Evaluation of the pesticide Oberon on a model organism Drosophila melanogaster via topical toxicity test on biochemical and reproductive parameters

Spiromesifen (Oberon® 240 SC), a pesticide widely used to control pests like mites and whiteflies, was investigated using Drosophila melanogaster Meigen, 1830 (Diptera, Drosophilidae) as a model organism. The compound was applied topically at two concentrations (LC₁₀: 21.45 and LC₂₅: 39.53 μg active ingredient/pupa), on newly molted pupae and assessed on morphometric measurements of ovaries and the progeny of surviving adults. Results showed that spiromesifen inhibited the growth and development of ovaries, reducing at the highest dose (LC₂₅) the number of oocytes, the volume of basal oocytes and ovarian weight. Biochemical analysis revealed that the tested compound reduced the ovarian levels of carbohydrates and glycogen during the sexual maturation. Moreover, fecundity, fertility and number of descendants from parents that survived to the treatment of pupae were significantly reduced. The sex ratio determined indicated a significant decrease in treated series and males seemed more sensitive to spiromesifen than females. Lastly, the compound was found to affect the sexual behavior.

Subpopulation of Macrophage-Like Plasmatocytes Attenuates Systemic Growth via JAK/STAT in the Drosophila Fat Body

Drosophila hemocytes, like those of mammals, are given rise from two distinctive phases during both the embryonic and larval hematopoiesis. Embryonically derived hemocytes, mostly composed of macrophage-like plasmatocytes, are largely identified by genetic markers. However, the cellular diversity and distinct functions of possible subpopulations within plasmatocytes have not been explored in Drosophila larvae. Here, we show that larval plasmatocytes exhibit differential expressions of Hemolectin (Hml) and Peroxidasin (Pxn) during development. Moreover, removal of plasmatocytes by overexpressing pro-apoptotic genes, hid and reaper in Hml-positive plasmatocytes, feeding high sucrose diet, or wasp infestation results in increased circulating hemocytes that are Hml-negative. Interestingly these Hml-negative plasmatocytes retain Pxn expression, and animals expressing Hml-negative and Pxn-positive subtype largely attenuate growth and abrogate metabolism. Furthermore, elevated levels of a cytokine, unpaired 3, are detected when Hml-positive hemocytes are ablated, which in turn activates JAK/STAT activity in several tissues including the fat body. Finally, we observed that insulin signaling is inhibited in this background, which can be recovered by concurrent loss of upd3. Overall, this study highlights heterogeneity in Drosophila plasmatocytes and a functional plasticity of each subtype, which reaffirms extension of their role beyond immunity into metabolic regulation for cooperatively maintaining internal homeostatic balance.

Sexual Dimorphisms in Innate Immunity and Responses to Infection in Drosophila melanogaster

The sexes show profound differences in responses to infection and the development of autoimmunity. Dimorphisms in immune responses are ubiquitous across taxa, from arthropods to vertebrates. Drosophila melanogaster shows strong sex dimorphisms in immune system responses at baseline, upon pathogenic challenge, and over aging. We have performed an exhaustive survey of peer-reviewed literature on Drosophila immunity, and present a database of publications indicating the sex(es) analyzed in each study. While we found a growing interest in the community in adult immunity and in reporting both sexes, the main body of work in this field uses only one sex, or does not stratify by sex. We synthesize evidence for sexually dimorphic responses to bacterial, viral, and fungal infections. Dimorphisms may be mediated by distinct immune compartments, and we review work on sex differences in behavioral, epithelial, cellular, and systemic (fat body-mediated) immunity. Emerging work on sexually dimorphic aging of immune tissues, immune senescence, and inflammation are examined. We consider evolutionary drivers for sex differences in immune investment, highlight the features of Drosophila biology that make it particularly amenable to studies of immune dimorphisms, and discuss areas for future exploration.

Ginseng protein protects against mitochondrial dysfunction and neurodegeneration by inducing mitochondrial unfolded protein response in Drosophila melanogaster PINK1 model of Parkinson's disease

ETHNOPHARMACOLOGICAL RELEVANCE

Historical literature and pharmacological studies demonstrate that ginseng, one of the most popular herbal medicines in China, holds potential benefits for Parkinson's disease (PD).

