Darwinian natural selection for orange bioluminescent color in a Jamaican click beetle

Multiple Origins of Bioluminescence in Beetles and Evolution of Luciferase Function

Bioluminescence in beetles has long fascinated biologists, with diverse applications in biotechnology. To date, however, our understanding of its evolutionary origin and functional variation mechanisms remains poor. To address these questions, we obtained high-quality reference genomes of luminous and nonluminous beetles in 6 Elateroidea families. We then reconstructed a robust phylogenetic relationship for all luminous families and related nonluminous families. Comparative genomic analyses and biochemical functional experiments suggested that gene evolution within Elateroidea played a crucial role in the origin of bioluminescence, with multiple parallel origins observed in the luminous beetle families. While most luciferase-like proteins exhibited a conserved nonluminous amino acid pattern (TLA346 to 348) in the luciferin-binding sites, luciferases in the different luminous beetle families showed divergent luminous patterns at these sites (TSA/CCA/CSA/LVA). Comparisons of the structural and enzymatic properties of ancestral, extant, and site-directed mutant luciferases further reinforced the important role of these sites in the trade-off between acyl-CoA synthetase and luciferase activities. Furthermore, the evolution of bioluminescent color demonstrated a tendency toward hypsochromic shifts and variations among the luminous families. Taken together, our results revealed multiple parallel origins of bioluminescence and functional divergence within the beetle bioluminescent system.

Creation of Artificial Luciferase 60s from Sequential Insights and Their Applications to Bioassays

In this study, a series of new artificial luciferases (ALucs) was created using sequential insights on missing peptide blocks, which were revealed using the alignment of existing ALuc sequences. Through compensating for the missing peptide blocks in the alignment, 10 sibling sequences were artificially fabricated and named from ALuc55 to ALuc68. The phylogenetic analysis showed that the new ALucs formed an independent branch that was genetically isolated from other natural marine luciferases. The new ALucs successfully survived and luminesced with native coelenterazine (nCTZ) and its analogs in living mammalian cells. The results showed that the bioluminescence (BL) intensities of the ALucs were interestingly proportional to the length of the appended peptide blocks. The computational modeling revealed that the appended peptide blocks created a flexible region near the active site, potentially modulating the enzymatic activities. The new ALucs generated various colors with maximally approximately 90 nm redshifted BL spectra in orange upon reaction with the authors' previously reported 1- and 2-series coelenterazine analogs. The utilities of the new ALucs in bioassays were demonstrated through the construction of single-chain molecular strain probes and protein fragment complementation assay (PCA) probes. The success of this study can guide new insights into how we can engineer and functionalize marine luciferases to expand the toolbox of optical readouts for bioassays and molecular imaging.

Molecular cloning, characterization, and evolution analysis of the luciferase genes from three sympatric sibling fireflies (Lampyridae: Lampyrinae, Diaphanes)

Firefly adult bioluminescence functions as signal communication between sexes. How sympatric sibling species with similar glow pattern recognize their conspecific mates remains largely unknown. To better understand the role of the luciferases of sympatric fireflies in recognizing mates, we cloned the luciferase genes of three sympatric forest dwelling fireflies (Diaphanes nubilus, Diaphanes pectinealis, and Diaphanes sp2) and evaluated their enzyme characteristics. Our data show that the amino acid (AA) sequences of all three luciferases are highly conserved, including the identities (D. nubilus vs D. pectinealis: 99%; D. nubilus vs Diaphanes sp2: 98.5%; D. pectinealis vs Diaphanes sp2: 99.4%) and the protein structures. Three recombinant luciferases produced in vitro all possess significant luminescence activity at pH 7.8, and similar maximum emission spectrum (D. nubilus: 562 nm; D. pectinealis and Diaphanes sp2: 564 nm). They show the highest activity at 10 °C (D. pectinealis, Diaphanes sp2) and 15 °C (D. nubilus), and completely inactivation at 45 °C. Their K_M for D-luciferin and ATP were 2.7 μM and 92 μM (D. nubilus), 3.7 μM and 49 μM (D. pectinealis), 3.5 μM and 46 μM (Diaphanes sp2). Phylogenetic analyses support that D. nubilus is sister to D. pectinealis with Diaphanes sp2 at their base, which further cluster with Pyrocoelia. All combined data indicate that sympatric Diaphanes species have similar luciferase characteristics, suggesting that other strategies (e.g., pheromone, active time, etc.) may be adopted to recognize mates. Our data provide new insights into Diaphanes luciferases and their evolution.

