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Parreira KS, Scarpelli P, Rezende Lima W, Garcia RS. Contribution of Transcriptome to Elucidate the Biology of Plasmodium spp. Curr Top Med Chem 2022; 22:169-187. [PMID: 35021974 DOI: 10.2174/1568026622666220111140803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 11/22/2022]
Abstract
In the present review, we discuss some of the new technologies that have been applied to elucidate how Plasmodium spp escape from the immune system and subvert the host physiology to orchestrate the regulation of its biological pathways. Our manuscript describes how techniques such as microarray approaches, RNA-Seq and single-cell RNA sequencing have contributed to the discovery of transcripts and changed the concept of gene expression regulation in closely related malaria parasite species. Moreover, the text highlights the contributions of high-throughput RNA sequencing for the current knowledge of malaria parasite biology, physiology, vaccine target and the revelation of new players in parasite signaling.
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Affiliation(s)
| | - Pedro Scarpelli
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo - USP, São Paulo, Brazil
| | - Wânia Rezende Lima
- Departamento de Medicina, Instituto de Biotecnologia-Universidade Federal de Catalão
| | - R S Garcia
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo - USP, São Paulo, Brazil
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2
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Huang F, Jacob CG, Takala-Harrison S, Adams M, Yang HL, Liu H, Xia ZG, Zhou SS, Tang LH, Plowe CV. Genomic Epidemiology of Antimalarial Drug Resistance in Plasmodium falciparum in Southern China. Front Cell Infect Microbiol 2021; 10:610985. [PMID: 33489939 PMCID: PMC7820777 DOI: 10.3389/fcimb.2020.610985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/20/2020] [Indexed: 12/05/2022] Open
Abstract
Emerging artemisinin resistance in Southeast Asia poses a significant risk to malaria control and eradication goals, including China’s plan to eliminate malaria nationwide by 2020. Plasmodium falciparum was endemic in China, especially in Southern China. Parasites from this region have shown decreased susceptibility to artemisinin and delayed parasite clearance after artemisinin treatment. Understanding the genetic basis of artemisinin resistance and identifying specific genetic loci associated with this phenotype is crucial for surveillance and containment of resistance. In this study, parasites were collected from clinical patients from Yunnan province and Hainan island. The parasites were genotyped using a P. falciparum-specific single nucleotide polymorphism (SNP) microarray. The SNP profiles examined included a total of 27 validated and candidate molecular markers of drug resistance. The structure of the parasite population was evaluated by principal component analysis by using the EIGENSOFT program, and ADMIXTURE was used to calculate maximum likelihood estimates for the substructure analysis. Parasites showed a high prevalence of resistance haplotypes of pfdhfr and pfdhps and moderate prevalence of pfcrt. There was no mutation identified on pfmdr1. Candidate SNPs on chromosomes 10, 13, and 14 that were associated with delayed parasite clearance showed a low prevalence of mutants. Parasites from Southern China were clustered and separated from those from Southeast Asia. Parasites from Yunnan province were substructured from parasites from Hainan island. This study provides evidence for a genomic population with drug resistance in Southern China and also illustrates the utility of SNP microarrays for large-scale parasite molecular epidemiology.
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Affiliation(s)
- Fang Huang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Chinese Center for Tropical Diseases Research, Key Laboratory of Parasite and Vector Biology, Ministry of Health, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, China
| | | | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Matthew Adams
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Heng-Lin Yang
- Malaria Department, Yunnan Institute of Parasitic Diseases, Puer, China
| | - Hui Liu
- Malaria Department, Yunnan Institute of Parasitic Diseases, Puer, China
| | - Zhi-Gui Xia
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Chinese Center for Tropical Diseases Research, Key Laboratory of Parasite and Vector Biology, Ministry of Health, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, China
| | - Shui-Sen Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Chinese Center for Tropical Diseases Research, Key Laboratory of Parasite and Vector Biology, Ministry of Health, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, China
| | - Lin-Hua Tang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Chinese Center for Tropical Diseases Research, Key Laboratory of Parasite and Vector Biology, Ministry of Health, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, China
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3
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Srisutham S, Suwannasin K, Mathema VB, Sriprawat K, Smithuis FM, Nosten F, White NJ, Dondorp AM, Imwong M. Utility of Plasmodium falciparum DNA from rapid diagnostic test kits for molecular analysis and whole genome amplification. Malar J 2020; 19:193. [PMID: 32460780 PMCID: PMC7251736 DOI: 10.1186/s12936-020-03259-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/15/2020] [Indexed: 11/10/2022] Open
Abstract
Background Rapid diagnostic tests (RDTs) have become the most common diagnostic tool for detection of Plasmodium falciparum malaria, in particular in remote areas. RDT blood spots provide a source of parasite DNA for molecular analysis. In this study, the utility of RDTs for molecular analysis and the performance of different methods for whole genome amplification were investigated. Methods Positive P. falciparum RDTs were collected from Kayin, Myanmar from August 2014 to January 2016. The RDT samples were stored for 6 months, 9 months, 20 months, 21 months, and 32 months before DNA extraction and subsequent molecular analysis of P. falciparum kelch 13 (pfkelch13) mutations, P. falciparum multidrug resistance 1 (pfmdr1), and P. falciparum plasmepsin 2 (pfplasmepsin2) gene amplification. In addition, performance of four whole genome amplification (WGA) kits were compared, including REPLI-g®, MALBACTM, PicoPLEX®, and GenomePlex®, for which DNA quantity and quality were compared between original DNA and post-WGA products. Results The proportion of successful amplification of the different molecular markers was similar between blood spots analysed from RDTs stored for 6, 9, 20, 21, or 32 months. Successful amplification was dependent on the molecular markers fragment length (p value < 0.05): 18% for a 1245 bp fragment of pfkelch13, 71% for 364 bp of pfkelch13, 81% for 87 bp of pfmdr1, 81% for 108 bp of pfplasmepsin2. Comparison of the four WGA assay kits showed that REPLI-g®, MALBACTM, and PicoPLEX® increased the quantity of DNA 60 to 750-fold, whereas the ratio of parasite DNA amplification over human DNA was most favourable for MALBAC®. Sequencing results of pfkelch13, P. falciparum chloroquine resistance transporter (pfcrt), P. falciparum dihydrofolate reductase (pfdhfr) and six microsatellite markers assessed from the post-WGA product was the same as from the original DNA. Conclusions Blood spots from RDTs are a good source for molecular analysis of P. falciparum, even after storage up to 32 months. WGA of RDT-derived parasite DNA reliably increase DNA quantity with sufficient quality for molecular analysis of resistance markers.
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Affiliation(s)
- Suttipat Srisutham
- Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kanokon Suwannasin
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Vivek Bhakta Mathema
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Frank M Smithuis
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Medical Action Myanmar, Yangon, Myanmar
| | - Francois Nosten
- Shoklo Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mallika Imwong
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. .,Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. .,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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4
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Simam J, Rono M, Ngoi J, Nyonda M, Mok S, Marsh K, Bozdech Z, Mackinnon M. Gene copy number variation in natural populations of Plasmodium falciparum in Eastern Africa. BMC Genomics 2018; 19:372. [PMID: 29783949 PMCID: PMC5963192 DOI: 10.1186/s12864-018-4689-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 04/17/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Gene copy number variants (CNVs), which consist of deletions and amplifications of single or sets of contiguous genes, contribute to the great diversity in the Plasmodium falciparum genome. In vitro studies in the laboratory have revealed their important role in parasite fitness phenotypes such as red cell invasion, transmissibility and cytoadherence. Studies of natural parasite populations indicate that CNVs are also common in the field and thus may facilitate adaptation of the parasite to its local environment. RESULTS In a survey of 183 fresh field isolates from three populations in Eastern Africa with different malaria transmission intensities, we identified 94 CNV loci using microarrays. All CNVs had low population frequencies (minor allele frequency < 5%) but each parasite isolate carried an average of 8 CNVs. Nine CNVs showed high levels of population differentiation (FST > 0.3) and nine exhibited significant clines in population frequency across a gradient in transmission intensity. The clearest example of this was a large deletion on chromosome 9 previously reported only in laboratory-adapted isolates. This deletion was present in 33% of isolates from a population with low and highly seasonal malaria transmission, and in < 9% of isolates from populations with higher transmission. Subsets of CNVs were strongly correlated in their population frequencies, implying co-selection. CONCLUSIONS These results support the hypothesis that CNVs are the target of selection in natural populations of P. falciparum. Their environment-specific patterns observed here imply an important role for them in conferring adaptability to the parasite thus enabling it to persist in its highly diverse ecological environment.
