Transcriptional profiling of the chick pineal gland, a photoreceptive circadian oscillator and pacemaker

Influence of Different Light Spectra on Melatonin Synthesis by the Pineal Gland and Influence on the Immune System in Chickens

It is well known that the pineal gland in birds influences behavioural and physiological functions, including those of the immune system. The purpose of this research is to examine the endocrine-immune correlations between melatonin and immune system activity. Through a description of the immune-pineal axis, we formulated the objective to determine and describe: the development of the pineal gland; how light influences secretory activity; and how melatonin influences the activity of primary and secondary lymphoid organs. The pineal gland has the ability to turn light information into an endocrine signal suitable for the immune system via the membrane receptors Mel1a, Mel1b, and Mel1c, as well as the nuclear receptors RORα, RORβ, and RORγ. We can state the following findings: green monochromatic light (560 nm) increased serum melatonin levels and promoted a stronger humoral and cellular immune response by proliferating B and T lymphocytes; the combination of green and blue monochromatic light (560-480 nm) ameliorated the inflammatory response and protected lymphoid organs from oxidative stress; and red monochromatic light (660 nm) maintained the inflammatory response and promoted the growth of pathogenic bacteria. Melatonin can be considered a potent antioxidant and immunomodulator and is a critical element in the coordination between external light stimulation and the body's internal response.

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.

A transcriptome analysis for 24-hour continuous sampled uterus reveals circadian regulation of the key pathways involved in eggshell formation of chicken

Circadian timing system controlled the rhythmic events, for example, ovulation and oviposition in chickens. However, how biological clock mediates eggshell formation remains obscure. Here, A 24-h mRNA transcriptome analysis was carried out in the uterus of 18 chickens with similar oviposition time points to identify the rhythmic genes and to reveal critical genes and biological pathways involved in the eggshell biomineralization. JTK_CYCLE analysis and real-time PCR revealed a total of 1,793 genes from the sequencing database with 23,513 genes (FPKM>1) were rhythmic genes regulating the rhythmic system and the expression of typical clock genes Per2, Cry1, Bmal1, Clock, Per3, and Rev-erbβ were rhythmically expressed, which suggested that endogenous clock in uterus might control the eggshell mineralization. Time of peak expression of the rhythmic genes was analyzed based on their acrophase. The main phases clustered at the periods from Zeitgeber time 0 (ZT0) to ZT4 (6:00–10:00) and from ZT10 to ZT14 (16:00-20:00). The rhythmic genes were annotated to the following Gene Ontology terms rhythmic process, lyase, ATP binding, cell membrane component. KEGG pathway enrichment analysis revealed the top 15 rhythmic genes were involved in vital biological pathways, including syndecan (1, 2, 3)-mediated signaling, post-translational regulation of adheres junction stability and disassembly, FoxO family signaling, TGF-β receptor and transport of small molecular pathways. 166 of total 1,235 genes (13.4%) were defined as rhythmic transfer factors (TFs) and they were investigated expression time distribution of cis-elements of circadian clock system D-box, E-box, B-site, and Y-Box within 24 h. Results indicated that rhythmic TFs at each phase are potential drivers of their circadian transcription activities. Compared with the control, the expression abundances of ion transport elements SCNN1G, CA2, SPP1, and ATP1B1 were significantly decreased after the interference of Bmal1 gene in synchronized uterine tubular gland cells. Clock genes changed their expression along with the eggshell formation, indicating that there is circadian clock in the uterus of chicken and it regulates the expression of eggshell formation genes.

Role of BMAL1 and CLOCK in regulating the secretion of melatonin in chick retina under monochromatic green light

As the circadian pacemaker of birds, the retina possesses the ability to receive light information, generate circadian oscillation, and secrete melatonin. Previous studies have confirmed that monochromatic green light can accelerate the circadian rhythmic expression of clock genes in the chick retina, thereby increasing cAanat mRNA level and melatonin secretion. However, as the core components of the transcriptional-translational negative feedback loop, the role that cBmal1 and cClock plays in the regulation of the retinal molecular clock system and melatonin secretion under monochromatic green light is unknown. To explore their in these processes, embryonic chick retinal cells at six embryo ages were isolated and cultured under light-dark (LD) 12:12 monochromatic green light with, and the role of cBmal1 and cClock in the regulation of the retinal molecular clock and melatonin secretion in the chick retina was explored by siRNA interference and overexpression. The results showed siRNA interference and overexpression of cBmal1 obliterated the circadian rhythm of cCry1, cPer2, cPer3, cAanat, and melatonin secretion. Moreover, the siRNA interference of cBmal1 significantly reduced the average expression levels of the positive clock genes cBmal2 and cClock, positive clock protein CLOCK, negative clock genes cCry1, cCry2, cPer2, cPer3, as well as cAanat and retinal melatonin. The over-expression of cBmal1 increased the average levels of the above-detected targets. However, siRNA interference and overexpression of cClock did not change the rhythm of all of the clock genes, clock proteins, cAanat, and melatonin secretion, while it only affected the circadian mesors (24 h time series means), amplitudes, and acrophases (peak times) of cCry1, cPer2, cPer3, cAanat, and melatonin, as well as the average levels of arrhythmic cBmal2 and cCry2. Moreover, interference and overexpression of cClock did not affect cBmal1 mRNA level and BMAL1 protein expression. The above results reveal interference and overexpression of cBmal1 completely abolished the molecular circadian oscillation and the rhythm of melatonin output signal of chick retinal cells, indicating that cBmal1 is on the top of the avian retinal molecular clock feedback loop and regulates the downstream molecular clock oscillation and output under monochromatic green light. cClock plays a subordinate role in maintaining the circadian oscillation of the molecular clock and melatonin secretion in retinal cells, and it has a stabilizing and amplifying effect on molecular clock oscillation.

Resource: A multi-species multi-timepoint transcriptome database and webpage for the pineal gland and retina

The website and database https://snengs.nichd.nih.gov provides RNA sequencing data from multi-species analysis of the pineal glands from zebrafish (Danio rerio), chicken (White Leghorn), rat (Rattus novegicus), mouse (Mus musculus), rhesus macaque (Macaca mulatta), and human (Homo sapiens); in most cases, retinal data are also included along with results of the analysis of a mixture of RNA from tissues. Studies cover day and night conditions; in addition, a time series over multiple hours, a developmental time series and pharmacological experiments on rats are included. The data have been uniformly re-processed using the latest methods and assemblies to allow for comparisons between experiments and to reduce processing differences. The website presents search functionality, graphical representations, Excel tables, and track hubs of all data for detailed visualization in the UCSC Genome Browser. As more data are collected from investigators and improved genomes become available in the future, the website will be updated. This database is in the public domain and elements can be reproduced by citing the URL and this report. This effort makes the results of 21st century transcriptome profiling widely available in a user-friendly format that is expected to broadly influence pineal research.

