Expressed sequence tag analysis of guinea pig (Cavia porcellus) eye tissues for NEIBank

Molecular Vision

Volumn 14, Issue , 2008, Pages 2413-2427

  Simpanya, Mukoma F ^a   Wistow, Graeme ^b   Gao, James ^b   David, Larry L ^c   Giblin, Frank J ^a   Mitton, Kenneth P ^a  

^a OAKLAND UNIVERSITY   (United States)

^b NATIONAL EYE INSTITUTE   (United States)

^c OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA ENOLASE; ALPHAA CRYSTALLIN; BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR; BETAA2 CRYSTALLIN; BETAA4 CRYSTALLIN; BETAB1 CRYSTALLIN; BETAB2 CRYSTALLIN; BETAB3 CRYSTALLIN; CARBONATE DEHYDRATASE III; COMPLEMENTARY DNA; CRYSTALLIN; DECORIN; FILENSIN; GAMMAA CRYSTALLIN; GAMMAB CRYSTALLIN; GAMMAC CRYSTALLIN; GAMMAD CRYSTALLIN; GAMMAE CRYSTALLIN; GAMMAF CRYSTALLIN; GAMMAN CRYSTALLIN; GAMMAS CRYSTALLIN; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; GRIFIN; KERATIN; LENGSIN; LENS PROTEIN; RETINA S ANTIGEN; RHODOPSIN; TRANSDUCIN; UNCLASSIFIED DRUG;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DNA LIBRARY; DNA SEQUENCE; ELECTROSPRAY MASS SPECTROMETRY; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENE EXPRESSION; GENE IDENTIFICATION; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENETIC TRANSDUCTION; GENOME ANALYSIS; GUINEA PIG; LENS; LENS NUCLEUS; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PHOTORECEPTOR; PHOTOTRANSDUCTION; PRIORITY JOURNAL; RETINA; RNA EXTRACTION; SEQUENCE ANALYSIS; TWO DIMENSIONAL ELECTROPHORESIS;

ALTERNATIVE SPLICING; ANIMALS; DATABASES, GENETIC; DNA, COMPLEMENTARY; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; EXPRESSED SEQUENCE TAGS; EYE; EYE PROTEINS; GAMMA-CRYSTALLINS; GENE LIBRARY; GENOME; GUINEA PIGS; HUMANS; LENS, CRYSTALLINE; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; NUCLEAR PROTEINS; OPEN READING FRAMES; RETINA; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA; SOLUBILITY;

EID: 58049200685     PISSN: None     EISSN: 10900535     Source Type: Journal    
DOI: None     Document Type: Article

References (80)

