Circadian timing in central and peripheral tissues in a migratory songbird: dependence on annual life-history states

Avian migration clocks in a changing world

Avian long-distance migration requires refined programming to orchestrate the birds' movements on annual temporal and continental spatial scales. Programming is particularly important as long-distance movements typically anticipate future environmental conditions. Hence, migration has long been of particular interest in chronobiology. Captivity studies using a proxy, the shift to nocturnality during migration seasons (i.e., migratory restlessness), have revealed circannual and circadian regulation, as well as an innate sense of direction. Thanks to rapid development of tracking technology, detailed information from free-flying birds, including annual-cycle data and actograms, now allows relating this mechanistic background to behaviour in the wild. Likewise, genomic approaches begin to unravel the many physiological pathways that contribute to migration. Despite these advances, it is still unclear how migration programmes are integrated with specific environmental conditions experienced during the journey. Such knowledge is imminently important as temporal environments undergo rapid anthropogenic modification. Migratory birds as a group are not dealing well with the changes, yet some species show remarkable adjustments at behavioural and genetic levels. Integrated research programmes and interdisciplinary collaborations are needed to understand the range of responses of migratory birds to environmental change, and more broadly, the functioning of timing programmes under natural conditions.

Understanding the role of temperature in seasonal timing: Effects on behavioural, physiological and molecular phenotypes

Organisms adapt to daily and seasonal environmental changes to maximise their metabolic and reproductive fitness. For seasonally breeding animals, photoperiod is considered the most robust cue to drive these changes. It, however, does not explain the interannual variations in different seasonal phenotypes. Several studies have repeatedly shown the influence of ambient temperature on the timing of different seasonal physiologies including the timing of migration, reproduction and its associated behaviours, etc. In the present review, we have discussed the effects of changes in ambient temperature on different seasonal events in endotherms with a focus on migratory birds as they have evolved to draw benefits from distinct but largely predictable seasonal patterns of natural resources. We have further discussed the physiological and molecular mechanisms by which temperature affects seasonal timings. The primary brain area involved in detecting temperature changes is the hypothalamic preoptic area. This area receives thermal inputs via sensory neurons in the peripheral ganglia that measure changes in thermoregulatory tissues such as the skin and spinal cord. For the input signals, several thermal sensory TRP (transient receptor potential ion channels) channels have been identified across different classes of vertebrates. These channels are activated at specific thermal ranges. Once perceived, this information should activate an effector function. However, the link between temperature sensation and the effector pathways is not properly understood yet. Here, we have summarised the available information that may help us understand how temperature information is translated into seasonal timing.

White-throated sparrow (Zonotrichia albicollis) liver and pectoralis flight muscle transcriptomic changes in preparation for migration

Migratory songbirds undertake challenging journeys to reach their breeding grounds each spring. They accomplish these nonstop flapping feats of endurance through a suite of physiological changes, including the development of substantial fat stores and flight muscle hypertrophy and an increased capacity for fat catabolism. In addition, migratory birds may show large reductions in organ masses during flight, including the flight muscle and liver, which they must rapidly rebuild during their migratory stopover before replenishing their fat stores. However, the molecular basis of this capacity for rapid tissue remodeling and energetic output has not been thoroughly investigated. We performed RNA-sequencing analysis of the liver and pectoralis flight muscle of captive white-throated sparrows in experimentally photostimulated migratory and nonmigratory condition to explore the mechanisms of seasonal change to metabolism and tissue mass regulation that may facilitate these migratory journeys. Based on transcriptional changes, we propose that tissue-specific adjustments in preparation for migration may alleviate the damaging effects of long-duration activity, including a potential increase to the inflammatory response in the muscle. Furthermore, we hypothesize that seasonal hypertrophy balances satellite cell recruitment and apoptosis, while little evidence appeared in the transcriptome to support myostatin-, insulin-like growth factor 1-, and mammalian target of rapamycin-mediated pathways for muscle growth. These findings can encourage more targeted molecular studies on the unique integration of pathways that we find in the development of the migratory endurance phenotype in songbirds.NEW & NOTEWORTHY Migratory songbirds undergo significant physiological changes to accomplish their impressive migratory journeys. However, we have a limited understanding of the regulatory mechanisms underlying these changes. Here, we explore the transcriptomic changes to the flight muscle and liver of white-throated sparrows as they develop the migratory condition. We use these patterns to develop hypotheses about metabolic flexibility and tissue restructuring in preparation for migration.

Time trees and clock genes: a systematic review and comparative analysis of contemporary avian migration genetics

Timing is a crucial aspect for survival and reproduction in seasonal environments leading to carefully scheduled annual programs of migration in many species. But what are the exact mechanisms through which birds (class: Aves) can keep track of time, anticipate seasonal changes, and adapt their behaviour? One proposed mechanism regulating annual behaviour is the circadian clock, controlled by a highly conserved set of genes, collectively called 'clock genes' which are well established in controlling the daily rhythmicity of physiology and behaviour. Due to diverse migration patterns observed within and among species, in a seemingly endogenously programmed manner, the field of migration genetics has sought and tested several candidate genes within the clock circuitry that may underlie the observed differences in breeding and migration behaviour. Among others, length polymorphisms within genes such as Clock and Adcyap1 have been hypothesised to play a putative role, although association and fitness studies in various species have yielded mixed results. To contextualise the existing body of data, here we conducted a systematic review of all published studies relating polymorphisms in clock genes to seasonality in a phylogenetically and taxonomically informed manner. This was complemented by a standardised comparative re-analysis of candidate gene polymorphisms of 76 bird species, of which 58 are migrants and 18 are residents, along with population genetics analyses for 40 species with available allele data. We tested genetic diversity estimates, used Mantel tests for spatial genetic analyses, and evaluated relationships between candidate gene allele length and population averages for geographic range (breeding- and non-breeding latitude), migration distance, timing of migration, taxonomic relationships, and divergence times. Our combined analysis provided evidence (i) of a putative association between Clock gene variation and autumn migration as well as a putative association between Adcyap1 gene variation and spring migration in migratory species; (ii) that these candidate genes are not diagnostic markers to distinguish migratory from sedentary birds; and (iii) of correlated variability in both genes with divergence time, potentially reflecting ancestrally inherited genotypes rather than contemporary changes driven by selection. These findings highlight a tentative association between these candidate genes and migration attributes as well as genetic constraints on evolutionary adaptation.

Genetic Control of Avian Migration: Insights from Studies in Latitudinal Passerine Migrants

Twice-a-year, large-scale movement of billions of birds across latitudinal gradients is one of the most fascinating behavioral phenomena seen among animals. These seasonal voyages in autumn southwards and in spring northwards occur within a discrete time window and, as part of an overall annual itinerary, involve close interaction of the endogenous rhythm at several levels with prevailing photoperiod and temperature. The overall success of seasonal migrations thus depends on their close coupling with the other annual sub-cycles, namely those of the breeding, post-breeding recovery, molt and non-migratory periods. There are striking alterations in the daily behavior and physiology with the onset and end of the migratory period, as shown by the phase inversions in behavioral (a diurnal passerine bird becomes nocturnal and flies at night) and neural activities. Interestingly, there are also differences in the behavior, physiology and regulatory strategies between autumn and spring (vernal) migrations. Concurrent molecular changes occur in regulatory (brain) and metabolic (liver, flight muscle) tissues, as shown in the expression of genes particularly associated with 24 h timekeeping, fat accumulation and the overall metabolism. Here, we present insights into the genetic basis of migratory behavior based on studies using both candidate and global gene expression approaches in passerine migrants, with special reference to Palearctic-Indian migratory blackheaded and redheaded buntings.

