Applications of proteomics in ecology and evolution;Aplicaciones de proteómica en ecología y evolución

Ecosistemas

Volumn 18, Issue 1, 2009, Pages 34-43

  Cieslak, A ^a   Ribera, I ^b  

^a MUSEO NACIONAL DE CIENCIAS NATURALES   (Spain)

^b INSTITUTE OF EVOLUTIONARY BIOLOGY CSIC UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

Bidimensional electrophoresis; Ecological differentiation; Non model organisms; Protein expression; Protein sequencing; Speciation

Indexed keywords

EID: 78650577913     PISSN: None     EISSN: 16972473     Source Type: Journal    
DOI: None     Document Type: Article

References (59)

1. Anderson, N.L., Matheson, A.D., Steiner, S., 2000. Proteomics: applications in basic and applied biology. Current Opinion in Biotechnology 11:408-412.
2. Aquadro, C.F., Avise, J.C., 1981. Genetic-divergence between rodent species assessed by using two-dimensional electrophoresis. Proceedings of the National Academy of Sciences of the United States of America-Biological Sciences 78: 3784-3788.
3. Banfield, J.F., Verberkmoes, N.C., Hettich, R.L., Thelen, M.P., 2005. Proteogenomic approaches for the molecular characterization of natural microbial communities. Omics - a Journal of Integrative Biology 9:301-333.
4. Barneah, O., Benayahu, Y., Weis, V., 2006. Comparative proteomics of symbiotic and aposymbiotic juvenile soft corals. Marine Biotechnology 8:11-16.
5. Biron, D.G., Loxdale, H.D., Ponton, F., Moura, H., Marche, L., Brugidou, C., Thomas, F., 2006. Population proteomics: An emerging discipline to study metapopulation ecology. Proteomics 6:1712-1715.
6. Biron, D.G., Marche, L., Ponton, F., Loxdale, H.D., Galeotti, N., Renault, L., Joly, C., Thomas, F., 2005. Behavioural manipulation in a grasshopper harbouring hairworm: a proteomics approach. Proceedings of the Royal Society B-Biological Sciences 272:2117-2126.
7. Bjellqvist B, Ek K, Righetti PG, Gianazza E, Görg A, Westermeier R, Postel W. 1982. Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. Journal of Biochemical and Biophysical Methods 6(4):317-339.
8. Blank, M., Bastrop, R., Jurss, K., 2006. Stress protein response in two sibling species of Marenzelleria (Polychaeta, Spionidae) Is there an influence of acclimation salinity? Comparative Biochemistry and Physiology B-Biochemistry y Molecular Biology 144:451-462.
9. Blank, M., Fulda, S., Bastrop, R., Jurss, K., 2005. Variation in protein patterns within and among polychaete sibling species of the genus Marenzelleria (Spionidae): a preliminary survey. Marine Biology 146:943-950.
10. Brower, V. 2001. Proteomics: biology in the post-genomic era. EMBO reports 21:558-560.
11. Calvo, E., Flores-Romero, P., López, J.A., Navás, A., 2005. Identification of proteins expressing differences among isolates of Meloidogyne spp. (Nematoda: Meloidogynidae) by nano-liquid chromatography coupled to ion-trap mass spectrometry. Journal of Proteome Research 4:1017-1021.
12. Chan, Q.W.T., Foster, L.J., 2008. Changes in protein expression during honey bee larval development. Genome Biology 9:R156.
13. Cieslak, A., Vogler, A.P., Lafranchi-Tristem, N., Dunn, M.J., Westbrook, J.A., 2007. Investigation of hormone activity in butterfly imaginal wing discs by protein expression pattern changes. Electrophoresis 28:535-544.
14. Denef, V.J., Shah, M.B., VerBerkmoes, N.C., Hettich, R.L., Banfield, J.F., 2007. Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysis. Journal of Proteome Research 6:3152-3161.
15. Diz, A.P., Skibinski, D.O.F., 2007. Evolution of 2-DE protein patterns in a mussel hybrid zone. Proteomics 7:2111-2120.
16. Edman P. and Begg G. 1967. A protein sequenator. European Journal of Biochemistry 1:80-91.
17. Eng, J.K., McCormack, A.L., Yates, J.R. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry 5:976-89.
18. Fox, J.W., Serrano, S.M.T., 2008. Exploring snake venom proteomes: multifaceted analyses for complex toxin mixtures. Proteomics 8:909-920.
