A chick retinal proteome database and differential retinal protein expressions during early ocular development

Journal of Proteome Research

Volumn 5, Issue 4, 2006, Pages 771-784

  Lam, Thomas C ^a   Li, King Kit ^a   Lo, Samuel Chun Lap ^a,b   Guggenheim, Jeremy A ^c   To, Chi Ho ^a  

^a HONG KONG POLYTECHNIC UNIVERSITY   (Hong Kong)

^b State Key Laboratory of Chinese Medicine and Molecular Pharmacology   (China)

^c CARDIFF UNIVERSITY   (United Kingdom)

Author keywords

Chick; Development; Mass spectrometry; Proteome; Proteomics; Retina; Two dimensional gel electrophoresis

Indexed keywords

PROTEOME; RETINA PROTEIN; UNCLASSIFIED DRUG;

ANALYTIC METHOD; ANIMAL TISSUE; ARTICLE; CHICK; EYE DEVELOPMENT; EYE DISEASE; EYE RESEARCH; HIGH THROUGHPUT SCREENING; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MEDICAL RESEARCH; NEWBORN; NONHUMAN; NUCLEOTIDE SEQUENCE; PEPTIDE MASS FINGERPRINTING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEOME DATABASE; PROTEOMICS; RETINA; TWO DIMENSIONAL GEL ELECTROPHORESIS; UNINDEXED SEQUENCE;

ANIMALS; ANIMALS, NEWBORN; CHICKENS; DATABASES, PROTEIN; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; EYE; EYE PROTEINS; PEPTIDE MAPPING; PROTEOME; PROTEOMICS; RETINA; ROBOTICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TIME FACTORS;

ANIMALIA;

EID: 33645779008     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr050280n     Document Type: Article

References (70)