Photoperiodic modulation of melatonin receptor and immune genes in migratory redheaded bunting

The transcriptional regulation of innate immune function across annual life history states (LHS) remains obscure in avian migrants. We, therefore, investigated this in a migratory passerine songbird, redheaded bunting (Emberiza bruniceps), which exhibits long-distance vernal migration from India to Central Asia. We exposed the birds (N = 10) to differential photoperiodic conditions to induce a non-migratory (NM), pre-migratory (PM), migratory (MIG), and refractory (REF) state, and performed gene expression assays of melatonin receptors (MEL1A and MEL1B), and innate immunity-linked genes (IL1B, IL6, TLR4, and NFKB) in spleen and blood. We found a significant reduction in splenic mass and volume, and a parallel increase in fat accumulation, and testicular growth in birds under migratory state. The gene expression assay revealed an upregulation of MEL1A and MEL1B mRNA levels in both the tissues in MIG. Additionally, we found a nocturnal increase of splenic IL1B expression, and IL1B, IL6, and TLR4 expression in the blood. The mRNA expression of melatonin receptors and proinflammatory cytokine showed a positive correlation. These results suggest that melatonin relays the photoperiodic signal to peripheral immune organs, which shows LHS-dependent changes in mRNA expression of immune genes.

Photoperiod-driven concurrent changes in hypothalamic and brainstem transcription of sleep and immune genes in migratory redheaded bunting

The molecular regulation of sleep in avian migrants is still obscure. We thus investigated this in migratory redheaded buntings, where four life-history states (LHS; i.e. non-migratory, pre-migratory, migratory and refractory states) were induced. There was increased night-time activity (i.e. Zugunruhe) during the migratory state with reduced daytime activity. The recordings of the sleep-wake cycle in buntings showed increased night-time active wakefulness coupled with drastically reduced front and back sleep during migratory phase. Interestingly, we found the buntings to feed and drink even after lights-off during migration. Gene expression studies revealed increased hypothalamic expression of glucocorticoid receptor (nr3c1), and pro-inflammatory cytokines (il1b and il6) in pre-migratory and migratory states, respectively, whereas in brainstem Ca2+/calmodulin-dependent protein kinase 2 (camk2) was upregulated during the migratory state. This suggested a heightened pro-inflammatory state during migration which is a feature of chronic sleep loss, and a possible role of Ca2+ signalling in promoting wakefulness. In both the hypothalamus and brainstem, the expression of melatonin receptors (mel1a and mel1b) was increased in the pre-migratory state, and growth hormone-releasing hormone (ghrh, known to induce sleep) was reduced during the migratory state. The current results demonstrate key molecules involved in the regulation of sleep-wake cycle across LHS in migratory songbirds.

Hypothalamic molecular correlates of photoperiod-induced spring migration in intact and castrated male redheaded buntings

This study investigated the molecular changes associated with neural plasticity in photoperiodic induction of spring migration in intact and castrated redheaded bunting, Emberiza bruniceps. We measured the hypothalamic mRNA expression of genes in birds that were photostimulated into winter non-migratory and spring (vernal) migratory phenotypes under short and long photoperiods, respectively. These included genes associated with the appetitive phase of reproduction (spring migration drive, th and ddc genes encoding for tyrosine hydroxylase and dopamine decarboxylase enzymes, respectively), sleep/awake state (pmch gene encoding for pro-melanin concentrating hormone; hcrt and hcrtr2 encoding for the hypocretin/orexin and its receptor, respectively) and neurogenesis (dcx and neuN coding for doublecortin and neuronal nuclear proteins, respectively). Higher th mRNA levels suggested an upregulated dopamine synthesis in the hypothalamus of spring migrants. Similarly, elevated hcrt and hcrtr2 mRNA levels suggested an increased wakefulness, and those of dcx and neuN genes suggested an enhanced neurogenesis during the spring migration state. Further, compared to intact birds, the lower th and pmch, and higher hcrtr2 and neuN mRNA levels in castrates suggested a role of testicular steroids in modulation of the appetitive phase of reproduction, sleep and awake states, and neurogenesis during spring migration period. These results provide insights into molecular changes linked with important hypothalamic molecular pathways and steroidal influence in the photoperiodic induction of spring migration in obligate migratory songbirds.

TRH and NPY Interact to Regulate Dynamic Changes in Energy Balance in the Male Zebra Finch

In contrast to mammals, birds have a higher basal metabolic rate and undertake wide range of energy-demanding activities. As a consequence, food deprivation for birds, even for a short period, poses major energy challenge. The energy-regulating hypothalamic homeostatic mechanisms, although extensively studied in mammals, are far from clear in the case of birds. We focus on the interplay between neuropeptide Y (NPY) and thyrotropin-releasing hormone (TRH), 2 of the most important hypothalamic signaling agents, in modulating the energy balance in a bird model, the zebra finch, Taeniopygia guttata. TRH neurons were confined to a few nuclei in the preoptic area and hypothalamus, and fibers widely distributed. The majority of TRH neurons in the hypothalamic paraventricular nucleus (PVN) whose axons terminate in median eminence were contacted by NPY-containing axons. Compared to fed animals, fasting significantly reduced body weight, PVN pro-TRH messenger RNA (mRNA) and TRH immunoreactivity, but increased NPY mRNA and NPY immunoreactivity in the infundibular nucleus (IN, avian homologue of mammalian arcuate nucleus) and PVN. Refeeding for a short duration restored PVN pro-TRH and IN NPY mRNA, and PVN NPY innervation to fed levels. Compared to control tissues, treatment of the hypothalamic superfused slices with NPY or an NPY-Y1 receptor agonist significantly reduced TRH immunoreactivity, a response blocked by treatment with a Y1-receptor antagonist. We describe a detailed neuroanatomical map of TRH-equipped elements, identify new TRH-producing neuronal groups in the avian brain, and demonstrate rapid restoration of the fasting-induced suppression of PVN TRH following refeeding. We further show that NPY via Y1 receptors may regulate PVN TRH neurons to control energy balance in T. guttata.

Control and adaptability of seasonal changes in behavior and physiology of latitudinal avian migrants: Insights from laboratory studies in Palearctic-Indian migratory buntings

Twice-a-year migrations, one in autumn and the other in spring, occur within a discrete time window with striking alterations in the behavior and physiology, as regulated by the interaction of endogenous rhythms with prevailing photoperiod. These seasonal voyages are not isolated events; rather, they are part of an overall annual itinerary and remain closely coupled to the other annual subcycles, called seasonal life history states (LHSs). The success of migration depends on appropriate timing of the initiation and termination of each LHS, for example, reproduction, molt, summer nonmigratory, preautumn migratory (fattening and weight gain), autumn migratory, winter nonmigratory (wnM), prevernal (spring) migratory (fattening and weight gain), and spring migratory LHSs. Migration-linked photoperiod-induced changes include the body fattening and weight gain, nocturnal Zugunruhe (migratory restlessness), elevated triglycerides and free fatty acids, triiodothyronine and corticosterone levels. Hypothalamic expression of the thyroid hormone-responsive dio2 and dio3, light-responsive per2, cry1, and adcyap1 and th (tyrosine hydroxylase, involved in dopamine biosynthesis) genes also show significant changes with transition from wnM to the vernal migratory LHS. Concurrent changes in the expression of genes associated with lipid metabolism and its transport also occur in the liver and flight muscles, respectively. Interestingly, there are clear differences in the behavioral and physiological phenotypes, and associated molecular changes, between the autumn and vernal migrations. In this review, we discuss seasonal changes in the behavior and physiology, and present molecular insights into the development of migratory phenotypes in latitudinal avian migrants, with special reference to Palearctic-Indian migratory buntings.

