Exploring Novel Antidepressants Targeting G Protein-Coupled Receptors and Key Membrane Receptors Based on Molecular Structures.

Major Depressive Disorder (MDD) is a complex mental disorder that involves alterations in signal transmission across multiple scales and structural abnormalities. The development of effective antidepressants (ADs) has been hindered by the dominance of monoamine hypothesis, resulting in slow progress. Traditional ADs have undesirable traits like delayed onset of action, limited efficacy, and severe side effects. Recently, two categories of fast-acting antidepressant compounds have surfaced, dissociative anesthetics S-ketamine and its metabolites, as well as psychedelics such as lysergic acid diethylamide (LSD). This has led to structural research and drug development of the receptors that they target. This review provides breakthroughs and achievements in the structure of depression-related receptors and novel ADs based on these. Cryo-electron microscopy (cryo-EM) has enabled researchers to identify the structures of membrane receptors, including the N-methyl-D-aspartate receptor (NMDAR) and the 5-hydroxytryptamine 2A (5-HT2A) receptor. These high-resolution structures can be used for the development of novel ADs using virtual drug screening (VDS). Moreover, the unique antidepressant effects of 5-HT1A receptors in various brain regions, and the pivotal roles of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) and tyrosine kinase receptor 2 (TrkB) in regulating synaptic plasticity, emphasize their potential as therapeutic targets. Using structural information, a series of highly selective ADs were designed based on the different role of receptors in MDD. These molecules have the favorable characteristics of rapid onset and low adverse drug reactions. This review offers researchers guidance and a methodological framework for the structure-based design of ADs.

Engineered exosomes as drug and RNA co-delivery system: new hope for enhanced therapeutics?

Chemotherapy often faces some obstacles such as low targeting effects and drug resistance, which introduce the low therapeutic efficiency and strong side effects. Recent advances in nanotechnology allows the use of novel nanosystems for targeted drug delivery, although the chemically synthesized nanomaterials always show unexpected low biocompability. The emergence of exosome research has offered a better understanding of disease treatment and created novel opportunities for developing effective drug delivery systems with high biocompability. Moreover, RNA interference has emerged as a promising strategy for disease treatments by selectively knocking down or over-expressing specific genes, which allows new possibilities to directly control cell signaling events or drug resistance. Recently, more and more interests have been paid to develop optimal delivery nanosystems with high efficiency and high biocompability for drug and functional RNA co-delivery to achieve enhanced chemotherapy. In light of the challenges for developing drug and RNA co-delivery system, exosomes have been found to show very attractive prospects. This review aims to explore current technologies and challenges in the use of exosomes as drug and RNA co-delivery system with a focus on the emerging trends and issues associated with their further applications, which may contribute to the accelerated developments of exosome-based theraputics.

Zoonotic pathogens identified in rodents and shrews from four provinces, China, 2015-2022.

Rodents and shrews are major reservoirs of various pathogens that are related to zoonotic infectious diseases. The purpose of this study was to investigate co-infections of zoonotic pathogens in rodents and shrews trapped in four provinces of China. We sampled different rodent and shrew communities within and around human settlements in four provinces of China and characterised several important zoonotic viral, bacterial, and parasitic pathogens by PCR methods and phylogenetic analysis. A total of 864 rodents and shrews belonging to 24 and 13 species from RODENTIA and EULIPOTYPHLA orders were captured, respectively. For viral pathogens, two species of hantavirus (Hantaan orthohantavirus and Caobang orthohantavirus) were identified in 3.47% of rodents and shrews. The overall prevalence of Bartonella spp., Anaplasmataceae, Babesia spp., Leptospira spp., Spotted fever group Rickettsiae, Borrelia spp., and Coxiella burnetii were 31.25%, 8.91%, 4.17%, 3.94%, 3.59%, 3.47%, and 0.58%, respectively. Furthermore, the highest co-infection status of three pathogens was observed among Bartonella spp., Leptospira spp., and Anaplasmataceae with a co-infection rate of 0.46%. Our results suggested that species distribution and co-infections of zoonotic pathogens were prevalent in rodents and shrews, highlighting the necessity of active surveillance for zoonotic pathogens in wild mammals in wider regions.

