Using fluorescence anisotropy to monitor chaperone dispersal of RNA-binding protein condensates.

Heat stress triggers a specific set of proteins in budding yeast to form solid-like biomolecular condensates, which are dispersed by molecular chaperones. Here, we describe a protocol to study the kinetics of chaperone-facilitated condensate dispersal using biochemical reconstitution and fluorescence anisotropy. Although the current protocol is tailored to study heat-induced condensates of poly(A)-binding protein (Pab1), the protocol can be modified to study any protein which shows differential substrate binding activity upon condensation. For complete details on the use and execution of this protocol, please refer to Yoo et al. (2022).

Post-synthetic ligand cyclization in metal-organic frameworks through functional group connection with regioisomerism.

A covalent connection between two orthogonal functional groups (-NH2 and -OH) in metal-organic frameworks (MOFs) has been developed. This post-synthetic ligand cyclization (PSLC) was successfully demonstrated to synthesize a benzoxazole-functionalized MOF from a Zr-based UiO-66-2,3-(NH2)(OH) under microwave irradiation. In contrast, the regioisomeric UiO-66-2,5-(NH2)(OH) only produces a non-cyclized formamide-functionalized MOF.

Chaperones directly and efficiently disperse stress-triggered biomolecular condensates.

Stresses such as heat shock trigger the formation of protein aggregates and the induction of a disaggregation system composed of molecular chaperones. Recent work reveals that several cases of apparent heat-induced aggregation, long thought to be the result of toxic misfolding, instead reflect evolved, adaptive biomolecular condensation, with chaperone activity contributing to condensate regulation. Here we show that the yeast disaggregation system directly disperses heat-induced biomolecular condensates of endogenous poly(A)-binding protein (Pab1) orders of magnitude more rapidly than aggregates of the most commonly used misfolded model substrate, firefly luciferase. Beyond its efficiency, heat-induced condensate dispersal differs from heat-induced aggregate dispersal in its molecular requirements and mechanistic behavior. Our work establishes a bona fide endogenous heat-induced substrate for long-studied heat shock proteins, isolates a specific example of chaperone regulation of condensates, and underscores needed expansion of the proteotoxic interpretation of the heat shock response to encompass adaptive, chaperone-mediated regulation.

Reversible amyloids of pyruvate kinase couple cell metabolism and stress granule disassembly.

Cells respond to stress by blocking translation, rewiring metabolism and forming transient messenger ribonucleoprotein assemblies called stress granules (SGs). After stress release, re-establishing homeostasis and disassembling SGs requires ATP-consuming processes. However, the molecular mechanisms whereby cells restore ATP production and disassemble SGs after stress remain poorly understood. Here we show that upon stress, the ATP-producing enzyme Cdc19 forms inactive amyloids, and that their rapid re-solubilization is essential to restore ATP production and disassemble SGs in glucose-containing media. Cdc19 re-solubilization is initiated by the glycolytic metabolite fructose-1,6-bisphosphate, which directly binds Cdc19 amyloids, allowing Hsp104 and Ssa2 chaperone recruitment and aggregate re-solubilization. Fructose-1,6-bisphosphate then promotes Cdc19 tetramerization, which boosts its activity to further enhance ATP production and SG disassembly. Together, these results describe a molecular mechanism that is critical for stress recovery and directly couples cellular metabolism with SG dynamics via the regulation of reversible Cdc19 amyloids.

Reusable surface amplified nanobiosensor for the sub PFU/mL level detection of airborne virus.

We developed a reusable surface-amplified nanobiosensor for monitoring airborne viruses with a sub-PFU/mL level detection limit. Here, sandwich structures consisted of magnetic particles functionalized with antibodies, target viruses, and alkaline phosphatases (ALPs) were formed, and they were magnetically concentrated on Ni patterns near an electrochemical sensor transducer. Then, the electrical signals from electrochemical markers generated by ALPs were measured with the sensor transducer, enabling highly-sensitive virus detection. The sandwich structures in the used sensor chip could be removed by applying an external magnetic field, and we could reuse the sensor transducer chip. As a proof of concepts, the repeated detection of airborne influenza virus using a single sensor chip was demonstrated with a detection limit down to a sub-PFU/mL level. Using a single reusable sensor transducer chip, the hemagglutinin (HA) of influenza A (H1N1) virus with different concentrations were measured down to 10 aM level. Importantly, our sensor chip exhibited reliable sensing signals even after more than 18 times of the repeated HA sensing measurements. Furthermore, airborne influenza viruses collected from the air could be measured down to 0.01 PFU/mL level. Interestingly, the detailed quantitative analysis of the measurement results revealed the degradation of HA proteins on the viruses after the air exposure. Considering the ultrasensitivity and reusability of our sensors, it can provide a powerful tool to help preventing epidemics by airborne pathogens in the future.

