Cold adaptation shapes the robustness of metabolic networks in Drosophila melanogaster

Effects of duration and type of cold acclimation on the subsequent cold tolerance of a tenebrionid beetle

The effects of cold acclimation on the subsequent survival and recovery of cold-exposed adults of Alphitobius diaperinus (Coleoptera: Tenebrionidae) was examined. Acclimation conditions were: 1, 2, 4 and 8 days at 5, 10, 15, 25 °C and fluctuating temperatures of 5-10-15 °C (8:8:8 h). Acute and chronic cold stresses were induced by keeping beetles at -8 °C for 8 h and 0 °C for 2, 3, 4, 5 and 6 days respectively. Survival was recorded after 5 days of recovery at 25 °C. The insects acclimated to 5, 10, 15 and 25 °C for 1 and 4 days were selected for metabolic response studies which was performed by gas chromatography-mass spectrophotometry (GC-MS). Beetles acclimated at 25 °C (control) and beetles acclimated at 5 °C for 1 or 8 days did not survive after acute cold stress. Survival increased to 100 % after acute cold stress in beetles acclimated to fluctuating temperatures for 2 days. The lethal times for 50 % of the population (Lt50) were calculated for beetles after chronic cold stress and range from 4.89 days in beetles acclimated to fluctuating temperatures for 4 days-0.018 days in beetles acclimated to 5 °C for 8 days. The metabolic profile analysis showed that proline exhibited the highest concentration in all experimental groups. Increases of alanine and glycine in cold acclimated beetles were observed. Glutamic acid had opposite pattern and decreased significantly in acclimated beetles at 5 °C for 4 days. Alanine accumulation and glutamic acid decrease suggest that alanine has derived from transamination of glutamic acid and pyruvate. Erythritol, sorbitol, arabitol, adonitol, xylitol, glucose and maltose were the polyols and sugars that have been accumulated in cold acclimated beetles especially at 5 °C. Mannose has only accumulated in 1d acclimated beetles.

Metabolomic signatures associated with cold adaptation and seasonal acclimation of Drosophila: profiling of 43 species

Cold tolerance is a key determinant of poleward colonization in insects. However, the physiological basis underlying interspecific differences in cold tolerance is not fully understood. Here, we analyzed cold tolerance and metabolomic profiles in warm- and cold-acclimated phenotypes of 43 Drosophila species representing a latitudinal gradient from the tropics to the boreal zone. We found a strong positive correlation between cold tolerance and climatic variables associated with habitat seasonality and temperature. Including the effects of cold acclimation, we found most species have similar 'safety margins', measured as the difference between the average environmental temperature and the lower lethal temperature. Searching for metabolomic signatures of cold tolerance, we found that the warm-acclimated flies of cold-hardy species had moderately but significantly higher constitutive signals of putative cryoprotectants such as trehalose, glucose, glycerol and mannitol/sorbitol. Cold acclimation (and the transition to a winter dormant phenotype) resulted in a strong accumulation of myo-inositol, which occurred only in species of the virilis group. Other temperate and boreal species either showed only moderate, idiosyncratic accumulations of sugars/polyols and free amino acids, or did not accumulate any 'classical' cryoprotectant at all. Thus, our results suggest that the colonization of boreal regions by Drosophila does not necessarily depend on the seasonal accumulation of classical cryoprotectants. In contrast, virtually all cold-acclimated species showed a significant increase in products of phospholipid catabolism, suggesting that remodeling of biological membranes is a clear and ubiquitous signature of cold acclimation in Drosophila.

Metabolomes of bumble bees reared in common garden conditions suggest constitutive differences in energy and toxin metabolism across populations

Cold tolerance of ectotherms can vary strikingly among species and populations. Variation in cold tolerance can reflect differences in genomes and transcriptomes that confer cellular-level protection from cold; additionally, shifts in protein function and abundance can be altered by other cellular constituents as cold-exposed insects often have shifts in their metabolomes. Even without a cold challenge, insects from different populations may vary in cellular composition that could alter cold tolerance, but investigations of constitutive differences in metabolomes across wild populations remain rare. To address this gap, we reared Bombus vosnesenskii queens collected from Oregon and California (USA) that differ in cold tolerance (CTmin = -6 °C and 0 °C, respectively) in common garden conditions, and measured offspring metabolomes using untargeted LC-MS/MS. Oregon bees had higher levels of metabolites associated with carbohydrate (sorbitol, lactitol, maltitol, and sorbitol-6-phosphate) and amino acid (hydroxyproline, ornithine, and histamine) metabolism. Exogenous metabolites, likely derived from the diet, also varied between Oregon and California bees, suggesting population-level differences in toxin metabolism. Overall, our results reveal constitutive differences in metabolomes for bumble bees reared in common garden conditions from queens collected in different locations despite no previous cold exposure.

The Impact of Climate on the Energetics of Overwintering Paper Wasp Gynes (Polistes dominula and Polistes gallicus)

Gynes of paper wasps (Polistes sp.) spend the cold season in sheltered hibernacles. These hibernacles protect against predators and adverse weather conditions but offer only limited protection against low temperatures. During overwintering diapause, wasps live on the energy they store. We investigated the hibernacles' microclimate conditions of species from the Mediterranean (Italy, P. dominula, P. gallicus) and temperate (Austria, P. dominula) climates in order to describe the environmental conditions and calculate the energetic demand of overwintering according to standard metabolic rate functions. The temperatures at the hibernacles differed significantly between the Mediterranean and temperate habitats (average in Austria: 3.2 ± 5.71 °C, in Italy: 8.5 ± 5.29 °C). In both habitats, the hibernacle temperatures showed variance, but the mean hibernacle temperature corresponded closely to the meteorological climate data. Cumulative mass-specific energetic costs over the studied period were the lowest for the temperate P. dominula population compared with both Mediterranean species. The lower costs of the temperate species were a result of the lower hibernacle temperature and acclimation to lower environmental temperatures. Model calculations with an increased mean temperature of up to 3 °C due to climate change indicate a dramatic increase of up to 40% in additional costs.

Evolutionary Adaptation of Protein Turnover in White Muscle of Stenothermal Antarctic Fish: Elevated Cold Compensation at Reduced Thermal Responsiveness

Protein turnover is highly energy consuming and overall relates to an organism's growth performance varying largely between species, e.g., due to pre-adaptation to environmental characteristics such as temperature. Here, we determined protein synthesis rates and capacity of protein degradation in white muscle of the cold stenothermal Antarctic eelpout (Pachycara brachycephalum) and its closely related temperate counterpart, the eurythermal common eelpout (Zoarces viviparus). Both species were exposed to acute warming (P. brachycephalum, 0 °C + 2 °C day-1; Z. viviparus, 4 °C + 3 °C day-1). The in vivo protein synthesis rate (Ks) was monitored after injection of 13C-phenylalanine, and protein degradation capacity was quantified by measuring the activity of cathepsin D in vitro. Untargeted metabolic profiling by nuclear magnetic resonance (NMR) spectroscopy was used to identify the metabolic processes involved. Independent of temperature, the protein synthesis rate was higher in P. brachycephalum (Ks = 0.38-0.614 % day-1) than in Z. viviparus (Ks= 0.148-0.379% day-1). Whereas protein synthesis remained unaffected by temperature in the Antarctic species, protein synthesis in Z. viviparus increased to near the thermal optimum (16 °C) and tended to fall at higher temperatures. Most strikingly, capacities for protein degradation were about ten times higher in the Antarctic compared to the temperate species. These differences are mirrored in the metabolic profiles, with significantly higher levels of complex and essential amino acids in the free cytosolic pool of the Antarctic congener. Together, the results clearly indicate a highly cold-compensated protein turnover in the Antarctic eelpout compared to its temperate confamilial. Constant versus variable environments are mirrored in rigid versus plastic functional responses of the protein synthesis machinery.

