scholarly journals Design and Evaluation of Synthetic RNA-Based Incoherent Feed-Forward Loop Circuits

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1182
Author(s):  
Seongho Hong ◽  
Dohyun Jeong ◽  
Jordan Ryan ◽  
Mathias Foo ◽  
Xun Tang ◽  
...  

RNA-based regulators are promising tools for building synthetic biological systems that provide a powerful platform for achieving a complex regulation of transcription and translation. Recently, de novo-designed synthetic RNA regulators, such as the small transcriptional activating RNA (STAR), toehold switch (THS), and three-way junction (3WJ) repressor, have been utilized to construct RNA-based synthetic gene circuits in living cells. In this work, we utilized these regulators to construct type 1 incoherent feed-forward loop (IFFL) circuits in vivo and explored their dynamic behaviors. A combination of a STAR and 3WJ repressor was used to construct an RNA-only IFFL circuit. However, due to the fast kinetics of RNA–RNA interactions, there was no significant timescale difference between the direct activation and the indirect inhibition, that no pulse was observed in the experiments. These findings were confirmed with mechanistic modeling and simulation results for a wider range of conditions. To increase delay in the inhibition pathway, we introduced a protein synthesis process to the circuit and designed an RNA–protein hybrid IFFL circuit using THS and TetR protein. Simulation results indicated that pulse generation could be achieved with this RNA–protein hybrid model, and this was further verified with experimental realization in E. coli. Our findings demonstrate that while RNA-based regulators excel in speed as compared to protein-based regulators, the fast reaction kinetics of RNA-based regulators could also undermine the functionality of a circuit (e.g., lack of significant timescale difference). The agreement between experiments and simulations suggests that the mechanistic modeling can help debug issues and validate the hypothesis in designing a new circuit. Moreover, the applicability of the kinetic parameters extracted from the RNA-only circuit to the RNA–protein hybrid circuit also indicates the modularity of RNA-based regulators when used in a different context. We anticipate the findings of this work to guide the future design of gene circuits that rely heavily on the dynamics of RNA-based regulators, in terms of both modeling and experimental realization.

2011 ◽  
Vol 391-392 ◽  
pp. 1324-1329
Author(s):  
Ying Ying Shi ◽  
Qiang Hua Zhang ◽  
Liang Dong Feng ◽  
Qing Ping Xiong ◽  
Fei Liu

By using Palygorskite as matrix and introducing the surface ion-imprinting concept to the synthesis process, a Palygorskite-supported organic–inorganic hybrid polymer for selective separation of Pb2+ from aqueous solutio was prepared. The prepared polymer was characterized with techniques of SEM, XRD and FT-IR. The effects of contact time, pH value and temperature of the initial solution on the adsorption characters of Pb2+ were investigated. Under the optimum conditions, the ions-imprinted polymer offered a fast kinetics for the adsorption of Pb2+ and the maximum capacity was 4.51 mg/g. And the pseudo-second order model bestly described the kinetics of adsorption of Pb2+ onto the as-prepared materials.


2013 ◽  
Vol 104 (2) ◽  
pp. 533a-534a
Author(s):  
Timothy Strovas ◽  
Alexander B. Rosenberg ◽  
Georg Seelig

Author(s):  
Xu Han ◽  
Zeyun Zhang ◽  
Xuefei Xu

To suppress the shuttle effect of lithium polysulfides and promote fast kinetics of charge−discharge process in Li−S batteries, it is essential to search promising catalysts with sufficient stability and high...


Author(s):  
Pascal A. Pieters ◽  
Bryan L. Nathalia ◽  
Ardjan J. van der Linden ◽  
Peng Yin ◽  
Jongmin Kim ◽  
...  

2016 ◽  
Vol 27 (24) ◽  
pp. 3791-3799 ◽  
Author(s):  
Hafida Sellou ◽  
Théo Lebeaupin ◽  
Catherine Chapuis ◽  
Rebecca Smith ◽  
Anna Hegele ◽  
...  

Chromatin relaxation is one of the earliest cellular responses to DNA damage. However, what determines these structural changes, including their ATP requirement, is not well understood. Using live-cell imaging and laser microirradiation to induce DNA lesions, we show that the local chromatin relaxation at DNA damage sites is regulated by PARP1 enzymatic activity. We also report that H1 is mobilized at DNA damage sites, but, since this mobilization is largely independent of poly(ADP-ribosyl)ation, it cannot solely explain the chromatin relaxation. Finally, we demonstrate the involvement of Alc1, a poly(ADP-ribose)- and ATP-dependent remodeler, in the chromatin-relaxation process. Deletion of Alc1 impairs chromatin relaxation after DNA damage, while its overexpression strongly enhances relaxation. Altogether our results identify Alc1 as an important player in the fast kinetics of the NAD+- and ATP-dependent chromatin relaxation upon DNA damage in vivo.


2015 ◽  
Vol 48 (3) ◽  
pp. 827-835 ◽  
Author(s):  
Mingliang Tang ◽  
Xuerun Li ◽  
Yusheng Shen ◽  
Xiaodong Shen

Modeling of the kinetics of the synthesis process for calcium sulfate α-hemihydrate from gypsum formed by flue gas desulfurization (FGD) is important to produce high-performance products with minimal costs and production cycles under hydrothermal conditions. In this study, a model was established by horizontally translating the obtained crystal size distribution (CSD) to the CSD of the stable phase during the transformation process. A simple method was used to obtain the nucleation and growth rates. A nonlinear optimization algorithm method was employed to determine the kinetic parameters. The model can be successfully used to analyze the transformation kinetics of FGD gypsum to α-hemihydrate in an isothermal batch crystallizer. The results showed that the transformation temperature and stirring speed exhibit a significant influence on the crystal growth and nucleation rates of α-hemihydrate, thus altering the transformation time and CSD of the final products. The characteristics obtained by the proposed model can potentially be used in the production of α-hemihydrate.


2019 ◽  
Vol 1 (1) ◽  
pp. 1
Author(s):  
Yu.V. Yudin ◽  
M.V. Maisuradze ◽  
A.A. Kuklina ◽  
P.D. Lebedev

An algorithm was developed for the simulation of a phase transition in solid state whichmakes it possible to obtain the kinetic curves of transformation under different initialconditions (the number and arrangement of new phase nuclei, the distance betweenthe nearest nuclei). The simulation results were analyzed using the Kolmogorov-Johnson-Mehl-Avrami equation and the corresponding coefficients were determined.The correlation between the simulation results and the experimental kinetics of theaustenite isothermal transformation in alloyed steels was shown.


2013 ◽  
Vol 123 (7) ◽  
pp. 3183-3183 ◽  
Author(s):  
Sampurna Chatterjee ◽  
Lukas C. Heukamp ◽  
Maike Siobal ◽  
Jakob Schöttle ◽  
Caroline Wieczorek ◽  
...  

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