Effect of monochromatic light on the temporal expression of N-acetyltransferase in chick pineal gland

The avian pineal gland is an independent molecular oscillator that receives external light information that regulates the synthesis and secretion of melatonin. Arylalkylamine N-acetyltransferase plays an important role in the pineal gland by controlling the rhythmic production of melatonin. Previous study showed that monochromatic light influences the secretion of melatonin, which is regulated by the molecular circadian clock genes in chick pineal gland. This study was designed to investigate the effect of monochromatic light on the circadian rhythm of levels of cAanat, clock protein (CLOCK and BMAL1), cCreb, and opsins (cOpnp, Pinopsin; cOpn4-1, Melanopsin-1; cOpn4-2, Melanopsin-2) in chick pineal gland. A total of 240 post-hatching day (P) 0 broiler chickens were reared under white (WL), red (RL), green (GL), and blue light (BL) with light (L)-dark (D) cycle of 12L:12D for 14 d. The results show significant circadian rhythms in the expression of cAanat, CLOCK, BMAL1, cCreb, cOpnp, cOpn4-1, and cOpn4-2, but not for cOpnp under RL. Compared with WL, GL increased the level of cAanat mRNA, while RL decreased it. Meanwhile, CLOCK and BMAL1 proteins were expressed at high levels in GL. Furthermore, the peak of the 24 h pattern of cOpnp mRNA in GL was earlier than that of in WL, RL, and BL. These results demonstrated that monochromatic light affects the daily expression of cAanat in the chick pineal gland via the biological clock. GL activates the transcription of cAanat, while RL suppresses the transcription of cAanat. Meanwhile, GL appears to induce the peak of cOpnp mRNA in advance to affect the transmission of light. Thus, monochromatic light regulates cAanat in the chick pineal gland by affecting the levels of clock regulators via entraining the expression of pineal gland opsins.

Differential gene expression profiling of the goose pineal gland

1. The present study was conducted to obtain a better understanding of the molecular mechanisms underlying broodiness in a commercial breed, Tianfu geese, as little is known about the role of the pineal gland in this period. The aim was to identify genes which are differentially expressed in the pineal gland between the laying and broodiness periods by performing a transcriptome screen.2. After sequencing cDNA derived from the pineal gland and annotation of the results, a sequencing depth of 14.82 and 18.17 million mapped tags was obtained during the laying and broodiness periods, respectively, and a total of 120 differentially expressed genes were identified. Of these, 32 genes showing up-regulated expression and 88 genes showing down-regulated expression were identified in broodiness period vs. laying period libraries.3. Gene ontology (GO) analyses showed that these genes were related to the visual process, phototransduction, and lipoprotein metabolism. Kyoto Encyclopaedia of Genes and Genome (KEGG) analyses showed that phototransduction and tryptophan metabolism pathways exhibited the largest enrichment factors. The reliability of the RNA sequence data was confirmed by quantitative real-time PCR analysis of five genes, and the results were mostly consistent with those from the high-throughput RNA sequencing.4. The goose transcriptome and the identification of differentially expressed genes provided comprehensive gene expression information that enables a better understanding of the molecular mechanisms underlying the broodiness period of geese.

Circadian regulation of membrane physiology in neural oscillators throughout the brain

Twenty-four-hour rhythmicity in physiology and behavior are driven by changes in neurophysiological activity that vary across the light-dark and rest-activity cycle. Although this neural code is most prominent in neurons of the primary circadian pacemaker in the suprachiasmatic nucleus (SCN) of the hypothalamus, there are many other regions in the brain where region-specific function and behavioral rhythmicity may be encoded by changes in electrical properties of those neurons. In this review, we explore the existing evidence for molecular clocks and/or neurophysiological rhythms (i.e., 24 hr) in brain regions outside the SCN. In addition, we highlight the brain regions that are ripe for future investigation into the critical role of circadian rhythmicity for local oscillators. For example, the cerebellum expresses rhythmicity in over 2,000 gene transcripts, and yet we know very little about how circadian regulation drives 24-hr changes in the neural coding responsible for motor coordination. Finally, we conclude with a discussion of how our understanding of circadian regulation of electrical properties may yield insight into disease mechanisms which may lead to novel chronotherapeutic strategies in the future.

Effect of pinealectomy on the circadian clock of the chick retina under different monochromatic lights

The avian circadian rhythm pacemaker is composed of the retina, pineal gland and suprachiasmatic nucleus. As an intact input-pacemaker-output system, each of these structures is linked within a neuroendocrine loop to influence downstream processes and peripheral oscillations. While our previous study found that monochromatic light affected the circadian rhythms of clock genes in the chick retina, the effect of the pineal gland on the response of the retinal circadian clock under monochromatic light still remains unclear. In this study, a total of 144 chicks, including sham-operated and pinealectomized groups, were exposed to white, red, green or blue light. After 2 weeks of light illumination, the circadian expression of six core clock genes (cClock, cBmal1, cCry1, cCry2, cPer2 and cPer3), melanopsin (cOpn4-1, cOpn4-2), Arylalkylamine N-acetyltransferase (cAanat) and melatonin was examined in the retina. The cBmal1, cCry1, cPer2, cPer3, cOpn4-1, cOpn4-2 and cAanat genes as well as melatonin had circadian rhythmic expression in both the sham-operated and pinealectomized groups under different monochromatic lights, while cClock and cCry2 had arrhythmic 24 h profiles in all of the light-treated groups. After pinealectomy, the rhythmicity of the clock genes, melanopsins, cAanat and melatonin in the chick retina did not change, especially the mesors, amplitudes and phases of cBmal1, cOpn4-1, cOpn4-2, cAanat and melatonin. Compared to the white light group, however, green light increased the mRNA expression of the positive-regulating clock genes cBmal1, cAanat, cOpn4-1 and cOpn4-2 as well as the melatonin content in pinealectomized chicks, whereas red light decreased their expression. These results suggest that the chick retina is a relatively independent circadian oscillator from the pineal gland, whose circadian rhythmicity (including photoreception, molecular clock and melatonin output) is not altered after pinealectomization. Moreover, green light increases ocular cAanat expression and melatonin synthesis by accelerating the expression of melanopsin and positive-regulating clock genes cBmal1 and cClock.

Single Cell Sequencing of the Pineal Gland: The Next Chapter

The analysis of pineal cell biology has undergone remarkable development as techniques have become available which allow for sequencing of entire transcriptomes and, most recently, the sequencing of the transcriptome of individual cells. Identification of at least nine distinct cell types in the rat pineal gland has been made possible, allowing identification of the precise cells of origin and expression of transcripts for the first time. Here the history and current state of knowledge generated by these transcriptomic efforts is reviewed, with emphasis on the insights suggested by the findings.

Diurnal and circadian variations in indole contents in the goose pineal gland

The diurnal and circadian profiles of pineal indoles, except melatonin, are poorly characterized in birds. Moreover, there are no data on the effect of sudden changes in the light-dark cycle on these profiles. Therefore, we investigated the diurnal (Experiment I) and circadian variation (Experiment II) of nine pineal indoles (tryptophan, 5-hydroxytryptophan, serotonin, N-acetylserotonin, melatonin, 5-hydroxyindole acetic acid, 5-methoxytryptophol, 5-methoxyindole acetic acid, 5-methoxytryptamine) in geese, as well as the changes in the profiles of these substances in geese subjected to a reversed light-dark cycle (Experiment III). For the first 12 weeks of life, all geese were kept under a diurnal cycle of 12 h of light and 12 h of darkness (12L:12D). In Experiment I (n = 48), they were kept under these conditions for another 14 days before being sacrificed at 2-h intervals for sampling of the pineal glands. In Experiment II, the geese (n = 48) were divided into three groups (12L:12D, 24L:0D, 0L:24D) for 10 days before sampling at 6-h intervals. In Experiment III, 24 geese were exposed to a reversed light-dark cycle before sampling at 14:00 and 02:00 on the first, second and third days after light-dark cycle reversal. To determine the content of the indoles in the goose pineals, HPLC with fluorescence detection was used. We found that, with the exception of tryptophan, all the investigated indoles showed statistically significant diurnal variation. When geese were kept in constant darkness, most of the indoles continued to show this variation, but when geese were kept in constant light, the indoles did not show significant variation. When the light-dark cycle was reversed (12L:12D to 12D:12L), the profiles of NAS, melatonin, 5-MTAM and 5-MTOL reflected the new cycle within 2 days. The content of serotonin in geese in 12L:12D was higher than that observed in other birds under these conditions, which suggests that this compound may play a special role in the pineal physiology of this species. In conclusion, our results show that the daily variations in the metabolism of melatonin-synthesis-related indoles in the goose pineal gland are generated endogenously and controlled by environmental light conditions, as in other birds. However, comparison of the results obtained with the goose to those obtained with other species (chicken, duck) unambiguously shows that the profiles of pineal indoles differ markedly between species, in both the quantitative proportions of the compounds and the characteristics of the diurnal changes. These findings provide strong arguments for the need for comparative studies.

