Membrane lipid physiology and toxin catabolism underlie ethanol and acetic acid tolerance in Drosophila melanogaster

Comparison of Preference for Chemicals Associated with Fruit Fermentation between Drosophila melanogaster and Drosophila suzukii and between Virgin and Mated D. melanogaster

Two taxonomically similar Drosophila species, Drosophila melanogaster and Drosophila suzukii, are known to have distinct habitats: D. melanogaster is mostly found near overripe and fermented fruits, whereas D. suzukii is attracted to fresh fruits. Since chemical concentrations are typically higher in overripe and fermented fruits than in fresh fruits, D. melanogaster is hypothesized to be attracted to higher concentrations of volatiles than D. suzukii. Therefore, the chemical preferences of the two flies were compared via Y-tube olfactometer assays and electroantennogram (EAG) experiments using various concentrations of 2-phenylethanol, ethanol, and acetic acid. D. melanogaster exhibited a higher preference for high concentrations of all the chemicals than that of D. suzukii. In particular, since acetic acid is mostly produced at the late stage of fruit fermentation, the EAG signal distance to acetic acid between the two flies was higher than those to 2-phenylethanol and ethanol. This supports the hypothesis that D. melanogaster prefers fermented fruits compared to D. suzukii. When comparing virgin and mated female D. melanogaster, mated females showed a higher preference for high concentrations of chemicals than that of virgin females. In conclusion, high concentrations of volatiles are important attraction factors for mated females seeking appropriate sites for oviposition.

Changes in the Bio-Compounds and Biological Activities of Eight Whole Grains Fermentation Starter with Different Oxidized Chin-Shin Oolong Teas

Chin-shin oolong tea is the most widely planted variety in Taiwan. This study fermented eight whole grains fermentation starter (EGS) with light (LOT), medium (MOT), and fully (FOT) oxidized Chin-shin oolong teas for ten weeks. Comparing the three fermentation beverages, it was found that LOT fermentation can obtain the highest catechins (1644.56 ± 60.15 ppm) among the functional and antioxidant components. MOT can obtain the highest glucuronic acid (19,040.29 ± 2903.91 ppm), tannins, total phenols, flavonoids, and angiotensin-converting enzyme (ACE) inhibitory activity. FOT can obtain the highest GABA (1360.92 ± 123.24 ppm). In addition, both the LOT and MOT showed a significant increase in their ability to scavenge DPPH radicals after fermentation. EGS fermented with lightly or moderately oxidized Chin-shin oolong tea may be considered a novel Kombucha.

Ethanol resistance in Drosophila melanogaster has increased in parallel cold-adapted populations and shows a variable genetic architecture within and between populations

Understanding the genetic properties of adaptive trait evolution is a fundamental crux of biological inquiry that links molecular processes to biological diversity. Important uncertainties persist regarding the genetic predictability of adaptive trait change, the role of standing variation, and whether adaptation tends to result in the fixation of favored variants. Here, we use the recurrent evolution of enhanced ethanol resistance in Drosophila melanogaster during this species' worldwide expansion as a promising system to add to our understanding of the genetics of adaptation. We find that elevated ethanol resistance has evolved at least three times in different cooler regions of the species' modern range-not only at high latitude but also in two African high-altitude regions. Applying a bulk segregant mapping framework, we find that the genetic architecture of ethanol resistance evolution differs substantially not only between our three resistant populations, but also between two crosses involving the same European population. We then apply population genetic scans for local adaptation within our quantitative trait locus regions, and we find potential contributions of genes with annotated roles in spindle localization, membrane composition, sterol and alcohol metabolism, and other processes. We also apply simulation-based analyses that confirm the variable genetic basis of ethanol resistance and hint at a moderately polygenic architecture. However, these simulations indicate that larger-scale studies will be needed to more clearly quantify the genetic architecture of adaptive evolution and to firmly connect trait evolution to specific causative loci.

Xanthohumol prolongs lifespan and decreases stress-induced mortality in Drosophila melanogaster

Aging is a significant risk factor that links to the genesis of human diseases. The capacity to scavenge free radicals and adapt to various stresses is essential for expanding living organisms' lifespan. The evidences on the promotion of longevity by dietary supplementation are growing. Drosophila or fruit fly is one of the most effective models for the evaluation of anti-aging compounds. Xanthohumol (XN) is a potential bioactive substance for the prevention and treatment of many diseases. The previous studies have reported its potent activities as antioxidant, anticancer, anti-inflammatory, antiviral, antibacterial antiplasmodial, and antiobesity. In this study, the effect of XN supplementation on the lifespan extension was investigated in Drosophila melanogaster. The effects of XN on the improvement of the recovery from cold and heat shock, the resistance to starvation stress, and free radical-induced oxidative stress in XN-treated flies were also evaluated. Results showed that supplementation with XN at 0.5 mg/mL diet extended the mean lifespan by 14.89%. This was consistent with a significant improvement of locomotor activity of the Drosophila fed with an XN-mixed diet compared with those fed with a control diet. XN supplementation significantly increased the antioxidant enzyme activities at both 25 and 40 days. Drosophila treated with XN exhibited increased survival after exposure to hydrogen peroxide and paraquat. Finally, XN supplementation improved the recovery from cold and heat shock, the resistance to starvation stress, and acetic acid-induced stress. The present study shows that dietary supplementation with XN revealed the longevity effect and ameliorated stress-induced mortality in Drosophila.

