Evidence for the adaptive significance of circadian rhythms

Measuring honey bee feeding rhythms with the BeeBox, a platform for nectar foraging insects

In honey bees, most studies of circadian rhythms involve a locomotion test performed in a small tube, a tunnel, or at the hive entrance. However, despite feeding playing an important role in honey bee health or fitness, no demonstration of circadian rhythm on feeding has been performed until recently. Here, we present the BeeBox, a new laboratory platform for bees based on the concept of the Skinner box, which dispenses discrete controlled amounts of food (sucrose syrup) following entrance into an artificial flower. We compared caged groups of bees in 12 h-12 h light/dark cycles, constant darkness and constant light and measured average hourly syrup consumption per living bee. Food intake was higher in constant light and lower in constant darkness; mortality increased in constant light. We observed rhythmic consumption with a period longer than 24 h; this is maintained in darkness without environmental cues, but is damped in the constant light condition. The BeeBox offers many new research perspectives and numerous potential applications in the study of nectar foraging animals.

Measuring activity-rest rhythms under different acclimation periods in a marine fish using automatic deep learning-based video tracking

Most organisms synchronize to an approximately 24-hour (circadian) rhythm. This study introduces a novel deep learning-powered video tracking method to assess the stability, fragmentation, robustness and synchronization of activity rhythms in Xyrichtys novacula. Experimental X. novacula were distributed into three groups and monitored for synchronization to a 14/10 hours of light/dark to assess acclimation to laboratory conditions. Group GP7 acclimated for 1 week and was tested from days 7 to 14, GP14 acclimated for 14 days and was tested from days 14 to 21 and GP21 acclimated for 21 days and was tested from days 21 to 28. Telemetry data from individuals in the wild depicted their natural behavior. Wild fish displayed a robust and minimally fragmented rhythm, entrained to the natural photoperiod. Under laboratory conditions, differences in activity levels were observed between light and dark phases. However, no differences were observed in activity rhythm metrics among laboratory groups related to acclimation period. Notably, longer acclimation (GP14 and GP21) led to a larger proportion of individuals displaying rhythm synchronization with the imposed photoperiod. Our work introduces a novel approach for monitoring biological rhythms in laboratory conditions, employing a specifically engineered video tracking system based on deep learning, adaptable for other species.

Nocturnal stomatal behaviour and its impact on water use strategies of desert herbs in the Gurbantunggut Desert, Northwest China

Nocturnal stomatal behaviour has the potential to exert a profound influence on plant-water relations, especially water use efficiency. However, we know very less about plant functional type differences in nocturnal stomatal conductance and their roles in plant stress adaptation, especially drought adaptation. To address this critical knowledge gap, we assessed diel leaf gas exchanges in eight ephemeral and perennial herbs growing on the southern edge of the Gurbantunggut Desert, Northwest China. For both ephemeral and perennial herbs, the nocturnal stomatal conductance (gs) exceeded 30 % of daytime gs, except for an ephemeral herb (Malcolmia scorpioides). The nocturnal gs in the studied perennial herbs were significantly higher than it in the ephemeral herbs. The results suggest that circadian-driven stomatal priming plays a pivotal role in accelerating the attainment of steady-state gs during the morning for perennial herbs, thereby enhancing their capacity for carbon capture. Moreover, the nocturnal stomatal behaviour of the ephemeral herbs favored water retention in the morning, consequently enhanced intrinsic water use efficiency and long-term water use efficiency. In summary, plant functional type differences in the magnitude of nocturnal stomatal opening were related to differences in water acquisition and utilization and highlighted diverse water use strategies in the desert plants.

Cell Signaling in the Circadian Pacemaker: New Insights from in vivo Imaging

BACKGROUND

"One for all, and all for one," the famous rallying cry of the Three Musketeers, in Alexandre Dumas's popular novel, certainly applies to the 20,000 cells composing the suprachiasmatic nuclei (SCN). These cells work together to form the central clock that coordinates body rhythms in tune with the day-night cycle. Like virtually every body cell, individual SCN cells exhibit autonomous circadian oscillations, but this rhythmicity only reaches a high level of precision and robustness when the cells are coupled with their neighbors. Therefore, understanding the functional network organization of SCN cells beyond their core rhythmicity is an important issue in circadian biology.

SUMMARY

The present review summarizes the main results from our recent study demonstrating the feasibility of recording SCN cells in freely moving mice and the significance of variations in intracellular calcium over several timescales.

KEY MESSAGE

We discuss how in vivo imaging at the cell level will be pivotal to interrogate the mammalian master clock, in an integrated context that preserves the SCN network organization, with intact inputs and outputs.

Short-time exposure to light at night affects incubation patterns and correlates with subsequent body weight in great tits (Parus major)

Artificial light at night (ALAN) widely affects wildlife by blurring light-dark differences, including transitions such as sunrise and sunset, thereby affecting regulation of diel rhythms. As a result, activity onsets in many wild diurnal songbirds advance under ALAN. From chronobiological studies, it is known that the direction and strength of the response to light depends on when during the night exposure takes place. However, these experiments are mostly done under continuous light conditions, when animals have free-running rhythms. It remains unclear whether phase-dependence also holds in entrained, wild songbirds; i.e., does the effect of ALAN on activity patterns differ between exposure in the morning compared to the evening? This information is essential to assess the effects of mitigation measures by limiting ALAN to selected times of the night. We exposed incubating great tits (Parus major) inside the nest-box to 4 h of dim light, of which 1 h overlapped with dawn before sunrise or dusk after sunset. We found a small advancing effect of morning-light on activity onset and of evening-light on offset compared to dark controls but not vice versa. Breeding success and chick condition were unaffected by the light treatments. However, light-treated females had lower weights 9-18 days after the end of the treatment compared to the controls, independent of whether ALAN occurred in the morning or the evening, indicating possible costs of ALAN. Despite the weak behavioral response, ALAN might have affected the females' circadian clock or physiology resulting in lower body condition.

Plasticity of circadian and circatidal rhythms in activity and transcriptomic dynamics in a freshwater snail

Organisms have diverse biological clocks synchronised with environmental cycles depending on their habitats. Anticipation of tidal changes has driven the evolution of circatidal rhythms in some marine species. In the freshwater snail, Semisulcospira reiniana, individuals in nontidal areas exhibit circadian rhythms, whereas those in tidal areas exhibit both circadian and circatidal rhythms. We investigated whether the circatidal rhythms are genetically determined or induced by environmental cycles. The exposure to a simulated tidal cycle did not change the intensity of circatidal rhythm in individuals in the nontidal population. However, snails in the tidal population showed different activity rhythms depending on the presence or absence of the exposure. Transcriptome analysis revealed that genes with circatidal oscillation increased due to entrainment to the tidal cycle in both populations and dominant rhythmicity was consistent with the environmental cycle. These results suggest plasticity in the endogenous rhythm in the gene expression in both populations. Note that circatidal oscillating genes were more abundant in the tidal population than in the nontidal population, suggesting that a greater number of genes are associated with circatidal clocks in the tidal population compared to the nontidal population. This increase of circatidal clock-controlled genes in the tidal population could be caused by genetic changes in the biological clock or the experience of tidal cycle in the early life stage. Our findings suggest that the plasticity of biological rhythms may have contributed to the adaptation to the tidal environment in S. reiniana.

Protocols for in vitro reconstitution of the cyanobacterial circadian clock

Circadian clocks are intracellular systems that orchestrate metabolic processes in anticipation of sunrise and sunset by providing an internal representation of local time. Because the ~24-h metabolic rhythms they produce are important to health across diverse life forms there is growing interest in their mechanisms. However, mechanistic studies are challenging in vivo due to the complex, that is, poorly defined, milieu of live cells. Recently, we reconstituted the intact circadian clock of cyanobacteria in vitro. It oscillates autonomously and remains phase coherent for many days with a fluorescence-based readout that enables real-time observation of individual clock proteins and promoter DNA simultaneously under defined conditions without user intervention. We found that reproducibility of the reactions required strict adherence to the quality of each recombinant clock protein purified from Escherichia coli. Here, we provide protocols for preparing in vitro clock samples so that other labs can ask questions about how changing environments, like temperature, metabolites, and protein levels are reflected in the core oscillator and propagated to regulation of transcription, providing deeper mechanistic insights into clock biology.