1. Dwek, M. V.; Rawlings, S. L. Current perspectives in cancer proteomics. Mol. Biotechnol. 2002, 22 (2), 139-152.
2. Hanash, S. M.; Madoz-Gurpide, J.; Misek, D. E. Identification of novel targets for cancer therapy using expression proteomics. Leukemia 2002, 16 (4), 478-485.
3. Michener, C. M.; Ardekani, A. M.; Petricoin, E. F., III; Liotta, L. A.; Kohn, E. C. Genomics and proteomics: application of novel technology to early detection and prevention of cancer. Cancer Detect. Prev. 2002, 26 (4), 249-255.
4. Wu, W.; Hu, W.; Kavanagh, J. J. Proteomics in cancer research. Int. J. Gynecol. Cancer 2002, 12 (5), 409-423.
5. Butterfield, D. A.; Boyd-Kimball, D. Proteomics analysis in Alzheimer's disease: new insights into mechanisms of neurodegeneration. Int. Rev. Neurobiol. 2004, 61, 159-188.
6. Nicolls, M. R.; D'Antonio, J. M.; Hutton, J. C.; Gill, R. G.; Czwornog, J. L.; Duncan, M. W. Proteomics as a tool for discovery: proteins implicated in Alzheimer's disease are highly expressed in normal pancreatic islets. J. Proteome Res. 2003, 2 (2), 199-205.
7. Ying, W.; Hao, Y.; Zhang, Y.; Peng, W.; Qin, E.; Cai, Y.; Wei, K.; Wang, J.; Chang, G.; Sun, W.; Dai, S.; Li, X.; Zhu, Y.; Li, J.; Wu, S.; Guo, L; Dai, J.; Wang, J.; Wan, P.; Chen, T.; Du, C.; Li, D.; Wan, J.; Kuai, X.; Li, W.; Shi, R.; Wei, H.; Cao, C.; Yu, M.; Liu, H.; Dong, F.; Wang, D.; Zhang, X.; Qian, X.; Zhu, Q.; He, F. Proteomic analysis on structural proteins of Severe Acute Respiratory Syndrome coronavirus. Proteomics 2004, 4 (2), 492-504.
8. Langman, R. E.; Cohn, M. A theory of the ontogeny of the chicken humoral immune system: the consequences of diversification by gene hyperconversion and its extension to rabbit. Res. Immunol. 1993, 144, (6-7), 422-446.
9. Okano, T.; Fukada, Y. Photoreception and arcadian clock system of the chicken pineal gland. Microsc. Res. Tech. 2001, 53 (1), 72-80.
10. Wolburg, H.; Liebner, S.; Reichenbach, A.; Gerhardt, H. The pecten oculi of the chicken: a model system for vascular differentiation and barrier maturation. Int. Rev. Cytol. 1999, 187, 111-159.
11. Schmid, K. L.; Wildsoet, C. F. Effects on the compensatory responses to positive and negative lenses of intermittent lens wear and ciliary nerve section in chicks. Vision Res. 1996, 36 (7), 1023-1036.
12. Norton, T. T. Animal models of myopia: learning how vision controls the size of the eye. ILAR J. 1999, 40, (2), 59-77.
13. Schaeffel, F.; Diether, S. The growing eye: an autofocus system that works on very poor images. Vision Res. 1999, 39, (9), 1585-1589.
14. Wildsoet, C. F.; Schmid, K. L. Emmetropization in chicks uses optical vergence and relative distance cues to decode defocus. Vision Res. 2001, 41 (24), 3197-3204.
15. Soh, B. M.; Fox, L. E.; Moscona, A. A. Changes in patterns and synthesis of proteins in embryonic neural retina studied by 2-dimensional gel electrophoresis. Brain Res. 1982, 255 (3), 329-340.
16. Schaeffel, F.; Glasser, A.; Howland, H. C. Accommodation, refractive error and eye growth in chickens. Vision Res. 1988, 28, (5), 639-657.
17. Yan, J. X.; Wait, R.; Berkelman, T.; Harry, R. A.; Westbrook, J. A.; Wheeler, C. H.; Dunn, M. J. A modified silver staining protocol for visualization of proteins compatible with matrix-assisted laser desorption/ionization and electrospray ionization-mass spectrometry. Electrophoresis 2000, 21 (17), 3666-3672.
18. Schuerenberg, M.; Luebbert, C.; Eickhoff, H.; Kalkum, M.; Lehrach, H.; Nordhoff, E. Prestructured MALDI-MS sample supports. Anal Chem. 2000, 72 (15), 3436-3442.
19. Johnson, T.; Bergquist, J.; Ekman, R.; Nordhoff, E.; Schurenberg, M.; Kloppel, K. D.; Muller, M.; Lehrach, H.; Gobom, J. A CEMALDI interface based on the use of prestructured sample supports. Anal. Chem. 2001, 73 (8), 1670-1675.
20. Gobom, J.; Schuerenberg, M.; Mueller, M.; Theiss, D.; Lehrach, H.; Nordhoff, E. α-Cyano-4-hydroxycinnamic acid affinity sample preparation. A protocol for MALDI-MS peptide analysis in proteomics. Anal. Chem. 2001, 73, (3), 434-438.
21. Ashburner, M.; Ball, C. A.; Blake, J. A.; Botstein, D.; Butler, H.; Cherry, J. M.; Davis, A. P.; Dolinski, K.; Dwight, S. S.; Eppig, J. T.; Harris, M. A.; Hill, D. P.; Issel-Tarver, L.; Kasarskis, A.; Lewis, S.; Matese, J. C.; Richardson, J. E.; Ringwald, M.; Rubin, G. M.; Sherlock, G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25 (1), 25-29.
