A comparison of the transcriptome of Drosophila melanogaster in response to entomopathogenic fungus, ionizing radiation, starvation and cold shock

Polyploidy promotes transformation of epithelial cells into non-professional phagocytes

Removal of dead and damaged cells is critical for organismal health. Under stress conditions such as nutritional deprivation, infection, or temperature shift, the clearance of nonessential cells becomes a universal strategy to conserve energy and maintain tissue homeostasis. Typically, this task is performed by professional phagocytes such as macrophages. However, non-professional phagocytes (NPPs) can also adopt a phagocytic fate under specific circumstances. Similar to professional phagocytes, NPPs undergo transitions from immature to mature states and activation, but the precise cellular and molecular mechanisms governing their maturation, induction and phagocytic execution remain largely unknown. A notable example of stress-induced phagocytosis is the removal of germline cells by follicle cell-derived NPPs during oogenesis in Drosophila . In this study, we report that the transformation of follicle cells into NPPs is dependent on Notch signaling activation during mid-oogenesis. Moreover, Notch overactivation is sufficient to trigger germline cell death and clearance (GDAC). We further show that polyploidy, driven by Notch signaling-induced endoreplication, is essential for the transformation of follicle cells into NPPs. Polyploidy facilitates the activation of JNK signaling, which is crucial for the phagocytic behavior of these cells. Additionally, we show that polyploidy in epidermal cells, another type of NPPs, is important for their engulfment of dendrites during induced degeneration. Together, these findings suggest that polyploidy is a critical factor in the transformation of epithelial cells into NPPs, enabling their phagocytic functions, which are essential for maintaining cellular and organismal homeostasis during stress conditions.

SIGNIFICANCE

The ability to remove dead and damaged cells is essential for maintaining tissue homeostasis and organismal health. While this task is typically performed by professional phagocytes such as macrophages, non-professional phagocytes (NPPs) can also acquire phagocytic functions during development or in response to stress conditions. Using Drosophila oogenesis as a model, we reveal that the transformation of follicle cells into NPPs is driven by Notch signaling and is critically dependent on polyploidy. Our findings show that polyploidy, induced through Notch signaling-mediated endoreplication, is required for activating JNK signaling, a pathway essential for the phagocytic behavior of NPPs. Furthermore, we show that polyploidy also facilitates the phagocytic activity of epidermal cells in clearing degenerating dendrites. Together, these results suggest that polyploidy plays an important role in enabling epithelial cells to adopt NPP functions and in maintaining tissue and organismal homeostasis under stress conditions.

Wolbachia enhances the survival of Drosophila infected with fungal pathogens

BACKGROUND

Wolbachia bacteria of arthropods are at the forefront of basic and translational research on multipartite host-symbiont-pathogen interactions. These vertically transmitted microbes are the most widespread endosymbionts on the planet due to factors including host reproductive manipulation and fitness benefits. Importantly, some strains of Wolbachia can inhibit viral pathogenesis within and between arthropod hosts. Mosquitoes carrying the wMel Wolbachia strain of Drosophila melanogaster have a greatly reduced capacity to spread viruses like dengue and Zika to humans. While significant research efforts have focused on viruses, relatively little attention has been given to Wolbachia-fungal interactions despite the ubiquity of fungal entomopathogens in nature.

RESULTS

Here, we demonstrate that Wolbachia increase the longevity of their Drosophila melanogaster hosts when challenged with a spectrum of yeast and filamentous fungal pathogens. We find that this pattern can vary based on host genotype, sex, and fungal species. Further, Wolbachia correlates with higher fertility and reduced pathogen titers during initial fungal infection, indicating a significant fitness benefit. Finally, RNA sequencing results show altered expression of many immune and stress response genes in the context of Wolbachia and fungal infection, suggesting host immunity may be involved in the mechanism.

CONCLUSIONS

This study demonstrates Wolbachia's protective role in diverse fungal pathogen interactions and determines that the phenotype is broad, but with several variables that influence both the presence and strength of the phenotype. It also is a critical step forward to understanding how symbionts can protect their hosts from a variety of pathogens.

Nutritional stress in larvae induces adaptive responses that transcend generations in males of a model insect

The ability of organisms to cope with poor quality nutrition is essential for their persistence. For species with a short generation time, the nutritional environments can transcend generations, making it beneficial for adults to prime their offspring to particular diets. However, our understanding of adaptive generational responses, including those to diet quality, are still very limited. Here, we used the vinegar fly, Drosophila melanogaster, to investigate whether females developing as larvae on a nutritionally poor diet produce offspring that are primed for nutrient deficiencies in the following generations. We found that females developed on low-quality diets produced offspring that, on similarly low-quality diets, had both increased egg-to-adult viability and starvation tolerance compared with offspring of females experiencing a nutrient-rich diet. When testing the persistence of such generational priming, we found that just one generation of high-quality diet is sufficient to erase the signal of priming. A global transcriptomic profile analysis on male offspring suggests that the observed phenotypic priming is not a constitutive transcriptomic adjustment of adults; instead, offspring are probably primed as larvae, enabling them to initiate an adaptive response as adults when exposed to low-quality diets. Our results support that generational priming is an important adaptive mechanism that enables organisms to cope with transient nutritional fluctuations.

Drosophila melanogaster experimental model to test new antimicrobials: a methodological approach

Given the increasing concern about antimicrobial resistance among the microorganisms that cause infections in our society, there is an urgent need for new drug discovery. Currently, this process involves testing many low-quality compounds, resulting from the in vivo testing, on mammal models, which not only wastes time, resources, and money, but also raises ethical questions. In this review, we have discussed the potential of D. melanogaster as an intermediary experimental model in this drug discovery timeline. We have tackled the topic from a methodological perspective, providing recommendations regarding the range of drug concentrations to test based on the mechanism of action of each compound; how to treat D. melanogaster, how to monitor that treatment, and what parameters we should consider when designing a drug screening protocol to maximize the study's benefits. We also discuss the necessary improvements needed to establish the D. melanogaster model of infection as a standard technique in the drug screening process. Overall, D. melanogaster has been demonstrated to be a manageable model for studying broad-spectrum infection treatment. It allows us to obtain valuable information in a cost-effective manner, which can improve the drug screening process and provide insights into our current major concern. This approach is also in line with the 3R policy in biomedical research, in particular on the replacement and reduce the use of vertebrates in preclinical development.

Glucocerebrosidase deficiency leads to neuropathology via cellular immune activation

Mutations in GBA (glucosylceramidase beta), which encodes the lysosomal enzyme glucocerebrosidase (GCase), are the strongest genetic risk factor for the neurodegenerative disorders Parkinson's disease (PD) and Lewy body dementia. Recent work has suggested that neuroinflammation may be an important factor in the risk conferred by GBA mutations. We therefore systematically tested the contributions of immune-related genes to neuropathology in a Drosophila model of GCase deficiency. We identified target immune factors via RNA-Seq and proteomics on heads from GCase-deficient flies, which revealed both increased abundance of humoral factors and increased macrophage activation. We then manipulated the identified immune factors and measured their effect on head protein aggregates, a hallmark of neurodegenerative disease. Genetic ablation of humoral (secreted) immune factors did not suppress the development of protein aggregation. By contrast, re-expressing Gba1b in activated macrophages suppressed head protein aggregation in Gba1b mutants and rescued their lifespan and behavioral deficits. Moreover, reducing the GCase substrate glucosylceramide in activated macrophages also ameliorated Gba1b mutant phenotypes. Taken together, our findings show that glucosylceramide accumulation due to GCase deficiency leads to macrophage activation, which in turn promotes the development of neuropathology.

