Review
Plant Sciences
Debao Huang, Pawel Z. Kosentka, Wusheng Liu
Summary: Recent advances in plant synthetic biology have focused on regulating gene expression at various levels including transcription, mRNA stability, translation, and protein degradation. These developments provide a solid foundation for functional genomics research and crop trait improvement.
CURRENT OPINION IN PLANT BIOLOGY
(2021)
Article
Biochemical Research Methods
Jonas Kretz, Vera Israel, Matthew McIntosh
Summary: Inducible gene expression is valuable for biotechnological applications and gene regulation studies in bacteria. However, many systems that work well in model organisms like Escherichia coli show poor performance in other biotechnologically relevant bacteria due to weak or leaky expression. To address this, a new invention named ACIT (Alphaproteobacteriahromosomally integrating transcription-control cassette) is described, which allows tight transcription control over any gene or gene cluster of interest through homologous recombination.
ACS SYNTHETIC BIOLOGY
(2023)
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.
Article
Biochemical Research Methods
Zhou Guo, Hongyi Yin, Lu Ma, Jieyi Li, Jiajun Ma, Yi Wu, Yingjin Yuan
Summary: The method of transferring and consolidating synthetic yeast chromosomes through abortive mating and chromosome elimination provides a novel route for large DNA assembly in donor yeast and direct transfer to receptor yeast, enriching the tools for synthetic genomics manipulation.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Zhou Guo, Hongyi Yin, Lu Ma, Jieyi Li, Jiajun Ma, Yi Wu, Yingjin Yuan
Summary: The transfer and consolidation of synthetic yeast chromosomes have been achieved through abortive mating and chromosome elimination. This provides a new route for assembling large DNA in the donor yeast and directly transferring it to the receptor yeast, enriching the manipulation tools for synthetic genomics.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biology
Lucy Ham, Marcel Jackson, Michael P. H. Stumpf
Summary: Single-cell expression profiling reveals extensive cell-to-cell variability at the transcriptomic and proteomic level, posing challenges in inferring dynamics and causes of variability. New mathematical models and experimental set-ups are proposed to distinguish intrinsic and extrinsic noise, providing insights into understanding the origins and effects of cell-to-cell variability.
Review
Biotechnology & Applied Microbiology
Natalie Chia, Sang Yup Lee, Yaojun Tong
Summary: Optogenetics technique provides a solution to chemical induction with dynamic control and low cost. It utilizes genetically encodable light-sensing modules to fine tune gene expression and protein activity. Recent advancements in microbial synthetic biology have been achieved, but more portable optogenetic tools need to be developed.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Computer Science, Hardware & Architecture
Mohamed Ibrahim, Zhanwei Zhong, Bhargab B. Bhattacharya, Krishnendu Chakrabarty
Summary: Microfluidic platforms play a crucial role in studying synthetic biology by emulating complex molecular networks on a chip. This article proposes a comprehensive framework called BioScan for implementing biocircuit-regulatory scanning assays, which enable the exploration of biocircuit parameters. The framework includes statistical methods, high-level synthesis, translation techniques, and a regressor to construct the parameter space. Simulation results demonstrate that the framework efficiently explores the parameter space while reducing completion time and reagent cost.
IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS
(2022)
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.
Review
Biotechnology & Applied Microbiology
Sai Sumanjali Yarra, Ganapathy Ashok, Utpal Mohan
Summary: Toehold switches are newly designed riboregulators with two RNA components and linear-linear RNA interactions, providing regulation of gene expression. They are highly versatile, orthogonal, programmable, and find applications in various fields of synthetic biology.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Physics, Fluids & Plasmas
F. E. Garbuzov, V. V. Gursky
Summary: A study on short-range repression mechanisms of transcription factors is presented, introducing a nonequilibrium model using graph formalism for transitions between gene states. The new model outperforms the equilibrium model in analyzing gene regulatory regions, allowing separation of two basic mechanisms of short-range repression. It displays better performance in predicting gene expression data for transcription factors controlling Drosophila development, suggesting the first repression mechanism is the most favorable in this system.
Review
Chemistry, Physical
Claire Husser, Natacha Dentz, Michael Ryckelynck
Summary: RNA plays a crucial role in cell life, particularly in gene expression regulation. Riboswitches, as cis-acting molecules, are able to specifically sense a target ligand and control the expression of downstream genes without the need for cellular factors, making them highly portable and potentially useful in various applications such as gene therapy and biosensing of small molecules.
Article
Biochemistry & Molecular Biology
Jingwen Zhu, Pan Chu, Xiongfei Fu
Summary: Global regulation of cell growth rate on gene expression perturbs gene networks and impacts cell-fate determination. Using a synthetic circuit, researchers discovered that growth rates can induce a bifurcation in the landscape, leading to changes in cell-fate decisions. This bifurcation is caused by unbalanced gene expression response to growth variations. These findings highlight the importance of growth regulation in cell-fate determination processes.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Ana P. Teixeira, Pascal Stucheli, Simon Auslander, David Auslander, Pascal Schonenberger, Samuel Hurlemann, Martin Fussenegger
Summary: The researchers have developed an antibiotic-free selection system for generating stable transgenic cell lines, which utilizes cellobiose as the primary energy source. By combining this system with a PiggyBac transposase-based integration strategy, they were able to efficiently generate stable transgenic cell lines that expressed high levels of cargo proteins. This strategy was successfully validated by integrating sequences encoding two biopharmaceutical proteins, erythropoietin and the monoclonal antibody rituximab, and confirmed their efficient production in both cellobiose- and glucose-containing medium.
METABOLIC ENGINEERING
(2022)
Review
Biotechnology & Applied Microbiology
Bozhidar-Adrian Stefanov, Martin Fussenegger
Summary: Current clinical therapies for chronic diseases carry the risk of under or overdosing, leading to ineffective treatment or undesirable side effects. To provide personalized treatment, synthetic systems that can generate calibrated therapeutic responses are necessary. These closed-loop devices should incorporate sensors to track disease severity and evaluate treatment effectiveness, as well as components for bio computing and delivering appropriate therapeutic outputs.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Alvaro Banderas, Mihaly Koltai, Alexander Anders, Victor Sourjik
NATURE COMMUNICATIONS
(2016)
Article
Biochemistry & Molecular Biology
Doreen Blueher, Annekathrin Reinhardt-Tews, Martin Hey, Hauke Lilie, Ralph Golbik, Karin D. Breunig, Alexander Anders
BIOLOGICAL CHEMISTRY
(2014)
Article
Biochemistry & Molecular Biology
Mandy Jeske, Bodo Moritz, Alexander Anders, Elmar Wahle
Article
Multidisciplinary Sciences
Alexander Anders, Bhaswar Ghosh, Timo Glatter, Victor Sourjik
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Alexander Anders, Remy Colin, Alvaro Banderas, Victor Sourjik
Summary: Studying yeast, it was found that different mating types exhibited asymmetrical responses in pheromone secretion, leading to enhanced mating efficiency and potential selective advantage.
Article
Biochemistry & Molecular Biology
Alexander Anders, Hauke Lilie, Kathlen Franke, Lutz Kapp, Joerg Stelling, Ernst D. Gilles, Karin D. Breunig
JOURNAL OF BIOLOGICAL CHEMISTRY
(2006)