Curated Optogenetic Publication Database

Abstract: Recent advances in experimental model systems have improved our ability to study cardiovascular development, function, and disease with high spatial and temporal resolution. The zebrafish (Danio rerio) has emerged as a powerful vertebrate model for cardiovascular research due to its transparency, genetic tractability, and conserved cardiac physiology, similar to humans. These features allow real-time in vivo imaging, the functional assessment of cardiac performance, and the tracking of signaling pathways that are fundamental in cardiovascular development and disease. Recent advances in nanotechnology and optogenetics have introduced complementary tools for probing and manipulating cardiovascular systems with high spatial and temporal precision. Nanoparticle-based platforms enable the tunable delivery of drugs, nucleic acids, and imaging agents, while optogenetic systems allow the light-mediated control of gene expression, signaling pathways, and cardiac electrophysiology. In this review, we summarize recent progress in the application of nanoparticle-based technologies and the emerging optogenetic tools in zebrafish cardiovascular research, including the optical control of cardiac signaling and electrophysiology. We briefly discuss emerging complementary efforts toward nanoparticle and optogenetic approaches, how to overcome key technical limitations, such as light penetration and gene delivery, and how to facilitate the development of fully optical platforms for cardiovascular disease modeling and drug screening.

Abstract: Evolving dynamic, multi-state, and computational protein functionalities is challenging because it requires selection pressure on all the states of a protein of interest (POI) and the transitions between them. To create a continuous directed evolution paradigm for such properties, we genetically engineered budding yeast for optogenetic input to switch a POI "on" and "off," which, in turn, controls a Cdk1 cyclin that is essential for one cell-cycle stage but detrimental for another. The method, "optovolution," generates dynamic selection pressure on POI cycling at the timescale of tens of minutes. We used it to evolve 19 new variants of the LOV transcription factor El222, including in vivo green-light-responsive variants allowing LOV color-multiplexing. Evolving the PhyB-Pif3 optogenetic system, we discovered that loss of YOR1 makes supplementing phycocyanobilin (PCB) unnecessary. Finally, we demonstrated the generality of the method by evolving a non-light-responsive AND gate (PEST-rtTA). Optovolution makes difficult-to-engineer protein functionalities continuously evolvable.

Abstract: As an interdisciplinary frontier integrating optical technologies and genetic principles, optogenetics enables precise spatiotemporal control of gene expression and neuronal activity via light-sensitive molecular assemblies, thereby driving transformative advancements in biomedical fields. Red/far-red light optogenetic tools, by virtue of the advantages of long wavelengths, have emerged as powerful platforms for deep-tissue manipulations for both basic researches and clinical applications. Although a number of in-depth studies on various red/far-red light optogenetic tools and their biomedical applications have been published, there has not yet been a comprehensive review that systematically summarizes the advancements of diverse researches on this type of optogenetics. This article systematically delineates the technology of red/far-red light optogenetics, focusing on the molecular mechanisms and biomedical applications of two core photoreceptor protein families: phytochromes and channelrhodopsins. Phytochromes distributed in plants, bacteria and fungi undergo reversible red/far-red light-driven conformational conversion, initiating downstream signaling cascades that support various optogenetic technologies. Channelrhodopsins, originally microalgal blue-light-gated cation channels, are engineered into red-shifted variants, enabling rapid and non-invasive red/far-red light-controlled neuronal excitability manipulation at precise spatiotemporal resolution. The representative case studies of applications of phytochromes-based optogenetic tools in gene editing, transcriptional regulation, light-gated drug delivery and deep tissue imaging and diagnosis; as well as applications of red-shifted channelrhodopsins-based optogenetic tools in spatiotemporally precise neuromodulation are discussed in detail. Moreover, the main technical challenges in the utilization of red/far-red light optogenetic tools are analyzed. With continuous advancements of wavelength-optimized actuators and closed-loop control architectures, red/far-red light optogenetic techniques are poised to drive multidisciplinary convergence, offering unprecedented tools for decoding cellular dynamics and accelerating therapeutic discoveries.

