Drosophila Research Research Articles

Unveiling GATOR2 Function: Novel Insights from Drosophila Research

The multiprotein Target of Rapamycin (TOR) Complex 1 (TORC1) is a serine/threonine kinase that stimulates anabolic metabolism and suppresses catabolism. Deregulation of TORC1 is implicated in various human pathologies, including cancer, epilepsy, and neurodegenerative disorders. The Gap Activity Towards Rags (GATOR) complex contains two subcomplexes: GATOR1, which inhibits TORC1 activity; and GATOR2, which counteracts GATOR1s function. Structural and biochemical studies have elucidated how GATOR1 regulates TORC1 activity by acting as a GTPase activating protein for Rag GTPase. However, while cryogenic electron microscopy has determined that the structure of the multi-protein GATOR2 complex is conserved from yeast to humans, how GATOR2 inhibits GATOR1 remains unclear. Here, we describe recent whole-animal studies in Drosophila that have yielded novel insights into GATOR2 function, including identifying a novel role for the GATOR2 subunit WDR59, redefining the core proteins sufficient for GATOR2 activity, and defining a TORC1-independent role for GATOR2 in the regulation of the lysosomal autophagic endomembrane system. Additionally, the recent characterization of a novel methionine receptor in Drosophila that acts through the GATOR2 complex suggests an attractive model for the evolution of species-specific nutrient sensors. Research on GATOR2 function in Drosophila highlights how whole-animal genetic models can be used to dissect intracellular signaling pathways to identify tissue-specific functions and functional redundancies that may be missed in studies confined to rapidly proliferating cell lines.

The Study of Sensorimotor Circuit Assembly in Drosophila melanogaster Embryos and Larvae.

In animals, movement is generated by the activity of motor circuits housed in the vertebrate spinal cord or the arthropod nerve cord. How motor circuits form is a fundamental question, with wide-ranging impacts on the fields of development, neurobiology, medicine, evolution, and beyond. Until recently, studying circuit assembly had been experimentally difficult, with a paucity of suitable models. Due to the introduction of novel neuroscience tools (calcium imaging, optogenetics, connectomics), Drosophila embryos and larvae can be used as models to study motor circuit assembly. Here, we briefly review the knowledge relevant to motor circuit assembly in Drosophila larvae. We discuss the larval body and its movements, larval neurons and circuits in the motor system, and how the generation of neural diversity starting from stem cells relates to circuit formation. The long-term goal of Drosophila research in this field is to identify developmental rules, determine when the rules apply, generate an integrated understanding of motor circuit development, and uncover molecular mechanisms driving the assembly process. Motor circuits are an ancient part of the nervous system, and so far, the developmental programs guiding motor circuit assembly appear to be largely conserved across phyla. Thus, as methods improve in other systems, findings in Drosophila will provide foundational concepts that will inspire hypotheses in those systems.

NeuronBridge: an intuitive web application for neuronal morphology search across large data sets

BackgroundNeuroscience research in Drosophila is benefiting from large-scale connectomics efforts using electron microscopy (EM) to reveal all the neurons in a brain and their connections. To exploit this knowledge base, researchers relate a connectome’s structure to neuronal function, often by studying individual neuron cell types. Vast libraries of fly driver lines expressing fluorescent reporter genes in sets of neurons have been created and imaged using confocal light microscopy (LM), enabling the targeting of neurons for experimentation. However, creating a fly line for driving gene expression within a single neuron found in an EM connectome remains a challenge, as it typically requires identifying a pair of driver lines where only the neuron of interest is expressed in both. This task and other emerging scientific workflows require finding similar neurons across large data sets imaged using different modalities.ResultsHere, we present NeuronBridge, a web application for easily and rapidly finding putative morphological matches between large data sets of neurons imaged using different modalities. We describe the functionality and construction of the NeuronBridge service, including its user-friendly graphical user interface (GUI), extensible data model, serverless cloud architecture, and massively parallel image search engine.ConclusionsNeuronBridge fills a critical gap in the Drosophila research workflow and is used by hundreds of neuroscience researchers around the world. We offer our software code, open APIs, and processed data sets for integration and reuse, and provide the application as a service at http://neuronbridge.janelia.org.

DrosOMA: the Drosophila Orthologous Matrix browser.

Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking. Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes. We developed and deployed a dedicated instance of the OMA browser to facilitate intuitive exploration, visualisation, and downloading of the genus-wide orthology delineation results. DrosOMA - the Drosophila Orthologous Matrix browser, accessible from https://drosoma.dcsr.unil.ch/ - presents the results of orthology delineation for 36 drosophilids from across the genus and four outgroup dipterans. It enables querying and browsing of the orthology data through a feature-rich web interface, with gene-view, orthologous group-view, and genome-view pages, including comprehensive gene name and identifier cross-references together with available functional annotations and protein domain architectures, as well as tools to visualise local and global synteny conservation. The DrosOMA browser demonstrates the deployability of the OMA browser framework for building user-friendly orthology databases with dense sampling of a selected taxonomic group. It provides the Drosophila research community with a tailored resource of browsable results from genus-wide orthology delineation.

Boosting life sciences research in Brazil: building a case for a local Drosophila stock center.

Drosophila melanogaster is undoubtedly one of the most useful model organisms in biology. Initially used in solidifying the principles of heredity, and establishing the basic concepts of population genetics and of the synthetic theory of evolution, it can currently offer scientists much more: the possibility of investigating a plethora of cellular and biological mechanisms, from development and function of the immune system to animal neurogenesis, tumorigenesis and beyond. Extensive resources are available for the community of Drosophila researchers worldwide, including an ever-growing number of mutant, transgenic and genomically-edited lines currently carried by stock centers in North America, Europe and Asia. Here, we provide evidence for the importance of stock centers in sustaining the substantial increase in the output of Drosophila research worldwide in recent decades. We also discuss the challenges that Brazilian Drosophila scientists face to keep their research projects internationally competitive, and argue that difficulties in importing fly lines from international stock centers have significantly stalled the progression of all Drosophila research areas in the country. Establishing a local stock center might be the first step towards building a strong local Drosophila community that will likely contribute to all areas of life sciences research.

Mosaic Analysis with a Repressible Cell Marker (MARCM) Clone Generation in Drosophila Dendritic Arborization Neurons.

Mosaic analysis with a repressible cell marker (MARCM) is used in Drosophila research to create labeled homozygous mutant clones of cells in an otherwise heterozygous fly. It allows the study of the effect of embryonically lethal genes and the determination of cell autonomy for a mutant phenotype. When used in dendritic arborization (da) neurons with a fluorescent protein targeted to the plasma membrane, MARCM allows the identification of homozygous mutant neurons and clear imaging of the dendrite arbor in both live and fixed preparations. Previous protocols that outlined experimental procedures to create MARCM clones in da neurons used a heat shock promoter to drive Flippase (FLP) expression; such an approach requires laborious embryo collection and heat shock steps, and it creates clones in other tissues besides the da neurons. The updated protocol described here outlines the use of FLP expression driven by a sensory organ precursor promoter (SOP-FLP); it requires no embryo collection or manipulation steps and creates clones exclusively in the peripheral sensory neuron lineage.

Telomere Checkpoint in Development and Aging

The maintenance of genome integrity through generations is largely determined by the stability of telomeres. Increasing evidence suggests that telomere dysfunction may trigger changes in cell fate, independently of telomere length. Telomeric multiple tandem repeats are potentially highly recombinogenic. Heterochromatin formation, transcriptional repression, the suppression of homologous recombination and chromosome end protection are all required for telomere stability. Genetic and epigenetic defects affecting telomere homeostasis may cause length-independent internal telomeric DNA damage. Growing evidence, including that based on Drosophila research, points to a telomere checkpoint mechanism that coordinates cell fate with telomere state. According to this scenario, telomeres, irrespective of their length, serve as a primary sensor of genome instability that is capable of triggering cell death or developmental arrest. Telomeric factors released from shortened or dysfunctional telomeres are thought to mediate these processes. Here, we discuss a novel signaling role for telomeric RNAs in cell fate and early development. Telomere checkpoint ensures genome stability in multicellular organisms but aggravates the aging process, promoting the accumulation of damaged and senescent cells.

DrosOMA: the Drosophila Orthologous Matrix browser

Background: Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking. Methods: Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes. We developed and deployed a dedicated instance of the OMA browser to facilitate intuitive exploration, visualisation, and downloading of the genus-wide orthology delineation results. Results: DrosOMA - the Drosophila Orthologous Matrix browser, accessible from https://drosoma.dcsr.unil.ch/ - presents the results of orthology delineation for 36 drosophilids from across the genus and four outgroup dipterans. It enables querying and browsing of the orthology data through a feature-rich web interface, with gene-view, orthologous group-view, and genome-view pages, including comprehensive gene name and identifier cross-references together with available functional annotations and protein domain architectures, as well as tools to visualise local and global synteny conservation. Conclusions: The DrosOMA browser demonstrates the deployability of the OMA browser framework for building user-friendly orthology databases with dense sampling of a selected taxonomic group. It provides the Drosophila research community with a tailored resource of browsable results from genus-wide orthology delineation.

