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1.  Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila 
Systems biology aims to describe the complex interplays between cellular building blocks which, in their concurrence, give rise to the emergent properties observed in cellular behaviors and responses. This approach tries to determine the molecular players and the architectural principles of their interactions within the genetic networks that control certain biological processes. Large-scale loss-of-function screens, applicable in various different model systems, have begun to systematically interrogate entire genomes to identify the genes that contribute to a certain cellular response. In particular, RNA interference (RNAi)-based high-throughput screens have been instrumental in determining the composition of regulatory systems and paired with integrative data analyses have begun to delineate the genetic networks that control cell biological and developmental processes. Through the creation of tools for both, in vitro and in vivo genome-wide RNAi screens, Drosophila melanogaster has emerged as one of the key model organisms in systems biology research and over the last years has massively contributed to and hence shaped this discipline.
PMCID: PMC3560415  PMID: 21197652
2.  Identification of Genes That Promote or Antagonize Somatic Homolog Pairing Using a High-Throughput FISH–Based Screen 
PLoS Genetics  2012;8(5):e1002667.
The pairing of homologous chromosomes is a fundamental feature of the meiotic cell. In addition, a number of species exhibit homolog pairing in nonmeiotic, somatic cells as well, with evidence for its impact on both gene regulation and double-strand break (DSB) repair. An extreme example of somatic pairing can be observed in Drosophila melanogaster, where homologous chromosomes remain aligned throughout most of development. However, our understanding of the mechanism of somatic homolog pairing remains unclear, as only a few genes have been implicated in this process. In this study, we introduce a novel high-throughput fluorescent in situ hybridization (FISH) technology that enabled us to conduct a genome-wide RNAi screen for factors involved in the robust somatic pairing observed in Drosophila. We identified both candidate “pairing promoting genes” and candidate “anti-pairing genes,” providing evidence that pairing is a dynamic process that can be both enhanced and antagonized. Many of the genes found to be important for promoting pairing are highly enriched for functions associated with mitotic cell division, suggesting a genetic framework for a long-standing link between chromosome dynamics during mitosis and nuclear organization during interphase. In contrast, several of the candidate anti-pairing genes have known interphase functions associated with S-phase progression, DNA replication, and chromatin compaction, including several components of the condensin II complex. In combination with a variety of secondary assays, these results provide insights into the mechanism and dynamics of somatic pairing.
Author Summary
In addition to their number and structure, the position and spatial dynamics of chromosomes are under tight control, as direct interactions between chromosomes can contribute to the activation or repression of genes. Here, we focus on a particular type of interaction, known as somatic homolog pairing, which occurs between the maternal and paternal copies of chromosomes. While the role of somatic pairing on downstream homology-driven processes is well-established, there is much to be learned about how homologous chromosome segments find each other, physically align, and form stable pairing interactions within somatic cells. Taking advantage of a novel high-throughput FISH technology and the fact that homologous chromosomes are intimately paired along their lengths in the somatic cells of Drosophila, we have conducted a screen for factors that are important for the fidelity of somatic pairing. Ultimately, the characterization of these pairing genes will shed light on the mechanism of pairing, as well as pairing-mediated processes that have implications for development and disease. Finally, the efficacy of our screen for pairing genes suggests that the high-throughput FISH technology described here will prove useful for studying forms of nuclear organization and chromosome positioning beyond pairing.
PMCID: PMC3349724  PMID: 22589731
3.  Flightless Flies: Drosophila models of neuromuscular disease 
The fruit fly, Drosophila melanogaster, has a long and rich history as an important model organism for biologists. In particular, study of the fruit fly has been essential to much of our fundamental understanding of the development and function of the nervous system. In recent years, studies using fruit flies have provided important insights into the pathogenesis of neurodegenerative and neuromuscular diseases. Fly models of spinal muscular atrophy, spinobulbar muscular atrophy, myotonic dystrophy, dystrophinopathies and other inherited neuromuscular diseases recapitulate many of the key pathologic features of the human disease. The ability to perform genetic screens holds promise for uncovering the molecular mechanisms of disease, and indeed, for identifying novel therapeutic targets. This review will summarize recent progress in developing fly models of neuromuscular diseases and will emphasize the contribution that Drosophila has made to our understanding of these diseases.