Seasonality in tropical birds

The survival of offspring depends on environmental conditions. Many organisms have evolved with seasonality, characterized as initiation-termination-reinitiation of several physiological processes (i.e., body fattening, molt, plumage coloration, reproduction, etc). It is an adaptation for the survival of many species. Predominantly seasonal breeders use photoperiod as the most reliable environmental cue to adapt to seasonal changes but supplementary factors like temperature and food are synergistically involved in seasonal processes. Studies from diverse vertebrate systems have contributed to understanding the mechanism involved in seasonal reproduction at the molecular and endocrine levels. Long-day induced thyrotropin (thyroid-stimulating hormone) released from the pars tuberalis of the pituitary gland triggers local thyroid hormone activation within the mediobasal hypothalamus. This locally produced thyroid hormone, T3, regulates seasonal gonadotropin-releasing hormone secretion. Most of the bird species studied are seasonal in reproduction and linked behavior and, therefore, need to adjust reproductive decisions to environmental fluctuations. Reproductive strategies of the temperate zone breeders are well-documented, but less is known about tropical birds' reproduction and factors stimulating the annual breeding strategies. Here, we address seasonality in tropical birds with reference to seasonal reproduction and the various environmental factors influencing seasonal breeding.

Molecular expression of clock genes in central and peripheral tissues of white-rumped munia (Lonchura striata)

To synchronize with the fluctuating environment, organisms have evolved an endogenous time tracking mechanism referred to as the biological clock(s). This clock machinery has been identified in almost all cells of vertebrates and categorized as central and peripheral clocks. In birds, three independent circadian clocks have been identified in the hypothalamus, the pineal and the retina which interact and generate circadian time at a functional level. However, there is a limited knowledge of molecular clockwork and integration between central and peripheral clocks in birds. Therefore, we studied the daily expression of clock genes (Bmal1, Clock, Per2, Cry1, Npas2, Rev-Erbα, E4bp4, Pparα, Hlf and Tef) in three central circadian clocks (hypothalamus, pineal and retina), other brain areas (cerebellum, optic tectum and telencephalon) and in the peripheral tissues (liver, intestine, muscle and blood) of white-rumped munia. Adult birds were exposed to equinox photoperiod (12 L:12D) for 2 weeks and were then sampled (N = 5 per time point) at six-time points (ZT1, ZT5, ZT9, ZT13, ZT17 and ZT21). Daily expressions of clock genes were studied using qPCR. We observed daily variations and tissue-specific expression patterns for clock genes. These results are consistent with the autoregulatory circadian feedback loop proposed for the mammalian system and thus suggest a conserved tissue-level circadian time generation in white-rumped munia.

Photoperiodically driven transcriptome-wide changes in the hypothalamus reveal transcriptional differences between physiologically contrasting seasonal life-history states in migratory songbirds

We investigated time course of photoperiodically driven transcriptional responses in physiologically contrasting seasonal life-history states in migratory blackheaded buntings. Birds exhibiting unstimulated winter phenotype (photosensitive state; responsive to photostimulation) under 6-h short days, and regressed summer phenotype (photorefractory state; unresponsiveness to photostimulation) under 16-h long days, were released into an extended light period up to 22 h of the day. Increased tshβ and dio2, and decreased dio3 mRNA levels in hypothalamus, and low prdx4 and high il1β mRNA levels in blood confirmed photoperiodic induction by hour 18 in photosensitive birds. Further, at hours 10, 14, 18 and 22 of light exposure, the comparison of hypothalamus RNA-Seq results revealed transcriptional differences within and between states. Particularly, we found reduced expression at hour 14 of transthyretin and proopiomelanocortin receptor, and increased expression at hour 18 of apolipoprotein A1 and carbon metabolism related genes in the photosensitive state. Similarly, valine, leucine and isoleucine degradation pathway genes and superoxide dismutase 1 were upregulated, and cocaine- and amphetamine-regulated transcript and gastrin-releasing peptide were downregulated in the photosensitive state. These results show life-history-dependent activation of hypothalamic molecular pathways involved in initiation and maintenance of key biological processes as early as on the first long day.

Molecular changes associated with migratory departure from wintering areas in obligate songbird migrants

Day length regulates the development of spring migratory and subsequent reproductive phenotypes in avian migrants. This study used molecular approaches, and compared mRNA and proteome-wide expression in captive redheaded buntings that were photostimulated under long-day (LD) conditions for 4 days (early stimulated, LD-eS) or for ∼3 weeks until each bird had shown 4 successive nights of Zugunruhe (stimulated, LD-S); controls were maintained under short days. After ∼3 weeks of LD, photostimulated indices of the migratory preparedness (fattening, weight gain and Zugunruhe) were paralleled with upregulated expression of acc, dgat2 and apoa1 genes in the liver, and of cd36, fabp3 and cpt1 genes in the flight muscle, suggesting enhanced fatty acid (FA) synthesis and transport in the LD-S state. Concurrently, elevated expression of genes involved in the calcium ion signalling and transport (camk1 and atp2a2; camk2a in LD-eS), cellular stress (hspa8 and sod1, not nos2) and metabolic pathways (apoa1 and sirt1), but not of genes associated with migratory behaviour (adcyap1 and vps13a), were found in the mediobasal hypothalamus (MBH). Further, MBH-specific quantitative proteomics revealed that out of 503 annotated proteins, 28 were differentially expressed (LD-eS versus LD-S: 21 up-regulated and 7 down-regulated) and they enriched five physiological pathways that are associated with FA transport and metabolism. These first comprehensive results on gene and protein expression suggest that changes in molecular correlates of FA transport and metabolism may aid the decision for migratory departure from wintering areas in obligate songbird migrants.

Ambient temperature affects multiple drivers of physiology and behaviour: adaptation for timely departure of obligate spring migrants

We investigated the role of ambient temperature in departure from wintering areas of migratory black-headed buntings in spring. Birds transferred at 22 and 35°C to long days were compared with one another and with controls held on short days for indices of readiness to migrate (Zugunruhe, fattening, mass gain), levels of testosterone and gonadal recrudescence. Temperature affected the development of migratory behaviour and physiology: buntings under long days at 35°C, compared with those at 22°C, showed altered migratory behaviour (daily activity and Zugunruhe onset), and enhanced muscle growth and plasma testosterone levels, but showed no effect on testis growth. Temperature was perceived at both peripheral and central levels, and affected multiple molecular drivers culminating into the migratory phenotype. This was evidenced by post-mortem comparison of the expression of 13 genes with known functions in the skin (temperature-sensitive TRP channels: trpv4 and trpm8), hypothalamus and/or midbrain (migration-linked genes: th, ddc, adcyap1 and vps13a) and flight muscles (muscle growth associated genes: ar, srd5a3, pvalb, mtor, myod, mstn and hif1a). In photostimulated birds, the expression of trpv4 in skin, th in the hypothalamus and midbrain, and srd5a3, ar, pvalb and mtor in flight muscle, in parallel with testosterone levels, was greater at 35°C than at 22°C. These results demonstrate the role of ambient temperature in development of the spring migration phenotype, and suggest that transcriptional responsiveness to temperature is a component of the overall adaptive strategy in latitudinal songbird migrants for timely departure from wintering areas in spring.

