Login to MyKarger

New to MyKarger? Click here to sign up.



Login with Facebook

Forgot your password?

Authors, Editors, Reviewers

For Manuscript Submission, Check or Review Login please go to Submission Websites List.

Submission Websites List

Institutional Login
(Shibboleth or Open Athens)

For the academic login, please select your country in the dropdown list. You will be redirected to verify your credentials.

Aging and Health - A Systems Biology Perspective

Editor(s): Yashin A.I. (Durham, N.C.) 
Jazwinski S.M. (New Orleans, La.) 
Cover
Yashin AI, Jazwinski SM (eds): Aging and Health - A Systems Biology Perspective. Interdiscipl Top Gerontol. Basel, Karger, 2015, vol 40, pp 18-34
(DOI:10.1159/000364925)

Applications to Aging Networks

Wimble C. · Witten T.M.

Author affiliations

Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Va., USA

Corresponding Author

Tarynn M. Witten

Center for the Study of Biological Complexity, Virginia Commonwealth University

PO Box 842030, 1000 West Cary Street

Richmond, VA 23284 (USA)

E-Mail tmwitten@vcu.edu

Do you have an account?

Login Information





Contact Information










I have read the Karger Terms and Conditions and agree.



Abstract

This chapter will introduce a few additional network concepts, and then it will focus on the application of the material in the previous chapter to the study of systems biology of aging. In particular, we will examine how the material can be used to study aging networks in two sample species: Caenorhabditis elegans and Saccharomyces cerevisiae.

