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Aleksander SA, Anagnostopoulos AV, Antonazzo G, Arnaboldi V, Attrill H, Becerra A, Bello SM, Blodgett O, Bradford YM, Bult CJ, Cain S, Calvi BR, Carbon S, Chan J, Chen WJ, Cherry JM, Cho J, Crosby MA, De Pons JL, D’Eustachio P, Diamantakis S, Dolan ME, dos Santos G, Dyer S, Ebert D, Engel SR, Fashena D, Fisher M, Foley S, Gibson AC, Gollapally VR, Gramates LS, Grove CA, Hale P, Harris T, Hayman GT, Hu Y, James-Zorn C, Karimi K, Karra K, Kishore R, Kwitek AE, Laulederkind SJF, Lee R, Longden I, Luypaert M, Markarian N, Marygold SJ, Matthews B, McAndrews MS, Millburn G, Miyasato S, Motenko H, Moxon S, Muller HM, Mungall CJ, Muruganujan A, Mushayahama T, Nash RS, Nuin P, Paddock H, Pells T, Perrimon N, Pich C, Quinton-Tulloch M, Raciti D, Ramachandran S, Richardson JE, Gelbart SR, Ruzicka L, Schindelman G, Shaw DR, Sherlock G, Shrivatsav A, Singer A, Smith CM, Smith CL, Smith JR, Stein L, Sternberg PW, Tabone CJ, Thomas PD, Thorat K, Thota J, Tomczuk M, Trovisco V, Tutaj MA, Urbano JM, Van Auken K, Van Slyke CE, Vize PD, Wang Q, Weng S, Westerfield M, Wilming LG, Wong ED, Wright A, Yook K, Zhou P, Zorn A, Zytkovicz M. Updates to the Alliance of Genome Resources central infrastructure. Genetics 2024; 227:iyae049. [PMID: 38552170 DOI: 10.1093/genetics/iyae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/09/2024] Open
Abstract
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).
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Affiliation(s)
| | | | | | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Valerio Arnaboldi
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Andrés Becerra
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Susan M Bello
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Olin Blodgett
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | | | - Carol J Bult
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Scott Cain
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Brian R Calvi
- Department of Biology, Indiana University , Bloomington, IN 47408 , USA
| | - Seth Carbon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
| | - Juancarlos Chan
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Wen J Chen
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - J Michael Cherry
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Jaehyoung Cho
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Madeline A Crosby
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Jeffrey L De Pons
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | | | - Stavros Diamantakis
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Mary E Dolan
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Gilberto dos Santos
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Dustin Ebert
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Stacia R Engel
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - David Fashena
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Malcolm Fisher
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
| | - Saoirse Foley
- Department of Biological Sciences, Carnegie Mellon University , 5000 Forbes Ave, Pittsburgh, PA 15203
| | - Adam C Gibson
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Varun R Gollapally
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - L Sian Gramates
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Christian A Grove
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Paul Hale
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Todd Harris
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - G Thomas Hayman
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Yanhui Hu
- Department of Genetics, Howard Hughes Medical Institute , Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 , USA
| | - Christina James-Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
| | - Kalpana Karra
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Ranjana Kishore
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Anne E Kwitek
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Stanley J F Laulederkind
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Raymond Lee
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Ian Longden
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Manuel Luypaert
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Nicholas Markarian
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Steven J Marygold
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Beverley Matthews
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Monica S McAndrews
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Gillian Millburn
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Stuart Miyasato
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Howie Motenko
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Sierra Moxon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
| | - Hans-Michael Muller
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
| | - Anushya Muruganujan
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Tremayne Mushayahama
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Robert S Nash
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Paulo Nuin
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Holly Paddock
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Troy Pells
- Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
| | - Norbert Perrimon
- Department of Genetics, Howard Hughes Medical Institute , Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 , USA
| | - Christian Pich
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Mark Quinton-Tulloch
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Daniela Raciti
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | | | | | - Susan Russo Gelbart