Olfactory Ensheathing Cell Ameliorate Neuroinflammation Following Spinal Cord Injury Through Upregulating REV-ERBα in Microglia

Circadian dysregulation involved in the pathophysiology of spinal cord injury (SCI). Modulation of circadian rhythms hold promise for the SCI treatment. Here, we aim to investigated the mechanism of olfactory ensheathing cells (OEC) in alleviating neuroinflammation via modulating clock gene expression in microglia. In this study, SCI rats were randomly divided into OEC group and vehicle group. At 1 day after the surgery, OECs were intravenously transplanted into OEC group SCI rat, while the rats in vehicle group received culture medium. After 7 days post of OEC transplantation, tissues were collected from the brain (prefrontal cortex, hypothalamus, spinal cord) for PCR, western blotting and immunohistochemistry (IHC) assay at zeitgeber time (ZT) 6, ZT 12, ZT 18, and ZT 24. The roles of OEC in modulating REV-ERBα in microglia were studied by experimental inhibition of gene expression and the co-culture experiment. In the vehicle group, IHC showed a significant increase of Iba-1 expression in the cerebral white matter and spinal cord compared with control group (P < 0.0001 for all comparisons). The expression of Iba-1 was significantly decreased (P < 0.0001 for all comparisons). In the OEC group, the expression of PER 1, PER 2, CLOCK, and REV-ERBα was in a rhythmical manner in both spinal cord and brain regions. SCI disrupted their typical rhythms. And OECs transplantation could modulate those dysregulations by upregulating REV-ERBα. In vitro study showed that OECs couldn't reduce the activation of REV-ERBα inhibited microglia. The intravenous transplantation of OECs can mediate cerebral and spinal microglia activation through upregulation REV-ERBα after SCI.

Temperature variation in caves and its significance for subterranean ecosystems

Climate change affects all ecosystems, but subterranean ecosystems are repeatedly neglected from political and public agendas. Cave habitats are home to unknown and endangered species, with low trait variability and intrinsic vulnerability to recover from human-induced disturbances. We studied the annual variability and cyclicity of temperatures in caves vis-à-vis surface in different climatic areas. We hypothesize that cave temperatures follow the average temperature pattern at the surface for each location with a slight delay in the signal, but we found three different thermal patterns occurring in caves: (1) high positive correlation and a similar thermal pattern to the surface, (2) low correlation and a slight thermal delay of the signal from the surface, and (3) high negative correlation with an extreme delay from the surface. We found daily thermal cycles in some caves, which may potentially control the circadian rhythms of cave organisms. Our results show that caves had lower thermal amplitude than the surface, and that thermal averages within caves approximately correspond to the to the annual average of surface temperature. Caves buffer external temperature and act as refugia for biota in extreme climatic events. Likewise, temperature increases at surface will lead to increment in caves, threatening subterranean biota and ecosystem services.

An Inexpensive System to Investigate the Daily Rhythms of Insects

Insects' daily rhythms occur in response to their surrounding environment. Recognizing the daily rhythms of pathogen vectors can be helpful in developing effective, safe, and sustainable management strategies to control vector insects and reduce the spread of pathogens. However, studying the daily rhythm of insects often requires costly or labor-intensive trapping, and few tools are available to quantify daily rhythms in the field. We developed a simple collection system to study the flight activity of mosquitoes and biting midges using a contained, programmable, rotating, automatic pet feeder. A diverse assemblage of nuisance and vector species were collected with our system, including mosquitoes of the genera Aedes, Anopheles, Culex, and Deinocerites and biting midges (Ceratopogonidae) such as the coastal pest Culicoides furens. Surprisingly, mosquitoes and biting midges were less active during crepuscular periods (1800-2100h; 0600-0900h) than during dark periods (2100h-2400h; 0300h-0600h). A number of urban and agricultural pest insects were captured, including Coleoptera, Hymenoptera, Isoptera and Lepidoptera. This study shows that relatively inexpensive products can be adapted to study the daily rhythms of flying vectors and nuisance arthropods, with implications for vector-borne disease transmission and control. The collection system could also be used with flight intercept or pitfall traps, permitting study of the circadian activity patterns of a diverse array of arthropods.

Circadian gene variation in relation to breeding season and latitude in allochronic populations of two pelagic seabird species complexes

Annual cues in the environment result in physiological changes that allow organisms to time reproduction during periods of optimal resource availability. Understanding how circadian rhythm genes sense these environmental cues and stimulate the appropriate physiological changes in response is important for determining the adaptability of species, especially in the advent of changing climate. A first step involves characterizing the environmental correlates of natural variation in these genes. Band-rumped and Leach's storm-petrels (Hydrobates spp.) are pelagic seabirds that breed across a wide range of latitudes. Importantly, some populations have undergone allochronic divergence, in which sympatric populations use the same breeding sites at different times of year. We investigated the relationship between variation in key functional regions of four genes that play an integral role in the cellular clock mechanism-Clock, Bmal1, Cry2 and Per2-with both breeding season and absolute latitude in these two species complexes. We discovered that allele frequencies in two genes, Clock and Bmal1, differed between seasonal populations in one archipelago, and also correlated with absolute latitude of breeding colonies. These results indicate that variation in these circadian rhythm genes may be involved in allochronic speciation, as well as adaptation to photoperiod at breeding locations.

Bumble Bees (Bombus terrestris) Use Time-Memory to Associate Reward with Color and Time of Day

Circadian clocks regulate ecologically important complex behaviors in honey bees, but it is not clear whether similar capacities exist in other species of bees. One key behavior influenced by circadian clocks is time-memory, which enables foraging bees to precisely time flower visitation to periods of maximal pollen or nectar availability and reduces the costs of visiting a non-rewarding flower patch. Bumble bees live in smaller societies and typically forage over shorter distances than honey bees, and it is therefore not clear whether they can similarly associate reward with time of day. We trained individually marked bumble bee (Bombus terrestris) workers to forage for sugar syrup in a flight cage with yellow or blue feeders rewarding either during the morning or evening. After training for over two weeks, we recorded all visitations to colored feeders filled with only water. We performed two experiments, each with a different colony. We found that bees tended to show higher foraging activity during the morning and evening training sessions compared to other times during the day. During the test day, the trained bees were more likely to visit the rewarding rather than the non-rewarding colored feeders at the same time of day during the test sessions, indicating that they associated time of day and color with the sugar syrup reward. These observations lend credence to the hypothesis that bumble bees have efficient time-memory, indicating that this complex behavior is not limited to honey bees that evolved sophisticated social foraging behaviors over large distances.

Characterizing the circadian connectome of Ocimum tenuiflorum using an integrated network theoretic framework

Across the three domains of life, circadian clock is known to regulate vital physiological processes, like, growth, development, defence etc. by anticipating environmental cues. In this work, we report an integrated network theoretic methodology comprising of random walk with restart and graphlet degree vectors to characterize genome wide core circadian clock and clock associated raw candidate proteins in a plant for which protein interaction information is available. As a case study, we have implemented this framework in Ocimum tenuiflorum (Tulsi); one of the most valuable medicinal plants that has been utilized since ancient times in the management of a large number of diseases. For that, 24 core clock (CC) proteins were mined in 56 template plant genomes to build their hidden Markov models (HMMs). These HMMs were then used to identify 24 core clock proteins in O. tenuiflorum. The local topology of the interologous Tulsi protein interaction network was explored to predict the CC associated raw candidate proteins. Statistical and biological significance of the raw candidates was determined using permutation and enrichment tests. A total of 66 putative CC associated proteins were identified and their functional annotation was performed.

