Mobius Assembly for Plant Systems highlights promoter-terminator interaction in gene regulation

Plant synthetic biology is a fast-evolving field that employs engineering principles to empower research and bioproduction in plant systems. Nevertheless, in the whole synthetic biology landscape, plant systems lag compared to microbial and mammalian systems. When it comes to multigene delivery to plants, the predictability of the outcome is decreased since it depends on three different chassis: E.coli, Agrobacterium, and the plant species. Here we aimed to develop standardised and streamlined tools for genetic engineering in plant synthetic biology. We have devised Mobius Assembly for Plant Systems (MAPS), a user-friendly Golden Gate Assembly system for fast and easy generation of complex DNA constructs. MAPS is based on a new group of small plant binary vectors (pMAPs) that contains an origin of replication from a cryptic plasmid of Paracoccuspantotrophus. The functionality of the pMAP vectors was confirmed by transforming the MM1 cell culture, demonstrating for the first time that plant transformation is dependent on the Agrobacterium strains and plasmids; plasmid stability was highly dependent on the plasmid and bacterial strain. We made a library of new short promoters and terminators and characterised them using a high-throughput protoplast expression assay. Our results underscored the strong influence of terminators in gene expression, and they altered the strength of promoters in some combinations and indicated the presence of synergistic interactions between promoters and terminators. Overall this work will further facilitate plant synthetic biology and contribute to improving its predictability, which is challenged by combinatorial interactions among the genetic parts, vectors, and chassis.

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GondenBraid2.0: A comprehensive toolkit for plant synthetic biology

Planta Medica ◽

10.1055/s-0033-1351820 ◽

2013 ◽

Vol 79 (13) ◽

Author(s):

A Sarrion-Perdigones ◽

M Vazquez-Vilar ◽

J Palaci ◽

A Granell ◽

D Orzáez

Keyword(s):

Synthetic Biology ◽

Plant Synthetic Biology

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Probing the Substrate Promiscuity of Isopentenyl Phosphate Kinase as a Platform for Hemiterpene Analogue Production

10.26434/chemrxiv.7765241 ◽

2019 ◽

Author(s):

Sean Lund ◽

Taylor Courtney ◽

Gavin Williams

Keyword(s):

Synthetic Biology ◽

Building Blocks ◽

Isoprenoid Biosynthesis ◽

Thermoplasma Acidophilum ◽

Substrate Promiscuity ◽

Enzymatic Pathways ◽

First Time ◽

Rate Limiting ◽

Alcohol Dependent ◽

Isopentenyl Phosphate

Isoprenoids are a large class of natural products with wide-ranging applications. Synthetic biology approaches to the manufacture of isoprenoids and their new-to-nature derivatives are limited due to the provision in Nature of just two hemiterpene building blocks for isoprenoid biosynthesis. To address this limitation, artificial chemo-enzymatic pathways such as the alcohol-dependent hemiterpene pathway (ADH) serve to leverage consecutive kinases to convert exogenous alcohols to pyrophosphates that could be coupled to downstream isoprenoid biosynthesis. To be successful, each kinase in this pathway should be permissive of a broad range of substrates. For the first time, we have probed the promiscuity of the second enzyme in the ADH pathway, isopentenyl phosphate kinase from Thermoplasma acidophilum, towards a broad range of acceptor monophosphates. Subsequently, we evaluate the suitability of this enzyme to provide non-natural pyrophosphates and provide a critical first step in characterizing the rate limiting steps in the artificial ADH pathway.<br>

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Integrating virtual reality in qualitative research methods: Making a case for the VR-assisted interview

Methodological Innovations ◽

10.1177/20597991211030778 ◽

2021 ◽

Vol 14 (2) ◽

pp. 205979912110307

Author(s):

Dennis Mathysen ◽

Ignace Glorieux

Keyword(s):