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Leyla Ruzicka
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Gary Schindelman
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - David R Shaw
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Ajay Shrivatsav
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Amy Singer
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Constance M Smith
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Cynthia L Smith
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Jennifer R Smith
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Lincoln Stein
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Paul W Sternberg
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Christopher J Tabone
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Paul D Thomas
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Ketaki Thorat
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Jyothi Thota
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Monika Tomczuk
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Vitor Trovisco
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Marek A Tutaj
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Jose-Maria Urbano
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Kimberly Van Auken
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Ceri E Van Slyke
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
| | - Qinghua Wang
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Shuai Weng
- Department of Genetics, Stanford University , Stanford, CA 94305
| | | | - Laurens G Wilming
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Edith D Wong
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Adam Wright
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Karen Yook
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Pinglei Zhou
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Aaron Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
| | - Mark Zytkovicz
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
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Aleksander SA, Anagnostopoulos AV, Antonazzo G, Arnaboldi V, Attrill H, Becerra A, Bello SM, Blodgett O, Bradford YM, Bult CJ, Cain S, Calvi BR, Carbon S, Chan J, Chen WJ, Michael Cherry J, Cho J, Crosby MA, De Pons JL, D’Eustachio P, Diamantakis S, Dolan ME, Santos GD, Dyer S, Ebert D, Engel SR, Fashena D, Fisher M, Foley S, Gibson AC, Gollapally VR, Sian Gramates L, Grove CA, Hale P, Harris T, Thomas Hayman G, Hu Y, James-Zorn C, Karimi K, Karra K, Kishore R, Kwitek AE, Laulederkind SJF, Lee R, Longden I, Luypaert M, Markarian N, Marygold SJ, Matthews B, McAndrews MS, Millburn G, Miyasato S, Motenko H, Moxon S, Muller HM, Mungall CJ, Muruganujan A, Mushayahama T, Nash RS, Nuin P, Paddock H, Pells T, Perrimon N, Pich C, Quinton-Tulloch M, Raciti D, Ramachandran S, Richardson JE, Gelbart SR, Ruzicka L, Schindelman G, Shaw DR, Sherlock G, Shrivatsav A, Singer A, Smith CM, Smith CL, Smith JR, Stein L, Sternberg PW, Tabone CJ, Thomas PD, Thorat K, Thota J, Tomczuk M, Trovisco V, Tutaj MA, Urbano JM, Auken KV, Van Slyke CE, Vize PD, Wang Q, Weng S, Westerfield M, Wilming LG, Wong ED, Wright A, Yook K, Zhou P, Zorn A, Zytkovicz M. Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium. bioRxiv 2023:2023.11.20.567935. [PMID: 38045425 PMCID: PMC10690154 DOI: 10.1101/2023.11.20.567935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, C. elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and APIs. Here we focus on developments over the last two years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse. We describe our progress towards a central persistent database to support curation, the data modeling that underpins harmonization, and progress towards a state-of-the art literature curation system with integrated Artificial Intelligence and Machine Learning (AI/ML).
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Agapite J, Albou LP, Aleksander SA, Alexander M, Anagnostopoulos AV, Antonazzo G, Argasinska J, Arnaboldi V, Attrill H, Becerra A, Bello SM, Blake JA, Blodgett O, Bradford YM, Bult CJ, Cain S, Calvi BR, Carbon S, Chan J, Chen WJ, Michael Cherry J, Cho J, Christie KR, Crosby MA, Davis P, da Veiga Beltrame E, De Pons JL, D’Eustachio P, Diamantakis S, Dolan ME, dos Santos G, Douglass E, Dunn B, Eagle A, Ebert D, Engel SR, Fashena D, Foley S, Frazer K, Gao S, Gibson AC, Gondwe F, Goodman J, Sian Gramates L, Grove CA, Hale P, Harris T, Thomas Hayman G, Hill DP, Howe DG, Howe KL, Hu Y, Jha S, Kadin JA, Kaufman TC, Kalita P, Karra K, Kishore R, Kwitek AE, Laulederkind SJF, Lee R, Longden I, Luypaert M, MacPherson KA, Martin R, Marygold SJ, Matthews B, McAndrews MS, Millburn G, Miyasato S, Motenko H, Moxon S, Muller HM, Mungall CJ, Muruganujan A, Mushayahama T, Nalabolu HS, Nash RS, Ng P, Nuin P, Paddock H, Paulini M, Perrimon N, Pich C, Quinton-Tulloch M, Raciti D, Ramachandran S, Richardson JE, Gelbart SR, Ruzicka L, Schaper K, Schindelman G, Shimoyama M, Simison M, Shaw DR, Shrivatsav A, Singer A, Skrzypek M, Smith CM, Smith CL, Smith JR, Stein L, Sternberg PW, Tabone CJ, Thomas PD, Thorat K, Thota J, Toro S, Tomczuk M, Trovisco V, Tutaj MA, Tutaj M, Urbano JM, Van Auken K, Van Slyke CE, Wang Q, Wang SJ, Weng S, Westerfield M, Williams G, Wilming LG, Wong ED, Wright A, Yook K, Zarowiecki M, Zhou P, Zytkovicz M. Harmonizing model organism data in the Alliance of Genome Resources. Genetics 2022; 220:iyac022. [PMID: 35380658 PMCID: PMC8982023 DOI: 10.1093/genetics/iyac022] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/26/2022] [Indexed: 02/06/2023] Open
Abstract
The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein-protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.
