Identification of genes involved in Drosophila melanogaster geotaxis, a complex behavioral trait

A Drosophila DEG/ENaC channel subunit is required for male response to female pheromones

Odorants and pheromones as well as sweet- and bitter-tasting small molecules are perceived through activation of G protein-coupled chemosensory receptors. In contrast, gustatory detection of salty and sour tastes may involve direct gating of sodium channels of the DEG/ENaC family by sodium and hydrogen ions, respectively. We have found that ppk25, a Drosophila melanogaster gene encoding a DEG/ENaC channel subunit, is expressed at highest levels in the male appendages responsible for gustatory and olfactory detection of female pheromones: the legs, wings, and antennae. Mutations in the ppk25 gene reduce or even abolish male courtship response to females in the dark, conditions under which detection of female pheromones is an essential courtship-activating sensory input. In contrast, the same mutations have no effect on other behaviors tested. Importantly, ppk25 mutant males that show no response to females in the dark execute all of the normal steps of courtship behavior in the presence of visible light, suggesting that ppk25 is required for activation of courtship behavior by chemosensory perception of female pheromones. Finally, a ppk25 mutant allele predicted to encode a truncated protein has dominant-negative properties, suggesting that the normal Ppk25 protein acts as part of a multiprotein complex. Together, these results indicate that ppk25 is necessary for response to female pheromones by D. melanogaster males, and suggest that members of the DEG/ENaC family of genes play a wider role in chemical senses than previously suspected.

DROSOPHILANUTRIGENOMICS CAN PROVIDE CLUES TO HUMAN GENE-NUTRIENT INTERACTIONS

Nutrigenomics refers to the complex effects of the nutritional environment on the genome, epigenome, and proteome of an organism. The diverse tissue- and organ-specific effects of diet include gene expression patterns, organization of the chromatin, and protein post-translational modifications. Long-term effects of diet range from obesity and associated diseases such as diabetes and cardiovascular disease to increased or decreased longevity. Furthermore, the diet of the mother can potentially have long-term health impacts on the children, possibly through inherited diet-induced chromatin alterations. Drosophila is a unique and ideal model organism for conducting nutrigenomics research for numerous reasons. Drosophila, yeast, and Caenorhabditis elegans all have sophisticated genetics as well as sequenced genomes, and researchers working with all three organisms have made valuable discoveries in nutrigenomics. However, unlike yeast and C. elegans, Drosophila has adipose-like tissues and a lipid transport system, making it a closer model to humans. This review summarizes what has already been learned in Drosophila nutrigenomics (with an emphasis on lipids and sterols), critically evaluates the data, and discusses fruitful areas for future research.

The use of transcriptomics to address questions in behaviour: production of a suppression subtractive hybridisation library from dominance hierarchies of rainbow trout

Microarrays, or gene chips, are transforming the way that gene expression is measured by allowing us to determine the expression of thousands of genes from a sample. This gives immense power to examine gene expression on a global scale within individual animals and between animals. The scope for analysing complex animal functions at the molecular level is within our grasp. Relatively few studies have examined complex behaviours and correlated them with gene expression in the central nervous system. Here, we review the use of microarray technology in the dissection of behaviour and focus specifically on dominance status. A cDNA library using suppression subtraction hybridisation on rainbow trout Oncorhynchus mykiss of differing status has been produced to enrich the cDNA library for genes that are differentially expressed between individuals of different dominance status. A preliminary analysis demonstrated that there were 1,165 genes that differed between fish of different dominance status. Therefore, there is the potential of correlating gene expression profile with rank position within dominance hierarchies, thus identifying targets for candidate gene approaches.

Generating phenotypic variation: prospects from "evo-devo" research on Bicyclus anynana wing patterns

Understanding the generation of phenotypic variation is an important challenge for modern evolutionary biology, and butterfly wing patterns are an exciting system that can shed some light on this issue. Here, we report on recent advances in the genetics of Bicyclus anynana butterflies. This system provides the potential for a fully integrated study of the evolutionary and developmental processes underlying diversity in morphology.

