sahadeo NSD, Nicholls S, Moreira FRR, O'Toole Á, Ramkissoon V, Whittaker C, Hill V, McCrone JT, Mohammed N, Ramjag A, Jordan AB, Hill SC, Singh R, Nathaniel-Girdharrie SM, Hinds A, Ramkissoon N, Parag KV, Nandram N, Parasram R, Khan-Mohammed Z, Edghill L, Indar L, Andrewin A, Sealey-Thomas R, McMillan P, Oyinloye A, George K, Potter I, Lee J, Johnson D, Charles S, Singh N, Bisesor-McKenzie J, Laws H, Belmar-George S, Keizer-Beache S, Greenaway-Duberry S, Ashwood N, Foster JE, Georges K, Naidu R, Ivey M, Giddings S, Haraksingh R, Ramsubhag A, Jayaraman J, Chinnadurai C, Oura C, Pybus OG, St John J, Gonzalez-Escobar G, Faria NR, Carrington CVF. Correction: Implementation of Genomic Surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings. PLOS Glob Public Health 2023; 3:e0002393. [PMID: 37695757 PMCID: PMC10495005 DOI: 10.1371/journal.pgph.0002393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
[This corrects the article DOI: 10.1371/journal.pgph.0001455.].
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Pustam A, Jayaraman J, Ramsubhag A. Comparative genomics and virulome analysis reveal unique features associated with clinical strains of Klebsiella pneumoniae and Klebsiella quasipneumoniae from Trinidad, West Indies. PLoS One 2023; 18:e0283583. [PMID: 37428714 DOI: 10.1371/journal.pone.0283583] [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] [Received: 12/09/2022] [Accepted: 03/12/2023] [Indexed: 07/12/2023] Open
Abstract
Klebsiella pneumoniae and Klebsiella quasipneumoniae are closely related human pathogens of global concern. The more recently described K. quasipneumoniae shares similar morphological characteristics with K. pneumoniae and is commonly misidentified as this species using traditional laboratory techniques. The vast mobilome in these pathogenic bacteria influences the dissemination of virulence factors in high-risk environments and it is, therefore, critical to monitor strains for developing effective clinical management strategies. Herein, this study utilized Illumina sequencing to characterize the whole genomes of nine clinical K. pneumoniae and one K. quasipneumoniae isolate obtained from patients of 3 major hospitals in Trinidad, West Indies. Reconstruction of the assembled genomes and implementation of several bioinformatic tools revealed unique features such as high pathogenicity islands associated with the isolates. The K. pneumoniae isolates were categorized as classical (n = 3), uropathogenic (n = 5), or hypervirulent (n = 1) strains. In silico multilocus sequence typing, and phylogenetic analysis showed that isolates were related to several international high-risk genotypes, including sequence types ST11, ST15, ST86, and ST307. Analysis of the virulome and mobilome of these pathogens showed unique and clinically important features including the presence of genes associated with Type 1 and Type 3 fimbriae, the aerobactin and yersiniabactin siderophore systems, the K2 and O1/2, and the O3 and O5 serotypes. These genes were either on or in close proximity to insertion sequence elements, phage sequences, and plasmids. Several secretion systems including the Type VI system and relevant effector proteins were prevalent in the local isolates. This is the first comprehensive study investigating the genomes of clinical K. pneumoniae and K. quasipneumoniae isolates from Trinidad, West Indies. The data presented illustrate the diversity of Trinidadian clinical K. pneumoniae isolates as well as significant virulence biomarkers and mobile elements associated with these isolates. Additionally, the genomes of the local isolates will add to global databases and thus can be used in future surveillance or genomic studies in this country and the wider Caribbean region.
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Affiliation(s)
- Aarti Pustam
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
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Ramnarine SDBJ, Jayaraman J, Ramsubhag A. copLAB gene prevalence and diversity among Trinidadian Xanthomonas spp. black-rot lesion isolates with variable copper resistance profiles. PeerJ 2023; 11:e15657. [PMID: 37397015 PMCID: PMC10312155 DOI: 10.7717/peerj.15657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023] Open
Abstract
Background There has been limited exploration of copLAB genotypes and associated copper resistance phenotypes in Xanthomonas spp. in the southern Caribbean region. An earlier study highlighted a variant copLAB gene cluster found in one Trinidadian Xanthomonas campestris pv. campestris (Xcc) strain (BrA1), with <90% similarity to previously reported Xanthomonas copLAB genes. With only one report describing this copper resistance genotype, the current study investigated the distribution of the BrA1 variant copLAB gene cluster and previously reported forms of copper resistance genes in local Xanthomonas spp. Methods Xanthomonas spp. were isolated from black-rot infected lesions on leaf tissue from crucifer crops at intensively farmed sites with high agrochemical usage in Trinidad. The identity of morphologically identified isolates were confirmed using a paired primer PCR based screen and 16s rRNA partial gene sequencing. MGY agar amended with CuSO4.5H2O up to 2.4 mM was used to establish MIC's for confirmed isolates and group strains as sensitive, tolerant, or resistant to copper. Separate primer pairs targeting the BrA1 variant copLAB genes and those predicted to target multiple homologs found in Xanthomonas and Stenotrophomonas spp. were used to screen copper resistant isolates. Select amplicons were sanger sequenced and evolutionary relationships inferred from global reference sequences using a ML approach. Results Only four copper sensitive/tolerant Xanthomonas sp. strains were isolated, with 35 others classed as copper-resistant from a total population of 45 isolates. PCR detection of copLAB genes revealed two PCR negative copper-resistant resistant strains. Variant copLAB genes were only found in Xcc from the original source location of the BrA1 strain, Aranguez. Other copper-resistant strains contained other copLAB homologs that clustered into three distinct clades. These groups were more similar to genes from X. perforans plasmids and Stenotrophomonas spp. chromosomal homologs than reference Xcc sequences. This study highlights the localisation of the BrA1 variant copLAB genes to one agricultural community and the presence of three distinct copLAB gene groupings in Xcc and related Xanthomonas spp. with defined CuSO4.5H2O MIC. Further characterisation of these gene groups and copper resistance gene exchange dynamics on and within leaf tissue between Xcc and other Xanthomonas species are needed as similar gene clusters showed variable copper sensitivity profiles. This work will serve as a baseline for copper resistance gene characterisation in Trinidad and the wider Caribbean region and can be used to boost already lacking resistant phytopathogen management in the region.
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Sahadeo NSD, Nicholls S, Moreira FRR, O’Toole Á, Ramkissoon V, Whittaker C, Hill V, McCrone JT, Mohammed N, Ramjag A, Brown Jordan A, Hill SC, Singh R, Nathaniel-Girdharrie SM, Hinds A, Ramkissoon N, Parag KV, Nandram N, Parasram R, Khan-Mohammed Z, Edghill L, Indar L, Andrewin A, Sealey-Thomas R, McMillan P, Oyinloye A, George K, Potter I, Lee J, Johnson D, Charles S, Singh N, Bisesor-McKenzie J, Laws H, Belmar-George S, Keizer-Beache S, Greenaway-Duberry S, Ashwood N, Foster JE, Georges K, Naidu R, Ivey M, Giddings S, Haraksingh R, Ramsubhag A, Jayaraman J, Chinnadurai C, Oura C, Pybus OG, St. John J, Gonzalez-Escobar G, Faria NR, Carrington CVF. Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings. PLOS Glob Public Health 2023; 3:e0001455. [PMID: 36963002 PMCID: PMC10022082 DOI: 10.1371/journal.pgph.0001455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/26/2023] [Indexed: 02/24/2023]
Abstract
The COVID-19 pandemic highlighted the importance of global genomic surveillance to monitor the emergence and spread of SARS-CoV-2 variants and inform public health decision-making. Until December 2020 there was minimal capacity for viral genomic surveillance in most Caribbean countries. To overcome this constraint, the COVID-19: Infectious disease Molecular epidemiology for PAthogen Control & Tracking (COVID-19 IMPACT) project was implemented to establish rapid SARS-CoV-2 whole genome nanopore sequencing at The University of the West Indies (UWI) in Trinidad and Tobago (T&T) and provide needed SARS-CoV-2 sequencing services for T&T and other Caribbean Public Health Agency Member States (CMS). Using the Oxford Nanopore Technologies MinION sequencing platform and ARTIC network sequencing protocols and bioinformatics pipeline, a total of 3610 SARS-CoV-2 positive RNA samples, received from 17 CMS, were sequenced in-situ during the period December 5th 2020 to December 31st 2021. Ninety-one Pango lineages, including those of five variants of concern (VOC), were identified. Genetic analysis revealed at least 260 introductions to the CMS from other global regions. For each of the 17 CMS, the percentage of reported COVID-19 cases sequenced by the COVID-19 IMPACT laboratory ranged from 0·02% to 3·80% (median = 1·12%). Sequences submitted to GISAID by our study represented 73·3% of all SARS-CoV-2 sequences from the 17 CMS available on the database up to December 31st 2021. Increased staffing, process and infrastructural improvement over the course of the project helped reduce turnaround times for reporting to originating institutions and sequence uploads to GISAID. Insights from our genomic surveillance network in the Caribbean region directly influenced non-pharmaceutical countermeasures in the CMS countries. However, limited availability of associated surveillance and clinical data made it challenging to contextualise the observed SARS-CoV-2 diversity and evolution, highlighting the need for development of infrastructure for collecting and integrating genomic sequencing data and sample-associated metadata.
