Epigallocatechin-3-gallate derived polymer coated Prussian blue for synergistic ROS elimination and antibacterial therapy.

Reactive oxygen species (ROS) play a vital role in wound healing process by fighting against invaded bacteria. However, excess ROS at the wound sites lead to oxidative stress that can trigger deleterious effects, causing cell death, tissue damage and chronic inflammation. Therefore, we fabricated a core-shell structured nanomedicine with antibacterial and antioxidant properties via a facile and green strategy. Specifically, Prussian blue (PB) nanozyme was fabricated and followed by coating a layer of epigallocatechin-3-gallate (EGCG)-derived polymer via polyphenolic condensation reaction and self-assembly process, resulting in PB@EGCG. The introduction of PB core endowed EGCG-based polyphenol nanoparticles with excellent NIR-triggered photothermal properties. Besides, owing to multiple enzyme-mimic activity of PB and potent antioxidant capacity of EGCG-derived polymer, PB@EGCG exhibited a remarkable ROS-scavenging ability, mitigated intracellular ROS level and protected cells from oxidative damage. Under NIR irradiation (808 nm, 1.5 W/cm2), PB@EGCG (50 µg/mL) exerted synergistic EGCG-derived polymer-photothermal antibacterial activity against Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus aureus (S. aureus). In vivo therapeutic effect was evaluated using a S. aureus-infected rat model indicated PB@EGCG with a prominent bactericidal ability could modulate the inflammatory microenvironment and accelerate wound healing. Overall, this dual-functional nanomedicine provides a promising strategy for efficient antibacterial therapy.

Extracellular RNA: A new perspective on the human pre-implantation embryos.

It is currently a challenge to perform noninvasive molecular biological analysis of in vitro fertilized embryos. In this issue of Cell Genomics, Wu et al.1 developed a non-invasive method to evaluate human pre-implantation embryos by characterizing the extracellular RNAs in spent media from the culture of in vitro fertilization embryos.

Deep-Cloud: A Deep Neural Network-Based Approach for Analyzing Differentially Expressed Genes of RNA-seq Data.

Presently, the field of analyzing differentially expressed genes (DEGs) of RNA-seq data is still in its infancy, with new approaches constantly being proposed. Taking advantage of deep neural networks to explore gene expression information on RNA-seq data can provide a novel possibility in the biomedical field. In this study, a novel approach based on a deep learning algorithm and cloud model was developed, named Deep-Cloud. Its main advantage is not only using a convolutional neural network and long short-term memory to extract original data features and estimate gene expression of RNA-seq data but also combining the statistical method of the cloud model to quantify the uncertainty and carry out in-depth analysis of the DEGs between the disease groups and the control groups. Compared with traditional analysis software of DEGs, the Deep-cloud model further improves the sensitivity and accuracy of obtaining DEGs from RNA-seq data. Overall, the proposed new approach Deep-cloud paves a new pathway for mining RNA-seq data in the biomedical field.

Thrombin and Thrombin-Incorporated Biomaterials for Disease Treatments.

Thrombin, a coagulation-inducing protease, has long been used in the hemostatic field. During the past decades, many other therapeutic uses of thrombin have been developed. For instance, burn treatment, pseudoaneurysm therapy, wound management, and tumor vascular infarction (or tumor vasculature blockade therapy) can all utilize the unique and powerful function of thrombin. Based on their therapeutic effects, many thrombin-associated products have been certificated by the Food and Drug Administration, including bovine thrombin, human thrombin, recombinant thrombin, fibrin glue, etc. Besides, several thrombin-based drugs are currently undergoing clinical trials. In this article, the therapeutic uses of thrombin (from the initial hemostasis to the latest cancer therapy), the commercially available drugs associated with thrombin, and the pros and cons of thrombin-based therapeutics (e.g., adverse immune responses related to bovine thrombin, thromboinflammation, and vasculogenic "rebounds") are summarized. Further, the current challenges and possible future research directions of thrombin-incorporated biomaterials and therapies are discussed. It is hoped that this review may provide a valuable reference for researchers in this field and help them to design safer and more effective thrombin-based drugs for fighting against various intractable diseases.