Pathogen infection alters the gene expression landscape of transposable elements in Drosophila melanogaster

Transposable elements make up substantial proportions of eukaryotic genomes and many are thought to be remnants of ancient viral infections. Current research has begun to highlight the role transposable elements can play in the immune system response to infections. However, most of our knowledge about transposable element expression during infection is limited by the specific host and pathogen factors from each study, making it difficult to compare studies and develop broader patterns regarding the role of transposable elements during infection. Here, we use the tools and resources available in the model, Drosophila melanogaster, to analyze multiple gene expression datasets of flies subject to bacterial, fungal, and viral infections. We analyzed differences in pathogen species, host genotype, host tissue, and sex to understand how these factors impact transposable element expression during infection. Our results highlight both shared and unique transposable element expression patterns between pathogens and suggest a larger effect of pathogen factors over host factors for influencing transposable element expression.

Analysis of X-ray irradiation effects on the mortality values and hemolymph immune cell composition of Apis mellifera and its parasite, Varroa destructor

Varroa destructor is one of the most destructive enemies of the honey bee, Apis mellifera all around the world. Several control methods are known to control V. destructor, but the efficacy of several alternative control methods remains unexplored. Irradiation can be one of these unknown solutions but before practical application, the effectiveness, and the physiological effects of ionizing radiation on the host and the parasite are waiting to be tested. Therefore, the objective of our study was to investigate the effects of different doses (15, 50, 100, and 150 Gy) of high-energy X-ray irradiation through mortality rates and hemocyte composition changes in A. mellifera workers and record the mortality rates of the parasite. The mortality rate was recorded during short-term (12, 24, and 48 h) and long-term periods (3, 6, 12, 18, and 24d). The sensitivity of the host and the parasite in case of the higher doses of radiation tested (50, 100, and 150 Gy) been demonstrated by total mortality of the host and 90 % of its parasite has been observed on the 18th day after the irradiation. V. destructor showed higher sensitivity (1.52-times higher than the adult honey bee workers) at the lowest dose (15 Gy). A. mellifera hemocytes were influenced significantly by radiation dosage and the elapsed time after treatment. The higher radiation doses increased plasmatocyte numbers in parallel with the decrease in prohemocyte numbers. On the contrary, the numbers of granulocytes and oencoytes increased in the treated samples, but the putative effects of the different dosages on the recorded number of these hemocyte types could not be statistically proven. In summary, based on the outcome of our study X-ray irradiation can be deemed an effective tool for controlling phoretic V. destructor. However, further research is needed to understand the physiological response of the affected organisms.

Impact of tRNA-induced proline-to-serine mistranslation on the transcriptome of Drosophila melanogaster

Mistranslation is the misincorporation of an amino acid into a polypeptide. Mistranslation has diverse effects on multicellular eukaryotes and is implicated in several human diseases. In Drosophila melanogaster, a serine transfer RNA (tRNA) that misincorporates serine at proline codons (P→S) affects male and female flies differently. The mechanisms behind this discrepancy are currently unknown. Here, we compare the transcriptional response of male and female flies to P→S mistranslation to identify genes and cellular processes that underlie sex-specific differences. Both males and females downregulate genes associated with various metabolic processes in response to P→S mistranslation. Males downregulate genes associated with extracellular matrix organization and response to negative stimuli such as wounding, whereas females downregulate aerobic respiration and ATP synthesis genes. Both sexes upregulate genes associated with gametogenesis, but females also upregulate cell cycle and DNA repair genes. These observed differences in the transcriptional response of male and female flies to P→S mistranslation have important implications for the sex-specific impact of mistranslation on disease and tRNA therapeutics.

The tardigrade Hypsibius exemplaris dramatically upregulates DNA repair pathway genes in response to ionizing radiation

Tardigrades can survive remarkable doses of ionizing radiation, up to about 1,000 times the lethal dose for humans. How they do so is incompletely understood. We found that the tardigrade Hypsibius exemplaris suffers DNA damage upon gamma irradiation, but the damage is repaired. We show that this species has a specific and robust response to ionizing radiation: irradiation induces a rapid upregulation of many DNA repair genes. This upregulation is unexpectedly extreme-making some DNA repair transcripts among the most abundant transcripts in the animal. By expressing tardigrade genes in bacteria, we validate that increased expression of some repair genes can suffice to increase radiation tolerance. We show that at least one such gene is important in vivo for tardigrade radiation tolerance. We hypothesize that the tardigrades' ability to sense ionizing radiation and massively upregulate specific DNA repair pathway genes may represent an evolved solution for maintaining DNA integrity.

Lipidome Unsaturation Affects the Morphology and Proteome of the Drosophila Eye

Organisms respond to dietary and environmental challenges by altering the molecular composition of their glycerolipids and glycerophospholipids (GPLs), which may favorably adjust the physicochemical properties of lipid membranes. However, how lipidome changes affect the membrane proteome and, eventually, the physiology of specific organs is an open question. We addressed this issue in Drosophila melanogaster, which is not able to synthesize sterols and polyunsaturated fatty acids but can acquire them from food. We developed a series of semisynthetic foods to manipulate the length and unsaturation of fatty acid moieties in GPLs and singled out proteins whose abundance is specifically affected by membrane lipid unsaturation in the Drosophila eye. Unexpectedly, we identified a group of proteins that have muscle-related functions and increased their abundances under unsaturated eye lipidome conditions. In contrast, the abundance of two stress response proteins, Turandot A and Smg5, is decreased by lipid unsaturation. Our findings could guide the genetic dissection of homeostatic mechanisms that maintain visual function when the eye is exposed to environmental and dietary challenges.

Glucocerebrosidase deficiency leads to neuropathology via cellular immune activation

Mutations in GBA (glucosylceramidase beta), which encodes the lysosomal enzyme glucocerebrosidase (GCase), are the strongest genetic risk factor for the neurodegenerative disorders Parkinson's disease (PD) and Lewy body dementia. Recent work has suggested that neuroinflammation may be an important factor in the risk conferred by GBA mutations. We therefore systematically tested the contributions of immune-related genes to neuropathology in a Drosophila model of GCase deficiency. We identified target immune factors via RNA-Seq and proteomics on heads from GCase-deficient flies, which revealed both increased abundance of humoral factors and increased macrophage activation. We then manipulated the identified immune factors and measured their effect on head protein aggregates, a hallmark of neurodegenerative disease. Genetic ablation of humoral (secreted) immune factors did not suppress the development of protein aggregation. By contrast, re-expressing Gba1b in activated macrophages suppressed head protein aggregation in Gba1b mutants and rescued their lifespan and behavioral deficits. Moreover, reducing the GCase substrate glucosylceramide in activated macrophages also ameliorated Gba1b mutant phenotypes. Taken together, our findings show that glucosylceramide accumulation due to GCase deficiency leads to macrophage activation, which in turn promotes the development of neuropathology.

Exploring cross-protective effects between cold and immune stress in Drosophila melanogaster

It is well established that environmental and biotic stressors like temperature and pathogens/parasites are essential for the life of small ectotherms. There are complex interactions between cold stress and pathogen infection in insects. Possible cross-protective mechanisms occur between both stressors, suggesting broad connectivity in insect stress responses. In this study, the functional significance of these interactions was tested, as well as the potential role of newly uncovered candidate genes, turandot. This was done using an array of factorial experiments exposing Drosophila melanogaster flies to a combination of different cold stress regimes (acute or chronic) and infections with the parasitic fungus Beauveria bassiana. Following these crossed treatments, phenotypic and molecular responses were assessed by measuring 1) induced cold tolerance, 2) immune resistance to parasitic fungus, and 3) activation of turandot genes. We found various responses in the phenotypic outcomes according to the various treatment combinations with higher susceptibility to infection following cold stress, but also significantly higher acute cold survival in flies that were infected. Regarding molecular responses, we found overexpression of turandot genes in response to most treatments, suggesting reactivity to both cold and infection. Moreover, maximum peak expressions were distinctly observed in the combined treatments (infection plus cold), indicating a marked synergistic effect of the stressors on turandot gene expression patterns. These results reflect the great complexity of cross-tolerance reactions between infection and abiotic stress, but could also shed light on the mechanisms underlying the activation of these responses.

