Article
Biochemistry & Molecular Biology
Alison G. Tebo, Benjamien Moeyaert, Marion Thauvin, Irene Carlon-Andres, Dorothea Boken, Michel Volovitch, Sergi Padilla-Parra, Peter Dedecker, Sophie Vriz, Arnaud Gautier
Summary: Spectrally separated fluorophores enable the observation of multiple targets in living cells simultaneously for a deeper understanding of cell functions. Engineered fluorogen-activating tags based on the FAST system offer orthogonality in recognition and spectral properties, allowing efficient multicolor imaging of proteins in live cells.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Microbiology
Caetanie F. Tchagang, Thien-Fah Mah, Francois-Xavier Campbell-Valois
Summary: Pseudomonas aeruginosa, a bacteria commonly found in the airways of individuals with cystic fibrosis, forms biofilms resistant to immune clearance and antibiotic treatment. In low-oxygen conditions, P. aeruginosa can use nitrate instead of oxygen to grow. Current fluorescent reporters for studying P. aeruginosa require oxygen for their chromophore maturation, limiting their use in anaerobic conditions. This study evaluated alternative fluorescent proteins and identified two that successfully labeled P. aeruginosa in anoxic environments, enabling the study of P. aeruginosa in biofilms and similar low-oxygen niches.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Vincent Grenier, Kayli N. Martinez, Brittany R. Benlian, Derek M. Garcia-Almedina, Benjamin K. Raliski, Steven C. Boggess, Johnathan C. Maza, Samantha J. Yang, Anneliese M. M. Gest, Evan W. Miller
Summary: This study demonstrates a molecular prosthetic approach that can substantially prolong imaging in neurons and cardiomyocytes.
ACS CENTRAL SCIENCE
(2022)
Article
Biology
Prashant Vaidyanathan, Evan Appleton, David Tran, Alexander Vahid, George Church, Douglas Densmore
Summary: Molecular biologists rely on fluorescent probes for measurements, and selecting an ideal set of fluorophores is a multidimensional problem with suboptimal choices leading to unreliable results. Vaidyanathan et al. present an algorithm to design optimized multi-color fluorophore panels for biologists, demonstrating its efficacy through computational predictions and experimental observations.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemical Research Methods
Alicia Climent-Catala, Ivan Casas-Rodrigo, Suhasini Iyer, Rodrigo Ledesma-Amaro, Thomas E. Ouldridge
Summary: This study investigates the performance of RNA light-up aptamers as transcriptional fluorescent reporters and compares them to protein-based reporters. The researchers found that RNA light-up aptamers exhibit suitable characteristics as transcriptional reporters over time and at the single-cell level, with higher variability in a population compared to protein-based reporters. Additionally, these RNA aptamers may offer faster dynamics compared to fluorescent proteins in E. coli. The implementation of these transcriptional reporters can facilitate transcription-based studies and expand the use of RNA-based circuits in bacterial cells.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Developmental Biology
Colin J. Dinsmore, Philippe Soriano
Summary: Understanding how cells activate intracellular signaling pathways in response to external signals is an important goal in cell and developmental biology. Live-cell signaling reporters have greatly contributed to our understanding of signaling dynamics. Translocation reporters have received attention due to their ease of use and fast response times. This study created two new mouse reporter lines to investigate the ERK1/2 and AKT signaling pathways.
DEVELOPMENTAL BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Anne C. Lyons, Sohum Mehta, Jin Zhang
Summary: This review introduces the complex spatiotemporal regulation of cell signaling and the design of fluorescent biosensors, highlighting the importance of spatial regulation in cell signaling.
BIOCHEMICAL JOURNAL
(2023)
Editorial Material
Genetics & Heredity
Kevin M. Brindle
Summary: MRI-based gene reporters can image gene expression at depth and high resolution, and may be translated to clinical applications. They exploit either endogenous contrast mechanisms or modulate the response to an introduced exogenous contrast agent.
TRENDS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Pavithran T. Ravindran, Sarah McFann, Richard H. Thornton, Jared E. Toettcher
Summary: Cells employ intracellular signaling pathways to sense and respond to changes in their external environment. Live-cell biosensors have revealed complex pulsatile dynamics in many pathways, but studies of these dynamics are limited by the necessity of live-cell imaging at high resolution. This study describes a method to infer pulsatile signaling dynamics in fixed cells using a pulse-detecting gene circuit. The circuit, implemented experimentally for the Erk signaling pathway, allows sensitive detection of Erk pulses and provides a way to permanently label transient, dynamic cell populations for further investigation of signaling dynamics.
