Novel features of drosophila period Transcription revealed by real-time luciferase reporting

Post-translational enzyme activation in an animal via optimized conditional protein splicing

Control over the timing, location and level of protein activity in vivo is crucial to understanding biological function. Living systems are able to respond to external and internal stimuli rapidly and in a graded fashion by maintaining a pool of proteins whose activities are altered through post-translational modifications. Here we show that the process of protein trans-splicing can be used to modulate enzymatic activity both in cultured cells and in Drosophila melanogaster. We used an optimized conditional protein splicing system to rapidly trigger the in vivo ligation of two inactive fragments of firefly luciferase in a tunable manner. This technique provides a means of controlling enzymatic function with greater speed and precision than with standard genetic techniques and is a useful tool for probing biological processes.

The circadian timekeeping system of Drosophila

Daily rhythms in behavior, physiology and metabolism are controlled by endogenous circadian clocks. At the heart of these clocks is a circadian oscillator that keeps circadian time, is entrained by environmental cues such as light and activates rhythmic outputs at the appropriate time of day. Genetic and molecular analyses in Drosophila have revealed important insights into the molecules and mechanisms underlying circadian oscillator function in all organisms. In this review I will describe the intracellular feedback loops that form the core of the Drosophila circadian oscillator and consider how they are entrained by environmental light cycles, where they operate within the fly and how they are thought to control overt rhythms in physiology and behavior. I will also discuss where work remains to be done to give a comprehensive picture of the circadian clock in Drosophila and likely many other organisms.

Real-time monitoring of chloroplast gene expression by a luciferase reporter: evidence for nuclear regulation of chloroplast circadian period

Chloroplast-encoded genes, like nucleus-encoded genes, exhibit circadian expression. How the circadian clock exerts its control over chloroplast gene expression, however, is poorly understood. To facilitate the study of chloroplast circadian gene expression, we developed a codon-optimized firefly luciferase gene for the chloroplast of Chlamydomonas reinhardtii as a real-time bioluminescence reporter and introduced it into the chloroplast genome. The bioluminescence of the reporter strain correlated well with the circadian expression pattern of the introduced gene and satisfied all three criteria for circadian rhythms. Moreover, the period of the rhythm was lengthened in per mutants, which are phototactic rhythm mutants carrying a long-period gene in their nuclear genome. These results demonstrate that chloroplast gene expression rhythm is a bona fide circadian rhythm and that the nucleus-encoded circadian oscillator determines the period length of the chloroplast rhythm. Our reporter strains can serve as a powerful tool not only for analysis of the circadian regulation mechanisms of chloroplast gene expression but also for a genetic approach to the molecular oscillator of the algal circadian clock.

Neural circuits underlying circadian behavior in Drosophila melanogaster

Circadian clocks include control systems for organizing daily behavior. Such a system consists of a time-keeping mechanism (the clock or pacemaker), input pathways for entraining the clock, and output pathways for producing overt rhythms in behavior and physiology. In Drosophila melanogaster, as in mammals, neural circuits play vital roles in all three functional subdivisions of the circadian system. Regarding the pacemaker, multiple clock neurons, each with cell-autonomous pacemaker capability, are coupled to each other in a network. The outputs of different sets of clock neurons in this network combine to produce the normal bimodal pattern of locomotor activity observed in Drosophila. Regarding input, multiple sensory modalities (including light, temperature, and pheromones) use their own circuitry to entrain the clock. Regarding output, distinct circuits are likely involved for controlling the timing of eclosion and for generating the locomotor activity rhythms. This review summarizes work on all of these circadian circuits, and discusses the broader utility of studying the fly's circadian system.

Photonic Monitoring in Real Time of Vascular Endothelial Growth Factor Receptor 2 Gene Expression under Relaxin-Induced Conditions in a Novel Murine Wound Model

Relaxin is known to promote vascular endothelial growth factor (VEGF) expression in reproductive tissue, and successful wound healing depends on good vascularization of wound sites, a process that relaxin may facilitate. Thus, the objective of this study was to evaluate the efficacy of relaxin on the development of vascular tissue at wound sites in a novel VEGF receptor 2-luc (VEGFR2-luc) transgenic mouse wound model by monitoring the rate of VEGFR2-luc-mediated gene expression using bioluminescence and real-time imaging. To this end, 12 FVB/N VEGFR2-luc transgenic male mice were assigned to treatments (six per group): saline alone or relaxin (1 g/6 h/14 days) administered intraperitoneally (i.p.). On day 0, a set of full-thickness wounds (6-mm punch) were generated under anesthesia on the dorsal aspect of each mouse. Photonic emissions were recorded (5-min collection of photons) from wound sites 10 min after the administration of luciferin (150 mg/kg i.p.) on day 0 and on days 1, 2, 4, 7, 9, 11, and 14 postwounding to quantify luciferase activity using an IVIS 100 biophotonic imaging system. Animals were sacrificed (three per group) on day 7 or 14, and wound tissue specimens were recovered for molecular and histologic analyses. Although photonic emission from wound sites increased (P < .001) over time with peak values obtained by day 7, no significant (P > .05) effect of relaxin treatment on VEGFR2-luc gene expression was noted at wound sites. Whereas measuring relaxin's effect on angiogenesis indirectly via the VEGFR2 model was not successful, photonic imaging provides an exciting new tool using alternative models (i.e., VEGF-luc mouse) to study relaxin-induced gene expression in normal (i.e., wound healing) or tumorigenic tissues in real time.

Circadian clocks — the fall and rise of physiology

Circadian clocks control the daily life of most light-sensitive organisms - from cyanobacteria to humans. Molecular processes generate cellular rhythmicity, and cellular clocks in animals coordinate rhythms through interaction (known as coupling). This hierarchy of clocks generates a complex, approximately 24-hour temporal programme that is synchronized with the rotation of the Earth. The circadian system ensures anticipation and adaptation to daily environmental changes, and functions on different levels - from gene expression to behaviour. Circadian research is a remarkable example of interdisciplinarity, unravelling the complex mechanisms that underlie a ubiquitous biological programme. Insights from this research will help to optimize medical diagnostics and therapy, as well as adjust social and biological timing on the individual level.

