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Su X, Stadler RV, Xu F, Wu J. Malaria Genomics, Vaccine Development, and Microbiome. Pathogens 2023; 12:1061. [PMID: 37624021 PMCID: PMC10459703 DOI: 10.3390/pathogens12081061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
Recent advances in malaria genetics and genomics have transformed many aspects of malaria research in areas of molecular evolution, epidemiology, transmission, host-parasite interaction, drug resistance, pathogenicity, and vaccine development. Here, in addition to introducing some background information on malaria parasite biology, parasite genetics/genomics, and genotyping methods, we discuss some applications of genetic and genomic approaches in vaccine development and in studying interactions with microbiota. Genetic and genomic data can be used to search for novel vaccine targets, design an effective vaccine strategy, identify protective antigens in a whole-organism vaccine, and evaluate the efficacy of a vaccine. Microbiota has been shown to influence disease outcomes and vaccine efficacy; studying the effects of microbiota in pathogenicity and immunity may provide information for disease control. Malaria genetics and genomics will continue to contribute greatly to many fields of malaria research.
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Affiliation(s)
- Xinzhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (R.V.S.); (F.X.); (J.W.)
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2
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Rougeron V, Boundenga L, Arnathau C, Durand P, Renaud F, Prugnolle F. A population genetic perspective on the origin, spread and adaptation of the human malaria agents Plasmodium falciparum and Plasmodium vivax. FEMS Microbiol Rev 2021; 46:6373923. [PMID: 34550355 DOI: 10.1093/femsre/fuab047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/06/2021] [Indexed: 01/20/2023] Open
Abstract
Malaria is considered one of the most important scourges that humanity has faced during its history, being responsible every year for numerous deaths worldwide. The disease is caused by protozoan parasites, among which two species are responsible of the majority of the burden, Plasmodium falciparum and Plasmodium vivax. For these two parasite species, the questions of their origin (how and when they appeared in humans), of their spread throughout the world, as well as how they have adapted to humans have long been of interest to the scientific community. Here, we review the current knowledge that has accumulated on these different questions, thanks in particular to the analysis of the genetic and genomic variability of these parasites and comparison with related Plasmodium species infecting other host species (like non-human primates). In this paper we review the existing body of knowledge, including current research dealing with these questions, focusing particularly on genetic analysis and genomic variability of these parasites and comparison with related Plasmodium species infecting other species of host (such as non-human primates).
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Affiliation(s)
- Virginie Rougeron
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Larson Boundenga
- CIRMF, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Céline Arnathau
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Patrick Durand
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - François Renaud
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Franck Prugnolle
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
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3
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Su XZ, Zhang C, Joy DA. Host-Malaria Parasite Interactions and Impacts on Mutual Evolution. Front Cell Infect Microbiol 2020; 10:587933. [PMID: 33194831 PMCID: PMC7652737 DOI: 10.3389/fcimb.2020.587933] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/22/2020] [Indexed: 12/22/2022] Open
Abstract
Malaria is the most deadly parasitic disease, affecting hundreds of millions of people worldwide. Malaria parasites have been associated with their hosts for millions of years. During the long history of host-parasite co-evolution, both parasites and hosts have applied pressure on each other through complex host-parasite molecular interactions. Whereas the hosts activate various immune mechanisms to remove parasites during an infection, the parasites attempt to evade host immunity by diversifying their genome and switching expression of targets of the host immune system. Human intervention to control the disease such as antimalarial drugs and vaccination can greatly alter parasite population dynamics and evolution, particularly the massive applications of antimalarial drugs in recent human history. Vaccination is likely the best method to prevent the disease; however, a partially protective vaccine may have unwanted consequences that require further investigation. Studies of host-parasite interactions and co-evolution will provide important information for designing safe and effective vaccines and for preventing drug resistance. In this essay, we will discuss some interesting molecules involved in host-parasite interactions, including important parasite antigens. We also discuss subjects relevant to drug and vaccine development and some approaches for studying host-parasite interactions.
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Affiliation(s)
- Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Cui Zhang
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Deirdre A Joy
- Parasitology and International Programs Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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Human unconventional T cells in Plasmodium falciparum infection. Semin Immunopathol 2020; 42:265-277. [PMID: 32076813 PMCID: PMC7223888 DOI: 10.1007/s00281-020-00791-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 02/07/2020] [Indexed: 12/22/2022]
Abstract
Malaria is an old scourge of humankind and has a large negative impact on the economic development of affected communities. Recent success in malaria control and reduction of mortality seems to have stalled emphasizing that our current intervention tools need to be complemented by malaria vaccines. Different populations of unconventional T cells such as mucosal-associated invariant T (MAIT) cells, invariant natural killer T (iNKT) cells and γδ T cells are gaining attention in the field of malaria immunology. Significant advances in our basic understanding of unconventional T cell biology in rodent malaria models have been made, however, their roles in humans during malaria are less clear. Unconventional T cells are abundant in skin, gut and liver tissues, and long-lasting expansions and functional alterations were observed upon malaria infection in malaria naïve and malaria pre-exposed volunteers. Here, we review the current understanding of involvement of unconventional T cells in anti-Plasmodium falciparum immunity and highlight potential future research avenues.
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Riggle BA, Miller LH, Pierce SK. Desperately Seeking Therapies for Cerebral Malaria. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:327-334. [PMID: 31907275 PMCID: PMC6951433 DOI: 10.4049/jimmunol.1900829] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023]
Abstract
Malaria is a deadly infectious disease caused by parasites of the Plasmodium spp. that takes an estimated 435,000 lives each year, primarily among young African children. For most children, malaria is a febrile illness that resolves with time, but in ∼1% of cases, for reasons we do not understand, malaria becomes severe and life threatening. Cerebral malaria (CM) is the most common form of severe malaria, accounting for the vast majority of childhood deaths from malaria despite highly effective antiparasite chemotherapy. Thus, CM is one of the most prevalent lethal brain diseases, and one for which we have no effective therapy. CM is, in part, an immune-mediated disease, and to fully understand CM, it is essential to appreciate the complex relationship between the malarial parasite and the human immune system. In this study, we provide a primer on malaria for immunologists and, in this context, review progress identifying targets for therapeutic intervention.
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Affiliation(s)
- Brittany A Riggle
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852; and
| | - Louis H Miller
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - Susan K Pierce
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852; and
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Plasmodium Genomics and Genetics: New Insights into Malaria Pathogenesis, Drug Resistance, Epidemiology, and Evolution. Clin Microbiol Rev 2019; 32:32/4/e00019-19. [PMID: 31366610 DOI: 10.1128/cmr.00019-19] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Protozoan Plasmodium parasites are the causative agents of malaria, a deadly disease that continues to afflict hundreds of millions of people every year. Infections with malaria parasites can be asymptomatic, with mild or severe symptoms, or fatal, depending on many factors such as parasite virulence and host immune status. Malaria can be treated with various drugs, with artemisinin-based combination therapies (ACTs) being the first-line choice. Recent advances in genetics and genomics of malaria parasites have contributed greatly to our understanding of parasite population dynamics, transmission, drug responses, and pathogenesis. However, knowledge gaps in parasite biology and host-parasite interactions still remain. Parasites resistant to multiple antimalarial drugs have emerged, while advanced clinical trials have shown partial efficacy for one available vaccine. Here we discuss genetic and genomic studies of Plasmodium biology, host-parasite interactions, population structures, mosquito infectivity, antigenic variation, and targets for treatment and immunization. Knowledge from these studies will advance our understanding of malaria pathogenesis, epidemiology, and evolution and will support work to discover and develop new medicines and vaccines.
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Nkhoma SC, Banda RL, Khoswe S, Dzoole-Mwale TJ, Ward SA. Intra-host dynamics of co-infecting parasite genotypes in asymptomatic malaria patients. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 65:414-424. [PMID: 30145390 PMCID: PMC6219893 DOI: 10.1016/j.meegid.2018.08.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/13/2018] [Accepted: 08/20/2018] [Indexed: 11/22/2022]
Abstract
Malaria-infected individuals often harbor mixtures of genetically distinct parasite genotypes. We studied intra-host dynamics of parasite genotypes co-infecting asymptomatic adults in an area of intense malaria transmission in Chikhwawa, Malawi. Serial blood samples (5 ml) were collected over seven consecutive days from 25 adults with asymptomatic Plasmodium falciparum malaria and analyzed to determine whether a single peripheral blood sample accurately captures within-host parasite diversity. Blood samples from three of the participants were also analyzed by limiting dilution cloning and SNP genotyping of the parasite clones isolated to examine both the number and relatedness of co-infecting parasite haplotypes. We observed rapid turnover of co-infecting parasite genotypes in 88% of the individuals sampled (n = 22) such that the genetic composition of parasites infecting these individuals changed dramatically over the course of seven days of follow up. Nineteen of the 25 individuals sampled (76%) carried multiple parasite genotypes at baseline. Analysis of serial blood samples from three of the individuals revealed that they harbored 6, 12 and 17 distinct parasite haplotypes respectively. Approximately 70% of parasite haplotypes recovered from the three extensively sampled individuals were unrelated (proportion of shared alleles <83.3%) and were deemed to have primarily arisen from superinfection (inoculation of unrelated parasite haplotypes through multiple mosquito bites). The rest were related at the half-sib level or greater and were deemed to have been inoculated into individual human hosts via parasite co-transmission from single mosquito bites. These findings add further to the growing weight of evidence indicating that a single blood sample poorly captures within-host parasite diversity and underscore the importance of repeated blood sampling to accurately capture within-host parasite ecology. Our data also demonstrate a more pronounced role for parasite co-transmission in generating within-host parasite diversity in high transmission settings than previously assumed. Taken together, these findings have important implications for understanding the evolution of drug resistance, malaria transmission, parasite virulence, allocation of gametocyte sex ratios and acquisition of malaria immunity.
