Continuous Cell-Free Replication and Evolution of Artificial Genomic DNA in a Compartmentalized Gene Expression System.

In all living organisms, genomic DNA continuously replicates by the proteins encoded in itself and undergoes evolution through many generations of replication. This continuous replication coupled with gene expression and the resultant evolution are fundamental functions of living things, but they have not previously been reconstituted in cell-free systems. In this study, we combined an artificial DNA replication scheme with a reconstituted gene expression system and microcompartmentalization to realize these functions. Circular DNA replicated through rolling-circle replication followed by homologous recombination catalyzed by the proteins, phi29 DNA polymerase, and Cre recombinase expressed from the DNA. We encapsulated the system in microscale water-in-oil droplets and performed serial dilution cycles. Isolated circular DNAs at Round 30 accumulated several common mutations, and the isolated DNA clones exhibited higher replication abilities than the original DNA due to its improved ability as a replication template, increased polymerase activity, and a reduced inhibitory effect of polymerization by the recombinase. The artificial genomic DNA, which continuously replicates using self-encoded proteins and autonomously improves its sequence, provides a useful starting point for the development of more complex artificial cells.

Minimization of Elements for Isothermal DNA Replication by an Evolutionary Approach.

DNA replication is one of the central functions of the cell. The complexity of modern DNA replication systems raises a question: is it possible to achieve a simpler continuous isothermal DNA replication using fewer proteins? Here, we searched such replication using an evolutionary approach. Through a long-term serial dilution experiment with phi29 DNA polymerase, we found that large repetitive DNAs spontaneously appear and continuously replicate. The repetitive sequence is critical for replication. Arbitrary sequences can replicate if they contain many repeats. We also demonstrated continuous DNA replication using expressed polymerase from the DNA for 10 rounds. This study revealed that continuous isothermal DNA replication can be achieved in a scheme simpler than that employed by modern organisms, providing an alternative strategy for simpler artificial cell synthesis and a clue to possible primitive forms of DNA replication.

Dietary natural cocoa ameliorates disrupted circadian rhythms in locomotor activity and sleep-wake cycles in mice with chronic sleep disorders caused by psychophysiological stress.

OBJECTIVES: Cocoa contains many chemical compounds that affect the physiological functions of experimental animals and humans. The present study used a mouse model characterized by disrupted circadian rhythms of locomotor activity and sleep-wake cycles to determine whether natural cocoa improves chronic sleep disorders (CSDs) induced by psychophysiological stress. METHODS: Mice were fed a high-fat, high-sucrose diet supplemented with 2.0% natural cocoa and stressed for 30 d to induce CSDs. RESULTS: Dietary cocoa restored the amplitude reduction of day-night activity rhythms by improving reduced nocturnal wheel-running activities during CSDs. Electroencephalography revealed that dietary cocoa significantly ameliorated CSD-induced increases in wakefulness during the first half of the inactive phase and in nonrapid eye movement sleep during the first half of the active phase. The attenuation of circadian rapid eye movement sleep rhythms and increased electroencephalography slow-wave activity (a marker of nonrapid eye movement sleep intensity) induced by CSDs improved in mice supplemented with cocoa. Dietary cocoa notably did not affect wheel-running activity rhythms or sleep-wake cycles under normal conditions. Dietary cocoa significantly increased the hypothalamic mRNA expression of Hspa1 a that encodes HSP70 and is associated with sleep regulation. Furthermore, Hspa1 a expression was not induced by CSDs in mice supplemented with cocoa. CONCLUSIONS: These findings suggest that dietary cocoa exerts beneficial effects on insomnia and circadian sleep disorders induced by psychophysiological stress.

Chronically skipping breakfast impairs hippocampal memory-related gene expression and memory function accompanied by reduced wakefulness and body temperature in mice.

