Applied systems biology and malaria

One of the goals of systems-biology research is to discover networks and interactions by integrating diverse data sets. So far, systems-biology research has focused on model organisms, which are well characterized and therefore suited to testing new methods. Systems biology has great potential for use in the search for therapies for disease. Here, the potential of systems-biology approaches in the search for new drugs and vaccines to treat malaria is examined.

[1]  J. Vanderberg,et al.  Protective Immunity produced by the Injection of X-irradiated Sporozoites of Plasmodium berghei , 1967, Nature.

[2]  Kei-Hoi Cheung,et al.  Large-scale analysis of the yeast genome by transposon tagging and gene disruption , 1999, Nature.

[3]  B. Birren,et al.  Sequencing and comparison of yeast species to identify genes and regulatory elements , 2003, Nature.

[4]  Jonathan E. Allen,et al.  Genome sequence of the human malaria parasite Plasmodium falciparum , 2002, Nature.

[5]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[6]  J. Baird,et al.  Effectiveness of antimalarial drugs. , 2005, The New England journal of medicine.

[7]  L. Fulton,et al.  Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting , 2003, Science.

[8]  R. Carter,et al.  A genetic approach to the de novo identification of targets of strain-specific immunity in malaria parasites. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[9]  A. E. Hirsh,et al.  Evolutionary Rate in the Protein Interaction Network , 2002, Science.

[10]  Travis Harrison,et al.  A Host-Targeting Signal in Virulence Proteins Reveals a Secretome in Malarial Infection , 2004, Science.

[11]  G. Church,et al.  Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. , 2000, Genome research.

[12]  Matthias Mann,et al.  Proteome Analysis of Separated Male and Female Gametocytes Reveals Novel Sex-Specific Plasmodium Biology , 2005, Cell.

[13]  P. Brown,et al.  Exploring the metabolic and genetic control of gene expression on a genomic scale. , 1997, Science.

[14]  D. Roos Genetics. Themes and variations in apicomplexan parasite biology. , 2005, Science.

[15]  Koen J. Dechering,et al.  Isolation and Functional Characterization of Two Distinct Sexual-Stage-Specific Promoters of the Human Malaria Parasite Plasmodium falciparum , 1999, Molecular and Cellular Biology.

[16]  R. Rosenberg,et al.  Continuous in vitro propagation of the malaria parasite Plasmodium vivax. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[17]  David L. Tabb,et al.  A proteomic view of the Plasmodium falciparum life cycle , 2002, Nature.

[18]  T. McCutchan,et al.  Sequence variation in putative functional domains of the circumsporozoite protein of Plasmodium falciparum. Implications for vaccine development. , 1987, The Journal of biological chemistry.

[19]  Huji Xu,et al.  Development and regulation of cell-mediated immune responses to the blood stages of malaria: implications for vaccine research. , 2005, Annual review of immunology.

[20]  W. Trager,et al.  Human malaria parasites in continuous culture. , 1976, Science.

[21]  H. Lichtenthaler,et al.  Inhibitors of the nonmevalonate pathway of isoprenoid biosynthesis as antimalarial drugs. , 1999, Science.

[22]  Patricia De la Vega,et al.  Discovery of Gene Function by Expression Profiling of the Malaria Parasite Life Cycle , 2003, Science.

[23]  R. Karp,et al.  Conserved pathways within bacteria and yeast as revealed by global protein network alignment , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[24]  D. Carucci,et al.  High-throughput generation of P. falciparum functional molecules by recombinational cloning. , 2004, Genome research.

[25]  K. Matuschewski,et al.  High efficiency transfection of Plasmodium berghei facilitates novel selection procedures. , 2006, Molecular and biochemical parasitology.

[26]  Inacio Mandomando,et al.  Efficacy of the RTS,S/AS02A vaccine against Plasmodium falciparum infection and disease in young African children: randomised controlled trial , 2004, The Lancet.

[27]  E. O’Shea,et al.  Global analysis of protein expression in yeast , 2003, Nature.

[28]  A. Scherf,et al.  Antigenic variation in malaria: in situ switching, relaxed and mutually exclusive transcription of var genes during intra‐erythrocytic development in Plasmodium falciparum , 1998, The EMBO journal.

[29]  T. Wellems,et al.  Transformation of Plasmodium falciparum malaria parasites by homologous integration of plasmids that confer resistance to pyrimethamine. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[30]  T. McCutchan,et al.  Analysis of sequence diversity in the Plasmodium falciparum merozoite surface protein-1 (MSP-1). , 1993, Molecular and biochemical parasitology.

[31]  D. Conway,et al.  Strong diversifying selection on domains of the Plasmodium falciparum apical membrane antigen 1 gene. , 2001, Genetics.

[32]  Daniel R. Richards,et al.  Direct allelic variation scanning of the yeast genome. , 1998, Science.

[33]  I. McGregor,et al.  Gamma-Globulin and Acquired Immunity to Human Malaria , 1961, Nature.