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Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby MA, dos Santos G, Goodman JL, Goutte-Gattat D, Jenkins VK, Kaufman T, Larkin A, Matthews BB, Millburn G, Strelets VB. FlyBase: a guided tour of highlighted features. Genetics 2022; 220:6546290. [PMID: 35266522 PMCID: PMC8982030 DOI: 10.1093/genetics/iyac035] [Citation(s) in RCA: 196] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/23/2022] [Indexed: 11/23/2022] Open
Abstract
FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster. As FlyBase enters our fourth decade of service to the research community, we reflect on our unique aspects and look forward to our continued collaboration with the larger research and model organism communities. In this study, we emphasize the dedicated reports and tools we have constructed to meet the specialized needs of fly researchers but also to facilitate use by other research communities. We also highlight ways that we support the fly community, including an external resources page, help resources, and multiple avenues by which researchers can interact with FlyBase.
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Affiliation(s)
- L Sian Gramates
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA,Corresponding author: Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge MA 02138, USA.
| | - Julie Agapite
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 1TN, UK
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Madeline A Crosby
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gilberto dos Santos
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joshua L Goodman
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Damien Goutte-Gattat
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 1TN, UK
| | - Victoria K Jenkins
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thomas Kaufman
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Aoife Larkin
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 1TN, UK
| | - Beverley B Matthews
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gillian Millburn
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 1TN, UK
| | - Victor B Strelets
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Larkin A, Marygold SJ, Antonazzo G, Attrill H, Dos Santos G, Garapati PV, Goodman JL, Gramates LS, Millburn G, Strelets VB, Tabone CJ, Thurmond J. FlyBase: updates to the Drosophila melanogaster knowledge base. Nucleic Acids Res 2021; 49:D899-D907. [PMID: 33219682 PMCID: PMC7779046 DOI: 10.1093/nar/gkaa1026] [Citation(s) in RCA: 257] [Impact Index Per Article: 85.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/13/2020] [Accepted: 10/22/2020] [Indexed: 01/04/2023] Open
Abstract
FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction of several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports and overview displays ('ribbons') of expression and disease data. We also describe a variety of recent important updates, including incorporation of a developmental proteome, upgrades to the GAL4 search tab, additional Experimental Tool Reports, migration to JBrowse for genome browsing and improvements to batch queries/downloads and the Fast-Track Your Paper tool.