Article
Biochemical Research Methods
Maria L. Sorkin, Kathleen K. Markham, Stevan Zorich, Ananda Menon, Kristen N. Edgeworth, Angela Ricono, Douglas Bryant, Rebecca Bart, Dmitri A. Nusinow, Kathleen Greenham
Summary: We have developed two self-assembled imaging systems that can be used for continuously monitoring in vivo reporter systems in various plant species, which is valuable for researchers interested in physiological and transcriptional responses in plants.
Review
Chemistry, Analytical
Muhammad Sohail, Lingyun Qin, Shuxian Li, Yue Chen, Muhammad Haidar Zaman, Xing Zhang, Bingzhi Li, He Huang
Summary: The CRISPR/Cas machinery has revolutionized the analytical platform for precise detection. This review highlights the role of reporter engineering in improving the CRISPR/Cas-based detection platform, focusing on reporter elements, nucleic acid sequences, and transducers for multiplexing and target differentiation. The review discusses the significance of reporters, their impact on signal generation, working principles, limitations of CRISPR technology, and future investigations.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Wenhua Li, Zhao Ma, Jiwei Chen, Gaopan Dong, Lupei Du, Minyong Li
Summary: A series of new fluorescent ligands with high binding affinity and visualizing ability for beta-adrenergic receptors (beta-ARs) have been successfully developed. Compound L5 showed the most favorable combination of properties, including high affinity, remarkable fluorescence enhancement upon binding, and the ability to visualize beta-ARs in living cells without wash steps. Additionally, a NanoLuc-based binding assay using compound 1,5 has been developed for high-throughput screening of beta-ARs.
ANALYTICAL CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Atul Goyal, Binh Vu, Vijay Maranholkar, Ujwal Patil, Katerina Kourentzi, Richard C. Willson
Summary: This article reports a technology for continuous monitoring of IgG in flowing clarified cell culture fluid. By adding immobilized fluorescein-labeled binding ligands to the column effluent, the breakthrough of IgG can be detected in real-time. The technology is suitable for process development and allows rapid and reliable monitoring of IgG without prior sample preparation.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biology
Michelina Kierzek, Parker E. Deal, Evan W. Miller, Shatanik Mukherjee, Dagmar Wachten, Arnd Baumann, U. Benjamin Kaupp, Timo Struenker, Christoph Brenker
Summary: FAST(M) is a novel technique for simultaneous recording of multiple probes with high sensitivity and minimal crosstalk. It is suitable for rapid kinetic stopped-flow fluorimetry, single-cell microscopy, and optochemical tools, opening new opportunities for studying cellular signaling pathways.
Article
Multidisciplinary Sciences
Brian Tenner, Jason Z. Zhang, Yonghoon Kwon, Veronica Pessino, Siyu Feng, Bo Huang, Sohum Mehta, Jin Zhang
Summary: FluoSTEPs is a novel class of biosensors that combines self-complementing split green fluorescent protein, CRISPR-mediated knock-in, and fluorescence resonance energy transfer technology to probe compartmentalized signaling dynamics in situ. It can simultaneously highlight endogenous microdomains and report domain-specific, real-time signaling events, including kinase activities, guanosine triphosphatase activation, and second messenger dynamics. FluoSTEPs have been shown to be useful in probing spatiotemporal regulation within endogenous signaling architectures, as demonstrated by a FluoSTEP for 3',5'-cyclic adenosine monophosphate (cAMP) revealing distinct cAMP dynamics within clathrin microdomains in response to stimulation of G protein-coupled receptors.
Review
Nanoscience & Nanotechnology
Wakana Sato, Tomasz Zajkowski, Felix Moser, Katarzyna P. Adamala
Summary: Synthetic cells can mimic various life-like behaviors and offer unique advantages in nanomedicine, but face key challenges before being deployed as drugs.
WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Rebecca Mackelprang, Katarzyna P. Adamala, Emily R. Aurand, James C. Diggans, Andrew D. Ellington, Samuel Weiss Evans, J. L. Clem Fortman, Nathan J. Hillson, Albert W. Hinman, Farren J. Isaacs, June Medford, Shadi Mamaghani, Tae Seok Moon, Megan J. Palmer, Jean Peccoud, Elizabeth A. Vitalis, India Hook-Barnard, Douglas C. Friedman
Summary: The rapid development of synthetic biology technologies has led to breakthrough applications with far-reaching implications, particularly in the development of diagnostics, therapeutics, and vaccines for COVID-19. However, there are risks associated with the publication of synthetic biology research and techniques, especially when it comes to the safety and distribution of pathogenic viruses. It is recommended to implement mandatory safety and security reviews for the de novo synthesis of certain pathogenic viruses and to include discussions or review processes regarding security considerations in the published papers, in order to enhance security and minimize negative outcomes.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Nathaniel J. Gaut, Jose Gomez-Garcia, Joseph M. Heili, Brock Cash, Qiyuan Han, Aaron E. Engelhart, Katarzyna P. Adamala
Summary: Synthetic cells can mimic the complexities of live cells with less noise. This study demonstrates key functionalities of synthetic cells and provides tools for engineering and research.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Changyang Linghu, Bobae An, Monika Shpokayte, Orhan T. Celiker, Nava Shmoel, Ruihan Zhang, Chi Zhang, Demian Park, Won Min Park, Steve Ramirez, Edward S. Boyden
Summary: Observing cellular physiological histories is crucial for understanding normal and disease-related processes. Researchers have developed a fully genetically encoded method called expression recording islands, which allows continuous digital recording of biological information within cells and high-throughput readout in fixed cells. This method stores information in growing intracellular protein chains and enables the reading of physiological history along the ordered subunits of protein chains using conventional optical microscopy. The researchers successfully used this method to record gene expression timecourse downstream of specific pharmacological and physiological stimuli in cultured neurons and living mouse brain, with a time resolution of a fraction of a day over periods of days to weeks.
NATURE BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Wakana Sato, Melanie Rasmussen, Nathaniel Gaut, Mahima Devarajan, Kaitlin Stokes, Christopher Deich, Aaron E. Engelhart, Katarzyna P. Adamala
Summary: Synthetic cells express proteins using cell-free transcription-translation technology and this method is utilized for various applications such as investigating natural gene pathways, metabolic engineering, drug development, and bioinformatics. However, there is a need for further advancements in gene-specific and straightforward regulation methods. This study presents a method of controlling gene expression in synthetic cells using a silencing oligo and demonstrates the transfection of various payloads to synthetic cell liposomes.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Oksana M. M. Subach, Anna V. V. Vlaskina, Yulia K. K. Agapova, Alena Y. Y. Nikolaeva, Konstantin V. V. Anokhin, Kiryl D. D. Piatkevich, Maxim V. V. Patrushev, Konstantin M. M. Boyko, Fedor V. V. Subach
Summary: This article introduces the characteristics and applications of true genetically encoded monomeric fluorescent timers (tFTs) and tandem timers (tdFTs). The researchers successfully engineered blue-to-red tFTs and green-to-far-red tdFTs. They also observed the brightness and stability of these timers in living organisms and developed the FucciFT2 system to monitor cell cycle phase transitions. Lastly, they determined the X-ray crystal structure of the mTagFT timer and analyzed it using directed mutagenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Neurosciences
Kevin R. Duffy, Nathan A. Crowder, Arnold J. Heynen, Mark F. Bear
Summary: During a critical period after birth, monocular deprivation (MD) reduces the size of neurons in the dorsal lateral geniculate nucleus (dLGN) connected to the deprived eye and shifts cortical ocular dominance in favor of the non-deprived eye. Temporary inactivation of the non-deprived eye, known as monocular inactivation (MI), can promote better recovery from long-term MD effects compared to conventional occlusion therapy. MI has a significant impact on neuron size in the dLGN, especially when applied during the peak of the critical period. Unlike MD, MI induces structural plasticity in both the binocular and monocular segments of the dLGN. The effectiveness of MI decreases with age but still produces significant effects even beyond the critical period, showing double the magnitude and efficacy compared to MD. The effects of MI can be fully remedied with a short period of binocular experience, leading to full recovery of vision in the previously inactivated eye. These findings highlight the potential of MI to modify the visual pathway and its ability to ameliorate visual system disorders like amblyopia.
JOURNAL OF COMPARATIVE NEUROLOGY
(2023)
Review
Biochemistry & Molecular Biology
Shuchang Zhao, Kiryl D. Piatkevich
Summary: Neuronal circuits in the brain that use serotonin are crucial for regulating mood and emotions. Disruptions in serotonin signaling contribute to neuropsychiatric disorders like depression and anxiety. However, the mechanisms underlying serotonergic signaling in healthy and diseased states are not fully understood. To address this, new techniques such as genetically encoded serotonin indicators have been developed to provide better resolution in studying serotonergic circuits and their role in neuropsychiatric disorders.