Mutations and Natural Genetic Variation in the Courtship Song of Drosophila

All Drosophila species have a courtship repertoire by which a male stimulates a female to mate with him. In many species, males vibrate their wings to produce courtship song, an element of courtship that plays an important role in female choice. Each species has a unique courtship song, with the major differences among species songs being in timing and/or structure. Analysis of genetic mutations has revealed 17 genes that affect courtship song in Drosophila melanogaster. Most of the genes were first identified as affecting another trait and were subsequently shown to affect song. Quantitative genetic studies have demonstrated a polygenetic additive genetic architecture for many song traits. Few candidate genes, identified through the classical genetic approach, coincide with the regions implicated as affecting natural variation. With many new tools in genetic analysis and the multiple Drosophila genome projects currently underway, the ability to relate mutational and quantitative analyses will improve.

Genetics and genomics of Drosophila mating behavior

The first steps of animal speciation are thought to be the development of sexual isolating mechanisms. In contrast to recent progress in understanding the genetic basis of postzygotic isolating mechanisms, little is known about the genetic architecture of sexual isolation. Here, we have subjected Drosophila melanogaster to 29 generations of replicated divergent artificial selection for mating speed. The phenotypic response to selection was highly asymmetrical in the direction of reduced mating speed, with estimates of realized heritability averaging 7%. The selection response was largely attributable to a reduction in female receptivity. We assessed the whole genome transcriptional response to selection for mating speed using Affymetrix GeneChips and a rigorous statistical analysis. Remarkably, >3,700 probe sets (21% of the array elements) exhibited a divergence in message levels between the Fast and Slow replicate lines. Genes with altered transcriptional abundance in response to selection fell into many different biological process and molecular function Gene Ontology categories, indicating substantial pleiotropy for this complex behavior. Future functional studies are necessary to test the extent to which transcript profiling of divergent selection lines accurately predicts genes that directly affect the selected trait.

Flexibility in a gene network affecting a simple behavior in Drosophila melanogaster

Gene interactions are emerging as central to understanding the realization of any phenotype. To probe the flexibility of interactions in a defined gene network, we isolated a set of 16 interacting genes in Drosophila, on the basis of their alteration of a quantitative behavioral phenotype-the loss of coordination in a temperature-sensitive allele of Syntaxin1A. The interactions inter se of this set of genes were then assayed in the presence and in the absence of the original Syntaxin1A mutation to ask whether the relationships among the 16 genes remain stable or differ after a change in genetic context. The pattern of epistatic interactions that occurs within this set of variants is dramatically altered in the two different genetic contexts. The results imply considerable flexibility in the network interactions of genes.

Quantitative genomics of starvation stress resistance in Drosophila

The efficacy of transcriptional profiling for identifying networks of pleiotropic genes regulating complex traits was assessed. The transcriptional response to starvation stress in males and females of the Oregon-R and 2b Drosophila strains, as well as four recombinant inbred lines derived from them, was shown to be different between the sexes and to involve approximately 25% of the genome.

Background

A major challenge of modern biology is to understand the networks of interacting genes regulating complex traits, and the subset of these genes that affect naturally occurring quantitative genetic variation. Previously, we used P-element mutagenesis and quantitative trait locus (QTL) mapping in Drosophila to identify candidate genes affecting resistance to starvation stress, and variation in resistance to starvation stress between the Oregon-R (Ore) and 2b strains. Here, we tested the efficacy of whole-genome transcriptional profiling for identifying genes affecting starvation stress resistance.

Results

We evaluated whole-genome transcript abundance for males and females of Ore, 2b, and four recombinant inbred lines derived from them, under control and starved conditions. There were significant differences in transcript abundance between the sexes for nearly 50% of the genome, while the transcriptional response to starvation stress involved approximately 25% of the genome. Nearly 50% of P-element insertions in 160 genes with altered transcript abundance during starvation stress had mutational effects on starvation tolerance. Approximately 5% of the genome exhibited genetic variation in transcript abundance, which was largely attributable to regulation by unlinked genes. Genes exhibiting variation in transcript abundance among lines did not cluster within starvation resistance QTLs, and none of the candidate genes affecting variation in starvation resistance between Ore and 2b exhibited significant differences in transcript abundance between lines.

Conclusions

Expression profiling is a powerful method for identifying networks of pleiotropic genes regulating complex traits, but the relationship between variation in transcript abundance among lines used to map QTLs and genes affecting variation in quantitative traits is complicated.

