Light regulates widespread plant alternative polyadenylation through the chloroplast.

Transcription of eukaryotic protein-coding genes generates immature mRNAs that are subjected to a series of processing events, including capping, splicing, cleavage, and polyadenylation (CPA), and chemical modifications of bases. Alternative polyadenylation (APA) greatly contributes to mRNA diversity in the cell. By determining the length of the 3' untranslated region, APA generates transcripts with different regulatory elements, such as miRNA and RBP binding sites, which can influence mRNA stability, turnover, and translation. In the model plant Arabidopsis thaliana, APA is involved in the control of seed dormancy and flowering. In view of the physiological importance of APA in plants, we decided to investigate the effects of light/dark conditions and compare the underlying mechanisms to those elucidated for alternative splicing (AS). We found that light controls APA in approximately 30% of Arabidopsis genes. Similar to AS, the effect of light on APA requires functional chloroplasts, is not affected in mutants of the phytochrome and cryptochrome photoreceptor pathways, and is observed in roots only when the communication with the photosynthetic tissues is not interrupted. Furthermore, mitochondrial and TOR kinase activities are necessary for the effect of light. However, unlike AS, coupling with transcriptional elongation does not seem to be involved since light-dependent APA regulation is neither abolished in mutants of the TFIIS transcript elongation factor nor universally affected by chromatin relaxation caused by histone deacetylase inhibition. Instead, regulation seems to correlate with changes in the abundance of constitutive CPA factors, also mediated by the chloroplast.

A Low-Power High-Sensitivity Photocurrent Sensory Circuit with Capacitive Feedback Transimpedance for Photoplethysmography Sensing.

This study presents an integrated analog front-end (AFE) tailored for photoplethysmography (PPG) sensing. The AFE module introduces a novel transimpedance amplifier (TIA) that incorporates capacitive feedback techniques alongside common drain feedback (CDF) TIA. The unique TIA topology achieves both high gain and high sensitivity while maintaining low power consumption. The resultant PPG sensor module demonstrates impressive specifications, including an input noise current of 4.81 pA/sqrt Hz, a transimpedance gain of 18.43 MΩ, and a power consumption of 68 µW. Furthermore, the sensory system integrates an LED driver featuring automatic light control (ALC), which dynamically adjusts the LED power based on the strength of the received signal. Employing 0.35 µm CMOS technology, the AFE implementation occupies a compact footprint of 1.98 mm × 2.475 mm.

Adaptive urban traffic signal control based on enhanced deep reinforcement learning.

One of the focal points in the field of intelligent transportation is the intelligent control of traffic signals (TS), aimed at enhancing the efficiency of urban road networks through specific algorithms. Deep Reinforcement Learning (DRL) algorithms have become mainstream, yet they suffer from inefficient training sample selection, leading to slow convergence. Additionally, enhancing model robustness is crucial for adapting to diverse traffic conditions. Hence, this paper proposes an enhanced method for traffic signal control (TSC) based on DRL. This approach utilizes dueling network and double q-learning to alleviate the overestimation issue of DRL. Additionally, it introduces a priority sampling mechanism to enhance the utilization efficiency of samples in memory. Moreover, noise parameters are integrated into the neural network model during training to bolster its robustness. By representing high-dimensional real-time traffic information as matrices, and employing a phase-cycled action space to guide the decision-making of intelligent agents. Additionally, utilizing a reward function that closely mirrors real-world scenarios to guide model training. Experimental results demonstrate faster convergence and optimal performance in metrics such as queue length and waiting time. Testing experiments further validate the method's robustness across different traffic flow scenarios.

Research on optimization method for traffic signal control at intersections in smart cities based on adaptive artificial fish swarm algorithm.

The transportation environment of smart cities is complex and ever-changing, and traffic flow is influenced by various factors. With the increase of traffic flow in smart cities, optimizing traffic intersection signal control has become an important method to improve traffic efficiency and reduce congestion. To this end, a smart city traffic intersection(SCTI) signal control optimization method based on adaptive artificial fish swarm algorithm was studied. Establish the Equation of state of traffic flow at SCTIs to understand the actual traffic flow at SCTIs. On this basis, design SCTI signal control parameters, with the minimum average delay and average number of stops as objective functions, and construct an optimization model for SCTI signal control. By combining chaotic search theory and adaptively improving the artificial fish swarm algorithm, based on the adaptive artificial fish swarm algorithm, the intelligent city traffic intersection signal control optimization model is solved to achieve intelligent city traffic intersection signal control optimization. The experimental results show that the average delay of this method is 7.8 ms, the average number of stops is 2, and the travel time is 68.4 s s. Thus, it is proved that the method in this paper has a good optimization effect of traffic signal control at smart city intersections, which can improve the optimization efficiency of traffic signal control at smart city intersections and reduce traffic congestion at smart city intersections.

