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Alvarez-Jarreta J, Amos B, Aurrecoechea C, Bah S, Barba M, Barreto A, Basenko EY, Belnap R, Blevins A, Böhme U, Brestelli J, Brown S, Callan D, Campbell LI, Christophides GK, Crouch K, Davison HR, DeBarry JD, Demko R, Doherty R, Duan Y, Dundore W, Dyer S, Falke D, Fischer S, Gajria B, Galdi D, Giraldo-Calderón GI, Harb OS, Harper E, Helb D, Howington C, Hu S, Humphrey J, Iodice J, Jones A, Judkins J, Kelly SA, Kissinger JC, Kittur N, Kwon DK, Lamoureux K, Li W, Lodha D, MacCallum RM, Maslen G, McDowell MA, Myers J, Nural MV, Roos DS, Rund SSC, Shanmugasundram A, Sitnik V, Spruill D, Starns D, Tomko SS, Wang H, Warrenfeltz S, Wieck R, Wilkinson PA, Zheng J. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023. Nucleic Acids Res 2024; 52:D808-D816. [PMID: 37953350 PMCID: PMC10767879 DOI: 10.1093/nar/gkad1003] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/09/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023] Open
Abstract
The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with additional funding from the Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Since 2004, VEuPathDB has analyzed omics data from the public domain using contemporary bioinformatic workflows, including orthology predictions via OrthoMCL, and integrated the analysis results with analysis tools, visualizations, and advanced search capabilities. The unique data mining platform coupled with >3000 pre-analyzed data sets facilitates the exploration of pertinent omics data in support of hypothesis driven research. Comparisons are easily made across data sets, data types and organisms. A Galaxy workspace offers the opportunity for the analysis of private large-scale datasets and for porting to VEuPathDB for comparisons with integrated data. The MapVEu tool provides a platform for exploration of spatially resolved data such as vector surveillance and insecticide resistance monitoring. To address the growing body of omics data and advances in laboratory techniques, VEuPathDB has added several new data types, searches and features, improved the Galaxy workspace environment, redesigned the MapVEu interface and updated the infrastructure to accommodate these changes.
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Affiliation(s)
| | - Beatrice Amos
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | | | - Saikou Bah
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | | | - Ana Barreto
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Evelina Y Basenko
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | | | - Ann Blevins
- University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | | | | | - Stuart Brown
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | | - Kathryn Crouch
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Helen R Davison
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | | | - Richard Demko
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ryan Doherty
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yikun Duan
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Sarah Dyer
- European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | - Dave Falke
- University of Georgia, Athens, GA 30602, USA
| | - Steve Fischer
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bindu Gajria
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel Galdi
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Omar S Harb
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Danica Helb
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Sufen Hu
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - John Iodice
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - John Judkins
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Kelly
- Imperial College London, South Kensington, London SW7 2BU, UK
| | | | | | - Dae Kun Kwon
- University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Wei Li
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Disha Lodha
- European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | | | - Gareth Maslen
- Imperial College London, South Kensington, London SW7 2BU, UK
| | | | - Jeremy Myers
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - David S Roos
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Achchuthan Shanmugasundram
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Genomics England Limited, London E14 5AB, UK
| | - Vasily Sitnik
- European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | | | - David Starns
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | | | | | | | - Robert Wieck
- University of Notre Dame, Notre Dame, IN 46556, USA
| | - Paul A Wilkinson
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jie Zheng
- University of Pennsylvania, Philadelphia, PA 19104, USA
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2
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Farinella DN, Kaur S, Tran V, Cabrera-Mora M, Joyner CJ, Lapp SA, Pakala SB, Nural MV, DeBarry JD, Kissinger JC, Jones DP, Moreno A, Galinski MR, Cordy RJ. Malaria disrupts the rhesus macaque gut microbiome. Front Cell Infect Microbiol 2023; 12:1058926. [PMID: 36710962 PMCID: PMC9880479 DOI: 10.3389/fcimb.2022.1058926] [Citation(s) in RCA: 3] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/12/2022] [Indexed: 01/14/2023] Open
Abstract
Previous studies have suggested that a relationship exists between severity and transmissibility of malaria and variations in the gut microbiome, yet only limited information exists on the temporal dynamics of the gut microbial community during a malarial infection. Here, using a rhesus macaque model of relapsing malaria, we investigate how malaria affects the gut microbiome. In this study, we performed 16S sequencing on DNA isolated from rectal swabs of rhesus macaques over the course of an experimental malarial infection with Plasmodium cynomolgi and analyzed gut bacterial taxa abundance across primary and relapsing infections. We also performed metabolomics on blood plasma from the animals at the same timepoints and investigated changes in metabolic pathways over time. Members of Proteobacteria (family Helicobacteraceae) increased dramatically in relative abundance in the animal's gut microbiome during peak infection while Firmicutes (family Lactobacillaceae and Ruminococcaceae), Bacteroidetes (family Prevotellaceae) and Spirochaetes amongst others decreased compared to baseline levels. Alpha diversity metrics indicated decreased microbiome diversity at the peak of parasitemia, followed by restoration of diversity post-treatment. Comparison with healthy subjects suggested that the rectal microbiome during acute malaria is enriched with commensal bacteria typically found in the healthy animal's mucosa. Significant changes in the tryptophan-kynurenine immunomodulatory pathway were detected at peak infection with P. cynomolgi, a finding that has been described previously in the context of P. vivax infections in humans. During relapses, which have been shown to be associated with less inflammation and clinical severity, we observed minimal disruption to the gut microbiome, despite parasites being present. Altogether, these data suggest that the metabolic shift occurring during acute infection is associated with a concomitant shift in the gut microbiome, which is reversed post-treatment.