Cretophengodidae, a new Cretaceous beetle family, sheds light on the evolution of bioluminescence

Bioluminescent beetles of the superfamily Elateroidea (fireflies, fire beetles, glow-worms) are the most speciose group of terrestrial light-producing animals. The evolution of bioluminescence in elateroids is associated with unusual morphological modifications, such as soft-bodiedness and neoteny, but the fragmentary nature of the fossil record discloses little about the origin of these adaptations. We report the discovery of a new bioluminescent elateroid beetle family from the mid-Cretaceous of northern Myanmar (ca 99 Ma), Cretophengodidae fam. nov. Cretophengodes azari gen. et sp. nov. belongs to the bioluminescent lampyroid clade, and would appear to represent a transitional fossil linking the soft-bodied Phengodidae + Rhagophthalmidae clade and hard-bodied elateroids. The fossil male possesses a light organ on the abdomen which presumably served a defensive function, documenting a Cretaceous radiation of bioluminescent beetles coinciding with the diversification of major insectivore groups such as frogs and stem-group birds. The discovery adds a key branch to the elateroid tree of life and sheds light on the evolution of soft-bodiedness and the historical biogeography of elateroid beetles.

Shining light on the electronic structure and relaxation dynamics of the isolated oxyluciferin anion

Firefly bioluminescence is exploited widely in imaging in the biochemical and biomedical sciences; however, our fundamental understanding of the electronic structure and relaxation processes of the oxyluciferin that emits the light is still rudimentary. Here, we employ photoelectron spectroscopy and quantum chemistry calculations to investigate the electronic structure and relaxation of a series of model oxyluciferin anions. We find that changing the deprotonation site has a dramatic influence on the relaxation pathway following photoexcitation of higher lying electronically excited states. The keto form of the oxyluciferin anion is found to undergo internal conversion to the fluorescent S₁ state, whereas we find evidence to suggest that the enol and enolate forms undergo internal conversion to a dipole bound state, possibly via the fluorescent S₁ state. Partially resolved vibrational structure points towards the involvement of out-of-plane torsional motions in internal conversion to the dipole bound state, emphasising the combined electronic and structural role that the microenvironment plays in controlling the electronic relaxation pathway in the enzyme.

Enzymatic promiscuity and the evolution of bioluminescence

Bioluminescence occurs when an enzyme, known as a luciferase, oxidizes a small-molecule substrate, known as a luciferin. Nature has evolved multiple distinct luciferases and luciferins independently, all of which accomplish the impressive feat of light emission. One of the best-known examples of bioluminescence is exhibited by fireflies, a class of beetles that use d-luciferin as their substrate. The evolution of bioluminescence in beetles is thought to have emerged from ancestral fatty acyl-CoA synthetase (ACS) enzymes present in all insects. This theory is supported by multiple lines of evidence: Beetle luciferases share high sequence identity with these enzymes, often retain ACS activity, and some ACS enzymes from nonluminous insects can catalyze bioluminescence from synthetic d-luciferin analogues. Recent sequencing of firefly genomes and transcriptomes further illuminates how the duplication of ACS enzymes and subsequent diversification drove the evolution of bioluminescence. These genetic analyses have also uncovered candidate enzymes that may participate in luciferin metabolism. With the publication of the genomes and transcriptomes of fireflies and related insects, we are now better positioned to dissect and learn from the evolution of bioluminescence in beetles.