Concurrent changes in photoperiod-induced seasonal phenotypes and hypothalamic CART peptide-containing systems in night-migratory redheaded buntings

This study tested the hypothesis whether hypothalamic cocaine-and amphetamine-regulated transcript (CART)-containing systems were involved in photoperiod-induced responses associated with spring migration (hyperphagia and weight gain) and reproduction (gonadal maturation) in migratory songbirds. We specifically chose CART to examine neural mechanism(s) underlying photoperiod-induced responses, since it is a potent anorectic neuropeptide and involved in the regulation of changes in the body mass and reproduction in mammals. We first studied the distribution of CART-immunoreactivity in the hypothalamus of migratory redheaded buntings (Emberiza bruniceps). CART-immunoreactive neurons were found extensively distributed in the preoptic, lateral hypothalamic (LHN), anterior hypothalamic (AN), suprachiasmatic (SCN), paraventricular (PVN), dorsomedialis hypothalami (DMN), inferior hypothalamic (IH), and infundibular (IN) nuclei. Then, we correlated hypothalamic CART-immunoreactivity in buntings with photostimulated seasonal states, particularly winter non-migratory/non-breeding (NMB) state under short days, and spring premigratory/pre-breeding (PMB) and migratory/breeding (MB) states under long days. There were significantly increased CART-immunoreactive cells, and percent fluorescent area of CART-immunoreactivity was significantly increased in all mapped hypothalamic areas, except the SCN, PVN, AN, and DMN in photostimulated PMB and MB states, as compared to the non-stimulated NMB state. In particular, CART was richly expressed in the medial preoptic nucleus, LHN, IH and IN during MB state in which buntings showed reduced food intake and increased night-time activity. These results suggest that changes in the activity of the CART-containing system in different brain regions were associated with heightened energy needs of the photoperiod-induced seasonal responses during spring migration and reproduction in migratory songbirds.

Wavelength-specific artificial light disrupts molecular clock in avian species: A power-calibrated statistical approach

Nighttime lighting is an increasingly important anthropogenic environmental stress on plants and animals. Exposure to unnatural lighting environments may disrupt the circadian rhythm of organisms. However, the sample size of relevant studies, e.g. disruption of the molecular circadian clock by light pollution, was small (<10), which led to low statistical power and difficulties in replicating prior results. Here, we developed a power-calibrated statistical approach to overcome these weaknesses. The results showed that the effect size of 2.48 in clock genes expression induced by artificial light would ensure the reproducibility of the results as high as 80%. Long-wavelength light (560-660 nm) entrained expressions of the positive core clock genes (e.g. cClock) and negative core clock genes (e.g. cCry1, cPer2) in robust circadian rhythmicity, whereas those clock genes were arrhythmic in short-wavelength light (380-480 nm). Further, we found artificial light could entrain the transcriptional-translational feedback loop of the molecular clock in a wavelength-dependent manner. The expression of the positive core clock genes (cBmal1, cBmal2 and cClock), cAanat gene and melatonin were the highest in short-wavelength light and lowest in long-wavelength light. For the negative regulators of the molecular clock (cCry1, cCry2, cPer2 and cPer3), the expression of which was the highest in long-wavelength light and lowest in short-wavelength light. Our statistical approach opens new opportunities to understand and strengthen conclusions, comparing with the studies with small sample sizes. We also provide comprehensive insight into the effect of wavelength-specific artificial light on the circadian rhythm of the molecular clock in avian species. Especially, the global lighting is shifting from "yellow" sodium lamps, which is more like the long-wavelength light, toward short-wavelength light (blue light)-enriched "white" light-emitting diodes (LEDs).

Developmental effects of constant light on circadian behaviour and gene expressions in zebra finches: Insights into mechanisms of metabolic adaptation to aperiodic environment in diurnal animals

A most crucial feature of biological adaptation is the maintenance of a close temporal relationship of behaviour and physiology with prevailing 24-h light-dark environment, which is rapidly changing with increasing nighttime illumination. This study investigated developmental effects of the loss of night on circadian behaviour, metabolism and gene expressions in diurnal zebra finches born and raised under LL, with controls on 12L:12D. Birds under LD were entrained, and showed normal body mass and a significant 24-h rhythm in both activity-rest pattern and mRNA expression of candidate genes that we measured. But, under LL, birds gained weight and accumulated lipid in the liver. Intriguingly, at the end of the experiment, the majority (4/5th) of birds under LL were rhythmic in activity despite arrhythmic expression in the hypothalamus of c-Fos (neuronal activity), Rhodopsin and Mel1-a genes (light perception), and clock genes (Bmal1, Per2 and Rev-erb β). In peripheral tissues, LL induced variable clock gene expressions. Whereas 24-h mRNA rhythm was abolished for Bmal1 in both liver and gut, it persisted for Per2 and Rev-erb β in liver, and for Per2 in gut. Further, we found under LL, the loss of 24-h rhythm in hepatic expression of Fasn and Cd36/Fat (biosynthesis and its uptake), and gut expression of Sglt1, Glut5, Cd36 and Pept1 (nutrient absorption) genes. As compared to LD, baseline mRNA levels of Fasn and Cd36 genes were attenuated under LL. Among major transporter genes, Sglt1 (glucose) and Cd36 (fat) genes were arrhythmic, while Glut5 (glucose) and Pept1 (protein) genes were rhythmic but with phase differences under LL, compared to LD. These results demonstrate dissociation of circadian behaviour from clock gene rhythms, and provide molecular insights into possible mechanisms at different levels (behaviour and physiology) that diurnal animals might employ in order to adapt to an emerging overly illuminated-night urban environment.

Season dependent effects of urban environment on circadian clock of tree sparrow (Passer montanus)

Great efforts have been made recently to understand the effect(s) of urban environments on the circadian and seasonal physiology of wild animals, but the mechanisms involved remain largely unknown.

Metabolic plasticity mediates differential responses to spring and autumn migrations: Evidence from gene expression patterns in migratory buntings

NEW FINDINGS

What is the central question of this study? What are the molecular underpinnings of seasonal metabolic plasticity during spring and autumn migrations in songbirds? What is the main finding and its importance? We report differences in mRNA levels of genes involved in the regulation of glucose and fat metabolism between photoinduced non-migratory and migratory states and between the spring and autumn migratory states. Higher expression of genes associated with fat mobilization and energy generation in the spring than in the autumn migration suggests differential activation of the metabolic pathways or alteration in the efficiency of existing functional machinery during annual journeys between nearly fixed destinations.