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Affiliation(s)
| | - Sukhpreet Kaur
- Department of Biology, Wake Forest University, Winston-Salem, NC, United States
| | - ViLinh Tran
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States
| | - Monica Cabrera-Mora
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States,Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Chester J. Joyner
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States,Department of Infectious Diseases, University of Georgia, Athens, GA, United States
| | - Stacey A. Lapp
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States,Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Suman B. Pakala
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Mustafa V. Nural
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Jeremy D. DeBarry
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States,Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Jessica C. Kissinger
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States,Department of Genetics, University of Georgia, Athens, GA, United States
| | - Dean P. Jones
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States
| | - Alberto Moreno
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States,Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States,Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Mary R. Galinski
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States,Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States,Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Regina Joice Cordy
- Department of Biology, Wake Forest University, Winston-Salem, NC, United States,Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States,*Correspondence: Regina Joice Cordy,
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3
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DeBarry JD, Nural MV, Pakala SB, Nayak V, Warrenfeltz S, Humphrey J, Lapp SA, Cabrera-Mora M, Brito CFA, Jiang J, Saney CL, Hankus A, Stealey HM, DeBarry MB, Lackman N, Legall N, Lee K, Tang Y, Gupta A, Trippe ED, Bridger RR, Weatherly DB, Peterson MS, Jiang X, Tran V, Uppal K, Fonseca LL, Joyner CJ, Karpuzoglu E, Cordy RJ, Meyer EVS, Wells LL, Ory DS, Lee FEH, Tirouvanziam R, Gutiérrez JB, Ibegbu C, Lamb TJ, Pohl J, Pruett ST, Jones DP, Styczynski MP, Voit EO, Moreno A, Galinski MR, Kissinger JC. MaHPIC malaria systems biology data from Plasmodium cynomolgi sporozoite longitudinal infections in macaques. Sci Data 2022; 9:722. [PMID: 36433985 PMCID: PMC9700667 DOI: 10.1038/s41597-022-01755-y] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/10/2022] [Indexed: 11/27/2022] Open
Abstract
Plasmodium cynomolgi causes zoonotic malarial infections in Southeast Asia and this parasite species is important as a model for Plasmodium vivax and Plasmodium ovale. Each of these species produces hypnozoites in the liver, which can cause relapsing infections in the blood. Here we present methods and data generated from iterative longitudinal systems biology infection experiments designed and performed by the Malaria Host-Pathogen Interaction Center (MaHPIC) to delve deeper into the biology, pathogenesis, and immune responses of P. cynomolgi in the Macaca mulatta host. Infections were initiated by sporozoite inoculation. Blood and bone marrow samples were collected at defined timepoints for biological and computational experiments and integrative analyses revolving around primary illness, relapse illness, and subsequent disease and immune response patterns. Parasitological, clinical, haematological, immune response, and -omic datasets (transcriptomics, proteomics, metabolomics, and lipidomics) including metadata and computational results have been deposited in public repositories. The scope and depth of these datasets are unprecedented in studies of malaria, and they are projected to be a F.A.I.R., reliable data resource for decades.
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Affiliation(s)
- Jeremy D DeBarry
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Mustafa V Nural
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Suman B Pakala
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Vishal Nayak
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Cancer Data Science Initiatives, Frederick National Laboratory for Cancer Research, Post Office Box B, Frederick, MD, 21702, USA
| | - Susanne Warrenfeltz
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Jay Humphrey
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Stacey A Lapp
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Monica Cabrera-Mora
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Cristiana F A Brito
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Laboratório de Malária, Instituto René Rachou/Fiocruz Minas, Av. Augusto de Lima 1715, Belo Horizonte, MG, 30190 009, Brazil
| | - Jianlin Jiang
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Celia L Saney
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, 30605, USA
| | - Allison Hankus
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Senior Public Health Informaticist, MITRE Corp, Atlanta, GA, 30345, USA
| | - Hannah M Stealey
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Megan B DeBarry
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Nicolas Lackman
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Noah Legall
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Interdisciplinary Disease Ecology Across Scales Research Traineeship Program, Institute of Bioinformatics, Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Kevin Lee
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Yan Tang
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Anuj Gupta
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Valted Seq, 704 Quince Orchard Rd, Gaithersburg, MD, 20878, USA
| | - Elizabeth D Trippe
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Federal Drug Administration, Silver Spring, MD, 20993, USA
| | - Robert R Bridger
- Complex Carbohydrate Research Center, Department of Biochemistry, University of Georgia, Athens, GA, 30602, USA
| | - Daniel Brent Weatherly
- Complex Carbohydrate Research Center, Department of Biochemistry, University of Georgia, Athens, GA, 30602, USA
| | - Mariko S Peterson
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Xuntian Jiang
- Division of Endocrinology, Metabolism & Lipid Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - ViLinh Tran
- Division of Pulmonary, Allergy, Critical Care, & Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Karan Uppal
- Division of Pulmonary, Allergy, Critical Care, & Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Luis L Fonseca
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Florida, Gainesville, FL, 32603, USA
| | - Chester J Joyner
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Center for Tropical and Emerging Global Disease, University of Georgia, Athens, GA, 30602, USA
- Center for Vaccines and Immunology, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Ebru Karpuzoglu
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Biosciences and Diagnostic Imaging, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Regina J Cordy
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Biology, Wake Forest University, Winston Salem, NC, 27103, USA
| | - Esmeralda V S Meyer
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Institutional Animal Care and Use Committee, Research Compliance and Research Integrity Office, Emory University, Atlanta, GA, 30322, USA
| | - Lance L Wells
- Complex Carbohydrate Research Center, Department of Biochemistry, University of Georgia, Athens, GA, 30602, USA
| | - Daniel S Ory
- Division of Endocrinology, Metabolism & Lipid Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Casma Therapeutics, Cambridge, MA, 02139, USA
| | - F Eun-Hyung Lee
- Division of Pulmonary, Allergy, Critical Care, & Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, 30322, USA
| | - Rabindra Tirouvanziam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Juan B Gutiérrez
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Department of Mathematics, Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Chris Ibegbu
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Tracey J Lamb
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Pathology, University of Utah, Salt Lake City, UT, 84112, USA
| | - Jan Pohl
- Biotechnology Core Facility Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Sarah T Pruett
- Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- University of Tennessee, Knoxville, TN, 37996, USA
| | - Dean P Jones
- Division of Pulmonary, Allergy, Critical Care, & Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Eberhard O Voit
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Alberto Moreno
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Mary R Galinski
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jessica C Kissinger
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, 30602, USA.