Artificial light at night at environmental intensities disrupts daily rhythm of the oyster Crassostrea gigas

Artificial Light At Night (ALAN) masks the natural light cycles and thus can disturb the synchronization of organisms' biological rhythms with their environment. Although coastlines are highly exposed to this growing threat, studies concerning the impacts of ALAN on coastal organisms remain scarce. In this study, we investigated the ALAN exposure effects at environmentally realistic intensities (0.1, 1, 10, 25 lx) on the oyster Crassostrea gigas, a sessile bivalve subject to light pollution on shores. We focused on the effects on oyster's daily rhythm at behavioral and molecular levels. Our results showed that ALAN disrupts the oyster's daily rhythm by increasing valve activity and annihilating day / night differences of expression of circadian clock and clock-associated genes. ALAN effects occur starting from 0.1 lx, in the range of artificial skyglow illuminances. We concluded that realistic ALAN exposure affects oysters' biological rhythm, which could lead to severe physiological and ecological consequences.

Widespread psychoactive pollutant augments daytime restfulness and disrupts diurnal activity rhythms in fish

Pharmaceutical pollution is a major driver of global change, with the capacity to alter key behavioural and physiological traits in exposed animals. Antidepressants are among the most commonly detected pharmaceuticals in the environment. Despite well-documented pharmacological effects of antidepressants on sleep in humans and other vertebrates, very little is known about their ecologically relevant impacts as pollutants on non-target wildlife. Accordingly, we investigated the effects of acute 3-day exposure of eastern mosquitofish (Gambusia holbrooki) to field-realistic levels (nominal concentrations: 30 and 300 ng/L) of the widespread psychoactive pollutant, fluoxetine, on diurnal activity patterns and restfulness, as indicators of disruptions to sleep. We show that exposure to fluoxetine disrupted diel activity patterns, which was driven by augmentation of daytime inactivity. Specifically, unexposed control fish were markedly diurnal, swimming farther during the day and exhibiting longer periods and more bouts of inactivity at night. However, in fluoxetine-exposed fish, this natural diel rhythm was eroded, with no differences in activity or restfulness observed between the day and night. As a misalignment in the circadian rhythm has been shown to adversely affect fecundity and lifespan in animals, our findings reveal a potentially serious threat to the survival and reproductive success of pollutant-exposed wildlife.

Biological rhythms and task allocation in ant colonies

Task allocation in ant colonies, mediated by social interactions, regulates which individuals perform each task, and when they are active, in response to the current situation. Many tasks are performed in a daily temporal pattern. An ant's biological clock depends on patterns of gene expression that are regulated using a negative feedback loop which is synchronized to earth's rotation by external cues. An individual's biological clock can shift in response to social cues, and this plasticity contributes to task switching. Daily rhythms in individual ant behavior combine, via interactions within and across task groups, to adjust the collective behavior of colonies. Further work is needed to elucidate how the social cues that lead to task switching influence the molecular mechanisms that generate clock outputs associated with each task, and to investigate the evolution of temporal patterns in task allocation in relation to ecological factors.

Daily activity timing in the Anthropocene

Animals are facing novel 'timescapes' in which the stimuli entraining their daily activity patterns no longer match historical conditions due to anthropogenic disturbance. However, the ecological effects (e.g., altered physiology, species interactions) of novel activity timing are virtually unknown. We reviewed 1328 studies and found relatively few focusing on anthropogenic effects on activity timing. We suggest three hypotheses to stimulate future research: (i) activity-timing mismatches determine ecological effects, (ii) duration and timing of timescape modification influence effects, and (iii) consequences of altered activity timing vary biogeographically due to broad-scale variation in factors compressing timescapes. The continued growth of sampling technologies promises to facilitate the study of the consequences of altered activity timing, with emerging applications for biodiversity conservation.

Microhabitat-specific diurnal metabolomic responses of the intertidal limpet Cellana toreuma to winter low temperature

High-throughput determination of circadian rhythms in metabolic response and their divergent patterns in various microhabitats are crucial for understanding how organisms respond to environmental stresses. A mid-intertidal limpet Cellana toreuma was collected at various time points across both daytime and nighttime in winter during low tide for investigating the diurnal metabolomic responses to cold stress and elucidating the divergent metabolic responses to temperature variations across microhabitats. Temperatures of emergent rock microhabitats were lower than the tidal pool and even aggravated at night. A series of metabolomic responses exhibited coordinated diurnal changes in winter. Metabolic responses which were associated with cellular stress responses and energy metabolism of emergent rock microhabitat individuals were highly induced compared to the tidal pool ones. This study shed light on the diurnal patterns of metabolomic responses of intertidal molluscs in the field and emphasized the variations in metabolic responses between microhabitats.

Rhythms and Clocks in Marine Organisms

The regular movements of waves and tides are obvious representations of the oceans' rhythmicity. But the rhythms of marine life span across ecological niches and timescales, including short (in the range of hours) and long (in the range of days and months) periods. These rhythms regulate the physiology and behavior of individuals, as well as their interactions with each other and with the environment. This review highlights examples of rhythmicity in marine animals and algae that represent important groups of marine life across different habitats. The examples cover ecologically highly relevant species and a growing number of laboratory model systems that are used to disentangle key mechanistic principles. The review introduces fundamental concepts of chronobiology, such as the distinction between rhythmic and endogenous oscillator-driven processes. It also addresses the relevance of studying diverse rhythms and oscillators, as well as their interconnection, for making better predictions of how species will respond to environmental perturbations, including climate change. As the review aims to address scientists from the diverse fields of marine biology, ecology, and molecular chronobiology, all of which have their own scientific terms, we provide definitions of key terms throughout the article.

Chromosome-level genome of black cutworm provides novel insights into polyphagy and seasonal migration in insects

BACKGROUND

The black cutworm, Agrotis ipsilon, is a serious global underground pest. Its distinct phenotypic traits, especially its polyphagy and ability to migrate long distances, contribute to its widening distribution and increasing difficulty of control. However, knowledge about these traits is still limited.

RESULTS

We generated a high-quality chromosome-level assembly of A. ipsilon using PacBio and Hi-C technology with a contig N50 length of ~ 6.7 Mb. Comparative genomic and transcriptomic analyses showed that detoxification-associated gene families were highly expanded and induced after insects fed on specific host plants. Knockout of genes that encoded two induced ABC transporters using CRISPR/Cas9 significantly reduced larval growth rate, consistent with their contribution to host adaptation. A comparative transcriptomic analysis between tethered-flight moths and migrating moths showed expression changes in the circadian rhythm gene AiCry2 involved in sensing photoperiod variations and may receipt magnetic fields accompanied by MagR and in genes that regulate the juvenile hormone pathway and energy metabolism, all involved in migration processes.

CONCLUSIONS

This study provides valuable genomic resources for elucidating the mechanisms involved in moth migration and developing innovative control strategies.

How Does Chronobiology Contribute to the Development of Diseases in Later Life

An increasingly older population is one of the major social and medical challenges we currently face. Between 2010 and 2050, it is estimated that the proportion of adults over 65 years of age will double from 8% to 16% of the global population. A major concern associated with aging is the changes in health that can lead to various diseases such as cancer and neurogenerative diseases, which are major burdens on individuals and societies. Thus, it is imperative to better understand changes in sleep and circadian rhythms that accompany aging to improve the health of an older population and target diseases associated with aging. Circadian rhythms play a role in most physiological processes and can contribute to age-related diseases. Interestingly, there is a relationship between circadian rhythms and aging. For example, many older adults have a shift in chronotype, which is an individual's natural inclination to sleep certain times of the day. As adults age, most people tend to go to sleep earlier while also waking up earlier. Numerous studies also suggest that disrupted circadian rhythms may be indicative of developing age-related diseases, like neurodegenerative disorders and cancer. Better understanding the relationship between circadian rhythms and aging may allow us to improve current treatments or develop novel ones that target diseases commonly associated with aging.