Acute or chronic effects of consuming or skipping breakfast on cognitive performance in humans are controversial. To evaluate the effects of chronically skipping breakfast (SB) on hippocampus-dependent long-term memory formation, we examined hippocampal gene expression and applied the novel object recognition test (NORT) after two weeks of repeated fasting for six hours from lights off to mimic SB in mice. We also examined the effects of SB on circadian rhythms of locomotor activity, food intake, core body temperature (CBT) and sleep-wake cycles. Skipping breakfast slightly but significantly decreased total daily food intake without affecting body weight gain. Locomotor activity and CBT significantly decreased during the fasting period under SB. The degree of fasting-dependent CBT reduction gradually increased and then became stabilized after four days of SB. Electroencephalographic data revealed that repeated SB significantly decreased the duration of wakefulness and increased that of rapid eye movement (REM) and of non-REM (NREM) sleep during the period of SB. Furthermore, total daily amounts of wakefulness and NREM sleep were significantly decreased and increased, respectively, under SB, suggesting that SB disrupts sleep homeostasis. Skipping breakfast significantly suppressed mRNA expression of the memory-related genes, Camk2a, Fkbp5, Gadd45b, Gria1, Sirt1 and Tet1 in the hippocampus. Recognition memory assessed by NORT was impaired by SB in accordance with the gene expression profiles. These findings suggested that chronic SB causes dysregulated CBT, sleep-wake cycles and hippocampal gene expression, which results in impaired long-term memory formation.

Food deprivation during active phase induces skeletal muscle atrophy via IGF-1 reduction in mice.

Skeletal muscle mass is largely influenced by nutritional status and physical activity. Although feeding at specific times of the day (time-restricted feeding, TRF) modulates obesity and other metabolic functions, its effects on skeletal muscles remain unclear. We explored the effects of feeding mice only during the inactive (daytime feeding, DF) or active (nighttime feeding, NF) phases for one week. Daytime feeding did not abolish the nocturnal activity rhythm, although total daily activity was reduced in these mice. Temporal expression of the circadian clock genes, Per2 and Rev-erbα, became synchronized to the feeding cycle in the liver, but not in skeletal muscle. Skeletal muscle mass, grip strength, and cross-sectional area were significantly lower in DF, than in NF mice, although DF increased body weight gain and lipid accumulation. Expression of the atrophy-related ubiquitin ligases, Atrogin-1 and Murf1 and the autophagy-related genes, Lc3b and Bnip3, was induced during the active phase in the gastrocnemius muscles of DF, compared with those of NF mice. Plasma IGF-1 concentrations and Igf-1 expression in the livers and gastrocnemius muscles during the active phase were lower in DF, than in NF mice. Furthermore, exogenous IGF-1 injection significantly suppressed DF-induced reduction in gastrocnemius muscle mass, which might at least partly explain the association between decreased plasma IGF-1 concentrations and reductions in the skeletal muscle mass of DF mice. These findings suggest that feeding only during the inactive phase reduces skeletal muscle mass via a decrease in plasma IGF-1 concentrations during the active phase.

Functional CLOCK Is Not Essentially Associated with Metabolic Disruption Caused by Sleep Phase Feeding in Mice.

Consuming food at uncommon times during the day might be associated with obesity in experimental animals and humans. We previously reported that mice become obese and their metabolism becomes disrupted when they consume food during the daytime (sleep phase feeding; SPF), but not during the nighttime (active phase feeding; APF). The goal of the present study was to clarify whether the molecular circadian clock is associated with the mechanisms that underly the metabolic disorders in mice brought about by SPF. We compared the effects of dominant negative Clock gene mutation on metabolic disruption and obesity brought about by SPF in mice. The consumption of food during SP increased body weight, adipose tissue mass and lipogenic gene expression in metabolic tissues, as well as hyperinsulinemia, hyperleptinemia and hepatic lipid accumulation in wild-type and Clock mutant mice, and there were no significant differences between genotypes except for the body weight increase which was attenuated by the Clock mutation. Temporal expression of Per2 was synchronized to feeding rhythms in the liver of both genotypes, although the expression of Dbp, a representative clock-controlled gene, was significantly damped in peripheral tissues of Clock mutant mice. These findings suggest that the molecular clock is not essentially associated with metabolic disruption caused by SPF. Desynchronized food consumption and central clock-dependent behaviour as well as rhythmic metabolic mechanisms might be associated with the metabolic disruption caused by SPF.

Timing of food intake is more potent than habitual voluntary exercise to prevent diet-induced obesity in mice.

