Human airway and nasal organoids reveal escalating replicative fitness of SARS-CoV-2 emerging variants.

The high transmissibility of SARS-CoV-2 Omicron subvariants was generally ascribed to immune escape. It remained unclear whether the emerging variants have gradually acquired replicative fitness in human respiratory epithelial cells. We sought to evaluate the replicative fitness of BA.5 and earlier variants in physiologically active respiratory organoids. BA.5 exhibited a dramatically increased replicative capacity and infectivity than B.1.1.529 and an ancestral strain wildtype (WT) in human nasal and airway organoids. BA.5 spike pseudovirus showed a significantly higher entry efficiency than that carrying WT or B.1.1.529 spike. Notably, we observed prominent syncytium formation in BA.5-infected nasal and airway organoids, albeit elusive in WT- and B.1.1.529-infected organoids. BA.5 spike-triggered syncytium formation was verified by lentiviral overexpression of spike in nasal organoids. Moreover, BA.5 replicated modestly in alveolar organoids, with a significantly lower titer than B.1.1.529 and WT. Collectively, the higher entry efficiency and fusogenic activity of BA.5 spike potentiated viral spread through syncytium formation in the human airway epithelium, leading to enhanced replicative fitness and immune evasion, whereas the attenuated replicative capacity of BA.5 in the alveolar organoids may account for its benign clinical manifestation.

MYB Transcription Factor CDC5 Activates CBF3 Expression to Positively Regulates Freezing Tolerance via Cooperating With ICE1 and Histone Modification in Arabidopsis.

The freezing temperature greatly limits the growth, development and productivity of plants. The C-repeat/DRE binding factor (CBF) plays a major role in cold acclimation, enabling plants to increase their freezing tolerance. Notably, the INDUCER OF CBF EXPRESSION1 (ICE1) protein has garnered attention for its pivotal role in bolstering plants' resilience against freezing through transcriptional upregulation of DREB1A/CBF3. However, the research on the interaction between ICE1 and other transcription factors and its function in regulating cold stress tolerance is largely inadequate. In this study, we found that a R2R3 MYB transcription factor CDC5 interacts with ICE1 and regulates the expression of CBF3 by recruiting RNA polymerase II, overexpression of ICE1 can complements the freezing deficient phenotype of cdc5 mutant. CDC5 increases the expression of CBF3 in response to freezing. Furthermore, CDC5 influences the expression of CBF3 by altering the chromatin status through H3K4me3 and H3K27me3 modifications. Our work identified a novel component that regulates CBF3 transcription in both ICE1-dependent and ICE1-independent manner, improving the understanding of the freezing signal transduction in plants.

Design and application of dual-emission metal-organic framework-based ratiometric fluorescence sensors.

Metal-organic frameworks (MOFs) are novel inorganic-organic hybridized crystals with a wide range of applications. In the last twenty years, fluorescence sensing based on MOFs has attracted much attention. MOFs can exhibit luminescence from metal nodes, ligands or introduced guests, which provides an excellent fluorescence response in sensing. However, single-signal emitting MOFs are susceptible to interference from concentration, environment, and excitation intensity, resulting in poor accuracy. To overcome the shortcomings, dual-emission MOF-based ratiometric fluorescence sensors have been proposed and rapidly developed. In this review, we first introduce the luminescence mechanisms, synthetic methods, and detection mechanisms of dual-emission MOFs, highlight the strategies for constructing ratiometric fluorescence sensors based on dual-emission MOFs, and classify them into three categories: intrinsic dual-emission and single-emission MOFs with luminescent guests, and non-emission MOFs with other luminescent materials. Then, we summarize the recent advances in dual-emission MOF-based ratiometric fluorescence sensors in various analytical industries. Finally, we discuss the current challenges and prospects for the future development of these sensors.

Discovery of novel 20S proteasome subunit ß5 PROTAC degraders as potential therapeutics for pharyngeal carcinoma and Bortezomib-resistant multiple myeloma.