Light Control in Microbial Systems.

Light is a key environmental component influencing many biological processes, particularly in prokaryotes such as archaea and bacteria. Light control techniques have revolutionized precise manipulation at molecular and cellular levels in recent years. Bacteria, with adaptability and genetic tractability, are promising candidates for light control studies. This review investigates the mechanisms underlying light activation in bacteria and discusses recent advancements focusing on light control methods and techniques for controlling bacteria. We delve into the mechanisms by which bacteria sense and transduce light signals, including engineered photoreceptors and light-sensitive actuators, and various strategies employed to modulate gene expression, protein function, and bacterial motility. Furthermore, we highlight recent developments in light-integrated methods of controlling microbial responses, such as upconversion nanoparticles and optical tweezers, which can enhance the spatial and temporal control of bacteria and open new horizons for biomedical applications.

Perspectives: Light Control of Magnetism and Device Development.

Accurately controlling magnetic and spin states presents a significant challenge in spintronics, especially as demands for higher data storage density and increased processing speeds grow. Approaches such as light control are gradually supplanting traditional magnetic field methods. Traditionally, the modulation of magnetism was predominantly achieved through polarized light with the help of ultrafast light technologies. With the growing demand for energy efficiency and multifunctionality in spintronic devices, integrating photovoltaic materials into magnetoelectric systems has introduced more physical effects. This development suggests that sunlight will play an increasingly pivotal role in manipulating spin orientation in the future. This review introduces and concludes the influence of various light types on magnetism, exploring mechanisms such as magneto-optical (MO) effects, light-induced magnetic phase transitions, and spin photovoltaic effects. This review briefly summarizes recent advancements in the light control of magnetism, especially sunlight, and their potential applications, providing an optimistic perspective on future research directions in this area.

AwSclB regulates a network for Aspergillus westerdijkiae asexual sporulation and secondary metabolism independent of the fungal light control.

As a prevalent pathogenic fungus, Aspergillus westerdijkiae poses a threat to both food safety and human health. The fungal growth, conidia production and ochratoxin A (OTA) in A. weterdijkiae are regulated by many factors especially transcription factors. In this study, a transcription factor AwSclB in A. westerdijkiae was identified and its function in asexual sporulation and OTA biosynthesis was investigated. In addition, the effect of light control on AwSclB regulation was also tested. The deletion of AwSclB gene could reduce conidia production by down-regulation of conidia genes and increase OTA biosynthesis by up-regulation of cluster genes, regardless under light or dark conditions. It is worth to note that the inhibitory effect of light on OTA biosynthesis was reversed by the knockout of AwSclB gene. The yeast one-hybrid assay indicated that AwSclB could interact with the promoters of BrlA, ConJ and OtaR1 genes. This result suggests that AwSclB in A. westerdijkiae can directly regulate asexual conidia formation by activating the central developmental pathway BrlA-AbaA-WetA through up-regulating the expression of AwBrlA, and promote the light response of the strain by activating ConJ. However, AwSclB itself is unable to respond to light regulation. This finding will deepen our understanding of the molecular regulation of A. westerdijkiae development and secondary metabolism, and provide potential targets for the development of new fungicides.

Photoactivatable Nanobody Conjugate Dimerizer Temporally Resolves Tiam1-Rac1 Signaling Axis.

