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)
Article
Multidisciplinary Sciences
Tianchi Chen, M. Ali Al-Radhawi, Christopher A. Voigt, Eduardo D. Sontag
Summary: A design for genetically encoded counters using repressor-based circuits is proposed, allowing for scalable computation and bypassing limitations on maximal circuit genes per cell. The design utilizes distributed computation with specialized cell types and connector modules for interconnecting single-bit counters to achieve an N-bit counter. An optimization framework is used to determine gate parameters and guide the construction of novel gates, moving towards circuits capable of finite automaton computation akin to central processing units.
Article
Biochemistry & Molecular Biology
Julius D. D. Stuart, Natalie R. R. Wickenkamp, Kaleb A. A. Davis, Camden Meyer, Rebekah C. C. Kading, Christopher D. D. Snow
Summary: Synthetic DNA barcodes are designed to carry recoverable information and can track objects and organisms. These barcodes offer robust detection using standard techniques and can be constructed from smaller interchangeable blocks. Using this modular approach, we can generate barcode libraries with less dependency on external entities. Next generation sequencing allows for high-throughput detection of multiple samples, demonstrating the multiplexing capability of the modular barcode design.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Kevin Jahnke, Vanessa Huth, Ulrike Mersdorf, Na Liu, Kerstin Goepfrich
Summary: In this study, artificial DNA-based cytoskeletons with programmed multifunctionality were assembled inside synthetic cells using light-controlled assembly and disassembly. By using molecular crowders, ordered bundling of DNA filaments and formation of ring-like cortical structures similar to actin rings during cell division were achieved. Additionally, DNA filaments were programmably linked to the compartment periphery using cholesterol-tagged DNA and were able to deform GUVs from within.
Review
Biology
Stefano Rosa, Chiara Bertaso, Paolo Pesaresi, Simona Masiero, Andrea Tagliani
Summary: Protein-protein interactions play a key role in regulating cell physiology and metabolism. By utilizing protein domains in genetic circuits, synthetic biology has enabled the design of circuits that can impact transcriptional outputs and cellular metabolism, with potential applications in biosensing and diagnostics. Additionally, engineered PPIs can be utilized in the development of new drugs targeting specific cellular and extracellular proteins.
Article
Biochemistry & Molecular Biology
Meghan D. J. Bragdon, Nikit Patel, James Chuang, Ethan Levien, Caleb J. Bashor, Ahmad S. Khalil
Summary: This study demonstrates that high regulatory specificity can be achieved through cooperative multivalent interactions among artificial zinc-finger-based transcription factors. This mechanism effectively prevents aberrant misregulation of the host cell genome, resulting in genetic and functional stability of synthetic gene circuits.
Editorial Material
Oncology
Krishneel Prasad, Ryan S. Cross, Misty R. Jenkins
Summary: Synthetic biology has allowed for rewiring natural cellular responses to treat disease, as exemplified by CAR T cells as immunotherapy for cancer. Current research focuses on using noncanonical signaling pathways and synthetic gene circuitry to enhance the antitumor properties of engineered T cells. Two recent studies explore how these new technologies can achieve this goal, one using machine learning to predict CAR T cell phenotype and the other engineering controllable transcriptional regulators using synthetic zinc fingers. These studies expand the possibilities for future gene circuits and demonstrate how cellular therapy can respond to various environmental cues.
MOLECULAR ONCOLOGY
(2023)
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
Multidisciplinary Sciences
Oskar Staufer, Franziska Dietrich, Rahul Rimal, Martin Schroeter, Sebastian Fabritz, Heike Boehm, Smriti Singh, Martin Moeller, Ilia Platzman, Joachim Pius Spatz
Summary: Extracellular vesicles play a crucial role in intercellular communication and cell physiology, but quantitative knowledge on their signaling mechanisms is lacking, hampering their therapeutic applications. By using a synthetic approach, researchers have shown that synthetic EVs have functionalities similar to natural EVs and can be used for therapeutic purposes in wound healing and neovascularization. Transcriptome profiling has enabled a systematic decoding of synergistic effects between individual EV constituents, leading to a better understanding of EV signaling.
Review
Cell Biology
Harold M. McNamara, Beatrice Ramm, Jared E. Toettcher
Summary: Technological advances have contributed to recent developments in developmental biology, such as light sheet imaging for studying single-cell dynamics and single-cell genomic methods for cataloguing cell types and gene expression states. Synthetic approaches are also emerging to understand development processes from the bottom up, including synthetic circuits for signaling delivery and recording, and synthetic reconstitution of pattern formation on multicellular scales.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Review
Plant Sciences
Savio S. Ferreira, Mauricio S. Antunes
Summary: Efforts to manipulate the biosynthesis of phenylpropanoids for various applications have faced challenges such as pathway complexity and metabolic burden. The use of biosensors and genetic circuits could be a promising approach to dynamically regulate the metabolic status of the pathway and enhance the development of phenylpropanoid-producing plant biofactories in plant synthetic biology.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Immunology
Daniel Hoces, Jesus Miguens Blanco, Rogelio A. Hernandez-Lopez
Summary: A synthetic circuit involves assembling genetic elements, biomolecules, or cells to create a defined function. In cancer therapeutics, engineering T cells with circuits has the potential to overcome current challenges by allowing specific targeting and killing of cancer cells.