A simple joint detection platform for high-throughput single-cell heterogeneity screening.

Single cell heterogeneity plays an important role in many biological phenomena and distinguishing cells that exhibit certain mutation in sample could benefit clinical diagnose and drug screening. Typical single cell detection methods such as flow cytometry, in-situ hybridization, real-time amplification or sequencing test either protein or nucleic acid as target and usually require specialized instruments. Joint measurement of the both types of targets could be done by combining the above strategies precisely but also unwieldly. Methods for rapidly and parallelly screening single cells with target genotype and antigen is needed. In this study, we describe a gel plate platform to distinguish cell types based on their phenotypes on target gene and antigen with low equipment requirement. Integrated cell lysis and immobilization were done in the gel solidification step, after which antibody hybridization and real-time amplification were sequentially carried out without losing the original loci information of individual single cells so the three types of information of individual single cells could be combined to distinguished cells with expected genotype and phenotype. The easy-to-use gel platform has potential in point-of-care circumstances and single-cell stimulation response that have high requirements on efficiency and simplicity.

Recent advances in droplet sequential monitoring methods for droplet sorting.

Droplet microfluidics is an attractive technology to run parallel experiments with high throughput and scalability while maintaining the heterogeneous features of individual samples or reactions. Droplet sorting is utilized to collect the desired droplets based on droplet characterization and in-droplet content evaluation. A proper monitoring method is critical in this process, which governs the accuracy and maximum frequency of droplet handling. Until now, numerous monitoring methods have been integrated in the microfluidic devices for identifying droplets, such as optical spectroscopy, mass spectroscopy, electrochemical monitoring, and nuclear magnetic resonance spectroscopy. In this review, we summarize the features of various monitoring methods integrated into droplet sorting workflow and discuss their suitable condition and potential obstacles in use. We aim to provide a systematic introduction and an application guide for choosing and building a droplet monitoring platform.

Spatial Transcriptomic Analysis Reveals Regional Transcript Changes in Early and Late Stages of rd1 Model Mice with Retinitis Pigmentosa.

Retinitis pigmentosa (RP) is the leading cause of inherited blindness with a genetically heterogeneous disorder. Currently, there is no effective treatment that can protect vision for those with RP. In recent decades, the rd1 mouse has been used to study the pathological mechanisms of RP. Molecular biological studies using rd1 mice have clarified the mechanism of the apoptosis of photoreceptor cells in the early stage of RP. However, the pathological changes in RP over time remain unclear. The unknown pathology mechanism of RP over time and the difficulty of clinical treatment make it urgent to perform more refined and spatially informed molecular biology studies of RP. In this study, spatial transcriptomic analysis is used to study the changes in different retinal layers of rd1 mice at different ages. The results demonstrate the pattern of photoreceptor apoptosis between rd1 mice and the control group. Not only was oxidative stress enhanced in the late stage of RP, but it was accompanied by an up-regulation of the VEGF pathway. Analysis of temporal kinetic trends has further identified patterns of changes in the key pathways of the early and late stages, to help understand the important pathogenesis of RP. Overall, the application of spatial transcriptomics to rd1 mice can help to elucidate the important pathogenesis of RP involving photoreceptor apoptosis and retinal remodeling.

Genome-wide identification of the heat shock transcription factor gene family in two kiwifruit species.

High temperatures have a significant impact on plant growth and metabolism. In recent years, the fruit industry has faced a serious threat due to high-temperature stress on fruit plants caused by global warming. In the present study, we explored the molecular regulatory mechanisms that contribute to high-temperature tolerance in kiwifruit. A total of 36 Hsf genes were identified in the A. chinensis (Ac) genome, while 41 Hsf genes were found in the A. eriantha (Ae) genome. Phylogenetic analysis revealed the clustering of kiwifruit Hsfs into three distinct groups (groups A, B, and C). Synteny analysis indicated that the expansion of the Hsf gene family in the Ac and Ae genomes was primarily driven by whole genome duplication (WGD). Analysis of the gene expression profiles revealed a close relationship between the expression levels of Hsf genes and various plant tissues and stress treatments throughout fruit ripening. Subcellular localization analysis demonstrated that GFP-AcHsfA2a/AcHsfA7b and AcHsfA2a/AcHsfA7b -GFP were localized in the nucleus, while GFP-AcHsfA2a was also observed in the cytoplasm of Arabidopsis protoplasts. The results of real-time quantitative polymerase chain reaction (RT-qPCR) and dual-luciferase reporter assay revealed that the majority of Hsf genes, especially AcHsfA2a, were expressed under high-temperature conditions. In conclusion, our findings establish a theoretical foundation for analyzing the potential role of Hsfs in high-temperature stress tolerance in kiwifruit. This study also offers valuable information to aid plant breeders in the development of heat-stress-resistant plant materials.