Virtual Reality ◽

Social Science ◽

Social Science Research ◽

Science Research ◽

Structured Interview ◽

Good Effect ◽

Valuable Alternative ◽

Specialized Hardware ◽

User Friendly ◽

First Time

Virtual reality (VR) is still very much a niche technology despite its increasing popularity since recent years. VR has now reached a point where it can offer photorealistic experiences, while also being consumer-friendly and affordable. However, so far only a very limited amount of software has been developed for the specific purpose of conducting (social science) research. In this article, we illustrate that integrating virtual reality to good effect in social science research does not necessarily require specialized hardware or software, an abundance of expertise regarding VR-technology or even a large budget. We do this by discussing our use of a method we have come to call ‘VR-assisted interviews’: conducting a (semi-structured) interview while respondents are confronted with a virtual environment viewed via a VR-headset. This method allows respondents to focus on what they are seeing and experiencing, instead of having them worry about how to operate a device and navigate an interface they are using for the first time. ‘VR-assisted interviews’ are very user-friendly for respondents but also limits options for interactiveness. We believe this method can be a valuable alternative, both because of methodological and practical considerations, for more complex applications of VR-technology in social science research.

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Enabling plant synthetic biology through genome engineering

Trends in Biotechnology ◽

10.1016/j.tibtech.2014.11.008 ◽

2015 ◽

Vol 33 (2) ◽

pp. 120-131 ◽

Cited By ~ 131

Author(s):

Nicholas J. Baltes ◽

Daniel F. Voytas

Keyword(s):

Synthetic Biology ◽

Genome Engineering ◽

Plant Synthetic Biology

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Towards a sustainable bio-based economy: Redirecting primary metabolism to new products with plant synthetic biology

Plant Science ◽

10.1016/j.plantsci.2018.03.012 ◽

2018 ◽

Vol 273 ◽

pp. 84-91 ◽

Cited By ~ 10

Author(s):

Patrick M. Shih

Keyword(s):

Synthetic Biology ◽

New Products ◽

Primary Metabolism ◽

Plant Synthetic Biology

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The Multiplanetary Future of Plant Synthetic Biology

Genes ◽

10.3390/genes9070348 ◽

2018 ◽

Vol 9 (7) ◽

pp. 348 ◽

Cited By ~ 8

Author(s):

Briardo Llorente ◽

Thomas Williams ◽

Hugh Goold

Keyword(s):

Synthetic Biology ◽

Plant Synthetic Biology

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Streamlined Construction of the Cyanobacterial CO2-Fixing Organelle via Protein Domain Fusions for Use in Plant Synthetic Biology

The Plant Cell ◽

10.1105/tpc.15.00329 ◽

2015 ◽

Vol 27 (9) ◽

pp. 2637-2644 ◽

Cited By ~ 31

Author(s):

C. Raul Gonzalez-Esquer ◽

Tyler B. Shubitowski ◽

Cheryl A. Kerfeld

Keyword(s):

Synthetic Biology ◽

Protein Domain ◽

Plant Synthetic Biology

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SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts

Nucleic Acids Research ◽

10.1093/nar/gkz1024 ◽

2019 ◽

Vol 48 (D1) ◽

pp. D1164-D1170 ◽

Cited By ~ 17

Author(s):

Esteban Martínez-García ◽

Angel Goñi-Moreno ◽

Bryan Bartley ◽

James McLaughlin ◽

Lucas Sánchez-Sampedro ◽

...