Abstract: Precise control of gene expression is one of the fundamental goals of synthetic biology. Whether the objective is to modify endogenous cellular function or induce the expression of molecules for diagnostic and therapeutic purposes, gene regulation remains a key aspect of biological systems. Over time, advances in protein engineering and molecular biology have led to the creation of gene circuits capable of inducing the expression of specific proteins in response to external stimulus such as light. These optogenetic, or light-activated circuits hold significant potential for gene therapy as a tool for regulating the expression of therapeutic genes within cells. However, the applications of optogenetic systems can be limited by the lack of efficient ways to deliver light into cells or tissue. Our approach to address this challenge is to harness the power of bioluminescence to produce light directly inside cells using a luminescent enzyme. Combined with a photosensitive transcription factor, we report the development of a genetically encoded optogenetic circuit for the control of gene expression. Furthermore, we utilized a magneto-sensitive protein to engineer a split-protein version of this luminescent enzyme, where its reconstitution is driven by a 50 mT magnetic stimulus. Thus, resulting in a gene circuit activated by a combination of light and magnetic stimulus. We expect this work to advance the implementation of light-controlled systems without the need of external light sources, as well as serve as a basis for the development of future magneto-sensitive tools.

Abstract: The bacterial flagellar motor drives bacterial swimming and chemotaxis by rotating helical flagellar filaments. When Escherichia coli navigates chemical gradients, the motor switches from counterclockwise (CCW) during forward swimming to clockwise (CW) during direction-changing tumbles. The motor responds indirectly to extracellular chemosensory input to membrane-bound chemoreceptors using an intervening intracellular signaling pathway. How the motor responds to its direct input signal-the diffusible messenger phosphorylated CheY (CheY-P)-remains poorly understood. Steady-state motor measurements have been modeled as an allosteric switch between CCW/CW states that depends on mean CheY-P levels. Allosteric models have suggested that as many as 20 CheY-P molecules can be bound to the motor when it switches rotational direction. But steady-state models cannot predict the sensitivity of the motor to dynamic changes in CheY-P that essentially modulate chemotactic behavior. We present an optogenetic reagent that precisely controls the direct dynamical input signal to the motor. We designed a "caged" molecule, Opto-CheY, that is transiently activated by photon absorption. We find that activation and binding of one to three additional CheY-P molecules is sufficient to switch the motor from the CCW to CW state. The sensitivity of the motor to small changes in CheY-P occupancy helps resolve a long-standing paradox about the high sensitivity of the chemotactic response to external sensory input. Optogenetic biochemistry by light-activated uncaging of signal molecules is a new strategy to dissect information-processing in the living cell.

Abstract: In plants, the regulation of transgene transcription is typically achieved using chemical agents. A safe alternative to chemically induced systems may be optogenetic systems. The BphP1-QPAS1 system has distinct advantages over other optogenetic systems, as it is activated by near-infrared (NIR, 780 nm) light, which is beyond the spectrum of plant photoreceptors. This system is based on the use of a split transcription factor (TF), consisting of the DNA-binding and dimerization domains of the yeast TF Gal4, fused to the QPAS1 component, along with the transactivation domain VP16 fused to BphP1. Under NIR light, BphP1 interacts with QPAS1, leading to the formation of the functional TF Gal4-VP16. A primary obstacle to using optogenetic systems in plants is their undesired activation under white light, which is vital for normal plant growth. A potential solution to this issue is temporarily removing one component of the split TF from the nucleus under white light. We modified the BphP1-QPAS1 system to activate reporter gene expression in Nicotiana benthamiana leaves using NIR light. We combined BphP1-QPAS1 with several variants of LOV domain-containing proteins activated by blue light (460-480 nm). The best results were achieved by combining the BphP1-QPAS1 system with the AsLOV2 domain, which carries the degron sequence RRRG at the C-terminal Jα helix and initiates the degradation of the chimeric protein NES-Gal4-QPAS1-AsLOV2-RRRG under white light. This modification induced the BphP1-QPAS1 system in tobacco leaves only under NIR light, but not in the dark or under white light. We believe that, in the future, the BphP1-QPAS1 system could be applied to enhance plant resistance to adverse environmental conditions, pests, and viral diseases.