AIM OF THE STUDY

Studies in Drosophila melanogaster (Dm) have highlighted mitochondrial dysfunction upon loss of PTEN-induced putative kinase 1 (PINK1) as a central mechanism of PD pathogenesis. Using PINK1^B9 mutant Dm, we aimed to explore the therapeutic action of ginseng total protein (GTP) on PD and provide in-depth scientific interpretation about the traditional efficacy of ginseng.

MATERIALS AND METHODS

We first used gel chromatography to purify GTP and confirmed its molecular weight by SDS-PAGE. Effects of GTP on PINK1^B9 mutants, which were supplied with standard diet from larvae to adult stages, were assayed in flies aged 3-6 (I), 10-15 (II), and 20-25 (III) days. Parkinson-like phenotypes were analyzed by evaluating lifespan, dopaminergic neurons, dopamine levels, and locomotor ability. Mitochondrial function was assessed by evaluating ATP production, respirometry, and mitochondrial DNA. In addition, reactive oxygen species were measured using dihydroethidium and 2',7'-dichlorodihydrofluorescein diacetate staining. PD-related oxidative stress was simulated by paraquat and rotenone, and mitochondrial membrane potential was measured using JC-10 reagent. Protein and mRNA expression was detected by Western blot and real-time quantitative reverse transcription polymerase chain reaction, respectively.

RESULTS

This study demonstrates for the first time that GTP treatment delays the onset of a Parkinson-like phenotype in PINK1^B9 Dm, including prolongation of lifespan and rescue of climbing ability, as well as rescue of the progressive loss of a cluster of dopaminergic neurons in the protocerebral posterior lateral 1 region, which was accompanied by a significant increase of dopamine content in the brain. In addition, GTP notably reduced the penetrance of abnormal wing position, indicating a strong inhibitory effect on indirect flight muscle degeneration. We further showed that GTP could promote maintenance of mitochondrial function and protect mitochondria from PD-associated oxidative stress by activating the mitochondrial unfolded protein response (UPR^mt).

CONCLUSIONS

GTP protected against mitochondrial dysfunction and neurodegeneration by inducing UPR^mt in the Dm PINK1^B9 model of PD. Our results suggest that GTP is a promising candidate for PD, and reveal a new mechanism by which ginseng is neuroprotective.

Painting of Fourth and the X-Linked 1.688 Satellite in D. melanogaster is Involved in Chromosome-Wide Gene Regulation

Chromosome-specific regulatory mechanisms provide a model to understand the coordinated regulation of genes on entire chromosomes or on larger genomic regions. In fruit flies, two chromosome-wide systems have been characterized: The male-specific lethal (MSL) complex, which mediates dosage compensation and primarily acts on the male X-chromosome, and Painting of fourth (POF), which governs chromosome-specific regulation of genes located on the 4th chromosome. How targeting of one specific chromosome evolves is still not understood; but repeated sequences, in forms of satellites and transposable elements, are thought to facilitate the evolution of chromosome-specific targeting. The highly repetitive 1.688 satellite has been functionally connected to both these systems. Considering the rapid evolution and the necessarily constant adaptation of regulatory mechanisms, such as dosage compensation, we hypothesised that POF and/or 1.688 may still show traces of dosage-compensation functions. Here, we test this hypothesis by transcriptome analysis. We show that loss of Pof decreases not only chromosome 4 expression but also reduces the X-chromosome expression in males. The 1.688 repeat deletion, Zhr¹ (Zygotic hybrid rescue), does not affect male dosage compensation detectably; however, Zhr¹ in females causes a stimulatory effect on X-linked genes with a strong binding affinity to the MSL complex (genes close to high-affinity sites). Lack of pericentromeric 1.688 also affected 1.688 expression in trans and was linked to the differential expression of genes involved in eggshell formation. We discuss our results with reference to the connections between POF, the 1.688 satellite and dosage compensation, and the role of the 1.688 satellite in hybrid lethality.

Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance

Predicting antibiotic efficacy within microbial communities remains highly challenging. Interspecies interactions can impact antibiotic activity through many mechanisms, including alterations to bacterial physiology. Here, we studied synthetic communities constructed from the core members of the fruit fly gut microbiota. Co-culturing of Lactobacillus plantarum with Acetobacter species altered its tolerance to the transcriptional inhibitor rifampin. By measuring key metabolites and environmental pH, we determined that Acetobacter species counter the acidification driven by L. plantarum production of lactate. Shifts in pH were sufficient to modulate L. plantarum tolerance to rifampin and the translational inhibitor erythromycin. A reduction in lag time exiting stationary phase was linked to L. plantarum tolerance to rifampicin, opposite to a previously identified mode of tolerance to ampicillin in E. coli. This mechanistic understanding of the coupling among interspecies interactions, environmental pH, and antibiotic tolerance enables future predictions of growth and the effects of antibiotics in more complex communities.

