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Abstract
Three common systemic human fungal pathogens--Cryptococcus neoformans, Candida albicans and Aspergillus fumigatus--have retained all the machinery to engage in sexual reproduction, and yet their populations are often clonal with limited evidence for recombination. Striking parallels have emerged with four protozoan parasites that infect humans: Toxoplasma gondii, Trypanosoma brucei, Trypanosoma cruzi and Plasmodium falciparum. Limiting sexual reproduction appears to be a common virulence strategy, enabling generation of clonal populations well adapted to host and environmental niches, yet retaining the ability to engage in sexual or parasexual reproduction and respond to selective pressure. Continued investigation of the sexual nature of microbial pathogens should facilitate both laboratory investigation and an understanding of the complex interplay between pathogens, hosts, vectors, and their environments.
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Affiliation(s)
- Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA.
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Mohammed AO, Attalla B, Bashir FMK, Ahmed FE, El Hassan AM, Ibnauf G, Jiang W, Cavalli-Sforza LL, Karrar ZAA, Ibrahim ME. Relationship of the sickle cell gene to the ethnic and geographic groups populating the Sudan. Public Health Genomics 2006; 9:113-20. [PMID: 16612062 DOI: 10.1159/000091489] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The presence of a geographical pattern in the distribution of the sickle cell gene (S gene) and its association with malaria is well documented. To study the distribution of the S gene among various ethnic and linguistic groups in the Sudan we analyzed a hospital-based sample of 189 sickle cell anemia (SCA) patients who reported to the Khartoum Teaching Hospital between June 1996 and March 2000 and 118 controls with other complaints, against their ethnic and linguistic affiliations and geographic origin. Electrophoresis for hemoglobin S and sickling tests were carried out on all patients and controls as a prerequisite for inclusion. The majority of patients (93.7%) belonged to families of single ethnic descent, indicating the high degree of within-group marriages and thus the higher risk of augmenting the gene. SCA was found to be predominant among the Afro-Asiatic-speaking groups (68.4%) including nomadic groups of Arab and non- Arab descent that migrated to the Sudan in various historical epochs. Those patients clustered in western Sudan (Kordofan and Darfur) from where 73% of all cases originate. The proportion of patients reporting from other geographic areas like the south (3.1%), which is primarily inhabited by Nilo-Saharan-speaking groups (19% of the whole sample) who populated the country in previous times, is disproportionate to their total population in the country (chi(2) = 71.6; p = 0.0001). Analysis of the haplotypes associated with the S gene indicated that the most abundant haplotypes are the Cameroon, Benin, Bantu and Senegal haplotypes, respectively. No relationship was seen between haplotypes and the various hematological parameters in the sub-sample analyzed for such association. These results provide an insight into the distribution of the sickle cell gene in the Sudan, and highlight the strong link of the middle Nile Valley with West Africa through the open plateau of the Sahel and the nomadic cattle herders and also probably the relatively young age of the S gene.
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Affiliation(s)
- Abdelrahim O Mohammed
- Department of Biochemistry, Faculty of Medicine University of Khartoum, Khartoum, Sudan.
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53
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Gomez A, Suarez CF, Martinez P, Saravia C, Patarroyo MA. High polymorphism in Plasmodium vivax merozoite surface protein-5 (MSP5). Parasitology 2006; 133:661-72. [PMID: 16978450 DOI: 10.1017/s0031182006001168] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Revised: 06/16/2006] [Accepted: 06/21/2006] [Indexed: 11/07/2022]
Abstract
A key issue relating to developing multi-component anti-malarial vaccines, lies in studying Plasmodium vivax surface proteins' genetic variation. The present work was aimed at amplifying, cloning and sequencing the gene encoding P. vivax merozoite surface protein 5 (PvMSP5) in samples obtained from infected patients from Colombian areas having varying malaria transmission rates. Nucleotide sequence data reported in this paper are available in the GenBank, EMBL and DDBJ databases under Accessions numbers DQ341586 to DQ341601. Our results have revealed that PvMSP5 is one of the P. vivax surface proteins having greater polymorphism, this being restricted to specific protein regions. The intron and exon II (which includes the GPI anchor and EGF-like domain) were both highly conserved when compared to exon I; exon I displayed the greatest variation and most of the recombination events occurred within it. No geographical grouping was observed. The Nei-Gojobori test revealed significant positive selection in the samples analysed here, whereas Tajima and Fu and Li tests presented a neutral selection pattern. The results reflected a localized variation pattern, recombination between PvMSP5 alleles and also functional and immune pressures, where stronger selective forces might be acting on exon I than on exon II, suggesting that the latter could be an important region to be included in an anti-malarial vaccine.
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Affiliation(s)
- A Gomez
- Molecular Biology Department, Fundacion Instituto de Inmunologia de Colombia, Carrera 50#26-00, Bogota, Colombia
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54
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Volkman SK, Lozovsky E, Barry AE, Bedford T, Bethke L, Myrick A, Day KP, Hartl DL, Wirth DF, Sawyer SA. Genomic heterogeneity in the density of noncoding single-nucleotide and microsatellite polymorphisms in Plasmodium falciparum. Gene 2006; 387:1-6. [PMID: 17005334 PMCID: PMC2593462 DOI: 10.1016/j.gene.2006.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Revised: 07/06/2006] [Accepted: 07/24/2006] [Indexed: 11/25/2022]
Abstract
The density and distribution of single-nucleotide polymorphisms (SNPs) across the genome has important implications for linkage disequilibrium mapping and association studies, and the level of simple-sequence microsatellite polymorphisms has important implications for the use of oligonucleotide hybridization methods to genotype SNPs. To assess the density of these types of polymorphisms in P. falciparum, we sampled introns and noncoding DNA upstream and downstream of coding regions among a variety of geographically diverse parasites. Across 36,229 base pairs of noncoding sequence representing 41 genetic loci, a total of 307 polymorphisms including 248 polymorphic microsatellites and 39 SNPs were identified. We found a significant excess of microsatellite polymorphisms having a repeat unit length of one or two, compared to those with longer repeat lengths, as well as a nonrandom distribution of SNP polymorphisms. Almost half of the SNPs localized to only three of the 41 genetic loci sampled. Furthermore, we find significant differences in the frequency of polymorphisms across the two chromosomes (2 and 3) examined most extensively, with an excess of SNPs and a surplus of polymorphic microsatellites on chromosome 3 as compared to chromosome 2 (P=0.0001). Furthermore, at some individual genetic loci we also find a nonrandom distribution of polymorphisms between coding and flanking noncoding sequences, where completely monomorphic regions may flank highly polymorphic genes. These data, combined with our previous findings of nonrandom distribution of SNPs across chromosome 2, suggest that the Plasmodium falciparum genome may be a mosaic with regard to genetic diversity, containing chromosomal regions that are highly polymorphic interspersed with regions that are much less polymorphic.