Abstract: Light is a pivotal environmental signal regulating diverse plant developmental and physiological processes, including seed germination, hypocotyl elongation, phototropism, metabolite biosynthesis, stress resistance, temperature response, and circadian rhythms. Multiple signal transduction pathways of ultraviolet, blue light, and red/far-red light as well as related protein interaction networks in plants have been identified. Deciphering the mechanisms of light perception and signal transduction is of great significance to crop breeding and optogenetic manipulation. Structural biology has profoundly advanced the studies of light signal transduction by elucidating high-resolution three-dimensional (3D) structures of photoreceptors and their downstream signaling components. These studies uncover the molecular basis underlying perception and transduction of different light signals by plants. This review summarizes key structural findings of plant light signal transduction, highlighting the architectures and molecular functions of photoreceptors and associated signaling factors. We also outline the mechanisms underlying photoreceptor activation, inhibition, and regulatory interactions within light signaling networks and discuss the challenges in this field.

Abstract: An optogenetic split-GAL4 system, ShineGAL4, allows genes to be manipulated with unprecedented spatiotemporal precision. Here, we convert a panel of 14 GAL4 drivers widely used in Drosophila research into their ShineGAL4 counterparts. Homology assisted CRISPR knock-in (HACK) is used to replace GAL4 with the GAL4 DNA binding domain fused to a Magnet photoswitch. We show that the resulting ShineGAL4 drivers enable gene expression to be rapidly induced by light specifically in fat body, muscles, enterocytes, oenocytes, Malpighian tubules, neurons, neuroblast lineages, glial subtypes or in all glia. We also develop an optogenetic cassette for photoactivation of GAL4 in 'silent' FLP-out clones. This panel of optogenetic tools will enable precise spatiotemporal control of gene expression in a wide range of different Drosophila tissues and cell-types.

Abstract: Microbial optogenetic tools can regulate gene expression with spatial and temporal precision, offering excellent potential for single-cell resolution studies. However, bacterial optogenetic systems have primarily been deployed for population-level experiments. It is not always clear how these tools perform in single cells, where stochastic effects can be substantial. In this study, we focus on optogenetic Cre recombinase and compare the performance of three variants (OptoCre-REDMAP, OptoCre-Vvd, and PA-Cre) for their population-level and single-cell activity. We quantify recombination efficiency, expression variability, and activation dynamics using reporters which produce changes in fluorescence or antibiotic resistance following light-induced Cre activity. We find that optogenetic recombinase performance can be reporter-dependent. Further, single-cell analysis reveals highly heterogeneous activity, with substantial variation in the efficiency and timing of recombinase activity from cell to cell. These findings suggest important criteria for selecting optogenetic recombinases and indicate areas for optimization to improve single-cell capabilities of bacterial optogenetic tools.

Abstract: Estrogen receptor (ER)-mediated genomic actions are crucial for maintaining various physiological functions, and their dysfunction is associated with numerous human diseases. Traditional estrogen replacement therapy (ERT) is commonly used to manage estrogen deficiency-related conditions, such as vulvovaginal atrophy during menopause, but its systemic effects pose notable risks. This study introduces OptoER, an optogenetic tool engineered to precisely modulate ER-mediated genomic pathways through light-induced transcription regulation, offering spatial-temporal control over ER-dependent gene expression. Our in vitro studies demonstrate that OptoER significantly enhances ER-specific gene transcription and protein synthesis, leading to improved cell proliferation and migration. In a proof-of-principle study using ovariectomized (OVX) mice, OptoER demonstrated considerable therapeutic potential for vaginal atrophy, with observed improvement in epithelial thickness and keratinization. These findings suggest that OptoER provides a targeted therapeutic strategy for estrogen deficiency conditions, with significant implications for treating vaginal atrophy and promoting regenerative healing in estrogen-deprived tissues.