The tardigrade Dsup protein enhances radioresistance in Drosophila melanogaster and acts as an unspecific repressor of transcription

The tardigrade-unique damage suppressor protein (Dsup) can protect DNA from ionizing radiation and reactive oxygen species (ROS). In this study, we generated Dsup-expressing lines of Drosophila melanogaster and demonstrated that Dsup increased the survival rate after γ-ray irradiation and hydrogen peroxide treatment in flies too, but reduced the level of their locomotor activity. The transcriptome analyses of Dsup-expressing lines revealed a significant number of DEGs, >99% of which were down-regulated. Moreover, Dsup could bind RNA. These findings suggest that Dsup can act not only as a DNA protector but also as a non-specific transcriptional repressor and RNA-binding protein, that may lead to disturbance of a number of biological processes in D. melanogaster. The obtained data demonstrate features of the Dsup protein action in non-tardigrade organisms and can be used to understand the impact of other unspecific DNA/RNA-binding proteins on ROS and radiation resistance, gene expression, and epigenetic processes.

Lipidome unsaturation affects the morphology and proteome of the Drosophila eye

While the proteome of an organism is largely determined by the genome, the lipidome is shaped by a poorly understood interplay of environmental factors and metabolic processes. To gain insights into the underlying mechanisms, we analyzed the impacts of dietary lipid manipulations on the ocular proteome of Drosophila melanogaster . We manipulated the lipidome with synthetic food media that differed in the supplementation of an equal amount of saturated or polyunsaturated triacylglycerols. This allowed us to generate flies whose eyes had a highly contrasting length and unsaturation of glycerophospholipids, the major lipid class of biological membranes, while the abundance of other membrane lipid classes remained unchanged. By bioinformatically comparing the resulting ocular proteomic trends and contrasting them with the impacts of vitamin A deficiency, we identified ocular proteins whose abundances are differentially affected by lipid saturation and unsaturation. For instance, we unexpectedly identified a group of proteins that have muscle-related functions and increase their abundances in the eye upon lipidome unsaturation but are unaffected by lipidome saturation. Moreover, we identified two differentially lipid-responsive proteins involved in stress responses, Turandot A and Smg5, whose abundances decrease with lipid unsaturation. Lastly, we discovered that the ocular lipid class composition is robust to dietary changes and propose that this may be a general homeostatic feature of the organization of eukaryotic tissues, while the length and unsaturation of fatty acid moieties is more variable to compensate environmental challenges. We anticipate that these insights into the molecular responses of the Drosophila eye proteome to specific lipid manipulations will guide the genetic dissection of the mechanisms that maintain visual function when the eye is exposed to dietary challenges.

A functional study of the role of Turandot genes in Drosophila melanogaster: An emerging candidate mechanism for inducible heat tolerance

Plastic responses to heat stress have been shown to temporarily increase heat stress tolerance in many small ectotherms. Heat shock proteins (Hsps) have previously been shown to play a role in this induced heat stress tolerance. The heat shock response is fast but short lived, with the cellular Hsp concentration peaking within a few hours after induction. Induced heat stress tolerance, on the other hand, peaks 16-32 h after induction. Therefore, the inducible heat stress response must depend on additional mechanisms. The Turandot gene family has been suggested as a candidate. It contains eight genes that are all upregulated to some degree following heat stress in Drosophila melanogaster. Previously, Turandot A (totA) and Turandot X (totX) have been linked to induced heat stress tolerance. The study presented here aimed to investigate the temporal dynamics of Turandot expression and the functional role of totA and totC for heat stress tolerance. This was done by assaying the temporal heat tolerance and Turandot gene expression after a heat insult, and by exposing Turandot gene knock down flies to a range of heat hardening treatments, and evaluating the effects on heat tolerance. Successful gene knock down was verified by gene expression assays. In addition, expression of hsp70A was included. Both totA, totC, and hsp70A expression increased following a heat hardening treatment, while the results for totX were less clear. The expression of totC temporally co-occurred with and was functionally linked to increased heat tolerance. Expression of totA did not have a significant effect on heat stress tolerance. The complexity of inducible heat tolerance was underlined by the result that knock down of Turandot genes led to increased expression of hsp70. The results suggest that heat tolerance is determined by the interaction between several mechanisms, of which Turandot genes constitute one such mechanism.

Transcriptome analysis of the response to low temperature acclimation in Calliptamus italicus eggs

Background

Calliptamus italicus is a dominant species in the desert and semi-desert grassland. It is widely distributed throughout many regions such as Asia, Europe, North Africa and the Mediterranean, and has enormous destructive potential for agriculture and animal husbandry. The C. italicus overwintering as eggs in the soil through diapause, and the cold tolerance of locust eggs is the key to their ability to survive the winter smoothly to maintain the population.

Results

Transcriptome analysis of C. italicus eggs was carried out in this paper in constant low temperature acclimation, natural low temperature acclimation and room temperature. The differentially expressed genes related to cold tolerance were screened out, the differences in expression patterns under different low temperature acclimation were analyzed, and the genes in the significantly up-regulated pathways may play an important role in cold tolerance. The results show that different domestication modes can induce C. italicus eggs to express a large number of genes to alleviate low temperature damage, but C. italicus eggs are more sensitive to changes in temperature. Compared with the control, there are 8689 DEGs at constant low temperature and 14,994 DEGs at natural low temperature. KEGG analysis showed that DEGs were mainly enriched in pathways related to metabolism and biological systems under constant low temperature, and were mainly enriched in pathways related to biological systems and environmental information processing under natural low temperature. In addition, RNAi technology was used to further verify the regulation of genes in the significantly enriched up-regulated pathways on C. italicus eggs, and it was confirmed that the hatching rate of C. italicus eggs at low temperature was significantly reduced after interference.

Conclusions

Transcriptome analysis of C. italicus eggs treated at different temperatures provided a theoretical basis for further understanding the adaptation mechanism of C. italicus eggs to low temperature. In addition, four potential RNAi target genes were verified in the eggs of C. italicus for the first time, providing new ideas for effective control of this species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08705-3.

Deletions of the cystathionine-β-synthase (CBS) and cystathionine-γ-lyase (CSE) genes, involved in the control of hydrogen sulfide biosynthesis, significantly affect lifespan and fitness components of Drosophila melanogaster

The gasotransmitter hydrogen sulfide (H2S) is an important biological mediator, playing an essential role in many physiological and pathological processes. It is produced by transsulfuration - an evolutionarily highly conserved pathway for the metabolism of sulfur-containing amino acids methionine and cysteine. Cystathionine-β-synthase (CBS) and cystathionine-γ-lyase (CSE) enzymes play a central role in cysteine metabolism and H2S production. Here we investigated the fitness components (longevity, stress resistance, viability of preimaginal stages, and reproductive function parameters) in D. melanogaster lines containing deletions of the CBS and CSE genes. Surprisingly, in most tests, CSE deletion improved, and CBS worsened the fitness. Lines with deletion of both CBS and CSE demonstrated better stress resistance and longevity than lines with single CBS deletion. At the same time, deletion of both CBS and CSE genes causes more serious disturbances of reproductive function parameters than single CBS deletion. Thus, a complex interaction of H2S-producing pathways and cellular stress response in determining the lifespan and fitness components of the whole organism was revealed.

Fitness Analysis and Transcriptome Profiling Following Repeated Mild Heat Stress of Varying Frequency in Drosophila melanogaster Females

Simple Summary

We studied the effect of mild heat stress (38 °C, 1 h) occurring once a day or once a week on D. melanogaster fertility, longevity, body composition metabolism and differential gene expression in fat body and adjacent tissues. Weekly stress in the first two weeks did not affect longevity but caused a decrease in fat content and an increase in the total level of fertility. Daily stress caused a significant longevity, fertility and fat content decrease, but an increase in carbohydrate levels compared with the control group. These data agree well with the results of transcriptome analysis, which demonstrated significant changes in expression levels of genes involved in proteolysis/digestion following daily stress. Heat shock protein 23 and stress-inducible humoral factor Turandot gene network are also involved. It is notable that daily and weekly heat stress resulted in different changes in metabolism, fitness and differential gene expression.

