PartsGenie: an integrated tool for optimising and sharing synthetic biology parts

AbstractSynthetic biology is typified by developing novel genetic constructs from the assembly of reusable synthetic DNA parts, which contain one or more features such as promoters, ribosome binding sites, coding sequences and terminators. While repositories of such parts exist to promote their reuse, there is still a need to design novel parts from scratch.PartsGenie, freely available at http://parts.synbiochem.co.uk, is introduced to facilitate the computational design of such synthetic biology parts. PartsGenie has been designed to bridge the gap between optimisation tools for the design of novel parts, the representation of such parts in community-developed data standards such as Synthetic Biology Open Language (SBOL), and their sharing in journal-recommended data repositories.Consisting of a drag-and-drop web interface, a number of DNA optimisation algorithms, and an interface to the well-used data repository JBEI ICE, PartsGenie facilitates the design, optimisation and dissemination of reusable synthetic biology parts through a single, integrated application. PartsGenie can therefore be used as a single, stand-alone tool, or integrated into larger synthetic biology pipelines that are being developed in the SYNBIOCHEM centre and elsewhere.

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A standard-enabled workflow for synthetic biology

Biochemical Society Transactions ◽

10.1042/bst20160347 ◽

2017 ◽

Vol 45 (3) ◽

pp. 793-803 ◽

Cited By ~ 24

Author(s):

Chris J. Myers ◽

Jacob Beal ◽

Thomas E. Gorochowski ◽

Hiroyuki Kuwahara ◽

Curtis Madsen ◽

...

Keyword(s):

Systems Biology ◽

Synthetic Biology ◽

Markup Language ◽

Design Tools ◽

Data Standards ◽

Data Repositories ◽

Simulation Tools ◽

Systems Biology Markup Language ◽

Visualization Tools ◽

Synthetic Biology Open Language

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.

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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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Design of Ribosome Binding Sites in Streptomyces coelicolor

Current Proteomics ◽

10.2174/1570164614666170724120325 ◽

2017 ◽

Vol 14 (4) ◽

Cited By ~ 1

Author(s):

Hong-Dou Luo ◽

Yang Tao ◽

Wen-Guang Wang ◽

Tao Lin ◽

Yue-Yue Wang ◽

...

Keyword(s):

Binding Sites ◽

Streptomyces Coelicolor ◽

Ribosome Binding ◽

Ribosome Binding Sites

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Tuning a bi-enzymatic cascade reaction in Escherichia coli to facilitate NADPH regeneration for ε-caprolactone production

Bioresources and Bioprocessing ◽

10.1186/s40643-021-00370-w ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Jinghui Xiong ◽

Hefeng Chen ◽

Ran Liu ◽

Hao Yu ◽

Min Zhuo ◽

...

Keyword(s):

Escherichia Coli ◽

Binding Sites ◽

Regeneration System ◽

Nadph Regeneration ◽

Whole Cell ◽

Cyclohexanone Monooxygenase ◽

Ribosome Binding ◽

Ribosome Binding Sites ◽

Whole Cell Biocatalyst ◽

Substrate Tolerance

Abstractε-Caprolactone is a monomer of poly(ε-caprolactone) which has been widely used in tissue engineering due to its biodegradability and biocompatibility. To meet the massive demand for this monomer, an efficient whole-cell biocatalytic approach was constructed to boost the ε-caprolactone production using cyclohexanol as substrate. Combining an alcohol dehydrogenase (ADH) with a cyclohexanone monooxygenase (CHMO) in Escherichia coli, a self-sufficient NADPH-cofactor regeneration system was obtained. Furthermore, some improved variants with the better substrate tolerance and higher catalytic ability to ε-caprolactone production were designed by regulating the ribosome binding sites. The best mutant strain exhibited an ε-caprolactone yield of 0.80 mol/mol using 60 mM cyclohexanol as substrate, while the starting strain only got a conversion of 0.38 mol/mol when 20 mM cyclohexanol was supplemented. The engineered whole-cell biocatalyst was used in four sequential batches to achieve a production of 126 mM ε-caprolactone with a high molar yield of 0.78 mol/mol.

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A method for mapping RNA initiation, termination, splice, and protein binding sites. Ribosome binding sites on beta-globin messenger RNA.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)32765-0 ◽

1983 ◽

Vol 258 (6) ◽

pp. 3991-3995

Author(s):

J R Patton ◽

C B Chae

Keyword(s):

Protein Binding ◽

Binding Sites ◽

Messenger Rna ◽

Beta Globin ◽

Protein Binding Sites ◽

Ribosome Binding ◽

Ribosome Binding Sites

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Expression of synthetic calcitonin genes in plasmid vectors containing tandemly repeated non-overlapping ribosome binding sites

International Journal of Biochemistry ◽

10.1016/0020-711x(89)90231-0 ◽

1989 ◽

Vol 21 (9) ◽

pp. 987-996 ◽

Cited By ~ 6

Author(s):

Krassimir Alexciev ◽

Anna Uscheva ◽

Maja Pavlova ◽

Libert Yavachev ◽

Ivan Ivanov

Keyword(s):

Binding Sites ◽

Plasmid Vectors ◽

Ribosome Binding ◽

Ribosome Binding Sites

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Chances and challenges of a long-term data repository in multiple sclerosis: 20th birthday of the German MS registry

Scientific Reports ◽

10.1038/s41598-021-92722-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Lisa-Marie Ohle ◽

David Ellenberger ◽

Peter Flachenecker ◽

Tim Friede ◽

Judith Haas ◽

...

Keyword(s):

Multiple Sclerosis ◽

Sociodemographic Factors ◽

Healthcare Research ◽

Structure Design ◽

Data Repository ◽

Research Projects ◽

Real World Data ◽

Data Repositories ◽

Term Data

AbstractIn 2001, the German Multiple Sclerosis Society, facing lack of data, founded the German MS Registry (GMSR) as a long-term data repository for MS healthcare research. By the establishment of a network of participating neurological centres of different healthcare sectors across Germany, GMSR provides observational real-world data on long-term disease progression, sociodemographic factors, treatment and the healthcare status of people with MS. This paper aims to illustrate the framework of the GMSR. Structure, design and data quality processes as well as collaborations of the GMSR are presented. The registry’s dataset, status and results are discussed. As of 08 January 2021, 187 centres from different healthcare sectors participate in the GMSR. Following its infrastructure and dataset specification upgrades in 2014, more than 196,000 visits have been recorded relating to more than 33,000 persons with MS (PwMS). The GMSR enables monitoring of PwMS in Germany, supports scientific research projects, and collaborates with national and international MS data repositories and initiatives. With its recent pharmacovigilance extension, it aligns with EMA recommendations and helps to ensure early detection of therapy-related safety signals.

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