Review
Biotechnology & Applied Microbiology
Sant Kumar, Mustafa Khammash
Summary: Harnessing the potential of optogenetics in biology requires methodologies from different disciplines and suitable light stimulation platforms. This review explores the evolution of light-induction hardware-software platforms, discusses their advantages and disadvantages, and examines design approaches in optogenetic experiments. The development of automated measurement and stimulation schemes on these platforms enables computer-controlled living systems.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Scott A. Wegner, Rachel M. Barocio-Galindo, Jose L. Avalos
Summary: Optogenetic systems from the field of optogenetics have been successfully applied to various areas of metabolic engineering, enabling unprecedented control over microbial fermentations. This new field of metabolic optogenetics has the potential to challenge existing paradigms and impact metabolic engineering in new directions.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Review
Developmental Biology
Akinobu Nakamura, Yuhei Goto, Yohei Kondo, Kazuhiro Aoki
Summary: This review provides an overview of the use of genetically encoded fluorescent biosensors for visualizing ERK activity in live cells, as well as their applications in developmental studies of model organisms. It discusses the current understanding of how ERK dynamics are encoded and decoded for cell fate decision-making.
Review
Biochemistry & Molecular Biology
Manoj Kumar Mahata, Ranjit De, Kang Taek Lee
Summary: The article reviews the progress and potential of lanthanide-doped upconverting nanoparticles in biomedical applications, focusing on their applications in optogenetics, oncotherapy, bioimaging, etc. The unique properties of UCNPs make them accurate, sensitive, multifunctional nanoprobes, leading to significant advancements in therapy and diagnosis. Emerging bioapplications and challenges in clinical translation of UCNP-based nanotechnology research are also discussed.
Review
Chemistry, Applied
Shannon M. Hoffman, Allison Y. Tang, Jose L. Avalos
Summary: Optogenetics has been widely used in microbial engineering, providing precise control and enabling new approaches in studying complex biological systems. Future research directions include the development of orthogonal multichromatic controls.
ANNUAL REVIEW OF CHEMICAL AND BIOMOLECULAR ENGINEERING
(2022)
Review
Plant Sciences
Kai R. Konrad, Shiqiang Gao, Matias D. Zurbriggen, Georg Nagel
Summary: Optogenetics is a technique that uses light-sensitive receptors in transgenic organisms to manipulate biological activities. It allows for fine-tuning of cellular processes using light in a noninvasive and spatiotemporally resolved manner. Despite its success in various model organisms, optogenetic tools have been rarely applied in plants. Recent progress has overcome the challenges of plant dependency on light and the absence of the rhodopsin chromophore, allowing for the establishment of plant optogenetics.
ANNUAL REVIEW OF PLANT BIOLOGY
(2023)
Article
Chemistry, Analytical
Lorico D. S. Lapitan Jr, Mariusz Pietrzak, Marek Krawczyk, Elzbieta Malinowska
Summary: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death globally in 2020. The complexity of the disease and the low survival rate are due to late-stage diagnosis. Therefore, developing simple, sensitive, and rapid screening methods for early detection is necessary. Recent studies have shown promising HCC biomarkers and ultrasensitive biosensor technologies that could significantly improve diagnosis.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Biotechnology & Applied Microbiology
Filipp Bezold, Johannes Scheffer, Philipp Wendering, Zahra Razaghi-Moghadam, Jonathan Trauth, Bastian Pook, Hagen Nusshaer, Sophia Hasenjaeger, Zoran Nikoloski, Lars-Oliver Essen, Christof Taxis
Summary: Dynamic metabolic engineering is a strategy to switch key metabolic pathways in microbial cell factories to increase production of valuable chemicals. In this study, optogenetic intervention was used to arrest the cell cycle of budding yeast, resulting in increased production of terpenoid and nucleoside analog. Proteomic analysis revealed significant changes in metabolic key enzymes, and integration of the data in metabolic models demonstrated modulation of fluxes associated with product synthesis. These results highlight the potential of optogenetically triggered cell cycle intervention in improving compound yields in cellular factories.
METABOLIC ENGINEERING
(2023)
Review
Materials Science, Biomaterials
Armin Baumschlager, Mustafa Khammash
Summary: Light has become an established tool in biology for visualizing, investigating, and steering biological systems. This review discusses the unique features of light in biology, its progression in control mechanisms, and focuses on the application of transcriptional light regulators in synthetic biology.
