Day-night and seasonal variation of human gene expression across tissues

Investigation of seasonality of human spontaneous physical activity and energy expenditure in respiratory chamber in Phoenix, Arizona

OBJECTIVE

The existence of seasonal changes in energy metabolism is uncertain. We investigated the relationship between the seasons and spontaneous physical activity (SPA), energy expenditure (EE), and other components measured in a respiratory chamber.

METHODS

Between 1985-2005, 671 healthy adults (aged 28.8 ± 7.1 years; 403 men) in Phoenix, Arizona had a 24-hour stay in the respiratory chamber equipped with radar sensors; SPA (expressed as a percentage over the time interval), the energy cost of SPA, EE, and respiratory exchange ratio (RER) were measured.

RESULTS

In models adjusted for known covariates, SPA (%) was lower during summer (7.2 ± 2.9, p = 0.0002), spring (7.5 ± 2.9, p = 0.025), and fall (7.6 ± 3, p = 0.038) compared to winter (8.3 ± 3.5, reference). Conversely, energy cost of SPA (kcal/h/%) was higher during summer (2.18 ± 0.83, p = 0.0008), spring (2.186 ± 0.83, p = 0.017), and fall (2.146 ± 0.75, p = 0.038) compared to winter (2.006 ± 0.76). Protein (292 ± 117 kcal/day, β = -21.2, p = 0.08) oxidation rates was lower in the summer compared to winter. Carbohydrate and lipid oxidation rates (kcal/day) did not differ across seasons. RER and 24-h EE did not differ by season.

CONCLUSION

SPA, representing fidgeting-like behavior in the chamber, demonstrated a winter peak and summer nadir in humans living in a desert climate. These findings indicate that the physiological propensity for movement may be affected by seasonal factors.

CLINICAL TRIAL REGISTRATION

ClinicalTrials.gov identifiers: NCT00340132, NCT00342732.

Seasonality of brain function: role in psychiatric disorders

Seasonality patterns are reported in various psychiatric disorders. The current paper summarizes findings on brain adaptations associated with seasonal changes, factors that contribute to individual differences and their implications for psychiatric disorders. Changes in circadian rhythms are likely to prominently mediate these seasonal effects since light strongly entrains the internal clock modifying brain function. Inability of circadian rhythms to accommodate to seasonal changes might increase the risk for mood and behavior problems as well as worse clinical outcomes in psychiatric disorders. Understanding the mechanisms that account for inter-individual variations in seasonality is relevant to the development of individualized prevention and treatment for psychiatric disorders. Despite promising findings, seasonal effects are still understudied and only controlled as a covariate in most brain research. Rigorous neuroimaging studies with thoughtful experimental designs, powered sample sizes and high temporal resolution alongside deep characterization of the environment are needed to better understand the seasonal adaptions of the human brain as a function of age, sex, and geographic latitude and to investigate the mechanisms underlying the alterations in seasonal adaptation in psychiatric disorders.

Assessing Genetic Diversity and Searching for Selection Signatures by Comparison between the Indigenous Livni and Duroc Breeds in Local Livestock of the Central Region of Russia

Indigenous pig breeds are mainly associated with the adaptive capacity that is necessary to respond adequately to climate change, food security, and livelihood needs, and natural resources conservation. Livni pigs are an indigenous fat-type breed farmed in a single farm in the Orel region and located in the Central European part of the Russian Federation. To determine the genomic regions and genes that are affected by artificial selection, we conducted the comparative study of two pig breeds with different breeding histories and breeding objectives, i.e., the native fat-type Livni and meat-type Duroc breeds using the Porcine GGP HD BeadChip, which contains ~80,000 SNPs. To check the Livni pigs for possible admixture, the Landrace and the Large White breeds were included into the study of genetic diversity as these breeds participated in the formation of the Livni pigs. We observed the highest level of genetic diversity in Livni pigs compared to commercial breeds (UHE = 0.409 vs. 0.319–0.359, p < 0.001; AR = 1.995 vs. 1.894–1.964, p < 0.001). A slight excess of heterozygotes was found in all of the breeds. We identified 291 candidate genes, which were localized within the regions under putative selection, including 22 and 228 genes, which were specific for Livni and Duroc breeds, respectively, and 41 genes common for both breeds. A detailed analysis of the molecular functions identified the genes, which were related to the formation of meat and fat traits, and adaptation to environmental stress, including extreme temperatures, which were different between breeds. Our research results are useful for conservation and sustainable breeding of Livni breed, which shows a high level of genetic diversity. This makes Livni one of the valuable national pig genetic resources.

Impacts of seasonality on gene expression in the Chinese horseshoe bat

Seasonality can cause changes in many environmental factors which potentially affects gene expression. Here, we used a bat species (Rhinolophus sinicus) from eastern China as a model to explore the molecular mechanisms of seasonal effects, in particular during phenological shifts in the spring and autumn. Based on the analysis of 45 RNA‐seq samples, we found strong seasonal effects on gene expression, with a large number of genes identified as either specific or biased to each season. Weighted gene co‐expression network analysis also identified multiple modules significantly associated with each season. These seasonal genes were further enriched into different functional categories. Consistent with effects of phenological shifts on bats, we found that genes related to promoting food intake were highly expressed in both autumn and spring. In addition, immunity genes were also highly expressed in both seasons although this seasonal immune response had tissue specificity in different seasons. In female bats, genes related to the delay of ovulation (e.g., NPPC, natriuretic peptide precursor type C) were highly expressed in October, while genes associated with the promotion of reproduction (e.g., DIO2, iodothyronine deiodinase 2) were biasedly expressed in April. Lastly, we found multiple known core clock genes in both October‐biased and April‐biased expressed genes, which may be involved in regulating the start and end of hibernation, respectively. Overall, together with studies in other land and aquatic animals, our work supports that seasonal gene expression variations may be a general evolutionary response to environmental changes in wild animals.