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
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4
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Peterson MS, Joyner CJ, Lapp SA, Brady JA, Wood JS, Cabrera-Mora M, Saney CL, Fonseca LL, Cheng WT, Jiang J, Soderberg SR, Nural MV, Hankus A, Machiah D, Karpuzoglu E, DeBarry JD, Tirouvanziam R, Kissinger JC, Moreno A, Gumber S, Voit EO, Gutierrez JB, Cordy RJ, Galinski MR. Plasmodium knowlesi Cytoadhesion Involves SICA Variant Proteins. Front Cell Infect Microbiol 2022; 12:888496. [PMID: 35811680 PMCID: PMC9260704 DOI: 10.3389/fcimb.2022.888496] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Plasmodium knowlesi poses a health threat throughout Southeast Asian communities and currently causes most cases of malaria in Malaysia. This zoonotic parasite species has been studied in Macaca mulatta (rhesus monkeys) as a model for severe malarial infections, chronicity, and antigenic variation. The phenomenon of Plasmodium antigenic variation was first recognized during rhesus monkey infections. Plasmodium-encoded variant proteins were first discovered in this species and found to be expressed at the surface of infected erythrocytes, and then named the Schizont-Infected Cell Agglutination (SICA) antigens. SICA expression was shown to be spleen dependent, as SICA expression is lost after P. knowlesi is passaged in splenectomized rhesus. Here we present data from longitudinal P. knowlesi infections in rhesus with the most comprehensive analysis to date of clinical parameters and infected red blood cell sequestration in the vasculature of tissues from 22 organs. Based on the histopathological analysis of 22 tissue types from 11 rhesus monkeys, we show a comparative distribution of parasitized erythrocytes and the degree of margination of the infected erythrocytes with the endothelium. Interestingly, there was a significantly higher burden of parasites in the gastrointestinal tissues, and extensive margination of the parasites along the endothelium, which may help explain gastrointestinal symptoms frequently reported by patients with P. knowlesi malarial infections. Moreover, this margination was not observed in splenectomized rhesus that were infected with parasites not expressing the SICA proteins. This work provides data that directly supports the view that a subpopulation of P. knowlesi parasites cytoadheres and sequesters, likely via SICA variant antigens acting as ligands. This process is akin to the cytoadhesive function of the related variant antigen proteins, namely Erythrocyte Membrane Protein-1, expressed by Plasmodium falciparum.
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Affiliation(s)
- Mariko S. Peterson
- Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Chester J. Joyner
- Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
| | - Stacey A. Lapp
- Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Jessica A. Brady
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA, United States
| | - Jennifer S. Wood
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Monica Cabrera-Mora
- Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Celia L. Saney
- Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Luis L. Fonseca
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Wayne T. Cheng
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
| | - Jianlin Jiang
- Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Stephanie R. Soderberg
- Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Mustafa V. Nural
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Allison Hankus
- Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Deepa Machiah
- Division of Pathology, Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Ebru Karpuzoglu
- Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Jeremy D. DeBarry
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Rabindra Tirouvanziam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Jessica C. Kissinger
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Alberto Moreno
- Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Sanjeev Gumber
- Division of Pathology, Yerkes National Primate Research Center, Atlanta, GA, United States
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Atlanta, GA, United States
| | - Eberhard O. Voit
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Juan B. Gutierrez
- Department of Mathematics, University of Georgia, Athens, GA, United States
| | - Regina Joice Cordy
- Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Mary R. Galinski
- Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States
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5
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Peterson MS, Joyner CJ, Brady JA, Wood JS, Cabrera-Mora M, Saney CL, Fonseca LL, Cheng WT, Jiang J, Lapp SA, Soderberg SR, Nural MV, Humphrey JC, Hankus A, Machiah D, Karpuzoglu E, DeBarry JD, Tirouvanziam R, Kissinger JC, Moreno A, Gumber S, Voit EO, Gutiérrez JB, Cordy RJ, Galinski MR. Clinical recovery of Macaca fascicularis infected with Plasmodium knowlesi. Malar J 2021; 20:486. [PMID: 34969401 PMCID: PMC8719393 DOI: 10.1186/s12936-021-03925-6] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/24/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Kra monkeys (Macaca fascicularis), a natural host of Plasmodium knowlesi, control parasitaemia caused by this parasite species and escape death without treatment. Knowledge of the disease progression and resilience in kra monkeys will aid the effective use of this species to study mechanisms of resilience to malaria. This longitudinal study aimed to define clinical, physiological and pathological changes in kra monkeys infected with P. knowlesi, which could explain their resilient phenotype. METHODS Kra monkeys (n = 15, male, young adults) were infected intravenously with cryopreserved P. knowlesi sporozoites and the resulting parasitaemias were monitored daily. Complete blood counts, reticulocyte counts, blood chemistry and physiological telemetry data (n = 7) were acquired as described prior to infection to establish baseline values and then daily after inoculation for up to 50 days. Bone marrow aspirates, plasma samples, and 22 tissue samples were collected at specific time points to evaluate longitudinal clinical, physiological and pathological effects of P. knowlesi infections during acute and chronic infections. RESULTS As expected, the kra monkeys controlled acute infections and remained with low-level, persistent parasitaemias without anti-malarial intervention. Unexpectedly, early in the infection, fevers developed, which ultimately returned to baseline, as well as mild to moderate thrombocytopenia, and moderate to severe anaemia. Mathematical modelling and the reticulocyte production index indicated that the anaemia was largely due to the removal of uninfected erythrocytes and not impaired production of erythrocytes. Mild tissue damage was observed, and tissue parasite load was associated with tissue damage even though parasite accumulation in the tissues was generally low. CONCLUSIONS Kra monkeys experimentally infected with P. knowlesi sporozoites presented with multiple clinical signs of malaria that varied in severity among individuals. Overall, the animals shared common mechanisms of resilience characterized by controlling parasitaemia 3-5 days after patency, and controlling fever, coupled with physiological and bone marrow responses to compensate for anaemia. Together, these responses likely minimized tissue damage while supporting the establishment of chronic infections, which may be important for transmission in natural endemic settings. These results provide new foundational insights into malaria pathogenesis and resilience in kra monkeys, which may improve understanding of human infections.