Infrared optical and thermal properties of microstructures in butterfly wings

While surface microstructures of butterfly wings have been extensively studied for their structural coloration or optical properties within the visible spectrum, their properties in infrared wavelengths with potential ties to thermoregulation are relatively unknown. The midinfrared wavelengths of 7.5 to 14 µm are particularly important for radiative heat transfer in the ambient environment, because of the overlap with the atmospheric transmission window. For instance, a high midinfrared emissivity can facilitate surface cooling, whereas a low midinfrared emissivity can minimize heat loss to surroundings. Here we find that the midinfrared emissivity of butterfly wings from warmer climates such as Archaeoprepona demophoon (Oaxaca, Mexico) and Heliconius sara (Pichincha, Ecuador) is up to 2 times higher than that of butterfly wings from cooler climates such as Celastrina echo (Colorado) and Limenitis arthemis (Florida), using Fourier-transform infrared (FTIR) spectroscopy and infrared thermography. Our optical computations using a unit cell approach reproduce the spectroscopy data and explain how periodic microstructures play a critical role in the midinfrared. The emissivity spectrum governs the temperature of butterfly wings, and we demonstrate that C. echo wings heat up to 8 °C more than A. demophoon wings under the same sunlight in the clear sky of Irvine, CA. Furthermore, our thermal computations show that butterfly wings in their respective habitats can maintain a moderate temperature range through a balance of solar absorption and infrared emission. These findings suggest that the surface microstructures of butterfly wings potentially contribute to thermoregulation and provide an insight into butterflies' survival.

Firefly genomes illuminate parallel origins of bioluminescence in beetles

Fireflies and their luminous courtships have inspired centuries of scientific study. Today firefly luciferase is widely used in biotechnology, but the evolutionary origin of bioluminescence within beetles remains unclear. To shed light on this long-standing question, we sequenced the genomes of two firefly species that diverged over 100 million-years-ago: the North American Photinus pyralis and Japanese Aquatica lateralis. To compare bioluminescent origins, we also sequenced the genome of a related click beetle, the Caribbean Ignelater luminosus, with bioluminescent biochemistry near-identical to fireflies, but anatomically unique light organs, suggesting the intriguing hypothesis of parallel gains of bioluminescence. Our analyses support independent gains of bioluminescence in fireflies and click beetles, and provide new insights into the genes, chemical defenses, and symbionts that evolved alongside their luminous lifestyle.

Luciferase Genes as Reporter Reactions: How to Use Them in Molecular Biology?

: The latest advances in molecular biology have made available several biotechnological tools that take advantage of the high detectability and quantum efficiency of bioluminescence (BL), with an ever-increasing number of novel applications in environmental, pharmaceutical, food, and forensic fields. Indeed, BL proteins are being used to develop ultrasensitive binding assays and cell-based assays, thanks to their high detectability and to the availability of highly sensitive BL instruments. The appealing aspect of molecular biology tools relying on BL reactions is their general applicability in both in vitro assays, such as cell cultures or purified proteins, and in vivo settings, such as in whole-animal BL imaging. The aim of this chapter is to provide the reader with an overview of state-of-the-art bioluminescent tools based on luciferase genes, highlighting molecular biology strategies that have been applied so far, together with some selected examples.

1001 lights: luciferins, luciferases, their mechanisms of action and applications in chemical analysis, biology and medicine

Bioluminescence (BL) is a spectacular phenomenon involving light emission by live organisms. It is caused by the oxidation of a small organic molecule, luciferin, with molecular oxygen, which is catalysed by the enzyme luciferase. In nature, there are approximately 30 different BL systems, of which only 9 have been studied to various degrees in terms of their reaction mechanisms. A vast range of in vitro and in vivo analytical techniques have been developed based on BL, including tests for different analytes, immunoassays, gene expression assays, drug screening, bioimaging of live organisms, cancer studies, the investigation of infectious diseases and environmental monitoring. This review aims to cover the major existing applications for bioluminescence in the context of the diversity of luciferases and their substrates, luciferins. Particularly, the properties and applications of d-luciferin, coelenterazine, bacterial, Cypridina and dinoflagellate luciferins and their analogues along with their corresponding luciferases are described. Finally, four other rarely studied bioluminescent systems (those of limpet Latia, earthworms Diplocardia and Fridericia and higher fungi), which are promising for future use, are also discussed.

