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Antonazzo G, Urbano JM, Marygold SJ, Millburn GH, Brown NH. Building a pipeline to solicit expert knowledge from the community to aid gene summary curation. Database (Oxford) 2020; 2020:baz152. [PMID: 31960022 PMCID: PMC6971343 DOI: 10.1093/database/baz152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/29/2019] [Accepted: 12/12/2019] [Indexed: 11/25/2022]
Abstract
Brief summaries describing the function of each gene's product(s) are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. However, manually writing such summaries, even for a single species, is a daunting task; for example, the Drosophila melanogaster genome contains almost 14 000 protein-coding genes. One solution is to use computational methods to generate summaries, but this often fails to capture the key functions or express them eloquently. Here, we describe how we solicited help from the research community to generate manually written summaries of D. melanogaster gene function. Based on the data within the FlyBase database, we developed a computational pipeline to identify researchers who have worked extensively on each gene. We e-mailed these researchers to ask them to draft a brief summary of the main function(s) of the gene's product, which we edited for consistency to produce a 'gene snapshot'. This approach yielded 1800 gene snapshot submissions within a 3-month period. We discuss the general utility of this strategy for other databases that capture data from the research literature. Database URL: https://flybase.org/.
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Affiliation(s)
- Giulia Antonazzo
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Jose M Urbano
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Steven J Marygold
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Gillian H Millburn
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Nicholas H Brown
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
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Kishore R, Arnaboldi V, Van Slyke CE, Chan J, Nash RS, Urbano JM, Dolan ME, Engel SR, Shimoyama M, Sternberg PW, Genome Resources TAO. Automated generation of gene summaries at the Alliance of Genome Resources. Database (Oxford) 2020; 2020:baaa037. [PMID: 32559296 PMCID: PMC7304461 DOI: 10.1093/database/baaa037] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/06/2020] [Accepted: 04/29/2020] [Indexed: 12/28/2022]
Abstract
Short paragraphs that describe gene function, referred to as gene summaries, are valued by users of biological knowledgebases for the ease with which they convey key aspects of gene function. Manual curation of gene summaries, while desirable, is difficult for knowledgebases to sustain. We developed an algorithm that uses curated, structured gene data at the Alliance of Genome Resources (Alliance; www.alliancegenome.org) to automatically generate gene summaries that simulate natural language. The gene data used for this purpose include curated associations (annotations) to ontology terms from the Gene Ontology, Disease Ontology, model organism knowledgebase (MOK)-specific anatomy ontologies and Alliance orthology data. The method uses sentence templates for each data category included in the gene summary in order to build a natural language sentence from the list of terms associated with each gene. To improve readability of the summaries when numerous gene annotations are present, we developed a new algorithm that traverses ontology graphs in order to group terms by their common ancestors. The algorithm optimizes the coverage of the initial set of terms and limits the length of the final summary, using measures of information content of each ontology term as a criterion for inclusion in the summary. The automated gene summaries are generated with each Alliance release, ensuring that they reflect current data at the Alliance. Our method effectively leverages category-specific curation efforts of the Alliance member databases to create modular, structured and standardized gene summaries for seven member species of the Alliance. These automatically generated gene summaries make cross-species gene function comparisons tenable and increase discoverability of potential models of human disease. In addition to being displayed on Alliance gene pages, these summaries are also included on several MOK gene pages.