IMMUNOLOGICAL REVIEWS
(2023)
Review
Chemistry, Multidisciplinary
Qiwen Wang, Zhehui Hu, Zhixuan Li, Tiangang Liu, Guangkai Bian
Summary: Engineered living materials (ELMs) represent a significant paradigm shift in material design, possessing unique living attributes and unprecedented potential in various fields. This review provides an overview of the latest research progress and design strategies for ELMs derived from bacteria, fungi, and plants, and offers valuable references for future ELM design and application. The investigation into synergistic application possibilities among different species of ELMs provides beneficial information for researchers and practitioners in this field.
ADVANCED MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Desiree Sauter, Martin Schroeter, Christoph Frey, Cornelia Weber, Ulrike Mersdorf, Jan-Willi Janiesch, Ilia Platzman, Joachim P. Spatz
Summary: This study introduces a method for assembling an artificial cytoskeleton in a synthetic cell model system, and investigates the temperature-mediated contraction/release behavior of the cytoskeleton. The results show that the deformation induced by hydrogel can be used to controllably manipulate the motility of droplet-based synthetic cells.
MACROMOLECULAR BIOSCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Rosanna Young, Matthew Haines, Marko Storch, Paul S. Freemont
Summary: Synthetic Biology is a rapidly growing interdisciplinary field that considers living systems as programmable at the genetic level, defining new platform technologies and methodological advances. A key concept driving the field is the Design-Build Test-Learn cycle, which provides a systematic framework for building new biological systems, with a major application area being biosynthetic pathway engineering requiring modular assembly of genetic elements and enzymes.
METABOLIC ENGINEERING
(2021)
Article
Biophysics
Kyung Hyuk Kim, Herbert M. Sauro
BIOPHYSICAL JOURNAL
(2011)
Editorial Material
Biology
Kyung Hyuk Kim, Herbert M. Sauro
Article
Chemistry, Physical
Kyung Hyuk Kim, Hong Qian, Herbert M. Sauro
JOURNAL OF CHEMICAL PHYSICS
(2013)
Article
Biotechnology & Applied Microbiology
Wilbert B. Copeland, Bryan A. Bartley, Deepak Chandran, Michal Galdzicki, Kyung H. Kim, Sean C. Sleight, Costas D. Maranas, Herbert M. Sauro
METABOLIC ENGINEERING
(2012)
Editorial Material
Multidisciplinary Sciences
Herbert M. Sauro, Kyung Hyuk Kim
Letter
Biotechnology & Applied Microbiology
Jean Peccoud, J. Christopher Anderson, Deepak Chandran, Douglas Densmore, Michal Galdzicki, Matthew W. Lux, Cesar A. Rodriguez, Guy-Bart Stan, Herbert M. Sauro
NATURE BIOTECHNOLOGY
(2011)
Article
Biochemistry & Molecular Biology
Song Yang, Sean C. Sleight, Herbert M. Sauro
NUCLEIC ACIDS RESEARCH
(2013)
Article
Multidisciplinary Sciences
Michal Galdzicki, Cesar Rodriguez, Deepak Chandran, Herbert M. Sauro, John H. Gennari
Article
Biochemical Research Methods
Deepak Chandran, Herbert M. Sauro
ACS SYNTHETIC BIOLOGY
(2012)
Article
Biochemical Research Methods
Sean C. Sleight, Herbert M. Sauro
ACS SYNTHETIC BIOLOGY
(2013)
Article
Biochemical Research Methods
Dagmar Waltemath, Richard Adams, Daniel A. Beard, Frank T. Bergmann, Upinder S. Bhalla, Randall Britten, Vijayalakshmi Chelliah, Michael T. Cooling, Jonathan Cooper, Edmund J. Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter Hunter, Edda Klipp, Camille Laibe, Andrew K. Miller, Ion Moraru, David Nickerson, Poul Nielsen, Macha Nikolski, Sven Sahle, Herbert M. Sauro, Henning Schmidt, Jacky L. Snoep, Dominic Tolle, Olaf Wolkenhauer, Nicolas Le Novere
PLOS COMPUTATIONAL BIOLOGY
(2011)
Article
Biochemical Research Methods
Kyung H. Kim, Herbert M. Sauro
PLOS COMPUTATIONAL BIOLOGY
(2012)
Proceedings Paper
Automation & Control Systems
Kyung Hyuk Kim, Herbert M. Sauro
2012 IEEE 51ST ANNUAL CONFERENCE ON DECISION AND CONTROL (CDC)
(2012)
Proceedings Paper
Computer Science, Software Engineering
Natasa Miskov-Zivanov, James R. Faeder, Chris J. Myers, Herbert M. Sauro
2012 IEEE/ACM INTERNATIONAL CONFERENCE ON COMPUTER-AIDED DESIGN (ICCAD)
(2012)