The nocturnal life of the great scallops (Pecten maximus, L.): First description of their natural daily valve opening cycle

Valvometry techniques used to monitor bivalve gaping activity have elucidated numerous relationships with environmental fluctuations, along with biological rhythms ranging from sub-daily to seasonal. Thus, a precise understanding of the natural activity of bivalves (i.e., not exposed to stressful environmental variations) is necessary as a baseline for detecting abnormal behaviors (deviations). This knowledge is also needed to reliably interpret observations of bivalve gaping behavior and associated biological processes (e.g., respiration, nutrition) acquired over time-limited periods. With this in mind, we investigated the natural daily gaping activity of the great scallop (Pecten maximus) by continuously monitoring 35 individuals in several individual tanks and in situ (Bay of Saint-Brieuc, Brittany, France) using fully autonomous Hall effect sensors. Our results revealed a circadian cycle (τ = 24.0h) in scallop gaping activity. Despite significant inter-individual variability in mean opening and cycle amplitude, almost all individuals (87.5%) exhibited nocturnal activity, with valves more open at night than during the day. A shift in light regime in the tanks triggered an instantaneous change in opening pattern, indicating that light levels strongly determine scallop activity. Based on the opening status of scallops, we also identified several gaping behaviors deviating from the regular daily pattern (lack of rhythmicity, high daytime opening), potentially reflecting physiological weakness. While further long-term studies are required to fully understand the natural activity of scallops, these findings pave the way for studies focused on the scallop response to external factors and introduce further research into the detection of abnormal behaviors. Coupling observations of diel valve gaping cycles with other daily variations in organismal and environmental parameters could help explain mechanisms driving the growth patterns of scallops observed in their shell striations. From a technical perspective, our field-based monitoring demonstrates the suitability of autonomous valvometry sensors for studying mobile subtidal bivalve activity in remote offshore environments.

Endogenous rhythm variation and adaptation to the tidal environment in the freshwater snail, Semisulcospira reiniana

Organisms have endogenous timekeeping system(s) to coordinate their biological processes with environmental cycles, allowing adaptation to external rhythmic changes in their environment. The change in endogenous rhythms could contribute to range expansion in a novel rhythmic environment. We hypothesized that populations of the freshwater snail near estuaries show a circatidal rhythm to synchronize with the tidal cycle. We compared the behavioral and gene expression rhythms between non-tidal and tidal populations of the freshwater snail, Semisulcospira reiniana. Individuals inhabiting tidal areas exhibited a rhythmic activity pattern coordinated with the tidal cycle under both field and laboratory conditions, but individuals inhabiting upstream non-tidal areas showed a circadian activity pattern. The proportion of circadian oscillating genes was greater in non-tidal than in tidal individuals, while that of circatidal oscillating genes was greater in tidal than in non-tidal individuals. Additionally, transcriptome-wide population genetic analyses revealed that these two adjacent populations can be clearly distinguished genetically, though the genetic distance was very small. Our results provide evidence of the shift in an endogenous rhythm via range expansion to a novel rhythmic environment. The changes in a small number of genes and/or phenotypic plasticity may contribute to the difference in the endogenous rhythms between non-tidal and tidal populations.

The 5'-3' mRNA Decay Pathway Modulates the Plant Circadian Network in Arabidopsis

Circadian rhythms enable organisms to anticipate and adjust their physiology to periodic environmental changes. These rhythms are controlled by biological clocks that consist of a set of clock genes that regulate each other's expression. Circadian oscillations in messenger RNA (mRNA) levels require the regulation of mRNA production and degradation. While transcription factors controlling clock function have been well characterized from cyanobacteria to humans, the role of factors controlling mRNA decay is largely unknown. Here, we show that mutations in SM-LIKE PROTEIN 1 (LSM1) and exoribonucleases 4 (XRN4), components of the 5'-3' mRNA decay pathway, alter clock function in Arabidopsis. We found that lsm1 and xrn4 mutants display long-period phenotypes for clock gene expression. In xrn4, these circadian defects were associated with changes in circadian phases of expression, but not overall mRNA levels, of several core-clock genes. We then used noninvasive transcriptome-wide mRNA stability analysis to identify genes and pathways regulated by XRN4. Among genes affected in the xrn4 mutant at the transcriptional and posttranscriptional level, we found an enrichment in genes involved in auxin, ethylene and drought recovery. Large effects were not observed for canonical core-clock genes, although the mRNAs of several auxiliary clock genes that control the pace of the clock were stabilized in xrn4 mutants. Our results establish that the 5'-3' mRNA decay pathway constitutes a novel posttranscriptional regulatory layer of the circadian gene network, which probably acts through a combination of small effects on mRNA stability of several auxiliary and some core-clock genes.

Time restricted feeding modifies leukocyte responsiveness and improves inflammation outcome

Time restricted eating, the dietary approach limiting food intake to a maximal 10-hour period of daytime is considered beneficial in metabolic dysfunctions, such as obesity and diabetes. Rhythm of food intake and parallel changes in serum nutrient levels are also important entrainment signals for the circadian clock, particularly in tissues involved in metabolic regulation. As both the metabolic state and the circadian clock have large impact on immune functions, we investigated in mice whether time restricted feeding (TRF) affects systemic inflammatory potential. TRF slackened the symptoms in K/BxN serum-transfer arthritis, an experimental model of human autoimmune joint inflammation. Compared to ad libitum conditions TRF reduced the expression of inflammatory mediators in visceral adipose tissue, an integrator and coordinator of metabolic and inflammatory processes. Furthermore, TRF strengthened the oscillation of peripheral leukocyte counts and alongside decreased the pool of both marginated and tissue leukocytes. Our data suggest that the altered leukocyte distribution in TRF mice is related to the attenuated expression of adhesion molecules on the surface of neutrophils and monocytes. We propose that TRF modifies both rhythm and inflammatory potential of leukocytes which contribute to the milder reactivity of the immune system and therefore time-restricted eating could serve as an effective complementary tool in the therapy of autoinflammatory processes.

The diurnal emission of floral scent in Oncidium hybrid orchid is controlled by CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) through the direct regulation on terpene synthase

BACKGROUND

To adapt the periodic fluctuation of environmental factors, plants are subtle to monitor the natural variation for the growth and development. The daily activities and physiological functions in coordination with the natural variation are regulated by circadian clock genes. The circadian emission of floral scents is one of the rhythmic physiological activities controlled by circadian clock genes. Here, we study the molecular mechanism of circadian emission pattern of ocimene and linalool compounds in Oncidium Sharry Baby (Onc. SB) orchid.

RESULTS

GC-Mass analysis revealed that Onc. SB periodically emitted ocimene and linalool during 6 to 14 o'clock daily. Terpene synthase, one of the key gene in the terpenoid biosynthetic pathway is expressed in coordination with scent emission. The promoter structure of terpene synthase revealed a circadian binding sequence (CBS), 5'-AGATTTTT-3' for CIRCADIAN CLOCK ASSOCIATED1 (CCA1) transcription factor. EMSA data confirms the binding affinity of CCA1. Transactivation assay further verified that TPS expression is regulated by CCA1. It suggests that the emission of floral scents is controlled by CCA1.

CONCLUSIONS

The work validates that the mechanism of circadian emission of floral scents in Onc. Sharry Baby is controlled by the oscillator gene, CCA1(CIRCADIAN CLOCK ASSOCIATED 1) under light condition. CCA1 transcription factor up-regulates terpene synthase (TPS) by binding on CBS motif, 5'-AGATTTTT-3' of promoter region to affect the circadian emission of floral scents in Onc. SB.