Behavioral and Genomic Sensory Adaptations Underlying the Pest Activity of Drosophila suzukii

Studying how novel phenotypes originate and evolve is fundamental to the field of evolutionary biology as it allows us to understand how organismal diversity is generated and maintained. However, determining the basis of novel phenotypes is challenging as it involves orchestrated changes at multiple biological levels. Here, we aim to overcome this challenge by using a comparative species framework combining behavioral, gene expression, and genomic analyses to understand the evolutionary novel egg-laying substrate-choice behavior of the invasive pest species Drosophila suzukii. First, we used egg-laying behavioral assays to understand the evolution of ripe fruit oviposition preference in D. suzukii compared with closely related species D. subpulchrella and D. biarmipes as well as D. melanogaster. We show that D. subpulchrella and D. biarmipes lay eggs on both ripe and rotten fruits, suggesting that the transition to ripe fruit preference was gradual. Second, using two-choice oviposition assays, we studied how D. suzukii, D. subpulchrella, D. biarmipes, and D. melanogaster differentially process key sensory cues distinguishing ripe from rotten fruit during egg-laying. We found that D. suzukii's preference for ripe fruit is in part mediated through a species-specific preference for stiff substrates. Last, we sequenced and annotated a high-quality genome for D. subpulchrella. Using comparative genomic approaches, we identified candidate genes involved in D. suzukii's ability to seek out and target ripe fruits. Our results provide detail to the stepwise evolution of pest activity in D. suzukii, indicating important cues used by this species when finding a host, and the molecular mechanisms potentially underlying their adaptation to a new ecological niche.

Identification of transcriptional responsive genes to acetic acid, ethanol, and 2-phenylethanol exposure in Drosophila melanogaster

The fruit fly, Drosophila melanogaster, is predominantly found in overripe, rotten, fermenting, or decaying fruits and is constantly exposed to chemical stressors such as acetic acid, ethanol, and 2-phenylethanol. D. melanogaster has been employed as a model system for studying the molecular bases of various types of chemical-induced tolerance. Expression profiling using Illumina sequencing has been performed for identifying changes in gene expression that may be associated with evolutionary adaptation to exposure of acetic acid, ethanol, and 2-phenylethanol. We identified a total of 457 differentially expressed genes that may affect sensitivity or tolerance to three chemicals in the chemical treatment group as opposed to the control group. Gene-set enrichment analysis revealed that the genes involved in metabolism, multicellular organism reproduction, olfaction, regulation of signal transduction, and stress tolerance were over-represented in response to chemical exposure. Furthermore, we also detected a coordinated upregulation of genes in the Toll- and Imd-signaling pathways after the chemical exposure. Quantitative reverse transcription PCR analysis revealed that the expression levels of nine genes within the set of genes identified by RNA sequencing were up- or downregulated owing to chemical exposure. Taken together, our data suggest that such differentially expressed genes are coordinately affected by chemical exposure. Transcriptional analyses after exposure of D. melanogaster with three chemicals provide unique insights into subsequent functional studies on the mechanisms underlying the evolutionary adaptation of insect species to environmental chemical stressors.

Fitness effects but no temperature-mediated balancing selection at the polymorphic Adh gene of Drosophila melanogaster

What factors maintain genetic variation in natural populations? Opposing selection pressures on protein stability and catalytic activity are thought to maintain variation along thermal gradients in many enzymes. We examined a classic hypothesis of temperature-mediated balancing selection, the alcohol dehydrogenase enzyme of Drosophila melanogaster, in which 2 latitudinally distributed variants are thought to be maintained by an activity/stability trade-off. Using in vitro and in vivo assays and population genetic analyses, we found no evidence of the predicted biochemical or fitness trade-offs and no signature of balancing selection. Rather, one variant confers greater activity and survival in the presence of ethanol, irrespective of temperature. Variation in Adh, and possibly other enzymes, must therefore be caused by other factors correlated with temperature.

Polymorphism in the alcohol dehydrogenase (ADH) protein of Drosophila melanogaster, like genetic variation in many other enzymes, has long been hypothesized to be maintained by a selective trade-off between thermostability and enzyme activity. Two major Adh variants, named Fast and Slow, are distributed along latitudinal clines on several continents. The balancing selection trade-off hypothesis posits that Fast is favored at high latitudes because it metabolizes alcohol faster, whereas Slow is favored at low latitudes because it is more stable at high temperatures. Here we use biochemical and physiological assays of precisely engineered genetic variants to directly test this hypothesis. As predicted, the Fast protein has higher catalytic activity than Slow, and both the Fast protein and regulatory variants linked to it confer greater ethanol tolerance on transgenic animals. But we found no evidence of a temperature-mediated trade-off: The Fast protein is not less stable or active at high temperatures, and Fast alleles increase ethanol tolerance and survivorship at all temperatures tested. Further, analysis of a population genomic dataset reveals no signature of balancing selection in the Adh gene. These results provide strong evidence against balancing selection driven by a stability/activity trade-off in Adh, and they justify caution about this hypothesis for other enzymes except those for which it has been directly tested. Our findings tentatively suggest that environment-specific selection for the Fast allele, coupled with demographic history, may have produced the observed pattern of Adh variation.

