BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis
- Autores
- Perez-Pepe, M.; Slomiansky, V.; Loschi, M.; Luchelli, L.; Neme, M.; Thomas, M.G.; Boccaccio, G.L.
- Año de publicación
- 2012
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- The spontaneous and reversible formation of foci and filaments that contain proteins involved in different metabolic processes is common in both the nucleus and the cytoplasm. Stress granules (SGs) and processing bodies (PBs) belong to a novel family of cellular structures collectively known as mRNA silencing foci that harbour repressed mRNAs and their associated proteins. SGs and PBs are highly dynamic and they form upon stress and dissolve thus releasing the repressed mRNAs according to changes in cell physiology. In addition, aggregates containing abnormal proteins are frequent in neurodegenerative disorders. In spite of the growing relevance of these supramolecular aggregates to diverse cellular functions a reliable automated tool for their systematic analysis is lacking. Here we report a MATLAB Script termed BUHO for the high-throughput image analysis of cellular foci. We used BUHO to assess the number, size and distribution of distinct objects with minimal deviation from manually obtained parameters. BUHO successfully addressed the induction of both SGs and PBs in mammalian and insect cells exposed to different stress stimuli. We also used BUHO to assess the dynamics of specific mRNA-silencing foci termed Smaug 1 foci (S-foci) in primary neurons upon synaptic stimulation. Finally, we used BUHO to analyze the role of candidate genes on SG formation in an RNAi-based experiment. We found that FAK56D, GCN2 and PP1 govern SG formation. The role of PP1 is conserved in mammalian cells as judged by the effect of the PP1 inhibitor salubrinal, and involves dephosphorylation of the translation factor eIF2α. All these experiments were analyzed manually and by BUHO and the results differed in less than 5% of the average value. The automated analysis by this user-friendly method will allow high-throughput image processing in short times by providing a robust, flexible and reliable alternative to the laborious and sometimes unfeasible visual scrutiny. © 2012 Perez-Pepe et al.
Fil:Slomiansky, V. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.
Fil:Loschi, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.
Fil:Luchelli, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.
Fil:Thomas, M.G. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.
Fil:Boccaccio, G.L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. - Fuente
- PLoS ONE 2012;7(12)
- Materia
-
focal adhesion kinase
focal adhesion kinase 56D
initiation factor 2alpha
messenger RNA
phosphoprotein phosphatase 1
transcription factor
translation initiation factor 2alpha
unclassified drug
analytic method
article
BUHO
cell function
cell granule
cell size
cell stimulation
cell stress
cell structure
cellular distribution
gene silencing
image analysis
image processing
information processing
insect cell
mammal cell
molecular dynamics
molecular imaging
processing body
protein phosphorylation
RNA interference
stress granule
synapse
Algorithms
Animals
Drosophila melanogaster
Image Processing, Computer-Assisted
Molecular Imaging
Organelles
Oxidative Stress
RNA Interference
RNA, Messenger
Software
Synapses
Time Factors
Hexapoda
Mammalia - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- http://creativecommons.org/licenses/by/2.5/ar
- Repositorio
- Institución
- Universidad Nacional de Buenos Aires. Facultad de Ciencias Exactas y Naturales
- OAI Identificador
- paperaa:paper_19326203_v7_n12_p_PerezPepe
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BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image AnalysisPerez-Pepe, M.Slomiansky, V.Loschi, M.Luchelli, L.Neme, M.Thomas, M.G.Boccaccio, G.L.focal adhesion kinasefocal adhesion kinase 56Dinitiation factor 2alphamessenger RNAphosphoprotein phosphatase 1transcription factortranslation initiation factor 2alphaunclassified druganalytic methodarticleBUHOcell functioncell granulecell sizecell stimulationcell stresscell structurecellular distributiongene silencingimage analysisimage processinginformation processinginsect cellmammal cellmolecular dynamicsmolecular imagingprocessing bodyprotein phosphorylationRNA interferencestress granulesynapseAlgorithmsAnimalsDrosophila melanogasterImage Processing, Computer-AssistedMolecular ImagingOrganellesOxidative StressRNA InterferenceRNA, MessengerSoftwareSynapsesTime FactorsHexapodaMammaliaThe spontaneous and reversible formation of foci and filaments that contain proteins involved in different metabolic processes is common in both the nucleus and the cytoplasm. Stress granules (SGs) and processing bodies (PBs) belong to a novel family of cellular structures collectively known as mRNA silencing foci that harbour repressed mRNAs and their associated proteins. SGs and PBs are highly dynamic and they form upon stress and dissolve thus releasing the repressed mRNAs according to changes in cell physiology. In addition, aggregates containing abnormal proteins are frequent in neurodegenerative disorders. In spite of the growing relevance of these supramolecular aggregates to diverse cellular functions a reliable automated tool for their systematic analysis is lacking. Here we report a MATLAB Script termed BUHO for the high-throughput image analysis of cellular foci. We