Article
Multidisciplinary Sciences
Thomas A. Dixon, Thomas C. Williams, Isak S. Pretorius
Summary: Synthetic biology practices are now integrated into 'multiscale' designs, facilitating two-way communication between organic and inorganic information substrates in biological, digital, and cyber-physical system integrations. Novel applications of bio-informational engineering will emerge in environmental monitoring, precision agriculture, precision medicine, and next-generation biomanufacturing.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Eunji Hong, Christopher Glynn, Qianbin Wang, Siyuan Rao
Summary: Electroretinography (ERG) is a non-invasive electrophysiological recording technique used to detect neuronal cell signaling in the visual system. We have developed an advanced ERG recording system integrated with a programmable optogenetic stimulation method, which allows for the dissection of neural dynamics under different physiological and pathological conditions.
Review
Chemistry, Physical
Muthusankar Eswaran, Bavatharani Chokkiah, Santosh Pandit, Shadi Rahimi, Ragupathy Dhanusuraman, Mahaboobbatcha Aleem, Ivan Mijakovic
Summary: Field effect transistor (FET)-based nanoelectronic biosensors provide a viable route for cancer biomarker detection. Researchers have made significant efforts to address issues such as sensitivity, selectivity, and operational conditions to improve the sensing performance of FETs. This review discusses the fabrication of FETs, choice of bioreceptors, operational conditions, and strategies for improving the sensing performance of FET-based diagnostic devices.
Review
Chemistry, Multidisciplinary
Saqer Al Abdullah, Lubna Najm, Liane Ladouceur, Farbod Ebrahimi, Amid Shakeri, Nadine Al-Jabouri, Tohid F. F. Didar, Kristen Dellinger
Summary: Alzheimer's disease (AD) is a significant cause of dementia worldwide, and current diagnostic methods only detect the disease after clinical symptoms appear. However, research suggests that AD pathology may begin before symptoms manifest, such as the formation of amyloid beta plaques and neurofibrillary tangles. Biomarkers like Aβ(40), Aβ(42), and tau protein show promise for early AD diagnosis. This review summarizes the emerging nanobiosensor approaches for detecting these AD biomarkers and discusses the application of electrochemical, optical, and colorimetric biosensors using nanoparticle-based and nanostructure-based materials. The criteria for incorporating these nanomaterials in clinical settings are also presented.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Endocrinology & Metabolism
Aurelien Michau, Chrystel Lafont, Paula Bargi-Souza, Yasmine Kemkem, Anne Guillou, Magalie A. Ravier, Gyslaine Bertrand, Annie Varrault, Tatiana Fiordelisio, David J. Hodson, Patrice Mollard, Marie Schaeffer
Summary: Pancreatic islet vascular cells, particularly pericytes, play a crucial role in regulating insulin release and maintaining beta cell function. However, metabolic stress, such as obesity, can lead to pericyte hypertrophy and impaired vascular responses, which may contribute to beta cell failure in type 2 diabetes.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Hyun Gyu Hwang, Dae-Yeol Ye, Gyoo Yeol Jung
Summary: Genetically encoded biosensors have been developed to efficiently screen enzymes with desired phenotypes, expanding enzyme discovery and engineering strategies.
BIOTECHNOLOGY ADVANCES
(2023)
Article
Engineering, Chemical
Robert J. Lovelett, Jose L. Avalos, Ioannis G. Kevrekidis
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2020)
Article
Biochemical Research Methods
Sarah K. Hammer, Yanfei Zhang, Jose L. Avalos
ACS SYNTHETIC BIOLOGY
(2020)
Review
Medicine, Research & Experimental
Therese C. Kichuk, Cesar Carrasco-Lopez, Jose L. Avalos
Summary: Optogenetics utilizes light-sensitive proteins to manipulate cellular function and structure, offering novel ways to control subcellular organization. By targeting specific organelles, researchers can precisely manipulate cellular functions like nuclear translocation and plasma membrane morphology, while also exploring organelle dynamics and function. This technology has the potential to revolutionize biological research and bioengineering applications by providing spatiotemporal control over cellular processes.