Effect of Sequential Acclimation to Various Carbon Sources on the Proteome of Acetobacter senegalensis LMG 23690T and Its Tolerance to Downstream Process Stresses

Acetic acid bacteria are very vulnerable to environmental changes; hence, they should get acclimated to different kinds of stresses when they undergo downstream processing. In the present study, Acetobacter senegalensis LMG 23690^T, a thermo-tolerant strain, was acclimated sequentially to different carbon sources including glucose (condition Glc), a mixture of glucose and ethanol (condition EtOH) and a mixture of glucose and acetic acid (condition GlcAA). Then, the effects of acclimation on the cell proteome profiles and some phenotypic characteristics such as growth in culture medium containing ethanol, and tolerance to freeze-drying process were evaluated. Based on the obtained results, despite the cells acclimated to Glc or EtOH conditions, 86% of acclimated cells to GlcAA condition were culturable and resumed growth with a short lag phase in a culture medium containing ethanol and acetic acid. Interestingly, if A. senegalensis LMG 23690^T had been acclimated to condition GlcAA, 92% of cells exhibited active cellular dehydrogenases, and 59% of cells were culturable after freeze-drying process. Proteome profiles comparison by 2D-DiGE and MS analysis, revealed distinct physiological status between cells exposed to different acclimation treatments, possibly explaining the resulting diversity in phenotypic characteristics. Results of proteome analysis by 2D-DiGE also showed similarities between the differentially expressed proteins of acclimated cells to EtOH condition and the proteome of acclimated cells to GlcAA condition. Most of the differentially regulated proteins are involved in metabolism, folding, sorting, and degradation processes. In conclusion, acclimation under appropriate sub-lethal conditions can be used as a method to improve cell phenotypic characteristics such as viability, growth under certain conditions, and tolerance to downstream processes.

Centrosome Loss Triggers a Transcriptional Program To Counter Apoptosis-Induced Oxidative Stress

Centrosomes play a critical role in mitotic spindle assembly through their role in microtubule nucleation and bipolar spindle assembly. Loss of centrosomes can impair the ability of some cells to properly conduct mitotic division, leading to chromosomal instability, cell stress, and aneuploidy. Multiple aspects of the cellular response to mitotic error associated with centrosome loss appear to involve activation of JNK signaling. To further characterize the transcriptional effects of centrosome loss, we compared gene expression profiles of wild-type and acentrosomal cells from Drosophila wing imaginal discs. We found elevation of expression of JNK target genes, which we verified at the protein level. Consistent with this, the upregulated gene set showed significant enrichment for the AP-1 consensus DNA-binding sequence. We also found significant elevation in expression of genes regulating redox balance. Based on those findings, we examined oxidative stress after centrosome loss, revealing that acentrosomal wing cells have significant increases in reactive oxygen species (ROS). We then performed a candidate genetic screen and found that one of the genes upregulated in acentrosomal cells, glucose-6-phosphate dehydrogenase, plays an important role in buffering acentrosomal cells against increased ROS and helps protect those cells from cell death. Our data and other recent studies have revealed a complex network of signaling pathways, transcriptional programs, and cellular processes that epithelial cells use to respond to stressors, like mitotic errors, to help limit cell damage and maintain normal tissue development.

Dynamic changes in gene expression and alternative splicing mediate the response to acute alcohol exposure in Drosophila melanogaster

Environmental changes typically cause rapid gene expression responses in the exposed organisms, including changes in the representation of gene isoforms with different functions or properties. Identifying the genes that respond to environmental change, including in genotype-specific ways, is an important step in treating the undesirable physiological effects of stress, such as exposure to toxins or ethanol. Ethanol is a unique environmental stress in that chronic exposure results in permanent physiological changes and the development of alcohol use disorders. Drosophila is a classic model for deciphering the mechanisms of the response to alcohol exposure, as it meets the criteria for the development of alcohol use disorders, and has similar physiological underpinnings with vertebrates. Because many studies on the response to ethanol have relied on a priori candidate genes, broad surveys of gene expression and splicing are required and have been investigated here. Further, we expose Drosophila to ethanol in an environment that is genetically, socially, and ecologically relevant. Both expression and splicing differences, inasmuch as they can be decomposed, contribute to the response to ethanol in Drosophila melanogaster. However, we find that while D. melanogaster responds to ethanol, there is very little genetic variation in how it responds to ethanol. In addition, the response to alcohol over time is dynamic, suggesting that incorporating time into studies on the response to the environment is important.

Sex differences in oxidative stress resistance in relation to longevity in Drosophila melanogaster

Gender differences in lifespan and aging are known across species. Sex differences in longevity within a species can be useful to understand sex-specific aging. Drosophila melanogaster is a good model to study the problem of sex differences in longevity since females are longer lived than males. There is evidence that stress resistance influences longevity. The objective of this study was to investigate if there is a relationship between sex differences in longevity and oxidative stress resistance in D. melanogaster. We observed a progressive age-dependent decrease in the activity of SOD and catalase, major antioxidant enzymes involved in defense mechanisms against oxidative stress in parallel to the increased ROS levels over time. Longer-lived females showed lower ROS levels and higher antioxidant enzymes than males as a function of age. Using ethanol as a stressor, we have shown differential susceptibility of the sexes to ethanol wherein females exhibited higher resistance to ethanol-induced mortality and locomotor behavior compared to males. Our results show strong correlation between sex differences in oxidative stress resistance, antioxidant defenses and longevity. The study suggests that higher antioxidant defenses in females may confer resistance to oxidative stress, which could be a factor that influences sex-specific aging in D. melanogaster.

Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster

Identifying the genetic basis for adaptive differences between species requires explicit tests of historical hypotheses concerning the effects of past changes in gene sequence on molecular function, organismal phenotype and fitness. We address this challenge by combining ancestral protein reconstruction with biochemical experiments and physiological analysis of transgenic animals that carry ancestral genes. We tested a widely held hypothesis of molecular adaptation-that changes in the alcohol dehydrogenase protein (ADH) along the lineage leading to Drosophila melanogaster increased the catalytic activity of the enzyme and thereby contributed to the ethanol tolerance and adaptation of the species to its ethanol-rich ecological niche. Our experiments strongly refute the predictions of the adaptive ADH hypothesis and caution against accepting intuitively appealing accounts of historical molecular adaptation that are based on correlative evidence. The experimental strategy we employed can be used to decisively test other adaptive hypotheses and the claims they entail about past biological causality.

Oviposition preferences for ethanol depend on spatial arrangement and differ dramatically among closely related Drosophila species

Recent work on the model fly Drosophila melanogaster has reported inconsistencies in their preference for laying eggs on intermediate concentrations of ethanol. In this study, we resolve this discrepancy by showing that this species strongly prefers ovipositing on ethanol when it is close to a non-ethanol substrate, but strongly avoids ethanol when options are farther apart. We also show fluidity of these behaviors among other Drosophila species: D. melanogaster is more responsive to ethanol than close relatives in that it prefers ethanol more than other species in the close-proximity case, but avoids ethanol more than other species in the distant case. In the close-proximity scenario, the more ethanol-tolerant species generally prefer ethanol more, with the exception of the island endemic D. santomea. This species has the lowest tolerance in the clade, but behaves like D. melanogaster. We speculate that this could be an adaptation to protect eggs from parasites or predators such as parasitoid wasps, as larvae migrate to non-toxic substrates after hatching. These natural differences among species are an excellent opportunity to study how genes and brains evolve to alter ethanol preferences, and provide an interesting model for genetic variation in preferences in other organisms, including humans.

Summary:Drosophila species make dramatically different egg-laying decisions depending on ethanol concentration and the distances between options. Surprisingly, we find that the species with the lowest ethanol tolerance prefers ethanol the most.

Modeling trade-offs between plant fiber and toxins: a framework for quantifying risks perceived by foraging herbivores

When selecting habitats, herbivores must weigh multiple risks, such as predation, starvation, toxicity, and thermal stress, forcing them to make fitness trade-offs. Here, we applied the method of paired comparisons (PC) to investigate how herbivores make trade-offs between habitat features that influence selection of food patches. The method of PC measures utility and the inverse of utility, relative risk, and makes trade-offs and indifferences explicit by forcing animals to make choices between two patches with different types of risks. Using a series of paired-choice experiments to titrate the equivalence curve and find the marginal rate of substitution for one risk over the other, we evaluated how toxin-tolerant (pygmy rabbit Brachylagus idahoensis) and fiber-tolerant (mountain cottontail rabbit Sylviagus nuttallii) herbivores differed in their hypothesized perceived risk of fiber and toxins in food. Pygmy rabbits were willing to consume nearly five times more of the toxin 1,8-cineole in their diets to avoid consuming higher levels of fiber than were mountain cottontails. Fiber posed a greater relative risk for pygmy rabbits than cottontails and cineole a greater risk for cottontails than pygmy rabbits. Our flexible modeling approach can be used to (1) quantify how animals evaluate and trade off multiple habitat attributes when the benefits and risks are difficult to quantify, and (2) integrate diverse risks that influence fitness and habitat selection into a single index of habitat value. This index potentially could be applied to landscapes to predict habitat selection across several scales.

Evidence that Environmental Heterogeneity Maintains a Detoxifying Enzyme Polymorphism in Drosophila melanogaster

Environmental heterogeneity is thought to be an important process maintaining genetic variation in populations [1-4]: if alternative alleles are favored in different environments, a stable polymorphism can be maintained [1, 5, 6]. This situation has been hypothesized to occur in genes encoding multi-substrate enzymes [7], in which changes that increase activity with one substrate typically decrease activity with others [8-10], but examples of polymorphisms maintained by this mechanism are rare. Here, we present evidence that a polymorphism in an enzyme gene in Drosophila melanogaster is maintained by such a trade-off. The mitochondrially localized aldehyde dehydrogenase in D. melanogaster has two important functions: detoxifying acetaldehyde derived from dietary ethanol [11] and detoxifying larger aldehydes produced as byproducts of oxidative phosphorylation [12]. A derived variant of the enzyme, Leu479Phe, is present in moderate frequencies in most temperate populations but is rare in more ethanol-averse tropical populations. Using purified recombinant protein, we show that the Leu-Phe substitution increases turnover rate of acetaldehyde but decreases turnover rate of larger aldehydes. Furthermore, using transgenic fly lines, we show that the substitution increases lifetime fitness on medium supplemented with an ecologically relevant ethanol concentration but decreases fitness on medium lacking ethanol. The strong, opposing selection pressures, coupled with documented highly variable ethanol concentrations in breeding sites of temperate populations, implicate an essential role for environmental heterogeneity in maintaining the polymorphism.