Effect of Monochromatic Light on Circadian Rhythm of Clock Genes in Chick Pinealocytes

The avian circadian system is a complex of mutually coupled pacemakers residing in pineal gland, retina and suprachiasmatic nucleus. In this study, the self-regulation mechanism of pineal circadian rhythm was investigated by culturing chick primary pinealocytes exposed to red light (RL), green light (GL), blue light (BL), white light (WL) and constant darkness (DD), respectively. All illuminations were set up with a photoperiod of 12 light: 12 dark. The 24-h expression profiles of seven core clock genes (cBmal1/2, cClock, cCry1/2 and cPer2/3), cAanat and melatonin showed significant circadian oscillation in all groups, except for the loss of cCry1 rhythm in BL. Compared to WL, GL increased the amplitudes and mesors of positive elements (cClock and cBmal1/2) and reduced those of negative elements (cCry1/2 and cPer2/3), in contrast to RL. The temporal patterns of cAanatmRNA and melatonin secretion have always been consistent with the positive genes. Besides, GL advanced the acrophases of the positive elements, cAanat and melatonin, but RL and BL showed the opposite effect. Thereby, GL could promote the secretion of melatonin by enhancing the expressions of positive clock genes and repressing the expressions of negative clock genes.

DNA methylation profiles in red blood cells of adult hens correlate with their rearing conditions

Stressful conditions are common in the environment where production animals are reared. Stress in animals is usually determined by the levels of stress-related hormones. A big challenge, however, is in determining the history of exposure of an organism to stress, because the release of stress hormones can show an acute (and recent) but not a sustained exposure to stress. Epigenetic tools provide an alternative option to evaluate past exposure to long-term stress. Chickens provide a unique model to study stress effects in the epigenome of red blood cells (RBCs), a cell type of easy access and nucleated in birds. The present study investigated whether two different rearing conditions in chickens can be identified by looking at DNA methylation patterns in their RBCs later in life. These conditions were rearing in open aviaries versus in cages, which are likely to differ regarding the amount of stress they generate. Our comparison revealed 115 genomic windows with significant changes in RBC DNA methylation between experimental groups, which were located around 53 genes and within 22 intronic regions. Our results set the ground for future detection of long-term stress in live production animals by measuring DNA methylation in a cell type of easy accessibility.

Effect of monochromatic light on circadian rhythmic expression of clock genes in the hypothalamus of chick

To clarify the effect of monochromatic light on circadian clock gene expression in chick hypothalamus, a total 240 newly hatched chickens were reared under blue light (BL), green light (GL), red light (RL) and white light (WL), respectively. On the post-hatched day 14, 24-h profiles of seven core clock genes (cClock, cBmal1, cBmal2, cCry1, cCry2, cPer2 and cPer3) were measured at six time points (CT 0, CT 4, CT 8, CT 12, CT 16, CT 20, circadian time). We found all these clock genes expressed with a significant rhythmicity in different light wavelength groups. Meanwhile, cClock and cBmal1 showed a high level under GL, and followed a corresponding high expression of cCry1. However, RL decreased the expression levels of these genes. Be consistent with the mRNA level, CLOCK and BMAL1 proteins also showed a high level under GL. The CLOCK-like immunoreactive neurons were observed not only in the SCN, but also in the non-SCN brain region such as the nucleus anterior medialis hypothalami, the periventricularis nucleus, the paraventricular nucleus and the median eminence. All these results are consistent with the auto-regulatory circadian feedback loop, and indicate that GL may play an important role on the circadian time generation and development in the chick hypothalamus. Our results also suggest that the circadian clock in the chick hypothalamus such as non-SCN brain region were involved in the regulation of photo information.

Effects of continuous white light and 12h white-12h blue light-cycles on the expression of clock genes in diencephalon, liver, and skeletal muscle in chicks

The core circadian clock mechanism relies on a feedback loop comprised of clock genes, such as the brain and muscle Arnt-like 1 (Bmal1), chriptochrome 1 (Cry1), and period 3 (Per3). Exposure to the light-dark cycle synchronizes the master circadian clock in the brain, and which then synchronizes circadian clocks in peripheral tissues. Birds have long been used as a model for the investigation of circadian rhythm in human neurobiology. In the present study, we examined the effects of continuous light and the combination of white and blue light on the expression of clock genes (Bmal1, Cry1, and Per3) in the central and peripheral tissues in chicks. Seventy two day-old male chicks were weighed, allocated to three groups and maintained under three light schedules: 12h white light-12h dark-cycles group (control); 24h white light group (WW group); 12h white light-12h blue light-cycles group (WB group). The mRNA levels of clock genes in the diencephalon were significantly different between the control and WW groups. On the other hand, the alteration in the mRNA levels of clock genes was similar between the control and WB groups. Similar phenomena were observed in the liver and skeletal muscle (biceps femoris). These results suggest that 12h white-12h blue light-cycles did not disrupt the circadian rhythm of clock gene expression in chicks.

Avian biological clock - Immune system relationship

Biological rhythms in birds are driven by the master clock, which includes the suprachiasmatic nucleus, the pineal gland and the retina. Light/dark cycles are the cues that synchronize the rhythmic changes in physiological processes, including immunity. This review summarizes our investigations on the bidirectional relationships between the chicken pineal gland and the immune system. We demonstrated that, in the chicken, the main pineal hormone, melatonin, regulates innate immunity, maintains the rhythmicity of immune reactions and is involved in the seasonal changes in immunity. Using thioglycollate-induced peritonitis as a model, we showed that the activated immune system regulates the pineal gland by inhibition of melatonin production at the level of the key enzyme in its biosynthetic pathway, arylalkylamine-N-acetyltransferase (AANAT). Interleukin 6 and interleukin 18 seem to be the immune mediators influencing the pineal gland, directly inhibiting Aanat gene transcription and modulating expression of the clock genes Bmal1 and Per3, which in turn regulate Aanat.

