Application of High-Throughput Technologies to Aging-Related Research

Handbook of Models for Human Aging

Volumn , Issue , 2006, Pages 109-119

  Kaeberlein, Matt ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33746336387     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-012369391-4/50011-4     Document Type: Chapter

References (68)

1. J.H. Bauer, S. Goupil, G.B. Garber and S.L. Helfand (2004) An accelerated assay for the identification of lifespan-extending interventions in Drosophila melanogaster. Proc Natl Acad Sci U S A 101 12980-12985.
2. D. Bellizzi, G. Rose, P. Cavalcante, G. Covello, S. Dato, F. De Rango, et al. (2005) A novel VNTR enhancer within the SIRT3 gene, a human homologue of SIR2, is associated with survival at oldest ages. Genomics 85 258-263.
3. M. Bluher, M.E. Patti, S. Gesta, B.B. Kahn and C.R. Kahn (2004) Intrinsic heterogeneity in adipose tissue of fatspecific insulin receptor knock-out mice is associated with differences in patterns of gene expression. J Biol Chem 279 31891-31901.
4. M.T. Borra, B.C. Smith and J.M. Denu (2005) Mechanism of human SIRT1 activation by resveratrol. J Biol Chem 280 17187-17195.
5. R.N. Butler, R. Sprott, H. Warner, J. Bland, R. Feuers, M. Forster, et al. (2004) Biomarkers of aging: From primitive organisms to humans. J Gerontol A Biol Sci Med Sci 59 B560-B567.
6. C. Chen, S. Dewaele, B. Braeckman, L. Desmyter, J. Verstraelen, G. Borgonie, et al. (2003) A high-throughput screening system for genes extending life-span. Exp Gerontol 38 1051-1063.
7. G.A. Churchill (2002) Fundamentals of experimental design for cDNA microarrays. Nat Genet 32 490-495. Suppl
8. A.B. Csoka, S.B. English, C.P. Simkevich, D.G. Ginzinger, A.J. Butte, G.P. Schatten, et al. (2004) Genome-scale expression profiling of Hutchinson-Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis. Aging Cell 3 235-243.
9. G. de Haan and R.W. Williams (2005) A genetic and genomic approach to identify longevity genes in mice. Mech Ageing Dev 126 133-138.
10. J.M. Dhahbi, H.J. Kim, P.L. Mote, R.J. Beaver and S.R. Spindler (2004) Temporal linkage between the phenotypic and genomic responses to caloric restriction. Proc Natl Acad Sci USA 101 5524-5529.
11. I. Dozmorov, A. Bartke and R.A. Miller (2001) Array-based expression analysis of mouse liver genes: Effect of age and of the longevity mutant Propldf. J Gerontol A Biol Sci Med Sci 56 B72-B80.
12. P. Fabrizio and V.D. Longo (2003) The chronological life span of Saccharomyces cerevisiae. Aging Cell 2 73-81.
13. P. Fabrizio, F. Pozza, S.D. Pletcher, C.M. Gendron and V.D. Longo (2001) Regulation of longevity and stress resistance by Sch9 in yeast. Science 292 288-290.
14. B.J. Geesaman, E. Benson, S.J. Brewster, L.M. Kunkel, H. Blanche, G. Thomas, et al. (2003) Haplotype-based identification of a microsomal transfer protein marker associated with the human lifespan. Proc. Natl Acad Sci USA 100 14115-14120.
15. M.S. Gill, A. Olsen, J.N. Sampayo and G.J. Lithgow (2003) An automated high-throughput assay for survival of the nematode Caenorhabditis elegans. Free Radic Biol Med 35 558-565.
16. J. Halaschek-Wiener, J.S. Khattra, S. McKay, A. Pouzyrev, J.M. Stott, G.S. Yang, et al. (2005) Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression. Genome Res. 15 603-615.
17. K.T. Howitz, K.J. Bitterman, H.Y. Cohen, D.W. Lamming, S. Lavu, J.G. Wood, et al. (2003) Small molecule activators of sirtuins extend Saccharomyces cerevisiae lifespan. Nature 425 191-196.
18. F.N. Hudson, M. Kaeberlein, N. Linford, D. Pritchard, R.P. Beyer and P.S. Rabinovitch (Eds) (2005) Microarray Analysis of Gene Expression Changes in Aging 6th ed. Academic Press
19. S. Imai, C.M. Armstrong, M. Kaeberlein and L. Guarente (2000) Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403 795-800.
20. S. Jarolim, J. Millen, G. Heeren, P. Laun, D.S. Goldfarb and M. Breitenbach (2004) A novel assay for replicative lifespan in Saccharomyces cerevisiae. FEMS Yeast Res 5 169-177.
