Quantification of Information Encoded by Gene Expression Levels During Lifespan Modulation Under Broad-range Dietary Restriction in <em>C. elegans</em>

Abstract

Sensory systems allow animals to detect, process, and respond to their environment. Food abundance is an environmental cue that has profound effects on animal physiology and behavior. Recently, we showed that modulation of longevity in the nematode Caenorhabditis elegans by food abundance is more complex than previously recognized. The responsiveness of the lifespan to changes in food level is determined by specific genes that act by controlling information processing within a neural circuit. Our framework combines genetic analysis, high-throughput quantitative imaging and information theory. Here, we describe how these techniques can be used to characterize any gene that has a physiological relevance to broad-range dietary restriction. Specifically, this workflow is designed to reveal how a gene of interest regulates lifespan under broad-range dietary restriction; then to establish how the expression of the gene varies with food level; and finally, to provide an unbiased quantification of the amount of information conveyed by gene expression about food abundance in the environment. When several genes are examined simultaneously under the context of a neural circuit, this workflow can uncover the coding strategy employed by the circuit.

A Multicellular Network Mechanism for Temperature-Robust Food Sensing

“…The L4-stage progeny of the F2 generation were then transferred to RNAi plates seeded with bacteria expressing double-stranded RNA (dsRNA) targeting the egg-5 gene, which is critical for egg-shell formation (47,48), for 24 hours at 20 °C. This short period of exposure to egg-5 RNAi is sufficient to prevent progeny production in the majority of animals throughout their reproductive period (18,19). This step is especially necessary for tph-1(-) and daf-7(-) mutants, as well as the double mutant of these genes, as they have an impaired egg-laying phenotype which results in the premature death of the adult worm from matricide.…”

“…This step is especially necessary for tph-1(-) and daf-7(-) mutants, as well as the double mutant of these genes, as they have an impaired egg-laying phenotype which results in the premature death of the adult worm from matricide. After the 24-hour egg-5 RNAi exposure the 1-day old adults were moved to NGM culture plates supplemented with the antibiotics streptomycin and carbenicillin (NSC) seeded with our baseline food level, antibiotic-inactivated OP50 at a concentration of 2x10 9 cells/ml (18,19), for 24 hours at 20 °C. All manipulations away from the baseline temperature and food level occurred on day 2 of adulthood ( Fig.…”

“…1B). Animals at each temperature were manually transferred to new NSC plates seeded with the appropriate food concentration according to the schedule laid out in Patel et al (19). Animals were scored for death at every transfer point and then daily after the final transfer point for each temperature.…”

“…For quantitative imaging, strains were cultured using a procedure similar to that in lifespan studies (18,19). Animals were initially raised on large NGM plates (10 cm diameter) for two generations.…”

“…The eggs were then deposited on to new large NGM plates seeded with live OP50 and left to hatch and grow at 20 °C till the animals reached the L4-stage. The daf-7(ok3125) mutation causes animals to constitutively enter a transient dauer arrest (18,19). For this reason, strains harboring daf-7(ok3125) were prepared 24 hours before strains without this mutation, to ensure sufficient numbers of animals exited dauer and reached the L4-stage.…”