Fabrication of a New Lineage of Artificial Luciferases from Natural Luciferase Pools

The fabrication of artificial luciferases (ALucs) with unique optical properties has a fundamental impact on bioassays and molecular imaging. In this study, we developed a new lineage of ALucs with unique substrate preferences by extracting consensus amino acids from the alignment of 25 copepod luciferase sequences available in natural luciferase pools. The primary sequence was first created with a sequence logo generator resulting in a total of 11 sibling sequences. Phylogenetic analysis shows that the newly fabricated ALucs form an independent branch, genetically isolated from the natural luciferases, and from a prior series of ALucs produced by our laboratory using a smaller basis set. The new lineage of ALucs were strongly luminescent in living mammalian cells with specific substrate selectivity to native coelenterazine. A single-residue-level comparison of the C-terminal sequences of new ALucs reveals that some amino acids in the C-terminal ends are greatly influential on the optical intensities but limited in the color variance. The success of this approach guides on how to engineer and functionalize marine luciferases for bioluminescence imaging and assays.

A new orange emitting luciferase from the Southern-Amazon Pyrophorus angustus (Coleoptera: Elateridae) click-beetle: structure and bioluminescence color relationship, evolutional and ecological considerations

Bioluminescent click-beetles display a wide variation of bioluminescence colors ranging from green to orange, including an unusual intra-specific color variation in the Jamaican Pyrophorus plagiophthalamus. Recently, we collected individuals of the Pyrophorus angustus species from the Southern Amazon forest, in Brazil, which displays an orange light emitting abdominal lantern. This species was also previously described from Central America, but displaying a bioluminescence spectrum from 536 nm (dorsal) to 578 nm (ventral). The biogeographic variation of the bioluminescence color in this species could be an adaptation to environmental reflectance and inter/intraspecific sexual competition. Here, we cloned, sequenced, characterized and performed site-direct mutagenesis of this new orange emitting luciferase. The in vitro luciferase spectrum displayed a peak at 594 nm, KM values for ATP and d-luciferin of 160 μM and 17 μM, respectively, and an optimum pH of approximately 8.5. Comparative multialignment and site-directed mutagenesis using different color emitting click-beetle luciferases from P. angustus, Fulgeochlizus bruchi and Pyrearinus termitilluminans luciferases cloned by our group showed an integral role of residue 247 in bioluminescence color modulation.

Eco-evo bioluminescence on land and in the sea

This review discusses the evolution of bioluminescence organisms that inhabit various environments based on the current understanding of their unique ecologies and biochemistries. As shown here, however, there are still many unanswered questions regarding the functions and mechanisms of bioluminescence, which should be investigated in further studies. To facilitate future research in this field, we introduce our recent attempt, the bioluminescent organism DNA barcode initiative. This genetic reference library will provide resources for other scientists to efficiently identify unstudied bioluminescent organisms, focus their biochemical and genetic research goals, and will generally promote bioluminescence as a field of scientific study.

Bioengineered bioluminescent magnetotactic bacteria as a powerful tool for chip-based whole-cell biosensors

This paper describes the generation of genetically engineered bioluminescent magnetotactic bacteria (BL-MTB) and their integration into a microfluidic analytical device to create a portable toxicity detection system. Magnetospirillum gryphiswaldense strain MSR-1 was bioengineered to constitutively express a red-emitting click beetle luciferase whose bioluminescent signal is directly proportional to bacterial viability. The magnetic properties of these bacteria have been exploited as "natural actuators" to transfer the cells in the chip from the reaction to the detection area, optimizing the chip's analytical performance. A robust and cost-effective biosensor for the evaluation of sample toxicity, named MAGNETOX, based on lens-free contact imaging detection, has been developed. A microfluidic chip has been fabricated using multilayered black and transparent polydimethyl siloxane (PDMS) in which BL-MTB are incubated for 30 min with the sample, then moved by microfluidics, trapped, and concentrated in detection chambers by an array of neodymium-iron-boron magnets. The chip is placed in contact with a cooled CCD via a fiber optic taper to perform quantitative bioluminescence imaging after addition of luciferin substrate. A model toxic compound (dimethyl sulfoxide, DMSO) and a bile acid (taurochenodeoxycholic acid, TCDCA) were used to investigate the analytical performance of the MAGNETOX. Incubation with DMSO and TCDCA drastically reduces the bioluminescent signal in a dose-related manner. The generation of bacteria that are both magnetic and bioluminescent combines the advantages of easy 2D cell handling with ultra sensitive detection, offering undoubted potential to develop cell-based biosensors integrated into microfluidic chips.