Metabolomics as a tool to elucidate biochemical cold adaptation in insects

Metabolomics is an incredibly valuable tool in helping understand insect responses to cold. It not only characterizes how low temperature disrupts metabolic homeostasis, but also how it triggers fundamental adaptive responses, for example, homeoviscous adaptation and cryoprotectant accumulation. This review outlines the advantages and disadvantages of different metabolomic technologies (nuclear magnetic resonance- versus mass spectrometry-based) and screening approaches (targeted versus untargeted). We emphasize the importance of time-series and tissue-specific data, as well as the challenges of disentangling insect versus microbiome responses. In addition, we set out the need to move beyond simple correlations between metabolite abundance and tolerance phenotypes by undertaking functional assessments, for example, using dietary supplementation or injections. We highlight studies at the vanguard of employing these approaches, and where key knowledge gaps remain.

Clinal variation as a tool to understand climate change

Clines are observable gradients that reflect continuous change in biological traits of species across geographical ranges. Clinal gradients could vary at geographic scales (latitude and altitude). Since clinal variations represent active genomic responses at the population level they (clines) provide an immense power to address questions related to climatic change. With the fast pace of climate change i.e. warming, populations are also likely to exhibit rapid responses; at both the phenotypic and genotypic levels. We seek to understand how clinal variation could be used to anticipate climatic responses using Drosophila, a pervasively used inter-disciplinary model system owing to its molecular repertoire. The genomic information coupled with the phenotypic variation greatly facilitates our understanding of the Drosophilidae response to climate change. We discuss traits associated with clinal variation at the phenotypic level as well as their underlying genetic regulators. Given prevailing climatic conditions and future projections for climate change, clines could emerge as monitoring tools to track the cross-talk between climatic variables and organisms.

Intestinal Flora-Derived Kynurenic Acid Protects Against Intestinal Damage Caused by Candida albicans Infection via Activation of Aryl Hydrocarbon Receptor

Colonization of the intestinal tract by Candida albicans (C. albicans) can lead to invasive candidiasis. Therefore, a functional intestinal epithelial barrier is critical for protecting against invasive C. albicans infections. We collected fecal samples from patients with Candida albicans bloodstream infection and healthy people. Through intestinal flora 16sRNA sequencing and intestinal metabolomic analysis, we found that C. albicans infection resulted in a significant decrease in the expression of the metabolite kynurenic acid (KynA). We used a repeated C. albicans intestinal infection mouse model, established following intake of 3% dextran sulfate sodium salt (DSS) for 9 days, and found that KynA, a tryptophan metabolite, inhibited inflammation, promoted expression of intestinal tight junction proteins, and protected from intestinal barrier damage caused by invasive Candida infections. We also demonstrated that KynA activated aryl hydrocarbon receptor (AHR) repressor in vivo and in vitro. Using Caco-2 cells co-cultured with C. albicans, we showed that KynA activated AHR, inhibited the myosin light chain kinase-phospho-myosin light chain (MLCK-pMLC) signaling pathway, and promoted tristetraprolin (TTP) expression to alleviate intestinal inflammation. Our findings suggest that the metabolite KynA which is differently expressed in patients with C. albicans infection and has a protective effect on the intestinal epithelium, via activating AHR, could be explored to provide new potential therapeutic strategies for invasive C. albicans infections.

Adaptive changes in energy reserves and effects of body melanization on thermal tolerance in Drosophila simulans

Seasonally polyphenic types have been documented in many Drosophilids, which differ significantly during thermal stress. Although Drosophila simulans is a sibling species to Drosophila melanogaster, both thrive in the temperate and tropical climates, but various climatic factors are expected to impact their distribution and abundance. As a result, D. simulans may use phenotypic plasticity to adapt to colder and drier circumstances in temperate zones, although such studies are less known. In the present study, our main aim was to find a link between adaptive plasticity and thermal tolerance in D. simulans. We characterized two morphs in D. simulans flies based on the abdominal melanization collected from the same locality and season, as this trait is highly associated with the larval developmental conditions. Our results suggested that flies reared from dark and light morph showed significant differences in the basal level of proline, carbohydrates (trehalose, glycogen), and lipids (cuticular lipids and total body lipids) within simulated seasons and morph lineages in D. simulans flies. We further showed that D. simulans reared from dark morph are better adapted to cold conditions, whereas light flies are more adapted to warm conditions. The flies, both from light and dark morph lineages, when reared at 15 °C, showed an increase in the level of total body lipids after acclimation at 0 °C but a decrease in the level of proline and carbohydrates (trehalose, glycogen). Heat acclimation increases glycogen levels in the flies from light morph lineage while decreases trehalose and proline.

Linking body condition and thermal physiology in limping crickets: Does limb autotomy incur costs concerning behavioral thermal tolerance?

Many ectotherms have the ability to voluntarily detach a body part, known as autotomy, usually in response to predator attacks. Autotomy can have an immediate benefit for survival, but it can also involve costs related to the individual's body condition. Even though the effects of autotomy have been studied in many ecophysiological aspects, its short-term costs on the ability to tolerate high environmental temperatures are still unexplored. Herein, we evaluated the effects of autotomy on the behavioral thermal tolerance (VT_Max ) in the cricket Gryllus assimilis. We hypothesized that, due to the increased energetic costs to maintain homeostasis, autotomized crickets have a lower VT_Max than intact ones. Additionally, we investigated differences in VT_Max between sexes, as well as the effects of heating rates and body mass on their VT_Max . Contrary to our hypothesis, we found no differences between VT_Max of autotomized and intact individuals. However, we observed that females have a higher VT_Max than males, regardless of their condition (i.e., autotomized and intact). Moreover, we detected significant effects of body mass and heating rate on behavioral thermal tolerances. The results of our study indicate that costs associated with limb autotomy at high environmental temperatures might be intricate and not immediately impactful. Furthermore, important aspects of reproduction and ecology might be responsible for differences in VT_Max between males and females. Our results contribute to understanding the ecological and physiological aspects of ectotherms and how they respond to changing climatic conditions.

Exercise and/or Cold Exposure Alters the Gene Expression Profile in the Fat Body and Changes the Heart Function in Drosophila

The major reason of human morbidity and mortality is obesity and related diseases. Brown adipose tissue (BAT) is associated with low total adipose tissue content and a lower risk of type 2 diabetes mellitus. Studies have shown that exercise and cold expose may induce browning. In this study, we verified (1) whether exercise and/or cold exposure can improve the expression level of ucp4c, serca, ampkα, camkII, sirt1, octβ3r, and hamlet; (2) if these interventions can save cardiac dysfunction induced by a high-fat diet (HFD) in Drosophila. w1118 (wild-type) virgin female flies collected within 8 h after eclosion were divided into eight groups: the normal feed control group (NFD-C), the normal feed exercise group (NFD-E), the normal feed cold exposure group (NFD-CA), the normal feed exercise/cold exposure group (NFD-EC), the HFD control group (HFD-C), the HFD exercise group (HFD-E), the HFD cold exposure group (HFD-CA), and the HFD exercise/cold exposure group (HFD-EC). After exercise and/or cold exposure for 7 days, the mRNA expression levels of ucp4c, serca, ampkα, camk II, sirt1, octβ3r, and hamlet were tested by qRT-PCR, and m-mode was used to assess cardiac function. In addition, we assessed the triacylglycerol (TAG) levels, motor ability, fat mass (by Oil Red O [ORO] staining), and morphological features. The results of TAG, ORO staining, and morphological features all indicate that after interventions, body size of Drosophila was smaller compared with the control group, irrespective of the feeding patterns. The mRNA expression levels of ucp4c, serca, octβ3r, hamlet, ampkα, camkII, and sirt1 were changed to varying degrees under different intervention states (exercise and/or cold exposure). Cold exposure and exercise/cold exposure partly improved cardiac function and the normal fruit flies' cardiac function and exercise ability. However, after exercise intervention, exercise ability and heart function were improved in both HFD and normal-fat diet (NFD) fruit flies. In conclusion, different intervention states (exercise and/or cold exposure) can change the mRNA expression levels of ucp4c, serca, octβ3r, hamlet, ampkα, camkII, and sirt1. Exercise is the most effective way to restore HFD-induced cardiac dysfunction.