The neuropeptide Drosulfakinin regulates social isolation-induced aggression in Drosophila

Social isolation strongly modulates behavior across the animal kingdom. We utilized the fruit fly Drosophila melanogaster to study social isolation-driven changes in animal behavior and gene expression in the brain. RNA-seq identified several head-expressed genes strongly responding to social isolation or enrichment. Of particular interest, social isolation downregulated expression of the gene encoding the neuropeptide Drosulfakinin (Dsk), the homologue of vertebrate cholecystokinin (CCK), which is critical for many mammalian social behaviors. Dsk knockdown significantly increased social isolation-induced aggression. Genetic activation or silencing of Dsk neurons each similarly increased isolation-driven aggression. Our results suggest a U-shaped dependence of social isolation-induced aggressive behavior on Dsk signaling, similar to the actions of many neuromodulators in other contexts.

Thioester-containing Proteins in the Drosophila melanogaster Immune Response against the Pathogen Photorhabdus

The fruit fly Drosophila melanogaster forms a magnificent model for interpreting conserved host innate immune signaling and functional processes in response to microbial assaults. In the broad research field of host-microbe interactions, model hosts are used in conjunction with a variety of pathogenic microorganisms to disentangle host immune system activities and microbial pathogenicity strategies. The pathogen Photorhabdus is considered an established model for analyzing bacterial virulence and symbiosis due to its unique life cycle that extends between two invertebrate hosts: an insect and a parasitic nematode. In recent years, particular focus has been given to the mechanistic participation of the D. melanogaster thioester-containing proteins (TEPs) in the overall immune capacity of the fly upon response against the pathogen Photorhabdus alone or in combination with its specific nematode vector Heterorhabditis bacteriophora. The original role of certain TEPs in the insect innate immune machinery was linked to the antibacterial and antiparasite reaction of the mosquito malaria vector Anopheles gambiae; however, revamped interest in the immune competence of these molecules has recently emerged from the D. melanogaster-Photorhabdus infection system. Here, we review the latest findings on this topic with the expectation that such information will refine our understanding of the evolutionary immune role of TEPs in host immune surveillance.

The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster

BACKGROUND

The piwi-interacting RNAs (piRNAs) are small non-coding RNAs that specifically repress transposable elements (TEs) in the germline of Drosophila. Despite our expanding understanding of TE:piRNA interaction, whether there is an evolutionary arms race between TEs and piRNAs was unclear.

RESULTS

Here, we studied the population genomics of TEs and piRNAs in the worldwide strains of D. melanogaster. By conducting a correlation analysis between TE contents and the abundance of piRNAs from ovaries of representative strains of D. melanogaster, we find positive correlations between TEs and piRNAs in six TE families. Our simulations further highlight that TE activities and the strength of purifying selection against TEs are important factors shaping the interactions between TEs and piRNAs. Our studies also suggest that the de novo generation of piRNAs is an important mechanism to repress the newly invaded TEs.

CONCLUSIONS

Our results revealed the existence of an evolutionary arms race between the copy numbers of TEs and the abundance of antisense piRNAs at the population level. Although the interactions between TEs and piRNAs are complex and many factors should be considered to impact their interaction dynamics, our results suggest the emergence, repression specificity and strength of piRNAs on TEs should be considered in studying the landscapes of TE insertions in Drosophila. These results deepen our understanding of the interactions between piRNAs and TEs, and also provide novel insights into the nature of genomic conflicts of other forms.

Diverse biological processes coordinate the transcriptional response to nutritional changes in a Drosophila melanogaster multiparent population

Background

Environmental variation in the amount of resources available to populations challenge individuals to optimize the allocation of those resources to key fitness functions. This coordination of resource allocation relative to resource availability is commonly attributed to key nutrient sensing gene pathways in laboratory model organisms, chiefly the insulin/TOR signaling pathway. However, the genetic basis of diet-induced variation in gene expression is less clear.

