KMT2D-mediated H3K4me1 recruits YBX1 to facilitate triple-negative breast cancer progression through epigenetic activation of c-Myc.

BACKGROUND: Lysine methyltransferase 2D (KMT2D) mediates mono-methylation of histone H3 lysine 4 (H3K4me1) in mammals. H3K4me1 mark is involved in establishing an active chromatin structure to promote gene transcription. However, the precise molecular mechanism underlying the KMT2D-mediated H3K4me1 mark modulates gene expression in triple-negative breast cancer (TNBC) progression is unresolved. METHODS AND RESULTS: We recognized Y-box-binding protein 1 (YBX1) as a "reader" of the H3K4me1 mark, and a point mutation of YBX1 (E121A) disrupted this interaction. We found that KMT2D and YBX1 cooperatively promoted cell growth and metastasis of TNBC cells in vitro and in vivo. The expression levels of KMT2D and YBX1 were both upregulated in tumour tissues and correlated with poor prognosis for breast cancer patients. Combined analyses of ChIP-seq and RNA-seq data indicated that YBX1 was co-localized with KMT2D-mediated H3K4me1 in the promoter regions of c-Myc and SENP1, thereby activating their expressions in TNBC cells. Moreover, we demonstrated that YBX1 activated the expressions of c-Myc and SENP1 in a KMT2D-dependent manner. CONCLUSION: Our results suggest that KMT2D-mediated H3K4me1 recruits YBX1 to facilitate TNBC progression through epigenetic activation of c-Myc and SENP1. These results together unveil a crucial interplay between histone mark and gene regulation in TNBC progression, thus providing novel insights into targeting the KMT2D-H3K4me1-YBX1 axis for TNBC treatment. HIGHLIGHTS: YBX1 is a KMT2D-mediated H3K4me1-binding effector protein and mutation of YBX1 (E121A) disrupts its binding to H3K4me1. KMT2D and YBX1 cooperatively promote TNBC proliferation and metastasis by activating c-Myc and SENP1 expression in vitro and in vivo. YBX1 is colocalized with H3K4me1 in the c-Myc and SENP1 promoter regions in TNBC cells and increased YBX1 expression predicts a poor prognosis in breast cancer patients.

Ferrocene Derivatives for Photothermal Applications.

Ferrocene (Fc) and Fc derivatives have gained popularity in recent years due to their unique structure and characteristics. Among Fc's diverse performances, photothermal conversion, as a primary source of energy conversion, has sparked substantial study attention. This review summaries Fc and Fc derivatives with photothermal characteristics, as well as their applications developed recently. First, methods for the synthesis of Fc-based materials are systematically discussed. Then, the photothermal conversion mechanism based on nonradiative relaxation is summarized. Furthermore, the most recent advances in Fc-based materials in photothermal applications are described, including photothermal degradation, photothermal antibacterial, photothermal therapies, photothermal catalysis, solar-driven water production, and photothermal CO2 separation. Finally, a summary and insights on the photothermal application of Fc-based materials are provided. This paper seeks to provide researchers with a better knowledge of photothermal behavior while also highlighting the potential of Fc and its derivatives in photothermal fields.

Octanoic acid mitigates busulfan-induced blood-testis barrier damage by alleviating oxidative stress and autophagy.