Local thermal environment and warming influence supercooling and drive widespread shifts in the metabolome of diapausing Pieris rapae butterflies

Global climate change has the potential to negatively impact biological systems as organisms are exposed to novel temperature regimes. Increases in annual mean temperature have been accompanied by disproportionate rates of change in temperature across seasons, and winter is the season warming most rapidly. Yet, we know relatively little about how warming will alter the physiology of overwintering organisms. Here, we simulated future warming conditions by comparing diapausing Pieris rapae butterfly pupae collected from disparate thermal environments and by exposing P. rapae pupae to acute and chronic increases in temperature. First, we compared internal freezing temperatures (supercooling points) of diapausing pupae that were developed in common-garden conditions but whose parents were collected from northern Vermont, USA, or North Carolina, USA. Matching the warmer winter climate of North Carolina, North Carolina pupae had significantly higher supercooling points than Vermont pupae. Next, we measured the effects of acute and chronic warming exposure in Vermont pupae and found that warming induced higher supercooling points. We further characterized the effects of chronic warming by profiling the metabolomes of Vermont pupae via untargeted LC-MS metabolomics. Warming caused significant changes in abundance of hundreds of metabolites across the metabolome. Notably, there were warming-induced shifts in key biochemical pathways, such as pyruvate metabolism, fructose and mannose metabolism, and β-alanine metabolism, suggesting shifts in energy metabolism and cryoprotection. These results suggest that warming affects various aspects of overwintering physiology in P. rapae and may be detrimental depending on the frequency and variation of winter warming events. Further research is needed to ascertain the extent to which the effects of warming are felt among a broader set of populations of P. rapae, and among other species, in order to better predict how insects may respond to changes in winter thermal environments.

Complementary Nuclear Magnetic Resonance-Based Metabolomics Approaches for Glioma Biomarker Identification in a Drosophila melanogaster Model

Human malignant gliomas are the most common type of primary brain tumor. Composed of glial cells and their precursors, they are aggressive and highly invasive, leading to a poor prognosis. Due to the difficulty of surgically removing tumors and their resistance to treatments, novel therapeutic approaches are needed to improve patient life expectancy and comfort. Drosophila melanogaster is a compelling genetic model to better understanding human neurological diseases owing to its high conservation in signaling pathways and cellular content of the brain. Here, glioma has been induced in Drosophila by co-activating the epidermal growth factor receptor and the phosphatidyl-inositol-3 kinase signaling pathways. Complementary nuclear magnetic resonance (NMR) techniques were used to obtain metabolic profiles in the third instar larvae brains. Fresh organs were directly studied by ¹H high resolution-magic angle spinning (HR-MAS) NMR, and brain extracts were analyzed by solution-state ¹H-NMR. Statistical analyses revealed differential metabolic signatures, impacted metabolic pathways, and glioma biomarkers. Each method was efficient to determine biomarkers. The highlighted metabolites including glucose, myo-inositol, sarcosine, glycine, alanine, and pyruvate for solution-state NMR and proline, myo-inositol, acetate, and glucose for HR-MAS show very good performances in discriminating samples according to their nature with data mining based on receiver operating characteristic curves. Combining results allows for a more complete view of induced disturbances and opens the possibility of deciphering the biochemical mechanisms of these tumors. The identified biomarkers provide a means to rebalance specific pathways through targeted metabolic therapy and to study the effects of pharmacological treatments using Drosophila as a model organism.

Sestrin regulates acute chill coma recovery in Drosophila melanogaster

When chill-susceptible insects are exposed to low temperatures they enter a temporary state of paralysis referred to as a chill coma. The most well-studied physiological mechanism of chill coma onset and recovery involves regulation of ion homeostasis. Previous studies show that changes in metabolism may also underlie the ability to recovery quickly, but the roles of genes that regulate metabolic homeostasis in chill coma recovery time (CCRT) are not well understood. Here, we investigate the roles of Sestrin and Spargel (Drosophila homolog of PGC-1α), which are involved in metabolic homeostasis and substrate oxidation, on CCRT in Drosophila melanogaster. We find that sestrin and spargel mutants have impaired CCRT. sestrin is required in the muscle and nervous system tissue for normal CCRT and spargel is required in muscle and adipose. On the basis that exercise induces sestrin and spargel, we also test the interaction of cold and exercise. We find that pre-treatment with one of these stressors does not consistently confer acute protection against the other. We conclude that Sestrin and Spargel are important in the chill coma response, independent of their role in exercise.

Divergent metabolomic profiles of cold-exposed mature and immature females of tropical versus temperate Drosophila species

Temperate species, contrary to their tropical counterparts, are exposed not only to thermally variable environments with low temperatures but also to long winters. Different selective pressures may have driven divergent physiological adaptations in closely related species with different biogeographic origins. To survive unfavourable winter conditions, Drosophila species in temperate areas generally undergo a period of reproductive dormancy, associated with a cold-induced cessation of oogenesis and metabolic reorganization. This work aims to compare cold tolerance and metabolic signatures of cold-exposed females exhibiting different reproductive maturity status (mature and immature females) of four Drosophila species from tropical vs. temperate origins. We expected that the capacity for delayed reproduction of immature females could result in the redirection of the energy-related metabolites to be utilized for surviving the cold season. To do so, we studied an array of 45 metabolites using quantitative target GC-MS profiling. Reproductively immature females of temperate species showed the lower CT_min and the faster chill coma recovery time (i.e. the most cold-tolerant group). Principal component analysis captured differences across species, but also between reproductive maturity states. Notably, temperate species exhibited significantly higher levels of glucose, alanine, and gluconolactone than tropical ones. As proline and glycerol showed higher abundances in immature females of temperate species compared to the levels exhibited by the rest of the groups, we reasoned that glucose and alanine could serve as intermediates in the synthesis of these compatible solutes. All in all, our findings suggest that cold-exposed females of temperate species accumulate energy-related and protective metabolites (e.g. glycerol and proline) while delaying reproduction, and that these metabolites are relevant to cold tolerance even at modest concentrations.

Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster

While several studies in a diverse set of species have shed light on the genes underlying adaptation, our knowledge on the selective pressures that explain the observed patterns lags behind. Drosophila melanogaster is a valuable organism to study environmental adaptation because this species originated in Southern Africa and has recently expanded worldwide, and also because it has a functionally well-annotated genome. In this study, we aimed to decipher which environmental variables are relevant for adaptation of D. melanogaster natural populations in Europe and North America. We analysed 36 whole-genome pool-seq samples of D. melanogaster natural populations collected in 20 European and 11 North American locations. We used the BayPass software to identify single nucleotide polymorphisms (SNPs) and transposable elements (TEs) showing signature of adaptive differentiation across populations, as well as significant associations with 59 environmental variables related to temperature, rainfall, evaporation, solar radiation, wind, daylight hours, and soil type. We found that in addition to temperature and rainfall, wind related variables are also relevant for D. melanogaster environmental adaptation. Interestingly, 23%-51% of the genes that showed significant associations with environmental variables were not found overly differentiated across populations. In addition to SNPs, we also identified 10 reference transposable element insertions associated with environmental variables. Our results showed that genome-environment association analysis can identify adaptive genetic variants that are undetected by population differentiation analysis while also allowing the identification of candidate environmental drivers of adaptation.