1. Brubaker RF, Bourne WM, Bachman LA, McLaren JW. Ascorbic acid content of human corneal epithelium. Invest Ophthalmol Vis Sci 2000; 41:1681-3.
2. Yokoyama T, Sasaki H, Giblin FJ, Reddy VN. A physiological level of ascorbate inhibits galactose cataract in guinea pigs by decreasing polyol accumulation in the lens epithelium: a dehydroascorbate-linked mechanism. Exp Eye Res 1994; 58:207-18.
3. Mackic JB, Ross-Cisneros IN, McComb JG, Bekhor I, Weiss MH, Kannan R, Zlokovic BV. Galactose-induced cataract formation in guinea pigs: morphologic changes and accumulation of galactitol. Invest Ophthalmol Vis Sci 1994; 35:804-10.
4. Reddy VN, Giblin FJ, Lin LR, Chakrapani B. The effect of aqueous humor ascorbate on ultraviolet-B-induced DNA damage in lens epithelium. Invest Ophthalmol Vis Sci 1998; 39:344-50.
5. Malik A, Kojima M, Sasaki K. Morphological and biochemical changes in lenses of guinea pigs after vitamin-C-deficient diet and UV-B radiation. Ophthalmic Res 1995; 27:189-96.
6. Wu K, Kojima M, Shui YB, Sasaki H, Sasaki K. Ultraviolet B-induced corneal and lens damage in guinea pigs on low-ascorbic acid diet. Ophthalmic Res 2004; 36:277-83.
7. Campbell FW, Ferguson ID, Garry RC. Ascorbic acid and healing of heat injuries in the guinea pig cornea. Br J Nutr 1950; 4:32-42.
8. Truscott RJ. Age-related nuclear cataract-oxidation is the key. Exp Eye Res 2005; 80:709-25.
9. Yu NT, DeNagel DC, Pruett PL, Kuck JF Jr. Disulfide bond formation in the eye lens. Proc Natl Acad Sci USA 1985; 82:7965-8.
10. Askren CC, Yu NT, Kuck JF Jr. Variation of the concentration of sulfhydryl along the visual axis of aging lenses by laser Raman optical dissection technique. Exp Eye Res 1979; 29:647-54.
11. Kuck JF, Yu NT, Askren CC. Total sulfhydryl by raman spectroscopy in the intact lens of several species: variations in the nucleus and along the optical axis during aging. Exp Eye Res 1982; 34:23-37.
12. Rao PV, Zigler JS Jr. Extremely high levels of NADPH in guinea pig lens: correlation with zeta-crystallin concentration. Biochem Biophys Res Commun 1990; 167:1221-8.
13. Zigler JS Jr, Rao PV. Enzyme/crystallins and extremely high pyridine nucleotide levels in the eye lens. FASEB J 1991; 5:223-5.
14. Francis Simpanya M, Ansari RR, Leverenz V, Giblin FJ. Measurement of Lens Protein Aggregation in Vivo Using Dynamic Light Scattering in a Guinea Pig/UVA Model for Nuclear Cataract. Photochem Photobiol 2008; 84:1589-95.
15. Giblin FJ, Leverenz VR, Padgaonkar VA, Unakar NJ, Dang L, Lin LR, Lou MF, Reddy VN, Borchman D, Dillon JP. UVA light in vivo reaches the nucleus of the guinea pig lens and produces deleterious, oxidative effects. Exp Eye Res 2002; 75:445-58.
16. Palmquist BM, Philipson B, Barr PO. Nuclear cataract and myopia during hyperbaric oxygen therapy. Br J Ophthalmol 1984; 68:113-7.
17. Giblin FJ, Padgaonkar VA, Leverenz VR, Lin LR, Lou W, Unakar NJ, Dang L, Dickerson JE Jr, Reddy VN. Nuclear light scattering, disulfide formation and membrane damage in lenses of older guinea pigs treated with hyperbaric oxygen. Exp Eye Res 1995; 60:219-35.
18. Bantseev V, Oriowo OM, Giblin FJ, Leverenz VR, Trevithick JR, Sivak JG. Effect of hyperbaric oxygen on guinea pig lens optical quality and on the refractive state of the eye. Exp Eye Res 2004; 78:925-31.
19. Padgaonkar VA, Lin LR, Leverenz VR, Rinke A, Reddy VN, Giblin FJ. Hyperbaric oxygen in vivo accelerates the loss of cytoskeletal proteins and MIP26 in guinea pig lens nucleus. Exp Eye Res 1999; 68:493-504.
20. Simpanya MF, Ansari RR, Suh KI, Leverenz VR, Giblin FJ. Aggregation of lens crystallins in an in vivo hyperbaric oxygen guinea pig model of nuclear cataract: dynamic light-scattering and HPLC analysis. Invest Ophthalmol Vis Sci 2005; 46:4641-51.