Baicalein Inhibits the Staphylococcus aureus Biofilm and the LuxS/AI-2 System in vitro.

Introduction: Staphylococcus aureus (S. aureus) is a common cause of mastitis in dairy cows, a condition that has a significant economic impact. S. aureus displays quorum sensing (QS) system-controlled virulence characteristics, like biofilm formation, that make therapy challenging. In order to effectively combat S. aureus, one potential technique is to interfere with quorum sensing. Methods: This study evaluated the effects of different Baicalin (BAI) concentrations on the growth and the biofilm of S. aureus isolates, including the biofilm formation and mature biofilm clearance. The binding activity of BAI to LuxS was verified by molecular docking and kinetic simulations. The secondary structure of LuxS in the formulations was characterized using fluorescence quenching and Fourier transform infrared (FTIR) spectroscopy. Additionally, using fluorescence quantitative PCR, the impact of BAI on the transcript levels of the luxS and biofilm-related genes was investigated. The impact of BAI on LuxS at the level of protein expression was also confirmed by a Western blotting investigation. Results: According to the docking experiments, they were able to engage with the amino acid residues in LuxS and BAI through hydrogen bonding. The results of molecular dynamics simulations and the binding free energy also confirmed the stability of the complex and supported the experimental results. BAI showed weak inhibitory activity against S. aureus but significantly reduced biofilm formation and disrupted mature biofilms. BAI also downregulated luxS and biofilm-associated genes' mRNA expression. Successful binding was confirmed using fluorescence quenching and FTIR. Discussion: We thus report that BAI inhibits the S. aureus LuxS/AI-2 system for the first time, which raises the possibility that BAI could be employed as a possible antimicrobial drug to treat S. aureus strain-caused biofilms.

Promising Roles of Circular RNAs as Biomarkers and Targets for Potential Diagnosis and Therapy of Tuberculosis.

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) infection, remains one of the most threatening infectious diseases worldwide. A series of challenges still exist for TB prevention, diagnosis and treatment, which therefore require more attempts to clarify the pathological and immunological mechanisms in the development and progression of TB. Circular RNAs (circRNAs) are a large class of non-coding RNA, mostly expressed in eukaryotic cells, which are generated by the spliceosome through the back-splicing of linear RNAs. Accumulating studies have identified that circRNAs are widely involved in a variety of physiological and pathological processes, acting as the sponges or decoys for microRNAs and proteins, scaffold platforms for proteins, modulators for transcription and special templates for translation. Due to the stable and widely spread characteristics of circRNAs, they are expected to serve as promising prognostic/diagnostic biomarkers and therapeutic targets for diseases. In this review, we briefly describe the biogenesis, classification, detection technology and functions of circRNAs, and, in particular, outline the dynamic, and sometimes aberrant changes of circRNAs in TB. Moreover, we further summarize the recent progress of research linking circRNAs to TB-related pathogenetic processes, as well as the potential roles of circRNAs as diagnostic biomarkers and miRNAs sponges in the case of Mtb infection, which is expected to enhance our understanding of TB and provide some novel ideas about how to overcome the challenges associated TB in the future.

Characterizing chemical signaling between engineered "microbial sentinels" in porous microplates.

Living materials combine a material scaffold, that is often porous, with engineered cells that perform sensing, computing, and biosynthetic tasks. Designing such systems is difficult because little is known regarding signaling transport parameters in the material. Here, the development of a porous microplate is presented. Hydrogel barriers between wells have a porosity of 60% and a tortuosity factor of 1.6, allowing molecular diffusion between wells. The permeability of dyes, antibiotics, inducers, and quorum signals between wells were characterized. A "sentinel" strain was constructed by introducing orthogonal sensors into the genome of Escherichia coli MG1655 for IPTG, anhydrotetracycline, L-arabinose, and four quorum signals. The strain's response to inducer diffusion through the wells was quantified up to 14 mm, and quorum and antibacterial signaling were measured over 16 h. Signaling distance is dictated by hydrogel adsorption, quantified using a linear finite element model that yields adsorption coefficients from 0 to 0.1 mol m-3 . Parameters derived herein will aid the design of living materials for pathogen remediation, computation, and self-organizing biofilms.