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Affiliation(s)
| | - Martin Rono
- KEMRI-Wellcome Trust Research Program, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Pwani University Bioscience Research Centre, Pwani University, Kilifi, Kenya
| | - Joyce Ngoi
- KEMRI-Wellcome Trust Research Program, Kilifi, Kenya
| | - Mary Nyonda
- Department of Microbiology and Molecular Medicine, Medical Faculty, University of Geneva, Geneva, Switzerland
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University, New York, USA
| | - Kevin Marsh
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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5
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Frith KA, Fogel R, Goldring JPD, Krause RGE, Khati M, Hoppe H, Cromhout ME, Jiwaji M, Limson JL. Towards development of aptamers that specifically bind to lactate dehydrogenase of Plasmodium falciparum through epitopic targeting. Malar J 2018; 17:191. [PMID: 29724225 PMCID: PMC5934816 DOI: 10.1186/s12936-018-2336-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/26/2018] [Indexed: 11/19/2022] Open
Abstract
Background Early detection is crucial for the effective treatment of malaria, particularly in those cases infected with Plasmodium falciparum. There is a need for diagnostic devices with the capacity to distinguish P. falciparum from other strains of malaria. Here, aptamers generated against targeted species-specific epitopes of P. falciparum lactate dehydrogenase (rPfLDH) are described. Results Two classes of aptamers bearing high binding affinity and specificity for recombinant P. falciparum lactate dehydrogenase (rPfLDH) and P. falciparum-specific lactate dehydrogenase epitopic oligopeptide (LDHp) were separately generated. Structurally-relevant moieties with particular consensus sequences (GGTAG and GGCG) were found in aptamers reported here and previously published, confirming their importance in recognition of the target, while novel moieties particular to this work (ATTAT and poly-A stretches) were identified. Aptamers with diagnostically-supportive functions were synthesized, prime examples of which are the aptamers designated as LDHp 1, LDHp 11 and rLDH 4 and rLDH 15 in work presented herein. Of the sampled aptamers raised against the recombinant protein, rLDH 4 showed the highest binding to the target rPfLDH in the ELONA assay, with both rLDH 4 and rLDH 15 indicating an ability to discriminate between rPfLDH and rPvLDH. LDHp 11 was generated against a peptide selected as a unique P. falciparum LDH peptide. The aptamer, LDHp 11, like antibodies against the same peptide, only detected rPfLDH and discriminated between rPfLDH and rPvLDH. This was supported by affinity binding experiments where only aptamers generated against a unique species-specific epitope showed an ability to preferentially bind to rPfLDH relative to rPvLDH rather than those generated against the whole recombinant protein. In addition, rLDH 4 and LDHp 11 demonstrated in situ binding to P. falciparum cells during confocal microscopy. Conclusions The utilization and application of LDHp 11, an aptamer generated against a unique species-specific epitope of P. falciparum LDH indicated the ability to discriminate between recombinant P. falciparum and Plasmodium vivax LDH. This aptamer holds promise as a biorecognition element in malaria diagnostic devices for the detection, and differentiation, of P. falciparum and P. vivax malaria infections. This study paves the way to explore aptamer generation against targeted species-specific epitopes of other Plasmodium species.
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Affiliation(s)
- Kelly-Anne Frith
- Biotechnology Innovation Centre, Rhodes University, P.O. Box 94, Grahamstown, 6140, Eastern Cape, South Africa
| | - Ronen Fogel
- Biotechnology Innovation Centre, Rhodes University, P.O. Box 94, Grahamstown, 6140, Eastern Cape, South Africa
| | - J P Dean Goldring
- Department of Biochemistry, Genetics and Microbiology, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, KwaZulu-Natal, South Africa
| | - Robert G E Krause
- Department of Biochemistry, Genetics and Microbiology, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, KwaZulu-Natal, South Africa
| | - Makobetsa Khati
- Emerging Health Technologies Platform, Biosciences Division, Council for Scientific and Industrial Research, PO Box 395, Pretoria, 0001, Gauteng, South Africa
| | - Heinrich Hoppe
- Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown, 6140, Eastern Cape, South Africa
| | - Mary E Cromhout
- Biotechnology Innovation Centre, Rhodes University, P.O. Box 94, Grahamstown, 6140, Eastern Cape, South Africa
| | - Meesbah Jiwaji
- Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown, 6140, Eastern Cape, South Africa
| | - Janice L Limson
- Biotechnology Innovation Centre, Rhodes University, P.O. Box 94, Grahamstown, 6140, Eastern Cape, South Africa.
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6
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Plasmodium Helical Interspersed Subtelomeric (PHIST) Proteins, at the Center of Host Cell Remodeling. Microbiol Mol Biol Rev 2016; 80:905-27. [PMID: 27582258 DOI: 10.1128/mmbr.00014-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During the asexual cycle, Plasmodium falciparum extensively remodels the human erythrocyte to make it a suitable host cell. A large number of exported proteins facilitate this remodeling process, which causes erythrocytes to become more rigid, cytoadherent, and permeable for nutrients and metabolic products. Among the exported proteins, a family of 89 proteins, called the Plasmodium helical interspersed subtelomeric (PHIST) protein family, has been identified. While also found in other Plasmodium species, the PHIST family is greatly expanded in P. falciparum. Although a decade has passed since their first description, to date, most PHIST proteins remain uncharacterized and are of unknown function and localization within the host cell, and there are few data on their interactions with other host or parasite proteins. However, over the past few years, PHIST proteins have been mentioned in the literature at an increasing rate owing to their presence at various localizations within the infected erythrocyte. Expression of PHIST proteins has been implicated in molecular and cellular processes such as the surface display of PfEMP1, gametocytogenesis, changes in cell rigidity, and also cerebral and pregnancy-associated malaria. Thus, we conclude that PHIST proteins are central to host cell remodeling, but despite their obvious importance in pathology, PHIST proteins seem to be understudied. Here we review current knowledge, shed light on the definition of PHIST proteins, and discuss these proteins with respect to their localization and probable function. We take into consideration interaction studies, microarray analyses, or data from blood samples from naturally infected patients to combine all available information on this protein family.
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7
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Obaldía N, Dow GS, Gerena L, Kyle D, Otero W, Mantel PY, Baro N, Daniels R, Mukherjee A, Childs LM, Buckee C, Duraisingh MT, Volkman SK, Wirth DF, Marti M. Altered drug susceptibility during host adaptation of a Plasmodium falciparum strain in a non-human primate model. Sci Rep 2016; 6:21216. [PMID: 26880111 PMCID: PMC4754742 DOI: 10.1038/srep21216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 01/19/2016] [Indexed: 01/07/2023] Open
Abstract
Infections with Plasmodium falciparum, the most pathogenic of the Plasmodium species affecting man, have been reduced in part due to artemisinin-based combination therapies. However, artemisinin resistant parasites have recently emerged in South-East Asia. Novel intervention strategies are therefore urgently needed to maintain the current momentum for control and elimination of this disease. In the present study we characterize the phenotypic and genetic properties of the multi drug resistant (MDR) P. falciparum Thai C2A parasite strain in the non-human Aotus primate model, and across multiple passages. Aotus infections with C2A failed to clear upon oral artesunate and mefloquine treatment alone or in combination, and ex vivo drug assays demonstrated reduction in drug susceptibility profiles in later Aotus passages. Further analysis revealed mutations in the pfcrt and pfdhfr loci and increased parasite multiplication rate (PMR) across passages, despite elevated pfmdr1 copy number. Altogether our experiments suggest alterations in parasite population structure and increased fitness during Aotus adaptation. We also present data of early treatment failures with an oral artemisinin combination therapy in a pre-artemisinin resistant P. falciparum Thai isolate in this animal model.
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Affiliation(s)
- Nicanor Obaldía
- Department of Immunology and Infectious Diseases, Harvard
- T.H. Chan School of Public Health, Boston, MA, United States.,Center for the Evaluation of Antimalarial Drugs and Vaccines, Tropical Medicine Research/Instituto Conmemorativo Gorgas de Estudios de la Salud, Panamá City, Republic of Panama
| | - Geoffrey S Dow
- Walter Reed Army Institute of Research, Silver Springs, MD, United States
| | - Lucia Gerena
- Walter Reed Army Institute of Research, Silver Springs, MD, United States
| | - Dennis Kyle
- Department of Global Health, University of South Florida, Tampa, FL, United States
| | - William Otero
- Center for the Evaluation of Antimalarial Drugs and Vaccines, Tropical Medicine Research/Instituto Conmemorativo Gorgas de Estudios de la Salud, Panamá City, Republic of Panama
| | - Pierre-Yves Mantel
- Department of Immunology and Infectious Diseases, Harvard
- T.H. Chan School of Public Health, Boston, MA, United States
| | - Nicholas Baro
- Department of Immunology and Infectious Diseases, Harvard
- T.H. Chan School of Public Health, Boston, MA, United States
| | - Rachel Daniels
- Department of Immunology and Infectious Diseases, Harvard
- T.H. Chan School of Public Health, Boston, MA, United States
| | - Angana Mukherjee
- Department of Immunology and Infectious Diseases, Harvard
- T.H. Chan School of Public Health, Boston, MA, United States
| | - Lauren M Childs
- Center for Communicable Disease Dynamics and Harvard
- T.H. Chan School of Public Health, Boston, MA, United States.,Department of Epidemiology, Harvard
- T.H. Chan School of Public Health, Boston, MA, United States
| | - Caroline Buckee
- Center for Communicable Disease Dynamics and Harvard
- T.H. Chan School of Public Health, Boston, MA, United States.,Department of Epidemiology, Harvard
- T.H. Chan School of Public Health, Boston, MA, United States
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard
- T.H. Chan School of Public Health, Boston, MA, United States
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard
- T.H. Chan School of Public Health, Boston, MA, United States.,The Broad Institute of MIT and Harvard, Cambridge, MA, United States.,School of Nursing and Health Sciences, Simmons College, Boston, MA United States
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard
- T.H. Chan School of Public Health, Boston, MA, United States.,The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Matthias Marti
- Department of Immunology and Infectious Diseases, Harvard
- T.H. Chan School of Public Health, Boston, MA, United States
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8
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Cheeseman IH, Miller B, Tan JC, Tan A, Nair S, Nkhoma SC, De Donato M, Rodulfo H, Dondorp A, Branch OH, Mesia LR, Newton P, Mayxay M, Amambua-Ngwa A, Conway DJ, Nosten F, Ferdig MT, Anderson TJC. Population Structure Shapes Copy Number Variation in Malaria Parasites. Mol Biol Evol 2015; 33:603-20. [PMID: 26613787 PMCID: PMC4760083 DOI: 10.1093/molbev/msv282] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.
