Jane M Carlton, Ph.D.

Why Is Plasmodium vivax a Neglected Tropical Disease?
Carlton, Jane M; Sina, Barbara J; Adams, John H
2011 Jun;5(6):e1160-e1160, PLoS neglected tropical diseases
— id: 135263, year: 2011, vol: 5, page: e1160, stat: Journal Article,

Microsatellite polymorphism in the sexually transmitted human pathogen Trichomonas vaginalis indicates a genetically diverse parasite
Conrad, Melissa; Zubacova, Zuzana; Dunn, Linda A; Upcroft, Jacqui; Sullivan, Steven A; Tachezy, Jan; Carlton, Jane M
2011 Jan;175(1):30-38, Molecular & biochemical parasitology
Given the growing appreciation of serious health sequelae from widespread Trichomonas vaginalis infection, new tools are needed to study the parasite's genetic diversity. To this end we have identified and characterized a panel of 21 microsatellites and six single-copy genes from the T. vaginalis genome, using seven laboratory strains of diverse origin. We have (1) adapted our microsatellite typing method to incorporate affordable fluorescent labeling, (2) determined that the microsatellite loci remain stable in parasites continuously cultured for up to 17 months, and (3) evaluated microsatellite marker coverage of the six chromosomes that comprise the T. vaginalis genome, using fluorescent in situ hybridization (FISH). We have used the markers to show that T. vaginalis is a genetically diverse parasite in a population of commonly used laboratory strains. In addition, we have used phylogenetic methods to infer evolutionary relationships from our markers in order to validate their utility in future population analyses. Our panel is the first series of robust polymorphic genetic markers for T. vaginalis that can be used to classify and monitor lab strains, as well as provide a means to measure the genetic diversity and population structure of extant and future T. vaginalis isolates
— id: 114173, year: 2011, vol: 175, page: 30, stat: Journal Article,

Linkage maps from multiple genetic crosses and loci linked to growth-related virulent phenotype in Plasmodium yoelii
Li, Jian; Pattaradilokrat, Sittiporn; Zhu, Feng; Jiang, Hongying; Liu, Shengfa; Hong, Lingxian; Fu, Yong; Koo, Lily; Xu, Wenyue; Pan, Weiqing; Carlton, Jane M.; Kaneko, Osamu; Carter, Richard; Wootton, John C.; Su, Xin-zhuan
2011 AUG 2 ;108(31):E374-E382, Proceedings of the National Academy of Sciences of the United States of America
Plasmodium yoelii is an excellent model for studying malaria pathogenesis that is often intractable to investigate using human parasites; however, genetic studies of the parasite have been hindered by lack of genome-wide linkage resources. Here, we performed 14 genetic crosses between three pairs of P. yoelii clones/subspecies, isolated 75 independent recombinant progeny from the crosses, and constructed a high-resolution linkage map for this parasite. Microsatellite genotypes from the progeny formed 14 linkage groups belonging to the 14 parasite chromosomes, allowing assignment of sequence contigs to chromosomes. Growth-related virulent phenotypes from 25 progeny of one of the crosses were significantly associated with a major locus on chromosome 13 and with two secondary loci on chromosomes 7 and 10. The chromosome 10 and 13 loci are both linked to day 5 parasitemia, and their effects on parasite growth rate are independent but additive. The locus on chromosome 7 is associated with day 10 parasitemia. The chromosome 13 locus spans similar to 220 kb of DNA containing 51 predicted genes, including the P. yoelii erythrocyte binding ligand, in which a C741Y substitution in the R6 domain is implicated in the change of growth rate. Similarly, the chromosome 10 locus spans similar to 234 kb with 71 candidate genes, containing a member of the 235-kDa rhoptry proteins (Py235) that can bind to the erythrocyte surface membrane. Atypical virulent phenotypes among the progeny were also observed. This study provides critical tools and information for genetic investigations of virulence and biology of P. yoelii
— id: 136614, year: 2011, vol: 108, page: E374, stat: Journal Article,

Phylogeny of Parasitic Parabasalia and Free-Living Relatives Inferred from Conventional Markers vs. Rpb1, a Single-Copy Gene
Malik, Shehre-Banoo; Brochu, Cynthia D; Bilic, Ivana; Yuan, Jing; Hess, Michael; Logsdon, John M Jr; Carlton, Jane M
2011 ;6(6):e20774-e20774, PLoS ONE
BACKGROUND: Parabasalia are single-celled eukaryotes (protists) that are mainly comprised of endosymbionts of termites and wood roaches, intestinal commensals, human or veterinary parasites, and free-living species. Phylogenetic comparisons of parabasalids are typically based upon morphological characters and 18S ribosomal RNA gene sequence data (rDNA), while biochemical or molecular studies of parabasalids are limited to a few axenically cultivable parasites. These previous analyses and other studies based on PCR amplification of duplicated protein-coding genes are unable to fully resolve the evolutionary relationships of parabasalids. As a result, genetic studies of Parabasalia lag behind other organisms. PRINCIPAL FINDINGS: Comparing parabasalid EF1alpha, alpha-tubulin, enolase and MDH protein-coding genes with information from the Trichomonas vaginalis genome reveals difficulty in resolving the history of species or isolates apart from duplicated genes. A conserved single-copy gene encodes the largest subunit of RNA polymerase II (Rpb1) in T. vaginalis and other eukaryotes. Here we directly sequenced Rpb1 degenerate PCR products from 10 parabasalid genera, including several T. vaginalis isolates and avian isolates, and compared these data by phylogenetic analyses. Rpb1 genes from parabasalids, diplomonads, Parabodo, Diplonema and Percolomonas were all intronless, unlike intron-rich homologs in Naegleria, Jakoba and Malawimonas. CONCLUSIONS/SIGNIFICANCE: The phylogeny of Rpb1 from parasitic and free-living parabasalids, and conserved Rpb1 insertions, support Trichomonadea, Tritrichomonadea, and Hypotrichomonadea as monophyletic groups. These results are consistent with prior analyses of rDNA and GAPDH sequences and ultrastructural data. The Rpb1 phylogenetic tree also resolves species- and isolate-level relationships. These findings, together with the relative ease of Rpb1 isolation, make it an attractive tool for evaluating more extensive relationships within Parabasalia
— id: 134471, year: 2011, vol: 6, page: e20774, stat: Journal Article,

The evolution of infectious agents in relation to sex in animals and humans: Brief discussions of some individual organisms
Reed D.L.; Currier R.W.; Walton S.F.; Conrad M.; Sullivan S.A.; Carlton J.M.; Read T.D.; Severini A.; Tyler S.; Eberle R.; Johnson W.E.; Silvestri G.; Clarke I.N.; Lagergard T.; Lukehart S.A.; Unemo M.; Shafer W.M.; Beasley R.P.; Bergstrom T.; Norberg P.; Davison A.J.; Sharp P.M.; Hahn B.H.; Blomberg J.
2011 ;1230(1):74-107, Annals of the New York Academy of Sciences
The following series of concise summaries addresses the evolution of infectious agents in relation to sex in animals and humans from the perspective of three specific questions: (1) what have we learned about the likely origin and phylogeny, up to the establishment of the infectious agent in the genital econiche, including the relative frequency of its sexual transmission; (2) what further research is needed to provide additional knowledge on some of these evolutionary aspects; and (3) what evolutionary considerations might aid in providing novel approaches to the more practical clinical and public health issues facing us currently and in the future? 2011 New York Academy of Sciences
— id: 136621, year: 2011, vol: 1230, page: 74, stat: Journal Article,

Genome sequences reveal divergence times of malaria parasite lineages
Silva, Joana C; Egan, Amy; Friedman, Robert; Munro, James B; Carlton, Jane M; Hughes, Austin L
2011 Nov;138(13):1737-1749, Parasitology
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
— id: 146230, year: 2011, vol: 138, page: 1737, stat: Journal Article,

Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle
Mitrofanova, Antonina; Kleinberg, Samantha; Carlton, Jane; Kasif, Simon; Mishra, Bud
2010 Jul;49(3):167-176, Artificial intelligence in medicine
OBJECTIVE: Even though a vaccine for malaria infections has been under intense study for many years, it has resisted several different lines of attack attempted by biologists. More than half of Plasmodium proteins still remain uncharacterized and therefore cannot be used in clinical trials. The task is further complicated by the metamorphic life-cycle of the parasite, which allows for rapid evolutionary changes and diversity among related strains, thus making precise targeting of the appropriate proteins for vaccination a technical challenge. We propose an automated method for predicting functions for the malaria parasite, which capitalizes on the importance of the intraerythrocytic developmental cycle data and expression changes during its five phases, as determined computationally by our segmentation algorithm. MATERIALS AND METHODS: Our method combines temporal gene expression profiles with protein-protein interaction data, sequence similarity scores, and metabolic pathway information to produce a set of predicted protein functions that can be used as targets for vaccine development. We use a Bayesian approach, which assigns a probability of having (or not having) a particular function to each protein, given the various sources of evidence. In our method, each data source is represented by either a functional linkage graph or a categorical feature vector. RESULTS AND CONCLUSIONS: The methods are tested on Plasmodium falciparum, the species responsible for the deadliest malaria infections. The algorithm was able to assign meaningful functions to 628 out of 1439 previously unannotated proteins, which are first-choice candidates for experimental vaccine research. We conclude that analyzing time-course gene expression profiles in separate phases leads to much higher prediction accuracy when compared with Pearson correlation coefficients computed across the time course as a whole. Additionally, we demonstrate that temporal expression profiles alone are able to improve the predictive power of the integrated data
— id: 141874, year: 2010, vol: 49, page: 167, stat: Journal Article,

A systems-based analysis of Plasmodium vivax lifecycle transcription from human to mosquito
Westenberger, Scott J; McClean, Colleen M; Chattopadhyay, Rana; Dharia, Neekesh V; Carlton, Jane M; Barnwell, John W; Collins, William E; Hoffman, Stephen L; Zhou, Yingyao; Vinetz, Joseph M; Winzeler, Elizabeth A
2010 ;4(4):e653-e653, PLoS neglected tropical diseases
BACKGROUND: Up to 40% of the world's population is at risk for Plasmodium vivax malaria, a disease that imposes a major public health and economic burden on endemic countries. Because P. vivax produces latent liver forms, eradication of P. vivax malaria is more challenging than it is for P. falciparum. Genetic analysis of P. vivax is exceptionally difficult due to limitations of in vitro culture. To overcome the barriers to traditional molecular biology in P. vivax, we examined parasite transcriptional changes in samples from infected patients and mosquitoes in order to characterize gene function, define regulatory sequences and reveal new potential vaccine candidate genes. PRINCIPAL FINDINGS: We observed dramatic changes in transcript levels for various genes at different lifecycle stages, indicating that development is partially regulated through modulation of mRNA levels. Our data show that genes involved in common biological processes or molecular machinery are co-expressed. We identified DNA sequence motifs upstream of co-expressed genes that are conserved across Plasmodium species that are likely binding sites of proteins that regulate stage-specific transcription. Despite their capacity to form hypnozoites we found that P. vivax sporozoites show stage-specific expression of the same genes needed for hepatocyte invasion and liver stage development in other Plasmodium species. We show that many of the predicted exported proteins and members of multigene families show highly coordinated transcription as well. CONCLUSIONS: We conclude that high-quality gene expression data can be readily obtained directly from patient samples and that many of the same uncharacterized genes that are upregulated in different P. vivax lifecycle stages are also upregulated in similar stages in other Plasmodium species. We also provide numerous examples of how systems biology is a powerful method for determining the likely function of genes in pathogens that are neglected due to experimental intractability
— id: 111957, year: 2010, vol: 4, page: e653, stat: Journal Article,

GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis
Aurrecoechea, Cristina; Brestelli, John; Brunk, Brian P; Carlton, Jane M; Dommer, Jennifer; Fischer, Steve; Gajria, Bindu; Gao, Xin; Gingle, Alan; Grant, Greg; Harb, Omar S; Heiges, Mark; Innamorato, Frank; Iodice, John; Kissinger, Jessica C; Kraemer, Eileen; Li, Wei; Miller, John A; Morrison, Hilary G; Nayak, Vishal; Pennington, Cary; Pinney, Deborah F; Roos, David S; Ross, Chris; Stoeckert, Christian J Jr; Sullivan, Steven; Treatman, Charles; Wang, Haiming
2009 Jan;37(Database issue):D526-D530, Nucleic acids research
GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data
— id: 96130, year: 2009, vol: 37, page: D526, stat: Journal Article,