22. Sullivan, K. F.; Lau, J. T.; Cleveland, D. W. Apparent gene conversion between beta-tubulin genes yields multiple regulatory pathways for a single beta-tubulin polypeptide isotype. Mol. Cell. Biol. 1985, 5 (9), 2454-2465.
23. Cleveland, D. W.; Sullivan, K. F., Molecular biology and genetics of tubulin. Annu. Rev. Biochem. 1985, 54, 331-365.
24. Yamagata, K.; Goto, K.; Kuo, C. H.; Kondo, H.; Miki, N. Visinin: a novel calcium binding protein expressed in retinal cone cells. Neuron 1990, 4 (3), 469-476.
25. Rogers, J. H. Calretinin: a gene for a novel calcium-binding protein expressed principally in neurons. J. Cell Biol. 1987, 105 (3), 1343-1353.
26. Ellis, J. H.; Richards, D. E.; Rogers, J. H. Calretinin and calbindin in the retina of the developing chick. Cell Tissue Res. 1991, 264 (2), 197-208.
27. Pasteels, B.; Rogers, J.; Blachier, F.; Pochet, R. Calbindin and calretinin localization in retina from different species. Vision Neurosci. 1990, 5 (1), 1-16.
28. Nakajo, S.; Shioda, S.; Nakai, Y.; Nakaya, K. Localization of phosphoneuroprotein 14 (PNP 14) and its mRNA expression in rat brain determined by immunocytochemistry and in situ hybridization. Brain Res. Mol. Brain Res. 1994, 27 (1), 81-86.
29. Lavedan, C.; Leroy, E.; Torres, R.; Dehejia, A.; Dutra, A.; Buchholtz, S.; Nussbaum, R. L; Polymeropoulos, M. H. Genomic organization and expression of the human beta-synuclein gene (SNCB). Genomics 1988, 54 (1), 173-175.
30. Norenberg, M. D.; Dutt, K.; Reif-Lehrer, L. Glutamine synthetase localization in cortisol-induced chick embryo retinas. J. Cell Biol. 1980, 84 (3), 803-807.
31. Linser, P.; Moscona, A. A. Induction of glutamine synthetase in embryonic neural retina: localization in Muller fibers and dependence on cell interactions. Proc. Natl. Acad. Sci. U.S.A. 1979, 76 (12), 6476-6480.
32. Tanaka, M.; Maeda, K.; Nakashima, K. Chicken alpha-enolase but not beta-enolase has a Src-dependent tyrosine-phosphorylation site: cDNA cloning and nucleotide sequence analysis. J. Biochem. (Tokyo) 1995, 117 (3), 554-559.
33. Eder, M.; Schlattner, U.; Becker, A.; Wallimann, T.; Kabsch, W.; Fritz-Wolf, K. Crystal structure of brain-type creatine kinase at 1.41 Å resolution. Protein Sci. 1999, 8 (11), 2258-2269.
34. Bessman, S. P.; Carpenter, C. L. The creatine-creatine phosphate energy shuttle. Annu. Rev. Biochem. 1985, 54, 831-862.
35. Meighan-Mantha, R. L.; Tolan, D. R. Noncoordinate changes in the steady-state mRNA expressed from aldolase A and aldolase C genes during differentiation of chicken myoblasts. J. Cell. Biochem. 1995, 57 (3), 423-431.
36. Rogers, J. H.; Hunt, S. P. Carbonic anhydrase-II messenger RNA in neurons and glia of chick brain: mapping by in situ hybridization. Neuroscience 1987, 23 (1), 343-361.
37. West, K. A.; Yan, L.; Shadrach, K.; Sun, J.; Hasan, A.; Miyagi, M.; Crabb, J. S.; Hollyfleld, J. G.; Marmorstein, A. D.; Crabb, J. W. Protein database, human retinal pigment epithelium. Mol. Cell. Proteomics 2003, 2 (1), 37-49.
38. Morel, V.; Poschet, R.; Traverso, V.; Deretic, D. Towards the proteome of the rhodopsin-bearing post-Golgi compartment of retinal photoreceptor cells. Electrophoresis 2000, 21 (16), 3460-3469.
39. Hauck, S. M.; Suppmann, S.; Ueffing, M. Proteomic profiling of primary retinal Muller glia cells reveals a shift in expression patterns upon adaptation to in vitro conditions. Glia 2003, 44 (3), 251-263.
40. Beranova-Giorgianni, S.; Pabst, M. J.; Russell, T. M.; Giorgianni, F.; Goldowitz, D.; Desiderio, D. M., Preliminary analysis of the mouse cerebellum proteome. Brain Res. Mol. Brain Res. 2002, 98 (1-2), 135-140.
41. Fountoulakis, M.; Schuller, E.; Hardmeier, R.; Berndt, P.; Lubec, G., Rat brain proteins: two-dimensional protein database and variations in the expression level. Electrophoresis 1999, 20 (18), 3572-3579.
42. Langen, H.; Berndt, P.; Roder, D.; Cairns, N.; Lubec, G.; Fountoulakis, M. Two-dimensional map of human brain proteins. Electrophoresis 1999, 20 (4-5), 907-916.
43. Banks, M. S. Infant refraction and accommodation. Int. Ophthalmol. Clin. 1980, 20 (1), 205-232.
44. Edwards, M. The refractive status of Hong Kong Chinese infants. Ophthalmic Physiol. Opt. 1991, 11, (4), 297-303.
45. Wallman, J.; Adams, J. I.; Trachtman, J. N. The eyes of young chickens grow toward emmetropia. Invest. Ophthalmol. Visual Sci. 1981, 20 (4), 557-561.
46. Irving, E. L.; Sivak, J. G.; Curry, T. A.; Callender, M. G. Chick eye optics: zero to fourteen days. J. Comp. Physiol, A 1998, 179 (2), 185-194.
47. Shackelford, J. E.; Lebherz, H. G. Regulation of apolipoprotein Al synthesis in avian muscles. J. Biol. Chem .1983, 258 (24), 14829-14833.