The precise spatiotemporal dynamics of protein activities play a crucial role in cell signaling pathways. To control cellular functions in a spatiotemporal manner, a powerful method called photoactivatable chemically induced dimerization (pCID) is used. In this study, photoactivatable nanobody conjugate inducers of dimerization (PANCIDs) is introduced, which combine pCID with nanobody technology. A PANCID consists of a nanobody module that directly binds to an antigenic target, a photocaged small molecule ligand, and a cyclic decaarginine (cR10 *) cell-penetrating peptide (CPP) for efficient nonendocytic intracellular delivery. Therefore, PANCID photodimerizers also benefit from nanobodies, such as their high affinities (in the nm or pm range), specificities, and ability to modulate endogenous proteins. Additionally it is demonstrated that the nanobody moiety can be easily replaced with alternative ones, expanding the potential applications. By using PANCIDs, the dynamics of the Tiam1-Rac1 signaling cascade is investigated and made an interesting finding. It is found that Rac1 and Tiam1 exhibit distinct behaviors in this axis, acting as time-resolved "molecular oscillators" that transit between different functions in the signaling cascade when activated either slowly or rapidly.

A sensing platform for ascorbic acid based on the spatial confinement of covalent organic frameworks.

Essential to many activities in our bodies, ascorbic acid is a small molecule essential to human health and physiological processes. In this study, a covalent organic framework called TpNda-COF was synthesized, which is composed of Tp (triformylephloroglucinol) and Nda (1, 5-napthalenediamine). This framework acts as a mimic enzyme and displays excellent oxidase-like activity when stimulated with purple light (at = 405 nm). It catalyzes the oxidation of 3,3',5,5'-tetramethylbenzydine (TMB) by generating O2- free radicals in the presence of oxygen. The resulting oxTMB shows a characteristic absorption peak at 652 nm. The biomimetic catalysis efficiency is significantly improved due to spatial restriction. By introducing ascorbic acid (AA) in the system, the blue oxTMB is reduced to colorless TMB. The decrease in absorption peak intensity can be quantitatively measured using a UV-Vis spectrophotometer, enabling the detection of AA. The sensing platform demonstrates excellent selectivity and sensitivity. It has a wide linear detection range from 5 µM to 50 µM, with a low detection limit of 1.44 µM. Advantages such as the easy control of light, high stability and efficient oxidation are provided by the TpNda-COF mimic oxidase. This innovative method presents a promising and cost-effective approach for rapid detection of ascorbic acid, with potential applications across various fields.

Progress and Prospects in Metallic FexGeTe2 (3 ≤ x ≤ 7) Ferromagnets.

Thermal fluctuations in two-dimensional (2D) isotropy systems at non-zero finite temperatures can destroy the long-range (LR) magnetic order due to the mechanisms addressed in the Mermin-Wanger theory. However, the magnetic anisotropy related to spin-orbit coupling (SOC) may stabilize magnetic order in 2D systems. Very recently, 2D FexGeTe2 (3 ≤ x ≤ 7) with a high Curie temperature (TC) has not only undergone significant developments in terms of synthetic methods and the control of ferromagnetism (FM), but is also being actively explored for applications in various devices. In this review, we introduce six experimental methods, ten ferromagnetic modulation strategies, and four spintronic devices for 2D FexGeTe2 materials. In summary, we outline the challenges and potential research directions in this field.

Applications of genetic code expansion and photosensitive UAAs in studying membrane proteins.

Membrane proteins are the targets for most drugs and play essential roles in many life activities in organisms. In recent years, unnatural amino acids (UAAs) encoded by genetic code expansion (GCE) technology have been widely used, which endow proteins with different biochemical properties. A class of photosensitive UAAs has been widely used to study protein structure and function. Combined with photochemical control with high temporal and spatial resolution, these UAAs have shown broad applicability to solve the problems of natural ion channels and receptor biology. This review will focus on several application examples of light-controlled methods to integrate GCE technology to study membrane protein function in recent years. We will summarize the typical research methods utilizing some photosensitive UAAs to provide common strategies and further new ideas for studying protein function and advancing biological processes.

Optogenetic Calcium Ion Influx in Myoblasts and Myotubes by Near-Infrared Light Using Upconversion Nanoparticles.