BACKGROUND: The management of male infertility continues to encounter an array of challenges and constraints, necessitating an in-depth exploration of novel therapeutic targets to enhance its efficacy. As an eight-carbon medium-chain fatty acid, octanoic acid (OCA) shows promise for improving health, yet its impact on spermatogenesis remains inadequately researched. METHODS: Mass spectrometry was performed to determine the fatty acid content and screen for a pivotal lipid component in the serum of patients with severe spermatogenesis disorders. The sperm quality was examined, and histopathological analysis and biotin tracer tests were performed to assess spermatogenesis function and the integrity of the blood-testis barrier (BTB) in vivo. Cell-based in vitro experiments were carried out to investigate the effects of OCA administration on Sertoli cell dysfunction. This research aimed to elucidate the mechanism by which OCA may influence the function of Sertoli cells. RESULTS: A pronounced reduction in OCA content was observed in the serum of patients with severe spermatogenesis disorders, indicating that OCA deficiency is related to spermatogenic disorders. The protective effect of OCA on reproduction was tested in a mouse model of spermatogenic disorder induced by busulfan at a dose 30 mg/kg body weight (BW). The mice in the study were separated into distinct groups and administered varying amounts of OCA, specifically at doses of 32, 64, 128, and 256 mg/kg BW. After evaluating sperm parameters, the most effective dose was determined to be 32 mg/kg BW. In vivo experiments showed that treatment with OCA significantly improved sperm quality, testicular histopathology and BTB integrity, which were damaged by busulfan. Moreover, OCA intervention reduced busulfan-induced oxidative stress and autophagy in mouse testes. In vitro, OCA pretreatment (100 µM) significantly ameliorated Sertoli cell dysfunction by alleviating busulfan (800 µM)-induced oxidative stress and autophagy. Moreover, rapamycin (5 µM)-induced autophagy led to Sertoli cell barrier dysfunction, while OCA administration exerted a protective effect by alleviating autophagy. CONCLUSIONS: This study demonstrated that OCA administration suppressed oxidative stress and autophagy to alleviate busulfan-induced BTB damage. These findings provide a deeper understanding of the toxicology of busulfan and a promising avenue for the development of novel OCA-based therapies for male infertility.

Effects of WuHuTang on the function and autophagy of dendritic cells treated with exosomes induced by RSV.

ETHNOPHARMACOLOGICAL RELEVANCE: WuHuTang (WHT) is a traditional Chinese medicine compound for treating asthma, and the evidence supports that it has a good effect on acute asthma attacks in children and adults. Respiratory syncytial virus (RSV) is an important factor in the pathogenesis of acute asthma attacks, and the effect on dendritic cells is the key to its pathogenesis. Previous studies have confirmed that the pathogenesis of viruses is related to exosomes. However, there are few studies on the exosomes induced by RSV. Whether WHT can improve the changes caused by RSV-induced exosomes or not is worthy of further exploration. AIM OF THE STUDY: We aim to study the effects of RSV-induced exosomes on the function and autophagy of dendritic cells, and to observe the intervention effect of WHT serum on the above effects. METHODS: The co-culture model of exosomes derived from bone marrow mesenchymal stem cells induced by RSV (BMSCs-Exo-RSV) and dendritic cells was established, and then WHT serum was used to intervene. After 24 h of intervention, the CCK-8 method, flow cytometry, Elisa, RT-qCPR, and Western blot were used to detect the above-mentioned culture model. RESULTS: RSV-induced exosomes had certain effects on viability, apoptosis, and costimulatory molecules generation of dendritic cells. At the same time, the levels of IL-6, IL-12, TNF-α, and autophagy increased, while the levels of IL-4, IL-10, and TGF-ß decreased, and the AKT/TSC/mTOR pathway was inhibited. WHT serum could activate this pathway and reverse the above changes in dendritic cells. CONCLUSION: This study reveals that the pathogenic effect of RSV is related to the exosomes induced by RSV. The exosomes induced by RSV affect the function of dendritic cells by inhibiting the AKT/TSC/mTOR pathway, which can be activated by WHT to reverse the effects caused by RSV-induced exosomes.

LiCl in situ decorated metal-organic framework (MOF)-derived porous carbon for efficient solar-driven atmospheric water harvesting.