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Affiliation(s)
- Mariko S Peterson
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory University School of Medicine, Atlanta, GA, USA
| | - Chester J Joyner
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Center for Vaccines and Immunology, Department of Infectious Diseases, University of Georgia, Athens, GA, USA
- Center for Vaccines and Immunology, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Jessica A Brady
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA, USA
- Eli Lilly and Company, Indianapolis, IN, USA
| | - Jennifer S Wood
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Monica Cabrera-Mora
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Celia L Saney
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Luis L Fonseca
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Wayne T Cheng
- Center for Vaccines and Immunology, Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Jianlin Jiang
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Stacey A Lapp
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Stephanie R Soderberg
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Thermo Fisher Scientific, South San Francisco, CA, USA
| | - Mustafa V Nural
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Jay C Humphrey
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Allison Hankus
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- The MITRE Corporation, Atlanta, GA, USA
| | - Deepa Machiah
- Division of Pathology, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Ebru Karpuzoglu
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Department of Biosciences and Diagnostic Imaging, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Jeremy D DeBarry
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Center for Topical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | | | - Jessica C Kissinger
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Alberto Moreno
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Sanjeev Gumber
- Division of Pathology, Yerkes National Primate Research Center, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Atlanta, GA, USA
- Pathology, Drug Safety, and DMPK, Boehringer Ingelheim Animal Health USA, Inc., Athens, GA, USA
| | - Eberhard O Voit
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Juan B Gutiérrez
- Department of Mathematics, University of Georgia, Athens, GA, USA
- Department of Mathematics, University of Texas at San Antonio, San Antonio, TX, USA
| | - Regina Joice Cordy
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Department of Biology, Wake Forest University, Winston-Salem, NC, USA
| | - Mary R Galinski
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
- Emory Vaccine Center, Emory University, Atlanta, GA, USA.
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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6
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Cordy RJ, Patrapuvich R, Lili LN, Cabrera-Mora M, Chien JT, Tharp GK, Khadka M, Meyer EV, Lapp SA, Joyner CJ, Garcia A, Banton S, Tran V, Luvira V, Rungin S, Saeseu T, Rachaphaew N, Pakala SB, DeBarry JD, Kissinger JC, Ortlund EA, Bosinger SE, Barnwell JW, Jones DP, Uppal K, Li S, Sattabongkot J, Moreno A, Galinski MR. Distinct amino acid and lipid perturbations characterize acute versus chronic malaria. JCI Insight 2019; 4:125156. [PMID: 31045574 DOI: 10.1172/jci.insight.125156] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 04/02/2019] [Indexed: 12/21/2022] Open
Abstract
Chronic malaria is a major public health problem and significant challenge for disease eradication efforts. Despite its importance, the biological factors underpinning chronic malaria are not fully understood. Recent studies have shown that host metabolic state can influence malaria pathogenesis and transmission, but its role in chronicity is not known. Here, with the goal of identifying distinct modifications in the metabolite profiles of acute versus chronic malaria, metabolomics was performed on plasma from Plasmodium-infected humans and nonhuman primates with a range of parasitemias and clinical signs. In rhesus macaques infected with Plasmodium coatneyi, significant alterations in amines, carnitines, and lipids were detected during a high parasitemic acute phase and many of these reverted to baseline levels once a low parasitemic chronic phase was established. Plasmodium gene expression, studied in parallel in the macaques, revealed transcriptional changes in amine, fatty acid, lipid and energy metabolism genes, as well as variant antigen genes. Furthermore, a common set of amines, carnitines, and lipids distinguished acute from chronic malaria in plasma from human Plasmodium falciparum cases. In summary, distinct host-parasite metabolic environments have been uncovered that characterize acute versus chronic malaria, providing insights into the underlying host-parasite biology of malaria disease progression.
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Affiliation(s)
- Regina Joice Cordy
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA.,Department of Biology, Wake Forest University, Winston-Salem, North Carolina, USA
| | | | - Loukia N Lili
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA.,Department of Genetics and Genomic Sciences, Institute for Next Generation Healthcare, Icahn School of Medicine, Mount Sinai, New York, New York, USA
| | - Monica Cabrera-Mora
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Jung-Ting Chien
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Gregory K Tharp
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Manoj Khadka
- Emory Integrated Lipidomics Core, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Esmeralda Vs Meyer
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Stacey A Lapp
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Chester J Joyner
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - AnaPatricia Garcia
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Sophia Banton
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - ViLinh Tran
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Viravarn Luvira
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Siriwan Rungin
- Mahidol Vivax Research Unit, Mahidol University, Bangkok, Thailand
| | - Teerawat Saeseu
- Mahidol Vivax Research Unit, Mahidol University, Bangkok, Thailand
| | | | | | | | | | - Jessica C Kissinger
- Institute of Bioinformatics.,Center for Tropical and Emerging Global Diseases, and.,Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Eric A Ortlund
- Emory Integrated Lipidomics Core, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Steven E Bosinger
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA.,Department of Pathology and Laboratory Medicine, Emory School of Medicine, Atlanta, Georgia, USA
| | - John W Barnwell
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dean P Jones
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Karan Uppal
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Shuzhao Li
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | | | - Alberto Moreno
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA.,Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Mary R Galinski
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA.,Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
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7
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Baptista RP, Reis-Cunha JL, DeBarry JD, Chiari E, Kissinger JC, Bartholomeu DC, Macedo AM. Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231. Microb Genom 2018; 4. [PMID: 29442617 PMCID: PMC5989580 DOI: 10.1099/mgen.0.000156] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing (NGS) methods are low-cost high-throughput technologies that produce thousands to millions of sequence reads. Despite the high number of raw sequence reads, their short length, relative to Sanger, PacBio or Nanopore reads, complicates the assembly of genomic repeats. Many genome tools are available, but the assembly of highly repetitive genome sequences using only NGS short reads remains challenging. Genome assembly of organisms responsible for important neglected diseases such as Trypanosoma cruzi, the aetiological agent of Chagas disease, is known to be challenging because of their repetitive nature. Only three of six recognized discrete typing units (DTUs) of the parasite have their draft genomes published and therefore genome evolution analyses in the taxon are limited. In this study, we developed a computational workflow to assemble highly repetitive genomes via a combination of de novo and reference-based assembly strategies to better overcome the intrinsic limitations of each, based on Illumina reads. The highly repetitive genome of the human-infecting parasite T. cruzi 231 strain was used as a test subject. The combined-assembly approach shown in this study benefits from the reference-based assembly ability to resolve highly repetitive sequences and from the de novo capacity to assemble genome-specific regions, improving the quality of the assembly. The acceptable confidence obtained by analyzing our results showed that our combined approach is an attractive option to assemble highly repetitive genomes with NGS short reads. Phylogenomic analysis including the 231 strain, the first representative of DTU III whose genome was sequenced, was also performed and provides new insights into T. cruzi genome evolution.