Abstract: Synthetic microbial consortia (SMCs) represent a paradigm shift from monocultures to multi-strain systems that leverage ecological interactions for enhanced environmental adaptation and bioproduction. This review systematically sorts out engineering strategies for constructing stable SMCs, focusing on three core principles regarding host selection based on obligate mutualism (e.g., auxotrophs), pathway modularization to resolve metabolic conflicts, and dynamic regulation using tools like quorum sensing and optogenetics. We demonstrate the efficacy of SMCs in diverse applications including high-value compound synthesis and lignocellulosic biomass conversion through consolidated bioprocessing and inhibitor mitigation. SMCs enabling advanced functions in engineered living materials, environmental remediation, and biomedical innovation via division of labor are also described. Despite such progress, challenges in scalability and real-time control of SMCs under industrial conditions remain. We conclude that SMCs serve to bridge evolutionary ecology and biotechnology, offering robust solutions for sustainable biomanufacturing and beyond.

Abstract: Light-induced membrane fusion has become a pivotal technique for constructing and functionalizing synthetic cells by enabling precise control over membrane merging events. Traditional fusion approaches that rely on chemical, physical, and mechanical stimuli frequently lack both specificity and reversibility, limiting their utility in mimicking dynamic cellular processes. Here, we review advances employing photosensitive molecules and optogenetic tools that facilitate spatiotemporally controlled fusion of lipid and polymer vesicles, enabling dynamic content exchange and membrane remodeling. These approaches have enhanced synthetic cell assembly, molecular transport, and signal transduction, with applications extending to drug delivery and biosensing. Despite challenges in efficiency and biocompatibility, ongoing innovations in photosensitizer design and light activation strategies promise to expand the capabilities of synthetic biology platforms. This work underscores the potential of light-induced fusion to advance the development of intelligent nanomaterials and functional synthetic cellular systems.

Abstract: Numerous organisms have evolved the ability to utilize light through photoreceptor proteins that mediate diverse biological processes. Currently, several optogenetic sensor systems are widely used in yeast. However, when these systems are applied for gene repression to regulate endogenous yeast gene expression, they typically require the insertion of corresponding target sites near the native promoter of the gene of interest to achieve precise modulation. To address these constraints, a novel blue light-inducible optogenetic tool designated iLight9 was developed, a single-component optogenetic biosensor integrated with the CRISPR-dCas9 platform. The stability of the iLight9 system was further enhanced by employing a strategy involving the addition of a protein degradation tag. The resulting system was designated as iLight9O, which facilitated programmable regulation of distinct genes through the introduction of specific sgRNAs. Subsequently, systematic metabolic engineering strategies were employed to construct an efficient patchoulol-producing cell factory in Saccharomyces cerevisiae. Moreover, a two-step isoprenol utilization (IU) pathway was introduced into the recombinant strain to enhance its capacity for patchoulol biosynthesis. Crucially, the iLight9O system was adopted to dynamically downregulate squalene synthase, a key enzyme in the competing squalene biosynthetic pathway. This optogenetic flux control strategy increased patchoulol titers by 66 % in the IU-optimized strain and 24 % in the MVAIU2 strain, demonstrating significant improvements over static engineering approaches.

Abstract: Autophagy, a conserved recycling process, manages intracellular quality control to mitigate stress. To determine the rapid effects of autophagy perturbation, we developed the first optogenetic tool to rapidly inhibit autophagy, termed ASAP. Our approach selectively inhibits autophagy within 5 minutes, providing a precise and dynamic approach to study autophagy regulation. Proteomic profiling with ASAP revealed the most tightly regulated autophagy substrates along with novel, previously unidentified substrates, including nuclear pore complex (NPC) proteins. Interestingly, autophagy regulates quality control of incomplete NPCs still in the cytoplasm via specific LC3-interacting regions (LIRs), sparing NPCs embedded in the nuclear envelope. Upon rapid autophagy inhibition, incomplete NPCs accumulate and instead of undergoing autophagic degradation, cytoplasmic NPCs aggregate in processing bodies. Using ASAP, we demonstrate rapid and specific inhibition of autophagy, revealing that the nuclear pore complex is a tightly regulated autophagy substrate.