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Affiliation(s)
- Nikita S. D. Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Soren Nicholls
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Filipe R. R. Moreira
- MRC Centre for Global Infectious Disease Analysis, Department for Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Áine O’Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Vernie Ramkissoon
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department for Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - John T. McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Nicholas Mohammed
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Anushka Ramjag
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Arianne Brown Jordan
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Sarah C. Hill
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Risha Singh
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | | | - Avery Hinds
- Ministry of Health, Port of Spain, Republic of Trinidad and Tobago
| | - Nuala Ramkissoon
- Ministry of Health, Port of Spain, Republic of Trinidad and Tobago
| | - Kris V. Parag
- MRC Centre for Global Infectious Disease Analysis, Department for Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Naresh Nandram
- Ministry of Health, Port of Spain, Republic of Trinidad and Tobago
| | - Roshan Parasram
- Ministry of Health, Port of Spain, Republic of Trinidad and Tobago
| | | | - Lisa Edghill
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | - Lisa Indar
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | | | | | | | | | | | - Irad Potter
- Ministry of Health and Social Development, Road Town, Tortola, British Virgin Islands
| | - John Lee
- Ministry of Health and Wellness, George Town, Grand Cayman, Cayman Islands
| | - David Johnson
- Ministry of Health, Wellness and New Health Investment, Roseau, Dominica
| | | | | | | | - Hazel Laws
- Ministry of Health, Basseterre, Saint Kitts and Nevis
| | | | - Simone Keizer-Beache
- Ministry of Health, Wellness and the Environment, Kingstown, Saint Vincent and the Grenadines
| | | | - Nadia Ashwood
- Ministry of Health, Agriculture, Sports and Human Services, Grand Turk, Turks and Caicos Islands
| | - Jerome E. Foster
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Karla Georges
- School of Veterinary Medicine, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Rahul Naidu
- School of Dentistry, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Marsha Ivey
- Department of Clinical Medical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Stanley Giddings
- Department of Clinical Medical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Rajini Haraksingh
- Department of Life Sciences, Faculty of Sciences of Technology, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Sciences of Technology, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Sciences of Technology, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Chinnaraja Chinnadurai
- Department of Life Sciences, Faculty of Sciences of Technology, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Christopher Oura
- School of Veterinary Medicine, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Joy St. John
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | - Gabriel Gonzalez-Escobar
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Department for Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Christine V. F. Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
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Ali O, Ramsubhag A, Jayaraman J. Transcriptome-wide modulation by Sargassum vulgare and Acanthophora spicifera extracts results in a prime-triggered plant signalling cascade in tomato and sweet pepper. AoB Plants 2022; 14:plac046. [PMID: 36483312 PMCID: PMC9724562 DOI: 10.1093/aobpla/plac046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/04/2022] [Indexed: 06/17/2023]
Abstract
Seaweed extracts (SWEs) are becoming integrated into crop production systems due to their multiple beneficial effects including growth promotion and induction of defence mechanisms. However, the comprehensive molecular mechanisms of these effects are yet to be elucidated. The current study investigated the transcriptomic changes induced by SWEs derived from Sargassum vulgare and Acanthophora spicifera on tomato and sweet pepper plants. Tomato and sweet pepper plants were subjected to foliar treatment with alkaline extracts prepared from the above seaweeds. Transcriptome changes in the plants were assessed 72 h after treatments using RNA sequencing. The treated plants were also analysed for defence enzyme activities, nutrient composition and phytohormonal profiles. The results showed the significant enrichment of genes associated with several growth and defence processes including photosynthesis, carbon and nitrogen metabolism, plant hormone signal transduction, plant-pathogen interaction, secondary metabolite metabolism, MAPK signalling and amino acid biosynthesis. Activities of defence enzymes were also significantly increased in SWE-treated plants. Plant nutrient profiling showed significant increases in calcium, potassium, nitrogen, sulphur, boron, copper, iron, manganese, zinc and phosphorous levels in SWE-treated plants. Furthermore, the levels of auxins, cytokinins and gibberellins were also significantly increased in the treated plants. The severity of bacterial leaf spot and early blight incidence in plants treated with SWE was significantly reduced, in addition to other effects like an increase in chlorophyll content, plant growth, and fruit yield. The results demonstrated the complex effect of S. vulgare and A. spicifera extracts on the plants' transcriptome and provided evidence of a strong role of these extracts in increasing plant growth responses while priming the plants against pathogenic attack simultaneously. The current study contributes to the understanding of the molecular mechanisms of SWEs in plants and helps their usage as a viable organic input for sustainable crop production.
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Affiliation(s)
- Omar Ali
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine TTO, 00000, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine TTO, 00000, Trinidad and Tobago
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Ali O, Ramsubhag A, Daniram Benn Jr Ramnarine S, Jayaraman J. Transcriptomic changes induced by applications of a commercial extract of Ascophyllum nodosum on tomato plants. Sci Rep 2022; 12:8042. [PMID: 35577794 PMCID: PMC9110418 DOI: 10.1038/s41598-022-11263-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 04/18/2022] [Indexed: 11/24/2022] Open
Abstract
Extracts of Ascophyllum nodosum are commonly used as commercial biostimulants in crop production. To further understand the seaweed extract-induced phenomena in plants, a transcriptomic study was conducted. RNA-seq differential gene expression analysis of tomato plants treated with a commercial A. nodosum extract formulation (Stimplex) revealed the up-regulation of 635 and down-regulation of 456 genes. Ontology enrichment analysis showed three gene categories were augmented, including biological processes, cellular components, and molecular functions. KEGG pathway analysis revealed that the extract had a strong influence on the expression of genes involved in carbon fixation, secondary metabolism, MAPK-signalling, plant hormone signal transduction, glutathione metabolism, phenylpropanoid and stilbenoid metabolism, and plant-pathogen interactions. qRT-PCR validation analysis using 15 genes established a strong correlation with the RNA sequencing results. The activities of defence enzymes were also significantly enhanced by seaweed extract treatment. Furthermore, AN-SWE treated tomato plants had significantly higher chlorophyll and growth hormone content and showed improved plant growth parameters and nutrient profiles than the control. It is postulated that seaweed extract-induced gene regulation was responsible for favourable plant responses that enabled better growth and tolerance to stress conditions. This study provides evidence at the transcriptomic level for the positive effects of foliar application of the Ascophyllum nodosum extract (Stimplex) observed in treated tomato plants.
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Affiliation(s)
- Omar Ali
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Stephen Daniram Benn Jr Ramnarine
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago.
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11
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Ramnarine SDBJ, Jayaraman J, Ramsubhag A. Comparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profiles. PeerJ 2022; 9:e12632. [PMID: 35036136 PMCID: PMC8734464 DOI: 10.7717/peerj.12632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022] Open
Abstract
Black-rot disease caused by the phytopathogen Xanthomonas campestris pv. campestris (Xcc) continues to have considerable impacts on the productivity of cruciferous crops in Trinidad and Tobago and the wider Caribbean region. While the widespread occurrence of resistance of Xcc against bactericidal agrochemicals can contribute to the high disease burdens, the role of virulence and pathogenicity features of local strains on disease prevalence and severity has not been investigated yet. In the present study, a comparative genomic analysis was performed on 6 pathogenic Xcc and 4 co-isolated non-pathogenic Xanthomonas melonis (Xmel) strains from diseased crucifer plants grown in fields with heavy chemical use in Trinidad. Native isolates were grouped into two known and four newly assigned ribosomal sequence types (rST). Mobile genetic elements were identified which belonged to the IS3, IS5 family, Tn3 transposon, resolvases, and tra T4SS gene clusters. Additionally, exogenous plasmid derived sequences with origins from other bacterial species were characterised. Although several instances of genomic rearrangements were observed, native Xcc and Xmel isolates shared a significant level of structural homology with reference genomes, Xcc ATCC 33913 and Xmel CFBP4644, respectively. Complete T1SS hlyDB, T2SS, T4SS vir and T5SS xadA, yapH and estA gene clusters were identified in both species. Only Xmel strains contained a complete T6SS but no T3SS. Both species contained a complex repertoire of extracellular cell wall degrading enzymes. Native Xcc strains contained 37 T3SS and effector genes but a variable and unique profile of 8 avr, 4 xop and 1 hpa genes. Interestingly, Xmel strains contained several T3SS effectors with low similarity to references including avrXccA1 (~89%), hrpG (~73%), hrpX (~90%) and xopAZ (~87%). Furthermore, only Xmel genomes contained a CRISPR-Cas I-F array, but no lipopolysaccharide wxc gene cluster. Xmel strains were confirmed to be non-pathogenic by pathogenicity assays. The results of this study will be useful to guide future research into virulence mechanisms, agrochemical resistance, pathogenomics and the potential role of the co-isolated non-pathogenic Xanthomonas strains on Xcc infections.
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Affiliation(s)
- Stephen D B Jr Ramnarine
- Department of Life Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
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Shreeve N, Traherne JA, Sovio U, Hawkes D, Depierreux D, Huhn O, Jayaraman J, Horowitz A, Ghadially H, Perry JRB, Moffett A, Sled JG, Sharkey AM, Colucci F. NKG2A educates uterine NK cells to optimise pregnancy outcomes in humans and mice. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.55.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Abstract
The conserved CD94/NKG2A receptor binds HLA-E in humans and Qa-1 in mice. Besides inhibiting natural killer (NK) cell activation, NKG2A drives NK-cell education, a process influenced by HLA-B alleles that promotes NK cell function. In human populations some individuals are genetically programmed to favour NKG2A education and have more robust NK cell function. NKG2A is expressed by nearly all human and roughly half mouse uterine NK cells (uNK), but the importance of NK-cell education in physiology is unknown.
Here we show that NKG2A was required for uNK cell-education in dams. Genetic ablation of NKG2A caused sub-optimal vascular responses in pregnancy, increased rate of smaller fetuses, which grew asymmetrically with abnormal brain development, and changes in placental gene expression consistent with stress. These are features of the human syndrome pre-eclampsia. In a genome-wide association study of 7,219 cases and 155,660 control pregnancies, we found that the maternal HLA-B allele that does not favour NKG2A education, was associated with a 7% greater relative risk of pre-eclampsia (P=0.005, OR= 1.07).
These results establish the relevance of NK cell education in physiology and show that the maternal HLA-B –> HLA-E –> NKG2A pathway contributes to healthy pregnancy and may influence offspring health.