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Affiliation(s)
- Ian H Cheeseman
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Becky Miller
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - John C Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Asako Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Shalini Nair
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Marcos De Donato
- Lab. Genetica Molecular, IIBCAUDO, Universidad De Oriente, Cumana, Venezuela
| | - Hectorina Rodulfo
- Lab. Genetica Molecular, IIBCAUDO, Universidad De Oriente, Cumana, Venezuela
| | - Arjen Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Oralee H Branch
- Division of Parasitology, Department of Microbiology, New York University School of Medicine
| | - Lastenia Ruiz Mesia
- Laboratorio De Investigaciones De Productos Naturales Y Antiparasitarios, Universidad Nacional De La Amazonia Peruana, Iquitos, Peru
| | - Paul Newton
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao PDR
| | | | - David J Conway
- Medical Research Council Unit, Fajara, Banjul, The Gambia Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - François Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Michael T Ferdig
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Tim J C Anderson
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
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9
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Whole-genome amplification: a useful approach to characterize new genes in unculturable protozoan parasites such as Bonamia exitiosa. Parasitology 2015; 142:1523-34. [PMID: 26282916 DOI: 10.1017/s0031182015000967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Bonamia exitiosa is an intracellular parasite (Haplosporidia) that has been associated with mass mortalities in oyster populations in the Southern hemisphere. This parasite was recently detected in the Northern hemisphere including Europe. Some representatives of the Bonamia genus have not been well categorized yet due to the lack of genomic information. In the present work, we have applied Whole-Genome Amplification (WGA) technique in order to characterize the actin gene in the unculturable protozoan B. exitiosa. This is the first protein coding gene described in this species. Molecular analysis revealed that B. exitiosa actin is more similar to Bonamia ostreae actin gene-1. Actin phylogeny placed the Bonamia sp. infected oysters in the same clade where the herein described B. exitiosa actin resolved, offering novel information about the classification of the genus. Our results showed that WGA methodology is a promising and valuable technique to be applied to unculturable protozoans whose genomic material is limited.
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10
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Cai H, Zhou Z, Gu J, Wang Y. Comparative Genomics and Systems Biology of Malaria Parasites Plasmodium.. Curr Bioinform 2012; 7. [PMID: 24298232 DOI: 10.2174/157489312803900965] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Malaria is a serious infectious disease that causes over one million deaths yearly. It is caused by a group of protozoan parasites in the genus Plasmodium. No effective vaccine is currently available and the elevated levels of resistance to drugs in use underscore the pressing need for novel antimalarial targets. In this review, we survey omics centered developments in Plasmodium biology, which have set the stage for a quantum leap in our understanding of the fundamental processes of the parasite life cycle and mechanisms of drug resistance and immune evasion.
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Affiliation(s)
- Hong Cai
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
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11
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Gobert GN, You H, Jones MK, McInnes R, McManus DP. Differences in genomic architecture between two distinct geographical strains of the blood fluke Schistosoma japonicum reveal potential phenotype basis. Mol Cell Probes 2012; 27:19-27. [PMID: 22940009 DOI: 10.1016/j.mcp.2012.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 08/10/2012] [Accepted: 08/11/2012] [Indexed: 10/28/2022]
Abstract
The Chinese (SjC) and Philippine (SjP) strains of the blood fluke Schistosoma japonicum have been shown to present clearly different phenotypes in fecundity, pathology, drug sensitivity and immunology. We used microarray based comparative genomic hybridisation (aCGH) to investigate structural differences in the genomes of the two strains and identified seven distinct regions of the S. japonicum genome that present differential aCGH representing either deletion or duplication regions in SjP. Within these regions, genes predicted to be associated with the recognised phenotypic differences were identified and that may provide new insights into the biology and evolution of the two strains, with implications for the epidemiology and control of schistosomiasis japonica in China and the Philippines.
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Affiliation(s)
- Geoffrey N Gobert
- Queensland Institute of Medical Research-QIMR, 300 Herston Road, Herston, Qld 4006, Australia.
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12
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Mwai L, Diriye A, Masseno V, Muriithi S, Feltwell T, Musyoki J, Lemieux J, Feller A, Mair GR, Marsh K, Newbold C, Nzila A, Carret CK. Genome wide adaptations of Plasmodium falciparum in response to lumefantrine selective drug pressure. PLoS One 2012; 7:e31623. [PMID: 22384044 PMCID: PMC3288012 DOI: 10.1371/journal.pone.0031623] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 01/16/2012] [Indexed: 01/08/2023] Open
Abstract
The combination therapy of the Artemisinin-derivative Artemether (ART) with Lumefantrine (LM) (Coartem®) is an important malaria treatment regimen in many endemic countries. Resistance to Artemisinin has already been reported, and it is feared that LM resistance (LMR) could also evolve quickly. Therefore molecular markers which can be used to track Coartem® efficacy are urgently needed. Often, stable resistance arises from initial, unstable phenotypes that can be identified in vitro. Here we have used the Plasmodium falciparum multidrug resistant reference strain V1S to induce LMR in vitro by culturing the parasite under continuous drug pressure for 16 months. The initial IC50 (inhibitory concentration that kills 50% of the parasite population) was 24 nM. The resulting resistant strain V1SLM, obtained after culture for an estimated 166 cycles under LM pressure, grew steadily in 378 nM of LM, corresponding to 15 times the IC50 of the parental strain. However, after two weeks of culturing V1SLM in drug-free medium, the IC50 returned to that of the initial, parental strain V1S. This transient drug tolerance was associated with major changes in gene expression profiles: using the PFSANGER Affymetrix custom array, we identified 184 differentially expressed genes in V1SLM. Among those are 18 known and putative transporters including the multidrug resistance gene 1 (pfmdr1), the multidrug resistance associated protein and the V-type H+ pumping pyrophosphatase 2 (pfvp2) as well as genes associated with fatty acid metabolism. In addition we detected a clear selective advantage provided by two genomic loci in parasites grown under LM drug pressure, suggesting that all, or some of those genes contribute to development of LM tolerance – they may prove useful as molecular markers to monitor P. falciparum LM susceptibility.
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Affiliation(s)
- Leah Mwai
- Kenya Medical Research Institute, Welcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Abdi Diriye
- Kenya Medical Research Institute, Welcome Trust Research Programme, Kilifi, Kenya
| | - Victor Masseno
- Kenya Medical Research Institute, Welcome Trust Research Programme, Kilifi, Kenya
| | - Steven Muriithi
- Kenya Medical Research Institute, Welcome Trust Research Programme, Kilifi, Kenya
| | - Theresa Feltwell
- Pathogen Microarrays group, The Welcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Jennifer Musyoki
- Kenya Medical Research Institute, Welcome Trust Research Programme, Kilifi, Kenya
| | - Jacob Lemieux
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Avi Feller
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Gunnar R. Mair
- Molecular Parasitology Unit, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Kevin Marsh
- Kenya Medical Research Institute, Welcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Chris Newbold
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Alexis Nzila
- Kenya Medical Research Institute, Welcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Céline K. Carret
- Molecular Parasitology Unit, Instituto de Medicina Molecular, Lisboa, Portugal
- * E-mail:
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Samarakoon U, Gonzales JM, Patel JJ, Tan A, Checkley L, Ferdig MT. The landscape of inherited and de novo copy number variants in a Plasmodium falciparum genetic cross. BMC Genomics 2011; 12:457. [PMID: 21936954 PMCID: PMC3191341 DOI: 10.1186/1471-2164-12-457] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 09/22/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number is a major source of genome variation with important evolutionary implications. Consequently, it is essential to determine copy number variant (CNV) behavior, distributions and frequencies across genomes to understand their origins in both evolutionary and generational time frames. We use comparative genomic hybridization (CGH) microarray and the resolution provided by a segregating population of cloned progeny lines of the malaria parasite, Plasmodium falciparum, to identify and analyze the inheritance of 170 genome-wide CNVs. RESULTS We describe CNVs in progeny clones derived from both Mendelian (i.e. inherited) and non-Mendelian mechanisms. Forty-five CNVs were present in the parent lines and segregated in the progeny population. Furthermore, extensive variation that did not conform to strict Mendelian inheritance patterns was observed. 124 CNVs were called in one or more progeny but in neither parent: we observed CNVs in more than one progeny clone that were not identified in either parent, located more frequently in the telomeric-subtelomeric regions of chromosomes and singleton de novo CNVs distributed evenly throughout the genome. Linkage analysis of CNVs revealed dynamic copy number fluctuations and suggested mechanisms that could have generated them. Five of 12 previously identified expression quantitative trait loci (eQTL) hotspots coincide with CNVs, demonstrating the potential for broad influence of CNV on the transcriptional program and phenotypic variation. CONCLUSIONS CNVs are a significant source of segregating and de novo genome variation involving hundreds of genes. Examination of progeny genome segments provides a framework to assess the extent and possible origins of CNVs. This segregating genetic system reveals the breadth, distribution and dynamics of CNVs in a surprisingly plastic parasite genome, providing a new perspective on the sources of diversity in parasite populations.
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Affiliation(s)
- Upeka Samarakoon
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
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14
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Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum. PLoS Genet 2011; 7:e1001383. [PMID: 21533027 PMCID: PMC3080868 DOI: 10.1371/journal.pgen.1001383] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 03/25/2011] [Indexed: 11/25/2022] Open
Abstract
The Plasmodium falciparum parasite's ability to adapt to
environmental pressures, such as the human immune system and antimalarial drugs,
makes malaria an enduring burden to public health. Understanding the genetic
basis of these adaptations is critical to intervening successfully against
malaria. To that end, we created a high-density genotyping array that assays
over 17,000 single nucleotide polymorphisms (∼1 SNP/kb), and applied it to
57 culture-adapted parasites from three continents. We characterized genome-wide
genetic diversity within and between populations and identified numerous loci
with signals of natural selection, suggesting their role in recent adaptation.