Resistance to proteasome inhibitors like Bortezomib is a major challenge in the treatment of multiple myeloma (MM). Proteolysis targeting chimeras (PROTACs), an emerging therapeutic approach that induces selective degradation of target proteins, offer a promising solution to overcome drug resistance. In this study, we designed and synthesized novel small-molecule PROTACs that induce 20S proteasome subunit ß5 degradation as a strategy to overcome Bortezomib resistance. These 20S proteasome subunit ß5 PROTACs demonstrated considerable binding affinity to 20S proteasome subunit ß5 and cereblon (CRBN), effectively induced 20S proteasome subunit ß5 degradation, and exhibited potent antiproliferative activity against a panel of cancer cell lines. Notably, PROTACs 12f and 14 displayed robust antitumor effects against both the pharyngeal carcinoma cell line FaDu and the Bortezomib-resistant MM cell line KM3/BTZ in vitro and in vivo with excellent safety profiles. Taken together, our findings highlight the potential of PROTACs 12f and 14 as novel 20S proteasome subunit ß5-degrading agents for the treatment of pharyngeal carcinoma and overcoming Bortezomib resistance in MM.

Absent in Melanoma 2 Mediates Inflammasome Signaling Activation against Clostridium perfringens Infection.

Absent in melanoma 2 (AIM2), a key component of the IFI20X/IFI16 (PYHIN) protein family, is characterized as a DNA sensor to detect cytosolic bacteria and DNA viruses. However, little is known about its immunological role during pathogenic Clostridium perfringens (C. perfringens) infection, an extracellular bacterial pathogen. In a pathogenic C. perfringens gas gangrene model, Aim2-/- mice are more susceptible to pathogenic C. perfringens soft tissue infection, revealing the importance of AIM2 in host protection. Notably, Aim2 deficiency leads to a defect in bacterial killing and clearance. Our in vivo and in vitro findings further establish that inflammasome signaling is impaired in the absence of Aim2 in response to pathogenic C. perfringens. Mechanistically, inflammasome signaling downstream of active AIM2 promotes pathogen control. Importantly, pathogenic C. perfringens-derived genomic DNA triggers inflammasome signaling activation in an AIM2-dependent manner. Thus, these observations uncover a central role for AIM2 in host defense and triggering innate immunity to combat pathogenic C. perfringens infections.

Expanding the Hydrophobic Cavity Surface of Azocalix[4]arene to Enable Biotin/Avidin Affinity with Controlled Release.

The development of artificial receptors that combine ultrahigh-affinity binding and controllable release for active guests holds significant importance in biomedical applications. On one hand, a complex with an exceedingly high binding affinity can resist unwanted dissociation induced by dilution effect and complex interferents within physiological environments. On the other hand, stimulus-responsive release of the guest is essential for precisely activating its function. In this context, we expanded hydrophobic cavity surface of a hypoxia-responsive azocalix[4]arene, affording Naph-SAC4A. This modification significantly enhanced its aqueous binding affinity to 1013 M-1, akin to the naturally occurring strongest recognition pair, biotin/(strept-)avidin. Consequently, Naph-SAC4A emerges as the first artificial receptor to simultaneously integrate ultrahigh recognition affinity and actively controllable release. The markedly enhanced affinity not only improved Naph-SAC4A's sensitivity in detecting rocuronium bromide in serum, but also refined the precision of hypoxia-responsive doxorubicin delivery at the cellular level, demonstrating its immense potential for diverse practical applications.

A Facile Strategy for Constructing High-Performance Polymer Electrolytes via Anion Modification and Click Chemistry for Rechargeable Magnesium Batteries.

Polymer electrolytes play a crucial role in advancing rechargeable magnesium batteries (RMBs) owing to their exceptional characteristics, including high flexibility, superior interface compatibility, broad electrochemical stability window, and enhanced safety features. Despite these advantages, research in this domain remains nascent, plagued by single preparation approaches and challenges associated with the compatibility between polymer electrolytes and Mg metal anode. In this study, we present a novel synthesis strategy to fabricate a glycerol α,α'-diallyl ether-3,6-dioxa-1,8-octanedithiol-based composite gel polymer electrolyte supported by glass fiber substrate (GDT@GF CGPE) through anion modification and thiol-ene click chemistry polymerization. The developed route exhibits novelty and high efficiency, leading to the production of GDT@GF CGPEs featuring exceptional mechanical properties, heightened ionic conductivity, elevated Mg2+ transference number, and commendable compatibility with Mg anode. The assembled modified Mo6S8||GDT@GF||Mg cells exhibit outstanding performance across a wide temperature range and address critical safety concerns, showcasing the potential for applications under extreme conditions. Our innovative preparation strategy offers a promising avenue for the advancement of polymer electrolytes in high-performance rechargeable magnesium batteries, while also opens up possibilities for future large-scale applications and the development of flexible electronic devices.