Abstract

Understanding how repeated stress affects metabolic and physiological functions in the long run is of crucial importance for evaluating anthropogenic pressure on the environment. We investigated fertility, longevity and metabolism in D. melanogaster females exposed to short-term heat stress (38 °C, 1 h) repeated daily or weekly. Daily stress was shown to cause a significant decrease in both fertility and longevity, as well as in body mass and triglyceride (fat) content, but a significant increase in trehalose and glucose content. Weekly stress did not affect longevity and carbohydrate metabolism but resulted in a significant decrease in body mass and fat content. Weekly stress did not affect the total level of fertility, despite sharp fertility drops on the exact days of stressing. However, stressing insects weekly, only in the first two weeks after eclosion, caused a significant increase in the total level of fertility. The analysis of differentially expressed genes in the fat bodies and adjacent tissues of researched groups with the use of RNA-Seq profiling revealed changes in signal pathways related to proteolysis/digestion, heat shock protein 23, and in the tightly linked stress-inducible humoral factor Turandot gene network.

Mifepristone Increases Life Span of Virgin Female Drosophila on Regular and High-fat Diet Without Reducing Food Intake

Background: The synthetic steroid mifepristone is reported to have anti-obesity and anti-diabetic effects in mammals on normal and high-fat diets (HFD). We previously reported that mifepristone blocks the negative effect on life span caused by mating in female Drosophila melanogaster. Methods: Here we asked if mifepristone could protect virgin females from the life span-shortening effect of HFD. Mifepristone was assayed for effects on life span in virgin females, in repeated assays, on regular media and on media supplemented with coconut oil (HFD). The excrement quantification (EX-Q) assay was used to measure food intake of the flies after 12 days mifepristone treatment. In addition, experiments were conducted to compare the effects of mifepristone in virgin and mated females, and to identify candidate mifepristone targets and mechanisms. Results: Mifepristone increased life span of virgin females on regular media, as well as on media supplemented with either 2.5 or 5% coconut oil. Food intake was not reduced in any assay, and was significantly increased by mifepristone in half of the assays. To ask if mifepristone might rescue virgin females from all life span-shortening stresses, the oxidative stressor paraquat was tested, and mifepristone produced little to no rescue. Analysis of extant metabolomics and transcriptomics data suggested similarities between effects of mifepristone in virgin and mated females, including reduced tryptophan breakdown and similarities to dietary restriction. Bioinformatics analysis identified candidate mifepristone targets, including transcription factors Paired and Extra-extra. In addition to shortening life span, mating also causes midgut hypertrophy and activation of the lipid metabolism regulatory factor SREBP. Mifepristone blocked the increase in midgut size caused by mating, but did not detectably affect midgut size in virgins. Finally, mating increased activity of a SREBP reporter in abdominal tissues, as expected, but reporter activity was not detectably reduced by mifepristone in either mated or virgin females. Conclusion: Mifepristone increases life span of virgin females on regular and HFD without reducing food intake. Metabolomics and transcriptomics analyses suggest some similar effects of mifepristone between virgin and mated females, however reduced midgut size was observed only in mated females. The results are discussed regarding possible mifepristone mechanisms and targets.

Circadian regulation of the Drosophila astrocyte transcriptome

Recent studies have demonstrated that astrocytes cooperate with neurons of the brain to mediate circadian control of many rhythmic processes including locomotor activity and sleep. Transcriptional profiling studies have described the overall rhythmic landscape of the brain, but few have employed approaches that reveal heterogeneous, cell-type specific rhythms of the brain. Using cell-specific isolation of ribosome-bound RNAs in Drosophila, we constructed the first circadian “translatome” for astrocytes. This analysis identified 293 “cycling genes” in astrocytes, most with mammalian orthologs. A subsequent behavioral genetic screen identified a number of genes whose expression is required in astrocytes for normal sleep behavior. In particular, we show that certain genes known to regulate fly innate immune responses are also required for normal sleep patterns.

First transcriptome profiling of D. melanogaster after development in a deep underground low radiation background laboratory

Natural background radiation is a permanent multicomponent factor. It has an influence on biological organisms, but effects of its deprivation still remain unclear. The aim of our work was to study for the first time responses of D. melanogaster to conditions of the Deep Underground Low-Background Laboratory DULB-4900 (BNO, INR, RAS, Russia) at the transcriptome level by RNA-seq profiling. Overall 77 transcripts demonstrated differential abundance between flies exposed to low and natural background radiation. Enriched biological process functional categories were established for all genes with differential expression. The results showed down-regulation of primary metabolic processes and up-regulation of both the immune system process and the response to stimuli. The comparative analysis of our data and publicly available transcriptome data on D. melanogaster exposed to low and high doses of ionizing radiation did not reveal common DEGs in them. We hypothesize that the observed changes in gene expression can be explained by the influence of the underground conditions in DULB-4900, in particular, by the lack of stimuli. Thus, our study challenges the validity of the LNT model for the region of background radiation doses below a certain level (~16.4 nGy h-1) and the presence of a dose threshold for D. melanogaster.

Transcriptome Profiling of Starvation in the Peripheral Chemosensory Organs of the Crop Pest Spodoptera littoralis Caterpillars

Simple Summary

Starvation increases olfactory sensitivity in a manner that enhances the search for food in animals, including insects. However, the molecular mechanisms via which starvation modulates olfactory receptor neuron function are poorly understood. In this study, we sequenced and compared the whole transcriptomes of the main olfactory organs (antennae and palps) of fed and starved caterpillars from the species Spodoptera littoralis. We revealed that transcripts involved in several biological processes are regulated upon starvation. These processes include glucose metabolism, immune defense, foraging activity, and olfaction. In this last process, we evidenced regulation of chemosensory proteins and odorant-degrading enzymes, known to play a role in the dynamics and the sensitivity of the olfactory receptor neuron response. Our results identify new elements in the cascade of olfactory neuron modulation, in addition to insulin, GABA, and short neuropeptide F signaling.

Abstract

Starvation is frequently encountered by animals under fluctuating food conditions in nature, and response to it is vital for life span. Many studies have investigated the behavioral and physiological responses to starvation. In particular, starvation is known to induce changes in olfactory behaviors and olfactory sensitivity to food odorants, but the underlying mechanisms are not well understood. Here, we investigated the transcriptional changes induced by starvation in the chemosensory tissues of the caterpillar Spodoptera littoralis, using Illumina RNA sequencing. Gene expression profiling revealed 81 regulated transcripts associated with several biological processes, such as glucose metabolism, immune defense, response to stress, foraging activity, and olfaction. Focusing on the olfactory process, we observed changes in transcripts encoding proteins putatively involved in the peri-receptor events, namely, chemosensory proteins and odorant-degrading enzymes. Such modulation of their expression may drive fluctuations in the dynamics and the sensitivity of the olfactory receptor neuron response. In combination with the enhanced presynaptic activity mediated via the short neuropeptide F expressed during fasting periods, this could explain an enhanced olfactory detection process. Our observations suggest that a coordinated transcriptional response of peripheral chemosensory organs participates in the regulation of olfactory signal reception and olfactory-driven behaviors upon starvation.

ERp44/CG9911 promotes fat storage in Drosophila adipocytes by regulating ER Ca2+ homeostasis

Fat storage is one of the important strategies employed in regulating energy homeostasis. Impaired lipid storage causes metabolic disorders in both mammals and Drosophila. In this study, we report CG9911, the Drosophila homolog of ERp44 (endoplasmic reticulum protein 44) plays a role in regulating adipose tissue fat storage. Using the CRISPR/Cas9 system, we generated a CG9911 mutant line deleting 5 bp of the coding sequence. The mutant flies exhibit phenotypes of lower bodyweight, fewer lipid droplets, reduced TAG level and increased expression of lipolysis related genes. The increased lipolysis phenotype is enhanced in the presence of ER stresses and suppressed by a reduction of the ER Ca²⁺. Moreover, loss of CG9911 per se results in a decrease of ER Ca²⁺ in the fat body. Together, our results reveal a novel function of CG9911 in promoting fat storage via regulating ER Ca²⁺ signal in Drosophila.