Circadian activity of small brown bear populations living in human-dominated landscapes

Whereas numerous studies on large carnivores have focused on analyzing spatial patterns and habitat use, the temporal dimension of their activity has been relatively little investigated, making this a topic of growing interest, especially in human-dominated landscapes. Relict and isolated Apennine brown bears (Ursus arctos marsicanus) have been living in a human-modified landscape since millennia, but no information is available on their activity patterns. By means of GPS telemetry (26,880 GPS locations collected from 18 adult Apennine brown bears) we investigated their circadian rhythms, using hourly movement rates as an index of bear activity. Based on a Bayesian modeling approach, circadian activity of Apennine brown bears was described by a bimodal curve, with peaks of activity around sunrise and sunset. We revealed seasonal effects, with bears exhibiting higher movement rates throughout the mating season, but no relevant influence of sex. In addition, bears increased their movement rate at distances < 100–500 m to roads and settlements exclusively during spring and late summer, suggesting a trade-off between foraging opportunities and risk avoidance. The absence of a marked nocturnality in Apennine brown bears suggests a relatively low degree of habitat encroachment and disturbance by humans. Yet, the occurrence of crepuscular activity patterns and the responses in proximity of anthropogenic landscape features likely indicate a coadaptation by bears to human presence through a shift in their temporal niche. Further studies should aim to unveil fitness implications of such modifications in activity patterns.

Temporal gene expression patterns in the coral Euphyllia paradivisa reveal the complexity of biological clocks in the cnidarian-algal symbiosis

Studying chronobiology in reef-building corals is challenging due to the tightly coupled symbiosis with their photosynthetic algae, Symbiodiniaceae. Although symbiosis requires metabolic synchronization and coordination of cellular processes in the holobiont, the cross-talk between the host and symbiont's clocks is still puzzling. Here, we use the mesophotic coral Euphyllia paradivisa to examine temporal gene expression patterns in symbiotic and aposymbiotic morphs exposed to natural light/dark cycles and constant darkness. Our comparative transcriptomic analyses revealed circadian and circatidal cycles of gene expression with a predominant diel pattern in both coral morphs. We found a substantial number of transcripts consistently rhythmic under both light conditions, including genes likely involved in the cnidarians' circadian clock, thus indicating that an endogenous clock, which can oscillate independently from the Symbiodiniaceae clock, exists in E. paradivisa. The analysis further manifests the remarkable impacts of symbiosis on transcriptional rhythms and implies that the algae's presence influences the host's biorhythm.

Naturally segregating genetic variation in circadian period exhibits a regional elevational and climatic cline

Circadian clocks confer adaptation to predictable 24-h fluctuations in the exogenous environment, but it has yet to be determined what ecological factors maintain natural genetic variation in endogenous circadian period outside of the hypothesized optimum of 24 h. We estimated quantitative genetic variation in circadian period in leaf movement in 30 natural populations of the Arabidopsis relative Boechera stricta sampled within only 1° of latitude but across an elevation gradient spanning 2460-3300 m in the Rocky Mountains. Measuring ~3800 plants from 473 maternal families (7-20 per population), we found that genetic variation was of similar magnitude among versus within populations, with population means varying between 21.9 and 24.9 h and maternal family means within populations varying by up to ~6 h. After statistically accounting for spatial autocorrelation at a habitat extreme, we found that elevation explained a significant proportion of genetic variation in the circadian period, such that higher-elevation populations had shorter mean period lengths and reduced intrapopulation ranges. Environmental data indicate that these spatial trends could be related to steep regional climatic gradients in temperature, precipitation, and their intra-annual variability. Our findings suggest that spatially fine-grained environmental heterogeneity contributes to naturally occurring genetic variation in circadian traits in wild populations.

Cryptochrome 1 as a state variable of the circadian clockwork of the suprachiasmatic nucleus: Evidence from translational switching

The suprachiasmatic nucleus (SCN) of the hypothalamus is the principal clock driving circadian rhythms of physiology and behavior that adapt mammals to environmental cycles. Disruption of SCN-dependent rhythms compromises health, and so understanding SCN time keeping will inform management of diseases associated with modern lifestyles. SCN time keeping is a self-sustaining transcriptional/translational delayed feedback loop (TTFL), whereby negative regulators inhibit their own transcription. Formally, the SCN clock is viewed as a limit-cycle oscillator, the simplest being a trajectory of successive phases that progresses through two-dimensional space defined by two state variables mapped along their respective axes. The TTFL motif is readily compatible with limit-cycle models, and in Neurospora and Drosophila the negative regulators Frequency (FRQ) and Period (Per) have been identified as state variables of their respective TTFLs. The identity of state variables of the SCN oscillator is, however, less clear. Experimental identification of state variables requires reversible and temporally specific control over their abundance. Translational switching (ts) provides this, the expression of a protein of interest relying on the provision of a noncanonical amino acid. We show that the negative regulator Cryptochrome 1 (CRY1) fulfills criteria defining a state variable: ts-CRY1 dose-dependently and reversibly suppresses the baseline, amplitude, and period of SCN rhythms, and its acute withdrawal releases the TTFL to oscillate from a defined phase. Its effect also depends on its temporal pattern of expression, although constitutive ts-CRY1 sustained (albeit less stable) oscillations. We conclude that CRY1 has properties of a state variable, but may operate among several state variables within a multidimensional limit cycle.

Administration time-dependent effects of poly (I:C) on antioxidant and immune responses along the diurnal time scale in zebrafish

The circadian clock of vertebrates regulates many biological processes, including the immune system. This paper investigated whether responsiveness to poly (I:C), a synthetic analog of double-stranded RNA used as an immunostimulant, exhibits day/night differences in zebrafish. Fish were intraperitoneally (IP) injected with either phosphate-buffered saline (PBS) or poly (I:C) at two different time points: "Zeitgeber Time" (ZT) 4 (day) and ZT16 (night). Then, 6 h later, fish were euthanized, and tissue samples (skin, liver and kidney) were collected. A control group (intact fish) was also sampled at the same time points. The effect of poly (I:C) on the expression of antioxidant and immune genes was time-of-day-dependent, and the response was stronger following poly (I:C) administration in the day than at night. Time-dependent differences were observed for some genes in the PBS and control groups. However, these differences were tissue-specific. In liver, almost all the genes were affected by time of day. In kidney, poly (I:C) affected the expression of all the gene markers regardless of administration time. These findings highlight the importance of considering the time to administer poly (I:C) when evaluating the fish immune response.

Extrinsic and intrinsic factors influencing the emergence and return of the Asian particolored bat Vespertilio sinensis to the summer roost

Circadian rhythms play a crucial role in the health and survival of organisms. However, little is known concerning how intrinsic and extrinsic factors affect animal daily rhythms in the field, especially in nocturnal animals. Here, we investigated the first emergence, mid-emergence, and return times of Vespertilio sinensis, and also integrated environmental conditions (temperature, humidity, and light intensity) and biotic factors (reproductive status and predation risk) to determine causes of variation in the activity rhythms of the bats. We found that variation in the first emergence time, the mid-emergence time, and the final return time were distinct. The results demonstrated that the emergence and return times of bats were affected by light intensity, reproductive status, and predation risk in a relatively complex pattern. Light intensity had the greatest contribution to activity rhythms. Moreover, we first investigated the effects of actual predators on the activity rhythms of bats; the results showed that the mid-emergence time of bats was earlier as predators were hunting, but the final return time was later when predators were present. Finally, our results also highlighted the importance of higher energy demands during the lactation in bats to variation in activity rhythms. These results improve our understanding of the patterns and causes of variation in activity rhythms in bats and other nocturnal animals.

Cross-species transcriptomes reveal species-specific and shared molecular adaptations for plants development on iron-rich rocky outcrops soils

Background

Canga is the Brazilian term for the savanna-like vegetation harboring several endemic species on iron-rich rocky outcrops, usually considered for mining activities. Parkia platycephala Benth. and Stryphnodendron pulcherrimum (Willd.) Hochr. naturally occur in the cangas of Serra dos Carajás (eastern Amazonia, Brazil) and the surrounding forest, indicating high phenotypic plasticity. The morphological and physiological mechanisms of the plants’ establishment in the canga environment are well studied, but the molecular adaptative responses are still unknown. To understand these adaptative responses, we aimed to identify molecular mechanisms that allow the establishment of these plants in the canga environment.

