DNA Framework-Programmed Nanoscale Enzyme Assemblies.

Multienzyme assemblies mediated by multivalent interaction play a crucial role in cellular processes. However, the three-dimensional (3D) programming of an enzyme complex with defined enzyme activity in vitro remains unexplored, primarily owing to limitations in precisely controlling the spatial topological configuration. Herein, we introduce a nanoscale 3D enzyme assembly using a tetrahedral DNA framework (TDF), enabling the replication of spatial topological configuration and maintenance of an identical edge-to-edge distance akin to natural enzymes. Our results demonstrate that 3D nanoscale enzyme assemblies in both two-enzyme systems (glucose oxidase (GOx)/horseradish peroxidase (HRP)) and three-enzyme systems (amylglucosidase (AGO)/GOx/HRP) lead to enhanced cascade catalytic activity compared to the low-dimensional structure, resulting in ∼5.9- and ∼7.7-fold enhancements over homogeneous diffusional mixtures of free enzymes, respectively. Furthermore, we demonstrate the enzyme assemblies for the detection of the metabolism biomarkers creatinine and creatine, achieving a low limit of detection, high sensitivity, and broad detection range.

A new strategy based on a cascade amplification strategy biosensor for on-site eDNA detection and outbreak warning of crown-of-thorns starfish.

Population outbreaks of the crown-of-thorns starfish (COTS) seriously threaten the sustainability of coral reef ecosystems. However, traditional ecological monitoring techniques cannot provide early warning before the outbreaks, thus preventing timely intervention. Therefore, there is an urgent need for a more accurate and faster technology to predict the outbreaks of COTS. In this work, we developed an electrochemical biosensor based on a programmed catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR) cyclic amplification strategy for sensitive and selective detection of COTS environmental DNA (eDNA) in water bodies. This biosensor exhibited excellent electrochemical characteristics, including a low limit of detection (LOD = 18.4 fM), low limit of quantification (LOQ = 41.1 fM), and wide linear range (50 fM - 10 nM). The biosensing technology successfully allowed the detection of COTS eDNA in the aquarium environment, and the results also demonstrated a significant correlation between eDNA concentration and COTS number (r = 0.990; P < 0.001). The reliability and accuracy of the biosensor results have been further validated through comparison with digital droplet PCR (ddPCR). Moreover, the applicability and accuracy of the biosensor were reconfirmed in field tests at the COTS outbreak site in the South China Sea, which has shown potential application in dynamically monitoring the larvae before the COTS outbreak. Therefore, this efficient electrochemical biosensing technology offers a new solution for on-site monitoring and early warning of the COTS outbreak.

Quantitative assessment of retinochoroidal microvasculature in patients with carotid artery stenosis using OCT angiography.

PURPOSE: To investigate the alterations in retinochoroidal parameters measured by optical coherence tomography (OCT) and OCT angiography (OCTA) in patients with carotid artery stenosis (CAS) and assess their associations with digital subtraction angiography (DSA) data. METHOD: This study enrolled patients diagnosed with CAS and age-matched healthy controls. Both groups underwent OCT and OCTA examinations. DSA and assessment of carotid artery stenosis were performed only in the CAS group. The study evaluated various retinochoroidal parameters from OCT and OCTA, including linear vessel density (LVD), foveal avascular zone (FAZ), choroidal thickness (ChT), and retinal nerve fiber layer (RNFL) thickness. DSA-derived measures included cervical segment (C1) diameter, cavernous segment (C4) diameter, stenosis percentage, ophthalmic artery (OA) filling time, C1-OA filling time, and residual stenosis. RESULTS: A total of 42 eyes from 30 CAS patients and 60 eyes from 30 healthy controls were included. Patients with CAS displayed significantly decreased LVD compared to controls (p < 0.001). Additionally, the CAS group had thinner choroid and RNFL (p = 0.047 and p < 0.001, respectively). Macular LVD negatively correlated with both stenosis percentage and C1-OA filling time (p = 0.010 and p = 0.014, respectively). In patients who underwent carotid artery stenting, preoperative ChT significantly correlated with residual stenosis (Pearson r = -0.480, p = 0.020). CONCLUSION: OCT and OCTA provide a quantitative assessment of retinochoroidal microstructural changes associated with CAS, suggesting potential for noninvasive evaluation of the disease. This might contribute to the prevention of irreversible ocular complications and early detection of CAS. Furthermore, ChT may not only aid in diagnosing CAS more reliably but also offer prognostic information.