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Affiliation(s)
| | | | - U Sovio
- 1University of Cambridge, UK
| | | | | | - O Huhn
- 1University of Cambridge, UK
- 2AstraZeneca, Cambridge, UK
| | | | - A Horowitz
- 3Icahn School of Medicine at Mount Sinai, New York, USA
| | | | | | | | - JG Sled
- 4University Hospital for Sick Children, Toronto, Canada
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Chinnadurai C, Kollam M, Ramsubhag A, Jayaraman J. Genome characterization of zucchini yellow mosaic virus infecting cucurbits reveals the presence of a new genotype in Trinidad and Tobago in the Caribbean region. Arch Virol 2021; 166:1661-1669. [PMID: 33811529 DOI: 10.1007/s00705-021-05048-4] [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] [Received: 12/05/2020] [Accepted: 02/08/2021] [Indexed: 10/21/2022]
Abstract
Zucchini yellow mosaic virus (ZYMV) is a member of the genus Potyvirus that is becoming a serious pathogen of pumpkin and other cucurbits in Trinidad and Tobago and the entire Caribbean region. In this study, four ZYMV isolates infecting pumpkin in Trinidad and Tobago were characterized by complete genome sequencing. Phylogenetic analysis showed 5.9-6.0% nt and 7.7-7.9% aa sequence divergence in comparison to the most closely related isolates NAT and AG from Israel and SE04T from Slovakia. Based on the variations in the complete genome sequence as well as individual gene sequences, a new genotype, designated ZYMV-Trini, is proposed for these isolates. Among the gene sequences of ZYMV-Trini isolates, the greatest variation was observed in the HC-Pro gene, with 20.8% aa sequence divergence from their closest relatives, whereas the least variation was observed in the NIb, P3, and CP genes, with 1.8-2.2% aa sequence divergence. This study also showed that transmission of ZYMV can occur through seeds, but this was less common than transmission via the aphid Aphis gossypii. The progression of ZYMV in pumpkin seedlings was quantified by RT-qPCR, which showed a rapid surge in viral load after 37 days. From recombination analysis, it could be concluded that the isolates SE04T from Slovakia, NAT from Israel, and AG from Israel have made major contributions to the genome architecture of ZYMV-Trini isolates.
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Affiliation(s)
- Chinnaraja Chinnadurai
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, WI, Trinidad and Tobago
| | - Mounika Kollam
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, WI, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, WI, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, WI, Trinidad and Tobago.
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Ali O, Ramsubhag A, Jayaraman J. Biostimulant Properties of Seaweed Extracts in Plants: Implications towards Sustainable Crop Production. Plants (Basel) 2021; 10:531. [PMID: 33808954 PMCID: PMC8000310 DOI: 10.3390/plants10030531] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/19/2021] [Accepted: 01/23/2021] [Indexed: 02/01/2023]
Abstract
The use of seaweed-based bioproducts has been gaining momentum in crop production systems owing to their unique bioactive components and effects. They have phytostimulatory properties that result in increased plant growth and yield parameters in several important crop plants. They have phytoelicitor activity as their components evoke defense responses in plants that contribute to resistance to several pests, diseases, and abiotic stresses including drought, salinity, and cold. This is often linked to the upregulation of important defense-related genes and pathways in the plant system, priming the plant defenses against future attacks. They also evoke phytohormonal responses due to their specific components and interaction with plant growth regulation. Treatment by seaweed extracts and products also causes significant changes in the microbiome components of soil and plant in support of sustainable plant growth. Seaweed extracts contain a plethora of substances which are mostly organic, but trace levels of inorganic nutrient elements are also present. Fractionation of seaweed extracts into their components and their respective bioassays, however, has not yielded favorable growth effects. Only the whole seaweed extracts have been consistently proven to be very effective, which highlights the role of multiple components and their complex interactive effects on plant growth processes. Since seaweed extracts are highly organic, they are ideally suited for organic farming and environmentally sensitive crop production. They are also very compatible with other crop inputs, paving the way for an integrated management approach geared towards sustainability. The current review discusses the growth and functional effects evoked by seaweed extracts and their modes and mechanisms of action in crop plants which are responsible for elicitor and phytostimulatory activities. The review further analyses the potential value of seaweed extracts in integrated crop management systems towards sustainable crop production.
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Affiliation(s)
| | | | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago; (O.A.); (A.R.)
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Nagendrababu V, Kishen A, Murray PE, Nekoofar MH, de Figueiredo JAP, Priya E, Jayaraman J, Pulikkotil SJ, Jakovljevic A, Dummer PMH. PRIASE 2021 guidelines for reporting animal studies in Endodontology: explanation and elaboration. Int Endod J 2021; 54:858-886. [PMID: 33492704 DOI: 10.1111/iej.13481] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/13/2022]
Abstract
Laws and ethics require that before conducting human clinical trials, a new material, device or drug may have to undergo testing in animals in order to minimize health risks to humans, unless suitable supporting grandfather data already exist. The Preferred Reporting Items for Animal Studies in Endodontology (PRIASE) 2021 guidelines were developed exclusively for the specialty of Endodontology by integrating and adapting the ARRIVE (Animals in Research: Reporting In Vivo Experiments) guidelines and the Clinical and Laboratory Images in Publications (CLIP) principles using a validated consensus-based methodology. Implementation of the PRIASE 2021 guidelines will reduce potential sources of bias and thus improve the quality, accuracy, reproducibility, completeness and transparency of reports describing animal studies in Endodontology. The PRIASE 2021 guidelines consist of a checklist with 11 domains and 43 individual items and a flowchart. The aim of the current document is to provide an explanation for each item in the PRIASE 2021 checklist and flowchart and is supplemented with examples from the literature in order for readers to understand their significance and to provide usage guidance. A link to the PRIASE 2021 explanation and elaboration document and PRIASE 2021 checklist and flowchart is available on the Preferred Reporting Items for study Designs in Endodontology (PRIDE) website (http://pride-endodonticguidelines.org/priase/).
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Affiliation(s)
- V Nagendrababu
- Department of Preventive and Restorative Dentistry, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - A Kishen
- Faculty of Dentistry, University of Toronto, Toronto, ON, Canada
| | - P E Murray
- Private Consultant, Fort Lauderdale, FL, USA
| | - M H Nekoofar
- Department of Endodontics, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran
| | | | - E Priya
- Division of Children and Community Oral Health, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - J Jayaraman
- Department of Developmental Dentistry, University of Texas Health School of Dentistry, San Antonio, TX, USA
| | - S J Pulikkotil
- Division of Clinical Dentistry, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - A Jakovljevic
- Department of Pathophysiology, School of Dental Medicine, University of Belgrade, Belgrade, Serbia
| | - P M H Dummer
- School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
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Nagendrababu V, Jakovljevic A, Jacimovic J, Duncan HF, Jayaraman J, Dummer PMH. Critical analysis of the reporting quality of randomized trials within Endodontics using the Preferred Reporting Items for RAndomized Trials in Endodontics (PRIRATE) 2020 quality standard checklist. Int Endod J 2021; 54:1083-1104. [PMID: 33544911 DOI: 10.1111/iej.13489] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/02/2021] [Indexed: 01/08/2023]
Abstract
AIM To critically evaluate the reporting quality of a random sample of clinical trials published in Endodontics against the PRIRATE 2020 checklist and to analyse the association between the quality of reported trials and a variety of parameters. METHODOLOGY Fifty randomized clinical trials relating to Endodontics were randomly selected from the PubMed database from 2015 to 2019 and evaluated by two independent reviewers. For each trial, a score of '1' was awarded when it fully reported each item in the PRIRATE guidelines whereas a score of '0' was awarded when an item was not reported; when the item was reported inadequately a score of '0.5' was awarded. For the items that were not relevant to the trial, 'Not Applicable (NA)' was given. Based on the interquartile range of the overall scores received, trials were categorized into 'Low' (0-58.4%), 'Moderate' (58.5-72.8%) and 'High' (72.9-100%) quality. The associations between characteristics and quality of clinical trials were investigated. Descriptive statistics, frequency analysis and percentage analyses were used to describe the data. To determine the significance of categorical data, the chi-square test was used. The probability value 0.05 was considered as the level of significance. RESULTS Based on the overall scores, 13 (26%), 25(50%) and 12 (24%) of the reports of clinical trials were categorized as 'High', 'Moderate' and 'Low' quality, respectively. Three items (1b, 6d, 11e) were adequately reported in all manuscripts whilst two items (5k, 5m) were scored 'NA' in all the reports. The reports published from Europe had a significantly greater percentage of 'High'-quality scores, compared to Asia, Middle East, North America and South America (P = 0.0002). The 'High'-quality reports were published significantly more often in impact factor journals (P = 0.045). Reports of clinical trials published in journals that adhered to the CONSORT guidelines had significantly more 'High' scores compared to those that did not (P = 0.008). Clinical trials with protocols registered a priori had a significantly greater percentage of 'High' scores compared to the trials that were not registered in advance (P = 0.003). No significant difference occurred between the quality of clinical trials and the number of authors, journal (Endodontic specialty vs. Non-Endodontic specialty) or year of publication. CONCLUSIONS Reports of randomized clinical trials published in the speciality of Endodontics had a substantial number of deficiencies. To create high-quality reports of clinical trials, authors should comply with the PRIRATE 2020 guidelines.