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Affiliation(s)
- Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK; Wellcome Trust-Liverpool-Glasgow Centre for Global Health Research, 70 Pembroke Place, Liverpool L69 3GF, UK.
| | - Rachel L Banda
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Stanley Khoswe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Tamika J Dzoole-Mwale
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Stephen A Ward
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
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Molina-Cruz A, Zilversmit MM, Neafsey DE, Hartl DL, Barillas-Mury C. Mosquito Vectors and the Globalization of Plasmodium falciparum Malaria. Annu Rev Genet 2016; 50:447-465. [PMID: 27732796 DOI: 10.1146/annurev-genet-120215-035211] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plasmodium falciparum malaria remains a devastating public health problem. Recent discoveries have shed light on the origin and evolution of Plasmodium parasites and their interactions with their vertebrate and mosquito hosts. P. falciparum malaria originated in Africa from a single horizontal transfer between an infected gorilla and a human, and became global as the result of human migration. Today, P. falciparum malaria is transmitted worldwide by more than 70 different anopheline mosquito species. Recent studies indicate that the mosquito immune system can be a barrier to malaria transmission and that the P. falciparum Pfs47 gene allows the parasite to evade mosquito immune detection. Here, we review the origin and globalization of P. falciparum and integrate this history with analysis of the biology, evolution, and dispersal of the main mosquito vectors. This new perspective broadens our understanding of P. falciparum population structure and the dispersal of important parasite genetic traits.
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Affiliation(s)
- Alvaro Molina-Cruz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852;
| | - Martine M Zilversmit
- Richard Guilder Graduate School and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024
| | - Daniel E Neafsey
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Carolina Barillas-Mury
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852;
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Arnot DE, Jensen ATR. Antigenic Variation and the Genetics and Epigenetics of the PfEMP1 Erythrocyte Surface Antigens in Plasmodium falciparum Malaria. ADVANCES IN APPLIED MICROBIOLOGY 2016; 74:77-96. [PMID: 21459194 DOI: 10.1016/b978-0-12-387022-3.00007-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
How immunity to malaria develops remains one of the great unresolved issues in bio-medicine and resolution of its various paradoxes is likely to be the key to developing effective malaria vaccines. The basic epidemiological observations are; under conditions of intense natural transmission, humans do become immune to P. falciparum malaria, but this is a slow process requiring multiple disease episodes which many, particularly young children, do not survive. Adult survivors are immune to the symptoms of malaria, and unless pregnant, can control the growth of most or all new inoculations. Sterile immunity is not achieved and chronic parasitization of apparently healthy adults is the norm. In this article, we analyse the best understood malaria "antigenic variation" system, that based on Plasmodium falciparum's PfEMP1-type cytoadhesion antigens, and critically review recent literature on the function and control of this multi-gene family of parasite variable surface antigens.
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Affiliation(s)
- David E Arnot
- Centre for Medical Parasitology, Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, CSS Oester Farimagsgade 5, Copenhagen K, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), CSS Oester Farimagsgade 5, Copenhagen K, Denmark; Institute of Immunology and Infection Research, School of Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
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10
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Huang B, Deng C, Yang T, Xue L, Wang Q, Huang S, Su XZ, Liu Y, Zheng S, Guan Y, Xu Q, Zhou J, Yuan J, Bacar A, Abdallah KS, Attoumane R, Mliva AMSA, Zhong Y, Lu F, Song J. Polymorphisms of the artemisinin resistant marker (K13) in Plasmodium falciparum parasite populations of Grande Comore Island 10 years after artemisinin combination therapy. Parasit Vectors 2015; 8:634. [PMID: 26667053 PMCID: PMC4678476 DOI: 10.1186/s13071-015-1253-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/10/2015] [Indexed: 12/03/2022] Open
Abstract
Background Plasmodium falciparum malaria is a significant public health problem in Comoros, and artemisinin combination therapy (ACT) remains the first choice for treating acute uncomplicated P. falciparum. The emergence and spread of artemisinin-resistant P. falciparum in Southeast Asia, associated with mutations in K13-propeller gene, poses a potential threat to ACT efficacy. Detection of mutations in the P. falciparum K13-propeller gene may provide the first-hand information on changes in parasite susceptibility to artemisinin. The objective of this study is to determinate the prevalence of mutant K13-propeller gene among the P. falciparum isolates collected from Grande Comore Island, Union of Comoros, where ACT has been in use since 2004. Methods A total of 207 P. falciparum clinical isolates were collected from the island during March 2006 and October 2007 (n = 118) and March 2013 and December 2014 (n = 89). All isolates were analysed for single nucleotide polymorphisms (SNPs) and haplotypes in the K13-propeller gene using nested PCR and DNA sequencing. Results Only three 2006–2007 samples carried SNPs in the K13-propeller gene, one having a synonymous (G538G) and the other having two non-synonymous (S477Y and D584E) substitutions leading to two mutated haplotypes (2.2 %, 2/95). Three synonymous mutations (R471R, Y500Y, and G538G) (5.9 %, 5/85) and 7 non-synonymous substitutions (21.2 %, 18/85) with nine mutated haplotypes (18.8 %, 16/85) were found in isolates from 2013 to 2014. However, none of the polymorphisms associated with artemisinin-resistance in Southeast Asia was detected from any of the parasites examined. Conclusion This study showed increased K13-propeller gene diversity among P. falciparum populations on the Island over the course of 8 years (2006–2014). Nevertheless, none of the polymorphisms known to be associated with artemisinin resistance in Asia was detected in the parasite populations examined. Our data suggest that P. falciparum populations in Grande Comore are still effectively susceptible to artemisinin. Our results provide insights into P. falciparum populations regarding mutations in the gene associated with artemisinin resistance and will be useful for developing and updating anti-malarial guidance in Comoros.
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Affiliation(s)
- Bo Huang
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Changsheng Deng
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Tao Yang
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Linlu Xue
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Qi Wang
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Shiguang Huang
- School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, PR China.
| | - Xin-zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA. .,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361005, Fujian, PR China.
| | - Yajun Liu
- The first affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Shaoqin Zheng
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Yezhi Guan
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Qin Xu
- Research Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Jiuyao Zhou
- Traditional Chinese Medicine Collage, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Jie Yuan
- Traditional Chinese Medicine Collage, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Afane Bacar
- National Malaria Control Programme, Moroni, Union of Comoros.
| | | | | | | | - Yanchun Zhong
- Traditional Chinese Medicine Collage, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Fangli Lu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, Guangdong, PR China.
| | - Jianping Song
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
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11
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Paquette AM, Harahap A, Laosombat V, Patnode JM, Satyagraha A, Sudoyo H, Thompson MK, Yusoff NM, Wilder JA. The evolutionary origins of Southeast Asian Ovalocytosis. INFECTION GENETICS AND EVOLUTION 2015; 34:153-9. [PMID: 26047685 DOI: 10.1016/j.meegid.2015.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/25/2015] [Accepted: 06/01/2015] [Indexed: 11/30/2022]
Abstract
Southeast Asian Ovalocytosis (SAO) is a common red blood cell disorder that is maintained as a balanced polymorphism in human populations. In individuals heterozygous for the SAO-causing mutation there are minimal detrimental effects and well-documented protection from severe malaria caused by Plasmodium vivax and Plasmodium falciparum; however, the SAO-causing mutation is fully lethal in utero when homozygous. The present-day high frequency of SAO in Island Southeast Asia indicates the trait is maintained by strong heterozygote advantage. Our study elucidates the evolutionary origin of SAO by characterizing DNA sequence variation in a 9.5 kilobase region surrounding the causal mutation in the SLC4A1 gene. We find substantial haplotype diversity among SAO chromosomes and estimate the age of the trait to be approximately 10,005 years (95% CI: 4930-23,200 years). This date is far older than any other human malaria-resistance trait examined previously in Southeast Asia, and considerably pre-dates the widespread adoption of agriculture associated with the spread of speakers of Austronesian languages some 4000 years ago. Using a genealogy-based method we find no evidence of historical positive selection acting on SAO (s=0.0, 95% CI: 0.0-0.03), in sharp contrast to the strong present-day selection coefficient (e.g., 0.09) estimated from the frequency of this recessively lethal trait. This discrepancy may be due to a recent increase in malaria-driven selection pressure following the spread of agriculture, with SAO targeted as a standing variant by positive selection in malarial populations.
