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An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular "breadboard" system

Zoltan A. Tuza, Vipul Singhal, Jongmin Kim, Richard M. Murray
2013 52nd IEEE Conference on Decision and Control  
In this paper, we develop an experimentally validated MATLAB software toolbox as an accompaniment to an in vitro cell-free biomolecular "breadboard" system.  ...  The toolbox gives insight into the dynamics of unmeasured states in the cell-free system, accounting especially for the resource usage.  ...  The developed model also has predictive capability because the parameters have been validated experimentally.  ... 
doi:10.1109/cdc.2013.6760079 dblp:conf/cdc/TuzaSKM13 fatcat:opjzq6cswfatlkjuzljaqtzff4

Effective Biophysical Modeling of Cell Free Transcription and Translation Processes

Abhinav Adhikari, Michael Vilkhovoy, Sandra Vadhin, Ha Eun Lim, Jeffrey D. Varner
2020 Frontiers in Bioengineering and Biotechnology  
In this study, we developed an effective biophysical modeling approach to simulate transcription and translation processes.  ...  Transcription and translation are at the heart of metabolism and signal transduction.  ...  Arguably, the most widely used cell free technology is cell free protein synthesis (CFPS), an in vitro platform for protein transcription (TX) and translation (TL).  ... 
doi:10.3389/fbioe.2020.539081 pmid:33324619 pmcid:PMC7726328 fatcat:pzemdrnygbcidl57mvu4kichvi

Kinetic analysis of aptazyme-regulated gene expression in a cell-free translation system: Modeling of ligand-dependent and -independent expression

S. Kobori, N. Ichihashi, Y. Kazuta, T. Matsuura, T. Yomo
2012 RNA: A publication of the RNA Society  
We performed switching of gene expression using two onswitch aptazymes with different properties in a cell-free translation system, and constructed a kinetic model that quantitatively describes the dynamics  ...  Aptazymes are useful as RNA-based switches of gene expression responsive to several types of compounds.  ...  This research was supported in part by the Global COE (Centers of Excellence) Program of the Ministry of Education, Culture, Sports, Science, and Technology, Japan.  ... 
doi:10.1261/rna.032748.112 pmid:22733807 pmcid:PMC3404367 fatcat:s2kj4m5tp5grhns3q2qfpgxs3m

Implementation and System Identification of a Phosphorylation-Based Insulator in a Cell-Free Transcription-Translation System [article]

Shaobin Guo, Enoch Yeung, Richard M Murray
2017 bioRxiv   pre-print
This paper describes the implementation of such a biological circuit in a cell-free transcription-translation system and the structural identifiability of the PBI in the system.  ...  We performed standard system identification analysis and determined that the model is globally identifiable with respect to three critical parameters.  ...  If we had a way of quantifying the rate of transcription, translation, and folding of the individual proteins in the transcription-translation system, we could predictively estimate the trajectories of  ... 
doi:10.1101/122606 fatcat:zl43gqm4abgcxnx2y3n6brpndq

Modeling Cell-Free Protein Synthesis Systems—Approaches and Applications

Jan Müller, Martin Siemann-Herzberg, Ralf Takors
2020 Frontiers in Bioengineering and Biotechnology  
In vitro systems are ideal setups to investigate the basic principles of biochemical reactions and subsequently the bricks of life.  ...  Cell-free protein synthesis (CFPS) systems mimic the transcription and translation processes of whole cells in a controlled environment and allow the detailed study of single components and reaction networks  ...  An equally complex system was developed to describe the synthesis of a short Met-Gly-Gly peptide in an E. colibased in vitro system by incorporating 968 reactions and 241 components (Matsuura et al.,  ... 
doi:10.3389/fbioe.2020.584178 pmid:33195146 pmcid:PMC7655533 fatcat:esynrf2ltbch3mfe4wihe5dt2e

Improving prediction fidelity of cellular metabolism with kinetic descriptions

Anupam Chowdhury, Ali Khodayari, Costas D Maranas
2015 Current Opinion in Biotechnology  
In addition to substratelevel kinetic regulatory information, the integration of a number of additional layers of regulation at the transcription, translation, and post-translation levels is sought after  ...  In addition to substrate-26 level kinetic regulatory information, the integration of a number of additional layers of regulation 27 at the transcription, translation, and post-translation levels is sought  ...  cell-free systems due to the relatively small size of the reaction networks and higher reliability of the estimated kinetic 48 parameters for in vitro systems.  ... 
doi:10.1016/j.copbio.2015.08.011 pmid:26318076 fatcat:q3owgtvvdfdgziul3ayqgzvgxy

Effective Biophysical Modeling of Cell Free Transcription and Translation Processes [article]

Abhinav Adhikari, Michael Vilkhovoy, Sandra Vadhin, Ha Eun Lim, Jeffrey Varner
2020 bioRxiv   pre-print
In this study, we developed an effective biophysical model of transcription and translation processes for the cell free operation of two synthetic circuits.  ...  Transcription and translation are at the heart of metabolism and signal transduction.  ...  Next, we used the ensemble of P70a, time constant and degradation parameters 317 estimated for the P70 -deGFP model to constrain the analysis of the more biophysical transcription and translation model  ... 
doi:10.1101/2020.02.25.964841 fatcat:iheohm5i5ngflfcxzj4sqacnbm

Positive regulatory dynamics by a small noncoding RNA: speeding up responses under temperature stress

