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Bioinformatics. 2019 Jan 2. doi: 10.1093/bioinformatics/bty1064. [Epub ahead of print] AnnoFly: Annotating Drosophila Embryonic Images Based on an Attention-Enhanced RNN Model. Yang Y1,2, Zhou M1, Fang Q3, Shen HB4,5. Author information Abstract MOTIVATION: In the post-genomic era, image-based transcriptomics have received huge attention, because the visualization of gene expression distribution is able to reveal spatial and temporal expression pattern, which is significantly important for understanding biological mechanisms. The Berkeley Drosophila Genome Project (BDGP) has collected a large-scale spatial gene expression database for studying Drosophila embryogenesis. Given the expression images, how to annotate them for the study of Drosophila embryonic development is the next urgent task. In order to speed up the labor-intensive labeling work, automatic tools are highly desired. However, conventional image annotation tools are not applicable here, because the labeling is at the gene-level rather than the image-level, where each gene is represented by a bag of multiple related images, showing a multi-instance phenomenon, and the image quality varies by image orientations and experiment batches. Moreover, different local regions of an image correspond to different CV annotation terms, i.e. an image has multiple labels. Designing an accurate annotation tool in such a multi-instance multi-label (MIML) scenario is a very challenging task.
RESULTS: To address these challenges, we develop a new annotator for the fruit fly embryonic images, called AnnoFly. Driven by an attention-enhanced RNN model, it can weight images of different qualities, so as to focus on the most informative image patterns. We assess the new model on three standard data sets. The experimental results reveal that the attention-based model provides a transparent approach for identifying the important images for labeling, and it substantially enhances the accuracy compared with the existing annotation methods, including both single-instance and multi-instance learning methods.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
PMID: 30601935 DOI: 10.1093/bioinformatics/bty1064
High throughput in vivo functional validation of candidate congenital heart disease genes in Drosophila
Elife. 2017 Jan 20;6. pii: e22617. doi: 10.7554/eLife.22617.
Zhu JY1, Fu Y1, Nettleton M1, Richman A1, Han Z1,2.
Genomic sequencing has implicated large numbers of genes and de novo mutations as potential disease risk factors. A high throughput in vivo model system is needed to validate gene associations with pathology. We developed a Drosophila-based functional system to screen candidate disease genes identified from Congenital Heart Disease (CHD) patients. 134 genes were tested in the Drosophila heart using RNAi-based gene silencing. Quantitative analyses of multiple cardiac phenotypes demonstrated essential structural, functional, and developmental roles for more than 70 genes, including a subgroup encoding histone H3K4 modifying proteins. We also demonstrated the use of Drosophila to evaluate cardiac phenotypes resulting from specific, patient-derived alleles of candidate disease genes. We describe the first high throughput in vivo validation system to screen candidate disease genes identified from patients. This approach has the potential to facilitate development of precision medicine approaches for CHD and other diseases associated with genetic factors. KEYWORDS: D. melanogaster; Drosophila; congenital heart disease; developmental biology; heart development; histone modification; human biology; in vivo validation; medicine; stem cells
PMID 28084990 DOI: 10.7554/eLife.22617
Lineage-associated tracts defining the anatomy of the drosophila first instar larval brain
Dev Biol. 2015 Jun 30. pii: S0012-1606(15)30027-0. doi: 10.1016/j.ydbio.2015.06.021. [Epub ahead of print]
Hartenstein V1, Younossi-Hartenstein A2, Lovick J2, Kong A2, Omoto J2, Ngo K2, Viktorin G3.
Fixed lineages derived from unique, genetically specified neuroblasts form the anatomical building blocks of the Drosophila brain. Neurons belonging to the same lineage project their axons in a common tract, which is labeled by neuronal markers. In this paper, we present a detailed atlas of the lineage-associated tracts forming the brain of the early Drosophila larva, based on the use of global markers (anti-Neuroglian, anti-Neurotactin, Inscuteable-Gal4>UAS-chRFP-Tub) and lineage-specific reporters. We describe 68 discrete fiber bundles that contain axons of one lineage or pairs/small sets of adjacent lineages. Bundles enter the neuropil at invariant locations, the lineage tract entry portals. Within the neuropil, these fiber bundles form larger fascicles that can be classified, by their main orientation, into longitudinal, transverse, and vertical (ascending/descending) fascicles. We present 3D digital models of lineage tract entry portals and neuropil fascicles, set into relationship to commonly used, easily recognizable reference structures such as the mushroom body, the antennal lobe, the optic lobe, and the Fasciclin II-positive fiber bundles that connect the brain and ventral nerve cord. Correspondences and differences between early larval tract anatomy and the previously described late larval and adult lineage patterns are highlighted. Our L1 neuro-anatomical atlas of lineages constitutes an essential step towards following morphologically defined lineages to the neuroblasts of the early embryo, which will ultimately make it possible to link the structure and connectivity of a lineage to the expression of genes in the particular neuroblast that gives rise to that lineage. Furthermore, the L1 atlas will be important for a host of ongoing work that attempts to reconstruct neuronal connectivity at the level of resolution of single neurons and their synapses. Copyright © 2015. Published by Elsevier Inc. KEYWORDS: Brain; Development; Drosophila; Larval; Lineage
Germ cell migration - Montell
Notch for detachment Jak/stat defines population Growth factors for migration
Cell-cell adhesion beta-catenin. Allows the to attach to each other.