ABSTRACT

The molecular underpinnings of metabolic plasticity underlying differential responses to spring and autumn migrations are not well understood. We investigated this by examining the differences in mRNA levels of metabolic genes in the liver, muscle and adipose tissues of night-migratory red-headed buntings between photostimulated non-migratory and migratory states and between spring and autumn migratory states. Buntings accumulated more subcutaneous fat and hepatic lipid, had higher body mass, larger adipose cells and higher circulating triglyceride and free fatty acid levels and exhibited more intense Zugunruhe in the spring migratory state than in the autumn migratory state. More importantly, we found differences in the hepatic expression of pdc and pdk genes, indicating a differential acetyl-CoA requirement, and of the mdh and ogdh genes, suggesting differential oxidative phosphorylation between the non-migratory and migratory states and between the spring and autumn migratory states. Differences in fasn, bmal1 and glut1 mRNA levels were consistent with this and suggested seasonal differences in lipogenesis and/or glucose uptake. Likewise, differences in mRNA levels of genes coding for lipases (atgl and lpl) suggested that adipose triglycerides and free fatty acids serve largely as the metabolic substrate. Furthermore, changes in mRNA levels of genes coding for the fatty acid binding protein (fabp3) and fatty acid translocases (cd36) were consistent with differential fat fuel supply (via circulating free fatty acids) to aerobically exercising flight muscles between the spring and autumn migrations. These results show seasonal adaptation of genetic pathway(s) underlying seasonal metabolic plasticity that seems to mediate differential responses to spring and autumn migrations in latitudinal migratory songbirds.

Effect of melatonin on monochromatic light-induced changes in clock gene circadian expression in the chick liver

Light is the most prominent zeitgeber of the circadian system, which contains central and peripheral oscillators. Our previous studies found that light wavelength could influence the rhythms of melatonin synthesis and clock gene expression in the central oscillator of chicks. However, the effect of monochromatic light on the peripheral oscillator and the role of melatonin have yet to be clarified. In this study, 216 newly hatched chicks were divided into three groups (intact, sham operation and pinealectomy) and were raised under white (WL), red (RL), green (GL) or blue (BL) light for 14 days. Their plasma and livers were sampled at 6 time points with 4-h intervals. Plasma melatonin concentration and liver clock gene expression (cClock, cBmal1, cBmal2, cCry1, cCry2, cPer2, cPer3) were measured for circadian rhythm analysis. In intact and sham operation chicks under WL, all liver clock genes showed circadian expression along with oscillations in plasma melatonin. However, positive clock genes peaked at subjective night along with melatonin, while negative clock genes peaked at subjective day or the shifting time of day-night. Chick exposure to monochromatic light led to an unaltered circadian rhythmicity in plasma melatonin and liver clock genes; however, their rhythmic parameters were notably influenced. Compared to WL, GL enhanced the mesor and amplitude of melatonin and all kinds of clock genes, whereas RL had the opposite effect. Pinealectomy significantly decreased expression of liver clock genes, which was consistent with the reduction in plasma melatonin concentration, especially for the GL group, and resulted in the expression of liver clock genes showing low-mesor and low-amplitude oscillations as well as no statistically significant differences among the monochromatic light groups. Thus, we speculated that melatonin plays a key role in the effects of light wavelength on clock gene rhythm in the chick liver.

Temporal expression of genes coding for aryl-alkamine-N-acetyltransferase and melatonin receptors in circadian clock tissues: Circadian rhythm dependent role of melatonin in seasonal responses

We investigated at the transcriptional level the role of daily rhythm in melatonin secretion in seasonal responses in the migratory blackheaded bunting (Emberiza melanocephala), which when exposed to short (SP) and long (LP) photoperiods exhibits distinct seasonal life-history states (LHSs). We reproduced the seasonal LHS by subjecting buntings to SP (8 h light: 16 h darkness, 8 L:16D), which maintained the nonmigratory/ nonbreeding phenotype, and to LP (16 L:8D), which induced the premigratory/ prebreeding, migratory/ breeding and nonmigratory/ postbreeding phenotypes. Plasma melatonin measured at 4 h intervals showed loss of the daily rhythm in the LP-induced premigratory/ prebreeding and migratory/ breeding LHSs. Subsequently, mRNA expression of genes coding for the aryl-alkamine-N-acetyltransferase (AANAT; the rate-liming enzyme of melatonin biosynthesis) and for the receptors for melatonin (Mel1A, Mel1B and Mel1C) was examined in the retina, pineal and hypothalamus; the interacting independent circadian clocks comprising the songbird circadian timing system. Except AANAT that was not amplified in the hypothalamus, we found significant alterations in both, the level and persistence of 24 h rhythm in mRNA expression of all genes, albeit with photoperiod and seasonal differences between three circadian clock tissues. Particularly, 24 h mRNA expression pattern of all genes, except retinal Mel1A, lacked a significant daily rhythm in the LP-induced migratory/ breeding LHS. These results underscore the overall importance of the circadian rhythm in the role of melatonin in photoperiodically-controlled seasonal responses in migratory songbirds.

Transcriptome-wide changes in testes reveal molecular differences in photoperiod-induced seasonal reproductive life-history states in migratory songbirds

We investigated the molecular basis of seasonal testicular states in black-headed buntings (Emberiza melanocephala), in which seasonal migrations limit reproduction to a narrow time-window during the year. We examined testicular gene expressions in buntings during short day-induced photosensitive nonreproductive state (SDSE), and during long day-induced early (LDES) and late (LDLS) gonadal maturation and regressed photorefractory (LDRF) seasonal states. Using Kallisto, we pseudoaligned the RNA-Seq transcripts and calculated the transcript abundance. We found 1,799 differentially expressed genes (DEGs) between the four photoperiod-induced seasonal states. Further pairwise comparison with SDSE revealed 1,187, 1,224, and 1,238 DEGs in LDES, LDLS, and LDRF, respectively; 852 genes were common to three comparisons. We then identified genetic pathways putatively involved in seasonal testicular cycle. DEGs that enriched calcium ion binding were highly expressed in testicular maturation states. Similarly, DEGs that enriched glycolytic pathway were highly expressed in LDES and LDRF states. More specifically, quantitative polymerase chain reaction showed significant differences between the photoperiod-induced states in testicular expression of genes (HOOK1, RGS2, PRDX4, BCL6, CYFIP2, PDCD4, P2RX4, and GABRA1) involved in gametogenesis and associated pathways. Overall, these results show significant transcriptional differences, and provide insights into the molecular basis of seasonal changes in the reproductive life-history states in a photoperiodic species.

Development of vernal migration in redheaded buntings: concurrent behavioral, physiological and neural changes under stimulatory photoperiods

We investigated changes in behavior, physiology and selected brain regions during the development of vernal migration and reproduction phenotypes in migratory redheaded buntings.

Transcriptional Signatures in Liver Reveal Metabolic Adaptations to Seasons in Migratory Blackheaded Buntings

The molecular underpinnings of metabolic adaptation to seasons are poorly understood in long- distance migrants. We measured changes in physiology and performed de novo sequencing of RNA extracted from liver samples collected at 4-h intervals over a period of 24 h from a long-distance avian migrant, the blackheaded bunting (Emberiza melanocephala), during two states: photostimulated vernal migratory (M) state and photorefractory non-migratory (nM) state. The M state was differentiated from the nM state based on body fattening and weight gain, as well as on Zugunruhe, that is, nocturnal migratory restlessness in caged birds. We found that baseline blood glucose and triglyceride levels were significantly higher in the M state than the nM state; conversely, surface body temperature was higher in the nM state than the M state. In a total of 6 liver samples that were sequenced from each state, 11,246 genes were annotated, including 4448 genes that were cyclic over 24 h. We found 569 differentially expressed genes (DEGs) between the M and the nM state, and the M state showed 131 upregulated and 438 downregulated genes. These DEGs formed core gene hubs associated with specific biological processes in both the states. In addition, weighted gene coexpression network analysis revealed two discrete modules of coexpressed genes, with a significant difference in the expression pattern of metab olism-associated genes between M and nM states. These results demonstrate, for the first time, transcriptome-wide changes in the liver between two distinct physiological states and give molecular insights into seasonal metabolic adaptations in latitudinal migrants.