An automated apparatus for the real-time monitoring of bioluminescence in plants

We developed an automated, high-throughput, bioluminescence-monitoring apparatus that can monitor 1920 individual plant seedlings under uniform light conditions. The apparatus is composed of five units: (i) a plate platform that can hold 20 96-well microplates under uniform light conditions, (ii) a scintillation counter, (iii) a robot that conveys plates between the plate platform and a scintillation counter, (iv) a sequence controller, and (v) an external computer that collects and analyzes bioluminescence data automatically. The apparatus gave reproducible and reliable results for both bioluminescence photon counts and period length of bioluminescence rhythms; neither was affected by the well position in a plate or the plate position on the platform. The apparatus is a powerful tool for both large-scale detailed analysis of gene expression and large-scale screening of mutants.

Temperature Synchronization of the Drosophila Circadian Clock

BACKGROUND

Circadian clocks are synchronized by both light:dark cycles and by temperature fluctuations. Although it has long been known that temperature cycles can robustly entrain Drosophila locomotor rhythms, nothing is known about the molecular mechanisms involved.

RESULTS

We show here that temperature cycles induce synchronized behavioral rhythms and oscillations of the clock proteins PERIOD and TIMELESS in constant light, a situation that normally leads to molecular and behavioral arrhythmicity. We show that expression of the Drosophila clock gene period can be entrained by temperature cycles in cultured body parts and isolated brains. Further, we show that the phospholipase C encoded by the norpA gene contributes to thermal entrainment, suggesting that a receptor-coupled transduction cascade signals temperature changes to the circadian clock. We initiated the further genetic dissection of temperature-entrainment and isolated the novel Drosophila mutation nocte, which is defective in molecular and behavioral entrainment by temperature cycles but synchronizes normally to light:dark cycles.

CONCLUSIONS

We conclude that temperature synchronization of the circadian clock is a tissue-autonomous process that is able to override the arrhythmia-inducing effects of constant light. Our data suggest that it involves a cell-autonomous signal-transduction cascade from a thermal receptor to the circadian clock. This process includes the function of phospholipase C and the product specified by the novel mutation nocte.

Bioluminescence imaging in living organisms

Luciferase enzymes catalyze the emission of light from a substrate -- a phenomenon known as bioluminescence -- and have been employed as reporters of many biological functions. Luminescent reporters are much dimmer than fluorescent reporters, and therefore provide relatively modest spatial and temporal resolution. Yet, they are generally more sensitive and less toxic, making them particularly useful for long-term longitudinal studies of living cells, tissues and whole animals. Bioluminescence imaging has proven useful for detecting protein-protein interactions, for tracking cells in vivo, and for monitoring the transcriptional and post-transcriptional regulation of specific genes. Recent applications have included longitudinal monitoring of tumor progression in vivo, and monitoring circadian rhythms with single-cell resolution.

Light-dependent development of circadian gene expression in transgenic zebrafish

The roles of environmental stimuli in initiation and synchronization of circadian oscillation during development appear to vary among different rhythmic processes. In zebrafish, a variety of rhythms emerge in larvae only after exposure to light-dark (LD) cycles, whereas zebrafish period3 (per3) mRNA has been reported to be rhythmic from day 1 of development in constant conditions. We generated transgenic zebrafish in which expression of the firefly luciferase (luc) gene is driven by the zebrafish per3 promoter. Live larvae from these lines are rhythmically bioluminescent, providing the first vertebrate system for high-throughput measurement of circadian gene expression in vivo. Circadian rhythmicity in constant conditions was observed only after 5-6 d of development, and only if the fish were exposed to LD signals after day 4. Regardless of light exposure, a novel developmental profile was observed, with low expression during the first few days and a rapid increase when active swimming begins. Ambient temperature affected the developmental profile and overall levels of per3 and luc mRNA, as well as the critical days in which LD cycles were needed for robust bioluminescence rhythms. In summary, per3-luc zebrafish has revealed complex interactions among developmental events, light, and temperature in the expression of a clock gene.

Techniques that Revealed the Network of the Circadian Clock of Drosophila

The techniques are reviewed that revealed the neuronal network of the circadian clock in the brain of the fruit fly as well as the function and localization of peripheral oscillators. Three principal techniques helped characterize the circadian clock network of Drosophila consisting of pacemaker centers in the brain and oscillators in peripheral tissues: (1) Immunolabeling with antibodies raised against specific clock proteins detected the tissues and cells that express the clock proteins, revealed the subcellular localization of clock molecules, and illuminated their abundance at different time points during the day; (2) reporter genes unraveled the network of clock neurons and reported the circadian cycling of the clock genes in vivo; and (3) genetic manipulations of clock gene expression elucidated the function of specific clock genes and clock cells. These techniques and the results gained by them are reviewed briefly.

Real-time reporting of circadian-regulated gene expression by luciferase imaging in plants and mammalian cells

Luciferase enzymes have been used as reporters of circadian rhythms in organisms as diverse as cyanobacteria, plants, fruit flies, and mice. This article details methodology for real-time reporting of circadian-regulated gene expression by imaging of luciferase bioluminescence in plants and mammalian cells.

Systems approaches to biological rhythms in Drosophila

The chronobiological system of Drosophila is considered from the perspective of rhythm-regulated genes. These factors are enumerated and discussed not so much in terms of how the gene products are thought to act on behalf of circadian-clock mechanisms, but with special emphasis on where these molecules are manufactured within the organism. Therefore, with respect to several such cell and tissue types in the fly head, what is the "systems meaning" of a given structure's function insofar as regulation of rest-activity cycles is concerned? (Systematic oscillation of daily behavior is the principal overt phenotype analyzed in studies of Drosophila chronobiology). In turn, how do the several separate sets of clock-gene-expressing cells interact--or in some cases act in parallel--such that intricacies of the fly's sleep-wake cycles are mediated? Studying Drosophila chrono-genetics as a system-based endeavor also encompasses the fact that rhythm-related genes generate their products in many tissues beyond neural ones and during all stages of the life cycle. What, then, is the meaning of these widespread gene-expression patterns? This question is addressed with regard to circadian rhythms outside the behavioral arena, by considering other kinds of temporally based behaviors, and by contemplating how broadly systemic expression of rhythm-related genes connects with even more pleiotropic features of Drosophila biology. Thus, chronobiologically connected factors functioning within this insect comprise an increasingly salient example of gene versatility--multi-faceted usages of, and complex interactions among, entities that set up an organism's overall wherewithal to form and function. A corollary is that studying Drosophila development and adult-fly actions, even when limited to analysis of rhythm-systems phenomena, involves many of the animal's tissues and phenotypic capacities. It follows that such chronobiological experiments are technically demanding, including the necessity for investigators to possess wide-ranging expertise. Therefore, this chapter includes several different kinds of Methods set-asides. These techniques primers necessarily lack comprehensiveness, but they include certain discursive passages about why a given method can or should be applied and concerning real-world applicability of the pertinent rhythm-related technologies.

