Turing patterns with cellular computers.

Turing patterns are a key theoretical foundation for understanding organ development and organization. While they have been found to occur in natural systems, implementing new biological systems that form Turing patterns has remained challenging. To address this, Tica et al.

Workflow to Select Functional Promoter DNA Baits and Screen Arrayed Gene Libraries in Yeast.

The yeast one-hybrid system (Y1H) is used extensively to identify DNA-protein interactions. The generation of large collections of open reading frames (ORFs) to be used as prey in screenings is not a bottleneck nowadays and can be carried out in-house or offered as a service by companies. However, the straightforward use of full gene promoters as baits to identify interacting proteins undermines the accuracy and sensitivity of the assay, especially in the case of multicellular eukaryotes.

The Laboratory Automation Protocol (LAP) Format and Repository: A Platform for Enhancing Workflow Efficiency in Synthetic Biology.

Laboratory automation deals with eliminating manual tasks in high-throughput protocols. It therefore plays a crucial role in allowing fast and reliable synthetic biology. However, implementing open-source automation solutions often demands experimental scientists to possess scripting skills, and even when they do, there is no standardized toolkit available for their use.

GENETTA: a Network-Based Tool for the Analysis of Complex Genetic Designs.

GENETTA is a software tool that transforms synthetic biology designs into networks using graph theory for analysis and manipulation. By representing complex data as interconnected points, GENETTA allows dynamic customization of visualizations, including interaction networks and parts hierarchies. It can also merge design data from multiple databases, providing a unified perspective.

pBLAM1-x: standardized transposon tools for high-throughput screening.

The engineering of pre-defined functions in living cells requires increasingly accurate tools as synthetic biology efforts become more ambitious. Moreover, the characterization of the phenotypic performance of genetic constructs demands meticulous measurements and extensive data acquisition for the sake of feeding mathematical models and matching predictions along the design-build-test lifecycle. Here, we developed a genetic tool that eases high-throughput transposon insertion sequencing (TnSeq): the pBLAM1-x plasmid vectors carrying the Himar1 Mariner transposase system.

Pressure-dependent growth controls 3D architecture of Pseudomonas putida microcolonies.

Colony formation is key to many ecological and biotechnological processes. In its early stages, colony formation involves the concourse of a number of physical and biological parameters for generation of a distinct 3D structure-the specific influence of which remains unclear. We focused on a thus far neglected aspect of the process, specifically the consequences of the differential pressure experienced by cells in the middle of a colony versus that endured by bacteria located in the growing periphery.

SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes.

The SEVA platform (https://seva-plasmids.com) was launched one decade ago, both as a database (DB) and as a physical repository of plasmid vectors for genetic analysis and engineering of Gram-negative bacteria with a structure and nomenclature that follows a strict, fixed architecture of functional DNA segments. While the current update keeps the basic features of earlier versions, the platform has been upgraded not only with many more ready-to-use plasmids but also with features that expand the range of target species, harmonize DNA assembly methods and enable new applications.

An electrogenetic toggle switch model.

Synthetic biology uses molecular biology to implement genetic circuits that perform computations. These circuits can process inputs and deliver outputs according to predefined rules that are encoded, often entirely, into genetic parts. However, the field has recently begun to focus on using mechanisms beyond the realm of genetic parts for engineering biological circuits.

A Network Approach to Genetic Circuit Designs.

As genetic circuits become more sophisticated, the size and complexity of data about their designs increase. The data captured goes beyond genetic sequences alone; information about circuit modularity and functional details improves comprehension, performance analysis, and design automation techniques. However, new data types expose new challenges around the accessibility, visualization, and usability of design data (and metadata).

Fast biofoundries: coping with the challenges of biomanufacturing.

Biofoundries are highly automated facilities that enable the rapid and efficient design, build, test, and learn cycle of biomanufacturing and engineering biology, which is applicable to both research and industrial production. However, developing a biofoundry platform can be expensive and time consuming. A biofoundry should grow organically, starting from a basic platform but with a vision for automation, equipment interoperability, and efficiency.