In addition, we performed a genome-wide association study (GWAS), searching for
loci correlated with resistance to thirteen antimalarials; we detected both
known and novel resistance loci, including a new halofantrine resistance locus,
PF10_0355. Through functional testing we demonstrated that
PF10_0355 overexpression decreases sensitivity to
halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated
antimalarials, and that increased gene copy number mediates resistance. Our GWAS
and follow-on functional validation demonstrate the potential of genome-wide
studies to elucidate functionally important loci in the malaria parasite
genome. Malaria infection with the human pathogen Plasmodium falciparum
results in almost a million deaths each year, mostly in African children.
Efforts to eliminate malaria are underway, but the parasite is adept at eluding
both the human immune response and antimalarial treatments. Thus, it is
important to understand how the parasite becomes resistant to drugs and to
develop strategies to overcome resistance mechanisms. Toward this end, we used
population genetic strategies to identify genetic loci that contribute to
parasite adaptation and to identify candidate genes involved in drug resistance.
We examined over 17,000 genetic variants across the parasite genome in over 50
strains in which we also measured responses to many known antimalarial
compounds. We found a number of genetic loci showing signs of recent natural
selection and a number of loci potentially involved in modulating the
parasite's response to drugs. We further demonstrated that one of the novel
candidate genes (PF10_0355) modulates resistance to the
antimalarial compounds halofantrine, mefloquine, and lumefantrine. Overall, this
study confirms that we can use genome-wide approaches to identify clinically
relevant genes and demonstrates through functional testing that at least one of
these candidate genes is indeed involved in antimalarial drug resistance.
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15
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Tan JC, Miller BA, Tan A, Patel JJ, Cheeseman IH, Anderson TJC, Manske M, Maslen G, Kwiatkowski DP, Ferdig MT. An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations. Genome Biol 2011; 12:R35. [PMID: 21477297 PMCID: PMC3218861 DOI: 10.1186/gb-2011-12-4-r35] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 03/04/2011] [Accepted: 04/08/2011] [Indexed: 11/13/2022] Open
Abstract
We present an optimized probe design for copy number variation (CNV) and SNP genotyping in the Plasmodium falciparum genome. We demonstrate that variable length and isothermal probes are superior to static length probes. We show that sample preparation and hybridization conditions mitigate the effects of host DNA contamination in field samples. The microarray and workflow presented can be used to identify CNVs and SNPs with 95% accuracy in a single hybridization, in field samples containing up to 92% human DNA contamination.
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Affiliation(s)
- John C Tan
- The Eck Institute for Global Health, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA
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16
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Tan JC, Tan A, Checkley L, Honsa CM, Ferdig MT. Variable numbers of tandem repeats in Plasmodium falciparum genes. J Mol Evol 2010; 71:268-78. [PMID: 20730584 DOI: 10.1007/s00239-010-9381-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 08/09/2010] [Indexed: 11/29/2022]
Abstract
Genome variation studies in Plasmodium falciparum have focused on SNPs and, more recently, large-scale copy number polymorphisms and ectopic rearrangements. Here, we examine another source of variation: variable number tandem repeats (VNTRs). Interspersed low complexity features, including the well-studied P. falciparum microsatellite sequences, are commonly classified as VNTRs; however, this study is focused on longer coding VNTR polymorphisms, a small class of copy number variations. Selection against frameshift mutation is a main constraint on tandem repeats (TRs) in coding regions, while limited propagation of TRs longer than 975 nt total length is a minor restriction in coding regions. Comparative analysis of three P. falciparum genomes reveals that more than 9% of all P. falciparum ORFs harbor VNTRs, much more than has been reported for any other species. Moreover, genotyping of VNTR loci in a drug-selected line, progeny of a genetic cross, and 334 field isolates demonstrates broad variability in these sequences. Functional enrichment analysis of ORFs harboring VNTRs identifies stress and DNA damage responses along with chromatin modification activities, suggesting an influence on genome mutability and functional variation. Analysis of the repeat units and their flanking regions in both P. falciparum and Plasmodium reichenowi sequences implicates a replication slippage mechanism in the generation of TRs from an initially unrepeated sequence. VNTRs can contribute to rapid adaptation by localized sequence duplication. They also can confound SNP-typing microarrays or mapping short-sequence reads and therefore must be accounted for in such analyses.
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Affiliation(s)
- John C Tan
- The Eck Institute for Global Health, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
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17
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Hwang SY, Kim SH, Kho WG. Genetic characteristics of polymorphic antigenic markers among Korean isolates of Plasmodium vivax. THE KOREAN JOURNAL OF PARASITOLOGY 2010; 47 Suppl:S51-8. [PMID: 19885335 DOI: 10.3347/kjp.2009.47.s.s51] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 09/28/2009] [Accepted: 09/28/2009] [Indexed: 11/23/2022]
Abstract
Plasmodium vivax, a protozoan malaria parasite of humans, represents a major public health concern in the Republic of Korea (= South Korea). However, little is known about the genetic properties and population structures of the P. vivax isolates circulating in South Korea. This article reviews known polymorphic genetic markers in South Korean isolates of P. vivax and briefly summarizes the current issues surrounding the gene and population structures of this parasite. The critical genetic characteristics of major antigens of the parasite, such as circumsporozoite protein (CSP), merozoite surface protein 1 (MSP-1) and MSP-3, Duffy binding protein (DBP), apical membrane antigen 1 (AMA-1), and GAM-1, are also discussed.
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Affiliation(s)
- Seung-Young Hwang
- Department of Parasitology, Inje University College of Medicine, Busan 614-735, Korea
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18
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Mackinnon MJ, Li J, Mok S, Kortok MM, Marsh K, Preiser PR, Bozdech Z. Comparative transcriptional and genomic analysis of Plasmodium falciparum field isolates. PLoS Pathog 2009; 5:e1000644. [PMID: 19898609 PMCID: PMC2764095 DOI: 10.1371/journal.ppat.1000644] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 10/05/2009] [Indexed: 11/18/2022] Open
Abstract
Mechanisms for differential regulation of gene expression may underlie much of the phenotypic variation and adaptability of malaria parasites. Here we describe transcriptional variation among culture-adapted field isolates of Plasmodium falciparum, the species responsible for most malarial disease. It was found that genes coding for parasite protein export into the red cell cytosol and onto its surface, and genes coding for sexual stage proteins involved in parasite transmission are up-regulated in field isolates compared with long-term laboratory isolates. Much of this variability was associated with the loss of small or large chromosomal segments, or other forms of gene copy number variation that are prevalent in the P. falciparum genome (copy number variants, CNVs). Expression levels of genes inside these segments were correlated to that of genes outside and adjacent to the segment boundaries, and this association declined with distance from the CNV boundary. This observation could not be explained by copy number variation in these adjacent genes. This suggests a local-acting regulatory role for CNVs in transcription of neighboring genes and helps explain the chromosomal clustering that we observed here. Transcriptional co-regulation of physical clusters of adaptive genes may provide a way for the parasite to readily adapt to its highly heterogeneous and strongly selective environment.
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19
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Cheeseman IH, Gomez-Escobar N, Carret CK, Ivens A, Stewart LB, Tetteh KKA, Conway DJ. Gene copy number variation throughout the Plasmodium falciparum genome. BMC Genomics 2009; 10:353. [PMID: 19653891 PMCID: PMC2732925 DOI: 10.1186/1471-2164-10-353] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Accepted: 08/04/2009] [Indexed: 11/17/2022] Open
Abstract
Background Gene copy number variation (CNV) is responsible for several important phenotypes of the malaria parasite Plasmodium falciparum, including drug resistance, loss of infected erythrocyte cytoadherence and alteration of receptor usage for erythrocyte invasion. Despite the known effects of CNV, little is known about its extent throughout the genome. Results We performed a whole-genome survey of CNV genes in P. falciparum using comparative genome hybridisation of a diverse set of 16 laboratory culture-adapted isolates to a custom designed high density Affymetrix GeneChip array. Overall, 186 genes showed hybridisation signals consistent with deletion or amplification in one or more isolate. There is a strong association of CNV with gene length, genomic location, and low orthology to genes in other Plasmodium species. Sub-telomeric regions of all chromosomes are strongly associated with CNV genes independent from members of previously described multigene families. However, ~40% of CNV genes were located in more central regions of the chromosomes. Among the previously undescribed CNV genes, several that are of potential phenotypic relevance are identified. Conclusion CNV represents a major form of genetic variation within the P. falciparum genome; the distribution of gene features indicates the involvement of highly non-random mutational and selective processes. Additional studies should be directed at examining CNV in natural parasite populations to extend conclusions to clinical settings.
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Affiliation(s)
- Ian H Cheeseman
- Department of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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20
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Anderson TJC, Patel J, Ferdig MT. Gene copy number and malaria biology. Trends Parasitol 2009; 25:336-43. [PMID: 19559648 DOI: 10.1016/j.pt.2009.04.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 03/26/2009] [Accepted: 04/03/2009] [Indexed: 12/16/2022]
Abstract
Alteration in gene copy number provides a simple way to change expression levels and alter phenotype. This was fully appreciated by bacteriologists more than 25 years ago, but the extent and implications of copy number polymorphism (CNP) have only recently become apparent in other organisms. New methods demonstrate the ubiquity of CNPs in eukaryotes and their medical importance in humans. CNP is also widespread in the Plasmodium falciparum genome and has an important and underappreciated role in determining phenotype. In this review, we summarize the distribution of CNP, its evolutionary dynamics within populations, its functional importance and its mode of evolution.
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Affiliation(s)
- Tim J C Anderson
- Southwest Foundation for Biomedical Research, San Antonio, TX 78245, USA.
