Physical Forces Shape Group Identity of Swimming Pseudomonas putida Cells

The often striking macroscopic patterns developed by motile bacterial populations on agar plates are a consequence of the environmental conditions where the cells grow and spread. Parameters such as medium stiffness and nutrient concentration have been reported to alter cell swimming behavior, while mutual interactions among populations shape collective patterns. One commonly observed occurrence is the mutual inhibition of clonal bacteria when moving toward each other, which results in a distinct halt at a finite distance on the agar matrix before having direct contact. The dynamics behind this phenomenon (i.e., intolerance to mix in time and space with otherwise identical others) has been traditionally explained in terms of cell-to-cell competition/cooperation regarding nutrient availability. In this work, the same scenario has been revisited from an alternative perspective: the effect of the physical mechanics that frame the process, in particular the consequences of collisions between moving bacteria and the semi-solid matrix of the swimming medium. To this end, we set up a simple experimental system in which the swimming patterns of Pseudomonas putida were tested with different geometries and agar concentrations. A computational analysis framework that highlights cell-to-medium interactions was developed to fit experimental observations. Simulated outputs suggested that the medium is compressed in the direction of the bacterial front motion. This phenomenon generates what was termed a compression wave that goes through the medium preceding the swimming population and that determines the visible high-level pattern. Taken together, the data suggested that the mechanical effects of the bacteria moving through the medium created a factual barrier that impedes to merge with neighboring cells swimming from a different site. The resulting divide between otherwise clonal bacteria is thus brought about by physical forces—not genetic or metabolic programs.This work was supported by the EVOPROG (FP7-ICT-610730), ARISYS (ERC-2012-ADG-322797), and EmPowerPutida (EU-H2020-BIOTEC-2014-2015-635536) Contracts of the European Union, and the CAMBIOS (RTC-2014-1777-3) and CONTIBUGS (PCIN-2013-040) Projects of the Spanish Ministry of Economy and Competitiveness.Peer Reviewe

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

8 Pág.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. Previously, this standard has only been used to represent designs in systems where the same design is implemented in every cell; however, there is also much interest in multicellular systems, in which designs involve a mixture of different types of cells with differing genotype and phenotype. Here, we show how the SBOL standard can be used to represent multicellular systems, and, hence, how researchers can better share designs with the community and reliably document intended system functionality.This work was supported in part by NSF Expeditions in Computing Program Award No. 1522074 as part of the Living Computing Project and by the Defense Advanced Research Projects Agency under Contract No. W911NF-17-2-0098. The views, opinions, and/or findings expressed are of the author(s) and should not be interpreted as representing official views or policies of the Department of Defense or the U.S. Government. A.G.-M. was supported by the SynBio3D project of the UK Engineering and Physical Sciences Research Council (No.EP/R019002/1) and the European CSA on biological standardization BIOROBOOST (EU Grant No. 820699)Peer reviewe

A born-again global firm: Inés Rosales SAU in the traditional sector of pastry production

The literature on internationalisation processes in family businesses has boomed with the emergence of new approaches and different perspectives. One of these schemes analyses the so-called born-again global firms, mostly technology companies, which experienced an internationalisation process after one or more serious incidents affecting it. The case of Ines Rosales extends the frontier of the meaning of a global born-again firm to firms in industries and traditional products. One of its most striking aspects is that the flagship product is centennial and based on basic ingredients. In addition, the production process of the firm mix production by hand and mechanised developments. Inés Rosales shows the ability of a family Small and Medium Enterprise (SME) in a process of internationalisation even in culturally distant markets through the traditional cake of olive oil.Universidad Pablo de Olavide. Departamento de Economía, Métodos Cuantitativos e Historia EconómicaPreprin