Results

To describe the natural genetic variation underlying nutrient-dependent differences, we used an outbred panel derived from a multiparental population, the Drosophila Synthetic Population Resource. We analyzed RNA sequence data from multiple female tissue samples dissected from flies reared in three nutritional conditions: high sugar (HS), dietary restriction (DR), and control (C) diets. A large proportion of genes in the experiment (19.6% or 2471 genes) were significantly differentially expressed for the effect of diet, and 7.8% (978 genes) for the effect of the interaction between diet and tissue type (LRT, P_adj. < 0.05). Interestingly, we observed similar patterns of gene expression relative to the C diet, in the DR and HS treated flies, a response likely reflecting diet component ratios. Hierarchical clustering identified 21 robust gene modules showing intra-modularly similar patterns of expression across diets, all of which were highly significant for diet or diet-tissue interaction effects (FDR P_adj. < 0.05). Gene set enrichment analysis for different diet-tissue combinations revealed a diverse set of pathways and gene ontology (GO) terms (two-sample t-test, FDR < 0.05). GO analysis on individual co-expressed modules likewise showed a large number of terms encompassing many cellular and nuclear processes (Fisher exact test, P_adj. < 0.01). Although a handful of genes in the IIS/TOR pathway including Ilp5, Rheb, and Sirt2 showed significant elevation in expression, many key genes such as InR, chico, most insulin peptide genes, and the nutrient-sensing pathways were not observed.

Conclusions

Our results suggest that a more diverse network of pathways and gene networks mediate the diet response in our population. These results have important implications for future studies focusing on diet responses in natural populations.

Absence of reproduction-immunity trade-off in male Drosophila melanogaster evolving under differential sexual selection

Background

The theory of trade-off suggests that limited resources should lead to trade-off in resource intensive traits such as, immunity related and sexually selected traits in males. Alternatively, sexual exaggerations can also act as an honest indicator of underlying immunocompetence, leading to positive correlations between these traits. Evidences in support of either hypothesis in invertebrates are equivocal. Whereas several studies have addressed this question, few have used naturally occurring pathogens and realized post infection realized immunity (e.g., survivorship) to assay the fitness correlations between these two sets of traits.

Results

Adopting an experimental evolution approach, we evolved replicate populations of Drosophila melanogaster under high and low sexual selection regimes for over a hundred generations and found the following in virgin and mated males in three separate assays:

Post infection survivorship against two natural pathogens - Pseudomonas entomophila (Pe) and Staphylococcus succinus (Ss): Mated males survived better against Pe, but were no different than virgins against Ss.

Bacterial clearance ability against a third natural pathogen Providencia rettgeri (Pr): Mated males had significantly lower CFUs than virgins.

However, sexual selection history had no effect on realized immunity of either virgin or mated males.

Conclusion

We show that while mating can affect realized immunity in a pathogen specific way, sexual selection did not affect the same. The results highlight that complex polygenic traits such as immunity and reproductive traits not necessarily evolve following a binary trade-off model. We also stress the importance natural pathogens while studying sexual selection-immunity correlations.

Food restriction reconfigures naïve and learned choice behavior in Drosophila larvae

In many animals, the establishment and expression of food-related memory is limited by the presence of food and promoted by its absence, implying that this behavior is driven by motivation. In the past, this has already been demonstrated in various insects including honeybees and adult Drosophila. For Drosophila larvae, which are characterized by an immense growth and the resulting need for constant food intake, however, knowledge is rather limited. Accordingly, we have analyzed whether starvation modulates larval memory formation or expression after appetitive classical olfactory conditioning, in which an odor is associated with a sugar reward. We show that odor-sugar memory of starved larvae lasts longer than in fed larvae, although the initial performance is comparable. 80 minutes after odor fructose conditioning, only starved but not fed larvae show a reliable odor-fructose memory. This is likely due to a specific increase in the stability of anesthesia-resistant memory (ARM). Furthermore, we observe that starved larvae, in contrast to fed ones, prefer sugars that offer a nutritional benefit in addition to their sweetness. Taken together our work shows that Drosophila larvae adjust the expression of learned and naïve choice behaviors in the absence of food. These effects are only short-lasting probably due to their lifestyle and their higher internal motivation to feed. In the future, the extensive use of established genetic tools will allow us to identify development-specific differences arising at the neuronal and molecular level.