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Affiliation(s)
- A M Paquette
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - A Harahap
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - V Laosombat
- Division of Pediatric Hematology & Oncology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkla 90110, Thailand
| | - J M Patnode
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - A Satyagraha
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - H Sudoyo
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - M K Thompson
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - N M Yusoff
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Kepala Batas, Pulau Pinang, Malaysia
| | - J A Wilder
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA.
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Crompton PD, Moebius J, Portugal S, Waisberg M, Hart G, Garver LS, Miller LH, Barillas-Mury C, Pierce SK. Malaria immunity in man and mosquito: insights into unsolved mysteries of a deadly infectious disease. Annu Rev Immunol 2014; 32:157-87. [PMID: 24655294 DOI: 10.1146/annurev-immunol-032713-120220] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Malaria is a mosquito-borne disease caused by parasites of the obligate intracellular Apicomplexa phylum the most deadly of which, Plasmodium falciparum, prevails in Africa. Malaria imposes a huge health burden on the world's most vulnerable populations, claiming the lives of nearly one million children and pregnant women each year. Although there is keen interest in eradicating malaria, we do not yet have the necessary tools to meet this challenge, including an effective malaria vaccine and adequate vector control strategies. Here we review what is known about the mechanisms at play in immune resistance to malaria in both the human and mosquito hosts at each step in the parasite's complex life cycle with a view toward developing the tools that will contribute to the prevention of disease and death and, ultimately, to the goal of malaria eradication. In so doing, we hope to inspire immunologists to participate in defeating this devastating disease.
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13
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Ferreira KAM, Fajardo EF, Baptista RP, Macedo AM, Lages-Silva E, Ramírez LE, Pedrosa AL. Species-specific markers for the differential diagnosis of Trypanosoma cruzi and Trypanosoma rangeli and polymorphisms detection in Trypanosoma rangeli. Parasitol Res 2014; 113:2199-207. [PMID: 24728520 DOI: 10.1007/s00436-014-3872-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
Abstract
Trypanosoma cruzi and Trypanosoma rangeli are kinetoplastid parasites which are able to infect humans in Central and South America. Misdiagnosis between these trypanosomes can be avoided by targeting barcoding sequences or genes of each organism. This work aims to analyze the feasibility of using species-specific markers for identification of intraspecific polymorphisms and as target for diagnostic methods by PCR. Accordingly, primers which are able to specifically detect T. cruzi or T. rangeli genomic DNA were characterized. The use of intergenic regions, generally divergent in the trypanosomatids, and the serine carboxypeptidase gene were successful. Using T. rangeli genomic sequences for the identification of group-specific polymorphisms and a polymorphic AT(n) dinucleotide repeat permitted the classification of the strains into two groups, which are entirely coincident with T. rangeli main lineages, KP1 (+) and KP1 (-), previously determined by kinetoplast DNA (kDNA) characterization. The sequences analyzed totalize 622 bp (382 bp represent a hypothetical protein sequence, and 240 bp represent an anonymous sequence), and of these, 581 (93.3%) are conserved sites and 41 bp (6.7%) are polymorphic, with 9 transitions (21.9%), 2 transversions (4.9%), and 30 (73.2%) insertion/deletion events. Taken together, the species-specific markers analyzed may be useful for the development of new strategies for the accurate diagnosis of infections. Furthermore, the identification of T. rangeli polymorphisms has a direct impact in the understanding of the population structure of this parasite.
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Affiliation(s)
- Keila Adriana Magalhães Ferreira
- Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Avenida Frei Paulino, 30, Bairro Abadia, Uberaba, Minas Gerais, 38025-180, Brazil
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Golassa L, Enweji N, Erko B, Aseffa A, Swedberg G. High prevalence of pfcrt-CVIET haplotype in isolates from asymptomatic and symptomatic patients in south-central Oromia, Ethiopia. Malar J 2014; 13:120. [PMID: 24674605 PMCID: PMC3986696 DOI: 10.1186/1475-2875-13-120] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 03/25/2014] [Indexed: 01/01/2023] Open
Abstract
Background As a result of extensive chloroquine resistance (CQR) in Plasmodium falciparum in late 1990s, Ethiopia replaced CQ with sulphadoxine-pyrimethamine (SP) as first-line drug, which in turn was replaced by artemisinin combination therapy in 2004. Plasmodium falciparum resistance to CQ is determined by the mutation at K76T of the P. falciparum chloroquine resistance transporter (pfcrt) gene. Understanding diversity in the P. falciparum genome is crucial since it has the potential to influence important phenotypes of the parasite such as drug resistance. Limited data is available regarding the type of pfcrt mutant allelic type, the effect of CQ withdrawal and diversity of the parasite population in south-central Oromia, Ethiopia. Methods Finger-pricked blood spotted on Whatman 3MM filter papers were collected from falciparum malaria patients. Parasite DNA was extracted from individual blood spots on the filter papers. The presence of K76T mutations was determined using nested PCR for all isolates. Complete sequencing of mutations in pfcrt 72-76 was done for a set of randomly selected resistant isolates. Four microsatellite (MS) markers were analysed to determine the heterozygosity. Results Although CQ was withdrawn for more than a decade, 100% of the parasites still carried the pfcrt K76T mutation. All isolates were mutant at the K76T polymorphism. Based on combinations of MS markers, seven different Ethiopian CQR variants (E1-E7) were identified. Heterozygosity (He) for MS flanking the pfcrt chloroquine resistance allele ranged from 0.00 (mscrt -29, -29.268 kb) to 0.21 (mscrt -2, -2.814 kb). He ranged from 0.00 (msint 3, 0 kb) to 0.19 (msint 2, 0 kb) for MS within the pfcrt gene. Both intronic and MS flanking the pfcrt gene showed low levels of diversity. Conclusion pfcrt CQR allele seems to be fixed in the study area. Of the different haplotypes associated with CQR, only the CVIET genotype was identified. No reversal to the wild-type has occurred in Ethiopia unlike in many Africa countries where CQR parasites declined after cessation of CQ use. Decreased diversity in CQR isolates surrounding pfcrt suggests CQ selection and homogenization among CQR parasite population. While mutation in msint 3 and mscrt -29 of the mutant pfcrt allele is being fixed, it seems that mutations in msint 2 and mscrt -2 are still evolving and may indicate the start of re-diversification of the population from a fixed 76 T population.
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Affiliation(s)
- Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
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Lin S, Li T, Zhu D, Ma C, Wang Y, He L, Zhu C, Xing Q. The association between GAD1 gene polymorphisms and cerebral palsy in Chinese infants. CYTOL GENET+ 2013. [DOI: 10.3103/s0095452713050071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Prajapati SK, Joshi H, Carlton JM, Rizvi MA. Neutral polymorphisms in putative housekeeping genes and tandem repeats unravels the population genetics and evolutionary history of Plasmodium vivax in India. PLoS Negl Trop Dis 2013; 7:e2425. [PMID: 24069480 PMCID: PMC3777877 DOI: 10.1371/journal.pntd.0002425] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/01/2013] [Indexed: 11/18/2022] Open
Abstract
The evolutionary history and age of Plasmodium vivax has been inferred as both recent and ancient by several studies, mainly using mitochondrial genome diversity. Here we address the age of P. vivax on the Indian subcontinent using selectively neutral housekeeping genes and tandem repeat loci. Analysis of ten housekeeping genes revealed a substantial number of SNPs (n = 75) from 100 P. vivax isolates collected from five geographical regions of India. Neutrality tests showed a majority of the housekeeping genes were selectively neutral, confirming the suitability of housekeeping genes for inferring the evolutionary history of P. vivax. In addition, a genetic differentiation test using housekeeping gene polymorphism data showed a lack of geographical structuring between the five regions of India. The coalescence analysis of the time to the most recent common ancestor estimate yielded an ancient TMRCA (232,228 to 303,030 years) and long-term population history (79,235 to 104,008) of extant P. vivax on the Indian subcontinent. Analysis of 18 tandem repeat loci polymorphisms showed substantial allelic diversity and heterozygosity per locus, and analysis of potential bottlenecks revealed the signature of a stable P. vivax population, further corroborating our ancient age estimates. For the first time we report a comparable evolutionary history of P. vivax inferred by nuclear genetic markers (putative housekeeping genes) to that inferred from mitochondrial genome diversity.