Quantitative evolutionary genomics: differential gene expression and male reproductive success in Drosophila melanogaster

We combined traditional quantitative genetics and oligonucleotide microarrays to examine within-population genetic variation in a trait closely related to fitness. The trait, male reproductive success under competitive conditions (MCRS), is of central importance to both life-history and sexual-selection theory. We identified 27 candidate genes whose expression levels were associated with within-population variation in MCRS. "High" MCRS was associated with low expression of a cytochrome P450 that causes pesticide resistance, suggesting a fitness cost to resistance. Two groups of metabolic proteins (glutathione transferases and phosphatases) were significantly over-represented, and a large portion of the candidates are genes involved in oxidative stress resistance, energy acquisition or energy storage. Genes expressed in accessory glands and testes were not over-represented among differentially expressed genes, but testis-expressed genes were significantly more likely to be upregulated in high MCRS genotypes. Finally, nine candidate genes that we identified had no previous functional annotation, and this experiment suggests that they play a role in male reproductive success.

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.

Quantitative genetic analyses of complex behaviours in Drosophila

Behaviours are exceptionally complex quantitative traits. Sensitivity to environmental variation and genetic background, the presence of sexual dimorphism, and the widespread functional pleiotropy that is inherent in behavioural phenotypes pose daunting challenges for unravelling their underlying genetics. Drosophila melanogaster provides an attractive system for elucidating the unifying principles of the genetic architectures that drive behaviours, as genetically identical individuals can be reared rapidly in controlled environments and extensive publicly accessible genetic resources are available. Recent advances in quantitative genetic and functional genomic approaches now enable the extensive characterization of complex genetic networks that mediate behaviours in this important model organism.

Expression of cardiac myosin-binding protein-C (cMyBP-C) in Drosophila as a model for the study of human cardiomyopathies

Mutations in the MYBPC3 gene encoding human cardiac myosin-binding protein-C (cMyBP-C) are associated with familial hypertrophic cardiomyopathy (FHC), but the molecular mechanisms involved are not fully understood. In addition, development of FHC is sensitive to genetic background, and the search for candidate modifier genes is crucial with a view to proposing diagnosis and exploring new therapies. We used Drosophila as the model to investigate the in vivo consequences of human cMyBP-C mutations. We first produced transgenic flies that specifically express human wild-type or two C-terminal truncated cMyBP-Cs in indirect flight muscles (IFM), a tissue particularly amenable to genetic and molecular analyses. First, incorporation of human cMyBP-C into the IFM led to sarcomeric structural abnormalities and to a flightless phenotype aggravated by age and human gene dosage. Second, transcriptome analysis of transgenic IFM using nylon microarrays showed the remodelling of a transcriptional program involving 97 out of 3570 Drosophila genes. Among them, the Calmodulin gene encoding a key component of muscle contraction, found up-regulated in transgenic IFM, was evaluated as a potential modifier gene. Calmodulin mutant alleles rescued the flightless phenotype, and therefore behave as dominant suppressors of the flightless phenotype suggesting that Calmodulin might be a modifier gene in the context of human FHC. In conclusion, we suggest that the combination of heterologous transgenesis and transcriptome analysis in Drosophila could be of great value as a way to glean insights into the molecular mechanisms underlying FHC and to propose potential candidate modifier genes.

E pluribus unum, ex uno plura: quantitative and single-gene perspectives on the study of behavior

Genetic studies of behavior have traditionally come in two flavors: quantitative genetic studies of natural variants and single-gene studies of induced mutants. Each employed different techniques and methods of analysis toward the common, ultimate goal of understanding how genes influence behavior. With the advent of new genomic technologies, and also the realization that mechanisms underlying behavior involve a considerable degree of complex gene interaction, the traditionally separate strands of behavior genetics are merging into a single, synthetic strategy.

Discovering genes: the use of microarrays and laser capture microdissection in pain research

The DNA microarray is a powerful, high throughput technique for assessing gene expression on a system-wide genomic scale. It has great potential in pain research for determining the network of gene regulation in different pain conditions, and also for producing detailed gene expression maps in anatomical areas that process nociceptive stimuli. However, for the potential of this high throughput technology to be realised in pain research, microarrays need to be combined with other technologies. Laser capture microdissection is capable of isolating small populations of homogenous cells, allowing distinct areas involved in nociceptive processing to be examined. In combination with sophisticated PCR-based amplification protocols this technique provides sufficient amounts of messenger RNA (mRNA) for application to microarrays. Aside from the technological issues, a difficult task in any microarray study is the analysis of the resulting enormous data set to reveal the key genes, whose regulation is central to the phenotypic changes observed. For this to be achieved, the methods of data analysis, pattern searching and feature recognition, and bioinformatics have to be properly deployed all within the context of an appropriate statistical design. These issues are especially relevant to pain research where interindividual and interpopulation variation is likely to be high, and where polymorphisms can greatly affect nociceptive sensitivity and susceptibility to pain conditions. Methods for assessing the function of new candidate genes identified in microarray screening experiments are also discussed.

