Review
Biochemical Research Methods
Martijn Diender, Ivette Parera Olm, Diana Z. Sousa
Summary: Synthetic microbial co-cultivation is an increasingly explored approach in biotechnology, which enhances the metabolic potential and process capabilities of microbes. The research findings suggest that co-cultivation can reduce undesired side reactions, promote microbial interactions, and open up new possibilities in areas like waste conversion.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Review
Biochemical Research Methods
Pei-Ru Chen, Peng-Fei Xia
Summary: Carbon dioxide plays a crucial role in mitigating global climate change and supporting life on Earth. Synthetic biology and metabolic engineering offer a promising approach to enhance CO2 fixation by combining the advantages of autotrophic and heterotrophic organisms. This article reviews the current progress in constructing synthetic CO2 fixation pathways, discusses the underlying design principles and challenges, and provides insights into the future of carbon recycling through engineered synthetic carbon fixation pathways.
CURRENT OPINION IN BIOTECHNOLOGY
(2024)
Article
Biochemistry & Molecular Biology
Fang Ba, Yushi Liu, Wan-Qiu Liu, Xintong Tian, Jian Li
Summary: Serine integrases are powerful tools in synthetic biology, and this study introduces a versatile method called SYMBIOSIS that can manipulate DNA parts both in vivo and in vitro. By proposing a 'keys match locks' model, the researchers demonstrate the ability of three orthogonal serine integrases to accurately switch on synthetic biobricks. They also show that purified integrases can facilitate plasmid assembly in vitro, leading to the creation of colored Escherichia coli.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biotechnology & Applied Microbiology
Govinda R. Navale, Mahesh S. Dharne, Sandip S. Shinde
Summary: Isoprenoids, also known as terpenoids, are diverse organic compounds found abundantly in nature, with various applications in pharmaceutical, nutraceutical, and chemical industries. Recent advancements in metabolic engineering have enabled the production of isoprenoids in heterologous host systems like Escherichia coli and Saccharomyces cerevisiae. Challenges and strategies for scale-up and engineering of isoprenoids in heterologous host systems have been discussed in detail.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Akshay J. Maheshwari, Jonathan Calles, Sean K. Waterton, Drew Endy
Summary: Using physics-based tools and evolutionary algorithms, the authors designed translation systems with different tRNA abundances, and successfully validated the expected outcomes through experiments.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Enrico Orsi, Nico J. Claassens, Pablo Nikel, Steffen N. Lindner
Summary: Synthetic biology has revolutionized the ability to redesign microbial metabolic networks by combining metabolic pathway-modularization with growth-coupled selection schemes. This powerful tool enables deep rewiring of cell factories' biochemistry for rational bioproduction.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Carolyn N. Bayer, Maja Rennig, Anja K. Ehrmann, Morten H. H. Norholm
Summary: The article introduces a simple genome engineering method called SEGA, which combines DNA and bacterial cells for synthesis, and then identifies recombinant clones through color change occurring on agar plates. The modular nature of SEGA allows for standardization of genetic designs and broad application range to be achieved.
NATURE COMMUNICATIONS
(2021)
Review
Biotechnology & Applied Microbiology
Jens Nielsen, Christian Brix Tillegreen, Dina Petranovic
Summary: Microbial fermentation plays a crucial role in sustainable production of food, chemicals, and natural products, with significant potential in new start-ups.
TRENDS IN BIOTECHNOLOGY
(2022)
Review
Nanoscience & Nanotechnology
Tzu-Chieh Tang, Bolin An, Yuanyuan Huang, Sangita Vasikaran, Yanyi Wang, Xiaoyu Jiang, Timothy K. Lu, Chao Zhong
Summary: Synthetic biology utilizes genetic tools to engineer living cells and organisms, similar to machine programming; materials synthetic biology integrates principles from synthetic biology and materials science to redesign living systems into dynamic and responsive materials.
NATURE REVIEWS MATERIALS
(2021)
Article
Multidisciplinary Sciences
Behzad D. Karkaria, Alex J. H. Fedorec, Chris P. Barnes
Summary: In naturally occurring microbial systems, there is a positive relationship between species diversity and community productivity; researchers performed model selection to discover potential amensal interactions that lead to robust stable synthetic microbial consortia.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Agris Pentjuss, Emils Bolmanis, Anastasija Suleiko, Elina Didrihsone, Arturs Suleiko, Konstantins Dubencovs, Janis Liepins, Andris Kazaks, Juris Vanags
Summary: This study focuses on optimizing the high-yield production of leghemoglobin protein and heme in Pichia pastoris by studying glycerol and methanol cultivation conditions, as well as using in-silico metabolic modeling analysis. The research suggests specific metabolic gene regulation strategies and provides recommendations for reaction regulation to increase heme production yields.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Phyana Litovco, Natalia Barger, Ximing Li, Ramez Daniel
Summary: The study demonstrates that indirect coherent feedforward loop and mutual inhibition designs can experimentally improve the fold change of promoters. Applying these designs to E. coli, up to ten times improvement in activation fold change was observed in multiple promoters.