© 2015 S. Karger AG, Basel


References

  1. Witten TM: (M,R)-systems, (P,M,C)-nets, hierarchical decay and biological aging: reminiscences of Robert Rosen. Chem Biodivers 2007;4:2332-2344.
  2. Witten TM, Bonchev DG: Predicting aging/longevity-related genes in the nematode C. elegans. Chem Biodivers 2007;4:2639-2655.
  3. Breitenbach M, Jazwinski SM, Laun P: Aging research in yeast. Springer Cell Cycle 2012;10:1385-1396.
    External Resources
  4. Longo VD, Shadel GS, Kaeberlein M, Kennedy B: Replicative and chronological aging in Saccharomyces cerevisiae. Cell Metab 2012;16:18-31.
  5. Steffen KK, Kennedy BK, Kaeberlein M: Measuring replicative life span in the budding yeast. J Vis Exp 2009;28:1209.
  6. Anderson RM, Bitterman KJ, Wood JG, Medvedik O, Sinclair DA: Nicotinamide and PNC1 govern lifespan extension by calorie restriction in Saccharomyces cerevisiae. Nature 2003;423:181-185.
  7. The Basic Biology of Aging. http://www.uwaging.org/genesdb/.
  8. Burtner CR, Murakami CJ, Olsen B, Kennedy BK, Kaeberlein M: A genomic analysis of chronological longevity factors in budding yeast. Cell Cycle 2011;10:1385-1396.
  9. Defossez PA, Prusty R, Kaeberlein M, Lin SJ, Ferrigno P, et al: Elimination of replication block protein Fob1 extends the life span of yeast mother cells. Mol Cell 1999;3:447-455.
  10. Delaney J, Murakami CJ, Olsen B, Kennedy BK, Kaeberlein M: Quantitative evidence for early life fitness defects from 32 longevity-associated alleles in yeast. Cell Cycle 2011;10:156-165.
  11. D'Mello NP, Childress AM, Franklin DS, Kale SP, Pinswasdi C, et al: Cloning and characterization of LAG1, a longevity-assurance gene in yeast. J Biol Chem 1994;269:15451-15459.
    External Resources
  12. Fabrizio P, Pozza F, Pletcher SD, Gendron CM, Longo VD: Regulation of longevity and stress resistance by Sch9 in yeast. Science 2001;292:288-290.
  13. Fabrizio P, Liou LL, Moy VN, Diaspro A, Valentine J, et al: SOD2 functions downstream of Sch9 to extend longevity in yeast. Genetics 2003;163:35-46.
    External Resources
  14. Gourlay CW, Carpp LN, Timpson P, Winder SJ, Ayscough KR: A role for the actin cytoskeleton in cell death and aging in yeast. J Cell Biol 2004;164:803-809.
  15. Hoopes LL, Budd M, Choe W, Weitao T, Campbell JL: Mutations in DNA replication genes reduce yeast life span. Mol Cell Biol 2002;22:4136-4146.
  16. Institute of bioinformatics and Systems biology. http://www.helmholtz-muenchen.de/en/ibis.
  17. Kaeberlein M, McVey M, Guarente L: The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev 1999;13:2570-2580.
  18. Kaeberlein M, Kirkland KT, Fields S, Kennedy BK: Genes determining yeast replicative life span in a long-lived genetic background. Mech Ageing Dev 2005;126:491-504.
  19. Kennedy BK, Austriaco NR, Zhang J, Guarente L: Mutation in the silencing gene SIR4 can delay aging in S. cerevisiae. Cell 1995;80:485-496.
  20. Kim S, Benguria A, Lai CY, Jazwinski SM: Modulation of life-span by histone deacetylase genes in Saccharomyces cerevisiae. Mol Biol Cell 1999;10:3125-3136.
  21. Kruegel U, Robison B, Dangel T, et al: Elevated proteasome capacity extends replicative lifespan in Saccharomyces cerevisiae. PLoS Genet 2011;7:1-16.
  22. Lin SJ, Defossez PA, Guarente L: Requirement of NAD and SIR2 for life-span extension by calorie restriction in Saccharomyces cerevisiae. Science 2000;289:2126-2128.
  23. Lu JY, Lin YY, Sheu JC, et al: Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction. Cell 2011;146:968-979.
  24. Managbanag JR, Witten TM, Bonchev DG, Fox LA, Tsuchiya M, Kennedy BK, Kaeberlein M: Shortest-path network analysis is a useful approach towards identifying genetic determinants of longevity. PLoS One 2008;3:e3802.
  25. Murakami CJ, Burtner CR, Kennedy BK, Kaeberlein M: A method for high-throughput quantitative analysis of yeast chronological life span. J Gerontol Biol Sci Med Sci 2008;63:113-121.
  26. Roy N, Runge KW: Two paralogs involved in transcriptional silencing that antagonistically control yeast life span. Curr Biol 2000;1:111-114.
  27. Scheckhuber CQ, Erjavec N, Tinazli A, Hamann A, et al: Reducing mitochondrial fission results in increased life span and fitness of two fungal ageing models. Nat Cell Biol 2007;9:99-105.
  28. Sinclair DA, Mills K, Guarente L: Accelerated aging and nucleolar fragmentation in yeast sgs1 mutants. Science 1997;277:1313-1316.
  29. Sinclair DA, Guarente L: Extrachromosomal rDNA circles - a cause of aging in yeast. Cell 1997;91:1033-1042.
  30. Smith DL, McClure JM, Matecic M, Smith JS: Calorie restriction extends the chronological lifespan of Saccharomyces cerevisiae independently of the Sirtuins. Aging Cell 2007;6:649-662.
  31. Smith ED, Tsuchiya M, Fox L, et al: Quantitative evidence for conserved longevity pathways between divergent eukaryotic species. Gene Res 2008;18:564-570.
  32. Steffen KK, MacKay VL, Kerr EO, Tsuchiya M, et al: Yeast life span extension by depletion of 60s ribosomal subunits is mediated by Gcn4. Cell 2008;133:292-302.
  33. Sun J, Kale SP, Childress AM, Pinswasdi C, Jazwinski SM: Divergent roles of RAS1 and RAS2 in yeast longevity. J Biol Chem 1994;269:18638-18645.
    External Resources
  34. Tsuchiya M, Dang N, Kerr EO, Hu D, et al: Sirtuin-independent effects of nicotinamide on lifespan extension from calorie restriction in yeast. Aging Cell 2006;5:505-514.
  35. AmiGO: http://amigo.geneontology.org/cgi-bin/amigo/go.cgi.
  36. Kaeberlein M, Powers RW, Steffen KK, Westman EA, Hu D, et al: Regulation of yeast replicative life span by TOR and Sch9 in response to nutrients. Science 2005;310:1193-1196.
  37. SGD, The Saccharomyces Genome Database. http://www.yeastgenome.org/.
  38. Witten TM: Reliability theoretic methods and aging: critical elements, hierarchies, and longevity - interpreting survival curves; in Woodhead A, Blackett A, Setlow R (eds): The Molecular Biology of Aging. New York, Plenum Press, 1985a.
  39. Witten TM: A return to time, cells, systems and aging. III. Critical elements, hierarchies, and Gompertzian dynamics. Mech Ageing Dev 1985;32:141-177.
  40. Agoston V, Csermely P, Pongor S: Multiple, weak hits confuse complex systems. Phys Rev E Stat Nonlin Soft Matter Phys 2005;71:051909.
  41. Basset DS, Bullmore E: Small-world brain networks. Neuroscientist 2006;12:512-523.
  42. Chan KP, Zhen D, Hui PM: Effects of aging and links removal on epidemic dynamics in scale-free networks. Int J Modern Phys B 2004;18:2534.
    External Resources
  43. Csermely P: Strong links are important but weak links stabilize them. Trends Biochem Sci 2004;29:331-334.
  44. Csermely P: Creative elements: network-based predictions of active centres in proteins and cellular and social networks. Trends Biochem Sci 2008;33:569-576.
  45. Gallos LK, Makse HA, Sigman M: A small world of weak ties provides optimal global integration of self-similar modules in functional brain networks. Proc Natl Acad Sci USA 2012;109:2825-2830.
  46. Gavrilov LA, Gavrilova NS: Models of systems failure in aging; in Conn PM (ed): Handbook of Models for Human Aging. Burlington, Elsevier Academic Press, 2006, pp 45-68.
    External Resources
  47. Kriete A: Robustness and aging - a systems-level perspective. Biosystems 2013;112:37-48.
  48. Lemke N, Heredia F, Barcellos CK, Dos Reis AN, Mombach JC: Essentiality and damage in metabolic networks. Bioinformatics 2004;20:115-119.
  49. Saavedra S, Reed-Tsochas F, Uzzi B: Asymmetric disassembly and robustness in declining networks. Proc Natl Acad Sci USA 2008;105:16466-16471.
  50. Huang X, Gao J, Buldyrev SV, Havlin S, Stanley HD: Robustness of interdependent networks under targeted attack. 2010. http://arxiv.org/abs/1010.5829v1.

Article / Publication Details

First-Page Preview
Abstract of  

Published online: October 13, 2014
Cover Date: 2015

Number of Print Pages: 17
Number of Figures: 11
Number of Tables: 3

ISBN: 978-3-318-02729-7 (Print)
eISBN: 978-3-318-02730-3 (Online)