title: FMAj: a tool for high content analysis of muscle dynamics in Drosophila metamorphosis.
abstract: BACKGROUND
  During metamorphosis in Drosophila melanogaster, larval muscles undergo two different developmental fates; one population is removed by cell death, while the other persistent subset undergoes morphological remodeling and survives to adulthood. Thanks to the ability to perform live imaging of muscle development in transparent pupae and the power of genetics, metamorphosis in Drosophila can be used as a model to study the regulation of skeletal muscle mass. However, time-lapse microscopy generates sizeable image data that require new tools for high throughput image analysis.
  
  
  RESULTS
  We performed targeted gene perturbation in muscles and acquired 3D time-series images of muscles in metamorphosis using laser scanning confocal microscopy. To quantify the phenotypic effects of gene perturbations, we designed the Fly Muscle Analysis tool (FMAj) which is based on the ImageJ and MySQL frameworks for image processing and data storage, respectively. The image analysis pipeline of FMAj contains three modules. The first module assists in adding annotations to time-lapse datasets, such as genotypes, experimental parameters and temporal reference points, which are used to compare different datasets. The second module performs segmentation and feature extraction of muscle cells and nuclei. Users can provide annotations to the detected objects, such as muscle identities and anatomical information. The third module performs comparative quantitative analysis of muscle phenotypes. We applied our tool to the phenotypic characterization of two atrophy related genes that were silenced by RNA interference. Reduction of Drosophila Tor (Target of Rapamycin) expression resulted in enhanced atrophy compared to control, while inhibition of the autophagy factor Atg9 caused suppression of atrophy and enlarged muscle fibers of abnormal morphology. FMAj enabled us to monitor the progression of atrophic and hypertrophic phenotypes of individual muscles throughout metamorphosis.
  
  
  CONCLUSIONS
  We designed a new tool to visualize and quantify morphological changes of muscles in time-lapse images of Drosophila metamorphosis. Our in vivo imaging experiments revealed that evolutionarily conserved genes involved in Tor signalling and autophagy, perform similar functions in regulating muscle mass in mammals and Drosophila. Extending our approach to a genome-wide scale has the potential to identify new genes involved in muscle size regulation.
authors.forename: Yadav
authors.initials: Y
authors.lastname: Kuleesha
authors.forename: Wee Choo
authors.initials: WC
authors.lastname: Puah
authors.forename: Feng
authors.initials: F
authors.lastname: Lin
authors.forename: Martin
authors.initials: M
authors.lastname: Wasser
mesh_terms: D000818:Animals; D000071183:Autophagy-Related Proteins; D002467:Cell Nucleus / Q000235:genetics; D029721:Drosophila Proteins / Q000037:antagonists & inhibitors / Q000235:genetics*; D004331:Drosophila melanogaster / Q000502:physiology*; D005260:Female; D018507:Gene Expression Regulation, Developmental; D007091:Image Processing, Computer-Assisted; D021621:Imaging, Three-Dimensional; D007814:Larva / Q000235:genetics*; D008297:Male; D008565:Membrane Proteins / Q000037:antagonists & inhibitors / Q000235:genetics; D008675:Metamorphosis, Biological / Q000235:genetics*; D018613:Microscopy, Confocal / Q000379:methods; D024510:Muscle Development / Q000235:genetics; D018482:Muscle, Skeletal / Q000502:physiology*; D010641:Phenotype; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000235:genetics; D012984:Software
chemical_list: C557894:Atg9 protein, Drosophila; D000071183:Autophagy-Related Proteins; D029721:Drosophila Proteins; D008565:Membrane Proteins; D034741:RNA, Small Interfering