Results

Plants were grown in canga and forest substrates collected in the Carajás Mineral Province. RNA was extracted from pooled leaf tissue, and RNA-seq paired-end reads were assembled into representative transcriptomes for P. platycephala and S. pulcherrimum containing 31,728 and 31,311 primary transcripts, respectively. We identified both species-specific and core molecular responses in plants grown in the canga substrate using differential expression analyses. In the species-specific analysis, we identified 1,112 and 838 differentially expressed genes for P. platycephala and S. pulcherrimum, respectively. Enrichment analyses showed that unique biological processes and metabolic pathways were affected for each species. Comparative differential expression analysis was based on shared single-copy orthologs. The overall pattern of ortholog expression was species-specific. Even so, we identified almost 300 altered genes between plants in canga and forest substrates with conserved responses in the two species. The genes were functionally associated with the response to light stimulus and the circadian rhythm pathway.

Conclusions

Plants possess species-specific adaptative responses to cope with the substrates. Our results also suggest that plants adapted to both canga and forest environments can adjust the circadian rhythm in a substrate-dependent manner. The circadian clock gene modulation might be a central mechanism regulating the plants’ development in the canga substrate in the studied legume species. The mechanism may be shared as a common mechanism to abiotic stress compensation in other native species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08449-0.

A Perspective Emphasizing Circadian Rhythm Entrainment to Ensure Sustainable Crop Production in Controlled Environment Agriculture: Dynamic Use of LED Cues

World-wide, sustainable crop production is increasingly dependent on the protection of crops from adverse local climate conditions by using controlled environment agriculture (CEA) facilities. Today's greenhouses and plant factories are becoming very technologically advanced. Important breakthroughs in our understanding of the deployment of affordable artificial lighting systems that can supplement and even replace solar radiation is the subject of this perspective article. The key to improving sustainable CEA is to synchronize those environmental cues that best entrain the natural circadian rhythm of the crop. Patterns of circadian rhythms reflect the balance of daily metabolic cycles and phenological stages of development that integrate and anticipate environmental changes for all complex organisms. Within the last decade, our understanding of the use of light-emitting diodes (LEDs) as spectrally tunable tools for stimulating plant responses has expanded rapidly. This perspective proposes that extending the photoperiod in CEA is an economically sustainable goal to for year-round productivity of tomato, using dynamic LED shifts that entrain the circadian rhythm. When the photoperiod is extended too far, tomato experiences injury. To avoid yield reduction, we look to nature for clues, and how circadian rhythms evolved in general to long-photoperiods during the summer in high-latitudes. It follows that circadian rhythm traits are good targets for breeders to select new tomato cultivars suitable for CEA. Circadian rhythm entrainment, using dynamic LED cues, can be tailored to any latitude-of-origin crop, and thus expands the strategies ensuring sustainable food security including healthy diets locally in any region of the world.

Strong parallel differential gene expression induced by hatchery rearing weakly associated with methylation signals in adult Coho Salmon (O. kisutch)

Human activities and resource exploitation led to a massive decline of wild salmonid populations, consequently, numerous conservation programs have been developed to supplement wild populations. However, many studies documented reduced fitness of hatchery-born relative to wild fish. Here, by using both RNA sequencing and Whole Genome Bisulfite Sequencing of hatchery and wild-born adult Coho salmon (Oncorhynchus kisutch) originating from two previously studied river systems, we show that early-life hatchery-rearing environment-induced significant and parallel gene expression differentiation is maintained until Coho come back to their natal river for reproduction. A total of 3,643 genes differentially expressed and 859 coexpressed genes were downregulated in parallel in hatchery-born fish from both rivers relative to their wild congeners. Among those genes, 26 displayed a significant relationship between gene expression and the median gene body methylation and 669 single CpGs displayed a significant correlation between methylation level and the associated gene expression. The link between methylation and gene expression was weak suggesting that DNA methylation is not the only player in mediating hatchery-related expression differences. Yet, significant gene expression differentiation was observed despite 18 months spent in a common environment (i.e., the sea). Finally, the differentiation is observed in parallel in two different river systems, highlighting the fact that early-life environment may account for at least some of the reduced fitness of the hatchery salmon in the wild. These results illustrate the relevance and importance of considering both epigenome and transcriptome to evaluate the costs and benefits of large-scale supplementation programs.

Transcriptomic and Metabolomic Analyses Reveal Key Metabolites, Pathways and Candidate Genes in Sophora davidii (Franch.) Skeels Seedlings Under Drought Stress

Soil aridification and desertification are particularly prominent in China's karst areas, severely limiting crop yields and vegetation restoration. Therefore, it is very important to identify naturally drought-tolerant plant species. Sophora davidii (Franch.) Skeels is resistant to drought and soil infertility, is deeply rooted and is an excellent plant material for soil and water conservation. We studied the transcriptomic and metabolomic changes in S. davidii in response to drought stress (CK, control; LD, mild drought stress; MD, moderate drought stress; and SD, severe drought stress). Sophora davidii grew normally under LD and MD stress but was inhibited under SD stress; the malondialdehyde (MDA), hydrogen peroxide (H₂O₂), soluble sugar, proline, chlorophyll a, chlorophyll b and carotenoid contents and ascorbate peroxidase (APX) activity significantly increased, while the superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities and soluble protein content significantly decreased. In the LD/CK, MD/CK and SD/CK comparison groups, there were 318, 734 and 1779 DEGs, respectively, and 100, 168 and 281 differentially accumulated metabolites, respectively. Combined analysis of the transcriptomic and metabolomic data revealed the metabolic regulation of S. davidii in response to drought stress. First, key candidate genes such as PRR7, PRR5, GI, ELF3, PsbQ, PsaK, INV, AMY, E2.4.1.13, E3.2.1.2, NCED, PP2C, PYL, ABF, WRKY33, P5CS, PRODH, AOC3, HPD, GPX, GST, CAT and SOD1 may govern the drought resistance of S. davidii. Second, three metabolites (oxidised glutathione, abscisic acid and phenylalanine) were found to be related to drought tolerance. Third, several key candidate genes and metabolites involved in 10 metabolic pathways were identified, indicating that these metabolic pathways play an important role in the response to drought in S. davidii and possibly other plant species.

Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor

Background

Circadian clocks allow organisms to anticipate daily fluctuations in their environment by driving rhythms in physiology and behavior. Inter-organismal differences in daily rhythms, called chronotypes, exist and can shift with age. In ants, age, caste-related behavior and chronotype appear to be linked. Brood-tending nurse ants are usually younger individuals and show “around-the-clock” activity. With age or in the absence of brood, nurses transition into foraging ants that show daily rhythms in activity. Ants can adaptively shift between these behavioral castes and caste-associated chronotypes depending on social context. We investigated how changes in daily gene expression could be contributing to such behavioral plasticity in Camponotus floridanus carpenter ants by combining time-course behavioral assays and RNA-Sequencing of forager and nurse brains.

Results

We found that nurse brains have three times fewer 24 h oscillating genes than foragers. However, several hundred genes that oscillated every 24 h in forager brains showed robust 8 h oscillations in nurses, including the core clock genes Period and Shaggy. These differentially rhythmic genes consisted of several components of the circadian entrainment and output pathway, including genes said to be involved in regulating insect locomotory behavior. We also found that Vitellogenin, known to regulate division of labor in social insects, showed robust 24 h oscillations in nurse brains but not in foragers. Finally, we found significant overlap between genes differentially expressed between the two ant castes and genes that show ultradian rhythms in daily expression.

