Genome projects, genetic analysis, and the changing landscape of malaria research

Current Opinion in Microbiology

Volumn 2, Issue 4, 1999, Pages 415-419

  Wellems, Thomas E ^a   Su, Xin Zhuan ^a   Ferdig, Michael ^a   Fidock, David A ^a  

^a NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME MAP; GENETIC ANALYSIS; GENETIC LINKAGE; GENOME; LIFE CYCLE; MALARIA; MEDICAL RESEARCH; NONHUMAN; PLASMODIUM FALCIPARUM; REVIEW;

EID: 0033179319     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5274(99)80073-3     Document Type: Review

References (58)

1. World Health Organization: World malaria situation in 1994. Part I. Population at risk. Wkly Epidemiol Rec 1997, 72:269-274.
2. Litsios S: The Tomorrow of Malaria. New Zealand: Pacific Press; 1996.
3. Dame JB, Arnot DE, Bourke PF, Chakrabarti D, Christodoulou Z, Coppel RL, Cowman AF, Craig AG, Fischer K, Foster J et al.: Current status of the Plasmodium falciparum genome project. Mol Biochem Parasitol 1996, 79:1-12.
4. Su X, Wellems TE: Genome discovery and malaria research: Current status and promise. In Malaria: Parasite Biology, Pathogenesis, Protection. Edited by Sherman IW. Washington DC: American Society of Microbiology Press; 1998:253-266. This chapter, in a comprehensive and timely book on malaria, reviews Plasmodium falciparum genomics and challenges ahead in the 'post-genomics' era.
5. Fidock DA, Su X, Deitsch KW, Wellems TE: Genetic approaches to the determinants of drug response, pathogenesis and infectivity in Plasmodium falciparum malaria. In Malaria: Molecular and Clinical Aspects. Edited by Wahlgren M, Perlmann P. Chur, Switzerland: Harwood Academic Publishing; 1999:217-248. A review of genetic studies of Plasmodium falciparum and their contributions to malaria research.
6. Hill WG, Babiker HA, Ranford-Cartwright LC, Walliker D: Estimation of inbreeding coefficients from genotypic data on multiple alleles, and application to estimation of clonality in malaria parasites. Genet Res 1995, 65:53-61.
7. Day KP, Koella JC, Nee S, Gupta S, Read AF: Population genetics and dynamics of Plasmodium falciparum: An ecological view. Parasitology 1992, 104 (suppl):S35-S52.
8. Wu Y, Sifri CD, Lei H, Su X, Wellems TE: Transfection of Plasmodium falciparum within human red blood cells. Proc Natl Acad Sci USA 1995, 92:973-977.
9. Wu Y, Kirkman L, Wellems TE: Transformation of Plasmodium falciparum malaria parasites by homologous integration of plasmids that confer resistance to pyrimethamine. Proc Natl Acad Sci USA 1996, 93:1130-1134.
10. Crabb BS, Cooke BM, Reeder JC, Waller RF, Caruana SR, Davern KM, Wickham ME, Brown GV, Coppel RL, Cowman AF: Targeted gene disruption shows that knobs enable malaria-infected red cells to cytoadhere under physiological shear stress. Cell 1997, 89:287-296.
11. Fidock DA, Nomura T, Wellems TE: Cycloguanil and its parent compound proguanil demonstrate distinct activities against Plasmodium falciparum malaria parasites transformed with human dihydrofolate reductase. Mol Pharmacol 1998, 54:1140-1147. A report showing the complementation of parasite dihydrofolate reductase by expression of the human enzyme from transfected plasmid DNA. The results identify distinct activities of proguanil and cycloguanil against malaria parasites.
12. Triglia T, Wang P, Sims PF, Hyde JE, Cowman AF: Allelic exchange at the endogenous genomic locus in Plasmodium falciparum proves the role of dihydropteroate synthase in sulfadoxine-resistant malaria. EMBO J 1998, 17:3807-3815. A report on the genetic modification of the P. falciparum dhps gene and the effect of point mutations on sulfadoxine response.
13. van Dijk MR, Waters AP, Janse CJ: Stable transfection of malaria parasite blood stages. Science 1995, 268:1358-1362.
14. van Dijk MR, Janse CJ, Waters AP: Expression of a Plasmodium gene introduced into subtelomeric regions of Plasmodium berghei chromosomes. Science 1996, 271:662-665.
15. Menard R, Sultan AA, Cortes C, Altszuler R, van Dijk MR, Janse CJ, Waters AP, Nussenzweig RS, Nussenzweig V: Circumsporozoite protein is required for development of malaria sporozoites in mosquitoes. Nature 1997, 385:336-340.