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21
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Duffy MF, Byrne TJ, Carret C, Ivens A, Brown GV. Ectopic recombination of a malaria var gene during mitosis associated with an altered var switch rate. J Mol Biol 2009; 389:453-69. [PMID: 19389407 PMCID: PMC3898907 DOI: 10.1016/j.jmb.2009.04.032] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 04/14/2009] [Accepted: 04/16/2009] [Indexed: 01/27/2023]
Abstract
The Plasmodium falciparum var multigene family encodes P. falciparum erythrocyte membrane protein 1, which is responsible for the pathogenic traits of antigenic variation and adhesion of infected erythrocytes to host receptors during malaria infection. Clonal antigenic variation of P. falciparum erythrocyte membrane protein 1 is controlled by the switching between exclusively transcribed var genes. The tremendous diversity of the var gene repertoire both within and between parasite strains is critical for the parasite's strategy of immune evasion. We show that ectopic recombination between var genes occurs during mitosis, providing P. falciparum with opportunities to diversify its var repertoire, even during the course of a single infection. We show that the regulation of the recombined var gene has been disrupted, resulting in its persistent activation although the regulation of most other var genes is unaffected. The var promoter and intron of the recombined var gene are not responsible for its atypically persistent activity, and we conclude that altered subtelomeric cis sequence is the most likely cause of the persistent activity of the recombined var gene.
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Affiliation(s)
- Michael F Duffy
- Department of Medicine at RMH, University of Melbourne, Parkville 3050, Australia.
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22
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Optimizing comparative genomic hybridization probes for genotyping and SNP detection in Plasmodium falciparum. Genomics 2009; 93:543-50. [PMID: 19285129 DOI: 10.1016/j.ygeno.2009.02.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 01/16/2009] [Accepted: 02/26/2009] [Indexed: 02/03/2023]
Abstract
Microarray-based comparative genomic hybridizations (CGH) interrogate genomic DNA to identify structural differences such as amplifications and deletions that are easily detected as large signal aberrations. Subtle signal deviations caused by single nucleotide polymorphisms (SNPs) can also be detected but is challenged by a high AT content (81%) in P. falciparum. We compared genome-wide CGH signal to sequence polymorphisms between parasite strains 3D7, HB3, and Dd2 using NimbleGen microarrays. From 23,191 SNPs (excluding var/rif/stevor genes), our CGH probe set detected SNPs with >99.9% specificity but low (<10%) sensitivity. Probe length, melting temperature, GC content, SNP location in the probe, mutation type, and hairpin structures affected SNP sensitivity. Previously unrecognized variable number tandem repeats (VNTRs) also were detected by this method. These findings will guide the redesign of a probe set to optimize an openly available CGH microarray platform for high-resolution genotyping suitable for population genomics studies.
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23
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Dharia NV, Sidhu ABS, Cassera MB, Westenberger SJ, Bopp SE, Eastman RT, Plouffe D, Batalov S, Park DJ, Volkman SK, Wirth DF, Zhou Y, Fidock DA, Winzeler EA. Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum. Genome Biol 2009; 10:R21. [PMID: 19216790 PMCID: PMC2688282 DOI: 10.1186/gb-2009-10-2-r21] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2008] [Revised: 01/05/2009] [Accepted: 02/13/2009] [Indexed: 11/29/2022] Open
Abstract
Using tiling microarrays, a mechanism by which Plasmodium falciparum parasites acquire resistance to the antimalarial fosmidomycin has been elucidated Background The identification of genetic changes that confer drug resistance or other phenotypic changes in pathogens can help optimize treatment strategies, support the development of new therapeutic agents, and provide information about the likely function of genes. Elucidating mechanisms of phenotypic drug resistance can also assist in identifying the mode of action of uncharacterized but potent antimalarial compounds identified in high-throughput chemical screening campaigns against Plasmodium falciparum. Results Here we show that tiling microarrays can detect de novo a large proportion of the genetic changes that differentiate one genome from another. We show that we detect most single nucleotide polymorphisms or small insertion deletion events and all known copy number variations that distinguish three laboratory isolates using readily accessible methods. We used the approach to discover mutations that occur during the selection process after transfection. We also elucidated a mechanism by which parasites acquire resistance to the antimalarial fosmidomycin, which targets the parasite isoprenoid synthesis pathway. Our microarray-based approach allowed us to attribute in vitro derived fosmidomycin resistance to a copy number variation event in the pfdxr gene, which enables the parasite to overcome fosmidomycin-mediated inhibition of isoprenoid biosynthesis. Conclusions We show that newly emerged single nucleotide polymorphisms can readily be detected and that malaria parasites can rapidly acquire gene amplifications in response to in vitro drug pressure. The ability to define comprehensively genetic variability in P. falciparum with a single overnight hybridization creates new opportunities to study parasite evolution and improve the treatment and control of malaria.
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Affiliation(s)
- Neekesh V Dharia
- Department of Cell Biology, ICND 202, The Scripps Research Institute, North Torrey Pines Road, La Jolla, CA 92037, USA
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Wang Y, Nair S, Nosten F, Anderson TJC. Multiple displacement amplification for malaria parasite DNA. J Parasitol 2009; 95:253-5. [PMID: 18601578 PMCID: PMC2759105 DOI: 10.1645/ge-1706.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Accepted: 07/05/2008] [Indexed: 11/10/2022] Open
Abstract
Multiple displacement amplification (MDA) using Phi29 has proved to be an efficient, high-fidelity method for whole genome amplification in many organisms. This project was designed to evaluate this approach for use with the malaria parasite Plasmodium falciparum. In particular, we were concerned that the AT richness and presence of contaminating human DNA could limit efficiency of MDA in this system. We amplified 60 DNA samples using phi29 and scored 14 microsatellites, 9 single-nucleotide polymorphisms (SNPs), and gene copy number at GTP-cyclohydrolase I both before and after MDA. We observed 100% concordance in 829 microsatellite genotypes and in 499 SNP genotypes. Furthermore, copy number estimates for the GTP-cyclohydrolase I gene were correlated (r(2) = 0.67) in pre- and postamplification samples. These data confirm that MDA permits scoring of a range of different types of polymorphisms in P. falciparum malaria and can be used to extend the life of valuable DNA stocks.
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Affiliation(s)
| | | | - F. Nosten
- Shoklo Malaria Research Unit (SMRU), Mae Sot, Tak, Thailand
- Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Vaccinology, Churchill Hospital, Oxford, U.K
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25
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Kim JH, Lee WM, Ryoo NH, Ha JS, Jeon DS, Kim JR, Kim JS, Lee SY. A Case of Partial Trisomy 15q25.3-qter. Ann Lab Med 2009; 29:66-70. [DOI: 10.3343/kjlm.2009.29.1.66] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Ji-Hae Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Won-Mok Lee
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Nam-Hee Ryoo
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Jung-Sook Ha
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Dong-Seok Jeon
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Jae-Ryong Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Joon-Sik Kim
- Department of Pediatrics, Keimyung University School of Medicine, Daegu, Korea
| | - So-Young Lee
- Department of Rehabilitation Medicine, Keimyung University School of Medicine, Daegu, Korea
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Cunningham D, Fonager J, Jarra W, Carret C, Preiser P, Langhorne J. Rapid changes in transcription profiles of the Plasmodium yoelii yir multigene family in clonal populations: lack of epigenetic memory? PLoS One 2009; 4:e4285. [PMID: 19173007 PMCID: PMC2628738 DOI: 10.1371/journal.pone.0004285] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Accepted: 12/04/2008] [Indexed: 11/18/2022] Open
Abstract
The pir multigene family, found in the genomes of Plasmodium vivax, P. knowlesi and the rodent malaria species, encode variant antigens that could be targets of the immune response. Individual parasites of the rodent malaria Plasmodium yoelii, selected by micromanipulation, transcribe only 1 to 3 different pir (yir) suggesting tight transcriptional control at the level of individual cells. Using microarray and quantitative RT-PCR, we show that despite this very restricted transcription in a single cell, many yir genes are transcribed throughout the intra-erythrocytic asexual cycle. The timing and level of transcription differs between genes, with some being more highly transcribed in ring and trophozoite stages, whereas others are more highly transcribed in schizonts. Infection of immunodeficient mice with single infected erythrocytes results in populations of parasites each with transcriptional profiles different from that of the parent parasite population and from each other. This drift away from the original 'set' of transcribed genes does not appear to follow a preset pattern and "epigenetic memory" of the yir transcribed in the parent parasite can be rapidly lost. Thus, regulation of pir gene transcription may be different from that of the well-characterised multigene family, var, of Plasmodium falciparum.