In vitro characterization of Fluorescence by Unbound Excitation from Luminescence: broadening the scope of energy transfer

Energy transfer mechanisms represent the basis for an array of valuable tools to infer interactions in vitro and in vivo, enhance detection or resolve interspecies distances such as with resonance. Based upon our own previously published studies and new results shown here we present a novel framework describing for the first time a model giving a view of the biophysical relationship between Fluorescence by Unbound Excitation from Luminescence (FUEL), a conventional radiative excitation-emission process, and bioluminescence resonance energy transfer. We show here that in homogeneous solutions and in fluorophore-targeted bacteria, FUEL is the dominant mechanism responsible for the production of red-shifted photons. The minor resonance contribution was ascertained by comparing the intensity of the experimental signal to its theoretical resonance counterpart. Distinctive features of the in vitro FUEL signal include a macroscopic depth dependency, a lack of enhancement upon targeting at a constant fluorophore concentration cf and a non-square dependency on cf. Significantly, FUEL is an important, so far overlooked, component of all resonance phenomena which should guide the design of appropriate controls when elucidating interactions. Last, our results highlight the potential for FUEL as a means to enhance in vivo and in vitro detection through complex media while alleviating the need for targeting.

Cloning and characterization of luciferase from a Fijian luminous click beetle

Luminous click beetle is distributed almost exclusively in Central and South America with a single genus in Melanesia. Among these click beetles, the description of Melanesian species has been fragmentary, and its luciferase gene and phylogenetic relation to other click beetles still remain uncertain. We collected a living luminous click beetle, Photophorus jansonii in Fiji. It emits green-yellow light from two spots on the pronotum and has no ventral luminous organ. Here, we cloned a luciferase gene from this insect by RT-PCR. The deduced amino acid sequence showed high identity of ~85% to the luciferases derived from other click beetle species. The luciferase of the Fijian click beetle was produced as a recombinant protein to characterize its biochemical properties. The Km for D-luciferin and ATP were 173 and 270 μm, respectively. The luciferase was pH-insensitive and the spectrum measured at pH 8.0 showed a peak at 559 nm, which was in the range of green-yellow light as seen in the luminous spot of the living Fijian click beetle. The Fijian click beetle luciferase was assigned to the Elateridae clade by a phylogenetic analysis, but it made a clearly different branch from Pyrophorus group examined in this study.

Current advanced bioluminescence technology in drug discovery

BACKGROUND

Bioluminescence technology is based on the luciferin-luciferase reaction and is generally well known as a reporter gene assay system that uses firefly luciferase. It has revolutionized the field of transcriptional analysis owing to its usability and quantitative capability. Several methods for transcription analysis have emerged in the past two decades. Recently, novel bioluminescence techniques that differ from typical approaches were developed for the detection of transcriptional regulation or direct protein-protein interactions.

OBJECTIVE

As each method has its own characteristics, this review summarizes the latest bioluminescence methods that are applicable to the field of drug discovery research.

METHODS

Considering the diversity of related techniques, this review covers several aspects that have been divided into the following classes: variation of reporter gene assays, secretion properties, protein-protein interaction assays in living cells and bioluminescence imaging of living cells.

RESULTS/CONCLUSIONS

The practical application of several luciferins and/or luciferases and the generation of novel applications by incorporating fluorescent molecules into bioluminescence techniques will become increasingly important because bioluminescence technology has a significant potential depending on how we use it.