Reproduction stage specific dysregulation of Daphnia magna metabolites as an early indicator of reproductive endocrine disruption

Rapid biomolecular observation in model indicator organisms has been considered as a potential predictor of water pollution from chronic and trace toxicants. This study evaluated the use of Daphnia magna metabolomic measurements as indicators for exposure to reproductive endocrine disruptors by using the model juvenile hormone analogue fenoxycarb. Because D. magna reproduction controls metabolic regulation, the reproduction stage was also carefully considered in metabolic observations and data analysis to examine differences. Comparisons of metabolite abundance regulation between 1 and 12 days of fenoxycarb exposure were performed to investigate the predictability of the sub-chronic (12 days) adverse impacts on reproduction and metabolic regulation based on acute (1 day) metabolic observations. ANOVA-simultaneous component analysis (ASCA) detected reversed patterns in direction of time-course metabolite abundance regulation with fenoxycarb exposure. For example, decreases in the abundances of leucine, asparagine, methionine, and isoleucine which then changed to increases were observed with time during fenoxycarb exposures. The reversed regulation pattern was observed at the last reproduction stage (stage 3), exclusively. Pearson correlation analysis showed that correlations of pairwise metabolites were disrupted with fenoxycarb exposure. Similar to ASCA, data normalization based on the reproduction stage improved the detectability of significant correlations. The disruption on ambient metabolite regulation patterns and pairwise metabolite correlations was consistently observed with both 1 and 12 days of fenoxycarb exposures for sets of select metabolites. The observed regulatory disruptions to these specific metabolites suggest altered oogenesis as the affected metabolites and the specific reproduction stage are related to successful oogenesis. This study demonstrates that D. magna metabolic dysregulation is a predictor of water contamination by endocrine disrupting compounds. The high predictability of sub-chronic (12 days) endocrine disruption was confirmed based on acute (1 day) metabolic observations. Furthermore, integration of the reproduction cycle information in D. magna metabolomics was validated by observing a reproduction stage specific dysregulation in metabolite abundance regulation, which was not observable from the broader data analysis. Consequently, this study confirms the potential for establishing a quantitative relationship between water quality and indicator species metabolic observations. Additionally, it was found that constraining variables relevant to toxicity mechanisms of interest, such as the reproduction stage, is a key consideration for extraction of ecologically meaningful information in environmental metabolomics.

Transcriptome analysis of Drosophila melanogaster laboratory strains of different geographical origin after long-term laboratory maintenance

Positive selection may be the main factor of the between-population divergence in gene expression. Expression profiles of two Drosophila melanogaster laboratory strains of different geographical origin and long-term laboratory maintenance were analyzed using microchip arrays encompassing probes for 18,500 transcripts. The Russian strain D18 and the North American strain Canton-S were compared. A set of 223 known or putative genes demonstrated significant changes in expression levels between these strains. Differentially expressed genes (DEG) were enriched in response to DDT (p = .0014), proteolysis (p = 2.285E-5), transmembrane transport (p = 1.03E-4), carbohydrate metabolic process (p = .0317), protein homotetramerization (p = .0444), and antibacterial humoral response (p = 425E-4). The expression in subset of genes from different categories was verified by qRT-PCR. Analysis of transcript abundance between Canton-S and D18 strains allowed to select several genes to estimate their participation in latitude adaptation. Expression of selected genes was analyzed in five D. melanogaster lines of different geographic origins by qRT-PCR, and we found two candidate genes that may be associated with latitude adaptation in adult flies-smp-30 and Cda9. Quite possible that several alleles of these genes may be important for insect survival in the environments of global warming. It is interesting that the number of genes involved in local adaptation demonstrates expression level appropriate to their geographical origin even after decades of laboratory maintenance.

Intraspecific variation in thermal acclimation and tolerance between populations of the winter ant, Prenolepis imparis

Thermal phenotypic plasticity, otherwise known as acclimation, plays an essential role in how organisms respond to short-term temperature changes. Plasticity buffers the impact of harmful temperature changes; therefore, understanding variation in plasticity in natural populations is crucial for understanding how species will respond to the changing climate. However, very few studies have examined patterns of phenotypic plasticity among populations, especially among ant populations. Considering that this intraspecies variation can provide insight into adaptive variation in populations, the goal of this study was to quantify the short-term acclimation ability and thermal tolerance of several populations of the winter ant, Prenolepis imparis. We tested for correlations between thermal plasticity and thermal tolerance, elevation, and body size. We characterized the thermal environment both above and below ground for several populations distributed across different elevations within California, USA. In addition, we measured the short-term acclimation ability and thermal tolerance of those populations. To measure thermal tolerance, we used chill-coma recovery time (CCRT) and knockdown time as indicators of cold and heat tolerance, respectively. Short-term phenotypic plasticity was assessed by calculating acclimation capacity using CCRT and knockdown time after exposure to both high and low temperatures. We found that several populations displayed different chill-coma recovery times and a few displayed different heat knockdown times, and that the acclimation capacities of cold and heat tolerance differed among most populations. The high-elevation populations displayed increased tolerance to the cold (faster CCRT) and greater plasticity. For high-temperature tolerance, we found heat tolerance was not associated with altitude; instead, greater tolerance to the heat was correlated with increased plasticity at higher temperatures. These current findings provide insight into thermal adaptation and factors that contribute to phenotypic diversity by revealing physiological variance among populations.

Three Quantitative Trait Loci Explain More than 60% of Variation for Chill Coma Recovery Time in a Natural Population of Drosophila ananassae

Ectothermic species such as insects are particularly vulnerable to climatic fluctuations. Nevertheless, many insects that evolved and diversified in the tropics have successfully colonized temperate regions all over the globe. To shed light on the genetic basis of cold tolerance in such species, we conducted a quantitative trait locus (QTL) mapping experiment for chill coma recovery time (CCRT) in Drosophila ananassae, a cosmopolitan species that has expanded its range from tropical to temperate regions. We created a mapping population of recombinant inbred advanced intercross lines (RIAILs) from two founder strains with diverging CCRT phenotypes. The RIAILs were phenotyped for their CCRT and, together with the founder strains, genotyped for polymorphic markers with double-digest restriction site-associated DNA (ddRAD) sequencing. Using a hierarchical mapping approach that combined standard interval mapping and a multiple-QTL model, we mapped three QTL which altogether explained 64% of the phenotypic variance. For two of the identified QTL, we found evidence of epistasis. To narrow down the list of cold tolerance candidate genes, we cross-referenced the QTL intervals with genes that we previously identified as differentially expressed in response to cold in D. ananassae, and with thermotolerance candidate genes of D. melanogaster. Among the 58 differentially expressed genes that were contained within the QTL, GF15058 showed a significant interaction of the CCRT phenotype and gene expression. Further, we identified the orthologs of four D. melanogaster thermotolerance candidate genes, MtnA, klarsicht, CG5246 (D.ana/GF17132) and CG10383 (D.ana/GF14829) as candidates for cold tolerance in D. ananassae.

Reproduction Stage Differentiates the Time-Course Regulation of Metabolites in Daphnia magna

Daphnia magna is a keystone indicator zooplankton used in environmental quality assessments. Comparative metabolomics, which contrasts small biomolecular regulations under different conditions, has emerged as a sensitive and informative investigation tool for the assessment of environmental stressors on D. magna. Baseline metabolomic variation is likely impacted by the asexual reproduction cycle of D. magna; however, the relationship between metabolite concentration regulation and reproduction cycle has not been investigated. This study investigated the time-course regulation of 51 metabolites during different reproduction stages to determine how the reproduction cycle controlled the metabolite profile of D. magna. Two-way analysis of variance (ANOVA) results reveal that most metabolites show significantly differentiated concentrations by individual or a combination of reproduction stages and sampling time. On the basis of the partial least-squares-discriminant analysis (PLS-DA) and ANOVA-simultaneous component analysis (ANOVA-SCA), stages 2 and 3 of reproduction show similarity in metabolite abundance regulation compared to stage 1. Metabolites were classified as being either dependent or independent of reproduction in the pairwise concentration correlation based on Pearson correlation coefficients. This study observed that the D. magna reproduction stage is an important consideration and potential variable and should be considered carefully when conducting metabolomic experiments using D. magna.