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Affiliation(s)
- V Nagendrababu
- Department of Preventive and Restorative Dentistry, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - A Jakovljevic
- Department of Pathophysiology, School of Dental Medicine, University of Belgrade, Belgrade, Serbia
| | - J Jacimovic
- Central Library, School of Dental Medicine, University of Belgrade, Belgrade, Serbia
| | - H F Duncan
- Division of Restorative Dentistry and Periodontology, Dublin Dental University Hospital, Trinity College Dublin, Dublin, Ireland
| | - J Jayaraman
- Department of Developmental Dentistry, University of Texas Health School of Dentistry, San Antonio, TX, USA
| | - P M H Dummer
- School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
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Nagendrababu V, Kishen A, Murray PE, Nekoofar MH, de Figueiredo JAP, Priya E, Jayaraman J, Pulikkotil SJ, Camilleri J, Silva RM, Dummer PMH. PRIASE 2021 guidelines for reporting animal studies in Endodontology: a consensus-based development. Int Endod J 2021; 54:848-857. [PMID: 33450080 DOI: 10.1111/iej.13477] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 01/10/2023]
Abstract
Animal testing is crucial in situations when research on humans is not allowed because of unknown health risks and ethical concerns. The current project aims to develop reporting guidelines exclusively for animal studies in Endodontology, using an established consensus-based methodology. The guidelines have been named: Preferred Reporting Items for Animal Studies in Endodontology (PRIASE) 2021. Nine individuals (PD, VN, AK, PM, MN, JF, EP, JJ and SJ), including the project leaders (PD, VN) formed a steering committee. The steering committee developed a novel checklist by adapting and integrating their animal testing and peer review experience with the Animals in Research: Reporting In Vivo Experiments (ARRIVE) guidelines and also the Clinical and Laboratory Images in Publications (CLIP) principles. A PRIASE Delphi Group (PDG) and PRIASE Online Meeting Group (POMG) were also formed. Thirty-one PDG members participated in the online Delphi process and achieved consensus on the checklist items and flowchart that were used to formulate the PRIASE guidelines. The novel PRIASE 2021 guidelines were discussed with the POMG on 9 September 2020 via a Zoom online video call attended by 21 individuals from across the globe and seven steering committee members. Following the discussions, the guidelines were modified and then piloted by several authors whilst writing a manuscript involving research on animals. The PRIASE 2021 guidelines are a checklist consisting of 11 domains and 43 individual items together with a flowchart. The PRIASE 2021 guidelines are focused on improving the methodological principles, reproducibility and quality of animal studies in order to enhance their reliability as well as repeatability to estimate the effects of endodontic treatments and usefulness for guiding future clinical studies on humans.
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Affiliation(s)
- V Nagendrababu
- Department of Preventive and Restorative Dentistry, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - A Kishen
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - P E Murray
- Private Consultant, Fort Lauderdale, FL, USA
| | - M H Nekoofar
- Department of Endodontics, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran
| | | | - E Priya
- Division of Children and Community Oral Health, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - J Jayaraman
- Department of Developmental Dentistry, University of Texas Health School of Dentistry, San Antonio, TX, USA
| | - S J Pulikkotil
- Division of Clinical Dentistry, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - J Camilleri
- School of Dentistry, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - R M Silva
- Department of Endodontics, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - P M H Dummer
- School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
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Nagendrababu V, Duncan HF, Fouad AF, Kirkevang LL, Parashos P, Pigg M, Væth M, Jayaraman J, Dummer PMH. Preferred Reporting items for OBservational studies in Endodontics (PROBE) guidelines: a development protocol. Int Endod J 2020; 53:1199-1203. [DOI: 10.1111/iej.13318] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 11/29/2022]
Affiliation(s)
- V. Nagendrababu
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - H. F. Duncan
- Division of Restorative Dentistry Dublin Dental University Hospital Trinity College Dublin Dublin Ireland
| | - A. F. Fouad
- Division of Comprehensive Oral Health Adams School of Dentistry University of North Carolina at Chapel Hill Chapel Hill NC USA
| | - L. L. Kirkevang
- Department of Dentistry and Oral Health Aarhus University Aarhus Denmark
| | - P. Parashos
- Melbourne Dental School University of Melbourne Melbourne Vic. Australia
| | - M. Pigg
- Department of Endodontics Faculty of Odontology Malmo University Malmo Sweden
| | - M. Væth
- Department of Public Health Aarhus University Aarhus Denmark
| | - J. Jayaraman
- Department of Developmental Dentistry University of Texas Health School of Dentistry San Antonio TX USA
| | - P. M. H. Dummer
- School of Dentistry College of Biomedical and Life Sciences Cardiff University Cardiff UK
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Nagendrababu V, Duncan HF, Bjørndal L, Kvist T, Priya E, Jayaraman J, Pulikkotil SJ, Dummer PMH. PRIRATE 2020 guidelines for reporting randomized trials in Endodontics: explanation and elaboration. Int Endod J 2020; 53:774-803. [DOI: 10.1111/iej.13304] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 12/11/2022]
Affiliation(s)
- V. Nagendrababu
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - H. F. Duncan
- Division of Restorative Dentistry & Periodontology Dublin Dental University Hospital Trinity College Dublin Dublin Ireland
| | - L. Bjørndal
- Cariology and Endodontics Department of Odontology Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - T. Kvist
- Department of Endodontology Institute of Odontology Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - E. Priya
- Division of Children and Community Oral Health School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - J. Jayaraman
- Department of Developmental Dentistry University of Texas Health School of Dentistry San Antonio USA
| | - S. J. Pulikkotil
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - P. M. H. Dummer
- School of Dentistry College of Biomedical and Life Sciences Cardiff University Cardiff UK
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Nagendrababu V, Chong BS, McCabe P, Shah PK, Priya E, Jayaraman J, Pulikkotil SJ, Dummer PMH. PRICE 2020 guidelines for reporting case reports in Endodontics: explanation and elaboration. Int Endod J 2020; 53:922-947. [PMID: 32221975 DOI: 10.1111/iej.13300] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 12/17/2022]
Abstract
Case reports play a key role in showcasing new, unusual or rare disease(s), and the impact of newer therapeutic approaches or interventions. The Preferred Reporting Items for Case reports in Endodontics (PRICE) 2020 guidelines are being introduced exclusively for Endodontics by adapting and integrating the CAse REport (CARE) guidelines and Clinical and Laboratory Images in Publications principles. The PRICE 2020 guidelines have been developed to help authors improve the completeness, accuracy and transparency of case reports in Endodontics and thus enhance the standard of manuscripts submitted for publication. The aim of this document is to provide a comprehensive explanation for each item in the PRICE 2020 checklist along with examples from the literature that demonstrate compliance with these guidelines. This information will highlight the importance of each item and provide practical examples to help authors understand the necessity of providing comprehensive information when preparing case reports. A link to this PRICE 2020 explanation and elaboration document is available on the Preferred Reporting Items for study Designs in Endodontology website at http://www.pride-endodonticguidelines.org.
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Affiliation(s)
- V Nagendrababu
- Division of Clinical Dentistry, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - B S Chong
- Institute of Dentistry, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - P McCabe
- Oranhill Dental Suite, Galway, Ireland
| | - P K Shah
- Institute of Dentistry, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - E Priya
- Division of Community and Children Oral Health, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - J Jayaraman
- Department of Developmental Dentistry, University of Texas Health School of Dentistry, San Antonio, TX, USA
| | - S J Pulikkotil
- Division of Clinical Dentistry, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - P M H Dummer
- School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
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Nagendrababu V, Kishen A, Chong BS, Priya E, Duncan HF, Rôças IN, Jayaraman J, Figueiredo JAP, Siqueira JF, Bjørndal L, Nekoofar MH, Peters OA, McCabe P, Murray PE, Shah PK, Ordinola‐Zapata R, Pulikkotil SJ, Kvist T, Dummer PMH. Preferred Reporting Items for study Designs in Endodontology (PRIDE): guiding authors to identify and correct reporting deficiencies in their manuscripts prior to peer review. Int Endod J 2020; 53:589-590. [DOI: 10.1111/iej.13276] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- V. Nagendrababu
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - A. Kishen
- Faculty of Dentistry University of Toronto Toronto ON Canada
| | - B. S. Chong
- Institute of Dentistry Barts & The London School of Medicine and Dentistry Queen Mary University of London London UK
| | - E. Priya
- Division of Children and Community Oral Health School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - H. F. Duncan
- Division of Restorative Dentistry Dublin Dental University Hospital Trinity College Dublin Dublin Ireland
| | - I. N. Rôças
- Dental Research Department Iguaçu University Nova Iguaçu RJ Brazil
| | - J. Jayaraman
- Department of Developmental Dentistry University of Texas Health School of Dentistry San Antonio TX USA
| | | | - J. F. Siqueira
- Dental Research Department Iguaçu University Nova Iguaçu RJ Brazil
| | - L. Bjørndal
- Cariology and Endodontics Department of Odontology Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - M. H. Nekoofar
- Department of Endodontics School of Dentistry Tehran University of Medical Sciences Tehran Iran
- School of Dentistry College of Biomedical and Life Sciences Cardiff University Cardiff UK
| | - O. A. Peters
- Department of Endodontics Arthur A Dugoni School of Dentistry University of the Pacific San Francisco CA USA
- Oral Health Centre University of Queensland Herston QLD Australia
| | - P. McCabe
- Oranhill Dental Suite Galway Ireland
| | - P. E. Murray
- Department of Periodontics College of Dental Medicine Nova Southeastern University Fort Lauderdale FL USA
| | - P. K. Shah
- Institute of Dentistry Barts & The London School of Medicine and Dentistry Queen Mary University of London London UK
| | - R. Ordinola‐Zapata
- Division of Endodontics University of Minnesota School of Dentistry Minneapolis MN USA
| | - S. J. Pulikkotil
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - T. Kvist
- Department of Endodontology Institute of Odontology Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - P. M. H. Dummer
- School of Dentistry College of Biomedical and Life Sciences Cardiff University Cardiff UK