Reduction in the cumulative effect of stress-induced inbreeding depression due to intragenerational purging in Drosophila melanogaster

Environmental stress generally exacerbates the harmful effects of inbreeding and it has been proposed that this could be exploited in purging deleterious alleles from threatened inbred populations. However, understanding what factors contribute to variability in the strength of inbreeding depression (ID) observed across adverse environmental conditions remains a challenge. Here, we examined how the nature and timing of stress affects ID and the potential for purging using inbred and outbred Drosophila melanogaster larvae exposed to biotic (larval competition, bacteria infection) and abiotic (ethanol, heat) stressors compared with unstressed controls. ID was measured during (larval survival) and after (male mating success) stress exposure. The level of stress imposed by each stressor was approximately equal, averaging a 42% reduction in outbred larval survival relative to controls. All stressors induced on average the same ID, causing a threefold increase in lethal equivalents for larval survival relative to controls. However, stress-induced ID in larval success was followed by a 30% reduction in ID in mating success of surviving males. We propose that this fitness recovery is due to 'intragenerational purging' whereby fitness correlations facilitate stress-induced purging that increases the average fitness of survivors in later life history stages. For biotic stressors, post-stress reductions in ID are consistent with intragenerational purging, whereas for abiotic stressors, there appeared to be an interaction between purging and stress-induced physiological damage. For all stressors, there was no net effect of stress on lifetime ID compared with unstressed controls, undermining the prediction that stress enhances the effectiveness of population-level purging across generations.

Preference for ethanol in feeding and oviposition in temperate and tropical populations of Drosophila melanogaster

The natural habitat of Drosophila melanogaster Meigen (Diptera: Drosophilidae) is fermenting fruits, which can be rich in ethanol. For unknown reasons, temperate populations of this cosmopolitan species have higher ethanol resistance than tropical populations. To determine whether this difference is accompanied by a parallel difference in preference for ethanol, we compared two European and two tropical African populations in feeding and oviposition preference for ethanol-supplemented medium. Although females of all populations laid significantly more eggs on medium with ethanol than on control medium, preference of European females for ethanol increased as ethanol concentration increased from 2 to 6%, whereas that of African females decreased. In feeding tests, African females preferred control medium over medium with 4% ethanol, whereas European females showed no preference. Males of all populations strongly preferred control medium. The combination of preference for ethanol in oviposition, and avoidance or neutrality in feeding, gives evidence that adults choose breeding sites with ethanol for the benefit of larvae, rather than for their own benefit. The stronger oviposition preference for ethanol of temperate than tropical females suggests that this benefit may be more important in temperate populations. Two possible benefits of ethanol for which there is some experimental evidence are cryoprotection and protection against natural enemies.

Mechanisms of naturally evolved ethanol resistance in Drosophila melanogaster

The decaying fruit in which Drosophila melanogaster feed and breed can contain ethanol in concentrations as high as 6-7%. In this cosmopolitan species, populations from temperate regions are consistently more resistant to ethanol poisoning than populations from the tropics, but little is known about the physiological basis of this difference. I show that when exposed to low levels of ethanol vapor, flies from a tropical African population accumulated 2-3 times more internal ethanol than flies from a European population, giving evidence that faster ethanol catabolism by European flies contributes to the resistance difference. Using lines differing only in the origin of their third chromosome, however, I show that faster ethanol elimination cannot fully explain the resistance difference, because relative to African third chromosomes, European third chromosomes confer substantially higher ethanol resistance, while having little effect on internal ethanol concentrations. European third chromosomes also confer higher resistance to acetic acid, a metabolic product of ethanol, than African third chromosomes, suggesting that the higher ethanol resistance conferred by the former might be due to increased resistance to deleterious effects of ethanol-derived acetic acid. In support of this hypothesis, when ethanol catabolism was blocked with an Alcohol dehydrogenase mutant, there was no difference in ethanol resistance between flies with European and African third chromosomes.

A transposable element insertion confers xenobiotic resistance in Drosophila

The increase in availability of whole genome sequences makes it possible to search for evidence of adaptation at an unprecedented scale. Despite recent progress, our understanding of the adaptive process is still very limited due to the difficulties in linking adaptive mutations to their phenotypic effects. In this study, we integrated different levels of biological information to pinpoint the ecologically relevant fitness effects and the underlying molecular and biochemical mechanisms of a putatively adaptive TE insertion in Drosophila melanogaster: the pogo transposon FBti0019627. We showed that other than being incorporated into Kmn1 transcript, FBti0019627 insertion also affects the polyadenylation signal choice of CG11699 gene. Consequently, only the short 3'UTR transcript of CG11699 gene is produced and the expression level of this gene is higher in flies with the insertion. Our results indicated that increased CG11699 expression leads to xenobiotic stress resistance through increased ALDH-III activity: flies with FBti0019627 insertion showed increased survival rate in response to benzaldehyde, a natural xenobiotic, and to carbofuran, a synthetic insecticide. Although differences in survival rate between flies with and without the insertion were not always significant, when they were, they were consistent with FBti0019627 mediating resistance to xenobiotics. Taken together, our results provide a plausible explanation for the increase in frequency of FBti0019627 in natural populations of D. melanogaster and add to the limited number of examples in which a natural genetic mutation has been linked to its ecologically relevant phenotype. Furthermore, the widespread distribution of TEs across the tree of life and conservation of stress response pathways across organisms make our results relevant not only for Drosophila, but for other organisms as well.