PMCID: PMC3062507  PMID: 20329357
4.  The FLIGHT Drosophila RNAi database 
Fly  2010;4(4):344-348.
FLIGHT ( is an online resource compiling data from high-throughput Drosophila in vivo and in vitro RNAi screens. FLIGHT includes details of RNAi reagents and their predicted off-target effects, alongside RNAi screen hits, scores and phenotypes, including images from high-content screens. The latest release of FLIGHT is designed to enable users to upload, analyze, integrate and share their own RNAi screens. Users can perform multiple normalizations, view quality control plots, detect and assign screen hits and compare hits from multiple screens using a variety of methods including hierarchical clustering. FLIGHT integrates RNAi screen data with microarray gene expression as well as genomic annotations and genetic/physical interaction datasets to provide a single interface for RNAi screen analysis and datamining in Drosophila.
PMCID: PMC3174485  PMID: 20855970
RNAi; database; integration; bioinformatics; phenotype
5.  High-throughput Computer Method for 3D Neuronal Structure Reconstruction from the Image Stack of the Drosophila Brain and Its Applications 
PLoS Computational Biology  2012;8(9):e1002658.
Drosophila melanogaster is a well-studied model organism, especially in the field of neurophysiology and neural circuits. The brain of the Drosophila is small but complex, and the image of a single neuron in the brain can be acquired using confocal microscopy. Analyzing the Drosophila brain is an ideal start to understanding the neural structure. The most fundamental task in studying the neural network of Drosophila is to reconstruct neuronal structures from image stacks. Although the fruit fly brain is small, it contains approximately 100 000 neurons. It is impossible to trace all the neurons manually. This study presents a high-throughput algorithm for reconstructing the neuronal structures from 3D image stacks collected by a laser scanning confocal microscope. The proposed method reconstructs the neuronal structure by applying the shortest path graph algorithm. The vertices in the graph are certain points on the 2D skeletons of the neuron in the slices. These points are close to the 3D centerlines of the neuron branches. The accuracy of the algorithm was verified using the DIADEM data set. This method has been adopted as part of the protocol of the FlyCircuit Database, and was successfully applied to process more than 16 000 neurons. This study also shows that further analysis based on the reconstruction results can be performed to gather more information on the neural network.
Author Summary
It is now possible to image a single neuron in the fruit fly brain. However, manually reconstructing neuronal structures is tremendously time consuming. The proposed method avoids user interventions by first automatically identifying the end points and detecting the appropriate representative point of the soma, and then, by finding the shortest paths from the soma to the end points in an image stack. In the proposed algorithm, a tailor-made weighting function allows the resulting reconstruction to represent the neuron appropriately. Accuracy analysis and a robustness test demonstrated that the proposed method is accurate and robust to handle the noisy image data. Tract discovery is one of the most frequently mentioned potentials of reconstructed results. In addition to a method for neuronal structure reconstruction, this study presents a method for tract discovery and explores the tract-connecting olfactory neuropils using the reconstructed results. The discovered tracts are in agreement with the results of previous studies in the literature. Software for reconstructing the neuronal structures and the reconstruction results can be downloaded from the Web site More details on acquiring the software and the reconstruction results are provided in Text S1.
PMCID: PMC3441491  PMID: 23028271
6.  The Drosophila visual system 
Cell Adhesion & Migration  2013;7(4):333-344.
A compact genome and a tiny brain make Drosophila the prime model to understand the neural substrate of behavior. The neurogenetic efforts to reveal neural circuits underlying Drosophila vision started about half a century ago, and now the field is booming with sophisticated genetic tools, rich behavioral assays, and importantly, a greater number of scientists joining from different backgrounds. This review will briefly cover the structural anatomy of the Drosophila visual system, the animal’s visual behaviors, the genes involved in assembling these circuits, the new and powerful techniques, and the challenges ahead for ultimately identifying the general principles of biological computation in the brain.