19. Fullaondo, A., Vicario, A., Aguirre, A., Barrena, I., Salazar, A., 2001. Quantitative analysis of two-dimensional gel electrophoresis protein patterns: a method for studying genetic relationships among Globodera pallida populations. Heredity 87:266-272.
20. Gardestrom, J., Elfwing, T., Lof, M., Tedengren, M., Davenport, J.L., Davenport, J., 2007. The effect of thermal stress on protein composition in dogwhelks (Nucella lapillus) under non-normoxic and hyperoxic conditions. Comparative Biochemistry and Physiology a-Molecular y Integrative Physiology 148:869-875.
21. Görg, A., y Weiss, W. 2006. High resolution two-dimensional electrophoresis with immobilized pH gradients for proteome analysis. En: J.E. Celis, (Ed.), Cell Biology. A Laboratory Manual, Vol. IV, Ch. 23, 3rd edition, pp. 175-188. Elsevier Science y Academic Press, Amsterdam, The Netherlands.
22. Hansen, B.T., Jones, J.A., Mason, D.E. and Liebler, D.C. 2001. SALSA: a pattern recognition algorithm to detect electrophileadducted peptides by automated evaluation of CIDspectra in LC-MS-MS analyses. Analytical Chemistry 73:1676-83.
23. Henry, C., Bernard, D. and Depieds, R. 1968. 2 dimensional electrophoresis in agar and acrylamide-agar. Comptes Rendus des Seances de la Societe de Biologie et de Ses Filiales 162(2):494-497.
24. Karr, T.L., 2008. Application of proteomics to ecology and population biology. Heredity 100:200-206.
25. Kraj, A. y Silberring, J. 2008. Introduction to Proteomics. pp. 352. Wiley-Interscience Series on Mass Spectrometry, Hoboken, New Jersey. USA.
26. Krogh, M., Liu, Y., Waldemarson, S., Valastro, B., James, P., 2007. Analysis of DIGE data using a linear mixed model allowing for protein-specific dye effects. Proteomics 7:4235-4244.
27. Kültz, D., Fiol, D., Valkova, N., Gomez-Jimenez, S., Chan, S.Y., Lee, J., 2007. Functional genomics and proteomics of the cellular osmotic stress response in 'non-model' organisms. Journal of Experimental Biology 210:1593-1601.
28. Kumarathasan, P., Mohottalage, S., Goegan, P. and Vincent, R. 2005. An optimized protein in-gel digest method for reliable proteome characterization by MALDI–TOF–MS analysis. Analytical Biochemistry 346:85-89.
29. Laemmli, U.K. 1970. Cleavage of structural proteins during the assembly of the head of the bacteriophage T4. Nature 227 (5259):680-685.
30. López, J.L., 2005. Role of proteomics in taxonomy: the Mytilus complex as a model of study. Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences 815:261-274.
31. López, J.L., 2007. Applications of proteomics in marine ecology. Marine Ecology-Progress Series 332:275-279.
32. Mackessy, S.P., 2002. Biochemistry and pharmacology of colubrid snake venoms. Journal of Toxicology-Toxin Reviews 21:43-83.
33. Martinez-Fernandez, M., Rodriguez-Pineiro, A.M., Oliveira, E., de la Cadena, M.P., Rolan-Alvarez, E., 2008. Proteomic comparison between two marine snail ecotypes reveals details about the biochemistry of adaptation. Journal of Proteome Research 7:4926-4934.
34. Miyazaki, J.I., Shintaku, M., Kyuno, A., Fujiwara, Y., Hashimoto, J., Iwasaki, H., 2004. Phylogenetic relationships of deep-sea mussels of the genus Bathymodiolus (Bivalvia: Mytilidae). Marine Biology 144:527-535.
35. Mullis, K., Faloona, F., Scharf, S., Saiki, R., Horn, G., Erlich, H., 1986. Specific enzymatic amplification of DNA in vitro - the Polymerase Chain-Reaction. Cold Spring Harbor Symposia on Quantitative Biology 51:263-273.
36. Murphy, W., Sites, J.W., Buth, D.G. y Haufer, C.H. 1996. Proteins: Siozyme electrophoresis. En: Hillis, D.M., Mortiz, C. y Mable, B.K. (eds.) Molecular systematics, 2nd ed., pp. 51-120. Sinauer Associates, Sunderland MA, USA.
37. Nascimento, D.G., Rates, B., Santos, D.M., Verano-Braga, T., Barbosa-Silva, A., Dutra, A.A.A., Biondi, I., Martin-Eauclaire, M.F., De Lima, M.E., Pimenta, A.M.C., 2006. Moving pieces in a taxonomic puzzle: Venom 2D-LC/MS and data clustering analyses to infer phylogenetic relationships in some scorpions from the Buthidae family (Scorpiones). Toxicon 47:628-639.