Conclusion

This study provides a first look at the chronobiological differences in gene expression between forager and nurse ant brains. This endeavor allowed us to identify a putative molecular mechanism underlying plastic timekeeping: several components of the ant circadian clock and its output can seemingly oscillate at different harmonics of the circadian rhythm. We propose that such chronobiological plasticity has evolved to allow for distinct regulatory networks that underlie behavioral castes, while supporting swift caste transitions in response to colony demands. Behavioral division of labor is common among social insects. The links between chronobiological and behavioral plasticity that we found in C. floridanus, thus, likely represent a more general phenomenon that warrants further investigation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08282-x.

Mechanisms behind the Madness: How Do Zombie-Making Fungal Entomopathogens Affect Host Behavior To Increase Transmission?

Transmission is a crucial step in all pathogen life cycles. As such, certain species have evolved complex traits that increase their chances to find and invade new hosts. Fungal species that hijack insect behaviors are evident examples. Many of these "zombie-making" entomopathogens cause their hosts to exhibit heightened activity, seek out elevated positions, and display body postures that promote spore dispersal, all with specific circadian timing. Answering how fungal entomopathogens manipulate their hosts will increase our understanding of molecular aspects underlying fungus-insect interactions, pathogen-host coevolution, and the regulation of animal behavior. It may also lead to the discovery of novel bioactive compounds, given that the fungi involved have traditionally been understudied. This minireview summarizes and discusses recent work on zombie-making fungi of the orders Hypocreales and Entomophthorales that has resulted in hypotheses regarding the mechanisms that drive fungal manipulation of insect behavior. We discuss mechanical processes, host chemical signaling pathways, and fungal secreted effectors proposed to be involved in establishing pathogen-adaptive behaviors. Additionally, we touch on effectors' possible modes of action and how the convergent evolution of host manipulation could have given rise to the many parallels in observed behaviors across fungus-insect systems and beyond. However, the hypothesized mechanisms of behavior manipulation have yet to be proven. We, therefore, also suggest avenues of research that would move the field toward a more quantitative future.

Social synchronization of circadian rhythms with a focus on honeybees

Many animals benefit from synchronizing their daily activities with conspecifics. In this hybrid paper, we first review recent literature supporting and extending earlier evidence for a lack of clear relationship between the level of sociality and social entrainment of circadian rhythms. Social entrainment is specifically potent in social animals that live in constant environments in which some or all individuals do not experience the ambient day-night cycles. We next focus on highly social honeybees in which there is good evidence that social cues entrain the circadian clocks of nest bees and can override the influence of conflicting light-dark cycles. The current understanding of social synchronization in honeybees is consistent with self-organization models in which surrogates of forager activity, such as substrate-borne vibrations and colony volatiles, entrain the circadian clocks of bees dwelling in the dark cavity of the nest. Finally, we present original findings showing that social synchronization is effective even in an array of individually caged callow bees placed on the same substrate and is improved for bees in connected cages. These findings reveal remarkable sensitivity to social time-giving cues and show that bees with attenuated rhythms (weak oscillators) can nevertheless be socially synchronized to a common phase of activity. This article is part of the theme issue 'Synchrony and rhythm interaction: from the brain to behavioural ecology'.

The impact of stress and stress hormones on endogenous clocks and circadian rhythms

In mammals, daily rhythms in physiology and behavior are under control of a circadian pacemaker situated in the suprachiasmatic nucleus (SCN). This master clock receives photic input from the retina and coordinates peripheral oscillators present in other tissues, maintaining all rhythms in the body synchronized to the environmental light-dark cycle. In line with its function as a master clock, the SCN appears to be well protected against unpredictable stressful stimuli. However, available data indicate that stress and stress hormones at certain times of day are capable of shifting peripheral oscillators in, e.g., liver, kidney and heart, which are normally under control of the SCN. Such shifts of peripheral oscillators may represent a temporary change in circadian organization that facilitates adaptation to repeated stress. Alternatively, these shifts of internal rhythms may represent an imbalance between precisely orchestrated physiological and behavioral processes that may have severe consequences for health and well-being.

Diel Patterns of Pheromone Release By Male Sea Lamprey

Costs to producing sexual signals can create selective pressures on males to invest signaling effort in particular contexts. When the benefits of signaling vary consistently across time, males can optimize signal investment to specific temporal contexts using biological rhythms. Sea lamprey, Petromyzon marinus, have a semelparous life history, are primarily nocturnal, and rely on pheromone communication for reproduction; however, whether male investment in pheromone transport and release matches increases in spawning activity remains unknown. By measuring 1) 3keto-petromyzonol sulfate (3kPZS, a main pheromone component) and its biosynthetic precursor petromyzonol sulfate (PZS) in holding water and tissue samples at 6 points over the course of 24 hours, and 2) 3kPZS release over the course of several days, we demonstrate that 3kPZS release exhibits a consistent diel pattern across several days with elevated pheromone release just prior to sunset and at night. Trends in hepatic concentrations and circulatory transport of PZS and 3kPZS were consistent with patterns of 3kPZS release and suggest the possibility of direct upregulation in pheromone transport and release rather than observed release patterns being solely a byproduct of increased behavioral activity. Our results suggest males evolved a signaling strategy that synchronizes elevated pheromone release with nocturnal increases in sea lamprey behavior. This may be imperative to ensure that male signaling effort is not wasted in a species having a single, reproductive event.

Light exposure mediates circadian rhythms of rhizosphere microbial communities

Microbial community circadian rhythms have a broad influence on host health and even though light-induced environmental fluctuations could regulate microbial communities, the contribution of light to the circadian rhythms of rhizosphere microbial communities has received little attention. To address this gap, we monitored diel changes in the microbial communities in rice (Oryza sativa L.) rhizosphere soil under light-dark and constant dark regimes, identifying microbes with circadian rhythms caused by light exposure and microbial circadian clocks, respectively. While rhizosphere microbial communities displayed circadian rhythms under light-dark and constant dark regimes, taxa possessing circadian rhythms under the two conditions were dissimilar. Light exposure concealed microbial circadian clocks as a regulatory driver, leading to fewer ecological niches in light versus dark communities. These findings disentangle regulation mechanisms for circadian rhythms in the rice rhizosphere microbial communities and highlight the role of light-induced regulation of rhizosphere microbial communities.

Molecular basis of synchronous replication of malaria parasites in the blood stage

The search for host factors that leads to malaria parasite synchronization has been the focus of several laboratories. The host hormone melatonin synchronizes Plasmodium falciparum in culture by increasing the number of mature parasite stages through a PLC-IP3 activation. Melatonin signaling is linked to crosstalk between Ca²⁺-cAMP that results in PKA activation. Two other kinases, PfPK7 and PfeIK1, and the nuclear protein PfMORC that lacks melatonin sensitivity in the inducible knock-down parasites are also identified as part of the hormone-signal transduction pathways. Melatonin also modulates P. falciparum mitochondrial fission genes FIS1, DYN1, and DYN2 in a stage-specific manner. How these multiple molecular mechanisms are orchestrated to lead to parasite synchronization is a fascinating and opened biological question.

Characterizing the modern light environment and its influence on circadian rhythms

Humans have largely supplanted natural light cycles with a variety of electric light sources and schedules misaligned with day-night cycles. Circadian disruption has been linked to a number of disease processes, but the extent of circadian disruption among the population is unknown. In this study, we measured light exposure and wrist temperature among residents of an urban area during each of the four seasons, as well as light illuminance in nearby outdoor locations. Daily light exposure was significantly lower for individuals, compared to outdoor light sensors, across all four seasons. There was also little seasonal variation in the realized photoperiod experienced by individuals, with the only significant difference occurring between winter and summer. We tested the hypothesis that differential light exposure impacts circadian phase timing, detected via the wrist temperature rhythm. To determine the influence of light exposure on circadian rhythms, we modelled the impact of morning and night-time light exposure on the timing of the maximum wrist temperature. We found that morning and night-time light exposure had significant but opposing impacts on maximum wrist temperature timing. Our results demonstrate that, within the range of exposure seen in everyday life, night-time light can delay the onset of the maximum wrist temperature, while morning light can lead to earlier onset. Our results demonstrate that humans are minimizing natural seasonal differences in light exposure, and that circadian shifts and disruptions may be a more regular occurrence in the general population than is currently recognized.