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Affiliation(s)
- Rodrigo P Baptista
- 1Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
- 2Institute of Bioinformatics, University of Georgia, Athens, USA
| | - Joao Luis Reis-Cunha
- 3Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jeremy D DeBarry
- 1Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Egler Chiari
- 3Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jessica C Kissinger
- 1Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
- 2Institute of Bioinformatics, University of Georgia, Athens, USA
- 4Department of Genetics, University of Georgia, Athens, USA
| | - Daniella C Bartholomeu
- 3Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Andrea M Macedo
- 5Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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8
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Tang Y, Joyner CJ, Cabrera-Mora M, Saney CL, Lapp SA, Nural MV, Pakala SB, DeBarry JD, Soderberg S, Kissinger JC, Lamb TJ, Galinski MR, Styczynski MP. Correction to: Integrative analysis associates monocytes with insufficient erythropoiesis during acute Plasmodium cynomolgi malaria in rhesus macaques. Malar J 2017; 16:486. [PMID: 29202752 PMCID: PMC5715518 DOI: 10.1186/s12936-017-2134-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 11/27/2017] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yan Tang
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.,Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Chester J Joyner
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Monica Cabrera-Mora
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Celia L Saney
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Stacey A Lapp
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Mustafa V Nural
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, USA.,Department of Computer Science, University of Georgia, Athens, GA, USA
| | - Suman B Pakala
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Jeremy D DeBarry
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Stephanie Soderberg
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | | | - Jessica C Kissinger
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, USA.,Department of Genetics, University of Georgia, Athens, GA, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA.,Department of Computer Science, University of Georgia, Athens, GA, USA
| | - Tracey J Lamb
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Mary R Galinski
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA. .,Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
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9
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Tang Y, Joyner CJ, Cabrera-Mora M, Saney CL, Lapp SA, Nural MV, Pakala SB, DeBarry JD, Soderberg S, Kissinger JC, Lamb TJ, Galinski MR, Styczynski MP. Integrative analysis associates monocytes with insufficient erythropoiesis during acute Plasmodium cynomolgi malaria in rhesus macaques. Malar J 2017; 16:384. [PMID: 28938907 PMCID: PMC5610412 DOI: 10.1186/s12936-017-2029-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/12/2017] [Indexed: 01/06/2023] Open
Abstract
Background Mild to severe anaemia is a common complication of malaria that is caused in part by insufficient erythropoiesis in the bone marrow. This study used systems biology to evaluate the transcriptional and alterations in cell populations in the bone marrow during Plasmodium cynomolgi infection of rhesus macaques (a model of Plasmodium vivax malaria) that may affect erythropoiesis. Results An appropriate erythropoietic response did not occur to compensate for anaemia during acute cynomolgi malaria despite an increase in erythropoietin levels. During this period, there were significant perturbations in the bone marrow transcriptome. In contrast, relapses did not induce anaemia and minimal changes in the bone marrow transcriptome were detected. The differentially expressed genes during acute infection were primarily related to ongoing inflammatory responses with significant contributions from Type I and Type II Interferon transcriptional signatures. These were associated with increased frequency of intermediate and non-classical monocytes. Recruitment and/or expansion of these populations was correlated with a decrease in the erythroid progenitor population during acute infection, suggesting that monocyte-associated inflammation may have contributed to anaemia. The decrease in erythroid progenitors was associated with downregulation of genes regulated by GATA1 and GATA2, two master regulators of erythropoiesis, providing a potential molecular basis for these findings. Conclusions These data suggest the possibility that malarial anaemia may be driven by monocyte-associated disruption of GATA1/GATA2 function in erythroid progenitors resulting in insufficient erythropoiesis during acute infection. Electronic supplementary material The online version of this article (doi:10.1186/s12936-017-2029-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Tang
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.,Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Chester J Joyner
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Monica Cabrera-Mora
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Celia L Saney
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Stacey A Lapp
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Mustafa V Nural
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, USA.,Department of Computer Science, University of Georgia, Athens, GA, USA
| | - Suman B Pakala
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Jeremy D DeBarry
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Stephanie Soderberg
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | | | - Jessica C Kissinger
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, USA.,Department of Genetics, University of Georgia, Athens, GA, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA.,Department of Computer Science, University of Georgia, Athens, GA, USA
| | - Tracey J Lamb
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Mary R Galinski
- Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA. .,Malaria Host-Pathogen Interaction Center, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
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10
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Nyasa RB, Kimbi HK, Zofou D, DeBarry JD, Kissinger JC, Titanji VPK. An evolutionary approach to identify potentially protective B cell epitopes involved in naturally acquired immunity to malaria and the role of EBA-175 in protection amongst denizens of Bolifamba, Cameroon. Malar J 2016; 15:281. [PMID: 27207101 PMCID: PMC4875671 DOI: 10.1186/s12936-016-1337-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 09/15/2015] [Accepted: 05/11/2016] [Indexed: 11/17/2022] Open
Abstract
Background The search for a vaccine against malaria caused by Plasmodium falciparum has lasted for more than 100 years, with considerable progress in the identification of a number of vaccine candidates. The post-genomic era offers new opportunities for an expedited search using rational vaccine design and prioritization of key B-cell epitopes involved in natural acquired immunity. Methods Malaria vaccine candidate genes that have reached clinical trial were searched on an evolutionary relationship tree, to determine their level of lineage-specificity. Ten other genes with similar protein features and level of lineage specificity to the vaccine candidates were randomly selected, and computationally evaluated for the presence of B-cell epitopes. The protein fragment with maximum probability of putative epitopes were synthesized and used in an ELISA experiment to determine the presence of antibodies to these peptides, in the serum of malaria patients and healthy malaria uninfected inhabitants from a malaria endemic region (Bolifamba), alongside with a vaccine candidate EBA-175. Results Two peptide fragments of 25 and 30 amino acid length from PF3D7_1233400 and PF3D7_1437500 respectively, coded as PF4-123 and PF4-143 were shown to contain B-cell epitope(s). Total IgG antibodies to these peptides were not significantly different between sick and healthy participants, but cytophilic antibodies to these peptides were significantly higher in healthy participants (p < 0.03). Total IgG to the vaccine candidate EBA-175 was significantly higher in sick participants than in healthy participants, likewise cytophilic antibodies (p < 0.04). Antibodies to the peptides PF4-123 and PF4-143 correlated negatively (p = 0.025 and 0.008 and r = −0.291 and −0.345, respectively) to parasite load. Total IgG antibodies to EBA-175 showed a negative correlation to parasite load (r = −0.144), which was not significant (p = 0.276). Duration of stay in Bolifamba also negatively correlated with parasite load (p = 0.026, r = −0.419) and total IgG to PF4-143 was significantly associated with prolonged duration of stay in the locality of Bolifamba, Cameroon (p = 0.006, r = 0.361). Conclusions The present study has identified two genes PF3D7_1233400 and PF3D7_1437500 containing peptide fragment (PF4-123 and PF4-143) with B-cell epitopes that are correlated with naturally acquired immunity to malaria. A pipeline has been developed for rapid identification of other B-cell epitopes involved in naturally acquired immunity.
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Affiliation(s)
- Raymond B Nyasa
- Biotechnology Unit, Faculty of Science, University of Buea, Buea, Cameroon.
| | - Helen K Kimbi
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Bamenda, Bamenda, NWR, Cameroon
| | - Denis Zofou
- Biotechnology Unit, Faculty of Science, University of Buea, Buea, Cameroon
| | - Jeremy D DeBarry
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, USA.,Department of Genetics, University of Georgia, Athens, USA
| | - Jessica C Kissinger
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, USA.,Department of Genetics, University of Georgia, Athens, USA.,Institute of Bioinformatics, University of Georgia, Athens, USA
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11
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Bensch S, Canbäck B, DeBarry JD, Johansson T, Hellgren O, Kissinger JC, Palinauskas V, Videvall E, Valkiūnas G. The Genome of Haemoproteus tartakovskyi and Its Relationship to Human Malaria Parasites. Genome Biol Evol 2016; 8:1361-73. [PMID: 27190205 PMCID: PMC4898798 DOI: 10.1093/gbe/evw081] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [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] [Indexed: 12/14/2022] Open
Abstract
The phylogenetic relationships among hemosporidian parasites, including the origin of Plasmodium falciparum, the most virulent malaria parasite of humans, have been heavily debated for decades. Studies based on multiple-gene sequences have helped settle many of these controversial phylogenetic issues. However, denser taxon sampling and genome-wide analyses are needed to confidently resolve the evolutionay relationships among hemosporidian parasites. Genome sequences of several Plasmodium parasites are available but only for species infecting primates and rodents. To root the phylogenetic tree of Plasmodium, genomic data from related parasites of birds or reptiles are required. Here, we use a novel approach to isolate parasite DNA from microgametes and describe the first genome of a bird parasite in the sister genus to Plasmodium, Haemoproteus tartakovskyi. Similar to Plasmodium parasites, H. tartakovskyi has a small genome (23.2 Mb, 5,990 genes) and a GC content (25.4%) closer to P. falciparum (19.3%) than to Plasmodium vivax (42.3%). Combined with novel transcriptome sequences of the bird parasite Plasmodium ashfordi, our phylogenomic analyses of 1,302 orthologous genes demonstrate that mammalian-infecting malaria parasites are monophyletic, thus rejecting the repeatedly proposed hypothesis that the ancestor of Laverania parasites originated from a secondary host shift from birds to humans. Genes and genomic features previously found to be shared between P. falciparum and bird malaria parasites, but absent in other mammal malaria parasites, are therefore signatures of maintained ancestral states. We foresee that the genome of H. tartakovskyi will open new directions for comparative evolutionary analyses of malarial adaptive traits.