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Affiliation(s)
- Sarah K. Volkman
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA USA
| | - Elena Lozovsky
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA USA
| | - Alyssa E. Barry
- Department of Medical Parasitology, New York University School of Medicine, New York, NY USA
| | - Trevor Bedford
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA USA
| | - Lara Bethke
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA USA
| | - Alissa Myrick
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA USA
| | - Karen P. Day
- Department of Medical Parasitology, New York University School of Medicine, New York, NY USA
| | - Daniel L. Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA USA
| | - Dyann F. Wirth
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA USA
- *Address for Correspondence 665 Huntington Avenue, I-703, Boston, MA 02115 USA, Tel: 617 432 4629, Fax: 617 432 4766,
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55
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Templeton AR. Haplotype trees and modern human origins. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2006; Suppl 41:33-59. [PMID: 16369961 DOI: 10.1002/ajpa.20351] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A haplotype is a multisite haploid genotype at two or more polymorphic sites on the same chromosome in a defined DNA region. An evolutionary tree of the haplotypes can be estimated if the DNA region had little to no recombination. Haplotype trees can be used to reconstruct past human gene-flow patterns and historical events, but any single tree captures only a small portion of evolutionary history, and is subject to error. A fuller view of human evolution requires multiple DNA regions, and errors can be minimized by cross-validating inferences across loci. An analysis of 25 DNA regions reveals an out-of-Africa expansion event at 1.9 million years ago. Gene flow with isolation by distance was established between African and Eurasian populations by about 1.5 million years ago, with no detectable interruptions since. A second out-of-Africa expansion occurred about 700,000 years ago, and involved interbreeding with at least some Eurasian populations. A third out-of-Africa event occurred around 100,000 years ago, and was also characterized by interbreeding, with the hypothesis of a total Eurasian replacement strongly rejected (P < 10(-17)). This does not preclude the possibility that some Eurasian populations could have been replaced, and the status of Neanderthals is indecisive. Demographic inferences from haplotype trees have been inconsistent, so few definitive conclusions can be made at this time. Haplotype trees from human parasites offer additional insights into human evolution and raise the possibility of an Asian isolate of humanity, but once again not in a definitive fashion. Haplotype trees can also indicate which genes were subject to positive selection in the lineage leading to modern humans. Genetics provides many insights into human evolution, but those insights need to be integrated with fossil and archaeological data to yield a fuller picture of the origin of modern humans.
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Affiliation(s)
- Alan R Templeton
- Department of Biology, Washington University, St. Louis, Missouri 63130-4899, USA.
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56
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Barry AE, Leliwa-Sytek A, Man K, Kasper JM, Hartl DL, Day KP. Variable SNP density in aspartyl-protease genes of the malaria parasite Plasmodium falciparum. Gene 2006; 376:163-73. [PMID: 16784823 DOI: 10.1016/j.gene.2006.02.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2005] [Revised: 02/14/2006] [Accepted: 02/14/2006] [Indexed: 10/24/2022]
Abstract
An analysis of the diversity of the aspartyl proteases of Plasmodium falciparum, known as plasmepsins (PMs), was completed in view of their possible role as drug targets. DNA sequence polymorphisms were identified in nine pm genes including their non-coding (introns and 5' flanking) sequences. All genes contained at least one single nucleotide polymorphism (SNP). Extensive microsatellite diversity was observed predominantly in non-coding sequences. All but one non-synonymous polymorphism (a conservative substitution) were mapped to the surface of the predicted protein, contradicting a possible role in enzymatic activity. The distribution of SNPs was found to be non-random among pm genes, with pm6 and pm10 having significantly higher SNP densities, suggesting they were under selection. For pm6 the majority of the SNPs were in introns and some of these may contribute to splice site variation. SNPs were found at a high density in both the coding and non-coding sequences of pm10. Recombination was important in generating additional diversity at this locus. Although direct selection for pm10 mutations could not be ruled out, the presence of balancing selection and a high density of SNPs in non-coding sequence led us to propose that another gene under selection may be influencing the diversity in the region. By sequencing short DNA tags in a 200 kb region flanking pm10 we show that a cluster of antigen genes, known to be under diversifying selection, may contribute to the observed diversity. We discuss the importance of diversity and local selection effects when choosing drug targets for intervention strategies.
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Affiliation(s)
- Alyssa E Barry
- Peter Medawar Building for Pathogen Research and Zoology Department, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK.
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57
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Kidgell C, Volkman SK, Daily J, Borevitz JO, Plouffe D, Zhou Y, Johnson JR, Le Roch KG, Sarr O, Ndir O, Mboup S, Batalov S, Wirth DF, Winzeler EA. A systematic map of genetic variation in Plasmodium falciparum. PLoS Pathog 2006; 2:e57. [PMID: 16789840 PMCID: PMC1480597 DOI: 10.1371/journal.ppat.0020057] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Accepted: 04/28/2006] [Indexed: 11/25/2022] Open
Abstract
Discovering novel genes involved in immune evasion and drug resistance in the human malaria parasite, Plasmodium falciparum, is of critical importance to global health. Such knowledge may assist in the development of new effective vaccines and in the appropriate use of antimalarial drugs. By performing a full-genome scan of allelic variability in 14 field and laboratory strains of P. falciparum, we comprehensively identified ≈500 genes evolving at higher than neutral rates. The majority of the most variable genes have paralogs within the P. falciparum genome and may be subject to a different evolutionary clock than those without. The group of 211 variable genes without paralogs contains most known immunogens and a few drug targets, consistent with the idea that the human immune system and drug use is driving parasite evolution. We also reveal gene-amplification events including one surrounding pfmdr1, the P. falciparum multidrug-resistance gene, and a previously uncharacterized amplification centered around the P. falciparum GTP cyclohydrolase gene, the first enzyme in the folate biosynthesis pathway. Although GTP cyclohydrolase is not the known target of any current drugs, downstream members of the pathway are targeted by several widely used antimalarials. We speculate that an amplification of the GTP cyclohydrolase enzyme in the folate biosynthesis pathway may increase flux through this pathway and facilitate parasite resistance to antifolate drugs. Variability in the genome of the human malaria parasite, Plasmodium falciparum, is key to the parasite's ability to cause disease and overcome therapeutic interventions such as drugs and vaccines. Elucidating the extent of genetic variation in the malaria parasite will therefore be central to decreasing the malaria disease burden. The authors performed a full-genome scan of variability in different strains of P. falciparum and observed a nonrandom distribution of variation. In particular, those genes that are predicted to have roles in evading the host immune response or antimalarial drugs show significantly higher levels of variation. In addition, the authors speculate that a previously unreported genome amplification in the folate biosynthesis pathway correlates with resistance to the antimalarial drug sulfadoxine. Such data enable hypotheses to be made about the function of many of the unknown elements in the parasite's genome, which may permit the identification of new targets that can be investigated for incorporation into a malaria vaccine and may aid in the understanding of how the parasite withstands drug pressure.
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Affiliation(s)
- Claire Kidgell
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Johanna Daily
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Justin O Borevitz
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - David Plouffe
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Yingyao Zhou
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Jeffrey R Johnson
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Karine G. Le Roch
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Ousmane Sarr
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Omar Ndir
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Soulyemane Mboup
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Serge Batalov
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Elizabeth A Winzeler
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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58
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Pearce-Duvet JMC. The origin of human pathogens: evaluating the role of agriculture and domestic animals in the evolution of human disease. Biol Rev Camb Philos Soc 2006; 81:369-82. [PMID: 16672105 DOI: 10.1017/s1464793106007020] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Revised: 02/23/2006] [Accepted: 02/24/2006] [Indexed: 11/06/2022]
Abstract
Many significant diseases of human civilization are thought to have arisen concurrently with the advent of agriculture in human society. It has been hypothesised that the food produced by farming increased population sizes to allow the maintenance of virulent pathogens, i.e. civilization pathogens, while domestic animals provided sources of disease to humans. To determine the relationship between pathogens in humans and domestic animals, I examined phylogenetic data for several human pathogens that are commonly evolutionarily linked to domestic animals: measles, pertussis, smallpox, tuberculosis, taenid worms, and falciparal malaria. The majority are civilization pathogens, although I have included others whose evolutionary origins have traditionally been ascribed to domestic animals. The strongest evidence for a domestic-animal origin exists for measles and pertussis, although the data do not exclude a non-domestic origin. As for the other pathogens, the evidence currently available makes it difficult to determine if the domestic-origin hypothesis is supported or refuted; in fact, intriguing data for tuberculosis and taenid worms suggests that transmission may occur as easily from humans to domestic animals. These findings do not abrogate the importance of agriculture in disease transmission; rather, if anything, they suggest an alternative, more complex series of effects than previously elucidated. Rather than domestication, the broader force for human pathogen evolution could be ecological change, namely anthropogenic modification of the environment. This is supported by evidence that many current emerging infectious diseases are associated with human modification of the environment. Agriculture may have changed the transmission ecology of pre-existing human pathogens, increased the success of pre-existing pathogen vectors, resulted in novel interactions between humans and wildlife, and, through the domestication of animals, provided a stable conduit for human infection by wildlife diseases.