Difference in control between spring and autumn migration in birds: insight from seasonal changes in hypothalamic gene expression in captive buntings

We hypothesized differences in molecular strategies for similar journeys that migrants undertake to reproduce in spring and to overwinter in autumn. We tested this in redheaded buntings (Emberiza bruniceps) photoinduced into spring and autumn migratory states, with winter and summer non-migratory states as controls. Compared with controls, buntings fattened, gained weight and showed Zugunruhe (nocturnal migratory restlessness) in the migratory state. Spring migration was associated with greater fat and body mass, and higher intensity of Zugunruhe, compared with autumn migration. Circulating corticosterone levels were higher in spring, while T3 levels were higher in autumn. Hypothalamic expression of thyroid hormone-responsive (dio2, dio3), light-responsive (per2, cry1, adcyap1) and th (tyrosine hydroxylase, involved in dopamine biosynthesis) genes showed significant changes with transition from non-migratory to the migratory state. There were significantly higher mRNA expressions in autumn, except for higher th levels in the spring. Furthermore, the expression patterns of dnmt3a (not dnmt3b) and tet2 genes suggested an epigenetic difference between the non-migrant and migrant periods, and the spring and autumn migrant periods. These results demonstrate for the first time seasonal transition in hypothalamic gene expressions, and suggest differences in regulatory strategies at the transcriptional level for spring and autumn migrations in songbirds.

Expression patterns of cryptochrome genes in avian retina suggest involvement of Cry4 in light-dependent magnetoreception

The light-dependent magnetic compass of birds provides orientation information about the spatial alignment of the geomagnetic field. It is proposed to be located in the avian retina, and be mediated by a light-induced, biochemical radical-pair mechanism involving cryptochromes as putative receptor molecules. At the same time, cryptochromes are known for their role in the negative feedback loop in the circadian clock. We measured gene expression of Cry1, Cry2 and Cry4 in the retina, muscle and brain of zebra finches over the circadian day to assess whether they showed any circadian rhythmicity. We hypothesized that retinal cryptochromes involved in magnetoreception should be expressed at a constant level over the circadian day, because birds use a light-dependent magnetic compass for orientation not only during migration, but also for spatial orientation tasks in their daily life. Cryptochromes serving in circadian tasks, on the other hand, are expected to be expressed in a rhythmic (circadian) pattern. Cry1 and Cry2 displayed a daily variation in the retina as expected for circadian clock genes, while Cry4 expressed at constant levels over time. We conclude that Cry4 is the most likely candidate magnetoreceptor of the light-dependent magnetic compass in birds.

Hypothalamic and liver transcriptome from two crucial life-history stages in a migratory songbird

NEW FINDINGS

What is the central question of this study? What are the molecular underpinnings of the seasonal adaptation in a latitudinal migratory songbird? What is the main finding and its importance? We found changes in mRNA levels after a photoperiod-induced alteration of seasonal state in a captive long-distance latitudinal avian migrant. The hypothalamus and liver transcriptomes revealed genes involved in the regulatory and functional pathways between non-migratory and migratory states. Our results provide insights into mechanisms underlying homeostasis during seasonal changes that are conserved across most species, including humans.

ABSTRACT

Very little is understood about genetic mechanisms underlying the onset of spring migration in latitudinal avian migrants. To gain insight into the genetic architecture of the hypothalamus and liver tissues of a long-distance migrant, we examined and compared the transcriptome profile of captive night-migratory black-headed buntings (Emberiza melanocephala) between photoperiod-induced winter non-migratory (WnM) and spring migratory (SM) life-history states under short and long days, respectively. High-throughput 454 pyrosequenced transcripts were mapped initially with reference to the genome of two phylogenetically close species, Taeniopygia guttata and Ficedula albicollis. The F. albicollis genome gave higher annotation results and was used for further analysis. A total of 216 (78 in hypothalamus; 138 in liver) genes were found to be expressed differentially between the WnM and SM life-history states. These genes were enriched for physiological pathways that might be involved in the regulation of seasonal migrations in birds. For example, genes for the ATP binding pathway in the hypothalamus were expressed at a significantly higher level in SM than in the WnM life-history state. Likewise, upregulated genes associated with the myelin sheath and focal adhesion were enriched in the hypothalamus, and those with cell-to-cell junction, intracellular protein transport, calcium ion transport and small GTPase-mediated signal transduction were enriched in the liver. Many of these genes are a part of physiological pathways potentially involved in the regulation of seasonal migration in birds. These results show molecular changes at the regulatory and metabolic levels associated with seasonal transitions in a long-distance migrant and provide the basis for future studies aimed at unravelling the genetic control of migration in birds.

Temporal expression of clock genes in central and peripheral tissues of spotted munia under varying light conditions: Evidence for circadian regulation of daily physiology in a non-photoperiodic circannual songbird species

We investigated if the duration and/or frequency of the light period affect 24-h rhythm of circadian clock genes in central and peripheral tissues of a non-photoperiodic songbird, the spotted munia (Lonchura punctulata), in which a circannual rhythm regulates the reproductive cycle. We monitored activity-rest pattern and measured 24-h mRNA oscillation of core clock (Bmal1, Clock, Per2, Cry1 and Cry2) and clock-controlled (E4bp4, Rorα and Rev-erbα) genes in the hypothalamus, retina, liver and gut of spotted munia subjected to an aberrant light-dark (LD) cycle (3.5L:3.5D; T7, T = period length of LD cycle) and continuous light (LL, 24L:0D), with controls on 24-h LD cycle (T24, 12L:12D). Munia exhibited rhythmic activity-rest pattern with period matched to T7 or T24 under an LD cycle and were arrhythmic with a scattered activity pattern and higher activity duration under LL. At the transcriptional level, both clock and clock-controlled genes showed a significant 24-h rhythm in all four tissues (except Clock in the liver) under 12L:12D, suggesting a conserved tissue-level circadian time generation in spotted munia. An exposure to 3.5L:3.5D or LL induced arrhythmicity in transcriptional oscillation of all eight genes in the hypothalamus (except Rev-erbα) and liver (except Bmal1 and Rev-erbα under T7 and Cry1 under LL). In the retina, however, all genes showed arrhythmic 24-h mRNA expression under LL, but not under T7 (except in E4bp4 and Rorα). Interestingly, unlike in the liver, Bmal1, Per2, Cry1, Rorα and Rev-erbα mRNA expressions were rhythmic in the gut under both T7 (except Rorα) and LL conditions. These results showed variable relationship of internal circadian clocks with the external light environment and suggested a weak coupling of circadian clocks between the central (hypothalamus and retina) and peripheral (liver and gut) tissues. We suggest tissue-level circadian clock regulation of daily physiology and behavior in the spotted munia.

