Standardsinsybio

Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress

Pseudomonas putida is a soil bacterium that is frequently found in sites polluted with toxic chemicals. It is able to survive in these sites because of its ability to tolerate high levels of endogenous and exogenous oxidative stress. But, how? The answer to this question remains largely unknown. A study, recently published in The ISME Journal, … Leer más

Modelling co-translational dimerization for programmable nonlinearity in synthetic biology

Nonlinearity is fundamental in the performance of natural and synthetic biological networks, as many key functional motifs in microbial systems rely on nonlinear molecular dynamics. Nevertheless, the rational design of nonlinearity is an unmet challenge due to the lack of mathematical modelling that accounts for the mechanistic basis of nonlinearity. In this study, a model … Leer más

Quantitative assessment of morphological traits of planktonic bacterial aggregates

Planktonic flocs composed of multiple bacterial strains can be used biocatalytic agents in aqueous media for industrial applications and environmental cleanup. Microbial consortia are characterized by including division of labour among the different microbial species that compose the biofilm, allowing to perform complex biochemical transformations. But this division of labour is not the only think … Leer más

An automated DIY framework for experimental evolution of Pseudomonas putida

Adaptive laboratory evolution is a general and effective strategy for optimizing the design of engineered genetic circuits and upgrading metabolic phenotypes. However, the specific characteristics of each microorganism typically require the use of exclusive conditions that must be adjusted to the biological chassis at stake. In this work, a do‐it‐yourself (DIY) approach has been used … Leer más

A standardized inverter package borne by broad host range plasmids for genetic circuit design in Gram-negative bacteria

Genetically encoded logic gates (and, in particular, inverters or NOT gates) are the main building blocks for designing circuits, engineering biosensors, or decision-making devices in synthetic biology. Nevertheless, the repertoire of inverters readily available for different species is limited. In this work, a variety of NOT gates were recreated as broad host range constructs assembled … Leer más

Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL)

Synthetic biology aims to develop novel biological systems and increase their reproducibility using engineering principles such as standardisation and modularisation. It is important to represent and share these systems in a standard way to ensure that they can be easily understood, reproduced, and used by other researchers. The Synthetic Biology Open Language (SBOL) is a … Leer más

For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is!

The role of synthetic biology as a fuel for the bioeconomy requires clarification of the terms typically adopted by this growing scientific-technical field. In particular, the concept of ‘chassis’ as a defined, reusable biological frame where non-native components can be plugged in and out to create new functionalities lies at the boundary between frontline bioengineering … Leer más

Naked Bacterium: Emerging Properties of a Surfome-Streamlined Pseudomonas putida Strain

Environmental bacteria are usually equipped with native surface-attachment elements that can hinder the engineering of biofilms. In this work, the genome of Pseudomonas putida KT2440 was engineered to strip the cells of most of their outer-facing structures, involved in motion, binding to surfaces and biofilm formation. In particular, 23 segments were deleted, resulting in a … Leer más

Mismatch repair hierarchy of Pseudomonas putida revealed by mutagenic ssDNA recombineering of the pyrF gene

The mismatch repair (MMR) system is one of the key molecular devices that prokaryotic cells have for ensuring fidelity of DNA replication. While the canonical MMR of E . coli involves 3 proteins (encoded by mutS , mutL and mutH), the soil bacterium Pseudomonads putida has only 2 bona fide homologues (mutS and mutL ) … Leer más