Noninvasive detection of brain gliomas using plasma cell-free DNA 5-hydroxymethylcytosine sequencing.

Liquid biopsy techniques based on deep sequencing of plasma cell-free DNA (cfDNA) could detect the low-frequency somatic mutations and provide an accurate diagnosis for many cancers. However, for brain gliomas, reliable performance of these techniques currently requires obtaining cfDNA from patients' cerebral spinal fluid, which is cumbersome and risky. Here we report a liquid biopsy method based on sequencing of plasma cfDNA fragments carrying 5-hydroxymethylcytosine (5hmC) using selective chemical labeling (hMe-Seal). We first constructed a dataset including 180 glioma patients and 229 non-glioma controls. We found marked concordance between cfDNA hydroxymethylome and the aberrant transcriptome of the underlying gliomas. Functional analysis also revealed overrepresentation of the differentially hydroxymethylated genes (DhmGs) in oncogenic and neural pathways. After splitting our dataset into training and test cohort, we showed that a penalized logistic model constructed with training set DhmGs could distinguish glioma patients from healthy controls in both our test set (AUC = 0.962) and an independent dataset (AUC = 0.930) consisting of 111 gliomas and 111 controls. Additionally, the DhmGs between gliomas with mutant and wild-type isocitrate dehydrogenase (IDH) could be used to train a cfDNA predictor of the IDH mutation status of the underlying tumor (AUC = 0.816), and patients with predicted IDH mutant gliomas had significantly better outcome (P = .01). These results indicate that our plasma cfDNA 5hmC sequencing method could obtain glioma-specific signals, which may be used to noninvasively detect these patients and predict the aggressiveness of their tumors.

Fully Integrated Ratiometric Fluorescence Enrichment Platform for High-Sensitivity POC Testing of Salivary Cancer Biomarkers.

The point-of-care (POC) testing of cancer biomarkers in saliva with both high sensitivity and accuracy remains a serious challenge in modern clinical medicine. Herein, we develop a new fully integrated ratiometric fluorescence enrichment platform that utilizes acoustic radiation forces to enrich dual-emission sandwich immune complexes for a POC visual assay. As a result, the color signals from red and green fluorescence (capture probe and report probe, respectively) are enhanced by nearly 10 times, and colorimetric sensitivity is effectively improved. When illuminated using a portable UV lamp, the fluorescence color changing from red to green can be clearly seen with the naked eye, which allows a semiqualitative assessment of the carcinoembryonic antigen (CEA) level. In combination with a homemade smartphone-based portable device, cancer biomarkers like CEA are quantified, achieving a limit of detection as low as 0.012 ng/mL. We also directly quantify CEA in human saliva samples to investigate the reliability of this fully integrated platform, thus validating the usefulness of the proposed strategy for clinical diagnosis and home monitoring of physical conditions.

High-Energy Aqueous Magnesium Ion Batteries with Capacity-Compensation Evolved from Dynamic Copper Ion Redox.

The low specific capacity and low voltage plateau are significant challenges in the advancement of practical magnesium ion batteries (MIBs). Here, a superior aqueous electrolyte combining with a copper foam interlayer between anode and separator is proposed to address these drawbacks. Notably, with the dynamic redox of copper ions, the weakened solvation of Mg2+ cations in the electrolyte and the enhanced electronic conductivity of anode, which may offer effective capacity-compensation to the 3,4,9,10-perylenetetracarboxylic diimide (PTCDI)-Mg conversion reactions during the long-term cycles. As a result, the unique MIBs using expanded graphite cathode coupled with PTCDI anode demonstrate exceptional performance with an ultra-high capacity (205 mAh g-1 , 243 Wh kg-1 at 5 A g-1 ) as well as excellent cycling stability after 600 cycles and rate capability (138 mAh g-1 , 81 Wh kg-1 at 10 A g-1 ).

Intronic microRNA-directed regulation of mitochondrial reactive oxygen species enhances plant stress tolerance in Arabidopsis.