Bioactuators made of cultured skeletal muscle cells are generally driven by electrical or visible light stimuli. Among these, the technology to control skeletal muscle consisting of myoblasts genetically engineered to express photoreceptor proteins with visible light is very promising, as there is no risk of cell contamination by electrodes, and the skeletal muscle bioactuator can be operated remotely. However, due to the low biopermeability of visible light, it can only be applied to thin skeletal muscle films, making it difficult to realize high-power bioactuators consisting of thick skeletal muscle. To solve this problem, it is desirable to realize thick skeletal muscle bioactuators that can be driven by near-infrared (NIR) light, to which living tissue is highly permeable. In this study, as a promising first step, upconversion nanoparticles (UCNPs) capable of converting NIR light into blue light were bound to C2C12 myoblasts expressing the photoreceptor protein channelrhodopsin-2 (ChR2), and the myoblasts calcium ion (Ca2+) influx was remotely manipulated by NIR light exposure. UCNP-bound myoblasts and UCNP-bound differentiated myotubes were exposed to NIR light, and the intracellular Ca2+ concentrations were measured and compared to myoblasts exposed to blue light. Exposure of the UCNP-bound cells to NIR light was found to be more efficient than exposure to blue light in terms of stimulating Ca2+ influx.

Design principles for engineering light-controlled antibodies.

Engineered antibodies are essential tools for research and advanced pharmacy. In the development of therapeutics, antibodies are excellent candidates as they offer both target recognition and modulation. Thanks to the latest advances in biotechnology, light-activated antibody fragments can be constructed to control spontaneous antigen interaction with high spatiotemporal precision. To implement conditional antigen binding, several optogenetic and optochemical engineering concepts have recently been developed. Here, we highlight the various strategies and discuss the features of opto-conditional antibodies. Each concept offers intrinsic advantages beneficial to different applications. In summary, the novel design approaches constitute a complementary toolset to promote current and upcoming antibody technologies with ultimate precision.

Effect of Controlling Light on Cashmere Growth and Harmful Gas Parameters in Shanbei White Cashmere Goats.

The quality and yield of cashmere closely affect the economic benefits of cashmere goat farming. Studies have shown that controlling light can have an important impact on cashmere but can also affect the concentration of harmful gases. In order to explore the impact of a short photoperiod on the growth of cashmere and harmful gases in goat houses, 130 female (non-pregnant) Shanbei white cashmere goats, aged 4-5 years with similar body weights, were randomly divided into a control group and a treatment group, with 65 goats in each group. The dietary nutrition levels of the experimental goats were the same, and completely natural light was used in the control group; the light control group received light for 7 h every day (9:30-16:30), and the rest of the time (16:30-9:30 the next day) they did not receive light. The light control treatment was carried out in a control house, and the gas content was analyzed. It was found that a shortened period of light exposure could increase the annual average cashmere production by 34.5%. The content of each gas has a certain functional relationship with the measurement time period, but at the same time, we found that the content of NH3 also changes seasonally. In summary, the use of shortened light periods when raising cashmere goats can significantly increase cashmere production and quality, but at the same time, it will increase the concentration of harmful gases in the goat barn, and ventilation should be increased to ensure the health of the goats and the air quality in the barn.

Light control of droplets on photo-induced charged surfaces.

The manipulation of droplets plays a vital role in fundamental research and practical applications, from chemical reactions to bioanalysis. As an intriguing and active format, light control of droplets, typically induced by photochemistry, photomechanics, light-induced Marangoni effects or light-induced electric fields, enables remote and contactless control with remarkable spatial and temporal accuracy. However, current light control of droplets suffers from poor performance and limited reliability. Here we develop a new superamphiphobic material that integrates the dual merits of light and electric field by rationally preparing liquid metal particles/poly(vinylidene fluoride-trifluoroethylene) polymer composites with photo-induced charge generation capability in real time, enabling light control of droplets on the basis of photo-induced dielectrophoretic force. We demonstrate that this photo-induced charged surface (PICS) imparts a new paradigm for controllable droplet motion, including high average velocity (∼35.9 mm s-1), unlimited distance, multimode motions (e.g. forward, backward and rotation) and single-to-multiple droplet manipulation, which are otherwise unachievable in conventional strategies. We further extend light control of droplets to robotic and bio-applications, including transporting a solid cargo in a closed tube, crossing a tiny tunnel, avoiding obstacles, sensing the changing environment via naked-eye color shift, preparing hydrogel beads, transporting living cells and reliable biosensing. Our PICS not only provides insight into the development of new smart interface materials and microfluidics, but also brings new possibilities for chemical and biomedical applications.

Implementation of a Novel Optogenetic Tool in Mammalian Cells Based on a Split T7 RNA Polymerase.

