Review
Biotechnology & Applied Microbiology
Roberto Di Blasi, Annalise Zouein, Tom Ellis, Francesca Ceroni
Summary: Construction of DNA-encoded programs is crucial in synthetic biology, with Golden Gate toolkits now dominating due to their modular design. Future advances include accessory packs for cloning toolkits to facilitate editing, orthogonality, advanced regulation, and integration into synthetic chromosome construction.
TRENDS IN BIOTECHNOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Camila Guindani, Lucas Caire da Silva, Shoupeng Cao, Tsvetomir Ivanov, Katharina Landfester
Summary: Bottom-up synthetic biology is the scientific approach of building systems that imitate the structure and function of living cells from the ground up. Recent developments have allowed scientists to engineer synthetic cells and organelles that mimic the essential functions and behaviors of natural cells.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Sudarshan Pinglay, Dylan P. Rahe, Emily Huang, Ran Brosh, Nicholas E. Mamrak, Benjamin R. King, Sergei German, John A. Cadley, Lila Rieber, Nicole Easo, Timothee Lionnet, Shaun Mahony, Matthew T. Maurano, Liam J. Holt, Esteban O. Mazzoni, Jef D. Boeke
Summary: Precise Hox gene expression is essential for embryonic patterning. This study utilizes synthetic regulatory reconstitution to study gene regulation and focuses on the HoxA cluster. The researchers synthesized and delivered variant rat HoxA clusters to an ectopic location in the mouse genome, and found that a minimal HoxA cluster could reproduce the correct patterns of chromatin remodeling and transcription in response to patterning signals, while the addition of distal enhancers was necessary for full transcriptional output.
Review
Biochemistry & Molecular Biology
J. Craig Venter, John I. Glass, Clyde A. Hutchison, Sanjay Vashee
Summary: Synthetic genomics involves synthesizing complete genomes or chromosomes to create viruses, bacteria, and eukaryotic cells. This field has revolutionized viral reverse genetics, vaccine design, and bacterial resistance. Future advances in DNA synthesis will open up extraordinary opportunities in medicine, industry, agriculture, and research.
Article
Biochemistry & Molecular Biology
Mariha Islam, Haixing P. Kehoe, Jacob B. Lissoos, Manjie Huang, Christopher E. Ghadban, Greg Berumen Sanchez, Hanan Z. Lane, James A. Van Deventer
Summary: The study demonstrates that antibody specificity can be mediated by a single complementarity determining region (CDR) while showing that the incorporation of noncanonical amino acids (ncAAs) is reasonably well tolerated. By introducing ncAAs into yeast displayed antibodies, small molecule functionality can be effectively introduced and protein-based covalent target binding can be evaluated.
ACS CHEMICAL BIOLOGY
(2021)
Review
Cell Biology
Maysam Mansouri, Martin Fussenegger
Summary: Cell therapy approaches utilizing engineered mammalian cells for on-demand production of therapeutic agents in the patient's body have advanced beyond proof-of-concept in translational medicine. Customized therapeutic cells can sense user-defined signals, process them, and respond programmably. Various methods of controlling cell behavior, including open-loop and closed-loop systems, are discussed, along with therapeutic applications of engineered cells in early disease diagnosis and treatment. Emerging technologies like digital devices also show potential for future incorporation into cell-based therapies.
Article
Biochemical Research Methods
Breschine Cummins, Justin Vrana, Robert C. Moseley, Hamed Eramian, Anastasia Deckard, Pedro Fontanarrosa, Daniel Bryce, Mark Weston, George Zheng, Joshua Nowak, Francis C. Motta, Mohammed Eslami, Kara Layne Johnson, Robert P. Goldman, Chris J. Myers, Tessa Johnson, Matthew W. Vaughn, Niall Gaffney, Joshua Urrutia, Shweta Gopaulakrishnan, Vanessa Biggers, Trissha R. Higa, Lorraine A. Mosqueda, Marcio Gameiro, Tomas Gedeon, Konstantin Mischaikow, Jacob Beal, Bryan Bartley, Tom Mitchell, Tramy T. Nguyen, Nicholas Roehner, Steven B. Haase
Summary: This article introduces an end-to-end sequence of tools called DART for the construction of synthetic genetic networks. DART covers the entire design-build-test-learn (DBTL) loop and provides rational selection and refinement of genetic parts. The Design Assemble (DA) part of DART improves previous techniques by screening thousands of network topologies using a novel robustness score and introduces experimental support software for genetic circuit assembly.