Engineering living and regenerative fungal-bacterial biocomposite structures.

Engineered living materials could have the capacity to self-repair and self-replicate, sense local and distant disturbances in their environment, and respond with functionalities for reporting, actuation or remediation. However, few engineered living materials are capable of both responsivity and use in macroscopic structures. Here we describe the development, characterization and engineering of a fungal-bacterial biocomposite grown on lignocellulosic feedstocks that can form mouldable, foldable and regenerative living structures. We have developed strategies to make human-scale biocomposite structures using mould-based and origami-inspired growth and assembly paradigms. Microbiome profiling of the biocomposite over multiple generations enabled the identification of a dominant bacterial component, Pantoea agglomerans, which was further isolated and developed into a new chassis. We introduced engineered P. agglomerans into native feedstocks to yield living blocks with new biosynthetic and sensing-reporting capabilities. Bioprospecting the native microbiota to develop engineerable chassis constitutes an important strategy to facilitate the development of living biomaterials with new properties and functionalities.

The Establishment and Application of Mobile Electronic Surveillance System for Infectious Diseases with the Help of China - Sierra Leone, 2016-Present.

INTRODUCTION: Infectious disease surveillance has long been a challenge for low-income countries like Sierra Leone. Traditional approaches based on paper and Short Message Service (SMS) were subject to severe delays in obtaining, transmitting, and analyzing information. METHODS: During the China aid operation for fighting Ebola since the end of 2014, a mobile electronic surveillance system for infectious diseases (MESSID) was developed in collaboration with the Republic of Sierra Leone Armed Forces (RSLAF), which comprised an Android-based reporting system and a complementary web-based program designed by Active Server Page.NET (ASP.NET) with the main functions including surveillance, real-time reporting, and risk assessment of infectious diseases. RESULTS: MESSID was successfully registered in June 2016 and had been used by all medical and health institutions in RSLAF. From June 1, 2016 to July 5, 2021, 34,419 cases were diagnosed with 47 infectious diseases of 5 categories, with a total of 42 clinical symptoms. Compared to traditional approaches based on paper and SMS, the MESSID showed flexibility, high efficiency, convenience, and acceptability. DISCUSSION: MESSID is an accessible tool for surveillance of infectious diseases in Sierra Leone and possibly in other African countries with similar needs, capable of improving timeliness of disease reporting, thus rendering a timely outbreak detection and response.

Conformational Control of DNA Origami by DNA Oligomers, Intercalators and UV Light.

DNA origami has garnered great attention due to its excellent programmability and precision. It offers a powerful means to create complex nanostructures which may not be possible by other methods. The macromolecular structures may be used as static templates for arranging proteins and other molecules. They are also capable of undergoing structural transformation in response to external signals, which may be exploited for sensing and actuation at the nanoscale. Such on-demand reconfigurations are executed mostly by DNA oligomers through base-pairing and/or strand displacement, demonstrating drastic shape changes between two different states, for example, open and close. Recent studies have developed new mechanisms to modulate the origami conformation in a controllable, progressive manner. Here we present several methods for conformational control of DNA origami nanostructures including chemical adducts and UV light as well as widely applied DNA oligomers. The detailed methods should be useful for beginners in the field of DNA nanotechnology.

Topological Assembly of a Deployable Hoberman Flight Ring from DNA.

Deployable geometries are finite auxetic structures that preserve their overall shapes during expansion and contraction. The topological behaviors emerge from intricately arranged elements and their connections. Despite the considerable utility of such configurations in nature and in engineering, deployable nanostructures have never been demonstrated. Here a deployable flight ring, a simplified planar structure of Hoberman sphere is shown, using DNA origami. The DNA flight ring consists of topologically assembled six triangles in two layers that can slide against each other, thereby switching between two distinct (open and closed) states. The origami topology is a trefoil knot, and its auxetic reconfiguration results in negative Poisson's ratios. This work shows the feasibility of deployable nanostructures, providing a versatile platform for topological studies and opening new opportunities for bioengineering.