Common variants in the 5' region of the leptin gene are associated with body mass index in men from the National Heart, Lung, and Blood Institute Family Heart Study

Linkage of body mass index (BMI) to a broad region of chromosome 7q22-35 has been reported in multiple studies. We previously published a multipoint LOD score of 4.9 at D7S1804 for BMI from the National Heart, Lung, and Blood Institute Family Heart Study. Leptin (LEP), the human homolog of the mouse obesity (ob) gene, is positioned near the linkage peak and is the most prominent candidate gene in this region. Interest in LEP as a susceptibility gene for human obesity has led to numerous linkage and association studies, but the results of these studies are still controversial. In the present study, we employed family-based tests of association with both a quantitative measure of BMI adjusted for age and sex and a dichotomously defined obesity trait. We genotyped 29 single-nucleotide polymorphisms (SNPs) spanning 240 kb around the LEP gene in the 82 extended pedigrees with the strongest evidence for linkage. When the programs TRANSMIT and FBAT were used, a number of SNPs showed association in men but not women, for both the quantitative and qualitative trait definitions (P<.05). Five SNPs (H1328084, H1328083, H1328082, H1328081, and H1328080) positioned 2 kb beyond the previously defined promoter region showed strong association in single-marker and multiple-marker haplotype analysis. This five-marker haplotype (frequency 49% in this sample) is overtransmitted to obese offspring (P=.00005). All five of these SNPs are predicted to modify transcription-factor binding sites. This may indicate new functional variants in an extended promoter region of LEP.

Waddington's widget: Hsp90 and the inheritance of acquired characters

Conrad Waddington published an influential model for evolution in his 1942 paper, Canalization of Development and Inheritance of Acquired Characters. In this classic, albeit controversial, paper, he proposed that an unknown mechanism exists that conceals phenotypic variation until the organism is stressed. Recent studies have proposed that the highly conserved chaperone Hsp90 could function as a "capacitor," or an "adaptively inducible canalizer," that masks silent phenotypic variation of either genetic or epigenetic origin. This review will discuss evidence for, and arguments against, the role of Hsp90 as a capacitor for morphological evolution, and as a key component of what we call "Waddington's widget."

Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae

BACKGROUND

The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood. Identifying how many phenotypes are associated with differences in gene expression and how many gene-expression differences are associated with a phenotype is important to understanding the molecular basis and evolution of complex traits.

RESULTS

We compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown either in the presence or absence of copper sulfate. Of the nine strains, two show a reduced growth rate and two others are rust colored in the presence of copper sulfate. We identified 633 genes that show significant differences in expression among strains. Of these genes, 20 were correlated with resistance to copper sulfate and 24 were correlated with rust coloration. The function of these genes in combination with their expression pattern suggests the presence of both correlative and causative expression differences. But the majority of differentially expressed genes were not correlated with either phenotype and showed the same expression pattern both in the presence and absence of copper sulfate. To determine whether these expression differences may contribute to phenotypic variation under other environmental conditions, we examined one phenotype, freeze tolerance, predicted by the differential expression of the aquaporin gene AQY2. We found freeze tolerance is associated with the expression of AQY2.

CONCLUSIONS

Gene expression differences provide substantial insight into the molecular basis of naturally occurring traits and can be used to predict environment dependent phenotypic variation.

What have two decades of laboratory life-history evolution studies on Drosophila melanogaster taught us?