Real-time luminescence reporting of circadian gene expression in mammals

Luminescence reporters have been used successfully in studies of circadian rhythms. Real-time measurements of circadian variations in gene expression were made in living cells, cultured tissues, and whole organisms. Because this technique is relatively easy and continuous noninvasive measurement from tissue cultures allows for a drastic reduction in the number of experimental animals, we believe this method will become a common technique for studying circadian rhythms. Using a multichannel recording apparatus, it may also become a powerful tool for the discovery of new drugs. In the past, measurements were done using hand-made apparatuses or by modifying commercially available equipment. We, along with other investigators, have developed user-friendly equipment for performing circadian rhythms experiments, and these systems are now available commercially. This article describes the use of luminescence reporters in circadian research and provides detailed methods used in these experiments. One of our goals in this article is to reduce experimental variability in different laboratories by proposing standard protocols.

Analysis of Circadian Rhythms in Zebrafish

The zebrafish probably constitutes the best animal system to study the complexity of the circadian clock machinery and the influence that light has on it. The possibilities of producing transgenic fishes, to establish light-responsive cultured cells, and to directly explore light phototransduction on single clock cells are all remarkable features of this circadian system. This article describes some of the most useful methodologies to analyze the behavioral, cellular, and molecular aspects of the zebrafish circadian clock system.

Genetic screens for clock mutants in Drosophila

The isolation and analysis of mutant flies (Drosophila melanogaster) with altered circadian rhythms have led to an understanding of circadian rhythms at the molecular level. This molecular mechanism elucidated in fruit flies is similar to the mechanism of the human circadian clock, which confers 24-h rhythmicity to our sleep/wake behavior, as well as to many other aspects of our cellular and organismal physiology. In fruit flies, genes can be mutated to abolish circadian rhythms (i.e., produce arrhythmia) or alter the period of the circadian rhythm; these genes encode key components of the circadian oscillator mechanism. Other mutations have identified components of the input pathways (by which light and temperature synchronize the circadian clock to environmental cycles) or output pathways (which connect the circadian oscillator to the physiological response). Mutations in genes are typically generated by chemical mutagenesis or mutagenesis with transposable elements. Flies with mutagenized chromosomes are processed in a series of genetic crosses, which allow specific chromosomes to be screened for semidominant mutations, recessive mutations, enhancer/suppressor mutations, or genes that can be overexpressed to alter circadian rhythms. Circadian phenotypes, which are assayed to identify mutants, include eclosion (emergence of the adult from the pupal case), locomotor activity (similar to human sleep?wake behavior), and circadian oscillations of gene expression. It is argued that screens for new circadian genes will continue to reveal novel components of the circadian mechanism.

The novel Drosophila tim(blind) mutation affects behavioral rhythms but not periodic eclosion

Circadian clock function depends on the tightly regulated exclusion or presence of clock proteins within the nucleus. A newly induced long-period timeless mutant, tim(blind), encodes a constitutively hypophosphorylated TIM protein. The mutant protein is not properly degraded by light, and tim(blind) flies show abnormal behavioral responses to light pulses. This is probably caused by impaired nuclear accumulation of TIM(BLIND) protein, which we observed in brain pacemaker neurons and photoreceptor cells of the compound eye. tim(blind) encodes two closely spaced amino acid changes compared to the wild-type TIM protein; one of them is within a putative nuclear export signal of TIM. Under constant conditions, tim(blind) flies exhibit 26-hr free-running locomotor rhythms, which are not correlated with a period lengthening of eclosion rhythms and period-luciferase reporter-gene oscillations. Therefore it seems possible that TIM--in addition to its well-established role as core clock factor--functions as a clock output factor, involved in determining the period length of adult locomotor rhythms.

The Doubletime and CKII Kinases Collaborate to Potentiate Drosophila PER Transcriptional Repressor Activity

In all genetically studied model organisms, a negative feedback loop of gene expression contributes to the circadian rhythm mechanism. In the Drosophila system, it has been proposed that the delay between the synthesis and function of clock proteins is due to phosphorylation-regulated nuclear entry. To test this hypothesis, we assayed the relationship between PER phosphorylation, nuclear localization, and transcriptional repression activity in cultured S2 cells. The results indicate that the two putative PER kinases DBT and CKII work together to phosphorylate PER and increase repression activity. Experiments combining kinase inhibition with inhibition of PER nuclear export suggest that phosphorylation directly affects PER repression activity and that PER nuclear localization is an indirect consequence of the association of active PER with DNA or chromatin. This interpretation suggests further that the circadian regulation of PER nuclear localization in flies reflects changes in PER transcriptional activity rather than in PER nuclear import or export activity.

A recessive mutant of Drosophila Clock reveals a role in circadian rhythm amplitude

The transcription factor Clock (Clk) plays a critical role in animal circadian rhythms. Genetic studies defining its function have relied on two dominant negative alleles, one in Drosophila and one in mice. Here we describe a novel recessive allele of Drosophila Clock, Clk(ar). Homozygous Clk(ar) flies are viable and behaviorally arrhythmic. The Clk(ar) phenotype is caused by a splice site mutation that severely disrupts splicing and reduces Clk activity. Despite the behavioral arrhythmicity, molecular oscillations are still detectable in Clk(ar) flies. Transcription analysis indicates potent effects of Clk(ar) on levels and amplitude of transcriptional oscillations. Taken together with other data, we propose that Clk makes a major contribution to the strength and amplitude of circadian rhythms.