Automated design and implementation of a NOR gate in Pseudomonas putida.

Boolean NOR gates have been widely implemented in as transcriptional regulatory devices for building complex genetic circuits. Yet, their portability to other bacterial hosts/chassis is generally hampered by frequent changes in the parameters of the INPUT/OUTPUT response functions brought about by new genetic and biochemical contexts. Here, we have used the circuit design tool CELLO for assembling a NOR gate in the soil bacterium and the metabolic engineering platform with components tailored for To this end, we capitalized on the functional parameters of 20 genetic inverters for each host and the resulting compatibility between NOT pairs.

Subcellular Architecture of the Gene Expression Flow of the TOL Catabolic Plasmid of Pseudomonas putida mt-2.

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.

Contextual dependencies expand the re-usability of genetic inverters.

The implementation of Boolean logic circuits in cells have become a very active field within synthetic biology. Although these are mostly focussed on the genetic components alone, the context in which the circuit performs is crucial for its outcome. We characterise 20 genetic NOT logic gates in up to 7 bacterial-based contexts each, to generate 135 different functions.

A Standardized Inverter Package Borne by Broad Host Range Plasmids for Genetic Circuit Design in Gram-Negative Bacteria.

Genetically encoded logic gates, especially inverters-NOT gates-are the building blocks for designing circuits, engineering biosensors, or decision-making devices in synthetic biology. However, the repertoire of inverters readily available for different species is rather limited. In this work, a large whole of NOT gates that was shown to function previously in a specific strain of , was recreated as broad host range (BHR) collection of constructs assembled in low, medium, and high copy number plasmid backbones of the SEVA (Standard European Vector Architecture) collection.

Modelling co-translational dimerization for programmable nonlinearity in synthetic biology.

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.

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 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.

The long journey towards standards for engineering biosystems: Are the Molecular Biology and the Biotech communities ready to standardise?

Synthetic biology needs to adopt sound scientific and industry-like standards in order to achieve its ambitious goals of efficient and accurate engineering of biological systems.

ShortBOL: A Language for Scripting Designs for Engineered Biological Systems Using Synthetic Biology Open Language (SBOL).

The Synthetic Biology Open Language (SBOL) is an emerging synthetic biology data exchange standard, designed primarily for unambiguous and efficient machine-to-machine communication. However, manual editing of SBOL is generally difficult for nontrivial designs. Here, we describe ShortBOL, a lightweight SBOL scripting language that bridges the gap between manual editing, visual design tools, and direct programming.

Digitalizing heterologous gene expression in Gram-negative bacteria with a portable ON/OFF module.

While prokaryotic promoters controlled by signal-responding regulators typically display a range of input/output ratios when exposed to cognate inducers, virtually no naturally occurring cases are known to have an OFF state of zero transcription-as ideally needed for synthetic circuits. To overcome this problem, we have modelled and implemented a simple digitalizer module that completely suppresses the basal level of otherwise strong promoters in such a way that expression in the absence of induction is entirely impeded. The circuit involves the interplay of a translation-inhibitory sRNA with the translational coupling of the gene of interest to a repressor such as LacI.

Pathways to cellular supremacy in biocomputing.

Synthetic biology uses living cells as the substrate for performing human-defined computations. Many current implementations of cellular computing are based on the "genetic circuit" metaphor, an approximation of the operation of silicon-based computers. Although this conceptual mapping has been relatively successful, we argue that it fundamentally limits the types of computation that may be engineered inside the cell, and fails to exploit the rich and diverse functionality available in natural living systems.

A Model for the Spatiotemporal Design of Gene Regulatory Circuits †.

Mathematical modeling assists the design of synthetic regulatory networks by providing a detailed mechanistic understanding of biological systems. Models that can predict the performance of a design are fundamental for synthetic biology since they minimize iterations along the design-build-test lifecycle. Such predictability depends crucially on what assumptions (, biological simplifications) the model considers.