Thermal adaptation of cellular membranes in natural populations of Drosophila melanogaster

Changes in temperature disrupt the fluidity of cellular membranes, which can negatively impact membrane integrity and cellular processes. Many ectotherms, including Drosophila melanogaster (Meigen), adjust the glycerophospholipid composition of their membranes to restore optimal fluidity when temperatures change, a type of trait plasticity termed homeoviscous adaptation.Existing data suggest that plasticity in the relative abundances of the glycerophospholipids phosphatidylethanolamine (PE) and phosphatidylcholine (PC) underlies cellular adaptation to temporal variability in the thermal environment. For example, laboratory populations of D. melanogaster evolved in the presence of temporally variable temperatures have greater developmental plasticity of the ratio of PE to PC (PE/PC) and greater fecundity than do populations evolved at constant temperatures.Here, we extend this work to natural populations of D. melanogaster by evaluating thermal plasticity of glycerophospholipid composition at different life stages, in genotypes isolated from Vermont, Indiana and North Carolina, USA. We also quantify the covariance between developmental and adult (reversible) plasticity, and between adult responses of the membrane to cool and warm thermal shifts.As predicted by physiological models of homeoviscous adaptation, flies from all populations decrease PE/PC and the degree of lipid unsaturation in response to warm temperatures. Furthermore, these populations have diverged in their degree of membrane plasticity. Flies from the most variable thermal environment (Vermont, USA) decrease PE/PC to a greater extent than do other populations when developed at a warm temperature, a pattern that matches our previous observation in laboratory-evolved populations. We also find that developmental plasticity and adult plasticity of PE/PC covary across genotypes, but that adult responses to cool and warm thermal shifts do not.When combined with our previous observations of laboratory-evolved populations, our findings implicate developmental plasticity of PE/PC as a mechanism of thermal adaptation in temporally variable environments. While little is known about the genetic bases of plastic responses to temperature, our observations suggest that both environmentally sensitive and environmentally specific alleles contribute to thermal adaptation of membranes, and that costs of plasticity may arise when the adult environment differs from that experienced during development.

Heritability and inter-population differences in lipid profiles of Drosophila melanogaster

Characterizing and understanding the complex spectrum of lipids in higher organisms lags far behind our analysis of genome and transcriptome sequences. Here we generate and evaluate comprehensive lipid profiles (>200 lipids) of 92 inbred lines from five different Drosophila melanogaster populations. We find that the majority of lipid species are highly heritable, and even lipids with odd-chain fatty acids, which cannot be generated by the fly itself, also have high heritabilities. Abundance of the endosymbiont Wolbachia, a potential provider of odd-chained lipids, was positively correlated with this group of lipids. Additionally, we show that despite years of laboratory rearing on the same medium, the lipid profiles of the five geographic populations are sufficiently distinct for population discrimination. Our data predicts a strikingly different membrane fluidity for flies from the Netherlands, which is supported by their increased ethanol tolerance. We find that 18% of lipids show strong concentration differences between males and females. Through an analysis of the correlation structure of the lipid classes, we find modules of co-regulated lipids and begin to associate these with metabolic constraints. Our data provide a foundation for developing associations between variation in lipid composition with variation in other metabolic attributes, with genome-wide variation, and with metrics of health and overall reproductive fitness.

Profiling and quantification of Drosophila melanogaster lipids using liquid chromatography/mass spectrometry

We present here the findings of global profiling of Drosophila lipids using liquid chromatography/tandem mass spectrometry (LC/MS/MS) on an LTQ-Orbitrap instrument. In addition, we present a multiple reaction monitoring (LC-MRM) method for the absolute quantification of the major phosphatidylethanolamine (PE) and phosphatidylcholine (PC) lipids of Drosophila. Using both normal- and reversed-phase LC followed by accurate mass analysis and MS/MS on an LTQ-Orbitrap instrument, we evaluated the lipid composition of the fruit fly Drosophila melanogaster. A total of 74 lipid species were identified consisting of glycerphospholipids belonging to the PE, PC, phosphatidylglycerol (PG), phosphatidylinositol (PI) and phosphatidylserine (PS) classes including several plasmanyl PE species, as well as triacylglycerides, cardiolipins, ceramides, and PE ceramides. Individual PE and PC phospholipids were then quantified using an LC-MRM approach. Reversed-phase chromatography followed by monitoring on a QTrap 4000 instrument of 21 MRM transitions combined with calibration curves constructed using internal standards enabled the absolute quantification of 28 PE and PC lipid species with limits of quantification of 3 and 5 pg/μL, respectively. Internal standards accounted for the differences in ionization efficiencies of PE and PC phospholipids, facilitating more accurate lipid abundance measurements. The method presented here builds on previous Drosophila work by making the quantification of absolute lipid abundance possible and will be of interest to scientists who study variation and changes in the degree of unsaturation, fatty acid carbon length, and head-group concentration among individuals of different genotypes in response to environmental, genetic, or physiological perturbation in small insects. It will also be particularly useful to biologists interested in adaptation and acclimation of cellular membranes in response to thermal heterogeneity.

Drug resistance marker-aided genome shuffling to improve acetic acid tolerance in Saccharomyces cerevisiae

Acetic acid existing in a culture medium is one of the most limiting constraints in yeast growth and viability during ethanol fermentation. To improve acetic acid tolerance in Saccharomyces cerevisiae strains, a drug resistance marker-aided genome shuffling approach with higher screen efficiency of shuffled mutants was developed in this work. Through two rounds of genome shuffling of ultraviolet mutants derived from the original strain 308, we obtained a shuffled strain YZ2, which shows significantly faster growth and higher cell viability under acetic acid stress. Ethanol production of YZ2 (within 60 h) was 21.6% higher than that of 308 when 0.5% (v/v) acetic acid was added to fermentation medium. Membrane integrity, higher in vivo activity of the H+-ATPase, and lower oxidative damage after acetic acid treatment are the possible reasons for the acetic acid-tolerance phenotype of YZ2. These results indicated that this novel genome shuffling approach is powerful to rapidly improve the complex traits of industrial yeast strains.