NUCLEIC ACIDS RESEARCH
(2021)
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.
Article
Multidisciplinary Sciences
Puhua Niu, Maria J. Soto, Byung-Jun Yoon, Edward R. Dougherty, Francis J. Alexander, Ian Blaby, Xiaoning Qian
Summary: Extensive research has been done on predictive modeling of genome-scale metabolic reaction networks. Living systems involve complex stochastic processes, and for more accurate predictions, both metabolic reactions and genetic regulatory relationships should be modeled. TRIMER is a new modeling and simulation pipeline that integrates transcription regulation with metabolic regulation, demonstrating applicability to both simulated and experimental data.
Article
Multidisciplinary Sciences
Ryan T. Santilli, John E. Williamson, Yoshitaka Shibata, Rosalie P. Sowers, Andrew N. Fleischman, Song Tan
Summary: The Penn State Protein Ladder system produces protein molecular weight markers through plasmid expression in E. coli, allowing for easy migration, purification, and detection on SDS-PAGE gels. Additionally, polycistronic expression vectors have been designed for more efficient production and as positive controls for recombinant protein expression and purification in research laboratories.
SCIENTIFIC REPORTS
(2021)
Article
Engineering, Chemical
Yun Liu, Guangze Yang, Da Zou, Yue Hui, Krishna Nigam, Anton P. J. Middelberg, Chun-Xia Zhao
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2020)
Article
Multidisciplinary Sciences
Yue Hui, Xin Yi, David Wibowo, Guangze Yang, Anton P. J. Middelberg, Huajian Gao, Chun-Xia Zhao
Editorial Material
Immunology
Gregory A. Poland, Nicolette van Dijk, Danny Altmann, Ray Borrow, Ivan Hung, Ken Ishii, Steve Jacobsen, Florian Krammer, Heidi Larson, Linda Lua, Anton Middelberg, Jennifer Nelson, Kathy Neuzil, Hanna Nohynek, Art Reingold, Sylvia van den Hurk, Rick B. Kennedy, Sapna Sadarangani
Review
Biochemical Research Methods
Sathish Nadar, Gary Shooter, Balaji Somasundaram, Evan Shave, Kym Baker, Linda H. L. Lua
Summary: The article reviews the application of membrane-based technologies in the bioprocessing of monoclonal antibodies, focusing on the recent progress towards developing intensified end-to-end bioprocesses and the critical role membrane technology will play in achieving this goal. Membrane technologies show promise in fulfilling industry needs due to their operational flexibility and ease of implementation, especially as the industry moves towards continuous operations and single use processes.
BIOTECHNOLOGY JOURNAL
(2021)
Article
Biotechnology & Applied Microbiology
Lukas Gerstweiler, Jingxiu Bi, Anton Peter Jacob Middelberg
Summary: Expression of viral capsomeres in bacterial systems and their subsequent assembly into virus-like particles can be a cost-effective option for future vaccines. However, purification is challenging due to poor binding to chromatography media. This study shows that protein-DNA interactions in bacterial lysates can lead to the formation of complexes that hinder proper purification, but can be modulated by controlling ionic strength to enhance bind-elute behavior on salt-tolerant chromatography media. DNA-protein interactions negatively impact in vitro assembly, forming worm-like structures instead of virus-like particles. Controlling DNA-protein interactions is crucial for downstream viral vaccine process development.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Biochemical Research Methods
Lukas Gerstweiler, Jagan Billakanti, Jingxiu Bi, Anton Middelberg
Summary: The study optimized a purification strategy for modular virus-like particles and capsomeres, allowing efficient removal of contaminants without the need for size exclusion polishing chromatography step, while achieving high purity of the purified product.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Engineering, Chemical
Lukas Gerstweiler, Jingxiu Bi, Anton P. J. Middelberg
Summary: Continuous production offers higher productivity and better quality compared to traditional batch-wise approaches, but has not yet fully guided biomanufacturing industry to the 21st century advanced manufacturing status. Despite advancements in upstream processing, the lack of development in continuous processing for downstream operations remains a hindrance to modernization and process system integration. Hopeful advances in continuous chromatographic purification and other unit operations are on the horizon, signaling a turning point in process intensification research.