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Affiliation(s)
- Deirdre Cunningham
- Division of Parasitology, National Institute for Medical Research, London, United Kingdom
| | - Jannik Fonager
- Division of Parasitology, National Institute for Medical Research, London, United Kingdom
| | - William Jarra
- Division of Parasitology, National Institute for Medical Research, London, United Kingdom
| | - Celine Carret
- Pathogen Microarrays Group, The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Peter Preiser
- Bioscience Research Centre, Nanyang Technical University, Singapore
| | - Jean Langhorne
- Division of Parasitology, National Institute for Medical Research, London, United Kingdom
- * E-mail:
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Gonzales JM, Patel JJ, Ponmee N, Jiang L, Tan A, Maher SP, Wuchty S, Rathod PK, Ferdig MT. Regulatory hotspots in the malaria parasite genome dictate transcriptional variation. PLoS Biol 2008; 6:e238. [PMID: 18828674 PMCID: PMC2553844 DOI: 10.1371/journal.pbio.0060238] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 08/18/2008] [Indexed: 11/19/2022] Open
Abstract
The determinants of transcriptional regulation in malaria parasites remain elusive. The presence of a well-characterized gene expression cascade shared by different Plasmodium falciparum strains could imply that transcriptional regulation and its natural variation do not contribute significantly to the evolution of parasite drug resistance. To clarify the role of transcriptional variation as a source of stain-specific diversity in the most deadly malaria species and to find genetic loci that dictate variations in gene expression, we examined genome-wide expression level polymorphisms (ELPs) in a genetic cross between phenotypically distinct parasite clones. Significant variation in gene expression is observed through direct co-hybridizations of RNA from different P. falciparum clones. Nearly 18% of genes were regulated by a significant expression quantitative trait locus. The genetic determinants of most of these ELPs resided in hotspots that are physically distant from their targets. The most prominent regulatory locus, influencing 269 transcripts, coincided with a Chromosome 5 amplification event carrying the drug resistance gene, pfmdr1, and 13 other genes. Drug selection pressure in the Dd2 parental clone lineage led not only to a copy number change in the pfmdr1 gene but also to an increased copy number of putative neighboring regulatory factors that, in turn, broadly influence the transcriptional network. Previously unrecognized transcriptional variation, controlled by polymorphic regulatory genes and possibly master regulators within large copy number variants, contributes to sweeping phenotypic evolution in drug-resistant malaria parasites. Development of the malaria parasite, Plasmodium falciparum, in the blood is driven by a number of different genes expressed at different times and at different levels. Exactly what influences such transcriptional changes remains elusive, particularly in regard to important phenotypes like drug resistance. Using cDNA microarray hybridizations from the progeny of a Plasmodium genetic cross, we mapped gene expression quantitative trait loci (eQTLs) in an experimental population of malaria parasites. Each gene's transcript level was used as a segregating phenotype to identify regions of the Plasmodium genome dictating transcriptional variation. Several regulatory hotspots controlled the majority of gene expression variation, mostly via trans-acting mechanisms. One, influencing the largest number of transcripts, coincided with an amplified region of the genome traditionally associated with multiple drug resistance (MDR). Overall, integration of two functional genomic tools (gene mapping and transcript quantitation) has revealed a system-wide rewiring of the parasite transcription network: pleiotropic phenotypic variation, driven by drug selection on genome structure that may be attributed in large part to adaptive copy number polymorphisms in the parasite. These structural variants alter the expression of genes within the amplicon as well as many genes scattered across the Plasmodium genome. Heritable levels of transcriptional variation, predominantly regulated by genomic copy number variants via trans mechanisms, are surprisingly abundant in drug-resistant malaria parasites.
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Affiliation(s)
- Joseph M Gonzales
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Jigar J Patel
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Napawan Ponmee
- Department of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Lei Jiang
- Department of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Asako Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Steven P Maher
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Stefan Wuchty
- Northwestern Institute of Complexity, Northwestern University, Evanston, Illinois, United States of America
| | - Pradipsinh K Rathod
- Department of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Michael T Ferdig
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- * To whom correspondence should be addressed. E-mail:
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Abstract
For many pathogens the availability of genome sequence, permitting genome-dependent methods of research, can partially substitute for powerful forward genetic methods (genome-independent) that have advanced model organism research for decades. In 2002 the genome sequence of Plasmodium falciparum, the parasite causing the most severe type of human malaria, was completed, eliminating many of the barriers to performing state-of-the-art molecular biological research on malaria parasites. Although new, licensed therapies may not yet have resulted from genome-dependent experiments, they have produced a wealth of new observations about the basic biology of malaria parasites, and it is likely that these will eventually lead to new therapeutic approaches. This review will focus on the basic research discoveries that have depended, in part, on the availability of the Plasmodium genome sequences.
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Affiliation(s)
- Elizabeth Ann Winzeler
- Genomics Institute of the Novartis Research Foundation, San Diego, California and The Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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Hayton K, Su XZ. Drug resistance and genetic mapping in Plasmodium falciparum. Curr Genet 2008; 54:223-39. [PMID: 18802698 DOI: 10.1007/s00294-008-0214-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2008] [Revised: 08/27/2008] [Accepted: 08/28/2008] [Indexed: 11/30/2022]
Abstract
Drug resistance in malaria parasites is a serious public health burden, and resistance to most of the antimalarial drugs currently in use has been reported. A better understanding of the molecular mechanisms of drug resistance is urgently needed to slow or circumvent the spread of resistance, to allow local treatments to be deployed more effectively to prolong the life span of the current drugs, and to develop new drugs. Although mutations in genes determining resistance to drugs such as chloroquine and the antifolates have been identified, we still do not have a full understanding of the resistance mechanisms, and genes that contribute to resistance to many other drugs remain to be discovered. Genetic mapping is a powerful tool for the identification of mutations conferring drug resistance in malaria parasites because most drug-resistant phenotypes were selected within the past 60 years. High-throughput methods for genotyping large numbers of single nucleotide polymorphisms (SNPs) and microsatellites (MSs) are now available or are being developed, and genome-wide association studies for malaria traits will soon become a reality. Here we discuss strategies and issues related to mapping genes contributing to drug resistance in the human malaria parasite Plasmodium falciparum.
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Affiliation(s)
- Karen Hayton
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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Highly sensitive amperometric immunosensor for detection of Plasmodium falciparum histidine-rich protein 2 in serum of humans with malaria: comparison with a commercial kit. J Clin Microbiol 2008; 46:3759-65. [PMID: 18799699 DOI: 10.1128/jcm.01022-08] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A disposable amperometric immunosensor was developed for the detection of Plasmodium falciparum histidine-rich protein 2 (PfHRP-2) in the sera of humans with P. falciparum malaria. For this purpose, disposable screen-printed electrodes (SPEs) were modified with multiwall carbon nanotubes (MWCNTs) and Au nanoparticles. The electrodes were characterized by cyclic voltammetry, scanning electron microscopy, and Raman spectroscopy. In order to study the immunosensing performances of modified electrodes, a rabbit anti-PfHRP-2 antibody (as the capturing antibody) was first immobilized on an electrode. Further, the electrode was exposed to a mouse anti-PfHRP-2 antibody from a serum sample (as the revealing antibody), followed by a rabbit anti-mouse immunoglobulin G-alkaline phosphatase conjugate. The immunosensing experiments were performed on bare SPEs, MWCNT-modified SPEs, and Au nanoparticle- and MWCNT-modified SPEs (Nano-Au/MWCNT/SPEs) for the amperometric detection of PfHRP-2 in a solution of 0.1 M diethanolamine buffer, pH 9.8, by applying a potential of 450 mV at the working electrode. Nano-Au/MWCNT/SPEs yielded the highest-level immunosensing performance among the electrodes, with a detection limit of 8 ng/ml. The analytical results of immunosensing experiments with human serum samples were compared with the results of a commercial Paracheck Pf test, as well as the results of microscopy. The specificities, sensitivities, and positive and negative predictive values of the Paracheck Pf and amperometric immunosensors were calculated by taking the microscopy results as the "gold standard." The Paracheck Pf kit exhibited a sensitivity of 79% (detecting 34 of 43 positive samples; 95% confidence interval [CI], 75 to 86%) and a specificity of 81% (correctly identifying 57 of 70 negative samples; 95% CI, 76 to 92%), whereas the developed amperometric immunosensor showed a sensitivity of 96% (detecting 41 of 43 positive samples; 95% CI, 93 to 98%) and a specificity of 94% (correctly identifying 66 of 70 negative samples; 95% CI, 92 to 99%). The developed method is more sensitive and specific than the Paracheck Pf kit.
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Jiang H, Yi M, Mu J, Zhang L, Ivens A, Klimczak LJ, Huyen Y, Stephens RM, Su XZ. Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray. BMC Genomics 2008; 9:398. [PMID: 18724869 PMCID: PMC2543026 DOI: 10.1186/1471-2164-9-398] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 08/25/2008] [Indexed: 12/21/2022] Open
Abstract
Background Genetic mapping is a powerful method to identify mutations that cause drug resistance and other phenotypic changes in the human malaria parasite Plasmodium falciparum. For efficient mapping of a target gene, it is often necessary to genotype a large number of polymorphic markers. Currently, a community effort is underway to collect single nucleotide polymorphisms (SNP) from the parasite genome. Here we evaluate polymorphism detection accuracy of a high-density 'tiling' microarray with 2.56 million probes by comparing single feature polymorphisms (SFP) calls from the microarray with known SNP among parasite isolates. Results We found that probe GC content, SNP position in a probe, probe coverage, and signal ratio cutoff values were important factors for accurate detection of SFP in the parasite genome. We established a set of SFP calling parameters that could predict mSFP (SFP called by multiple overlapping probes) with high accuracy (≥ 94%) and identified 121,087 mSFP genome-wide from five parasite isolates including 40,354 unique mSFP (excluding those from multi-gene families) and ~18,000 new mSFP, producing a genetic map with an average of one unique mSFP per 570 bp. Genomic copy number variation (CNV) among the parasites was also cataloged and compared. Conclusion A large number of mSFP were discovered from the P. falciparum genome using a high-density microarray, most of which were in clusters of highly polymorphic genes at chromosome ends. Our method for accurate mSFP detection and the mSFP identified will greatly facilitate large-scale studies of genome variation in the P. falciparum parasite and provide useful resources for mapping important parasite traits.