Unexpected reactivity of cyclometalated iridium(III) dimers. Direct synthesis of a mononuclear luminescent complex.

A new synthetic method has been developed for the preparation of unexpected emissive iridium(III) complexes (A and B), directly obtained from the established [Ir(ppy)2(µ-Cl)]2 dimer, under reaction conditions in which such compounds are usually considered stable. Complex A ([Ir(ppy)2(Oppy)], where Hppy = 2-phenylpyridine and HOppy = 2-(o-hydroxyphenyl)pyridine) was obtained from the dimer without the addition of further ancillary ligands in the reaction environment, but in the presence of a basic water environment in 2-ethoxyethanol as solvent at 165 °C. The complex evidences the unexpected insertion of an oxygen atom between the iridium(III) center and the carbon atom of one ppy moiety. Under specific reaction conditions, the mer-[Ir(ppy)3] complex (B) was obtained. The presence of the right amount of water is important to maximize the formation of A relative to B. Both compounds were fully characterized by NMR spectroscopy and mass spectrometry (MS), and the X-ray structure of A was also determined. DFT calculations were used to shed light on the reaction mechanism leading to the unexpected formation of A, suggesting that the Oppy ligand is generated intramolecularly once the [Ir(ppy)2(µ-OH)]2 dimer is formed. The process is probably assisted by a redox reaction involving the second iridium(III) center in the dimer. The electrochemical and photophysical properties of complexes A and B were investigated in comparison with the well-known fac-[Ir(ppy)3] analogue (C). Complex A displays a green emission (λmax = 545 nm) with a photoluminescence quantum yield (PLQY) of nearly 40%, whereas the oxygen-free counterpart B is poorly emissive, exhibiting an orange emission (λmax = 605 nm) with a PLQY below 10%. These findings may pave the way for the direct synthesis of neutral luminescent complexes with the general formula [Ir(C^N)2(OC^N)], even using dimers with non-commercial or highly substituted C^N ligands, without the need for synthesizing the corresponding hydroxyl-substituted ancillary ligand, which may be hardly obtainable.

2D Covalent Organic Frameworks with Kagome Lattice: Synthesis and Applications.

2D covalent organic frameworks with Kagome (kgm) topology are a promising class of crystalline frameworks that possess both triangular and hexagonal pores. These dual-pore structures enable kgm COFs to exhibit unique advantages in selective separation, mass transfer, and targeted drug release. However, the synthesis of 2D kgm COFs has been hindered by the reliance on empirical methods. This review systematically summarizes the conventional macrocycle-to-framework strategy, typical [4+2] co-polymerization synthetic strategy, and bifunctional molecules self-condensation approach for constructing 2D kgm COFs. Factors influencing the formation of kgm lattice are surveyed, such as monomer type, solvent polarity, substrate concentration, etc., and highlight the representative examples on targeted synthesis. Additionally, applications of 2D kgm COFs and relationships between structure and performances are summarized. Finally, key fundamental perspectives are proposed to accelerate the further development of this intriguing material.

Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data.