Ethanol-regulated genes that contribute to ethanol sensitivity and rapid tolerance in Drosophila

BACKGROUND

Increased ethanol intake, a major predictor for the development of alcohol use disorders, is facilitated by the development of tolerance to both the aversive and pleasurable effects of the drug. The molecular mechanisms underlying ethanol tolerance development are complex and are not yet well understood.

METHODS

To identify genetic mechanisms that contribute to ethanol tolerance, we examined the time course of gene expression changes elicited by a single sedating dose of ethanol in Drosophila, and completed a behavioral survey of strains harboring mutations in ethanol-regulated genes.

RESULTS

Enrichment for genes in metabolism, nucleic acid binding, olfaction, regulation of signal transduction, and stress suggests that these biological processes are coordinately affected by ethanol exposure. We also detected a coordinate up-regulation of genes in the Toll and Imd innate immunity signal transduction pathways. A multi-study comparison revealed a small set of genes showing similar regulation, including increased expression of 3 genes for serine biosynthesis. A survey of Drosophila strains harboring mutations in ethanol-regulated genes for ethanol sensitivity and tolerance phenotypes revealed roles for serine biosynthesis, olfaction, transcriptional regulation, immunity, and metabolism. Flies harboring deletions of the genes encoding the olfactory co-receptor Or83b or the sirtuin Sir2 showed marked changes in the development of ethanol tolerance.

CONCLUSIONS

Our findings implicate novel roles for these genes in regulating ethanol behavioral responses.

The effect of environmental temperature on olfactory perception in Drosophila melanogaster

Olfaction provides chemical information to an animal about its environment. When environmental conditions change, individuals should be able to adequately maintain function. Temperature may influence olfaction in a double manner, as it modifies the concentrations of gaseous compounds and affects biological processes. Here, we address acclimatization to environmental temperature in the olfactory system of Drosophila melanogaster using heat and cold treatments. Because the consequences of temperature shifts persist for some time after the treatment's end, comparison of olfactory behaviors at the same temperature in treated and untreated flies allows us to infer the biological effects of temperature in olfaction. At intermediate odorant concentrations heat always generates a reduction of olfactory sensitivity, as they would be expected to compensate for the increase of volatiles in the air. Cold produces the opposite effect. These changes are observed in both sexes and in natural populations as well as in standard laboratory stocks. Short applications suffice to cause detectable olfactory perception changes, but even prolonged temperature treatments have only a transitory effect. Together, these results suggest that olfaction in Drosophila underlies acclimatization to environmental temperature. However, sensitivity changes are not immediate and may cause imperfect adjustment of olfactory function for short time periods.

Direct evidence that genetic variation in glycerol-3-phosphate and malate dehydrogenase genes (Gpdh and Mdh1) affects adult ethanol tolerance in Drosophila melanogaster

Many studies of alcohol adaptation in Drosophila melanogaster have focused on the Adh polymorphism, yet the metabolic elimination of alcohol should involve many enzymes and pathways. Here we evaluate the effects of glycerol-3-phosphate dehydrogenase (Gpdh) and cytosolic malate dehydrogenase (Mdh1) genotype activity on adult tolerance to ethanol. We have created a set of P-element-excision-derived Gpdh, Mdh1, and Adh alleles that generate a range of activity phenotypes from full to zero activity. Comparisons of paired Gpdh genotypes possessing 10 and 60% normal activity and 66 and 100% normal activity show significant effects where higher activity increases tolerance. Mdh1 null allele homozygotes show reductions in tolerance. We use piggyBac FLP-FRT site-specific recombination to create deletions and duplications of Gpdh. Duplications show an increase of 50% in activity and an increase of adult tolerance to ethanol exposure. These studies show that the molecular polymorphism associated with GPDH activity could be maintained in natural populations by selection related to adaptation to alcohols. Finally, we examine the interactions between activity genotypes for Gpdh, Mdh1, and Adh. We find no significant interlocus interactions. Observations on Mdh1 in both Gpdh and Adh backgrounds demonstrate significant increases in ethanol tolerance with partial reductions (50%) in cytosolic MDH activity. This observation strongly suggests the operation of pyruvate-malate and, in particular, pyruvate-citrate cycling in adaptation to alcohol exposure. We propose that an understanding of the evolution of tolerance to alcohols will require a system-level approach, rather than a focus on single enzymes.

Intoxicated fly brains: neurons mediating ethanol-induced behaviors

In free nature, animals rarely become alcoholics. Only when humans interfere do they develop some aspects of dependence. In humans, it is thought that 40-60% of the risk to become an alcoholic is influenced by genetic factors. The interplay between the genetic predisposition and the environment is thought to promote addictive behaviors to ethanol (Schuckit, 2000). Animal models are widely used to functionally dissect behaviors that are associated with alcohol dependence and to characterize the related ethanol responsive genes (Lovinger & Crabbe, 2005). Thus, brain regions and neurons have been identified that mediate ethanol-induced behaviors (Rothenfluh & Heberlein, 2002). This review aims to give an overview of ethanol-induced behaviors and the correlating neurons/neuronal structures in Drosophila melanogaster mediating these behaviors and discusses the possible significance of these results.

Phenotypic and transcriptional response to selection for alcohol sensitivity in Drosophila melanogaster

Gene-expression profiling combined with selection for genetically divergent Drosophila lines either highly sensitive or resistant to ethanol exposure has been used to identify candidate genes that affect alcohol sensitivity, including 23 novel genes that have human orthologs.