Corrosion Degradation Mechanism of Cr-Coated Zr-4 Alloy under Simulated Nuclear Conditions for Accident-Tolerant Fuel.

Cr coatings with a thickness of about 19 µm were synthesized on Zr-4 cladding using plasma-enhanced arc ion plating. A Zr-Cr micro-diffusion layer was formed via Cr ion cleaning before deposition to enhance the interface bonding strength. Cr coatings exhibit an obvious columnar crystal structure with an average grain size of 1.26 µm using SEM (scanning electron microscopy) and EBSD (electron backscatter diffraction) with a small amount of nanoscale pores on the surface. A long-term aqueous test at 420 ± 3 °C, 10.3 ± 0.7 MPa and isothermal oxidation tests at 900~1300 °C in air were conducted to evaluate the Cr-coated Zr-4 cladding. All the results showed that the Cr coatings had a significant protective effect to the Zr-4 alloy. However, the corrosion deterioration mechanism is different. A gradual thinning of the Cr coating was observed in a long-term aqueous test, but a cyclic corrosion mechanism of void initiation-propagation-cracking at the oxide film interface is the main corrosion characteristic of the Cr coating in isothermal oxidation. Different corrosion models are constructed to explain the corrosion mechanism.

The Protective Effects of Curcumin against Renal Toxicity.

Curcumin is a naturally polyphenolic compound used for hepatoprotective, thrombosuppressive, neuroprotective, cardioprotective, antineoplastic, antiproliferative, hypoglycemic, and antiarthritic effects. Kidney disease is a major public health problem associated with severe clinical complications worldwide. The protective effects of curcumin against nephrotoxicity have been evaluated in several experimental models. In this review, we discussed how curcumin exerts its protective effect against renal toxicity and also illustrated the mechanisms of action such as anti-inflammatory, antioxidant, regulating cell death, and anti-fibrotic. This provides new perspectives and directions for the clinical guidance and molecular mechanisms for the treatment of renal diseases by curcumin.

Tangshen formula targets the gut microbiota to treat non-alcoholic fatty liver disease in HFD mice: A 16S rRNA and non-targeted metabolomics analyses.

BACKGROUND: Tangshen formula (TSF) has an ameliorative effect on hepatic lipid metabolism in non-alcoholic fatty liver disease (NAFLD), but the role played by the gut microbiota in this process is unknown. METHOD: We conducted three batches of experiments to explore the role played by the gut microbiota: TSF administration, antibiotic treatment, and fecal microbial transplantation. NAFLD mice were induced with a high-fat diet to investigate the ameliorative effects of TSF on NAFLD features and intestinal barrier function. 16S rRNA sequencing and serum untargeted metabolomics were performed to further investigate the modulatory effects of TSF on the gut microbiota and metabolic dysregulation in the body. RESULTS: TSF ameliorated insulin resistance, hypercholesterolemia, lipid metabolism disorders, inflammation, and impairment of intestinal barrier function. 16S rRNA sequencing analysis revealed that TSF regulated the composition of the gut microbiota and increased the abundance of beneficial bacteria. Antibiotic treatment and fecal microbiota transplantation confirmed the importance of the gut microbiota in the treatment of NAFLD with TSF. Subsequently, untargeted metabolomics identified 172 differential metabolites due to the treatment of TSF. Functional predictions suggest that metabolisms of choline, glycerophospholipid, linoleic acid, alpha-linolenic acid, and arachidonic acid are the key metabolic pathways by which TSF ameliorates NAFLD and this may be influenced by the gut microbiota. CONCLUSION: TSF treats the NAFLD phenotype by remodeling the gut microbiota and improving metabolic profile, suggesting that TSF is a functional gut microbial and metabolic modulator for the treatment of NAFLD.

A marine heatwave changes the stabilizing effects of biodiversity in kelp forests.

