Decreased Indy activity extends lifespan in D. melanogaster without significant reduction in fecundity, metabolic rate, or locomotion. To understand the underlying mechanisms leading to lifespan extension in this mutant strain, we compared the genome-wide gene expression changes in the head and thorax of adult Indy mutant with control flies over the course of their lifespan. A signature enrichment analysis of metabolic and signaling pathways revealed that expression levels of genes in the oxidative phosphorylation pathway are significantly lower in Indy starting at day 20. We confirmed experimentally that complexes I and III of the electron transport chain have lower enzyme activity in Indy longlived flies by Day 20 and predicted that reactive oxygen species (ROS) production in mitochondria could be reduced. Consistently, we found that both ROS production and protein damage are reduced in Indy with respect to control. However, we did not detect significant differences in total ATP, a phenotype that could be explained by our finding of a higher mitochondrial density in Indy mutants. Thus, one potential mechanism by which Indy mutants extend life span could be through an alteration in mitochondrial physiology leading to an increased efficiency in the ATP/ROS ratio.electron transport chain ͉ mitochondria ͉ oxidative phosphorylation ͉ Drosophila ͉ aging U nderstanding the biological and physiological underpinnings of aging and the development of interventions to ameliorate its deleterious effects has been the subject of much interest. Identification and examination of specific genetic alterations that extend life span is one common approach for uncovering mechanisms underlying normal aging. A number of single gene alterations that extend healthy life span in model organisms have been isolated, but delineating the specific physiological changes responsible for their life span extending effects has been challenging (1).High throughput genomic analyses have emerged as an unbiased method for providing information of the physiological changes involved in mediating complex biological phenomena such as longevity. In particular, whole genome transcriptional studies (microarrays) to identify specific genes or physiological systems important in longevity determination have been successfully used in both nematodes and flies. Microarray studies of daf-2 long-lived nematodes identified specific genes that were then functionally verified as causally related to the daf-2 life span extension (2).Restricting the examination of microarrays to only those genes identically shared between different interventions may limit the ability to detect some of the physiologically relevant changes important in complex biological phenomena such as life span extension. As more data becomes available from high throughput gene expression studies, analyses have shifted from a gene centric model to a pathway centric approach. It has been realized that reproducibility of experiments, and comparison across interventions that should have resulted in simil...