Role of monochromatic light on daily variation of clock gene expression in the pineal gland of chick

The avian pineal gland is a master clock that can receive external photic cues and translate them into output rhythms. To clarify whether a shift in light wavelength can influence the circadian expression in chick pineal gland, a total of 240 Arbor Acre male broilers were exposed to white light (WL), red light (RL), green light (GL) or blue light (BL). After 2weeks light illumination, circadian expressions of seven core clock genes in pineal gland and the level of melatonin in plasma were examined. The results showed after illumination with monochromatic light, 24h profiles of all clock gene mRNAs retained circadian oscillation, except that RL tended to disrupt the rhythm of cCry2. Compared to WL, BL advanced the acrophases of the negative elements (cCry1, cCry2, cPer2 and cPer3) by 0.1-1.5h and delayed those of positive elements (cClock, cBmal1 and cBmal2) by 0.2-0.8h. And, RL advanced all clock genes except cClock and cPer2 by 0.3-2.1h, while GL delayed all clock genes by 0.5-1.5h except cBmal2. Meanwhile, GL increased the amplitude and mesor of positive and reduced both parameters of negative clock genes, but RL showed the opposite pattern. Although the acrophase of plasma melatonin was advanced by both GL and RL, the melatonin level was significantly increased in GL and decreased in RL. This tendency was consistent with the variations in the positive clock gene mRNA levels under monochromatic light and contrasted with those of negative clock genes. Therefore, we speculate that GL may enhance positive clock genes expression, leading to melatonin synthesis, whereas RL may enhance negative genes expression, suppressing melatonin synthesis.

Clock-Controlled Regulation of the Acute Effects of Norepinephrine on Chick Pineal Melatonin Rhythms

The chicken pineal gland synthesizes and releases melatonin rhythmically in light/dark (LD) cycles, with high melatonin levels during the dark phase, and in constant darkness (DD) for several cycles before it gradually damps to arrhythmicity in DD. Daily administration of norepinephrine (NE) in vivo and in vitro prevents the damping and restores the melatonin rhythm. To investigate the role of the circadian clock on melatonin rhythm damping and of its restoration by NE, the effects of NE administration at different phases of the melatonin cycle revealed a robust rhythm in NE sensitivity in which NE efficacy in increasing melatonin amplitude peaked in late subjective night and early subjective day, suggesting a clock underlying NE sensitivity. However, NE itself had no effect on circadian phase or period of the melatonin rhythms. Transcriptional analyses indicated that even though the rhythm of melatonin output damped to arrhythmicity, messenger RNA (mRNA) encoding clock genes gper2, gper3, gBmal1, gclock, gcry1, and gcry2; enzymes associated with melatonin biosynthesis; and enzymes involved in cyclic nucleotide signaling remained robustly rhythmic. Of these, only gADCY1 (adenylate cyclase 1) and gPDE4D (cAMP-specific 3',5'-cyclic phosphodiesterase 4D) were affected by NE administration at the mRNA levels, and only ADCY1 was affected at the protein level. The data strongly suggest that damping of the melatonin rhythm in the chick pineal gland occurs at the posttranscriptional level and that a major role of the clock is to regulate pinealocytes' sensitivity to neuronal input from the brain.

Breakthrough in neuroendocrinology by discovering novel neuropeptides and neurosteroids: 2. Discovery of neurosteroids and pineal neurosteroids

Bargmann-Scharrer's discovery of "neurosecretion" in the first half of the 20th century has since matured into the scientific discipline of neuroendocrinology. Identification of novel neurohormones, such as neuropeptides and neurosteroids, is essential for the progress of neuroendocrinology. Our studies over the past two decades have significantly broadened the horizons of this field of research by identifying novel neuropeptides and neurosteroids in vertebrates that have opened new lines of scientific investigation in neuroendocrinology. We have established de novo synthesis and functions of neurosteroids in the brain of various vertebrates. Recently, we discovered 7α-hydroxypregnenolone (7α-OH PREG), a novel bioactive neurosteroid that acts as a key regulator for inducing locomotor behavior by means of the dopaminergic system. We further discovered that the pineal gland, an endocrine organ located close to the brain, is an important site of production of neurosteroids de novo from cholesterol (CHOL). The pineal gland secretes 7α-OH PREG and 3α,5α-tetrahydroprogesterone (3α,5α-THP; allopregnanolone) that are involved in locomotor rhythms and neuronal survival, respectively. Subsequently, we have demonstrated their mode of action and functional significance. This review summarizes the discovery of these novel neurosteroids and its contribution to the progress of neuroendocrinology.

Avian circadian organization: a chorus of clocks

In birds, biological clock function pervades all aspects of biology, controlling daily changes in sleep: wake, visual function, song, migratory patterns and orientation, as well as seasonal patterns of reproduction, song and migration. The molecular bases for circadian clocks are highly conserved, and it is likely the avian molecular mechanisms are similar to those expressed in mammals, including humans. The central pacemakers in the avian pineal gland, retinae and SCN dynamically interact to maintain stable phase relationships and then influence downstream rhythms through entrainment of peripheral oscillators in the brain controlling behavior and peripheral tissues. Birds represent an excellent model for the role played by biological clocks in human neurobiology; unlike most rodent models, they are diurnal, they exhibit cognitively complex social interactions, and their circadian clocks are more sensitive to the hormone melatonin than are those of nocturnal rodents.

Pineal oscillator functioning in the chicken--effect of photoperiod and melatonin

The avian pineal gland, apart from the hypothalamic master clock (suprachiasmatic nuclei, SCN) and retina, functions as an independent circadian oscillator, receiving external photic cues that it translates into the rhythmical synthesis of melatonin, a biochemical signal of darkness. Functional similarity to the mammalian SCN makes the avian pineal gland a convenient model for studies on biological clock mechanisms in general. Pineal melatonin is produced not only in a light-dependent manner but also remains under the control of the endogenous oscillator, while the possible involvement of melatonin in maintaining cyclic expression of the avian clock genes remains to be elucidated. The aim of the present study was to characterize the diurnal profiles of main clock genes transcription in the pineal glands of chickens exposed to continuous light (LL) and supplemented with exogenous melatonin. We hypothesized that rearing chickens from the day of hatch under LL conditions would evoke a functional pinealectomy, influencing, in turn, pineal clock function. To verify this hypothesis, we examined the diurnal transcriptional profiles of selected clock genes as well as the essential parameters of pineal gland function: transcription of the genes encoding arylalkylamine N-acetyltransferase (Aanat), a key enzyme in melatonin biosynthesis, and the melatonin receptor (Mel1c), along with the blood melatonin level. Chickens hatched in summer or winter were maintained under LD 16:8 and 8:16, corresponding to the respective photoperiods, as the seasonal control groups. Another set of chickens was kept in parallel under LL conditions and some were supplemented with melatonin to check the ability of exogenous hormone to antagonize the effects evoked by continuous light. Twelve-day-old chickens were sacrificed every 3 h over a 24-h period and the mRNAs of selected clock genes, Bmal1, Cry1, Per3, E4bp4, together with those of Aanat and Mel1c, were quantified in the isolated pineal glands. Our results indicate that the profiles of clock gene transcription are not dependent on the duration of the light phase, while LL conditions decrease the amplitude of diurnal changes, but do not abolish them entirely. Melatonin supplied in drinking water to the birds kept in LL seems to desynchronize transcription of the majority of clock genes in the summer, while in the winter, it restores the pattern, but not the diurnal rhythmicity. Rhythmic expression of Bmal1 appears to provide a direct link between the circadian clock and the melatonin output pathway, while the availability of cyclic melatonin is clearly involved in the canonical transcription pattern of Per3 in the chicken pineal gland. Regardless of the experimental conditions, a negative correlation was identified between the transcription of genes involved in melatonin biosynthesis (Aanat) and melatonin signal perception (Mel1c receptor).