Hundreds of microsatellites for genotyping Plasmodium yoelii parasites
Li, J; Zhang, YH; Liu, SF; Hong, LX; Sullivan, M; McCutchan, TF; Carlton, JM; Su, XZA
2009 AUG ;166(2):153-158, Molecular & biochemical parasitology
Genetic crosses have been employed to study various traits of rodent malaria parasites and to locate loci that contribute to drug resistance, immune protection, and disease virulence. Compared with human malaria parasites, genetic crossing of rodent malaria parasites is more easily performed; however, genotyping methods using microsatellites (MSs) or large-scale single nucleotide polymorphisms (SNPs) that have been widely used in typing Plasmodium falciparum are not available for rodent malaria species. Here we report a genome-wide search of the Plasmodium yoelii yoelii (P. yoelii) genome for simple sequence repeats (SSRs) and the identification of nearly 600 polymorphic MS markers for typing the genomes of P, yoelii and Plasmodium berghei. The MS markers are randomly distributed across the 14 physical chromosomes assembled from genome sequences of three rodent malaria species, although some variations in the numbers of MS expected according to chromosome size exist. The majority of the MS markers are AT-rich repeats, similar to those found in the P. falciparum genome. The MS markers provide an important resource for genotyping, lay a foundation for developing linkage maps, and will greatly facilitate genetic studies of P. yoelii. Published by Elsevier B.V
— id: 100444, year: 2009, vol: 166, page: 153, stat: Journal Article,

Key gaps in the knowledge of Plasmodium vivax, a neglected human malaria parasite
Mueller, I; Galinski, MR; Baird, JK; Carlton, JM; Kochar, DK; Alonso, PL; del Portillo, HA
2009 SEP ;9(9):555-566, Lancet infectious diseases
Plasmodium vivax is geographically the most widely distributed cause of malaria in people, with up to 2.5 billion people at risk and an estimated 80 million to 300 million clinical cases every year-including severe disease and death. Despite this large burden of disease, P vivax is overlooked and left in the shadow of the enormous problem caused by Plasmodium falciparum in sub-Saharan Africa. The technological advances enabling the sequencing of the P vivax genome and a recent call for worldwide malaria eradication have together placed new emphasis on the importance of addressing P vivax as a major public health problem. However, because of this parasite's biology, it is especially difficult to interrupt the transmission of P vivax, and experts agree that the available methods for preventing and treating infections with P vivax are inadequate. It is thus imperative that the development of new methods and strategies become a priority. Advancing the development of such methods needs renewed emphasis on understanding the biology, pathogenesis, and epidemiology of P vivax. This Review critically examines what is known about P vivax, focusing on identifying the crucial gaps that create obstacles to the elimination of this parasite in human populations
— id: 102287, year: 2009, vol: 9, page: 555, stat: Journal Article,

Carotenoid biosynthesis in intraerythrocytic stages of plasmodium falciparum
Tonhosolo, Renata; D'Alexandri, Fabio L; de Rosso, Veridiana V; Gazarini, Marcos L; Matsumura, Miriam Y; Peres, Valnice J; Merino, Emilio F; Carlton, Jane M; Wunderlich, Gerhard; Mercadante, Adriana Z; Kimura, Emilia A; Katzin, Alejandro M
2009 Apr 10;284(15):9974-9985, Journal of biological chemistry
Carotenoids are widespread lipophilic pigments synthesized by all photosynthetic organisms and some nonphotosynthetic fungi and bacteria. All carotenoids are derived from the C40 isoprenoid precursor geranylgeranyl pyrophosphate and their chemical and physical properties are associated with light absorption, free radical scavenging and antioxidant activity. Carotenoids are generally synthesized in well-defined subcellular organelles, the plastids, which are also present in the phylum Apicomplexa that comprises of a number of important human parasites such as Plasmodium or Toxoplasma. Recently, it was demonstrated that Toxoplasma gondii synthesizes abscisic acid. We therefore asked if Plasmodium falciparum is also capable to synthesize carotenoids. Herein, biochemical findings demonstrated the presence of carotenoid biosynthesis in the intraerythrocytic stages of the apicomplexan parasite P. falciparum. Using metabolic labeling with radioisotopes, in vitro inhibition tests with norflurazon, a specific inhibitor of plant carotenoid biosynthesis, the results showed that intraerythrocytic stages of P. falciparum synthesize carotenoid compounds. A plasmodial enzyme that presented phytoene synthase activity was also identified and characterized. These findings not only contribute to the current understanding of P. falciparum evolution, but shed light on a pathway that could serve as a chemotherapeutic target
— id: 96125, year: 2009, vol: 284, page: 9974, stat: Journal Article,

The transcriptome of Plasmodium vivax reveals divergence and diversity of transcriptional regulation in malaria parasites
Bozdech, Zbynek; Mok, Sachel; Hu, Guangan; Imwong, Mallika; Jaidee, Anchalee; Russell, Bruce; Ginsburg, Hagai; Nosten, Francois; Day, Nicholas P J; White, Nicholas J; Carlton, Jane M; Preiser, Peter R
2008 Oct 21;105(42):16290-16295, Proceedings of the National Academy of Sciences of the United States of America
Plasmodium vivax causes over 100 million clinical infections each year. Primarily because of the lack of a suitable culture system, our understanding of the biology of this parasite lags significantly behind that of the more deadly species P. falciparum. Here, we present the complete transcriptional profile throughout the 48-h intraerythrocytic cycle of three distinct P. vivax isolates. This approach identifies strain specific patterns of expression for subsets of genes predicted to encode proteins associated with virulence and host pathogen interactions. Comparison to P. falciparum revealed significant differences in the expression of genes involved in crucial cellular functions that underpin the biological differences between the two parasite species. These data provide insights into the biology of P. vivax and constitute an important resource for the development of therapeutic approaches
— id: 96128, year: 2008, vol: 105, page: 16290, stat: Journal Article,

Comparative genomics of the neglected human malaria parasite Plasmodium vivax
Carlton, Jane M; Adams, John H; Silva, Joana C; Bidwell, Shelby L; Lorenzi, Hernan; Caler, Elisabet; Crabtree, Jonathan; Angiuoli, Samuel V; Merino, Emilio F; Amedeo, Paolo; Cheng, Qin; Coulson, Richard M R; Crabb, Brendan S; Del Portillo, Hernando A; Essien, Kobby; Feldblyum, Tamara V; Fernandez-Becerra, Carmen; Gilson, Paul R; Gueye, Amy H; Guo, Xiang; Kang'a, Simon; Kooij, Taco W A; Korsinczky, Michael; Meyer, Esmeralda V-S; Nene, Vish; Paulsen, Ian; White, Owen; Ralph, Stuart A; Ren, Qinghu; Sargeant, Tobias J; Salzberg, Steven L; Stoeckert, Christian J; Sullivan, Steven A; Yamamoto, Marcio M; Hoffman, Stephen L; Wortman, Jennifer R; Gardner, Malcolm J; Galinski, Mary R; Barnwell, John W; Fraser-Liggett, Claire M
2008 Oct 9;455(7214):757-763, Nature
The human malaria parasite Plasmodium vivax is responsible for 25-40% of the approximately 515 million annual cases of malaria worldwide. Although seldom fatal, the parasite elicits severe and incapacitating clinical symptoms and often causes relapses months after a primary infection has cleared. Despite its importance as a major human pathogen, P. vivax is little studied because it cannot be propagated continuously in the laboratory except in non-human primates. We sequenced the genome of P. vivax to shed light on its distinctive biological features, and as a means to drive development of new drugs and vaccines. Here we describe the synteny and isochore structure of P. vivax chromosomes, and show that the parasite resembles other malaria parasites in gene content and metabolic potential, but possesses novel gene families and potential alternative invasion pathways not recognized previously. Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected species
— id: 96129, year: 2008, vol: 455, page: 757, stat: Journal Article,

Comparative evolutionary genomics of human malaria parasites
Carlton, Jane M; Escalante, Ananias A; Neafsey, Daniel; Volkman, Sarah K
2008 Dec;24(12):545-550, Trends in parasitology
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?
— id: 96127, year: 2008, vol: 24, page: 545, stat: Journal Article,

Metabolic and molecular evidence of adenosine kinase activity in Plasmodium falciparum
Cassera, MB; Merino, EF; Hazleton, KZ; Carlton, JM; Schramm, VL
2008 JAN ;38(1):S69-S69, International journal for parasitology
— id: 76167, year: 2008, vol: 38, page: S69, stat: Journal Article,

Metabolic and molecular evidence of adenosine kinase activity in Plasmodium falciparum
Cassera, MB; Merino, EF; Hazleton, KZ; Carlton, JM; Schramm, VL
2008 JAN ;38(1):S73-S73, International journal for parasitology
— id: 76168, year: 2008, vol: 38, page: S73, stat: Journal Article,

Carotenoid biosynthesis in the intraerythrocytic stages of Plasmodium falciparum
D'Alexandri, FL; Tonhosolo, R; de Rosso, VV; Dutra, MG; Merino, EF; Wunderlich, G; Carlton, JM; Mercadante, AZ; Kimura, EA; Katzin, AM
2008 JAN ;38(1):S81-S82, International journal for parasitology
— id: 76169, year: 2008, vol: 38, page: S81, stat: Journal Article,

IDEA: Interactive Display for Evolutionary Analyses
Egan, Amy; Mahurkar, Anup; Crabtree, Jonathan; Badger, Jonathan H; Carlton, Jane M; Silva, Joana C
2008 ;9:524-524, BMC bioinformatics
BACKGROUND: The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are codeml and baseml, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency. RESULTS: We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with codeml and baseml for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly. CONCLUSION: IDEA provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data
— id: 96126, year: 2008, vol: 9, page: 524, stat: Journal Article,

PRODUCTION OF RETICULOCYTES FROM HEMATOPOIETIC STEM CELLS FOR DEVELOPMENT OF A CONTINUOUS IN VITRO CULTURE SYSTEM FOR PLASMODIUM VIVAX
Furuya, T; Carlton, JM; Rajapandi, T; Stedman, T; Ma, W
2008 DEC ;79(6):276-276, American journal of tropical medicine & hygiene
— id: 91863, year: 2008, vol: 79, page: 276, stat: Journal Article,

Plasmodium vivax in India
Joshi, Hema; Prajapati, Surendra K; Verma, Anju; Kang'a, Simon; Carlton, Jane M
2008 May;24(5):228-235, Trends in parasitology
Four Plasmodium species cause malaria in humans: Plasmodium vivax is the most widespread and results in pronounced morbidity. India (population >1 billion) is a major contributor to the burden of vivax malaria. With a resurgence in interest concerning the neglected burden of vivax malaria and the completion of the P. vivax genome, it is timely to review what is known concerning P. vivax in India. The P. vivax population is highly diverse in terms of relapse patterns, drug response and clinical profiles, and highly genetically variable according to studies of antigen genes, isoenzyme markers and microsatellites. The unique epidemiology of malaria in India, where P. vivax predominates over Plasmodium falciparum, renders this location ideal for studying the dynamics of co-infection
— id: 78753, year: 2008, vol: 24, page: 228, stat: Journal Article,

