Article
Biotechnology & Applied Microbiology
Xuekun Wang, Mario Andrea Marchisio
Summary: This study highlights the importance of coordinated, high-level, and stable expression of multiple genes for engineering biosynthetic circuits and metabolic pathways. The use of IRES and 2 A peptides allows for co-expression of various genes in polycistronic vectors, enabling reliable expression in eukaryotic cells. Ribosome-skipping events mediated by 2 A peptides facilitate the generation of multiple independent proteins from a single open reading frame.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xiaofan Feng, Mario Andrea Marchisio
Summary: New synthetic constitutive promoters for Saccharomyces cerevisiae were constructed and optimized by utilizing foreign core promoters as templates and manipulating the TATA box composition, leading to an expanded pool of yeast promoters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
News Item
Multidisciplinary Sciences
Philip Ball
Summary: A pair of studies highlight ethical and legal concerns surrounding the status of lab-grown human embryo models.
Article
Biotechnology & Applied Microbiology
Alexis Casas, Matthieu Bultelle, Charles Motraghi, Richard Kitney
Summary: cMatch is a software tool for reconstructing and identifying synthetic genetic constructs based on their modular structure and libraries of components. It addresses the quality control bottleneck in combinatorial pathway engineering problems and automates the construct-matching operation. Two algorithms are provided, which yield accurate results within a few minutes and provide metrics to improve the decision-making process.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Kangsan Kim, Minjeong Kang, Byung-Kwan Cho
Summary: In recent years, there has been increasing interest in gut commensal engineering for therapeutic applications. Recent advancements in synthetic biology and systems biology have enabled effective utilization of gut commensals for therapy and diagnosis, including the rational design of synthetic microbial consortia and the construction of synthetic cells that can detect specific signals in the intestine and deliver therapeutic drugs in real-time.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Editorial Material
Biochemical Research Methods
Michael B. Sheets, Joshua T. Atkinson, Mark P. Styczynski, Emily R. Aurand
Summary: As engineering biology continues to have increasing impacts, it is crucial to introduce the field early on in an accessible manner. However, teaching engineering biology faces challenges such as limited representation in widely used scientific textbooks or curricula, as well as its interdisciplinary nature. To address this, we have developed an adaptable curriculum module that provides a versatile slide deck designed by engineering biology experts to cover the fundamental principles and applications of the field. Free and accessible through a public website, this module can be used independently or integrated into existing curricula, aiming to enhance the ease of teaching current engineering biology topics and promote public engagement with the field.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemical Research Methods
Salva Duran-Nebreda, Jordi Pla, Blai Vidiella, Jordi Pinero, Nuria Conde-Pueyo, Ricard Sole
Summary: This article discusses the characteristics of multicellular entities and their spatial patterns related to functions, as well as the repeating distributions in biological structures. It introduces patterning modules and synthetic gene circuits, along with the phenomenon of symmetry-breaking demonstrated through experimental results.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Yuval Elani
Summary: The construction of artificial cells is a major challenge today, with potential applications in clinical and industrial settings. Artificial cells currently cannot match the complexity of biological cells, leading researchers to explore hybrid living/synthetic systems that combine the advantages of both.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Biochemistry & Molecular Biology
Bagrat A. Shainyan, Larisa Zhilitskaya, Nina O. Yarosh
Summary: This review focuses on the synthesis, structural modification, reaction mechanisms, and potential pharmacological activity of C-2-substituted benzothiazoles, including traditional multistep reactions and one-pot atom economy processes using green chemistry principles.
Article
Chemistry, Multidisciplinary
Layla Malouf, Diana A. Tanase, Giacomo Fabrini, Ryan A. Brady, Miguel Paez-Perez, Adrian Leathers, Michael J. Booth, Lorenzo Di Michele
Summary: This paper demonstrates how microphase separation can be used to engineer synthetic cells with programmable morphology and compartment-targeted activity. The synthetic cells are self-assembled from amphiphilic DNA nanostructures and can undergo lipid deposition and phase-selective etching to generate core-shell condensates, a porous pseudo-membrane, cytoplasm analog, and membrane-less organelles. The research exemplifies how architectural and functional complexity can emerge from a limited number of distinct building blocks.
Article
Biochemical Research Methods
Jing Wui Yeoh, Neil Swainston, Peter Vegh, Valentin Zulkower, Pablo Carbonell, Maciej B. Holowko, Gopal Peddinti, Chueh Loo Poh
Summary: Advances in hardware automation in synthetic biology laboratories have outpaced those in software development. The development of software solutions is crucial for automated laboratories to assist with specialized tasks. Many labs are independently developing similar software solutions, highlighting the need for standardized open-source software packages.