Solar-powered sorption-based atmospheric water harvesting (AWH) technology is a promising solution to the freshwater scarcity in arid regions. Existing adsorbent materials still face challenges in aspects such as cycling stability and adsorption kinetics and require further development. Herein, we presented a strategy for the in situ fabrication of high-performance adsorbents, lithium chloride (LiCl)-decorated metal-organic framework (MOF)-derived porous carbon sorbents (PCl), via high-temperature pyrolysis and hydrogen chloride (HCl) vapor treatment. The sorbents display high adsorption capacity across a wide range of humidity water adsorption capacities in a wide humidity range with the maximum adsorption capacity of 7.87 g g-1, and rapid response to the solar-driven process and excellent cyclic stability. The LiCl nanocrystals in PCl can be utilized efficiently and decorated within the porous framework stably, and demonstrate water adsorption at 20%, 40%, 60% and 80% RH, of 1.34, 1.69, 2.56 and 4.23 gH2O·gLiCl-1, respectively, and significantly higher water uptake and release rates than bulk LiCl. This may provide new guides for designing efficient solar-driven AWH.

Epigenetic modifications of DNA and RNA in Alzheimer's disease.

Alzheimer's disease (AD) is a complex neurodegenerative disorder and the most common form of dementia. There are two main types of AD: familial and sporadic. Familial AD is linked to mutations in amyloid precursor protein (APP), presenilin-1 (PSEN1), and presenilin-2 (PSEN2). On the other hand, sporadic AD is the more common form of the disease and has genetic, epigenetic, and environmental components that influence disease onset and progression. Investigating the epigenetic mechanisms associated with AD is essential for increasing understanding of pathology and identifying biomarkers for diagnosis and treatment. Chemical covalent modifications on DNA and RNA can epigenetically regulate gene expression at transcriptional and post-transcriptional levels and play protective or pathological roles in AD and other neurodegenerative diseases.

Lipidomics random forest algorithm of seminal plasma is a promising method for enhancing the diagnosis of necrozoospermia.

BACKGROUND: Despite the clear clinical diagnostic criteria for necrozoospermia in andrology, the fundamental mechanisms underlying it remain elusive. This study aims to profile the lipid composition in seminal plasma systematically and to ascertain the potential of lipid biomarkers in the accurate diagnosis of necrozoospermia. It also evaluates the efficacy of a lipidomics-based random forest algorithm model in identifying necrozoospermia. METHODS: Seminal plasma samples were collected from patients diagnosed with necrozoospermia (n = 28) and normozoospermia (n = 28). Liquid chromatography-mass spectrometry (LC-MS) was used to perform lipidomic analysis and identify the underlying biomarkers. A lipid functional enrichment analysis was conducted using the LION lipid ontology database. The top 100 differentially significant lipids were subjected to lipid biomarker examination through random forest machine learning model. RESULTS: Lipidomic analysis identified 46 lipid classes comprising 1267 lipid metabolites in seminal plasma. The top five enriched lipid functions as follows: fatty acid (FA) with ≤ 18 carbons, FA with 16-18 carbons, monounsaturated FA, FA with 18 carbons, and FA with 16 carbons. The top 100 differentially significant lipids were subjected to machine learning analysis and identified 20 feature lipids. The random forest model identified lipids with an area under the curve > 0.8, including LPE(20:4) and TG(4:0_14:1_16:0). CONCLUSIONS: LPE(20:4) and TG(4:0_14:1_16:0), were identified as differential lipids for necrozoospermia. Seminal plasma lipidomic analysis could provide valuable biochemical information for the diagnosis of necrozoospermia, and its combination with conventional sperm analysis may improve the accuracy and reliability of the diagnosis.

A combined pre- and intra-operative nomogram in evaluation of degrees of liver cirrhosis predicts post-hepatectomy liver failure: a multicenter prospective study.