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Affiliation(s)
- Aoife Larkin
- 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
| | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Gilberto Dos Santos
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Phani V Garapati
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Joshua L Goodman
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - L Sian Gramates
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Gillian Millburn
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Victor B Strelets
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Christopher J Tabone
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Jim Thurmond
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Thurmond J, Goodman JL, Strelets VB, Attrill H, Gramates LS, Marygold SJ, Matthews BB, Millburn G, Antonazzo G, Trovisco V, Kaufman TC, Calvi BR. FlyBase 2.0: the next generation. Nucleic Acids Res 2020; 47:D759-D765. [PMID: 30364959 PMCID: PMC6323960 DOI: 10.1093/nar/gky1003] [Citation(s) in RCA: 484] [Impact Index Per Article: 121.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/09/2018] [Indexed: 01/01/2023] Open
Abstract
FlyBase (flybase.org) is a knowledge base that supports the community of researchers that use the fruit fly, Drosophila melanogaster, as a model organism. The FlyBase team curates and organizes a diverse array of genetic, molecular, genomic, and developmental information about Drosophila. At the beginning of 2018, ‘FlyBase 2.0’ was released with a significantly improved user interface and new tools. Among these important changes are a new organization of search results into interactive lists or tables (hitlists), enhanced reference lists, and new protein domain graphics. An important new data class called ‘experimental tools’ consolidates information on useful fly strains and other resources related to a specific gene, which significantly enhances the ability of the Drosophila researcher to design and carry out experiments. With the release of FlyBase 2.0, there has also been a restructuring of backend architecture and a continued development of application programming interfaces (APIs) for programmatic access to FlyBase data. In this review, we describe these major new features and functionalities of the FlyBase 2.0 site and how they support the use of Drosophila as a model organism for biological discovery and translational research.
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Affiliation(s)
- Jim Thurmond
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Joshua L Goodman
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Victor B Strelets
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - L Sian Gramates
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Steven J Marygold
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Beverley B Matthews
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Gillian Millburn
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Vitor Trovisco
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Thomas C Kaufman
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
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7
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Gramates LS, Marygold SJ, Santos GD, Urbano JM, Antonazzo G, Matthews BB, Rey AJ, Tabone CJ, Crosby MA, Emmert DB, Falls K, Goodman JL, Hu Y, Ponting L, Schroeder AJ, Strelets VB, Thurmond J, Zhou P. FlyBase at 25: looking to the future. Nucleic Acids Res 2017; 45:D663-D671. [PMID: 27799470 PMCID: PMC5210523 DOI: 10.1093/nar/gkw1016] [Citation(s) in RCA: 400] [Impact Index Per Article: 57.1] [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: 09/30/2016] [Revised: 10/14/2016] [Accepted: 10/18/2016] [Indexed: 01/12/2023] Open
Abstract
Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interactions, and reagents such as stocks and cDNAs. Access to data is provided through a number of tools, reports, and bulk-data downloads. Looking to the future, FlyBase is expanding its focus to serve a broader scientific community. In this update, we describe new features, datasets, reagent collections, and data presentations that address this goal, including enhanced orthology data, Human Disease Model Reports, protein domain search and visualization, concise gene summaries, a portal for external resources, video tutorials and the FlyBase Community Advisory Group.
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Affiliation(s)
- L Sian Gramates
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Steven J Marygold
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Gilberto Dos Santos
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Jose-Maria Urbano
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Beverley B Matthews
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Alix J Rey
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Christopher J Tabone
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Madeline A Crosby
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - David B Emmert
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Kathleen Falls
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Joshua L Goodman
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Laura Ponting
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Andrew J Schroeder
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Victor B Strelets
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jim Thurmond
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Pinglei Zhou
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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8
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Abstract
The use of Drosophila melanogaster as a model for studying human disease is well established, reflected by the steady increase in both the number and proportion of fly papers describing human disease models in recent years. In this article, we highlight recent efforts to improve the availability and accessibility of the disease model information in FlyBase (http://flybase.org), the model organism database for Drosophila. FlyBase has recently introduced Human Disease Model Reports, each of which presents background information on a specific disease, a tabulation of related disease subtypes, and summaries of experimental data and results using fruit flies. Integrated presentations of relevant data and reagents described in other sections of FlyBase are incorporated into these reports, which are specifically designed to be accessible to non-fly researchers in order to promote collaboration across model organism communities working in translational science. Another key component of disease model information in FlyBase is that data are collected in a consistent format – using the evolving Disease Ontology (an open-source standardized ontology for human-disease-associated biomedical data) – to allow robust and intuitive searches. To facilitate this, FlyBase has developed a dedicated tool for querying and navigating relevant data, which include mutations that model a disease and any associated interacting modifiers. In this article, we describe how data related to fly models of human disease are presented in individual Gene Reports and in the Human Disease Model Reports. Finally, we discuss search strategies and new query tools that are available to access the disease model data in FlyBase. Drosophila Collection:Drosophila melanogaster is well established as a model for studying human disease. Here, we highlight recent efforts to enhance the availability and accessibility of disease model data in FlyBase, the model organism database for Drosophila.