Inappropriate eating habits such as skipping breakfast and eating late at night are associated with risk for abnormal weight-gain and adiposity. We previously reported that time-imposed feeding during the daytime (inactive phase) induces obesity and metabolic disorders accompanied by physical inactivity in mice. The present study compares metabolic changes induced in mice by time-imposed feeding under voluntary wheel-running (RW) and sedentary (SED) conditions to determine the effects of voluntary wheel-running activity on obesity induced in mice by feeding at inappropriate times. Mice were individually housed in cages with or without running-wheels. We compared food consumption, core body temperature, hormonal and metabolic variables in the blood, lipid accumulation in the liver, circadian expression of clock and metabolic genes in peripheral tissues, and gains in body weight between mice allowed access to food only during the sleep phase (daytime feeding; DF) or only during the active phase (nighttime feeding; NF) under SED or RW conditions. Only a high-fat high-sucrose diet was available to the mice throughout restricted feeding. Nocturnal activity was maintained in both NF and DF mice under RW conditions, but significantly suppressed during the latter half of the dark phase in DF mice. Nocturnal fluctuations in core body temperature were maintained in DF and NF mice under both SED and RW conditions, although DF attenuated the day-night amplitude more under SED, than RW conditions. The degrees of DF-induced increases in body weight gain, food efficiency, adipose tissue mass, lipogenic gene expression in metabolic tissues, and hepatic lipid accumulation were essentially identical between SED and RW conditions. Daytime feeding also induced hyperinsulinemia and hyperleptinemia under both SED and RW conditions, although DF-induced hyperleptinemia was slightly attenuated by wheel-running. The temporal expression of circadian clock genes became synchronized to feeding cycles in the liver but not in the skeletal muscle of mice under both SED and RW conditions. Chronic voluntary exercise on running-wheels minimally affected obesity and adiposity in mice caused by daily feeding at unusual times. The timing of food intake might be more important than physical exercise for preventing metabolic disorders. Abbreviations: ANOVA: analysis of variance; DF: daytime feeding; FFA: free fatty acid; GLP-1: glucagon-like peptide-1; HOMA-IR: homeostasis model assessment of insulin resistance; NEAT: non-exercise activity thermogenesis; NF: nighttime feeding; RF: restricted feeding; RW: running-wheel; SCN: suprachiasmatic nucleus; SE: standard error of the mean; SED: sedentary; SPA: spontaneous physical activity; T-Cho: total cholesterol; TG: triglyceride; WAT: white adipose tissues.

Determination of reference genes that are independent of feeding rhythms for circadian studies of mouse metabolic tissues.

Real-time reverse transcription-polymerase chain reaction (RT-PCR) analysis is a popular method for the measurement of mRNA expression level and is a critical tool for basic research. The identification of suitable reference genes that are stable and not affected by experimental conditions is a critical step in the accurate normalization of RT-PCR. On the other hand, the levels of numerous transcripts exhibit circadian oscillation in various peripheral tissues and it is thought to be regulated by feeding rhythms in addition to the molecular circadian clock. Here, we investigated the effects of feeding schedule on the temporal expression profiles of 13 common housekeeping genes in metabolic tissues of mice fed during either the sleep or the active phase. The expression of most of these genes fluctuated dependently on feeding rhythms in the liver and WAT, but not in skeletal muscle. Two-way analyses of variance (ANOVA) identified 18S ribosomal RNA (Rn18s) as the only gene that was stably expressed throughout the day independently of feeding schedules in the liver and WAT, although RefFinder software showed that peptidylprolyl isomerase A (Ppia) was the most stably expressed housekeeping gene. Both ANOVA and RefFinder software determined that Actb was the preferred reference gene for skeletal muscle. Furthermore, NormFinder proposed that the optimal pairs of reference genes were beta-2 microglobulin (B2m)-Ppia in the liver, Ppia-TATA box binding protein (Tbp) in WAT, and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide (Ywhaz)-glyceraldehyde-3-phosphate dehydrogenase (Gapdh) in skeletal muscle, and that their stability value was better than that of a single stable gene. The appropriate reference gene pairs for normalizing genes of interest in mouse circadian studies are B2m-Ppia in the liver, Ppia-Tbp in WAT, and Ywhaz-Gapdh in skeletal muscle.