38. Navás, A., Albar, J.P., 2003. Application of proteomics in phylogenetic and evolutionary studies, En: Seminar in Proteomics UCO-2003, pp. 299-302, Universidad de Córdoba, Córdoba, Spain.
39. Navás, A., Lopez, J.A., Esparrago, G., Camafeita, E., Albar, J.P., 2002. Protein variability in Meloidogyne spp. (Nematoda: Meloidogynidae) revealed by two-dimensional gel electrophoresis and mass spectrometry. Journal of Proteome Research 1:421-427.
40. Nunn, B.L., Timperman, A.T., 2007. Marine proteomics. Marine Ecology-Progress Series 332, 281-289.
41. Panchaud, A., Affolder, M., Moreillon, P. and Kussmann, M. 2008. Experimental and computational approaches to quantitative proteomics: Status quo and outlook. Journal of Proteomics 71:19-33.
42. Perkins, D.N., Pappin, D.J. and Creasy, D.M. 1999. Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551-67.
43. Petrak, J., Ivanek, R., Toman, O., Cmejla, R., Cmejlova, J., Vyoral, D., Zivny, J., Vulpe, C.D., 2008. Deja vu in proteomics. A hit parade of repeatedly identified differentially expressed proteins. Proteomics 8:1744-1749.
44. Pörtner, H.O., Farrell, A.P., 2008. Physiology and Climate Change. Science 322:690-692.
45. Ramm, S.A., McDonald, L., Hurst, J.L., Beynon, R.J., Stockley, P., 2009. Comparative proteomics reveals evidence for evolutionary diversification of rodent seminal fluid and its functional significance in sperm competition. Molecular Biology and Evolution 26:189-198.
46. Rousch, J.M., Bingham, S.E., Sommerfeld, M.R., 2004. Protein expression during heat stress in thermo-intolerant and thermo-tolerant diatoms. Journal of Experimental Marine Biology and Ecology 306:231-243.
47. Sanger, F., Nicklen, S., Coulson, A.R., 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America 74:5463-5467.
48. Singh, N.P., Matta, N.K., 2008. Variation studies on seed storage proteins and phylogenetics of the genus Cucumis. Plant Systematics and Evolution 275:209-218.
49. Sunyaev, S., Liska, A.J., Golod, A., Shevchenko, A. and Shevchenko A. 2003. MultiTag: multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry. Analytical Chemistry 75:1307-15.
50. Tabb, D.L., Saraf, A. and Yates, III J.R. 2003. GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. Analytical Chemistry 75:6415-21.
51. Taylor, C.F. et al. [29 autores]. 2007. The minimum information about proteomics experiment (MIAPE). Nature biotechnology 25:887-893.
52. Toni, M., Alibardi, L., 2007. Alpha-and beta-keratins of the snake epidermis. Zoology 110:41-47.
53. Ünlü, M., Morgan, M.E., Minden, J.S., 1997. Difference gel electrophoresis: A single gel method for detecting changes in protein extracts. Electrophoresis 18:2071-2077.
54. Valcu, C.M., Lalanne, C., Muller-Starck, G., Plomion, C., Schlink, K., 2008. Protein polymorphism between 2 Picea abies populations revealed by 2-dimensional gel electrophoresis and tandem mass spectrometry. Journal of Heredity 99:364-375.
55. Van der Beek, J.G., Folkertsma, R., Poleij, L.M., vanKoert, P.H.G., Bakker, J., 1997. Molecular evidence that Meloidogyne hapla, M. chitwoodi, and M. fallax are distinct biological entities. Fundamental and Applied Nematology 20:513-520.
56. Wang, X.Q., Yang, P.F., Gao, Q., Liu, X.L., Kuang, T.Y., Shen, S.H., He, Y.K., 2008. Proteomic analysis of the response to high-salinity stress in Physcomitrella patens. Planta 228:167-177.
57. Westermeier, R., Naven, T. y Höpker, H.R. 2008. Proteomics in practice: a guide to successful experimental design, 2nd ed. Wiley-VCH, Weinheim, Germany.
58. Yuan, C.H., Jin, Q.H., Tang, X., Hu, W.J., Cao, R., Yang, S.Q., Xiong, J.X., Xie, C.L., Xie, J.Y., Liang, S.P., 2007. Proteomic and peptidomic characterization of the venom from the Chinese bird spider, Ornithoctonus huwena Wang. Journal of Proteome Research 6:2792-2801.
59. Zhang, W. and Chait, B.T. 2000. ProFound an expert system for protein identification using mass spectrometric peptide mapping information. Analytical Chemistry 72:2482-9.