Hardware científico abierto y tecnologías libres

Sin tecnología no hay ciencia. El movimiento global por el hardware científico abierto (GOSH) plantea como punto de partida para imaginar un futuro diferente para la ciencia que los planos, protocolos y materiales de los instrumentos deben ser compartidos, a fin de que puedan replicarse. Esta activa y diversa comunidad nacida en 2016 ya ha realizado dos encuentros globales, cuenta con un Manifiesto y actualmente está en proceso de redacción de un Mapa de ruta para hacer el hardware científico abierto ubicuo para el 2025, mientras se prepara para un nuevo encuentro en 2018.Facultad de Informátic

Hardware científico abierto y tecnologías libres

Sin tecnología no hay ciencia. El movimiento global por el hardware científico abierto (GOSH) plantea como punto de partida para imaginar un futuro diferente para la ciencia que los planos, protocolos y materiales de los instrumentos deben ser compartidos, a fin de que puedan replicarse. Esta activa y diversa comunidad nacida en 2016 ya ha realizado dos encuentros globales, cuenta con un Manifiesto y actualmente está en proceso de redacción de un Mapa de ruta para hacer el hardware científico abierto ubicuo para el 2025, mientras se prepara para un nuevo encuentro en 2018.Facultad de Informátic

Intercellular adhesion promotes clonal mixing in growing bacterial populations

Dense bacterial communities, known as biofilms, can have functional spatial organization driven by self-organizing chemical and physical interactions between cells, and their environment. In this work, we investigated intercellular adhesion, a pervasive property of bacteria in biofilms, to identify effects on the internal structure of bacterial colonies. We expressed the self-recognizing ag43 adhesin protein in Escherichia coli to generate adhesion between cells, which caused aggregation in liquid culture and altered microcolony morphology on solid media. We combined the adhesive phenotype with an artificial colony patterning system based on plasmid segregation, which marked clonal lineage domains in colonies grown from single cells. Engineered E. coli were grown to colonies containing domains with varying adhesive properties, and investigated with microscopy, image processing and computational modelling techniques. We found that intercellular adhesion elongated the fractal-like boundary between cell lineages only when both domains within the colony were adhesive, by increasing the rotational motion during colony growth. Our work demonstrates that adhesive intercellular interactions can have significant effects on the spatial organization of bacterial populations, which can be exploited for biofilm engineering. Furthermore, our approach provides a robust platform to study the influence of intercellular interactions on spatial structure in bacterial populations.For this research, A.K. and T.J.R. were supported by the EC FP7project no. 612146 (PLASWIRES) awarded to J.P.H., A.K. has also been supported by a BBSRC CASE studentship in partnership with Microsoft Research, F.F. was supported by the UK Biotechnological and Biological Sciences Research Council (BBSRC) Synthetic Biology Research Centre ‘OpenPlant’ award (BB/L014130/1), CONICYT-PAI/Concurso Nacional de Apoyo al Retorno de Investigadores/as desde el Extranjero Folio 182130027, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation 1(15090007), Millennium Nucleus Center for Plant Systems and Synthetic Biology 1(NC130030) and Fondecyt Iniciación 111140776. T.J.R. has also been supported by Fondecyt Iniciación 11161046

Decentralizing Cell-Free RNA Sensing With the Use of Low-Cost Cell Extracts.

Cell-free gene expression systems have emerged as a promising platform for field-deployed biosensing and diagnostics. When combined with programmable toehold switch-based RNA sensors, these systems can be used to detect arbitrary RNAs and freeze-dried for room temperature transport to the point-of-need. These sensors, however, have been mainly implemented using reconstituted PURE cell-free protein expression systems that are difficult to source in the Global South due to their high commercial cost and cold-chain shipping requirements. Based on preliminary demonstrations of toehold sensors working on lysates, we describe the fast prototyping of RNA toehold switch-based sensors that can be produced locally and reduce the cost of sensors by two orders of magnitude. We demonstrate that these in-house cell lysates provide sensor performance comparable to commercial PURE cell-free systems. We further optimize these lysates with a CRISPRi strategy to enhance the stability of linear DNAs by knocking-down genes responsible for linear DNA degradation. This enables the direct use of PCR products for fast screening of new designs. As a proof-of-concept, we develop novel toehold sensors for the plant pathogen Potato Virus Y (PVY), which dramatically reduces the yield of this important staple crop. The local implementation of low-cost cell-free toehold sensors could enable biosensing capacity at the regional level and lead to more decentralized models for global surveillance of infectious disease

Loop assembly: a simple and open system for recursive fabrication of DNA circuits.

High efficiency methods for DNA assembly have enabled routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customisation, elaborate vector sets or serial manipulations for the different stages of assembly. We have developed Loop assembly based on a recursive approach to DNA fabrication. The system makes use of two Type IIS restriction endonucleases and corresponding vector sets for efficient and parallel assembly of large DNA circuits. Standardised level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets. The vectors also contain modular sites for hybrid assembly using sequence overlap methods. Loop assembly enables efficient and versatile DNA fabrication for plant transformation. We show construction of plasmids up to 16 genes and 38 Kb with high efficiency (>80%). We have characterized Loop assembly on over 200 different DNA constructs and validated the fidelity of the method by high-throughput Illumina plasmid sequencing. Our method provides a simple generalised solution for DNA construction with standardised parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access. This article is protected by copyright. All rights reserved.Support for the authors was provided by Becas Chile and the Cambridge Trust (to B.P.), University of Cambridge BBSRC DTP programme (to M.D.), and the Biotechnology and Biological Sciences Research Council and Engineering and Physical Sciences Research Council [OpenPlant Grant No. BB/L014130/1] (to N.P., F.F. and J.H.). Laboratory automation, nextgeneration sequencing and library construction was delivered via the BBSRC National Capability in Genomics (BB/CCG1720/1) at Earlham Institute. F.F. acknowledges funding from CONICYT Fondecyt Iniciación 11140776. F.F. and R.A.G. acknowledge funding from Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007) and Millennium Nucleus Center for Plant Systems and Synthetic Biology (NC130030)