Journal ArticleDOI
Response to Comment on "Oscillations in NF-kappa B signaling control the dynamics of gene expression"
David E. Nelson,Caroline A. Horton,Violaine Sée,James R. Johnson,Glyn Nelson,David G. Spiller,Douglas B. Kell,Michael R. H. White +7 more
TLDR
In this paper, the experimental data showed no correlation between NF-kappa B (ReLA) expression level and oscillation dynamics, and a small change to the computational model used by Barken et al. to generate their theoretical data reduced the apparent discrepancies.Abstract:
Our experimental data shows no correlation between NF-kappa B (ReLA) expression level and oscillation dynamics. We show that a small change to the computational model used by Barken et al. to generate their theoretical data reduces the apparent discrepancies. Cell system differences and possible compensatory changes to normal signaling in their genetically engineered knockout cells may explain differences between the two studies.read more
Citations
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Journal ArticleDOI
Pulsatile Stimulation Determines Timing and Specificity of NF-κB-Dependent Transcription
Louise Ashall,Caroline A. Horton,David E. Nelson,Pawel Paszek,Claire V. Harper,Kate Sillitoe,Sheila Ryan,David G. Spiller,John Unitt,David S. Broomhead,Douglas B. Kell,David A. Rand,Violaine Sée,Michael R. H. White +13 more
TL;DR: Altering the stimulation intervals gave different patterns of NF-κB–dependent gene expression, which supports the idea that oscillation frequency has a functional role in nuclear factor κB regulation.
Journal ArticleDOI
A Noisy Paracrine Signal Determines the Cellular NF-κB Response to Lipopolysaccharide
Timothy K. Lee,Elissa M. Denny,Jayodita C. Sanghvi,Jahlionais E. Gaston,Nathaniel D. Maynard,Jacob J. Hughey,Markus W. Covert +6 more
TL;DR: It is shown that mammalian cells can create “noisy” environments to produce diversified responses to stimuli and be linked to a secondary paracrine signal secreted at low concentrations, such that not all cells undergo a second round of NF-κB activation.
Journal ArticleDOI
Enhanced Characteristics of Genetically Modified Switchgrass (Panicum virgatum L.) for High Biofuel Production
Hui Shen,Charleson R. Poovaiah,Charleson R. Poovaiah,Angela Ziebell,Angela Ziebell,Timothy J. Tschaplinski,Sivakumar Pattathil,Sivakumar Pattathil,Erica Gjersing,Erica Gjersing,Nancy L. Engle,Rui Katahira,Rui Katahira,Yunqiao Pu,Yunqiao Pu,Robert W. Sykes,Robert W. Sykes,Fang Chen,Arthur J. Ragauskas,Arthur J. Ragauskas,Jonathan R. Mielenz,Michael G. Hahn,Michael G. Hahn,Mark F. Davis,Mark F. Davis,C. Neal Stewart,C. Neal Stewart,Richard A. Dixon,Richard A. Dixon +28 more
TL;DR: The results have demonstrated that overexpression of PvMYB4, a general transcriptional repressor of the phenylpropanoid/lignin biosynthesis pathway, can lead to very high yield ethanol production through dramatic reduction of recalcitrance.
Journal ArticleDOI
Physiological levels of TNFα stimulation induce stochastic dynamics of NF-κB responses in single living cells
David A. Turner,Pawel Paszek,Dan J. Woodcock,David E. Nelson,Caroline A. Horton,Yunjiao Wang,David G. Spiller,David A. Rand,Michael R. H. White,Claire V. Harper +9 more
TL;DR: Deterministic and stochastic models simulated the experimentally observed activation threshold and gave rise to new predictions about the structure of the system and open the way for better mechanistic understanding of physiological TNFα activation of inflammatory responses in cells and tissues.
Journal ArticleDOI
Stochastic Regulation in Early Immune Response
TL;DR: This article reformulate the model of the NF-kappaB regulatory module to analyze a single cell regulation and hypothesize that this synchronization is crucial for proper activation of early genes controlling inflammation.
References
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Journal ArticleDOI
A synthetic oscillatory network of transcriptional regulators
TL;DR: This work used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli, which periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells.
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The IκB-NF-κB Signaling Module: Temporal Control and Selective Gene Activation
TL;DR: A computational model is presented that describes the temporal control of NF-κB activation by the coordinated degradation and synthesis of IκB proteins and demonstrates that IπκBα is responsible for strong negative feedback that allows for a fast turn-off of the NF-σB response.
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Requirement for glycogen synthase kinase-3β in cell survival and NF-κB activation
TL;DR: It is shown that disruption of the murine GSK-3β gene results in embryonic lethality caused by severe liver degeneration during mid-gestation, a phenotype consistent with excessive tumour necrosis factor (TNF) toxicity, as observed in mice lacking genes involved in the activation of the transcription factor activation NF-κB.
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Studying protein dynamics in living cells.
TL;DR: Live cell imaging, in combination with photobleaching, energy transfer or fluorescence correlation spectroscopy are providing unprecedented insights into the movement of proteins and their interactions with cellular components.
Journal ArticleDOI
Oscillations in NF-κB Signaling Control the Dynamics of Gene Expression
David E. Nelson,Adaoha E. C. Ihekwaba,M Elliott,James R. Johnson,C. A. Gibney,B. E. Foreman,Glyn Nelson,Violaine Sée,Caroline A. Horton,David G. Spiller,Steven W. Edwards,H. P. McDowell,John Unitt,Elaine Sullivan,Rachel L. Grimley,Neil Benson,David S. Broomhead,Douglas B. Kell,Michael R. H. White +18 more
TL;DR: Single-cell time-lapse imaging and computational modeling of NF-κB (RelA) localization showed asynchronous oscillations following cell stimulation that decreased in frequency with increased IκBα transcription.
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Oscillations in NF-κB Signaling Control the Dynamics of Gene Expression
David E. Nelson,Adaoha E. C. Ihekwaba,M Elliott,James R. Johnson,C. A. Gibney,B. E. Foreman,Glyn Nelson,Violaine Sée,Caroline A. Horton,David G. Spiller,Steven W. Edwards,H. P. McDowell,John Unitt,Elaine Sullivan,Rachel L. Grimley,Neil Benson,David S. Broomhead,Douglas B. Kell,Michael R. H. White +18 more