Biodiversity can stabilize ecological communities through biological insurance, but climate and other environmental changes may disrupt this process via simultaneous ecosystem destabilization and biodiversity loss. While changes to diversity-stability relationships (DSRs) and the underlying mechanisms have been extensively explored in terrestrial plant communities, this topic remains largely unexplored in benthic marine ecosystems that comprise diverse assemblages of producers and consumers. By analyzing two decades of kelp forest biodiversity survey data, we discovered changes in diversity, stability, and their relationships at multiple scales (biological organizational levels, spatial scales, and functional groups) that were linked with the most severe marine heatwave ever documented in the North Pacific Ocean. Moreover, changes in the strength of DSRs during/after the heatwave were more apparent among functional groups than both biological organizational levels (population vs. ecosystem levels) and spatial scales (local vs. broad scales). Specifically, the strength of DSRs decreased for fishes, increased for mobile invertebrates and understory algae, and were unchanged for sessile invertebrates during/after the heatwave. Our findings suggest that biodiversity plays a key role in stabilizing marine ecosystems, but the resilience of DSRs to adverse climate impacts primarily depends on the functional identities of ecological communities.

High-throughput DNA synthesis for data storage.

With the explosion of digital world, the dramatically increasing data volume is expected to reach 175 ZB (1 ZB = 1012 GB) in 2025. Storing such huge global data would consume tons of resources. Fortunately, it has been found that the deoxyribonucleic acid (DNA) molecule is the most compact and durable information storage medium in the world so far. Its high coding density and long-term preservation properties make itself one of the best data storage carriers for the future. High-throughput DNA synthesis is a key technology for "DNA data storage", which encodes binary data stream (0/1) into quaternary long DNA sequences consisting of four bases (A/G/C/T). In this review, the workflow of DNA data storage and the basic methods of artificial DNA synthesis technology are outlined first. Then, the technical characteristics of different synthesis methods and the state-of-the-art of representative commercial companies, with a primary focus on silicon chip microarray-based synthesis and novel enzymatic DNA synthesis are presented. Finally, the recent status of DNA storage and new opportunities for future development in the field of high-throughput, large-scale DNA synthesis technology are summarized.

Towards mechanistic integration of the causes and consequences of biodiversity.

The global biodiversity crisis has stimulated decades of research on three themes: species coexistence, biodiversity-ecosystem functioning relationships (BEF), and biodiversity-ecosystem functional stability relationships (BEFS). However, studies on these themes are largely independent, creating barriers to an integrative understanding of the causes and consequences of biodiversity. Here we review recent progress towards mechanistic integration of coexistence, BEF, and BEFS. Mechanisms underlying the three themes can be linked in various ways, potentially creating either positive or negative relationships between them. That said, we generally expect positive associations between coexistence and BEF, and between BEF and BEFS. Our synthesis represents an initial step towards integrating causes and consequences of biodiversity; future developments should include more mechanistic approaches and broader ecological contexts.

A novel biosensing strategy on the dynamic and on-site detection of Vibrio coralliilyticus eDNA for coral health warnings.

Heat stress and coral diseases are the predominant factors causing the degradation of coral reef ecosystems. Over recent years, Vibrio coralliilyticus was identified as a temperature-dependent pathogen causing tissue lysis in Pocillopora damicornis and one of the primary pathogens causing bleaching and mortality in other corals. Yet current detection techniques for V. coralliilyticus rely primarily on qPCR and ddPCR, which cannot meet the requirements for non-invasive and real-time detection. Herein, we developed an effective electrochemical biosensor modified by an Au-MoS2/rGO (AMG) nanocomposites and a specific capture probe to dynamically detect V. coralliilyticus environment DNA (eDNA) in aquarium experiments, with a lower limit of detection (0.28 fM) for synthetic DNA and a lower limit of quantification (9.8 fg/µL, ∼0.86 copies/µL) for genomic DNA. Its reliability and accuracy were verified by comparison with the ddPCR method (P > 0.05). Notably, coral tissue started to lyse at only 29 °C when the concentration of V. coralliilyticus increased abruptly to 880 copies/µL, indicating the biosensor could reflect the types of pathogen and health risks of corals under heat stress. Overall, the novel and reliable electrochemical biosensing technology provides an efficient strategy for the on-site monitoring and early warning of coral health in the context of global warming.