Host-Microbe-Pathogen Interactions: A Review of Vibrio cholerae Pathogenesis in Drosophila

Most animals maintain mutually beneficial symbiotic relationships with their intestinal microbiota. Resident microbes in the gastrointestinal tract breakdown indigestible food, provide essential nutrients, and, act as a barrier against invading microbes, such as the enteric pathogen Vibrio cholerae. Over the last decades, our knowledge of V. cholerae pathogenesis, colonization, and transmission has increased tremendously. A number of animal models have been used to study how V. cholerae interacts with host-derived resources to support gastrointestinal colonization. Here, we review studies on host-microbe interactions and how infection with V. cholerae disrupts these interactions, with a focus on contributions from the Drosophila melanogaster model. We will discuss studies that highlight the connections between symbiont, host, and V. cholerae metabolism; crosstalk between V. cholerae and host microbes; and the impact of the host immune system on the lethality of V. cholerae infection. These studies suggest that V. cholerae modulates host immune-metabolic responses in the fly and improves Vibrio fitness through competition with intestinal microbes.

Flavonoids from Epimedium pubescens: extraction and mechanism, antioxidant capacity and effects on CAT and GSH-Px of Drosophila melanogaster

Background

Epimedium is a famous medicinal plant in China, Southeast Asian and some other regions. Flavonoids are regarded as its supremely important active constituents used in phytomedicines and/or functional foods. It is of theoretical and applied significance to optimize the procedure for extraction of flavonoids with high bioactivity from Epimedium, to unveil extraction mechanism, to identify chemical composition of flavonoids, to analyze free radical-scavenging ability of flavonoids, and to investigate their effects on the model organism Drosophila melanogaster.

Methods

Box-Behnken design was applied to optimization of extraction procedure. Laser diffraction particle size analysis was used to clarify extraction mechanism. Chemical composition of flavonoids was analyzed using high-performance liquid chromatography. Antiradical capacities of flavonoids were determined by chemical-based assay. Then, effects of flavonoids on catalase (CAT) and glutathione peroxidase (GSH-Px) in D. melanogaster were investigated for the first time.

Results

The optimal condition for ultrasonic extraction of antioxidant flavonoids from Epimedium pubescens was achieved and extraction mechanism was discussed. Epimedium flavonoids contained icariin, epimedin A, epimedin B and epimedin C. Epimedium flavonoids exhibited the ability to scavenge ABTS⁺ and DPPH^⋅ radicals with EC₅₀ values of 55.8 and 52.1 µg/ml, respectively. Moreover, Epimedium flavonoids were able to increase activities of CAT and GSH-Px in D. melanogaster. For females, oral administration of flavonoids improved CAT and GSH-Px activities by 13.58% and 5.18%, respectively. For males, oral administration of flavonoids increased CAT and GSH-Px activities by 13.90% and 5.65%, respectively.

Conclusion

Flavonoids ultrasonically extracted from E. pubescens considerably affected antioxidant defense system in D. melanogaster. Flavonoids of E. pubescens showed great potential for becoming a natural antioxidant because of their antiradical ability and effects on CAT and GSH-Px of the model organism.

High-Resolution Infection Kinetics of Entomopathogenic Nematodes Entering Drosophila melanogaster

Entomopathogenic nematodes (EPNs) have been a useful model for studying wound healing in insects due to their natural mechanism of entering an insect host either through the cuticle or an orifice. While many experiments have shed light on nematode and host behavior, as well as the host immune response, details regarding early nematode entry and proliferative events have been limited. Using high-resolution microscopy, we provide data on the early infection kinetics of Heterorhabditis bacteriophora and its symbiotic bacteria, Photorhabdus luminescens. EPNs appendage themselves to the host and enter through the host cuticle with a drill-like mechanism while leaving their outer sheath behind. EPNs immediately release their symbiotic bacteria in the host which leads to changes in host behavior and septicemia within 6 h while EPNs travel through the host in a predictable manner, congregating in the anterior end of the host. This paper sheds light on the entry and proliferative events of EPN infection, which will further aid in our understanding of wound healing and host immune activation at a high spatiotemporal resolution.

Enteric infection induces Lark-mediated intron retention at the 5' end of Drosophila genes

BACKGROUND

RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, we employ a systems approach to study alternative splicing changes upon enteric infection in females from classical Drosophila melanogaster strains as well as 38 inbred lines.