Daily expression of six clock genes in central and peripheral tissues of a night-migratory songbird: evidence for tissue-specific circadian timing

In birds, independent circadian clocks reside in the retina, pineal, and hypothalamus, which interact with each other and produce circadian time at the functional level. However, less is known of the molecular clockwork, and of the integration between central and peripheral clocks in birds. The present study investigated this, by monitoring the timed expression of five core clock genes (Per2. Cry1. Cry2. Bmal1, and Clock) and one clock-controlled gene (E4bp4) in a night-migratory songbird, the redheaded bunting (rb; Emberiza bruniceps). The authors first partially cloned these six genes, and then measured their 24-h profiles in central (retina, hypothalamus) and peripheral (liver, heart, stomach, gut, testes) tissues, collected at six times (zeitgeber time 2 [ZT2], ZT6, ZT11, ZT13, ZT18, and ZT23; ZT0 = lights on) from birds (n = 5 per ZT) on 12 h:12 h light-dark cycle. rbPer2. rbCry1. rbBmal1, and rbClock were expressed with a significant rhythm in all the tissues, except in the retina (only rbClock) and testes. rbCry2, however, had tissue-specific expression pattern: a significant rhythm in the hypothalamus, heart, and gut, but not in the retina, liver, stomach, and testes. rbE4bp4 had a significant mRNA rhythm in all the tissues, except retina. Further, rbPer2 mRNA peak was phase aligned with lights on, whereas rbCry1. rbBmal1, and rbE4bp4 mRNA peaks were phase aligned with lights off. rbCry2 and rbClock had tissue-specific scattered peaks. For example, both rbCry2 and rbClock peaks were close to rbCry1 and rbBmal1 peaks, respectively, in the hypothalamus, but not in other tissues. The results are consistent with the autoregulatory circadian feedback loop, and indicate a conserved tissue-level circadian time generation in buntings. Variable phase relationships between gene pairs forming positive and negative limbs of the feedback loop may suggest the tissue-specific contribution of individual core circadian genes in the circadian time generation.

Biological clocks in the duodenum and the diurnal regulation of duodenal and plasma serotonin

Serotonin in blood plasma is primarily synthesized in the duodenum, as brain derived serotonin does not cross the blood-brain barrier. Because serotonin in the brain and retina is synthesized under the control of a circadian clock, we sought to determine if a circadian clock in the duodenum regulates serotonin synthesis and release in blood. We examined gene expression in the duodenum of chickens at different times of the day and found that the duodenum rhythmically expresses molecular circadian clock genes and genes controlling serotonin biosynthesis, specifically tryptophan hydroxylase, in a light dark cycle (LD). Analysis of the duodenum and blood plasma showed that the amount of serotonin in the duodenum varies across the day and that serotonin profiles in blood plasma are also rhythmic in LD, but were not rhythmic in constant darkness. Because serotonin in the gut affects duodenal nutrient absorption and gut motility, the control of serotonin production in the duodenum by LD cycles could provide an additional mechanism by which the external environment controls nutrient uptake and digestive function. The diurnal regulation of plasma serotonin may also serve as an additional biochemical signal in the blood encoding time and could be used by target tissues to indicate the status of nutrient absorption.

Microarray resources for genetic and genomic studies in chicken: a review

Advent of microarray technologies revolutionized the nature and scope of genetic and genomic research in human and other species by allowing massively parallel analysis of thousands of genomic sites. They have been used for diverse purposes such as for transcriptome analysis, CNV detection, SNP and CNV genotyping, studying DNA-protein interaction, and detection of genome methylation. Microarrays have also made invaluable contributions to research in chicken which is an important model organism for studying embryology, immunology, oncology, virology, evolution, genetics, and genomics and also for other avian species. Despite their huge contributions in life science research, the future of microarrays is now being questioned with the advent of massively parallel next generation sequencing (NGS) technologies, which promise to overcome some of the limitations of microarray platforms. In this article we review the various microarray resources developed for chicken and their past and potential future applications. We also discuss about the future of microarrays in the NGS era particularly in the context of livestock genetics. We argue that even though NGS promises some major advantages-in particular, offers the opportunity to discover novel elements in the genome-microarrays will continue to be major tools for research and practice in the field of livestock genetics/genomics due to their affordability, high throughput nature, mature established technologies and ease of application. Moreover, with advent of new microarray technologies like capture arrays, the NGS and microarrays are expected to complement each other in future research in life science.

Biosynthesis and biological actions of pineal neurosteroids in domestic birds

The central and peripheral nervous systems have the capacity of synthesizing steroids de novo from cholesterol, the so-called 'neurosteroids'. De novo synthesis of neurosteroids from cholesterol appears to be a conserved property across the subphylum vertebrata. Until recently, it was generally believed that neurosteroids are produced in neurons and glial cells in the central and peripheral nervous systems. However, our recent studies on birds have demonstrated that the pineal gland, an endocrine organ located close to the brain, is an important site of production of neurosteroids de novo from cholesterol. 7α-Hydroxypregnenolone is a major pineal neurosteroid that stimulates locomotor activity of juvenile birds, connecting light-induced gene expression with locomotion. The other major pineal neurosteroid allopregnanolone is involved in Purkinje cell survival by suppressing the activity of caspase-3, a crucial mediator of apoptosis during cerebellar development. This review is an updated summary of the biosynthesis and biological actions of pineal neurosteroids.

Systematic identification of rhythmic genes reveals camk1gb as a new element in the circadian clockwork

A wide variety of biochemical, physiological, and molecular processes are known to have daily rhythms driven by an endogenous circadian clock. While extensive research has greatly improved our understanding of the molecular mechanisms that constitute the circadian clock, the links between this clock and dependent processes have remained elusive. To address this gap in our knowledge, we have used RNA sequencing (RNA–seq) and DNA microarrays to systematically identify clock-controlled genes in the zebrafish pineal gland. In addition to a comprehensive view of the expression pattern of known clock components within this master clock tissue, this approach has revealed novel potential elements of the circadian timing system. We have implicated one rhythmically expressed gene, camk1gb, in connecting the clock with downstream physiology of the pineal gland. Remarkably, knockdown of camk1gb disrupts locomotor activity in the whole larva, even though it is predominantly expressed within the pineal gland. Therefore, it appears that camk1gb plays a role in linking the pineal master clock with the periphery.

The circadian clock is a molecular pacemaker that drives rhythmic expression of genes with a ∼24-hour period. As a result, many physiological processes have daily rhythms. Many of the conserved elements that constitute the circadian clock are known, but the links between the clock and dependent processes have remained elusive. With its amenability to genetic manipulations and a variety of genetic tools, the zebrafish has become an attractive vertebrate model for the quest to identify and characterize novel clock components. Here, we take advantage of another attraction of the zebrafish, the fact that its pineal gland is the site of a central clock which directly receives light input and autonomously generates circadian rhythms that affect the physiology of the whole organism. We show that the systematic design and analysis of genome-wide experiments based on the zebrafish pineal gland can lead to the discovery of new clock elements. We have characterized one novel element, camk1gb, and show that this gene, predominantly expressed within the pineal gland and driven by the circadian clock, links circadian clock timing with locomotor activity in zebrafish larvae.

