Review
Biochemical Research Methods
Koray Malci, Emma Watts, Tania Michelle Roberts, Jamie Yam Auxillos, Behnaz Nowrouzi, Heloisa Oss Boll, Cibele Zolnier Sousa do Nascimento, Andreas Andreou, Peter Vegh, Sophie Donovan, Rennos Fragkoudis, Sven Panke, Edward Wallace, Alistair Elfick, Leonardo Rios-Solis
Summary: As redesigning organisms using engineering principles in synthetic biology becomes increasingly important, the standardization of experimental methods and DNA parts is necessary. The synthetic biology community focusing on Saccharomyces cerevisiae has developed well-characterized toolkits that have been widely adopted. These toolkits, along with standardized assembly strategies, have greatly contributed to the rapid development of metabolic engineering and diagnostics applications. However, there is still a long way to go for the yeast community to utilize synthetic biology in more sophisticated applications like bioautomation.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Mathematical & Computational Biology
Hiroaki Kitano
Summary: Scientific discovery is a driving force in our civilization, and accelerating the speed of discoveries is crucial. Implementing scientific discovery using AI systems is necessary to break the limitations of current scientific practice.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2021)
Article
Biochemical Research Methods
Matthew W. Lux, Elizabeth A. Strychalski, Gary J. Vora
Summary: Reproducibility is a significant challenge in synthetic biology, and addressing this challenge is crucial for the advancement of the field and its potential societal benefits. Commitment from researchers and institutions through education, incentivization, and infrastructure investment is necessary for the successful adoption of reproducibility as a routine aspect of research and development.
Article
Biochemical Research Methods
Bryan A. Bartley
Summary: With the increasing automation and data-driven nature of synthetic biology, tools that aid researchers in implementing FAIR data management practices are necessary. Tyto, a lightweight Python tool, addresses the difficulty of adopting standardized annotation practices by providing support for controlled vocabularies in everyday scripting practice.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Irene Otero-Muras, Pablo Carbonell
Summary: Metabolic engineering involves optimizing processes from single-cell to fermentation to increase production of valuable chemicals. A systems approach has accelerated scaling from rapid prototyping to industrial production, with automated DNA assembly reducing time from conception to production. The success of metabolic engineering often relies on retrobiosynthetic protocols and dynamic regulation strategies assembled as genetic circuits in host strains.
METABOLIC ENGINEERING
(2021)
Article
Medicine, General & Internal
Gert J. H. Snel, Sharon Poort, Birgitta K. Velthuis, Vincent M. van Deursen, Christopher T. Nguyen, David Sosnovik, Rudi A. J. O. Dierckx, Riemer H. J. A. Slart, Ronald J. H. Borra, Niek H. J. Prakken
Summary: Automating cardiac function assessment using cardiac magnetic resonance imaging is faster and more reproducible than manual contour-tracing, but accurately tracing basal contours remains challenging. Comparing three automated post-processing software packages to manual assessment, it was found that Level 1 automation had wider limits of agreement compared to manual. However, in Level 2 automation, there was a balance between speed and accuracy, with more reliable software packages obtaining more accurate measurements.
Article
Management
Barbara Ribeiro, Robert Meckin, Andrew Balmer, Philip Shapira
Summary: This paper examines the impact of automation and digitalisation on scientific work practices, particularly mundane knowledge work in the field of synthetic biology. The study finds that despite the aim of simplifying work processes, automation and digitalisation contribute to the persistence of mundane work through amplification and diversification processes.