Background: Adequate evaluation of degrees of liver cirrhosis is essential in surgical treatment of hepatocellular carcinoma (HCC) patients. The impact of the degrees of cirrhosis on prediction of post-hepatectomy liver failure (PHLF) remains poorly defined. This study aimed to construct and validate a combined pre- and intra-operative nomogram based on the degrees of cirrhosis in predicting PHLF in HCC patients using prospective multi-center's data. Methods: Consecutive HCC patients who underwent hepatectomy between May 18, 2019 and Dec 19, 2020 were enrolled at five tertiary hospitals. Preoperative cirrhotic severity scoring (CSS) and intra-operative direct liver stiffness measurement (DSM) were performed to correlate with the Laennec histopathological grading system. The performances of the pre-operative nomogram and combined pre- and intra-operative nomogram in predicting PHLF were compared with conventional predictive models of PHLF. Results: For 327 patients in this study, histopathological studies showed the rates of HCC patients with no, mild, moderate, and severe cirrhosis were 41.9%, 29.1%, 22.9%, and 6.1%, respectively. Either CSS or DSM was closely correlated with histopathological stages of cirrhosis. Thirty-three (10.1%) patients developed PHLF. The 30- and 90-day mortality rates were 0.9%. Multivariate regression analysis showed four pre-operative variables [HBV-DNA level, ICG-R15, prothrombin time (PT), and CSS], and one intra-operative variable (DSM) to be independent risk factors of PHLF. The pre-operative nomogram was constructed based on these four pre-operative variables together with total bilirubin. The combined pre- and intra-operative nomogram was constructed by adding the intra-operative DSM. The pre-operative nomogram was better than the conventional models in predicting PHLF. The prediction was further improved with the combined pre- and intra-operative nomogram. Conclusions: The combined pre- and intra-operative nomogram further improved prediction of PHLF when compared with the pre-operative nomogram. Trial Registration: Clinicaltrials.gov Identifier: NCT04076631.

Clinical significance of R-wave amplitude in lead V1 and inferobasal myocardial infarction in patients with inferior wall myocardial infarction.

OBJECTIVE: To assess electrocardiogram (ECG) for risk stratification in inferior ST-elevation myocardial infarction (STEMI) patients within 24 h. METHODS: Three hundred thirty-four patients were divided into four ECG-based groups: Group A: R V1 <0.3 mV with ST-segment elevation (ST↑) V7-V9, Group B: R V1 <0.3 mV without ST↑ V7-V9, Group C: R V1 ≥0.3 mV with ST↑ V7-V9, and Group D: R V1 ≥0.3 mV without ST↑ V7-V9. RESULTS: Group A demonstrated the longest QRS duration, followed by Groups B, C, and D. ECG signs for right ventricle (RV) infarction were more common in Groups A and B (p < .01). ST elevation in V6, indicative of left ventricle (LV) lateral injury, was more higher in Group C than in Group A, while the ∑ST↑ V3R + V4R + V5R, representing RV infarction, showed the opposite trend (p < .05). The estimated LV infarct size from ECG was similar between Groups A and C, yet Group A had higher creatine kinase MB isoform (CK-MB; p < .05). Cardiac troponin I (cTNI) was higher in Groups A and C than in B and D (p < .05 and p = .16, respectively). NT-proBNP decreased across groups (p = .20), with the highest left ventricular ejection fraction (LVEF) observed in Group D (p < .05). Group A notably demonstrated more cardiac dysfunction within 4 h post-onset. CONCLUSIONS: For inferior STEMI patients, concurrent R V1 <0.3 mV with ST↑ V7-V9 suggests prolonged ventricular activation and notable myocardial damage. RV infarction's dominance over LV lateral injury might explain these observations.

Automated identification of atrial fibrillation from single-lead ECGs using multi-branching ResNet.