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Affiliation(s)
- Gillian H Millburn
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Madeline A Crosby
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - L Sian Gramates
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Susan Tweedie
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J. Exploring FlyBase Data Using QuickSearch. Curr Protoc Bioinformatics 2016; 56:1.31.1-1.31.23. [PMID: 27930807 PMCID: PMC5152691 DOI: 10.1002/cpbi.19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
FlyBase (flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, mean that FlyBase now houses a huge quantity of data. Researchers need to be able to rapidly and intuitively query these data, 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 unit 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. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Steven J. Marygold
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Marta Costa
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Madeline A. Crosby
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Gilberto dos Santos
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Joshua L. Goodman
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - L. Sian Gramates
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Beverley B. Matthews
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Alix J. Rey
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Jim Thurmond
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, Park S, Wan KH, Schroeder AJ, Gramates LS, St. Pierre SE, Roark M, Wiley KL, Kulathinal RJ, Zhang P, Myrick KV, Antone JV, Celniker SE, Gelbart WM, Kellis M. Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genes Dev 2007; 17:1823-36. [PMID: 17989253 PMCID: PMC2099591 DOI: 10.1101/gr.6679507] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 09/21/2007] [Indexed: 11/24/2022]
Abstract
The availability of sequenced genomes from 12 Drosophila species has enabled the use of comparative genomics for the systematic discovery of functional elements conserved within this genus. We have developed quantitative metrics for the evolutionary signatures specific to protein-coding regions and applied them genome-wide, resulting in 1193 candidate new protein-coding exons in the D. melanogaster genome. We have reviewed these predictions by manual curation and validated a subset by directed cDNA screening and sequencing, revealing both new genes and new alternative splice forms of known genes. We also used these evolutionary signatures to evaluate existing gene annotations, resulting in the validation of 87% of genes lacking descriptive names and identifying 414 poorly conserved genes that are likely to be spurious predictions, noncoding, or species-specific genes. Furthermore, our methods suggest a variety of refinements to hundreds of existing gene models, such as modifications to translation start codons and exon splice boundaries. Finally, we performed directed genome-wide searches for unusual protein-coding structures, discovering 149 possible examples of stop codon readthrough, 125 new candidate ORFs of polycistronic mRNAs, and several candidate translational frameshifts. These results affect >10% of annotated fly genes and demonstrate the power of comparative genomics to enhance our understanding of genome organization, even in a model organism as intensively studied as Drosophila melanogaster.
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Affiliation(s)
- Michael F. Lin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
| | - Joseph W. Carlson
- Berkeley Drosophila Genome Project, Department of Genome Biology, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Madeline A. Crosby
- FlyBase, The Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Beverley B. Matthews
- FlyBase, The Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Charles Yu
- Berkeley Drosophila Genome Project, Department of Genome Biology, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Soo Park
- Berkeley Drosophila Genome Project, Department of Genome Biology, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kenneth H. Wan
- Berkeley Drosophila Genome Project, Department of Genome Biology, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Andrew J. Schroeder
- FlyBase, The Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, USA
| | - L. Sian Gramates
- FlyBase, The Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Susan E. St. Pierre
- FlyBase, The Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Margaret Roark
- FlyBase, The Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Kenneth L. Wiley
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Rob J. Kulathinal
- FlyBase, The Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Peili Zhang
- FlyBase, The Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Kyl V. Myrick
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jerry V. Antone
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Susan E. Celniker
- Berkeley Drosophila Genome Project, Department of Genome Biology, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - William M. Gelbart
- FlyBase, The Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts 02139, USA
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11
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Gorczyca D, Ashley J, Speese S, Gherbesi N, Thomas U, Gundelfinger E, Gramates LS, Budnik V. Postsynaptic membrane addition depends on the Discs-Large-interacting t-SNARE Gtaxin. J Neurosci 2007; 27:1033-44. [PMID: 17267557 PMCID: PMC4664082 DOI: 10.1523/jneurosci.3160-06.2007] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Targeted membrane addition is a hallmark of many cellular functions. In the nervous system, modification of synaptic membrane size has a major impact on synaptic function. However, because of the complex shape of neurons and the need to target membrane addition to very small and polarized synaptic compartments, this process is poorly understood. Here, we show that Gtaxin (GTX), a Drosophila t-SNARE (target-soluble N-ethylmaleimide-sensitive factor attachment protein receptor), is required for expansion of postsynaptic membranes during new synapse formation. Mutations in gtx lead to drastic reductions in postsynaptic membrane surface, whereas gtx upregulation results in the formation of complex membrane structures at ectopic sites. Postsynaptic GTX activity depends on its direct interaction with Discs-Large (DLG), a multidomain scaffolding protein of the PSD-95 (postsynaptic density protein-95) family with key roles in cell polarity and formation of cellular junctions as well as synaptic protein anchoring and trafficking. We show that DLG selectively determines the postsynaptic distribution of GTX to type I, but not to type II or type III boutons on the same cell, thereby defining sites of membrane addition to this unique set of glutamatergic synapses. We provide a mechanistic explanation for selective targeted membrane expansion at specific synaptic junctions.