Local adaptation and vector-mediated population structure in Plasmodium vivax malaria
Joy, Deirdre A; Gonzalez-Ceron, Lilia; Carlton, Jane M; Gueye, Amy; Fay, Michael; McCutchan, Thomas F; Su, Xin-zhuan
2008 Jun;25(6):1245-1252, Molecular biology & evolution
Plasmodium vivax in southern Mexico exhibits different infectivities to 2 local mosquito vectors, Anopheles pseudopunctipennis and Anopheles albimanus. Previous work has tied these differences in mosquito infectivity to variation in the central repeat motif of the malaria parasite's circumsporozoite (csp) gene, but subsequent studies have questioned this view. Here we present evidence that P. vivax in southern Mexico comprised 3 genetic populations whose distributions largely mirror those of the 2 mosquito vectors. Additionally, laboratory colony feeding experiments indicate that parasite populations are most compatible with sympatric mosquito species. Our results suggest that reciprocal selection between malaria parasites and mosquito vectors has led to local adaptation of the parasite. Adaptation to local vectors may play an important role in generating population structure in Plasmodium. A better understanding of coevolutionary dynamics between sympatric mosquitoes and parasites will facilitate the identification of molecular mechanisms relevant to disease transmission in nature and provide crucial information for malaria control
— id: 78754, year: 2008, vol: 25, page: 1245, stat: Journal Article,

Hunting down the genetic determinants of Plasmodium vivax chloroquine resistance
Kang'a, S; Merino, EF; Susanti, AI; Leksana, B; Maguire, JD; Carlton, JM
2008 JAN ;38(2):S77-S78, International journal for parasitology
— id: 98144, year: 2008, vol: 38, page: S77, stat: Journal Article,

A PANEL OF GENETIC MARKERS SUGGESTS GENETIC RELATEDNESS AND EVOLUTIONARY HISTORIES OF PLASMODIUM VIVAX LINEAGES, OLD WORLD AND NEW WORLD
Prajapati, SK; Joshi, H; Kang'a, S; Carlton, JM; Rizvi, MA; Dash, AP
2008 DEC ;79(6):66-66, American journal of tropical medicine & hygiene
— id: 91861, year: 2008, vol: 79, page: 66, stat: Journal Article,

Evidence-based annotation of the malaria parasite's genome using comparative expression profiling
Zhou, Yingyao; Ramachandran, Vandana; Kumar, Kota Arun; Westenberger, Scott; Refour, Phillippe; Zhou, Bin; Li, Fengwu; Young, Jason A; Chen, Kaisheng; Plouffe, David; Henson, Kerstin; Nussenzweig, Victor; Carlton, Jane; Vinetz, Joseph M; Duraisingh, Manoj T; Winzeler, Elizabeth A
2008 ;3(2):e1570-e1570, PLoS ONE
A fundamental problem in systems biology and whole genome sequence analysis is how to infer functions for the many uncharacterized proteins that are identified, whether they are conserved across organisms of different phyla or are phylum-specific. This problem is especially acute in pathogens, such as malaria parasites, where genetic and biochemical investigations are likely to be more difficult. Here we perform comparative expression analysis on Plasmodium parasite life cycle data derived from P. falciparum blood, sporozoite, zygote and ookinete stages, and P. yoelii mosquito oocyst and salivary gland sporozoites, blood and liver stages and show that type II fatty acid biosynthesis genes are upregulated in liver and insect stages relative to asexual blood stages. We also show that some universally uncharacterized genes with orthologs in Plasmodium species, Saccharomyces cerevisiae and humans show coordinated transcription patterns in large collections of human and yeast expression data and that the function of the uncharacterized genes can sometimes be predicted based on the expression patterns across these diverse organisms. We also use a comprehensive and unbiased literature mining method to predict which uncharacterized parasite-specific genes are likely to have roles in processes such as gliding motility, host-cell interactions, sporozoite stage, or rhoptry function. These analyses, together with protein-protein interaction data, provide probabilistic models that predict the function of 926 uncharacterized malaria genes and also suggest that malaria parasites may provide a simple model system for the study of some human processes. These data also provide a foundation for further studies of transcriptional regulation in malaria parasites
— id: 78755, year: 2008, vol: 3, page: e1570, stat: Journal Article,

Toward a malaria haplotype map
Carlton, Jane M
2007 Jan;39(1):5-6, Nature genetics
— id: 72024, year: 2007, vol: 39, page: 5, stat: Journal Article,

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis
Carlton, Jane M; Hirt, Robert P; Silva, Joana C; Delcher, Arthur L; Schatz, Michael; Zhao, Qi; Wortman, Jennifer R; Bidwell, Shelby L; Alsmark, U Cecilia M; Besteiro, Sebastien; Sicheritz-Ponten, Thomas; Noel, Christophe J; Dacks, Joel B; Foster, Peter G; Simillion, Cedric; Van de Peer, Yves; Miranda-Saavedra, Diego; Barton, Geoffrey J; Westrop, Gareth D; Muller, Sylke; Dessi, Daniele; Fiori, Pier Luigi; Ren, Qinghu; Paulsen, Ian; Zhang, Hanbang; Bastida-Corcuera, Felix D; Simoes-Barbosa, Augusto; Brown, Mark T; Hayes, Richard D; Mukherjee, Mandira; Okumura, Cheryl Y; Schneider, Rachel; Smith, Alias J; Vanacova, Stepanka; Villalvazo, Maria; Haas, Brian J; Pertea, Mihaela; Feldblyum, Tamara V; Utterback, Terry R; Shu, Chung-Li; Osoegawa, Kazutoyo; de Jong, Pieter J; Hrdy, Ivan; Horvathova, Lenka; Zubacova, Zuzana; Dolezal, Pavel; Malik, Shehre-Banoo; Logsdon, John M Jr; Henze, Katrin; Gupta, Arti; Wang, Ching C; Dunne, Rebecca L; Upcroft, Jacqueline A; Upcroft, Peter; White, Owen; Salzberg, Steven L; Tang, Petrus; Chiu, Cheng-Hsun; Lee, Ying-Shiung; Embley, T Martin; Coombs, Graham H; Mottram, Jeremy C; Tachezy, Jan; Fraser-Liggett, Claire M; Johnson, Patricia J
2007 Jan 12;315(5809):207-212, Science
We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria
— id: 72023, year: 2007, vol: 315, page: 207, stat: Journal Article,

Contrasting genetic structure in Plasmodium vivax populations from Asia and South America
Imwong, Mallika; Nair, Shalini; Pukrittayakamee, Sasithon; Sudimack, Daniel; Williams, Jeff T; Mayxay, Mayfong; Newton, Paul N; Kim, Jung Ryong; Nandy, Amitab; Osorio, Lyda; Carlton, Jane M; White, Nicholas J; Day, Nicholas P J; Anderson, Tim J C
2007 Jul;37(8-9):1013-1022, International journal for parasitology
Populations of Plasmodium falciparum show striking differences in linkage disequilibrium, population differentiation and diversity, but only fragmentary data exists on the genetic structure of Plasmodium vivax. We genotyped nine tandem repeat loci bearing 2-8bp motifs from 345 P. vivax infections collected from three Asian countries and from five locations in Colombia. We observed 9-37 alleles per locus and high diversity (H(e)=0.72-0.79, mean=0.75) in all countries. Numbers of multiple clone infections varied considerably: these were rare in Colombia and India, but > 60% of isolates carried multiple alleles in at least one locus in Thailand and Laos. However, only one or two of the nine loci show >1 allele in many samples, suggesting that mutation within infections may result in overestimation of true multiple carriage rates. Identical nine-locus genotypes were frequently found in Colombian populations, contributing to strong linkage disequilibrium. These identical genotypes were strongly clustered in time, consistent with epidemic transmission of clones and subsequent breakdown of allelic associations, suggesting high rates of inbreeding and low effective recombination rates in this country. In contrast, identical genotypes were rare and loci were randomly associated in all three Asian populations, consistent with higher rates of outcrossing and recombination. We observed low but significant differentiation between different Asian countries (standardized F(ST)=0.13-0.45). In comparison, we see greater differentiation between collection locations within Colombia (standardized F(ST)=0.4-0.7), and strong differentiation between continents (standardized F(ST)=0.48-0.79). The observed heterogeneity in multiple clone carriage rates, linkage disequilibrium and population differentiation are similar in some, but not all, respects to those observed in P. falciparum, and have important implications for the design of association mapping studies, and interpretation of P. vivax epidemiology
— id: 72021, year: 2007, vol: 37, page: 1013, stat: Journal Article,

Relapses of Plasmodium vivax infection usually result from activation of heterologous hypnozoites
Imwong, Mallika; Snounou, Georges; Pukrittayakamee, Sasithon; Tanomsing, Naowarat; Kim, Jung Ryong; Nandy, Amitab; Guthmann, Jean-Paul; Nosten, Francois; Carlton, Jane; Looareesuwan, Sornchai; Nair, Shalini; Sudimack, Daniel; Day, Nicholas P J; Anderson, Timothy J C; White, Nicholas J
2007 Apr 1;195(7):927-933, Journal of infectious diseases
BACKGROUND: Relapses originating from hypnozoites are characteristic of Plasmodium vivax infections. Thus, reappearance of parasitemia after treatment can result from relapse, recrudescence, or reinfection. It has been assumed that parasites causing relapse would be a subset of the parasites that caused the primary infection. METHODS: Paired samples were collected before initiation of antimalarial treatment and at recurrence of parasitemia from 149 patients with vivax malaria in Thailand (n=36), where reinfection could be excluded, and during field studies in Myanmar (n=75) and India (n=38). RESULTS: Combined genetic data from 2 genotyping approaches showed that novel P. vivax populations were present in the majority of patients with recurrent infection (107 [72%] of 149 patients overall [78% of patients in Thailand, 75% of patients in Myanmar {Burma}, and 63% of patients in India]). In 61% of the Thai and Burmese patients and in 55% of the Indian patients, the recurrent infections contained none of the parasite genotypes that caused the acute infection. CONCLUSIONS: The P. vivax populations emerging from hypnozoites commonly differ from the populations that caused the acute episode. Activation of heterologous hypnozoite populations is the most common cause of first relapse in patients with vivax malaria
— id: 72022, year: 2007, vol: 195, page: 927, stat: Journal Article,

Within-host and population-level genetic diversity of Plasmodium vivax in Peru
Sutton, PL; Kang'a, S; Hernandez, JN; Merino, EF; Vidal, CE; Carlton, J; Branch, OH
2007 NOV ;77(5):850-169, American journal of tropical medicine & hygiene
— id: 98152, year: 2007, vol: 77, page: 850, stat: Journal Article,

Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
Eisen, Jonathan A; Coyne, Robert S; Wu, Martin; Wu, Dongying; Thiagarajan, Mathangi; Wortman, Jennifer R; Badger, Jonathan H; Ren, Qinghu; Amedeo, Paolo; Jones, Kristie M; Tallon, Luke J; Delcher, Arthur L; Salzberg, Steven L; Silva, Joana C; Haas, Brian J; Majoros, William H; Farzad, Maryam; Carlton, Jane M; Smith, Roger K Jr; Garg, Jyoti; Pearlman, Ronald E; Karrer, Kathleen M; Sun, Lei; Manning, Gerard; Elde, Nels C; Turkewitz, Aaron P; Asai, David J; Wilkes, David E; Wang, Yufeng; Cai, Hong; Collins, Kathleen; Stewart, B Andrew; Lee, Suzanne R; Wilamowska, Katarzyna; Weinberg, Zasha; Ruzzo, Walter L; Wloga, Dorota; Gaertig, Jacek; Frankel, Joseph; Tsao, Che-Chia; Gorovsky, Martin A; Keeling, Patrick J; Waller, Ross F; Patron, Nicola J; Cherry, J Michael; Stover, Nicholas A; Krieger, Cynthia J; del Toro, Christina; Ryder, Hilary F; Williamson, Sondra C; Barbeau, Rebecca A; Hamilton, Eileen P; Orias, Eduardo
2006 Sep;4(9):e286-e286, PLoS biology
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance
— id: 68202, year: 2006, vol: 4, page: e286, stat: Journal Article,

Microsatellite variation, repeat array length, and population history of Plasmodium vivax
Imwong, M; Sudimack, D; Pukrittayakamee, S; Osorio, L; Carlton, J M; Day, N P J; White, N J; Anderson, T J C
2006 May;23(5):1016-1018, Molecular biology & evolution
— id: 66425, year: 2006, vol: 23, page: 1016, stat: Journal Article,

Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites
Sargeant, Tobias J; Marti, Matthias; Caler, Elisabet; Carlton, Jane M; Simpson, Ken; Speed, Terence P; Cowman, Alan F
2006 ;7(2):R12-R12, Genome biology
BACKGROUND: The apicomplexan parasite Plasmodium falciparum causes the most severe form of malaria in humans. After invasion into erythrocytes, asexual parasite stages drastically alter their host cell and export remodeling and virulence proteins. Previously, we have reported identification and functional analysis of a short motif necessary for export of proteins out of the parasite and into the red blood cell. RESULTS: We have developed software for the prediction of exported proteins in the genus Plasmodium, and identified exported proteins conserved between malaria parasites infecting rodents and the two major causes of human malaria, P. falciparum and P. vivax. This conserved 'exportome' is confined to a few subtelomeric chromosomal regions in P. falciparum and the synteny of these and surrounding regions is conserved in P. vivax. We have identified a novel gene family PHIST (for Plasmodium helical interspersed subtelomeric family) that shares a unique domain with 72 paralogs in P. falciparum and 39 in P. vivax; however, there is only one member in each of the three species studied from the P. berghei lineage. CONCLUSION: These data suggest radiation of genes encoding remodeling and virulence factors from a small number of loci in a common Plasmodium ancestor, and imply a closer phylogenetic relationship between the P. vivax and P. falciparum lineages than previously believed. The presence of a conserved 'exportome' in the genus Plasmodium has important implications for our understanding of both common mechanisms and species-specific differences in host-parasite interactions, and may be crucial in developing novel antimalarial drugs to this infectious disease
— id: 64340, year: 2006, vol: 7, page: R12, stat: Journal Article,

The genome of model malaria parasites, and comparative genomics
Carlton, Jane; Silva, Joana; Hall, Neil
2005 Jan;7(1):23-37, Current issues in molecular biology
The field of comparative genomics of malaria parasites has recently come of age with the completion of the whole genome sequences of the human malaria parasite Plasmodium falciparum and a rodent malaria model, Plasmodium yoelii yoelii. With several other genome sequencing projects of different model and human malaria parasite species underway, comparing genomes from multiple species has necessitated the development of improved informatics tools and analyses. Results from initial comparative analyses reveal striking conservation of gene synteny between malaria species within conserved chromosome cores, in contrast to reduced homology within subtelomeric regions, in line with previous findings on a smaller scale. Genes that elicit a host immune response are frequently found to be species-specific, although a large variant multigene family is common to many rodent malaria species and Plasmodium vivax. Sequence alignment of syntenic regions from multiple species has revealed the similarity between species in coding regions to be high relative to non-coding regions, and phylogenetic footprinting studies promise to reveal conserved motifs in the latter. Comparison of non-synonymous substitution rates between orthologous genes is proving a powerful technique for identifying genes under selection pressure, and may be useful for vaccine design. This is a stimulating time for comparative genomics of model and human malaria parasites, which promises to produce useful results for the development of antimalarial drugs and vaccines
— id: 64352, year: 2005, vol: 7, page: 23, stat: Journal Article,

Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages
Cui, Liwang; Fan, Qi; Hu, Yi; Karamycheva, Svetlana A; Quackenbush, John; Khuntirat, Benjawan; Sattabongkot, Jetsumon; Carlton, Jane M
2005 Nov;144(1):1-9, Molecular & biochemical parasitology
Despite the significance of Plasmodium vivax as the most widespread human malaria parasite and a major public health problem, gene expression in this parasite is poorly understood. To accelerate gene discovery and facilitate the annotation phase of the P. vivax genome project, we have undertaken a transcriptome approach to study gene expression in the mixed blood stages of a P. vivax field isolate. Using a cDNA library constructed from purified blood stages, we have obtained single-pass sequences for approximately 21,500 expressed sequence tags (ESTs), the largest number of transcript tags obtained so far for this species. Cluster analysis revealed that the library is highly redundant, resulting in 5407 clusters. Clustered ESTs were searched against public protein databases for functional annotation, and more than one-third showed a significant match, the majority of these to Plasmodium falciparum proteins. The most abundant clusters were to genes encoding ribosomal proteins and proteins involved in metabolism, consistent with the predominance of trophozoites in the field isolate sample. In spite of the scarcity of other parasite stages in the field isolate, we could identify genes that are expressed in rings, schizonts and gametocytes. This study should facilitate our understanding of the gene expression in P. vivax asexual stages and provide valuable data for gene prediction and annotation of the P. vivax genome sequence
— id: 64344, year: 2005, vol: 144, page: 1, stat: Journal Article,

Comparative genomics of trypanosomatid parasitic protozoa
El-Sayed, Najib M; Myler, Peter J; Blandin, Gaelle; Berriman, Matthew; Crabtree, Jonathan; Aggarwal, Gautam; Caler, Elisabet; Renauld, Hubert; Worthey, Elizabeth A; Hertz-Fowler, Christiane; Ghedin, Elodie; Peacock, Christopher; Bartholomeu, Daniella C; Haas, Brian J; Tran, Anh-Nhi; Wortman, Jennifer R; Alsmark, U Cecilia M; Angiuoli, Samuel; Anupama, Atashi; Badger, Jonathan; Bringaud, Frederic; Cadag, Eithon; Carlton, Jane M; Cerqueira, Gustavo C; Creasy, Todd; Delcher, Arthur L; Djikeng, Appolinaire; Embley, T Martin; Hauser, Christopher; Ivens, Alasdair C; Kummerfeld, Sarah K; Pereira-Leal, Jose B; Nilsson, Daniel; Peterson, Jeremy; Salzberg, Steven L; Shallom, Joshua; Silva, Joana C; Sundaram, Jaideep; Westenberger, Scott; White, Owen; Melville, Sara E; Donelson, John E; Andersson, Bjorn; Stuart, Kenneth D; Hall, Neil
2005 Jul 15;309(5733):404-409, Science
A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that-along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions-have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont
— id: 64345, year: 2005, vol: 309, page: 404, stat: Journal Article,

Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes
Gardner, Malcolm J; Bishop, Richard; Shah, Trushar; de Villiers, Etienne P; Carlton, Jane M; Hall, Neil; Ren, Qinghu; Paulsen, Ian T; Pain, Arnab; Berriman, Matthew; Wilson, Robert J M; Sato, Shigeharu; Ralph, Stuart A; Mann, David J; Xiong, Zikai; Shallom, Shamira J; Weidman, Janice; Jiang, Lingxia; Lynn, Jeffery; Weaver, Bruce; Shoaibi, Azadeh; Domingo, Alexander R; Wasawo, Delia; Crabtree, Jonathan; Wortman, Jennifer R; Haas, Brian; Angiuoli, Samuel V; Creasy, Todd H; Lu, Charles; Suh, Bernard; Silva, Joana C; Utterback, Teresa R; Feldblyum, Tamara V; Pertea, Mihaela; Allen, Jonathan; Nierman, William C; Taracha, Evans L N; Salzberg, Steven L; White, Owen R; Fitzhugh, Henry A; Morzaria, Subhash; Venter, J Craig; Fraser, Claire M; Nene, Vishvanath
2005 Jul 1;309(5731):134-137, Science
We report the genome sequence of Theileria parva, an apicomplexan pathogen causing economic losses to smallholder farmers in Africa. The parasite chromosomes exhibit limited conservation of gene synteny with Plasmodium falciparum, and its plastid-like genome represents the first example where all apicoplast genes are encoded on one DNA strand. We tentatively identify proteins that facilitate parasite segregation during host cell cytokinesis and contribute to persistent infection of transformed host cells. Several biosynthetic pathways are incomplete or absent, suggesting substantial metabolic dependence on the host cell. One protein family that may generate parasite antigenic diversity is not telomere-associated
— id: 64346, year: 2005, vol: 309, page: 134, stat: Journal Article,

Comparative genomics of malaria parasites
Hall, Neil; Carlton, Jane
2005 Dec;15(6):609-613, Current opinion in genetics & development
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
— id: 64342, year: 2005, vol: 15, page: 609, stat: Journal Article,

A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses
Hall, Neil; Karras, Marianna; Raine, J Dale; Carlton, Jane M; Kooij, Taco W A; Berriman, Matthew; Florens, Laurence; Janssen, Christoph S; Pain, Arnab; Christophides, Georges K; James, Keith; Rutherford, Kim; Harris, Barbara; Harris, David; Churcher, Carol; Quail, Michael A; Ormond, Doug; Doggett, Jon; Trueman, Holly E; Mendoza, Jacqui; Bidwell, Shelby L; Rajandream, Marie-Adele; Carucci, Daniel J; Yates, John R 3rd; Kafatos, Fotis C; Janse, Chris J; Barrell, Bart; Turner, C Michael R; Waters, Andrew P; Sinden, Robert E
2005 Jan 7;307(5706):82-86, Science
Plasmodium berghei and Plasmodium chabaudi are widely used model malaria species. Comparison of their genomes, integrated with proteomic and microarray data, with the genomes of Plasmodium falciparum and Plasmodium yoelii revealed a conserved core of 4500 Plasmodium genes in the central regions of the 14 chromosomes and highlighted genes evolving rapidly because of stage-specific selective pressures. Four strategies for gene expression are apparent during the parasites' life cycle: (i) housekeeping; (ii) host-related; (iii) strategy-specific related to invasion, asexual replication, and sexual development; and (iv) stage-specific. We observed posttranscriptional gene silencing through translational repression of messenger RNA during sexual development, and a 47-base 3' untranslated region motif is implicated in this process
— id: 64350, year: 2005, vol: 307, page: 82, stat: Journal Article,

A Plasmodium whole-genome synteny map: indels and synteny breakpoints as foci for species-specific genes
Kooij, Taco W A; Carlton, Jane M; Bidwell, Shelby L; Hall, Neil; Ramesar, Jai; Janse, Chris J; Waters, Andrew P
2005 Dec;1(4):e44-e44, PLoS pathogens
Whole-genome comparisons are highly informative regarding genome evolution and can reveal the conservation of genome organization and gene content, gene regulatory elements, and presence of species-specific genes. Initial comparative genome analyses of the human malaria parasite Plasmodium falciparum and rodent malaria parasites (RMPs) revealed a core set of 4,500 Plasmodium orthologs located in the highly syntenic central regions of the chromosomes that sharply defined the boundaries of the variable subtelomeric regions. We used composite RMP contigs, based on partial DNA sequences of three RMPs, to generate a whole-genome synteny map of P. falciparum and the RMPs. The core regions of the 14 chromosomes of P. falciparum and the RMPs are organized in 36 synteny blocks, representing groups of genes that have been stably inherited since these malaria species diverged, but whose relative organization has altered as a result of a predicted minimum of 15 recombination events. P. falciparum-specific genes and gene families are found in the variable subtelomeric regions (575 genes), at synteny breakpoints (42 genes), and as intrasyntenic indels (126 genes). Of the 168 non-subtelomeric P. falciparum genes, including two newly discovered gene families, 68% are predicted to be exported to the surface of the blood stage parasite or infected erythrocyte. Chromosomal rearrangements are implicated in the generation and dispersal of P. falciparum-specific gene families, including one encoding receptor-associated protein kinases. The data show that both synteny breakpoints and intrasyntenic indels can be foci for species-specific genes with a predicted role in host-parasite interactions and suggest that, besides rearrangements in the subtelomeric regions, chromosomal rearrangements may also be involved in the generation of species-specific gene families. A majority of these genes are expressed in blood stages, suggesting that the vertebrate host exerts a greater selective pressure than the mosquito vector, resulting in the acquisition of diversity
— id: 64341, year: 2005, vol: 1, page: e44, stat: Journal Article,