Introduction: Atrial fibrillation (AF) is the most common cardiac arrhythmia, which is clinically identified with irregular and rapid heartbeat rhythm. AF puts a patient at risk of forming blood clots, which can eventually lead to heart failure, stroke, or even sudden death. Electrocardiography (ECG), which involves acquiring bioelectrical signals from the body surface to reflect heart activity, is a standard procedure for detecting AF. However, the occurrence of AF is often intermittent, costing a significant amount of time and effort from medical doctors to identify AF episodes. Moreover, human error is inevitable, as even experienced medical professionals can overlook or misinterpret subtle signs of AF. As such, it is of critical importance to develop an advanced analytical model that can automatically interpret ECG signals and provide decision support for AF diagnostics. Methods: In this paper, we propose an innovative deep-learning method for automated AF identification using single-lead ECGs. We first extract time-frequency features from ECG signals using continuous wavelet transform (CWT). Second, the convolutional neural networks enhanced with residual learning (ReNet) are employed as the functional approximator to interpret the time-frequency features extracted by CWT. Third, we propose to incorporate a multi-branching structure into the ResNet to address the issue of class imbalance, where normal ECGs significantly outnumber instances of AF in ECG datasets. Results and Discussion: We evaluate the proposed Multi-branching Resnet with CWT (CWT-MB-Resnet) with two ECG datasets, i.e., PhysioNet/CinC challenge 2017 and ECGs obtained from the University of Oklahoma Health Sciences Center (OUHSC). The proposed CWT-MB-Resnet demonstrates robust prediction performance, achieving an F1 score of 0.8865 for the PhysioNet dataset and 0.7369 for the OUHSC dataset. The experimental results signify the model's superior capability in balancing precision and recall, which is a desired attribute for ensuring reliable medical diagnoses.

The effect of physical therapy and mechanical stimulation on dysfunction of lower extremities after total pelvic exenteration in cervical carcinoma patient with rectovesicovaginal fistula induced by radiotherapy: a case report.

BACKGROUND: Total pelvic exenteration is the ultimate solution for rectovesicovaginal fistula caused by radiation therapy, yet total pelvic exenteration frequently causes intraoperative complications and postoperative complications. These complications are responsible for the dysfunction of lower extremities, impaired quality of life, and even the high long-term morbidity rate, thus multidisciplinary cooperation and early intervention for prevention of complications are necessary. Physical therapy was found to reduce the postoperative complications and promote rehabilitation, yet the effect on how physiotherapy prevents and treats complications after total pelvic exenteration and pelvic lymphadenectomy remains unclear. CASE PRESENTATION: A 50-year-old Chinese woman gradually developed perianal and pelvic floor pain and discomfort, right lower limb numbness, and involuntary vaginal discharge owing to recurrence and metastasis of cervical cancer more than half a year ago. Diagnosed as rectovesicovaginal fistula caused by radiation, she received total pelvic exenteration and subsequently developed severe lower limb edema, swelling pain, obturator nerve injury, and motor dysfunction. The patient was referred to a physiotherapist who performed rehabilitation evaluation and found edema in both lower extremities, right inguinal region pain (numeric pain rate scale 5/10), decreased temperature sensation and light touch in the medial thigh of the right lower limb, decreased right hip adductor muscle strength (manual muscle test 1/5) and right hip flexor muscle strength (manual muscle test 1/5), inability actively to adduct and flex the right hip with knee extension, low de Morton mobility Index score (0/100), and low Modified Barthel Index score (35/100). Routine physiotherapy was performed in 2 weeks, including therapeutic exercises, mechanical stimulation and electrical stimulation as well as manual therapy. The outcomes showed that physiotherapy significantly reduced lower limb pain and swelling, and improved hip range of motion, motor function, and activities of daily living, but still did not prevent thrombosis. CONCLUSION: Standardized physical therapy demonstrates the effect on postoperative complications after total pelvic exenteration and pelvic lymphadenectomy. This supports the necessity of multidisciplinary cooperation and early physiotherapy intervention. Further research is needed to determine the causes of thrombosis after standardized intervention, and more randomized controlled trials are needed to investigate the efficacy of physical therapy after total pelvic exenteration.

Bridging the gap: R-loop mediated genomic instability and its implications in neurological diseases.