JOURNAL OF NEUROCHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Judee A. Sharon, Chelsea Dasrath, Aiden Fujiwara, Alessandro Snyder, Mace Blank, Sam O'Brien, Lauren M. Aufdembrink, Aaron E. Engelhart, Katarzyna P. Adamala
Summary: Trumpet is a biocomputing technology that builds complex logic gate circuits using DNA and enzymes, with amplified fluorescent readout. It combines the simplicity and robustness of in vitro biocomputing methods, with signal amplification and programmability, avoiding common shortcomings of live cell-based biocomputing solutions.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Christopher Deich, Nathaniel J. Gaut, Wakana Sato, Aaron E. Engelhart, Katarzyna P. Adamala
Summary: Recently, a new subset of fluorescent proteins from Aequorea jellyfish has been discovered. These proteins have been characterized in vivo but not validated in cell-free systems. Cell-free systems are crucial in various fields including foundational research, synthetic cells, bioengineering, biomanufacturing, and drug development, and they heavily rely on fluorescent proteins as reporters. In this study, we characterize and validate this new set of Aequorea proteins for their use in cell-free and synthetic cell expression platforms.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemical Research Methods
Andrei Sakai, Aafke J. Jonker, Frank H. T. Nelissen, Evan M. Kalb, Bob van Sluijs, Hans A. Heus, Katarzyna P. Adamala, John I. Glass, Wilhelm T. S. Huck
Summary: This article reports the successful creation of a CFE system derived from the minimal synthetic bacterium Syn3A, which is supported by an unusual cell lysis method that reduces ribonuclease activity. To improve protein yields, the researchers optimized the Syn3A CFE reaction mixture using an active machine learning tool. This is the first functional CFE system derived from a minimal synthetic bacterium, enabling further advancements in bottom-up synthetic biology.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Brock Cash, Nathaniel J. Gaut, Christopher Deich, Laura L. Johnson, Aaron E. Engelhart, Katarzyna P. Adamala
Summary: Synthetic minimal cells serve as a controllable and engineerable model for biological processes. By investigating host-pathogen interactions and mechanisms for acquiring immunity, this study expands the synthetic cell engineering toolbox and brings synthetic cell systems closer to providing a comprehensive model of complex, natural life.
Article
Biochemistry & Molecular Biology
Oksana M. Subach, Larisa Varfolomeeva, Anna V. Vlaskina, Yulia K. Agapova, Alena Y. Nikolaeva, Kiryl D. Piatkevich, Maxim V. Patrushev, Konstantin M. Boyko, Fedor V. Subach
Summary: Neurobiologists commonly use green genetically encoded calcium indicators (GECIs) to visualize neuronal activity. Ratiometric GECIs are less popular due to their inferior properties compared to intensiometric GCaMP GECIs. To address this issue, we engineered a ratiometric green calcium indicator called FNCaMP and compared its properties with FGCaMP7.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Neurosciences
Dustin J. Hayden, Peter S. B. Finnie, Aurore Thomazeau, Alyssa Y. Li, Samuel F. Cooke, Mark F. Bear
Summary: The study investigates the stimulus-selective response plasticity (SRP) in the mouse primary visual cortex and reveals the involvement of NMDA receptors and glutamatergic principal neurons in the expression of SRP. The results show the disruption of SRP when NMDA receptors are deleted in layer 6 principal neurons and suggest the modulation of neuronal activity in different layers of the visual cortex in response to familiar stimuli.
JOURNAL OF NEUROSCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Brock Cash, Nathaniel J. Gaut, Christopher Deich, Laura L. Johnson, Aaron E. Engelhart, Katarzyna P. Adamala
Summary: Synthetic minimal cells serve as controllable and engineerable models for biological processes, offering a simplified platform for investigating key chemical foundations of life. In this study, a synthetic cell system with host cells interacting with parasites and experiencing various degrees of infection was demonstrated. The engineered host cells were shown to resist infection, and the metabolic cost of carrying resistance was investigated. Furthermore, an inoculation method was employed to immunize the host against pathogens, expanding the toolbox for synthetic cell engineering and inching closer towards a comprehensive model of complex natural life.