used BUHO to assess the number, size and distribution of distinct objects with minimal deviation from manually obtained parameters. BUHO successfully addressed the induction of both SGs and PBs in mammalian and insect cells exposed to different stress stimuli. We also used BUHO to assess the dynamics of specific mRNA-silencing foci termed Smaug 1 foci (S-foci) in primary neurons upon synaptic stimulation. Finally, we used BUHO to analyze the role of candidate genes on SG formation in an RNAi-based experiment. We found that FAK56D, GCN2 and PP1 govern SG formation. The role of PP1 is conserved in mammalian cells as judged by the effect of the PP1 inhibitor salubrinal, and involves dephosphorylation of the translation factor eIF2α. All these experiments were analyzed manually and by BUHO and the results differed in less than 5% of the average value. The automated analysis by this user-friendly method will allow high-throughput image processing in short times by providing a robust, flexible and reliable alternative to the laborious and sometimes unfeasible visual scrutiny. © 2012 Perez-Pepe et al.Fil:Slomiansky, V. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.Fil:Loschi, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.Fil:Luchelli, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.Fil:Thomas, M.G. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.Fil:Boccaccio, G.L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.2012info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12110/paper_19326203_v7_n12_p_PerezPepePLoS ONE 2012;7(12)reponame:Biblioteca Digital (UBA-FCEN)instname:Universidad Nacional de Buenos Aires. Facultad de Ciencias Exactas y Naturalesinstacron:UBA-FCENenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by/2.5/ar2025-09-29T13:43:09Zpaperaa:paper_19326203_v7_n12_p_PerezPepeInstitucionalhttps://digital.bl.fcen.uba.ar/Universidad públicaNo correspondehttps://digital.bl.fcen.uba.ar/cgi-bin/oaiserver.cgiana@bl.fcen.uba.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:18962025-09-29 13:43:10.735Biblioteca Digital (UBA-FCEN) - Universidad Nacional de Buenos Aires. Facultad de Ciencias Exactas y Naturalesfalse |
dc.title.none.fl_str_mv |
BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis |
title |
BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis |
spellingShingle |
BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis Perez-Pepe, M. focal adhesion kinase focal adhesion kinase 56D initiation factor 2alpha messenger RNA phosphoprotein phosphatase 1 transcription factor translation initiation factor 2alpha unclassified drug analytic method article BUHO cell function cell granule cell size cell stimulation cell stress cell structure cellular distribution gene silencing image analysis image processing information processing insect cell mammal cell molecular dynamics molecular imaging processing body protein phosphorylation RNA interference stress granule synapse Algorithms Animals Drosophila melanogaster Image Processing, Computer-Assisted Molecular Imaging Organelles Oxidative Stress RNA Interference RNA, Messenger Software Synapses Time Factors Hexapoda Mammalia |
title_short |
BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis |
title_full |
BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis |
title_fullStr |
BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis |
title_full_unstemmed |
BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis |
title_sort |
BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis |
dc.creator.none.fl_str_mv |
Perez-Pepe, M. Slomiansky, V. Loschi, M. Luchelli, L. Neme, M. Thomas, M.G. Boccaccio, G.L. |
author |
Perez-Pepe, M. |
author_facet |
Perez-Pepe, M. Slomiansky, V. Loschi, M. Luchelli, L. Neme, M. Thomas, M.G. Boccaccio, G.L. |
author_role |
author |
author2 |
Slomiansky, V. Loschi, M. Luchelli, L. Neme, M. Thomas, M.G. Boccaccio, G.L. |
author2_role |
author author author author author author |
dc.subject.none.fl_str_mv |
focal adhesion kinase focal adhesion kinase 56D initiation factor 2alpha messenger RNA phosphoprotein phosphatase 1 transcription factor translation initiation factor 2alpha unclassified drug analytic method article BUHO cell function cell granule cell size cell stimulation cell stress cell structure cellular distribution gene silencing image analysis image processing information processing insect cell mammal cell molecular dynamics molecular imaging processing body protein phosphorylation RNA interference stress granule synapse Algorithms Animals Drosophila melanogaster Image Processing, Computer-Assisted Molecular Imaging Organelles Oxidative Stress RNA Interference RNA, Messenger Software Synapses Time Factors Hexapoda Mammalia |
topic |
focal adhesion kinase focal adhesion kinase 56D initiation factor 2alpha messenger RNA phosphoprotein phosphatase 1 transcription factor translation initiation factor 2alpha unclassified drug analytic method article BUHO cell function cell granule cell size cell stimulation cell stress cell structure cellular distribution gene silencing image analysis image processing information processing insect cell mammal cell molecular dynamics molecular imaging processing body protein phosphorylation RNA interference stress granule synapse Algorithms Animals Drosophila melanogaster Image Processing, Computer-Assisted Molecular Imaging Organelles Oxidative Stress RNA Interference RNA, Messenger Software Synapses Time Factors Hexapoda Mammalia |