21. Borchman D, Giblin FJ, Leverenz VR, Reddy VN, Lin LR, Yappert MC, Tang D, Li L. Impact of aging and hyperbaric oxygen in vivo on guinea pig lens lipids and nuclear light scatter. Invest Ophthalmol Vis Sci 2000; 41:3061-73.
22. Han J, Little M, David LL, Giblin FJ, Schey KL. Sequence and peptide map of guinea pig aquaporin 0. Mol Vis 2004; 10:215-22.
23. Racine J, Behn D, Lachapelle P. Structural and functional maturation of the retina of the albino Hartley guinea pig. Doc Ophthalmol 2008; 117:13-26.
24. Loeliger M, Rees S. Immunocytochemical development of the guinea pig retina. Exp Eye Res 2005; 80:9-21.
25. Rees S, Bainbridge A. The structural and neurochemical development of the fetal guinea pig retina and optic nerve in experimental growth retardation. Int J Dev Neurosci 1992; 10:93-108.
26. Franze K, Grosche J, Skatchkov SN, Schinkinger S, Foja C, Schild D, Uckermann O, Travis K, Reichenbach A, Guck J. Muller cells are living optical fibers in the vertebrate retina. Proc Natl Acad Sci USA 2007; 104:8287-92.
27. Cringle S, Yu DY, Alder V, Su EN, Yu P. Oxygen consumption in the avascular guinea pig retina. Am J Physiol 1996; 271:H1162-5.
28. Quiram PA, Leverenz VR, Baker RM, Dang L, Giblin FJ, Trese MT. Microplasmin-induced posterior vitreous detachment affects vitreous oxygen levels. Retina 2007; 27:1090-6.
29. Aydemir O, Celebi S, Yilmaz T, Yekeler H, Kukner AS. Protective effects of vitamin E forms (alpha-tocopherol, gamma-tocopherol and d-alpha-tocopherol polyethylene glycol 1000 succinate) on retinal edema during ischemia-reperfusion injury in the guinea pig retina. Int Ophthalmol 2004; 25:283-9.
30. Kannan R, Mackic JB, Zlokovic BV. Corneal transport of circulating glutathione in normal and galactosemic guinea pigs. Cornea 1999; 18:321-7.
31. Ardan T, Kovaceva J, Cejkova J. Comparative histochemical and immunohistochemical study on xanthine oxidoreductase/ xanthine oxidase in mammalian corneal epithelium. Acta Histochem 2004; 106:69-75.
32. Cejkova J, Ardan T, Filipec M, Midelfart A. Xanthine oxidoreductase and xanthine oxidase in human cornea. Histol Histopathol 2002; 17:755-60.
33. Carr RW, Pianova S, Fernandez J, Fallon JB, Belmonte C, Brock JA. Effects of heating and cooling on nerve terminal impulses recorded from cold-sensitive receptors in the guinea-pig cornea. J Gen Physiol 2003; 121:427-39.
34. Matsumoto K, Shimmura S, Goto E, Saito K, Takeuchi T, Miyajima S, Negi A, Tsubota K. Lecithin-bound superoxide dismutase in the prevention of neutrophil-induced damage of corneal tissue. Invest Ophthalmol Vis Sci 1998; 39:30-5.
35. Nishida S, Sears M. Fine structural innervation of the dilator muscle of the iris of the albino guinea pig studied with permanganate fixation. Exp Eye Res 1969; 8:292-6.
36. Yoshitomi T, Ito Y, Inomata H. Adrenergic excitatory and cholinergic inhibitory innervations in the human iris dilator. Exp Eye Res 1985; 40:453-9.
37. Cavallotti C, Artico M, Pescosolido N, Tranquilli Leali FM, Pacella E. Distribution of peptidergic nerve fibres in the guinea pig trabecular meshwork. Anat Histol Embryol 2000; 29:387-91.
38. Sasamoto M, Chen HB, Tsukahara S. Ultrastructural identification of substance P containing nerves in the guinea pig trabecular meshwork. Ophthalmic Res 1998; 30:127-34.
39. Zhou X, Wang W, Lu F, Hu S, Jiang L, Yan D, Zhang X, Yu X, Yu J, Qu J. A comparative gene expression profile of the whole eye from human, mouse, and guinea pig. Mol Vis 2007; 13:2214-21.