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Affiliation(s)
- David Gorczyca
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - James Ashley
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Sean Speese
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Norberto Gherbesi
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Ulrich Thomas
- Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany, and
| | | | - L. Sian Gramates
- Molecular and Cellular Biology Graduate Program, University of Massachusetts at Amherst, Amherst, Massachusetts 01003
| | - Vivian Budnik
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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12
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Abstract
The Darwin Centre
The Natural History Museum. Cromwell Road, London SW7 5BD, UK.
www.nhm.ac.uk/darwincentre/
The newest building at London's Natural History Museum in London combines storage facilities for the specimens preserved in alcohol and a behind-the-scenes view of museum work and research.
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Affiliation(s)
- L. Sian Gramates
- The author is in the Department of Biochemistry and Molecular Biology, Box 34505, University of Massachusetts, Amherst, MA 01003-4505, USA
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13
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Mathew D, Gramates LS, Packard M, Thomas U, Bilder D, Perrimon N, Gorczyca M, Budnik V. Recruitment of scribble to the synaptic scaffolding complex requires GUK-holder, a novel DLG binding protein. Curr Biol 2002; 12:531-9. [PMID: 11937021 PMCID: PMC4661175 DOI: 10.1016/s0960-9822(02)00758-3] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND Membrane-associated guanylate kinases (MAGUKs), such as Discs-Large (DLG), play critical roles in synapse maturation by regulating the assembly of synaptic multiprotein complexes. Previous studies have revealed a genetic interaction between DLG and another PDZ scaffolding protein, SCRIBBLE (SCRIB), during the establishment of cell polarity in developing epithelia. A possible interaction between DLG and SCRIB at synaptic junctions has not yet been addressed. Likewise, the biochemical nature of this interaction remains elusive, raising questions regarding the mechanisms by which the actions of both proteins are coordinated. RESULTS Here we report the isolation of a new DLG-interacting protein, GUK-holder, that interacts with the GUK domain of DLG and which is dynamically expressed during synaptic bouton budding. We also show that at Drosophila synapses DLG colocalizes with SCRIB and that this colocalization is likely to be mediated by direct interactions between GUKH and the PDZ2 domain of SCRIB. We show that DLG, GUKH, and SCRIB form a tripartite complex at synapses, in which DLG and GUKH are required for the proper synaptic localization of SCRIB. CONCLUSIONS Our results provide a mechanism by which developmentally important PDZ-mediated complexes are associated at the synapse.
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Affiliation(s)
- Dennis Mathew
- Department of Biology and Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts 01003
| | - L. Sian Gramates
- Department of Biology and Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts 01003
| | - Mary Packard
- Department of Biology and Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts 01003
| | - Ulrich Thomas
- Department of Neurochemistry, Leibniz Institute for Neurobiology, Brenneckestrasse 6, 39118 Magdeburg, Germany
| | - David Bilder
- Department of Genetics, Harvard Medical School, HHMI, Boston, Massachusetts 02115
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, HHMI, Boston, Massachusetts 02115
| | - Michael Gorczyca
- Department of Biology and Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts 01003
| | - Vivian Budnik
- Department of Biology and Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts 01003
- Correspondence:
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14
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Abstract
Understanding the mechanisms that mediate synaptic plasticity is a primary goal of molecular neuroscience. The Drosophila larval neuromuscular junction provides a particularly useful model for investigating the roles of synaptic components in both structural and functional plasticity. The powerful molecular genetics of this system makes it possible to uncover new synaptic components and signaling molecules, as well as their function in the intact organism. Together with the mouse hippocampus and Aplysia dissociated cell culture, the Drosophila larval neuromuscular junction has been among the most valuable model systems for examining the molecular and cellular basis of neuronal plasticity.