Genetics and molecular biology of rhythms in Drosophila and other insects

Application of generic variants (Sections II-IV, VI, and IX) and molecular manipulations of rhythm-related genes (Sections V-X) have been used extensively to investigate features of insect chronobiology that might not have been experimentally accessible otherwise. Most such tests of mutants and molecular-genetic xperiments have been performed in Drosophila melanogaster. Results from applying visual-system variants have revealed that environmental inputs to the circadian clock in adult flies are mediated by external photoreceptive structures (Section II) and also by direct light reception chat occurs in certain brain neurons (Section IX). The relevant light-absorbing molecuLes are rhodopsins and "blue-receptive" cryptochrome (Sections II and IX). Variations in temperature are another clock input (Section IV), as has been analyzed in part by use of molecular techniques and transgenes involving factors functioning near the heart of the circadian clock (Section VIII). At that location within the fly's chronobiological system, approximately a half-dozen-perhaps up to as many as 10-clock genes encode functions that act and interact to form the circadian pacemaker (Sections III and V). This entity functions in part by transcriptional control of certain clock genes' expressions, which result in the production of key proteins that feed back negatively to regulate their own mRNA production. This occurs in part by interactions of such proteins with others that function as transcriptional activators (Section V). The implied feedback loop operates such that there are daily variations in the abundances of products put out by about one-half of the core clock genes. Thus, the normal expression of these genes defines circadian rhythms of their own, paralleling the effects of mutations at the corresponding genetic loci (Section III), which are to disrupt or apparently eliminate clock functioning. The fluctuations in the abundance of gene products are controlled transciptionally and posttranscriptionally. These clock mechanisms are being analyzed in ways that are increasingly complex and occasionally obscure; not all panels of this picture are comprehensive or clear, including problems revolving round the biological meaning or a given features of all this molecular cycling (Section V). Among the complexities and puzzles that have recently arisen, phenomena that stand out are posttranslational modifications of certain proteins that are circadianly regulated and regulating; these biochemical events form an ancillary component of the clock mechanism, as revealed in part by genetic identification of Factors (Section III) that turned out to encode protein kinases whose substrates include other pacemaking polypeptides (Section V). Outputs from insect circadian clocks have been long defined on formalistic and in some cases concrete criteria, related to revealed rhythms such as periodic eclosion and daily fluctuations of locomotion (Sections II and III). Based on the reasoning that if clock genes can regulate circadian cyclings of their own products, they can do the same for genes that function along output pathways; thus clock-regulated genes have been identified in part by virtue of their products' oscillations (Section X). Those studied most intensively have their expression influenced by circadian-pacemaker mutations. The clock-regulated genes discovered on molecular criteria have in some instances been analyzed further in their mutant forms and found to affect certain features of overt whole-organismal rhythmicity (Sections IV and X). Insect chronogenetics touches in part on naturally occurring gene variations that affect biological rhythmicity or (in some cases) have otherwise informed investigators about certain features of the organism's rhythm system (Section VII). Such animals include at least a dozen insect species other than D. melanogaster in which rhythm variants have been encountered (although usually not looked for systematically). The chronobiological "system" in the fruit fly might better be graced with a plural appellation because there is a myriad of temporally related phenomena that have come under the sway of one kind of putative rhythm variant or the other (Section IV). These phenotypes, which range well beyond the bedrock eclosion and locomotor circadian rhythms, unfortunately lead to the creation of a laundry list of underanalyzed or occult phenomena that may or may not be inherently real, whether or not they might be meaningfully defective under the influence of a given chronogenetic variant. However, such mutants seem to lend themselves to the interrogation of a wide variety of time-based attributes-those that fall within the experimental confines of conventionally appreciated circadian rhythms (Sections II, III, VI, and X); and others that consist of 24-hr or nondaily cycles defined by many kinds of biological, physiological, or biochemical parameters (Section IV).

Circadian and light-induced expression of luciferase in Neurospora crassa

We have constructed a plasmid vector for expressing firefly luciferase in Neurospora crassa under control of the light- and clock-regulated ccg-2 (eas) promoter. The sequence of the luciferase gene in the vector has been modified to reflect the N. crassa codon bias. Both light-induced activity and circadian activity are demonstrated. Expression of luciferase in strains carrying mutant frequency alleles shows appropriate period length alterations. These data demonstrate that luciferase is a sensitive reporter of gene expression in N. crassa. Our results also show that the modified luciferase is expressed in Aspergillus nidulans.

The network of time: understanding the molecular circadian system

The circadian clock provides a temporal structure that modulates biological functions from the level of gene expression to performance and behaviour. Pioneering work on the fruitfly Drosophila has provided a basis for understanding how the temporal sequence of daily events is controlled in mammals. New insights have come from work on mammals, specifically from studying the daily activity profiles of clock mutant mice; from more detailed recordings of clock gene expression under different experimental conditions and in different tissues; and from the discovery and analysis of a growing number of additional clock genes. These new results are moving the model paradigm away from a simple negative feedback loop to a molecular network. Understanding the coupling and interactions of this network will help us to understand the evolution of the circadian system, advance medical diagnosis and treatment, improve the health of shift workers and frequent travellers, and will generally enable the treatment of clock-related pathologies.

Real-time analysis of rhythmic gene expression in immortalized suprachiasmatic nucleus cells

Immortalized cells derived from the suprachiasmatic nucleus (SCN) retain many properties of the SCN including the capacity to generate circadian rhythms. Stably transfected SCN2.2 cells expressing the human c- promoter linked to a luciferase reporter gene ( /luc) were examined for evidence of transgene responses to stimuli known to induce c- expression and of endogenous rhythmic variation. Bioluminescence-reported transgene expression was induced in SCN2.2 /luc cells following stimulation with fetal bovine serum or KCl. SCN2.2 /luc cells showed 24 h rhythms of bioluminescence with a 9- to 19-fold difference between peak and minimum levels. These results demonstrate that the regulation of /luc transgene expression in SCN2.2 cells is similar to that of the endogenous c- gene in the SCN.

Combined noninvasive imaging and luminometric quantification of luciferase-labeled human prostate tumors and metastases

Noninvasive imaging should facilitate the analysis of changes in experimental tumors and metastases-expressing photoproteins and result in improved data consistency and experimental animal welfare. We analyzed quantitative aspects of noninvasive imaging of luciferase-labeled tumors by comparing the efficiency of noninvasive light detection with in vitro quantification of luciferase activity. An intensified charge coupled device video camera was used to noninvasively image luciferase-expressing human prostate tumors and metastases in nude mice, after ip inoculation of luciferin. Repeated imaging of anesthetized animals after intervening growth periods allowed monitoring of tumor and metastases development. Comparison of photon events recorded in tumor images with the number of relative light units from luminometric quantification of homogenates from the same tumors, revealed that the efficiency with which light escapes tumors is inversely related to tumor size and that intensified charge coupled device images alone are not sufficient for quantitative evaluation of tumor growth. However, a combined videometric and luminometric approach did allow quantification and was used to show the cytostatic effects of paclitaxel in three different human prostate tumors growing in nude mice.