Identification of a very large Rab GTPase family in the parasitic protozoan Trichomonas vaginalis
Lal, Kalpana; Field, Mark C; Carlton, Jane M; Warwicker, Jim; Hirt, Robert P
2005 Oct;143(2):226-235, Molecular & biochemical parasitology
Rab proteins are pivotal components of the membrane trafficking machinery in all eukaryotes. Distinct Rab proteins locate to specific endomembrane compartments and genomic studies suggest that Rab gene diversity correlates with endomembrane system complexity; for example unicellular organisms generally possess 5-20 Rab family members and the size of the repertoire increases to 25-60 in multicellular systems. Here we report 65 open reading frames from the unicellular protozoan Trichomonas vaginalis that encode distinct Rab proteins (TvRabs), indicating a family with complexity that rivals Homo sapiens in number. The detection of gene transcripts for the majority of these genes and conservation of functional motifs strongly suggests that TvRabs retain functionality and likely roles in membrane trafficking. The T. vaginalis Rab family includes orthologues of the conserved subfamilies, Rab1, Rab5, Rab6, Rab7 and Rab11, but the majority of TvRabs are not represented by orthologues in other systems and includes six novel T. vaginalis specific Rab subfamilies (A-F). The extreme size of the T. vaginalis Rab family, the presence of novel subfamilies plus the divergent nature of many TvRab sequences suggest both the presence of a highly complex endomembrane system within Trichomonas and potentially novel Rab functionality. A family of more than 65 Rab genes in a unicellular genome is unexpected, but may be a requirement for progression though an amoeboid life-cycle phase as both Dictyostelium discoideum and Entamoeba histolytica share with T. vaginalis both an amoeboid life cycle stage and very large Rab gene families
— id: 64343, year: 2005, vol: 143, page: 226, stat: Journal Article,

Host switch leads to emergence of Plasmodium vivax malaria in humans
Mu, Jianbing; Joy, Deirdre A; Duan, Junhui; Huang, Yaming; Carlton, Jane; Walker, John; Barnwell, John; Beerli, Peter; Charleston, Michael A; Pybus, Oliver G; Su, Xin-zhuan
2005 Aug;22(8):1686-1693, Molecular biology & evolution
The geographical origin of Plasmodium vivax, the most widespread human malaria parasite, is controversial. Although genetic closeness to Asian primate malarias has been confirmed by phylogenetic analyses, genetic similarities between P. vivax and Plasmodium simium, a New World primate malaria, suggest that humans may have acquired P. vivax from New World monkeys or vice versa. Additionally, the near fixation of the Duffy-negative blood type (FY x B(null)/FY x B(null)) in West and Central Africa, consistent with directional selection, and the association of Duffy negativity with complete resistance to vivax malaria suggest a prolonged period of host-parasite coevolution in Africa. Here we use Bayesian and likelihood methods in conjunction with cophylogeny mapping to reconstruct the genetic and coevolutionary history of P. vivax from the complete mitochondrial genome of 176 isolates as well as several closely related Plasmodium species. Taken together, a haplotype network, parasite migration patterns, demographic history, and cophylogeny mapping support an Asian origin via a host switch from macaque monkeys
— id: 64348, year: 2005, vol: 22, page: 1686, stat: Journal Article,

A potentially functional mariner transposable element in the protist Trichomonas vaginalis
Silva, Joana C; Bastida, Felix; Bidwell, Shelby L; Johnson, Patricia J; Carlton, Jane M
2005 Jan;22(1):126-134, Molecular biology & evolution
Mariner transposable elements encoding a D,D34D motif-bearing transposase are characterized by their pervasiveness among, and exclusivity to, animal phyla. To date, several hundred sequences have been obtained from taxa ranging from cnidarians to humans, only two of which are known to be functional. Related transposons have been identified in plants and fungi, but their absence among protists is noticeable. Here, we identify and characterize Tvmar1, the first representative of the mariner family to be found in a species of protist, the human parasite Trichomonas vaginalis. This is the first D,D34D element to be found outside the animal kingdom, and its inclusion in the mariner family is supported by both structural and phylogenetic analyses. Remarkably, Tvmar1 has all the hallmarks of a functional element and has recently expanded to several hundred copies in the genome of T. vaginalis. Our results show that a new potentially active mariner has been found that belongs to a distinct mariner lineage and has successfully invaded a nonanimal, single-celled organism. The considerable genetic distance between Tvmar1 and other mariners may have valuable implications for the design of new, high-efficiency vectors to be used in transfection studies in protists
— id: 64354, year: 2005, vol: 22, page: 126, stat: Journal Article,

Spliceosomal introns in the deep-branching eukaryote Trichomonas vaginalis
Vanacova, Stepanka; Yan, Weihong; Carlton, Jane M; Johnson, Patricia J
2005 Mar 22;102(12):4430-4435, Proceedings of the National Academy of Sciences of the United States of America
Eukaryotes have evolved elaborate splicing mechanisms to remove introns that would otherwise destroy the protein-coding capacity of genes. Nuclear premRNA splicing requires sequence motifs in the intron and is mediated by a ribonucleoprotein complex, the spliceosome. Here we demonstrate the presence of a splicing apparatus in the protist Trichomonas vaginalis and show that RNA motifs found in yeast and metazoan introns are required for splicing. We also describe the first introns in this deep-branching lineage. The positions of these introns are often conserved in orthologous genes, indicating they were present in a common ancestor of trichomonads, yeast, and metazoa. All examined T. vaginalis introns have a highly conserved 12-nt 3' splice-site motif that encompasses the branch point and is necessary for splicing. This motif is also found in the only described intron in a gene from another deep-branching eukaryote, Giardia intestinalis. These studies demonstrate the conservation of intron splicing signals across large evolutionary distances, reveal unexpected motif conservation in deep-branching lineages that suggest a simplified mechanism of splicing in primitive unicellular eukaryotes, and support the presence of introns in the earliest eukaryote
— id: 64349, year: 2005, vol: 102, page: 4430, stat: Journal Article,

Immune responses to Plasmodium vivax pre-erythrocytic stage antigens in naturally exposed Duffy-negative humans: a potential model for identification of liver-stage antigens
Wang, Ruobing; Arevalo-Herrera, Myriam; Gardner, Malcolm J; Bonelo, Anilza; Carlton, Jane M; Gomez, Andres; Vera, Omaira; Soto, Liliana; Vergara, Juana; Bidwell, Shelby L; Domingo, Alexander; Fraser, Claire M; Herrera, Socrates
2005 Jun;35(6):1859-1868, European journal of immunology
Duffy antigen is the receptor used by Plasmodium vivax to invade erythrocytes. Consequently, individuals lacking Duffy antigen [Fy(-)] do not develop blood-stage infections. We hypothesized that naturally exposed Fy(-) humans may develop immune responses mainly to pre-erythrocytic stages and could be used to study acquired immunity to P. vivax and to identify liver-stage antigens. We report here that antibody and IFN-gamma responses to known sporozoite antigens were significantly induced by natural exposure in Fy(-) humans, whereas responses to blood-stage antigens were significantly induced in Fy(+) humans. IFN-gamma responses to sporozoite antigens were lower in Fy(+) than in Fy(-) humans, indicating that in Fy(+) humans blood-stage infections may have suppressed T cell responses to pre-erythrocytic stages. We evaluated the immune responses to 18 novel P. vivax homologs of P. falciparum sporozoite proteins identified from the P. vivax genome sequence. Eight proteins recalled IFN-gamma responses in P. vivax-exposed but not in unexposed individuals. Of these, 3 antigens elicited IFN-gamma responses in Fy(-) but not in Fy(+) individuals. These results suggest that differential immune responses observed in naturally exposed Fy(-) and Fy(+) individuals can be exploited to identify P. vivax stage-specific antigens
— id: 64347, year: 2005, vol: 35, page: 1859, stat: Journal Article,

Novel antigen identification method for discovery of protective malaria antigens by rapid testing of DNA vaccines encoding exons from the parasite genome
Haddad, Diana; Bilcikova, Erika; Witney, Adam A; Carlton, Jane M; White, Charles E; Blair, Peter L; Chattopadhyay, Rana; Russell, Joshua; Abot, Esteban; Charoenvit, Yupin; Aguiar, Joao C; Carucci, Daniel J; Weiss, Walter R
2004 Mar;72(3):1594-1602, Infection & immunity
We describe a novel approach for identifying target antigens for preerythrocytic malaria vaccines. Our strategy is to rapidly test hundreds of DNA vaccines encoding exons from the Plasmodium yoelii yoelii genomic sequence. In this antigen identification method, we measure reduction in parasite burden in the liver after sporozoite challenge in mice. Orthologs of protective P. y. yoelii genes can then be identified in the genomic databases of Plasmodium falciparum and Plasmodium vivax and investigated as candidate antigens for a human vaccine. A pilot study to develop the antigen identification method approach used 192 P. y. yoelii exons from genes expressed during the sporozoite stage of the life cycle. A total of 182 (94%) exons were successfully cloned into a DNA immunization vector with the Gateway cloning technology. To assess immunization strategies, mice were vaccinated with 19 of the new DNA plasmids in addition to the well-characterized protective plasmid encoding P. y. yoelii circumsporozoite protein. Single plasmid immunization by gene gun identified a novel vaccine target antigen which decreased liver parasite burden by 95% and which has orthologs in P. vivax and P. knowlesi but not P. falciparum. Intramuscular injection of DNA plasmids produced a different pattern of protective responses from those seen with gene gun immunization. Intramuscular immunization with plasmid pools could reduce liver parasite burden in mice despite the fact that none of the plasmids was protective when given individually. We conclude that high-throughput cloning of exons into DNA vaccines and their screening is feasible and can rapidly identify new malaria vaccine candidate antigens
— id: 64356, year: 2004, vol: 72, page: 1594, stat: Journal Article,

Chloroquine resistance in Plasmodium chabaudi: are chloroquine-resistance transporter (crt) and multi-drug resistance (mdr1) orthologues involved?
Hunt, Paul; Cravo, Pedro V L; Donleavy, Paul; Carlton, Jane M-R; Walliker, David
2004 Jan;133(1):27-35, Molecular & biochemical parasitology
We have identified in the rodent malaria parasite Plasmodium chabaudi orthologues of two Plasmodium falciparum genes, pfcrt and pfmdr1 which have been implicated as determinants of chloroquine resistance in the latter species. The sequences of the P. chabaudi genes, denoted, respectively, pccg10 and pcmdr1, were first determined in the chloroquine-sensitive clone AS, and found to be highly similar to those of P. falciparum. For pccg10, there was a nucleotide sequence identity of 68.6% and amino acid sequence identity of 75.1% within the predicted coding region. For pcmdr1, the sequence identities were 75.0% (nucleotide) and 78.1% (amino acid). The sequences of the genes were then determined in three P. chabaudi clones selected from clone AS which possessed three different levels of resistance to chloroquine. The sequences of both genes in all mutants were found to be identical to those of the sensitive AS from which they had been derived. Polymorphic sites were found in both genes between the AS clones and a genetically unrelated sensitive clone AJ. Analysis of genetic crosses between AJ and resistant AS clones showed no linkage between inherited parental alleles of pccrt and pcmdr1 and drug responses of the cloned progeny. This showed that neither of these genes, nor genes closely linked to them, were determinants of the chloroquine resistance in the P. chabaudi mutants
— id: 64357, year: 2004, vol: 133, page: 27, stat: Journal Article,

Gene synteny and chloroquine resistance in Plasmodium chabaudi
Hunt, Paul; Martinelli, Axel; Fawcett, Richard; Carlton, Jane; Carter, Richard; Walliker, David
2004 Aug;136(2):157-164, Molecular & biochemical parasitology
Chloroquine resistance in the rodent malaria parasite Plasmodium chabaudi has been shown to be caused by a gene on chromosome 11, and is not linked to orthologues of the Plasmodium falciparum chloroquine resistance transporter (pfcrt) or Pgh-1 (pfmdr1) genes. In the current work, the progeny of crosses between chloroquine-resistant and sensitive clones of P. chabaudi have been analysed for the inheritance of 658 AFLP markers. Markers linked to the chloroquine responses of the progeny, including two which are completely linked, have been genetically mapped, sequenced and their homologues, or closely linked loci, identified in P. falciparum. The chromosome 11 markers most closely linked to chloroquine resistance in P. chabaudi map to loci which are also closely linked in P. falciparum, although in two linkage groups on chromosomes 6 and 13 of this species. The P. falciparum orthologue of the gene conferring chloroquine resistance in P. chabaudi is predicted to lie within a 250 kb region of P. falciparum chromosome 6, containing approximately 50 genes. The genetic order of the markers in P. chabaudi is co-linear with the physical linkage represented in the P. falciparum genome database. The findings provide evidence for extensive conservation of synteny between the two species
— id: 64353, year: 2004, vol: 136, page: 157, stat: Journal Article,