A typical brain utilizes a great many compact neural circuits to collect and process information from the internal biological and external environmental worlds and generates motor commands for observable behaviors. The fruit fly Drosophila melanogaster, despite of its miniature body and tiny brain, can survive in almost any corner of the world.1 It can find food, court mate, fight rival conspecific, avoid predators, and amazingly fly without crashing into trees. Drosophila vision and its underlying neuronal machinery has been a key research model for at least half century for neurogeneticists.2 Given the efforts invested on the visual system, this animal model is likely to offer the first full understanding of how visual information is computed by a multi-cellular organism. Furthermore, research in Drosophila has revealed many genes that play crucial roles in the formation of functional brains across species. The architectural similarities between the visual systems of Drosophila and vertebrate at the molecular, cellular, and network levels suggest new principles discovered at the circuit level on the relationship between neurons and behavior in Drosophila shall also contribute greatly to our understanding of the general principles for how bigger brains work.3 I start with the anatomy of Drosophila visual system, which surprisingly still contains many uncharted areas.
PMCID: PMC3739809  PMID: 23880926
Drosophila; vision; neural circuits; behavior; neurogenetics
7.  Drosophila, Genetic Screens, and Cardiac Function 
Circulation research  2011;109(7):794-806.
The fruit fly, Drosophila melanogaster, has been used to study genetics, development, and signaling for nearly a century but only over the past few decades has this tremendous resource been the focus of cardiovascular research. Fly genetics offers sophisticated transgenic systems, molecularly-defined genomic deficiencies, genome-wide transgenic RNAi lines, and numerous curated mutants to perform genetic screens. As a genetically-tractable model, the fly facilitates gene discovery and can complement mammalian models of disease. The circulatory system in the fly is comprised of well-defined sets of cardiomyocytes and methodological advances have permitted accurate characterization of cardiac morphology and function. Thus, fly genetics and genomics offers new approaches for gene discovery of adult cardiac phenotypes to identify evolutionarily conserved molecular signals that drive cardiovascular disease.
PMCID: PMC3678974  PMID: 21921272
Drosophila; Cardiomyopathy; Genomics
8.  Integrative Approach Reveals Composition of Endoparasitoid Wasp Venoms 
PLoS ONE  2013;8(5):e64125.
The fruit fly Drosophila melanogaster and its endoparasitoid wasps are a developing model system for interactions between host immune responses and parasite virulence mechanisms. In this system, wasps use diverse venom cocktails to suppress the conserved fly cellular encapsulation response. Although numerous genetic tools allow detailed characterization of fly immune genes, lack of wasp genomic information has hindered characterization of the parasite side of the interaction. Here, we use high-throughput nucleic acid and amino acid sequencing methods to describe the venoms of two related Drosophila endoparasitoids with distinct infection strategies, Leptopilina boulardi and L. heterotoma. Using RNA-seq, we assembled and quantified libraries of transcript sequences from female wasp abdomens. Next, we used mass spectrometry to sequence peptides derived from dissected venom gland lumens. We then mapped the peptide spectral data against the abdomen transcriptomes to identify a set of putative venom genes for each wasp species. Our approach captured the three venom genes previously characterized in L. boulardi by traditional cDNA cloning methods as well as numerous new venom genes that were subsequently validated by a combination of RT-PCR, blast comparisons, and secretion signal sequence search. Overall, 129 proteins were found to comprise L. boulardi venom and 176 proteins were found to comprise L. heterotoma venom. We found significant overlap in L. boulardi and L. heterotoma venom composition but also distinct differences that may underlie their unique infection strategies. Our joint transcriptomic-proteomic approach for endoparasitoid wasp venoms is generally applicable to identification of functional protein subsets from any non-genome sequenced organism.
PMCID: PMC3662768  PMID: 23717546
9.  Sleep and wakefulness in Drosophila melanogaster 
Sleep is present and tightly regulated in every vertebrate species in which it has been carefully investigated, but what sleep is for remains a mystery. Sleep is also present in invertebrates, and an extensive analysis in Drosophila melanogaster has shown that sleep in fruit flies show most of the fundamental features that characterize sleep in mammals. In Drosophila, fly sleep consists of sustained periods of quiescence associated with an increased arousal threshold. Fly sleep is modulated by several of the same stimulants and hypnotics that affect mammalian sleep. Moreover, like in mammals, fly sleep shows remarkable interindividual variability. The expression of several genes involved in energy metabolism, synaptic plasticity, and the response to cellular stress varies in Drosophila between sleep and wakefulness, and the same occurs in rodents. Brain activity also changes in flies as a function of behavioral state. Furthermore, Drosophila sleep is tightly regulated in a circadian and homeostatic manner, and the homeostatic regulation is largely independent of the circadian regulation. After sleep deprivation recovery sleep in flies is longer in duration and more consolidated, as indicated by an increase in arousal threshold and fewer brief awakenings. Finally, sleep deprivation in flies impairs vigilance and performance. Because of the extensive similarities between flies and mammals, Drosophila is now being used as a promising model system for the genetic dissection of sleep. Over the last few years, mutagenesis screens have isolated several short sleeping mutants, a demonstration that that single genes can have a powerful effect on a complex trait like sleep.