Auxetic Two-Dimensional Nanostructures from DNA*.

Architectured materials exhibit negative Poisson's ratios and enhanced mechanical properties compared with regular materials. Their auxetic behaviors emerge from periodic cellular structures regardless of the materials used. The majority of such metamaterials are constructed by top-down approaches and macroscopic with unit cells of microns or larger. There are also molecular auxetics including natural crystals which are not designable. There is a gap from few nanometers to microns, which may be filled by biomolecular self-assembly. Herein, we demonstrate two-dimensional auxetic nanostructures using DNA origami. Structural reconfigurations are performed by two-step DNA reactions and complemented by mechanical deformation studies using molecular dynamics simulations. We find that the auxetic behaviors are mostly defined by geometrical designs, yet the properties of the materials also play an important role. From elasticity theory, we introduce design principles for auxetic DNA metamaterials.

Visible/near-infrared subdiffraction imaging reveals the stochastic nature of DNA walkers.

DNA walkers are designed with the structural specificity and functional diversity of oligonucleotides to actively convert chemical energy into mechanical translocation. Compared to natural protein motors, DNA walkers' small translocation distance (mostly <100 nm) and slow reaction rate (<0.1 nm s-1) make single-molecule characterization of their kinetics elusive. An important indication of single-walker kinetics is the rate-limiting reactions that a particular walker design bears. We introduce an integrated super-resolved fluorescence microscopy approach that is capable of long-term imaging to investigate the stochastic behavior of DNA walkers. Subdiffraction tracking and imaging in the visible and second near-infrared spectra resolve walker structure and reaction rates. The distributions of walker kinetics are analyzed using a stochastic model to reveal reaction randomness and the rate-limiting biochemical reaction steps.

Conformational Effects of UV Light on DNA Origami.

The responses of DNA origami conformation to UV radiation of different wavelengths and doses are investigated. Short- and medium-wavelength UV light can cause photo-lesions in DNA origami. At moderate doses, the lesions do not cause any visible defects in the origami, nor do they significantly affect the hybridization capability. Instead, they help relieve the internal stress in the origami structure and restore it to the designed conformation. At high doses, staple dissociation increases which causes structural disintegration. Long-wavelength UV does not show any effect on origami conformation by itself. We show that this UV range can be used in conjunction with photoactive molecules for photo-reconfiguration, while avoiding any damage to the DNA structures.

DNA Walkers as Transport Vehicles of Nanoparticles Along a Carbon Nanotube Track.

DNA-based molecular motors are synthetic analogs of naturally occurring protein motors. Typical DNA walkers are constructed from synthetic short DNA strands and are powered by various free energy changes during hybridization reactions. Due to the constraints set by their small physical dimension and slow kinetics, most DNA walkers are characterized by ensemble measurements that result in averaged kinetics data. Here we present a synthetic DNA walker system that exploits the extraordinary physicochemical properties of nanomaterials and the functionalities of DNA molecules, which enables real-time control and monitoring of single-DNA walkers over an extended period.

A DNAzyme-mediated logic gate for programming molecular capture and release on DNA origami.

Here we design a DNA origami-based site-specific molecular capture and release platform operated by a DNAzyme-mediated logic gate process. We show the programmability and versatility of this platform with small molecules, proteins, and nanoparticles, which may also be controlled by external light signals.

Dynamic and Progressive Control of DNA Origami Conformation by Modulating DNA Helicity with Chemical Adducts.