Mind the gap: bridging the divide between clinical and molecular studies of the trichomonads
Lyons, Emily J; Carlton, Jane M
2004 May;20(5):204-207, Trends in parasitology
— id: 64355, year: 2004, vol: 20, page: 204, stat: Journal Article,

Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment
Moran, Mary Ann; Buchan, Alison; Gonzalez, Jose M; Heidelberg, John F; Whitman, William B; Kiene, Ronald P; Henriksen, James R; King, Gary M; Belas, Robert; Fuqua, Clay; Brinkac, Lauren; Lewis, Matt; Johri, Shivani; Weaver, Bruce; Pai, Grace; Eisen, Jonathan A; Rahe, Elisha; Sheldon, Wade M; Ye, Wenying; Miller, Todd R; Carlton, Jane; Rasko, David A; Paulsen, Ian T; Ren, Qinghu; Daugherty, Sean C; Deboy, Robert T; Dodson, Robert J; Durkin, A Scott; Madupu, Ramana; Nelson, William C; Sullivan, Steven A; Rosovitz, M J; Haft, Daniel H; Selengut, Jeremy; Ward, Naomi
2004 Dec 16;432(7019):910-913, Nature
Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean
— id: 64351, year: 2004, vol: 432, page: 910, stat: Journal Article,

The Plasmodium vivax genome sequencing project
Carlton, Jane
2003 May;19(5):227-231, Trends in parasitology
With the successful completion of the project to sequence the Plasmodium falciparum genome, researchers are now turning their attention to other malaria parasite species. Here, an update on the Plasmodium vivax genome sequencing project is presented, as part of the Trends in Parasitology series of reviews expanding on various aspects of P. vivax research
— id: 64362, year: 2003, vol: 19, page: 227, stat: Journal Article,

Genome sequencing and comparative genomics of tropical disease pathogens
Carlton, Jane M
2003 Dec;5(12):861-873, Cellular microbiology
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
— id: 64358, year: 2003, vol: 5, page: 861, stat: Journal Article,

Genetics of mefloquine resistance in the rodent malaria parasite Plasmodium chabaudi
Cravo, Pedro V L; Carlton, Jane M-R; Hunt, Paul; Bisoni, Laura; Padua, Rose Ann; Walliker, David
2003 Feb;47(2):709-718, Antimicrobial agents & chemotherapy
The genetic determinants of resistance to mefloquine in malaria parasites are unclear. Some studies have implied that amplification of, or mutations in, the multidrug resistance gene pfmdr1 in Plasmodium falciparum may be involved. Using the rodent malaria model Plasmodium chabaudi, we investigated the role of the orthologue of this gene, pcmdr1, in a stable mefloquine-resistant mutant, AS(15MF/3), selected from a sensitive clone. pcmdr1 exists as a single copy gene on chromosome 12 of the sensitive clone. In AS(15MF/3), the gene was found to have undergone duplication, with one copy translocating to chromosome 4. mRNA levels of pcmdr1 were higher in the mutant than in the parent sensitive clone. A partial genetic map of the translocation showed that other genes in addition to pcmdr1 had been cotranslocated. The sequences of both copies of pcmdr1 of AS(15MF/3) were identical to that of the parent sensitive clone. A cross was made between AS(15MF/3) and an unrelated mefloquine-sensitive clone, AJ. Phenotypic and molecular analysis of progeny clones showed that duplication and overexpression of the pcmdr1 gene was an important determinant of resistance. However, not all mefloquine-resistant progeny contained the duplicated gene, showing that at least one other gene was involved in resistance
— id: 64363, year: 2003, vol: 47, page: 709, stat: Journal Article,

Plasmepsin 4, the food vacuole aspartic proteinase found in all Plasmodium spp. infecting man
Dame, John B; Yowell, Charles A; Omara-Opyene, Levi; Carlton, Jane M; Cooper, Roland A; Li, Tang
2003 Aug 11;130(1):1-12, Molecular & biochemical parasitology
Plasmepsins are aspartic proteinases of the malaria parasite, and seven groups of plasmepsins have been identified by comparing genomic sequence data available for the genes encoding these enzymes from Plasmodium falciparum, Plasmodium vivax, Plasmodium knowlesi, Plasmodium berghei, and Plasmodium yoelii. The food vacuole plasmepsins typified by plasmepsin 4 from P. falciparum (PfPM4) constitute one of these groups. Genes encoding the ortholog of PfPM4 have been cloned from Plasmodium ovale, Plasmodium malariae, and P. vivax. In addition, P. falciparum contains three paralagous food vacuole plasmepsins or plasmepsin-like enzymes that appear to have arisen by gene duplication, plasmepsins 1 (PfPM1), 2 (PfPM2) and HAP, and all four were localized to purified food vacuole preparations by two-dimensional gel electrophoresis and mass spectroscopic analysis. The three paralogs of PfPM4 do not have counterparts in the six other Plasmodium spp. examined by genomic DNA blot analysis and by review of available genomic sequence data. The presence of these paralogs among the food vacuole plasmepsins in P. falciparum as compared with the other three species causing malaria in man will impact efforts to rationally design antimalarials targeting the food vacuole plasmepsins
— id: 64360, year: 2003, vol: 130, page: 1, stat: Journal Article,

Single-nucleotide polymorphisms and genome diversity in Plasmodium vivax
Feng, Xiaorong; Carlton, Jane M; Joy, Deirdre A; Mu, Jianbing; Furuya, Tetsuya; Suh, Bernard B; Wang, Yufeng; Barnwell, John W; Su, Xin-Zhuan
2003 Jul 8;100(14):8502-8507, Proceedings of the National Academy of Sciences of the United States of America
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
— id: 64361, year: 2003, vol: 100, page: 8502, stat: Journal Article,

Identification of a polymorphic Plasmodium vivax microsatellite marker
Gomez, John C; McNamara, David T; Bockarie, Moses J; Baird, J Kevin; Carlton, Jane M; Zimmerman, Peter A
2003 Oct;69(4):377-379, American journal of tropical medicine & hygiene
Microsatellite markers derived from simple sequence repeats have been useful in studying a number of human pathogens, including the human malaria parasite Plasmodium falciparum. Genetic markers for P. vivax would likewise help elucidate the genetics and population characteristics of this other important human malaria parasite. We have identified a locus in a P. vivax telomeric clone that contains simple sequence repeats. Primers were designed to amplify this region using a two-step semi-nested polymerase chain reaction protocol. The primers did not amplify template obtained from non-infected individuals, nor DNA from primates infected with the other human malaria parasites (P. ovale, P. malariae, or P. falciparum). The marker was polymorphic in P. vivax-infected field isolates obtained from Papua New Guinea, Indonesia and Guyana. This microsatellite marker may be useful in genetic and epidemiologic studies of P. vivax malaria
— id: 64359, year: 2003, vol: 69, page: 377, stat: Journal Article,

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
Carlton, Jane M; Angiuoli, Samuel V; Suh, Bernard B; Kooij, Taco W; Pertea, Mihaela; Silva, Joana C; Ermolaeva, Maria D; Allen, Jonathan E; Selengut, Jeremy D; Koo, Hean L; Peterson, Jeremy D; Pop, Mihai; Kosack, Daniel S; Shumway, Martin F; Bidwell, Shelby L; Shallom, Shamira J; van Aken, Susan E; Riedmuller, Steven B; Feldblyum, Tamara V; Cho, Jennifer K; Quackenbush, John; Sedegah, Martha; Shoaibi, Azadeh; Cummings, Leda M; Florens, Laurence; Yates, John R; Raine, J Dale; Sinden, Robert E; Harris, Michael A; Cunningham, Deirdre A; Preiser, Peter R; Bergman, Lawrence W; Vaidya, Akhil B; van Lin, Leo H; Janse, Chris J; Waters, Andrew P; Smith, Hamilton O; White, Owen R; Salzberg, Steven L; Venter, J Craig; Fraser, Claire M; Hoffman, Stephen L; Gardner, Malcolm J; Carucci, Daniel J
2002 Oct 3;419(6906):512-519, Nature
Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease
— id: 64365, year: 2002, vol: 419, page: 512, stat: Journal Article,

Rodent models of malaria in the genomics era
Carlton, Jane M; Carucci, Daniel J
2002 Mar;18(3):100-102, Trends in parasitology
The Rodent Malaria Genomics Symposium: Current Status and Future Directions was held on 15-16 November 2001 in Atlanta, GA, USA
— id: 64369, year: 2002, vol: 18, page: 100, stat: Journal Article,

Fast algorithms for large-scale genome alignment and comparison
Delcher, Arthur L; Phillippy, Adam; Carlton, Jane; Salzberg, Steven L
2002 Jun 1;30(11):2478-2483, Nucleic acids research
We describe a suffix-tree algorithm that can align the entire genome sequences of eukaryotic and prokaryotic organisms with minimal use of computer time and memory. The new system, MUMmer 2, runs three times faster while using one-third as much memory as the original MUMmer system. It has been used successfully to align the entire human and mouse genomes to each other, and to align numerous smaller eukaryotic and prokaryotic genomes. A new module permits the alignment of multiple DNA sequence fragments, which has proven valuable in the comparison of incomplete genome sequences. We also describe a method to align more distantly related genomes by detecting protein sequence homology. This extension to MUMmer aligns two genomes after translating the sequence in all six reading frames, extracts all matching protein sequences and then clusters together matches. This method has been applied to both incomplete and complete genome sequences in order to detect regions of conserved synteny, in which multiple proteins from one organism are found in the same order and orientation in another. The system code is being made freely available by the authors
— id: 64367, year: 2002, vol: 30, page: 2478, stat: Journal Article,

Genome sequence of the human malaria parasite Plasmodium falciparum
Gardner, Malcolm J; Hall, Neil; Fung, Eula; White, Owen; Berriman, Matthew; Hyman, Richard W; Carlton, Jane M; Pain, Arnab; Nelson, Karen E; Bowman, Sharen; Paulsen, Ian T; James, Keith; Eisen, Jonathan A; Rutherford, Kim; Salzberg, Steven L; Craig, Alister; Kyes, Sue; Chan, Man-Suen; Nene, Vishvanath; Shallom, Shamira J; Suh, Bernard; Peterson, Jeremy; Angiuoli, Sam; Pertea, Mihaela; Allen, Jonathan; Selengut, Jeremy; Haft, Daniel; Mather, Michael W; Vaidya, Akhil B; Martin, David M A; Fairlamb, Alan H; Fraunholz, Martin J; Roos, David S; Ralph, Stuart A; McFadden, Geoffrey I; Cummings, Leda M; Subramanian, G Mani; Mungall, Chris; Venter, J Craig; Carucci, Daniel J; Hoffman, Stephen L; Newbold, Chris; Davis, Ronald W; Fraser, Claire M; Barrell, Bart
2002 Oct 3;419(6906):498-511, Nature
The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host-parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria
— id: 64366, year: 2002, vol: 419, page: 498, stat: Journal Article,

Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14
Gardner, Malcolm J; Shallom, Shamira J; Carlton, Jane M; Salzberg, Steven L; Nene, Vishvanath; Shoaibi, Azadeh; Ciecko, Anne; Lynn, Jeffery; Rizzo, Michael; Weaver, Bruce; Jarrahi, Behnam; Brenner, Michael; Parvizi, Babak; Tallon, Luke; Moazzez, Azita; Granger, David; Fujii, Claire; Hansen, Cheryl; Pederson, James; Feldblyum, Tamara; Peterson, Jeremy; Suh, Bernard; Angiuoli, Sam; Pertea, Mihaela; Allen, Jonathan; Selengut, Jeremy; White, Owen; Cummings, Leda M; Smith, Hamilton O; Adams, Mark D; Venter, J Craig; Carucci, Daniel J; Hoffman, Stephen L; Fraser, Claire M
2002 Oct 3;419(6906):531-534, Nature
The mosquito-borne malaria parasite Plasmodium falciparum kills an estimated 0.7-2.7 million people every year, primarily children in sub-Saharan Africa. Without effective interventions, a variety of factors-including the spread of parasites resistant to antimalarial drugs and the increasing insecticide resistance of mosquitoes-may cause the number of malaria cases to double over the next two decades. To stimulate basic research and facilitate the development of new drugs and vaccines, the genome of Plasmodium falciparum clone 3D7 has been sequenced using a chromosome-by-chromosome shotgun strategy. We report here the nucleotide sequences of chromosomes 10, 11 and 14, and a re-analysis of the chromosome 2 sequence. These chromosomes represent about 35% of the 23-megabase P. falciparum genome
— id: 64364, year: 2002, vol: 419, page: 531, stat: Journal Article,