Article
Biochemical Research Methods
Kristoffer Bach Falkenberg, Vivienne Mol, Arrate Sainz de la Maza Larrea, Ivan Pogrebnyakov, Morten H. H. Norholm, Alex Toftgaard Nielsen, Sheila Ingemann Jensen
Summary: Versatile DNA assembly standards and well-characterized part libraries are crucial tools in synthetic biology. Despite limitations in vector standards for Gram-positive hosts, the ProUSER2.0 toolbox provides a standardized platform for creating shuttle vectors in Bacillus subtilis. This system is semi-compatible with previously developed standards and allows for efficient insertion of cargo sequences. Through thorough characterization of integration sites and promoters, the toolbox facilitates the construction of signal peptide libraries for industrial proteins. Overall, the ProUSER2.0 toolbox is a powerful and flexible framework for use in B. subtilis.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemical Research Methods
Ibrahim Aldulijan, Jacob Beal, Sonja Billerbeck, Jeff Bouffard, Gael Chambonnier, Nikolaos Ntelkis, Isaac Guerreiro, Martin Holub, Paul Ross, Vinoo Selvarajah, Noah Sprent, Gonzalo Vidal, Alejandro Vignoni
Summary: Synthetic biologists have made significant progress in modular assembly of genetic sequences and engineering biological systems. However, the current approach of entangling sequence and functionality hinders abstraction and design reuse. Functional Synthetic Biology aims to overcome these challenges by prioritizing function over sequence and enabling greater flexibility, predictability, and cost reduction.
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
Biology
Shinichi Nakagawa, Malgorzata Lagisz
Summary: Canadian policymakers are concerned about the potential threat of farmed Atlantic salmon infected with PRV to wild salmon populations in the Pacific Northwest. The findings of a study published in BMC Biology by Polinksi and colleagues, suggesting that PRV has little impact on sockeye salmon, are disputed by Mordecai and colleagues in a correspondence article. To resolve this dispute, a registered multi-lab replication with adversaries is recommended.
Review
Polymer Science
Vid Potocnik, Selestina Gorgieva, Janja Trcek
Summary: Bacterial cellulose (BC), produced by certain species of Komagataeibacter and Novacetimonas genera, has versatile applications in various fields. BC synthesis has been extensively studied at the molecular level, with Komagataeibacter xylinus serving as a model species. BC exhibits higher purity compared to plant-derived cellulose and can be modified in situ during its synthesis. The utilization of organic substrates and food waste by Komagataeibacter and Novacetimonas species aligns with sustainable practices. Additionally, genetic engineering tools have enabled further intervention in BC synthesis, leading to the development of novel living biomaterials.
Article
Computer Science, Information Systems
Raiane Coelho, Regina Braga, Jose Maria N. David, Victor Stroele, Fernanda Campos, Mario Dantas
Summary: This study proposes an architecture called BlockFlow, based on blockchain, provenance, and cloud infrastructure, to provide traceability and trust in collaborative scientific experiments. The architecture is implemented on Hyperledger and evaluated using a scenario of genomic sequencing. The study discusses the benefits of providing traceability and trust in collaborative scientific experimentation and addresses the heterogeneity of shared data.
JOURNAL OF GRID COMPUTING
(2022)
Article
Engineering, Multidisciplinary
Shaffee Mayoof, Hasan Alaswad, Sameer Aljeshi, Ahmed Tarafa, Wael Elmedany
Summary: This paper introduces a hybrid-circuits cloud-based platform that enables students to design, simulate, and model both analog and digital electronic systems. The platform is ranked as number one in Google search for electronic circuit cloud tools, integrating IoT and cloud-based tools.
AIN SHAMS ENGINEERING JOURNAL
(2021)
Review
Chemistry, Multidisciplinary
Vittorio Saggiomo
Summary: Despite being increasingly common in households, 3D printers are still seen as toys rather than laboratory equipment in many laboratories worldwide. This review aims to challenge this conservative viewpoint, focusing on fused deposition modeling printers and their application in laboratories. 3D printers have become cheaper and easier to use, making them one of the most versatile pieces of equipment in a laboratory.