Visible Light Photochemical Reactions for Nucleic Acid-Based Technologies.

The expanding scope of chemical reactions applied to nucleic acids has diversified the design of nucleic acid-based technologies that are essential to medicinal chemistry and chemical biology. Among chemical reactions, visible light photochemical reaction is considered a promising tool that can be used for the manipulations of nucleic acids owing to its advantages, such as mild reaction conditions and ease of the reaction process. Of late, inspired by the development of visible light-absorbing molecules and photocatalysts, visible light-driven photochemical reactions have been used to conduct various molecular manipulations, such as the cleavage or ligation of nucleic acids and other molecules as well as the synthesis of functional molecules. In this review, we describe the recent developments (from 2010) in visible light photochemical reactions involving nucleic acids and their applications in the design of nucleic acid-based technologies including DNA photocleaving, DNA photoligation, nucleic acid sensors, the release of functional molecules, and DNA-encoded libraries.

Reusable surface plasmon resonance biosensor chip for the detection of H1N1 influenza virus.

We developed a reusable magnetic surface plasmon resonance (SPR) sensor chip for detecting various target molecules repeatedly in a conventional SPR system. Here, ferromagnetic patterns on a SPR sensor chip were utilized to trap a layer of magnetic particles, and they were utilized as a solid substrate for SPR sensing in a conventional SPR system. After a sensing experiment, the used magnetic particles were removed by external magnetic fields, and a new layer of magnetic particles was immobilized to the SPR sensor chip for additional sensing measurements. Since magnetic particles were trapped on the ferromagnetic patterns, we could use our reusable SPR chip for SPR sensing measurements in a traditional SPR system without any applied magnetic fields. Significantly, ferromagnetic patterns on the sensor chip surface deflected the strong external fields, so that the large aggregation of magnetic particles on the sensor surface was reduced. We demonstrated using a single reusable SPR sensor chip to measure the nucleoprotein (NP) of H1N1 influenza virus solution ranging repeatedly for more than 7 times without significant signal degradation. Also, different target molecules could be repeatedly measured in a single SPR chip. Since our reusable SPR sensor chip can be repeatedly used in a conventional SPR system without any chemical processes for refreshment, the cost for SPR sensing should be significantly reduced. In this case, our reusable SPR sensor chip can be a major breakthrough and can be used for versatile practical applications of SPR sensors.

Cellular sensing by phase separation: Using the process, not just the products.

Phase separation creates two distinct liquid phases from a single mixed liquid phase, like oil droplets separating from water. Considerable attention has focused on how the products of phase separation-the resulting condensates-might act as biological compartments, bioreactors, filters, and membraneless organelles in cells. Here, we expand this perspective, reviewing recent results showing how cells instead use the process of phase separation to sense intracellular and extracellular changes. We review case studies in phase separation-based sensing and discuss key features, such as extraordinary sensitivity, which make the process of phase separation ideally suited to meet a range of sensory challenges cells encounter.

Dye-functionalized Sol-gel Matrix on Carbon Nanotubes for Refreshable and Flexible Gas Sensors.

We report a colorimetric dye-functionalized sol-gel matrix on carbon nanotubes for use as a refreshable and flexible gas sensor with humidity calibration. Here, we fabricated gas sensors by functionalizing dye molecules on the top of carbon nanotube networks via a sol-gel method. Using hybrid gas sensors with different dye molecules, we could selectively detect various hazardous gases, such as NH3, Cl2 and SO2 gases, via optical and electrical signals. The sensors exhibited rather large conductance changes of more than 50% following exposure to gas species with concentrations even under the permissible exposure limit. Significantly, we could refresh used gas sensors by simply exposing them to fresh N2 gas without any heat treatment. Additionally, our sensors can be bent to form versatile practical sensor devices, such as tube-shape sensors for ventilation tubes. This work shows a simple but powerful method for building refreshable and selective gas sensors for versatile industrial and academic applications.