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Affiliation(s)
- Surendra K Prajapati
- Molecular Biology Division, National Institute of Malaria Research, New Delhi, India
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Abstract
Owing to the absence of antiparasitic vaccines and the constant threat of drug resistance, the development of novel antiparasitic chemotherapies remains of major importance for disease control. A better understanding of drug transport (uptake and efflux), drug metabolism and the identification of drug targets, and mechanisms of drug resistance would facilitate the development of more effective therapies. Here, we focus on malaria and African trypanosomiasis. We review existing drugs and drug development, emphasizing high-throughput genomic and genetic approaches, which hold great promise for elucidating antiparasitic mechanisms. We describe the approaches and technologies that have been influential for each parasite and develop new ideas for future research directions, including mode-of-action studies for drug target deconvolution.
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Affiliation(s)
- David Horn
- Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Manoj T. Duraisingh
- Harvard School of Public Health, 665 Huntington Avenue, Building 1, Room 715, Boston, Massachusetts 02115, USA
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Modulation of the immune and inflammatory responses by Plasmodium falciparum schizont extracts: role of myeloid dendritic cells in effector and regulatory functions of CD4+ lymphocytes. Infect Immun 2013; 81:1842-51. [PMID: 23509139 DOI: 10.1128/iai.01226-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The optimal immune response to malaria infection comprises rapid induction of inflammatory responses promptly counteracted by regulatory mechanisms to prevent immunopathology. To evaluate the role of dendritic cells (DC) in the balance of parasite-induced inflammatory/anti-inflammatory mechanisms, we studied the activity of monocyte-derived dendritic cells (MDDC), previously exposed to soluble extracts of Plasmodium falciparum-infected red blood cells (PfSE), in the differentiation of CD4 cells isolated from donors never exposed to malaria infection. We show that MDDC exposed to PfSE are extremely efficient to induce a contemporary differentiation of TH1 effector cells and T regulatory (Treg) cells in CD4 T cells even when exposed to low concentrations of parasitic extracts. Treg cells induced by MDDC infected with PfSE (MDDC-PfSE) produce transforming growth factor beta (TGF-β) and interleukin 10 (IL-10) and are endowed with strong suppressive properties. They also show phenotypical and functional peculiarities, such as the contemporary expression of markers of Treg and TH1 differentiation and higher sensitivity to TLR4 ligands both inducing an increasing production of suppressive cytokines. On the whole, our data indicate that MDDC exposed to PfSE orchestrate a well-balanced immune response with timely differentiation of TH1 and Treg cells in CD4 cells from nonimmune donors and suggest that, during the infection, the role of MDCC could be particularly relevant in low-parasitemia conditions.
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Katju V. In with the old, in with the new: the promiscuity of the duplication process engenders diverse pathways for novel gene creation. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:341932. [PMID: 23008799 PMCID: PMC3449122 DOI: 10.1155/2012/341932] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 06/03/2012] [Indexed: 01/26/2023]
Abstract
The gene duplication process has exhibited far greater promiscuity in the creation of paralogs with novel exon-intron structures than anticipated even by Ohno. In this paper I explore the history of the field, from the neo-Darwinian synthesis through Ohno's formulation of the canonical model for the evolution of gene duplicates and culminating in the present genomic era. I delineate the major tenets of Ohno's model and discuss its failure to encapsulate the full complexity of the duplication process as revealed in the era of genomics. I discuss the diverse classes of paralogs originating from both DNA- and RNA-mediated duplication events and their evolutionary potential for assuming radically altered functions, as well as the degree to which they can function unconstrained from the pressure of gene conversion. Lastly, I explore theoretical population-genetic considerations of how the effective population size (N(e)) of a species may influence the probability of emergence of genes with radically altered functions.
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Affiliation(s)
- Vaishali Katju
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
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Sexual recombination is a signature of a persisting malaria epidemic in Peru. Malar J 2011; 10:329. [PMID: 22039962 PMCID: PMC3231964 DOI: 10.1186/1475-2875-10-329] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 10/31/2011] [Indexed: 11/22/2022] Open
Abstract
Background The aim of this study was to consider the impact that multi-clone, complex infections have on a parasite population structure in a low transmission setting. In general, complexity of infection (minimum number of clones within an infection) and the overall population level diversity is expected to be minimal in low transmission settings. Additionally, the parasite population structure is predicted to be clonal, rather than sexual due to infrequent parasite inoculation and lack of recombination between genetically distinct clones. However, in this low transmission of the Peruvian Amazon, complex infections are becoming more frequent, in spite of decreasing infection prevalence. In this study, it was hypothesized that sexual recombination between distinct clonal lineages of Plasmodium falciparum parasites were altering the subpopulation structure and effectively maintaining the population-level diversity. Methods Fourteen microsatellite markers were chosen to describe the genetic diversity in 313 naturally occurring P. falciparum infections from Peruvian Amazon. The population and subpopulation structure was characterized by measuring: clusteredness, expected heterozygosity (He), allelic richness, private allelic richness, and linkage disequilibrium. Next, microsatellite haplotypes and alleles were correlated with P. falciparum merozoite surface protein 1 Block 2 (Pfmsp1-B2) to examine the presence of recombinant microsatellite haplotypes. Results The parasite population structure consists of six genetically diverse subpopulations of clones, called "clusters". Clusters 1, 3, 4, and 6 have unique haplotypes that exceed 70% of the total number of clones within each cluster, while Clusters 2 and 5 have a lower proportion of unique haplotypes, but still exceed 46%. By measuring the He, allelic richness, and private allelic richness within each of the six subpopulations, relatively low levels of genetic diversity within each subpopulation (except Cluster 4) are observed. This indicated that the number of alleles, and not the combination of alleles, are limited. Next, the standard index of association (IAS) was measured, which revealed a significant decay in linkage disequilibrium (LD) associated with Cluster 6, which is indicative of independent assortment of alleles. This decay in LD is a signature of this subpopulation approaching linkage equilibrium by undergoing sexual recombination. To trace possible recombination events, the two most frequent microsatellite haplotypes observed over time (defined by either a K1 or Mad20) were selected as the progenitors and then potential recombinants were identified in within the natural population. Conclusions Contrary to conventional low transmission models, this study provides evidence of a parasite population structure that is superficially defined by a clonal backbone. Sexual recombination does occur and even arguably is responsible for maintaining the substructure of this population.
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Protein-based signatures of functional evolution in Plasmodium falciparum. BMC Evol Biol 2011; 11:257. [PMID: 21917172 PMCID: PMC3197514 DOI: 10.1186/1471-2148-11-257] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 09/14/2011] [Indexed: 02/06/2023] Open
Abstract
Background It has been known for over a decade that Plasmodium falciparum proteins are enriched in non-globular domains of unknown function. The potential for these regions of protein sequence to undergo high levels of genetic drift provides a fundamental challenge to attempts to identify the molecular basis of adaptive change in malaria parasites. Results Evolutionary comparisons were undertaken using a set of forty P. falciparum metabolic enzyme genes, both within the hominid malaria clade (P. reichenowi) and across the genus (P. chabaudi). All genes contained coding elements highly conserved across the genus, but there were also a large number of regions of weakly or non-aligning coding sequence. These displayed remarkable levels of non-synonymous fixed differences within the hominid malaria clade indicating near complete release from purifying selection (dN/dS ratio at residues non-aligning across genus: 0.64, dN/dS ratio at residues identical across genus: 0.03). Regions of low conservation also possessed high levels of hydrophilicity, a marker of non-globularity. The propensity for such regions to act as potent sources of non-synonymous genetic drift within extant P. falciparum isolates was confirmed at chromosomal regions containing genes known to mediate drug resistance in field isolates, where 150 of 153 amino acid variants were located in poorly conserved regions. In contrast, all 22 amino acid variants associated with drug resistance were restricted to highly conserved regions. Additional mutations associated with laboratory-selected drug resistance, such as those in PfATPase4 selected by spiroindolone, were similarly restricted while mutations in another calcium ATPase (PfSERCA, a gene proposed to mediate artemisinin resistance) that reach significant frequencies in field isolates were located exclusively in poorly conserved regions consistent with genetic drift. Conclusion Coding sequences of malaria parasites contain prospectively definable domains subject to neutral or nearly neutral evolution on a scale that appears unrivalled in biology. This distinct evolutionary landscape has potential to confound analytical methods developed for other genera. Against this tide of genetic drift, polymorphisms mediating functional change stand out to such an extent that evolutionary context provides a useful signal for identifying the molecular basis of drug resistance in malaria parasites, a finding that is of relevance to both genome-wide and candidate gene studies in this genus.
