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Abstract RNA plays a crucial role not only in information transfer as messenger RNA during gene expression but also in various biological functions as non-coding RNAs. Understanding mechanical mechanisms of function needs tertiary structure information; however, experimental determination of three-dimensional RNA structures is costly and time-consuming, leading to a substantial gap between RNA sequence and structural data. To address this challenge, we developed NuFold, a novel computational approach that leverages state-of-the-art deep learning architecture to accurately predict RNA tertiary structures. NuFold is a deep neural network trained end-to-end for the output structure from the input sequence. NuFold incorporates a nucleobase center representation, which enables flexible conformation of ribose rings. Benchmark study showed that NuFold clearly outperformed energy-based methods and demonstrated comparable results with existing state-of-the-art deep-learning-based methods. NuFold exhibited a particular advantage in building correct local geometries of RNA. Analyses of individual components in the NuFold pipeline indicated that the performance improved by utilizing metagenome sequences for multiple sequence alignment and increasing the number of recycling. NuFold is also capable of predicting multimer complex structures of RNA by linking the input sequences.

Abstract Advanced smart polymer materials with the ability of reversible deformation under external stimuli hold great potential in robotics, soft machines, and flexible electronics. However, the complexity and low efficiency for fabricating actuators along with their limited functionality hinder further progress. Here an efficient and mild catalyst-free thiol-yne click polymerization was developed to fabricate photosensitive polyimide (PI) films. Then the fluorescent robust photoactuators with single-layered janus structure were directly obtained via UV assisted photo-crosslinking of the films, exhibiting reversible response driven by a pronounced mismatch in expansion between the front and back sides of the films. Achieving selective, non-uniform spatial distribution within the PI films, rapid and reversible complex morphing of the actuators, along with the capabilities for encrypting, reading, and erasing fluorescent information—all through the use of a single UV light source—becomes straightforward. The robust mechanical property and driving ability of these actuators enable the conversion of light energy into obvious motion even under heavy loads and the leaping through the storage and release of energy, ensuring their potential for practical applications that require durability and reliability.

3D-AF-Surfer is presented as a computational resource for real-time protein structure comparison search between AlphaFold2 models and PDB entries within seconds to a few minutes.

Abstract The vomeronasal type 2 receptor (V2R, also called OlfC) multigene family is found in a broad range of jawed vertebrates from cartilaginous fish to tetrapods. V2Rs encode receptors for food-related amino acids in teleost fish, whereas for peptide pheromones in mammals. In addition, V2Rs of teleost fish are phylogenetically distinct from those of tetrapods, implying a drastic change in the V2R repertoire during terrestrial adaptation. To understand the process of diversification of V2Rs in vertebrates from “fish-type” to “tetrapod-type”, we conducted an exhaustive search for V2Rs in cartilaginous fish (chimeras, sharks, and skates) and basal ray-finned fish (reedfish, sterlet, and spotted gar), and compared them with those of teleost, coelacanth, and tetrapods. Phylogenetic and synteny analyses on 1897 V2Rs revealed that basal ray-finned fish possess unexpectedly higher number of V2Rs compared with cartilaginous fish, implying that V2R gene repertoires expanded in the common ancestor of Osteichthyes. Furthermore, reedfish and sterlet possessed various V2Rs that belonged to both “fish-type” and “tetrapod-type”, suggesting that the common ancestor of Osteichthyes possess “tetrapod-type” V2Rs although they inhabited underwater environments. Thus, the unexpected diversity of V2Rs in basal ray-finned fish may provide insight into how the olfaction of osteichthyan ancestors adapt from water to land.

Abstract Fish possess one olfactory organ called the olfactory epithelium (OE), by which various chemical substances are detected. On the other hand, tetrapods possess two independent olfactory organs called the main olfactory epithelium (MOE) and vomeronasal organ (VNO), each of which mainly detects general odorants and pheromones, respectively. Traditionally, the VNO, so-called concentrations of vomeronasal neurons, was believed to have originated in tetrapods. However, recent studies have identified a primordial VNO in lungfish, implying that the origin of the VNO was earlier than traditionally expected. In this study, we examined the presence/absence of the VNO in the olfactory organ of bichir (Polypterus senegalus), which is the most ancestral group of extant bony vertebrates. In particular, we conducted a transcriptomic evaluation of the accessory olfactory organ (AOO), which is anatomically separated from the main olfactory organ (MOO) in bichir. As a result, several landmark genes specific to the VNO and MOE in tetrapods were both expressed in the MOO and AOO, suggesting that these organs were not functionally distinct in terms of pheromone and odorant detection. Instead, differentially expressed gene (DEG) analysis showed that DEGs in AOO were enriched in genes for cilia movement, implying its additional and specific function in efficient water uptake into the nasal cavity other than chemosensing. This transcriptomic study provides novel insight into the long-standing question of AOO function in bichir and suggests that VNO originated in the lineage of lobe-finned fish during vertebrate evolution.