21. S.J. Jones, D.L. Riddle, A.T. Pouzyrev, V.E. Velculescu, L. Hillier, S.R. Eddy, et al. (2001) Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. Genome Res 11 1346-1352.
22. M. Kaeberlein (2004) Aging-related research in the “-omics” age. Sci Aging Knowledge Environ pe39. 2004
23. M. Kaeberlein, T. McDonagh, B. Heltweg, J. Hixon, E.A. Westman, S. Caldwell, et al. (2005) Substrate specific activation of sirtuins by resveratrol. J Biol Chem 280 17038-17045.
24. M. Kaeberlein, M. McVey and L. Guarente (1999) The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev 13 2570-2580.
25. M. Kaeberlein, R.W. Powers, K.K. Steffen, E.A. Westman, D. Hu, N. Dang, et al. (2005) Regulation of yeast replication life span by TOR and Sch9 in response to nutrients. Science in press
26. S. Kammerer, L.L. Burns-Hamuro, Y. Ma, S.C. Hamon, J.M. Canaves, M.M. Shi, et al. (2003) Amino acid variant in the kinase binding domain of dual-specific A kinase-anchoring protein 2: A disease susceptibility polymorphism. Proc Natl Acad Sci USA 100 4066-4071.
27. P. Kapahi, B.M. Zid, T. Harper, D. Koslover, V. Sapin and S. Benzer (2004) Regulation of lifespan in Drosophila by modulation of genes in the TOR signaling pathway. Curr Biol 14 885-890.
28. T. Kayo, D.B. Allison, R. Weindruch and T.A. Prolla (2001) Influences of aging and caloric restriction on the transcriptional profile of skeletal muscle from rhesus monkeys. Proc Natl Acad Sci USA 98 5093-5098.
29. M.K. Kerr and G.A. Churchill (2001) Statistical design and the analysis of gene expression microarray data. Genet Res 77 123-128.
30. M.K. Kerr, M. Martin and G.A. Churchill (2000) Analysis of variance for gene expression microarray data. J Comput Biol 7 819-837.
31. K.J. Kyng, A. May, S. Kolvraa and V.A. Bohr (2003) Gene expression profiling in Werner syndrome closely resembles that of normal aging. Proc Natl Acad Sci USA 100 12259-12264.
32. G.N. Landis, D. Abdueva, D. Skvortsov, J. Yang, B.E. Rabin, J. Carrick, S. Tavare and J. Tower (2004) Similar gene expression patterns characterize aging and oxidative stress in Drosophila melanogaster. Proc Natl Acad Sci USA 101 7663-7668.
33. J. Landry, A. Sutton, S.T. Tafrov, R.C. Heller, J. Stebbins, L. Pillus and R. Sternglanz (2000) The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc Natl Acad Sci USA 97 5807-5811.
34. C.K. Lee, R.G. Klopp, R. Weindruch and T.A. Prolla (1999) Gene expression profile of aging and its retardation by caloric restriction. Science 285 1390-1393.
35. M.L. Lee and G.A. Whitmore (2002) Power and sample size for DNA microarray studies. Stat Med 21 3543-3570.
36. S.S. Lee, R.Y. Lee, A.G. Fraser, R.S. Kamath, J. Ahringer and G. Ruvkun (2003) A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity. Nat Genet 33 40-48.
37. T. Lu, Y. Pan, S.Y. Kao, C. Li, I. Kohane, J. Chan and B.A. Yankner (2004) Gene regulation and DNA damage in the ageing human brain. Nature 429 883-891.
38. W. Mair, P. Goymer, S.D. Pletcher and L. Partridge (2003) Demography of dietary restriction and death in Drosophila. Science 301 1731-1733.
39. S.A. McCarroll, C.T. Murphy, S. Zou, S.D. Pletcher, C.S. Chin, Y.N. Jan, et al. (2004) Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nat Genet 36 197-204.
40. J. McElwee, K. Bubb and J.H. Thomas (2003) Transcriptional outputs of the Caenorhabditis elegans forkhead protein DAF-16. Aging Cell 2 111-121.
41. S. Melov and A. Hubbard (2004) Microarrays as a tool to investigate the biology of aging: A retrospective and a look to the future. Sci Aging Knowledge Environ re7. 2004
42. R.A. Miller, Y. Chang, A.T. Galecki, K. Al-Regaiey, J.J. Kopchick and A. Bartke (2002) Gene expression patterns in calorically restricted mice: Partial overlap with long-lived mutant mice. Mol Endocrinol 16 2657-2666.
43. R.A. Miller, A. Galecki and R.J. Shmookler-Reis (2001) Interpretation, design, and analysis of gene array expression experiments. J Gerontol A Biol Sci Med Sci 56 B52-B57.
44. C.T. Murphy, S.A. McCarroll, C.I. Bargmann, A. Fraser, R.S. Kamath, J. Ahringer, et al. (2003) Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans. Nature 424 277-283.