Tissue-Specific Knockdown of Genes of the Argonaute Family Modulates Lifespan and Radioresistance in Drosophila Melanogaster

Small RNAs are essential to coordinate many cellular processes, including the regulation of gene expression patterns, the prevention of genomic instability, and the suppression of the mutagenic transposon activity. These processes determine the aging, longevity, and sensitivity of cells and an organism to stress factors (particularly, ionizing radiation). The biogenesis and activity of small RNAs are provided by proteins of the Argonaute family. These proteins participate in the processing of small RNA precursors and the formation of an RNA-induced silencing complex. However, the role of Argonaute proteins in regulating lifespan and radioresistance remains poorly explored. We studied the effect of knockdown of Argonaute genes (AGO1, AGO2, AGO3, piwi) in various tissues on the Drosophila melanogaster lifespan and survival after the γ-irradiation at a dose of 700 Gy. In most cases, these parameters are reduced or did not change significantly in flies with tissue-specific RNA interference. Surprisingly, piwi knockdown in both the fat body and the nervous system causes a lifespan increase. But changes in radioresistance depend on the tissue in which the gene was knocked out. In addition, analysis of changes in retrotransposon levels and expression of stress response genes allow us to determine associated molecular mechanisms.

Identification of key genes associated with overwintering in Anoplophora glabripennis larva using gene co-expression network analysis

BACKGROUND

Anoplophora glabripennis (Coleoptera: Cerambycidae) is a major quarantine pest in forestry. It is widely distributed throughout many regions such as Asia, Europe, and North America, and has enormous destructive potential for forests. The larvae of A. glabripennis overwinter in a dormant state with strong cold tolerance, and whether the larvae survive winter determines the population density in the following year. However, the molecular mechanisms of this process are not clear.

RESULTS

RNA sequencing (RNA-Seq) analysis of A. glabripennis larvae at five overwintering stages identified 6876 differentially expressed genes (DEGs). Among these, 46 functional genes that might respond to low temperature were identified. Weighted gene co-expression network analysis revealed that the MEturquoise module was correlated with the overwintering process. The STPK, PP2A, DGAT, and HSF genes were identified as hub genes using visualization of gene network. In addition, four genes related to sugar transport, gluconeogenesis and glycosylation were screened, which may be involved in the metabolic regulation of overwintering larvae. The protein-protein interaction network indicated that ribosomal protein and ATP synthase may play an important role in connecting with other proteins. The expression levels of fifteen hub genes were further validated by quantitative RT-PCR, and the results were consistent with RNA-Seq.

CONCLUSION

This study demonstrates key genes that may reveal the molecular mechanism of overwintering in A. glabripennis larvae. The genes may be the potential targets to prevent larvae from surviving the cold winter by developing new biological agents using genetic engineering.

Oxidative and radiation stress induces transposable element transcription in Drosophila melanogaster

It has been shown that stressors are capable of activating transposable elements (TEs). Currently, there is a hypothesis that stress activation of TEs may be involved in adaptive evolution, favouring the increase in genetic variability when the population is under adverse conditions. However, TE activation under stress is still poorly understood. In the present study, we estimated the fraction of differentially expressed TEs (DETEs) under ionizing radiation (144, 360 and 864 Gy) and oxidative stress (dioxin, formaldehyde and toluene) treatments. The stress intensity of each treatment was estimated by measuring the number of differentially expressed genes, and we show that several TEs families are activated by stress whereas others are repressed. The proportion of DETEs was positively related to stress intensity. However, even under the strongest stress, only a small fraction of TE families were activated (9.28%) and 17.72% were repressed. Considering all treatments together, the activated proportion was 19.83%. Nevertheless, as several TEs are incomplete or degenerated, only 10.55% of D. melanogaster mobilome is, at same time, activated by the stressors and able to transpose or at least code a protein. Thus, our study points out that although stress activates TEs, it is not a generalized activation process, and for some families, the stress induces repression.

Amyloid-β peptides slightly affect lifespan or antimicrobial peptide gene expression in Drosophila melanogaster

Background

Beta-amyloid peptide (Aβ) is the key protein in the pathogenesis of Alzheimer’s disease, the most common age-related neurodegenerative disorder in humans. Aβ peptide induced pathological phenotypes in different model organisms include neurodegeneration and lifespan decrease. However, recent experimental evidence suggests that Aβ may utilize oligomerization and fibrillization to function as an antimicrobial peptide (AMP), and protect the host from infections. We used the power of Drosophila model to study mechanisms underlying a dual role for Aβ peptides.

Results

We investigated the effects of Drosophila treatment with three Aβ42 peptide isoforms, which differ in their ability to form oligomers and aggregates on the lifespan, locomotor activity and AMP genes expression. Aβ42 slightly decreased female’s median lifespan (by 4.5%), but the effect was not related to the toxicity of peptide isoform. The lifespan and relative levels of AMP gene expression in male flies as well as locomotor activity in both sexes were largely unaffected by Aβ42 peptide treatment. Regardless of the effects on lifespan, Aβ42 peptide treatment induced decrease in AMP genes expression in females, but the effects were not robust.

Conclusions

The results demonstrate that chronic treatment with Aβ42 peptides does not drastically affect fly aging or immunity.

Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure.. [DOI: 10.1101/2020.10.06.328567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Numerous genome-wide association studies (GWAS) conducted to date revealed genetic variants associated with various diseases, including breast and prostate cancers. Despite the availability of these large-scale data, relatively few variants have been functionally characterized, mainly because the majority of single-nucleotide polymorphisms (SNPs) map to the non-coding regions of the human genome. The functional characterization of these non-coding variants and the identification of their target genes remain challenging. In this communication, we explore the potential functional mechanisms of non-coding SNPs by integrating GWAS with the high-resolution chromosome conformation capture (Hi-C) data for breast and prostate cancers. We show that more genetic variants map to regulatory elements through the 3D genome structure than the 1D linear genome lacking physical chromatin interactions. Importantly, the association of enhancers, transcription factors, and their target genes with breast and prostate cancers tends to be higher when these regulatory elements are mapped to high-risk SNPs through spatial interactions compared to simply using a linear proximity. Finally, we demonstrate that topologically associating domains (TADs) carrying high-risk SNPs also contain gene regulatory elements whose association with cancer is generally higher than those belonging to control TADs containing no high-risk variants. Our results suggest that many SNPs may contribute to the cancer development by affecting the expression of certain tumor-related genes through long-range chromatin interactions with gene regulatory elements. Integrating large-scale genetic datasets with the 3D genome structure offers an attractive and unique approach to systematically investigate the functional mechanisms of genetic variants in disease risk and progression.

Genetic Constraints, Transcriptome Plasticity, and the Evolutionary Response to Climate Change

In situ adaptation to climate change will be critical for the persistence of many ectotherm species due to their relative lack of dispersal capacity. Climate change is causing increases in both the mean and the variance of environmental temperature, each of which may act as agents of selection on different traits. Importantly, these traits may not be heritable or have the capacity to evolve independently from one another. When genetic constraints prevent the "baseline" values of thermal performance traits from evolving rapidly, phenotypic plasticity driven by gene expression might become critical. We review the literature for evidence that thermal performance traits in ectotherms are heritable and have genetic architectures that permit their unconstrained evolution. Next, we examine the relationship between gene expression and both the magnitude and duration of thermal stress. Finally, we identify genes that are likely to be important for adaptation to a changing climate and determine whether they show patterns consistent with thermal adaptation. Although few studies have measured narrow-sense heritabilities of thermal performance traits, current evidence suggests that the end points of thermal reaction norms (tolerance limits) are moderately heritable and have the potential to evolve rapidly. By contrast, performance at intermediate temperatures has substantially lower evolutionary potential. Moreover, evolution in many species appears to be constrained by genetic correlations such that populations can adapt to either increases in mean temperature or temperature variability, but not both. Finally, many species have the capacity for plastic expression of the transcriptome in response to temperature shifts, with the number of differentially expressed genes increasing with the magnitude, but not the duration, of thermal stress. We use these observations to develop a conceptual model that describes the likely trajectory of genome evolution in response to changes in environmental temperature. Our results indicate that extreme weather events, rather than gradual increases in mean temperature, are more likely to drive genetic and phenotypic change in wild ectotherms.

