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Subcellular Architecture of the Gene Expression Flow of the TOL Catabolic Plasmid of Pseudomonas putida mt-2.
mBio
February 2021
Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, Spain
Despite intensive research on the biochemical and regulatory features of the archetypal catabolic TOL system borne by pWW0 of strain mt-2, the physical arrangement and tridimensional logic of the gene expression flow remains unknown. In this work, the spatial distribution of specific mRNAs with respect to the host nucleoid, the TOL plasmid, and the ribosomal pool has been investigated. hybridization of target transcripts with fluorescent oligonucleotide probes revealed that mRNAs cluster in discrete foci, adjacent but clearly separated from the TOL plasmid and the cell nucleoid.
View Article and Find Full Text PDFModelling co-translational dimerization for programmable nonlinearity in synthetic biology.
J R Soc Interface
November 2020
School of Computing, Newcastle University, Urban Sciences Building, Science Square, Newcastle upon Tyne NE4 5TG, UK.
Nonlinearity plays a fundamental role in the performance of both natural and synthetic biological networks. Key functional motifs in living microbial systems, such as the emergence of bistability or oscillations, rely on nonlinear molecular dynamics. Despite its core importance, the rational design of nonlinearity remains an unmet challenge.
View Article and Find Full Text PDFCapturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL).
ACS Synth Biol
September 2020
School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, United Kingdom.
Synthetic biology aims to develop novel biological systems and increase their reproducibility using engineering principles such as standardization and modularization. It is important that these systems can be represented and shared in a standard way to ensure they can be easily understood, reproduced, and utilized by other researchers. The Synthetic Biology Open Language (SBOL) is a data standard for sharing biological designs and information about their implementation and characterization.
View Article and Find Full Text PDFSBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information.
ACS Synth Biol
July 2019
School of Computing , Newcastle University, Newcastle upon Tyne NE4 5TG , UK.
Standard representation of data is key for the reproducibility of designs in synthetic biology. The Synthetic Biology Open Language (SBOL) has already emerged as a data standard to represent information about genetic circuits, and it is based on capturing data using graphs. The language provides the syntax using a free text document that is accessible to humans only.
View Article and Find Full Text PDFA Metabolic Widget Adjusts the Phosphoenolpyruvate-Dependent Fructose Influx in .
mSystems
December 2016
Systems and Synthetic Biology Program, National Spanish Center for Biotechnology (CNB-CSIC), Madrid, Spain.
Fructose uptake in the soil bacterium occurs through a canonical phosphoenolpyruvate (PEP)-dependent sugar transport system (PTS). The logic of the genetic circuit that rules its functioning is puzzling: the transcription of the operon, encoding all the components of PTS, can escape the repression exerted by the catabolite repressor/activator protein Cra solely in the presence of intracellular fructose-1-P, an agonist formed only when fructose has been already transported. To study this apparently incongruous regulatory architecture, the changes in the transcriptome brought about by a seamless Δ deletion in strain KT2440 were inspected under different culture conditions.
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