PMCID: PMC2715168  PMID: 18591491
10.  Exploring prion protein biology in flies 
Prion  2010;4(1):1-8.
The fruit fly Drosophila melanogaster has been a favored tool for genetic studies for over 100 years and has become an excellent model system to study development, signal transduction, cell biology, immunity and behavior. The relevance of Drosophila to humans is perhaps best illustrated by the fact that more than 75% of the genes identified in human diseases have counterparts in Drosophila. During the last decade, many fly models of neurodegenerative disorders have contributed to the identification of novel pathways mediating pathogenesis. However, the development of prion disease models in flies has been remarkably challenging. We recently reported a Drosophila model of sporadic prion pathology that shares relevant features with the typical disease in mammals. This new model provides the basis to explore relevant aspects of the biology of the prion protein, such as uncovering the genetic mechanisms regulating prion protein misfolding and prion-induced neurodegeneration, in a dynamic, genetically tractable in vivo system.
PMCID: PMC2850413  PMID: 20083902
Drosophila model; prion protein; spontaneous misfolding; neurodegeneration; genetics
11.  In vivo RNAi: Today and Tomorrow 
RNA interference (RNAi) provides a powerful reverse genetics approach to analyze gene functions both in tissue culture and in vivo. Because of its widespread applicability and effectiveness it has become an essential part of the tool box kits of model organisms such as Caenorhabditis elegans, Drosophila, and the mouse. In addition, the use of RNAi in animals in which genetic tools are either poorly developed or nonexistent enables a myriad of fundamental questions to be asked. Here, we review the methods and applications of in vivo RNAi to characterize gene functions in model organisms and discuss their impact to the study of developmental as well as evolutionary questions. Further, we discuss the applications of RNAi technologies to crop improvement, pest control and RNAi therapeutics, thus providing an appreciation of the potential for phenomenal applications of RNAi to agriculture and medicine.
In vivo RNAi technology is replacing classical genetics in screens and conditional targeting of gene function. It also has applications in crop improvement, pest control, and medicine.
PMCID: PMC2908776  PMID: 20534712
12.  A whole genome RNAi screen of Drosophila S2 cell spreading performed using automated computational image analysis 
The Journal of Cell Biology  2010;191(3):471-478.
An automated, image-based RNAi screen for cell shape reveals roles for membrane secretion factors in cell spreading.
Recent technological advances in microscopy have enabled cell-based whole genome screens, but the analysis of the vast amount of image data generated by such screens usually proves to be rate limiting. In this study, we performed a whole genome RNA interference (RNAi) screen to uncover genes that affect spreading of Drosophila melanogaster S2 cells using several computational methods for analyzing the image data in an automated manner. Expected genes in the Scar-Arp2/3 actin nucleation pathway were identified as well as casein kinase I, which had a similar morphological RNAi signature. A distinct nonspreading morphological phenotype was identified for genes involved in membrane secretion or synthesis. In this group, we identified a new secretory peptide and investigated the functions of two poorly characterized endoplasmic reticulum proteins that have roles in secretion. Thus, this genome-wide screen succeeded in identifying known and unexpected proteins that are important for cell spreading, and the computational tools developed in this study should prove useful for other types of automated whole genome screens.
PMCID: PMC3003316  PMID: 21041442
13.  Drosophila endocytic neoplastic tumor suppressor genes regulate Sav/Wts/Hpo signaling and the c-Jun N-terminal kinase pathway 
Cell Cycle  2011;10(23):4110-4118.
