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
Edward Geeurickx, Lien Lippens, Pekka Rappu, Bruno G. De Geest, Olivier De Wever, An Hendrix
Summary: This study presents a protocol for using recombinant EV as a biological reference material to evaluate EV application performance, map technical variability, and promote inter-laboratory studies, which can be completed in about 4-5 days.
Article
Multidisciplinary Sciences
Luna Rizik, Loai Danial, Mouna Habib, Ron Weiss, Ramez Daniel
Summary: Researchers have utilized the perceptgene technology to create synthetic gene circuits based on the computational properties of neuronal networks. These circuits can perform non-binary logic computation and signal processing, and can be modified for different tasks by adjusting parameters.
NATURE COMMUNICATIONS
(2022)
Review
Biotechnology & Applied Microbiology
Brett J. Kagan, Christopher Gyngell, Tamra Lysaght, Victor M. Cole, Tsutomu Sawai, Julian Savulescu
Summary: This article reviews the key aspects of Synthetic Biological Intelligence (SBI), its potential applications, and the associated ethical concerns. It aims to provide a robust framework for the responsible research and application of SBI technology.
BIOTECHNOLOGY ADVANCES
(2023)
Article
Biochemistry & Molecular Biology
Bhavnita Soni, Shailza Singh
Summary: Macrophage phenotype plays a crucial role in the pathogenesis of Leishmanial infection, and the expression levels of cytokine signaling suppressors (SOCS) in correlation with the establishment of infection are not well understood. IL6 induces the expression of SOCS1 and SOCS3 through JAK-STAT signaling, and the immunological crosstalk between TLR2 and IL6 signaling pathways is established during the early stage of Leishmania major infection. Synthetic biology approaches can be used to target the activity of SOCS1 and restore pro-inflammatory cytokine expression during infection.
Review
Chemistry, Analytical
Changqing Mao, Yichun Mao, Xiaoli Zhu, Guifang Chen, Chang Feng
Summary: In recent years, synthetic biologists have developed biological elements and bioreactors composed of nucleotides using engineering methods. This paper reviews the biosensor components based on synthetic bioreactors and reporters, and discusses their applications in detecting heavy metal ions, nucleic acid, antibiotics, and other substances using cell and cell-free systems. It also examines the current bottlenecks faced by biosensors and potential directions for optimization.
CRITICAL REVIEWS IN ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Hector A. Plahar, Thomas N. Rich, Stephen D. Lane, William C. Morrell, Leanne Springthorpe, Oge Nnadi, Elena Aravina, Tiffany Dai, Michael J. Fero, Nathan J. Hillson, Christopher J. Petzold
Summary: The Web of Registries allows standalone ICE installations to securely connect and form a distributed parts database. Bioparts, a new search portal, combines the convenience of modern web search engines with the capabilities of bioinformatics search tools. It allows anyone to search for publicly accessible biological part information, including parts publicly accessible through ICE Registries.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemical Research Methods
Juan Ramon Melendez-Alvarez, Xiao-Jun Tian
Summary: The study revealed the existence of ultrasensitive growth feedback between cells and synthetic gene circuits. A mathematical model was developed to analyze the effect of ultrasensitive growth feedback on the host-circuit system. Bistability and high-order multistability were observed in different types of circuits. Understanding the impact of ultrasensitive growth feedback could help predict unexpected outcomes in gene circuits and formulate control strategies.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Alan Costello, Ahmed H. Badran
Summary: Researchers aim to control cellular behavior by reducing or eliminating unwanted interactions, in order to achieve reliable and predictable gene circuits and develop context-independent biological activities. Current focus is on biological orthogonalization, isolating researcher-specified bioactivities from host processes, with the potential to create an orthogonal central dogma and novel cellular functions.
TRENDS IN BIOTECHNOLOGY
(2021)
Article
History & Philosophy Of Science
Tarja Knuuttila, Rami Koskinen
Summary: The study focuses on two cases from synthetic biology that can be seen as concrete fictions, emphasizing their relative existence. Before their realizations, minimal cells and alternative genetic systems were not well-defined objects, and subsequent experimental work has enriched these initially schematic imaginings. It is uncertain whether individual members of these heterogeneous groups of functional synthetic constructs will eventually become fully realizable, partially realizable, or impossible.
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
Cell Biology
Mingxia Wang, Jinming Xu, Jialin Meng, Xinbo Huang
Summary: A novel gRNA design for rapid circular gRNA assembly inside cells is proposed in this study, which can effectively reduce off-target editing in the CRISPR system.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Hanrui Liu, Toni A. Baeumler, Kai Nakamura, Yuga Okada, Seojung Cho, Akihiro Eguchi, Daisuke Kuroda, Kouhei Tsumoto, Ryosuke Ueki, Shinsuke Sando
Summary: Cell membrane receptors play a crucial role in regulating cellular responses by detecting and transducing extracellular signals. Receptor engineering allows for directing cells to respond to specific external cues and perform programmed functions. This study introduces an aptamer-based signal transduction system that enables control and customization of engineered receptor functions.