MOTIVATION: Multiple displacement amplification (MDA) has become the most commonly used method of whole genome amplification, generating a vast amount of DNA with higher molecular weight and greater genome coverage. Coupling with long-read sequencing, it is possible to sequence the amplicons of over 20 kb in length. However, the formation of chimeric sequences (chimeras, expressed as structural errors in sequencing data) in MDA seriously interferes with the bioinformatics analysis but its influence on long-read sequencing data is unknown. RESULTS: We sequenced the phi29 DNA polymerase-mediated MDA amplicons on the PacBio platform and analyzed chimeras within the generated data. The 3rd-ChimeraMiner has been constructed as a pipeline for recognizing and restoring chimeras into the original structures in long-read sequencing data, improving the efficiency of using TGS data. Five long-read datasets and one high-fidelity long-read dataset with various amplification folds were analyzed. The result reveals that the mis-priming events in amplification are more frequently occurring than widely perceived, and the propor tion gradually accumulates from 42% to over 78% as the amplification continues. In total, 99.92% of recognized chimeric sequences were demonstrated to be artifacts, whose structures were wrongly formed in MDA instead of existing in original genomes. By restoring chimeras to their original structures, the vast majority of supplementary alignments that introduce false-positive structural variants are recycled, removing 97% of inversions on average and contributing to the analysis of structural variation in MDA-amplified samples. The impact of chimeras in long-read sequencing data analysis should be emphasized, and the 3rd-ChimeraMiner can help to quantify and reduce the influence of chimeras. AVAILABILITY AND IMPLEMENTATION: The 3rd-ChimeraMiner is available on GitHub, https://github.com/dulunar/3rdChimeraMiner.

Cytosine base editors (CBEs) for inducing targeted DNA base editing in Nicotiana benthamiana.

BACKGROUND: The base editors can introduce point mutations accurately without causing double-stranded DNA breaks or requiring donor DNA templates. Previously, cytosine base editors (CBEs) containing different deaminases are reported for precise and accurate base editing in plants. However, the knowledge of CBEs in polyploid plants is inadequate and needs further exploration. RESULTS: In the present study, we constructed three polycistronic tRNA-gRNA expression cassettes CBEs containing A3A, A3A (Y130F), and rAPOBEC1(R33A) to compare their base editing efficiency in allotetraploid N. benthamiana (n = 4x). We used 14 target sites to compare their editing efficiency using transient transformation in tobacco plants. The sanger sequencing and deep sequencing results showed that A3A-CBE was the most efficient base editor. In addition, the results showed that A3A-CBE provided most comprehensive editing window (C1 ~ C17 could be edited) and had a better editing efficiency under the base background of TC. The target sites (T2 and T6) analysis in transformed N. benthamiana showed that only A3A-CBE can have C-to-T editing events and the editing efficiency of T2 was higher than T6. Additionally, no off-target events were found in transformed N. benthamiana. CONCLUSIONS: All in all, we conclude that A3A-CBE is the most suitable vector for specific C to T conversion in N. benthamiana. Current findings will provide valuable insights into selecting an appropriate base editor for breeding polyploid plants.

LncRNA CDKN2B-AS1 interacts with LIN28B to exacerbate sepsis-induced acute lung injury by inducing HIF-1α/NLRP3-mediated pyroptosis.

Sepsis-associated acute lung injury (ALI) is a life-threatening condition in intensive care units with high mortality. LncRNAs have been confirmed to participate in the underlying pathogenesis of septic ALI. This study investigated the biological functions of lncRNA CDKN2B-AS1 in septic ALI and its potential mechanism.BEAS-2B cells were challenged with lipopolysaccharide (LPS) and mice were subjected to caecal ligation and puncture (CLP) to induce septic ALI in vitro and in vivo. The expression levels of CDKN2B-AS1, LIN28B, HIF-1α, and pyroptosis-related molecules were assessed by qRT-PCR or Western blotting. The production of IL-1ß and IL-18 was detected by ELISA. BEAS-2B cell pyroptosis was examined by flow cytometry. The interaction between LIN28B and CDKN2B-AS1/HIF-1α was validated by RIP and RNA pull-down assays. Colocalization of CDKN2B-AS1 and LIN28B was observed by FISH. ALI was determined by HE staining, the lung wet-to-dry (W/D) weight ratio, inflammatory cell numbers, and total protein concentration in bronchoalveolar lavage fluid (BALF). Caspase-1 expression in the lung tissues was examined by immunohistochemical staining.CDKN2B-AS1 was upregulated in BEAS-2B cells after LPS stimulation. CDKN2B-AS1 knockdown inhibited pyroptosis in LPS-exposed BEAS-2B cells in vitro and the lung tissues of septic mice in vivo. Mechanistically, CDKN2B-AS1 interacted with LIN28B to enhance HIF-1α stability. Rescue experiments showed that HIF-1α overexpression counteracted the inhibitory effect of sh-CDKN2B-AS1 on LPS-induced pyroptosis. CDKN2B-AS1 bound to LIN28B to trigger NLRP3-mediated pyroptosis by stabilizing HIF-1α, which promoted sepsis-induced ALI. CDKN2B-AS1 might be a novel therapeutic target for this disease.