R-loops, intricate three-stranded structures formed by RNA-DNA hybrids and an exposed non-template DNA strand, are fundamental to various biological phenomena. They carry out essential and contrasting functions within cellular mechanisms, underlining their critical role in maintaining cellular homeostasis. The specific cellular context that dictates R-loop formation determines their function, particularly emphasizing the necessity for their meticulous genomic regulation. Notably, the aberrant formation or misregulation of R-loops is implicated in numerous neurological disorders. This review focuses on the complex interactions between R-loops and double-strand DNA breaks, exploring how R-loop dysregulation potentially contributes to the pathogenesis of various brain disorders, which could provide novel insights into the molecular mechanisms underpinning neurological disease progression and identify potential therapeutic targets by highlighting these aspects.

R-loops are special structures inside our cells, made when a piece of RNA (a molecule similar to DNA) sticks to DNA, exposing a part of the DNA. These structures play important roles in how our cells work, helping to keep them healthy and functioning properly. However, when these R-loops do not form correctly or are not controlled well by the cell, they can cause problems. This is especially true in the brain, where mistakes in R-loop formation can lead to various neurological disorders, which are conditions that affect the brain and nerves. In our review, we examine how R-loops interact with certain types of DNA damage and how this can lead to brain disorders. We hope that by understanding these interactions better, scientists can find new ways to treat or prevent these conditions.

Pd NP-loaded covalent organic framework for pH-switched Pickering emulsion catalytic dechlorination.

Quinoline carboxylic acid-linked and Pd nanoparticle (NP)-loaded COF nanospheres were constructed via a three-component one-pot Doebner reaction and post-synthetic metalation. The obtained Pd@DhaTAPB-COOH solid stabilizer can greatly promote the pH-switched recyclable Pickering interfacial dechlorination reaction, which sheds light on the bright future of smart Pickering emulsion catalysis.

Mechanism of Bazi Bushen capsule in delaying the senescence of mesenchymal stem cells based on network pharmacology and experimental validation.

Ageing is becoming an increasingly serious problem; therefore, there is an urgent need to find safe and effective anti-ageing drugs. Aims: To investigate the effects of Bazi Bushen capsule (BZBS) on the senescence of mesenchymal stem cells (MSCs) and explore its mechanism of action. Methods: Network pharmacology was used to predict the targets of BZBS in delaying senescence in MSCs. For in vitro studies, MSCs were treated with D-gal, BZBS, and NMN, and cell viability, cell senescence, stemness-related genes, and cell cycle were studied using cell counting kit-8 (CCK-8) assay, SA-ß-galactosidase (SA-ß-gal) staining, Quantitative Real-Time PCR (qPCR) and flow cytometry (FCM), respectively. Alkaline phosphatase (ALP), alizarin red, and oil red staining were used to determine the osteogenic and lipid differentiation abilities of MSCs. Finally, the expression of senescence-related genes and cyclin-related factors was detected by qPCR and western blotting. Results: Network pharmacological analysis suggested that BZBS delayed cell senescence by interfering in the cell cycle. Our in vitro studies suggested that BZBS could significantly increase cell viability (P < 0.01), decrease the quantity of ß-galactosidase+ cells (P < 0.01), downregulate p16 and p21 (P < 0.05, P < 0.01), improve adipogenic and osteogenic differentiation, and upregulate Nanog, OCT4 and SOX2 genes (P < 0.05, P < 0.01) in senescent MSCs. Moreover, BZBS significantly reduced the proportion of senescent MSCs in the G0/G1 phase (P < 0.01) and enhanced the expression of CDK4, Cyclin D1, and E2F1 (P < 0.05, P < 0.01, respectively). Upon treatment with HY-50767A, a CDK4 inhibitor, the upregulation of E2F1 was no longer observed in the BZBS group. Conclusions: BZBS can protect MSCs against D-gal-induced senescence, which may be associated with cell cycle regulation via the Cyclin D1/CDK4/E2F1 signalling pathway.

Deep5hmC: Predicting genome-wide 5-Hydroxymethylcytosine landscape via a multimodal deep learning model.

