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Repeated Small Perturbation Approach Reveals Transcriptomic Steady States

The study of biological systems dynamics requires elucidation of the transitions of steady states. A “small perturbation” approach can provide important information on the “steady state” of a biological system. In our experiments, small perturbations were generated by applying a series of repeating...

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Detalles Bibliográficos
Autores principales: Huang, Ching-Lung, Shu, Wun-Yi, Tsai, Min-Lung, Chiang, Chi-Shiun, Chang, Cheng-Wei, Chang, Chiu-Ting, Hsu, Ian C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240659/
https://www.ncbi.nlm.nih.gov/pubmed/22195030
http://dx.doi.org/10.1371/journal.pone.0029241
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author Huang, Ching-Lung
Shu, Wun-Yi
Tsai, Min-Lung
Chiang, Chi-Shiun
Chang, Cheng-Wei
Chang, Chiu-Ting
Hsu, Ian C.
author_facet Huang, Ching-Lung
Shu, Wun-Yi
Tsai, Min-Lung
Chiang, Chi-Shiun
Chang, Cheng-Wei
Chang, Chiu-Ting
Hsu, Ian C.
author_sort Huang, Ching-Lung
collection PubMed
description The study of biological systems dynamics requires elucidation of the transitions of steady states. A “small perturbation” approach can provide important information on the “steady state” of a biological system. In our experiments, small perturbations were generated by applying a series of repeating small doses of ultraviolet radiation to a human keratinocyte cell line, HaCaT. The biological response was assessed by monitoring the gene expression profiles using cDNA microarrays. Repeated small doses (10 J/m2) of ultraviolet B (UVB) exposure modulated the expression profiles of two groups of genes in opposite directions. The genes that were up-regulated have functions mainly associated with anti-proliferation/anti-mitogenesis/apoptosis, and the genes that were down-regulated were mainly related to proliferation/mitogenesis/anti-apoptosis. For both groups of genes, repetition of the small doses of UVB caused an immediate response followed by relaxation between successive small perturbations. This cyclic pattern was suppressed when large doses (233 or 582.5 J/m2) of UVB were applied. Our method and results contribute to a foundation for computational systems biology, which implicitly uses the concept of steady state.
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spelling pubmed-32406592011-12-22 Repeated Small Perturbation Approach Reveals Transcriptomic Steady States Huang, Ching-Lung Shu, Wun-Yi Tsai, Min-Lung Chiang, Chi-Shiun Chang, Cheng-Wei Chang, Chiu-Ting Hsu, Ian C. PLoS One Research Article The study of biological systems dynamics requires elucidation of the transitions of steady states. A “small perturbation” approach can provide important information on the “steady state” of a biological system. In our experiments, small perturbations were generated by applying a series of repeating small doses of ultraviolet radiation to a human keratinocyte cell line, HaCaT. The biological response was assessed by monitoring the gene expression profiles using cDNA microarrays. Repeated small doses (10 J/m2) of ultraviolet B (UVB) exposure modulated the expression profiles of two groups of genes in opposite directions. The genes that were up-regulated have functions mainly associated with anti-proliferation/anti-mitogenesis/apoptosis, and the genes that were down-regulated were mainly related to proliferation/mitogenesis/anti-apoptosis. For both groups of genes, repetition of the small doses of UVB caused an immediate response followed by relaxation between successive small perturbations. This cyclic pattern was suppressed when large doses (233 or 582.5 J/m2) of UVB were applied. Our method and results contribute to a foundation for computational systems biology, which implicitly uses the concept of steady state. Public Library of Science 2011-12-15 /pmc/articles/PMC3240659/ /pubmed/22195030 http://dx.doi.org/10.1371/journal.pone.0029241 Text en Huang et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Huang, Ching-Lung
Shu, Wun-Yi
Tsai, Min-Lung
Chiang, Chi-Shiun
Chang, Cheng-Wei
Chang, Chiu-Ting
Hsu, Ian C.
Repeated Small Perturbation Approach Reveals Transcriptomic Steady States
title Repeated Small Perturbation Approach Reveals Transcriptomic Steady States
title_full Repeated Small Perturbation Approach Reveals Transcriptomic Steady States
title_fullStr Repeated Small Perturbation Approach Reveals Transcriptomic Steady States
title_full_unstemmed Repeated Small Perturbation Approach Reveals Transcriptomic Steady States
title_short Repeated Small Perturbation Approach Reveals Transcriptomic Steady States
title_sort repeated small perturbation approach reveals transcriptomic steady states
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240659/
https://www.ncbi.nlm.nih.gov/pubmed/22195030
http://dx.doi.org/10.1371/journal.pone.0029241
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