Trade-Offs in Cold Resistance at the Northern Range Edge of the Common Woodland Ant Aphaenogaster picea (Formicidae)

Geographic variation in low temperatures at poleward range margins of terrestrial species often mirrors population variation in cold resistance, suggesting that range boundaries may be set by evolutionary constraints on cold physiology. The northeastern woodland ant Aphaenogaster picea occurs up to approximately 45°N in central Maine. We combined presence/absence surveys with classification tree analysis to characterize its northern range limit and assayed two measures of cold resistance operating on different timescales to determine whether and how marginal populations adapt to environmental extremes. The range boundary of A. picea was predicted primarily by temperature, but low winter temperatures did not emerge as the primary correlate of species occurrence. Low summer temperatures and high seasonal variability predicted absence above the boundary, whereas high mean annual temperature (MAT) predicted presence in southern Maine. In contrast, assays of cold resistance across multiple sites were consistent with the hypothesis of local cold adaptation at the range edge: among populations, there was a 4-min reduction in chill coma recovery time across a 2° reduction in MAT. Baseline resistance and capacity for additional plastic cold hardening shifted in opposite directions, with hardening capacity approaching zero at the coldest sites. This trade-off between baseline resistance and cold-hardening capacity suggests that populations at range edges may adapt to colder temperatures through genetic assimilation of plastic responses, potentially constraining further adaptation and range expansion.

Cold adaptation does not alter ATP homeostasis during cold exposure in Drosophila melanogaster

In insects and other ectotherms, cold temperatures cause a coma resulting from loss of neuromuscular function, during which ionic and metabolic homeostasis are progressively lost. Cold adaptation improves homeostasis during cold exposure, but the ultimate targets of selection are still an open question. Cold acclimation and adaptation remodels mitochondrial metabolism in insects, suggesting that aerobic energy production during cold exposure could be a target of selection. Here, we test the hypothesis that cold adaptation improves the ability to maintain rates of aerobic energy production during cold exposure by using ³¹ P NMR on live flies. Using lines of Drosophila melanogaster artificially selected for fast and slow recovery from a cold coma, we show that cold exposure does not lower ATP levels and that cold adaptation does not alter aerobic ATP production during cold exposure. Cold-hardy and cold-susceptible lines both experienced a brief transition to anaerobic metabolism during cooling, but this was rapidly reversed during cold exposure, suggesting that oxidative phosphorylation was sufficient to meet energy demands below the critical thermal minimum, even in cold-susceptible flies. We thus reject the hypothesis that performance under mild low temperatures is set by aerobic ATP supply limitations in D. melanogaster, excluding oxygen and capacity limitation as a weak link in energy supply. This work suggests that the modulations to mitochondrial metabolism resulting from cold acclimation or adaptation may arise from selection on a biosynthetic product(s) of those pathways rather than selection on ATP supply during cold exposure.

Cold acclimation triggers lipidomic and metabolic adjustments in the spotted wing drosophila Drosophila suzukii (Matsumara)

Chronic cold exposure is detrimental to chill susceptible insects that may accumulate chill injuries. To cope with deleterious effects of cold temperature, insects employ a variety of physiological strategies and metabolic adjustments, such as production of cryoprotectants, or remodeling of cellular membranes. Cold tolerance is a key element determining the fundamental niche of species. Because Drosophila suzukii is an invasive fruit pest, originating from East Asia, knowledge about its thermal biology is urgently needed. Physiological mechanisms underlying cold tolerance plasticity remain poorly understood in this species. Here, we explored metabolic and lipidomic modifications associated with the acquisition of cold tolerance in D. suzukii using Omics technologies (LC- and GC-MS/MS). In both cold-acclimated males and females, we observed physiological changes consistent with homeoviscous/homeophasic adaptation of membranes: reshuffling of phospholipid head groups and increasing unsaturation rate of fatty acids. Modification of fatty acids unsaturation were also observed in triacylglycerides, which would likely increase accessibility of lipid reserves. At the metabolic level, we observed clear-cut differentiation of metabolic profiles with cold-acclimated metabotypes showing accumulation of several potential cryoprotectants (sugars and amino acids). Metabolic pathway analyses indicated a remodeling of various processes, including purine metabolism and aminoacyl tRNA biosynthesis. These data provide a large-scale characterization of lipid rearrangements and metabolic pathway modifications in D. suzukii in response to cold acclimation and contribute to characterizing the strategies used by this species to modulate cold tolerance.

Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer

BACKGROUND

Obesity is a complex disorder associated with an increased risk of developing several comorbid chronic diseases, including postmenopausal breast cancer. Although many studies have investigated this issue, the link between body weight and either risk or poor outcome of breast cancer is still to characterize. Systems biology approaches, based on the integration of multiscale models and data from a wide variety of sources, are particularly suitable for investigating the underlying molecular mechanisms of complex diseases. In this scenario, GEnome-scale metabolic Models (GEMs) are a valuable tool, since they represent the metabolic structure of cells and provide a functional scaffold for simulating and quantifying metabolic fluxes in living organisms through constraint-based mathematical methods. The integration of omics data into the structural information described by GEMs allows to build more accurate descriptions of metabolic states.

RESULTS

In this work, we exploited gene expression data of postmenopausal breast cancer obese and lean patients to simulate a curated GEM of the human adipocyte, available in the Human Metabolic Atlas database. To this aim, we used a published algorithm which exploits a data-driven approach to overcome the limitation of defining a single objective function to simulate the model. The flux solutions were used to build condition-specific graphs to visualise and investigate the reaction networks and their properties. In particular, we performed a network topology differential analysis to search for pattern differences and identify the principal reactions associated with significant changes across the two conditions under study.

CONCLUSIONS

Metabolic network models represent an important source to study the metabolic phenotype of an organism in different conditions. Here we demonstrate the importance of exploiting Next Generation Sequencing data to perform condition-specific GEM analyses. In particular, we show that the qualitative and quantitative assessment of metabolic fluxes modulated by gene expression data provides a valuable method for investigating the mechanisms associated with the phenotype under study, and can foster our interpretation of biological phenomena.

Larvae of Drosophila melanogaster exhibit transcriptional activation of immune response pathways and antimicrobial peptides during recovery from supercooling stress

The biochemical and molecular mechanisms underlying insect cold acclimation prior to cold stress are relatively well explored, but the mechanisms linked to recovery and repair after cold stress have received much less attention. Here we focus on recovery from cold stress in the larvae of the vinegar fly (Drosophila melanogaster) that were exposed to two physiologically distinct cold stress situations: supercooling (S, survival > 95%) and freezing (F, survival < 10%), both at -5 °C. We analysed the metabolic and transcriptomic responses to cold stress via GC-MS/LC-MS and whole-genome microarrays, respectively. Both stresses (S and F) caused metabolic perturbations which were transient in supercooled larvae but deeper and irreversible in frozen larvae. Differential gene expression analysis revealed a clear disparity in responses to supercooling and freezing (less than 10% of DE genes overlapped between S and F larvae). Using GO term enrichment analysis and KEGG pathway mapping, we identified the stimulation of immune response pathways as a strong candidate mechanism for coping with supercooling. Supercooling caused complex transcriptional activation of innate immunity potential: from Lysozyme-mediated degradation of bacterial cell walls, recognition of pathogen signals, through phagocytosis and lysosomal degradation, Toll and Imd signaling, to upregulation of genes coding for different antimicrobial peptides. The transcriptomic response to freezing was instead dominated by degradation of macromolecules and death-related processes such as autophagy and apoptosis. Of the 45 upregulated DE genes overlapping in responses to supercooling and freezing, 26 were broadly ascribable to defense and repair functions.