Advances in in vivo bioluminescence imaging of gene expression

To advance our understanding of biological processes as they occur in living animals, imaging strategies have been developed and refined that reveal cellular and molecular features of biology and disease in real time. One rapid and accessible technology for in vivo analysis employs internal biological sources of light emitted from luminescent enzymes, luciferases, to label genes and cells. Combining this reporter system with the new generation of charge coupled device (CCD) cameras that detect the light transmitted through the animal's tissues has opened the door to sensitive in vivo measurements of mammalian gene expression in living animals. Here, we review the development and application of this imaging strategy, in vivo bioluminescence imaging (BLI), together with in vivo fluorescence imaging methods, which has enabled the real-time study of immune cell trafficking, of various genetic regulatory elements in transgenic mice, and of in vivo gene transfer. BLI has been combined with fluorescence methods that together offer access to in vivo measurements that were not previously available. Such studies will greatly facilitate the functional analysis of a wide range of genes for their roles in health and disease.

Central and peripheral circadian oscillator mechanisms in flies and mammals

Circadian oscillators are cell-autonomous time-keeping mechanisms that reside in diverse tissues in many organisms. In flies and mice, the core molecular components that sustain these oscillators are highly conserved, but the functions of some of these components appear to have diverged significantly. One possible reason for these differences is that previous comparisons have focused primarily on the central oscillator of the mouse and peripheral oscillators in flies. Recent research on mouse and Drosophila peripheral oscillators shows that the function of the core components between these organisms may be more highly conserved than was first believed, indicating the following: (1) that central and peripheral oscillators in flies do not necessarily have the same molecular mechanisms; (2) that mammalian central oscillators are regulated differently from peripheral oscillators; and (3) that different peripheral oscillators within and across species show striking similarities. The core feedback loop in peripheral oscillators might therefore be functionally well conserved, and central oscillators could be specialized versions of a basic oscillator design.

Mapping of elements involved in regulating normal temporal period and timeless RNA expression patterns in Drosophila melanogaster

Although transcriptional regulation is a major force in generating circadian oscillations of clock molecules, posttranscriptional mechanisms also contribute to molecular rhythms. Applying novel transgenic period-luciferase constructs in transgenic Drosophila, the authors show that sequences within per's 5'-untranslated region mediate posttranscriptional regulation at the RNA level. Further mapping suggests that the relevant sequences for the correct phasing of period mRNA expression are located within the first intron. The results are consistent with a clock-regulated temporal stabilization of period mRNA during its daily upswing in the morning. This process is inferred to depend on a function of the PERIOD and TIMELESS proteins, and could further contribute to the observed delay between RNA and protein accumulation. Similarly, applying timeless-luciferase constructs led to the demonstration that regulatory elements for proper temporal timeless expression are present in a 4 kb promoter fragment and in sequences within the first intron. The results establish that, for normal rhythmicity, expression of clock genes requires regulation at the transcriptional, posttranscriptional, and posttranslational levels.

Trap a gene and find out its function: toward functional genomics in Drosophila

Many declared aims of the genome projects have been achieved. The total genomic sequences of several relatively noncomplex/complex organisms (such as E. coli, yeast, Caenorhabditis, Drosophila) are being determined, and the nucleotide sequencing of the entire human genome will be complete in the near future. However, this achievement is not the end of the road but rather the first step toward the functional understanding of the genome of humans and other organisms. The determined linear nucleotide sequences remain only lists of A, C, G and T, unless they are given functional significance. The coding sequences of genes can be identified in a relatively reliable manner by computational methods, but the exact function of their protein products can rarely be determined without obtaining much additional information, e.g., by biochemical or cell biological methods. Thus, following sequencing, the next step must be to assign functions to the identified genes. The final goal of genome research today may look futuristic, but the knowledge of the function of every single gene and the interactions between them will finally allow us to understand the development and functioning of an organism as a whole. Gene-trapping methodology is a powerful strategy for cloning and identifying functional genes, as it marks a gene with a tag and simultaneously generates a corresponding genetic variation for that particular locus. Therefore, gene trapping is an extremely useful tool for functional genomics, establishing a correlation between the physical and genetic maps of the genome. The relative simplicity of its genome and the availability of huge bodies of genetic and molecular information make Drosophila melanogaster one of the most important model organisms. Its genome will serve as a "reference" for the in-depth analysis of the organization of more complex eukaryotic genomes. Multifaceted approaches to Drosophila functional genomics and the dual-tagging gene trap system newly developed for functional analysis of Drosophila genes are discussed in this review.

Intercellular coupling mechanism for synchronized and noise-resistant circadian oscillators

The circadian clock in multicellular organisms consists of multiple autonomous single-cell oscillators. These individual oscillator cells produce coherent oscillations even in the presence of internal noise associated with rhythm-generating reaction rates and in the absence of external time cues such as light and temperature. Thus, an intercellular coupling mechanism must synchronize the cells to induce coherent circadian oscillations. We propose the roles of a synchronizing factor that is secreted from individual cells during subjective day to induce light-pulse-type phase shifts in the neighboring cells or, alternatively, a factor that is secreted during subjective night to induce dark-pulse-type phase shifts. Here, we present our multicellular stochastic model of Drosophila circadian rhythms that emulates the intercellular coupling mechanism and suggest that the mechanism facilitates the constancy of the circadian rhythm with possible functional redundancy among different synchronizing factors.

Advanced analysis of a cryptochrome mutation's effects on the robustness and phase of molecular cycles in isolated peripheral tissues of Drosophila

BACKGROUND

Previously, we reported effects of the cry(b) mutation on circadian rhythms in period and timeless gene expression within isolated peripheral Drosophila tissues. We relied on luciferase activity driven by the respective regulatory genomic elements to provide real-time reporting of cycling gene expression. Subsequently, we developed a tool kit for the analysis of behavioral and molecular cycles. Here, we use these tools to analyze our earlier results as well as additional data obtained using the same experimental designs.