16. Sultan AA, Thathy V, Frevert U, Robson KJ, Crisanti A, Nussenzweig V, Nussenzweig RS, Menard R: Trap is necessary for gliding motility and infectivity of Plasmodium sporozoites. Cell 1997, 90:511-522.
17. van der Wel AM, Tomas AM, Kocken CH, Malhotra P, Janse CJ, Waters AP, Thomas AW: Transfection of the primate malaria parasite Plasmodium knowlesi using entirely heterologous constructs. J Exp Med 1997, 185:1499-1503.
18. Waters AP, Thomas AW, van Dijk MR, Janse CJ: Transfection of malaria parasites. Methods 1997, 13:134-147.
19. Menard R, Janse C: Gene targeting in malaria parasites. Methods 1997, 13:148-157.
20. Barker RHJ, Metelev V, Rapaport E, Zamecnik P: Inhibition of Plasmodium falciparum malaria using antisense oligodeoxynucleotides. Proc Natl Acad Sci USA 1996, 93:514-518.
21. Flores MV, Atkins D, Wade D, O'Sullivan WJ, Stewart TS: Inhibition of Plasmodium falciparum proliferation in vitro by ribozymes. J Biol Chem 1997, 272:16940-16945.
22. Rapaport E, Misiura K, Agrawal S, Zamecnik P: Antimalarial activities of oligodeoxynucleotide phosphorothioates in chloroquine-resistant Plasmodium falciparum. Proc Natl Acad Sci USA 1992, 89:8577-8580.
23. Sharp PA: RNAi and double-strand RNA. Genes Dev 1999, 13:139-141. A review of the fascinating new findings on gene-specific silencing by double-strand RNA.
24. Lander ES, Schork NJ: Genetic dissection of complex traits. Science 1994, 265:2037-2048. [Published erratum appears in Science 1994, 266:353.]
25. Malaria Genetics and Genomics on World Wide Web URL: http://www.ncbi.nlm.nih.gov/Malaria/index.html A Web site providing information on malaria genetics and genomics at the National Center for Biotechnology Information.
26. Su X, Kirkman LA, Fujioka H, Wellems TE: Complex polymorphisms in an ∼330 kD protein are linked to chloroquine-resistant P. falciparum in Southeast Asia and Africa. Cell 1997, 91:593-603.
27. Prensier G, Slomianny C: The karyotype of Plasmodium falciparum determined by ultrastructural serial sectioning and 3D reconstruction. J Parasitol 1986, 72:731-736.
28. Wellems TE, Walliker D, Smith CL, do Rosario VE, Maloy WL, Howard RJ, Carter R, McCutchan TF: A histidine-rich protein gene marks a linkage group favored strongly in a genetic cross of Plasmodium falciparum. Cell 1987, 49:633-642.
29. Gu H, Inselburg JW, Bzik DJ, Li WB: Plasmodium falciparum: Analysis of chromosomes separated by contour-clamped homogenous electric fields. Exp Parasitol 1990, 71:189-198.
30. Triglia T, Wellems TE, Kemp DJ: Towards a high-resolution map of the Plasmodium falciparum genome. Parasitol Today 1992, 8:225-229.
31. Triglia T, Kemp DJ: Large fragments of Plasmodium falciparum DNA can be stable when cloned in yeast artificial chromosomes. Mol Biochem Parasitol 1991, 44:207-211.
32. de Bruin D, Lanzer M, Ravetch JV: Characterization of yeast artificial chromosomes from Plasmodium falciparum: Construction of a stable, representative library and cloning of telomeric DNA fragments. Genomics 1992, 14:332-339.
33. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M et al.: Life with 6000 genes. Science 1996, 274:546-567.
34. The C. elegans Sequencing Consortium: Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 1998, 282:2012-2018. A report and discussion of the implications of the first complete nematode genome sequence.
35. Pennisi E: First food-borne pathogen sequenced. Science 1999, 283:1243-1243.
36. Gardner MJ, Tettelin H, Carucci DJ, Cummings LM, Aravind L, Koonin EV, Shallom S, Mason T, Yu K, Fujii C et al.: Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science 1998, 282:1126-1132. [Published erratum appears in Science 1998, 282:1827.] Report, analysis and discussion of the first complete sequence of a P. falciparum chromosome.
37. Plasmodium falciparum Genome project on World Wide Web URL: http://www.sanger.ac.uk/Projects/P_falciparum/ A Web site providing information and data from the P. falciparum genome sequencing project at The Sanger Center.
38. The Plasmodium falciparum Genome Database (PFDB) on World Wide Web: http://www.tigr.org/tdb/edb/pfdb/pfdb.html A Web site providing information and data from the P. falciparum genome sequencing project at The Institute for Genome Research.
