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
Biblioteca Digital (UBA-FCEN)
Institución
Universidad Nacional de Buenos Aires. Facultad de Ciencias Exactas y Naturales
OAI Identificador
paperaa:paper_19326203_v7_n12_p_PerezPepe

id BDUBAFCEN_e7bb13f2b347db315ba2416f8966245a
oai_identifier_str paperaa:paper_19326203_v7_n12_p_PerezPepe
network_acronym_str BDUBAFCEN
repository_id_str 1896
network_name_str Biblioteca Digital (UBA-FCEN)
spelling 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
_version_ 1844618740736458752
score 13.070432