Genetic screens in the fruit fly Drosophila melanogaster have identified a class of neoplastic tumor suppressor genes (endocytic nTSGs) that encode proteins that localize to endosomes and facilitate the trafficking of membrane-bound receptors and adhesion molecules into the degradative lysosome. Loss of endocytic nTSGs transforms imaginal disc epithelia into highly proliferative, invasive tissues that fail to differentiate and display defects in cellular apicobasal polarity, adhesion and tissue architecture. As vertebrate homologs of some Drosophila nTSGs are linked to tumor formation, identifying molecular changes in signaling associated with nTSG loss could inform understanding of neoplastic transformation in vertebrates. Here, we show that mutations in genes that act at multiple steps of the endolysosomal pathway lead to autonomous activation of the Sav/Wts/Hpo (SWH) transcriptional effector Yki (YAP/TAZ in vertebrates) and the Jun N-terminal kinase (JNK), which is known to promote Yki activity in cells with disrupted polarity. Yki and JNK activity are elevated by mutations at multiple steps in the endolysosomal pathway, including mutations in the AP-2σ gene, which encodes a component of the AP-2 adaptor complex that recruits cargoes into clathrin-coated pits for subsequent internalization. Moreover, reduction of JNK activity can decrease elevated Yki signaling caused by altered endocytosis. These studies reveal a broad requirement for components of the endocytic pathway in regulating SWH and JNK outputs and place Drosophila endocytic nTSGs into a network that involves two major signaling pathways implicated in oncogenesis.
PMCID: PMC3272291  PMID: 22101275
Drosophila; endocytic tumor suppressor; Yki; JNK; Tsg101; AP-2; Hippo
14.  Aging: Dial M for Mitochondria 
Aging (Albany NY)  2010;2(1):69-73.
A major goal of aging research is to identify interventions that prolong lifespan in distantly related organisms. In recent years, genetic studies in both nematodes and rodents have reported that moderate inactivation of genes important for mitochondrial electron transport chain (ETC) function can promote longevity. We performed an RNAi screen to probe the role of ETC components in modulating lifespan in the fruit flyDrosophila melanogaster. In this Research Perspective, we discuss our findings and how they may relate to similar studies in worms and mice.
PMCID: PMC2837206  PMID: 20228940
Drosophila; longevity; C. elegans; respiratory chain
15.  Using Drosophila as a tool to identify Pharmacological Therapies for Fragile X Syndrome 
Drug discovery today. Technologies  2012;10(1):e129-e136.
Despite obvious differences such as the ability to fly, the fruit fly Drosophila melanogaster is similar to humans at many different levels of complexity. Studies of development, cell growth and division, metabolism, and even cognition, have borne out these similarities. For example, Drosophila bearing mutations in the fly gene homologue of the known human disease Fragile X, are affected in fundamentally similar ways as affected humans. The ramification of this degree of similarity is that Drosophila, as a model organism, is a rich resource for learning about human cells, development and even human cognition and behavior. Drosophila has a short generation time of ten days, is cheap to propagate and maintain and has a vast array of genetic tools available to it; making Drosophila an extremely attractive organism for the study of human disease. Here, we summarize research from our lab and others using Drosophila to understand the human neurological disease, called Fragile X. We focus on the Drosophila model of fragile X, its characterization, and use as a tool to identify potential drugs for the treatment of Fragile X. Several clinical trials are in progress now that were motivated by this research.
PMCID: PMC3667993  PMID: 23730322
Disease Modeling; Fragile X; Drosophila; Pharmacological Treatments; Autism; Cognitive impairment
16.  The Aedes aegypti Toll Pathway Controls Dengue Virus Infection 
PLoS Pathogens  2008;4(7):e1000098.
Aedes aegypti, the mosquito vector of dengue viruses, utilizes its innate immune system to ward off a variety of pathogens, some of which can cause disease in humans. To date, the features of insects' innate immune defenses against viruses have mainly been studied in the fruit fly Drosophila melanogaster, which appears to utilize different immune pathways against different types of viruses, in addition to an RNA interference–based defense system. We have used the recently released whole-genome sequence of the Ae. aegypti mosquito, in combination with high-throughput gene expression and RNA interference (RNAi)-based reverse genetic analyses, to characterize its response to dengue virus infection in different body compartments. We have further addressed the impact of the mosquito's endogenous microbial flora on virus infection. Our findings indicate a significant role for the Toll pathway in regulating resistance to dengue virus, as indicated by an infection-responsive regulation and functional assessment of several Toll pathway–associated genes. We have also shown that the mosquito's natural microbiota play a role in modulating the dengue virus infection, possibly through basal-level stimulation of the Toll immune pathway.