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Nagendrababu V, Chong BS, McCabe P, Shah PK, Priya E, Jayaraman J, Pulikkotil SJ, Setzer FC, Sunde PT, Dummer PMH. PRICE 2020 guidelines for reporting case reports in Endodontics: a consensus‐based development. Int Endod J 2020; 53:619-626. [DOI: 10.1111/iej.13285] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022]
Affiliation(s)
- V. Nagendrababu
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - B. S. Chong
- Institute of Dentistry Barts & The London School of Medicine & Dentistry Queen Mary University of London London UK
| | - P. McCabe
- Oranhill Dental Suite Galway Ireland
| | - P. K. Shah
- Institute of Dentistry Barts & The London School of Medicine & Dentistry Queen Mary University of London London UK
| | - E. Priya
- Division of Children and Community Oral Health School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - J. Jayaraman
- Department of Developmental Dentistry University of Texas Health School of Dentistry San Antonio Texas USA
| | - S. J. Pulikkotil
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - F. C. Setzer
- Department of Endodontics School of Dental Medicine University of Pennsylvania Philadelphia Pennsylvania USA
| | - P. T. Sunde
- Department of Endodontics Institute of Clinical Dentistry Faculty of Dentistry University of Oslo Oslo Norway
| | - P. M. H. Dummer
- School of Dentistry College of Biomedical and Life Sciences Cardiff University Cardiff UK
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Nagendrababu V, Duncan HF, Bjørndal L, Kvist T, Priya E, Jayaraman J, Pulikkotil SJ, Pigg M, Rechenberg DK, Væth M, Dummer PMH. PRIRATE 2020 guidelines for reporting randomized trials in Endodontics: a consensus‐based development. Int Endod J 2020; 53:764-773. [DOI: 10.1111/iej.13294] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 03/16/2020] [Indexed: 11/28/2022]
Affiliation(s)
- V. Nagendrababu
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - H. F. Duncan
- Division of Restorative Dentistry Dublin Dental University Hospital Trinity College Dublin Dublin Ireland
| | - L. Bjørndal
- Cariology and Endodontics Department of Odontology Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - T. Kvist
- Department of Endodontology Institute of Odontology Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - E. Priya
- Division of Children and Community Oral Health School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - J. Jayaraman
- Department of Developmental Dentistry University of Texas Health School of Dentistry San Antonio USA
| | - S. J. Pulikkotil
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - M. Pigg
- Department of Endodontics Faculty of Odontology Malmo University Malmo Sweden
| | - D. K. Rechenberg
- Department of Conservative and Preventive Dentistry University of Zürich Zürich Switzerland
| | - M. Væth
- Department of Public Health, Section for Biostatistics Aarhus University Aarhus Denmark
| | - P. M. H. Dummer
- School of Dentistry College of Biomedical and Life Sciences Cardiff University Cardiff UK
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Ali R, Mohammed A, Jayaraman J, Nandram N, Feng RS, Lezcano RD, Seeramsingh R, Daniel B, Lovin DD, Severson DW, Ramsubhag A. Changing patterns in the distribution of the Mayaro virus vector Haemagogus species in Trinidad, West Indies. Acta Trop 2019; 199:105108. [PMID: 31351893 DOI: 10.1016/j.actatropica.2019.105108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/21/2019] [Accepted: 07/22/2019] [Indexed: 10/26/2022]
Abstract
The Mayaro virus disease (MAYVD) is an emerging mosquito borne zoonosis that was first reported on the island of Trinidad in 1954. The viral agent for this disease is known to presently be endemic to Central and South America. The enzootic cycle of the Mayaro virus (MAYV) is not fully characterized, though primates are thought to be the main reservoir with Haemagogus species of mosquitoes as the primary vector. This virus has been responsible for several sporadic cases of infections and limited outbreaks, but it is postulated that the MAYVD will become a major epidemic in the future, following in the steps of the recent pandemics caused by Chikungunya and Zika viruses. Mitigating possible major outbreaks of MAYVD in the future would require effective strategies for vector control, for which knowledge on the ecology and distribution of the Haemagogus mosquitoes would be vitally important. In Trinidad, Haemagogus species have only been reported in the northwestern peninsula of the island based on studies up to 1995. However, no recent investigations have been completed to determine the status of this important vector on the island. The aim of this study was to investigate the current spatial distribution of Haemagogus species in the island of Trinidad, West Indies. Adult Haemagogus (Hag.) mosquitoes and larvae were surveyed during a twenty-month period using human bait trapping and ovitraps in major forested areas on the island. Mosquito species were identified using classical taxonomic keys. Haemagogus species were widespread and found in all forest types surveyed. Hag. janthinomys (85.7%) was the most widely distributed and dominant species on the island. Lower levels of Hag. leucocelaneus (7.3%), Hag. equinus (6.4%) and Hag. celeste (0.6%) were also collected. Overall, the proportion of mosquitoes collected in the wet season (June-December) was 3.5 times more than in the dry season (January-May). Mangroves, young secondary forests, semi-evergreen and evergreen forest types had relatively high mean abundance levels of Haemagogus species as compared to deciduous and montane forests. Proximity analysis suggests that population settlements within a 1 km buffer of the forest peripherals may be at risk for any emerging arboviral disease associated with these mosquito vectors. Haemagogus species showed a much wider distribution in Trinidad as compared to previous reports from up to 20 years ago and were prevalent in areas with no known presence of non-human primates. Since the MAYV has been previously implicated in causing infections in vertebrate hosts like rodents, birds and small mammals, the findings of this study suggest that there may be alternative hosts and reservoirs of this virus in the sylvatic cycle in Trinidad, other than primates. This has significant epidemiological implications for mosquito-borne viral infections in the region.
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Ali O, Ramsubhag A, Jayaraman J. Biostimulatory activities of Ascophyllum nodosum extract in tomato and sweet pepper crops in a tropical environment. PLoS One 2019; 14:e0216710. [PMID: 31086398 PMCID: PMC6516672 DOI: 10.1371/journal.pone.0216710] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [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: 12/20/2018] [Accepted: 04/28/2019] [Indexed: 12/01/2022] Open
Abstract
This study evaluated the effectiveness of a commercially available Ascophyllum nodosum alkaline extract as a plant growth stimulant and defense elicitor against foliar diseases of tomato and sweet pepper caused by Xanthomonas campestris pv. vesicatoria and Alternaria solani in a tropical environment. Foliar applications of 0.5% A. nodosum extract (AN) at 10-day intervals resulted in significant (P < 0.05) increase in plant growth parameters, including plant height (40%), leaf number (50%), plant dry biomass (52%), root length (59%) and chlorophyll content (20%) compared to control. Treated plants also had a significantly higher number of flower clusters, flower numbers, fruits per cluster and total harvested fruit yield. The Ascophyllum extract significantly (P < 0.05) reduced disease incidence by the pathogens in both crops under greenhouse and field conditions. The combinatory treatment of seaweed extract and a minimum dose of contact fungicide in field trials, recorded the overall lowest disease levels (60% reduction) and highest yield (57% increase). Investigations into the mechanisms of disease suppression revealed the effects of the extract in inducing the activities of defense-related enzymes including phenylalanine ammonia lyase, peroxidase, polyphenol oxidase, chitinase and β-1,3-glucanase, as well as the levels of total phenolic compounds. The effect on SA, JA and ET-mediated signalling defense pathways was examined by quantifying expression levels of marker genes including PR1-a, PinII and ETR-1, for the above pathways respectively. Both crop plants treated with A. nodosum extract had significantly higher expression levels of the PinII and ETR-1 marker genes than controls. This was coupled with a marked increase in gene transcripts involved in auxin (IAA), gibberellin (Ga2Ox) and cytokinin (IPT) biosynthesis, which provides possible evidence for induced growth in plants treated with AN extract. Cross-talks between growth and defense responses as a result of seaweed extract application could evidently implicate the benefits of seaweed extract usage in sustainable crop production.
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Affiliation(s)
- Omar Ali
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
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Nagendrababu V, Kishen A, Murray PE, Nekoofar MH, de Figueiredo JAP, Priya E, Jayaraman J, Pulikkotil SJ, Dummer PMH. Preferred Reporting Items for Animal Studies in Endodontology: a development protocol. Int Endod J 2019; 52:1290-1296. [PMID: 30985938 DOI: 10.1111/iej.13125] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 04/10/2019] [Indexed: 12/11/2022]
Abstract
The regulated use of animals in endodontic research is often necessary to investigate the biological mechanisms of endodontic diseases and to measure the preclinical efficacy, biocompatibility, toxicology and safety of new treatments, biomaterials, sealers, drugs, disinfectants, irrigants, devices and instruments. Animal testing is most crucial in situations when research on humans is not ethical, practical or has unknown health risks. Currently, there is a wide variability in the quality of manuscripts that report the results of animal studies. Towards the goal of improving the quality of publications, guidelines for preventing disability, pain, and suffering to animals, and enhanced reporting requirements for animal research have been developed. These guidelines are referred to as Animals in Research: Reporting In Vivo Experiments (ARRIVE). Henceforth, causing any form of animal suffering for research purposes is not acceptable and cannot be justified under any circumstances. The present report describes a protocol for the development of welfare and reporting guidelines for animal studies conducted in the specialty of Endodontology: the Preferred Reporting Items for Animal Studies in Endodontology (PRIASE) guidelines. The PRIASE guidelines will be developed by adapting and modifying the ARRIVE guidelines and the Clinical and Laboratory Images in Publication (CLIP) principles. The development of the new PRIASE guidelines will include a five-step consensus process. An initial draft of the PRIASE guidelines will be developed by a steering committee. Each item in the draft guidelines will then be evaluated by members of a PRIASE Delphi Group (PDG) for its clarity using a dichotomous scale (yes or no) and suitability for its inclusion using a 9-point Likert scale. The online surveys will continue until each item achieves this standard, and a set of items are agreed for further analysis by a PRIASE Face-to-face Consensus Meeting Group (PFCMG). Following the consensus meeting, the steering committee will finalize and confirm the PRIASE guidelines taking into account the responses and comments of the PFCMG. The PRIASE guidelines will be published and disseminated internationally and updated periodically based on feedback from stakeholders.