Review
Biotechnology & Applied Microbiology
Chun-Qiang Li, Hong-Mei Lei, Qian-Yi Hu, Guo-Hong Li, Pei-Ji Zhao
Summary: The review outlines recent advances in synthetic biology of natural drugs, focusing on optimization and reconstruction of biosynthetic pathways for mass production of certain drugs. The study provides new strategies for large-scale preparation of rare natural plant metabolites and highly bioactive microbial compounds. Additionally, it discusses the potential advantages and disadvantages of using synthetic biology and various expression systems for heterologous expression of natural drugs.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Chemistry, Medicinal
Monica de Gaetano, Catherine Tighe, Kevin Gahan, Andrea Zanetti, Jianmin Chen, Justine Newson, Antonino Cacace, Mariam Marai, Andrew Gaffney, Eoin Brennan, Phillip Kantharidis, Mark E. Cooper, Xavier Leroy, Mauro Perretti, Derek Gilroy, Catherine Godson, Patrick J. Guiry
Summary: The failure to resolve inflammation underlies many prevalent pathologies. Lipid mediators like lipoxins have been identified as drivers of inflammation resolution, suggesting potential therapeutic benefit. The novel quinoxaline-containing synthetic-LXA(4)-mimetic (R)-6 shows potent anti-inflammatory properties, attenuating inflammatory responses both in vitro and in vivo.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Thomas O. Richardson, Thomas E. Gorochowski
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2015)
Article
Biochemistry & Molecular Biology
Thomas E. Gorochowski, Zoya Ignatova, Roel A. L. Bovenberg, Johannes A. Roubos
NUCLEIC ACIDS RESEARCH
(2015)
Article
Biochemical Research Methods
Jesus Fernandez-Rodriguez, Lei Yang, Thomas E. Gorochowski, D. Benjamin Gordon, Christopher A. Voigt
ACS SYNTHETIC BIOLOGY
(2015)
Review
Biochemistry & Molecular Biology
Thomas E. Gorochowski
SYNTHETIC BIOLOGY-BOOK
(2016)
Article
Biochemistry & Molecular Biology
Lauren B. A. Woodruff, Thomas E. Gorochowski, Nicholas Roehner, Tarjei S. Mikkelsen, Douglas Densmore, D. Benjamin Gordon, Robert Nicol, Christopher A. Voigt
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemical Research Methods
Bryan S. Der, Emerson Glassey, Bryan A. Bartley, Casper Enghuus, Daniel B. Goodman, D. Benjamin Gordon, Christopher A. Voigt, Thomas E. Gorochowski
ACS SYNTHETIC BIOLOGY
(2017)
Article
Biochemical Research Methods
Thomas E. Gorochowski, Irem Aycilar-Kucukgoze, Roel A. L. Bovenberg, Johannes A. Roubos, Zoya Ignatova
ACS SYNTHETIC BIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Thomas E. Gorochowski, Amin Espah Borujeni, Yongjin Park, Alec A. K. Nielsen, Jing Zhang, Bryan S. Der, D. Benjamin Gordon, Christopher A. Voigt
MOLECULAR SYSTEMS BIOLOGY
(2017)
Article
Multidisciplinary Sciences
Thomas E. Gorochowski, Claire S. Grierson, Mario di Bernardo
Article
Behavioral Sciences
Thomas Jahans-Price, Thomas E. Gorochowski, Matthew A. Wilson, Matthew W. Jones, Rafal Bogacz
FRONTIERS IN BEHAVIORAL NEUROSCIENCE
(2014)
Editorial Material
Biotechnology & Applied Microbiology
Thomas E. Gorochowski, Tom Ellis
NATURE BIOTECHNOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Thomas E. Gorochowski, Irina Chelysheva, Mette Eriksen, Priyanka Nair, Steen Pedersen, Zoya Ignatova
MOLECULAR SYSTEMS BIOLOGY
(2019)
Article
Multidisciplinary Sciences
Lewis Grozinger, Martyn Amos, Thomas E. Gorochowski, Pablo Carbonell, Diego A. Oyarzun, Ruud Stoof, Harold Fellermann, Paolo Zuliani, Huseyin Tas, Angel Goni-Moreno
NATURE COMMUNICATIONS
(2019)
Review
Biochemistry & Molecular Biology
Chris J. Myers, Jacob Beal, Thomas E. Gorochowski, Hiroyuki Kuwahara, Curtis Madsen, James Alastair McLaughlin, Goksel Misirli, Tramy Nguyen, Ernst Oberortner, Meher Samineni, Anil Wipat, Michael Zhang, Zach Zundel
BIOCHEMICAL SOCIETY TRANSACTIONS
(2017)