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Systems biology via redescription and ontologies (III): Protein classification using malaria parasite's temporal transcriptomic profiles
Chapter by: Mitrofanova, Antonina; Kleinberg, Samantha; Carlton, Jane; Kasif, Simon; Mishra, Bud
in: Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 by
[S.l.] : Cell Press subs@cell.com, 2008
pp. 278-283
ISBN: 9780769534527
CID: 2809212
A PANEL OF GENETIC MARKERS SUGGESTS GENETIC RELATEDNESS AND EVOLUTIONARY HISTORIES OF PLASMODIUM VIVAX LINEAGES, OLD WORLD AND NEW WORLD [Meeting Abstract]
Prajapati, SK; Joshi, H; Kang'a, S; Carlton, JM; Rizvi, MA; Dash, AP
ISI:000261644600225
ISSN: 0002-9637
CID: 91861
PRODUCTION OF RETICULOCYTES FROM HEMATOPOIETIC STEM CELLS FOR DEVELOPMENT OF A CONTINUOUS IN VITRO CULTURE SYSTEM FOR PLASMODIUM VIVAX [Meeting Abstract]
Furuya, T; Carlton, JM; Rajapandi, T; Stedman, T; Ma, W
ISI:000261644601304
ISSN: 0002-9637
CID: 91863
Comparative evolutionary genomics of human malaria parasites
Carlton, Jane M; Escalante, Ananias A; Neafsey, Daniel; Volkman, Sarah K
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?
PMID: 18938107
ISSN: 1471-4922
CID: 96127
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
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
PMCID:2571024
PMID: 18852452
ISSN: 1091-6490
CID: 96128
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
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
PMCID:2651158
PMID: 18843361
ISSN: 1476-4687
CID: 96129
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
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
PMCID:2386084
PMID: 18385220
ISSN: 1537-1719
CID: 78754
Plasmodium vivax in India
Joshi, Hema; Prajapati, Surendra K; Verma, Anju; Kang'a, Simon; Carlton, Jane M
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
PMID: 18403267
ISSN: 1471-4922
CID: 78753
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
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
PMCID:2215772
PMID: 18270564
ISSN: 1932-6203
CID: 78755
Metabolic and molecular evidence of adenosine kinase activity in Plasmodium falciparum [Meeting Abstract]
Cassera, MB; Merino, EF; Hazleton, KZ; Carlton, JM; Schramm, VL
ISI:000253127600185
ISSN: 0020-7519
CID: 76167