Engineering and In Vivo Applications of Riboswitches.

Riboswitches are common gene regulatory units mostly found in bacteria that are capable of altering gene expression in response to a small molecule. These structured RNA elements consist of two modular subunits: an aptamer domain that binds with high specificity and affinity to a target ligand and an expression platform that transduces ligand binding to a gene expression output. Significant progress has been made in engineering novel aptamer domains for new small molecule inducers of gene expression. Modified expression platforms have also been optimized to function when fused with both natural and synthetic aptamer domains. As this field expands, the use of these privileged scaffolds has permitted the development of tools such as RNA-based fluorescent biosensors. In this review, we summarize the methods that have been developed to engineer new riboswitches and highlight applications of natural and synthetic riboswitches in enzyme and strain engineering, in controlling gene expression and cellular physiology, and in real-time imaging of cellular metabolites and signals.

Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs.

Tumor necrosis factor-α (TNF-α) is the most potent proinflammatory cytokine in mammals. The degradation of TNF-α mRNA is critical for restricting TNF-α synthesis and involves a constitutive decay element (CDE) in the 3' UTR of the mRNA. Here, we demonstrate that the CDE folds into an RNA stem-loop motif that is specifically recognized by Roquin and Roquin2. Binding of Roquin initiates degradation of TNF-α mRNA and limits TNF-α production in macrophages. Roquin proteins promote mRNA degradation by recruiting the Ccr4-Caf1-Not deadenylase complex. CDE sequences are highly conserved and are found in more than 50 vertebrate mRNAs, many of which encode regulators of development and inflammation. In macrophages, CDE-containing mRNAs were identified as the primary targets of Roquin on a transcriptome-wide scale. Thus, Roquin proteins act broadly as mediators of mRNA deadenylation by recognizing a conserved class of stem-loop RNA degradation motifs.

A large-scale microelectromechanical-systems-based silicon photonics LiDAR.

Three-dimensional (3D) imaging sensors allow machines to perceive, map and interact with the surrounding world1. The size of light detection and ranging (LiDAR) devices is often limited by mechanical scanners. Focal plane array-based 3D sensors are promising candidates for solid-state LiDARs because they allow electronic scanning without mechanical moving parts. However, their resolutions have been limited to 512 pixels or smaller2. In this paper, we report on a 16,384-pixel LiDAR with a wide field of view (FoV, 70° × 70°), a fine addressing resolution (0.6° × 0.6°), a narrow beam divergence (0.050° × 0.049°) and a random-access beam addressing with sub-MHz operation speed. The 128 × 128-element focal plane switch array (FPSA) of grating antennas and microelectromechanical systems (MEMS)-actuated optical switches are monolithically integrated on a 10 × 11-mm2 silicon photonic chip, where a 128 × 96 subarray is wire bonded and tested in experiments. 3D imaging with a distance resolution of 1.7 cm is achieved with frequency-modulated continuous-wave (FMCW) ranging in monostatic configuration. The FPSA can be mass-produced in complementary metal-oxide-semiconductor (CMOS) foundries, which will allow ubiquitous 3D sensors for use in autonomous cars, drones, robots and smartphones.

Obstructive sleep apnea in a mouse model is associated with tissue-specific transcriptomic changes in circadian rhythmicity and mean 24-hour gene expression.

Intermittent hypoxia (IH) is a major clinical feature of obstructive sleep apnea (OSA). The mechanisms that become dysregulated after periods of exposure to IH are unclear, particularly in the early stages of disease. The circadian clock governs a wide array of biological functions and is intimately associated with stabilization of hypoxia-inducible factors (HIFs) under hypoxic conditions. In patients, IH occurs during the sleep phase of the 24-hour sleep-wake cycle, potentially affecting their circadian rhythms. Alterations in the circadian clock have the potential to accelerate pathological processes, including other comorbid conditions that can be associated with chronic, untreated OSA. We hypothesized that changes in the circadian clock would manifest differently in those organs and systems known to be impacted by OSA. Using an IH model to represent OSA, we evaluated circadian rhythmicity and mean 24-hour expression of the transcriptome in 6 different mouse tissues, including the liver, lung, kidney, muscle, heart, and cerebellum, after a 7-day exposure to IH. We found that transcriptomic changes within cardiopulmonary tissues were more affected by IH than other tissues. Also, IH exposure resulted in an overall increase in core body temperature. Our findings demonstrate a relationship between early exposure to IH and changes in specific physiological outcomes. This study provides insight into the early pathophysiological mechanisms associated with IH.

