Biophysical and Quantitative Principles of Centrosome Biogenesis and Structure.

The centrosome is a main orchestrator of the animal cellular microtubule cytoskeleton. Dissecting its structure and assembly mechanisms has been a goal of cell biologists for over a century. In the last two decades, a good understanding of the molecular constituents of centrosomes has been achieved. Moreover, recent breakthroughs in electron and light microscopy techniques have enabled the inspection of the centrosome and the mapping of its components with unprecedented detail. However, we now need a profound and dynamic understanding of how these constituents interact in space and time. Here, we review the latest findings on the structural and molecular architecture of the centrosome and how its biogenesis is regulated, highlighting how biophysical techniques and principles as well as quantitative modeling are changing our understanding of this enigmatic cellular organelle.

Orthogonal Control of Nucleic Acid Function via Chemical Caging-Decaging Strategies.

The ability to precisely control the function of nucleic acids plays an important role in biosensing and biomedicine. In recent years, novel strategies employing biological, physical, and chemical triggers have been developed to modulate the function of nucleic acids spatiotemporally. These approaches commonly involve the incorporation of stimuli-responsive groups onto nucleic acids to block their functions until triggers-induced decaging restore activity. These inventive strategies deepen our comprehension of nucleic acid molecules' dynamic behavior and provide new techniques for precise disease diagnosis and treatment. Focusing on the spatiotemporal regulation of nucleic acid molecules through the chemical caging-decaging strategy, we here present an overview of the innovative triggered control mechanisms and accentuate their implications across the fields of chemical biology, biomedicine, and biosensing.

Chemical tools for the opioids.

The opioids are potent and widely used pain management medicines despite also possessing severe liabilities that have fueled the opioid crisis. The pharmacological properties of the opioids primarily derive from agonism or antagonism of the opioid receptors, but additional effects may arise from specific compounds, opioid receptors, or independent targets. The study of the opioids, their receptors, and the development of remediation strategies has benefitted from derivatization of the opioids as chemical tools. While these studies have primarily focused on the opioids in the context of the opioid receptors, these chemical tools may also play a role in delineating mechanisms that are independent of the opioid receptors. In this review, we describe recent advances in the development and applications of opioid derivatives as chemical tools and highlight opportunities for the future.

Modular Weaving DNAzyme in Skeleton of DNA Nanocages for Photoactivatable Catalytic Activity Regulation.

DNAzymes exhibit tremendous application potentials in the field of biosensing and gene regulation due to its unique catalytic function. However, spatiotemporally controlled regulation of DNAzyme activity remains a daunting challenge, which may cause nonspecific signal leakage or gene silencing of the catalytic systems. Here, we report a photochemical approach via modular weaving active DNAzyme into the skeleton of tetrahedral DNA nanocages (TDN) for light-triggered on-demand liberation of DNAzyme and thus conditional control of gene regulation activity. We demonstrate that the direct encoding of DNAzyme in TDN could improve the biostability of DNAzyme and ensure the delivery efficiency, comparing with the conventional surface anchoring strategy. Furthermore, the molecular weaving of the DNA nanostructures allows remote control of DNAzyme-mediated gene regulation with high spatiotemporal precision of light. In addition, we demonstrate that the approach is applicable for controlled regulation of the gene editing functions of other functional nucleic acids.

MicroRNA-Triggered Programmable DNA-Encoded Pre-PROTACs for Cell-Selective and Controlled Protein Degradation.

Proteolysis-targeting chimeras (PROTACs) have accelerated drug development; however, some challenges still exist owing to their lack of tumor selectivity and on-demand protein degradation. Here, we developed a miRNA-initiated assembled pre-PROTAC (miRiaTAC) platform that enables the on-demand activation and termination of target degradation in a cell type-specific manner. Using miRNA-21 as a model, we engineered DNA hairpins labeled with JQ-1 and pomalidomide and facilitated the modular assembly of DNA-encoded pre-PROTACs through a hybridization chain reaction. This configuration promoted the selective polyubiquitination and degradation of BRD4 upon miR-21 initiation, highlighting significant tumor selectivity and minimal systemic toxicity. Furthermore, the platform incorporates photolabile groups, enabling the precise optical control of pre-PROTACs during DNA assembly/disassembly, mitigating the risk of excessive protein degradation. Additionally, by introducing a secondary ligand targeting CDK6, these pre-PROTACs were used as a modular scaffold for the programmable assembly of active miRiaTACs containing two different warheads in exact stoichiometry, enabling orthogonal multitarget degradation. The integration of near-infrared light-mediated photodynamic therapy through an upconversion nanosystem further enhanced the efficacy of the platform with potent in vivo anticancer activity. We anticipate that miRiaTAC represents a significant intersection between dynamic DNA nanotechnology and PROTAC, potentially expanding the versatility of PROTAC toolkit for cancer therapy.