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Affiliation(s)
- V Nagendrababu
- Division of Clinical Dentistry, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - A Kishen
- University of Toronto, Toronto, ON, Canada
| | - P E Murray
- Department of Periodontics, College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - M H Nekoofar
- Department of Endodontics, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran.,School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | | | - E Priya
- Division of Children and Community Oral Health, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - J Jayaraman
- Division of Children and Community Oral Health, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - S J Pulikkotil
- Division of Clinical Dentistry, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - P M H Dummer
- School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
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Nagendrababu V, Murray PE, Ordinola‐Zapata R, Peters OA, Rôças IN, Siqueira JF, Priya E, Jayaraman J, Pulikkotil SJ, Dummer PMH. A protocol for developing reporting guidelines for laboratory studies in Endodontology. Int Endod J 2019; 52:1090-1095. [DOI: 10.1111/iej.13123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 11/27/2022]
Affiliation(s)
- V. Nagendrababu
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - P. E. Murray
- Department of Periodontics College of Dental Medicine Nova Southeastern University Fort Lauderdale FL USA
| | - R. Ordinola‐Zapata
- Division of Endodontics University of Minnesota School of Dentistry Minneapolis MN USA
| | - O. A. Peters
- Department of Endodontics Arthur A Dugoni School of Dentistry University of the Pacific San Francisco CA USA
- Oral Health Centre University of Queensland Herston Australia
| | - I. N. Rôças
- Department of Endodontics Faculty of Dentistry Estácio de Sá University Rio de Janeiro RJ Brazil
| | - J. F. Siqueira
- Department of Endodontics Faculty of Dentistry Estácio de Sá University Rio de Janeiro RJ Brazil
| | - E. Priya
- Division of Children and Community Oral Health School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - J. Jayaraman
- Division of Children and Community Oral Health School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - S. J. Pulikkotil
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - P. M. H. Dummer
- School of Dentistry College of Biomedical and Life Sciences Cardiff University Cardiff UK
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Pulikkotil SJ, Jayaraman J, Nagendrababu V. Quality of abstract of systematic reviews and meta-analyses in paediatric dentistry journals. Eur Arch Paediatr Dent 2019; 20:383-391. [PMID: 30887462 DOI: 10.1007/s40368-019-00432-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 03/11/2019] [Indexed: 12/31/2022]
Abstract
AIM To systematically evaluate the reporting quality of the abstract of systematic reviews and meta-analyses in paediatric dentistry journals. MATERIALS AND METHODS Systematic reviews with meta-analyses in paediatric dentistry were searched in PubMed and Scopus databases from inception to December 2017. Selection of studies by title and abstract screening followed by full-text assessment was independently done by two reviewers. The quality of abstracts was assessed by PRISMA-Abstract checklist comprising of 12 items; one each for title and objective, three items for methods, three items for results, two items for discussion and two items for others. PRISMA-A median scores were calculated and compared with the article characteristics. Statistical significance was set at p < 0.05 and multi-variate analysis was performed using Kruskal-Wallis test. RESULTS A total of 24 studies were included in the analysis. The mean PRISMA-Abstract score was 7.46 ± 1.19. None of the studies were of high quality (score 10-12), 20 were of moderate (score 7-9), and 4 were of low quality (score 1-6). Journals that adhered to PRISMA guidelines showed significantly higher quality (p < 0.05). No association was found between the quality and the number of authors, country, journals, year of publication, word count and focus of study. CONCLUSION Majority of abstracts of systematic reviews and meta-analyses in paediatric dentistry journals were of moderate quality. Adoption and adherence to PRISMA-Abstract checklist by the journal editors and authors will enhance the reporting quality of abstracts.
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Affiliation(s)
- S J Pulikkotil
- Division of Clinical Dentistry, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - J Jayaraman
- Children's Dentistry and Orthodontics, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia.
| | - V Nagendrababu
- Division of Clinical Dentistry, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
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Nagendrababu V, Duncan HF, Bjørndal L, Kvist T, Priya E, Pulikkotil SJ, Jayaraman J, Dummer PMH. Preferred Reporting Items for RAndomized Trials in Endodontics (
PRIRATE
) guidelines: a development protocol. Int Endod J 2019; 52:974-978. [DOI: 10.1111/iej.13087] [Citation(s) in RCA: 16] [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] [Received: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 12/13/2022]
Affiliation(s)
- V. Nagendrababu
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - H. F. Duncan
- Division of Restorative Dentistry Dublin Dental University Hospital Trinity College Dublin Dublin Ireland
| | - L. Bjørndal
- Faculty of Health and Medical Sciences Cariology and Endodontics, Department of Odontology University of Copenhagen Copenhagen Denmark
| | - T. Kvist
- Department of Endodontology Institute of Odontology Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - E. Priya
- Division of Children and Community Oral Health School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - S. J. Pulikkotil
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - J. Jayaraman
- Division of Children and Community Oral Health School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - P. M. H. Dummer
- School of Dentistry College of Biomedical and Life Sciences Cardiff University Cardiff UK
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30
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Nagendrababu V, Chong BS, McCabe P, Shah PK, Priya E, Jayaraman J, Pulikkotil SJ, Dummer PMH. Guidelines for reporting the quality of clinical case reports in Endodontics: a development protocol. Int Endod J 2019; 52:775-778. [DOI: 10.1111/iej.13067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 12/16/2022]
Affiliation(s)
- V. Nagendrababu
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - B. S. Chong
- Institute of Dentistry Barts & The London School of Medicine & Dentistry Queen Mary University of London London UK
| | - P. McCabe
- Oranhill Dental Suite Galway Ireland
| | - P. K. Shah
- Institute of Dentistry Barts & The London School of Medicine & Dentistry Queen Mary University of London London UK
| | - E. Priya
- Division of Children and Community Oral Health School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - J. Jayaraman
- Division of Children and Community Oral Health School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - S. J. Pulikkotil
- Division of Clinical Dentistry School of Dentistry International Medical University Kuala Lumpur Malaysia
| | - P. M. H. Dummer
- School of Dentistry College of Biomedical and Life Sciences Cardiff University Cardiff UK
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31
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Nagendrababu V, Pulikkotil SJ, Sultan OS, Jayaraman J, Soh JA, Dummer PMH. Effectiveness of technology-enhanced learning in Endodontic education: a systematic review and meta-analysis. Int Endod J 2018; 52:181-192. [DOI: 10.1111/iej.12995] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/06/2018] [Indexed: 01/25/2023]
Affiliation(s)
- V. Nagendrababu
- Division of Clinical Dentistry; School of Dentistry; International Medical University; Kuala Lumpur Malaysia
| | - S. J. Pulikkotil
- Division of Clinical Dentistry; School of Dentistry; International Medical University; Kuala Lumpur Malaysia
| | - O. S. Sultan
- Division of Clinical Dentistry; School of Dentistry; International Medical University; Kuala Lumpur Malaysia
| | - J. Jayaraman
- Division of Community and Children Oral Health; School of Dentistry; International Medical University; Kuala Lumpur Malaysia
| | - J. A. Soh
- School of Dentistry; International Medical University; Kuala Lumpur Malaysia
| | - P. M. H. Dummer
- School of Dentistry; College of Biomedical and Life Sciences; Cardiff University; Cardiff UK
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Jamil KM, Hydes TJ, Cheent KS, Cassidy SA, Traherne JA, Jayaraman J, Trowsdale J, Alexander GJ, Little AM, McFarlane H, Heneghan MA, Purbhoo MA, Khakoo SI. STAT4-associated natural killer cell tolerance following liver transplantation. Gut 2017; 66:352-361. [PMID: 26887815 PMCID: PMC5284485 DOI: 10.1136/gutjnl-2015-309395] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 09/29/2015] [Accepted: 10/20/2015] [Indexed: 01/15/2023]
Abstract
OBJECTIVE Natural killer (NK) cells are important mediators of liver inflammation in chronic liver disease. The aim of this study was to investigate why liver transplants (LTs) are not rejected by NK cells in the absence of human leukocyte antigen (HLA) matching, and to identify a tolerogenic NK cell phenotype. DESIGN Phenotypic and functional analyses on NK cells from 54 LT recipients were performed, and comparisons made with healthy controls. Further investigation was performed using gene expression analysis and donor:recipient HLA typing. RESULTS NK cells from non-HCV LT recipients were hypofunctional, with reduced expression of NKp46 (p<0.05) and NKp30 (p<0.001), reduced cytotoxicity (p<0.001) and interferon (IFN)-γ secretion (p<0.025). There was no segregation of this effect with HLA-C, and these functional changes were not observed in individuals with HCV. Microarray and RT-qPCR analysis demonstrated downregulation of STAT4 in NK cells from LT recipients (p<0.0001). Changes in the expression levels of the transcription factors Helios (p=0.06) and Hobit (p=0.07), which control NKp46 and IFNγ expression, respectively, were also detected. Hypofunctionality of NK cells was associated with impaired STAT4 phosphorylation and downregulation of the STAT4 target microRNA-155. Conversely in HCV-LT NK cell tolerance was reversed, consistent with the more aggressive outcome of LT for HCV. CONCLUSIONS LT is associated with transcriptional and functional changes in NK cells, resulting in reduced activation. NK cell tolerance occurs upstream of major histocompatibility complex (MHC) class I mediated education, and is associated with deficient STAT4 phosphorylation. STAT4 therefore represents a potential therapeutic target to induce NK cell tolerance in liver disease.