Abstract: The light-mediated, specific, and precise control of cell functions enabled by optogenetics has become a versatile method for investigating and combatting cancer. An increasing set of optogenetic tools enables tightly controlled regulation of ion flux across biological membranes, gene expression, gene editing, and protein-protein interactions and is being used to interrogate hallmark traits of cancer at the cellular, subcellular, and organismic level. This enables, on the one hand, the identification of critical signaling circuits required for cancer development and progression in vitro and in animal models and can flag potential intervention points for pharmacologic interference. On the other hand, optogenetics can improve the level of control in cell-based therapeutics. The current article provides a review of optogenetic tools and approaches used in the cancer research field and their multiple applications for improving our understanding of signal transduction pathways, modulating immune functions in the tumor microenvironment, facilitating drug screening, or directly attacking cancer cells. Key advantages and achievements of optogenetics in the cancer research field and remaining barriers for clinical applications are discussed.

Abstract: Endoplasmic reticulum-plasma membrane (ER-PM) contact sites are essential signaling hubs that regulate lipid transport, calcium homeostasis, and spatially organized signal transduction. Emerging evidence indicates that not only the presence but also the dynamics, stability, and geometry of ER-PM contacts critically shape cellular functions; however, tools that enable simultaneous high-fidelity visualization and reversible, quantitative control of these contacts in living cells remain limited. Here, we introduce a modular toolkit for inducible ER-PM contact-site reconstitution based on complementary chemical and optical dimerization strategies. We develop a nontoxic and reversible abscisic acid (ABA)-inducible system using the plant-derived ABIcs/PYLcs pair, and a rapidly reversible optogenetic system based on the iLID/SspB module, both of which allow robust visualization and dose-dependent control over contact-site formation kinetics, increasing contact-site density and total area fraction per cell without altering the size of individual contacts. In contrast, systematic variation of rigid α-helical linker length or inducible tether abundance selectively tunes the lateral growth, stability, and lifetime of individual contact sites, without changing their density. By combining these two orthogonal strategies, we achieve independent control of both individual contact-site size and overall contact-site density, providing complementary mechanisms to adjust total contact area per cell. This versatile platform enables quantitative dissection of ER-PM contact site structure-function relationships and offers broad utility in studies of lipid exchange, calcium signaling, membrane repair, metabolic regulation, and disease-relevant dysregulation.

Abstract: Light-oxygen-voltage (LOV) domain proteins represent a versatile class of photoreceptors capable of regulating a wide range of light-dependent biological functions. While a lot of studies have focused on the photochemistry of LOV domains, the mechanisms of signal generation and propagation in multidomain LOV proteins remain incompletely understood. Here, we investigated two multidomain proteins, using time-resolved infrared spectroscopy. The measurements resolve the entire photocycle dynamics from picoseconds to hours and uncover distinct patterns of local and global structural responses. The two multidomain proteins under study, YF1 and PAL, exhibit nearly identical dynamics during excitation and intersystem crossing on the nanosecond timescale, reflecting conserved local interactions between the chromophore and its highly conserved binding pocket. Multiscale simulations attribute minor spectral differences in this regime to a phenylalanine residue located near the chromophore present only in one of the two LOV domains. The similarities, however, end at the microsecond timescale, where adduct formation already involves global structural adaptations. By experimentally isolating the response of the histidine kinase effector domain in the synthetic photoreceptor YF1, we show that major structural adaptions of the effector domain occur concurrently with cysteine-adduct formation and that the Jα-helix putatively mediates unidirectional communication between domains. In PAL, light-induced opening of the RNA binding site during the adduct formation is additionally followed by a subsequent rearrangement in the distal PAS domain after 3 s. This highlights the pivotal yet distinct roles of the Jα-helix in signal transmission, which depend on the domain topology. Ultimately, our study not only deepens the current understanding of signal transduction in full-length LOV proteins, but also contributes to the fundamental framework for the future application of LOV domains in optogenetic engineering.