A series of laboratory selection experiments on Drosophila melanogaster over the past two decades has provided insights into the specifics of life-history tradeoffs in the species and greatly refined our understanding of how ecology and genetics interact in life-history evolution. Much of what has been learnt from these studies about the subtlety of the microevolutionary process also has significant implications for experimental design and inference in organismal biology beyond life-history evolution, as well as for studies of evolution in the wild. Here we review work on the ecology and evolution of life-histories in laboratory populations of D. melanogaster, emphasizing how environmental effects on life-history-related traits can influence evolutionary change. We discuss life-history tradeoffs - many unexpected - revealed by selection experiments, and also highlight recent work that underscores the importance to life-history evolution of cross-generation and cross-life-stage effects and interactions, sexual antagonism and sexual dimorphism, population dynamics, and the possible role of biological clocks in timing life-history events. Finally, we discuss some of the limitations of typical selection experiments, and how these limitations might be transcended in the future by a combination of more elaborate and realistic selection experiments, developmental evolutionary biology, and the emerging discipline of phenomics.

Chipping away at brain function: mining for insights with microarrays

The impact of microarray studies on neurobiology has been limited because, with the exception of a few outstanding papers, most reports provide little more than lists of genes, often leaving the reader at a loss to understand which and how many of the identified transcripts will be true positives with significant biological impact. However, some recent papers have offered considerable biological insight by providing independent in vivo confirmation of the roles of candidate genes, offering a glimpse of the potential power of microarrays in neurobiological research.

Genetic modules and networks for behavior: lessons fromDrosophila

Behaviors are quantitative traits determined through actions of multiple genes and subject to genome-environment interactions. Early studies concentrated on analyzing the effects of single genes on behaviors, often generating views of simplified linear genetic pathways. The genome era has generated a profound paradigm shift enabling us to identify all the genes that contribute to expression of a behavioral phenotype, to investigate how they are organized as functional ensembles and to begin to identify polymorphisms that contribute to phenotypic variation and are targets for natural selection. Recent studies show that the genetic architecture of behavior is determined by dynamic and plastic modular networks of pleiotropic genes and that the behavioral phenotype manifests itself as an emergent property of such networks. Such networks are exquisitely sensitive to genetic background and sex effects. This review describes how Drosophila can serve as a model for uncovering fundamental principles of the genetic architecture of behavior.

Allelic variations in gene expression

PURPOSE OF REVIEW

Genetic variants determine phenotypic variability. Many genetic studies suggest that protein structural variations predispose the population to more than 1000 different hereditary diseases. Unfortunately, despite the study of genetic polymorphisms for many decades, the milder phenotypic variations believed to account for most human physical and behavioral differences and underlying the most common human genetic diseases (including cancers) cannot be accounted for easily by these variations in the protein coding sequences. Thus, it has been hypothesized that the study of natural differential expression presenting within and among populations may enhance understanding of human phenotypic variation.

RECENT FINDINGS

During the last year, reports identifying variations in gene expression in different organisms and finding subtle changes of gene expression associated with common genetic disease have pointed to variations in gene expression as playing a central role in molecular evolution and human disease. Advances in the functional analysis of gene regulatory networks-in particular, new methods for distinguishing cis-acting components from trans-acting factors-have provided the impetus for these discoveries.

SUMMARY

This review represents current knowledge about allelic variation in gene expression and its increasingly important role in understanding the genotype-phenotype relation. Characterization of these allelic variations may open largely uncharted territory in genomics for biomedical researchers and may eventually lead to the discovery of the causative genes of common hereditary diseases and their mechanism of action.

Microarray analysis: genome-scale hypothesis scanning

Microarrays can survey genome-wide expression patterns. Not only can these gene expression profiles be used to identify a few genes of interest, they are now being creatively applied for hypothesis generation and testing

Gene Expression Profiles in the Brain Predict Behavior in Individual Honey Bees

We show that the age-related transition by adult honey bees from hive work to foraging is associated with changes in messenger RNA abundance in the brain for 39% of approximately 5500 genes tested. This result, discovered using a highly replicated experimental design involving 72 microarrays, demonstrates more extensive genomic plasticity in the adult brain than has yet been shown. Experimental manipulations that uncouple behavior and age revealed that messenger RNA changes were primarily associated with behavior. Individual brain messenger RNA profiles correctly predicted the behavior of 57 out of 60 bees, indicating a robust association between brain gene expression in the individual and naturally occurring behavioral plasticity.