Review
Biotechnology & Applied Microbiology
Javad Aminian-Dehkordi, Shadi Rahimi, Mehdi Golzar-Ahmadi, Amritpal Singh, Javiera Lopez, Rodrigo Ledesma-Amaro, Ivan Mijakovic
Summary: Synthetic biology offers new solutions for environmental protection by developing remediation systems using genetically engineered microbes and plants, and utilizing computational methods for design and application to detect and respond to specific pollutants.
BIOTECHNOLOGY ADVANCES
(2023)
Article
Green & Sustainable Science & Technology
Indu Jatain, Kashyap Kumar Dubey, Manisha Sharma, Zeba Usmani, Minaxi Sharma, Vijai Kumar Gupta
Summary: Continuous combustion of fossil fuels leads to significant contribution of CO2 to climate change and global warming, posing a major concern for the future of our planet. Different biological CO2 fixation strategies are being employed to mitigate these challenges, with the use of synthetic biology tools to increase production efficiency and reduce atmospheric CO2 levels. These strategies offer a promising solution to both the increasing temperature concern and the improvement of renewable energy sources.
JOURNAL OF CLEANER PRODUCTION
(2021)
Article
Chemistry, Inorganic & Nuclear
Meghamala Sarkar, Ramamoorthy Boomishankar
Summary: This study reports the structures of two neutral tetrahedral cages and investigates the reaction pathway of their formation. The cages possess intrinsic cavities that can encapsulate various guest molecules, with a higher binding affinity for C6H5F and C6H6 compared to other halogenated guests.
INORGANIC CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Ana P. Teixeira, Pascal Stucheli, Simon Auslander, David Auslander, Pascal Schonenberger, Samuel Hurlemann, Martin Fussenegger
Summary: The researchers have developed an antibiotic-free selection system for generating stable transgenic cell lines, which utilizes cellobiose as the primary energy source. By combining this system with a PiggyBac transposase-based integration strategy, they were able to efficiently generate stable transgenic cell lines that expressed high levels of cargo proteins. This strategy was successfully validated by integrating sequences encoding two biopharmaceutical proteins, erythropoietin and the monoclonal antibody rituximab, and confirmed their efficient production in both cellobiose- and glucose-containing medium.
METABOLIC ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Ari Dwijayanti, Marko Storch, Guy-Bart Stan, Geoff S. Baldwin
Summary: This article introduces a modular artificial RNA interference method called mARi, which enables robust, portable and multiplexed post-transcriptional regulation in Escherichia coli. The study demonstrates the independence and extensibility of mARi and provides new insights into RNA-based regulation design in E. coli.
NUCLEIC ACIDS RESEARCH
(2022)
Editorial Material
Multidisciplinary Sciences
Claudia E. Vickers, Paul S. Freemont
Summary: Synthetic biology has been crucial in tackling the current pandemic, and biofoundries are essential infrastructure that should be accessible to all nations as part of their independent bioengineering, biosecurity, and countermeasure response systems.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Alexis Casas, Matthieu Bultelle, Charles Motraghi, Richard Kitney
Summary: cMatch is a software tool for reconstructing and identifying synthetic genetic constructs based on their modular structure and libraries of components. It addresses the quality control bottleneck in combinatorial pathway engineering problems and automates the construct-matching operation. Two algorithms are provided, which yield accurate results within a few minutes and provide metrics to improve the decision-making process.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Alexis Casas, Matthieu Bultelle, Charles Motraghi, Richard Kitney
Summary: PASIV is a newly developed workflow designed to address the practical problem of an impaired scoping phase in the design of experiments. By combining biology and software, it allows for the identification of the region of interest and has shown promising results in the lycopene pathway.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Joshua M. Lawrence, Yutong Yin, Paolo Bombelli, Alberto Scarampi, Marko Storch, Laura T. Wey, Alicia Climent-Catala, Geoff S. Baldwin, Danny O'Hare, Christopher J. Howe, Jenny Z. Zhang, Thomas E. Ouldridge, Rodrigo Ledesma-Amaro
Summary: This study developed a strong redox-responsive promoter and derived a mutant promoter library with varying strengths. Using these tools, researchers demonstrated the electrochemical activation of gene expression in electrogenetic systems, providing new means for the design and improvement of electrogenetics.
Editorial Material
Multidisciplinary Sciences
Thomas A. Dixon, Paul S. Freemont, Richard A. Johnson, Isak S. Pretorius
Summary: A Global Forum on Synthetic Biology is necessary to facilitate dialogue between policymakers and practitioners across borders and discuss future policies in the age of engineering biology.