[34]  C. Ouzounis,et al.  Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. , 2004, Genome research.

[35]  R. Sinden,et al.  Complete Development of Mosquito Phases of the Malaria Parasite in Vitro , 2002, Science.

[36]  Ruben Abagyan,et al.  Excess Polymorphisms in Genes for Membrane Proteins in Plasmodium falciparum , 2002, Science.

[37]  A. Cowman,et al.  Characterization of promoters and stable transfection by homologous and nonhomologous recombination in Plasmodium falciparum. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Ronald W. Davis,et al.  A genome-wide transcriptional analysis of the mitotic cell cycle. , 1998, Molecular cell.

[39]  Joshua M. Stuart,et al.  A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules , 2003, Science.

[40]  Matthew Bogyo,et al.  A Role for the Protease Falcipain 1 in Host Cell Invasion by the Human Malaria Parasite , 2002, Science.

[41]  M. Gerstein,et al.  A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data , 2003, Science.

[42]  Lan V. Zhang,et al.  Evidence for dynamically organized modularity in the yeast protein–protein interaction network , 2004, Nature.

[43]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[44]  J. Sachs,et al.  The economic and social burden of malaria , 2002, Nature.

[45]  X. Su,et al.  The large diverse gene family var encodes proteins involved in cytoadherence and antigenic variation of plasmodium falciparum-infected erythrocytes , 1995, Cell.

[46]  Yingyao Zhou,et al.  Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. , 2004, Genome research.

[47]  T. Richie,et al.  Progress and challenges for malaria vaccines , 2002, Nature.

[48]  Karine Prat,et al.  Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eukaryotes , 2005, BMC Genomics.

[49]  J. Derisi,et al.  The Transcriptome of the Intraerythrocytic Developmental Cycle of Plasmodium falciparum , 2003, PLoS biology.

[50]  D. Soldati,et al.  Tetracycline analogue-regulated transgene expression in Plasmodium falciparum blood stages using Toxoplasma gondii transactivators. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[51]  G. Church,et al.  Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. , 2000, Journal of molecular biology.

[52]  Thomas E. Wellems,et al.  Frequent ectopic recombination of virulence factor genes in telomeric chromosome clusters of P. falciparum , 2000, Nature.

[53]  J. Vanderberg,et al.  Immunization of man against sporozite-induced falciparum malaria , 1973, The American journal of the medical sciences.

[54]  William Stafford Noble,et al.  Assessing computational tools for the discovery of transcription factor binding sites , 2005, Nature Biotechnology.

[55]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

[56]  T. Sullivan,et al.  Transfection of the malaria parasite and expression of firefly luciferase. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[57]  M. Gerstein,et al.  Global Analysis of Protein Activities Using Proteome Chips , 2001, Science.

[58]  Joseph D. Smith,et al.  Switches in expression of plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes , 1995, Cell.

[59]  G. Church,et al.  Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation , 1998, Nature Biotechnology.

[60]  C. Janse,et al.  Stable transfection of malaria parasite blood stages. , 1995, Science.

[61]  Dyann F. Wirth,et al.  The parasite genome: Biological revelations , 2002, Nature.

[62]  Christopher J. Tonkin,et al.  Localization of organellar proteins in Plasmodium falciparum using a novel set of transfection vectors and a new immunofluorescence fixation method. , 2004, Molecular and biochemical parasitology.

[63]  E. O’Shea,et al.  Global analysis of protein localization in budding yeast , 2003, Nature.

[64]  M. Vignali,et al.  A protein interaction network of the malaria parasite Plasmodium falciparum , 2005, Nature.

[65]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[66]  Jonathan E. Allen,et al.  Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii , 2002, Nature.

[67]  Ronald W. Davis,et al.  Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. , 1999, Science.

[68]  John R Yates,et al.  Proteome analysis of rhoptry-enriched fractions isolated from Plasmodium merozoites. , 2004, Journal of proteome research.

[69]  Melanie Rug,et al.  Targeting Malaria Virulence and Remodeling Proteins to the Host Erythrocyte , 2004, Science.

[70]  J R Yates,et al.  Utilization of genomic sequence information to develop malaria vaccines , 2003, Journal of Experimental Biology.

[71]  Neil Hall,et al.  Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry , 2002, Nature.

[72]  D. Hartl,et al.  Recent Origin of Plasmodium falciparum from a Single Progenitor , 2001, Science.

[73]  Yingyao Zhou,et al.  The Plasmodium falciparum sexual development transcriptome: a microarray analysis using ontology-based pattern identification. , 2005, Molecular and biochemical parasitology.

[74]  John R Yates,et al.  A Comprehensive Survey of the Plasmodium Life Cycle by Genomic, Transcriptomic, and Proteomic Analyses , 2005, Science.

[75]  C. Janse,et al.  The development of genetic tools for dissecting the biology of malaria parasites. , 2000, Annual review of microbiology.

[76]  John Sidney,et al.  Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[77]  David S. Roos,et al.  Themes and Variations in Apicomplexan Parasite Biology , 2005, Science.