Author Summary
The Aedes aegypti mosquito is largely responsible for the transmission of dengue viruses that cause disease in humans. The virus is taken up with an infected blood meal from which it will first infect the mosquito gut tissue. From the gut it will migrate to other parts of the mosquito, including the salivary glands, from where it can be transmitted to another human upon a second blood meal. In this study we show that the mosquito utilizes its innate immune system to control dengue virus infection. Infection with the virus will result in the activation of mosquito immune responses that are mainly controlled by the Toll pathway. These responses entail antiviral activities that limit infection with the virus. We also show that the mosquito's natural microbial flora play a role in modulating the dengue virus infection, possibly through the stimulation of the mosquito's immune system.
PMCID: PMC2435278  PMID: 18604274
17.  In situ electroporation of surface-bound siRNAs in microwell arrays† 
Lab on a Chip  2012;12(5):939-947.
Gene silencing using RNA interference (RNAi) has become a prominent biological tool for gene annotation, pathway analysis, and target discovery in mammalian cells. High-throughput screens conducted using whole-genome siRNA libraries have uncovered rich sets of new genes involved in a variety of biological processes and cellular models of disease. However, high-throughput RNAi screening is not yet a mainstream tool in life science research because current screening platforms are expensive and onerous. Miniaturizing the RNAi screening platform to reduce cost and increase throughput will enable its widespread use and harness its potential for rapid genome annotation. With this aim, we have combined semi-conductor microfabrication and nanolitre dispensing techniques to develop miniaturized electroporation-ready microwell arrays loaded with siRNA molecules in which multiplexed gene knockdown can be achieved. Arrays of microwells are created using high-aspect ratio biocompatible photoresists on optically transparent and conductive Indium-Tin Oxide (ITO) substrates with integrated micro-electrodes to enable in situ electroporation. Non-contact inkjet microarraying allows precise dispensing of nanolitre volumes into the microwell structures. We have achieved parallel electroporation of multiple mammalian cells cultured in these microwell arrays and observed efficient knockdown of genes with surface-bound, printed siRNAs. Further integration of microfabrication and non-contact nanolitre dispensing techniques described here may enable single-substrate whole-genome siRNA screening in mammalian cells.
PMCID: PMC3392120  PMID: 22245984
18.  The Tribolium spineless ortholog specifies both larval and adult antennal identity 
Development genes and evolution  2008;219(1):45-51.
The morphology of insect antennae varies widely among species, but our understanding of antennal development comes almost solely from studies of one species - the fruit fly, Drosophila melanogaster. Moreover, this knowledge applies mostly to adult structures, since Drosophila lacks external larval appendages. In contrast to Drosophila, the red flour beetle, Tribolium castaneum, has both larval and adult antennae, which are very different from one another in morphology. Thus, Tribolium provides an ideal system to compare modes of antennal development both within and between species. Here we report that the Tribolium ortholog of spineless (Tc-ss) is required in both the larval and adult antennae. Knockdown of Tc-ss by RNAi during either larval or imaginal development causes transformation of the distal portion of the antennae to legs. Thus, the function of ss is conserved between Drosophila and Tribolium with respect to adult antennal specification, and also between Tribolium larval and adult antennal development. The similarity of the Tc-ss RNAi phenotype to that of a classically described Tribolium mutation, antennapedia (ap) (of no relationship to the Drosophila Hox gene of the same name), led us to characterize the original ap mutation and two newly identified ap alleles. Our mapping and phenotypic data suggest Tc-ss is the best candidate for the ap locus. These results represent a first step in characterizing larval and adult antennal patterning in Tribolium, which should provide important insights into the evolution of insect antennal development.
PMCID: PMC2605184  PMID: 19030877
Tribolium; antenna; spineless; appendage; insect
19.  Autophagy in Drosophila melanogaster 
Biochimica et biophysica acta  2009;1793(9):1452-1460.
