Evaluation of differential gene expression in Leishmania major Friedlin procyclics and metacyclics using DNA microarray analysis

Molecular and Biochemical Parasitology

Volumn 129, Issue 1, 2003, Pages 103-114

  Saxena, Alka ^a   Worthey, Elizabeth A ^a   Yan, Shaofeng ^a   Leland, Aaron ^a   Stuart, Kenneth D ^a,b   Myler, Peter J ^a,b  

^a SEATTLE BIOMEDICAL RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

DNA microarray; Gene expression; Leishmania major; Metacyclic; Procyclic

Indexed keywords

FLUORESCENT DYE; RNA;

ARTICLE; CALCULATION; DATA ANALYSIS; DIFFERENTIATION; DNA DETERMINATION; DNA MICROARRAY; DOWN REGULATION; EVALUATION; GENE AMPLIFICATION; GENE EXPRESSION; GENE IDENTIFICATION; GENE LIBRARY; GENETIC ANALYSIS; HYBRIDIZATION; LEISHMANIA MAJOR; NONHUMAN; NORTHERN BLOTTING; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RANDOMIZATION; RNA ANALYSIS; STATISTICAL SIGNIFICANCE; UPREGULATION;

LEISHMANIA MAJOR; MASTIGOPHORA (FLAGELLATES); PROTOZOA;

EID: 0037836064     PISSN: 01666851     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0166-6851(03)00100-2     Document Type: Article

References (41)