Cold Acclimation Favors Metabolic Stability in Drosophila suzukii

The invasive fruit fly pest, Drosophila suzukii, is a chill susceptible species, yet it is capable of overwintering in rather cold climates, such as North America and North Europe, probably thanks to a high cold tolerance plasticity. Little is known about the mechanisms underlying cold tolerance acquisition in D. suzukii. In this study, we compared the effect of different forms of cold acclimation (at juvenile or at adult stage) on subsequent cold tolerance. Combining developmental and adult cold acclimation resulted in a particularly high expression of cold tolerance. As found in other species, we expected that cold-acclimated flies would accumulate cryoprotectants and would be able to maintain metabolic homeostasis following cold stress. We used quantitative target GC-MS profiling to explore metabolic changes in four different phenotypes: control, cold acclimated during development or at adult stage or during both phases. We also performed a time-series GC-MS analysis to monitor metabolic homeostasis status during stress and recovery. The different thermal treatments resulted in highly distinct metabolic phenotypes. Flies submitted to both developmental and adult acclimation were characterized by accumulation of cryoprotectants (carbohydrates and amino acids), although concentrations changes remained of low magnitude. After cold shock, non-acclimated chill-susceptible phenotype displayed a symptomatic loss of metabolic homeostasis, correlated with erratic changes in the amino acids pool. On the other hand, the most cold-tolerant phenotype was able to maintain metabolic homeostasis after cold stress. These results indicate that cold tolerance acquisition of D. suzukii depends on physiological strategies similar to other drosophilids: moderate changes in cryoprotective substances and metabolic robustness. In addition, the results add to the body of evidence supporting that mechanisms underlying the different forms of acclimation are distinct.

Mechanisms underpinning the beneficial effects of fluctuating thermal regimes in insect cold tolerance

Insects exposed to low temperature often have high mortality or exhibit sublethal effects. A growing number of recent studies have shown beneficial effects of exposing insects to recurrent brief warm pulses during low-temperature stress (fluctuating thermal regime, FTR). The physiological underpinnings of the beneficial effects of FTR on cold survival have been extensively studied over the past few years. Profiling with various ‘-omics’ techniques has provided supporting evidence for different physiological responses between insects exposed to FTR and constant low temperature. Evidence from transcriptomic, metabolomic and lipidomic studies points to a system-wide loss of homeostasis at low temperature that can be counterbalanced by repair mechanisms under FTR. Although there has been considerable progress in understanding the physiological mechanisms underlying the beneficial effects of FTR, here we discuss how many areas still lack clarity, such as the precise role(s) of heat shock proteins, compatible solutes or the identification of regulators and key players involved in the observed homeostatic responses. FTR can be particularly beneficial in applied settings, such as for model insects used in research, integrated pest management and pollination services. We also explain how the application of FTR techniques in large-scale facilities may require overcoming some logistical and technical constraints. FTR definitively enhances survival at low temperature in insects, but before it can be widely used, we suggest that the possible fitness and energy costs of FTR must be explored more thoroughly. Although FTR is not ecologically relevant, similar processes may operate in settings where temperatures fluctuate naturally.

Hormesis-like effect of mild larval crowding on thermotolerance in Drosophila flies

Crowding is a complex stress that can affect organisms' physiology, especially through decreased food quality and accessibility. Here, we evaluated the effect of larval density on several biological traits of Drosophila melanogaster An increasing gradient, from 1 to 1000 eggs per milliliter of food, was used to characterize life-history traits variations. Crowded conditions resulted in striking decreases of fresh mass (up to 6-fold) and viability, as well as delayed development. Next, we assessed heat and cold tolerance in L3 larvae reared at three selected larval densities: low (LD, 5 eggs ml^-1), medium (MD, 60 eggs ml^-1) and high (HD, 300 eggs ml^-1). LT₅₀ values of MD and, to a lesser extent, HD larvae were repeatedly higher than those from LD larvae, under both heat and cold stress. We investigated potential physiological correlates associated with this density-dependent thermotolerance shift. No marked pattern could be drawn from the expression of stress-related genes. However, a metabolomic analysis differentiated the metabotypes of the three density levels, with potential candidates associated with this clustering (e.g. glucose 6-phosphate, GABA, sugars and polyols). Under HD, signs of oxidative stress were noted but not confirmed at the transcriptional level. Finally, urea, a common metabolic waste, was found to accumulate substantially in food from MD and HD larvae. When supplemented in food, urea stimulated cold tolerance but reduced heat tolerance in LD larvae. This study highlights that larval crowding is an important environmental parameter that induces drastic consequences on flies' physiology and can affect thermotolerance in a density-specific way.

Evolution of the metabolome in response to selection for increased immunity in populations of Drosophila melanogaster

We used NMR-based metabolomics to test two hypotheses–(i) there will be evolved differences in the metabolome of selected and control populations even under un-infected conditions and (ii) post infection, the metabolomes of the selected and control populations will respond differently. We selected replicate populations of Drosophila melanogaster for increased survivorship (I) against a gram-negative pathogen. We subjected the selected (I) and their control populations (S) to three different treatments: (1) infected with heat-killed bacteria (i), (2) sham infected (s), and (3) untreated (u). We performed 1D and 2D NMR experiments to identify the metabolic differences. Multivariate analysis of the metabolic profiles of the untreated (Iu and Su) flies yielded higher concentrations of lipids, organic acids, sugars, amino acids, NAD and AMP in the Iu treatment as compared to the Su treatment, showing that even in the absence of infection, the metabolome of the I and S regimes was different. In the S and I regimes, post infection/injury, concentration of metabolites directly or indirectly associated with energy related pathways (lipids, organic acids, sugars) declined while the concentration of metabolites that are probably associated with immune response (amino acids) increased. However, in most cases, the I regime flies had a higher concentration of such metabolites even under un-infected conditions. The change in the metabolite concentration upon infection/injury was not always comparable between I and S regimes (in case of lactate, alanine, leucine, lysine, threonine) indicating that the I and S regimes had evolved to respond differentially to infection and to injury.

Methods for studying the metabolic basis of Drosophila development

The field of metabolic research has experienced an unexpected renaissance. While this renewed interest in metabolism largely originated in response to the global increase in diabetes and obesity, studies of metabolic regulation now represent the frontier of many biomedical fields. This trend is especially apparent in developmental biology, where metabolism influences processes ranging from stem cell differentiation and tissue growth to sexual maturation and reproduction. In this regard, the fruit fly Drosophila melanogaster has emerged as a powerful tool for dissecting conserved mechanisms that underlie developmental metabolism, often with a level of detail that is simply not possible in other animals. Here we describe why the fly is an ideal system for exploring the relationship between metabolism and development, and outline a basic experimental strategy for conducting these studies. WIREs Dev Biol 2017, 6:e280. doi: 10.1002/wdev.280 For further resources related to this article, please visit the WIREs website.

Similar post-stress metabolic trajectories in young and old flies

Homeostenosis (i.e. decline in stress resistance and resilience with age) is a fundamental notion of the biogerontology and physiology of aging. Stressful situations typically challenge metabolic homeostasis and the capacity to recover from a stress-induced metabolic disorder might be particularly compromised in senescent individuals. In the present work, we report the effects of aging on low temperature stress tolerance and metabolic profiles in Drosophila melanogaster females of different ages. Adult flies aged 4, 16, 30 and 44days were subjected to acute and chronic cold stress, and data confirmed a strong decline in cold tolerance and resilience of old flies compared to young counterparts. Using quantitative target GC-MS analysis, we found distinct metabolic phenotypes between young (4day-old) and old (44day-old) flies, with glycolytic pathways being differentially affected between the two age groups. We also compared the robustness of metabolic homeostasis in young vs. old flies when exposed to cold stress using time-series metabolic analysis. In both age groups, we found evidence of strong alteration of metabolic profiles when flies were exposed to low temperature stress. Interestingly, the temporal metabolic trajectories during the recovery period were similar in young and old flies, despite strong differences in thermotolerance. In conclusion, metabolic signatures markedly changed with age and homeostenosis was observed in the phenotypic response to cold stress. However, these changes did not reflect in different temporal homeostatic response at metabolic level.