Article
Biochemistry & Molecular Biology
Hideyuki Nakanishi, Tatsuyuki Yoshii, Shunsuke Kawasaki, Karin Hayashi, Keita Tsutsui, Choji Oki, Shinya Tsukiji, Hirohide Saito
Summary: Two types of photo-controllable translational activation systems compatible with modRNAs have been developed, one consisting of a heterodimerization domain-fused split translational activator protein and a photocaged heterodimerizer, and the other consisting of a destabilizing domain-fused translational activator protein and a photocaged stabilizer. These systems not only enable translational activation but also translational repression of modRNAs, expanding the application of mammalian synthetic biology research.
CELL CHEMICAL BIOLOGY
(2021)
Article
Engineering, Electrical & Electronic
Jamie A. Davies
Summary: Synthetic morphogenesis is a new engineering discipline that genetically engineers cells to create designed shapes and structures. Devices in this field utilize natural shape-generating processes from embryonic development, but artificially manipulate them according to a technologist's preferences. Synthetic morphogenesis enables the construction of two-way interfaces between living organisms and electronic devices, facilitating unprecedented information flow and control.
PROCEEDINGS OF THE IEEE
(2022)
Article
Mathematical & Computational Biology
Michael A. Crone, James T. MacDonald, Paul S. Freemont, Velia Siciliano
Summary: In this study, a computational software pipeline called gDesigner was developed to automate the selection of orthogonal gRNAs and minimize off-target effects and promoter crosstalk. A repression system based on dLbCas12a was engineered, and a library of orthogonal synthetic dCas12a-repressed promoters was created and experimentally validated in various cell lines. This system expands the toolkit of mammalian synthetic promoters and enables the design of synthetic promoter libraries for multiplex gene perturbation, facilitating the understanding of complex cellular phenotypes.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2022)
Article
Biochemical Research Methods
Rajkamal Srivastava, Kathakali Sarkar, Deepro Bonnerjee, Sangram Bagh
Summary: In this study, a synthetic genetic reversible Feynman gate was constructed in single E. coli cells, and the input-output relations were measured. The behavior of the circuit was found to be ultrasensitive and predictive. An application of this reversible genetic system in sensing, diagnostics, cellular computing, and synthetic biology was demonstrated.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Dariusz Abramczyk, Maria del Carmen Sanchez Olmos, Adan Andres Ramirez Rojas, Daniel Schindler, Daniel Robertson, Stephen McColm, Adele L. Marston, Paul N. Barlow
Summary: A linear nanochromosome has been developed in K. phaffii, allowing for stable integration of multiple foreign genes and potentially facilitating cost-effective biomanufacturing.
MICROBIAL CELL FACTORIES
(2023)
Review
Materials Science, Biomaterials
Hui Lin, Liyun Zhang, Qiyue Zhang, Qiang Wang, Xue Wang, Guangqi Yan
Summary: This review provides an overview of the fabrication methods and clinical applications of 3D-printed biodegradable bioceramic scaffolds, as well as discussing their mechanisms and new developments. Biodegradable bioceramic materials hold great potential in bone repair applications and have a wide range of research and application prospects.
BIOMATERIALS SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Federica Cella, Ilaria De Martino, Francesca Piro, Velia Siciliano
Summary: This review discusses the tools implemented for engineering programmable RNA-based synthetic circuits in mammalian cells, highlighting the limitations of RNA-encoded gene delivery and significant studies that improved payload expression and delivery efficiency. The article also touches on examples of RNA-based therapeutics and future perspectives.
CURRENT OPINION IN SYSTEMS BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
R. A. Vasilev, V. Yu Chernikovich, M. A. Evteeva, D. A. Sakharov, M. Patrushev
Summary: Synthetic biology is a field that utilizes engineering approaches to develop predetermined cell behaviors based on theoretically constructed regulatory networks. Cells can be analogs of computers, performing basic functions through sensory, information processing, and response formation functions. Endogenous and exogenous factors trigger information processing cascades, leading to changes in transcriptional and metabolic profiles.
MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY
(2021)