Macroautophagy (autophagy) is a bulk cytoplasmic degradation process that is conserved from yeast to mammals. Autophagy is an important cellular response to starvation and stress, and plays important roles in development, cell death, aging, immunity, and cancer. The fruit fly Drosophila melanogaster provides an excellent model system to study autophagy in vivo, in the context of a developing organism. Autophagy (atg) genes and their regulators are conserved in Drosophila, and autophagy is induced in response to nutrient starvation and hormones during development. In this review we provide an overview of how Drosophila research has contributed to our understanding of the role and regulation of autophagy in cell survival, growth, nutrient utilization, and cell death. Recent Drosophila research has also provided important mechanistic information about the role of autophagy in protein aggregation disorders, neurodegeneration, aging, and innate immunity. Differences in the role of autophagy in specific contexts and/or cell types suggest that there may be cell-context-specific regulators of autophagy, and studies in Drosophila are well-suited to yield discoveries about this specificity.
PMCID: PMC2739249  PMID: 19264097
20.  Inferring Gene Function and Network Organization in Drosophila Signaling by Combined Analysis of Pleiotropy and Epistasis 
G3: Genes|Genomes|Genetics  2013;3(5):807-814.
High-throughput genetic interaction screens have enabled functional genomics on a network scale. Groups of cofunctional genes commonly exhibit similar interaction patterns across a large network, leading to novel functional inferences for a minority of previously uncharacterized genes within a group. However, such analyses are often unsuited to cases with a few relevant gene variants or sparse annotation. Here we describe an alternative analysis of cell growth signaling using a computational strategy that integrates patterns of pleiotropy and epistasis to infer how gene knockdowns enhance or suppress the effects of other knockdowns. We analyzed the interaction network for RNAi knockdowns of a set of 93 incompletely annotated genes in a Drosophila melanogaster model of cellular signaling. We inferred novel functional relationships between genes by modeling genetic interactions in terms of knockdown-to-knockdown influences. The method simultaneously analyzes the effects of partially pleiotropic genes on multiple quantitative phenotypes to infer a consistent model of each genetic interaction. From these models we proposed novel candidate Ras inhibitors and their Ras signaling interaction partners, and each of these hypotheses can be inferred independent of network-wide patterns. At the same time, the network-scale interaction patterns consistently mapped pathway organization. The analysis therefore assigns functional relevance to individual genetic interactions while also revealing global genetic architecture.
PMCID: PMC3656728  PMID: 23550134
genetic interaction; pleiotropy; epistasis; genetic network; signaling network
21.  RNAi Screening for Host Factors Involved in Vaccinia Virus Infection using Drosophila Cells 
Viral pathogens represent a significant public health threat; not only can viruses cause natural epidemics of human disease, but their potential use in bioterrorism is also a concern. A better understanding of the cellular factors that impact infection would facilitate the development of much-needed therapeutics. Recent advances in RNA interference (RNAi) technology coupled with complete genome sequencing of several organisms has led to the optimization of genome-wide, cell-based loss-of-function screens. Drosophila cells are particularly amenable to genome-scale screens because of the ease and efficiency of RNAi in this system 1. Importantly, a wide variety of viruses can infect Drosophila cells, including a number of mammalian viruses of medical and agricultural importance 2,3,4. Previous RNAi screens in Drosophila have identified host factors that are required for various steps in virus infection including entry, translation and RNA replication 5. Moreover, many of the cellular factors required for viral replication in Drosophila cell culture are also limiting in human cells infected with these viruses 4,6,7,8, 9. Therefore, the identification of host factors co-opted during viral infection presents novel targets for antiviral therapeutics. Here we present a generalized protocol for a high-throughput RNAi screen to identify cellular factors involved in viral infection, using vaccinia virus as an example.
PMCID: PMC3156023  PMID: 20834214
22.  RNAi Screening in Drosophila Cells Identifies New Modifiers of Mutant Huntingtin Aggregation 
PLoS ONE  2009;4(9):e7275.