Spatiotemporal Investigation of Intercellular Heterogeneity via Multiple Photocaged Probes.

Intercellular heterogeneity occurs widely under both normal physiological environments and abnormal disease-causing conditions. Several attempts to couple spatiotemporal information to cell states in a microenvironment were performed to decipher the cause and effect of heterogeneity. Furthermore, spatiotemporal manipulation can be achieved with the use of photocaged/photoactivatable molecules. Here, we provide a platform to spatiotemporally analyze differential protein expression in neighboring cells by multiple photocaged probes coupled with homemade photomasks. We successfully established intercellular heterogeneity (photoactivable ROS trigger) and mapped the targets (directly ROS-affected cells) and bystanders (surrounding cells), which were further characterized by total proteomic and cysteinomic analysis. Different protein profiles were shown between bystanders and target cells in both total proteome and cysteinome. Our strategy should expand the toolkit of spatiotemporal mapping for elucidating intercellular heterogeneity.

A Conformational Restriction Strategy for the Control of CRISPR/Cas Gene Editing with Photoactivatable Guide RNAs.

The CRISPR/Cas system is one of the most powerful tools for gene editing. However, approaches for precise control of genome editing and regulatory events are still desirable. Here, we report the spatiotemporal and efficient control of CRISPR/Cas9- and Cas12a-mediated editing with conformationally restricted guide RNAs (gRNAs). This approach relied on only two or three pre-installed photo-labile substituents followed by an intramolecular cyclization, representing a robust synthetic method in comparison to the heavily modified linear gRNAs that often require extensive screening and time-consuming optimization. This tactic could direct the precise cleavage of the genes encoding green fluorescent protein (GFP) and the vascular endothelial growth factor A (VEGFA) protein within a predefined cutting region without notable editing leakage in live cells. We also achieved light-mediated myostatin (MSTN) gene editing in embryos, wherein a new bow-knot-type gRNA was constructed with excellent OFF/ON switch efficiency. Overall, our work provides a significant new strategy in CRISPR/Cas editing with modified circular gRNAs to precisely manipulate where and when genes are edited.

Photoactivated DNA Assembly and Disassembly for On-Demand Activation and Termination of cGAS-STING Signaling.

Despite significant progress in DNA self-assembly for interfacing with biology, spatiotemporally controlled regulation of biological process via in situ dynamic DNA assembly remains an outstanding challenge. Here, we report an optically triggered DNA assembly and disassembly strategy that enables on-demand activation and termination of the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling pathway. In the design, an activatable DNA hairpin is engineered with a photocleavable group at defined site to modulate its self-assembly activity. Light activation induces the configurational switching and consequent self-assembly of the DNA hairpins to form long linear double-stranded structures, allowing to stimulate cGAS protein to synthesize 2',3'-cyclic-GMP-AMP (cGAMP) for STING stimulation. Furthermore, by endowing the pre-assembled DNA scaffold with a built-in photolysis feature, we demonstrate that the cGAS-STING stimulation can be efficiently terminated through remote photo-triggering, providing for the first time a route to control the temporal "dose" on-demand for such a stimulation. We envision that this regulation strategy will benefit and inspire both fundamental research and therapeutic applications regarding the cGAS-STING pathway.

Precise modulation of embryonic development through optogenetics.

The past decade has witnessed enormous progress in optogenetics, which uses photo-sensitive proteins to control signal transduction in live cells and animals. The ever-increasing amount of optogenetic tools, however, could overwhelm the selection of appropriate optogenetic strategies. In this work, we summarize recent progress in this emerging field and highlight the application of opsin-free optogenetics in studying embryonic development, focusing on new insights gained into optical induction of morphogenesis, cell polarity, cell fate determination, tissue differentiation, neuronal regeneration, synaptic plasticity, and removal of cells during development.