5-hydroxymethylcytosine (5hmC), a critical epigenetic mark with a significant role in regulating tissue-specific gene expression, is essential for understanding the dynamic functions of the human genome. Using tissue-specific 5hmC sequencing data, we introduce Deep5hmC, a multimodal deep learning framework that integrates both the DNA sequence and the histone modification information to predict genome-wide 5hmC modification. The multimodal design of Deep5hmC demonstrates remarkable improvement in predicting both qualitative and quantitative 5hmC modification compared to unimodal versions of Deep5hmC and state-of-the-art machine learning methods. This improvement is demonstrated through benchmarking on a comprehensive set of 5hmC sequencing data collected at four time points during forebrain organoid development and across 17 human tissues. Notably, Deep5hmC showcases its practical utility by accurately predicting gene expression and identifying differentially hydroxymethylated regions in a case-control study of Alzheimer's disease.

NatD epigenetically activates FOXA2 expression to promote breast cancer progression by facilitating MMP14 expression.

N-α-acetyltransferase D (NatD) mediates N-α-terminal acetylation of histone H4 (Nt-Ac-H4), but its role in breast cancer metastasis remains unknown. Here, we show that depletion of NatD directly represses the expression of FOXA2, and is accompanied by a significant reduction in Nt-Ac-H4 enrichment at the FOXA2 promoter. We show that NatD is commonly upregulated in primary breast cancer tissues, where its expression level correlates with FOXA2 expression, enhanced invasiveness, and poor clinical outcomes. Furthermore, we show that FOXA2 promotes the migration and invasion of breast cancer cells by activating MMP14 expression. MMP14 is also upregulated in breast cancer tissues, where its expression level correlates with FOXA2 expression and poor clinical prognosis. Our study shows that the NatD-FOXA2-MMP14 axis functions as a key signaling pathway to promote the migratory and invasive capabilities of breast cancer cells, suggesting that NatD is a critical epigenetic modulator of cell invasion during breast cancer progression.

Effect of ozone sterilization on controlling leaf mildew and gray mold tomato disease in a glasshouse and its influence on other growth parameters.

BACKGROUND: In order to explore the effect of ozone sterilization treatment on tomato disease control and increase fruit setting rate, this study took 906 pink fruit tomato as test material, used a small ozone generator to carry out ozone treatment single-factor test, and then selected orthogonal table to guide the ozone treatment combination. The effects of different ozone treatment concentration, ozone treatment duration and ozone treatment times on the growth, disease and fruit setting rate of potted tomato were analyzed. RESULTS: Different ozone treatment had effects on leaf mildew, gray mold and fruit setting rate of tomato. The influence degree of three factors on leaf mildew, gray mold and fruit setting rate was from large to small, a > b > c, a > c > b, b > a > c. A quadratic regression model was established with the control effect of tomato leaf mildew, gray mold and fruit setting rate as response values, and the optimal parameter combination was determined: The ozone treatment concentration was 0.0465 g kg-1, the ozone treatment time was 30 min, and the ozone treatment times were twice a week. In this case, the control efficiency of tomato leaf mildew was 95.02%, the control effect of gray mold was 99.49%, and the fruit setting rate was 76.5%. The test parameters were accurate and reliable. CONCLUSION: The ozone sterilization method proposed in this article is safe and green, and can provide theoretical support for the recovery and reconstruction of tomato disease in a glasshouse. © 2024 Society of Chemical Industry.

scaDA: A Novel Statistical Method for Differential Analysis of Single-Cell Chromatin Accessibility Sequencing Data.