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Affiliation(s)
- Ranjana Kishore
- WormBase, Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Valerio Arnaboldi
- WormBase, Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Ceri E Van Slyke
- ZFIN, The Institute of Neuroscience, 222 Huestis Hall, University of Oregon, Eugene, OR 97403-1254, USA
| | - Juancarlos Chan
- WormBase, Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Robert S Nash
- Saccharomyces Genome Database, Department of Genetics, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, USA
| | - Jose M Urbano
- FlyBase, Department of Physiology, Development and Neuroscience, 7 Downing Pl, University of Cambridge, Cambridge CB2 3DY, UK
| | - Mary E Dolan
- MGI, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Stacia R Engel
- Saccharomyces Genome Database, Department of Genetics, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, USA
| | - Mary Shimoyama
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin and Marquette University, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Paul W Sternberg
- WormBase, Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
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Urbano JM, Naylor HW, Scarpa E, Muresan L, Sanson B. Suppression of epithelial folding at actomyosin-enriched compartment boundaries downstream of Wingless signalling in Drosophila. Development 2018; 145:dev155325. [PMID: 29691225 PMCID: PMC5964650 DOI: 10.1242/dev.155325] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 03/09/2018] [Indexed: 01/01/2023]
Abstract
Epithelial folding shapes embryos and tissues during development. Here, we investigate the coupling between epithelial folding and actomyosin-enriched compartmental boundaries. The mechanistic relationship between the two is unclear, because actomyosin-enriched boundaries are not necessarily associated with folds. Also, some cases of epithelial folding occur independently of actomyosin contractility. We investigated the shallow folds called parasegment grooves that form at boundaries between anterior and posterior compartments in the early Drosophila embryo. We demonstrate that formation of these folds requires the presence of an actomyosin enrichment along the boundary cell-cell contacts. These enrichments, which require Wingless signalling, increase interfacial tension not only at the level of the adherens junctions but also along the lateral surfaces. We find that epithelial folding is normally under inhibitory control because different genetic manipulations, including depletion of the Myosin II phosphatase Flapwing, increase the depth of folds at boundaries. Fold depth correlates with the levels of Bazooka (Baz), the Par-3 homologue, along the boundary cell-cell contacts. Moreover, Wingless and Hedgehog signalling have opposite effects on fold depth at the boundary that correlate with changes in Baz planar polarity.
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Affiliation(s)
- Jose M Urbano
- Department of Physiology, Development and Neuroscience, University of Cambridge, Anatomy Building, Downing Street, Cambridge, CB2 3DY, UK
| | - Huw W Naylor
- Department of Physiology, Development and Neuroscience, University of Cambridge, Anatomy Building, Downing Street, Cambridge, CB2 3DY, UK
| | - Elena Scarpa
- Department of Physiology, Development and Neuroscience, University of Cambridge, Anatomy Building, Downing Street, Cambridge, CB2 3DY, UK
| | - Leila Muresan
- Department of Physiology, Development and Neuroscience, University of Cambridge, Anatomy Building, Downing Street, Cambridge, CB2 3DY, UK
- Cambridge Advanced Imaging Centre, University of Cambridge, Anatomy Building, Downing Street, Cambridge, CB2 3DY, UK
| | - Bénédicte Sanson
- Department of Physiology, Development and Neuroscience, University of Cambridge, Anatomy Building, Downing Street, Cambridge, CB2 3DY, UK
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Urbano JM, Domínguez-Giménez P, Estrada B, Martín-Bermudo MD. PS integrins and laminins: key regulators of cell migration during Drosophila embryogenesis. PLoS One 2011; 6:e23893. [PMID: 21949686 PMCID: PMC3174947 DOI: 10.1371/journal.pone.0023893] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 07/27/2011] [Indexed: 01/16/2023] Open
Abstract
During embryonic development, there are numerous cases where organ or tissue formation depends upon the migration of primordial cells. In the Drosophila embryo, the visceral mesoderm (vm) acts as a substrate for the migration of several cell populations of epithelial origin, including the endoderm, the trachea and the salivary glands. These migratory processes require both integrins and laminins. The current model is that αPS1βPS (PS1) and/or αPS3βPS (PS3) integrins are required in migrating cells, whereas αPS2βPS (PS2) integrin is required in the vm, where it performs an as yet unidentified function. Here, we show that PS1 integrins are also required for the migration over the vm of cells of mesodermal origin, the caudal visceral mesoderm (CVM). These results support a model in which PS1 might have evolved to acquire the migratory function of integrins, irrespective of the origin of the tissue. This integrin function is highly specific and its specificity resides mainly in the extracellular domain. In addition, we have identified the Laminin α1,2 trimer, as the key extracellular matrix (ECM) component regulating CVM migration. Furthermore, we show that, as it is the case in vertebrates, integrins, and specifically PS2, contributes to CVM movement by participating in the correct assembly of the ECM that serves as tracks for migration.
