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A Simple Model to Control Growth Rate of Synthetic E. coli during the Exponential Phase: Model Analysis and Parameter Estimation [chapter]

Alfonso Carta, Madalena Chaves, Jean-Luc Gouzé
2012 Lecture Notes in Computer Science  
We develop and analyze a model of a minimal synthetic gene circuit, that describes part of the gene expression machinery in Escherichia coli, and enables the control of the growth rate of the cells during  ...  Moreover, an analytic expression of the growth rate during the exponential phase as function of the input is derived.  ...  the growth rate of E. coli cells during exponential phase.  ... 
doi:10.1007/978-3-642-33636-2_8 fatcat:4bihzkb7jjf3tah2hgdzzf2u7y

Phase space characterization for gene circuit design [article]

Macarena A. Muñoz Silva, Tamara Matute, Isaac Nuñez, Ambrosio Valdes, Carlos A. Ruiz, Gonzalo A. Vidal Peña, Fernán Federici, Timothy J. Rudge
2019 bioRxiv   pre-print
The dynamics of gene circuits were characterized by a trajectory through a multi-dimensional phase space parameterized by the expression levels of each of their constituent transcriptional units (TU).  ...  This will aid in genetic circuit design by providing simple models for the dynamics of gene circuits and their constituent TUs.  ...  ACKNOWLEDGMENT The authors would like to thank Guillermo Yañez for his help uploading to SynBioHub.  ... 
doi:10.1101/590299 fatcat:kaid7iib3ncshm3cme5iejfplm

The Adder Phenomenon Emerges from Independent Control of Pre- and Post-Start Phases of the Budding Yeast Cell Cycle

Devon Chandler-Brown, Kurt M. Schmoller, Yonatan Winetraub, Jan M. Skotheim
2017 Current Biology  
We use single-cell microscopy to parameterize a full cell-cycle model based on independent control of pre- and post-Start cell-cycle periods.  ...  We find that our model predicts the size-independent amount of cell growth during the full cell cycle.  ...  ), and a Genentech Pre-doctoral Fellowship (DCB).  ... 
doi:10.1016/j.cub.2017.08.015 pmid:28889980 pmcid:PMC5679121 fatcat:xnggubd2wfbc5fxcrujuqfjdle

TEARS: Spatial engineering of E. coli with addressable phase-separated RNAs [article]

Haotian Guo, Joseph C Ryan, Adeline Mallet, Xiaohu Song, Victor Pabst, Antoine Decrulle, Ariel B. Lindner
2020 bioRxiv   pre-print
TEARS are a simple and versatile tool for spatially controlling E. coli biochemistry.  ...  Here we demonstrate Transcriptionally Engineered Addressable RNA Solvent droplets (TEARS) as synthetic microdomains within the Escherichia coli.  ...  Chen for comments on modeling, and C. Li and E. H. Wintermute for the comments on the manuscript.  ... 
doi:10.1101/2020.07.02.182527 fatcat:eomp6rrm5vcv3grb32ydio5kdi

Measuring and modeling energy and power consumption in living microbial cells with a synthetic ATP reporter

Yijie Deng, Douglas Raymond Beahm, Steven Ionov, Rahul Sarpeshkar
2021 BMC Biology  
Here we describe a dynamic model and an ATP reporter that tracks ATP in E. coli over different growth phases.  ...  Bacteria turn over their cellular ATP pool a few times per second during the exponential phase and slow this rate by ~ 2–5-fold in lag and stationary phases.  ...  Brown, and Dan Clipca for their technical assistance. We are also thankful to reviewers for their useful feedback to improve the manuscript.  ... 
doi:10.1186/s12915-021-01023-2 pmid:34001118 pmcid:PMC8130387 fatcat:svqkvriskveodfugz65gnghywm

Molecular Characterization and Heterologous Production of the Bacteriocin Peocin, a DNA Starvation/Stationary Phase Protection Protein, from Paenibacillus ehimensis NPUST1

Tseng, Murni, Han, Arfiati, Shih, Hu
2019 Molecules  
For mass production of peocin, fed-batch cultivation of E. coli was performed using a pH-stat control system.  ...  The present study aimed to identify peocin and increase the peocin yield by heterologous expression in Escherichia coli BL21(DE3).  ...  The efficiency of peocin expression was estimated by IPTG induction at different growth phases.  ... 
doi:10.3390/molecules24132516 fatcat:2hyplaikarhojpq2652ds7rvme

Variability of bacterial behavior in the mammalian gut captured using a growth-linked single-cell synthetic gene oscillator [article]

David T Riglar, David L Richmond, Laurent Potvin-Trottier, Andrew A Verdegaal, Alexander D Naydich, Somenath Bakshi, Emanuele Leoncini, Johan Paulsson, Pamela A Silver
2018 bioRxiv   pre-print
In doing so, we demonstrate robust functionality and controllability of the oscillator circuit's activity during bacterial growth in vitro, in a simulated murine gut microfluidic environment, and in vivo  ...  We determine the phase of oscillation from individual bacteria using image analysis of resultant colonies and thereby infer the number of cell divisions elapsed.  ...  The form of f (r) is derived in Growth Model, using a simple model for the growth of the colonies.  ... 
doi:10.1101/472720 fatcat:edxsc4bu2ncj5c6yktttr7yona

Understanding the Control of a Vitamin B12 Riboswitch

Mohammad Abbadi, Sarah Spurgeon, Naziyat Khan, Martin Warren
2018 2018 UKACC 12th International Conference on Control (CONTROL)  
The paper first describes a simple model for the B12-riboswitch regulatory network in E. coli and applies the same analysis when changing the strain to S. enterica.  ...  Here methods for analysis of switched systems from control engineering are applied to the modelling and analysis of a riboswitch.  ...  ANALYSIS OF A SIMPLE MODEL OF THE VITAMIN B 12 RIBOSWITCH The mathematical model which is used in this paper is based on the riboswitch regulatory pathway.  ... 
doi:10.1109/control.2018.8516881 fatcat:as7gppan7jbztmg2k7m2pofnru

