RatDNA: DATABASE ON MICROARRAY STUDIES OF RATS BEARING GENES ASSOCIATED WITH AGE-RELATED DISEASES
Abstract
The purpose of the RatDNA database is the development of experimental methods for basic molecular studies of human age-related diseases in rats involving microarray tests of gene expression. Despite the obvious correlation between life expectancy and heredity and numerous biomedical studies on aging, little is known about genetic factors determining aging processes. People do not die of «healthy» aging: at any age conditions whose probability increases with age become the cause of their death. Age-related macular degeneration (AMD) becomes the main cause of vision problems and sight loss in people aged above 50. Structural and functional changes in the retina characteristic of aging are similar to those observed at early stages of AMD. They underlie the pathogenesis of this disease, but not always lead to its development. RatDNA database contains information on genes associated with age-related diseases, in particular AMD, and experimental data about their expression in tissues of a model rat strain. The database is available at http://pixie.bionet.nsc.ru/ratdna/rat/index.php.
About the Authors
O. S. Kozhevnikova
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
M. K. Martyschenko
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
M. A. Genaev
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
E. E. Korbolina
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
N. A. Muraleva
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
N. G. Kolosova
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Novosibirsk National Research State University, Novosibirsk, Russia
Russian Federation
Russian Federation
Y. L. Orlov
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Novosibirsk National Research State University, Novosibirsk, Russia
Russian Federation
Russian Federation
References
1. Веллинг Л., Томсон Л. Разработка Web-приложений с помощью PHP и MySQL. 3-е изд. М.: Издат. дом «Вильямс», 2008. 880 с.
2. Жданкина А.А., Фурсова А.Ж., Логвинов С.В., Колосова Н.Г. Клинико-морфологические особенности хориоретиальной дегенерации у преждевременно стареющих крыс линии OXYS // Бюл. эксперим. биол. и медицины. 2008. V. 146. № 10. P. 435–438.
3. Колосова Н., Лебедев П., Фурсова А. и др. Преждевременно стареющие крысы OXYS как модель сенильной катаракты человека // Усп. геронтологии. 2003. Т. 12. С. 143–148.
4. Либман Е.С., Толмачев Р.А., Шахова Е.В. Эпидемиологическая характеристика инвалидности вследствие основных форм макулопатий // Матер. II Всерос. семинара «Макула-2006» / Под ред. Ю.А. Иванишко, Ростов-на-Дону, 2006. С. 15–22.
5. Blagosklonny M.V. Why human lifespan is rapidly increasing: solving «longevity riddle» with «revealed-slow-aging » hypothesis // Aging (Albany NY). 2010. V. 2. No. 4. P. 177–182.
6. Bobko A., Sergeeva S., Bagryanskaya E. et al. 19F NMR measurements of NO production in hypertensive ISIAH and OXYS rats // Biochem. Biophys. Res. Commun. 2005. V. 330. No. 2. P. 367–370.
7. Booij J.C., van Soest S., Swagemakers S.M. et al. Functional annotation of the human retinal pigment epithelium transcriptome // BMC Genomics. 2009. V. 20. No. 10. 164.
8. Christensen K., Doblhammer G., Rau R., Vaupel J.W. Ageing populations: the challenges ahead // Lancet. 2009. V. 374. No. 9696. P. 1196–1208.
9. Ehrlich R., Kheradiya N.S., Winston et al. Age-related ocular vascular changes // Graefes Arch. Clin. Exp. Ophthalmol. 2009. V. 247. No. 5. P. 583–591.
10. Gibson G. Microarray analysis: genome-scale hypothesis scanning // PLoS Biol. 2003. V. 1. No. 1. E15.
11. Ishikawa K., Yoshida S., Kadota K. et al. Gene expression profi le of hyperoxic and hypoxic retinas in a mouse model of oxygen-induced retinopathy // Invest. Ophthalmol. Vis. Sci. 2010. V. 51. No. 8. P. 4307–4319.
12. Kalathur R.K., Gagniere N., Berthommier G. et al. RETINOBASE: a Web database, data mining and analysis platform for gene expression data on retina // BMC Genomics. 2008. V. 9. 208.
13. Katagiri F., Glazebrook J. Pattern discovery in expression profi ling data // Curr. Protoc. Mol. Biol. 2009. Chapter 22:Unit 22.5.
14. Korbolina E.E., Kozhevnikova O.S., Stefanova N.A., Kolosova N.G. Quantitative trait loci on chromosome 1 for cataract and AMD-like retinopathy in senescence-accelerated OXYS rats // Aging (Albany NY). 2012. V. 4. No. 1. P. 49–59.
15. Kurji K.H., Cui J.Z., Lin T. et al. Microarray analysis identifies changes in infl ammatory gene expression in response to amyloid-beta stimulation of cultured human retinal pigment epithelial cells // Invest. Ophthalmol. Vis. Sci. 2010. V. 51. No. 2. P. 1151–1163.
16. Maier A.B., Westendorp R.G. Relation between replicative senescence of human fi broblasts and life history characteristics // Ageing Res Rev. 2009. V. 8. No. 3. P. 237–243.
17. Markovets A.M., Fursova A.Z., Kolosova N.G. Therapeutic action of the mitochondria-targeted antioxidant SkQ1 on retinopathy in OXYS rats linked with improvement of VEGF and PEDF gene expression // PLoS One. 2011. V. 6. No. 7. e21682.
18. Muraleva N.A., Sadovoĭ M.A., Kolosova N.G. Effect of alendronate on bone tissue status of senescence-accelerated OXYS rats // Adv. Gerontol. 2011. V. 24. No. 1. P. 143–146.
19. Muraleva N.A., Sadovoĭ M.A., Kolosova N.G. Development of osteoporosis in prematurely aging OXYS rats // Adv. Gerontol. 2010. V. 23. Nо. 2. P. 233–242.
20. Obukhova L.A., Skulachev V.P., Kolosova N.G. Mitochondriatargeted antioxidant SkQ1 inhibits age-dependent involution of the thymus in normal and senescence-prone rats // Aging (Albany NY). 2009. V. 1. Nо. 4. P. 389–401.
21. Sander M., Avlund K., Lauritzen M. et al. Aging-from molecules to populations // Mech. Ageing Dev. 2008. V. 129. No. 10. P. 614–623.
22. Shevelev O.B., Rykova V.I., Fedoseeva L.A. et al. Expression of Ext1, Ext2, and heparanase genes in brain of senescence-accelerated OXYS rats in early ontogenesis and during development of neurodegenerative changes // Biochemistry (Mosc). 2012. V. 77. No. 1. P. 56–61.
23. Smith C.P., Steinle J.J. Changes in growth factor expression in normal aging of the rat retina // Exp. Eye Res. 2007. V. 85. No. 6. P. 817–824.
24. Takeda T. Senescence-accelerated mouse (SAM) with special references to neurodegeneration models, SAMP8 and SAMP10 mice // Neurochem. Res. 2009. V. 34. No. 4. P. 639–659.
25. Vaupel J.W. Biodemography of human ageing // Nature. 2010. V. 464. No. 7288. P. 536–542.
26. Yang L., Nie Y.H., Zhou L.H. et al. Microarray profi les on age-related genes in the earlier postnatal rat visual cortex // Chin. Med. J. (Engl). 2011. V. 124. No. 10. P. 1545–1550.
27. Yoshida S., Yashar B.M., Hiriyanna S., Swaroop A. Microarray analysis of gene expression in the aging human retina // Invest. Ophthalmol. Vis. Sci. 2002. V. 43. No. 8. P. 2554–2560.
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