Drosophila free-running rhythms require intercellular communication

Robust self-sustained oscillations are a ubiquitous characteristic of circadian rhythms. These include Drosophila locomotor activity rhythms, which persist for weeks in constant darkness (DD). Yet the molecular oscillations that underlie circadian rhythms damp rapidly in many Drosophila tissues. Although much progress has been made in understanding the biochemical and cellular basis of circadian rhythms, the mechanisms that underlie the differences between damped and self-sustaining oscillations remain largely unknown. A small cluster of neurons in adult Drosophila brain, the ventral lateral neurons (LN(v)s), is essential for self-sustained behavioral rhythms and has been proposed to be the primary pacemaker for locomotor activity rhythms. With an LN(v)-specific driver, we restricted functional clocks to these neurons and showed that they are not sufficient to drive circadian locomotor activity rhythms. Also contrary to expectation, we found that all brain clock neurons manifest robust circadian oscillations of timeless and cryptochrome RNA for many days in DD. This persistent molecular rhythm requires pigment-dispersing factor (PDF), an LN(v)-specific neuropeptide, because the molecular oscillations are gradually lost when Pdf(01) mutant flies are exposed to free-running conditions. This observation precisely parallels the previously reported effect on behavioral rhythms of the Pdf(01) mutant. PDF is likely to affect some clock neurons directly, since the peptide appears to bind to the surface of many clock neurons, including the LN(v)s themselves. We showed that the brain circadian clock in Drosophila is clearly distinguishable from the eyes and other rapidly damping peripheral tissues, as it sustains robust molecular oscillations in DD. At the same time, different clock neurons are likely to work cooperatively within the brain, because the LN(v)s alone are insufficient to support the circadian program. Based on the damping results with Pdf(01) mutant flies, we propose that LN(v)s, and specifically the PDF neuropeptide that it synthesizes, are important in coordinating a circadian cellular network within the brain. The cooperative function of this network appears to be necessary for maintaining robust molecular oscillations in DD and is the basis of sustained circadian locomotor activity rhythms.

Construction of a cDNA-based microarray forDrosophila melanogaster: a comparison of gene transcription profiles from SL2 and Kc167 cells

We have constructed a DNA microarray that represents approximately 6900 of the estimated 13 598 genes in the Drosophila melanogaster genome. The microarray contains 5756 target cDNAs from the Berkeley Drosophila Genome Project, 1078 cDNAs from the National Institutes of Health Drosophila testis cDNA library, and 546 gene fragments that were amplified from genomic DNA. The methods for DNA amplification and microarray manufacture are presented. Academic researchers can obtain the microarray from the Canadian Drosophila Microarray Centre. To evaluate the utility of these arrays, we compared the gene transcription profiles of two commonly used Drosophila cell lines. Analysis revealed that 5412 spot pairs gave signals consistently above the average background in Kc167 cells, whereas 5636 spot pairs met this criterion in SL2 cells. When the expression profiles of the cell lines were compared, 1437 genes displayed at least a 1.5-fold difference, and 170 genes had a threefold or greater difference between the two cell lines. In each case, with respect to Kc167 when compared with SL2 cells, the number of genes that were upregulated was nearly equal to the number of downregulated genes. This result demonstrates that despite the similar embryonic derivation of both cell lines, their transcriptional profiles are very different.Key words: DNA microarray, Drosophila, transcriptional regulation, SL2, Kc167.

A putative Drosophila pheromone receptor expressed in male-specific taste neurons is required for efficient courtship

Propagation in higher animals requires the efficient and accurate display of innate mating behaviors. In Drosophila melanogaster, male courtship consists of a stereotypic sequence of behaviors involving multiple sensory modalities, such as vision, audition, and chemosensation. For example, taste bristles located in the male forelegs and the labial palps are thought to recognize nonvolatile pheromones secreted by the female. Here, we report the identification of the putative pheromone receptor GR68a, which is expressed in chemosensory neurons of about 20 male-specific gustatory bristles in the forelegs. Gr68a expression is dependent on the sex determination gene doublesex, which controls many aspects of sexual differentiation and is necessary for normal courtship behavior. Tetanus toxin-mediated inactivation of Gr68a-expressing neurons or transgene-mediated RNA interference of Gr68a RNA leads to a significant reduction in male courtship performance, suggesting that GR68a protein is an essential component of pheromone-driven courtship behavior in Drosophila.

Evolutionary and ecological functional genomics

A unique combination of disciplines is emerging--evolutionary and ecological functional genomics--which focuses on the genes that affect ecological success and evolutionary fitness in natural environments and populations. Already this approach has provided new insights that were not available from its disciplinary components in isolation. However, future advances will necessitate the re-engineering of scientific attitudes, training and institutions, to achieve extensive multidisciplinarity.

