Feedback control of stochastic noise in the yeast galactose utilization pathway
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| Title: | Feedback control of stochastic noise in the yeast galactose utilization pathway |
|---|---|
| Authors: | Orrell, David1, Ramsey, Stephen1, Marelli, Marcello1, Smith, Jennifer J.1, Petersen, Timothy W.1, Atauri, Pedro de1, Aitchison, John D.1, Bolouri, Hamid hbolouri@systemsbiology.org |
| Source: | Physica D. May2006, Vol. 217 Issue 1, p64-76. 13p. |
| Subjects: | Feedback control systems, Electronic noise, Computer simulation, Loops (Group theory) |
| Abstract: | Abstract: Genetic networks are often affected by stochastic noise, due to the low number of molecules taking part in certain reactions. In complex regulatory networks, noise in any one chemical species may induce noise in the rest of the system. In this paper, we analyse the sources of stochastic noise in the yeast galactose utilization pathway at the level of the complete system, by using both computer simulations, and experimental comparisons between wild-type yeast and a modified strain. A computer model was first used to determine the sources of network noise, as well as mechanisms by which noise is controlled. Results from an estimation tool, confirmed by detailed stochastic simulations, show that noise is caused primarily by fluctuations in mRNA concentrations due to their stochastic creation and decay. The noise is controlled by feedback loops which regulate transcription of certain genes. To test the effect of the feedback loops on the rest of the system, a modified strain of yeast was prepared in which regulation of two key genes is eliminated. As predicted by the model, the mutant strain is induced by galactose in a manner similar to that for the wild-type, but with a higher degree of stochastic noise. [Copyright &y& Elsevier] |
| Copyright of Physica D is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 20728469 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Feedback control of stochastic noise in the yeast galactose utilization pathway – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Orrell%2C+David%22">Orrell, David</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Ramsey%2C+Stephen%22">Ramsey, Stephen</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Marelli%2C+Marcello%22">Marelli, Marcello</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Smith%2C+Jennifer+J%2E%22">Smith, Jennifer J.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Petersen%2C+Timothy+W%2E%22">Petersen, Timothy W.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Atauri%2C+Pedro+de%22">Atauri, Pedro de</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Aitchison%2C+John+D%2E%22">Aitchison, John D.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Bolouri%2C+Hamid%22">Bolouri, Hamid</searchLink><i> hbolouri@systemsbiology.org</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Physica+D%22">Physica D</searchLink>. May2006, Vol. 217 Issue 1, p64-76. 13p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Feedback+control+systems%22">Feedback control systems</searchLink><br /><searchLink fieldCode="DE" term="%22Electronic+noise%22">Electronic noise</searchLink><br /><searchLink fieldCode="DE" term="%22Computer+simulation%22">Computer simulation</searchLink><br /><searchLink fieldCode="DE" term="%22Loops+%28Group+theory%29%22">Loops (Group theory)</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Abstract: Genetic networks are often affected by stochastic noise, due to the low number of molecules taking part in certain reactions. In complex regulatory networks, noise in any one chemical species may induce noise in the rest of the system. In this paper, we analyse the sources of stochastic noise in the yeast galactose utilization pathway at the level of the complete system, by using both computer simulations, and experimental comparisons between wild-type yeast and a modified strain. A computer model was first used to determine the sources of network noise, as well as mechanisms by which noise is controlled. Results from an estimation tool, confirmed by detailed stochastic simulations, show that noise is caused primarily by fluctuations in mRNA concentrations due to their stochastic creation and decay. The noise is controlled by feedback loops which regulate transcription of certain genes. To test the effect of the feedback loops on the rest of the system, a modified strain of yeast was prepared in which regulation of two key genes is eliminated. As predicted by the model, the mutant strain is induced by galactose in a manner similar to that for the wild-type, but with a higher degree of stochastic noise. [Copyright &y& Elsevier] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Physica D is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1016/j.physd.2006.03.010 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 13 StartPage: 64 Subjects: – SubjectFull: Feedback control systems Type: general – SubjectFull: Electronic noise Type: general – SubjectFull: Computer simulation Type: general – SubjectFull: Loops (Group theory) Type: general Titles: – TitleFull: Feedback control of stochastic noise in the yeast galactose utilization pathway Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Orrell, David – PersonEntity: Name: NameFull: Ramsey, Stephen – PersonEntity: Name: NameFull: Marelli, Marcello – PersonEntity: Name: NameFull: Smith, Jennifer J. – PersonEntity: Name: NameFull: Petersen, Timothy W. – PersonEntity: Name: NameFull: Atauri, Pedro de – PersonEntity: Name: NameFull: Aitchison, John D. – PersonEntity: Name: NameFull: Bolouri, Hamid IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 05 Text: May2006 Type: published Y: 2006 Identifiers: – Type: issn-print Value: 01672789 Numbering: – Type: volume Value: 217 – Type: issue Value: 1 Titles: – TitleFull: Physica D Type: main |
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