Flying Together: Drosophila as a Tool to Understand the Genetics of Human Alcoholism

Alcohol use disorder (AUD) exacts an immense toll on individuals, families, and society. Genetic factors determine up to 60% of an individual's risk of developing problematic alcohol habits. Effective AUD prevention and treatment requires knowledge of the genes that predispose people to alcoholism, play a role in alcohol responses, and/or contribute to the development of addiction. As a highly tractable and translatable genetic and behavioral model organism, Drosophila melanogaster has proven valuable to uncover important genes and mechanistic pathways that have obvious orthologs in humans and that help explain the complexities of addiction. Vinegar flies exhibit remarkably strong face and mechanistic validity as a model for AUDs, permitting many advancements in the quest to understand human genetic involvement in this disease. These advancements occur via approaches that essentially fall into one of two categories: (1) discovering candidate genes via human genome-wide association studies (GWAS), transcriptomics on post-mortem tissue from AUD patients, or relevant physiological connections, then using reverse genetics in flies to validate candidate genes' roles and investigate their molecular function in the context of alcohol. (2) Utilizing flies to discover candidate genes through unbiased screens, GWAS, quantitative trait locus analyses, transcriptomics, or single-gene studies, then validating their translational role in human genetic surveys. In this review, we highlight the utility of Drosophila as a model for alcoholism by surveying recent advances in our understanding of human AUDs that resulted from these various approaches. We summarize the genes that are conserved in alcohol-related function between humans and flies. We also provide insight into some advantages and limitations of these approaches. Overall, this review demonstrates how Drosophila have and can be used to answer important genetic questions about alcohol addiction.

Predictive features of gene expression variation reveal mechanistic link with differential expression

For most biological processes, organisms must respond to extrinsic cues, while maintaining essential gene expression programmes. Although studied extensively in single cells, it is still unclear how variation is controlled in multicellular organisms. Here, we used a machine-learning approach to identify genomic features that are predictive of genes with high versus low variation in their expression across individuals, using bulk data to remove stochastic cell-to-cell variation. Using embryonic gene expression across 75 Drosophila isogenic lines, we identify features predictive of expression variation (controlling for expression level), many of which are promoter-related. Genes with low variation fall into two classes reflecting different mechanisms to maintain robust expression, while genes with high variation seem to lack both types of stabilizing mechanisms. Applying this framework to humans revealed similar predictive features, indicating that promoter architecture is an ancient mechanism to control expression variation. Remarkably, expression variation features could also partially predict differential expression after diverse perturbations in both Drosophila and humans. Differential gene expression signatures may therefore be partially explained by genetically encoded gene-specific features, unrelated to the studied treatment.

Limited influence of the microbiome on the transcriptional profile of female Aedes aegypti mosquitoes

The microbiome is an assemblage of microorganisms living in association with a multicellular host. Numerous studies have identified a role for the microbiome in host physiology, development, immunity, and behaviour. The generation of axenic (germ-free) and gnotobiotic model systems has been vital to dissecting the role of the microbiome in host biology. We have previously reported the generation of axenic Aedes aegypti mosquitoes, the primary vector of several human pathogenic viruses, including dengue virus and Zika virus. In order to better understand the influence of the microbiome on mosquitoes, we examined the transcriptomes of axenic and conventionally reared Ae. aegypti before and after a blood meal. Our results suggest that the microbiome has a much lower effect on the mosquito's gene expression than previously thought with only 170 genes influenced by the axenic state, while in contrast, blood meal status influenced 809 genes. The pattern of expression influenced by the microbiome is consistent with transient changes similar to infection rather than sweeping physiological changes. While the microbiome does seem to affect some pathways such as immune function and metabolism, our data suggest the microbiome is primarily serving a nutritional role in development with only minor effects in the adult.

Cyclophosphamide in Drosophila promotes genes and transposable elements differential expression and mitochondrial dysfunction

Cyclophosphamide (CPA) is an alkylating agent used for cancer chemotherapy, organ transplantation, and autoimmune disease treatment. Here, mRNA sequencing and high-resolution respirometry were performed to evaluate the alterations of Drosophila melanogaster gene expression fed with CPA under acute (0.1 mg/mL, for 24 h) and chronic (0.05 mg/mL, for 35 days) treatments. Differential expression analysis was performed using Cufflinks-Cuffdiff, DESeq2, and edgeR software. CPA affected genes are involved in several biological functions, including stress response and immune-related pathways, oxi-reduction and apoptotic processes, and cuticle and vitelline membrane formation. In particular, this is the first report of CPA-induced mitochondrial dysfunction caused by the downregulation of genes involved with mitochondria constituents. CPA treatment also changed the transcription pattern of transposable elements (TEs) from the gypsy and copia superfamilies. The results presented here provided evidence of CPA mitochondrial toxicity mechanisms and that CPA can modify TEs transcription in Drosophila flies.

Defensins: Transcriptional regulation and function beyond antimicrobial activity

Defensins are one the largest group of antimicrobial peptides and are part of the innate defence. Defensins are produced by animals, plants and fungi. In animals and plants, defensins can be constitutively or differentially expressed both locally or systemically which confer defence before and a stronger response after infection. Immune signalling pathways regulate the gene expression of defensins. These pathways include cellular receptors, which recognise pathogen-associated molecular patterns and are found both in plants and animals. After recognition, signalling pathways and, subsequently, transcriptional factors are activated. There is an increasing number of novel functions in defensins, such as immunomodulators and immune cell attractors. Identification of defensin triggers could help us to elucidate other new functions. The present article reviews the different elicitors of defensins with a main focus on human, fish and marine invertebrate defensins.

Sugar Promotes Feeding in Flies via the Serine Protease Homolog scarface

A balanced diet of macronutrients is critical for animal health. A lack of specific elements can have profound effects on behavior, reproduction, and lifespan. Here, we used Drosophila to understand how the brain responds to carbohydrate deprivation. We found that serine protease homologs (SPHs) are enriched among genes that are transcriptionally regulated in flies deprived of carbohydrates. Stimulation of neurons expressing one of these SPHs, Scarface (Scaf), or overexpression of scaf positively regulates feeding on nutritious sugars, whereas inhibition of these neurons or knockdown of scaf reduces feeding. This modulation of food intake occurs only in sated flies while hunger-induced feeding is unaffected. Furthermore, scaf expression correlates with the presence of sugar in the food. As Scaf and Scaf neurons promote feeding independent of the hunger state, and the levels of scaf are positively regulated by the presence of sugar, we conclude that scaf mediates the hedonic control of feeding.

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The fly brain responds to specific macronutrients via distinct signaling pathways

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Serine protease homologs act as neuromodulators under sugar deprivation

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Sugar is both necessary and sufficient to maintain expression levels of scarface

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Scarface and Scarface neurons mediate hedonic control of feeding in flies

Effects of starvation on respiratory metabolism and energy metabolism in the cotton bollworm Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae)

Intermittent food shortages are commonly encountered in the wild. To cope with the threat of starvation, insects initiate a suite of behavioral activities and physiological countermeasures. The cotton bollworm, Helicoverpa armigera, is a major agricultural pest worldwide, but how H. armigera modulates its metabolism under starvation remains ambiguous. In the present study, the respiratory rates (V̇_O2; ml g^-1 h^-1) from the third-larval instar to the pupal stage were first determined. Our results highlighted a transient rise during the larval-larval molt and larval-pupal transition, followed by a sharp decline in the pupal stage and, finally, an upward trend before eclosion. When subjected to food deprivation, the starved larvae experienced a significant decline in the rates of O₂ consumed and CO₂ produced, as well as in respiratory quotient (RQ) values, indicative of severe metabolic depression during starvation and a shift of metabolic substrates with prolonged starvation. For metabolic substrate analysis, an apparent decline in triglyceride and glycogen contents was observed in the starved larvae, and the hemolymph trehalose content was significantly reduced throughout starvation. In addition, comparative transcriptome analysis showed that 48 h of larval starvation caused substantial transcriptional regulations in several energetically costly processes, wherein the marked up-regulations were detected in the pathways of glycolysis and fatty acid metabolism. Overall, our work makes a comprehensive study on the respiratory rate and energy metabolism in the starved H. armigera larvae, and provides a deep insight into the physiological adaptive strategies to alleviate nutritional stress.