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

10 Pág.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. In particular, SEVA 4.0 includes (i) a sub-collection of plasmids for easing the composition of multiple DNA segments with MoClo/Golden Gate technology, (ii) vectors for Gram-positive bacteria and yeast and [iii] off-the-shelf constructs with built-in functionalities. A growing collection of plasmids that capture part of the standard-but not its entirety-has been compiled also into the DB and repository as a separate corpus (SEVAsib) because of its value as a resource for constructing and deploying phenotypes of interest. Maintenance and curation of the DB were accompanied by dedicated diffusion and communication channels that make the SEVA platform a popular resource for genetic analyses, genome editing and bioengineering of a large number of microorganisms.The SEVA repository has been developed and maintained with funds of the SYCOLIM [ERA-COBIOTECH 2018-PCI2019-111859-2] Project of the Spanish Ministry of Science and Innovation, SYNBIO4FLAV [H2020-NMBP-TR-IND/H2020-NMBP-BIO-2018-814650]; MIX-UP [MIX-UP H2020-BIO-CN-2019-870294] Contracts of the European Union; BIOSINT-CM [Y2020/TCS-6555] Project of the Comunidad de Madrid-European Structural and Investment Funds (FSE, FECER); P.I.N. acknowledges financial support by the Novo Nordisk Foundation [NNF20CC0035580, TARGET (NNF21OC0067996]; European Union's Horizon 2020 Research and Innovation Programme [814418 (SinFonia)]; M.H.H.N. acknowledges funding by the Novo Nordisk Foundation [NNF20CC0035580]; P.D. was funded by Czech Science Foundation Project 22-12505S; A.G.M. was supported by the Grants BioSinT-CM [Y2020/TCS-6555]; CONTEXT (Atracción de Talento Program) [2019-T1/BIO-14053] Projects of the Comunidad de Madrid, MULTI-SYSBIO [PID2020-117205GA-I00]; Severo Ochoa Program for Centres of Excellence in R&D [CEX2020-000999-S] funded by MCIN/AEI/10.13039/501100011033 and the ECCO (ERC-2021-COG-101044360) Contract of the EU. Funding for open access charge: European Commission Grant SYNBIO4FLAV [H2020-NMBP-TR-IND/H2020-NMBP-BIO-2018-814650].With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2020‐000999‐S) .Peer reviewe

Modelling co-translational dimerization for programmable nonlinearity in synthetic biology

8 Pág.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. This is largely due to a lack of mathematical modelling that accounts for the mechanistic basis of nonlinearity. We introduce a model for gene regulatory circuits that explicitly simulates protein dimerization-a well-known source of nonlinear dynamics. Specifically, our approach focuses on modelling co-translational dimerization: the formation of protein dimers during-and not after-translation. This is in contrast to the prevailing assumption that dimer generation is only viable between freely diffusing monomers (i.e. post-translational dimerization). We provide a method for fine-tuning nonlinearity on demand by balancing the impact of co- versus post-translational dimerization. Furthermore, we suggest design rules, such as protein length or physical separation between genes, that may be used to adjust dimerization dynamics in vivo. The design, build and test of genetic circuits with on-demand nonlinear dynamics will greatly improve the programmability of synthetic biological systems.This work was supported by the SynBio3D project of the UK Engineering and Physical Sciences Research Council (EP/R019002/1) and the European CSA on biological standardization BIOROBOOST (EU grant no. 820699). Á.G.-M. was also supported by grants from Comunidad de Madrid (Atraccion de Talento Program, grant no. 2019-T1/BIO-14053) and the Severo Ochoa Program for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain, grant no. SEV-2016-0672 (2017–2021).Peer reviewe

An electrogenetic toggle switch model

Special Issue: Microbial electrochemical technologies and Synthetic Biology. 14 Pág.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. We analyse the use of electrogenic processes for circuit design and present a model for a merged genetic and electrogenetic toggle switch operating in a biofilm attached to an electrode. Computational simulations explore conditions under which bistability emerges in order to identify the circuit design principles for best switch performance. The results provide a basis for the rational design and implementation of hybrid devices that can be measured and controlled both genetically and electronically.This work was supported by the grants BioSinT-CM (Y2020/TCS-6555) and CONTEXT (Atracción de Talento Program; 2019-T1/BIO-14053) Projects of the Comunidad de Madrid, MULTI-SYSBIO (PID2020-117205GA-I00) and the Severo Ochoa Program for Centres of Excellence in R&D (CEX2020-000999-S) from the Spanish MCIN/AEI /10.13039/501100011033, and the EPSRC studentship 2127432 (L.G.).With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2020‐000999‐S)Peer reviewe

A Network Approach to Genetic Circuit Designs

9 Pág. Centro de Biotecnología y Genómica de PlantasAs 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). Here, we present a method to transform circuit designs into networks and showcase its potential to enhance the utility of design data. Since networks are dynamic structures, initial graphs can be interactively shaped into subnetworks of relevant information based on requirements such as the hierarchy of biological parts or interactions between entities. A significant advantage of a network approach is the ability to scale abstraction, providing an automatic sliding level of detail that further tailors the visualization to a given situation. Additionally, several visual changes can be applied, such as coloring or clustering nodes based on types (e.g., genes or promoters), resulting in easier comprehension from a user perspective. This approach allows circuit designs to be coupled to other networks, such as metabolic pathways or implementation protocols captured in graph-like formats. We advocate using networks to structure, access, and improve synthetic biology information.This work was supported by the Grants BioSinT-CM (Y2020/TCS-6555) and CONTEXT (Atracción de Talento Program; 2019-T1/BIO-14053) Projects of the Comunidad de Madrid, MULTI-SYSBIO (PID2020-117205GA-I00) and the Severo Ochoa Program for Centres of Excellence in R&D (CEX2020-000999-S) funded by MCIN/AEI/10.13039/501100011033 and the EPSRC studentship 34000024085 (M.C.)Peer reviewe