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Mu J, Seydel KB, Bates A, Su XZ. Recent Progress in Functional Genomic Research in Plasmodium falciparum. Curr Genomics 2011; 11:279-86. [PMID: 21119892 PMCID: PMC2930667 DOI: 10.2174/138920210791233081] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 02/22/2010] [Accepted: 03/09/2010] [Indexed: 02/02/2023] Open
Abstract
With the completion and near completion of many malaria parasite genome-sequencing projects, efforts are now being directed to a better understanding of gene functions and to the discovery of vaccine and drug targets. Inter- and intraspecies comparisons of the parasite genomes will provide invaluable insights into parasite evolution, virulence, drug resistance, and immune invasion. Genome-wide searches for loci under various selection pressures may lead to discovery of genes conferring drug resistance or encoding for protective antigens. In addition, the Plasmodium falciparum genome sequence provides the basis for the development of various microarrays to monitor gene expression and to detect nucleotide substitution and deletion/amplification. Genome-wide profiling of the parasite proteome, chromatin modification, and nucleosome position also depend on availability of the parasite genome. In this brief review, we will highlight some recent advances and studies in characterizing gene function and related phenotype in P. falciparum that were made possible by the genome sequence, particularly the development of a genome-wide diversity map and various high-throughput genotyping methods for genome-wide association studies (GWAS).
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Affiliation(s)
- Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Han K, Lee TY, Nikitopoulos DE, Soper SA, Murphy MC. A vertically stacked, polymer, microfluidic point mutation analyzer: rapid high accuracy detection of low-abundance K-ras mutations. Anal Biochem 2011; 417:211-9. [PMID: 21771577 DOI: 10.1016/j.ab.2011.06.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 06/15/2011] [Accepted: 06/23/2011] [Indexed: 01/06/2023]
Abstract
Recognition of point mutations in the K-ras gene can be used for the clinical management of several types of cancers. Unfortunately, several assay and hardware concerns must be addressed to allow users not well trained in performing molecular analyses the opportunity to undertake these measurements. To provide for a larger user base for these types of molecular assays, a vertically stacked microfluidic analyzer with a modular architecture and process automation was developed. The analyzer employs a primary polymerase chain reaction (PCR) coupled to an allele-specific ligase detection reaction (LDR). Each functional device, including continuous flow thermal reactors for the PCR and LDR, passive micromixers, and ExoSAP-IT purification, was designed and tested. Individual devices were fabricated in polycarbonate using hot embossing and were assembled using adhesive bonding for system assembly. The system produced LDR products from a DNA sample in approximately 1h, an 80% reduction in time compared with conventional benchtop instrumentation. Purifying the post-PCR products with the ExoSAP-IT enzyme led to optimized LDR performance, minimizing false-positive signals and producing reliable results. Mutant alleles in genomic DNA were quantified to the level of 0.25 ng of mutant DNA in 50 ng of wild-type DNA for a 25-μl sample, equivalent to DNA from 42 mutant cells.
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Affiliation(s)
- Kyudong Han
- Department of Nanobiomedical Science and WCU Research Center, Dankook University, Cheonan 330-714, Republic of Korea.
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Abstract
OBJECTIVE The evolutionary history of human malaria parasites (genus Plasmodium) has long been a subject of speculation and controversy. The complete genome sequences of the two most widespread human malaria parasites, P. falciparum and P. vivax, and of the monkey parasite P. knowlesi are now available, together with the draft genomes of the chimpanzee parasite P. reichenowi, three rodent parasites, P. yoelii yoelli, P. berghei and P. chabaudi chabaudi, and one avian parasite, P. gallinaceum. METHODS We present here an analysis of 45 orthologous gene sequences across the eight species that resolves the relationships of major Plasmodium lineages, and provides the first comprehensive dating of the age of those groups. RESULTS Our analyses support the hypothesis that the last common ancestor of P. falciparum and the chimpanzee parasite P. reichenowi occurred around the time of the human-chimpanzee divergence. P. falciparum infections of African apes are most likely derived from humans and not the other way around. On the other hand, P. vivax, split from the monkey parasite P. knowlesi in the much more distant past, during the time that encompasses the separation of the Great Apes and Old World Monkeys. CONCLUSION The results support an ancient association between malaria parasites and their primate hosts, including humans.
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Branch OH, Sutton PL, Barnes C, Castro JC, Hussin J, Awadalla P, Hijar G. Plasmodium falciparum genetic diversity maintained and amplified over 5 years of a low transmission endemic in the Peruvian Amazon. Mol Biol Evol 2010; 28:1973-86. [PMID: 21109587 PMCID: PMC3112368 DOI: 10.1093/molbev/msq311] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Plasmodium falciparum entered into the Peruvian Amazon in 1994, sparking an epidemic between 1995 and 1998. Since 2000, there has been sustained low P. falciparum transmission. The Malaria Immunology and Genetics in the Amazon project has longitudinally followed members of the community of Zungarococha (N = 1,945, 4 villages) with active household and health center-based visits each year since 2003. We examined parasite population structure and traced the parasite genetic diversity temporally and spatially. We genotyped infections over 5 years (2003–2007) using 14 microsatellite (MS) markers scattered across ten different chromosomes. Despite low transmission, there was considerable genetic diversity, which we compared with other geographic regions. We detected 182 different haplotypes from 302 parasites in 217 infections. Structure v2.2 identified five clusters (subpopulations) of phylogenetically related clones. To consider genetic diversity on a more detailed level, we defined haplotype families (hapfams) by grouping haplotypes with three or less loci differences. We identified 34 different hapfams identified. The Fst statistic and heterozygosity analysis showed the five clusters were maintained in each village throughout this time. A minimum spanning network (MSN), stratified by the year of detection, showed that haplotypes within hapfams had allele differences and haplotypes within a cluster definition were more separated in the later years (2006–2007). We modeled hapfam detection and loss, accounting for sample size and stochastic fluctuations in frequencies overtime. Principle component analysis of genetic variation revealed patterns of genetic structure with time rather than village. The population structure, genetic diversity, appearance/disappearance of the different haplotypes from 2003 to 2007 provides a genome-wide “real-time” perspective of P. falciparum parasites in a low transmission region.
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Affiliation(s)
- Oralee H Branch
- Department of Medical Parasitology, New York University, USA.
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Sullivan D. Uncertainty in mapping malaria epidemiology: implications for control. Epidemiol Rev 2010; 32:175-87. [PMID: 20581219 DOI: 10.1093/epirev/mxq013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Malaria is a location-specific, dynamic infectious disease transmitted by mosquitoes to humans and is influenced by environmental, vector, parasite, and host factors. The principal purposes of malarial epidemiology are 1) to describe the malarial distribution in space and time along with the physical, biologic, and social etiologic factors and 2) to guide control objectives for either modeling impact or measuring progress of control tactics. Mapping malaria and many of its causative factors has been achieved on many different levels from global distribution to biologic quantitative trait localization in humans, parasites, and mosquitoes. Despite these important achievements, a large degree of uncertainty still exists on the annual burden of malarial cases. Accurate, sensitive detection and treatment of asymptomatic reservoirs important to infectious transmission are additional components necessary for future control measures. Presently spurred by the leadership and funding of Bill and Melinda Gates, the malarial community is developing and implementing plans for elimination of malaria. The challenge for malariologists is to digitally integrate and map epidemiologic factors and intervention measures in space and time to target effective, sustainable control alongside research efforts.
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Affiliation(s)
- David Sullivan
- The Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA.
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Malaria parasite sequences from chimpanzee support the co-speciation hypothesis for the origin of virulent human malaria (Plasmodium falciparum). Mol Phylogenet Evol 2010; 57:135-43. [PMID: 20541613 DOI: 10.1016/j.ympev.2010.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 05/24/2010] [Accepted: 06/04/2010] [Indexed: 11/22/2022]
Abstract
Phylogenetic analyses of the mitochondrial cytochrome b (cytb), apicoplast caseinolytic protease C (clpC), and 18S rRNA sequences of Plasmodium isolates from chimpanzees along with those of the virulent human malaria parasite P. falciparum showed that the common chimpanzee (Pan troglodytes) malaria parasites, assigned by Rich et al. (2009) to P. reichenowi, constitute a paraphyletic assemblage. The assumption that P. falciparum diverged from P. reichenowi as recently as 5000-50,000 years ago would require a rate of synonymous substitution/site/year in cytb and clpC on the order of 10(-5)-10(-6), several orders of magnitude higher than any known from eukaryotic organelle genomes, and would imply an unrealistically recent timing of the most recent common ancestor of P. falciparum mitochondrial genomes. The available data are thus most consistent with the hypothesis that P. reichenowi (in the strict sense) and P. falciparum co-speciated with their hosts about 5-7 million years ago.