PANGEA: a new gene set enrichment tool for Drosophila and common research organisms.

Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an 'omics' study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https://www.flyrnai.org/tools/pangea/), developed to allow a more flexible and configurable approach to data analysis using a variety of classification sets. PANGEA allows GO analysis to be performed on different sets of GO annotations, for example excluding high-throughput studies. Beyond GO, gene sets for pathway annotation and protein complex data from various resources as well as expression and disease annotation from the Alliance of Genome Resources (Alliance). In addition, visualizations of results are enhanced by providing an option to view network of gene set to gene relationships. The tool also allows comparison of multiple input gene lists and accompanying visualisation tools for quick and easy comparison. This new tool will facilitate GSEA for Drosophila and other major model organisms based on high-quality annotated information available for these species.

Exploring FlyBase Data Using QuickSearch.

FlyBase (www.flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, means that FlyBase now houses a huge quantity of data. Researchers need to be able to query these data rapidly and intuitively, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This article describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Using the "Search FlyBase" tab of QuickSearch Basic Protocol 2: Using the "Data Class" tab of QuickSearch Basic Protocol 3: Using the "References" tab of QuickSearch Basic Protocol 4: Using the "Gene Groups" tab of QuickSearch Basic Protocol 5: Using the "Pathways" tab of QuickSearch Basic Protocol 6: Using the "GO" tab of QuickSearch Basic Protocol 7: Using the "Protein Domains" tab of QuickSearch Basic Protocol 8: Using the "Expression" tab of QuickSearch Basic Protocol 9: Using the "GAL4 etc" tab of QuickSearch Basic Protocol 10: Using the "Phenotype" tab of QuickSearch Basic Protocol 11: Using the "Human Disease" tab of QuickSearch Basic Protocol 12: Using the "Homologs" tab of QuickSearch Support Protocol 1: Managing FlyBase hit lists.

The take-off of Drosophila research in 1930-1950s Edinburgh.

The fruit fly, Drosophila melanogaster, is a simple and powerful model organism. It has played a critical role over more than a century, for example in establishing the field of genetics, and in foundational insights into the molecular basis of development. From the 1930s until today, researchers at the University of Edinburgh have used Drosophila to tackle questions in basic and biomedical science. Here the history of the initial decades of this research is explored, beginning with the introduction of Drosophila research to Edinburgh by Francis Albert Eley Crew, in the newly established Institute of Animal Genetics. This period of research includes the discovery that chemicals can cause genetic mutation. This was demonstrated by research of the effects of mustard gas on flies by Charlotte Auerbach and colleagues, guided by the future Nobel laureate Hermann Muller. Drosophila research was also formative in Conrad Hal Waddington's conceptual thinking about developmental biology, including in his vision of the epigenetic landscape. This holistic, systems-level view of the control of development was far before its time and has continued to be influential to this day in our conceptualisation of developmental biology and in the increasingly important field of systems biology. Waddington's experiments with Drosophila in Edinburgh also gave rise to the evolutionary concept of genetic assimilation, in which an environmentally induced phenotype subsequently becomes genetically encoded.

Lifespan and ROS levels in different Drosophila melanogaster strains after 24 h hypoxia exposure.

ABSTRACTDuring recent decades, model organisms such as Drosophila melanogaster have made it possible to study the effects of different environmental oxygen conditions on lifespan and oxidative stress. However, many studies have often yielded controversial results usually assigned to variations in Drosophila genetic background and differences in study design. In this study, we compared longevity and ROS levels in young, unmated males of three laboratory wild-type lines (Canton-S, Oregon-R and Berlin-K) and one mutant line (Sod1n1) as a positive control of redox imbalance, under both normoxic and hypoxic (2% oxygen for 24 h) conditions. Lifespan was used to detect the effects of hypoxic treatment and differences were analysed by means of Kaplan–Meier survival curves and log-rank tests. Electron paramagnetic resonance spectroscopy was used to measure ROS levels and analysis of variance was used to estimate the effects of hypoxic treatment and to assess ROS differences between strains. We observed that the genetic background is a relevant factor involved in D. melanogaster longevity and ROS levels. Indeed, as expected, in normoxia Sod1n1 are the shortest-lived, while the wild-type strains, despite a longer lifespan, show some differences, with the Canton-S line displaying the lowest mortality rate. After hypoxic stress these variances are amplified, with Berlin-K flies showing the highest mortality rate and most evident reduction of lifespan. Moreover, our analysis highlighted differential effects of hypoxia on redox balance/unbalance. Canton-S flies had the lowest increase of ROS level compared to all the other strains, confirming it to be the less sensitive to hypoxic stress. Sod1n1 flies displayed the highest ROS levels in normoxia and after hypoxia. These results should be used to further standardize future Drosophila research models designed to investigate genes and pathways that may be involved in lifespan and/or ROS, as well as comparative studies on specific mutant strains.