Photoactivation of Innate Immunity Receptor TLR8 in Live Mammalian Cells by Genetic Encoding of Photocaged Tyrosine.

The effectiveness of innate immune responses relies on an intricate balance between activation and regulation. TLR8, a member of the Toll-like receptor (TLR) family, plays a fundamental role in host defense by sensing viral single-stranded RNAs (ssRNAs). However, the molecular recognition and regulatory mechanism of TLR8 is not fully understood, especially in a whole-cell environment. Here, we engineer the first light-controllable TLR8 model by genetically encoding a photocaged tyrosine, NBY, into specific sites of TLR8. In the caged forms, the activity of TLR8 is masked but can be restored upon decaging by exposure to UV light. To explain the mechanism clearly, we divide the sites with light responsiveness into three groups. They can separately block the ligands that bind to the pockets of TLR8, change the interaction modes between two TLR8 protomers, and interfere with the interactions between TLR8 cytosolic domains with its downstream adaptor. Specifically, we use this chemical caging strategy to probe and evaluate the function of several tyrosine sites located at the interface of TLR8 homodimers with a previously unknown regulatory mode, which may provide a new strategy for TLR8 modulator development. Effects on downstream signaling pathways are monitored at the transcriptional and translational levels in various cell lines. By photoactivating specific cells within a larger population, this powerful tool can provide novel mechanistic insights, with potential in biotechnological and pharmaceutical applications.

A Light-Activatable Photocaged Variant of the Ultra-High Affinity ALFA-Tag Nanobody.

Nanobodies against short linear peptide-epitopes are widely used to detect and bind proteins of interest (POI) in fusion constructs. Engineered nanobodies that can be controlled by light have found very recent attention for various extra- and intracellular applications. We here report the design of a photocaged variant of the ultra-high affinity ALFA-tag nanobody, also termed ALFA-tag photobody. ortho-Nitrobenzyl tyrosine was incorporated into the paratope region of the nanobody by genetic code expansion technology and resulted in a ≥9,200 to 100,000-fold impairment of the binding affinity. Irradiation with light (365 nm) leads to decaging and reconstitutes the native nanobody. We show the light-dependent binding of the ALFA-tag photobody to HeLa cells presenting the ALFA-tag. The generation of the first photobody directed against a short peptide epitope underlines the generality of our photobody design concept. We envision that this photobody will be useful for the spatiotemporal control of proteins in many applications using cultured cells.

High-intensity focused ultrasound-induced mechanochemical transduction in synthetic elastomers.

While study in the field of polymer mechanochemistry has yielded mechanophores that perform various chemical reactions in response to mechanical stimuli, there is not yet a triggering method compatible with biological systems. Applications such as using mechanoluminescence to generate localized photon flux in vivo for optogenetics would greatly benefit from such an approach. Here we introduce a method of triggering mechanophores by using high-intensity focused ultrasound (HIFU) as a remote energy source to drive the spatially and temporally resolved mechanical-to-chemical transduction of mechanoresponsive polymers. A HIFU setup capable of controlling the excitation pressure, spatial location, and duration of exposure is employed to activate mechanochemical reactions in a cross-linked elastomeric polymer in a noninvasive fashion. One reaction is the chromogenic isomerization of a naphthopyran mechanophore embedded in a polydimethylsiloxane (PDMS) network. Under HIFU irradiation evidence of the mechanochemical transduction is the observation of a reversible color change as expected for the isomerization. The elastomer exhibits this distinguishable color change at the focal spot, depending on ultrasonic exposure conditions. A second reaction is the demonstration that HIFU irradiation successfully triggers a luminescent dioxetane, resulting in localized generation of visible blue light at the focal spot. In contrast to conventional stimuli such as UV light, heat, and uniaxial compression/tension testing, HIFU irradiation provides spatiotemporal control of the mechanochemical activation through targeted but noninvasive ultrasonic energy deposition. Targeted, remote light generation is potentially useful in biomedical applications such as optogenetics where a light source is used to trigger a cellular response.

Spatiotemporal Thermal Control Effects on Thermal Grill Illusion.