High-Speed Lateral Flow Strategy for a Fast Biosensing with an Improved Selectivity and Binding Affinity.

We report a high-speed lateral flow strategy for a fast biosensing with an improved selectivity and binding affinity even under harsh conditions. In this strategy, biosensors were fixed at a location away from the center of a round shape disk, and the disk was rotated to create the lateral flow of a target solution on the biosensors during the sensing measurements. Experimental results using the strategy showed high reaction speeds, high binding affinity, and low nonspecific adsorptions of target molecules to biosensors. Furthermore, binding affinity between target molecules and sensing molecules was enhanced even in harsh conditions such as low pH and low ionic strength conditions. These results show that the strategy can improve the performance of conventional biosensors by generating high-speed lateral flows on a biosensor surface. Therefore, our strategy can be utilized as a simple but powerful tool for versatile bio and medical applications.

Magnetically-focusing biochip structures for high-speed active biosensing with improved selectivity.

We report a magnetically-focusing biochip structure enabling a single layered magnetic trap-and-release cycle for biosensors with an improved detection speed and selectivity. Here, magnetic beads functionalized with specific receptor molecules were utilized to trap target molecules in a solution and transport actively to and away from the sensor surfaces to enhance the detection speed and reduce the non-specific bindings, respectively. Using our method, we demonstrated the high speed detection of IL-13 antigens with the improved detection speed by more than an order of magnitude. Furthermore, the release step in our method was found to reduce the non-specific bindings and improve the selectivity and sensitivity of biosensors. This method is a simple but powerful strategy and should open up various applications such as ultra-fast biosensors for point-of-care services.

Fourier Transform Surface Plasmon Resonance of Nanodisks Embedded in Magnetic Nanorods.

In this study, we demonstrate the synthesis and application of magnetic plasmonic gyro-nanodisks (GNDs) for Fourier transform surface plasmon resonance based biodetection. Plasmonically active and magnetically responsive gyro-nanodisks were synthesized using electrochemical methods with anodized aluminum templates. Due to the unique properties of GNDs (magnetic responsiveness and surface plasmon bands), periodic extinction signals were generated under an external rotating magnetic field, which is, in turn, converted into frequency domains using Fourier transformation. After the binding of a target on GNDs, an increase in the shear force causes a shift in the frequency domain, which allows us to investigate biodetection for HA1 (the influenza virus). Most importantly, by modulating the number and the location of plasmonic nanodisks (a method for controlling the hydrodynamic forces by rationally designing the nanomaterial architecture), we achieved enhanced biodetection sensitivity. We expect that our results will contribute to improved sensing module performance, as well as a better understanding of dynamic nanoparticle systems, by harnessing the perturbed periodic fluctuation of surface plasmon bands under the modulated magnetic field.

Fourier Transform Surface Plasmon Resonance (FTSPR) with Gyromagnetic Plasmonic Nanorods.

An unprecedented active and dynamic sensing platform based on a LSPR configuration that is modulated by using an external magnetic field is reported. Electrochemically synthesized Au/Fe/Au nanorods exhibited plasmonically active behavior through plasmonic coupling, and the middle ferromagnetic Fe block responded to a magnetic impetus, allowing the nanorods to be modulated. The shear force variation induced by the specific binding events between antigens and antibodies on the nanorod surface is used to enhance the sensitivity of detection of antigens in the plasmonics-based sensor application. As a proof-of-concept, influenza A virus (HA1) was used as a target protein. The limit of detection was enhanced by two orders of magnitude compared to that of traditional LSPR sensing.

The cyanobacterial circadian clock follows midday in vivo and in vitro.

Circadian rhythms are biological oscillations that schedule daily changes in physiology. Outside the laboratory, circadian clocks do not generally free-run but are driven by daily cues whose timing varies with the seasons. The principles that determine how circadian clocks align to these external cycles are not well understood. Here, we report experimental platforms for driving the cyanobacterial circadian clock both in vivo and in vitro. We find that the phase of the circadian rhythm follows a simple scaling law in light-dark cycles, tracking midday across conditions with variable day length. The core biochemical oscillator comprised of the Kai proteins behaves similarly when driven by metabolic pulses in vitro, indicating that such dynamics are intrinsic to these proteins. We develop a general mathematical framework based on instantaneous transformation of the clock cycle by external cues, which successfully predicts clock behavior under many cycling environments.