RESULTS

Isolated antennal pairs, heads, bodies, wings and forelegs were evaluated under light-dark cycles. In these conditions, the cry(b) mutation significantly decreases the number of rhythmic specimens in each case except the wing. Moreover, among those specimens with detectable rhythmicity, mutant rhythms are significantly weaker than cry+ controls. In addition, cry(b) alters the phase of period gene expression in these tissues. Furthermore, peak phase of luciferase-reported period and timeless expression within cry+ samples is indistinguishable in some tissues, yet significantly different in others. We also analyze rhythms produced by antennal pairs in constant conditions.

CONCLUSIONS

These analyses further show that circadian clock mechanisms in Drosophila may vary in a tissue-specific manner, including how the cry gene regulates circadian gene expression.

A P element with a novel fusion of reporters identifies regular, a C2H2 zinc-finger gene downstream of the circadian clock

Elucidating the mechanisms that link the circadian pacemaker to the timing of behaviors it controls is one of the greatest challenges in circadian biology. We report the generation of a P element, Pluc+, containing a novel reporter fusion. Our fusion reporter capitalizes on the use of luciferase bioluminescence to easily analyze temporal expression as well as the strength of myc epitopes and GFP to identify spatial expression. Using Pluc+ we have identified and characterized a novel C2H2 zinc-finger gene, regular (rgr), that cycles circadianly in phase with period (per) gene expression, but shifts to light-dark regulation in Clk(Jrk) mutant flies. By following myc expression of the Pluc+ reporter, we demonstrate that Rgr is expressed in a discrete number of neurons in the brain which overlap with axons expressing pigment-dispersing factor.

Identification of circadian-clock-regulated enhancers and genes of Drosophila melanogaster by transposon mobilization and luciferase reporting of cyclical gene expression

A new way was developed to isolate rhythmically expressed genes in Drosophila by modifying the classic enhancer-trap method. We constructed a P element containing sequences that encode firefly luciferase as a reporter for oscillating gene expression in live flies. After generation of 1176 autosomal insertion lines, bioluminescence screening revealed rhythmic reporter-gene activity in 6% of these strains. Rhythmically fluctuating reporter levels were shown to be altered by clock mutations in genes that specify various circadian transcription factors or repressors. Intriguingly, rhythmic luminescence in certain lines was affected by only a subset of the pacemaker mutations. By isolating genes near 13 of the transposon insertions and determining their temporal mRNA expression pattern, we found that four of the loci adjacent to the trapped enhancers are rhythmically expressed. Therefore, this approach is suitable for identifying genetic loci regulated by the circadian clock. One transposon insert caused a mutation in the rhythmically expressed gene numb. This novel numb allele, as well as previously described ones, was shown to affect the fly's rhythm of locomotor activity. In addition to its known role in cell fate determination, this gene and the phosphotyrosine-binding protein it encodes are likely to function in the circadian system.

Signal analysis of behavioral and molecular cycles

BACKGROUND

Circadian clocks are biological oscillators that regulate molecular, physiological, and behavioral rhythms in a wide variety of organisms. While behavioral rhythms are typically monitored over many cycles, a similar approach to molecular rhythms was not possible until recently; the advent of real-time analysis using transgenic reporters now permits the observations of molecular rhythms over many cycles as well. This development suggests that new details about the relationship between molecular and behavioral rhythms may be revealed. Even so, behavioral and molecular rhythmicity have been analyzed using different methods, making such comparisons difficult to achieve. To address this shortcoming, among others, we developed a set of integrated analytical tools to unify the analysis of biological rhythms across modalities.

RESULTS

We demonstrate an adaptation of digital signal analysis that allows similar treatment of both behavioral and molecular data from our studies of Drosophila. For both types of data, we apply digital filters to extract and clarify details of interest; we employ methods of autocorrelation and spectral analysis to assess rhythmicity and estimate the period; we evaluate phase shifts using crosscorrelation; and we use circular statistics to extract information about phase.

CONCLUSION

Using data generated by our investigation of rhythms in Drosophila we demonstrate how a unique aggregation of analytical tools may be used to analyze and compare behavioral and molecular rhythms. These methods are shown to be versatile and will also be adaptable to further experiments, owing in part to the non-proprietary nature of the code we have developed.

Imaging transgenic animals

Transgenic and eugenic animals as small as 30 g can be studied non-invasively by radionuclides with resolutions of 1-2 mm, by MRI with resolution of 100 microns and by light fluorescence and bioluminescence with high sensitivities. The technologies of radionuclide emission, magnetic resonance imaging, magnetic resonance spectroscopy, optical tomography, optical fluorescence and optical bioluminescence are currently being applied to small-animal studies. These technologies and examples of their applications are reviewed in this chapter.

Peripheral clocks and their role in circadian timing: insights from insects

Impressive advances have been made recently in our understanding of the molecular basis of the cell-autonomous circadian feedback loop; however, much less is known about the overall organization of the circadian systems. How many clocks tick in a multicellular animal, such as an insect, and what are their roles and the relationships between them? Most attempts to locate clock-containing tissues were based on the analysis of behavioural rhythms and identified brain-located timing centres in a variety of animals. Characterization of several essential clock genes and analysis of their expression patterns revealed that molecular components of the clock are active not only in the brain, but also in many peripheral organs of Drosophila and other insects as well as in vertebrates. Subsequent experiments have shown that isolated peripheral organs can maintain self-sustained and light sensitive cycling of clock genes in vitro. This, together with earlier demonstrations that physiological output rhythms persist in isolated organs and tissues, provide strong evidence for the existence of functionally autonomous local circadian clocks in insects and other animals. Circadian systems in complex animals may include many peripheral clocks with tissue-specific functions and a varying degree of autonomy, which seems to be correlated with their sensitivity to external entraining signals.