45. P.N. Nair, T. Golden and S. Melov (2003) Microarray workshop on aging. Mech Ageing Dev 124 133-138.
46. S.K. Park and T.A. Prolla (2005) Gene expression profiling studies of aging in cardiac and skeletal muscles. Cardiovasc Res 66 205-212.
47. S.K. Park and T.A. Prolla (2005) Lessons learned from gene expression profile studies of aging and caloric restriction. Ageing Res Rev 4 55-65.
48. S.D. Pletcher, S.J. Macdonald, R. Marguerie, U. Certa, S.C. Stearns, D.B. Goldstein and L. Partridge (2002) Genome-wide transcript profiles in aging and calorically restricted Drosophila melanogaster. Curr Biol 12 712-723.
49. M.C. Popesco, A. Frostholm, K. Rejniak and A. Rotter (2004) Digital transcriptome analysis in the aging cerebellum. Ann N Y Acad Sci 1019 58-63.
50. T.A. Prolla (2005) Multiple roads to the aging phenotype: Insights from the molecular dissection of progerias through DNA microarray analysis. Mech Ageing Dev 126 461-465.
51. A.A. Puca, M.J. Daly, S.J. Brewster, T.C. Matise, J. Barrett, M. Shea-Drinkwater, et al. (2001) A genome-wide scan for linkage to human exceptional longevity identifies a locus on chromosome 4. Proc Natl Acad Sci USA 98 10505-10508.
52. G.E. Rodwell, R. Sonu, J.M. Zahn, J. Lund, J. Wilhelmy, L. Wang, et al. (2004) A transcriptional profile of aging in the human kidney. PLoS Biol 2 e427.
53. B. Rogina and S.L. Helfand (2004) Sir2 mediates longevity in the fly through a pathway related to calorie restriction. Proc Natl Acad Sci USA 101 15998-16003.
54. J.F. Rual, J. Ceron, J. Koreth, T. Hao, A.S. Nicot, T. Hirozane-Kishikawa, et al. (2004) Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res 14 2162-2168.
55. C. Schoneich (2003) Proteomics in gerontological research. Exp Gerontol 38 473-481.
56. K.G. Tanner, J. Landry, R. Sternglanz and J.M. Denu (2000) Silent information regulator 2 family of NAD-dependent histone/protein deacetylases generates a unique product, 1-O-acetyl-ADP-ribose. Proc Natl Acad Sci USA 97 14178-14182.
57. H.A. Tissenbaum and L. Guarente (2001) Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans. Nature 410 227-230.
58. T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke and S.R. Spindler (2004) Additive regulation of hepatic gene expression by dwarfism and caloric restriction. Physiol Genomics 17 307-315.
59. D. van Heemst, M. Beekman, S.P. Mooijaart, B.T. Heijmans, B.W. Brandt, B.J. Zwaan, et al. (2005) Reduced insulin/IGF-1 signalling and human longevity. Aging Cell 4 79-85.
60. V.E. Velculescu, L. Zhang, B. Vogelstein and K.W. Kinzler (1995) Serial analysis of gene expression. Science 270 484-487.
61. T. Vellai, K. Takacs-Vellai, Y. Zhang, A.L. Kovacs, L. Orosz and F. Muller (2003) Genetics: Influence of TOR kinase on lifespan in C. elegans. Nature 426 620.
62. R. Weindruch, T. Kayo, C.K. Lee and T.A. Prolla (2001) Microarray profiling of gene expression in aging and its alteration by caloric restriction in mice. J Nutr 131 918S-923S.
63. S. Welle, A. Brooks and C.A. Thornton (2001) Senescence-related changes in gene expression in muscle: Similarities and differences between mice and men. Physiol Genomics 5 67-73.
64. S. Welle, A.I. Brooks, J.M. Delehanty, N. Needler, K. Bhatt, B. Shah and C.A. Thornton (2004) Skeletal muscle gene expression profiles in 20–29 year old and 65–71 year old women. Exp Gerontol 39 369-377.
65. S. Welle, A.I. Brooks, J.M. Delehanty, N. Needler and C.A. Thornton (2003) Gene expression profile of aging in human muscle. Physiol Genomics 14 149-159.
66. J.G. Wood, B. Rogina, S. Lavu, K. Howitz, S.L. Helfand, M. Tatar and D. Sinclair (2004) Sirtuin activators mimic caloric restriction and delay ageing in metazoans. Nature 430 686-689.
67. S. Yoshida, B.M. Yashar, S. Hiriyanna and A. Swaroop (2002) Microarray analysis of gene expression in the aging human retina. Invest Ophthalmol Vis Sci 43 2554-2560.
68. S. Zou, S. Meadows, L. Sharp, L.Y. Jan and Y.N. Jan (2000) Genome-wide study of aging and oxidative stress response in Drosophila melanogaster. Proc Natl Acad Sci USA 97 13726-13731.