Keyword(s):

Synthetic Biology ◽

Bacterial Species ◽

Web Based ◽

Genomic Engineering ◽

Bioinformatic Tools ◽

Synthetic Biology Open Language ◽

User Friendly ◽

Machine Readable ◽

Genetic Constructs

Abstract The Standard European Vector Architecture 3.0 database (SEVA-DB 3.0, http://seva.cnb.csic.es) is the update of the platform launched in 2013 both as a web-based resource and as a material repository of formatted genetic tools (mostly plasmids) for analysis, construction and deployment of complex bacterial phenotypes. The period between the first version of SEVA-DB and the present time has witnessed several technical, computational and conceptual advances in genetic/genomic engineering of prokaryotes that have enabled upgrading of the utilities of the updated database. Novelties include not only a more user-friendly web interface and many more plasmid vectors, but also new links of the plasmids to advanced bioinformatic tools. These provide an intuitive visualization of the constructs at stake and a range of virtual manipulations of DNA segments that were not possible before. Finally, the list of canonical SEVA plasmids is available in machine-readable SBOL (Synthetic Biology Open Language) format. This ensures interoperability with other platforms and affords simulations of their behaviour under different in vivo conditions. We argue that the SEVA-DB will remain a useful resource for extending Synthetic Biology approaches towards non-standard bacterial species as well as genetically programming new prokaryotic chassis for a suite of fundamental and biotechnological endeavours.

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Support of Operational Decisions for Prelude’s Side-by-Side LNG Offloading

Volume 1: Offshore Technology; Offshore Geotechnics ◽

10.1115/omae2019-96090 ◽

2019 ◽

Author(s):

Erwan Auburtin ◽

Thiago Miliante ◽

Ewoud van Haaften ◽

Finlay McPhail

Keyword(s):

Numerical Simulations ◽

Line Tension ◽

Mooring Line ◽

Base Case ◽

Liquefied Petroleum Gas ◽

Operational Decisions ◽

Weather Forecasts ◽

Dynamic Time ◽

User Friendly ◽

First Time

Abstract Prelude floating liquefied natural gas (FLNG) facility reached a significant milestone in June 2018 when gas was introduced onboard for the first time as part of the facility startup process, loaded from an LNG Carrier (LNGC) moored in side-by-side (SBS) configuration. This first offshore LNG SBS operation allowed Prelude’s utilities to switch from running on diesel to running on gas. SBS mooring is the base case configuration for offloading both LNG and Liquefied Petroleum Gas (LPG) into product carriers using Marine Loading Arms (MLA) once the Prelude FLNG facility is fully operational. These complex and weather sensitive operations are expected to take place on a weekly basis. This means critical decisions about weather-window and timing should be supported as much as possible by predictive analysis and modelling of forecast environment to reduce the risks. There are multiple criteria for evaluating the operability of LNGC or LPGC SBS offloading. These criteria cover the various phases of an operation, such as personnel transfer to the visiting carrier, Terminal Team Leader (TTL) transfer, spool fitting and fender lowering, approach and mooring, connection and testing of the loading arms, ramp-up of product transfer, full rate cargo transfer, loading arm purging and recovery, de-berthing, and people and hardware recovery. The criteria have been tailored to be appropriate to the phase of the operation. They comprise both environment-based criteria (maximum acceptable wind and waves conditions), and criteria related to motion or mooring (carrier roll, MLA envelope, mooring line tension, fender deflection). Motion and mooring criteria are evaluated through dynamic time-domain simulations. This allows an accurate modelling of non-linear effects, including mooring characteristics and partially filled cargo tanks. Thrusters can be used to control Prelude FLNG facility position if needed. The required thruster force to maintain the selected heading is calculated with frequency-domain calculation for all possible headings. This paper presents a visual reporting tool, developed by TechnipFMC in partnership with Shell. This tool has been used to support operational decisions during commissioning and startup, for SBS LNG and LPG import to Prelude FLNG facility. The daily reports used weather forecasts, in combination with numerical simulations, to predict the maximum motion and mooring criteria which contribute to determine both the timing and the decision to proceed with the operation. The format of the report has been designed to be user friendly for offshore operational staff, summarizing efficiently and in a visual manner the usage factors for each criterion separately. An overall operability is also presented for a quick overview. This paper also presents the details of numerical simulations, summarizes the different studies carried out to ensure the reliability of these simulations and discusses the possibilities for future development.

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