Drosophila Hox and Sex-Determination Genes Control Segment Elimination through EGFR and extramacrochetae Activity
PLoS Genet. 2012 Aug;8(8):e1002874. Epub 2012 Aug 9.
Foronda D, Martín P, Sánchez-Herrero E. Source Centro de Biología Molecular Severo Ochoa (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
The formation or suppression of particular structures is a major change occurring in development and evolution. One example of such change is the absence of the seventh abdominal segment (A7) in Drosophila males. We show here that there is a down-regulation of EGFR activity and fewer histoblasts in the male A7 in early pupae. If this activity is elevated, cell number increases and a small segment develops in the adult. At later pupal stages, the remaining precursors of the A7 are extruded under the epithelium. This extrusion requires the up-regulation of the HLH protein Extramacrochetae and correlates with high levels of spaghetti-squash, the gene encoding the regulatory light chain of the non-muscle myosin II. The Hox gene Abdominal-B controls both the down-regulation of spitz, a ligand of the EGFR pathway, and the up-regulation of extramacrochetae, and also regulates the transcription of the sex-determining gene doublesex. The male Doublesex protein, in turn, controls extramacrochetae and spaghetti-squash expression. In females, the EGFR pathway is also down-regulated in the A7 but extramacrochetae and spaghetti-squash are not up-regulated and extrusion of precursor cells is almost absent. Our results show the complex orchestration of cellular and genetic events that lead to this important sexually dimorphic character change.
Gene regulatory networks controlling hematopoietic progenitor niche cell production and differentiation in the Drosophila lymph gland
PLoS One. 2012;7(7):e41604. Epub 2012 Jul 24.
Tokusumi Y, Tokusumi T, Shoue DA, Schulz RA. Source Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America.
Hematopoiesis occurs in two phases in Drosophila, with the first completed during embryogenesis and the second accomplished during larval development. The lymph gland serves as the venue for the final hematopoietic program, with this larval tissue well-studied as to its cellular organization and genetic regulation. While the medullary zone contains stem-like hematopoietic progenitors, the posterior signaling center (PSC) functions as a niche microenvironment essential for controlling the decision between progenitor maintenance versus cellular differentiation. In this report, we utilize a PSC-specific GAL4 driver and UAS-gene RNAi strains, to selectively knockdown individual gene functions in PSC cells. We assessed the effect of abrogating the function of 820 genes as to their requirement for niche cell production and differentiation. 100 genes were shown to be essential for normal niche development, with various loci placed into sub-groups based on the functions of their encoded protein products and known genetic interactions. For members of three of these groups, we characterized loss- and gain-of-function phenotypes. Gene function knockdown of members of the BAP chromatin-remodeling complex resulted in niche cells that do not express the hedgehog (hh) gene and fail to differentiate filopodia believed important for Hh signaling from the niche to progenitors. Abrogating gene function of various members of the insulin-like growth factor and TOR signaling pathways resulted in anomalous PSC cell production, leading to a defective niche organization. Further analysis of the Pten, TSC1, and TSC2 tumor suppressor genes demonstrated their loss-of-function condition resulted in severely altered blood cell homeostasis, including the abundant production of lamellocytes, specialized hemocytes involved in innate immune responses. Together, this cell-specific RNAi knockdown survey and mutant phenotype analyses identified multiple genes and their regulatory networks required for the normal organization and function of the hematopoietic progenitor niche within the lymph gland.
Functional study of mammalian Neph proteins in Drosophila melanogaster
PLoS One. 2012;7(7):e40300. Epub 2012 Jul 6.
Helmstädter M, Lüthy K, Gödel M, Simons M, Ashish, Nihalani D, Rensing SA, Fischbach KF, Huber TB. Source Renal Division, University Hospital Freiburg, Freiburg, Germany.
Neph molecules are highly conserved immunoglobulin superfamily proteins (IgSF) which are essential for multiple morphogenetic processes, including glomerular development in mammals and neuronal as well as nephrocyte development in D. melanogaster. While D. melanogaster expresses two Neph-like proteins (Kirre and IrreC/Rst), three Neph proteins (Neph1-3) are expressed in the mammalian system. However, although these molecules are highly abundant, their molecular functions are still poorly understood. Here we report on a fly system in which we overexpress and replace endogenous Neph homologs with mammalian Neph1-3 proteins to identify functional Neph protein networks required for neuronal and nephrocyte development. Misexpression of Neph1, but neither Neph2 nor Neph3, phenocopies the overexpression of endogenous Neph molecules suggesting a functional diversity of mammalian Neph family proteins. Moreover, structure-function analysis identified a conserved and specific Neph1 protein motif that appears to be required for the functional replacement of Kirre. Hereby, we establish D. melanogaster as a genetic system to specifically model molecular Neph1 functions in vivo and identify a conserved amino acid motif linking Neph1 to Drosophila Kirre function.
Scanning electron microscopy of Drosophila
- Scanning electron microscopy of Drosophila embryogenesis. I. The structure of the egg envelopes and the formation of the cellular blastoderm. Turner FR, Mahowald AP. Dev Biol. 1976 May;50(1):95-108. No abstract available. PMID: 817949
- Scanning electron microscopy of Drosophila melanogaster embryogenesis. II. Gastrulation and segmentation. Turner FR, Mahowald AP. Dev Biol. 1977 Jun;57(2):403-16. No abstract available. PMID: 406152
- Scanning electron microscopy of Drosophila melanogaster embryogenesis. III. Formation of the head and caudal segments. Turner FR, Mahowald AP. Dev Biol. 1979 Jan;68(1):96-109. PMID: 1081572