RESULTS

We find that infection leads to extensive differences in isoform ratios, which results in a more diverse transcriptome with longer 5' untranslated regions (5'UTRs). We establish a role for genetic variation in mediating inter-individual splicing differences, with local splicing quantitative trait loci (local-sQTLs) being preferentially located at the 5' end of transcripts and directly upstream of splice donor sites. Moreover, local-sQTLs are more numerous in the infected state, indicating that acute stress unmasks a substantial number of silent genetic variants. We observe a general increase in intron retention concentrated at the 5' end of transcripts across multiple strains, whose prevalence scales with the degree of pathogen virulence. The length, GC content, and RNA polymerase II occupancy of these introns with increased retention suggest that they have exon-like characteristics. We further uncover that retained intron sequences are enriched for the Lark/RBM4 RNA binding motif. Interestingly, we find that lark is induced by infection in wild-type flies, its overexpression and knockdown alter survival, and tissue-specific overexpression mimics infection-induced intron retention.

CONCLUSION

Our collective findings point to pervasive and consistent RNA splicing changes, partly mediated by Lark/RBM4, as being an important aspect of the gut response to infection.

The DNA polymerases of Drosophila melanogaster

DNA synthesis during replication or repair is a fundamental cellular process that is catalyzed by a set of evolutionary conserved polymerases. Despite a large body of research, the DNA polymerases of Drosophila melanogaster have not yet been systematically reviewed, leading to inconsistencies in their nomenclature, shortcomings in their functional (Gene Ontology, GO) annotations and an under-appreciation of the extent of their characterization. Here, we describe the complete set of DNA polymerases in D. melanogaster, applying nomenclature already in widespread use in other species, and improving their functional annotation. A total of 19 genes encode the proteins comprising three replicative polymerases (alpha-primase, delta, epsilon), five translesion/repair polymerases (zeta, eta, iota, Rev1, theta) and the mitochondrial polymerase (gamma). We also provide an overview of the biochemical and genetic characterization of these factors in D. melanogaster. This work, together with the incorporation of the improved nomenclature and GO annotation into key biological databases, including FlyBase and UniProtKB, will greatly facilitate access to information about these important proteins.

Lactobacillus probiotics improved the gut microbiota profile of a Drosophila melanogaster Alzheimer's disease model and alleviated neurodegeneration in the eye

Alzheimer's disease (AD) is a progressive disease and one of the most common forms of neurodegenerative disorders. Emerging evidence is supporting the use of various strategies that modulate gut microbiota to exert neurological and psychological changes. This includes the utilisation of probiotics as a natural and dietary intervention for brain health. Here, we showed the potential AD-reversal effects of Lactobacillus probiotics through feeding to our Drosophila melanogaster AD model. The administration of Lactobacillus strains was able to rescue the rough eye phenotype (REP) seen in AD-induced Drosophila, with a more prominent effect observed upon the administration of Lactobacillus plantarum DR7 (DR7). Furthermore, we analysed the gut microbiota of the AD-induced Drosophila and found elevated levels of Wolbachia. The administration of DR7 restored the gut microbiota diversity of AD-induced Drosophila with a significant reduction in Wolbachia's relative abundance, accompanied by an increase of Stenotrophomonas and Acetobacter. Through functional predictive analyses, Wolbachia was predicted to be positively correlated with neurodegenerative disorders, such as Parkinson's, Huntington's and Alzheimer's diseases, while Stenotrophomonas was negatively correlated with these neurodegenerative disorders. Altogether, our data exhibited DR7's ability to ameliorate the AD effects in our AD-induced Drosophila. Thus, we propose that Wolbachia be used as a potential biomarker for AD.

The Impact of Protein Architecture on Adaptive Evolution

Adaptive mutations play an important role in molecular evolution. However, the frequency and nature of these mutations at the intramolecular level are poorly understood. To address this, we analyzed the impact of protein architecture on the rate of adaptive substitutions, aiming to understand how protein biophysics influences fitness and adaptation. Using Drosophila melanogaster and Arabidopsis thaliana population genomics data, we fitted models of distribution of fitness effects and estimated the rate of adaptive amino-acid substitutions both at the protein and amino-acid residue level. We performed a comprehensive analysis covering genome, gene, and protein structure, by exploring a multitude of factors with a plausible impact on the rate of adaptive evolution, such as intron number, protein length, secondary structure, relative solvent accessibility, intrinsic protein disorder, chaperone affinity, gene expression, protein function, and protein-protein interactions. We found that the relative solvent accessibility is a major determinant of adaptive evolution, with most adaptive mutations occurring at the surface of proteins. Moreover, we observe that the rate of adaptive substitutions differs between protein functional classes, with genes encoding for protein biosynthesis and degradation signaling exhibiting the fastest rates of protein adaptation. Overall, our results suggest that adaptive evolution in proteins is mainly driven by intermolecular interactions, with host-pathogen coevolution likely playing a major role.