The role of DNA repair genes in radiation-induced adaptive response in Drosophila melanogaster is differential and conditional

Studies in human and mammalian cell cultures have shown that induction of DNA repair mechanisms is required for the formation of stimulation effects of low doses of ionizing radiation, named "hormesis". Nevertheless, the role of cellular defense mechanisms in the formation of radiation-induced hormesis at the level of whole organism remains poorly studied. The aim of this work was to investigate the role of genes involved in different mechanisms and stages of DNA repair in radioadaptive response and radiation hormesis by lifespan parameters in Drosophila melanogaster. We studied genes that control DNA damage sensing (D-Gadd45, Hus1, mnk), nucleotide excision repair (mei-9, mus210, Mus209), base excision repair (Rrp1), DNA double-stranded break repair by homologous recombination (Brca2, spn-B, okr) and non-homologous end joining (Ku80, WRNexo), and the Mus309 gene that participates in several mechanisms of DNA repair. The obtained results demonstrate that in flies with mutations in studied genes radioadaptive response and radiation hormesis are absent or appear to a lesser extent than in wild-type Canton-S flies. Chronic exposure of γ-radiation in a low dose during pre-imaginal stages of development leads to an increase in expression of the studied DNA repair genes, which is maintained throughout the lifespan of flies. However, the activation of conditional ubiquitous overexpression of DNA repair genes does not induce resistance to an acute exposure to γ-radiation and reinforces its negative impact.

Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution

Mitochondria are involved in a number of diverse cellular functions, including energy production, metabolic regulation, apoptosis, calcium homeostasis, cell proliferation, and motility, as well as free radical generation. Mitochondrial DNA (mtDNA) is present at hundreds to thousands of copies per cell in a tissue-specific manner. mtDNA copy number also varies during aging and disease progression and therefore might be considered as a biomarker that mirrors alterations within the human body. Here, we present a new quantitative, highly sensitive droplet digital PCR (ddPCR) method, droplet digital mitochondrial DNA measurement (ddMDM), to measure mtDNA copy number not only from cell populations but also from single cells. Our developed assay can generate data in as little as 3 h, is optimized for 96-well plates, and also allows the direct use of cell lysates without the need for DNA purification or nuclear reference genes. We show that ddMDM is able to detect differences between samples whose mtDNA copy number was close enough as to be indistinguishable by other commonly used mtDNA quantitation methods. By utilizing ddMDM, we show quantitative changes in mtDNA content per cell across a wide variety of physiological contexts including cancer progression, cell cycle progression, human T cell activation, and human aging.

Transcriptome Analysis of Long-lived Drosophila melanogaster E(z) Mutants Sheds Light on the Molecular Mechanisms of Longevity

The E(z) histone methyltransferase heterozygous mutation in Drosophila is known to increase lifespan and stress resistance. However, the longevity mechanisms of E(z) mutants have not been revealed. Using genome-wide transcriptome analysis, we demonstrated that lifespan extension, increase of resistance to hyperthermia, oxidative stress and endoplasmic reticulum stress, and fecundity enhancement in E(z) heterozygous mutants are accompanied by changes in the expression level of 239 genes (p < 0.05). Our results demonstrated sex-specific effects of E(z) mutation on gene expression, which, however, did not lead to differences in lifespan extension in both sexes. We observed that a mutation in an E(z) gene leads to perturbations in gene expression, most of which participates in metabolism, such as Carbohydrate metabolism, Lipid metabolism, Drug metabolism, Nucleotide metabolism. Age-dependent changes in the expression of genes involved in pathways related to immune response, cell cycle, and ribosome biogenesis were found.

Studying alcohol use disorder using Drosophila melanogaster in the era of 'Big Data'

Our understanding of the networks of genes and protein functions involved in Alcohol Use Disorder (AUD) remains incomplete, as do the mechanisms by which these networks lead to AUD phenotypes. The fruit fly (Drosophila melanogaster) is an efficient model for functional and mechanistic characterization of the genes involved in alcohol behavior. The fly offers many advantages as a model organism for investigating the molecular and cellular mechanisms of alcohol-related behaviors, and for understanding the underlying neural circuitry driving behaviors, such as locomotor stimulation, sedation, tolerance, and appetitive (reward) learning and memory. Fly researchers are able to use an extensive variety of tools for functional characterization of gene products. To understand how the fly can guide our understanding of AUD in the era of Big Data we will explore these tools, and review some of the gene networks identified in the fly through their use, including chromatin-remodeling, glial, cellular stress, and innate immunity genes. These networks hold great potential as translational drug targets, making it prudent to conduct further research into how these gene mechanisms are involved in alcohol behavior.

The Neuronal Overexpression of Gclc in Drosophila melanogaster Induces Life Extension With Longevity-Associated Transcriptomic Changes in the Thorax

Some effects of aging in animals are tissue-specific. In D. melanogaster neuronal overexpression of Gclc increases lifespan and improves certain physiological parameters associated with health benefits such as locomotor activity, circadian rhythmicity, and stress resistance. Our previous transcriptomic analyses of Drosophila heads, primarily composed of neuronal tissue, revealed significant changes in expression levels of genes involved in aging-related signaling pathways (Jak-STAT, MAPK, FOXO, Notch, mTOR, TGF-beta), translation, protein processing in endoplasmic reticulum, proteasomal degradation, glycolysis, oxidative phosphorylation, apoptosis, regulation of circadian rhythms, differentiation of neurons, synaptic plasticity, and transmission. Considering that various tissues age differently and age-related gene expression changes are tissue-specific, we investigated the effects of neuronal Gclc overexpression on gene expression levels in the imago thorax, which is primarily composed of muscles. A total of 58 genes were found to be differentially expressed between thoraces of control and Gclc overexpressing flies. The Gclc level demonstrated associations with expression of genes involved in the circadian rhythmicity, the genes in categories related to the muscle system process and the downregulation of genes involved in proteolysis. Most of the functional categories altered by Gclc overexpression related to metabolism including Drug metabolism, Metabolism of xenobiotics by cytochrome P450, Glutathione metabolism, Starch and sucrose metabolism, Citrate cycle (TCA cycle), One carbon pool by folate. Thus, the transcriptomic changes caused by neuron-specific Gclc overexpression in the thorax were less pronounced than in the head and affected pathways also differed from previous results. Although these pathways don't belong to the canonical longevity pathways, we suggest that they could participate in the delay of aging of Gclc overexpressing flies.