CHEMICAL ENGINEERING SCIENCE
(2021)
Article
Biochemical Research Methods
Kuok Yap, Junqiao Du, Fabian B. H. Rehm, Shyn Ric Tang, Yan Zhou, Jing Xie, Conan K. Wang, Simon J. de Veer, Linda H. L. Lua, Thomas Durek, David J. Craik
Summary: The protocol outlines a method for producing cyclic peptide precursors in Pichia pastoris that can be enzymatically matured into cyclic peptides, suitable for drug development and biotechnology applications. The process is versatile, allowing for the generation of cyclic peptides of varying classes and sizes, with production and purification taking approximately 24 days.
Article
Genetics & Heredity
Maci L. Mueller, John B. Cole, Natalie K. Connors, David J. Johnston, Imtiaz A. S. Randhawa, Alison L. Van Eenennaam
Summary: The study demonstrates that strong selection pressure on polled will be necessary due to the limited number of polled Australian Brahman bulls in order to significantly increase the number of polled animals in this population. Additionally, these scenarios illustrate how gene editing could be used as a tool to accelerate the development of high-genetic-merit homozygous polled sires in the Australian Brahman population to mitigate the trade-off of slower genetic gain associated with decreasing HORNED allele frequency.
FRONTIERS IN GENETICS
(2021)
Review
Biotechnology & Applied Microbiology
Manya Mittal, Manidipa Banerjee, Linda H. L. Lua, Anurag S. Rathore
Summary: Virus-like particles (VLPs) have great potential as vaccines, but face challenges in production. Continuous bioprocessing offers new opportunities for manufacturing VLPs. The biopharmaceutical industry is gradually shifting towards continuous production.
JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY
(2022)
Article
Engineering, Biomedical
Shuxiong Chen, Benjamin Evert, Adetayo Adeniyi, Merce Salla-Martret, Linda H. -L. Lua, Victoria Ozberk, Manisha Pandey, Michael F. Good, Andreas Suhrbier, Peter Halfmann, Yoshihiro Kawaoka, Bernd H. A. Rehm
Summary: The biopolymer particle (BP) vaccine technology offers a promising solution to the unmet need for safe and effective SARS-CoV-2 vaccines that can be produced at large scale. These vaccines, utilizing coronavirus antigen-coated BPs, have shown safety and immunogenicity in mice and induced protective immunity in a hamster SARS-CoV-2 infection model. The BP platform enables rapid design and cost-effective manufacture of ambient temperature stable vaccines to combat the COVID-19 pandemic.
ADVANCED HEALTHCARE MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Joanne L. Allard, Katherine A. Shields, Trent P. Munro, Linda H. L. Lua
Summary: Organophosphorus nerve agents pose a serious chemical threat due to their ease of production and large-scale impact. Current medical countermeasures are limited and prohibitively expensive. This review evaluates previous attempts and recent advances in producing a cost-effective bioscavenger using recombinant human butyrylcholinesterase, identifying potential strategies for achieving the desired efficacy and cost.
CHEMICO-BIOLOGICAL INTERACTIONS
(2022)
Article
Biotechnology & Applied Microbiology
Sathish Nadar, Balaji Somasundaram, Marcela Charry, Jagan Billakanti, Evan Shave, Kym Baker, Linda H. L. Lua
Summary: This study demonstrates that an optimized process development strategy can alleviate the capacity limitations of membrane chromatography in separating product-related variants. The results show that an optimized process consisting of anion exchange and cation exchange membrane chromatography can effectively reduce acidic variants and clear HCP.
BIOTECHNOLOGY PROGRESS
(2022)
Meeting Abstract
Biochemical Research Methods
M. L. Mueller, J. B. Cole, N. K. Connors, D. J. Johnston, I. A. S. Randhawa, A. L. Van Eenennaam
TRANSGENIC RESEARCH
(2020)
Article
Chemistry, Multidisciplinary
Kuok Yap, Junqiao Du, Fong Yang Looi, Shyn Ric Tang, Simon J. de Veer, Anuja R. Bony, Fabian B. H. Rehm, Jing Xie, Lai Yue Chan, Conan K. Wang, David J. Adams, Linda H. L. Lua, Thomas Durek, David J. Craik