The shikimate pathway and its branches in apicomplexan parasites
Roberts, Craig W; Roberts, Fiona; Lyons, Russell E; Kirisits, Michael J; Mui, Ernest J; Finnerty, John; Johnson, Jennifer J; Ferguson, David J P; Coggins, John R; Krell, Tino; Coombs, Graham H; Milhous, Wilbur K; Kyle, Dennis E; Tzipori, Saul; Barnwell, John; Dame, John B; Carlton, Jane; McLeod, Rima
2002 Feb 15;185 Suppl 1:S25-S36, Journal of infectious diseases
The shikimate pathway is essential for production of a plethora of aromatic compounds in plants, bacteria, and fungi. Seven enzymes of the shikimate pathway catalyze sequential conversion of erythrose 4-phosphate and phosphoenol pyruvate to chorismate. Chorismate is then used as a substrate for other pathways that culminate in production of folates, ubiquinone, napthoquinones, and the aromatic amino acids tryptophan, phenylalanine, and tyrosine. The shikimate pathway is absent from animals and present in the apicomplexan parasites Toxoplasma gondii, Plasmodium falciparum, and Cryptosporidium parvum. Inhibition of the pathway by glyphosate is effective in controlling growth of these parasites. These findings emphasize the potential benefits of developing additional effective inhibitors of the shikimate pathway. Such inhibitors may function as broad-spectrum antimicrobial agents that are effective against bacterial and fungal pathogens and apicomplexan parasites
— id: 64368, year: 2002, vol: 185 Suppl 1, page: S25, stat: Journal Article,

Co-ordinated programme of gene expression during asexual intraerythrocytic development of the human malaria parasite Plasmodium falciparum revealed by microarray analysis
Ben Mamoun C; Gluzman IY; Hott C; MacMillan SK; Amarakone AS; Anderson DL; Carlton JM; Dame JB; Chakrabarti D; Martin RK; Brownstein BH; Goldberg DE
2001 Jan;39(1):26-36, Molecular microbiology
Plasmodium falciparum is a protozoan parasite responsible for the most severe forms of human malaria. All the clinical symptoms and pathological changes seen during human infection are caused by the asexual blood stages of Plasmodium. Within host red blood cells, the parasite undergoes enormous developmental changes during its maturation. In order to analyse the expression of genes during intraerythrocytic development, DNA microarrays were constructed and probed with stage-specific cDNA. Developmental upregulation of specific mRNAs was found to cluster into functional groups and revealed a co-ordinated programme of gene expression. Those involved in protein synthesis (ribosomal proteins, translation factors) peaked early in development, followed by those involved in metabolism, most dramatically glycolysis genes. Adhesion/invasion genes were turned on later in the maturation process. At the end of intraerythrocytic development (late schizogony), there was a general shut-off of gene expression, although a small set of genes, including a number of protein kinases, were turned on at this stage. Nearly all genes showed some regulation over the course of development. A handful of genes remained constant and should be useful for normalizing mRNA levels between stages. These data will facilitate functional analysis of the P. falciparum genome and will help to identify genes with a critical role in parasite progression and multiplication in the human host
— id: 66433, year: 2001, vol: 39, page: 26, stat: Journal Article,

Mycoplasma alligatoris sp. nov., from American alligators
Brown DR; Farley JM; Zacher LA; Carlton JM; Clippinger TL; Tully JG; Brown MB
2001 Mar;51(Pt 2):419-424, International journal of systematic & evolutionary microbiology
Mycoplasmas were isolated from multiple tissues of diseased American alligators (Alligator mississippiensis). This paper presents biochemical, serological and molecular genetic characterizations of a lethal pathogen of alligators for which the name Mycoplasma alligatoris sp. nov. is proposed. The type strain is A21JP2T (ATCC 700619T)
— id: 66430, year: 2001, vol: 51, page: 419, stat: Journal Article,

Conservation of a novel vacuolar transporter in Plasmodium species and its central role in chloroquine resistance of P. falciparum
Carlton JM; Fidock DA; Djimde A; Plowe CV; Wellems TE
2001 Aug;4(4):415-420, Current opinion in microbiology
Chloroquine resistance in Plasmodium falciparum has recently been shown to result from mutations in the novel vacuolar transporter, PfCRT. Field studies have demonstrated the importance of these mutations in clinical resistance. Although a pfcrt ortholog has been identified in Plasmodiumvivax, there is no association between in vivo chloroquine resistance and codon mutations in the P. vivax gene. This is consistent with lines of evidence that suggest alternative mechanisms of chloroquine resistance among various malaria parasite species
— id: 66427, year: 2001, vol: 4, page: 415, stat: Journal Article,

Of mice and malaria mutants: unravelling the genetics of drug resistance using rodent malaria models
Carlton JM; Hayton K; Cravo PV; Walliker D
2001 May;17(5):236-242, Trends in parasitology
It is well recognized that drug resistance is the most significant obstacle to gaining effective malaria control. Despite the enormous advances in the knowledge of the biochemistry and molecular biology of malaria parasites, only a few genes determining resistance to the commonly used drugs have been identified. The idea that rodent malaria parasites should be exploited more widely for such work, in view of the practical problems of studying this subject experimentally in human malaria, is presented
— id: 66429, year: 2001, vol: 17, page: 236, stat: Journal Article,

Profiling the malaria genome: a gene survey of three species of malaria parasite with comparison to other apicomplexan species
Carlton JM; Muller R; Yowell CA; Fluegge MR; Sturrock KA; Pritt JR; Vargas-Serrato E; Galinski MR; Barnwell JW; Mulder N; Kanapin A; Cawley SE; Hide WA; Dame JB
2001 Dec;118(2):201-210, Molecular & biochemical parasitology
We have undertaken the first comparative pilot gene discovery analysis of approximately 25,000 random genomic and expressed sequence tags (ESTs) from three species of Plasmodium, the infectious agent that causes malaria. A total of 5482 genome survey sequences (GSSs) and 5582 ESTs were generated from mung bean nuclease (MBN) and cDNA libraries, respectively, of the ANKA line of the rodent malaria parasite Plasmodium berghei, and 10,874 GSSs generated from MBN libraries of the Salvador I and Belem lines of Plasmodium vivax, the most geographically wide-spread human malaria pathogen. These tags, together with 2438 Plasmodium falciparum sequences present in GenBank, were used to perform first-pass assembly and transcript reconstruction, and non-redundant consensus sequence datasets created. The datasets were compared against public protein databases and more than 1000 putative new Plasmodium proteins identified based on sequence similarity. Homologs of previously characterized Plasmodium genes were also identified, increasing the number of P. vivax and P. berghei sequences in public databases at least 10-fold. Comparative studies with other species of Apicomplexa identified interesting homologs of possible therapeutic or diagnostic value. A gene prediction program, Phat, was used to predict probable open reading frames for proteins in all three datasets. Predicted and non-redundant BLAST-matched proteins were submitted to InterPro, an integrated database of protein domains, signatures and families, for functional classification. Thus a partial predicted proteome was created for each species. This first comparative analysis of Plasmodium protein coding sequences represents a valuable resource for further studies on the biology of this important pathogen
— id: 66426, year: 2001, vol: 118, page: 201, stat: Journal Article,

Biomagnetic separation of contaminating host leukocytes from plasmodium-infected erythrocytes
Carlton JM; Yowell CA; Sturrock KA; Dame JB
2001 Feb;97(2):111-114, Experimental parasitology
Carlton, J. M-R., Yowell, C. A., Sturrock, K. A., and Dame, J. B. 2001. Biomagnetic separation of contaminating host leukocytes from Plasmodium-infected erythrocytes. Experimental Parasitology 97, 111-114
— id: 66431, year: 2001, vol: 97, page: 111, stat: Journal Article,

Host sequences in Plasmodium falciparum and Plasmodium vivax genomic DNA: horizontal transfer or contamination artifact?
Deitsch KW; Carlton JM; Wootton JC; Wellems TE
2001 Feb 23;491(1-2):164-165, FEBS letters
— id: 66432, year: 2001, vol: 491, page: 164, stat: Journal Article,

Evidence for different mechanisms of chloroquine resistance in 2 Plasmodium species that cause human malaria
Nomura T; Carlton JM; Baird JK; del Portillo HA; Fryauff DJ; Rathore D; Fidock DA; Su X; Collins WE; McCutchan TF; Wootton JC; Wellems TE
2001 Jun 1;183(11):1653-1661, Journal of infectious diseases
Chloroquine (CQ)-resistant Plasmodium vivax malaria was first reported 12 years ago, nearly 30 years after the recognition of CQ-resistant P. falciparum. Loss of CQ efficacy now poses a severe problem for the prevention and treatment of both diseases. Mutations in a digestive vacuole protein encoded by a 13-exon gene, pfcrt, were shown recently to have a central role in the CQ resistance (CQR) of P. falciparum. Whether mutations in pfcrt orthologues of other Plasmodium species are involved in CQR remains an open question. This report describes pfcrt homologues from P. vivax, P. knowlesi, P. berghei, and Dictyostelium discoideum. Synteny between the P. falciparum and P. vivax genes is demonstrated. However, a survey of patient isolates and monkey-adapted lines has shown no association between in vivo CQR and codon mutations in the P. vivax gene. This is evidence that the molecular events underlying P. vivax CQR differ from those in P. falciparum
— id: 66428, year: 2001, vol: 183, page: 1653, stat: Journal Article,

The ves multigene family of B. bovis encodes components of rapid antigenic variation at the infected erythrocyte surface
Allred DR; Carlton JM; Satcher RL; Long JA; Brown WC; Patterson PE; O'Connor RM; Stroup SE
2000 Jan;5(1):153-162, Molecular cell
B. bovis, an intraerythrocytic protozoal parasite, establishes chronic infections in cattle in part through rapid variation of the polymorphic, heterodimeric VESA1 protein on the infected erythrocyte surface and sequestration of mature parasites. We describe the characterization of the ves1 alpha gene encoding the VESA1a subunit, thus providing a description of a gene whose product is involved in rapid antigenic variation in a babesial parasite. This three-exon gene, a member of a multigene family (ves), encodes a polypeptide with no cleavable signal sequence, a single predicted transmembrane segment, and a cysteine/lysine-rich domain. Variation appears to involve creation and modification or loss of a novel, transcribed copy of the gene
— id: 66436, year: 2000, vol: 5, page: 153, stat: Journal Article,

The plasmodium vivax and P. berghei gene sequence tag projects
Carlton JM; Dame JB
2000 Oct;16(10):409-409, Parasitology today
— id: 66434, year: 2000, vol: 16, page: 409, stat: Journal Article,

Genome display and typing of Plasmodium parasites using anchored PolyA and PolyT oligonucleotides
Su X; Carlton JM
2000 Apr;94(4):273-278, Experimental parasitology
— id: 66435, year: 2000, vol: 94, page: 273, stat: Journal Article,

Gene synteny across Plasmodium spp: could 'operon-like' structures exist?
Carlton JM
1999 May;15(5):178-179, Parasitology today
— id: 66438, year: 1999, vol: 15, page: 178, stat: Journal Article,