The early history of the eye-antennal disc of Drosophila melanogaster.

A pair of eye-antennal imaginal discs give rise to nearly all external structures of the adult Drosophila head including the compound eyes, ocelli, antennae, maxillary palps, head epidermis, and bristles. In the earliest days of Drosophila research, investigators would examine thousands of adult flies in search of viable mutants whose appearance deviated from the norm. The compound eyes are dispensable for viability and perturbations to their structure are easy to detect. As such, the adult compound eye and the developing eye-antennal disc emerged as focal points for studies of genetics and developmental biology. Since few tools were available at the time, early researchers put an enormous amount of thought into models that would explain their experimental observations-many of these hypotheses remain to be tested. However, these "ancient" studies have been lost to time and are no longer read or incorporated into today's literature despite the abundance of field-defining discoveries that are contained therein. In this FlyBook chapter, I will bring these forgotten classics together and draw connections between them and modern studies of tissue specification and patterning. In doing so, I hope to bring a larger appreciation of the contributions that the eye-antennal disc has made to our understanding of development as well as draw the readers' attention to the earliest studies of this important imaginal disc. Armed with the today's toolkit of sophisticated genetic and molecular methods and using the old papers as a guide, we can use the eye-antennal disc to unravel the mysteries of development.

High-resolution 3D spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae.

Drosophila has long been a successful model organism in multiple biomedical fields. Spatial gene expression patterns are critical for the understanding of complex pathways and interactions, whereas temporal gene expression changes are vital for studying highly dynamic physiological activities. Systematic studies in Drosophila are still impeded by the lack of spatiotemporal transcriptomic information. Here, utilizing spatialenhancedresolutionomics-sequencing (Stereo-seq), we dissected the spatiotemporal transcriptomic changes of developing Drosophila with high resolution and sensitivity. We demonstrated that Stereo-seq data can be used for the 3D reconstruction of the spatial transcriptomes of Drosophila embryos and larvae. With these 3D models, we identified functional subregions in embryonic and larval midguts, uncovered spatial cell state dynamics of larval testis, and revealed known and potential regulons of transcription factors within their topographic background. Our data provide the Drosophila research community with useful resources of organism-wide spatiotemporally resolved transcriptomic information across developmental stages.

The power of Drosophila in modeling human disease mechanisms.

Six years ago, DMM launched a subject collection called ‘Drosophila as a Disease Model’. This collection features Review-type articles and original research that highlight the power of Drosophila research in many aspects of human disease modeling. In the ensuing years, Drosophila research has further expanded to capitalize on genome editing, development of resources, and further interest in studying rare disease mechanisms. In the current issue of DMM, we again highlight the versatility, breadth, and scope of Drosophila research in human disease modeling and translational medicine. While many researchers have embraced the power of the fly, many more could still be encouraged to appreciate the strengths of Drosophila and how such research can integrate across species in a multi-pronged approach. Only when we truly acknowledge that all models contribute to our understanding of human biology, can we take advantage of the scope of current research endeavors.

Investigating local and systemic intestinal signalling in health and disease with Drosophila.

ABSTRACTWhole-body health relies on complex inter-organ signalling networks that enable organisms to adapt to environmental perturbations and to changes in tissue homeostasis. The intestine plays a major role as a signalling centre by producing local and systemic signals that are relayed to the body and that maintain intestinal and organismal homeostasis. Consequently, disruption of intestinal homeostasis and signalling are associated with systemic diseases and multi-organ dysfunction. In recent years, the fruit fly Drosophila melanogaster has emerged as a prime model organism to study tissue-intrinsic and systemic signalling networks of the adult intestine due to its genetic tractability and functional conservation with mammals. In this Review, we highlight Drosophila research that has contributed to our understanding of how the adult intestine interacts with its microenvironment and with distant organs. We discuss the implications of these findings for understanding intestinal and whole-body pathophysiology, and how future Drosophila studies might advance our knowledge of the complex interplay between the intestine and the rest of the body in health and disease.