Production of 3',3'-cGAMP by a Bdellovibrio bacteriovorus promiscuous GGDEF enzyme, Bd0367, regulates exit from prey by gliding motility.

Bacterial second messengers are important for regulating diverse bacterial lifestyles. Cyclic di-GMP (c-di-GMP) is produced by diguanylate cyclase enzymes, named GGDEF proteins, which are widespread across bacteria. Recently, hybrid promiscuous (Hypr) GGDEF proteins have been described in some bacteria, which produce both c-di-GMP and a more recently identified bacterial second messenger, 3',3'-cyclic-GMP-AMP (cGAMP). One of these proteins was found in the predatory Bdellovibrio bacteriovorus, Bd0367. The bd0367 GGDEF gene deletion strain was found to enter prey cells, but was incapable of leaving exhausted prey remnants via gliding motility on a solid surface once predator cell division was complete. However, it was unclear which signal regulated this process. We show that cGAMP signalling is active within B. bacteriovorus and that, in addition to producing c-di-GMP and some c-di-AMP, Bd0367 is a primary producer of cGAMP in vivo. Site-directed mutagenesis of serine 214 to an aspartate rendered Bd0367 into primarily a c-di-GMP synthase. B. bacteriovorus strain bd0367S214D phenocopies the bd0367 deletion strain by being unable to glide on a solid surface, leading to an inability of new progeny to exit from prey cells post-replication. Thus, this process is regulated by cGAMP. Deletion of bd0367 was also found to be incompatible with wild-type flagellar biogenesis, as a result of an acquired mutation in flagellin chaperone gene homologue fliS, implicating c-di-GMP in regulation of swimming motility. Thus the single Bd0367 enzyme produces two secondary messengers by action of the same GGDEF domain, the first reported example of a synthase that regulates multiple second messengers in vivo. Unlike roles of these signalling molecules in other bacteria, these signal to two separate motility systems, gliding and flagellar, which are essential for completion of the bacterial predation cycle and prey exit by B. bacteriovorus.

2024 Statement from Asia expert operators on transcatheter pulmonary valve replacement.

Transcatheter pulmonary valve replacement (TPVR), also known as percutaneous pulmonary valve implantation, refers to a minimally invasive technique that replaces the pulmonary valve by delivering an artificial pulmonary prosthesis through a catheter into the diseased pulmonary valve under the guidance of X-ray and/or echocardiogram while the heart is still beating not arrested. In recent years, TPVR has achieved remarkable progress in device development, evidence-based medicine proof and clinical experience. To update the knowledge of TPVR in a timely fashion, and according to the latest research and further facilitate the standardized and healthy development of TPVR in Asia, we have updated this consensus statement. After systematical review of the relevant literature with an in-depth analysis of eight main issues, we finally established eight core viewpoints, including indication recommendation, device selection, perioperative evaluation, procedure precautions, and prevention and treatment of complications.

Clinical pharmacology considerations for first-in-human clinical trials for enzyme replacement therapy.

Inborn errors of metabolism (IEM) such as lysosomal storage disorders (LSDs) are conditions caused by deficiency of one or more key enzymes, cofactors, or transporters involved in a specific metabolic pathway. Enzyme replacement therapy (ERT) provides an exogenous source of the affected enzyme and is one of the most effective treatment options for IEMs. In this paper, we review the first-in-human (FIH) protocols for ERT drug development programs supporting 20 Biologic License Applications (BLA) approved by the Center for Drug Evaluation and Research (CDER) at the US Food and Drug Administration (FDA) in the period of May 1994 to September 2023. We surveyed study design elements across these FIH protocols including study population, dosage form, dose selection, treatment duration, immunogenicity, biomarkers, and study follow-up. A total of 18 FIH trials from 20 BLAs were identified and of those, 72% (13/18) used single ascending dose (SAD) and/or multiple ascending dose (MAD) study design, 83% (15/18) had a primary objective of assessing the safety and tolerability, 72% (13/18) included clinical endpoint assessments, and 94% (17/18) included biomarker assessments as secondary or exploratory endpoints. Notably, the majority of ERT products tested the approved route of administration and the approved dose was tested in 83% (15/18) of FIH trials. At last, we offer considerations for the design of FIH studies.