dc.description.none.fl_txt_mv |
The spontaneous and reversible formation of foci and filaments that contain proteins involved in different metabolic processes is common in both the nucleus and the cytoplasm. Stress granules (SGs) and processing bodies (PBs) belong to a novel family of cellular structures collectively known as mRNA silencing foci that harbour repressed mRNAs and their associated proteins. SGs and PBs are highly dynamic and they form upon stress and dissolve thus releasing the repressed mRNAs according to changes in cell physiology. In addition, aggregates containing abnormal proteins are frequent in neurodegenerative disorders. In spite of the growing relevance of these supramolecular aggregates to diverse cellular functions a reliable automated tool for their systematic analysis is lacking. Here we report a MATLAB Script termed BUHO for the high-throughput image analysis of cellular foci. We used BUHO to assess the number, size and distribution of distinct objects with minimal deviation from manually obtained parameters. BUHO successfully addressed the induction of both SGs and PBs in mammalian and insect cells exposed to different stress stimuli. We also used BUHO to assess the dynamics of specific mRNA-silencing foci termed Smaug 1 foci (S-foci) in primary neurons upon synaptic stimulation. Finally, we used BUHO to analyze the role of candidate genes on SG formation in an RNAi-based experiment. We found that FAK56D, GCN2 and PP1 govern SG formation. The role of PP1 is conserved in mammalian cells as judged by the effect of the PP1 inhibitor salubrinal, and involves dephosphorylation of the translation factor eIF2α. All these experiments were analyzed manually and by BUHO and the results differed in less than 5% of the average value. The automated analysis by this user-friendly method will allow high-throughput image processing in short times by providing a robust, flexible and reliable alternative to the laborious and sometimes unfeasible visual scrutiny. © 2012 Perez-Pepe et al. Fil:Slomiansky, V. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Loschi, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Luchelli, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Thomas, M.G. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Boccaccio, G.L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. |
description |
The spontaneous and reversible formation of foci and filaments that contain proteins involved in different metabolic processes is common in both the nucleus and the cytoplasm. Stress granules (SGs) and processing bodies (PBs) belong to a novel family of cellular structures collectively known as mRNA silencing foci that harbour repressed mRNAs and their associated proteins. SGs and PBs are highly dynamic and they form upon stress and dissolve thus releasing the repressed mRNAs according to changes in cell physiology. In addition, aggregates containing abnormal proteins are frequent in neurodegenerative disorders. In spite of the growing relevance of these supramolecular aggregates to diverse cellular functions a reliable automated tool for their systematic analysis is lacking. Here we report a MATLAB Script termed BUHO for the high-throughput image analysis of cellular foci. We used BUHO to assess the number, size and distribution of distinct objects with minimal deviation from manually obtained parameters. BUHO successfully addressed the induction of both SGs and PBs in mammalian and insect cells exposed to different stress stimuli. We also used BUHO to assess the dynamics of specific mRNA-silencing foci termed Smaug 1 foci (S-foci) in primary neurons upon synaptic stimulation. Finally, we used BUHO to analyze the role of candidate genes on SG formation in an RNAi-based experiment. We found that FAK56D, GCN2 and PP1 govern SG formation. The role of PP1 is conserved in mammalian cells as judged by the effect of the PP1 inhibitor salubrinal, and involves dephosphorylation of the translation factor eIF2α. All these experiments were analyzed manually and by BUHO and the results differed in less than 5% of the average value. The automated analysis by this user-friendly method will allow high-throughput image processing in short times by providing a robust, flexible and reliable alternative to the laborious and sometimes unfeasible visual scrutiny. © 2012 Perez-Pepe et al. |
publishDate |
2012 |
dc.date.none.fl_str_mv |
2012 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/20.500.12110/paper_19326203_v7_n12_p_PerezPepe |
url |
http://hdl.handle.net/20.500.12110/paper_19326203_v7_n12_p_PerezPepe |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
http://creativecommons.org/licenses/by/2.5/ar |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
PLoS ONE 2012;7(12) reponame:Biblioteca Digital (UBA-FCEN) instname:Universidad Nacional de Buenos Aires. Facultad de Ciencias Exactas y Naturales instacron:UBA-FCEN |
reponame_str |
Biblioteca Digital (UBA-FCEN) |
collection |
Biblioteca Digital (UBA-FCEN) |
instname_str |
Universidad Nacional de Buenos Aires. Facultad de Ciencias Exactas y Naturales |
instacron_str |
UBA-FCEN |
institution |
UBA-FCEN |
repository.name.fl_str_mv |
Biblioteca Digital (UBA-FCEN) - Universidad Nacional de Buenos Aires. Facultad de Ciencias Exactas y Naturales |
repository.mail.fl_str_mv |
ana@bl.fcen.uba.ar |
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