39. Plasmodium falciparum Genome Project Sequencing at the Stanford DNA Sequence and Technology Center on World Wide Web URL: http://sequence-www.stanford.edu/group/malaria/index.html A Web site providing information and data from the P. falciparum genome sequencing project at Stanford University.
40. Plasmodium falciparum Gene Sequence Tag Project on World Wide Web URL: http://parasite.arf.ufl.edu/path/pfgstp/index.html A Web site providing information and data from the P. falciparum EST and GST projects at The University of Florida.
41. Chakrabarti D, Reddy GR, Dame JB, Almira EC, Laipis PJ, Ferl RJ, Yang TP, Rowe TC, Schuster SM: Analysis of expressed sequence tags from Plasmodium falciparum. Mol Biochem Parasitol 1994, 66:97-104.
42. Reddy GR, Chakrabarti D, Schuster SM, Ferl RJ, Almira EC, Dame JB: Gene sequence tags from Plasmodium falciparum genomic DNA fragments prepared by the "genease" activity of mung bean nuclease. Proc Natl Acad Sci USA 1993, 90:9867-9871.
43. Dame JB, Reddy GR, Yowell CA, Dunn BM, Kay J, Berry C: Sequence, expression and modeled structure of an aspartic proteinase from the human malaria parasite Plasmodium falciparum. Mol Biochem Parasitol 1994, 64:177-190.
44. Reddy GR: Cloning and characterization of a Plasmodium falciparum cyclophilin gene that is stage-specifically expressed. Mol Biochem Parasitol 1995, 73:111-121.
45. Berriman M, Fairlamb AH: Detailed characterization of a cyclophilin from the human malaria parasite Plasmodium falciparum. Biochem J 1998, 334:437-445.
46. Dobson S, May T, Berriman M, DelVecchio D, Fairlamb AH, Chakrabarti D, Barik S: Characterization of protein Ser/Thr phosphatases of the malaria parasite, Plasmodium falciparum: Inhibition of the parasitic calcineurin by cyclophilin-cyclosporin complex. Mol Biochem Parasitol 1999, 99:167-181.
47. Chakrabarti D, Azam T, DelVecchio C, Qiu L, Park YI, Allen CM: Protein prenyl transferase activities of Plasmodium falciparum. Mol Biochem Parasitol 1998, 94:175-184.
48. Woodrow CJ, Penny JI, Krishna S: Intraerythrocytic Plasmodium falciparum expresses a high-affinity facilitative hexose transporter. J Biol Chem 1999, 274:7272-7277.
49. Wahlgren M, Fernandez V, Chen Q, Svärd S, Hagblom P: Waves of malarial var-iations. Cell 1999, 96:603-606. An overview with selected references on variant antigen gene families involved in pathogenesis and immune evasion by malaria parasites.
50. Tatusov RL, Koonin EV, Lipman DJ: A genomic perspective on protein families. Science 1997, 278:631-637.
51. Koonin EV, Tatusov RL, Galperin MY: Beyond complete genomes: From sequence to structure and function. Curr Opin Struct Biol 1998, 8:355-363. A key article on the computational assignment of molecular function by sequence analysis.
52. WIT 39 Genomes on World Wide Web URL: http://wit.mcs.anl.gov/WIT2/ Interactive metabolic reconstruction on the web.
53. A Natural System of Gene Families from Complete Genomes on World Wide Web URL: http://www.ncbi.nlm.nih.gov/COG/ A natural system of gene families from complete genomes.
54. Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, et al.: Comparison of the complete protein sets of worm and yeast: Orthology and divergence. Science 1998, 282:2022-2028. Reciprocal comparative analysis of the full complement of predicted protein sequences from the complete genomes of two eukaryotes.
55. Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JCF, Trent JM, Staudt LM, Hudson JJ, Boguski MS et al: The transcriptional program in the response of human fibroblasts to serum. Science 1999, 283:83-87. A key article on the use of DNA microarrays to understand a cellular response to exogenous factors at the level of changes in gene expression.
56. Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H et al.: Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med 1998, 4:1293-1301. A landmark article on the use of microarrays to understand drug effect by gene expression analysis.
57. Schofield L, McConville MJ, Hansen D, Campbell AS, Fraser-Reid B, Grusby MJ, Tachado SD: CD1d-restricted immunoglobulin G formation to GPI-anchored antigens mediated by NKT cells. Science 1999, 283:225-229.
58. Ridley RG, Dorn A, Vippagunta SR, Vennerstrom JL: Haematin (haem) polymerization and its inhibition by quinoline antimalarials. Ann Trop Med Parasitol 1997, 91:559-566.