Understanding variation in migratory movements: A mechanistic approach

Spatial and temporal fluctuations in resource availability have led to the evolution of varied migration patterns. In order to appropriately time movements in relation to resources, environmental cues are used to provide proximate information for timing and the endocrine system serves to integrate these external cues and behavioral and physiological responses. Yet, the regulatory mechanisms underlying migratory timing have rarely been compared across a broad range of migratory patterns. First, we offer an updated nomenclature of migration using a mechanistic perspective to clarify terminology describing migratory types in relation to ecology, behavior and endocrinology. We divide migratory patterns into three types: obligate, nomadic, and fugitive. Obligate migration is characterized by regular and directed annual movements between locations, most commonly for breeding and overwintering, where resources are predictable and sufficient. Nomadic migrations occur less predictably than do obligate migrations as animals make use of potentially rich but ephemeral resources that occur unpredictably in space or time. Fugitive migrations move animals away from an area in response to severe disruption of environmental conditions and occur as part of an emergency life history stage. We also consider partially migratory populations, which include a mix of sedentary and migratory individuals; the movement patterns of partial migrants are expected to fall into one of the three types above. For these various forms of migration, we review our understanding of the environmental cues and endocrine mechanisms that underlie the expression of a migratory state. Several common hormonal mechanisms exist across the varied migratory forms, but there are also important areas where further investigations are needed in order to gain broad insight into the origin of movements and the diversity of migratory patterns. We propose that taking a comparative approach across the migratory types that considers endocrine mechanisms will advance a new understanding of migration biology.

Temporal Expression of c-fos and Genes Coding for Neuropeptides and Enzymes of Amino Acid and Amine Neurotransmitter Biosynthesis in Retina, Pineal and Hypothalamus of a Migratory Songbird: Evidence for Circadian Rhythm-Dependent Seasonal Responses

This study investigated whether, in photoperiodic songbirds, the circadian pacemaker system (CPS) connects to the seasonal photoperiodic responses, by changes at transcriptional level in the level and 24-h rhythm of its constituent neurotransmitters. We used black-headed buntings (Emberiza melanocephala), which exhibit distinct seasonal states in captivity under appropriate photoperiods and hence served as a useful model system. Under short days, buntings remain in the photosensitive state (Pse) (winter phenotype: non-migratory, non-breeding). Under long days, however, buntings undergo through early-photostimulated (spring phenotype: pre-migratory, pre-breeding), late photostimulated (summer phenotype: migratory, breeding) and photorefractory (autumn phenotype: post-breeding) states. During all four seasonal states, we measured in the retina, pineal and hypothalamus, which together form avian CPS, 4-hourly mRNA expression of c-fos (a neuronal-activity marker) and of genes coding for neuropeptides (vasoactive intestinal peptide, vip; somatostatin, sst; neuropeptide Y, npy) and for intermediary enzymes of amino acid (glutamate: glutaminase, gls and glutamic-oxaloacetic transaminase 2, got2; GABA: glutamic acid decarboxylase, gad65) and amine (dopamine: tyrosine hydroxylase, th) neurotransmitters biosynthetic pathway. There was a significant alteration in level and 24-h pattern of mRNA expression, albeit with seasonal differences in presence, waveform parameters and phase relationship of 24-h rhythm, of different genes. Particularly, mRNA expression of all candidate genes (except hypothalamic vip, pineal gls and retinal th) was arrhythmic in late photostimulated state. These results underscore that circadian rhythm of peptide, amino acid and amine neurotransmitter biosynthesis in CPS plays a critical role in the photoperiodic regulation of seasonal states in birds.

Circannual testis and moult cycles persist under photoperiods that disrupt circadian activity and clock gene cycles in spotted munia

We investigated whether circannual rhythms underlying annual testis maturation and moult cycles are independent of duration and frequency of the light period and circadian clock control in non-photoperiodic spotted munia. Birds were subjected to an aberrant light-dark (LD) cycle (3.5 h L:3.5 h D; T7, where T is the period length of the LD cycle) and continuous light (LL, 24 h L:0 h D), with controls on 12 h L:12 h D (T24, 24 h LD cycle). We measured the behavioural activity pattern of the birds and 24 h mRNA oscillations of circadian clock genes (bmal1, clock, per2, cry1, cry2) in the hypothalamus, the putative site of seasonal timing. Diurnal munia were rhythmic in behaviour with the period of the activity-rest cycle matched to T7 and T24, and became behaviourally arrhythmic with activity scattered throughout 24 h under LL. Similarly, exposure to 3.5 h L:3.5 h D and LL caused arrhythmicity in 24 h clock gene expression, suggesting disruption of internal circadian timing at the transcriptional level; a significant rhythm was found under 12 h L:12 h D. During an exposure of 80 weeks, munia showed two to three cycles of testis maturation and wing primaries moult under all photoperiods, although with a longer period under 12L:12D. Thus, the frequency of light period under 3.5 h L:3.5 h D or LL disrupted circadian clock gene cycles, but did not affect the generation of circannual testis and moult cycles. We conclude that the prevailing light environment and hypothalamic circadian gene cycles do not exert direct control on the timing of the annual reproductive cycle in spotted munia, suggesting independent generation of the circadian and circannual rhythms in seasonally breeding species.

Daily levels and rhythm in circulating corticosterone and insulin are altered with photostimulated seasonal states in night-migratory blackheaded buntings

The circadian rhythms are involved in the photostimulation of seasonal responses in migratory blackheaded buntings. Here, we investigated whether changes in daily levels and rhythm in corticosterone (cort) and insulin secretions were associated with transitions in the photoperiodic seasonal states. Buntings were exposed to short days to maintain the winter (photosensitive) non-migratory state, and to long days for varying durations to induce the premigratory, migratory (shown by migratory restlessness at night, Zugunruhe) and summer non-migratory (photorefractory) states. We monitored activity patterns, and measured plasma cort and insulin levels at six and four times, respectively, over 24h in each seasonal state. Buntings were fattened and weighed heavier, and exhibited intense nighttime activity in the migratory state. The daytime activity patterns also showed seasonal differences, with a bimodal pattern with morning and evening activity bouts only in the summer non-migratory state. Further, the average baseline hormone levels were significantly higher in premigratory and migratory than in the winter non-migratory state. Both cort and insulin levels showed a significant daily rhythm, but with seasonal differences. Whereas, cort rhythm acrophases (estimated time of peak secretion over 24h) were at night in the winter non-migratory, premigratory and migratory states, the insulin rhythm acrophases were found early in the day and night in winter and summer non-migratory states, respectively. These results suggest that changes in daily levels and rhythm in cort and insulin mediate changes in the physiology and behavior with photostimulated transition in seasonal states in migratory blackheaded buntings.