Making sense out of missense mutations: Mechanistic dissection of Notch receptors through structure-function studies in Drosophila

Notch signaling is involved in the development of almost all organ systems and is required post-developmentally to modulate tissue homeostasis. Rare variants in Notch signaling pathway genes are found in patients with rare Mendelian disorders, while unique or recurrent somatic mutations in a similar set of genes are identified in cancer. The human genome contains four genes that encode Notch receptors, NOTCH1-4, all of which are linked to genetic diseases and cancer. Although some mutations have been classified as clear loss- or gain-of-function alleles based on cellular or rodent based assay systems, the functional consequence of many variants/mutations in human Notch receptors remain unknown. In this review, I will first provide an overview of the domain structure of Notch receptors and discuss how each module is known to regulate Notch signaling activity in vivo using the Drosophila Notch receptor as an example. Next, I will introduce some interesting mutant alleles that have been isolated in the fly Notch gene over the past > 100 years of research and discuss how studies of these mutations have facilitated the understanding of Notch biology. By identifying unique alleles of the fly Notch gene through forward genetic screens, mapping their molecular lesions and characterizing their phenotypes in depth, one can begin to unravel new mechanistic insights into how different domains of Notch fine-tune signaling output. Such information can be useful in deciphering the functional consequences of rare variants/mutations in human Notch receptors, which in turn can influence disease management and therapy.

Bombardier Enables Delivery of Short-Form Bomanins in the Drosophila Toll Response

Toll mediates a robust and effective innate immune response across vertebrates and invertebrates. In Drosophila melanogaster, activation of Toll by systemic infection drives the accumulation of a rich repertoire of immune effectors in hemolymph, including the recently characterized Bomanins, as well as the classical antimicrobial peptides (AMPs). Here we report the functional characterization of a Toll-induced hemolymph protein encoded by the bombardier (CG18067) gene. Using the CRISPR/Cas9 system to generate a precise deletion of the bombardier transcriptional unit, we found that Bombardier is required for Toll-mediated defense against fungi and Gram-positive bacteria. Assaying cell-free hemolymph, we found that the Bomanin-dependent candidacidal activity is also dependent on Bombardier, but is independent of the antifungal AMPs Drosomycin and Metchnikowin. Using mass spectrometry, we demonstrated that deletion of bombardier results in the specific absence of short-form Bomanins from hemolymph. In addition, flies lacking Bombardier exhibited a defect in pathogen tolerance that we trace to an aberrant condition triggered by Toll activation. These results lead us to a model in which the presence of Bombardier in wild-type flies enables the proper folding, secretion, or intermolecular associations of short-form Bomanins, and the absence of Bombardier disrupts one or more of these steps, resulting in defects in both immune resistance and tolerance.

Dietary fatty acids promote sleep through a taste-independent mechanism

Consumption of foods that are high in fat contribute to obesity and metabolism-related disorders. Dietary lipids are comprised of triglycerides and fatty acids, and the highly palatable taste of dietary fatty acids promotes food consumption, activates reward centers in mammals and underlies hedonic feeding. Despite the central role of dietary fats in the regulation of food intake and the etiology of metabolic diseases, little is known about how fat consumption regulates sleep. The fruit fly, Drosophila melanogaster, provides a powerful model system for the study of sleep and metabolic traits, and flies potently regulate sleep in accordance with food availability. To investigate the effects of dietary fats on sleep regulation, we have supplemented fatty acids into the diet of Drosophila and measured their effects on sleep and activity. We found that flies fed a diet of hexanoic acid, a medium-chain fatty acid that is a by-product of yeast fermentation, slept more than flies starved on an agar diet. To assess whether dietary fatty acids regulate sleep through the taste system, we assessed sleep in flies with a mutation in the hexanoic acid receptor Ionotropic receptor 56D, which is required for fatty acid taste perception. We found that these flies also sleep more than agar-fed flies when fed a hexanoic acid diet, suggesting the sleep promoting effect of hexanoic acid is not dependent on sensory perception. Taken together, these findings provide a platform to investigate the molecular and neural basis for fatty acid-dependent modulation of sleep.