Metabolomic Studies in Drosophila

Metabolomic analysis provides a powerful new tool for studies of Drosophila physiology. This approach allows investigators to detect thousands of chemical compounds in a single sample, representing the combined contributions of gene expression, enzyme activity, and environmental context. Metabolomics has been used for a wide range of studies in Drosophila, often providing new insights into gene function and metabolic state that could not be obtained using any other approach. In this review, we survey the uses of metabolomic analysis since its entry into the field. We also cover the major methods used for metabolomic studies in Drosophila and highlight new directions for future research.

Cross-tolerance effects due to adult heat hardening, desiccation and starvation acclimation of tropical drosophilid-Zaprionus indianus

Some insect taxa from polar or temperate habitats have shown cross-tolerance for multiple stressors but tropical insect taxa have received less attention. Accordingly, we considered adult flies of a tropical drosophilid-Zaprionus indianus for testing direct as well as cross-tolerance effects of rapid heat hardening (HH), desiccation acclimation (DA) and starvation acclimation (SA) after rearing under warmer and drier season specific simulated conditions. We observed significant direct acclimation effects of HH, DA and SA; and four cases of cross-tolerance effects but no cross-tolerance between desiccation and starvation. Cross-tolerance due to heat hardening on desiccation showed 20% higher effect than its reciprocal effect. There is greater reduction of water loss in heat hardened flies (due to increase in amount of cuticular lipids) as compared with desiccation acclimated flies. However, cross-tolerance effect of SA on heat knockdown was two times higher than its reciprocal. Heat hardened and desiccation acclimated adult flies showed substantial increase in the level of trehalose and proline while body lipids increased due to heat hardening or starvation acclimation. However, maximum increase in energy metabolites was stressor specific i.e. trehalose due to DA; proline due to HH and total body lipids due to SA. Rapid changes in energy metabolites due to heat hardening seem compensatory for possible depletion of trehalose and proline due to desiccation stress; and body lipids due to starvation stress. Thus, observed cross-tolerance effects in Z. indianus represent physiological changes to cope with multiple stressors related to warmer and drier subtropical habitats.

Cold acclimation allows Drosophila flies to maintain mitochondrial functioning under cold stress

Environmental stress generally disturbs cellular homeostasis. Researchers have hypothesized that chilling injury is linked to a shortage of ATP. However, previous studies conducted on insects exposed to nonfreezing low temperatures presented conflicting results. In this study, we investigated the mitochondrial bioenergetics of Drosophila melanogaster flies exposed to chronic cold stress (4 °C). We assessed mitochondrial oxygen consumption while monitoring the rate of ATP synthesis at various times (0, 1, 2, and 3 days) during prolonged cold stress and at two assay temperatures (25 and 4 °C). We compared organelle responses between cold-susceptible and cold-acclimated phenotypes. Continuous exposure to low temperature provoked temporal declines in the rates of mitochondrial respiration and ATP synthesis. Respiratory control ratios (RCRs) suggested that mitochondria were not critically uncoupled. Nevertheless, after 3 days of continuous cold stress, a sharp decline in the mitochondrial ATP synthesis rate was observed in control flies when they were assayed at low temperature. This change was associated with reduced survival capacity in control flies. In contrast, cold-acclimated flies exhibited high survival and maintained higher rates of mitochondrial ATP synthesis and coupling (i.e., higher RCRs). Adaptive changes due to cold acclimation observed in the whole organism were thus manifested in isolated mitochondria. Our observations suggest that cold tolerance is linked to the ability to maintain bioenergetics capacity under cold stress.

CRISPR-induced null alleles show that Frost protects Drosophila melanogaster reproduction after cold exposure

The ability to survive and reproduce after cold exposure is important in all kingdoms of life. However, even in a sophisticated genetic model system like Drosophila melanogaster, few genes have been identified as functioning in cold tolerance. The accumulation of the Frost (Fst) gene transcript increases after cold exposure, making it a good candidate for a gene that has a role in cold tolerance. However, despite extensive RNAi knockdown analysis, no role in cold tolerance has been assigned to Fst. CRISPR is an effective technique for completely knocking down genes, and less likely to produce off-target effects than GAL4-UAS RNAi systems. We have used CRISPR-mediated homologous recombination to generate Fst null alleles, and these Fst alleles uncovered a requirement for FST protein in maintaining female fecundity following cold exposure. However, FST does not have a direct role in survival following cold exposure. FST mRNA accumulates in the Malpighian tubules, and the FST protein is a highly disordered protein with a putative signal peptide for export from the cell. Future work is needed to determine whether FST is exported from the Malpighian tubules and directly interacts with female reproductive tissues post-cold exposure, or if it is required for other repair/recovery functions that indirectly alter energy allocation to reproduction.

Considerations when choosing a genetic model organism for metabolomics studies

Model organisms are important in many areas of chemical biology. In metabolomics, model organisms can provide excellent samples for methods development as well as the foundation of comparative phylometabolomics, which will become possible as metabolomics applications expand. Comparative studies of conserved and unique metabolic pathways will help in the annotation of metabolites as well as provide important new targets of investigation in biology and biomedicine. However, most chemical biologists are not familiar with genetics, which needs to be considered when choosing a model organism. In this review we summarize the strengths and weaknesses of several genetic systems, including natural isolates, recombinant inbred lines, and genetic mutations. We also discuss methods to detect targets of selection on the metabolome.

Metabolomics with Nuclear Magnetic Resonance Spectroscopy in a Drosophila melanogaster Model of Surviving Sepsis

Patients surviving sepsis demonstrate sustained inflammation, which has been associated with long-term complications. One of the main mechanisms behind sustained inflammation is a metabolic switch in parenchymal and immune cells, thus understanding metabolic alterations after sepsis may provide important insights to the pathophysiology of sepsis recovery. In this study, we explored metabolomics in a novel Drosophila melanogaster model of surviving sepsis using Nuclear Magnetic Resonance (NMR), to determine metabolite profiles. We used a model of percutaneous infection in Drosophila melanogaster to mimic sepsis. We had three experimental groups: sepsis survivors (infected with Staphylococcus aureus and treated with oral linezolid), sham (pricked with an aseptic needle), and unmanipulated (positive control). We performed metabolic measurements seven days after sepsis. We then implemented metabolites detected in NMR spectra into the MetExplore web server in order to identify the metabolic pathway alterations in sepsis surviving Drosophila. Our NMR metabolomic approach in a Drosophila model of recovery from sepsis clearly distinguished between all three groups and showed two different metabolomic signatures of inflammation. Sham flies had decreased levels of maltose, alanine, and glutamine, while their level of choline was increased. Sepsis survivors had a metabolic signature characterized by decreased glucose, maltose, tyrosine, beta-alanine, acetate, glutamine, and succinate.

Chronic dietary salt stress mitigates hyperkalemia and facilitates chill coma recovery in Drosophila melanogaster

Chill susceptible insects like Drosophila lose the ability to regulate water and ion homeostasis at low temperatures. This loss of hemolymph ion and water balance drives a hyperkalemic state that depolarizes cells, causing cellular injury and death. The ability to maintain ion homeostasis at low temperatures and/or recover ion homeostasis upon rewarming is closely related to insect cold tolerance. We thus hypothesized that changes to organismal ion balance, which can be achieved in Drosophila through dietary salt loading, could alter whole animal cold tolerance phenotypes. We put Drosophila melanogaster in the presence of diets highly enriched in NaCl, KCl, xylitol (an osmotic control) or sucrose (a dietary supplement known to impact cold tolerance) for 24h and confirmed that they consumed the novel food. Independently of their osmotic effects, NaCl, KCl, and sucrose supplementation all improved the ability of flies to maintain K⁺ balance in the cold, which allowed for faster recovery from chill coma after 6h at 0°C. These supplements, however, also slightly increased the CT_min and had little impact on survival rates following chronic cold stress (24h at 0°C), suggesting that the effect of diet on cold tolerance depends on the measure of cold tolerance assessed. In contrast to prolonged salt stress, brief feeding (1.5h) on diets high in salt slowed coma recovery, suggesting that the long-term effects of NaCl and KCl on chilling tolerance result from phenotypic plasticity, induced in response to a salty diet, rather than simply the presence of the diet in the gut lumen.