Background

Alcoholism is a complex disorder determined by interactions between genetic and environmental risk factors. Drosophila represents a powerful model system to dissect the genetic architecture of alcohol sensitivity, as large numbers of flies can readily be reared in defined genetic backgrounds and under controlled environmental conditions. Furthermore, flies exposed to ethanol undergo physiological and behavioral changes that resemble human alcohol intoxication, including loss of postural control, sedation, and development of tolerance.

Results

We performed artificial selection for alcohol sensitivity for 35 generations and created duplicate selection lines that are either highly sensitive or resistant to ethanol exposure along with unselected control lines. We used whole genome expression analysis to identify 1,678 probe sets with different expression levels between the divergent lines, pooled across replicates, at a false discovery rate of q < 0.001. We assessed to what extent genes with altered transcriptional regulation might be causally associated with ethanol sensitivity by measuring alcohol sensitivity of 37 co-isogenic P-element insertional mutations in 35 candidate genes, and found that 32 of these mutants differed in sensitivity to ethanol exposure from their co-isogenic controls. Furthermore, 23 of these novel genes have human orthologues.

Conclusion

Combining whole genome expression profiling with selection for genetically divergent lines is an effective approach for identifying candidate genes that affect complex traits, such as alcohol sensitivity. Because of evolutionary conservation of function, it is likely that human orthologues of genes affecting alcohol sensitivity in Drosophila may contribute to alcohol-associated phenotypes in humans.

Inducible and constitutive heat shock gene expression responds to modification of Hsp70 copy number in Drosophila melanogaster but does not compensate for loss of thermotolerance in Hsp70 null flies

Background

The heat shock protein Hsp70 promotes inducible thermotolerance in nearly every organism examined to date. Hsp70 interacts with a network of other stress-response proteins, and dissecting the relative roles of these interactions in causing thermotolerance remains difficult. Here we examine the effect of Hsp70 gene copy number modification on thermotolerance and the expression of multiple stress-response genes in Drosophila melanogaster, to determine which genes may represent mechanisms of stress tolerance independent of Hsp70.

Results

Hsp70 copy number in four strains is positively associated with Hsp70 expression and inducible thermotolerance of severe heat shock. When assayed at carefully chosen temperatures, Hsp70 null flies are almost entirely deficient in thermotolerance. In contrast to expectations, increasing Hsp70 expression levels induced by thermal pretreatment are associated with increasing levels of seven other inducible Hsps across strains. In addition, complete Hsp70 loss causes upregulation of the inducible Hsps and six constitutive stress-response genes following severe heat shocks.

Conclusion

Modification of Hsp70 copy number quantitatively and qualitatively affects the expression of multiple other stress-response genes. A positive association between absolute expression levels of Hsp70 and other Hsps after thermal pretreatment suggests novel regulatory mechanisms. Severe heat shocks induce both novel gene expression patterns and almost total mortality in the Hsp70 null strain: alteration of gene expression in this strain does not compensate for Hsp70 loss but suggests candidates for overexpression studies.

A worldwide polymorphism in aldehyde dehydrogenase in Drosophila melanogaster: evidence for selection mediated by dietary ethanol

Clinally varying traits in Drosophila melanogaster provide good opportunities for elucidating the genetic basis of adaptation. Resistance to ethanol, a natural component of D. melanogaster's breeding sites, increases with latitude on multiple continents, indicating that the trait is under selection. Although the well-studied Alcohol dehydrogenase (Adh) polymorphism makes a contribution to the clines, it accounts for only a small proportion of the phenotypic variation. We describe an amino acid replacement polymorphism in Aldehyde dehydrogenase (Aldh), the gene encoding the second enzyme in the ethanol degradation pathway, that shows hallmarks of also contributing to the clines. The derived Aldh allele, like the Adh-Fast allele, increases in frequency in laboratory populations selected for ethanol resistance, and increases in frequency with latitude in wild populations. Moreover, strains with the derived allele have significantly higher ALDH enzyme activity with acetaldehyde (the breakdown product of ethanol) as a substrate than strains with the ancestral allele. As is the case with the Adh-Fast allele, chromosomes with the derived Aldh allele show markedly reduced molecular variation in the vicinity of the replacement polymorphism compared to those with the ancestral allele, suggesting a single, relatively recent origin. Nonetheless, the Aldh polymorphism differs from the Adh polymorphism in that the ethanol-associated allele remains in relatively low frequency in most populations. We present evidence that this is likely to be the result of a trade-off in catalytic activity, with the advantage of the derived allele in acetaldehyde detoxification being offset by a disadvantage in detoxification of other aldehydes.

Genotoxicity of three mouthwash products, Cepacol, Periogard, and Plax, in the Drosophila wing-spot test

Antiseptic mouthwashes used in biofilm control are widely available in the marketplace, despite inconsistent data concerning their genetic and cellular toxicity. In the present study, we investigated the genotoxic potential of three antiseptics currently used for odontologic treatment, Cepacol (containing cetylpyridinium chloride), Periogard (chlorhexidine digluconate), and Plax (triclosan). Genotoxicity was evaluated using the Somatic Mutation and Recombination Test (SMART) in Drosophila melanogaster, employing flies having normal bioactivation (the standard cross) and flies with increased cytochrome P450-dependent biotransformation capacity (the high bioactivation cross). Periogard and Plax produced negative responses in both types of flies; however, Cepacol (75 and 100%) produced positive responses in both the standard and high bioactivation assays, with the genotoxic responses mainly due to the induction of mitotic recombination. Assays performed with ethanol and cetylpirydinium chloride, two major ingredients of Cepacol, indicated that the genotoxicity of the mouthwash is likely to be due to ethanol.