Luciferase from Fulgeochlizus bruchi (Coleoptera:Elateridae), a Brazilian click-beetle with a single abdominal lantern: molecular evolution, biological function and comparison with other click-beetle luciferases

Bioluminescent click-beetles emit a wide range of bioluminescence colors (λ(Max) = 534-594 nm) from thoracic and abdominal lanterns, which are used for courtship. Only the luciferases from Pyrophorus and Pyrearinus species were cloned and sequenced. The Brazilian Fulgeochlizus bruchi click-beetle, which inhabits the Central-west Cerrado (Savannas), is noteworthy because, differently from other click-beetles, the adult stage displays only a functional abdominal lantern, which produces a bright green bioluminescence for sexual attraction purposes, and lacks functional thoracic lanterns. We cloned the cDNA for the abdominal lantern luciferase of this species. Notably, the primary sequence of this luciferase showed slightly higher identity with the green emitting dorsal lantern luciferases of the Pyrophorus genus instead of the abdominal lanterns luciferases. This luciferase displays a blue-shifted spectrum (λ(Max) = 540 nm), which is pH-insensitive from pH 7.5 to 9.5 and undergoes a slight red shift and broadening above this pH; the lowest K(M) for luciferin among studied click-beetle luciferases, and the highest optimum pH (9.0) ever reported for a beetle luciferase. At pH 9.0, the K(M) for luciferin increases, showing a decrease of affinity for this substrate, despite the higher activity. The slow luminescence decay rate of F. bruchi luciferase in vitro reaction could be an adaptation of this luciferase for the long and sustained in vivo luminescence display of the click-beetle during the courtship, and could be useful for in vivo intracellular imaging.

Firefly luciferase: an adenylate-forming enzyme for multicatalytic functions

Firefly luciferase is a member of the acyl-adenylate/thioester-forming superfamily of enzymes and catalyzes the oxidation of firefly luciferin with molecular oxygen to emit light. Knowledge of the luminescence mechanism catalyzed by firefly luciferase has been gathered, leading to the discovery of a novel catalytic function of luciferase. Recently, we demonstrated that firefly luciferase has a catalytic function of fatty acyl-CoA synthesis from fatty acids in the presence of ATP, Mg(2+) and coenzyme A. Based on identification of fatty acyl-CoA genes in firefly, Drosophila, and non-luminous click beetles, we then proposed that the evolutionary origin of firefly luciferase is a fatty acyl-CoA synthetase in insects. Further, we succeeded in converting the fatty acyl-CoA synthetase of non-luminous insects into functional luciferase showing luminescence activity by site-directed mutagenesis.

Labels and probes for live cell imaging: overview and selection guide

Fluorescence imaging is an important tool for molecular biology research. There is a wide array of fluorescent labels and activatable probes available for investigation of biochemical processes at a molecular level in living cells. Given the large number of potential imaging agents and numerous variables that can impact the utility of these fluorescent materials for imaging, selection of the appropriate probes can be a difficult task. In this report an overview of fluorescent imaging agents and details on their optical and physical properties that can impact their function are presented.

Characterization of luciferases and its paralogue in the Panamanian luminous click beetle Pyrophorus angustus: a click beetle luciferase lacks the fatty acyl-CoA synthetic activity

Two luciferase genes (dPaLuc and vPaLuc) and one paralogue of luciferase (PaLL) were isolated from the Panamanian luminous click beetle, Pyrophorus angustus (Elateridae, Pyrophorinae). The transcripts of dPaLuc and vPaLuc were predominantly detected in the body parts with dorsal photophore and ventral photophore, respectively, and the transcript of PaLL was detected in both parts. The gene products of dPaLuc and vPaLuc possessed luminescence activity with firefly luciferin (lambda(max)=536 and 566 nm, respectively) but did not show significant activity of fatty acyl-CoA synthesis. On the other hand, the gene product of PaLL had fatty acyl-CoA synthetic activity with very weak luminescence activity. The catalytic properties of click beetle luciferase are different from our previous results that firefly luciferase has both luminescence activity and fatty acyl-CoA synthetic activity. These results suggested that the ancestral fatty acyl-CoA synthetase in the Pyrophorinae lineage has undergone gene duplication event, followed by specialization of one copy in luciferase. Subsequently, the luciferase was duplicated again and the two copies diverged in their luminescent color and expression pattern.

