Genetically Distinct Behavioral Modules Underlie Natural Variation in Thermal Performance Curves

Integrated transcriptomics and metabolomics unravel the metabolic pathway variations for barley β-glucan before and after fermentation with L. plantarum DY-1

The results of our previous study showed that the structure and function of β-glucan in barley were changed after fermentation by L. plantarum DY-1. In this study, the antioxidant activities of RBG (regular barley β-glucan, unfermented) and FBG (barley β-glucan, fermented with L. plantarum DY-1) were evaluated by adopting an in vivo animal model, Caenorhabditis elegans (C. elegans). We also carried out an integrated transcriptomic and metabolomic profiling for RBG and FBG to delineate their signature pathways. RBG treatment has better effects on SOD enzyme activity and ROS levels than FBG, while FBG treatment has better effects on the CAT enzyme activity and MDA content than RBG in C. elegans. Transcription group analysis showed that FBG mainly decreases the expression of the Cyp-D gene to inhibit the calcium signaling pathway, promotes the Wnt signaling pathway by up-regulating the GSK-3β gene and improving the oxidative damage of C. elegans; RBG mainly inhibits calcium signal pathways by reducing the expression of ANT-solute carrier family 25 genes, promoting life adjustment pathways by reducing the expression of the HSP-12.6 gene to improve the oxidative stress of C. elegans. Joint analysis showed that the difference between FBG and RBG in the regulation of oxidative stress is mainly reflected in the metabolism pathway of arachidonic acid. Under the regulation of FBG, the expression of the C03H5.4 gene was decreased, the expression of leukotriene A4, prostaglandin G2, arachidonic acid and phosphatidylcholine was decreased, and the expression of 14,15-DiHETrE was increased. Under the regulation of RBG, the expression of gene C03H5.4 was up-regulated, the expression of metabolites such as leukotriene B4 was up-regulated, and the expression of arachidonic acid and phosphatidylcholine was down-regulated.

Cold Survival and Its Molecular Mechanisms in a Locally Adapted Nematode Population

Since Darwin, evolutionary biologists have sought to understand the drivers and mechanisms of natural trait diversity. The field advances toward this goal with the discovery of phenotypes that vary in the wild, their relationship to ecology, and their underlying genes. Here, we established resistance to extreme low temperature in the free-living nematode Caenorhabditis briggsae as an ecological and evolutionary model system. We found that C. briggsae strains of temperate origin were strikingly more cold-resistant than those isolated from tropical localities. Transcriptional profiling revealed expression patterns unique to the resistant temperate ecotype, including dozens of genes expressed at high levels even after multiple days of cold-induced physiological slowdown. Mutational analysis validated a role in cold resistance for seven such genes. These findings highlight a candidate case of robust, genetically complex adaptation in an emerging model nematode, and shed light on the mechanisms at play.

Variation in the response to exercise stimulation in Drosophila: marathon runner versus sprinter genotypes

Animals' behaviors vary in response to their environment, both biotic and abiotic. These behavioral responses have significant impacts on animal survival and fitness, and thus, many behavioral responses are at least partially under genetic control. In Drosophila, for example, genes impacting aggression, courtship behavior, circadian rhythms and sleep have been identified. Animal activity also is influenced strongly by genetics. My lab previously has used the Drosophila melanogaster Genetics Reference Panel (DGRP) to investigate activity levels and identified over 100 genes linked to activity. Here, I re-examined these data to determine whether Drosophila strains differ in their response to rotational exercise stimulation, not simply in the amount of activity, but in activity patterns and timing of activity. Specifically, I asked whether there are fly strains exhibiting either a 'marathoner' pattern of activity, i.e. remaining active throughout the 2 h exercise period, or a 'sprinter' pattern, i.e. carrying out most of the activity early in the exercise period. The DGRP strains examined differ significantly in how much activity is carried out at the beginning of the exercise period, and this pattern is influenced by both sex and genotype. Interestingly, there was no clear link between the activity response pattern and lifespan of the animals. Using genome-wide association studies (GWAS), I identified 10 high confidence candidate genes that control the degree to which Drosophila exercise behaviors fit a marathoner or sprinter activity pattern. This finding suggests that, similar to other aspects of locomotor behavior, the timing of activity patterns in response to exercise stimulation is under genetic control.

Genome structure predicts modular transcriptome responses to genetic and environmental conditions

Understanding the plasticity, robustness and modularity of transcriptome expression to genetic and environmental conditions is crucial to deciphering how organisms adapt in nature. To test how genome architecture influences transcriptome profiles, we quantified expression responses for distinct temperature-adapted genotypes of the nematode Caenorhabditis briggsae when exposed to chronic temperature stresses throughout development. We found that 56% of the 8,795 differentially expressed genes show genotype-specific changes in expression in response to temperature (genotype-by-environment interactions, GxE). Most genotype-specific responses occur under heat stress, indicating that cold vs. heat stress responses involve distinct genomic architectures. The 22 co-expression modules that we identified differ in their enrichment of genes with genetic vs. environmental vs. interaction effects, as well as their genomic spatial distributions, functional attributes and rates of molecular evolution at the sequence level. Genes in modules enriched for simple effects of either genotype or temperature alone tend to evolve especially rapidly, consistent with disproportionate influence of adaptation or weaker constraint on these subsets of loci. Chromosome-scale heterogeneity in nucleotide polymorphism, however, rather than the scale of individual genes predominates as the source of genetic differences among expression profiles, and natural selection regimes are largely decoupled between coding sequences and noncoding flanking sequences that contain cis-regulatory elements. These results illustrate how the form of transcriptome modularity and genome structure contribute to predictable profiles of evolutionary change.