MicroRNAs (miRNAs) play crucial roles in regulating plant development and stress responses. However, the functions and mechanism of intronic miRNAs in plants are poorly understood. This study reports a stress-responsive RNA splicing mechanism for intronic miR400 production, whereby miR400 modulates reactive oxygen species (ROS) accumulation and improves plant tolerance by downregulating its target expression. To monitor the intron splicing events, we used an intronic miR400 splicing-dependent luciferase transgenic line. Luciferase activity was observed to decrease after high cadmium concentration treatment due to the retention of the miR400-containing intron, which inhibited the production of mature miR400. Furthermore, we demonstrated that under Cd treatments, Pentatricopeptide Repeat Protein 1 (PPR1), the target of miR400, acts as a positive regulator by inducing ROS accumulation. Ppr1 mutation affected the Complex III activity in the electron transport chain and RNA editing of the mitochondrial gene ccmB. This study illustrates intron splicing as a key step in intronic miR400 production and highlights the function of intronic miRNAs as a 'signal transducer' in enhancing plant stress tolerance.

Selective Reduction Leading to 3,5-cis-3-Aminosugars: Synthesis and Stereoselective Glycosylation.

Synthesis of 3,5-cis-3-amino glycals with a cis-fused cyclic sulfamidate group has been achieved by selective reduction of sulfamidate ketimine groups. The efficient access to the structurally unique glycals allowed the subsequent divergent synthesis of various naturally occurring 3-amino-2,3,6-trideoxysugars. In addition, Lewis acid-promoted glycosylation of the glycals provided a simple solution for the stereoselective installation of O- and C-linked aglycons on the amino sugar scaffolds.

The maize ATP-binding cassette (ABC) transporter ZmMRPA6 confers cold and salt stress tolerance in plants.

KEY MESSAGE: ZmMRPA6 was cloned and characterized as the first ATP-binding cassette (ABC) transporter in maize to be proven to participate in cold and salt tolerance. Homologous genes AtABCC4 and AtABCC14 of ZmMRPA6 also responded to salt stress. ATP-binding cassette (ABC) proteins are major transmembrane transporters that play significant roles in plant development against various abiotic stresses. However, available information regarding stress-related ABC genes in maize is minimal. In this study, a maize ABC transporter gene, ZmMRPA6, was identified through genome-wide association analysis (GWAS) for cold tolerance in maize seeds germination and functionally characterized. During germination and seedling stages, the zmmrpa6 mutant exhibited enhanced resistance to cold or salt stress. Mutated of ZmMRPA6 did not affect the expression of downstream response genes related cold or salt response at the transcriptional level. Mass spectrometry analysis revealed that most of the differential proteins between zmmrpa6 and wild-type plants were involved in response to stress process including oxidative reduction, hydrolase activity, small molecule metabolism, and photosynthesis process. Meanwhile, the plants which lack the ZmMRPA6 homologous genes AtABCC4 or AtABCC14 were sensitive to salt stress in Arabidopsis. These results indicated that ZmMRPA6 and its homologous genes play a conserved role in cold and salt stress, and functional differentiation occurs in monocotyledonous and dicotyledonous plants. In summary, these findings dramatically improved our understanding of the function of ABC transporters resistance to abiotic stresses in plants.

Spinal cord stimulation and deep brain stimulation for disorders of consciousness: a systematic review and individual patient data analysis of 608 cases.

The application of spinal cord stimulation (SCS) and deep brain stimulation (DBS) for disorders of consciousness (DoC) has been increasingly reported. However, there is no sufficient evidence to determine how effective and safe SCS and DBS are for DoC owing to various methodological limitations. We conducted a systematic review to elucidate the safety and efficacy of SCS and DBS for DoC by systematically reviewing related literature by searching PubMed, EMBASE, Medline, and Cochrane Library. Twenty eligible studies with 608 patients were included in this study. Ten studies with 508 patients reported the efficacy of SCS for DoC, and the estimated overall effectiveness rate was 37%. Five studies with 343 patients reported the efficacy of SCS for VS, and the estimated effectiveness rate was 30%. Three studies with 53 patients reported the efficacy of SCS for MCS, and the estimated effectiveness rate was 63%. Five studies with 92 patients reported the efficacy of DBS for DoC, and the estimated overall effectiveness rate was 40%. Four studies with 63 patients reported the efficacy of DBS for VS, and the estimated effectiveness rate was 26%. Three studies with 19 patients reported the efficacy of DBS for MCS, and the estimated effectiveness rate was 74%. The adverse event rate of DoC was 8.1% and 18.2% after SCS and DBS, respectively. These results suggest that SCS and DBS can be considered reasonable treatments for DoC with considerable efficacy and safety.