40. Wistow G, Bernstein SL, Wyatt MK, Ray S, Behal A, Touchman JW, Bouffard G, Smith D, Peterson K. Expressed sequence tag analysis of human retina for the NEIBank Project: retbindin, an abundant, novel retinal cDNA and alternative splicing of other retina-preferred gene transcripts. Mol Vis 2002; 8:196-204.
41. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-10.
42. Wistow G, Bernstein SL, Touchman JW, Bouffard G, Wyatt MK, Peterson K, Behal A, Gao J, Buchoff P, Smith D. Grouping and identification of sequence tags (GRIST): bioinformatics tools for the NEIBank database. Mol Vis 2002; 8:164-70.
43. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002; 12:656-64.
44. Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 2008; 36:D773-9.
45. Wistow G, Peterson K, Gao J, Buchoff P, Jaworski C, Bowes-Rickman C, Ebright JN, Hauser MA, Hoover D. NEIBank: genomics and bioinformatics resources for vision research. Mol Vis 2008; 14:1327-37.
46. Ueda Y, Fukiage C, Shih M, Shearer TR, David LL. Mass measurements of C-terminally truncated alpha-crystallins from two-dimensional gels identify Lp82 as a major endopeptidase in rat lens. Mol Cell Proteomics 2002; 1:357-65.
47. Lampi KJ, Shih M, Ueda Y, Shearer TR, David LL. Lens proteomics: analysis of rat crystallin sequences and two-dimensional electrophoresis map. Invest Ophthalmol Vis Sci 2002; 43:216-24.
48. Ueda Y, Duncan MK, David LL. Lens proteomics: the accumulation of crystallin modifications in the mouse lens with age. Invest Ophthalmol Vis Sci 2002; 43:205-15.
49. Robertson LJ, David LL, Riviere MA, Wilmarth PA, Muir MS, Morton JD. Susceptibility of ovine lens crystallins to proteolytic cleavage during formation of hereditary cataract. Invest Ophthalmol Vis Sci 2008; 49:1016-22.
50. Matsui NM, Smith-Beckerman DM, Epstein LB. Staining of preparative 2-D gels. Coomassie blue and imidazole-zinc negative staining. Methods Mol Biol 1999; 112:307-11.
51. Fine BS, Yanoff M. Ocular Histology. A Text and Atlas. 2nd edn. Hagerstown, MD.: Harper and Row; 1979.
52. Kolb H, Fernandez E, Nelson R. The organization of the retina and visual system. 2008; .
53. Wistow G, Wyatt K, David L, Gao C, Bateman O, Bernstein S, Tomarev S, Segovia L, Slingsby C, Vihtelic T. gammaN-crystallin and the evolution of the betagamma-crystallin superfamily in vertebrates. FEBS J 2005; 272:2276-91.
54. Ida H, Boylan SA, Weigel AL, Smit-McBride Z, Chao A, Gao J, Buchoff P, Wistow G, Hjelmeland LM. EST analysis of mouse retina and RPE/choroid cDNA libraries. Mol Vis 2004; 10:439-44.
55. Sharon-Friling R, Richardson J, Sperbeck S, Lee D, Rauchman M, Maas R, Swaroop A, Wistow G. Lens-specific gene recruitment of zeta-crystallin through Pax6, Nrl-Maf, and brain suppressor sites. Mol Cell Biol 1998; 18:2067-76.
56. Duhaiman AS, Rabbani N, AlJafari AA, Alhomida AS. Purification and characterization of zeta-crystallin from the camel lens. Biochem Biophys Res Commun 1995; 215:632-40.
57. Rao PV, Gonzalez P, Persson B, Jornvall H, Garland D, Zigler JS Jr. Guinea pig and bovine zeta-crystallins have distinct functional characteristics highlighting replacements in otherwise similar structures. Biochemistry 1997; 36:5353-62.
58. Wistow G, Bernstein SL, Wyatt MK, Behal A, Touchman JW, Bouffard G, Smith D, Peterson K. Expressed sequence tag analysis of adult human lens for the NEIBank Project: over 2000 non-redundant transcripts, novel genes and splice variants. Mol Vis 2002; 8:171-84.
59. Ogden AT, Nunes I, Ko K, Wu S, Hines CS, Wang AF, Hegde RS, Lang RA. GRIFIN, a novel lens-specific protein related to the galectin family. J Biol Chem 1998; 273:28889-96.