48. Tarugi, P.; Reggiani, D.; Ottaviani, E.; Ferrari, S.; Tiozzo, R.; Calandra, S. Plasma lipoproteins, tissue cholesterol overload, and skeletal muscle apolipoprotein A-I synthesis in the developing chick. J. Lipid Res. 1989, 30 (1), 9-22.
49. Ferrari, S.; Drusiani, E.; Calandra, S.; Tarugi, P. Isolation of a cDNA clone for chick intestinal apolipoprotein AI (Apo-AI) and its use for detecting apo-AI rnRNA expression in several chick tissues. Gene 1986, 42 (2), 209-214.
50. Ferrari, S.; Tarugi, P.; Drusiani, E.; Calandra, S.; Fregni, M. The complete sequence of chick apolipoprotein AI mRNA and its expression in the developing chick. Gene 1987, 60 (1), 39-46.
51. Lemieux, M. J.; Mezei, C.; Breckenridge, W. C. Secretion and processing of apolipoprotein A-I in the avian sciatic nerve during development. J. Neurosci. Res. 1998, 44 (6), 594-605.
52. Godbout, R. Identification and characterization of transcripts present at elevated levels in the undifferentiated chick retina. Exp. Eye Res. 1993, 56 (1), 95-106.
53. Godbout, R.; Marusyk, H.; Bisgrove, D.; Dabbagh, L.; Poppema, S. Localization of a fatty acid binding protein and its transcript in the developing chick retina. Exp. Eye Res. 1995, 60 (6), 645-657.
54. Sellner, P. Developmental regulation of fatty acid binding protein in neural tissue. Dev. Dyn. 1994, 200 (4), 333-339.
55. Miranda, A. F.; Peterson, E. R.; Masurovsky, E. B. Differential expression of creatine kinase and phosphoglycerate mutase isozymes during development in aneural and innervated human muscle culture. Tissue Cell 1988, 20 (2), 179-191.
56. Granstrom, G. Isoenzyme changes during rat facial development. Scand. J. Dent. Res. 1986, 94 (1), 1-14.
57. Boraldi, F.; Bini, L.; Liberatori, S.; Armini, A.; Pallini, V.; Tiozzo, R.; Pasquali-Ronchetti, I.; Quaglino, D., Proteome analysis of dermal fibroblasts cultured in vitro from human healthy subjects of different ages. Proteomics 2003, 3 (6), 917-929.
58. Thornalley, P. J. The glyoxalase system in health and disease. Mol. Aspects Med. 1993, 14 (4), 287-371.
59. Sharma-Luthra, R.; Kale, R. K. Age related changes in the activity of the glyoxalase system. Mech. Ageing Dev. 1994, 73 (1), 39-45.
60. Deswal, R.; Chakaravarty, T. N.; Sopory, S. K. The glyoxalase system in higher plants: regulation in growth and differentiation. Biochem. Soc. Trans. 1993, 21 (2), 527-530.
61. Bamburg, J. R. Proteins of the ADF/cofilin family: essential regulators of actin dynamics. Annu. Rev. Cell Dev. Biol. 1999, 15, 185-230.
62. Ikeda, S.; Cunningham, L. A.; Boggess, D.; Hawes, N.; Hobson, C. D.; Sundberg, J. P.; Naggert, J. K.; Smith, R. S.; Nishina, P. M. Aberrant actin cytoskeleton leads to accelerated proliferation of corneal epithelial cells in mice deficient for destrin (actin depolymerizing factor). Hum. Mol. Genet. 2003, 12 (9), 1029-1037.
63. Gungabissoon, R. A.; Bamburg, J. R. Regulation of growth cone actin dynamics by ADF/cofilin. J. Histochem. Cytochem. 2003, 51 (4), 411-420.
64. Matsumoto, H.; Kahn, E. S.; Komori, N. The emerging role of mass spectrometry in molecular biosciences: studies of protein phosphorylation in fly eyes as an example. Novartis Found. Symp. 1999, 224, 225-244; discussion 244-248.
65. Cavusoglu, N.; Thierse, D.; Mohand-Said, S.; Chalmel, F.; Poch, O.; Van-Dorsselaer, A.; Sahel, J. A.; Leveillard, T. Differential proteomic analysis of the mouse retina: the induction of crystallin proteins by retinal degeneration in the rd1 mouse. Mol. Cell. Proteomics 2003, 2 (8), 494-505.
66. Vignaud, J. M.; Plenat, F.; Duprez, A. [In situ hybridization: principles, methods and applications]. Arch. Anat. Cytol. Pathol. 1990, 38 (4), 125-134.
67. Charuruks, N.; Voravud, N. In situ hybridization: a new tool in molecular medicine. J. Med. Assoc. Thailand 1996, 79 (6), 374-381.
68. Van Noorden, S. Advances in immunocytochemistry. Folia Histochem. Cytobiol. 2002, 40 (2), 121-124.
69. Bertrand, E. F.; Fritsch, C.; Schmid, K.; Schmid, P.; Muller, D.; Schindler, P.; Towbin, H.; van Oostrum, J.; Lambrou, G. N.; Voshol, H. Ocular axial growth control and proteomics: differential protein expression in an experimental animal model. Invest. Ophthalmol. Visual Sci. 2005, 46 (5), 3331.
70. Lam, C.; Li, K. K.; Lo, S. C. L.; To, C. H. Differential protein expressions in the emmetropization of chick retina by a proteomic approach. Invest. Ophthalmol. Vis. Sci. 2005, 46 (5), 3144.