Cold and desiccation stress induced changes in the accumulation and utilization of proline and trehalose in seasonal populations of Drosophila immigrans

Changes in the levels of energy metabolites can limit survival ability of Drosophila species under stressful conditions but this aspect has received less attention in wild populations collected in different seasons. We tested cold or desiccation triggered changes in the accumulation or utilization of two energy metabolites (trehalose and proline) in Drosophila immigrans flies reared under season specific environmental conditions. Such D.immigrans populations were subjected to different durations of cold (0°C) or desiccation stress (5% RH) or dual stress. We found stress induced effects of cold vs desiccation on the levels of trehalose as well as for proline. Different durations of cold stress led to accumulation of trehalose while desiccation stress durations revealed utilization of trehalose. In contrast, there was accumulation of proline under desiccation and utilization of proline with cold stress. Since accumulation levels were higher than utilization of each energy metabolite, the effects of dual stress showed additive effect. However, there was no utilization of total body lipids under cold or desiccation stress. We observed significant season specific differences in the amount of energy metabolites but the rate of metabolism did not vary across seasons. Stress triggered changes in trehalose and proline suggest possible link between desiccation and cold tolerance. Finally, stress specific (cold or desiccation) compensatory changes in the levels of trehalose and proline suggest possible energetic homeostasis in D.immigrans living under harsh climatic conditions of montane localities.

Head Transcriptomes of Two Closely Related Species of Fruit Flies of the Anastrepha fraterculus Group Reveals Divergent Genes in Species with Extensive Gene Flow

Several fruit flies species of the Anastrepha fraterculus group are of great economic importance for the damage they cause to a variety of fleshy fruits. Some species in this group have diverged recently, with evidence of introgression, showing similar morphological attributes that render their identification difficult, reinforcing the relevance of identifying new molecular markers that may differentiate species. We investigated genes expressed in head tissues from two closely related species: A. obliqua and A. fraterculus, aiming to identify fixed single nucleotide polymorphisms (SNPs) and highly differentiated transcripts, which, considering that these species still experience some level of gene flow, could indicate potential candidate genes involved in their differentiation process. We generated multiple libraries from head tissues of these two species, at different reproductive stages, for both sexes. Our analyses indicate that the de novo transcriptome assemblies are fairly complete. We also produced a hybrid assembly to map each species' reads, and identified 67,470 SNPs in A. fraterculus, 39,252 in A. obliqua, and 6386 that were common to both species. We identified 164 highly differentiated unigenes that had a mean interspecific index ([Formula: see text]) of at least 0.94. We selected unigenes that had Ka/Ks higher than 0.5, or had at least three or more highly differentiated SNPs as potential candidate genes for species differentiation. Among these candidates, we identified proteases, regulators of redox homeostasis, and an odorant-binding protein (Obp99c), among other genes. The head transcriptomes described here enabled the identification of thousands of genes hitherto unavailable for these species, and generated a set of candidate genes that are potentially important to genetically identify species and understand the speciation process in the presence of gene flow of A. obliqua and A. fraterculus.

Cold adaptation increases rates of nutrient flow and metabolic plasticity during cold exposure in Drosophila melanogaster

Metabolic flexibility is an important component of adaptation to stressful environments, including thermal stress and latitudinal adaptation. A long history of population genetic studies suggest that selection on core metabolic enzymes may shape life histories by altering metabolic flux. However, the direct relationship between selection on thermal stress hardiness and metabolic flux has not previously been tested. We investigated flexibility of nutrient catabolism during cold stress in Drosophila melanogaster artificially selected for fast or slow recovery from chill coma (i.e. cold-hardy or -susceptible), specifically testing the hypothesis that stress adaptation increases metabolic turnover. Using (13)C-labelled glucose, we first showed that cold-hardy flies more rapidly incorporate ingested carbon into amino acids and newly synthesized glucose, permitting rapid synthesis of proline, a compound shown elsewhere to improve survival of cold stress. Second, using glucose and leucine tracers we showed that cold-hardy flies had higher oxidation rates than cold-susceptible flies before cold exposure, similar oxidation rates during cold exposure, and returned to higher oxidation rates during recovery. Additionally, cold-hardy flies transferred compounds among body pools more rapidly during cold exposure and recovery. Increased metabolic turnover may allow cold-adapted flies to better prepare for, resist and repair/tolerate cold damage. This work illustrates for the first time differences in nutrient fluxes associated with cold adaptation, suggesting that metabolic costs associated with cold hardiness could invoke resource-based trade-offs that shape life histories.

Cold tolerance is unaffected by oxygen availability despite changes in anaerobic metabolism

Insect cold tolerance depends on their ability to withstand or repair perturbations in cellular homeostasis caused by low temperature stress. Decreased oxygen availability (hypoxia) can interact with low temperature tolerance, often improving insect survival. One mechanism proposed for such responses is that whole-animal cold tolerance is set by a transition to anaerobic metabolism. Here, we provide a test of this hypothesis in an insect model system (Thaumatotibia leucotreta) by experimental manipulation of oxygen availability while measuring metabolic rate, critical thermal minimum (CT_min), supercooling point and changes in 43 metabolites in moth larvae at three key timepoints (before, during and after chill coma). Furthermore, we determined the critical oxygen partial pressure below which metabolic rate was suppressed (c. 4.5 kPa). Results showed that altering oxygen availability did not affect (non-lethal) CT_min nor (lethal) supercooling point. Metabolomic profiling revealed the upregulation of anaerobic metabolites and alterations in concentrations of citric acid cycle intermediates during and after chill coma exposure. Hypoxia exacerbated the anaerobic metabolite responses induced by low temperatures. These results suggest that cold tolerance of T. leucotreta larvae is not set by oxygen limitation, and that anaerobic metabolism in these larvae may contribute to their ability to survive in necrotic fruit.

Arginine and proline applied as food additives stimulate high freeze tolerance in larvae of Drosophila melanogaster

The fruit fly Drosophila melanogaster is an insect of tropical origin. Its larval stage is evolutionarily adapted for rapid growth and development under warm conditions and shows high sensitivity to cold. In this study, we further developed an optimal acclimation and freezing protocol that significantly improves larval freeze tolerance (an ability to survive at −5°C when most of the freezable fraction of water is converted to ice). Using the optimal protocol, freeze survival to adult stage increased from 0.7% to 12.6% in the larvae fed standard diet (agar, sugar, yeast, cornmeal). Next, we fed the larvae diets augmented with 31 different amino compounds, administered in different concentrations, and observed their effects on larval metabolomic composition, viability, rate of development and freeze tolerance. While some diet additives were toxic, others showed positive effects on freeze tolerance. Statistical correlation revealed tight association between high freeze tolerance and high levels of amino compounds involved in arginine and proline metabolism. Proline- and arginine-augmented diets showed the highest potential, improving freeze survival to 42.1% and 50.6%, respectively. Two plausible mechanisms by which high concentrations of proline and arginine might stimulate high freeze tolerance are discussed: (i) proline, probably in combination with trehalose, could reduce partial unfolding of proteins and prevent membrane fusions in the larvae exposed to thermal stress (prior to freezing) or during freeze dehydration; (ii) both arginine and proline are exceptional among amino compounds in their ability to form supramolecular aggregates which probably bind partially unfolded proteins and inhibit their aggregation under increasing freeze dehydration.