Seasonal alterations in the daily rhythms in hypothalamic expression of genes involved in the photoperiodic transduction and neurosteroid-dependent processes in migratory blackheaded buntings

The present study investigated seasonal alterations in the daily rhythms of hypothalamic expression of genes involved in the photoperiodic regulation of annual cycles in birds. We measured the 4-hourly mRNA expression of genes involved in the photoperiodic transduction (OPN5, EYA3, CGA, TSHβ, DIO2, DIO3) and neurosteroid-dependent processes (AR, CYP19, ERα, ERβ) in the hypothalamus of migratory blackheaded buntings photoinduced with photosensitive, photostimulated (early and late stimulated) and photorefractory seasonal states. There were significant differences in daily mRNA profiles between the photoperiodic states. Particularly, increased CGA, TSHβ and DIO2 and decreased DIO3 mRNA levels in the early photostimulated state, compared to the photosensitive state, suggest that thyroid hormones have a role in photostimulation in buntings. Similar differences in the expression of genes coding for the aromatase enzyme (CYP19) and receptors for oestrogen (ERα, ERβ) (but not androgen; AR) indicate that there is seasonal alteration in the neuro-oestrogen-mediated functions. Furthermore, peak expression times of CGA, TSHβ and DIO2 genes at hours 14-15 of the day in the early stimulated state indicated molecular regulation of the daily rhythm of photoinducibility in buntings. Most significantly, however, we found an attenuated daily rhythm in thyroid hormone modulatory genes and a switch of peak expression time from day to night in CYP19 mRNA rhythm in the subsequent late photostimulated state, although testicular maturation still persisted. These alterations in daily rhythms may have signalled the initiation of processes underlying other seasonal phenologies in parallel with the gonadal response, such as a manifestation of the night-time flight in buntings. These results show alterations in daily rhythms underlying the transcriptional regulation of the photoperiod-induced seasonal states in migratory blackheaded buntings.

Proteus: a random forest classifier to predict disorder-to-order transitioning binding regions in intrinsically disordered proteins

The focus of the computational structural biology community has taken a dramatic shift over the past one-and-a-half decades from the classical protein structure prediction problem to the possible understanding of intrinsically disordered proteins (IDP) or proteins containing regions of disorder (IDPR). The current interest lies in the unraveling of a disorder-to-order transitioning code embedded in the amino acid sequences of IDPs/IDPRs. Disordered proteins are characterized by an enormous amount of structural plasticity which makes them promiscuous in binding to different partners, multi-functional in cellular activity and atypical in folding energy landscapes resembling partially folded molten globules. Also, their involvement in several deadly human diseases (e.g. cancer, cardiovascular and neurodegenerative diseases) makes them attractive drug targets, and important for a biochemical understanding of the disease(s). The study of the structural ensemble of IDPs is rather difficult, in particular for transient interactions. When bound to a structured partner, an IDPR adapts an ordered conformation in the complex. The residues that undergo this disorder-to-order transition are called protean residues, generally found in short contiguous stretches and the first step in understanding the modus operandi of an IDP/IDPR would be to predict these residues. There are a few available methods which predict these protean segments from their amino acid sequences; however, their performance reported in the literature leaves clear room for improvement. With this background, the current study presents ‘Proteus’, a random forest classifier that predicts the likelihood of a residue undergoing a disorder-to-order transition upon binding to a potential partner protein. The prediction is based on features that can be calculated using the amino acid sequence alone. Proteus compares favorably with existing methods predicting twice as many true positives as the second best method (55 vs. 27%) with a much higher precision on an independent data set. The current study also sheds some light on a possible ‘disorder-to-order’ transitioning consensus, untangled, yet embedded in the amino acid sequence of IDPs. Some guidelines have also been suggested for proceeding with a real-life structural modeling involving an IDPR using Proteus.

Genetic basis of allochronic differentiation in the fall armyworm

BACKGROUND

Very little is known on how changes in circadian rhythms evolve. The noctuid moth Spodoptera frugiperda (Lepidoptera: Noctuidae) consists of two strains that exhibit allochronic differentiation in their mating time, which acts as a premating isolation barrier between the strains. We investigated the genetic basis of the strain-specific timing differences to identify the molecular mechanisms of differentiation in circadian rhythms.

RESULTS

Through QTL analyses we identified one major Quantitative trait chromosome (QTC) underlying differentiation in circadian timing of mating activity. Using RADtags, we identified this QTC to be homologous to Bombyx mori C27, on which the clock gene vrille is located, which thus became the major candidate gene. In S. frugiperda, vrille showed strain-specific polymorphisms. Also, vrille expression differed significantly between the strains, with the rice-strain showing higher expression levels than the corn-strain. In addition, RT-qPCR experiments with the other main clock genes showed that pdp1, antagonist of vrille in the modulatory feedback loop of the circadian clock, showed higher expression levels in the rice-strain than in the corn-strain.

CONCLUSIONS

Together, our results indicate that the allochronic differentiation in the two strains of S. frugiperda is associated with differential transcription of vrille or a cis-acting gene close to vrille, which contributes to the evolution of prezygotic isolation in S. frugiperda.

Extra-hypothalamic brain clocks in songbirds: Photoperiodic state dependent clock gene oscillations in night-migratory blackheaded buntings, Emberiza melanocephala

The avian circadian pacemaker system is comprised of independent clocks in the retina, pineal and hypothalamus, as shown by daily and circadian oscillations of core clock genes (Per2, Cry1, Bmal1 and Clock) in several birds including migratory blackheaded buntings (Emberiza melanocephala). This study investigated the extra-hypothalamic brain circadian clocks in blackheaded buntings, and measured Per2, Cry1, Cry2, Bmal1 and Clock mRNA expressions at 4h intervals over 24h beginning 1h after light-on in the left and right telencephalon, optic tectum and cerebellum, the brain regions involved in several physiological and cognitive functions. Because of seasonal alterations in the circadian clock dependent brain functions, we measured daily clock gene oscillations in buntings photoperiod-induced with the non-migratory state under short days (SDnM), and the pre-migratory (LDpM), migratory (LDM) and post-migratory (refractory, LDR) states under long days. Daily Per2 oscillations were not altered with changes in the photoperiodic states, except for about 2-3h phase difference in the optic tectum between the SDnM and LDpM states. However, there were about 3-5h differences in the phase and 2 to 4 fold change in the amplitude of daily Bmal1 and Cry1 mRNA oscillations between the photoperiod-induced states. Further, Cry2 and Clock genes lacked a significant oscillation, except in Cb (Cry2) and TeO and Rt (Clock) under LDR state. Overall, these results show the presence of circadian clocks in extra-hypothalamic brain regions of blackheaded buntings, and suggest tissue-dependent alterations in the waveforms of mRNA oscillations with transitions in the photoperiod-induced seasonal states in a long-day species.

Concurrent hypothalamic gene expression under acute and chronic long days: Implications for initiation and maintenance of photoperiodic response in migratory songbirds

Hypothalamic expression of the thyroid hormone (TH) responsive gonadostimulatory (eya3, cga, tshβ, dio2, dio3, gnrh, gnih) and neurosteroid pathway genes (androgen receptor [ar], aromatase [cyp19], estrogen receptor [er] α and β) was examined in photosensitive redheaded buntings exposed to 2 (acute, experiment 1) or 12 (chronic, experiment 2) long days (16L:8D). Experiment 2 also included a photorefractory group. Acute long days caused a significant increase in eya3, cga, tshβ, dio2 and gnrh and decrease in dio3 mRNA levels. eya3, cga and tshβ expressions were unchanged after the chronic long days. We also found increased cyp19, erα and erβ mRNA levels after acute, and increased cyp19 and decreased erβ levels after the chronic long-day exposure. Photorefractory buntings showed expression patterns similar to that in the photosensitive state, except for high gnrh and gnih and low dio3 mRNA levels. Consistent with gene expression patterns, there were changes in fat deposition, body mass, testis size, and plasma levels of testosterone, tri-iodothyronine and thyroxine. These results show concurrent photostimulation of the TH-signalling and neurosteroid pathways, and extend the idea, based on differences in gene expression, that transitions in seasonal photoperiodic states are accomplished at the transcriptional levels in absolute photorefractory species.