Abstract Humans and bacteria have always been closely related. However, pathogenic bacteria and drug‐resistant bacteria pose a certain threat to human life and health. On the other hand, probiotics, such as intestinal flora, also affect our daily life. Understanding the microstructure of microorganisms is important for effective treatment of bacterial infections. Luminogens with aggregation‐induced emission properties are now recognized as potent fluorescent agents for the diagnosis and treatment of microorganisms. In this review, we summarized the most recent developments of AIEgen‐based biomaterials and discussed the advantages of AIE fluorescent probes for imaging. Their applications for rapid imaging of bacteria, differentiation of Gram‐ negative and positive bacteria, and specific imaging of intracellular bacteria and fungi are presented. The monitoring of bacteria‐cell interaction was also introduced. Finally, the design strategy of engineered bacteria‐AIEgen hybrid system and their role in anti‐cancer applications was discussed.

After complete spinal cord injury, spinal segments below the lesion maintain inter-segmental communication via the intraspinal propriospinal network. Here, the authors show that neurons in these circuits can be chemogenetically modulated to improve locomotor function in mice after spinal cord injury.

With the continuous development of power electronics technology, variable-speed offshore wind turbines that penetrated the grid system caused the problem of inertia reduction. This study investigates the frequency stability of synchronous, offshore wind-farm integration through a modular-multilevel-converter high-voltage direct-current (MMC–HVDC) transmission system. When full-scale converter wind turbines (type 4) penetrate the AC grid, the AC system debilitates, and it becomes difficult to maintain the AC system frequency stability. In this paper, we present an improved inertial-response-control method to solve this problem. The mathematical model of the synchronous generator is based on the swing equation and is theoretically derived by establishing a MMC–HVDC. Based on the above model, the inertia constant is analyzed using a model that integrates the MMC–HVDC and offshore synchronous generator. With the new improved control method, a more sensitive and accurate inertia index can be obtained using the formula related to the effective short-circuit ratio of the AC system. Moreover, it is advantageous to provide a more accurate inertial control evaluation for AC systems under various conditions. Furthermore, the impact of the MMC–HVDC on system safety is assessed based on the capacitor time constant. This simulation was implemented using the PSCAD/EMTDC platform.

Reporter genes have contributed to advancements in molecular biology. Binding of an upstream regulatory protein to a downstream reporter promoter allows quantification of the activity of the upstream protein produced from the corresponding gene. In studies of synthetic biology, analyses of reporter gene activities ensure control of the cell with synthetic genetic circuits, as achieved using a combination of in silico and in vivo experiments. However, unexpected effects of downstream reporter genes on upstream regulatory genes may interfere with in vivo observations. This phenomenon is termed as retroactivity. Using in silico and in vivo experiments, we found that a different copy number of regulatory protein-binding sites in a downstream gene altered the upstream dynamics, suggesting retroactivity of reporters in this synthetic genetic oscillator. Furthermore, by separating the two sources of retroactivity (titration of the component and competition for degradation), we showed that, in the dual-feedback oscillator, the level of the fluorescent protein reporter competing for degradation with the circuits’ components is important for the stability of the oscillations. Altogether, our results indicate that the selection of reporter promoters using a combination of in silico and in vivo experiments is essential for the advanced design of genetic circuits.

A brain-machine interface (BMI) is a neuroprosthetic device that can restore motor function of individuals with paralysis. Although the feasibility of BMI control of upper-limb neuroprostheses has been demonstrated, a BMI for the restoration of lower-limb motor functions has not yet been developed. The objective of this study was to determine if gait-related information can be captured from neural activity recorded from the primary motor cortex of rats, and if this neural information can be used to stimulate paralysed hindlimb muscles after complete spinal cord transection. Neural activity was recorded from the hindlimb area of the primary motor cortex of six female Sprague Dawley rats during treadmill locomotion before and after mid-thoracic transection. Before spinal transection there was a strong association between neural activity and the step cycle. This association decreased after spinal transection. However, the locomotive state (standing vs. walking) could still be successfully decoded from neural recordings made after spinal transection. A novel BMI device was developed that processed this neural information in real-time and used it to control electrical stimulation of paralysed hindlimb muscles. This system was able to elicit hindlimb muscle contractions that mimicked forelimb stepping. We propose this lower-limb BMI as a future neuroprosthesis for human paraplegics.