Circuit Mechanisms Underlying Chromatic Encoding in Drosophila Photoreceptors

Spectral information is commonly processed in the brain through generation of antagonistic responses to different wavelengths. In many species, these color opponent signals arise as early as photoreceptor terminals. Here, we measure the spectral tuning of photoreceptors in Drosophila. In addition to a previously described pathway comparing wavelengths at each point in space, we find a horizontal-cell-mediated pathway similar to that found in mammals. This pathway enables additional spectral comparisons through lateral inhibition, expanding the range of chromatic encoding in the fly. Together, these two pathways enable efficient decorrelation and dimensionality reduction of photoreceptor signals while retaining maximal chromatic information. A biologically constrained model accounts for our findings and predicts a spatio-chromatic receptive field for fly photoreceptor outputs, with a color opponent center and broadband surround. This dual mechanism combines motifs of both an insect-specific visual circuit and an evolutionarily convergent circuit architecture, endowing flies with the ability to extract chromatic information at distinct spatial resolutions.

DN1p or the "Fluffy" Cerberus of Clock Outputs

Drosophila melanogaster is a powerful genetic model to study the circadian clock. Recently, three drosophilists received the Nobel Prize for their intensive past and current work on the molecular clockwork (Nobel Prize 2017). The Drosophila brain clock is composed of about 150 clock neurons distributed along the lateral and dorsal regions of the protocerebrum. These clock neurons control the timing of locomotor behaviors. In standard light-dark (LD) conditions (12-12 h and constant 25°C), flies present a bi-modal locomotor activity pattern controlled by the clock. Flies increase their movement just before the light-transitions, and these behaviors are therefore defined as anticipatory. Two neuronal oscillators control the morning and evening anticipation. Knowing that the molecular clock cycles in phase in all clock neurons in the brain in LD, how can we explain the presence of two behavioral activity peaks separated by 12 h? According to one model, the molecular clock cycles in phase in all clock neurons, but the neuronal activity cycles with a distinct phase in the morning and evening oscillators. An alternative model takes the environmental condition into consideration. One group of clock neurons, the dorso-posterior clock neurons DN1p, drive two peaks of locomotor activity in LD even though their neuronal activity cycles with the same phase (late night/early morning). Interestingly, the locomotor outputs they control differ in their sensitivity to light and temperature. Hence, they must drive outputs to different neuropil regions in the brain, which also receive different inputs. Since 2010 and the presentation of the first specific DN1p manipulations, many studies have been performed to understand the role of this group of neurons in controlling locomotor behaviors. Hence, we review what we know about this heterogeneous group of clock neurons and discuss the second model to explain how clock neurons that oscillate with the same phase can drive behaviors at different times of the day.

MicroRNAs Regulate Multiple Aspects of Locomotor Behavior in Drosophila

Locomotion is an ancient and fundamental output of the nervous system required for animals to perform many other complex behaviors. Although the formation of motor circuits is known to be under developmental control of transcriptional mechanisms that define the fates and connectivity of the many neurons, glia and muscle constituents of these circuits, relatively little is known about the role of post-transcriptional regulation of locomotor behavior. MicroRNAs have emerged as a potentially rich source of modulators for neural development and function. In order to define the microRNAs required for normal locomotion in Drosophila melanogaster, we utilized a set of transgenic Gal4-dependent competitive inhibitors (microRNA sponges, or miR-SPs) to functionally assess ca. 140 high-confidence Drosophila microRNAs using automated quantitative movement tracking systems followed by multiparametric analysis. Using ubiquitous expression of miR-SP constructs, we identified a large number of microRNAs that modulate aspects of normal baseline adult locomotion. Addition of temperature-dependent Gal80 to identify microRNAs that act during adulthood revealed that the majority of these microRNAs play developmental roles. Comparison of ubiquitous and neural-specific miR-SP expression suggests that most of these microRNAs function within the nervous system. Parallel analyses of spontaneous locomotion in adults and in larvae also reveal that very few of the microRNAs required in the adult overlap with those that control the behavior of larval motor circuits. These screens suggest that a rich regulatory landscape underlies the formation and function of motor circuits and that many of these mechanisms are stage and/or parameter-specific.