Predicting and analyzing early wake-up associated gene expressions by integrating GWAS and eQTL studies

Circadian rhythms are endogenous 24-hour rhythmic oscillations affecting human behaviors, such as sleep, blood pressure and other biological processes, the disturbance of which lead to circadian rhythm sleep disorders (CRSDs). In this study, based on the data from genome-wide association studies (GWASs) and expression quantitative trait loci (eQTLs), we tried to identify novel gene expression patterns in brain tissues that were associated with early wake-up. First, the maximum-relevance-minimum-redundancy (mRMR) method was adopted to analyze the involved gene expression patterns, yielding a feature list. Second, the incremental feature selection (IFS) method and the Dagging algorithm were applied to extract important gene expression patterns, which yield the best performance for Dagging. As a result, 4374 gene expression patterns were obtained, and they were further used to build an optimal classifier with a good performance of a Matthews's correlation coefficient of 0.933. Furthermore, the most important 49 gene expression patterns were extensively analyzed. Four genes were found to be related to circadian rhythm, as reported in previous studies. As a first attempt in identifying the target genes whose expression levels are associated with sleep-wake rhythms through integrating GWAS and eQTL results, this study can motivate more investigations in this regard.This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.     

Circadian rhythms of omitted stimulus potentials in the crayfish brain

The omitted stimulus potential (OSP) is a type of event-related potentials elicited by cognitively-relevant stimuli associated with mental processes in humans. Crayfish also emit OSP when an expected stimulus does not arrive, although this is not considered to index a high-level cognitive event, but it is endogenous in nature because this depends on the recent history and arousal state of the animal. Although OSP is highly conserved in evolution, it had not been the subject of circadian study. Our hypothesis is that OSP, recorded in crayfish brain (Procambarus clarkii) has a circadian behaviour in its firing pattern. OSPs show circadian rhythms in both the latency and in the OSP/Sp ratio, under free-running (light:light, LL) and photoperiod (light:dark, LD) conditions, with main peaks during the daytime. This is the first report that shows a circadian pattern of OSP.     

Activity rhythms of the shallow-water octopuses Octopus laqueus and Abdopus aculeatus with special reference to its relation to light and tidal cycles

Patterns of activity and inactivity were experimentally measured for two shallow-water octopuses, Octopus laqueus (n = 8) and Abdopus aculeatus (n = 4), inhabiting the Ryukyu Archipelago. Octopuses that were collected from the coastal waters of Okinawa Island were held in experimental tanks under controlled light conditions (L, light; D, dark; 12L:12D, LD conditions; 12D:12D, DD conditions). Behaviors of these two species were continuously recorded for 9 to 10 days. Under LD conditions, O. laqueus were active for 7 to 14 min during daytime and 298 to 339 min at night, and under DD conditions, for 97 to 140 min during daytime and 71 to 169 min at night. A. aculeatus were active for 49 to 99 min during daytime and 138 to 185 min at night under LD conditions, whereas under DD conditions, they were active for 36 to 56 min during daytime and 55 to 154 min at night. Continuous duration for activity cycles was 39 ± 7.6 h under LD conditions and 42 ± 2.6 h under DD conditions in O. laqueus, and 38 ± 7.4 h under LD conditions and 42 ± 2.8 h under DD conditions in A. aculeatus. Ratios for active duration to inactive duration did not differ between LD condition and DD condition both in O. laqueus and A. aculeatus.     

Circadian rhythms of biomarkers of oxidative stress and their characteristics in broiler chickens reared under natural light/dark cycle

For the purpose of studying circadian rhythms of biomarkers of oxidative stress in broiler chickens maintained under natural photoperiod, we collected blood from the wing veins of 10 matured broiler chickens every three hours for a period of 24 h. The blood samples were analyzed for superoxide dismutase (SOD), catalase (CAT), and malondialdehyde (MDA). The fitting in of single cosinor procedure showed that CAT and MDA exhibited clear circadian rhythms, while SOD did not. The amplitude of daily rhythms for the parameters was small, while the acrophases were all restricted to the light phase of the light:dark cycle. In conclusion, to our knowledge, this is the first time investigation of the circadian rhythms of antioxidants in broilers chickens, reared under natural photoperiod in the tropics. The result may be exploited for a more precise targeting of reactive oxygen species, thereby offering better protection for the cells to combat oxidative stress.     

Creatine–facilitated protection of stress caused by disrupted circadian rhythm

Disturbances in natural Circadian rhythm are well-known stress factors, affecting a range of metabolic pathways in the living body including the brain. Hence, discovery of natural compounds that could help to prevent and cure of adverse changes is very important. One of the recently discussed substances is creatine, that is believed to have anti-stressor properties. Recent paper describes the impact of intraperitoneally injected creatine (140 mg/kg) into rats with a disturbed natural circadian rhythm for an extended period of time (30 days). Markedly, creatine-treated animals show positive changes in open-field behavioral parameters, and an increase in certain antioxidant enzymes’ (SOD, catalase) activity in the hippocampus, whereas the concentration of nitric oxide, H₂O₂, and Ca²⁺ are approximated to the control value. Similar findings were also observed in case of Na⁺/K⁺- and Ca²⁺-ATPases. To sum up, the recent findings allow the conclusion that oxidative stress induced by long-term disturbances in natural circadian rhythm is accompanied and likely provoked by an increase in Ca²⁺-cytotoxicity, which is supposedly normalized by the creatine’s indirect action on the NMDA receptor. Therefore, impact on energy mediating pathways has a positive effect on stabilization of antioxidant and various metabolic systems and protecting hippocampal cells from stress.     