A survey of FDA Approved Monoclonal Antibodies and Fc-fusion Proteins for Manufacturing Changes and Comparability Assessment.

OBJECTIVE: Manufacturing changes occur commonly throughout stages of biologics development and may result in product quality attribute changes. As changes in critical quality attributes have the potential to affect clinical safety and efficacy of products, it is imperative to ensure the quality and clinical performance before introducing the after-change products. Thus, we embarked on this project to understand what data have supported the manufacturing changes for licensed products with pre- and post-approval changes. METHODS: We surveyed the manufacturing changes of 85 monoclonal antibodies and 10 Fc fusion proteins approved by the Food and Drug Administration as of December 25, 2021. After collecting the type and timing of changes for these products, we investigated the approaches that provided supporting data for the changes. The source documents included reports submitted by applicants and FDA's regulatory reviews. RESULTS: Analytical comparability was assessed to support all identified manufacturing changes. Supporting clinical data were available in 92% of these manufacturing changes; including data from pharmacokinetic comparability studies alone (3%), other studies on efficacy or safety (70%) and a combination of both (19%). Clinical pharmacokinetic comparability data contributed to supporting substantial changes, such as host cell type or master cell bank changes, concentration or formulation changes, and changes from pre-filled syringes to autoinjectors, especially when introduced after completing pivotal studies. CONCLUSION: Our comprehensive retrospective analysis provides an understanding of the regulatory experience and industry practice, which could facilitate developing appropriate comparability approaches to support manufacturing changes in the future.

Time-restricted feeding protects the blood pressure circadian rhythm in diabetic mice.

The quantity and quality of food intake have been considered crucial for peoples' wellness. Only recently has it become appreciated that the timing of food intake is also critical. Nondipping blood pressure (BP) is prevalent in diabetic patients and is associated with increased cardiovascular events. However, the causes and mechanisms of nondipping BP in diabetes are not fully understood. Here, we report that food intake and BP were arrhythmic in diabetic db/db mice fed a normal chow diet ad libitum. Imposing a food intake diurnal rhythm by time-restricted feeding (TRF; food was only available for 8 h during the active phase) prevented db/db mice from developing nondipping BP and effectively restored the already disrupted BP circadian rhythm in db/db mice. Interestingly, increasing the time of food availability from 8 h to 12 h during the active dark phase in db/db mice prompted isocaloric feeding and still provided robust protection of the BP circadian rhythm in db/db mice. In contrast, neither 8-h nor 12-h TRF affected BP dipping in wild-type mice. Mechanistically, we demonstrate that TRF protects the BP circadian rhythm in db/db mice via suppressing the sympathetic activity during the light phase when they are inactive and fasting. Collectively, these data reveal a potentially pivotal role of the timing of food intake in the prevention and treatment of nondipping BP in diabetes.

Optoelectronic tweezers: a versatile toolbox for nano-/micro-manipulation.

The rapid development of micromanipulation technologies has opened exciting new opportunities for the actuation, selection and assembly of a variety of non-biological and biological nano/micro-objects for applications ranging from microfabrication, cell analysis, tissue engineering, biochemical sensing, to nano/micro-machines. To date, a variety of precise, flexible and high-throughput manipulation techniques have been developed based on different physical fields. Among them, optoelectronic tweezers (OET) is a state-of-art technique that combines light stimuli with electric field together by leveraging the photoconductive effect of semiconductor materials. Herein, the behavior of micro-objects can be directly controlled by inducing the change of electric fields on demand in an optical manner. Relying on this light-induced electrokinetic effect, OET offers tremendous advantages in micromanipulation such as programmability, flexibility, versatility, high-throughput and ease of integration with other characterization systems, thus showing impressive performance compared to those of many other manipulation techniques. A lot of research on OET have been reported in recent years and the technology has developed rapidly in various fields of science and engineering. This work provides a comprehensive review of the OET technology, including its working mechanisms, experimental setups, applications in non-biological and biological scenarios, technology commercialization and future perspectives.