Scribble is essential for olfactory behavior in Drosophila melanogaster

The ability to discriminate and respond to chemical signals from the environment is an almost universal prerequisite for survival. Here, we report that the scaffold protein Scribble is essential for odor-guided behavior in Drosophila. Previously, we identified a P-element insert line with generalized sexually dimorphic smell impairment, smi97B. We found that the transposon in this line is located between the predicted promoter region and the transcription initiation site of scrib. A deficiency in this region, Df(3R)Tl-X, and two scrib null alleles fail to complement the smell-impaired phenotype of smi97B. Wild-type behavior is restored by precise excision of the P element, scrib mRNA levels correspond with mutant and wild-type phenotypes, and introduction of a full-length scrib transgene in the smi97B mutant rescues the olfactory deficit. Expression of Scrib is widespread in olfactory organs and the central nervous system. Finally, alternative splicing of scrib generates transcripts that differ in the number of leucine-rich repeats and PDZ domains.

Cis-acting variation in the expression of a high proportion of genes in human brain

Much of the genetic component of human phenotypic diversity, including susceptibility to disease, is proposed to be the result of cis-acting influences on gene expression. If this hypothesis is correct, it implies that cis-acting regulatory variation is a common phenomenon. However, direct evidence in support of this view is scarce. We have applied highly quantitative measures of allele-specific expression in order to screen an average of 19 informative subjects (range 8-26) for the presence of common cis-acting influences on the expression of 15 genes by using RNA derived from human brain. We found that, in seven of the 15 assayed genes, at least one individual exhibited relative differences in allelic expression of 20% or more and, in one gene (DTNBP1), allelic expression differences exceeded 50%. These results suggest that cis-acting variation in gene expression commonly occurs in native tissue and hence provide empirical support for the hypothesis that this is potentially an important mechanism underlying human phenotypic diversity.

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).

Beyond phrenology, at last

Although integration is a widely acknowledged goal in neuroscience, our approach to the function of biological entities often places boundaries that defy integration. Mapping across systems - from the genome to cognitive function - will require innovative methods that can identify every contributing component to a function, and instantaneously scale numerous changes in large data sets to consequences over the entire biological hierarchy.

Evolution of gene expression in the Drosophila melanogaster subgroup

Little is known about broad patterns of variation and evolution of gene expression during any developmental process. Here we investigate variation in genome-wide gene expression among Drosophila simulans, Drosophila yakuba and four strains of Drosophila melanogaster during a major developmental transition--the start of metamorphosis. Differences in gene activity between these lineages follow a phylogenetic pattern, and 27% of all of the genes in these genomes differ in their developmental gene expression between at least two strains or species. We identify, on a gene-by-gene basis, the evolutionary forces that shape this variation and show that, both within the transcriptional network that controls metamorphosis and across the whole genome, the expression changes of transcription factor genes are relatively stable, whereas those of their downstream targets are more likely to have evolved. Our results demonstrate extensive evolution of developmental gene expression among closely related species.

Developmental genomic approaches in model organisms

Functional genomics technologies can help decipher how information encoded in the genome is translated into morphology, physiology, and behavior during the development of complex organisms. A number of researchers have begun to apply DNA microarrays and other functional genomics approaches to study development. Here we review recent studies that take the first steps toward relating genome-wide information to developmental events, we discuss recent genomics approaches taken in animal model systems used to study human disease, and we outline methods that may be useful for constructing genome-wide maps of developmental processes.

Experimental evolution of learning ability in fruit flies

The presence of genetic variation for learning ability in animals opens the way for experiments asking how and under what ecological circumstances improved learning ability should evolve. Here we report experimental evolution of learning ability in Drosophila melanogaster. We exposed experimental populations for 51 generations to conditions that we expected to favor associative learning with regard to oviposition substrate choice. Flies that learned to associate a chemical cue (quinine) with a particular substrate, and still avoided this substrate several hours after the cue had been removed, were expected to contribute more alleles to the next generation. From about generation 15 on, the experimental populations showed marked ability to avoid oviposition substrates that several hours earlier had contained the chemical cue. The improved response to conditioning was also expressed when the flies were faced with a choice of novel media. We demonstrate that these behavioral changes are caused by the evolution of both a higher learning rate and a better memory.