Body size mediates the functional potential of soil organisms by diversity and community assembly across soil aggregates.

Body size is an important life-history trait that affects organism niche occupancy and ecological interactions. However, it is still unclear to what extent the assembly process of organisms with different body sizes affects soil biogeochemical cycling processes at the aggregate level. Here, we examined the diversity and community assembly of soil microorganisms (bacteria, fungi, and protists) and microfauna (nematodes) with varying body sizes. The microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism within three soil aggregate sizes (large macroaggregates, > 2 mm; small macroaggregates, 0.25-2 mm; and microaggregates, < 0.25 mm) were determined by metagenomics. We found that the smallest microbes (bacteria) had higher α-diversity and lower ß-diversity and were mostly structured by stochastic processes, while all larger organisms (fungi, protists, and nematodes) had lower α-diversity and were relatively more influenced by deterministic processes. Structural equation modeling indicated that the microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism was mainly influenced by the bacterial and protist diversity in microaggregates. In contrast, the microbial functional potential was primarily mediated by the assembly processes of four organism groups, especially the nematode community in macroaggregates. This study reveals the important roles of soil organisms with different body sizes in the functional potential related to nutrient cycling, and provides new insights into the ecological processes structuring the diversity and community assembly of organisms of different body sizes at the soil aggregate level, with implications for soil nutrient cycling dynamics.

Label-Free Optical Imaging of Nanoscale Single Entities.

The advancement of optical microscopy technologies has achieved imaging of nanoscale objects, including nanomaterials, virions, organelles, and biological molecules, at the single entity level. Recently developed plasmonic and scattering based optical microscopy technologies have enabled label-free imaging of single entities with high spatial and temporal resolutions. These label-free methods eliminate the complexity of sample labeling and minimize the perturbation of the analyte native state. Additionally, these imaging-based methods can noninvasively probe the dynamics and functions of single entities with sufficient throughput for heterogeneity analysis. This perspective will review label-free single entity imaging technologies and discuss their principles, applications, and key challenges.

Functionalized tetrahedral DNA frameworks for the capture of circulating tumor cells.

Identification and characterization of circulating tumor cells (CTCs) from blood samples of patients with cancer can help monitor parameters such as disease stage, disease progression and therapeutic efficiency. However, the sensitivity and specificity of current multivalent approaches used for CTC capture is limited by the lack of control over the ligands' position. In this Protocol Update, we describe DNA-tetrahedral frameworks anchored with aptamers that can be configured with user-defined spatial arrangements and stoichiometries. The modified tetrahedral DNA frameworks, termed 'n-simplexes', can be used as probes to specifically target receptor-ligand interactions on the cell membrane. Here, we describe the synthesis and use of n-simplexes that target the epithelial cell adhesion molecule expressed on the surface of CTCs. The characterization of the n-simplexes includes measuring the binding affinity to the membrane receptors as a result of the spatial arrangement and stoichiometry of the aptamers. We further detail the capture of CTCs from patient blood samples. The procedure for the preparation and characterization of n-simplexes requires 11.5 h, CTC capture from clinical samples and data processing requires ~5 h per six samples and the downstream analysis of captured cells typically requires 5.5 h. The protocol is suitable for users with basic expertise in molecular biology and handling of clinical samples.

An alfalfa MYB-like transcriptional factor MsMYBH positively regulates alfalfa seedling drought resistance and undergoes MsWAV3-mediated degradation.

Drought is a major threat to alfalfa (Medicago sativa L.) production. The discovery of important alfalfa genes regulating drought response will facilitate breeding for drought-resistant alfalfa cultivars. Here, we report a genome-wide association study of drought resistance in alfalfa. We identified and functionally characterized an MYB-like transcription factor gene (MsMYBH), which increases the drought resistance in alfalfa. Compared with the wild-types, the biomass and forage quality were enhanced in MsMYBH overexpressed plants. Combined RNA-seq, proteomics and chromatin immunoprecipitation analysis showed that MsMYBH can directly bind to the promoters of MsMCP1, MsMCP2, MsPRX1A and MsCARCAB to improve their expression. The outcomes of such interactions include better water balance, high photosynthetic efficiency and scavenge excess H2O2 in response to drought. Furthermore, an E3 ubiquitin ligase (MsWAV3) was found to induce MsMYBH degradation under long-term drought, via the 26S proteasome pathway. Furthermore, variable-number tandem repeats in MsMYBH promoter were characterized among a collection of germplasms, and the variation is associated with promoter activity. Collectively, our findings shed light on the functions of MsMYBH and provide a pivotal gene that could be leveraged for breeding drought-resistant alfalfa. This discovery also offers new insights into the mechanisms of drought resistance in alfalfa.