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59
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Chookajorn T, Hartl DL. Position-specific polymorphism of Plasmodium falciparum Stuttering motif in a PHISTc PFI1780w. Exp Parasitol 2006; 114:126-8. [PMID: 16674945 DOI: 10.1016/j.exppara.2006.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Revised: 02/23/2006] [Accepted: 02/24/2006] [Indexed: 11/22/2022]
Abstract
Several genes of Plasmodium falciparum are positively selected due to the pressure from the host immune system. This is a pattern completely opposite to that found in most housekeeping genes, which have few synonymous mutations. The discrepancy is an important topic in Plasmodium biology. We searched for unique polymorphism patterns in P. falciparum and identified a repetitive Stuttering motif in PFI1780w which was recently grouped as a gene in the PHIST family. The repeat has a position-specific polymorphism pattern in the otherwise highly conserved gene. Its mutations are limited to only one small region, and they are not consistent with replication slippage or gene conversion commonly found in low complexity regions. The repeat variation was analyzed in different strains of P. falciparum. The PFI1780w Stuttering motif can be a model to study gene diversification and used as a tool for strain typing.
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Affiliation(s)
- Thanat Chookajorn
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
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60
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Ninokata A, Kimura R, Samakkarn U, Settheetham-Ishida W, Ishida T. Coexistence of five G6PD variants indicates ethnic complexity of Phuket islanders, Southern Thailand. J Hum Genet 2006; 51:424-428. [PMID: 16528451 DOI: 10.1007/s10038-006-0380-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Accepted: 01/16/2006] [Indexed: 10/24/2022]
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzymopathy in humans. The prevalence of G6PD deficiency and its molecular basis were studied in Phuket islanders, Southern Thailand. A total of 345 volunteers (123 males and 222 females) were recruited in this study. Infection with Plasmodium falciparum or Plasmodium vivax was not detected in any of these subjects by polymerase chain reaction (PCR)-based diagnosis. G6PD-deficient individuals were identified with the WST-8/1-methoxy PMS method. The molecular basis of G6PD deficiency was investigated by PCR-direct sequencing procedures or PCR-restriction enzyme fragment length polymorphism assays. The numbers of individuals showing severe and mild G6PD deficiency were 14 and 21, respectively. A high prevalence of G6PD deficiency was observed in subjects with Moken (15.4%) or Thai (15.5%) ethnic background. G6PD Mahidol (487G>A) (n=14), G6PD Viangchan (871G>A) (n=11), G6PD Gaohe (95A>G) (n=2), G6PD Kaiping (1388G>A) (n=1), and G6PD Kerala-Kalyan (949G>A) (n=1) were identified. The results suggest that several groups of people of the Asian Continent, such as Burmese, Laotian or Cambodian, Thai and Chinese, participated in the establishment of the ethnic identity of the current ethnic groups of Phuket Island.
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Affiliation(s)
- Aya Ninokata
- Department of Biological Sciences, Unit of Human Genetics, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryosuke Kimura
- Department of Human Genetics, School of International Health, Graduate School of Medical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | | | - Takafumi Ishida
- Department of Biological Sciences, Unit of Human Genetics, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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61
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Abstract
One of the goals of systems-biology research is to discover networks and interactions by integrating diverse data sets. So far, systems-biology research has focused on model organisms, which are well characterized and therefore suited to testing new methods. Systems biology has great potential for use in the search for therapies for disease. Here, the potential of systems-biology approaches in the search for new drugs and vaccines to treat malaria is examined.
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Affiliation(s)
- Elizabeth A Winzeler
- Department of Cell Biology, ICND202, The Scripps Research Institute, La Jolla, California 92037, USA.
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62
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Bhattacharya D, Haque R, Singh U. Coding and noncoding genomic regions of Entamoeba histolytica have significantly different rates of sequence polymorphisms: implications for epidemiological studies. J Clin Microbiol 2005; 43:4815-9. [PMID: 16145147 PMCID: PMC1234137 DOI: 10.1128/jcm.43.9.4815-4819.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To evaluate genetic variability among Entamoeba histolytica strains, we sequenced 9,077 bp from each of 14 isolates. The polymorphism rates from coding and noncoding regions were significantly different (0.07% and 0.37%, respectively), indicating that these regions are subject to different selection pressures. Additionally, single nucleotide polymorphisms (SNPs) potentially associated with specific clinical outcomes were identified.
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Affiliation(s)
- Dhruva Bhattacharya
- Department of Microbiology and Immunology, Division of Infectious Diseases, Stanford, CA 94305, USA
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63
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Lim CS, Tazi L, Ayala FJ. Plasmodium vivax: recent world expansion and genetic identity to Plasmodium simium. Proc Natl Acad Sci U S A 2005; 102:15523-8. [PMID: 16227436 PMCID: PMC1266129 DOI: 10.1073/pnas.0507413102] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plasmodium vivax causes the most geographically widespread human malaria, accounting annually for 70-80 million clinical cases throughout the tropical and subtropical regions of the world's continents. We have analyzed the DNA sequences of the Csp (circumsporozoite protein) gene in 24 geographically representative strains of P. vivax and 2 of P. simium, which parasitizes several species of New World monkeys. The Csp sequences are of two types, VK210 and VK247, which differ by three diagnostic amino acid replacements, one in each of the 5' and 3' terminal regions [5' nonrepeat (NR) and 3' NR] of the gene and in an insertion sequence that precedes the 3' NR region. The central region of the gene consists of approximately 38 repetitive "motifs," which are alternatively four and five amino acids long, which also are diagnostically different between the VK210 and VK247 types. There are very few synonymous substitutions within and between the two types of strains, which we hypothesize reflects that the worldwide spread of P. vivax is very recent. The two P. simium Csp sequences belong one to each of the two VK types and are genetically indistinguishable from the corresponding P. vivax strains, suggesting that at least two host transfers have occurred between humans and New World monkeys. We exclude as unlikely the possibility that the two types of sequences could have independently arisen in humans and platyrrhines by natural selection. There are reasons favoring each of the two possible directions of host transfer between humans and monkeys.
