Aging Cell (2007) 6, pp179–188 Doi: 10.1111/j.1474-9726.2007.00273.x BDlackwel PublrishingLatdmatic age-related changes in nuclear and genome copy number in the nematode Caenorhabditis elegans Tamara R. Golden,1 Kenneth B. Beckman,2 Andreia H. J. Lee,2 Nancy Dudek,1 Alan Hubbard,1,3 Enrique Samper1* and Simon Melov1 1Buck Institute for Age Research, 8001 Redwood Boulevard, Novato, CA 94945, USA 2Center for Genetics, Children’s Hospital Oakland Research Institute, Oakland, CA 94609, USA 3Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, 94720, USA Summary The nematode Caenorhabditis elegans has become one of the most widely used model systems for the study of aging, yet very little is known about how C. elegans age. The development of the worm, from egg to young adult has been completely mapped at the cellular level, but such detailed studies have not been extended throughout the adult lifespan. Numerous single gene mutations, drug treatments and environmental manipulations have been found to extend worm lifespan. To interpret the mechanism of action of such aging interventions, studies to charac- terize normal worm aging, similar to those used to study worm development are necessary. We have used 4′,6′- diamidino-2-phenylindole hydrochloride staining and quantitative polymerase chain reaction to investigate the integrity of nuclei and quantify the nuclear genome copy number of C. elegans with age. We report both systematic loss of nuclei or nuclear DNA, as well as dramatic age-related changes in nuclear genome copy number. These changes are delayed or attenuated in long-lived daf-2 mutants. We propose that these changes are important patho- biological characteristics of aging nematodes. Key words: aging; C. elegans; genome; nematode; oldest old, variability. Correspondence Simon Melov, Buck Institute for Age Research, 8001 Redwood Boulevard, Novato, CA 94945, USA. Tel.: 415-209-2268; fax: 415-209-2231; e-mail: smelov@buckinstitute.org *Present address: Centro Nacional de Biotecnologia, CSIC, Campus de la Universidad Autonoma de Madrid, Cantoblanco, E-28049 Madrid, Spain. Accepted for publication 26 November 2006 Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2·5, which does not permit commercial exploitation. © Blackwell Publishing Ltd/Anatomical Society of Great Britain and Ireland 2007 No claim to original US government works Introduction Aging is generally defined and studied as a population phenom- enon. Yet some aspects of aging, such as differences in individual lifespans, can only be understood through the study of individuals. An enigmatic aspect of aging is the heterogeneity in lifespan experienced by individuals of a synchronized population (Finch, 1990; Finch & Kirkwood, 2000). This heterogeneity, which can comprise up to 50% of the maximum lifespan of a species, is also observed in a clonal population of Caenorhabditis elegans, in which individuals are genetically identical and raised in an identical environment. The study of aging at the level of the individual organism is something for which C. elegans is well suited. In addition to being genetically identical, young adult worms are also essentially physically identical; studies of nematode development have mapped the cellular divisions and migrations leading to the final location of each of the 959 somatic nuclei in the young adult worm. However, such studies of worm morphology have not been applied to the remainder of the nematode lifespan. Only recently have studies begun to examine the structural integrity of older adult worms to investigate the pathobiology of worm aging (Garigan et al., 2002; Herndon et al., 2002). Herndon et al. (2002) found evidence of sarcopenia in aging worms, whereas neurons appeared to remain intact throughout the nematode lifespan. This study also observed a stochastic element to aging; various cells and tissues deteriorated at different rates between individuals, and no single pathology or series of pathogenic changes characterized aging in all individuals. Several mutations have been identified that extend the lifespan of C. elegans (Friedman & Johnson, 1988a,b; Johnson, 1990; Kenyon et al., 1993; Kimura et al., 1997; Lin et al., 1997; Ogg et al., 1997; Apfeld & Kenyon, 1999). The best-characterized single gene mutation that extends C. elegans lifespan is daf-2, which encodes an insulin-receptor homolog. Several mutations of daf-2 have been isolated, which fit into two broad classes, class 1 and class 2 mutations (Gems et al., 1998). In addition to other criteria, class 1 alleles have increased longevity, and lay a reduced number of unfertilized oocytes compared to wild-type worms, while class 2 alleles demonstrate these and additional traits, including reduced brood sizes, reduced adult motility, and production of late progeny (Gems et al., 1998). In this study we have examined both a class 1 (e1368) and a class 2 (e1370) allele of daf-2 for molecular heterogeneity over lifespan between individual nematodes. We have used three independent and complementary techniques to examine pathophysiology of aging and age-related 179