Growth of Wide-Bandgap Monolayer Molybdenum Disulfide for a Highly Sensitive Micro-Displacement Sensor.

Two-dimensional (2D) piezoelectric semiconductor materials are garnering significant attention in applications such as intelligent sensing and energy harvesting due to their exceptional physical and chemical properties. Among these, molybdenum disulfide (MoS2), a 2D wide-bandgap semiconductor, exhibits piezoelectricity in odd-layered structures due to the absence of an inversion symmetry center. In this study, we present a straightforward chemical vapor deposition (CVD) technique to synthesize monolayer MoS2 on a Si/SiO2 substrate, achieving a lateral size of approximately 50 µm. Second-harmonic generation (SHG) characterization confirms the non-centrosymmetric crystal structure of the wide-bandgap MoS2, indicative of its piezoelectric properties. We successfully transferred the triangular MoS2 to a polyethylene terephthalate (PET) flexible substrate using a wet-transfer method and developed a wide-bandgap MoS2-based micro-displacement sensor employing maskless lithography and hot evaporation techniques. Our testing revealed a piezoelectric response current of 5.12 nA in the sensor under a strain of 0.003% along the armchair direction of the monolayer MoS2. Furthermore, the sensor exhibited a near-linear relationship between the piezoelectric response current and the strain within a displacement range of 40-100 µm, with a calculated response sensitivity of 1.154 µA/%. This research introduces a novel micro-displacement sensor, offering potential for advanced surface texture sensing in various applications.

Degraders in epigenetic therapy: PROTACs and beyond.

Epigenetics refers to the reversible process through which changes in gene expression occur without changing the nucleotide sequence of DNA. The process is currently gaining prominence as a pivotal objective in the treatment of cancers and other ailments. Numerous drugs that target epigenetic mechanisms have obtained approval from the Food and Drug Administration (FDA) for the therapeutic intervention of diverse diseases; many have drawbacks, such as limited applicability, toxicity, and resistance. Since the discovery of the first proteolysis-targeting chimeras (PROTACs) in 2001, studies on targeted protein degradation (TPD)-encompassing PROTACs, molecular glue (MG), hydrophobic tagging (HyT), degradation TAG (dTAG), Trim-Away, a specific and non-genetic inhibitor of apoptosis protein (IAP)-dependent protein eraser (SNIPER), antibody-PROTACs (Ab-PROTACs), and other lysosome-based strategies-have achieved remarkable progress. In this review, we comprehensively highlight the small-molecule degraders beyond PROTACs that could achieve the degradation of epigenetic proteins (including bromodomain-containing protein-related targets, histone acetylation/deacetylation-related targets, histone methylation/demethylation related targets, and other epigenetic targets) via proteasomal or lysosomal pathways. The present difficulties and forthcoming prospects in this domain are also deliberated upon, which may be valuable for medicinal chemists when developing more potent, selective, and drug-like epigenetic drugs for clinical applications.

Recent Advances in Real-Time Label-Free Detection of Small Molecules.

The detection and analysis of small molecules, typically defined as molecules under 1000 Da, is of growing interest ranging from the development of small-molecule drugs and inhibitors to the sensing of toxins and biomarkers. However, due to challenges such as their small size and low mass, many biosensing technologies struggle to have the sensitivity and selectivity for the detection of small molecules. Notably, their small size limits the usage of labeled techniques that can change the properties of small-molecule analytes. Furthermore, the capability of real-time detection is highly desired for small-molecule biosensors' application in diagnostics or screening. This review highlights recent advances in label-free real-time biosensing technologies utilizing different types of transducers to meet the growing demand for small-molecule detection.

Deep Learning-Based Culture-Free Bacteria Detection in Urine Using Large-Volume Microscopy.