Optogenetic tools are widely used to control gene expression dynamics both in prokaryotic and eukaryotic cells. These tools are used in a variety of biological applications from stem cell differentiation to metabolic engineering. Despite some tools already available in bacteria, no light-inducible system currently exists to control gene expression independently from mammalian transcriptional and/or translational machineries thus working orthogonally to endogenous regulatory mechanisms. Such a tool would be particularly important in synthetic biology, where orthogonality is advantageous to achieve robust activation of synthetic networks. Here we implement, characterize, and optimize a new optogenetic tool in mammalian cells based on a previously published system in bacteria called Opto-T7RNAPs. The tool is orthogonal to the cellular machinery for transcription and consists of a split T7 RNA polymerase coupled with the blue light-inducible magnets system (mammalian OptoT7-mOptoT7). In our study we exploited the T7 polymerase's viral origins to tune our system's expression level, reaching up to an almost 20-fold change activation over the dark control. mOptoT7 is used here to generate mRNA for protein expression, shRNA for protein inhibition, and Pepper aptamer for RNA visualization. Moreover, we show that mOptoT7 can mitigate the gene expression burden when compared to another optogenetic construct. These properties make mOptoT7 a powerful new tool to use when orthogonality and viral RNA species (that lack endogenous RNA modifications) are desired.

Platforms for Optogenetic Stimulation and Feedback Control.

Harnessing the potential of optogenetics in biology requires methodologies from different disciplines ranging from biology, to mechatronics engineering, to control engineering. Light stimulation of a synthetic optogenetic construct in a given biological species can only be achieved via a suitable light stimulation platform. Emerging optogenetic applications entail a consistent, reproducible, and regulated delivery of light adapted to the application requirement. In this review, we explore the evolution of light-induction hardware-software platforms from simple illumination set-ups to sophisticated microscopy, microtiter plate and bioreactor designs, and discuss their respective advantages and disadvantages. Here, we examine design approaches followed in performing optogenetic experiments spanning different cell types and culture volumes, with induction capabilities ranging from single cell stimulation to entire cell culture illumination. The development of automated measurement and stimulation schemes on these platforms has enabled researchers to implement various in silico feedback control strategies to achieve computer-controlled living systems-a theme we briefly discuss in the last part of this review.

Engineering Light-Control in Biology.

Unraveling the transformative power of optogenetics in biology requires sophisticated engineering for the creation and optimization of light-regulatable proteins. In addition, diverse strategies have been used for the tuning of these light-sensitive regulators. This review highlights different protein engineering and synthetic biology approaches, which might aid in the development and optimization of novel optogenetic proteins (Opto-proteins). Focusing on non-neuronal optogenetics, chromophore availability, general strategies for creating light-controllable functions, modification of the photosensitive domains and their fusion to effector domains, as well as tuning concepts for Opto-proteins are discussed. Thus, this review shall not serve as an encyclopedic summary of light-sensitive regulators but aims at discussing important aspects for the engineering of light-controllable proteins through selected examples.

Optogenetic approaches in biotechnology and biomaterials.

Advances in genetic engineering, combined with the development of optical technologies, have allowed optogenetics to broaden its area of possible applications in recent years. However, the application of optogenetic tools in industry, including biotechnology and the production of biomaterials, is still limited, because each practical task requires the engineering of a specific optogenetic system. In this review, we discuss recent advances in the use of optogenetic tools in the production of biofuels and valuable chemicals, the synthesis of biomedical and polymer materials, and plant agrobiology. We also offer a comprehensive analysis of the properties and industrial applicability of light-controlled and other smart biomaterials. These data allow us to outline the prospects for the future use of optogenetics in bioindustry.

Solid-Phase-Supported Chemoenzymatic Synthesis of a Light-Activatable tRNA Derivative.

Herein, we present a multi-cycle chemoenzymatic synthesis of modified RNA with simplified solid-phase handling to overcome size limitations of RNA synthesis. It combines the advantages of classical chemical solid-phase synthesis and enzymatic synthesis using magnetic streptavidin beads and biotinylated RNA. Successful introduction of light-controllable RNA nucleotides into the tRNAMet sequence was confirmed by gel electrophoresis and mass spectrometry. The methods tolerate modifications in the RNA phosphodiester backbone and allow introductions of photocaged and photoswitchable nucleotides as well as photocleavable strand breaks and fluorophores.