Abstract: Notch signalling is a critical regulator of multiple developmental processes through its ability to control gene expression and thereby influence cell fate specification and cell proliferation through direct cell-cell communication. Although Notch signalling has been implicated in myogenesis during late embryogenesis, its role in early mesoderm development has been largely unexplored. Endocytosis of the Notch ligand Delta and the Notch receptor extracellular domain, a critical step in Notch pathway activation, has been extensively observed in the ventral mesoderm of the early Drosophila embryo, indicating a potential for Notch signalling activity in this early germ layer. Here, we present evidence that genes critical to mesoderm development require and are responsive to Notch signalling activity. Using a novel light-inducible Optogenetic variant of the Notch intracellular domain (OptoNotch), which affords precise spatial and temporal control over ectopic activation of Notch signalling, in combination with high-resolution fluorescent RNA in situ hybridization and qPCR, we identified a set of mesodermal genes whose expression is directly regulated by Notch signalling. We also provide evidence that Notch signalling indirectly regulates the dorsal-ventral patterning program mediated by the Toll signalling pathway through the Dorsal/Twist/Snail gene network. Our findings demonstrate that Notch signalling regulates ventral mesoderm patterning and is critical for establishing the mesoderm-mesectoderm-ectoderm boundary by regulating gene expression patterns and providing negative feedback on the upstream patterning network.

Abstract: Various blue-light photoreceptor proteins have photo-responsive domains known as light, oxygen, voltage (LOV) domains, which are extensively distributed in plants, algae, fungi, and bacteria. When exposed to blue light, the flavin chromophore and a highly conserved cysteine residue form a covalent adduct on a microsecond time scale. LOV domains are common photosensory modules that can be applied to optogenetics, regulated synthesis of reactive oxygen species, and fluorescence microscopy. This review explores the photocycle kinetics and applications of various LOV domains, which have been explored for confocal microscopy, two-photon microscopy, and super-resolution microscopy. Many LOV domains have been derived and modulated for use in different types of microscopic applications. Molecular understanding, diversity of LOV domains, and versatile photo-physical characteristics of these proteins have immense potential for the development of useful probes for various microscopy tools. There is a great demand for perspective research on LOV domain proteins for harnessing their possible optobiotechnological applications.

Abstract: Cancer is known to be a disease of altered cellular signaling; however, the relationship between mutation-specific changes to signal transduction and the phenotypic consequences produced remains poorly understood. Here, we investigate two common breast cancer driver mutations, the PIK3CAH1047R mutation and the ErbB2 amplification, both of which activate the PI3K-Akt pathway but paradoxically drive distinct cellular outcomes. Indeed, in nontransformed mammary epithelial cells, PI3KH1047R expression induced features of epithelial-mesenchymal transition (EMT), while ErbB2amp cells exhibited a hyperproliferative phenotype. Characterization of PI3K axis signaling revealed that ErbB2amp cells display prolonged, stimulus-dependent PI3K activation, whereas PI3KH1047R cells show constitutive, ligand-independent signaling. To test whether these distinct dynamics contribute to the phenotypic responses, we employed an iLID-based optogenetic system that enables precise, tunable control of endogenous PI3K activity. Using this tool to mimic the mutation-specific dynamics in MCF10A mammary epithelial cells, we found that PI3K signaling patterns alone were sufficient to reproduce key features of the PIK3CA H1047R-associated EMT phenotype but not the ErbB2-associated proliferative phenotype. These findings suggest that the temporal encoding of pathway activity, not merely its magnitude, can drive some phenotypic changes in oncogenic progression, explain how distinct mutations within a common signaling pathway can produce divergent cellular phenotypes, and provide a workflow for interrogating the functional consequences of changes in signaling dynamics.