Low-dose ionizing radiation alleviates Aβ42-induced cell death via regulating AKT and p38 pathways in Drosophila Alzheimer's disease models

Ionizing radiation is widely used in medicine and is valuable in both the diagnosis and treatment of many diseases. However, its health effects are ambiguous. Here, we report that low-dose ionizing radiation has beneficial effects in human amyloid-β42 (Aβ42)-expressing Drosophila Alzheimer's disease (AD) models. Ionizing radiation at a dose of 0.05 Gy suppressed AD-like phenotypes, including developmental defects and locomotive dysfunction, but did not alter the decreased survival rates and longevity of Aβ42-expressing flies. The same dose of γ-irradiation reduced Aβ42-induced cell death in Drosophila AD models through downregulation of head involution defective (hid), which encodes a protein that activates caspases. However, 4 Gy of γ-irradiation increased Aβ42-induced cell death without modulating pro-apoptotic genes grim, reaper and hid. The AKT signaling pathway, which was suppressed in Drosophila AD models, was activated by either 0.05 or 4 Gy γ-irradiation. Interestingly, p38 mitogen-activated protein-kinase (MAPK) activity was inhibited by exposure to 0.05 Gy γ-irradiation but enhanced by exposure to 4 Gy in Aβ42-expressing flies. In addition, overexpression of phosphatase and tensin homolog (PTEN), a negative regulator of the AKT signaling pathway, or a null mutant of AKT strongly suppressed the beneficial effects of low-dose ionizing radiation in Aβ42-expressing flies. These results indicate that low-dose ionizing radiation suppresses Aβ42-induced cell death through regulation of the AKT and p38 MAPK signaling pathways, suggesting that low-dose ionizing radiation has hormetic effects on the pathogenesis of Aβ42-associated AD.

Summary: Low-dose ionizing radiation can reduce cell death by regulating AKT/p38 signaling pathway and improve Aβ42-induced symptoms in Drosophila Alzheimer's disease, suggesting that low-dose ionizing radiation may be applicable for treatment.

Comparative analysis of the ftness of Drosophila virilis lines contrasting in response to stress

One of the crucial elements contributing to the adaptation of organisms to unfavorable environmental conditions is the reaction of stress. The study of its genetic control and role in adaptation to unfavorable conditions are of special interest. The juvenile hormone (JH) acts as a gonadotropic hormone in adult insects controlling the development of the ovaries, inducing vitellogenesis and oviposition. It was shown that a decrease in JH degradation in individuals reacting to adverse conditions by stress reaction (R­individuals) causes delay in egg laying and seems to allow the population to “wait out” the unfavorable conditions, thereby contributing to the adaptation at the population level. However, monitoring natural populations of D. melanogaster for the capability of stress reaction demonstrated that they have a high percentage of individuals incapable of it (NR­individuals). The study of reproductive characteristics of R­ and NR­individuals showed that under normal conditions R­individuals have the advantage of procreating offspring. Under unfavorable conditions, if the stressor is intense enough, NR­individuals die, but if its intensity is low, then they, unlike R­individuals, continue to produce offspring. Based on these data, it was hypothesized that the balance of R­ and NR­alleles in the population ensures its adaptation under frequent stresses of low intensity. To verify the hypothesis by an experiment, the ftness characteristics (lifespan, fecundity) of the R and NR lines of D. virilis were studied under normal conditions and under regular heat stress of various frequency.

Comparative analysis of the ftness of Drosophila virilis lines contrasting in response to stress

One of the crucial elements contributing to the adaptation of organisms to unfavorable environmental conditions is the reaction of stress. The study of its genetic control and role in adaptation to unfavorable conditions are of special interest. The juvenile hormone (JH) acts as a gonadotropic hormone in adult insects controlling the development of the ovaries, inducing vitellogenesis and oviposition. It was shown that a decrease in JH degradation in individuals reacting to adverse conditions by stress reaction (R­individuals) causes delay in egg laying and seems to allow the population to “wait out” the unfavorable conditions, thereby contributing to the adaptation at the population level. However, monitoring natural populations of D. melanogaster for the capability of stress reaction demonstrated that they have a high percentage of individuals incapable of it (NR­individuals). The study of reproductive characteristics of R­ and NR­individuals showed that under normal conditions R­individuals have the advantage of procreating offspring. Under unfavorable conditions, if the stressor is intense enough, NR­individuals die, but if its intensity is low, then they, unlike R­individuals, continue to produce offspring. Based on these data, it was hypothesized that the balance of R­ and NR­alleles in the population ensures its adaptation under frequent stresses of low intensity. To verify the hypothesis by an experiment, the ftness characteristics (lifespan, fecundity) of the R and NR lines of D. virilis were studied under normal conditions and under regular heat stress of various frequency.

Neuron-specific overexpression of core clock genes improves stress-resistance and extends lifespan of Drosophila melanogaster

Gene expression is much altered in aging. We observed age-dependent decline of core clock genes' expression in the whole body of the fruit fly. We hypothesized that inducible overexpression of clock genes (cry, per, tim, cyc and Clk) in the nervous system can improve healthspan of D. melanogaster. We studied the lifespan of transgenic Drosophila and showed life extension for cry, per, cyc and tim genes. It was also the significant positive changes in the stress-resistance of flies overexpressing core clock genes in conditions of hyperthermia, hyperoxia, starvation and persistent lighting. The overexpression of per and cry restore circadian rhythms of locomotor activity. The results presented support the hypotheses that the compensation of circadian oscillator genes expression can improve the healthspan in Drosophila melanogaster.

Effect of Larval Nutrition on Maternal mRNA Contribution to the Drosophila Egg

Embryonic development begins under the control of maternal gene products, mRNAs and proteins that the mother deposits into the egg; the zygotic genome is activated some time later. Maternal control of early development is conserved across metazoans. Gene products contributed by mothers are critical to many early developmental processes, and set up trajectories for the rest of development. Maternal deposition of these factors is an often-overlooked aspect of parental investment. If the mother experiences challenging environmental conditions, such as poor nutrition, previous studies in Drosophila melanogaster have demonstrated a plastic response wherein these mothers may produce larger eggs to buffer the offspring against the same difficult environment. This additional investment can produce offspring that are more fit in the challenging environment. With this study, we ask whether D. melanogaster mothers who experience poor nutrition during their own development change their gene product contribution to the egg. We perform mRNA-Seq on eggs at a stage where all mRNAs are maternally derived, from mothers with different degrees of nutritional limitation. We find that nutritional limitation produces similar transcript changes at all degrees of limitation tested. Genes that have lower transcript abundance in nutritionally limited mothers are those involved in translation, which is likely one of the most energetically costly processes occurring in the early embryo. We find an increase in transcripts for transport and localization of macromolecules, and for the electron transport chain. The eggs produced by nutrition-limited mothers show a plastic response in mRNA deposition, which may better prepare the future embryo for development in a nutrition-limited environment.

Concomitant changes in radiation resistance and trehalose levels during life stages of Drosophila melanogaster suggest radio-protective function of trehalose

PURPOSE

During development, various life stages of Drosophila melanogaster (D. melanogaster) show different levels of resistance to gamma irradiation, with the early pupal stage being the most radiation sensitive. This provides us an opportunity to explore the biochemical basis of such variations. The present study was carried out to understand the mechanisms underlying radiation resistance during life stages of D. melanogaster.

MATERIALS AND METHODS

Homogenates from all the life stages of D. melanogaster were prepared at stipulated age. These homogenates were used for the determination of (1) enzymatic antioxidants: superoxide dismutase (SOD), catalase, D. melanogaster glutathione peroxidase (DmGPx), and glutathione S-transferase (GST); (2) reducing non-enzymatic antioxidants: total antioxidant capacity (TAC), reduced glutathione (GSH) and non-reducing non-enzymatic antioxidant trehalose; and (3) levels of protein carbonyl (PC) content. Age-dependent changes in radiation resistance and associated biochemical changes were also studied in young (2 d) and old (20 and 30 d) flies.

RESULTS

TAC and GSH were found high in the early pupal stage, whereas catalase and DmGPx were found to increase in the early pupal stage. The non-feeding third instar (NFTI) larvae were found to have high levels of SOD and GST, besides NFTI larvae showed high levels of trehalose. A remarkable decrease was observed in radiation resistance and trehalose levels during the early pupal stage. The PC level was the highest during early pupal stage and was the lowest in NFTI larvae. Older flies showed high level of PC compared with young flies.

CONCLUSION

In vitro increments in trehalose concentration correspond to reduced formation of PCs, suggesting a protective role of trehalose against free radicals. A strong correlation between levels of trehalose and PC formation suggests amelioration of proteome damage due to ionizing radiation (IR). Stages with high trehalose levels showed protected proteome and high radiation resistance, suggesting a significant role for this disaccharide in radiation resistance.