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The Historical Ecology of Human and Wild Primate Malarias in the New World. DIVERSITY-BASEL 2010. [DOI: 10.3390/d2020256] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Genetic mapping of targets mediating differential chemical phenotypes in Plasmodium falciparum. Nat Chem Biol 2009; 5:765-71. [PMID: 19734910 PMCID: PMC2784992 DOI: 10.1038/nchembio.215] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Accepted: 07/09/2009] [Indexed: 11/08/2022]
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Weiss GE, Crompton PD, Li S, Walsh LA, Moir S, Traore B, Kayentao K, Ongoiba A, Doumbo OK, Pierce SK. Atypical memory B cells are greatly expanded in individuals living in a malaria-endemic area. THE JOURNAL OF IMMUNOLOGY 2009; 183:2176-82. [PMID: 19592645 DOI: 10.4049/jimmunol.0901297] [Citation(s) in RCA: 333] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Epidemiological observations in malaria endemic areas have long suggested a deficiency in the generation and maintenance of B cell memory to Plasmodium falciparum (Pf) in individuals chronically reinfected with the parasite. Recently, a functionally and phenotypically distinct population of FCRL4(+) hyporesponsive memory B cells (MBCs) was reported to be expanded in HIV-infected individuals with high viral loads. In this study, we provide evidence that a phenotypically similar atypical MBC population is significantly expanded in Pf-exposed Malian adults and children as young as 2 years of age as compared with healthy U.S. adult controls. The number of these atypical MBCs was higher in children with chronic asymptomatic Pf infections compared with uninfected children, suggesting that the chronic presence of the parasite may drive expansion of these distinct MBCs. This is the first description of an atypical MBC phenotype associated with malaria. Understanding the origin and function of these MBCs could be important in informing the design of malaria vaccines.
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Affiliation(s)
- Greta E Weiss
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
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Pierce SK, Miller LH. World Malaria Day 2009: what malaria knows about the immune system that immunologists still do not. THE JOURNAL OF IMMUNOLOGY 2009; 182:5171-7. [PMID: 19380759 DOI: 10.4049/jimmunol.0804153] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Malaria kills >1 million children each year, and there is little doubt that an effective vaccine would play a central role in preventing these deaths. However, the strategies that proved so successful in developing the vaccines we have today may simply not be adequate to confront complex, persistent infectious diseases, including malaria, AIDS, and tuberculosis. We believe that the development of a highly effective vaccine will require a better understanding of several features of the immune response to malaria. At the top of the list is the complex and ancient relationship between the parasite that causes malaria and the immune system that enables the parasite to persist in an otherwise functional immune system. A close second is the antigenic targets in malaria and how to overcome the enormous polymorphism of these targets. Meeting these challenges represents a call to arms of basic immunologists to advance our knowledge of malaria immunity.
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Affiliation(s)
- Susan K Pierce
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Twinbrook II, 12441 Parklawn Drive, Room 200B, Mail Stop Code 8180, Rockville, MD 20852, USA.
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Su XZ, Jiang H, Yi M, Mu J, Stephens RM. Large-scale genotyping and genetic mapping in Plasmodium parasites. THE KOREAN JOURNAL OF PARASITOLOGY 2009; 47:83-91. [PMID: 19488413 DOI: 10.3347/kjp.2009.47.2.83] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 04/03/2009] [Indexed: 11/23/2022]
Abstract
The completion of many malaria parasite genomes provides great opportunities for genomewide characterization of gene expression and high-throughput genotyping. Substantial progress in malaria genomics and genotyping has been made recently, particularly the development of various microarray platforms for large-scale characterization of the Plasmodium falciparum genome. Microarray has been used for gene expression analysis, detection of single nucleotide polymorphism (SNP) and copy number variation (CNV), characterization of chromatin modifications, and other applications. Here we discuss some recent advances in genetic mapping and genomic studies of malaria parasites, focusing on the use of high-throughput arrays for the detection of SNP and CNV in the P. falciparum genome. Strategies for genetic mapping of malaria traits are also discussed.
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Affiliation(s)
- Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
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Glycophorin B is the erythrocyte receptor of Plasmodium falciparum erythrocyte-binding ligand, EBL-1. Proc Natl Acad Sci U S A 2009; 106:5348-52. [PMID: 19279206 DOI: 10.1073/pnas.0900878106] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the war against Plasmodium, humans have evolved to eliminate or modify proteins on the erythrocyte surface that serve as receptors for parasite invasion, such as the Duffy blood group, a receptor for Plasmodium vivax, and the Gerbich-negative modification of glycophorin C for Plasmodium falciparum. In turn, the parasite counters with expansion and diversification of ligand families. The high degree of polymorphism in glycophorin B found in malaria-endemic regions suggests that it also may be a receptor for Plasmodium, but, to date, none has been identified. We provide evidence from erythrocyte-binding that glycophorin B is a receptor for the P. falciparum protein EBL-1, a member of the Duffy-binding-like erythrocyte-binding protein (DBL-EBP) receptor family. The erythrocyte-binding domain, region 2 of EBL-1, expressed on CHO-K1 cells, bound glycophorin B(+) but not glycophorin B-null erythrocytes. In addition, glycophorin B(+) but not glycophorin B-null erythrocytes adsorbed native EBL-1 from the P. falciparum culture supernatants. Interestingly, the Efe pygmies of the Ituri forest in the Democratic Republic of the Congo have the highest gene frequency of glycophorin B-null in the world, raising the possibility that the DBL-EBP family may have expanded in response to the high frequency of glycophorin B-null in the population.
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Charlesworth B. Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nat Rev Genet 2009; 10:195-205. [PMID: 19204717 DOI: 10.1038/nrg2526] [Citation(s) in RCA: 958] [Impact Index Per Article: 63.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The effective size of a population, N(e), determines the rate of change in the composition of a population caused by genetic drift, which is the random sampling of genetic variants in a finite population. N(e) is crucial in determining the level of variability in a population, and the effectiveness of selection relative to drift. This article reviews the properties of N(e) in a variety of different situations of biological interest, and the factors that influence it. In particular, the action of selection means that N(e) varies across the genome, and advances in genomic techniques are giving new insights into how selection shapes N(e).
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Affiliation(s)
- Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.
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Neafsey DE, Schaffner SF, Volkman SK, Park D, Montgomery P, Milner DA, Lukens A, Rosen D, Daniels R, Houde N, Cortese JF, Tyndall E, Gates C, Stange-Thomann N, Sarr O, Ndiaye D, Ndir O, Mboup S, Ferreira MU, Moraes SDL, Dash AP, Chitnis CE, Wiegand RC, Hartl DL, Birren BW, Lander ES, Sabeti PC, Wirth DF. Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence. Genome Biol 2008; 9:R171. [PMID: 19077304 PMCID: PMC2646275 DOI: 10.1186/gb-2008-9-12-r171] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 12/15/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun to elucidate the demographic history of the species, as well as patterns of population structure and patterns of linkage disequilibrium within its genome. Such studies will be greatly enhanced by new genomic tools and recent large-scale efforts to map genomic variation. To that end, we have developed a high throughput single nucleotide polymorphism (SNP) genotyping platform for P. falciparum. RESULTS Using an Affymetrix 3,000 SNP assay array, we found roughly half the assays (1,638) yielded high quality, 100% accurate genotyping calls for both major and minor SNP alleles. Genotype data from 76 global isolates confirm significant genetic differentiation among continental populations and varying levels of SNP diversity and linkage disequilibrium according to geographic location and local epidemiological factors. We further discovered that nonsynonymous and silent (synonymous or noncoding) SNPs differ with respect to within-population diversity, inter-population differentiation, and the degree to which allele frequencies are correlated between populations. CONCLUSIONS The distinct population profile of nonsynonymous variants indicates that natural selection has a significant influence on genomic diversity in P. falciparum, and that many of these changes may reflect functional variants deserving of follow-up study. Our analysis demonstrates the potential for new high-throughput genotyping technologies to enhance studies of population structure, natural selection, and ultimately enable genome-wide association studies in P. falciparum to find genes underlying key phenotypic traits.
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Affiliation(s)
- Daniel E Neafsey
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
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Catania F, Wurmser F, Potekhin AA, Przybos E, Lynch M. Genetic diversity in the Paramecium aurelia species complex. Mol Biol Evol 2008; 26:421-31. [PMID: 19023087 DOI: 10.1093/molbev/msn266] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Current understanding of the population genetics of free-living unicellular eukaryotes is limited, and the amount of genetic variability in these organisms is still a matter of debate. We characterized-reproductively and genetically-worldwide samples of multiple Paramecium species belonging to a cryptic species complex, Paramecium aurelia, whose species have been shown to be reproductively isolated. We found that levels of genetic diversity both in the nucleus and in the mitochondrion are substantial within groups of reproductively compatible P. aurelia strains but drop considerably when strains are partitioned according to their phylogenetic groupings. Our study reveals the existence of discrepancies between the mating behavior of a number of P. aurelia strains and their multilocus genetic profile, a controversial finding that has major consequences for both the current methods of species assignment and the species problem in the P. aurelia complex.