Two Bacillus spp. Strains Improve the Structure and Diversity of the Rhizosphere Soil Microbial Community of Lilium brownii var. viridulum.

Lily Fusarium wilt disease caused by Fusarium spp. spreads rapidly and is highly destructive, leading to a severe reduction in yield. In this study, lily (Lilium brownii var. viridulum) bulbs were irrigated after planting with suspensions of two Bacillus strains that effectively control lily Fusarium wilt disease to assess their effects on the rhizosphere soil properties and microbial community. A high-throughput sequencing of microorganisms in the rhizosphere soil was performed and the soil physicochemical properties were measured. The FunGuild and Tax4Fun tools were used for a functional profile prediction. The results showed that Bacillus amyloliquefaciens BF1 and B. subtilis Y37 controlled lily Fusarium wilt disease with control efficacies of 58.74% and 68.93%, respectively, and effectively colonized the rhizosphere soil. BF1 and Y37 increased the bacterial diversity and richness of the rhizosphere soil and improved the physicochemical properties of the soil, thereby favoring the proliferation of beneficial microbes. The relative abundance of beneficial bacteria was increased and that of pathogenic bacteria was decreased. Bacillus abundance in the rhizosphere was positively correlated with most soil physicochemical properties, whereas Fusarium abundance was negatively correlated with most physicochemical properties. Functional prediction revealed that irrigation with BF1 and Y37 significantly upregulated glycolysis/gluconeogenesis among metabolism and absorption pathways. This study provides insights into the mechanism by which two Bacillus strains with antifungal activity, BF1 and Y37, antagonize plant pathogenic fungi and lays the foundation for their effective application as biocontrol agents.

Discriminating Single Nucleotide Variations in Solid-State Nanopores by Evaluating the Combination Efficiency between DNA Polymerase and Its Substrate.

A single nucleotide variant present between two otherwise identical nucleic acids will have unexpected functional consequences frequently. Here, a neoteric single nucleotide variation (SNV) detection assay that integrates two complementary nanotechnology systems, nanoassembly technology and an ingenious nanopore biosensing platform, has been applied to this research. Specifically, we set up a detection system to reflect the binding efficiency of the polymerase and nanoprobe through the difference of nanopore signals and then explore the effect of base mutation at the binding site. In addition, machine learning based on support vector machines is used to automatically classify characteristic events mapped by nanopore signals. Our system reliably discriminates single nucleotide variants at binding sites, even possessing the recognition among transitions, transversions, and hypoxanthine (base I). Our results demonstrate the potential of solid-state nanopore detection for SNV and provide some ideas for expanding solid-state nanopore detection platforms.

Insights and future trends in bioanalysis: an interview with Jing Tu.

Jack Lodge, Commissioning Editor of Bioanalysis, and Neil Spooner, Editor in Chief, speak to Jing Tu.

Impact of metacognition on attitudes toward epilepsy in medical students.