Abstract: Crafting synthetic in vitro tissues with mammalian cells faces a shortage of methods to define spatial features. Optogenetic tissue engineering can provide the desired spatial and temporal control but requires stable genomic engineering to support long-term cultivation and high response resolution. Here, we developed BlueGENEs, a set of optimized optogenetic gene switches. BlueGENEs support rapid, stable cell line generation, including precision engineering into the human AAVS1 safe harbor locus. By combining a designer endonuclease and a phage integrase, the approach overcomes gene-disruptive effects of random gene delivery and enables reproducible cell line development. BlueGENEs comprise an optogenetic blue light-responsive gene switch, a synthetic response promoter, and selection strategies serving broad use scenarios. We generated various human cell lines for optical control of apoptotic cell fate, 3D tissue formation, and signals promoting cytoskeletal remodeling. Our results demonstrate the integration of optogenetic cells with bioprinting technologies, illustrating the potential of BlueGENEs in advancing the synthesis of de novo or patient-derived in vitro model systems.

Abstract: Single-cell resolution studies have transformed our understanding of microbial systems, revealing substantial cell-to-cell heterogeneity and complex dynamic behaviors. This review describes recent advances in using optogenetics, where light-sensitive proteins control cellular processes, to investigate microbial behavior at the individual cell level. We discuss studies where optogenetic approaches have enabled high-resolution analysis of properties such as relative cell positioning, subcellular localization, morphology, and gene expression dynamics. In addition, we highlight emerging feedback and event-driven control methods that dynamically modulate cellular states using light signals. By leveraging light's unique capabilities for spatial and temporal manipulation, researchers can now probe cellular characteristics with unprecedented precision. We anticipate significant advances as researchers introduce more sophisticated dynamically patterned light signals for single-cell microbial research.

Abstract: RNA-binding proteins (RBPs) with prion-like domains (PrLDs), such as FUS and TDP-43, condense into functional liquids, which can transform into pathological fibrils that underpin fatal neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD). Here, we define short RNAs that prevent FUS fibrillization by promoting liquid phases and distinct short RNAs that prevent and reverse FUS condensation and fibrillization. These activities require interactions with multiple RNA-binding domains of FUS and are encoded by RNA sequence, length, and structure. We define a short RNA that dissolves cytoplasmic FUS aggregates, restores nuclear FUS, and mitigates FUS toxicity in optogenetic models and ALS patient-derived motor neurons. Another short RNA dissolves cytoplasmic TDP-43 aggregates, restores nuclear TDP-43, and mitigates TDP-43 toxicity. Since short RNAs can be effectively delivered to the human brain, these oligonucleotides could have utility for ALS/FTD and related disorders.

Abstract: Mitochondria besides being the powerhouse of the cell are also involved in performing a multitude of critical cellular functions. Any failure in maintenance of these organelles is implicated in multiple human pathologies, including neurodegenerative disorders. Over the past two decades, significant efforts have been made to investigate the pharmacodynamic propensity of various potential compounds, which could be engaged as efficient therapeutic approach in modulating mitochondrial dynamics during neuronal dysfunctions.

Abstract: CRISPR/Cas9 is a powerful tool for targeted genome editing experiments. Using CRISPR/Cas9, genes can be deleted or modified by inserting specific DNA sequences, encoding for fluorescent proteins, small peptide tags, or other modifications. Such experiments are essential for detailed gene and protein characterization. However, designing and cloning the corresponding constructs can be repetitive, time-consuming, and laborious. To assist users in CRISPR/Cas9-based genome engineering, we developed CrisprBuildr, an open-source, web-based application for designing modifications to their target genes. CrisprBuildr guides users through creating guide RNAs and repair template vectors to generate cloning maps. The application is designed for the Drosophila melanogaster genome but can serve as a template for other available genomes. We also created new tagging vectors using EGFP and mCherry combined with the small peptide SspB-Q73R for use in iLID-based optogenetic experiments.