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Carlton JM, Escalante AA, Neafsey D, Volkman SK. Comparative evolutionary genomics of human malaria parasites. Trends Parasitol 2008; 24:545-50. [PMID: 18938107 DOI: 10.1016/j.pt.2008.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Revised: 09/10/2008] [Accepted: 09/12/2008] [Indexed: 10/21/2022]
Abstract
The parasites Plasmodium falciparum and Plasmodium vivax are responsible for the majority of human malaria cases worldwide. Despite many similarities in their biology, they frequently are studied in isolation. With the completion of the P. vivax genome and the generation of an initial P. falciparum genetic diversity map, attempts are being made to infer inter- and intra-species genome evolution. Here, we briefly review our current knowledge of comparative evolutionary genomics of the two species in the light of several presentations at the Molecular Approaches to Malaria 2008 meeting in Lorne, Australia and ask the question: can evolutionary genomics of one species inform the other?
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Affiliation(s)
- Jane M Carlton
- Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, USA.
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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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Weedall GD, Polley SD, Conway DJ. Gene-specific signatures of elevated non-synonymous substitution rates correlate poorly across the Plasmodium genus. PLoS One 2008; 3:e2281. [PMID: 18509456 PMCID: PMC2384006 DOI: 10.1371/journal.pone.0002281] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Accepted: 04/13/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Comparative genome analyses of parasites allow large scale investigation of selective pressures shaping their evolution. An acute limitation to such analysis of Plasmodium falciparum is that there is only very partial low-coverage genome sequence of the most closely related species, the chimpanzee parasite P. reichenowi. However, if orthologous genes have been under similar selective pressures throughout the Plasmodium genus then positive selection on the P. falciparum lineage might be predicted to some extent by analysis of other lineages. PRINCIPAL FINDINGS Here, three independent pairs of closely related species in different sub-generic clades (P. falciparum and P. reichenowi; P. vivax and P. knowlesi; P. yoelii and P. berghei) were compared for a set of 43 candidate ligand genes considered likely to be under positive directional selection and a set of 102 control genes for which there was no selective hypothesis. The ratios of non-synonymous to synonymous substitutions (dN/dS) were significantly elevated in the candidate ligand genes compared to control genes in each of the three clades. However, the rank order correlation of dN/dS ratios for individual candidate genes was very low, less than the correlation for the control genes. SIGNIFICANCE The inability to predict positive selection on a gene in one lineage by identifying elevated dN/dS ratios in the orthologue within another lineage needs to be noted, as it reflects that adaptive mutations are generally rare events that lead to fixation in individual lineages. Thus it is essential to complete the genome sequences of particular species of phylogenetic importance, such as P. reichenowi.
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Affiliation(s)
- Gareth D Weedall
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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ATHANASIADOU S, HUNTLEY JF. Emerging technologies and their applications in interactions between nutrition and immunity to gastrointestinal parasites in sheep. Parasite Immunol 2008; 30:101-11. [DOI: 10.1111/j.1365-3024.2008.00993.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Amodu OK, Hartl DL, Roy SW. Patterns of polymorphism in genomic regions flanking three highly polymorphic surface antigens in Plasmodium falciparum. Mol Biochem Parasitol 2007; 159:1-6. [PMID: 18291540 DOI: 10.1016/j.molbiopara.2007.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Revised: 12/04/2007] [Accepted: 12/10/2007] [Indexed: 10/22/2022]
Abstract
Many surface antigens of the human malaria parasite Plasmodium falciparum show extraordinary diversity, with different alleles being so divergent as to be unalignable in some coding regions. To better understand the population history and modes of selection on such loci, we sequenced genomic regions flanking the highly polymorphic genes merozoite surface protein-1, merozoite surface protein-2, and circumsporozoite protein, from reference isolates of P. falciparum. Diversity was much lower in genomic flanking regions than in the coding sequences. Average pairwise nucleotide diversity for these regions was 0.00088, similar to other genomic regions not thought to be evolving under balancing selection, suggesting against balancing selection acting on promoter regions of these genes. Most observed polymorphisms were singletons. A higher ratio of SNPs to indels than previously reported for P. falciparum was observed. An 11 bp repeat upstream of msp2 showed an intriguing pattern of polymorphism possibly suggestive of purifying selection on total allele length.
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Affiliation(s)
- Olukemi K Amodu
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Iriko H, Kaneko O, Otsuki H, Tsuboi T, Su XZ, Tanabe K, Torii M. Diversity and evolution of the rhoph1/clag multigene family of Plasmodium falciparum. Mol Biochem Parasitol 2007; 158:11-21. [PMID: 18155305 DOI: 10.1016/j.molbiopara.2007.11.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Revised: 11/05/2007] [Accepted: 11/06/2007] [Indexed: 11/19/2022]
Abstract
A complex of high-molecular-mass proteins (PfRhopH) of the human malaria parasite Plasmodium falciparum induces host protective immunity and therefore is a candidate for vaccine development. Understanding the level of polymorphism and the evolutionary processes is important for advancements in both vaccine design and knowledge of the evolution of cell invasion in this parasite. In the present study, we sequenced the entire open reading frames of seven genes encoding the proteins of the PfRhopH complex (rhoph2, rhoph3, and five rhoph1/clag gene paralogs). We found that four rhoph1/clag genes (clag2, 3.1, 3.2, and 8) were highly polymorphic. Amino acid substitutions and indels are predominantly clustered around amino acid positions 1000-1200 of these four rhoph1/clag genes. An excess of nonsynonymous substitutions over synonymous substitutions was detected for clag8 and 9, indicating positive selection. The McDonald-Kreitman test with a Plasmodium reichenowi orthologous sequence also supports positive selection on clag8. Based on the ratio of interspecific genetic distance to intraspecific distance, the time to the most recent common ancestor of the clag2 and 8 polymorphisms was estimated to be 1.89 and 0.87 million years ago, respectively, assuming divergence of P. falciparum and P. reichenowi 6 million years ago. In addition to a copy number polymorphism, gene conversion events were detected for the rhoph1/clag genes on chromosome 3, which likely play a role in increasing the diversity of each locus. Our results indicate that a high diversity of the PfRhopH1/Clag multigene family is maintained by diversifying selection forces over a considerably long period.
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Affiliation(s)
- Hideyuki Iriko
- Department of Molecular Parasitology, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
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Terzić N, Opsenica D, Milić D, Tinant B, Smith KS, Milhous WK, Solaja BA. Deoxycholic Acid-Derived Tetraoxane Antimalarials and Antiproliferatives. J Med Chem 2007; 50:5118-27. [PMID: 17887664 DOI: 10.1021/jm070684m] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis of deoxycholic acid (DCA)- and cholic acid (CA)-derived mixed tetraoxanes revealed that N-(2-dimethylamino)ethyl derivatives are potent antimalarials in vitro and in vivo. The tetraoxanes presented in this paper are dual inhibitors: besides curing mice in vivo without observed toxic effects, they kill cancer cell lines at very low concentrations. For example, DCA and CA derivatives 16 and 25 cured 3/5 (160 mg/kg/day) and 2/5 (40 mg/kg/day, MTD >960 mg/kg), respectively, and they were extremely active against melanoma LOX IMVI cancer, LC50 = 22 nM and 69 nM, respectively.
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Affiliation(s)
- Natasa Terzić
- Institute of Chemistry, Technology and Metallurgy, Belgrade, Serbia
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Teodorovic S, Braverman JM, Elmendorf HG. Unusually low levels of genetic variation among Giardia lamblia isolates. EUKARYOTIC CELL 2007; 6:1421-30. [PMID: 17557879 PMCID: PMC1951139 DOI: 10.1128/ec.00138-07] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Accepted: 05/29/2007] [Indexed: 11/20/2022]
Abstract
Giardia lamblia, an intestinal pathogen of mammals, including humans, is a significant cause of diarrheal disease around the world. Additionally, the parasite is found on a lineage which separated early from the main branch in eukaryotic evolution. The extent of genetic diversity among G. lamblia isolates is insufficiently understood, but this knowledge is a prerequisite to better understand the role of parasite variation in disease etiology and to examine the evolution of mechanisms of genetic exchange among eukaryotes. Intraisolate genetic variation in G. lamblia has never been estimated, and previous studies on interisolate genetic variation have included a limited sample of loci. Here we report a population genetics study of intra- and interisolate genetic diversity based on six coding and four noncoding regions from nine G. lamblia isolates. Our results indicate exceedingly low levels of genetic variation in two out of three G. lamblia groups that infect humans; this variation is sufficient to allow identification of isolate-specific markers. Low genetic diversity at both coding and noncoding regions, with an overall bias towards synonymous substitutions, was discovered. Surprisingly, we found a dichotomous haplotype structure in the third, more variable G. lamblia group, represented by a haplotype shared with one of the homogenous groups and an additional group-specific haplotype. We propose that the distinct patterns of genetic-variation distribution among lineages are a consequence of the presence of genetic exchange. More broadly, our findings have implications for the regulation of gene expression, as well as the mode of reproduction in the parasite.