PURPOSE: This study evaluated medical students' knowledge and attitudes toward epilepsy and the influence of metacognition thereon. METHOD: Valid questionnaires were administered to medical students including undergraduate, professional postgraduate, and standardized residency training students (N = 503). The questionnaire had 4 parts: demographic information, knowledge of epilepsy, attitudes toward epilepsy, and metacognitive assessment. The Chinese Public Attitudes Toward Epilepsy scale and 30-Item Metacognition Questionnaire were used to assess attitudes and metacognition, respectively. RESULTS: Almost all participants had heard of epilepsy; 38.8% had witnessed a seizure and 25% were acquainted with a person with epilepsy. The proportion of correct answers to epilepsy-related knowledge ranged from 40.6% (Putting an object into the mouth of a person experiencing an epileptic seizure) to 97% (Convulsion is a symptom of epilepsy). However, knowledge of epilepsy was not able to affect attitudes toward epilepsy. Age, years of clinical experience, having witnessed a seizure, positive belief of worry, and need to control thinking were correlated with the different domains of attitude toward epilepsy. When participants were divided into 2 groups-i.e., those with high and low knowledge of epilepsy, participants in the former group who had a positive belief of worry or had not witnessed any seizures were more likely to have negative attitudes toward epilepsy. CONCLUSION: Medical students showed good awareness of the etiology and symptoms of epilepsy. Overall, attitudes toward epilepsy were negative. A positive belief of worry was associated with a more negative attitude toward epilepsy among respondents with greater knowledge of epilepsy.

PHMB modified photothermally triggered nitric oxide release nanoplatform for precise synergistic therapy of wound bacterial infections.

Bacterial infection has been considered as a significant obstacle for wound healing. Nitric oxide (NO), as a novel alternative for antibiotics, has emerged as a promising antibacterial agent. However, the precise spatiotemporal controlled release of NO still remains a major challenge. Herein, a near-infrared (NIR) light triggered NO release nanoplatform (designated as PB-NO@PDA-PHMB) with enhanced broad-spectrum antibacterial and anti-biofilm properties was constructed. Given that PB-NO@PDA-PHMB has strong absorption in the NIR region and exhibits excellent photothermal effect, it can rapidly trigger NO release by NIR irradiation. PB-NO@PDA-PHMB can effectively contact and capture bacteria, and then exhibit synergistic effect of photothermal and gas therapy. In vitro and in vivo experiments indicated that PB-NO@PDA-PHMB exhibited excellent biocompatibility, satisfactory synergistic antibacterial efficacy and the capability of accelerating wound healing. Under NIR irradiation (808 nm, 1 W cm-2, 7 min), PB-NO@PDA-PHMB (80 µg mL-1) achieved 100% bactericidal activity against both Gram-negative bacteria Escherichia coli (E. coli) and Gram-positive bacteria Staphyloccocus aureus (S. aureus), removed 58.94% of S. aureus biofilm. Therefore, this all-in-one antibacterial nanoplatform with high NIR responsiveness provides a promising antibiotic-free strategy for bacterial infection treatment.

Photothermal/lysozyme-catalyzed hydrolysis dual-modality therapy via halloysite nanotube-based platform for effective bacterial eradication.

Bacterial biofilm seriously impedes the healing of infected wound, remaining a major challenge in wound repair. Antibiotic-free antibacterial strategies based on nanotechnology are emerging as promising tools to combat bacterial infections. Here, halloysite nanotube (HNT), as a natural clay mineral, was employed to fabricate a multifunctional platform (designated as HNTs@CuS@PDA-Lys) through a layer-by-layer strategy for treating bacterial infections by utilizing synergistic lysozyme (Lys)-photothermal therapy (PTT). Specifically, amino-modified HNTs were first decorated with copper sulfide (CuS), followed by coated with a polydopamine (PDA) layer, then functionalized with antimicrobial enzyme Lys onto the surface of PDA via cation-π interactions. The as-prepared HNTs@CuS@PDA-Lys at a low dose (200 µg/mL) exhibited excellent synergistic Lys-photothermal bactericidal activity against Escherichia coli (E. coli) (100.0 ± 0.2 %) and Staphyloccocus aureus (S. aureus) (99.9 ± 0.1 %), eliminated 75.9 ± 2.0 % of S. aureus biofilm under near-infrared (NIR) irradiation (808 nm, 1.5 W/cm2). In vivo experiments using a S. aureus-infected rat model showed HNTs@CuS@PDA-Lys could rapidly kill bacteria and accelerate wound healing process. Overall, this multifunctional nanoplatform combines the advantages of PTT and Lys, providing a cost-efficient, environmental friendly strategy for bacterial and biofilm eradication, demonstrating the potential applications in the field of biomedicine.