Rapid in vivo functional analysis of transgenes in mice using whole body imaging of luciferase expression

The use of transgenic animals in biomedical research is increasing rapidly and may be the best means of determining gene function. Generating transgenic animals typically requires time-consuming screening processes, and gene function is assessed by an array of difficult phenotypic and biochemical assays performed ex vivo. To address the unmet need in transgenic research for functional assays performed with ease in living animals, we demonstrate here that in vivo detection of luciferase enzyme as a transcriptional reporter facilitates rapid screening for both the presence and function of transgenes in intact living mice. Using this approach we identified three bioluminescent transgenic founders where the transgene consisted of the heme oxygenase promoter fused to the modified coding sequence of the luciferase gene. These founders were identified from 183 pups and confirmed by PCR analysis. Identification of HO-1-luc homozygotes from back- crossed F2 littermates was then accelerated by in vivo imaging. In another transgenic mouse line, where the transgene was comprised of the bone morphogenic-4 (BMP4) promoter fused to the modified luciferase gene, we were able to identify transgenic animals and in each line we were able to visualize patterns of expression in living animals over time. The light production from these transgenic mice indicated that the desired DNA fragment was functional and different expression profiles apparent at different ages and after gene induction.

Noninvasive optical imaging of firefly luciferase reporter gene expression in skeletal muscles of living mice

The ability to monitor reporter gene expression noninvasively offers significant advantages over current techniques such as postmortem tissue staining or enzyme activity assays. Here we demonstrate a novel method of repetitively tracking in vivo gene expression of firefly luciferase (FL) in skeletal muscles of mice using a cooled charged coupled device (CCD) camera. We first show that the cooled CCD camera provides consistent and reproducible results within +/-8% standard deviation from mean values, and a detection sensitivity (range tested: 1 x 10(4) - 1 x 10(9) plaque form-ing units (pfu)) of 1 x 10(6) pfu of E1-deleted adenovirus expressing FL driven by a cytomegalovirus promoter (Ad-CMV-FL). The duration and magnitude of adenoviral mediated (1 x 10(9) pfu) FL gene expression were then followed over time. FL gene expression in immunocompetent Swiss Webster mice peaks within the first 48 hours, falls by 98% after 20 days, and persists for >150 days. In contrast, FL activity in nude mice remains elevated for >110 days. Finally, transduced Swiss Webster and nude mice were sacrificed to show that the in vivo CCD signals correlate well with in vitro luciferase enzyme assays (r(2)=0.91 and 0.96, respectively). Our findings demonstrate the ability of the cooled CCD camera to sensitively and noninvasively track the location, magnitude, and persistence of FL gene expression. Monitoring of gene therapy studies in small animals may be aided considerably with further extensions of this technique.

Behavioral rhythmicity, age, division of labor and period expression in the honey bee brain

Young adult honey bees work inside the beehive "nursing" brood around the clock with no circadian rhythms; older bees forage for nectar and pollen outside with strong circadian rhythms. Previous research has shown that the development of an endogenous rhythm of activity is also seen in the laboratory in a constant environment. Newly emerging bees maintained in isolation are typically arrhythmic during the first few days of adult life and develop strong circadian rhythms by about a few days of age. In addition, average daily levels of period (per) mRNA in the brain are higher in foragers or forager-age bees (> 21 days of age) relative to young nest bees (approximately 7 days of age). The authors used social manipulations to uncouple behavioral rhythmicity, age, and task to determine the relationship between these factors and per. There was no obligate link between average daily levels of per brain mRNA and either behavioral rhythmicity or age. There also were no differences in per brain mRNA levels between nurse bees and foragers in social environments that promote precocious or reversed behavioral development. Nurses and other hive-age bees can have high or low levels of per mRNA levels in the brain, depending on the social environment, while foragers and foraging-age bees always have high levels. These findings suggest a link between honey bee foraging behavior and per up-regulation. Results also suggest task-related differences in the amplitude of per mRNA oscillation in the brain, with foragers having larger diurnal fluctuation in per than nurses, regardless of age. Taken together, these results suggest that social factors may exert potent influences on the regulation of clock genes.

Stopping time: the genetics of fly and mouse circadian clocks

Forward genetic analyses in flies and mice have uncovered conserved transcriptional feedback loops at the heart of circadian pacemakers. Conserved mechanisms of posttranslational regulation, most notably phosphorylation, appear to be important for timing feedback. Transcript analyses have indicated that circadian clocks are not restricted to neurons but are found in several tissues. Comparisons between flies and mice highlight important differences in molecular circuitry and circadian organization. Future studies of pacemaker mechanisms and their control of physiology and behavior will likely continue to rely on forward genetics.

A new role for cryptochrome in a Drosophila circadian oscillator

Cryptochromes are flavin/pterin-containing proteins that are involved in circadian clock function in Drosophila and mice. In mice, the cryptochromes Cry1 and Cry2 are integral components of the circadian oscillator within the brain and contribute to circadian photoreception in the retina. In Drosophila, cryptochrome (CRY) acts as a photoreceptor that mediates light input to circadian oscillators in both brain and peripheral tissue. A Drosophila cry mutant, cryb, leaves circadian oscillator function intact in central circadian pacemaker neurons but renders peripheral circadian oscillators largely arrhythmic. Although this arrhythmicity could be caused by a loss of light entrainment, it is also consistent with a role for CRY in the oscillator. A peripheral oscillator drives circadian olfactory responses in Drosophila antennae. Here we show that CRY contributes to oscillator function and physiological output rhythms in the antenna during and after entrainment to light-dark cycles and after photic input is eliminated by entraining flies to temperature cycles. These results demonstrate a photoreceptor-independent role for CRY in the periphery and imply fundamental differences between central and peripheral oscillator mechanisms in Drosophila.

Gene expression in transgenic mice using neural promoters

In the first part of this unit, major considerations for the analysis of neural promoters in transgenic mice are discussed. Detailed protocols on the production of transgenic mice are not described in this unit. Advantages and disadvantages of the transgenic approach for analysis of neural cis-acting elements are also presented. The concept of transient transgenic mice is then introduced; this method compensates for some disadvantages associated with the conventional transgenic approach. Finally, major factors influencing the efficiency of transgenic mouse production are discussed. The second part of the unit presents detailed information on a variety of neural-specific cis-acting elements that have been characterized by a transgenic approach. This information is useful both as a guide for carrying out the analysis of cis-acting elements and as a reference for selection of promoter/enhancer elements for designing an appropriate transgenic construct.