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Affiliation(s)
- Chae Seung Lim
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
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64
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Hall N, Carlton J. Comparative genomics of malaria parasites. Curr Opin Genet Dev 2005; 15:609-13. [PMID: 16182520 DOI: 10.1016/j.gde.2005.09.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Accepted: 09/09/2005] [Indexed: 11/20/2022]
Abstract
In the past few years, the area of comparative genomics of malaria parasites has begun to come of age, with the completion of genome sequencing projects of four Plasmodium species, and several functional genomics studies. A picture is emerging of a parasite genome that is highly adapted to its mammalian and vector hosts, and which uses post-transcriptional gene-silencing as one method for the control of gene expression. The genome is compartmentalized into a core of conserved housekeeping genes, sandwiched between subtelomerically located genes encoding surface antigens. Species-specific gene families shape the preference of the parasite for host cells, in addition to determining interactions with the host immune-system. Recent research has led to the description of a motif that is conserved across Plasmodium species and which plays a central role in protein export into the host cell.
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Affiliation(s)
- Neil Hall
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20851, USA.
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65
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Martin MJ, Rayner JC, Gagneux P, Barnwell JW, Varki A. Evolution of human-chimpanzee differences in malaria susceptibility: relationship to human genetic loss of N-glycolylneuraminic acid. Proc Natl Acad Sci U S A 2005; 102:12819-24. [PMID: 16126901 PMCID: PMC1200275 DOI: 10.1073/pnas.0503819102] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Chimpanzees are the closest evolutionary cousins of humans, sharing >99% identity in most protein sequences. Plasmodium falciparum is the major worldwide cause of malaria mortality. Plasmodium reichenowi, a morphologically identical and genetically very similar parasite, infects chimpanzees but not humans. Conversely, experimental P. falciparum infection causes brief moderate parasitization and no severe infection in chimpanzees. This surprising host specificity remains unexplained. We modified and enhanced traditional methods for measuring sialic acid (Sia)-dependent recognition of glycophorins by merozoite erythrocyte-binding proteins, eliminating interference caused by endogenous Sias on transfected cells, and by using erythroleukemia cells to allow experimental manipulation of Sia content. We present evidence that these remarkable differences among such closely related host-parasite pairs is caused by species-specific erythrocyte-recognition profiles, apparently related to the human-specific loss of the common primate Sia N-glycolylneuraminic acid. The major merozoite-binding protein erythrocyte-binding antigen-175 of P. falciparum apparently evolved to take selective advantage of the excess of the Sia N-acetylneuraminic acid (the precursor of N-glycolylneuraminic acid) on human erythrocytes. The contrasting preference of P. reichenowi erythrocyte-binding antigen-175 for N-glycolylneuraminic acid is likely the ancestral condition. The surprising ability of P. falciparum to cause disease in New World Aotus monkeys (geographically isolated from P. falciparum until arrival of peoples from the Old World) can be explained by parallel evolution of a human-like Sia expression pattern in these distantly related primates. These results also have implications for the prehistory of hominids and for the genetic origins and recent emergence of P. falciparum as a major human pathogen.
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Affiliation(s)
- Maria J Martin
- Glycobiology Research and Training Center and Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
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66
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Steiper ME, Wolfe ND, Karesh WB, Kilbourn AM, Bosi EJ, Ruvolo M. The population genetics of the alpha-2 globin locus of orangutans (Pongo pygmaeus). J Mol Evol 2005; 60:400-8. [PMID: 15871050 DOI: 10.1007/s00239-004-0201-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2004] [Accepted: 10/04/2004] [Indexed: 11/30/2022]
Abstract
In this study, the molecular population genetics of the orangutan's alpha-2 globin (HBA2) gene were investigated in order to test for the action of natural selection. Haplotypes from 28 orangutan chromosomes were collected from a 1.46-kilobase region of the alpha-2 globin locus. While many aspects of the data were consistent with neutrality, the observed heterogeneous distribution of polymorphisms was inconsistent with neutral expectations. Furthermore, a single amino acid variant, found in both the Bornean and the Sumatran orangutan subspecies, was associated with different alternative synonymous variants in each subspecies, suggesting that the allele may have spread separately through the two subspecies after two distinct origination events. This variant is not in Hardy-Weinberg equilibrium (HWE). These observations are consistent with neutral models that incorporate population structure and models that invoke selection. The orangutan Plasmodium parasite is a plausible selective agent that may underlie the variation at alpha-2 globin in orangutans.
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Affiliation(s)
- Michael E Steiper
- Department of Anthropology, Hunter College-City University of New York, New York, 10021, USA.
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67
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68
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Abstract
The population structure of Plasmodial parasites, especially Plasmodium falciparum, has received much attention in the recent years. Like many other micropathogens, the debate has focused on the clonality/sexuality question. Considered a panmictic species for very long, P. falciparum actually exhibits strong departures from panmictic expectations in many of its populations, which corroborates the proposal that it is able to undergo uniparental propagation.(1) The currently accepted idea to account for this surprising result is kind of "mechanical" self-fertilization due to the lack of availability of gametes with different genetic make-ups in low transmission areas. However, it could be misleading to make this simple working hypothesis a dogma, for many other explanations are possible (unknown cycles, sibling species, mating types) that deserve to be explored as well. The consequences of this combination of uniparental(1) and sexual propagation on the circulation of genes of interest (drug resistance, antigenic variability, pathogenicity) are discussed, together with the need to use more sophisticated technologies, analysing much broader samples and considering better the host and vector factors in P. falciparum population dynamics.
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Affiliation(s)
- C Gauthier
- Unit of Research 165 "Genetics and Evolution of Infectious Diseases", UMR CNRS/IRD 2724, IRD, BP 64501, 34394 Montpellier Cedex 5, France
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69
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Jongwutiwes S, Putaporntip C, Iwasaki T, Ferreira MU, Kanbara H, Hughes AL. Mitochondrial genome sequences support ancient population expansion in Plasmodium vivax. Mol Biol Evol 2005; 22:1733-9. [PMID: 15901839 DOI: 10.1093/molbev/msi168] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Examination of nucleotide diversity in 106 mitochondrial genomes of the most geographically widespread human malaria parasite, Plasmodium vivax, revealed a level of diversity similar to, but slightly higher than, that seen in the virulent human malaria parasite Plasmodium falciparum. The pairwise distribution of nucleotide differences among mitochondrial genome sequences supported the hypothesis that both these parasites underwent ancient population expansions. We estimated the age of the most recent common ancestor (MRCA) of the mitochondrial genomes of both P. vivax and P. falciparum at around 200,000-300,000 years ago. This is close to the previous estimates of the time of the human mitochondrial MRCA and the origin of modern Homo sapiens, consistent with the hypothesis that both these Plasmodium species were parasites of the hominid lineage before the origin of modern H. sapiens and that their population expansion coincided with the population expansion of their host.
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Affiliation(s)
- Somchai Jongwutiwes
- Department of Molecular Epidemiology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
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70
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Neafsey DE, Hartl DL, Berriman M. Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes. Mol Biol Evol 2005; 22:1621-6. [PMID: 15858207 DOI: 10.1093/molbev/msi154] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We compared levels of sequence divergence between fourfold synonymous coding sites and noncoding sites from the intergenic and intronic regions of the Plasmodium falciparum and Plasmodium reichenowi genomes. We observed significant differences in the level of divergence between these classes of silent sites. Fourfold synonymous coding sites exhibited the highest level of sequence divergence, followed by introns, and then intergenic sequences. This pattern of relative divergence rates has been observed in primate genomes but was unexpected in Plasmodium due to a paucity of variation at silent sites in P. falciparum and the corollary hypothesis that silent sites in this genome may be subject to atypical selective constraints. Exclusion of hypermutable CpG dinucleotides reduces the divergence level of synonymous coding sites to that of intergenic sites but does not diminish the significantly higher divergence level of introns relative to intergenic sites. A greater than expected incidence of CpG dinucleotides in intergenic regions less than 500 bp from genes may indicate selective maintenance of regulatory motifs containing CpGs. Divergence rates of different classes of silent sites in these Plasmodium genomes are determined by a combination of mutational and selective pressures.