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Affiliation(s)
- Jose M. Urbano
- Centro Andaluz de Biología del Desarrollo, (CSIC)-Universidad Pablo de Olavide, Sevilla, Spain
| | - Paloma Domínguez-Giménez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, (CSIC)-Universidad de Sevilla, Sevilla, Spain
| | - Beatriz Estrada
- Centro Andaluz de Biología del Desarrollo, (CSIC)-Universidad Pablo de Olavide, Sevilla, Spain
| | - María D. Martín-Bermudo
- Centro Andaluz de Biología del Desarrollo, (CSIC)-Universidad Pablo de Olavide, Sevilla, Spain
- * E-mail:
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Urbano JM, Torgler CN, Molnar C, Tepass U, López-Varea A, Brown NH, de Celis JF, Martín-Bermudo MD. Drosophila laminins act as key regulators of basement membrane assembly and morphogenesis. Development 2009; 136:4165-76. [PMID: 19906841 DOI: 10.1242/dev.044263] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Laminins are heterotrimeric molecules found in all basement membranes. In mammals, they have been involved in diverse developmental processes, from gastrulation to tissue maintenance. The Drosophila genome encodes two laminin alpha chains, one beta and one Gamma, which form two distinct laminin trimers. So far, only mutations affecting one or other trimer have been analysed. In order to study embryonic development in the complete absence of laminins, we mutated the gene encoding the sole laminin beta chain in Drosophila, LanB1, so that no trimers can be made. We show that LanB1 mutant embryos develop until the end of embryogenesis. Electron microscopy analysis of mutant embryos reveals that the basement membranes are absent and the remaining extracellular material appears disorganised and diffuse. Accordingly, abnormal accumulation of major basement membrane components, such as Collagen IV and Perlecan, is observed in mutant tissues. In addition, we show that elimination of LanB1 prevents the normal morphogenesis of most organs and tissues, including the gut, trachea, muscles and nervous system. In spite of the above structural roles for laminins, our results unravel novel functions in cell adhesion, migration and rearrangement. We propose that while an early function of laminins in gastrulation is not conserved in Drosophila and mammals, their function in basement membrane assembly and organogenesis seems to be maintained throughout evolution.
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Affiliation(s)
- Jose M Urbano
- Centro Andaluz de Biología de Desarrollo (CABD), Univ. Pablo de Olavide-CSIC, 41013 Sevilla, Spain.
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Abstract
A collection of 917 accessions of Spanish durum and bread wheat was screened for resistance to leaf rust (Puccinia triticina) under field conditions at three locations. Resistance levels ranged from very low to very high, high susceptibility being most frequent. Relative disease severity (referred to the most susceptible accession = 100%) was lower than 20% in about 6% of the accessions in each location. In the collection most of the lines (84%) displayed a susceptible infection type. A final selection of seven accessions (one of them durum) displaying low severity level in the field and high infection type in a growth chamber was chosen for further studies. High levels of partial resistant with longer latency period and high percentage of early aborted colonies without necrosis were found. They might be used in breeding programmes.
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Affiliation(s)
- F Martínez
- Instituto de Agricultura Sostenible (CSIC), Dpto. de Agronomía y Mejora Genética Vegetal, Apdo. 4084, 14080 Córdoba, Spain.
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Urbano JM, Benítez M, Romero J. [Bacteremia by Clostridium perfringens: complication of the manual extraction of a fecaloma]. Enferm Infecc Microbiol Clin 1999; 17:200. [PMID: 10365522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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