Single-cell ATAC-seq sequencing data (scATAC-seq) has been widely used to investigate chromatin accessibility on the single-cell level. One important application of scATAC-seq data analysis is differential chromatin accessibility analysis. However, the data characteristics of scATAC-seq such as excessive zeros and large variability of chromatin accessibility across cells impose a unique challenge for DA analysis. Existing statistical methods focus on detecting the mean difference of the chromatin accessible regions while overlooking the distribution difference. Motivated by real data exploration that distribution difference exists among cell types, we introduce a novel composite statistical test named "scaDA", which is based on zero-inflated negative binomial model (ZINB), for performing differential distribution analysis of chromatin accessibility by jointly testing the abundance, prevalence and dispersion simultaneously. Benefiting from both dispersion shrinkage and iterative refinement of mean and prevalence parameter estimates, scaDA demonstrates its superiority to both ZINB-based likelihood ratio tests and published methods by achieving the highest power and best FDR control in a comprehensive simulation study. In addition to demonstrating the highest power in three real sc-multiome data analyses, scaDA successfully identifies differentially accessible regions in microglia from sc-multiome data for an Alzheimer's disease (AD) study, regions which are most enriched in GO terms related to neurogenesis, the clinical phenotype of AD, and SNPs identified in AD-associated GWAS.

Anodic Electrodepositing Bioinspired Cu-BDC-NH2@Graphene Oxide Membrane for Efficient Uranium Extraction.

The challenge of removing trace levels of heavy metal ions, particularly uranium, from wastewater is a critical concern in environmental management. Uranium, a key element in long-term nuclear power generation, often poses significant extraction difficulties in wastewater due to its low concentration, interference from other ions, and the complexity of aquatic ecosystems. This study introduces an anodic electrodeposited hierarchical porous 2D metal-organic framework (MOF) Cu-BDC-NH2@graphene oxide (GO) membrane for effective uranium extraction by mimicking the function of the superb-uranyl-binding protein. This membrane is characterized by its hierarchical pillared-layer structures resulting from the controlled orientation of Cu-BDC-NH2 MOFs within the laminated GO layers during the electrodeposition process. The integration of amino groups from 2D Cu-BDC-NH2 and carboxylate groups from GO enables a high affinity to uranyl ions, achieving an unprecedented uranium adsorption capacity of 1078.4 mg/g and outstanding selectivity. Our findings not only demonstrate a breakthrough in uranium extraction technology but also pave the way for advancements in water purification and sustainable energy development, proposing a practical and efficient strategy for creating orientation-tunable 2D MOFs@GO membranes tailored for high-efficiency uranium extraction.

The putative RNA helicase DDX1 associates with the nuclear RNA exosome and modulates RNA/DNA hybrids (R-loops).

The RNA exosome is a ribonuclease complex that mediates both RNA processing and degradation. This complex is evolutionarily conserved, ubiquitously expressed, and required for fundamental cellular functions, including rRNA processing. The RNA exosome plays roles in regulating gene expression and protecting the genome, including modulating the accumulation of RNA-DNA hybrids (R-loops). The function of the RNA exosome is facilitated by cofactors, such as the RNA helicase MTR4, which binds/remodels RNAs. Recently, missense mutations in RNA exosome subunit genes have been linked to neurological diseases. One possibility to explain why missense mutations in genes encoding RNA exosome subunits lead to neurological diseases is that the complex may interact with cell- or tissue-specific cofactors that are impacted by these changes. To begin addressing this question, we performed immunoprecipitation of the RNA exosome subunit, EXOSC3, in a neuronal cell line (N2A), followed by proteomic analyses to identify novel interactors. We identified the putative RNA helicase, DDX1, as an interactor. DDX1 plays roles in double-strand break repair, rRNA processing, and R-loop modulation. To explore the functional connections between EXOSC3 and DDX1, we examined the interaction following double-strand breaks and analyzed changes in R-loops in N2A cells depleted for EXOSC3 or DDX1 by DNA/RNA immunoprecipitation followed by sequencing. We find that EXOSC3 interaction with DDX1 is decreased in the presence of DNA damage and that loss of EXOSC3 or DDX1 alters R-loops. These results suggest EXOSC3 and DDX1 interact during events of cellular homeostasis and potentially suppress unscrupulous expression of genes promoting neuronal projection.