Circadian activation of the mitogen-activated protein kinase MAK-1 facilitates rhythms in clock-controlled genes in Neurospora crassa

The circadian clock regulates the expression of many genes involved in a wide range of biological functions through output pathways such as mitogen-activated protein kinase (MAPK) pathways. We demonstrate here that the clock regulates the phosphorylation, and thus activation, of the MAPKs MAK-1 and MAK-2 in the filamentous fungus Neurospora crassa. In this study, we identified genetic targets of the MAK-1 pathway, which is homologous to the cell wall integrity pathway in Saccharomyces cerevisiae and the extracellular signal-regulated kinase 1/2 (ERK1/2) pathway in mammals. When MAK-1 was deleted from Neurospora cells, vegetative growth was reduced and the transcript levels for over 500 genes were affected, with significant enrichment for genes involved in protein synthesis, biogenesis of cellular components, metabolism, energy production, and transcription. Additionally, of the ~500 genes affected by the disruption of MAK-1, more than 25% were previously identified as putative clock-controlled genes. We show that MAK-1 is necessary for robust rhythms of two morning-specific genes, i.e., ccg-1 and the mitochondrial phosphate carrier protein gene NCU07465. Additionally, we show clock regulation of a predicted chitin synthase gene, NCU04352, whose rhythmic accumulation is also dependent upon MAK-1. Together, these data establish a role for the MAK-1 pathway as an output pathway of the circadian clock and suggest a link between rhythmic MAK-1 activity and circadian control of cellular growth.

Pineal arylalkylamine N-acetyltransferase (Aanat) gene expression as a target of inflammatory mediators in the chicken

Previously, we demonstrated that experimental peritonitis in chickens was attenuated by treatment with exogenous melatonin, while the developing inflammation decreased pineal AANAT activity. This suggested the existence of a bidirectional relationship between the activated immune system and pineal gland function. The aim of the present study was to identify the step(s) in the chicken pineal melatonin biosynthetic pathway that are affected by inflammation. Peritonitis was evoked by i.p. injection of thioglycollate solution, either 2h after the start, or 2h before the end of the light period, and the animals were sacrificed 4h later. The effect of inflammation on the expression of genes encoding enzymes participating in melatonin biosynthesis in the pineal gland, i.e. tryptophan hydroxylase 1 (Tph1), dopa decarboxylase (Ddc), arylalkylamine N-acetyltransferase (Aanat) and acetylserotonin O-methyltransferase (Asmt), was evaluated by qPCR. The pineal and serum melatonin concentration as well as the content of its precursors in the pineal gland were measured, along with the activity of the relevant biosynthetic enzymes. Developing peritonitis caused an increase in the pineal levels of the Tph1 mRNA during the night and the Asmt mRNA during the day, while nocturnal Aanat transcription was reduced. Both the pineal and serum melatonin level and the pineal content of N-acetylserotonin (NAS) were decreased during the night in birds with peritonitis. The amount and activity of pineal AANAT were significantly reduced, while the activity of HIOMT was increased under these experimental conditions. These results indicate that the observed decrease in MEL biosynthesis in chickens with developing inflammation is a result of transcriptional downregulation of the Aanat gene, followed by reduced synthesis and activity of the encoded enzyme.

Circadian Regulation of Bird Song, Call, and Locomotor Behavior by Pineal Melatonin in the Zebra Finch

As both a photoreceptor and pacemaker in the avian circadian clock system, the pineal gland is crucial for maintaining and synchronizing overt circadian rhythms in processes such as locomotor activity and body temperature through its circadian secretion of the pineal hormone melatonin. In addition to receptor presence in circadian and visual system structures, high-affinity melatonin binding and receptor mRNA are present in the song control system of male oscine passeriform birds. The present study explores the role of pineal melatonin in circadian organization of singing and calling behavior in comparison to locomotor activity under different lighting conditions. Similar to locomotor activity, both singing and calling behavior were regulated on a circadian basis by the central clock system through pineal melatonin, since these behaviors free-ran with a circadian period and since pinealectomy abolished them in constant environmental conditions. Further, rhythmic melatonin administration restored their rhythmicity. However, the rates by which these behaviors became arrhythmic and the rates of their entrainment to rhythmic melatonin administration differed among locomotor activity, singing and calling under constant dim light and constant bright light. Overall, the study demonstrates a role for pineal melatonin in regulating circadian oscillations of avian vocalizations in addition to locomotor activity. It is suggested that these behaviors might be controlled by separable circadian clockworks and that pineal melatonin entrains them all through a circadian clock.

The bird of time: cognition and the avian biological clock

Avian behavior and physiology are embedded in time at many levels of biological organization. Biological clock function in birds is critical for sleep/wake cycles, but may also regulate the acquisition of place memory, learning of song from tutors, social integration, and time-compensated navigation. This relationship has two major implications. First, mechanisms of the circadian clock should be linked in some way to the mechanisms of all these behaviors. How is not yet clear, and evidence that the central clock has effects is piecemeal. Second, selection acting on characters that are linked to the circadian clock should influence aspects of the clock mechanism itself. Little evidence exists for this in birds, but there have been few attempts to assess this idea. At its core, the avian circadian clock is a multi-oscillator system comprising the pineal gland, the retinae, and the avian homologs of the suprachiasmatic nuclei, whose mutual interactions ensure coordinated physiological functions, which are in turn synchronized to ambient light cycles (LD) via encephalic, pineal, and retinal photoreceptors. At the molecular level, avian biological clocks comprise a genetic network of "positive elements" clock and bmal1 whose interactions with the "negative elements" period 2 (per2), period 3 (per3), and the cryptochromes form an oscillatory feedback loop that circumnavigates the 24 h of the day. We assess the possibilities for dual integration of the clock with time-dependent cognitive processes. Closer examination of the molecular, physiological, and behavioral elements of the circadian system would place birds at a very interesting fulcrum in the neurobiology of time in learning, memory, and navigation.

Crx broadly modulates the pineal transcriptome

Cone-rod homeobox (Crx) encodes Crx, a transcription factor expressed selectively in retinal photoreceptors and pinealocytes, the major cell type of the pineal gland. In this study, the influence of Crx on the mammalian pineal gland was studied by light and electron microscopy and by use of microarray and qRTPCR technology, thereby extending previous studies on selected genes (Furukawa et al. 1999). Deletion of Crx was not found to alter pineal morphology, but was found to broadly modulate the mouse pineal transcriptome, characterized by a>2-fold down-regulation of 543 genes and a>2-fold up-regulation of 745 genes (p<0.05). Of these, one of the most highly up-regulated (18-fold) was Hoxc4, a member of the Hox gene family, members of which are known to control gene expression cascades. During a 24-h period, a set of 51 genes exhibited differential day/night expression in pineal glands of wild-type animals; only eight of these were also day/night expressed in the Crx⁻/⁻ pineal gland. However, in the Crx⁻/⁻ pineal gland 41 genes exhibited differential night/day expression that was not seen in wild-type animals. These findings indicate that Crx broadly modulates the pineal transcriptome and also influences differential night/day gene expression in this tissue. Some effects of Crx deletion on the pineal transcriptome might be mediated by Hoxc4 up-regulation.

Circadian melatonin production develops faster in birds than in mammals

The development of circadian rhythmicity of melatonin biosynthesis in the pineal gland starts during embryonic period in birds while it is delayed to the postnatal life in mammals. Daily rhythms of melatonin in isolated pinealocytes and in intact pineal glands under in vivo conditions were demonstrated during the last third of embryonic development in chick embryos, with higher levels during the dark (D) than during the light (L) phase. In addition to the LD cycle, rhythmic temperature changes with the amplitude of 4.5°C can entrain rhythmic melatonin biosynthesis in chick embryos, with higher concentrations found during the low-temperature phase (33.0 vs 37.5°C). Molecular clockwork starts to operate during the embryonic life in birds in line with the early development of melatonin rhythmicity. Expression of per2 and cry genes is rhythmic at least at day 16 and 18, respectively, and the circadian system operates in a mature-like manner soon after hatching. Rhythmic oscillations are detected earlier in the central oscillator (the pineal gland) than in the peripheral structures, reflecting the synchronization of individual cells which is necessary for detection of the rhythm. The early development of the circadian system in birds reflects an absence of rhythmic maternal melatonin which in mammals synchronizes physiological processes of offspring. Developmental consequences of modified development of circadian system for its stability later in development are not known and should be studied.