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Affiliation(s)
- Hongying Jiang
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Mok BW, Ribacke U, Sherwood E, Wahlgren M. A highly conserved segmental duplication in the subtelomeres of Plasmodium falciparum chromosomes varies in copy number. Malar J 2008; 7:46. [PMID: 18325124 PMCID: PMC2279139 DOI: 10.1186/1475-2875-7-46] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2007] [Accepted: 03/07/2008] [Indexed: 11/30/2022] Open
Abstract
Background Segmental duplications (SD) have been found in genomes of various organisms, often accumulated at the ends of chromosomes. It has been assumed that the sequence homology in-between the SDs allow for ectopic interactions that may contribute to the emergence of new genes or gene variants through recombinatorial events. Methods In silico analysis of the 3D7 Plasmodium falciparum genome, conducted to investigate the subtelomeric compartments, led to the identification of subtelomeric SDs. Sequence variation and copy number polymorphisms of the SDs were studied by DNA sequencing, real-time quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The levels of transcription and the developmental expression of copy number variant genes were investigated by qPCR. Results A block of six genes of >10 kilobases in size, including var, rif, pfmc-2tm and three hypothetical genes (n-, o- and q-gene), was found duplicated in the subtelomeric regions of chromosomes 1, 2, 3, 6, 7, 10 and 11 (SD1). The number of SD1 per genome was found to vary from 4 to 8 copies in between different parasites. The intragenic regions of SD1 were found to be highly conserved across ten distinct fresh and long-term cultivated P. falciparum. Sequence variation was detected in a ≈ 23 amino-acid long hypervariable region of a surface-exposed loop of PFMC-2TM. A hypothetical gene within SD1, the n-gene, encoding a PEXEL/VTS-containing two-transmembrane protein was found expressed in ring stage parasites. The n-gene transcription levels were found to correlate to the number of n-gene copies. Fragments of SD1 harbouring two or three of the SD1-genes (o-gene, pfmc-2tm, q-gene) were also found in the 3D7 genome. In addition a related second SD, SD2, of ≈ 55% sequence identity to SD1 was found duplicated in a fresh clinical isolate but was only present in a single copy in 3D7 and in other P. falciparum lines or clones. Conclusion Plasmodium falciparum carries multiple sequence conserved SDs in the otherwise highly variable subtelomeres of its chromosomes. The uniqueness of the SDs amongst plasmodium species, and the conserved nature of the genes within, is intriguing and suggests an important role of the SD to P. falciparum.
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Affiliation(s)
- Bobo W Mok
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77 Stockholm, Sweden.
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33
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Hu G, Liu I, Sham A, Stajich JE, Dietrich FS, Kronstad JW. Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans. Genome Biol 2008; 9:R41. [PMID: 18294377 PMCID: PMC2374700 DOI: 10.1186/gb-2008-9-2-r41] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 12/23/2007] [Accepted: 02/22/2008] [Indexed: 11/20/2022] Open
Abstract
Extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans is revealed through comparative genome hybridization between strains of different mating type, molecular subtype and ploidy. Background Genome variability can have a profound influence on the virulence of pathogenic microbes. The availability of genome sequences for two strains of the AIDS-associated fungal pathogen Cryptococcus neoformans presented an opportunity to use comparative genome hybridization (CGH) to examine genome variability between strains of different mating type, molecular subtype, and ploidy. Results Initially, CGH was used to compare the approximately 100 kilobase MATa and MATα mating-type regions in serotype A and D strains to establish the relationship between the Log2 ratios of hybridization signals and sequence identity. Subsequently, we compared the genomes of the environmental isolate NIH433 (MATa) and the clinical isolate NIH12 (MATα) with a tiling array of the genome of the laboratory strain JEC21 derived from these strains. In this case, CGH identified putative recombination sites and the origins of specific segments of the JEC21 genome. Similarly, CGH analysis revealed marked variability in the genomes of strains representing the VNI, VNII, and VNB molecular subtypes of the A serotype, including disomy for chromosome 13 in two strains. Additionally, CGH identified differences in chromosome content between three strains with the hybrid AD serotype and revealed that chromosome 1 from the serotype A genome is preferentially retained in all three strains. Conclusion The genomes of serotypes A, D, and AD strains exhibit extensive variation that spans the range from small differences (such as regions of divergence, deletion, or amplification) to the unexpected disomy for chromosome 13 in haploid strains and preferential retention of specific chromosomes in naturally occurring diploids.
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Affiliation(s)
- Guanggan Hu
- Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada .
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McNulty SN, Weil GJ, Heinz M, Crosby SD, Fischer PU. Brugia malayi: whole genome amplification for genomic characterization of filarial parasites. Exp Parasitol 2008; 119:256-63. [PMID: 18359019 DOI: 10.1016/j.exppara.2008.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 02/04/2008] [Accepted: 02/12/2008] [Indexed: 11/18/2022]
Abstract
Genetic characterization of field isolates and clinical specimens of filarial nematodes is often limited by a shortage of DNA; therefore, we evaluated a multiple displacement amplification (MDA) based whole genome amplification method. The quality of amplified DNA was examined by conventional PCR, real-time PCR, and DNA hybridization. MDA of 5.0 ng of adult Brugia malayi DNA and one-fifteenth of the DNA isolated from a single microfilaria resulted in 6.3 and 4.2 microg of amplified DNA, respectively. Amplified DNA was equivalent to native genomic DNA for hybridization to B. malayi BAC library clones or to an oligonucleotide microarray with approximately 18,000 filarial DNA sequences. MDA is useful for whole genome amplification of filarial DNA from very small amounts of starting material. This technology will permit detailed studies of genetic diversity that were not previously feasible.
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Affiliation(s)
- Samantha N McNulty
- Internal Medicine/Infectious Diseases Division, Washington University School of Medicine, Campus Mailbox 8051, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
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35
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Sherman IW. References. ADVANCES IN PARASITOLOGY 2008. [DOI: 10.1016/s0065-308x(08)00430-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Microarray-based method for detection of unknown genetic modifications. BMC Biotechnol 2007; 7:91. [PMID: 18088429 PMCID: PMC2225397 DOI: 10.1186/1472-6750-7-91] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Accepted: 12/18/2007] [Indexed: 11/10/2022] Open
Abstract
Background Due to the increased use of genetic modifications in crop improvement, there is a need to develop effective methods for the detection of both known and unknown transgene constructs in plants. We have developed a strategy for detection and characterization of unknown genetic modifications and we present a proof of concept for this method using Arabidopsis thaliana and Oryza sativa (rice). The approach relies on direct hybridization of total genomic DNA to high density microarrays designed to have probes tiled throughout a set of reference sequences. Results We show that by using arrays with 25 basepair probes covering both strands of a set of 235 vectors (2 million basepairs) we can detect transgene sequences in transformed lines of A. thaliana and rice without prior knowledge about the transformation vectors or the T-DNA constructs used to generate the studied plants. Conclusion The approach should allow the user to detect the presence of transgene sequences and get sufficient information for further characterization of unknown genetic constructs in plants. The only requirements are access to a small amount of pure transgene plant material, that the genetic construct in question is above a certain size (here ≥ 140 basepairs) and that parts of the construct shows some degree of sequence similarity with published genetic elements.
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Kidgell C, Winzeler EA. Using the genome to dissect the molecular basis of drug resistance. Future Microbiol 2007; 1:185-99. [PMID: 17661664 DOI: 10.2217/17460913.1.2.185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The need to understand the genetic basis of drug resistance in human pathogens has never been greater. The global incidence of drug-resistant organisms, such as those that cause malaria, continues to rise, while the repertoire of effective, inexpensive drugs is declining. Genomic technologies, such as DNA microarrays and full-genome sequencing offer new hope in advancing our understanding of the underlying genetic processes that facilitate a resistance phenotype. Importantly, evidence that drug resistance in many organisms can be a multigene, complex phenomenon implies that unbiased, genome-wide scans of diversity will be required to fully understand the molecular mechanisms of both established and novel resistance traits. While the potential application of full-genome approaches for deciphering mechanisms of drug resistance has yet to be fully realized, this review evaluates drug resistance in human malaria parasites and discusses the exciting role genome-based systems could play in monitoring drug resistance, as well as guiding the implementation of efficient therapeutic strategies for malaria. The approaches reviewed within this article will be applicable to all known or emerging microbial pathogens.
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Affiliation(s)
- Claire Kidgell
- The Scripps Research Institute, ICND 202, La Jolla, CA 92037, USA.
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38
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Ribacke U, Mok BW, Wirta V, Normark J, Lundeberg J, Kironde F, Egwang TG, Nilsson P, Wahlgren M. Genome wide gene amplifications and deletions in Plasmodium falciparum. Mol Biochem Parasitol 2007; 155:33-44. [PMID: 17599553 DOI: 10.1016/j.molbiopara.2007.05.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 04/13/2007] [Accepted: 05/15/2007] [Indexed: 11/24/2022]
Abstract
The extent to which duplications and deletions occur in the Plasmodium falciparum genome, outside of the subtelomeres, and their contribution to the virulence of the malaria parasite is not known. Here we show the presence of multiple genome wide copy number polymorphisms (CNPs) covering 82 genes, the most extensive spanning a cumulative size of 110kilobases. CNPs were identified in both laboratory strains and fresh clinical isolates using a 70-mer oligonucleotide microarray in conjunction with fluorescent in situ hybridizations and real-time quantitative PCR. The CNPs were found on all chromosomes except on chromosomes 6 and 8 and involved a total of 50 genes with increased copy numbers and 32 genes with decreased copy numbers relative to the 3D7 parasite. The genes, amplified in up to six copies, encode molecules involved in cell cycle regulation, cell division, drug resistance, erythrocyte invasion, sexual differentiation and unknown functions. These together with previous findings, suggest that the malaria parasite employs gene duplications and deletions as general strategies to enhance its survival and spread. Further analysis of the impact of discovered genetic differences and the underlying mechanisms is likely to generate a better understanding of the biology and the virulence of the malaria parasite.