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Affiliation(s)
| | | | - Jeremy D DeBarry
- The Center for Tropical and Emerging Global Diseases, Athens, Georgia, USA
| | | | | | - Jessica C Kissinger
- The Center for Tropical and Emerging Global Diseases, Athens, Georgia, USA Department of Genetics and Institute of Bioinformatics, University of Georgia
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12
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Lee KJ, Yin W, Arafat D, Tang Y, Uppal K, Tran V, Cabrera-Mora M, Lapp S, Moreno A, Meyer E, DeBarry JD, Pakala S, Nayak V, Kissinger JC, Jones DP, Galinski M, Styczynski MP, Gibson G. Comparative transcriptomics and metabolomics in a rhesus macaque drug administration study. Front Cell Dev Biol 2014; 2:54. [PMID: 25453034 PMCID: PMC4233942 DOI: 10.3389/fcell.2014.00054] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/08/2014] [Indexed: 01/02/2023] Open
Abstract
We describe a multi-omic approach to understanding the effects that the anti-malarial drug pyrimethamine has on immune physiology in rhesus macaques (Macaca mulatta). Whole blood and bone marrow (BM) RNA-Seq and plasma metabolome profiles (each with over 15,000 features) have been generated for five naïve individuals at up to seven timepoints before, during and after three rounds of drug administration. Linear modeling and Bayesian network analyses are both considered, alongside investigations of the impact of statistical modeling strategies on biological inference. Individual macaques were found to be a major source of variance for both omic data types, and factoring individuals into subsequent modeling increases power to detect temporal effects. A major component of the whole blood transcriptome follows the BM with a time-delay, while other components of variation are unique to each compartment. We demonstrate that pyrimethamine administration does impact both compartments throughout the experiment, but very limited perturbation of transcript or metabolite abundance was observed following each round of drug exposure. New insights into the mode of action of the drug are presented in the context of pyrimethamine's predicted effect on suppression of cell division and metabolism in the immune system.
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Affiliation(s)
- Kevin J Lee
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Weiwei Yin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology Atlanta, GA, USA
| | - Dalia Arafat
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Yan Tang
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Karan Uppal
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, Emory University Atlanta, GA, USA
| | - ViLinh Tran
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, Emory University Atlanta, GA, USA
| | - Monica Cabrera-Mora
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University Atlanta, GA, USA
| | - Stacey Lapp
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University Atlanta, GA, USA
| | - Alberto Moreno
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University Atlanta, GA, USA ; Division of Infectious Diseases, Department of Medicine, Emory University Atlanta, GA, USA
| | - Esmeralda Meyer
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University Atlanta, GA, USA
| | - Jeremy D DeBarry
- Center for Topical and Emerging Global Diseases, University of Georgia Athens, GA, USA
| | - Suman Pakala
- Institute of Bioinformatics, University of Georgia Athens, GA, USA
| | - Vishal Nayak
- Institute of Bioinformatics, University of Georgia Athens, GA, USA
| | - Jessica C Kissinger
- Center for Topical and Emerging Global Diseases, University of Georgia Athens, GA, USA ; Institute of Bioinformatics, University of Georgia Athens, GA, USA
| | - Dean P Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, Emory University Atlanta, GA, USA
| | - Mary Galinski
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University Atlanta, GA, USA ; Division of Infectious Diseases, Department of Medicine, Emory University Atlanta, GA, USA
| | - Mark P Styczynski
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology Atlanta, GA, USA
| | - Greg Gibson
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology Atlanta, GA, USA
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13
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Estep MC, DeBarry JD, Bennetzen JL. The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution. Heredity (Edinb) 2013; 110:194-204. [PMID: 23321774 PMCID: PMC3554455 DOI: 10.1038/hdy.2012.99] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [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: 06/18/2012] [Revised: 10/22/2012] [Accepted: 10/23/2012] [Indexed: 11/09/2022] Open
Abstract
Sample sequence analysis was employed to investigate the repetitive DNAs that were most responsible for the evolved variation in genome content across seven panicoid grasses with >5-fold variation in genome size and different histories of polyploidy. In all cases, the most abundant repeats were LTR retrotransposons, but the particular families that had become dominant were found to be different in the Pennisetum, Saccharum, Sorghum and Zea lineages. One element family, Huck, has been very active in all of the studied species over the last few million years. This suggests the transmittal of an active or quiescent autonomous set of Huck elements to this lineage at the founding of the panicoids. Similarly, independent recent activity of Ji and Opie elements in Zea and of Leviathan elements in Sorghum and Saccharum species suggests that members of these families with exceptional activation potential were present in the genome(s) of the founders of these lineages. In a detailed analysis of the Zea lineage, the combined action of several families of LTR retrotransposons were observed to have approximately doubled the genome size of Zea luxurians relative to Zea mays and Zea diploperennis in just the last few million years. One of the LTR retrotransposon amplification bursts in Zea may have been initiated by polyploidy, but the great majority of transposable element activations are not. Instead, the results suggest random activation of a few or many LTR retrotransposons families in particular lineages over evolutionary time, with some families especially prone to future activation and hyper-amplification.
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Affiliation(s)
- M C Estep
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - J D DeBarry
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - J L Bennetzen
- Department of Genetics, University of Georgia, Athens, GA, USA
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14
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Patel JC, Oberstaller J, Xayavong M, Narayanan J, DeBarry JD, Srinivasamoorthy G, Villegas L, Escalante AA, DaSilva A, Peterson DS, Barnwell JW, Kissinger JC, Udhayakumar V, Lucchi NW. Real-time loop-mediated isothermal amplification (RealAmp) for the species-specific identification of Plasmodium vivax. PLoS One 2013; 8:e54986. [PMID: 23349994 PMCID: PMC3551762 DOI: 10.1371/journal.pone.0054986] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [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: 09/12/2012] [Accepted: 12/17/2012] [Indexed: 11/18/2022] Open
Abstract
Plasmodium vivax infections remain a major source of malaria-related morbidity and mortality. Early and accurate diagnosis is an integral component of effective malaria control programs. Conventional molecular diagnostic methods provide accurate results but are often resource-intensive, expensive, have a long turnaround time and are beyond the capacity of most malaria-endemic countries. Our laboratory has recently developed a new platform called RealAmp, which combines loop-mediated isothermal amplification (LAMP) with a portable tube scanner real-time isothermal instrument for the rapid detection of malaria parasites. Here we describe new primers for the detection of P. vivax using the RealAmp method. Three pairs of amplification primers required for this method were derived from a conserved DNA sequence unique to the P. vivax genome. The amplification was carried out at 64°C using SYBR Green or SYTO-9 intercalating dyes for 90 minutes with the tube scanner set to collect fluorescence signals at 1-minute intervals. Clinical samples of P. vivax and other human-infecting malaria parasite species were used to determine the sensitivity and specificity of the primers by comparing with an 18S ribosomal RNA-based nested PCR as the gold standard. The new set of primers consistently detected laboratory-maintained isolates of P. vivax from different parts of the world. The primers detected P. vivax in the clinical samples with 94.59% sensitivity (95% CI: 87.48-98.26%) and 100% specificity (95% CI: 90.40-100%) compared to the gold standard nested-PCR method. The new primers also proved to be more sensitive than the published species-specific primers specifically developed for the LAMP method in detecting P. vivax.