The thermal grill illusion induces a pain sensation under a spatial display of warmth and coolness of approximately 40 °C; and 20 °C. To realize virtual pain display more universally during the virtual reality experience, we proposed a spatiotemporal control method to realize a variable thermal grill illusion and evaluated the effect of the method. First, we examined whether there was a change in the period until pain occurred due to the spatial temperature distribution of pre-warming and pre-cooling and verified whether the period until pain occurred became shorter as the temperature difference between pre-warming and pre-cooling increased. Next, we examined the effect of the number of grids on the illusion and verified the following facts. In terms of the pain area, the larger the thermal area, the larger the pain area. In terms of the magnitude of the pain, the larger the thermal area, the greater the magnitude of the sensation of pain.

Development and application of light-controlled inducible recombination systems.

The site-specific recombination systems are composed of recombinases and specific recognition sites, which are powerful tools for gene manipulation and have been extensively used in life sciences research. Inducible recombination systems have been developed to precisely regulate gene expression in a spatiotemporal manner in cells and animals for applications such as gene function research, cell lineage tracing and disease treatment. Based on different spatiotemporal expression methods of recombinases, inducible recombination systems can be divided into two categories: chemical- controlled and light-controlled inductions. Light-controlled inducible recombination systems that utilize light as inducer consist of photocage and optogenetics in accordance with optical control patterns and objects. Photocaged inducible recombination systems are using photosensitive groups to control chemical inducers or recombinases. Their activities are inhibited by photosensitive groups before light induction and recovered after specific light irradiation, leading to light-controlled inducible gene recombination. While optogenetic inducible recombination systems rely on reactivations of split recombinases that mediated by optogenetic switches. Optogenetic switches are composed of a series of gene-encoded photosensitive proteins, including cryptochromes, VIVID, phytochromes, etc. These types of light-controlled inducible recombination systems provide more possibilities for analyzing gene expression and function from the dimension of high spatiotemporal resolution to meet the increasingly complex demands of life science research. In this review, we summarize the developing principles and applications of different types of light-controlled inducible recombination systems, compare their advantages and disadvantages, and prospect the development of more light-controlled recombination systems in the future, with the aims to provide theoretical basis and guidance for system optimization and upgrade.

A Sonication-Activated Valence-Variable Sono-Sensitizer/Catalyst for Autography Inhibition/Ferroptosis-Induced Tumor Nanotherapy.

The effective deployment of reactive oxygen species (ROS)-mediated oncotherapy in practice remains challenging, mired by uncontrollable catalytic processes, stern reaction conditions and safety concerns. Herein, we develop a copper nanodot integrating sonodynamic and catalytic effects within one active center, which responds to exogenous ultrasound (US) and endogenous H2 O2 stimuli. US irradiation induces the valence conversion from CuII to CuI catalyzing H2 O2 into ⋅OH for chemodynamic therapy. Meanwhile, valence transformation results in electron-hole pairs separation, promoting ROS generation for sonodynamic therapy. Notably, copper nanodots not only block lysosome fusion and degradation leading to autophagy flux blockage, but also interfere with the glutathione peroxidase 4 and cystine-glutamate antiporter SLC7A11 function achieving ferroptosis. Furthermore, reversible valence changes, inherent hydrophilicity and renal clearance ultrasmall size guarantee biosafety.

Spatiotemporally Selective Molecular Imaging via Upconversion Luminescence-Controlled, DNA-Based Biosensor Technology.

DNA-based biosensor technologies have shown great potential in chemical and biological detection. These biosensors have been actively developed as probes for molecular imaging in live cells and in animals, allowing in situ detection of analytes in complex biological systems, elucidation of the roles of key molecules in biological processes, and the development of non-invasive diagnosis and image-guided surgery. Despite the progress made, improving the spatial-temporal precision remains a challenge in this field. In this Minireview, we describe the concepts behind spatiotemporally selective molecular imaging via the combination of engineered, light-activatable DNA-based biosensors and upconversion nanotechnology. We then highlight the application of the approach for the spatiotemporally controlled imaging of various targets in specific intracellular organelles, signal amplification, as well as the regulation of targeting activity to receptor proteins. We finally discuss the challenges and perspectives for possible future developments in this emerging field.