Expression pattern of clock under acute phase-delay of the light/dark cycle in the chicken pineal model

Shift workers have a higher risk of metabolic syndrome, a condition that also develops in mice carrying mutation in their circadian clock gene clock. To collect more data on the transcriptional changes of clock under phase-shifted light/dark LD conditions, we examined the 24h patterns of clock mRNA expression in vivo and in vitro in chickens exposed acutely to a reversed LD (DL) cycle. Under controlled LD conditions (lights on at 6:00, lights off at 20:00), clock mRNA expression peaked in vivo at 2:00 (Zeitgeber Time 20, ZT20) and in vitro at 22:00 (ZT16). Even higher mRNA contents were measured in the first cycle of in vivo DL conditions between 22:00 and 6:00 (lights at night), but in the second cycle by 2:00, lower mRNA contents were detected than the control peak values seen at this time point. Furthermore, no alterations were found in vitro in clock mRNA content during the first 12h of DL conditions (lights at night). The differences seen between the first and the second DL cycles in vivo and between the in vivo and in vitro data for the first DL cycle support the idea that neurohumoral signals perturbed by a phase-delayed light-dark cycle may also play a role in the in vivo rapid transcriptional resetting of the circadian clock in the chicken pineal model.

Light-dependent and circadian clock-regulated activation of sterol regulatory element-binding protein, X-box-binding protein 1, and heat shock factor pathways

The circadian clock is phase-delayed or -advanced by light when given at early or late subjective night, respectively. Despite the importance of the time-of-day-dependent phase responses to light, the underlying molecular mechanism is poorly understood. Here, we performed a comprehensive analysis of light-inducible genes in the chicken pineal gland, which consists of light-sensitive clock cells representing a prototype of the clock system. Light stimulated expression of 62 genes and 40 ESTs by >2.5-fold, among which genes responsive to the heat shock and endoplasmic reticulum stress as well as their regulatory transcription factors heat shock factor (HSF)1, HSF2, and X-box-binding protein 1 (XBP1) were strongly activated when a light pulse was given at late subjective night. In contrast, the light pulse at early subjective night caused prominent induction of E4bp4, a key regulator in the phase-delaying mechanism of the pineal clock, along with activation of a large group of cholesterol biosynthetic genes that are targets of sterol regulatory element-binding protein (SREBP) transcription factor. We found that the light pulse stimulated proteolytic formation of active SREBP-1 that, in turn, transactivated E4bp4 expression, linking SREBP with the light-input pathway of the pineal clock. As an output of light activation of cholesterol biosynthetic genes, we found light-stimulated pineal production of a neurosteroid, 7α-hydroxypregnenolone, demonstrating a unique endocrine function of the pineal gland. Intracerebroventricular injection of 7α-hydroxypregnenolone activated locomotor activities of chicks. Our study on the genome-wide gene expression analysis revealed time-of-day-dependent light activation of signaling pathways and provided molecular connection between gene expression and behavior through neurosteroid release from the pineal gland.

Inflammation in the avian spleen: timing is everything

Background

The synchrony of an organism with both its external and internal environment is critical to well-being and survival. As a result, organisms display daily cycles of physiology and behavior termed circadian rhythms. At the cellular level, circadian rhythms originate via interlocked autoregulatory feedback loops consisting of circadian clock genes and their proteins. These regulatory loops provide the molecular framework that enables the intracellular circadian timing system necessary to generate and maintain subsequent 24 hr rhythms. In the present study we examine the daily control of circadian clock genes and regulation of the inflammatory response by the circadian clock in the spleen.

Results

Our results reveal that circadian clock genes as well as proinflammatory cytokines, including Tnfά and IL-1β, display rhythmic oscillations of mRNA abundance over a 24 hr cycle. LPS-induced systemic inflammation applied at midday vs. midnight reveals a differential response of proinflammatory cytokine induction in the spleen, suggesting a daily rhythm of inflammation. Exogenous melatonin administration at midday prior to LPS stimulation conveys pleiotropic effects, enhancing and repressing inflammatory cytokines, indicating melatonin functions as both a pro- and anti-inflammatory molecule in the spleen.

Conclusion

In summary, a daily oscillation of circadian clock genes and inflammatory cytokines as well as the ability of melatonin to function as a daily mediator of inflammation provides valuable information to aid in deciphering how the circadian timing system regulates immune function at the molecular level. However, further research is needed to clarify the precise mechanisms by which the circadian clock and melatonin have an impact upon daily immune functions in the periphery.

Role of clock genes in gastrointestinal motility

Biological rhythms coordinate the timing of our internal bodily functions. Colonic motility follows a rhythm as well: most people will have a bowel movement in the morning and rarely during the night. Recent work provides a potential mechanism for this observation: the mouse colon possesses a functional circadian clock as well as a subset of rhythmically expressed genes that may directly impact on colonic motility. Furthermore, measures of colonic motility such as the colonic tissue contractile response to acetylcholine, stool output, and intracolonic pressure changes vary as a function of the time of day, but these variations are attenuated in mice with disrupted clock function. These laboratory findings are supported by clinical observations. Gastrointestinal symptoms such as diarrhea or constipation are prevalent among shift workers and time-zone travelers, both of which are conditions associated with disruptions in biological rhythms. This review will discuss new insights into the role of clock genes in colonic motility and their potential clinical relevance.

Functional genomics in chickens: development of integrated-systems microarrays for transcriptional profiling and discovery of regulatory pathways

The genetic networks that govern the differentiation and growth of major tissues of economic importance in the chicken are largely unknown. Under a functional genomics project, our consortium has generated 30 609 expressed sequence tags (ESTs) and developed several chicken DNA microarrays, which represent the Chicken Metabolic/Somatic (10 K) and Neuroendocrine/Reproductive (8 K) Systems (http://udgenome.ags.udel.edu/cogburn/). One of the major challenges facing functional genomics is the development of mathematical models to reconstruct functional gene networks and regulatory pathways from vast volumes of microarray data. In initial studies with liver-specific microarrays (3.1 K), we have examined gene expression profiles in liver during the peri-hatch transition and during a strong metabolic perturbation—fasting and re-feeding—in divergently selected broiler chickens (fast vs. slow-growth lines). The expression of many genes controlling metabolic pathways is dramatically altered by these perturbations. Our analysis has revealed a large number of clusters of functionally related genes (mainly metabolic enzymes and transcription factors) that control major metabolic pathways. Currently, we are conducting transcriptional profiling studies of multiple tissues during development of two sets of divergently selected broiler chickens (fast vs. slow growing and fat vs. lean lines). Transcriptional profiling across multiple tissues should permit construction of a detailed genetic blueprint that illustrates the developmental events and hierarchy of genes that govern growth and development of chickens. This review will briefly describe the recent acquisition of chicken genomic resources (ESTs and microarrays) and our consortium's efforts to help launch the new era of functional genomics in the chicken.

