Impact of Light Schedules and Model Parameters on the Circadian Outcomes of Individuals

Key differences exist between individuals in terms of certain circadian-related parameters, such as intrinsic period and sensitivity to light. These variations can differentially impact circadian timing, leading to challenges in accurately implementing time-sensitive interventions. In this work, we parse out these effects by investigating the impact of parameters from a macroscopic model of human circadian rhythms on phase and amplitude outputs. Using in silico light data designed to mimic commonly studied schedules, we assess the impact of parameter variations on model outputs to gain insight into the different effects of these schedules. We show that parameter sensitivity is heavily modulated by the lighting routine that a person follows, with darkness and shift work schedules being the most sensitive. We develop a framework to measure overall sensitivity levels of the given light schedule and furthermore decompose the overall sensitivity into individual parameter contributions. Finally, we measure the ability of the model to extract parameters given light schedules with noise and show that key parameters like the circadian period can typically be recovered given known light history. This can inform future work on determining the key parameters to consider when personalizing a model and the lighting protocols to use when assessing interindividual variability.

Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation

Background

One mechanism to account for robustness against gene knockouts or knockdowns is through buffering by gene duplicates, but the extent and general correlates of this process in organisms is still a matter of debate. To reveal general trends of this process, we provide a comprehensive comparison of gene essentiality, duplication and buffering by duplicates across seven bacteria (Mycoplasma genitalium, Bacillus subtilis, Helicobacter pylori, Haemophilus influenzae, Mycobacterium tuberculosis, Pseudomonas aeruginosa, Escherichia coli), and four eukaryotes (Saccharomyces cerevisiae (yeast), Caenorhabditis elegans (worm), Drosophila melanogaster (fly), Mus musculus (mouse)).

Results

In nine of the eleven organisms, duplicates significantly increase chances of survival upon gene deletion (P-value ≤ 0.05), but only by up to 13%. Given that duplicates make up to 80% of eukaryotic genomes, the small contribution is surprising and points to dominant roles of other buffering processes, such as alternative metabolic pathways. The buffering capacity of duplicates appears to be independent of the degree of gene essentiality and tends to be higher for genes with high expression levels. For example, buffering capacity increases to 23% amongst highly expressed genes in E. coli. Sequence similarity and the number of duplicates per gene are weak predictors of the duplicate's buffering capacity. In a case study we show that buffering gene duplicates in yeast and worm are somewhat more similar in their functions than non-buffering duplicates and have increased transcriptional and translational activity.

Conclusion

In sum, the extent of gene essentiality and buffering by duplicates is not conserved across organisms and does not correlate with the organisms' apparent complexity. This heterogeneity goes beyond what would be expected from differences in experimental approaches alone. Buffering by duplicates contributes to robustness in several organisms, but to a small extent – and the relatively large amount of buffering by duplicates observed in yeast and worm may be largely specific to these organisms. Thus, the only common factor of buffering by duplicates between different organisms may be the by-product of duplicate retention due to demands of high dosage.