Intergenic exchange, geographic isolation, and the evolution of bioluminescent color for Pyrophorus click beetles

Gene duplication is an evolutionary process in which the emergent property of the whole can become greater and different than the sum of its parts. One potential outcome for gene duplication is for loci to evolve different, yet related functions. In this case, intergenic exchange can shuffle blocks of differentiated nucleotides between paralogues to create new alleles and phenotypes rather than simply homogenize loci. Bioluminescent click beetles in the genus Pyrophorus (Coleoptera: Elateridae) provide an opportunity to explore the creative potential of intergenic exchange for gene family evolution. Pyrophorus beetles bioluminesce different light colors from a pair of dorsal light organs and a ventral light organ. The light organs are under the separate genetic control of dorsal and ventral luciferase loci. Here, we report that intergenic exchange is common between dorsal and ventral loci for beetles from Jamaica (P. plagiophthalamus), the Dominican Republic (P. mellifluous), Belize (P. luscus), and Trinidad (P. noctilucus). We also present evidence that periods of past geographic isolation for beetles on Jamaica, probably acting in concert with selection, built differentiated blocks of substitutions within dorsal and ventral P. plagiophthalamus luciferase loci. Gene flow and intergenic exchange subsequently shuffled these substitutions between dorsal and ventral loci to produce new color phenotypes on Jamaica, including a yellow-green polymorphism. We discuss the possibility of a previously unrecognized emergent evolutionary property of intergenic exchange for luciferase involving cycles of bioluminescent color change related to differences in selective constrains acting on dorsal versus ventral loci. We also explore whether intergenic exchange may commonly create novel variation and the potential for cyclic evolution in other multigene family systems.

Molecular pathology of malignant gliomas

Malignant gliomas, the most common type of primary brain tumor, are a spectrum of tumors of varying differentiation and malignancy grades. These tumors may arise from neural stem cells and appear to contain tumor stem cells. Early genetic events differ between astrocytic and oligodendroglial tumors, but all tumors have an initially invasive phenotype, which complicates therapy. Progression-associated genetic alterations are common to different tumor types, targeting growth-promoting and cell cycle control pathways and resulting in focal hypoxia, necrosis, and angiogenesis. Knowledge of malignant glioma genetics has already impacted clinical management of these tumors, and researchers hope that further knowledge of the molecular pathology of malignant gliomas will result in novel therapies.

Molecular imaging using visible light to reveal biological changes in the brain

Advances in imaging have enabled the study of cellular and molecular processes in the context of the living body that include cell migration patterns, location and extent of gene expression, degree of protein-protein interaction, and levels of enzyme activity. These tools, which operate over a range of scales, resolutions, and sensitivities, have opened up broad new areas of investigation where the influence of organ systems and functional circulation is intact. There are a myriad of imaging modalities available, each with its own advantages and disadvantages, depending on the specific application. Among these modalities, optical imaging techniques, including in vivo bioluminescence imaging and fluorescence imaging, use visible light to interrogate biology in the living body. Optimal imaging with these modalities require that the appropriate marker be used to tag the process of interest to make it uniquely visible using a particular imaging technology. For each optical modality, there are various labels to choose from that range from dyes that permit tissue contrast and dyes that can be activated by enzymatic activity, to gene-encoding proteins with optical signatures that can be engineered into specific biological processes. This article provides and overview of optical imaging technologies and commonly used labels, focusing on bioluminescence and fluorescence, and describes several examples of how these tools are applied to biological questions relating to the central nervous system.