Sugarcane DIRIGENT and O-methyltransferase promoters confer stem-regulated gene expression in diverse monocots

Transcription profiling analysis identified Saccharum hybrid DIRIGENT (SHDIR16) and Omicron-Methyltransferase (SHOMT), putative defense and fiber biosynthesis-related genes that are highly expressed in the stem of sugarcane, a major sucrose accumulator and biomass producer. Promoters (Pro) of these genes were isolated and fused to the beta-glucuronidase (GUS) reporter gene. Transient and stable transgene expression analyses showed that both Pro( DIR16 ):GUS and Pro( OMT ):GUS retain the expression characteristics of their respective endogenous genes in sugarcane and function in orthologous monocot species, including rice, maize and sorghum. Furthermore, both promoters conferred stem-regulated expression, which was further enhanced in the stem and induced in the leaf and root by salicylic acid, jasmonic acid and methyl jasmonate, key regulators of biotic and abiotic stresses. Pro( DIR16 ) and Pro( OMT ) will enable functional gene analysis in monocots, and will facilitate engineering monocots for improved carbon metabolism, enhanced stress tolerance and bioenergy production.

Reproducible RNA preparation from sugarcane and citrus for functional genomic applications

High-throughput functional genomic procedures depend on the quality of the RNA used. Copurifying molecules can negatively impact the functionality of some plant RNA preparations employed in these procedures. We present a simplified, rapid, and scalable SDS/phenol-based method that provides the high-quantity and -quality RNA required by the newly emerging biotechnology applications. The method is applied to isolating RNA from tissues of two biotechnologically important crop plants, sugarcane and citrus, which provide a challenge due to the presence of fiber, polysaccharides, or secondary metabolites. The RNA isolated by this method is suitable for several downstream applications including northern blot hybridization, microarray analysis, and quantitative RT-PCR. This method has been used in a diverse range of projects ranging from screening plant lines overexpressing mammalian genes to analyzing plant responses to viral infection and defense signaling molecules.

Pineal function: impact of microarray analysis

Microarray analysis has provided a new understanding of pineal function by identifying genes that are highly expressed in this tissue relative to other tissues and also by identifying over 600 genes that are expressed on a 24-h schedule. This effort has highlighted surprising similarity to the retina and has provided reason to explore new avenues of study including intracellular signaling, signal transduction, transcriptional cascades, thyroid/retinoic acid hormone signaling, metal biology, RNA splicing, and the role the pineal gland plays in the immune/inflammation response. The new foundation that microarray analysis has provided will broadly support future research on pineal function.

Transcriptome analysis of the zebrafish pineal gland

The zebrafish pineal gland (epiphysis) is a site of melatonin production, contains photoreceptor cells, and functions as a circadian clock pace maker. Here, we have used microarray technology to study the zebrafish pineal transcriptome. Analysis of gene expression at three larval and two adult stages revealed a highly dynamic transcriptional profile, revealing many genes that are highly expressed in the zebrafish pineal gland. Statistical analysis of the data based on Gene Ontology annotation indicates that many transcription factors are highly expressed during larval stages, whereas genes dedicated to phototransduction are preferentially expressed in the adult. Furthermore, several genes were identified that exhibit day/night differences in expression. Among the multiple candidate genes suggested by these data, we note the identification of a tissue-specific form of the unc119 gene with a possible role in pineal development.

Time's arrow flies like a bird: two paradoxes for avian circadian biology

Biological timekeeping in birds is a fundamental feature of avian physiology, behavior and ecology. The physiological basis for avian circadian rhythmicity has pointed to a multi-oscillator system of mutually coupled pacemakers in the pineal gland, eyes and hypothalamic suprachiasmatic nuclei (SCN). In passerines, the role of the pineal gland and its hormone melatonin is particularly important. More recent molecular biological studies have pointed to a highly conserved mechanism involving rhythmic transcription and translation of "clock genes". However, studies attempting to reconcile the physiological role of pineal melatonin with molecular studies have largely failed. Recent work in our laboratory has suggested that melatonin-sensitive physiological processes are only loosely coupled to transcriptional oscillations. Similarly, although the pineal gland has been shown to be critical for overt circadian behaviors, its role in annual cycles of reproductive function appears to be minimal. Recent work on the seasonal control of birdsong, however, suggests that, although the pineal gland does not directly affect gonadal cycles, it is important for seasonal changes in song. Experimental analyses that address these paradoxes will shed light on the roles the biological clock play in birds and in vertebrates in general.

Expression of Cry2 in the chicken pineal gland: effects of changes in light-dark conditions

Pineal expression of Cry2 mRNA has been examined in chickens under normal (LD) and reversed (DL) light-dark conditions. In vivo the peak of Cry2 mRNA content at late subjective day under LD diminished after switching to a DL schedule. In vitro, Cry2 mRNA levels showed a steady decrease during light exposure at subjective night. Our data show that light-sensitive clock components in the pinealocytes may be involved in the repression of Cry2 transcription at night, which may contribute to resetting the phase of the clock within 24 h.

Pineal melatonin acts as a circadian zeitgeber and growth factor in chick astrocytes

Melatonin is rhythmically synthesized and released by the avian pineal gland and retina during the night, targeting an array of tissues and affecting a variety of physiological and behavioral processes. Among these targets, astrocytes express two melatonin receptor subtypes in vitro, the Mel(1A) and Mel(1C) receptors, which play a role in regulating metabolic activity and calcium homeostasis in these cells. Molecular characterization of chick astrocytes has revealed the expression of orthologs of the mammalian clock genes including clock, cry1, cry2, per2, and per3. To test the hypothesis that pineal melatonin entrains molecular clockworks in downstream cells, we asked whether coculturing astrocytes with pinealocytes or administration of exogenous melatonin cycles would entrain metabolic rhythms of 2-deoxy [14C]-glucose (2DG] uptake and/or clock gene expression in cultured astrocytes. Rhythmic secretion of melatonin from light-entrained pinealocytes in coculture as well as cyclic administration of exogenous melatonin entrained rhythms of 2DG uptake and expression of Gallus per2 (gper2) and/or gper3, but not of gcry1 mRNA. Surprisingly, melatonin also caused a dose-dependent increase in mitotic activity of astrocytes, both in coculture and when administered exogenously. The observation that melatonin stimulates mitotic activity in diencephalic astrocytes suggests a trophic role of the hormone in brain development. The data suggest a dual role for melatonin in avian astrocytes: synchronization of rhythmic processes in these cells and regulation of growth and differentiation. These two processes may or may not be mutually exclusive.

Modulation of metabolic and clock gene mRNA rhythms by pineal and retinal circadian oscillators

Avian circadian organization involves interactions between three neural pacemakers: the suprachiasmatic nuclei (SCN), pineal, and retina. Each of these structures is linked within a neuroendocrine loop to influence downstream processes and peripheral oscillations. However, the contribution of each structure to drive or synchronize peripheral oscillators or circadian outputs in avian species is largely unknown. To explore these interactions in the chick, we measured 2-deoxy[(14)C]-glucose (2DG) uptake and mRNA expression of the chick clock genes bmal1, cry1, and per3 in three brain areas and in two peripheral organs in chicks that underwent pinealectomy, enucleation, or sham surgery. We found that 2DG uptake rhythms damp under constant darkness in intact animals, while clock gene mRNA levels continue to cycle, demonstrating that metabolic rhythms are not directly driven by clock gene transcription. Moreover, 2DG rhythms are not phase-locked to rhythms of clock gene mRNA. However, pinealectomy and enucleation had similar disruptive effects on both metabolic and clock gene rhythms, suggesting that both of these oscillators act similarly to reinforce molecular and physiological rhythms in the chicken. Finally, we show that the relative phasing of at least one clock gene, cry1, varies between central and peripheral oscillators in a tissue specific manner. These data point to a complex, differential orchestration of central and peripheral oscillators in the chick, and, importantly, indicate a disconnect between canonical clock gene regulation and circadian control of metabolism.