Raúl Guantes, Bastien Cayrol, Florent Busi, Véronique Arluison
2012 Molecular Biosystems  
Our analysis is based on the first absolute quantification of the copy number of both the sRNA and of its corresponding mRNA in combination with mathematical models for post-transcriptional regulation.  ...  In E. coli, most of those ncRNAs for which functional knowledge is available were shown to be dependent on the Hfq RNA chaperone and to act as inhibitors of translation by base pairing with their mRNA  ...  Lease (OSU, Columbus, OH, USA) for critical reading of the manuscript.  ... 
doi:10.1039/c2mb05479e pmid:22456827 fatcat:xqmszp4uujhgfdlzzl7jxn3zri

Optimization of an In Vitro Transcription/Translation System Based on Sulfolobus solfataricus Cell Lysate

Giada Lo Gullo, Rosanna Mattossovich, Giuseppe Perugino, Anna La Teana, Paola Londei, Dario Benelli
2019 Archaea  
A system is described which permits the efficient synthesis of proteins in vitro at high temperature.  ...  It is based on the use of an unfractionated cell lysate (S30) from Sulfolobus solfataricus previously well characterized in our laboratory for translation of pretranscribed mRNAs, and now adapted to perform  ...  mRNAs in Archaea" and by funds from "Sapienza" University of Rome to DB for the 2016 project "The 9 Archaea translational control of p53 executed by eIF5A", protocol number: RP116154B8B63CB0.  ... 
doi:10.1155/2019/9848253 fatcat:xvtriv2w6jc3bhe6svko7nrjde

Kinetic measurement of ribosome motor stalling force

Deepak Kumar Sinha, U. S. Bhalla, G. V. Shivashankar
2004 Applied Physics Letters  
, k oligo is the rate of translation when an oligomer of length ␦l is added to in vitro translation system, ⌬E is the hybridization energy of mRNA and DNA oligomer, W is the work done by the ribosome to  ...  We use TNT® T7 Coupled Wheat Germ Extract System-WGES from Promega for studying the kinetics of in vitro transcription coupled translation of luciferase gene. 14 1 l of antisense oligomers of three different  ... 
doi:10.1063/1.1821647 fatcat:zlpa354opfavflsns5bzytvr6q

Reconstruction of transcriptional dynamics from gene reporter data using differential equations

Bärbel Finkenstädt, Elizabeth A. Heron, Michal Komorowski, Kieron Edwards, Sanyi Tang, Claire V. Harper, Julian R. E. Davis, Michael R. H. White, Andrew J. Millar, David A. Rand
2008 Computer applications in the biosciences : CABIOS  
Conflict of Interest: none declared.  ...  An example of formulating and fitting an autoregulatory feedback system with transcriptional delay as a system of SDEs can be found in Heron et al. (2007) .  ...  Although the control data do not seem very dynamic they are useful in inferring the base rates of transcription and translation.  ... 
doi:10.1093/bioinformatics/btn562 pmid:18974172 pmcid:PMC2639297 fatcat:xp6zpkigt5dupospoyqkvsrr5i

Modeling of Rifampicin-Induced CYP3A4 Activation Dynamics for the Prediction of Clinical Drug-Drug Interactions from In Vitro Data

Fumiyoshi Yamashita, Yukako Sasa, Shuya Yoshida, Akihiro Hisaka, Yoshiyuki Asai, Hiroaki Kitano, Mitsuru Hashida, Hiroshi Suzuki, Randen Lee Patterson
2013 PLoS ONE  
Herein, we report the compilation of in vitro induction data for CYP3A4 by rifampicin in human hepatocytes, and the transcription/translation model developed for this enzyme using an extended least squares  ...  Although several DDI models have been proposed, none have comprehensively considered the effects of enzyme transcription/translation dynamics on induction-based DDI.  ...  To obtain non-biased parameters regarding transcription and translation of CYP3A4, we systematically collected in vitro data and analyzed them using an extended least squares method [21, 22] that allows  ... 
doi:10.1371/journal.pone.0070330 pmid:24086247 pmcid:PMC3782498 fatcat:x7sun4k7k5fvdcxsoue5sdfa4u

Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems

Daniel D. Lewis, Fernando D. Villarreal, Fan Wu, Cheemeng Tan
2014 Frontiers in Bioengineering and Biotechnology  
In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems.  ...  At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic  ...  This work is supported by Society-in-Science: Branco-Weiss Fellowship.  ... 
doi:10.3389/fbioe.2014.00066 pmid:25538941 pmcid:PMC4260521 fatcat:5462hdi3qzga5dnur7ibjhgypm

Kinetic modeling and simulation of in vitro transcription by phage T7 RNA polymerase

Sabine Arnold, Martin Siemann, Kai Scharnweber, Markus Werner, Sandra Baumann, Matthias Reuss
2001 Biotechnology and Bioengineering  
Model parameters and their precision are estimated using dynamic simulation and nonlinear regression analysis.  ...  This study provides a mathematical model of T7 RNA polymerase (T7 RNAP) kinetics under in vitro conditions targeted at application of this model to simulation of dynamic transcription performance.  ...  The authors thank all members of this consortium, represented by Prof. V. Erdmann (Institute of Biochemistry, FU Berlin, Germany), Prof. A.  ... 
doi:10.1002/1097-0290(20010305)72:5<548::aid-bit1019>3.0.co;2-2 pmid:11460245 fatcat:ulsg7j5drvh3zaezvglxlboyci

Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions

Duschak VG
2015 Current Synthetic and Systems Biology  
The specific applications of computational tools to the design of an in vitro gene expression platform known as the artificial cell, its components and the strategies developed to predict activities of  ...  By using computational models to set up quantitative differences between in vitro reactions and in vivo systems, could identify specific mechanisms in living organisms to be further used in in vitro reactions  ...  Additionally, a library of twenty one T7 promoters was characterized in cell-free platforms using an in vitro transcription/translation system [91] .  ... 
doi:10.4172/2332-0737.1000127 fatcat:bo7tsmpuabfcxmotarlxodyboq
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