Karyotype and synteny among the chromosomes of all four species of human malaria parasite
Carlton JM; Galinski MR; Barnwell JW; Dame JB
1999 Jun 25;101(1-2):23-32, Molecular & biochemical parasitology
The karyotype and chromosomes of the human malaria parasite Plasmodium falciparum have been well characterized in recent years. Here we present karyotype maps of the three other human malaria species, P. vivax, P. malariae and P. ovale. Chromosomes of these species were found to be of significantly higher molecular weight than those of P. falciparum. Some 14 P. vivax chromosomes were distinguishable, and 12-14 P. malariae and P. ovale chromosomes. The chromosome location of 15 genes, known to be present within five synteny groups between P. falciparum and the rodent malarias, were analyzed, and four of these synteny groups were found to be conserved between all of the human malaria species. In addition, a more detailed genome map of P. vivax was made using ten housekeeping and antigen genes. These data represent the first karyotype maps of all species of malaria which infect man
— id: 66437, year: 1999, vol: 101, page: 23, stat: Journal Article,

A chloroquine resistance locus in the rodent malaria parasite Plasmodium chabaudi
Carlton J; Mackinnon M; Walliker D
1998 May 15;93(1):57-72, Molecular & biochemical parasitology
We have located a possible chloroquine resistance locus in the genome of the rodent malaria parasite Plasmodium chabaudi. Two genetically distinct clones of the parasite were grown in vivo and allowed to undergo genetic crossing. The clones differed from each other in their susceptibility to chloroquine; AS(3CQ) had been selected for a low level of resistance to the drug whereas AJ is chloroquine-sensitive. Independent recombinant progeny (20) were cloned from the products of two crosses, phenotyped for their susceptibility to chloroquine, and genotyped for their inheritance of 46 chromosome-specific markers. No association was found between chloroquine susceptibility and the inheritance of pcmdr1, the P. chabaudi homologue of the pfmdr1 multi-drug resistance gene of P. falciparum. Also, there was no association between chloroquine susceptibility and the inheritance of a marker linked to a putative chloroquine resistance locus in a P. falciparum cross. However, 16 of the progeny clones showed co-segregation of four linked markers on chromosome 11 with their resistance phenotype. This result suggests that a locus for chloroquine resistance exists on this chromosome in P. chabaudi
— id: 66446, year: 1998, vol: 93, page: 57, stat: Journal Article,

Gene synteny in species of Plasmodium
Carlton JM; Vinkenoog R; Waters AP; Walliker D
1998 Jun 1;93(2):285-294, Molecular & biochemical parasitology
We have attempted to establish the degree of linkage conservation between different species of the malaria parasite Plasmodium. Initially, the chromosome locations of 42 homologous genes were established in parasites from a rodent malaria species and the human malaria parasite P. falciparum. Of these genes, 26 appeared to be conserved within ten synteny groups between the two genomes. Several synteny groups were analysed further by long-range restriction mapping of digested chromosomes. Finally, a fine restriction map of one of the linkage groups was made from the rodent malaria parasites P. berghei and from P. falciparum and from the simian malaria parasite P. knowlesi. The fine-scale organisation of this linkage group appears to have remained intact among the three species, despite the evolutionary distance between them. This provides the first example of linkage conservation between the rodent, simian and human malaria species, which represent three different branches of the inferred phylogenetic tree of the genus Plasmodium
— id: 66439, year: 1998, vol: 93, page: 285, stat: Journal Article,

Restoring abdominal wall integrity in contaminated tissue-deficient wounds using autologous fascia grafts
Disa, J J; Goldberg, N H; Carlton, J M; Robertson, B C; Slezak, S
1998 Apr;101(4):979-986, Plastic & reconstructive surgery
Necrotizing abdominal wall infections, enteric fistulae, or exposed prosthetic material after ventral hernia repair often results in a loss of abdominal wall integrity. Further surgical reconstruction with prosthetic material is usually contraindicated in the contaminated wound because of the high infection rate necessitating prosthetic removal and further abdominal wall debridement. Consequently, for the past 9 years, we have been using free grafts of autologous fascia lata to replace deficient abdominal wall fascia and muscle in situations where prosthetic material is contraindicated and local tissue rearrangement (i.e., component separation) would be inadequate. Thirty-two patients (mean age 59 years) underwent abdominal wall reconstruction with autologous fascia lata grafts. Indications included exposed mesh (31 percent), enteric fistulae (28 percent), enteric contamination (22 percent), wound infection (13 percent), and immunosuppression alone (6 percent); 31 percent of all patients were immunosuppressed secondary to either a solid organ transplant or a systemic inflammatory disorder. Fascia grafts (mean size 10 x 17 cm) were sutured to the surrounding abdominal wall and covered by local skin flap advancement and/or myocutaneous flap rotation. All abdominal reconstructions were initially successful. Subsequent local abdominal wall complications included cellulitis (n = 3), seroma (n = 2), and skin dehiscence with exposed fascia grafts (n = 7). Five of seven patients with skin dehiscence healed by secondary intention, whereas two had split-thickness skin grafts successfully applied to the granulating fascia. Thigh donor site complications included hematoma (n = 1), skin dehiscence (n = 1), and seroma (n = 2). There have been no cases of lateral knee instability. The average follow-up period is 27 months (range 3 to 106 months). Recurrent hernia has been seen in three patients (9 percent). Interestingly, laparotomy has been performed through an intact fascia lata patch in three patients for unrelated intra-abdominal conditions. In each case, the graft was intact and revascularized, confirming experimental animal data performed in our laboratory. Recurrent hernia has not been observed through the laparotomy site. Our 9-year experience has demonstrated that in the face of large, contaminated abdominal wounds where prosthetic material is contraindicated and local tissue rearrangement would be inadequate, fascia lata autografts are a reliable adjuvant to abdominal wall reconstruction
— id: 72025, year: 1998, vol: 101, page: 979, stat: Journal Article,

Adaptive changes in Plasmodium transmission strategies following chloroquine chemotherapy
Buckling AG; Taylor LH; Carlton JM; Read AF
1997 Apr 22;264(1381):553-559, Proceedings of the Royal Society. B. Biological sciences
Both theory and data suggest that malaria parasites divert resources from within-host replication to the production of transmission stages (gametocytes) when conditions deteriorate. Increased investment into transmission stages should therefore follow subcurative treatment with antimalarial drugs, but relevant clinical studies necessarily lack adequate control groups. We therefore carried out controlled experiments to test this hypothesis, using a rodent malaria (Plasmodium chabaudi) model. Infections treated with a subcurative dose of the antimalarial chloroquine showed an earlier peak and a greater rate of gametocyte production relative to untreated controls. These alterations led to correlated changes in infectivity to mosquitoes, with the consequence that chloroquine treatment had no effect on the proportion of mosquitoes infected. Treatment of human malaria commonly does not result in complete parasite clearance. If surviving parasites produce compensatory increases in their rate of gametocyte production similar to those reported here, such treatment may have minimal effect on decreasing, and may actually increase, transmission. Importantly, if increased investment in transmission is a generalized stress response, the effect might be observed following a variety of antimalarial treatments, including other drugs and potential vaccines. Similar parasite life history counter-adaptations to intervention strategies are likely to occur in many disease-causing organisms
— id: 66440, year: 1997, vol: 264, page: 553, stat: Journal Article,

Use of random amplified polymorphic DNA (RAPD) technique in inheritance studies of Plasmodium falciparum
Howard J; Carlton JM; Walliker D; Jensen JB
1996 Dec;82(6):941-946, Journal of parasitology
Effectiveness of random amplified polymorphic DNA (RAPD), a technique using 1 10-base primer to amplify random segments of genomic DNA, and some of its possible uses were tested in the A + T-rich genome of Plasmodium falciparum. The best concentrations of MgCl2, 60% G + C primer, and DNA were determined to be 4.0 mM, 0.4 microM, and 90-180 ng/15 microliters reaction, respectively. Use of 30% G + C primers did not allow amplification to occur. Application of RAPD to DNA of parent and progeny clones from a P. falciparum cross showed that polymorphisms identified in the parentals and tracked in the progeny were inherited in a Mendelian fashion and that RAPD-identified polymorphisms could be used as genetic markers. Some of these polymorphic markers were located on more than 1 chromosome, whereas others were specific for a single chromosome. Two of these markers, each located on chromosome 3 of 1 of the parental parasites, were missing from 2 of the 18 progeny, suggesting that deletions, or crossover events had occurred. RAPD markers also identified a higher number of nonparental-type progeny than expected, thus confirming previous observations for high genetic variability in malaria parasites
— id: 66441, year: 1996, vol: 82, page: 941, stat: Journal Article,

Sexual-stage-specific RNA expression of a new Plasmodium falciparum gene detected by in situ hybridisation
Baker DA; Thompson J; Daramola OO; Carlton JM; Targett GA
1995 Jun;72(1-2):193-201, Molecular & biochemical parasitology
A gene, Pf77, transcribed in the sexual stages of Plasmodium falciparum was isolated from a genomic expression library with a polyclonal antibody raised to gametocyte proteins. The entire coding region was obtained from a series of overlapping genomic and cDNA clones (from gametocyte RNA). A single open reading frame is present with no introns and no tandem repeat sequences. A Pf77 probe hybridised to a single transcript present in RNA prepared from purified gametocytes and could not be detected in RNA prepared from asexual blood stages. In situ hybridisation studies confirmed that the expression of Pf77 mRNA is sexual-stage-specific and in addition, showed that Pf77 mRNA is present only in female gametocytes during the vertebrate stages of the parasite's development
— id: 66442, year: 1995, vol: 72, page: 193, stat: Journal Article,

A rapid technique for the detection of DNA polymorphisms in Plasmodium
Carlton JM; Howard J; Jensen JB; Walliker D
1995 Feb;80(1):163-166, Experimental parasitology
— id: 66443, year: 1995, vol: 80, page: 163, stat: Journal Article,

Conserved location of genes on polymorphic chromosomes of four species of malaria parasites
Janse CJ; Carlton JM; Walliker D; Waters AP
1994 Dec;68(2):285-296, Molecular & biochemical parasitology
The number of chromosomes and the chromosomal location and linkage of more than 50 probes, mainly of genes, have been established in four species of Plasmodium which infect African murine rodents. We expected that the location and linkage of genes would not be conserved between these species of malaria parasites since extensive inter- and intraspecific size differences of the chromosomes existed and large scale internal rearrangements and chromosome translocations in parasites from laboratory lines had been reported. Our study showed that all four species contained 14 chromosomes, ranging in size between 0.5 and 3.5 Mb, which showed extensive size polymorphisms. The location and linkage of the genes on the polymorphic chromosomes, however, was conserved and nearly identical between these species. These results indicate that size polymorphisms of the chromosomes are more likely due to variation in non-coding (subtelomeric, repeat) sequences and show that a high plasticity of internal regions of chromosomes that may exist does not frequently affect chromosomal location and linkage of genes
— id: 66444, year: 1994, vol: 68, page: 285, stat: Journal Article,

Drug response and genetic characterization of Plasmodium falciparum clones recently isolated from a Sudanese village
Bayoumi RA; Creasey AM; Babiker HA; Carlton JM; Sultan AA; Satti G; Sohal AK; Walliker D; Jensen JB; Arnot DE
1993 Jul-Aug;87(4):454-458, Transactions of the Royal Society of Tropical Medicine & Hygiene
We have isolated 20 clones of Plasmodium falciparum from isolates from patients attending a village clinic in Sudan during 10 d in October-November 1989. The clones were genetically diverse, having highly variable molecular karyotypes and a wide range of drug responses. Chloroquine-sensitive (50% inhibitory concentration [IC50] in the 4-15 nM range) and chloroquine-resistant clones (IC50 in the 40-95 nM range) co-existed in the population, but no obvious amplification of the P-glycoprotein homologue gene, Pgh1 (previously known as the multi-drug resistance gene, mdr1) marked the chloroquine-resistant clones. Chloroquine resistance was reversible by verapamil in these clones, although they varied in their susceptibility to verapamil alone. These observations indicate that the biochemical characteristics of the Sudanese chloroquine-resistant P. falciparum are similar to those reported from south-east Asian and Latin American isolates, which is consistent with there being a similar molecular basis for this phenomenon
— id: 66445, year: 1993, vol: 87, page: 454, stat: Journal Article,