The fruitfly Drosophila melanogaster is well established as a model system in the study of human neurodegenerative diseases. Utilizing RNAi, we have carried out a high-throughput screen for modifiers of aggregate formation in Drosophila larval CNS-derived cells expressing mutant human Huntingtin exon 1 fused to EGFP with an expanded polyglutamine repeat (62Q). 7200 genes, encompassing around 50% of the Drosophila genome, were screened, resulting in the identification of 404 candidates that either suppress or enhance aggregation. These candidates were subjected to secondary screening in normal length (18Q)-expressing cells and pruned to remove dsRNAs with greater than 10 off-target effects (OTEs). De novo RNAi probes were designed and synthesized for the remaining 68 candidates. Following a tertiary round of screening, 21 high confidence candidates were analyzed in vivo for their ability to modify mutant Huntingtin-induced eye degeneration and brain aggregation. We have established useful models for the study of human HD using the fly, and through our RNAi screen, we have identified new modifiers of mutant human Huntingtin aggregation and aggregate formation in the brain. Newly identified modifiers including genes related to nuclear transport, nucleotide processes, and signaling, may be involved in polyglutamine aggregate formation and Huntington disease cascades.
PMCID: PMC2748703  PMID: 19789644
23.  Mutation in pre-mRNA adenosine deaminase markedly attenuates neuronal tolerance to O2 deprivation in Drosophila melanogaster 
Journal of Clinical Investigation  2001;107(6):685-693.
O2 deprivation can produce many devastating clinical conditions such as myocardial infarct and stroke. The molecular mechanisms underlying the inherent tissue susceptibility or tolerance to O2 lack are, however, not well defined. Since the fruit fly, Drosophila melanogaster, is extraordinarily tolerant to O2 deprivation, we have performed a genetic screen in the Drosophila to search for loss-of-function mutants that are sensitive to low O2. Here we report on the genetic and molecular characterization of one of the genes identified from this screen, named hypnos-2. This gene encodes a Drosophila pre-mRNA adenosine deaminase (dADAR) and is expressed almost exclusively in the adult central nervous system. Disruption of the dADAR gene results in totally unedited sodium (Para), calcium (Dmca1A), and chloride (DrosGluCl-α) channels, a very prolonged recovery from anoxic stupor, a vulnerability to heat shock and increased O2 demands, and neuronal degeneration in aged flies. These data clearly demonstrate that, through the editing of ion channels as targets, dADAR, for which there are mammalian homologues, is essential for adaptation to altered environmental stresses such as O2 deprivation and for the prevention of premature neuronal degeneration.
PMCID: PMC208948  PMID: 11254668
24.  Neurodegenerative diseases: Lessons from genome-wide screens in small model organisms 
EMBO Molecular Medicine  2009;1(8-9):360-370.
Various age-related neurodegenerative diseases, including Parkinson's disease, polyglutamine expansion diseases and Alzheimer's disease, are associated with the accumulation of misfolded proteins in aggregates in the brain. How and why these proteins form aggregates and cause disease is still poorly understood. Small model organisms—the baker's yeast Saccharomyces cerevisiae, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster—have been used to model these diseases and high-throughput genetic screens using these models have led to the identification of a large number of genes that modify aggregation and toxicity of the disease proteins. In this review, we revisit these models and provide a comprehensive comparison of the genetic screens performed so far. Our integrative analysis highlights alterations of a wide variety of basic cellular processes. Not all disease proteins are influenced by alterations in the same cellular processes and despite the unifying theme of protein misfolding and aggregation, the pathology of each of the age-related misfolding disorders can be induced or influenced by a disease-protein-specific subset of molecular processes.
PMCID: PMC3378155  PMID: 20049741
neurodegeneration; protein aggregation; genetic modifiers; small model organisms; meta-analysis
25.  More than just glue 
Cell Adhesion & Migration  2009;3(1):36-42.
Cell adhesion is the fundamental driving force that establishes complex cellular architectures, with the nervous system offering a striking, sophisticated case study. Developing neurons adhere to neighboring neurons, their synaptic partners, and to glial cells. These adhesive interactions are required in a diverse array of contexts, including cell migration, axon guidance and targeting, as well as synapse formation and physiology. Forward and reverse genetic screens in the fruit fly Drosophila have uncovered several adhesion molecules that are required for neural development, and detailed cell biological analyses are beginning to unravel how these factors shape nervous system connectivity. Here we review our current understanding of the most prominent of these adhesion factors and their modes of action.
PMCID: PMC2675147  PMID: 19372748
drosophila; cell adhesion; nervous system; glia; axon; synapse

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