Article
Biochemical Research Methods
Russel M. Vincent, Bradley W. Wright, Paul R. Jaschke
ACS SYNTHETIC BIOLOGY
(2019)
Article
Virology
Dominic Y. Logel, Paul R. Jaschke
Article
Biochemical Research Methods
Bradley W. Wright, Juanfang Ruan, Mark P. Molloy, Paul R. Jaschke
ACS SYNTHETIC BIOLOGY
(2020)
Review
Biotechnology & Applied Microbiology
Matthew J. McNulty, Yongao (Mary) Xiong, Kevin Yates, Kalimuthu Karuppanan, Jacob M. Hilzinger, Aaron J. Berliner, Jesse Delzio, Adam P. Arkin, Nancy E. Lane, Somen Nandi, Karen A. McDonald
Summary: This article highlights the assumption in space missions that the risk of spacecraft malfunction outweighs human system failure, but this assumption breaks down in longer duration exploration missions. It suggests using plants to produce pharmaceuticals to mitigate the risks in current space medical systems.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2021)
Article
Microbiology
Bradley W. Wright, Dominic Y. Logel, Mehdi Mirzai, Dana Pascovici, Mark P. Molloy, Paul R. Jaschke
Summary: By studying the proteomic and transcriptomic responses of Escherichia coli to Microviridae infections, this research provides insights into the host response mechanisms, such as membrane damage and remodeling, cellular chaperone activity, and lipoprotein processing. The upregulation of small heat shock proteins IbpA/B during infection and their potential role in viral infections are also highlighted.
Article
Virology
Ellina Trofimova, Paul R. Jaschke
Summary: PST is an automated command-line application that can detect and measure bacteriophage plaque sizes of different morphologies. It has shown compatibility with manual measurements and can be applied to a variety of lytic bacteriophages, making it valuable for the advancement of laboratory automation.
Article
Astronomy & Astrophysics
Aaron J. Berliner, Jacob M. Hilzinger, Anthony J. Abel, Matthew J. McNulty, George Makrygiorgos, Nils J. H. Averesch, Soumyajit Sen Gupta, Alexander Benvenuti, Daniel F. Caddell, Stefano Cestellos-Blanco, Anna Doloman, Skyler Friedline, Davian Ho, Wenyu Gu, Avery Hill, Paul Kusuma, Isaac Lipsky, Mia Mirkovic, Jorge Luis Meraz, Vincent Pane, Kyle B. Sander, Fengzhe Shi, Jeffrey M. Skerker, Alexander Styer, Kyle Valgardson, Kelly Wetmore, Sung-Geun Woo, Yongao Xiong, Kevin Yates, Cindy Zhang, Shuyang Zhen, Bruce Bugbee, Douglas S. Clark, Devin Coleman-Derr, Ali Mesbah, Somen Nandi, Robert M. Waymouth, Peidong Yang, Craig S. Criddle, Karen A. McDonald, Lance C. Seefeldt, Amor A. Menezes, Adam P. Arkin
Summary: The passage discusses the potential use of biotechnologies in a crewed mission to Mars, emphasizing the need for an integrated biomanufacturing plant. It outlines the goals and constraints guiding the design of such a plant, including modules for microbial resource utilization and production of necessary materials.
FRONTIERS IN ASTRONOMY AND SPACE SCIENCES
(2021)
Review
Genetics & Heredity
Bradley W. Wright, Mark P. Molloy, Paul R. Jaschke
Summary: The modern genome-scale methods have shown that gene overlap is widespread and functionally integrated in prokaryotic, eukaryotic, and viral genomes. This overlap can be utilized in bioengineering for building more robust synthetic strains. The authors focus on overlapping protein-coding and RNA-coding genes, highlighting their potential in controlling translation, compressing genetic constructs, and protecting against mutation in synthetic biology approaches.