DNA origami has received enormous attention for its ability to program complex nanostructures with a few nanometer precision. Dynamic origami structures that change conformation in response to environmental cues or external signals hold great promises in sensing and actuation at the nanoscale. The reconfiguration mechanism of existing dynamic origami structures is mostly limited to single-stranded hinges and relies almost exclusively on DNA hybridization or strand displacement. Here, we show an alternative approach by demonstrating on-demand conformation changes with DNA-binding molecules, which intercalate between base pairs and unwind DNA double helices. The unwinding effect modulates the helicity mismatch in DNA origami, which significantly influences the internal stress and the global conformation of the origami structure. We demonstrate the switching of a polymerized origami nanoribbon between different twisting states and a well-constrained torsional deformation in a monomeric origami shaft. The structural transformation is shown to be reversible, and binding isotherms confirm the reconfiguration mechanism. This approach provides a rapid and reversible means to change DNA origami conformation, which can be used for dynamic and progressive control at the nanoscale.

Nanomanufacturing of 2D Transition Metal Dichalcogenide Materials Using Self-Assembled DNA Nanotubes.

2D transition metal dichalcogenides (TMDCs) are nanomanufactured using a generalized strategy with self-assembled DNA nanotubes. DNA nanotubes of various lengths serve as lithographic etch masks for the dry etching of TMDCs. The nanostructured TMDCs are studied by atomic force microscopy, photoluminescence, and Raman spectroscopy. This parallel approach can be used to manufacture 2D TMDC nanostructures of arbitrary geometries with molecular-scale precision.

Design Principles of DNA Enzyme-Based Walkers: Translocation Kinetics and Photoregulation.

Dynamic DNA enzyme-based walkers complete their stepwise movements along the prescribed track through a series of reactions, including hybridization, enzymatic cleavage, and strand displacement; however, their overall translocation kinetics is not well understood. Here, we perform mechanistic studies to elucidate several key parameters that govern the kinetics and processivity of DNA enzyme-based walkers. These parameters include DNA enzyme core type and structure, upper and lower recognition arm lengths, and divalent metal cation species and concentration. A theoretical model is developed within the framework of single-molecule kinetics to describe overall translocation kinetics as well as each reaction step. A better understanding of kinetics and design parameters enables us to demonstrate a walker movement near 5 µm at an average speed of ∼1 nm s(-1). We also show that the translocation kinetics of DNA walkers can be effectively controlled by external light stimuli using photoisomerizable azobenzene moieties. A 2-fold increase in the cleavage reaction is observed when the hairpin stems of enzyme catalytic cores are open under UV irradiation. This study provides general design guidelines to construct highly processive, autonomous DNA walker systems and to regulate their translocation kinetics, which would facilitate the development of functional DNA walkers.

Recent progress on DNA based walkers.

DNA based synthetic molecular walkers are reminiscent of biological protein motors. They are powered by hybridization with fuel strands, environment induced conformational transitions, and covalent chemistry of oligonucleotides. Recent developments in experimental techniques enable direct observation of individual walkers with high temporal and spatial resolution. The functionalities of state-of-the-art DNA walker systems can thus be analyzed for various applications. Herein we review recent progress on DNA walker principles and characterization methods, and evaluate various aspects of their functions for future applications.

Understanding the mechanical properties of DNA origami tiles and controlling the kinetics of their folding and unfolding reconfiguration.

DNA origami represents a class of highly programmable macromolecules that can go through conformational changes in response to external signals. Here we show that a two-dimensional origami rectangle can be effectively folded into a short, cylindrical tube by connecting the two opposite edges through the hybridization of linker strands and that this process can be efficiently reversed via toehold-mediated strand displacement. The reconfiguration kinetics was experimentally studied as a function of incubation temperature, initial origami concentration, missing staples, and origami geometry. A kinetic model was developed by introducing the j factor to describe the reaction rates in the cyclization process. We found that the cyclization efficiency (j factor) increases sharply with temperature and depends strongly on the structural flexibility and geometry. A simple mechanical model was used to correlate the observed cyclization efficiency with origami structure details. The mechanical analysis suggests two sources of the energy barrier for DNA origami folding: overcoming global twisting and bending the structure into a circular conformation. It also provides the first semiquantitative estimation of the rigidity of DNA interhelix crossovers, an essential element in structural DNA nanotechnology. This work demonstrates efficient DNA origami reconfiguration, advances our understanding of the dynamics and mechanical properties of self-assembled DNA structures, and should be valuable to the field of DNA nanotechnology.