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Affiliation(s)
- Daniel E Neafsey
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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71
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Abstract
This minireview summarizes the historical development of bacterial population genetic concepts since the early 1980s. Initially multilocus enzyme electrophoresis was used to determine population structures but this technique is poorly portable between laboratories and was replaced in 1998 by multilocus sequence typing. Diverse population structures exist in different bacterial species. Two distinctive structures are described in greater detail. "Young" organisms, such as Yersinia pestis, have evolved or undergone a severe bottleneck in recent millennia and have not yet accumulated much sequence diversity. "genoclouds" in subgroup III Neisseria meningitidis arise because of the accumulation of diversity due to herd immunity, which is then purified during subsequent epidemic spread.
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Affiliation(s)
- Mark Achtman
- Department of Molecular Biology, Max-Planck Institut für Infektionsbiologie, Schumannstrasse 21122, D-10117 Berlin, Germany.
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72
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Escalante AA, Cornejo OE, Freeland DE, Poe AC, Durrego E, Collins WE, Lal AA. A monkey's tale: the origin of Plasmodium vivax as a human malaria parasite. Proc Natl Acad Sci U S A 2005; 102:1980-5. [PMID: 15684081 PMCID: PMC548581 DOI: 10.1073/pnas.0409652102] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2004] [Indexed: 01/24/2023] Open
Abstract
The high prevalence of Duffy negativity (lack of the Duffy blood group antigen) among human populations in sub-Saharan Africa has been used to argue that Plasmodium vivax originated on that continent. Here, we investigate the phylogenetic relationships among 10 species of Plasmodium that infect primates by using three genes, two nuclear (beta-tubulin and cell division cycle 2) and a gene from the plastid genome (the elongation factor Tu). We find compelling evidence that P. vivax is derived from a species that inhabited macaques in Southeast Asia. Specifically, those phylogenies that include P. vivax as an ancient lineage from which all of the macaque parasites could originate are significantly less likely to explain the data. We estimate the time to the most recent common ancestor at four neutral gene loci from Asian and South American isolates (a minimum sample of seven isolates per locus). Our analysis estimates that the extant populations of P. vivax originated between 45,680 and 81,607 years ago. The phylogeny and the estimated time frame for the origination of current P. vivax populations are consistent with an "out of Asia" origin for P. vivax as hominoid parasite. The current debate regarding how the Duffy negative trait became fixed in Africa needs to be revisited, taking into account not only human genetic data but also the genetic diversity observed in the extant P. vivax populations and the phylogeny of the genus Plasmodium.
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Affiliation(s)
- Ananias A Escalante
- Division of Parasitic Diseases, Centers for Disease Control and Prevention, Chamblee, GA 30341, USA.
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73
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Singh N, Preiser P, Rénia L, Balu B, Barnwell J, Blair P, Jarra W, Voza T, Landau I, Adams JH. Conservation and developmental control of alternative splicing in maebl among malaria parasites. J Mol Biol 2004; 343:589-99. [PMID: 15465047 DOI: 10.1016/j.jmb.2004.08.047] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Revised: 08/11/2004] [Accepted: 08/13/2004] [Indexed: 11/18/2022]
Abstract
Genes of malaria parasites and other unicellular organisms have larger exons with fewer and smaller introns than metaozoans. Such differences in gene structure are perceived to extend to simpler mechanisms for transcriptional control and mRNA processing. Instead, we discovered a surprisingly complex level of post-transcriptional mRNA processing in analysis of maebl transcripts in several Plasmodium species. Mechanisms for internal alternative cis-splicing and exon skipping were active in multiple life cycle stages to change exon structure in the deduced coding sequence (CDS). The major alternatively spliced transcript utilized a less favorable acceptor splice site, which shifted codon triplet usage to a different CDS with a hydrophilic C terminus, changing the canonical type I membrane MAEBL product to a predicted soluble isoform. We found that developmental control of the alternative splicing pattern was distinct from the canonical splicing pattern. Western blot analysis indicated that MAEBL expression was better correlated with the appearance of the canonical ORF1 transcript. Together these data reveal that RNA metabolism in unicellular eukaryotes like Plasmodium is more sophisticated than believed and may have a significant role regulating gene expression in Plasmodium.
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Affiliation(s)
- Naresh Singh
- Department of Biological Sciences, University of Notre Dame, 220 Galvin, PO Box 369, Notre Dame, IN 46556, USA
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74
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Tanabe K, Sakihama N, Hattori T, Ranford-Cartwright L, Goldman I, Escalante AA, Lal AA. Genetic Distance in Housekeeping Genes Between Plasmodium falciparum and Plasmodium reichenowi and Within P. falciparum. J Mol Evol 2004; 59:687-94. [PMID: 15693624 DOI: 10.1007/s00239-004-2662-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The time to the most recent common ancestor of the extant populations of Plasmodium falciparum is controversial. The controversy primarily stems from the limited availability of sequences from Plasmodium reichenowi, a chimpanzee malaria parasite closely related to P. falciparum. Since the rate of nucleotide substitution differs in different loci and DNA regions, the estimation of genetic distance between P. falciparum and P. reichenowi should be performed using orthologous sequences that are evolving neutrally. Here, we obtained full-length sequences of two housekeeping genes, sarcoplasmic and endoplasmic reticulum Ca2+ -ATPase (serca) and lactate dehydrogenase (ldh), from 11 isolates of P. falciparum and 1 isolate of P. reichenowi and estimate the interspecific genetic distance (divergence) between the two species and intraspecific genetic distance (polymorphism) within P. falciparum. Interspecific distance and intraspecific distance at synonymous sites of interspecies-conserved regions of serca and ldh were 0.0672 +/- 0.0088 and 0.0011 +/- 0.0007, respectively, using the Nei and Gojobori method. Based on the ratio of interspecific distance to intraspecific distance, the time to the most recent common ancestor of P. falciparum was estimated to be (8.30 +/- 5.40) x 10(4) and (11.62 +/- 7.56) x 10(4) years ago, assuming the divergence time of the two parasite species to be 5 and 7 million years ago, respectively.
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Affiliation(s)
- Kazuyuki Tanabe
- Laboratory of Biology, faculty of Engineering, Osaka Institute of Technology, Ohmiya 5-16-1, Asahi-ku, Osaka 535-8585, Japan.
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75
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Rich SM. The unpredictable past of Plasmodium vivax revealed in its genome. Proc Natl Acad Sci U S A 2004; 101:15547-8. [PMID: 15505201 PMCID: PMC524848 DOI: 10.1073/pnas.0405618101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Stephen M Rich
- Division of Infectious Diseases, Tufts University, North Grafton, MA 01536, USA.