Quantitative electrophysiological monitoring of anti-histamine drug effects on live cells via reusable sensor platforms.

We demonstrated the quantitative electrophysiological monitoring of histamine and anti-histamine drug effects on live cells via reusable sensor platforms based on carbon nanotube transistors. This method enabled us to monitor the real-time electrophysiological responses of a single HeLa cell to histamine with different concentrations. The measured electrophysiological responses were attributed to the activity of histamine type 1 receptors on a HeLa cell membrane by histamine. Furthermore, the effects of anti-histamine drugs such as cetirizine or chlorphenamine on the electrophysiological activities of HeLa cells were also evaluated quantitatively. Significantly, we utilized only a single device to monitor the responses of multiple HeLa cells to each drug, which allowed us to quantitatively analyze the antihistamine drug effects on live cells without errors from the device-to-device variation in device characteristics. Such quantitative evaluation capability of our method would promise versatile applications such as drug screening and nanoscale bio sensor researches.

"Bio-switch Chip" Based on Nanostructured Conducting Polymer and Entrapped Enzyme.

We report a switchable biochip strategy where enzymes were entrapped in conducting polymer layers and the enzymatic reaction of the entrapped enzymes was controlled in real-time via electrical stimuli on the polymer layers. This device is named here as a "bio-switch chip" (BSC). We fabricated BSC structures using polypyrrole (Ppy) with entrapped glucose oxidase (GOx) and demonstrated the switching of glucose oxidation reaction in real-time. We found that the introduction of a negative bias voltage on the BSC structure resulted in the enhanced glucose oxidation reaction by more than 20 times than that without a bias voltage. Moreover, because the BSC structures could be fabricated on specific regions, we could control the enzymatic reaction on specific regions. In view of the fact that enzymes enable very useful and versatile biochemical reactions, the ability to control the enzymatic reactions via conventional electrical signals could open up various applications in the area of biochips and other biochemical industries.

Magnetically-refreshable receptor platform structures for reusable nano-biosensor chips.

We developed a magnetically-refreshable receptor platform structure which can be integrated with quite versatile nano-biosensor structures to build reusable nano-biosensor chips. This structure allows one to easily remove used receptor molecules from a biosensor surface and reuse the biosensor for repeated sensing operations. Using this structure, we demonstrated reusable immunofluorescence biosensors. Significantly, since our method allows one to place receptor molecules very close to a nano-biosensor surface, it can be utilized to build reusable carbon nanotube transistor-based biosensors which require receptor molecules within a Debye length from the sensor surface. Furthermore, we also show that a single sensor chip can be utilized to detect two different target molecules simply by replacing receptor molecules using our method. Since this method does not rely on any chemical reaction to refresh sensor chips, it can be utilized for versatile biosensor structures and virtually-general receptor molecular species.

Drosophila Cappuccino alleles provide insight into formin mechanism and role in oogenesis.

During Drosophila development, the formin actin nucleator Cappuccino (Capu) helps build a cytoplasmic actin mesh throughout the oocyte. Loss of Capu leads to female sterility, presumably because polarity determinants fail to localize properly in the absence of the mesh. To gain deeper insight into how Capu builds this actin mesh, we systematically characterized seven capu alleles, which have missense mutations in Capu's formin homology 2 (FH2) domain. We report that all seven alleles have deleterious effects on fly fertility and the actin mesh in vivo but have strikingly different effects on Capu's biochemical activity in vitro. Using a combination of bulk and single- filament actin-assembly assays, we find that the alleles differentially affect Capu's ability to nucleate and processively elongate actin filaments. We also identify a unique "loop" in the lasso region of Capu's FH2 domain. Removing this loop enhances Capu's nucleation, elongation, and F-actin-bundling activities in vitro. Together our results on the loop and the seven missense mutations provides mechanistic insight into formin function in general and Capu's role in the Drosophila oocyte in particular.