WIRES MECHANISMS OF DISEASE
(2021)
Article
Biochemistry & Molecular Biology
Makoto A. Lalwani, Samantha S. Ip, Cesar Carrasco-Lopez, Catherine Day, Evan M. Zhao, Hinako Kawabe, Jose L. Avalos
Summary: By using OptoLAC circuits for light-controlled gene expression, improved metabolic engineering production and easier tunability of recombinant protein production can be achieved compared to IPTG induction.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Robert J. Lovelett, Evan M. Zhao, Makoto A. Lalwani, Jared E. Toettcher, Ioannis G. Kevrekidis, Jose L. Avalos
Summary: The dynamic control of engineered microbes using light through optogenetics has proven to be an effective strategy for increasing the yield of biofuels, chemicals, and other products. By utilizing light to manipulate microbial metabolism, the interface between biological and computer systems is simplified, allowing for in silico control of the microbe. Mechanistic models of yeast optogenetic circuits can predict short- and long-term responses to varying light inputs and are compatible with model predictive control for real-time control and optimization in microbial fermentations.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemical Research Methods
Evan M. Zhao, Makoto A. Lalwani, Jhong-Min Chen, Paulina Orillac, Jared E. Toettcher, Jose L. Avalos
Summary: OptoAMP is a new series of optogenetic circuits that amplify the transcriptional response to blue light up to 23-fold compared to the basal circuit (OptoEXP). These circuits show up to a 41-fold induction between dark and light conditions, efficient activation at light duty cycles as low as similar to 1%, and strong homogeneous light-induction in bioreactors of at least 5 L, with limited illumination at cell densities above 40 OD600.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Shannon M. Hoffman, Maria Alvarez, Gilad Alfassi, Dmitry M. Rein, Sergio Garcia-Echauri, Yachin Cohen, Jose L. Avalos
Summary: The use of cellulose emulsions has been shown to enhance cellulose hydrolysis quickly at temperatures tolerated by yeast, increasing saccharification rate. The development of an eSSF process allows for rapid and efficient production of cellulosic biofuels in short processing times, and can be extended to the production of other chemicals such as isobutanol. The transferability of this technology establishes the eSSF process as a platform for sustainable production of biofuels and chemicals.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Review
Microbiology
Jose Montano Lopez, Lisset Duran, Jose L. Avalos
Summary: Metabolic engineering plays a crucial role in improving the environmental sustainability of transportation and chemical manufacturing sectors by utilizing engineered microorganisms and overcoming physiological challenges. Understanding how host organism's physiological traits impact the performance of engineered metabolic pathways is essential.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Makoto A. Lalwani, Hinako Kawabe, Rebecca L. Mays, Shannon M. Hoffman, Jose L. Avalos
Summary: Microbial co-culture fermentations can be improved with optogenetics to dynamically control populations and increase chemical production. Adjusting population ratios with specific light duty cycles can enhance co-culture productivity.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemical Research Methods
Makoto A. Lalwani, Evan M. Zhao, Scott A. Wegner, Jose L. Avalos
Summary: The translation of yeast gene expression using bidirectional optogenetic control has potential applications in biotechnology. By applying the Q system in Saccharomyces cerevisiae, circuits inducible by quinic acid, darkness, or blue light have been developed, allowing for light-repressed and light-activated transcription as well as up to 39-fold induction. This system does not interfere with the GAL regulon, enabling simultaneous utilization of multiple optogenetic circuits for dynamic control and metabolic engineering applications in yeast.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Scott A. Wegner, Rachel M. Barocio-Galindo, Jose L. Avalos
Summary: Optogenetic systems from the field of optogenetics have been successfully applied to various areas of metabolic engineering, enabling unprecedented control over microbial fermentations. This new field of metabolic optogenetics has the potential to challenge existing paradigms and impact metabolic engineering in new directions.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yanfei Zhang, Jeremy D. Cortez, Sarah K. Hammer, Cesar Carrasco-Lopez, Sergio A. Garcia Echauri, Jessica B. Wiggins, Wei Wang, Jose L. Avalos
Summary: The authors report a genetically encoded biosensor for branched-chain amino acid (BCAA) metabolism based on the Leu3p transcriptional regulator in Saccharomyces cerevisiae. This biosensor is used to monitor yeast production of isobutanol and isopentanol. The biosensor configurations are effective in isolating high-producing strains and identifying enzymes with enhanced activity.
NATURE COMMUNICATIONS
(2022)
Review
Biochemical Research Methods
Pei-Ru Chen, Peng-Fei Xia
Summary: Carbon dioxide plays a crucial role in mitigating global climate change and supporting life on Earth. Synthetic biology and metabolic engineering offer a promising approach to enhance CO2 fixation by combining the advantages of autotrophic and heterotrophic organisms. This article reviews the current progress in constructing synthetic CO2 fixation pathways, discusses the underlying design principles and challenges, and provides insights into the future of carbon recycling through engineered synthetic carbon fixation pathways.
CURRENT OPINION IN BIOTECHNOLOGY
(2024)
