Article
Biochemical Research Methods
Daniel Stukenberg, Tobias Hensel, Josef Hoff, Benjamin Daniel, Rene Inckemann, Jamie N. Tedeschi, Franziska Nousch, Georg Fritz
Summary: Vibrio natriegens, known for its incredibly fast growth rate, is being explored as a potential replacement for E. coli in synthetic and molecular biology applications. The Marburg Collection, consisting of 191 genetic parts optimized for V. natriegens, provides a flexible and efficient toolbox for researchers to construct plasmids using de novo assembly. This collection also includes novel connector parts for modular circuit assembly and the inversion of transcription units, offering valuable resources for the V. natriegens community.
ACS SYNTHETIC BIOLOGY
(2021)
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
Infectious Diseases
Qingqing Sun, Lixin Shen, Bai-Ling Zhang, Jiaoyang Yu, Fu Wei, Yanmei Sun, Wei Chen, Shiwei Wang
Summary: Since the discovery of bacteriophages in the early 20th century, their study has experienced fluctuations in interest due to the discovery and overuse of antibiotics. However, their application in therapy of antibiotic-resistant strains is currently a hot topic. Synthetic biology has greatly contributed to the understanding of phage evolution, engineering modification, and control of phage-bacteria interactions. This review comprehensively introduces strategies for engineering and modifying the phage genome, discusses recent research and potential directions in phage synthetic biology, and outlines current applications of engineered phages.
INFECTION AND DRUG RESISTANCE
(2023)
Article
Biochemical Research Methods
Ichiro Matsumura
Summary: This study demonstrates two methylase-assisted methods, the 4R/2M discontinuous DNA assembly and the 5RM continuous DNA assembly, which streamline the BioBrick assembly workflows and improve the efficiency and specificity of recombinant plasmids.
Article
Biotechnology & Applied Microbiology
Nicolas Daffern, Irene M. Francino-Urdaniz, Zachary T. Baumer, Timothy A. Whitehead
Summary: A standardized Golden Gate method for building user-defined libraries is presented, allowing the construction of large, deeply mutagenized protein encoding libraries. This method is efficient and capable of generating libraries with a high number of protein encoding variants. It can be applied to different protein engineering systems and provides general-use destination vectors and detailed protocols for other researchers.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Immunology
Hai Xu, Ling Li, Ruiting Li, Zijie Guo, Mengzhou Lin, Yu Lu, Jibo Hou, Roshini Govinden, Bihua Deng, Hafizah Y. Y. Chenia
Summary: This study developed a DNA vaccine delivery system based on DC-targeting phages, which efficiently expressed the HA2 antigen in DCs, induced enhanced immune responses, and demonstrated the potential of DC-targeting phages as DNA vaccine delivery vehicles.
FRONTIERS IN IMMUNOLOGY
(2022)
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.
Article
Chemistry, Medicinal
Aurelija M. Grigonyte, Alexia Hapeshi, Chrystala Constantinidou, Andrew Millard
Summary: By engineering phage T7 with lung tissue targeting homing peptides, in vitro studies demonstrated a significant increase in association with lung epithelium cells compared to wild-type T7. The results suggest that appending phages with homing peptides could potentially lead to greater phage concentrations and efficacy at infection sites.
Article
Biotechnology & Applied Microbiology
Aaron J. Hinz, Benjamin Stenzler, Alexandre J. Poulain
Summary: Microbial bioreporters provide insight into cellular processes by producing quantifiable signals. In this study, a system for constructing novel Escherichia coli bioreporters was developed using Golden Gate assembly. The constructed bioreporters can produce fluorescent or luminescent signals either constitutively or in response to specific exposures. The study highlights the importance and versatility of microbial bioreporters in environmental toxicology.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Review
Biochemical Research Methods
Bryan R. Lenneman, Jonas Fernbach, Martin J. Loessner, Timothy K. Lu, Samuel Kilcher
Summary: Genetic engineering can improve phage therapy by redirecting receptor-binding proteins and reprogramming phages as gene therapy vectors. Additionally, utilizing big data and artificial intelligence-driven approaches to design synthetic phages is a promising direction for future advancements in phage therapy.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Immunology
Tong Yu, Zhe Sun, Xiangyu Cao, Qiuxiang Pang, Hongkuan Deng
Summary: The T7 phage, which parasitizes Escherichia coli, is a virulent phage that poses no threat to animals and plants. With its advantages of small genome, well elucidated functional genomics, fast life cycle, and high stability, the T7 phage has been widely used in various fields, including biology and medicine. This review focuses on the research of T7 phages in biological sciences and medicine, including their application in the treatment and diagnosis of infectious diseases and tumor diseases. It also introduces the therapeutic application of T7 phage in various diseases and discusses the future direction of T7 phage application in the biomedical field.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2022)
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
Engineering, Biomedical
Jochen Estebano Hernandez Buecher, Oskar Staufer, Lukas Ostertag, Ulrike Mersdorf, Ilia Platzman, Joachim Pius Spatz
Summary: This article describes a bottom-up approach for the controlled assembly of fully-synthetic immune-inspired cells using predefined molecular components, reducing the complexity of the immune system. The study demonstrates the effectiveness of these synthetic immune cells through structural and functional characterization, providing new learning-by-building approaches in synthetic immunology.
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)