Social isolation of mice: activity rhythm changes and the expression of clock

Social isolation usually affects the physical and mental health of the human and produces depression, whether it may relate with circadian rhythm still remains to be investigated. Two groups of mice were employed to this experiment to continuously monitoring their activities in a dark environment. Immunofluorescence was used to show the expression of the circadian clock gene in two groups of mice. The results demonstrate that the social isolation leads to decrease of mouse activities, phase advance of rhythm relatively and down-regulated of clock gene expression. We conclude that social isolation can affect the physiological function and the normal physiological rhythm of mice, which may be related to depression.     

Locomotor activity rhythm of Talitrus saltator (Crustacea,Amphipoda) on a progradating sandy beach

In the Maremma Natural Park (Grosseto, Italy), the Collelungo beach exhibits a clear morphodynamics gradient, resulting in a severe erosion to a gradual accretion along the shoreline. Here, three sub-populations of the sandhopper Talitrus saltator (Montagu) (Crustacea, Amphipoda) were studied to highlight eventual intra- and inter-population variation of the endogenous locomotor rhythm. Individual activity recordings were carried out for 21 days in constant darkness and controlled temperature and humidity conditions. The variation of the free-running period was analysed at individual and sub-population levels, and the dependence on intrinsic (individual features) and extrinsic (habitat of origin and season) factors was analysed. A seasonal variation was highlighted, related to the seasonal spontaneous activity of the species. In summer and autumn, a significant correlation between the behavioural variation in the sub-populations (period and definition of the period) and beach physical parameters (slope and width) defined the dependence of the behavioural gradient on the environmental gradient. The observed relationship may represent an adaptation to the local coastline dynamics, suggesting the importance of a plastic behaviour as adaptive response to a variable environment.     

A gene‐driven recovery mechanism: Drosophila larvae increase feeding activity for post‐stress weight recovery

Recovery from weight loss after stress is important for all organisms, although the recovery mechanisms are not fully understood. We are working to clarify these mechanisms. Here, we recorded enhanced feeding activity of Drosophila melanogaster larvae from 2 to 4 h after heat stress at 35°C for 1 h. During the post‐stress period, expression levels of sweet taste gustatory receptor genes (Grs), Gr5a, Gr43a, Gr64a, and Gr64f, were elevated, whereas bitter taste Grs, Gr66a, and Gr33a, were decreased in expression and expression of a non‐typical taste receptor Gr, Gr68a, was unchanged. Similar upregulation of Gr5a and downregulation of Gr66a was recorded after cold stress at 4°C. Expression levels of tropomyosin and ATP synthase ß subunit were significantly increased in larval mouth parts around 3 to 5 h after the heat stress. We infer that up‐regulation of post‐stress larval feeding activity, and weight recovery, is mediated by increasing capacity for mouth part muscular movements and changes in taste sensing physiology. We propose that Drosophila larvae, and likely insects generally, express an efficient mechanism to recover from weight loss during post‐stress periods.     

Features of the daily rhythms of blood melatonin and glucose in goats during different natural photoperiod

The scope of the present study was to explore the features of the daily rhythms of plasma melatonin and blood glucose in goats during different natural photoperiod imposed by the four seasons. Five Sarda breed pluriparus female goats, 2 years old, with a mean body weight 40.5 ± 2.3 kg, lead to a natural pasture, were cannulated the day before the start of the study for sample collection performed during spring and autumn equinoxes, and winter and summer solstices for a 48-h period. On blood samples, melatonin and glucose concentrations were assessed. Our results indicate a daily rhythm of both parameters studied which characteristics were influenced by the different photoperiod due to season. During the experimental period, the two parameters showed a negative correlation, despite the onset of melatonin concentration was linked to the sunset, whereas the onset and offset of glucose were not linked to the photoperiod. In conclusion, we can claim that the two parameters are driven by different entrainable systems, but further studies are necessary to establish their correlation.     

Physiological status of Drosophila suzukii (Diptera: Drosophilidae) affects their response to attractive odours

An improved understanding of the biology of the invasive pest, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae), is critical for the development of effective management strategies. Trapping is one technique used for both detection and control; however, the efficacy of trapping can vary depending on the target insect's physiological state, its behavioural priorities and the type of attractant used in the trap. We conducted a series of caged trapping experiments and a greenhouse trapping experiment to investigate the effects of D. suzukii feeding status, age, mating status, ovipositional status and seasonal morph type on the capture rate of traps baited with fermentation odours. Starved flies were trapped at greater rates compared to fed flies; more virgin flies were trapped than mated flies; flies deprived of an oviposition substrate were trapped more frequently than flies given an oviposition substrate. It is still unclear whether age or seasonal morphology affect bait response. Lastly, a caged choice experiment investigated the relationship between female reproductive status and attraction to fermentation or fruit odours. Fermentation‐based traps captured female flies regardless of their reproductive status but, ripe fruit‐based traps were more attractive to flies with more than seven eggs. In summary, studies that use fermentation‐based traps should recognize that capture rates of D. suzukii will depend on the feeding, mating and oviposition experiences of the population; also, fruit‐based traps may better target gravid females.