Wild-type circadian rhythmicity is dependent on closely spaced E boxes in the Drosophila timeless promoter

Transcriptional regulation plays an important role in Drosophila melanogaster circadian rhythms. The period promoter has been well studied, but the timeless promoter has not been analyzed in detail. Mutagenesis of the canonical E box in the timeless promoter reduces but does not eliminate timeless mRNA cycling or locomotor activity rhythms. This is because there are at least two other cis-acting elements close to the canonical E box, which can also be transactivated by the circadian transcription factor dCLOCK. These E-box-like sequences cooperate with the canonical E-box element to promote high-amplitude transcription, which is necessary for wild-type rhythmicity.

Dual-tagging gene trap of novel genes in Drosophila melanogaster

A gene-trap system is established for Drosophila. Unlike the conventional enhancer-trap system, the gene-trap system allows the recovery only of fly lines whose genes are inactivated by a P-element insertion, i.e., mutants. In the gene-trap system, the reporter gene expression reflects precisely the spatial and temporal expression pattern of the trapped gene. Flies in which gene trap occurred are identified by a two-step screening process using two independent markers, mini-w and Gal4, each indicating the integration of the vector downstream of the promoter of a gene (dual tagging). mini-w has its own promoter but lacks a polyadenylation signal. Therefore, mini-w mRNA is transcribed from its own promoter regardless of the vector integration site in the genome. However, the eyes of flies are not orange or red unless the vector is incorporated into a gene enabling mini-w to be spliced to a downstream exon of the host gene and polyadenylated at the 3' end. The promoter-less Gal4 reporter is expressed as a fusion mRNA only when it is integrated downstream of the promoter of a host gene. The exons of trapped genes can be readily cloned by vectorette RT-PCR, followed by RACE and PCR using cDNA libraries. Thus, the dual-tagging gene-trap system provides a means for (i) efficient mutagenesis, (ii) unequivocal identification of genes responsible for mutant phenotypes, (iii) precise detection of expression patterns of trapped genes, and (iv) rapid cloning of trapped genes.

The period E-box is sufficient to drive circadian oscillation of transcription in vivo

The minimum element from the Drosophila period promoter capable of driving in vivo cycling mRNA is the 69 bp circadian regulatory sequence (CRS). In cell culture, an 18 bp E-box element from the period promoter is regulated by five genes that are involved in the regulation of circadian expression in flies. This E-box is a target for transcriptional activation by bHLH-PAS proteins dCLOCK (dCLK) and CYCLE (CYC), this activation is inhibited by PERIOD (PER) and TIMELESS (TIM) together, and inhibition of dCLK/CYC by PER and TIM is blocked by CRYPTOCHROME (CRY) in the presence of light. Here, the same 18 bp E-box region generated rhythmic expression of luciferase in flies under both light-dark cycling and constant conditions. Flies heterozygous for the Clke(jrk) mutation maintained rhythmic expression from the E-box although at a lower level than wild type. Homozygous mutant Clk(jrk) animals had drastically lowered and arrhythmic expression. In a per01 background, expression from the E-box was high and not rhythmic. Transcription mediated by the per E-box was restricted to the same spatial pattern as the CRS. The per E-box DNA element and cognate binding proteins can confer per-like temporal and spatial expression. This demonstrates in vivo that the known circadian genes that form the core of the circadian oscillator in Drosophila integrate their activities at a single DNA element.

takeout, a novel Drosophila gene under circadian clock transcriptional regulation

We report the identification and characterization of a new Drosophila clock-regulated gene, takeout (to). to is a member of a novel gene family and is implicated in circadian control of feeding behavior. Its gene expression is down-regulated in all of the clock mutants tested. In wild-type flies, to mRNA exhibits daily cycling expression but with a novel phase, delayed relative to those of the better-characterized clock mRNAs, period and timeless. The E-box-containing sequence in the to promoter shows impressive similarities with those of period and timeless. However, our results suggest that the E box is not involved in the amplitude and phase of the transcriptional cycling of to. The circadian delayed transcriptional phase is therefore most likely the result of indirect regulation through unknown transcription factors.

Neuroanatomy of cells expressing clock genes in Drosophila: transgenic manipulation of the period and timeless genes to mark the perikarya of circadian pacemaker neurons and their projections

Subsets of brain neurons expressing the clock genes period (per) and timeless (tim) are involved in the generation of circadian behavioral rhythms. However, current knowledge of projection patterns of these neurons is limited to those immunoreactive to an antibody against a crustacean neuropeptide. The GAL4-expression system was utilized to visualize neuronal processes from all per and tim-expressing neurons in the central nervous system. Each of two types of GAL4-driver fusion genes, per-gal4 or tim-gal4, was combined in transgenic flies with marker genes-lacZ, and sequences encoding green fluorescent protein or TAU protein-under the control of the GAL4-responsive element UAS. This allowed visualization of the cytoplasm of GAL4-expressing cells. Thus, neurites of clock neurons in the adult brain as well as those of larvae and pupae were revealed. Among the anatomical patterns revealed by per-gal4- or tim-gal4-driven marker expression were a previously unknown, dorsally located neuronal cluster, along with the projections of these cells and of other dorsal neurons characterized in earlier studies only by the location of their perikarya. The similarity of projections from PER- or TIM-containing neurons during development to those in the adult implies that these features of mature clock neurons are established by the larval stages. Neurons that have never been identified as PER- or TIM-immunoreactive were also visualized in this assay system, indicating promoter activity of the clock genes in these cells and suggesting that their products cannot accumulate to detectable levels in certain neurons.

Molecular mechanism and cellular distribution of insect circadian clocks

Circadian clocks are endogenous timing mechanisms that control molecular, cellular, physiological, and behavioral rhythms in all organisms from unicellulars to humans. Circadian rhythms influence many aspects of insect biology, finetuning life functions to the light and temperature cycles associated with the solar day. Genetic studies in the fruit fly Drosophila melanogaster have led to the cloning and characterization of several genes involved in the mechanism of the circadian clock. Periodic transcription and translation of these clock genes form the basis of a molecular feedback loop that has a "circa" 24-hour period. Rhythmic expression of clock genes in specific brain neurons appears to control behavioral rhythms in adult flies. However, clock genes are also expressed in other tissues, both within and outside of the nervous system. These observations prompted chronobiologists to investigate whether nonneural tissues possess intrinsic circadian clocks, what role they may be playing, and what the relationships are between clocks in the nervous system and those in peripheral tissues. Answers to those questions are providing important insights into the overall organization of the circadian system in insects.