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76
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Leclerc MC, Durand P, Gauthier C, Patot S, Billotte N, Menegon M, Severini C, Ayala FJ, Renaud F. Meager genetic variability of the human malaria agent Plasmodium vivax. Proc Natl Acad Sci U S A 2004; 101:14455-60. [PMID: 15328406 PMCID: PMC521958 DOI: 10.1073/pnas.0405186101] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Malaria is a major human parasitic disease caused by four species of Plasmodium protozoa. Plasmodium vivax, the most widespread, affects millions of people across Africa, Asia, the Middle East, and Central and South America. We have studied the genetic variability of 13 microsatellite loci in 108 samples from 8 localities in Asia, Africa, South America, and New Guinea. Only one locus is polymorphic; nine are completely monomorphic, and the remaining three are monomorphic in all but one or two populations, which have a rare second allele. In contrast, Plasmodium falciparum displays extensive microsatellite polymorphism within and among populations. We further have analyzed, in 96 samples from the same 8 localities, 8 tandem repeats (TRs) located on a 100-kb contiguous chromosome segment described as highly polymorphic. Each locus exhibits 2-10 alleles in the whole sample but little intrapopulation polymorphism (1-5 alleles with a prevailing allele in most cases). Eight microsatellite loci monomorphic in P. vivax are polymorphic in three of five Plasmodium species related to P. vivax (two to seven individuals sampled). Plasmodium simium, a parasite of New World monkeys, is genetically indistinguishable from P. vivax. At 13 microsatellite loci and at 7 of the 8 TRs, both species share the same (or most common) allele. Scarce microsatellite polymorphism may reflect selective sweeps or population bottlenecks in recent evolutionary history of P. vivax; the differential variability of the TRs may reflect selective processes acting on particular regions of the genome. We infer that the world expansion of P. vivax as a human parasite occurred recently, perhaps <10,000 years ago.
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Affiliation(s)
- M C Leclerc
- Unité Mixte de Recherche 2724, Institut de Recherche pour le Développement et Centre National de la Recherche Scientifique, 911 Avenue Agropolis, 34394 Montpellier Cedex 5, France
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77
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Abstract
Over the past 35 years, the incidence of malaria has increased 2-3-fold. At present, it affects 300-500 million people and causes about 1 million deaths, primarily in Africa. The continuing upsurge has come from a coincidence of drug-resistant parasites, insecticide-resistant mosquitoes, global climate change and continuing poverty and political instability. An analogous rapid increase in malaria might have taken place about 10,000 years ago. Patterns of genetic variation in mitochondrial DNA support this model, but variation in nuclear genes gives an ambiguous message. Resolving these discrepancies has implications for the evolution of drug resistance and vaccine evasion.
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Affiliation(s)
- Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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78
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Affiliation(s)
- David J Conway
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
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79
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Abstract
The sequencing of eukaryotic genomes has lagged behind sequencing of organisms in the other domains of life, archae and bacteria, primarily due to their greater size and complexity. With recent advances in high-throughput technologies such as robotics and improved computational resources, the number of eukaryotic genome sequencing projects has increased significantly. Among these are a number of sequencing projects of tropical pathogens of medical and veterinary importance, many of which are responsible for causing widespread morbidity and mortality in peoples of developing countries. Uncovering the complete gene complement of these organisms is proving to be of immense value in the development of novel methods of parasite control, such as antiparasitic drugs and vaccines, as well as the development of new diagnostic tools. Combining pathogen genome sequences with the host and vector genome sequences is promising to be a robust method for the identification of host-pathogen interactions. Finally, comparative sequencing of related species, especially of organisms used as model systems in the study of the disease, is beginning to realize its potential in the identification of genes, and the evolutionary forces that shape the genes, that are involved in evasion of the host immune response.
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Affiliation(s)
- Jane M Carlton
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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80
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Barry AE, Leliwa A, Choi M, Nielsen KM, Hartl DL, Day KP. DNA sequence artifacts and the estimation of time to the most recent common ancestor (TMRCA) of Plasmodium falciparum. Mol Biochem Parasitol 2003; 130:143-7. [PMID: 12946852 DOI: 10.1016/s0166-6851(03)00164-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Alyssa E Barry
- The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK.
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81
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Su XZ, Mu J, Joy DA. The "Malaria's Eve" hypothesis and the debate concerning the origin of the human malaria parasite Plasmodium falciparum. Microbes Infect 2003; 5:891-6. [PMID: 12919857 DOI: 10.1016/s1286-4579(03)00173-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The debate over whether the human malaria parasite Plasmodium falciparum underwent a recent severe population bottleneck ("Malaria's Eve" hypothesis) has attracted great attention recently. Understanding the genetic diversity and evolutionary history of the parasite has practical implications for developing disease control measures.
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Affiliation(s)
- Xin Zhuan Su
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-0425, USA.
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82
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Feng X, Carlton JM, Joy DA, Mu J, Furuya T, Suh BB, Wang Y, Barnwell JW, Su XZ. Single-nucleotide polymorphisms and genome diversity in Plasmodium vivax. Proc Natl Acad Sci U S A 2003; 100:8502-7. [PMID: 12799466 PMCID: PMC166258 DOI: 10.1073/pnas.1232502100] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2003] [Indexed: 01/26/2023] Open
Abstract
The study of genetic variation in malaria parasites has practical significance for developing strategies to control the disease. Vaccines based on highly polymorphic antigens may be confounded by allelic restriction of the host immune response. In response to drug pressure, a highly plastic genome may generate resistant mutants more easily than a monomorphic one. Additionally, the study of the distribution of genomic polymorphisms may provide information leading to the identification of genes associated with traits such as parasite development and drug resistance. Indeed, the age and diversity of the human malaria parasite Plasmodium falciparum has been the subject of recent debate, because an ancient parasite with a complex genome is expected to present greater challenges for drug and vaccine development. The genome diversity of the important human pathogen Plasmodium vivax, however, remains essentially unknown. Here we analyze an approximately 100-kb contiguous chromosome segment from five isolates, revealing 191 single-nucleotide polymorphisms (SNPs) and 44 size polymorphisms. The SNPs are not evenly distributed across the segment with blocks of high and low diversity. Whereas the majority (approximately 63%) of the SNPs are in intergenic regions, introns contain significantly less SNPs than intergenic sequences. Polymorphic tandem repeats are abundant and are more uniformly distributed at a frequency of about one polymorphic tandem repeat per 3 kb. These data show that P. vivax has a highly diverse genome, and provide useful information for further understanding the genome diversity of the parasite.
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Affiliation(s)
- Xiaorong Feng
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - Jane M. Carlton
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - Deirdre A. Joy
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - Tetsuya Furuya
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - Bernard B. Suh
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - Yufeng Wang
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - John W. Barnwell
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - Xin-Zhuan Su
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
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83
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Charlesworth D. Effects of inbreeding on the genetic diversity of populations. Philos Trans R Soc Lond B Biol Sci 2003; 358:1051-70. [PMID: 12831472 PMCID: PMC1693193 DOI: 10.1098/rstb.2003.1296] [Citation(s) in RCA: 306] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The study of variability within species is important to all biologists who use genetic markers. Since the discovery of molecular variability among normal individuals, data have been collected from a wide range of organisms, and it is important to understand the major factors affecting diversity levels and patterns. Comparisons of inbreeding and outcrossing populations can contribute to this understanding, and therefore studying plant populations is important, because related species often have different breeding systems. DNA sequence data are now starting to become available from suitable plant and animal populations, to measure and compare variability levels and test predictions.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Cell, Animal and Population Biology (ICAPB), University of Edinburgh, Ashworth Laboratory, King's Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
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84
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Abstract
The protozoan parasite Toxoplasma gondii is endemic worldwide. For such a widespread pathogen that has few geographic or host boundaries, it possess an unexpected population structure comprised principally of three clonally propagated lineages. The origin and the evolutionary dynamics of these three lines are unclear. Recent population genetic analyses suggest that a meiotic recombination between two discrete gene pools produces a pandemic outbreak of three super-successful lines, which have recently come to dominate most other strains worldwide.