60. Wyatt K, White HE, Wang L, Bateman OA, Slingsby C, Orlova EV, Wistow G. Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens. Structure 2006; 14:1823-34.
61. Wyatt K, Gao C, Tsai JY, Fariss RN, Ray S, Wistow G. A role for lengsin, a recruited enzyme, in terminal differentiation in the vertebrate lens. J Biol Chem 2008; 283:6607-15.
62. Bloemendal H, Benedetti EL, Ramaekers F, Dunia I. The lens cytoskeleton. Intermediate-sized filaments, their biosynthesis and association with plasma membranes. Mol Biol Rep 1981; 7:167-8.
63. Clark JI, Matsushima H, David LL, Clark JM. Lens cytoskeleton and transparency: a model. Eye 1999; 13:417-24.
64. Bron AJ, Vrensen GF, Koretz J, Maraini G, Harding JJ. The ageing lens. Ophthalmologica 2000; 214:86-104.
65. Agre P. The aquaporin water channels. Proc Am Thorac Soc 2006; 3:5-13.
66. Lampi KJ, Ma Z, Shih M, Shearer TR, Smith JB, Smith DL, David LL. Sequence analysis of betaA3, betaB3, and betaA4 crystallins completes the identification of the major proteins in young human lens. J Biol Chem 1997; 272:2268-75.
67. Wilmarth PA, Taube JR, Riviere MA, Duncan MK, David LL. Proteomic and sequence analysis of chicken lens crystallins reveals alternate splicing and translational forms of beta B2 and beta A2 crystallins. Invest Ophthalmol Vis Sci 2004; 45:2705-15.
68. Bessant DA, Payne AM, Mitton KP, Wang QL, Swain PK, Plant C, Bird AC, Zack DJ, Swaroop A, Bhattacharya SS. A mutation in NRL is associated with autosomal dominant retinitis pigmentosa. Nat Genet 1999; 21:355-6.
69. Forrester JV, Dick DA, McMenamin PG, Lee WR. The Eye: Basic Sciences in Practice. W.B. Saunders; 2002.
70. Rattner A, Sun H, Nathans J. Molecular genetics of human retinal disease. Annu Rev Genet 1999; 33:89-131.
71. Wistow G. The NEIBank project for ocular genomics: data-mining gene expression in human and rodent eye tissues. Prog Retin Eye Res 2006; 25:43-77.
72. Szabo V, Kreienkamp HJ, Rosenberg T, Gal A. p.Gln200Glu, a putative constitutively active mutant of rod alpha-transducin (GNAT1) in autosomal dominant congenital stationary night blindness. Hum Mutat 2007; 28:741-2.
73. Rabinowitz YS, Dong L, Wistow G. Gene expression profile studies of human keratoconus cornea for NEIBank: a novel cornea-expressed gene and the absence of transcripts for aquaporin 5. Invest Ophthalmol Vis Sci 2005; 46:1239-46.
74. Danielson KG, Fazzio A, Cohen I, Cannizzaro LA, Eichstetter I, Iozzo RV. The human decorin gene: intron-exon organization, discovery of two alternatively spliced exons in the 5′ untranslated region, and mapping of the gene to chromosome 12q23. Genomics 1993; 15:146-60.
75. de Jong PT. Age-related macular degeneration. N Engl J Med 2006; 355:1474-85.
76. Gouras P, Kong J, Tsang SH. Retinal degeneration and RPE transplantation in Rpe65(-/-) mice. Invest Ophthalmol Vis Sci 2002; 43:3307-11.
77. Klaver CC, Kliffen M, van Duijn CM, Hofman A, Cruts M, Grobbee DE, van Broeckhoven C, de Jong PT. Genetic association of apolipoprotein E with age-related macular degeneration. Am J Hum Genet 1998; 63:200-6.
78. Tomarev SI, Wistow G, Raymond V, Dubois S, Malyukova I. Gene expression profile of the human trabecular meshwork: NEIBank sequence tag analysis. Invest Ophthalmol Vis Sci 2003; 44:2588-96.
79. Wistow G, Bernstein SL, Ray S, Wyatt MK, Behal A, Touchman JW, Bouffard G, Smith D, Peterson K. Expressed sequence tag analysis of adult human iris for the NEIBank Project: steroid-response factors and similarities with retinal pigment epithelium. Mol Vis 2002; 8:185-95.
80. Goh Y, Nakajima M, Azuma I, Hayaishi O. Prostaglandin D2 reduces intraocular pressure. Br J Ophthalmol 1988; 72:461-4.