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Affiliation(s)
- Y H Koh
- Biology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA
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15
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Affiliation(s)
- L S Gramates
- Department of Biology and Molecular and Cellular Biology Program, University of Massachusetts, Amherst 01003, USA
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16
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Phillis RW, Bramlage AT, Wotus C, Whittaker A, Gramates LS, Seppala D, Farahanchi F, Caruccio P, Murphey RK. Isolation of mutations affecting neural circuitry required for grooming behavior in Drosophila melanogaster. Genetics 1993; 133:581-92. [PMID: 8454205 PMCID: PMC1205345 DOI: 10.1093/genetics/133.3.581] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We have developed a screen for the isolation of mutations that produce neural defects in adult Drosophila melanogaster. In this screen, we identify mutants as flies unable to remove a light coating of applied dust in a 2-hr period. We have recovered and characterized six mutations and have found that they produce coordination defects and some have reduced levels of reflex responsiveness to the stimulation of single tactile sensory bristles. The grooming defects produced by all six of the mutations are recessive, and each of the mutations has been genetically mapped. We have also used our assay to test the grooming ability of stocks containing mutations that produce known neural defects.
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Affiliation(s)
- R W Phillis
- Department of Biology, University of Massachusetts, Amherst 01003
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17
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Abstract
Western immunoblots performed during separation of glycosylated prolactin from amniotic fluid revealed that some of the glycosylated prolactin is covalently bound to another protein. Using high performance liquid chromatography and other protein isolation techniques we have demonstrated that a glycosylated prolactin species is linked to immunoglobulin by disulfide bonds in amniotic fluid.
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Affiliation(s)
- L J Heffner
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA
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18
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Rosoff PM, Hall C, Gramates LS, Terlecky SR. 4,4'-Diisothiocyanatostilbene-2,2'-disulfonic acid inhibits CD3-T cell antigen receptor-stimulated Ca2+ influx in human T lymphocytes. J Biol Chem 1988; 263:19535-40. [PMID: 2974037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Stimulation of the CD3-T cell antigen receptor complex on T lymphocytes results in a rapid rise in intracellular calcium from both intra- and extracellular sources. The former is thought to be released from the endoplasmic reticulum in response to inositol trisphosphate, while the latter enters the cells through a membrane potential-sensitive transporter (Oettgen, H. C., Terhorst, C., Cantley, L. C., and Rosoff, P. M. (1985) Cell 40, 583-590). In this report we show that the stilbene disulfonate, DIDS (4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid), inhibited the ability of monoclonal anti-CD3 complex antibodies to stimulate an influx of calcium in the human T lymphocyte cell line, Jurkat. DIDS had no effect on either antibody binding to the receptor or receptor-stimulated phosphatidylinositol turnover. The Ki was approximately 25 microM in the presence of extracellular Cl- and 10 microM when labeling was performed in the absence of Cl-, suggesting that DIDS was competing with Cl- for binding to the cell membrane. The reduced form of DIDS, dihydroDIDS, was only 50% as effective as DIDS itself, and the monoisothiocyanate stilbene, 4-acetamido-4'-isothiocyantostilbene-2,2'-disulfonic acid, was totally ineffective, even to concentrations of 0.750 mM. Removal of extracellular Cl- also inhibited the antibody-stimulated influx of calcium. These data suggest that the function of the CD3-T cell receptor-activated calcium channel/transporter may be dependent on or regulated by extracellular Cl-.
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Affiliation(s)
- P M Rosoff
- Department of Physiology, Tufts University School of Medicine, Boston, Massachusetts 02111
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