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Affiliation(s)
- K M Jamil
- Department of Hepatology, Imperial College, London, UK
| | - T J Hydes
- Department of Hepatology, Southampton University, Southampton, UK
| | - K S Cheent
- Department of Hepatology, Imperial College, London, UK
| | - S A Cassidy
- Department of Hepatology, Imperial College, London, UK
| | - J A Traherne
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - J Jayaraman
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - J Trowsdale
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - G J Alexander
- Department of Hepatology, Addenbrookes Hospital, Cambridge, UK
| | - A-M Little
- Histocompatibility and Immunogenetics Service, Gartnavel General Hospital, Glasgow, UK
| | - H McFarlane
- Histocompatibility and Immunogenetics Service, Gartnavel General Hospital, Glasgow, UK
| | - M A Heneghan
- Institute of Liver Studies, Kings College Hospital London, London, UK
| | - M A Purbhoo
- Department of Hepatology, Imperial College, London, UK
| | - S I Khakoo
- Department of Hepatology, Imperial College, London, UK.,Department of Hepatology, Southampton University, Southampton, UK
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López-Álvarez MR, Jiang W, Jones DC, Jayaraman J, Johnson C, Cookson WO, Moffatt MF, Trowsdale J, Traherne JA. LILRA6 copy number variation correlates with susceptibility to atopic dermatitis. Immunogenetics 2016; 68:743-7. [PMID: 27333811 PMCID: PMC5026711 DOI: 10.1007/s00251-016-0924-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/10/2016] [Indexed: 02/06/2023]
Abstract
Leukocyte immunoglobulin-like receptors (LILR) are expressed mostly on myelomonocytic cells where they are mediators of immunological tolerance. Two LILR genes, LILRA3 and LILRA6, exhibit marked copy number variation. We assessed the contribution of these genes to atopic dermatitis (AD) by analysing transmission in 378 AD families. The data indicated that copies of LILRA6 were over-transmitted to affected patients. They are consistent with a contribution of LILR genes to AD. They could affect the equilibrium between activating and inhibitory signals in the immune response.
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Affiliation(s)
- M R López-Álvarez
- Immunology Division, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - W Jiang
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - D C Jones
- Immunology Division, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - J Jayaraman
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - C Johnson
- Immunology Division, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.,Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.,Molecular Genetics and Genomics Section, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW3 6LY, UK
| | - W O Cookson
- Molecular Genetics and Genomics Section, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW3 6LY, UK
| | - M F Moffatt
- Molecular Genetics and Genomics Section, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW3 6LY, UK
| | - J Trowsdale
- Immunology Division, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.,Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - J A Traherne
- Immunology Division, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK. .,Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.
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Traherne JA, Jiang W, Valdes AM, Hollenbach JA, Jayaraman J, Lane JA, Johnson C, Trowsdale J, Noble JA. KIR haplotypes are associated with late-onset type 1 diabetes in European-American families. Genes Immun 2015; 17:8-12. [PMID: 26492518 PMCID: PMC4746488 DOI: 10.1038/gene.2015.44] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 09/14/2015] [Accepted: 09/15/2015] [Indexed: 01/30/2023]
Abstract
Classical human leukocyte antigens (HLA) genes confer the strongest, but not the only, genetic susceptibility to type 1 diabetes. Killer cell immunoglobulin-like receptors (KIR), on natural killer (NK) cells, bind ligands including class I HLA. We examined presence or absence, with copy number, of KIR loci in 1698 individuals, from 339 multiplex type 1 diabetes families, from the Human Biological Data Interchange, previously genotyped for HLA. Combining family data with KIR copy number information allowed assignment of haplotypes using identity by descent. This is the first disease study to use KIR copy number typing and unambiguously define haplotypes by gene transmission. KIR A1 haplotypes were positively associated with T1D in the subset of patients without the high T1D risk HLA genotype, DR3/DR4 (odds ratio=1.29, P=0.0096). The data point to a role for KIR in type 1 diabetes risk in late-onset patients. In the top quartile (age of onset>14), KIR A2 haplotype was overtransmitted (63.4%, odds ratio=1.73, P=0.024) and KIR B haplotypes were undertransmitted (41.1%, odds ratio=0.70, P=0.0052) to patients. The data suggest that inhibitory ‘A' haplotypes are predisposing and stimulatory ‘B' haplotypes confer protection in both DR3/DR4-negative and late-onset patient groups.
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Affiliation(s)
- J A Traherne
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, UK.,Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - W Jiang
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - A M Valdes
- Academic Rheumatology, University of Nottingham, City Hospital, Nottingham, UK
| | - J A Hollenbach
- Department of Neurology, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - J Jayaraman
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - J A Lane
- Children's Hospital Oakland Research Institute, Oakland, California, USA
| | - C Johnson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - J Trowsdale
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, UK.,Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - J A Noble
- Children's Hospital Oakland Research Institute, Oakland, California, USA
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Dunphy SE, Guinan KJ, Chorcora CN, Jayaraman J, Traherne JA, Trowsdale J, Pende D, Middleton D, Gardiner CM. 2DL1, 2DL2 and 2DL3 all contribute to KIR phenotype variability on human NK cells. Genes Immun 2015; 16:301-10. [PMID: 25950617 DOI: 10.1038/gene.2015.15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 03/06/2015] [Accepted: 03/31/2015] [Indexed: 01/16/2023]
Abstract
Natural killer (NK) cells are lymphocytes that function as part of the innate immune system. Their activity is controlled by a range of inhibitory and activating receptors, including the important killer-cell immunoglobulin-like receptors (KIR). The KIR are a multi-gene family of receptors that interact with the human leukocyte antigen (HLA) class I family of molecules and are characterised by extensive allelic polymorphism. Their expression on the cell surface of NK cells is highly variable, but the factors responsible for this variability are not yet clearly understood. In the current study, we investigated KIR expression in a healthy human cohort that we had previously characterised in depth at a genetic level, with KIR allele typing and HLA class I ligand genotypes available for all donors (n=198). Allelic polymorphism significantly affected the phenotypic expression of all KIR analysed, whereas HLA ligand background influenced the expression levels of 2DL1 and 2DL3. In particular, we found that although 2DL2 may influence 2DL1 expression, this appears to be owing to variation in 2DL1 copy number. Finally, the inhibitory receptor LILRB1 had higher expression levels in individuals with B/B KIR genotypes, suggesting a possible relationship between KIR and non-KIR receptors, which serves to balance NK cell activation potential.
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Affiliation(s)
- S E Dunphy
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin 2, Ireland
| | - K J Guinan
- Current address: BioAtlantis Ltd., Kerry Technology Park, Tralee, Co. Kerry, Ireland
| | - C Ní Chorcora
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin 2, Ireland
| | - J Jayaraman
- Cambridge Institute for Medical Research, University of Cambridge; Division of Immunology, Cambridge, UK
| | - J A Traherne
- 1] Cambridge Institute for Medical Research, University of Cambridge; Division of Immunology, Cambridge, UK [2] Department of Pathology, University of Cambridge, Cambridge, UK
| | - J Trowsdale
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - D Pende
- Immunology Laboratory, IRCCS AOU San Martino-IST, Largo Rosanna Benzi 10, Genova, Italy
| | - D Middleton
- Transplant Immunology Laboratory, Royal Liverpool University Hospital, Liverpool, UK
| | - C M Gardiner
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin 2, Ireland
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36
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Jayaraman J, King NM, Roberts GJ, Wong HM. Dental age assessment: are Demirjian's standards appropriate for southern Chinese children? J Forensic Odontostomatol 2011; 29:22-28. [PMID: 22717910 PMCID: PMC5734851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Estimation of age is an important requisite in forensic, judicial and criminal proceedings. Dental age can be estimated from a dataset that has been prepared from a similar or a different population group. Demirjian and his co-workers proposed dental maturity scores from a French-Canadian population and this has served as a reference dataset for evaluation of age for various population groups. Considering the high number of illegal immigrants who have entered Hong Kong from neighboring countries, age estimation studies on southern Chinese is warranted. This study aimed to validate the applicability of Demirjian's dataset on a southern Chinese population. A total of 182 dental panoramic tomographs comprising an equal number of boys and girls with an age range from 3 to 16 years were scored. Dental maturity scores were obtained from the Demirjian's dataset and dental age was calculated. The difference in chronological and estimated dental ages was calculated using the paired t-test. There was a mean overestimation of dental age of 0.62 years for boys (p < 0.01) and 0.36 years for girls (p < 0.01). Demirjian's dataset is not suitable for estimating the age of 3-16 years old southern Chinese children.
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Affiliation(s)
- J Jayaraman
- Faculty of Dentistry,The University of Hong Kong, Pokfulam, Hong Kong.
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37
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Suresh N, Shivakumar K, Jayaraman J. The adaptation to salinity: protein synthesis and some aspects of energy transduction in fish gill mitochondria. J Bioenerg Biomembr 2008; 15:379-94. [PMID: 18251433 DOI: 10.1007/bf00751057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Exposure of freshwater fish to saline conditions brings about somewhat drastic changes in the mitochondrial energy metabolism. These include abolition of oxidative phosphorylation, ATP-induced contraction of swollen mitochondria and transhydrogenase activity. On the other hand the endogenous calcium levels and protein synthetic capacity are elevated. In vitro protein synthesis by mitochondria from freshwater and stressed fish shows qualitative and quantitative variations. Effluxing the excess calcium by treatment with NaCl or inhibiting the protein synthesis by chloramphenicol in stressed mitochondria restores almost all the functions. It is proposed that the energy potential formed by the mitochondrial membrane is channelized to perform different functions and that the ratio of channelization can be altered to suit the needs of the cell.
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Affiliation(s)
- N Suresh
- Department of Biochemistry, School of Biological Sciences, Madurai Kamraj University, Madurai-625021, India
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38
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Abstract
Plants are susceptible to infection by a broad range of fungal pathogens. Many horticulturally important crop species lack adequate genetic resistance to disease. Studies on potential mechanisms of disease resistance in plants have revealed the importance of a range of pathogenesis-related (PR) proteins with antifungal activity in reducing colonization of plant tissues by pathogens. We are evaluating a range of PR-proteins, through heterologous expression in transgenic carrot tissues, for their effects on fungal disease development. The protocols for carrot transformation with a thaumatin-like protein are described. In addition, the use of herbicide resistance as a selectable marker in carrot transformation is illustrated. In this protocol, petiole segments from carrot seedlings are exposed to Agrobacterium for 10-30 min and co-cultivated for 3 d, after which herbicide selection is imposed until embryogenic calli are produced after 8-12 wk. The transfer of the embryogenic calli to hormone-free medium yields transgenic plantlets. This genetic transformation protocol has supported the generation of transgenic carrot plants with defined T-DNA inserts at the rate of between 1 and 3 Southern positive independent events out of 100.