NATURE REVIEWS GENETICS
(2022)
Article
Microbiology
Matthew J. McNulty, Aaron J. Berliner, Patrick G. Negulescu, Liber McKee, Olivia Hart, Kevin Yates, Adam P. Arkin, Somen Nandi, Karen A. McDonald
Summary: This study examines the use of bioregenerative technology for pharmaceutical production to address medical treatment vulnerabilities in longer-duration space exploration missions. By evaluating different pharmaceutical purification processing strategies and technologies, key areas for future development of pharmaceutical life support technology and improvement of assessment frameworks were identified.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Astronomy & Astrophysics
Anthony J. Abel, Aaron J. Berliner, Mia Mirkovic, William D. Collins, Adam P. Arkin, Douglas S. Clark
Summary: Studies have shown that photovoltaics-based power systems can provide sufficient and practical energy for manned outposts on Mars. The analysis suggests that these systems would require a relatively low carry-along mass and outperform alternatives over a significant portion of the planet's surface.
FRONTIERS IN ASTRONOMY AND SPACE SCIENCES
(2022)
Article
Multidisciplinary Sciences
Davian Ho, Georgios Makrygiorgos, Avery Hill, Aaron J. Berliner
Summary: NASA mission systems are often compared using an equivalent system mass (ESM) framework, but the existing methods and tools fail to consider the complexities of multiple transit and operations stages, as well as the reliability differences of underlying technologies. This study proposes an extension of ESM (xESM) that allows for a direct analysis and comparison of different mission systems.
Article
Biotechnology & Applied Microbiology
Georgios Makrygiorgos, Aaron J. Berliner, Fengzhe Shi, Douglas S. Clark, Adam P. Arkin, Ali Mesbah
Summary: This paper presents a framework using flow-map (de)compositions to learn the dynamic behavior of biochemical systems. Data-driven flow-map models are flexible and can be used to derive fast-to-evaluate surrogates for expensive computational models or reconstruct system dynamics via experimental observations. The approach is demonstrated for various benchmark systems and uncertainty quantification of a microbial electrosynthesis reactor.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Education & Educational Research
Aaron J. Berliner, Jake Hecla
Summary: To address the lack of familiarity with nuclear history among nuclear engineers and physicists, a special-topics course called NE290: Nuclear History, Politics, and Futures was designed and deployed. This course contextualizes the importance of nuclear field throughout its history and in current affairs. The course aims to instill a sense of respect for the scientific, technical, and sociological consequences of nuclear technology, as well as its dangers.
FRONTIERS IN EDUCATION
(2023)
Article
Multidisciplinary Sciences
Nils J. H. Averesch, Aaron J. Berliner, Shannon N. Nangle, Spencer Zezulka, Gretchen L. Vengerova, Davian Ho, Cameran A. Casale, Benjamin A. E. Lehner, Jessica E. Snyder, Kevin B. Clark, Lewis R. Dartnell, Craig S. Criddle, Adam P. Arkin
Summary: As interest in human space exploration grows, it is becoming increasingly important to develop a coherent and modern strategy for mission design and planning. Biotechnology has emerged as a promising approach to enhance the resilience, flexibility, and efficiency of missions by utilizing in situ resources and reclaiming resources from waste streams. This article outlines four primary mission classes on the Moon and Mars and discusses the challenges and benefits of integrating biomanufacturing into these missions. The advancements in space-related technology development are likely to have significant implications for creating a sustainable circular bioeconomy on Earth.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Jake Hecla, Erik J. Kambarian, Robert Tubbs, Carla McKinley, Aaron Berliner, Kayla Russell, Gabrielle Spatola, Jordan Chertok, Weston Braun, Natalia Hank, Courtney Marquette, Jennifer Betz, Terry Paik, Marie Chenery, Alex Cagan, Carl Willis, Tim Mousseau
Summary: This report presents the results of a two-year study on the internal and external contamination levels of Cs-137 and beta-emitters in the feral dog population near the Chernobyl nuclear power plant. The purpose was to assess the potential human radiation exposure from this contamination. The study found varying levels of contamination, with some animals having high Cs-137 body burdens, but no external exposure hazards were identified.