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Affiliation(s)
- Michael E Grigg
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, 2733 Heather Street, BC, V5Z 3J5, Vancouver, Canada.
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85
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Abstract
Immune responses that kill pathogens or reduce their reproductive rate are generally important in protecting hosts from infection and disease. Pathogens that escape the full impact of such responses will survive, and any heritable genetic basis of this evasion will be selected. Due to the memory component of vertebrate immune responses, pathogens with rare alleles of a target antigen can have an advantage over those with common alleles, leading to the maintenance of a polymorphism. At the genetic level, there ought to be detectable signatures of balancing selection in the genes encoding these antigens. Here, methods for identifying these selective signatures are reviewed. Their practical utility for identifying which antigens are targets of protective immune responses is discussed.
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Affiliation(s)
- D J Conway
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT.
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86
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Joy DA, Feng X, Mu J, Furuya T, Chotivanich K, Krettli AU, Ho M, Wang A, White NJ, Suh E, Beerli P, Su XZ. Early origin and recent expansion of Plasmodium falciparum. Science 2003; 300:318-21. [PMID: 12690197 DOI: 10.1126/science.1081449] [Citation(s) in RCA: 248] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The emergence of virulent Plasmodium falciparum in Africa within the past 6000 years as a result of a cascade of changes in human behavior and mosquito transmission has recently been hypothesized. Here, we provide genetic evidence for a sudden increase in the African malaria parasite population about 10,000 years ago, followed by migration to other regions on the basis of variation in 100 worldwide mitochondrial DNA sequences. However, both the world and some regional populations appear to be older (50,000 to 100,000 years old), suggesting an earlier wave of migration out of Africa, perhaps during the Pleistocene migration of human beings.
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MESH Headings
- Africa
- Agriculture
- Animals
- Anopheles/classification
- Anopheles/genetics
- Asia
- DNA, Mitochondrial/genetics
- DNA, Protozoan/genetics
- Emigration and Immigration
- Evolution, Molecular
- Genes, Protozoan
- Genetic Variation
- Genome, Protozoan
- Haplotypes
- Humans
- Insect Vectors/classification
- Insect Vectors/genetics
- Introns
- Likelihood Functions
- Malaria, Falciparum/parasitology
- Malaria, Falciparum/transmission
- Mutation
- Pan troglodytes/genetics
- Papua New Guinea
- Plasmodium/genetics
- Plasmodium falciparum/genetics
- Plasmodium falciparum/physiology
- Polymorphism, Single Nucleotide
- Population Density
- RNA, Ribosomal/genetics
- Selection, Genetic
- Sequence Analysis, DNA
- South America
- Time
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Affiliation(s)
- Deirdre A Joy
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-0425, USA.
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87
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Wu Y, Wang X, Liu X, Wang Y. Data-mining approaches reveal hidden families of proteases in the genome of malaria parasite. Genome Res 2003; 13:601-16. [PMID: 12671001 PMCID: PMC430172 DOI: 10.1101/gr.913403] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The search for novel antimalarial drug targets is urgent due to the growing resistance of Plasmodium falciparum parasites to available drugs. Proteases are attractive antimalarial targets because of their indispensable roles in parasite infection and development, especially in the processes of host erythrocyte rupture/invasion and hemoglobin degradation. However, to date, only a small number of proteases have been identified and characterized in Plasmodium species. Using an extensive sequence similarity search, we have identified 92 putative proteases in the P. falciparum genome. A set of putative proteases including calpain, metacaspase, and signal peptidase I have been implicated to be central mediators for essential parasitic activity and distantly related to the vertebrate host. Moreover, of the 92, at least 88 have been demonstrated to code for gene products at the transcriptional levels, based upon the microarray and RT-PCR results, and the publicly available microarray and proteomics data. The present study represents an initial effort to identify a set of expressed, active, and essential proteases as targets for inhibitor-based drug design.
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Affiliation(s)
- Yimin Wu
- Department of Protistology, American Type Culture Collection, Manassas, Virginia 20110, USA
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88
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Hume JCC, Lyons EJ, Day KP. Human migration, mosquitoes and the evolution of Plasmodium falciparum. Trends Parasitol 2003; 19:144-9. [PMID: 12643998 DOI: 10.1016/s1471-4922(03)00008-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To date, coalescent analysis of the Plasmodium falciparum genome sequence has failed to provide a unifying theory regarding the parasite's evolution. While a better understanding of the evolution of the malaria genome will undoubtedly clarify the current controversy, the importance of the parasite's interplay with both the human host and mosquito vector cannot be underestimated. Changes in the population biology or ecology of either one of these species have consequences for malaria transmission and this was never more apparent than in the environmental changes brought about by the advent of agriculture.
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Affiliation(s)
- Jennifer C C Hume
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Oxford, UK OX1 3SY.
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89
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Abstract
The study of viral molecular genetics has produced a considerable body of research into the sequences and phylogenetic relationships of human and animal viruses. A review of this literature suggests that humans have been afflicted by viruses throughout their evolutionary history, although the number and types have changed. Some viruses show evidence of long-standing intimate relationship and cospeciation with hominids, while others are more recently acquired from other species, including African monkeys and apes while our line was evolving in that continent, and domesticated animals and rodents since the Neolithic. Viral selection for specific resistance polymorphisms is unlikely, but in conjunction with other parasites, viruses have probably contributed to selection pressure maintaining major histocompatibility complex (MHC) diversity and a strong immune response. They may also have played a role in the loss in our lineage of N-glycolylneuraminic acid (Neu5Gc), a cell-surface receptor for many infectious agents. Shared viruses could have affected hominid species diversity both by promoting divergence and by weeding out less resistant host populations, while viruses carried by humans and other animals migrating out of Africa may have contributed to declines in other populations. Endogenous retroviral insertions since the divergence between humans and chimpanzees were capable of directly affecting hominid evolution through changes in gene expression and development.
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90
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Gutacker MM, Smoot JC, Migliaccio CAL, Ricklefs SM, Hua S, Cousins DV, Graviss EA, Shashkina E, Kreiswirth BN, Musser JM. Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains. Genetics 2002; 162:1533-43. [PMID: 12524330 PMCID: PMC1462380 DOI: 10.1093/genetics/162.4.1533] [Citation(s) in RCA: 176] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Several human pathogens (e.g., Bacillus anthracis, Yersinia pestis, Bordetella pertussis, Plasmodium falciparum, and Mycobacterium tuberculosis) have very restricted unselected allelic variation in structural genes, which hinders study of the genetic relationships among strains and strain-trait correlations. To address this problem in a representative pathogen, 432 M. tuberculosis complex strains from global sources were genotyped on the basis of 230 synonymous (silent) single nucleotide polymorphisms (sSNPs) identified by comparison of four genome sequences. Eight major clusters of related genotypes were identified in M. tuberculosis sensu stricto, including a single cluster representing organisms responsible for several large outbreaks in the United States and Asia. All M. tuberculosis sensu stricto isolates of previously unknown phylogenetic position could be rapidly and unambiguously assigned to one of the eight major clusters, thus providing a facile strategy for identifying organisms that are clonally related by descent. Common clones of M. tuberculosis sensu stricto and M. bovis are distinct, deeply branching genotypic complexes whose extant members did not emerge directly from one another in the recent past. sSNP genotyping rapidly delineates relationships among closely related strains of pathogenic microbes and allows construction of genetic frameworks for examining the distribution of biomedically relevant traits such as virulence, transmissibility, and host range.