Eye movement influences on coupled and decoupled eye-hand coordination tasks.

Visually guided reaching precision and accuracy depend on the level of coupling between movements of the eyes and hand. In the present study, participants performed central fixations and either saccadic or smooth pursuit eye movements during fast and accurate reaching tasks involving eye-hand coupling and decoupling to better understand type of eye movement influence over upper limb control. Some eye-hand coupling and decoupling tasks also included hand reversals, where the hand moves away from the target to direct a cursor toward the target to account for various levels of hand-cursor and eye-cursor coupling. Regardless of eye-movement type, eye-hand-cursor coupling produced an endpoint accuracy advantage over decoupling. Use of hand reversal decreased peak speed and increased response time of the hand, whether considering fixation or a given eye movement. Use of smooth pursuit slowed hand movements relative to saccades, yet improved endpoint accuracy. Compared to central fixations, using smooth pursuit also slowed hand movements, while using saccades decreased, thus improved, hand reaction times. Data suggest an advantage, when using smooth pursuit to track the hand movement for the greatest endpoint accuracy, an advantage when using saccades for the fastest movements, and an eye-hand coupling advantage when using saccades for the shortest reactions. Researchers should provide clear eye-movement instructions for participants and/or monitor the eyes when assessing similar upper limb control to account for possible differences in eye movements used. Moreover, the type of eye movement chosen for participants should correspond to the primary goal of the task.

Macrophage-mediated degradable gelatin-coated mesoporous silica nanoparticles carrying pirfenidone for the treatment of rat spinal cord injury.

The treatment of spinal cord injury is still a challenge worldwide; there is still no effective method. Our strategy is to devise a macrophage-mediated degradable gelatin coated mesoporous silica nanoparticles, which could carry pirfenidone and realize spatiotemporal control of pirfenidone release in the lesion site. For the in vivo experiment, three groups of SD rats subjected to spinal cord contusion injury were injected with GNS-PFD, PFD or PBS. Spinal cord functions were observed. In vitro, we investigated the expression of inflammatory and anti-inflammatory factors. Spinal cord function and recovery were better in the GSN-PFD and PFD than the control group. In the in vitro study, the MMPs after SCI in lesion site were lower in the experimental group. Moreover, the expression of anti-inflammatory and inflammatory factors showed better in the experimental group. The inflammatory response of the PFD to time and space can be achieved with the loading of macrophage-mediated degradable gelatin coated mesoporous silica nanoparticles.

A Light-Controllable Chemical Modulation of m6 A RNA Methylation.

Bioactive small molecules with photo-removable protecting groups have provided spatial and temporal control of corresponding biological effects. We present the design, synthesis, computational and experimental evaluation of the first photo-activatable small-molecule methyltransferase agonist. By blocking the functional N-H group on MPCH with a photo-removable ortho-nitrobenzyl moiety, we have developed a promising photo-caged compound that had completely concealed its biological activity. Short UV light exposure of cells treated with that caged molecule in a few minutes resulted in a considerable hypermethylation of m6 A modification in transcriptome RNAs, implicating a rapid release of the parent active compound. This study validates for the first time the photo-activatable small organic molecular concept in the field of RNA epigenetic research, which represents a novel tool in spatiotemporal and cellular modulation approaches.

Spatiotemporal Dynamics of Aggregation-Induced Emission Enhancement Controlled by Optical Manipulation.

We present spatiotemporal control of aggregation-induced emission enhancement (AIEE) of a protonated tetraphenylethene derivative by optical manipulation. A single submicrometer-sized aggregate is initially confined by laser irradiation when its fluorescence is hardly detectable. The continuous irradiation of the formed aggregate leads to sudden and rapid growth, resulting in bright yellow fluorescence emission. The fluorescence intensity at the peak wavelength of 540 nm is tremendously enhanced with growth, meaning that AIEE is activated by optical manipulation. Amazingly, the switching on/off of the activation of AIEE is arbitrarily controlled by alternating the laser power. This result means that optical manipulation increases the local concentration, which overcomes the electrostatic repulsion between the protonated molecules, namely, optical manipulation changes the aggregate structure. The dynamics and mechanism in AIEE controlled by optical manipulation will be discussed from the viewpoint of molecular conformation and association depending on the laser power.