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Affiliation(s)
- Smilja Teodorovic
- Biology Department, 406 Reiss Bldg., 37th and O Sts. NW, Georgetown University, Washington, DC 20057, USA
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Su X, Hayton K, Wellems TE. Genetic linkage and association analyses for trait mapping in Plasmodium falciparum. Nat Rev Genet 2007; 8:497-506. [PMID: 17572690 DOI: 10.1038/nrg2126] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genetic studies of Plasmodium falciparum laboratory crosses and field isolates have produced valuable insights into determinants of drug responses, antigenic variation, disease virulence, cellular development and population structures of these virulent human malaria parasites. Full-genome sequences and high-resolution haplotype maps of SNPs and microsatellites are now available for all 14 parasite chromosomes. Rapidly increasing genetic and genomic information on Plasmodium parasites, mosquitoes and humans will combine as a rich resource for new advances in our understanding of malaria, its transmission and its manifestations of disease.
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Affiliation(s)
- Xinzhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike Bethesda, Maryland 20892-8132, USA
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Annan Z, Durand P, Ayala FJ, Arnathau C, Awono-Ambene P, Simard F, Razakandrainibe FG, Koella JC, Fontenille D, Renaud F. Population genetic structure of Plasmodium falciparum in the two main African vectors, Anopheles gambiae and Anopheles funestus. Proc Natl Acad Sci U S A 2007; 104:7987-92. [PMID: 17470800 PMCID: PMC1876559 DOI: 10.1073/pnas.0702715104] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We investigated patterns of genetic diversity of Plasmodium falciparum associated with its two main African vectors: Anopheles gambiae and Anopheles funestus. We dissected 10,296 wild-caught mosquitoes from three tropical sites, two in Cameroon (Simbock and Tibati, separated by 320 km) and one in Kenya (Rota, >2,000 km from the other two sites). We assayed seven microsatellite loci in 746 oocysts from 183 infected mosquito guts. Genetic polymorphism was very high in parasites isolated from both vector species. The expected heterozygosity (H(E)) was 0.79 in both species; the observed heterozygosities (H(O)) were 0.32 in A. funestus and 0.42 in A. gambiae, indicating considerable inbreeding within both vector species. Mean selfing (s) between genetically identical gametes was s = 0.33. Differences in the rate of inbreeding were statistically insignificant among sites and between the two vector species. As expected, because of the high rate of inbreeding, linkage disequilibrium was very high; it was significant for all 21 loci pairs in A. gambiae and for 15 of 21 pairs in A. funestus, although only two pairwise comparisons were between loci on the same chromosome. Overall, the genetic population structure of P. falciparum, as evaluated by F statistics, was predominantly clonal rather than panmictic, a population structure that facilitates the spread of antimalarial drug and vaccine resistance and thus may impair the effectiveness of malaria control efforts.
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Affiliation(s)
- Zeinab Annan
- *Génétique et Evolution des Maladies Infectieuses, Unité Mixte de Recherche-Institut de Recherche pour le Développement/Centre National de la Recherche Scientifique 2724, B.P. 64501, 34394 Montpellier Cedex 5, France
- Laboratoire de Lutte Contre les Insectes Nuisibles, Unité de Recherche 016-Institut de Recherche pour le Développement, B.P. 64501, 34394 Montpellier Cedex 5, France
| | - Patrick Durand
- *Génétique et Evolution des Maladies Infectieuses, Unité Mixte de Recherche-Institut de Recherche pour le Développement/Centre National de la Recherche Scientifique 2724, B.P. 64501, 34394 Montpellier Cedex 5, France
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
- To whom correspondence should be addressed at:
Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA 92697-2525. E-mail:
| | - Céline Arnathau
- *Génétique et Evolution des Maladies Infectieuses, Unité Mixte de Recherche-Institut de Recherche pour le Développement/Centre National de la Recherche Scientifique 2724, B.P. 64501, 34394 Montpellier Cedex 5, France
| | - Parfait Awono-Ambene
- Laboratoire de Recherche sur le Paludisme-Institut de Recherche pour le Développement, Organisation de Coordination pour la Lutte Contre les Endémies en Afrique Centrale, B.P. 288, Yaoundé, Cameroon
| | - Frédéric Simard
- Laboratoire de Recherche sur le Paludisme-Institut de Recherche pour le Développement, Organisation de Coordination pour la Lutte Contre les Endémies en Afrique Centrale, B.P. 288, Yaoundé, Cameroon
| | - Fabien G. Razakandrainibe
- Laboratoire de Parasitologie Evolutive, Unité Mixte de Recherche-Centre National de la Recherche Scientifique 7103, Université Pierre et Marie Curie, 75252 Paris, France; and
| | - Jacob C. Koella
- **Division of Biology, Imperial College London, Silwood Park, Ascot, Berkshire SL5 7PY, United Kingdom
| | - Didier Fontenille
- Laboratoire de Lutte Contre les Insectes Nuisibles, Unité de Recherche 016-Institut de Recherche pour le Développement, B.P. 64501, 34394 Montpellier Cedex 5, France
| | - François Renaud
- *Génétique et Evolution des Maladies Infectieuses, Unité Mixte de Recherche-Institut de Recherche pour le Développement/Centre National de la Recherche Scientifique 2724, B.P. 64501, 34394 Montpellier Cedex 5, France
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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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Flanagan JF, Blus BJ, Kim D, Clines KL, Rastinejad F, Khorasanizadeh S. Molecular implications of evolutionary differences in CHD double chromodomains. J Mol Biol 2007; 369:334-42. [PMID: 17433364 PMCID: PMC1948097 DOI: 10.1016/j.jmb.2007.03.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 03/09/2007] [Indexed: 11/16/2022]
Abstract
Double chromodomains occur in CHD proteins, which are ATP-dependent chromatin remodeling factors implicated in RNA polymerase II transcription regulation. Biochemical studies suggest important differences in the histone H3 tail binding of different CHD chromodomains. In human and Drosophila, CHD1 double chromodomains bind lysine 4-methylated histone H3 tail, which is a hallmark of transcriptionally active chromatin in all eukaryotes. Here, we present the crystal structure of the yeast CHD1 double chromodomains, and pinpoint their differences with that of the human CHD1 double chromodomains. The most conserved residues in these double chromodomains are the two chromoboxes that orient adjacently. Only a subset of CHD chromoboxes can form an aromatic cage for methyllysine binding, and methyllysine binding requires correctly oriented inserts. These factors preclude yeast CHD1 double chromodomains from interacting with the histone H3 tail. Despite great sequence similarity between the human CHD1 and CHD2 chromodomains, variation within an insert likely prevents CHD2 double chromodomains from binding lysine 4-methylated histone H3 tail as efficiently as in CHD1. By using the available structural and biochemical data we highlight the evolutionary specialization of CHD double chromodomains, and provide insights about their targeting capacities.
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Affiliation(s)
- John F Flanagan
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
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49
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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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50
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Mu J, Awadalla P, Duan J, McGee KM, Keebler J, Seydel K, McVean GAT, Su XZ. Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome. Nat Genet 2006; 39:126-30. [PMID: 17159981 DOI: 10.1038/ng1924] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Accepted: 11/02/2006] [Indexed: 11/09/2022]
Abstract
One goal in sequencing the Plasmodium falciparum genome, the agent of the most lethal form of malaria, is to discover vaccine and drug targets. However, identifying those targets in a genome in which approximately 60% of genes have unknown functions is an enormous challenge. Because the majority of known malaria antigens and drug-resistant genes are highly polymorphic and under various selective pressures, genome-wide analysis for signatures of selection may lead to discovery of new vaccine and drug candidates. Here we surveyed 3,539 P. falciparum genes ( approximately 65% of the predicted genes) for polymorphisms and identified various highly polymorphic loci and genes, some of which encode new antigens that we confirmed using human immune sera. Our collections of genome-wide SNPs ( approximately 65% nonsynonymous) and polymorphic microsatellites and indels provide a high-resolution map (one marker per approximately 4 kb) for mapping parasite traits and studying parasite populations. In addition, we report new antigens, providing urgently needed vaccine candidates for disease control.
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Affiliation(s)
- Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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