Integrating biogeographic and genetic approaches to investigate the history of bioluminescent colour alleles in the Jamaican click beetle, Pyrophorus plagiophthalamus

Bioluminescent colour in the Jamaican click beetle, Pyrophorus plagiophthalamus, is an ideal system for studies moving from gene to landscape to gain a holistic understanding of the molecular, ecological, and historical bases for adaptation. Previous studies have established the genetics of bioluminescent colour variation in the beetle to the level of the nucleotide base pair in the target gene luciferase. Three different luciferase colour alleles affecting ventral light organ colour [yellow-green (vYG), yellow (vYE), and orange (vOR)] were found segregating in P. plagiophthalamus populations. These alleles differ from each other in a number of replacement mutations (14 total), the majority of which (11) have a measurable effect on colour. Phylogenetic analysis revealed a long-term adaptive trend on Jamaica towards longer wavelength bioluminescence, culminating in the most recently derived vOR allele. Here, we further investigate the historical and geographic context of adaptive colour evolution by testing a vicariance model for the origins of the extant ventral light organ polymorphism: that the vOR allele arose and differentiated in an isolated deme on the east side of Jamaica before spreading westward. Comparisons of colour phenotypes, luciferase coding sequences, the third intron of the gene, mtDNA, and microsatellite data provided evidence for past population subdivision on Jamaica and ongoing gene flow, as has been found for other island endemics. However, the pattern of differentiation supported the allopatric divergence of vYG and vYE alleles. The vOR gene appears to have arisen relatively recently from a vYE precursor and postdates the period of major biogeographic isolation. We discuss the implications of the results for discerning ecological causation in the adaptive sequence from nucleotide to landscape to population change for bioluminescent colour.

Nocturnal colour vision--not as rare as we might think

The dual retina of humans and most vertebrates consists of multiple types of cone for colour vision in bright light and one single type of rod, leaving these animals colour-blind at night. Instead of comparing the signals from different spectral types of photoreceptors, they use one highly sensitive receptor, thus improving the signal-to-noise ratio. However, nocturnal moths and geckos can discriminate colours at extremely dim light intensities when humans are colour-blind, by sacrificing spatial and temporal rather than spectral resolution. The advantages of colour vision are just as obvious at night as they are during the day. Colour vision is much more reliable than achromatic contrast, not only under changing light intensities, but also under the colour changes occurring during dusk and dawn. It can be expected that nocturnal animals other than moths and geckos make use of the highly reliable colour signals in dim light.

Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies

Strategies for the identification of functional genetic variation underlying phenotypic traits of ecological and evolutionary importance have received considerable attention in the literature recently. This paper aims to bring together and compare the relative strengths and limitations of various potentially useful research strategies for dissecting functionally important genetic variation in a wide range of organisms. We briefly explore the relative strengths and limitations of traditional and emerging approaches and evaluate their potential use in free-living populations. While it is likely that much of the progress in functional genetic analyses will rely on progress in traditional model species, it is clear that with prudent choices of methods and appropriate sampling designs, much headway can be also made in a diverse range of species. We suggest that combining research approaches targeting different functional and biological levels can potentially increase understanding the genetic basis of ecological and evolutionary processes both in model and non-model organisms.

Plant eco-devo: the potential of poplar as a model organism

Ecological developmental genetics is the study of how ecologically significant traits originate in the genome and how the allelic combinations responsible are maintained in populations and species. Plant development involves a continuous feedback between growth and environment and the success of individual genotype x environment interactions determines the passage of alleles to the next generation: the adaptive recursion. Outbreeding plants contain a large amount of genetic variation, mostly in the form of single nucleotide polymorphisms (SNPs). One of the challenges of eco-devo is to distinguish neutral SNPs from those with ecological consequences. The complete genome sequence of Populus trichocarpa Torr. & A. Gray will be a significant aid in this endeavour. Occurring from California to Alaska, this is the first ecologically 'keystone' species to be sequenced. It has a rich natural history and is an obligate outbreeder. The individual sequenced, Nisqually-1, appears to be heterozygous on average about every 100 bp over the c. 500 million bp of the genome. Overlaid on this within-individual variation is some ecologically based between-individual genotypic variation evident across the distribution of the species. The synthesis of information from genomics and ecology is now in prospect. This 'ecomolecular synthesis' is likely to provide a rich insight into the genomic basis of plant adaptation.