Repeated evolution of circadian clock dysregulation in cavefish populations

Circadian rhythms are nearly ubiquitous throughout nature, suggesting they are critical for survival in diverse environments. Organisms inhabiting largely arrhythmic environments, such as caves, offer a unique opportunity to study the evolution of circadian rhythms in response to changing ecological pressures. Populations of the Mexican tetra, Astyanax mexicanus, have repeatedly invaded caves from surface rivers, where individuals must contend with perpetual darkness, reduced food availability, and limited fluctuations in daily environmental cues. To investigate the molecular basis for evolved changes in circadian rhythms, we investigated rhythmic transcription across multiple independently-evolved cavefish populations. Our findings reveal that evolution in a cave environment has led to the repeated disruption of the endogenous biological clock, and its entrainment by light. The circadian transcriptome shows widespread reductions and losses of rhythmic transcription and changes to the timing of the activation/repression of core-transcriptional clock. In addition to dysregulation of the core clock, we find that rhythmic transcription of the melatonin regulator aanat2 and melatonin rhythms are disrupted in cavefish under darkness. Mutants of aanat2 and core clock gene rorca disrupt diurnal regulation of sleep in A. mexicanus, phenocopying circadian modulation of sleep and activity phenotypes of cave populations. Together, these findings reveal multiple independent mechanisms for loss of circadian rhythms in cavefish populations and provide a platform for studying how evolved changes in the biological clock can contribute to variation in sleep and circadian behavior.

Biological rhythms are molecular, physiological, and behavioral changes that follow a daily cycle and allow for animals to coordinate critical biological processes with their external environment. While these clocks are ubiquitous from unicellular life through humans, little is known about how they evolve in the absence of daily cycling within an environment. In this study, we sought to understand the evolutionary response of the biological clock when organisms become established in an environment that lacks daily fluctuations in light, temperature, and other environmental factors. Astyanax mexicanus have repeatedly moved from surface rivers into caves where they live in complete darkness. We find that multiple populations of cavefish have disrupted biological clocks compared to their surface relatives, but that these clocks are disrupted via different molecular mechanisms in different populations. Our results suggest that changes to the biological clock in these populations may also affect aspects of cavefish behavior, like the sleep-wake cycle. This study demonstrates that moving into an environment without daily cycles has led to predictable disruptions to the biological clock among cavefish populations, but that the clock itself can be broken multiple ways.

Warm nights disrupt transcriptome rhythms in field-grown rice panicles

In rice, a small increase in nighttime temperature reduces grain yield and quality. How warm nighttime temperatures (WNT) produce these detrimental effects is not well understood, especially in field conditions where the typical day-to-night temperature fluctuation exceeds the mild increase in nighttime temperature. We observed genome-wide disruption of gene expression timing during the reproductive phase in field-grown rice panicles acclimated to 2 to 3 °C WNT. Transcripts previously identified as rhythmically expressed with a 24-h period and circadian-regulated transcripts were more sensitive to WNT than were nonrhythmic transcripts. The system-wide perturbations in transcript levels suggest that WNT disrupt the tight temporal coordination between internal molecular events and the environment, resulting in reduced productivity. We identified transcriptional regulators whose predicted targets are enriched for sensitivity to WNT. The affected transcripts and candidate regulators identified through our network analysis explain molecular mechanisms driving sensitivity to WNT and identify candidates that can be targeted to enhance tolerance to WNT.

Evolutionary conservations, changes of circadian rhythms and their effect on circadian disturbances and therapeutic approaches

The circadian rhythm is essential for the interaction of all living organisms with their environments. Several processes, such as thermoregulation, metabolism, cognition and memory, are regulated by the internal clock. Disturbances in the circadian rhythm have been shown to lead to the development of neuropsychiatric disorders, including attention-deficit hyperactivity disorder (ADHD). Interestingly, the mechanism of the circadian rhythms has been conserved in many different species, and misalignment between circadian rhythms and the environment results in evolutionary regression and lifespan reduction. This review summarises the conserved mechanism of the internal clock and its major interspecies differences. In addition, it focuses on effects the circadian rhythm disturbances, especially in cases of ADHD, and describes the possibility of recombinant proteins generated by eukaryotic expression systems as therapeutic agents as well as CRISPR/Cas9 technology as a potential tool for research and therapy. The aim is to give an overview about the evolutionary conserved mechanism as well as the changes of the circadian clock. Furthermore, current knowledge about circadian rhythm disturbances and therapeutic approaches is discussed.

Natural Zeitgebers Under Temperate Conditions Cannot Compensate for the Loss of a Functional Circadian Clock in Timing of a Vital Behavior in Drosophila

The adaptive significance of adjusting behavioral activities to the right time of the day seems obvious. Laboratory studies implicated an important role of circadian clocks in behavioral timing and rhythmicity. Yet, recent studies on clock-mutant animals questioned this importance under more naturalistic settings, as various clock mutants showed nearly normal diel activity rhythms under seminatural zeitgeber conditions. We here report evidence that proper timing of eclosion, a vital behavior of the fruit fly Drosophila melanogaster, requires a functional molecular clock under quasi-natural conditions. In contrast to wild-type flies, period01 mutants with a defective molecular clock showed impaired rhythmicity and gating in a temperate environment even in the presence of a full complement of abiotic zeitgebers. Although period01 mutants still eclosed during a certain time window during the day, this time window was much broader and loosely defined, and rhythmicity was lower or lost as classified by various statistical measures. Moreover, peak eclosion time became more susceptible to variable day-to-day changes of light. In contrast, flies with impaired peptidergic interclock signaling (Pdf01 and han5304 PDF receptor mutants) eclosed mostly rhythmically with normal gate sizes, similar to wild-type controls. Our results suggest that the presence of natural zeitgebers is not sufficient, and a functional molecular clock is required to induce stable temporal eclosion patterns in flies under temperate conditions with considerable day-to-day variation in light intensity and temperature. Temperate zeitgebers are, however, sufficient to functionally rescue a loss of PDF-mediated clock-internal and -output signaling.

The urban-adapted underground mosquito Culex pipiens form molestus maintains exogenously influenceable circadian rhythms

Genes known to affect circadian rhythms (i.e. 'clock genes') also influence the photoperiodic induction of overwintering reproductive diapause in the northern house mosquito, Culex pipiens f. pipiens. This suggests that molecular changes in one or more clock genes could contribute to the inability to diapause in a second form of this mosquito, Culex pipiens f. molestus. Temperate populations of Cx. pipiens f. molestus inhabit underground locations generally devoid of predictable photoperiods. For this reason, there could be limited fitness consequences if the hypothesized molecular changes to its clock genes also eliminated this mosquito's ability to regulate circadian rhythms in response to photoperiod variation. Here, we demonstrate that in contrast to this prediction, underground derived Cx. pipiens f. molestus retain exogenously influenceable circadian rhythms. Nonetheless, our genetic analyses indicate that the gene Helicase domino (dom) has a nine-nucleotide, in-frame deletion specific to Cx. pipiens f. molestus. Previous work has shown that splice variants in this gene differentially influence circadian behavior in Drosophila melanogaster. We also find derived, non-synonymous single nucleotide polymorphisms (SNPs) in eight genes that may also affect circadian rhythms and/or diapause induction in Cx. pipiens f. molestus. Finally, four putative circadian genes were found to have no quantifiable expression during any examined life stage, suggesting potential regulatory effects. Collectively, our findings indicate that the distinct, but molecularly interconnected life-history traits of diapause induction and circadian rhythms are decoupled in Cx. pipiens f. molestus and suggest this taxon may be a valuable tool for exploring exogenously influenced phenotypes in mosquitoes more broadly.