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Affiliation(s)
- Michaela M Gutacker
- Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, USA
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91
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Coluzzi M, Sabatini A, della Torre A, Di Deco MA, Petrarca V. A polytene chromosome analysis of the Anopheles gambiae species complex. Science 2002; 298:1415-8. [PMID: 12364623 DOI: 10.1126/science.1077769] [Citation(s) in RCA: 306] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Field-collected specimens of all known taxa in the Anopheles gambiae complex were analyzed on the basis of chromosome inversions with reference to a standard polytene chromosome map. The phylogenetic relationships among the seven described species in the complex could be inferred from the distribution of fixed inversions. Nonrandom patterns of inversion distribution were observed and, particularly on chromosome arm 2R, provided evidence for genetically distinct populations in A. gambiae, A. arabiensis, and A. melas. In A. gambiae from Mali, stable genetic differentiation was observed even in populations living in the same region, suggesting a process of incipient speciation which is being confirmed by studies with molecular markers. The possible role of chromosome differentiation in speciation of the A. gambiae complex and in the emergence of distinct chromosomal forms within the nominal species is discussed in relation to human malaria.
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Affiliation(s)
- Mario Coluzzi
- Dipartimento di Scienze di Sanità Pubblica and Istituto Pasteur-Cenci Bolognetti, Università "La Sapienza," Rome, Italy.
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92
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Bhasin VK. Plasmodium falciparum genetic diversity and ancestry. THE LANCET. INFECTIOUS DISEASES 2002; 2:657. [PMID: 12409044 DOI: 10.1016/s1473-3099(02)00436-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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93
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Volkman SK, Hartl DL, Wirth DF, Nielsen KM, Choi M, Batalov S, Zhou Y, Plouffe D, Le Roch KG, Abagyan R, Winzeler EA. Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science 2002; 298:216-8. [PMID: 12364807 DOI: 10.1126/science.1075642] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The detection of single-nucleotide polymorphisms in pathogenic microorganisms has normally been carried out by trial and error. Here we show that DNA hybridization with high-density oligonucleotide arrays provides rapid and convenient detection of single-nucleotide polymorphisms in Plasmodium falciparum, despite its exceptionally high adenine-thymine (AT) content (82%). A disproportionate number of polymorphisms are found in genes encoding proteins associated with the cell membrane. These genes are targets for only 22% of the oligonucleotide probes but account for 69% of the polymorphisms. Genetic variation is also enriched in subtelomeric regions, which account for 22% of the chromosome but 76% of the polymorphisms.
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Affiliation(s)
- Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
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94
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Abstract
Malaria is among the oldest of diseases. In one form or another, it has infected and affected our ancestors since long before the origin of the human line. During our recent evolution, its influence has probably been greater than that of any other infectious agent. Here we attempt to trace the forms and impacts of malaria from a distant past through historical times to the present. In the last sections, we review the current burdens of malaria across the world and discuss present-day approaches to its management. Only by following, or attempting to follow, malaria throughout its evolution and history can we understand its character and so be better prepared for our future management of this ancient ill.
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Affiliation(s)
- Richard Carter
- University of Edinburgh, Division of Biological Sciences, ICAPB, Ashworth Laboratories, Edinburgh EH9 3JT, United Kingdom.
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95
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Abstract
Rich and Ayala propose that the zero rate of non-amino-acid-changing (synonymous) mutations in some proteins of Plasmodium falciparum reflects a recent population bottleneck. Alternatively, Arnot and Saul propose sequence conservation in response to selective pressures other than the pressure to encode protein. Among these are fold pressure and purine-loading pressure. Genomes adapt to these by acquisition of introns and/or low-complexity (simple-sequence) segments in proteins. Adaptive explanations include facilitation of intragenic recombination (and hence diversification of the encoded protein) by DNA stem-loop secondary structures.
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Affiliation(s)
- Donald R Forsdyke
- Dept of Biochemistry, Queen's University, Kingston, Ontario, Canada K7L3N6.
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96
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Jongwutiwes S, Putaporntip C, Friedman R, Hughes AL. The extent of nucleotide polymorphism is highly variable across a 3-kb region on Plasmodium falciparum chromosome 2. Mol Biol Evol 2002; 19:1585-90. [PMID: 12200485 DOI: 10.1093/oxfordjournals.molbev.a004220] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genomic nucleotide polymorphism in the virulent human malarial parasite Plasmodium falciparum was surveyed by sequencing a 3-kb region of chromosome 2 from 21 isolates, including the MSP4 and MSP5 genes. Extensive sequence polymorphism was observed in the coding regions of these genes and in the region downstream to MSP5, and the average pairwise divergence time of haplotypes in this region was estimated to be at least about 200,000 years. But nucleotide polymorphism was not found in the introns and was much reduced in the intergenic region. Over the entire region, nucleotide diversity was negatively correlated with a nucleotide content skewed toward thymine. Together with the previous evidence of limited nucleotide polymorphism in introns of P. falciparum, these data suggest the existence of a mechanism suppressing single-nucleotide polymorphism in regions of the P. falciparum genome with highly skewed nucleotide content.
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Affiliation(s)
- Somchai Jongwutiwes
- Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok
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97
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Weatherall DJ, Clegg JB. Genetic variability in response to infection: malaria and after. Genes Immun 2002; 3:331-7. [PMID: 12209359 DOI: 10.1038/sj.gene.6363878] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2002] [Accepted: 02/22/2002] [Indexed: 11/09/2022]
Abstract
Recent studies have shown that the relatively short period of exposure of human populations to malaria has left in its wake a wide range of genetic diversity. And there is growing evidence that other infectious agents have, or are, having the same effect. By integrating further studies of human populations with genetic analyses of susceptibility to murine malaria it should now be possible to determine some of the mechanisms involved in the variation of susceptibility to infectious disease, information which may have important practical implications for both the diagnosis and better management of these conditions.
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Affiliation(s)
- D J Weatherall
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
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98
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Abstract
DNA sequence data reveal extensive polymorphism in the virulent, human malaria parasite Plasmodium falciparum. The extent of polymorphism at apparently neutral-evolving loci points to a common ancestor for this species that is no more recent than approximately 150,000-200,000 years ago. In addition, there is evidence of balanced polymorphisms at certain antigen-encoding loci, some of which have been maintained for millions of years. Thus, we can reject the hypothesis that this species underwent a recent extreme bottleneck (i.e. one in which the population was reduced to a single haploid genotype). However, it is possible that less-severe bottlenecks have occurred.
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Affiliation(s)
- Austin L Hughes
- Dept of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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99
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Plebanski M, Proudfoot O, Pouniotis D, Coppel RL, Apostolopoulos V, Flannery G. Immunogenetics and the design of Plasmodium falciparum vaccines for use in malaria-endemic populations. J Clin Invest 2002; 110:295-301. [PMID: 12163446 PMCID: PMC151095 DOI: 10.1172/jci16163] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Magdalena Plebanski
- Vaccine Development and Infectious Diseases Unit, The Austin Research Institute, A & RMC Hospital Campus, Heidelberg, Victoria, Australia.
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100
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Plebanski M, Proudfoot O, Pouniotis D, Coppel RL, Apostolopoulos V, Flannery G. Immunogenetics and the design of Plasmodium falciparum vaccines for use in malaria-endemic populations. J Clin Invest 2002. [DOI: 10.1172/jci0216163] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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