1. Kopyants N.S., Clifton S.W., Martin J., Pape D., Wylie T., Li L.et al. A survey of the Leishmania major Friedlin strain V1 genome by shotgun sequencing: a resource for DNA microarrays and expression profiling. Mol. Biochem. Parasitol. 113:2001;337-340.
2. Sacks D.L., Perkins P.V. Identification of an infective stage of Leishmania promastigotes. Science. 223:1984;1417-1419.
3. Sacks D.L., Hieny S., Sher A. Identification of cell surface carbohydrate and antigenic changes between non-infective and infective developmental stages of Leishmania major promastigotes. J. Immunol. 135:1985;564-569.
4. Wiese M. A mitogen-activated protein (MAP) kinase homologue of Leishmania mexicana is essential for parasite survival in the infected host. EMBO. 17:1998;2619-2628.
5. Flinn H.M., Smith D.F. Genomic organization and expression of differentially regulated gene family from Leishmania major. Nucleic Acids Res. 20:1992;755-762.
6. Myler P.J., Beverley S.M., Cruz A.K., Dobson D.E., Ivens A.C., McDonagh P.D.et al. The Leishmania genome project: new insights into gene organization and function. Med. Microbiol. Immunol. 190:2001;9-12.
7. Nourbakhsh F., Uliana S.R.B., Smith D.F. Characterisation and expression of a stage-regulated gene of Leishmania major. Mol. Biochem. Parasitol. 76:1996;201-213.
8. Brodin T.N., Heath S., Sacks D.L. Genes selectively expressed in the infectious (metacyclic) stage of Leishmania major promastigotes encode a potential basic-zipper structural motif. Mol. Biochem. Parasitol. 52:1992;241-250.
9. Thomas J.G., Olson J.M., Tapscott S.J., Zhao L.P. An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles. Genome Res. 11:2001;1227-1236.
10. Hochberg Y. A sharper Bonferroni procedure for multiple test of significance. Biometrika. 75:2002;800-802.
11. Lodes M.J., Merlin G., deVos T., Ghosh A., Madhubala R., Myler P.J.et al. Increased expression of LD1 genes transcribed by RNA polymerase I in Leishmania donovani as a result of duplication into the rRNA gene locus. Mol. Cell Biol. 15:1995;6845-6853.
12. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M.A.et al. Artemis: sequence visualisation and annotation. Bioinformatics. 16:2000;944-945.
13. Salzberg S.L., Delcher A.L., Kasif S., White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 26:1998;544-548.
14. Salzberg S.L., Pertea M., Delcher A.L., Gardner M.J., Tettelin H. Interpolated Markov models for eukaryotic gene finding. Genomics. 59:1999;24-31.
15. Fickett J.W. Recognition of protein coding regions in DNA sequences. Nucleic Acids Res. 10:1982;5303-5318.
16. Tiwari S., Ramachandran S., Bhattacharya A., Bhattacharya S., Ramaswamy R. Prediction of probable genes by Fourier analysis of genomic sequences. Comput. Appl. Biosci. 13:1997;263-270.
17. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
18. Tatusov R.L., Natale D.A., Garkavtsev I.V., Tatusova T.A., Shankavaram U.T., Rao B.S.et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29:2001;22-28.
19. Marchler-Bauer A., Panchenko A.R., Shoemaker B.A., Thiessen P.A., Geer L.Y., Bryant S.H. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 30:2002;281-283.
20. Godambe V.P. An optimum property of regular maximum likelihood estimation. Ann. Math. Stat. 31:1960;1208-1212.
21. Prentice R.L., Zhao L.P. Estimating equations for parameters in means and covariances of multivariate discrete continuous responses. Biometrics. 47:1991;825-839.
22. Mukhopadhyay N.K., Saha A.K., Lovelace J.K., Da Silva R., Sacks D.L., Glew R.H. Comparison of protein kinase and acid phosphotase activitiesof five species of Leishmania. J. Protozool. 35:1988;601-607.
23. Cool D.E., Blum J.J. Protein tyrosine phosphatase activity in Leishmania donovani. Mol. Cell Biochem. 127/128:1993;143-149.
24. Li S., Wilson M.E., Donelson J.E. Leishmania chagasi: a gene encoding a protein kinase with a catalytic domain structurally related to MAP kinase kinase. Exp. Parasitol. 82:1996;87-96.
25. Flinn H.M. Expression of a hydrophilic surface protein in infective stages of Leishmania major. Mol. Biochem. Parasitol. 65:1994;259-270.
26. Charest H., Matlashewski G. Developmental gene expression in Leishmania donovani: differential cloning and analysis of an amastigote-stage-specific gene. Mol. Cell Biol. 14:1994;2975-2984.
27. Marin M., Muskus C., Ramirez J.R., Arbelaez L.F., Alzate J.F., Berberich C. The gene encoding the metacyclogenesis-associated transcript Mat-1 is conserved in the genus Leishmania and shows a tendency to form dimers upon protein expression. Parasitol. Res. 86:2000;431-435.
28. Newton M.A., Kendziorski C.M., Richmond C.S., Blattner F.R., Tsui K.W. On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J. Comput. Biol. 8:2001;37-52.
29. Pavlidis P, Noble WS. Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol 2001;2:RESEARCH0042.
30. Kerr M.K., Churchill G.A. Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments. Proc. Natl. Acad. Sci. U.S.A. 98:2001;8961-8965.
31. DeRisi J.L., Iyer V.R., Brown P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 278:1997;680-686.
32. Wu Y., El Fakhry Y., Sereno D., Tamar S., Papadopoulou B. A new developmentally regulated gene family in Leishmania amastigotes encoding a homolog of amastin surface proteins. Mol. Biochem. Parasitol. 110:2000;345-357.
33. Burchmore R.J.S., Landfear S.M. Differential regulation of multiple glucose transporter genes in Leishmania mexicana. J. Biol. Chem. 272:1998;29118-29126.
34. Beetham J.K., Myung K.S., McCoy J.J., Donelson J.E. Glycoprotein 46 mRNA abundance is post-transcriptionally regulated during development of Leishmania chagasi promastigotes to an infectious form. J. Biol. Chem. 273:1997;17360-17366.
35. Belli S. Chromatin remodelling during the life cycle of trypanosomatids. Int. J. Parasitol. 30:2000;679-687.
36. Gygi S.P., Rochon Y., Franza B.R., Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 19:1999;1720-1730.
37. Pavesi A. Relationships between transcriptional and translational control of gene expression in Saccharomyces cerevisiae: a multiple regression analysis. Mol. Evol. 48:1999;133-141.
38. Lee M.L., Kuo F.C., Whitmore G.A., Sklar J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. U.S.A. 97:2000;9834-9839.
39. Handman E., Osborn A.H., Symons F., Van Driel R., Cappai R. The Leishmania promastigote surface antigen 2 complex is differentially expressed during the parasite life cycle. Mol. Biochem. Parasitol. 74:1995;189-200.
40. Rangarajan D., Gokool S., McCrossan M.V., Smith D.F. The gene B protein localises to the surface of Leishmania major parasites in the absence of metacyclic stage lipophosphoglycan. J. Cell Sci. 108:1995;3359-3366.
41. Almeida R., Norrish A., Levick M., Vetrie D., Freeman T., Vilo J.et al. From genomes to vaccines: Leishmania as a model. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 357:2002;5-11.