Bacterial variability in the mammalian gut captured by a single-cell synthetic oscillator

David T. Riglar, David L. Richmond, Laurent Potvin-Trottier, Andrew A. Verdegaal, Alexander D. Naydich, Somenath Bakshi, Emanuele Leoncini, Lorena G. Lyon, Johan Paulsson, Pamela A. Silver
2019 Nature Communications  
Synthetic gene oscillators have the potential to control timed functions and periodic gene expression in engineered cells.  ...  The oscillations provide a marker of bacterial growth at a single-cell level enabling quantification of bacterial dynamics in response to inflammation and underlying variations in the gut microbiota.  ...  Acknowledgements We thank E Libby and M Baym for helpful discussions. Next-generation sequencing was undertaken at The Bauer Core Facility at Harvard University. D.T.  ... 
doi:10.1038/s41467-019-12638-z pmid:31604953 pmcid:PMC6789134 fatcat:mad4qbykkff2ng2dp6ct5hi5tu

CO2 to succinic acid – Estimating the potential of biocatalytic routes

Ulf W. Liebal, Lars M. Blank, Birgitta E. Ebert
2018 Metabolic Engineering Communications  
This analysis provided insight into the economic feasibility and allowed to estimate the future industrial applicability by estimating overall production costs.  ...  The carbon dioxide assimilation can proceed by a variety of natural pathways and recently even synthetic CO2 fixation routes have been designed.  ...  Funding This work was supported by the Biotechnology Research and Information Network AG (BRAIN AG) and by the German Federal Ministry of Education and Research (BMBF) as part of the Strategic Alliance  ... 
doi:10.1016/j.mec.2018.e00075 pmid:30197864 pmcid:PMC6127376 fatcat:rkfcg4eyyzgdfmzzsa243jetui

A Soft Sensor for Bioprocess Control Based on Sequential Filtering of Metabolic Heat Signals

Dan Paulsson, Robert Gustavsson, Carl-Fredrik Mandenius
2014 Sensors  
The estimated specific growth rate signal obtained from the three stage sequential filter allowed controlled feeding of substrate during the fed-batch phase of the production process.  ...  Temperature sensor signals from the cooling system of the bioreactor were used for estimating the metabolic heat of the microbial culture and from that the specific growth rate and active biomass concentration  ...  Acknowledgments The authors are grateful to G Rajkai at Belach Bioteknik AB for programming work with the soft sensor implementation, to Jan-Peter Axelsson for advice and to Aber Instruments Ltd. for providing  ... 
doi:10.3390/s141017864 pmid:25264951 pmcid:PMC4239934 fatcat:ngaw7ev7sbepjibrndzvua2loy

The Interrelationship between Promoter Strength, Gene Expression, and Growth Rate

Matthew S. Bienick, Katherine W. Young, Justin R. Klesmith, Emily E. Detwiler, Kyle J. Tomek, Timothy A. Whitehead, Stephen S. Fong
2014 PLoS ONE  
(eGFP and amiE) in E. coli in different strains and growth media.  ...  We expand upon the previous theory by introducing a simple promoter activity model to quantitatively predict how basal promoter strength relates to growth rate and protein expression.  ...  to: a~a o (1{e {m m à ) ð20Þ where a o is the portion of the bundled promoter activity that is invariant with respect to growth rate and m* is a fitted parameter that describes the growth dependence on  ... 
doi:10.1371/journal.pone.0109105 pmid:25286161 pmcid:PMC4186888 fatcat:pgpojmjqe5dpdmi3vzs4v7al4e

Biological Implications of Dynamical Phases in Non-equilibrium Networks

Arvind Murugan, Suriyanarayanan Vaikuntanathan
2016 Journal of statistical physics  
The design principles and free energy trade-offs have been studied for a variety of such mechanisms.  ...  Dynamical phases can also provide an intuitive picture of the design principles behind such biological Maxwell Demons.  ...  SV acknowledges funding from the University of Chicago.  ... 
doi:10.1007/s10955-015-1445-0 fatcat:yobesctoivbsnb5b4g5tltuqty

Effect of Replication Fork Dynamics on Escherichia coli Cell Size [article]

Chaitanya A. Athale
2019 arXiv   pre-print
While temperature, population density and growth rate have all been shown to affect E. coli cell size distributions, and recent models have validated a link between growth rate and cell size through DNA  ...  In our model, multi-fork replication produces multiplicative 'noise' and provides a mechanism linking growth rate and cell size variability.  ...  Gangan performed the DIC microscopy of mutant E. coli strains and ran the image analysis code.  ... 
arXiv:1601.02240v4 fatcat:qu7uc4eczna6xhvbeayjlonshe

Component Characterization in a Growth-Dependent Physiological Context: Optimal Experimental Design

Nathan Braniff, Matthew Scott, Brian Ingalls
2019 Processes  
Our numerical results suggest that the intrinsic parameters of a genetic component can be more accurately estimated using optimal experimental designs, and that the choice of growth rates, sampling schedule  ...  Synthetic biology design challenges have driven the use of mathematical models to characterize genetic components and to explore complex design spaces.  ...  We use nutrient quality in exponential phase as a predictable controller of the cell's growth rate and relevant physiological state.  ... 
doi:10.3390/pr7010052 fatcat:myhh7wsj2jaivflwv4pag34z2y
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