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Affiliation(s)
- Owen Wally
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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39
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Jayaraman J. Exploiting indigenous technologies for unmanned air vehicle surveillance system(Review Paper). DEFENCE SCI J 2001. [DOI: 10.14429/dsj.51.2232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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40
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Silber JH, Fridman M, Shpilsky A, Even-Shoshan O, Smink DS, Jayaraman J, Fox KR, Pauly MV. Modeling the cost-effectiveness of granulocyte colony-stimulating factor use in early-stage breast cancer. J Clin Oncol 1998; 16:2435-44. [PMID: 9667261 DOI: 10.1200/jco.1998.16.7.2435] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [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: 11/20/2022] Open
Abstract
PURPOSE To model the cost-effectiveness (CE) of granulocyte colony-stimulating factor (G-CSF) in early-stage breast cancer when its use is directed to those most in need of the medication. METHODS A conditional CE model was developed for the use of G-CSF based on a ranking of patient need as determined by patient blood counts during the first cycle of chemotherapy. In the base case, no G-CSF was used. In the alternative case, G-CSF was used in the following manner. If the risk of a neutropenic event (as defined by a predictive model based on nadir absolute neutrophil count [ANC] and hemoglobin decrease in cycle 1) was equal to or exceeded a predetermined critical value "T," then patients would receive G-CSF in cycles 2 through 6 of chemotherapy. If the risk of an event was less than T, patients would not use G-CSF unless an event occurred, at which time G-CSF would be administered with every subsequent cycle. RESULTS A decision rule (T) that would allow the most needy 50% of early-stage breast cancer patients to receive G-CSF after the first cycle of chemotherapy resulted in a CE ratio of $34,297 dollars per life-year saved (LYS). If only the most needy 10% of patients received G-CSF, then the associated CE ratio was $23,748/LYS; if 90% of patients could receive the medication, the CE ratio would be $76,487/LYS. These estimates were relatively insensitive to inpatient hospital cost estimates (inpatient costs for fever and neutropenia of $3,090 to $7,726 per admission produced dollar per LYS figures of $34,297 to $32,415, respectively). However, the model was sensitive to assumptions about the shape of the relationship between dose reduction and disease-free survival (DFS) at 3 years. CONCLUSION Providing G-CSF to the neediest 50% of early-stage breast cancer patients (as defined by first-cycle blood counts) starting after the first cycle of chemotherapy is associated with a CE ratio of $34,297/LYS, which is well in the range of CE ratios for treatment of other common medical conditions. Furthermore, conditional CE studies, based on predictive models that incorporate individual patient risk, allow one to define populations for which therapy is, or is not, cost-effective. Limitations of our present understanding of the shape of the chemotherapy dose-response curve, especially at low levels of dose reductions, affect these results. Further work is required to define the shape of the dose-response curve in early-stage breast cancer.
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Affiliation(s)
- J H Silber
- University of Pennsylvania Cancer Center and the Leonard Davis Institute of Health Economics, Department of Pediatrics, School of Medicine, Philadelphia, USA.
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41
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Krishana PS, Panda PK, Jayaraman J. Unmanned Air Vehicle and Simulation . DEFENCE SCI J 1997. [DOI: 10.14429/dsj.47.4013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Abstract
Upon cellular DNA damage, the p53 tumor suppressor protein transmits a signal to genes that control the cell cycle and apoptosis. One function of p53 that is important for its role in this pathway is its ability to function as a sequence-specific transcriptional activator. We demonstrate here that short single DNA strands can markedly stimulate the ability of human and murine p53 proteins to bind specifically to a p53 response element in supercoiled DNA. We also show that single-stranded DNA does not stimulate binding by a truncated p53 that lacks the C-terminal domain. Finally, we establish that a peptide spanning the p53 C-terminus has the ability in trans to stimulate sequence-specific DNA binding by p53 dramatically. These data taken together suggest a model in which the p53 C-terminus can recognize DNA structures resulting from damage-induced lesions, and this interaction can be propagated to regulate positively p53 sequence-specific DNA binding.
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Affiliation(s)
- J Jayaraman
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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Rao AV, Reddy TK, Prabakar ER, Baskaran S, Swaminathan R, Belinda C, Andal G, Verghese A, Kulhara P, Sharma SD, Sathyavathy K, Prabakaran N, Jayaraman J, Luthra UK, Parhee R, Kumar N. COGNITIVE DISORDER AND DEPRESSION: (An Analysis of the Causal Relationship and Susceptibility to Relapses). Indian J Psychiatry 1989; 31:201-7. [PMID: 21927384 PMCID: PMC2992113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
A prospective study of 45 cases of unipolar depression was conducted with the aim to examine the hypothesis that cognitive disorder predisposes to depression. The data indicated that the absence of the cognitive disorder during remission was statistically significant in 41 cases who remitted. Of the latter, 27 were free from cognitive disorder, while 14 continued with it. This fails to support the causal role of the cognitive disorder. It was also observed that those with persisting cognitive disorder in remission ran the risk of early relapse. It is suggested that persistence of cognitive disorder in remission could be a predictor of early relapse and offers the possibility of using cognitive behavioural therapy for such select cases.
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Affiliation(s)
- A V Rao
- Emeritus Professor of Psychiatry and Officer-in-Charge, Centre for Advanced Research on 'Health and Behaviour', Madurai Medical College and Govt. Rajaji Hospital, Madurai-625 020
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Jebakumar SR, Kannan N, Subramanian BR, Jayaraman J. Residues of phosphamidon in rice fields. Environ Pollut 1989; 61:227-234. [PMID: 15092362 DOI: 10.1016/0269-7491(89)90243-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/1988] [Revised: 05/08/1989] [Accepted: 06/13/1989] [Indexed: 05/24/2023]
Abstract
Thirty-day-old seedlings of rice plants (IR-20 variety) from the nursery were transplanted into experimental plots and after 52 days were sprayed with phosphamidon (Dimecron 85% EC) at two dose-rates (0.38 kg a.i. ha(-1) and 0.76 kg a.i. ha(-1)). Residues of phosphamidon in the plant, soil and water were analysed by GLC, at various time intervals, and were found to decrease steadily up to 15 days. A second application of the pesticide was made on day 113 and grains harvested on day 138. The residue level in the plants was 0.12 microg g(-1) and in the grains 0.04 microg g(-1) with the high dose. This is slightly below the EPA prescribed tolerance level of 0.05 microg g(-1). The residues in both soil and water were very low, 24 h after spraying.
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Affiliation(s)
- S R Jebakumar
- Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai-625 021, India
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45
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Abstract
When the freshwater fish Sarotherodon mossambicus is exposed to an ionoosmotic stress, extensive changes take place in the energetics of the gill mitochondria. These changes are reversed when thyroxine is administered to the fish prior to exposure to stress [K. Shivakumar and J. Jayaraman (1984) Arch. Biochem. Biophys. 233, 728]. The presence of a thyroxine binding component in the mitochondrial inner membrane, its characteristics, and its possible involvement in the salinity adaptation process are discussed.
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46
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Rajaji D, Jayaraman J. Interaction of barbiturates with bimolecular lipid membranes. Indian J Biochem Biophys 1984; 21:365-8. [PMID: 6545523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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Nath I, Jayaraman J, Sathish M, Bhutani LK, Sharma AK. Inhibition of interleukin-2 production by adherent cell factors from lepromatous leprosy patients. Clin Exp Immunol 1984; 58:531-8. [PMID: 6334579 PMCID: PMC1577108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Twenty-four hour supernatants (MoF) were obtained from monocyte rich 2 h adherent cells of 19 leprosy patients and four healthy contacts. MoF from borderline and lepromatous patients produced 52-61% inhibition of human interleukin-2 (IL-2) production by a PHA conditioned T cell line (Jurkat). Non-adherent cell supernatants and MoF from tuberculoid and healthy individuals had little effect on IL-2 production. The suppression effected by MoF was in the first 12 h of initiation of PHA stimulated Jurkat cell cultures. Suppressive MoF did not interfere with (1) IL-2 release, (2) IL-2 utilization by Con A-induced T cell blasts or (3) constitutive proliferation of Jurkat cells. Such MoF were released spontaneously from adherent cells of bacilliferous leprosy patients but required in vitro antigen triggering in long term treated lepromatous patients. It is possible that the unresponsiveness associated with lepromatous leprosy is related to the inhibition of IL-2 production by suppressive factors, thereby, preventing the further expansion of antigen reactive T cells.
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Rajaji D, Jayaraman J. Lignocaine induces lithium transport across bimolecular lipid membrane. Indian J Biochem Biophys 1984; 21:392-3. [PMID: 6545528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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49
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Rajaji D, Ramarajan K, Jayaraman J. Influence of tranquilisers on ionic permeability of bimolecular lipid membranes. Indian J Biochem Biophys 1984; 21:369-72. [PMID: 6545524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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50
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Gopalan G, Jayaraman J, Rajamanickam C. Effect of exogenous addition of hemin on the biogenesis of mitochondrial membranes during glucose repression in Saccharomyces cerevisiae. Arch Biochem Biophys 1984; 235:159-66. [PMID: 6388505 DOI: 10.1016/0003-9861(84)90264-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Exogenous addition of hemin alleviated glucose repression by promoting mitochondrial membrane functions. It prevented the release of mitochondrial proteins into the cytosol by decreasing the activities of phospholipase C and phospholipase D. It restored oligomycin sensitivity of mitochondrial ATPase associated with repressed mitochondria. It enhanced cardiolipin content twofold, and decreased the sterol:phospholipid ratio. Studies on the amino acid incorporation into isolated mitochondria showed that hemin can also promote biogenesis of the organelle by stimulating amino acid incorporation into mitochondrial proteins, and this stimulation appeared to be mediated through some cytosolic factor(s).
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