SUMMARY
Mammals rely on a network of circadian clocks to control daily systemic metabolism and physiology. The central pacemaker in the suprachiasmatic nucleus (SCN) is considered hierarchically dominant over peripheral clocks, whose degree of independence, or tissue level autonomy, has never been ascertained in vivo. Using arrhythmic Bmal1-null mice, we generated animals with reconstituted circadian expression of BMAL1 exclusively in the liver (Liver-RE). High-throughput transcriptomics and metabolomics show that the liver has independent circadian functions, specific for metabolic processes such as the NAD+ salvage pathway and glycogen turnover. However, although BMAL1 occupies chromatin at most genomic targets in Liver-RE mice, circadian expression is restricted to ~ 10% of normally rhythmic transcripts. Finally, rhythmic clock gene expression is lost in Liver-RE mice under constant darkness. Hence, full circadian function in the liver depends on signals emanating from other clocks and light contributes to tissue-autonomous clock function.
While the timing of food intake is important, it is unclear whether the effects of exercise on energy metabolism are restricted to unique time windows. As circadian regulation is key to controlling metabolism, understanding the impact of exercise performed at different times of the day is relevant for physiology and homeostasis. Using high-throughput transcriptomic and metabolomic approaches, we identify distinct responses of metabolic oscillations that characterize exercise in either the early rest phase or the early active phase in mice. Notably, glycolytic activation is specific to exercise at the active phase. At the molecular level, HIF1a, a central regulator of glycolysis during hypoxia, is selectively activated in a time-dependent manner upon exercise, resulting in carbohydrate exhaustion, usage of alternative energy sources, and adaptation of systemic energy expenditure. Our findings demonstrate that the time of day is a critical factor to amplify the beneficial impact of exercise on both metabolic pathways within skeletal muscle and systemic energy homeostasis.
Rapid
antimicrobial susceptibility testing (AST) is an integral
tool to mitigate the unnecessary use of powerful and broad-spectrum
antibiotics that leads to the proliferation of multi-drug-resistant
bacteria. Using a sensor platform composed of surface-enhanced Raman
scattering (SERS) sensors with control of nanogap chemistry and machine
learning algorithms for analysis of complex spectral data, bacteria
metabolic profiles post antibiotic exposure are correlated with susceptibility.
Deep neural network models are able to discriminate the responses
of Escherichia coli and Pseudomonas aeruginosa to antibiotics from untreated cells in SERS data in 10 min after
antibiotic exposure with greater than 99% accuracy. Deep learning
analysis is also able to differentiate responses from untreated cells
with antibiotic dosages up to 10-fold lower than the minimum inhibitory
concentration observed in conventional growth assays. In addition,
analysis of SERS data using a generative model, a variational autoencoder,
identifies spectral features in the P. aeruginosa lysate data associated with antibiotic efficacy. From this insight,
a combinatorial dataset of metabolites is selected to extend the latent
space of the variational autoencoder. This culture-free dataset dramatically
improves classification accuracy to select effective antibiotic treatment
in 30 min. Unsupervised Bayesian Gaussian mixture analysis achieves
99.3% accuracy in discriminating between susceptible versus resistant to antibiotic cultures in SERS using the extended latent
space. Discriminative and generative models rapidly provide high classification
accuracy with small sets of labeled data, which enormously reduces
the amount of time needed to validate phenotypic AST with conventional
growth assays. Thus, this work outlines a promising approach toward
practical rapid AST.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.