Authentication of In Situ Measurements for Thoracic Aortic Aneurysms in Mice.

[Figure: see text].

The Signaling Pathway That cGAMP Riboswitches Found: Analysis and Application of Riboswitches to Study cGAMP Signaling in Geobacter sulfurreducens.

The Hypr cGAMP signaling pathway was discovered via the function of the riboswitch. In this study, we show the development of a method for affinity capture followed by sequencing to identify non-coding RNA regions that bind nucleotide signals such as cGAMP. The RNAseq of affinity-captured cGAMP riboswitches from the Geobacter sulfurreducens transcriptome highlights general challenges that remain for this technique. Furthermore, by applying riboswitch reporters in vivo, we identify new growth conditions and transposon mutations that affect cGAMP levels in G. sulfurreducens. This work reveals an extensive regulatory network and supports a second functional cGAMP synthase gene in G. sulfurreducens. The activity of the second synthase was validated using riboswitch-based fluorescent biosensors, and is the first known example of an active enzyme with a variant GGDDF motif.

Second messengers and divergent HD-GYP phosphodiesterases regulate 3',3'-cGAMP signaling.

3',3'-cyclic GMP-AMP (cGAMP) is the third cyclic dinucleotide (CDN) to be discovered in bacteria. No activators of cGAMP signaling have yet been identified, and the signaling pathways for cGAMP have been inferred to display a narrow distribution based upon the characterized synthases, DncV and Hypr GGDEFs. Here, we report that the ubiquitous second messenger cyclic AMP (cAMP) is an activator of the Hypr GGDEF enzyme GacB from Myxococcus xanthus. Furthermore, we show that GacB is inhibited directly by cyclic di-GMP, which provides evidence for cross-regulation between different CDN pathways. Finally, we reveal that the HD-GYP enzyme PmxA is a cGAMP-specific phosphodiesterase (GAP) that promotes resistance to osmotic stress in M. xanthus. A signature amino acid change in PmxA was found to reprogram substrate specificity and was applied to predict the presence of non-canonical HD-GYP phosphodiesterases in many bacterial species, including phyla previously not known to utilize cGAMP signaling.

Efficient spontaneous emission by metal-dielectric antennas; antenna Purcell factor explained.

The rate of spontaneous emission from an optical emitter can be greatly enhanced using a metallic optical antenna at the penalty of efficiency. In this paper we propose a metal-dielectric antenna that eliminates the tradeoff between spontaneous emission enhancement and radiative efficiency by using nanoscopic dielectric structures at the antenna tips. This tradeoff occurs due to Ohmic loss and is further exacerbated by electron surface collisions. We find that our metal-dielectric antenna can enhance spontaneous emission by a factor 5 × 105 with efficiency = 70%, greatly exceeding the radiative efficiency of a purely metallic antenna with similar enhancement. Moreover, the metal-dielectric antenna design strategy is naturally amenable to short-distance optical communications applications. We go on to discuss the Purcell effect within the context of antenna enhancement. Metallic optical antennas are best analyzed with conventional antenna circuit models, but if the Purcell enhancement were to be employed, we provide the effective mode volume, Veff = (3/4π2)2d2λ(λ/l)5, that would be needed.

RNA-based fluorescent biosensors for live cell detection of bacterial sRNA.

Bacteria contain a diverse set of RNAs to provide tight regulation of gene expression in response to environmental stimuli. Bacterial small RNAs (sRNAs) work in conjunction with protein cofactors to bind complementary mRNA sequences in the cell, leading to up- or downregulation of protein synthesis. In vivo imaging of sRNAs can aid in understanding their spatiotemporal dynamics in real time, which inspires new ways to manipulate these systems for a variety of applications including synthetic biology and therapeutics. Current methods for sRNA imaging are quite limited in vivo and do not provide real-time information about fluctuations in sRNA levels. Herein, we describe our efforts toward the development of an RNA-based fluorescent biosensor for bacterial sRNA both in vitro and in vivo. We validated these sensors for three different bacterial sRNAs in Escherichia coli and demonstrated that the designs provide a bright, sequence-specific signal output in response to exogenous and endogenous RNA targets.