MAC5, an RNA-binding protein, protects pri-miRNAs from SERRATE-dependent exoribonuclease activities.

MAC5 is a component of the conserved MOS4-associated complex. It plays critical roles in development and immunity. Here we report that MAC5 is required for microRNA (miRNA) biogenesis. MAC5 interacts with Serrate (SE), which is a core component of the microprocessor that processes primary miRNA transcripts (pri-miRNAs) into miRNAs and binds the stem-loop region of pri-miRNAs. MAC5 is essential for both the efficient processing and the stability of pri-miRNAs. Interestingly, the reduction of pri-miRNA levels in mac5 is partially caused by XRN2/XRN3, the nuclear-localized 5'-to-3' exoribonucleases, and depends on SE. These results reveal that MAC5 plays a dual role in promoting pri-miRNA processing and stability through its interaction with SE and/or pri-miRNAs. This study also uncovers that pri-miRNAs need to be protected from nuclear RNA decay machinery, which is connected to the microprocessor.

Automated approach for quality assessment of RDF resources.

INTRODUCTION: The Semantic Web community provides a common Resource Description Framework (RDF) that allows representation of resources such that they can be linked. To maximize the potential of linked data - machine-actionable interlinked resources on the Web - a certain level of quality of RDF resources should be established, particularly in the biomedical domain in which concepts are complex and high-quality biomedical ontologies are in high demand. However, it is unclear which quality metrics for RDF resources exist that can be automated, which is required given the multitude of RDF resources. Therefore, we aim to determine these metrics and demonstrate an automated approach to assess such metrics of RDF resources. METHODS: An initial set of metrics are identified through literature, standards, and existing tooling. Of these, metrics are selected that fulfil these criteria: (1) objective; (2) automatable; and (3) foundational. Selected metrics are represented in RDF and semantically aligned to existing standards. These metrics are then implemented in an open-source tool. To demonstrate the tool, eight commonly used RDF resources were assessed, including data models in the healthcare domain (HL7 RIM, HL7 FHIR, CDISC CDASH), ontologies (DCT, SIO, FOAF, ORDO), and a metadata profile (GRDDL). RESULTS: Six objective metrics are identified in 3 categories: Resolvability (1), Parsability (1), and Consistency (4), and represented in RDF. The tool demonstrates that these metrics can be automated, and application in the healthcare domain shows non-resolvable URIs (ranging from 0.3% to 97%) among all eight resources and undefined URIs in HL7 RIM, and FHIR. In the tested resources no errors were found for parsability and the other three consistency metrics for correct usage of classes and properties. CONCLUSION: We extracted six objective and automatable metrics from literature, as the foundational quality requirements of RDF resources to maximize the potential of linked data. Automated tooling to assess resources has shown to be effective to identify quality issues that must be avoided. This approach can be expanded to incorporate more automatable metrics so as to reflect additional quality dimensions with the assessment tool implementing more metrics.

Rapid establishment of murine gastrointestinal organoids using mechanical isolation method.

Gastrointestinal (GI) diseases, including pathological dysplasia, inflammation, neoplasia and injury, suffer millions of patients globally per year. Organoids, three-dimensional cell mass structures supported by biomaterials in dishes, are currently used as a research model for diseases of the small intestine. However, the traditional enzymatic-digestion method for establishing small-intestinal organoids (EnzyOs) is time consuming and often loses the bulk of crypts, a more efficient and reliable method needs to be developed. In this study, using mouse GI organoids as a model, we formulated a rapid mechanical isolation method that could efficiently isolate and culture villi-crypts into small intestinal organoids (MechOs). Primary duodenum organoids generated by MechOs displayed three types of morphology: spheroid, semi-budding and budding, while EnzyOs produced much less budding. Moreover, primary duodenum organoids from MechOs could be subcultured and presented similar gene expression profiles of small intestine specific markers as that from EnzyOs. Importantly, the MechOs method could also be used to generate other types of organoids derived from the stomach, jejunum-ileum, sigmoid-rectum and bile cysts. Taken together, the results show that MechOs could efficiently and economically generate digestive system organoids, providing a potential basis of epithelial organoids for the clinical treatment of gastroenterological diseases.