NATURE COMMUNICATIONS
(2022)
Letter
Biotechnology & Applied Microbiology
Tim Mercer, Neil Almond, Michael A. Crone, Patrick S. G. Chain, Alina Deshpande, Deepa Eveleigh, Paul Freemont, Sebastien Fuchs, Russell Garlick, Jim Huggett, Martin Kammel, Po-E Li, Mojca Milavec, Elizabeth M. Marlowe, Denise M. O'Sullivan, Mark Page, Gary A. Pestano, Sara Suliman, Birgitte Simen, John J. Sninsky, Lynne Sopchak, Cristina M. Tato, Peter M. Vallone, Jo Vandesompele, Thomas J. White, Heinz Zeichhardt, Marc Salit
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Joan Herisson, Thomas Duigou, Melchior du Lac, Kenza Bazi-Kabbaj, Mahnaz Sabeti Azad, Gizem Buldum, Olivier Telle, Yorgo El Moubayed, Pablo Carbonell, Neil Swainston, Valentin Zulkower, Manish Kushwaha, Geoff S. Baldwin, Jean-Loup Faulon
Summary: Introduced the Galaxy-SynBioCAD portal, a toolshed for synthetic biology, metabolic engineering, and industrial biotechnology. The portal provides tools and workflows to facilitate the design and engineering process of metabolic pathways, from strain and target selection to DNA part design and plasmid assembly.
NATURE COMMUNICATIONS
(2022)
Correction
Multidisciplinary Sciences
William M. Shaw, Lucie Studena, Kyler Roy, Piotr Hapeta, Nicholas S. McCarty, Alicia E. Graham, Tom Ellis, Rodrigo Ledesma-Amaro
NATURE COMMUNICATIONS
(2023)
Review
Multidisciplinary Sciences
Xin Xu, Felix Meier, Benjamin A. Blount, Isak S. Pretorius, Tom Ellis, Ian T. Paulsen, Thomas C. Williams
Summary: This review explores the potential of genome minimization and re-functionalization approaches for industrial applications, highlighting the advantages of minimal genomes in terms of engineerability and biosynthetic capacity.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Huadong Peng, Ruiqi Chen, William M. Shaw, Piotr Hapeta, Wei Jiang, David J. Bell, Tom Ellis, Rodrigo Ledesma-Amaro
Summary: Microbial-derived aromatics provide a sustainable and renewable alternative to petroleum-derived chemicals. This study utilized synthetic biology and modular approaches to produce a valuable fragrance compound, raspberry ketone (RK), in the model yeast Saccharomyces cerevisiae. The strategies employed included modular cloning, modular pathway engineering, and modular cocultures, resulting in the production of high levels of RK and its precursor. This research highlights the importance and potential of modularity in synthetic biology for industrial applications.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemical Research Methods
William M. Shaw, Ahmad S. Khalil, Tom Ellis
Summary: Synthetic biology toolkits are important foundations for the field, facilitating the reprogramming of cells and organisms for various biotechnological applications. The yeast Saccharomyces cerevisiae has been widely used in the field and has benefited from toolkits like the MoClo Yeast Toolkit (YTK). However, YTK has limitations in creating new strains of yeast. The newly developed Multiplex Yeast Toolkit (MYT) addresses these limitations and provides additional tools for strain engineering, enabling yeast synthetic biologists to take their engineering ambitions to new levels.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemical Research Methods
Matthew C. Haines, Benedict Carling, James Marshall, Vasily A. Shenshin, Geoff S. Baldwin, Paul Freemont, Marko Storch
Summary: Standardized DNA assembly methods provide a powerful framework to explore designs and iterate. BASIC DNA assembly uses modular parts and linkers, is highly accurate and easy to automate. This study presents basicsynbio software for designing BASIC constructs with drag-and-drop or programming. The software allows exporting sequence data and creating instructions. Successful assembly of 30 vectors using SEVA modules was demonstrated using basicsynbio.
Article
Biochemical Research Methods
Jacob Beal, Cheryl A. Telmer, Alejandro Vignoni, Yadira Boada, Geoff S. Baldwin, Liam Hallett, Taeyang Lee, Vinoo Selvarajah, Sonja Billerbeck, Bradley Brown, Guo-nan Cai, Liang Cai, Edward Eisenstein, Daisuke Kiga, David Ross, Nina Alperovich, Noah Sprent, Jaclyn Thompson, Eric M. Young, Drew Endy, Traci Haddock-Angelli
Summary: This study extends the previous calibration protocols to include red fluorescence with sulforhodamine-101 fluorescent dye, and blue fluorescence with Cascade Blue. The interlaboratory study shows that these calibrants provide comparable precision to the previous ones and enable effective cross-laboratory comparison of red and blue fluorescence measurements.