Evolutionary Conservation of Hox Genes in Vertebrate Brain Development

Hox genes, their conserved derivatives, and the pathways responsible for their expression have been extensively studied in the fruit fly, Drosophila melanogaster;the experimentation done in the Drosophila model system has given developmental biologists tools to better understand the role and significance of Hox genes and their derivatives in anterior-posterior axis determination in the Drosophila embryo. Along with this, Drosophila research opened up the door to investigation on the conservation of Hox genes between vertebrates and invertebrates. Comparative embryology in mice, chickens, pufferfish, and zebrafish have shown conserved Hox gene expression patterns specifically along the anterior-posterior axis. Recently, comparative analysis performed on dorsal-ventral axis formation showed that patterning and segmentation of the spinal cord is influenced by the action of Hox genes as well. This review will briefly consider the evolution of the vertebrate brain and the evolution and conservation of Hox genes in regulating hindbrain patterning and spinal cord development.

Cryopreservation method for Drosophila melanogaster embryos

The development of a widely adopted cryopreservation method remains a major challenge in Drosophila research. Here we report a robust and easily implemented cryopreservation protocol of Drosophila melanogaster embryos. We present innovations for embryo permeabilization, cryoprotectant agent loading, and rewarming. We show that the protocol is broadly applicable, successfully implemented in 25 distinct strains from different sources. We demonstrate that for most strains, >50% embryos hatch and >25% of the resulting larvae develop into adults after cryopreservation. We determine that survival can be significantly improved by outcrossing to mitigate the effect of genetic background for strains with low survival after cryopreservation. We show that flies retain normal sex ratio, fertility, and original mutation after successive cryopreservation of 5 generations and 6-month storage in liquid nitrogen. Lastly, we find that non-specialists are able to use this protocol to obtain consistent results, demonstrating potential for wide adoption.

Eco-genetics of desiccation resistance in Drosophila.

Climate change globally perturbs water circulation thereby influencing ecosystems including cultivated land. Both harmful and beneficial species of insects are likely to be vulnerable to such changes in climate. As small animals with a disadvantageous surface area to body mass ratio, they face a risk of desiccation. A number of behavioural, physiological and genetic strategies are deployed to solve these problems during adaptation in various Drosophila species. Over 100 desiccation-related genes have been identified in laboratory and wild populations of the cosmopolitan fruit fly Drosophila melanogaster and its sister species in large-scale and single-gene approaches. These genes are involved in water sensing and homeostasis, and barrier formation and function via the production and composition of surface lipids and via pigmentation. Interestingly, the genetic strategy implemented in a given population appears to be unpredictable. In part, this may be due to different experimental approaches in different studies. The observed variability may also reflect a rich standing genetic variation in Drosophila allowing a quasi-random choice of response strategies through soft-sweep events, although further studies are needed to unravel any underlying principles. These findings underline that D. melanogaster is a robust species well adapted to resist climate change-related desiccation. The rich data obtained in Drosophila research provide a framework to address and understand desiccation resistance in other insects. Through the application of powerful genetic tools in the model organism D. melanogaster, the functions of desiccation-related genes revealed by correlative studies can be tested and the underlying molecular mechanisms of desiccation tolerance understood. The combination of the wealth of available data and its genetic accessibility makes Drosophila an ideal bioindicator. Accumulation of data on desiccation resistance in Drosophila may allow us to create a world map of genetic evolution in response to climate change in an insect genome. Ultimately these efforts may provide guidelines for dealing with the effects of climate-related perturbations on insect population dynamics in the future.

Drosophila as a Model for Infectious Diseases.

The fruit fly, Drosophila melanogaster, has been used to understand fundamental principles of genetics and biology for over a century. Drosophila is now also considered an essential tool to study mechanisms underlying numerous human genetic diseases. In this review, we will discuss how flies can be used to deepen our knowledge of infectious disease mechanisms in vivo. Flies make effective and applicable models for studying host-pathogen interactions thanks to their highly conserved innate immune systems and cellular processes commonly hijacked by pathogens. Drosophila researchers also possess the most powerful, rapid, and versatile tools for genetic manipulation in multicellular organisms. This allows for robust experiments in which specific pathogenic proteins can be expressed either one at a time or in conjunction with each other to dissect the molecular functions of each virulent factor in a cell-type-specific manner. Well documented phenotypes allow large genetic and pharmacological screens to be performed with relative ease using huge collections of mutant and transgenic strains that are publicly available. These factors combine to make Drosophila a powerful tool for dissecting out host-pathogen interactions as well as a tool to better understand how we can treat infectious diseases that pose risks to public health, including COVID-19, caused by SARS-CoV-2.