Group IIc WRKY transcription factors regulate cotton resistance to Fusarium oxysporum by promoting GhMKK2-mediated flavonoid biosynthesis.

WRKY transcription factors (TFs) are crucial regulators in response to pathogen infection. However, the regulatory mechanisms of WRKY TFs in response to Fusarium oxysporum f. sp. vasinfectum (Fov), the most devastating pathogen of cotton, remain unclear. Here, transcriptome sequencing indicated that the group IIc WRKY TF subfamily was the most important TF subfamily in response to Fov. Gain-of-function and loss-of-function analyses showed that group IIc WRKY TFs positively regulated cotton resistance to Fov. A series of chromatin immunoprecipitation sequencing, yeast one-hybrid assay and electrophoresis mobility shift assay experiments indicated that group IIc WRKY TFs directly bound to the promoter of GhMKK2 and regulated its expression. Importantly, a novel mitogen-activated protein kinase (MAPK) cascade composed of GhMKK2, GhNTF6 and GhMYC2 was identified. The functional analysis indicated that group IIc WRKY TFs induced the GhMKK2-GhNTF6 pathway to increase resistance to Fov by upregulating the GhMYC2-mediated expression of several flavonoid biosynthesis-related genes, which led to flavonoid accumulation. In conclusion, our study demonstrated a novel disease defense mechanism by which the WRKY-MAPK pathway promotes flavonoid biosynthesis to defend against pathogen infection. This pathway improves our understanding of the interaction mode between WRKY TFs and MAPK cascades in plant immunity and the vital role of plant flavonoids in pathogen defense.

Physiological suitability of sulfate-reducing granules for the development of bioconcrete.

Regular monitoring and timely repair of concrete cracks are required to minimize further deterioration. Self-healing of cracks has been proposed as an alternative to the crack maintenance procedures. One of the proposed techniques is to use axenic cultures to exploit microbial-induced calcite precipitation (MICP). However, such healing agents are not cost-effective for in situ use. As the market for bio-based self-healing concrete necessitates a low-cost bio-agent, nonaxenic sulfate reducing bacterial (SRB) granules were investigated in this study through cultivation in an upflow anaerobic sludge blanket reactor. The compact granules can protect the bacteria from adverse conditions without encapsulation. This study investigated the microbial activities of SRB granules at different temperatures, pH, and chemical oxygen demand concentrations which the microbes would experience during the concrete casting and curing process. The attenuation and recovery of microbial activities were measured before and after the exposure. Moreover, the MICP yield was also tested for a possible use in self-healing bioconcrete. The results consistently showed that SRB granules were able to survive starvation, high temperature (50-60°C), and high pH (12), together with scanning electron microscope/energy dispersive spectrometry/X-ray diffraction analysis evidence. Microbial staining analysis demonstrated the formation of spores in the granules during their exposure to harsh conditions. SRB granule was thus demonstrated to be a viable self-healing nonaxenic agent for low-cost bioconcrete.

Association between household incense burning and executive function in Chinese children.

Incense burning is common in Asia including China. Research investigating the association between household incense burning and children's neurodevelopment is scarce. We aimed to examine this association in Chinese children. In 2019, we randomly enrolled 8293 children aged 6-12 years from 5 elementary schools in Guangzhou, southern China. Information on duration and frequency of household incense burning was collected using a questionnaire. Children's executive function was evaluated using the parental report of the Behavioral Rating Inventory of Executive Function. A general linear model was used to assess the associations between incense burning and executive function. Children who occasionally and frequently exposed to incense burning exhibited worse performance on executive function. For example, frequent incense burning was associated with increases in behavioral regulation index (BRI) of 1.77 (95%CI: 0.97, 2.58) points and metacognition index (MI) of 1.40 (95%CI: 0.60, 2.20) points, compared to never incense burning group. Parental smoking and household income were significant modifiers of the associations, with the stronger associations were observed in children having smoking parent(s) and poorer household income. The findings suggest that household incense burning was associated with poorer executive function, especially in children whose parent(s) were smokers and in those with low household income.