Myocardial-restricted ablation of the GTPase RAD results in a pro-adaptive heart response in mice.

Existing therapies to improve heart function target ß-adrenergic receptor (ß-AR) signaling and Ca2+ handling and often lead to adverse outcomes. This underscores an unmet need for positive inotropes that improve heart function without any adverse effects. The GTPase Ras associated with diabetes (RAD) regulates L-type Ca2+ channel (LTCC) current (ICa,L). Global RAD-knockout mice (gRAD-/-) have elevated Ca2+ handling and increased cardiac hypertrophy, but RAD is expressed also in noncardiac tissues, suggesting the possibility that pathological remodeling is due also to noncardiac effects. Here, we engineered a myocardial-restricted inducible RAD-knockout mouse (RADΔ/Δ). Using an array of methods and techniques, including single-cell electrophysiological and calcium transient recordings, echocardiography, and radiotelemetry monitoring, we found that RAD deficiency results in a sustained increase of inotropy without structural or functional remodeling of the heart. ICa,L was significantly increased, with RAD loss conferring a ß-AR-modulated phenotype on basal ICa,L Cardiomyocytes from RADΔ/Δ hearts exhibited enhanced cytosolic Ca2+ handling, increased contractile function, elevated sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA2a) expression, and faster lusitropy. These results argue that myocardial RAD ablation promotes a beneficial elevation in Ca2+ dynamics, which would obviate a need for increased ß-AR signaling to improve cardiac function.

Tuning the Innate Immune Response to Cyclic Dinucleotides by Using Atomic Mutagenesis.

Cyclic dinucleotides (CDNs) trigger the innate immune response in eukaryotic cells through the stimulator of interferon genes (STING) signaling pathway. To decipher this complex cellular process, a better correlation between structure and downstream function is required. Herein, we report the design and immunostimulatory effect of a novel group of c-di-GMP analogues. By employing an "atomic mutagenesis" strategy, changing one atom at a time, a class of gradually modified CDNs was prepared. These c-di-GMP analogues induce type-I interferon (IFN) production, with some being more potent than c-di-GMP, their native archetype. This study demonstrates that CDN analogues bearing modified nucleobases are able to tune the innate immune response in eukaryotic cells.

Laser frequency sweep linearization by iterative learning pre-distortion for FMCW LiDAR.

We report on a laser frequency sweep linearization method by iterative learning pre-distortion for frequency-modulated continuous-wave (FMCW) light detection and ranging (LiDAR) systems. A pre-distorted laser drive voltage waveform that results in a linear frequency sweep is obtained by an iterative learning controller, and then applied to the FMCW LiDAR system. We have also derived a fundamental figure of merit for the maximum residual nonlinearity needed to achieve the transform-limited range resolution. This method is experimentally tested using a commercial vertical cavity surface-emitting laser (VCSEL) and a distributed feedback (DFB) laser, achieving less than 0.005% relative residual nonlinearity of frequency sweep. With the proposed method, high-performance FMCW LiDAR systems can be realized without expensive linear lasers, complex linearization setups, or heavy post-processing.

Inverse design optimization for efficient coupling of an electrically injected optical antenna-LED to a single-mode waveguide.

Efficient high-speed nanoscale optical sources are required for low-power next-generation data communication. Here we propose an integrated antenna-LED on a single-mode optical waveguide. By leveraging inverse design optimization, we achieved a waveguide coupling efficiency of 94% and an antenna efficiency of 64%, while maintaining a high average enhancement of 144 - potentially enabling >100GHz direct modulation.

Multicast silicon photonic MEMS switches with gap-adjustable directional couplers.

We report on 4x20 silicon photonic MEMS switch that is capable of multicasting. The switch is built on passive optical crossbar network with gap-adjustable directional couplers. The switch has high on-off extinction ratio (59 dB), low insertion loss (< 4.0 dB), small footprint (1.2x4.5 mm2), and fast response (9.8 µs). The switching voltage is 9.6 V and 20 dB bandwidth is 31.5 nm. One-to-two and one-to-four multicast operations are demonstrated.