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Affiliation(s)
- Ulf Ribacke
- Swedish Institute for Infectious Disease Control, SE-17182 Solna, Sweden
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39
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Lavazec C, Sanyal S, Templeton TJ. Expression switching in thestevorandPfmc-2TMsuperfamilies inPlasmodium falciparum. Mol Microbiol 2007; 64:1621-34. [PMID: 17555442 DOI: 10.1111/j.1365-2958.2007.05767.x] [Citation(s) in RCA: 255] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plasmodium falciparum possesses two multigenic families, var and rif, the products of which are expressed on the surface of infected erythrocytes, where via antigenic variation they contribute to malaria pathogenesis and evasion of antibody-mediated host immunity. The products of two smaller gene families, stevor and Pfmc-2TM, also localize to the erythrocyte membrane, although it is not known if they undergo antigenic switching. Herein we use gene-specific quantitative reverse transcription polymerase chain reaction (RT-PCR) to investigate the transcription pattern of the stevor and Pfmc-2TM gene families, in both primary and second generation clonal lines of the P. falciparum isolate, NF54. We show that: (i) the expression of stevor and Pfmc-2TM families is clonally variant, (ii) the expression of stevor and Pfmc-2TM families undergoes switching, and (iii) switching rates vary among different variants and different isogenic clones at rates higher than 2% per generation. In addition, we show that chromosomal telomeric deletions are common in clonal lines and result in a spectrum of deletion genotypes. These findings provide evidence that the stevor and Pfmc-2TM gene families play a role in P. falciparum antigenic variation.
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Affiliation(s)
- Catherine Lavazec
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
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40
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Abstract
Malaria persists as an undiminished global problem, but the resources available to address it have increased. Many tools for understanding its biology and epidemiology are well developed, with a particular richness of comparative genome sequences. Targeted genetic manipulation is now effectively combined with in vitro culture assays on the most important human parasite, Plasmodium falciparum, and with in vivo analysis of rodent and monkey malaria parasites in their laboratory hosts. Studies of the epidemiology, prevention, and treatment of human malaria have already been influenced by the availability of molecular methods, and analyses of parasite polymorphisms have long had useful and highly informative applications. However, the molecular epidemiology of malaria is currently undergoing its most substantial revolution as a result of the genomic information and technologies that are available in well-resourced centers. It is a challenge for research agendas to face the real needs presented by a disease that largely exists in extremely resource-poor settings, but it is one that there appears to be an increased willingness to undertake. To this end, developments in the molecular epidemiology of malaria are reviewed here, emphasizing aspects that may be current and future priorities.
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Affiliation(s)
- David J Conway
- Medical Research Council Laboratories, Fajara, P.O. Box 273, Banjul, The Gambia.
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Jeffares DC, Pain A, Berry A, Cox AV, Stalker J, Ingle CE, Thomas A, Quail MA, Siebenthall K, Uhlemann AC, Kyes S, Krishna S, Newbold C, Dermitzakis ET, Berriman M. Genome variation and evolution of the malaria parasite Plasmodium falciparum. Nat Genet 2006; 39:120-5. [PMID: 17159978 PMCID: PMC2663918 DOI: 10.1038/ng1931] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Accepted: 11/02/2006] [Indexed: 11/09/2022]
Abstract
Infections with the malaria parasite Plasmodium falciparum result in more than 1 million deaths each year worldwide. Deciphering the evolutionary history and genetic variation of P. falciparum is critical for understanding the evolution of drug resistance, identifying potential vaccine candidates and appreciating the effect of parasite variation on prevalence and severity of malaria in humans. Most studies of natural variation in P. falciparum have been either in depth over small genomic regions (up to the size of a small chromosome) or genome wide but only at low resolution. In an effort to complement these studies with genome-wide data, we undertook shotgun sequencing of a Ghanaian clinical isolate (with fivefold coverage), the IT laboratory isolate (with onefold coverage) and the chimpanzee parasite P. reichenowi (with twofold coverage). We compared these sequences with the fully sequenced P. falciparum 3D7 isolate genome. We describe the most salient features of P. falciparum polymorphism and adaptive evolution with relation to gene function, transcript and protein expression and cellular localization. This analysis uncovers the primary evolutionary changes that have occurred since the P. falciparum-P. reichenowi speciation and changes that are occurring within P. falciparum.
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Affiliation(s)
- Daniel C. Jeffares
- Informatics Division, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus CB10 1SA, Hinxton, UK
| | - Arnab Pain
- Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus CB10 1SA, Hinxton, UK
| | - Andrew Berry
- Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus CB10 1SA, Hinxton, UK
| | - Anthony V. Cox
- Informatics Division, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus CB10 1SA, Hinxton, UK
| | - James Stalker
- Informatics Division, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus CB10 1SA, Hinxton, UK
| | - Catherine E. Ingle
- Informatics Division, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus CB10 1SA, Hinxton, UK
| | - Alan Thomas
- Biomedical Primate Research Centre, Lange Kleiweg 139, Rijswijk, Postbus 3306, 2280 GH Rijswijk, The Netherlands
| | - Michael A. Quail
- Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus CB10 1SA, Hinxton, UK
| | - Kyle Siebenthall
- Informatics Division, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus CB10 1SA, Hinxton, UK
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | | | - Sue Kyes
- The Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Sanjeev Krishna
- St George's, University of London, Cranmer Terrace, London SW17 ORE UK
| | - Chris Newbold
- The Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Emmanouil T. Dermitzakis
- Informatics Division, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus CB10 1SA, Hinxton, UK
- correspondence should be addressed to: Emmanouil T. Dermitzakis (; +44-1223-494866) or Matthew Berriman (; +44-1223-494975) Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus CB10 1SA, Hinxton, Cambs UK. Fax: +44-1223-494919
| | - Matthew Berriman
- Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus CB10 1SA, Hinxton, UK
- correspondence should be addressed to: Emmanouil T. Dermitzakis (; +44-1223-494866) or Matthew Berriman (; +44-1223-494975) Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus CB10 1SA, Hinxton, Cambs UK. Fax: +44-1223-494919
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42
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Kidgell C, Volkman SK, Daily J, Borevitz JO, Plouffe D, Zhou Y, Johnson JR, Le Roch KG, Sarr O, Ndir O, Mboup S, Batalov S, Wirth DF, Winzeler EA. A systematic map of genetic variation in Plasmodium falciparum. PLoS Pathog 2006; 2:e57. [PMID: 16789840 PMCID: PMC1480597 DOI: 10.1371/journal.ppat.0020057] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Accepted: 04/28/2006] [Indexed: 11/25/2022] Open
Abstract
Discovering novel genes involved in immune evasion and drug resistance in the human malaria parasite, Plasmodium falciparum, is of critical importance to global health. Such knowledge may assist in the development of new effective vaccines and in the appropriate use of antimalarial drugs. By performing a full-genome scan of allelic variability in 14 field and laboratory strains of P. falciparum, we comprehensively identified ≈500 genes evolving at higher than neutral rates. The majority of the most variable genes have paralogs within the P. falciparum genome and may be subject to a different evolutionary clock than those without. The group of 211 variable genes without paralogs contains most known immunogens and a few drug targets, consistent with the idea that the human immune system and drug use is driving parasite evolution. We also reveal gene-amplification events including one surrounding pfmdr1, the P. falciparum multidrug-resistance gene, and a previously uncharacterized amplification centered around the P. falciparum GTP cyclohydrolase gene, the first enzyme in the folate biosynthesis pathway. Although GTP cyclohydrolase is not the known target of any current drugs, downstream members of the pathway are targeted by several widely used antimalarials. We speculate that an amplification of the GTP cyclohydrolase enzyme in the folate biosynthesis pathway may increase flux through this pathway and facilitate parasite resistance to antifolate drugs. Variability in the genome of the human malaria parasite, Plasmodium falciparum, is key to the parasite's ability to cause disease and overcome therapeutic interventions such as drugs and vaccines. Elucidating the extent of genetic variation in the malaria parasite will therefore be central to decreasing the malaria disease burden. The authors performed a full-genome scan of variability in different strains of P. falciparum and observed a nonrandom distribution of variation. In particular, those genes that are predicted to have roles in evading the host immune response or antimalarial drugs show significantly higher levels of variation. In addition, the authors speculate that a previously unreported genome amplification in the folate biosynthesis pathway correlates with resistance to the antimalarial drug sulfadoxine. Such data enable hypotheses to be made about the function of many of the unknown elements in the parasite's genome, which may permit the identification of new targets that can be investigated for incorporation into a malaria vaccine and may aid in the understanding of how the parasite withstands drug pressure.
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Affiliation(s)
- Claire Kidgell
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Johanna Daily
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Justin O Borevitz
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - David Plouffe
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Yingyao Zhou
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Jeffrey R Johnson
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Karine G. Le Roch
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Ousmane Sarr
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Omar Ndir
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Soulyemane Mboup
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Serge Batalov
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Elizabeth A Winzeler
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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43
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Arora K, Chand S, Malhotra BD. Recent developments in bio-molecular electronics techniques for food pathogens. Anal Chim Acta 2006; 568:259-74. [PMID: 17761267 DOI: 10.1016/j.aca.2006.03.078] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Revised: 03/20/2006] [Accepted: 03/23/2006] [Indexed: 01/26/2023]
Abstract
Food borne illnesses contribute to the majority of infections caused by pathogenic microorganisms. Detection of these pathogens originating from different sources has led to increased interest of researchers. New bio-molecular techniques for food pathogen detection are being developed to improve the sensor characteristics such as sensitivity, reusability, simplicity and economic viability. Present article deals with the various methods of food pathogen detection with special emphasis on bio-molecular electronics techniques such as biosensors, microarrays, electronic nose, and nano-materials based methods.
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Affiliation(s)
- Kavita Arora
- Biomolecular Electronics and Conducting Polymer Research Group, National Physical Laboratory, K.S. Krishnan Road, New Delhi 110012, India.
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