21 Result(s)
within
Alfonso Jaramillo
English
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Article
Open AccessT7 phage-assisted evolution of riboswitches using error-prone replication and dual selection
Leveraging riboswitches, non-coding mRNA fragments pivotal to gene regulation, poses a challenge in effectively selecting and enriching these functional genetic sensors, which can toggle between ON and OFF sta...
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Protocol
Scarless Recombineering of Phage in Lysogenic State
We present a scarless recombineering-based method for introducing multiple point mutations into the genome of a temperate phage. The method uses the λ Red recombineering system to promote exogenous ssDNA oligo...
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Protocol
Lambda Red Recombineering of Bacteriophage in the Lysogenic State
We present a recombineering-based method for editing the genome of a temperate phage. The method uses the lambda Red recombination system to edit the genome of a lysogenized host with a prophage compatible wit...
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Article
Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication
This protocol describes a phagemid-based intracellular evolution approach to generate and select for proteins with improved biological characteristics.
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Article
Synthetic biology: Engineered stable ecosystems
Co-culture of bacterial cells engineered with quorum-sensing and self-lysis circuits allows coupled oscillatory dynamics and stable states, opening the way to engineered microbial ecosystems with targeted dyna...
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Article
Open AccessEngineering orthogonal dual transcription factors for multi-input synthetic promoters
Synthetic biology has seen an explosive growth in the capability of engineering artificial gene circuits from transcription factors (TFs), particularly in bacteria. However, most artificial networks still empl...
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Protocol
Regulatory RNA Design Through Evolutionary Computation and Strand Displacement
The discovery and study of a vast number of regulatory RNAs in all kingdoms of life over the past decades has allowed the design of new synthetic RNAs that can regulate gene expression in vivo. Riboregulators,...
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Protocol
Design and Characterization of Topological Small RNAs
RNA can self-assemble into complex structures through base pairing, as well as encode information and bind with proteins to induce enzymatic activity. Furthermore, RNA can possess intrinsic enzymatic-like (rib...
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Article
Open AccessAutomated design of bacterial genome sequences
Organisms have evolved ways of regulating transcription to better adapt to varying environments. Could the current functional genomics data and models support the possibility of engineering a genome with compl...
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Article
Pushing the limits of automatic computational protein design: design, expression, and characterization of a large synthetic protein based on a fungal laccase scaffold
The de novo engineering of new proteins will allow the design of complex systems in synthetic biology. But the design of large proteins is very challenging due to the large combinatorial sequence space to be e...
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Article
Synthetic biology gains momentum in Europe
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Article
Open AccessRobust dynamical pattern formation from a multifunctional minimal genetic circuit
A practical problem during the analysis of natural networks is their complexity, thus the use of synthetic circuits would allow to unveil the natural mechanisms of operation. Autocatalytic gene regulatory netw...
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Chapter
Computational Design in Synthetic Biology
One of the most ambitious goals in biological engineering is the ability to computationally design an organism using unsupervised algorithms. We discuss the development of new automatic methodologies to design...
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Article
Open AccessReverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions
Understanding the molecular mechanisms plants have evolved to adapt their biological activities to a constantly changing environment is an intriguing question and one that requires a systems biology approach. ...
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Article
Open AccessPROTDES: CHARMM toolbox for computational protein design
We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PRO...
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Article
Open AccessChanges in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus
Tobacco etch potyvirus (TEV) has been extensively used as model system for the study of positive-sense RNA virus infecting plants. TEV ability to infect Arabidopsis thaliana varies among ecotypes. In this study, ...
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Article
Open AccessAsmparts: assembly of biological model parts
We propose a new computational tool to produce models of biological systems by assembling models from biological parts. Our software not only takes advantage of modularity, but it also enforces standardisation...
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Article
Open AccessComputational design of digital and memory biological devices
The use of combinatorial optimization techniques with computational design allows the development of automated methods to design biological systems. Automatic design integrates design principles in an unsuperv...
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Article
Evolutionary mechanisms of circadian clocks
An intriguing question in biology is to know how circadian molecular networks could have evolved their particular topologies to adjust to a daily period. We analyze the mechanism of the evolution of such netwo...
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Article
Open AccessComputational design of proteins with new functions