Bacterial infections, increasingly resistant to common antibiotics, pose a global health challenge. Traditional diagnostics often depend on slow cell culturing, leading to empirical treatments that accelerate antibiotic resistance. We present a novel large-volume microscopy (LVM) system for rapid, point-of-care bacterial detection. This system, using low magnification (1-2×), visualizes sufficient sample volumes, eliminating the need for culture-based enrichment. Employing deep neural networks, our model demonstrates superior accuracy in detecting uropathogenic Escherichia coli compared to traditional machine learning methods. Future endeavors will focus on enriching our datasets with mixed samples and a broader spectrum of uropathogens, aiming to extend the applicability of our model to clinical samples.

Construction of Double-enzyme Complexes with DNA Framework Nanorulers for Improving Enzyme Cascade Catalytic Efficiency.

Efficient biocatalytic cascade reactions play a crucial role in guiding intricate, specific and selective intracellular transformation processes. However, the catalytic activity of the enzyme cascade reaction in bulk solution was greatly impacted by the spatial morphology and inter-enzyme distance. The programmability and addressability nature of framework nucleic acid (FNA) allows to be used as scaffold for immobilization and to direct the spatial arrangement of enzyme cascade molecules. Here, we used tetrahedral DNA framework (TDF) as nanorulers to assemble two enzymes for constructing a double-enzyme complex, which significantly enhance the catalytic efficiency of sarcosine oxidase (SOx)/horseradish peroxidase (HRP) cascade system. We synthesized four types of TDF nanorulers capable of programming the lateral distance between enzymes from 5.67 nm to 12.33 nm. Enzymes were chemical modified by ssDNA while preserving most catalytic activity. Polyacrylamide gel electrophoresis (PAGE), transmission electron microscopy (TEM) and atomic force microscopy (AFM) were used to verify the formation of double-enzyme complex. Four types of double-enzyme complexes with different enzyme distance were constructed, in which TDF26 (SOx+HRP) exhibited the highest relative enzyme cascade catalytic activity, ~3.11-fold of free-state enzyme. Importantly, all the double-enzyme complexes demonstrate a substantial improvement in enzyme cascade catalytic activity compared to free enzymes.

Efficacy and safety of intravitreal injections of conbercept for the treatment of idiopathic choroidal neovascularization.

BACKGROUND: To determine the efficacy and safety of intravitreally injected conbercept, a vascular endothelial growth factor receptor fusion protein, for the treatment of idiopathic choroidal neovascularization (ICNV). METHODS: This retrospective study analyzed outcomes in 40 patients (40 eyes) with ICNV who received intravitreal injections of conbercept 0.5 mg (0.05 ml) and were followed up for at least 12 months. All patients underwent full ophthalmic examinations, including best-corrected vision acuity (BCVA), intraocular pressure (IOP), slit-lamp examination, color fundus photography, optical coherence tomography angiography, multifocal electroretinogram, and fundus fluorescence angiography, if necessary, at baseline and after 1, 3, 6, and 12 months. BCVA, macular central retinal thickness (CRT), IOP, CNV blood flow area, thickness of the CNV-pigment epithelial detachment complex, thickness of the retinal nerve fiber layer (RNFL), and the first positive peak (P1) amplitude density in ring 1 before and after treatment were compared. RESULTS: Mean baseline BCVA (logMAR), CRT, CNV blood flow area, and CNV-pigment epithelial detachment complex thickness were significantly lower 1, 3, 6, and 12 months after than before conbercept treatment (P < 0.05 each). IOP and baseline RNFL thickness were unaffected by conbercept treatment. P1 amplitude density was significantly higher 1, 3, 6, and 12 months after than before conbercept treatment (P < 0.05 each). None of the 40 eyes showed obvious ocular adverse reactions, such as endophthalmitis, glaucoma, cataract progression, and retinal detachment, and none of the patients experienced systemic adverse events, such as cardiovascular and cerebrovascular accidents. CONCLUSIONS: Intravitreal injection of conbercept is beneficial to eyes with ICNV, inducing the recovery of macular structure and function and improving BCVA, while not damaging the neuroretina. Intravitreal conbercept is safe and effective for the treatment of ICNV.