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Affiliation(s)
- Jaymin C Patel
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
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15
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Abstract
Whole-genome comparisons provide insight into genome evolution by informing on gene repertoires, gene gains/losses, and genome organization. Most of our knowledge about eukaryotic genome evolution is derived from studies of multicellular model organisms. The eukaryotic phylum Apicomplexa contains obligate intracellular protist parasites responsible for a wide range of human and veterinary diseases (e.g., malaria, toxoplasmosis, and theileriosis). We have developed an in silico protein-encoding gene based pipeline to investigate synteny across 12 apicomplexan species from six genera. Genome rearrangement between lineages is extensive. Syntenic regions (conserved gene content and order) are rare between lineages and appear to be totally absent across the phylum, with no group of three genes found on the same chromosome and in the same order within 25 kb up- and downstream of any orthologous genes. Conserved synteny between major lineages is limited to small regions in Plasmodium and Theileria/Babesia species, and within these conserved regions, there are a number of proteins putatively targeted to organelles. The observed overall lack of synteny is surprising considering the divergence times and the apparent absence of transposable elements (TEs) within any of the species examined. TEs are ubiquitous in all other groups of eukaryotes studied to date and have been shown to be involved in genomic rearrangements. It appears that there are different criteria governing genome evolution within the Apicomplexa relative to other well-studied unicellular and multicellular eukaryotes.
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Affiliation(s)
- Jeremy D DeBarry
- Center for Tropical and Emerging Global Diseases, University of Georgia, USA.
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16
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DeBarry JD, Liu R, Bennetzen JL. Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm. BMC Bioinformatics 2008. [PMID: 18474116 DOI: 10.1186/1471‐2105‐9‐235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Higher eukaryotic genomes are typically large, complex and filled with both genes and multiple classes of repetitive DNA. The repetitive DNAs, primarily transposable elements, are a rapidly evolving genome component that can provide the raw material for novel selected functions and also indicate the mechanisms and history of genome evolution in any ancestral lineage. Despite their abundance, universality and significance, studies of genomic repeat content have been largely limited to analyses of the repeats in fully sequenced genomes. RESULTS In order to facilitate a broader range of repeat analyses, the Assisted Automated Assembler of Repeat Families algorithm has been developed. This program, written in PERL and with numerous adjustable parameters, identifies sequence overlaps in small shotgun sequence datasets and walks them out to create long pseudomolecules representing the most abundant repeats in any genome. Testing of this program in maize indicated that it found and assembled all of the major repeats in one or more pseudomolecules, including coverage of the major Long Terminal Repeat retrotransposon families. Both Sanger sequence and 454 datasets were appropriate. CONCLUSION These results now indicate that hundreds of higher eukaryotic genomes can be efficiently characterized for the nature, abundance and evolution of their major repetitive DNA components.
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Affiliation(s)
- Jeremy D DeBarry
- Department of Genetics, University of Georgia, Athens, GA 30602-7223, USA.
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17
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DeBarry JD, Liu R, Bennetzen JL. Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm. BMC Bioinformatics 2008; 9:235. [PMID: 18474116 PMCID: PMC2412881 DOI: 10.1186/1471-2105-9-235] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [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: 07/10/2007] [Accepted: 05/13/2008] [Indexed: 11/25/2022] Open
Abstract
Background Higher eukaryotic genomes are typically large, complex and filled with both genes and multiple classes of repetitive DNA. The repetitive DNAs, primarily transposable elements, are a rapidly evolving genome component that can provide the raw material for novel selected functions and also indicate the mechanisms and history of genome evolution in any ancestral lineage. Despite their abundance, universality and significance, studies of genomic repeat content have been largely limited to analyses of the repeats in fully sequenced genomes. Results In order to facilitate a broader range of repeat analyses, the Assisted Automated Assembler of Repeat Families algorithm has been developed. This program, written in PERL and with numerous adjustable parameters, identifies sequence overlaps in small shotgun sequence datasets and walks them out to create long pseudomolecules representing the most abundant repeats in any genome. Testing of this program in maize indicated that it found and assembled all of the major repeats in one or more pseudomolecules, including coverage of the major Long Terminal Repeat retrotransposon families. Both Sanger sequence and 454 datasets were appropriate. Conclusion These results now indicate that hundreds of higher eukaryotic genomes can be efficiently characterized for the nature, abundance and evolution of their major repetitive DNA components.
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Affiliation(s)
- Jeremy D DeBarry
- Department of Genetics, University of Georgia, Athens, GA 30602-7223, USA.
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18
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DeBarry JD, Ganko EW, McCarthy EM, McDonald JF. The Contribution of LTR Retrotransposon Sequences to Gene Evolution in Mus musculus. Mol Biol Evol 2005; 23:479-81. [PMID: 16368779 DOI: 10.1093/molbev/msj076] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Approximately 1.5% of mouse genes (Mus musculus) contain long terminal repeat retrotransposon sequences (LRS). Consistent with earlier findings in Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens, LRS are more likely to be associated with newly evolved genes. Evidence is presented that LRS are often recruited as novel exons or as spliced additions to existing exons. These novel gene configurations may be expressed initially as alternative transcripts providing an opportunity for the evolution of new gene function.
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