Epigenetic therapy inhibits metastases by disrupting premetastatic niches.

Cancer recurrence after surgery remains an unresolved clinical problem1-3. Myeloid cells derived from bone marrow contribute to the formation of the premetastatic microenvironment, which is required for disseminating tumour cells to engraft distant sites4-6. There are currently no effective interventions that prevent the formation of the premetastatic microenvironment6,7. Here we show that, after surgical removal of primary lung, breast and oesophageal cancers, low-dose adjuvant epigenetic therapy disrupts the premetastatic microenvironment and inhibits both the formation and growth of lung metastases through its selective effect on myeloid-derived suppressor cells (MDSCs). In mouse models of pulmonary metastases, MDSCs are key factors in the formation of the premetastatic microenvironment after resection of primary tumours. Adjuvant epigenetic therapy that uses low-dose DNA methyltransferase and histone deacetylase inhibitors, 5-azacytidine and entinostat, disrupts the premetastatic niche by inhibiting the trafficking of MDSCs through the downregulation of CCR2 and CXCR2, and by promoting MDSC differentiation into a more-interstitial macrophage-like phenotype. A decreased accumulation of MDSCs in the premetastatic lung produces longer periods of disease-free survival and increased overall survival, compared with chemotherapy. Our data demonstrate that, even after removal of the primary tumour, MDSCs contribute to the development of premetastatic niches and settlement of residual tumour cells. A combination of low-dose adjuvant epigenetic modifiers that disrupts this premetastatic microenvironment and inhibits metastases may permit an adjuvant approach to cancer therapy.

Chromosome-scale de novo genome assembly and annotation of three representative Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana.

Australian pine (Casuarina spp.) is extensively planted in tropical and subtropical regions for wood production, shelterbelts, environmental protection, and ecological restoration due to their superior biological characteristics, such as rapid growth, wind and salt tolerance, and nitrogen fixation. To analyze the genomic diversity of Casuarina, we sequenced the genomes and constructed de novo genome assemblies of the three most widely planted Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana. We generated chromosome-scale genome sequences using both Pacific Biosciences (PacBio) Sequel sequencing and chromosome conformation capture technology (Hi-C). The total genome sizes for C. equisetifolia, C. glauca, and C. cunninghamiana are 268 942 579 bp, 296 631 783 bp, and 293 483 606 bp, respectively, of which 25.91, 27.15, and 27.74% were annotated as repetitive sequences. We annotated 23 162, 24 673, and 24 674 protein-coding genes in C. equisetifolia, C. glauca, and C. cunninghamiana, respectively. We then collected branchlets from male and female individuals for whole-genome bisulfite sequencing (BS-seq) to explore the epigenetic regulation of sex determination in these three species. Transcriptome sequencing (RNA-seq) revealed differential expression of phytohormone-related genes between male and female plants. In summary, we generated three chromosome-level genome assemblies and comprehensive DNA methylation and transcriptome datasets from both male and female material for three Casuarina species, providing a basis for the comprehensive investigation of genomic diversity and functional gene discovery of Casuarina in the future.

Comprehensive bioinformation analysis of homeodomain-leucine zipper gene family and expression pattern of HD-Zip I under abiotic stress in Salix suchowensis.

BACKGROUND: Homeodomain-leucine zipper (HD-Zip) transcription factors are plant-specific and play important roles in plant defense against environmental stresses. Identification and functional studies have been carried out in model plants such as rice, Arabidopsis thaliana, and poplar, but comprehensive analysis on the HD-Zip family of Salix suchowensis have not been reported. RESULTS: A total of 55 HD-Zip genes were identified in the willow genome, unevenly distributed on 18 chromosomes except for chromosome 19. And segmental duplication events containing SsHD-Zip were detected on all chromosomes except chromosomes 13 and 19. The SsHD-Zip were classified into 4 subfamilies subfamilies (I-IV) according to the evolutionary analysis, and members of each subfamily shared similar domain structure and gene structure. The combination of GO annotation and promoter analysis showed that SsHD-Zip genes responded to multiple abiotic stresses. Furthermore, the results of qPCR analysis showed that the SsHD-Zip I gene exhibited different degrees of expression under salt stress, PEG treatment and heat treatment. Moreover, there was a synergistic effect between SsHD-Zip I genes under stress conditions based on coregulatory networks analysis. CONCLUSIONS: In this study, HD-Zip transcription factors were systematically identified and analyzed at the whole genome level. These results preliminarily clarified the structural characteristics and related functions of willow HD-Zip family members, and it was found that SsHox34, SsHox36 and SsHox51 genes were significantly involved in the response to various stresses. Together, these findings laid the foundation for further research on the resistance functions of willow HD-Zip genes.

Use of extreme gradient boosting, light gradient boosting machine, and deep neural networks to evaluate the activity stage of extraocular muscles in thyroid-associated ophthalmopathy.

PURPOSE: To develop a machine learning model to evaluate the activity stage of extraocular muscles in thyroid-associated ophthalmopathy (TAO). METHODS: This study retrospectively analysed data from patients with TAO who underwent contrast-enhanced magnetic resonance imaging (MRI) from 2015 to 2022. Three independent machine learning models, namely, extreme gradient boosting (XGBoost), light gradient boosting machine (LightGBM), and deep neural networks (DNNs), were constructed using common clinical features. The performance of these models was compared using evaluation metrics such as the area under the receiver operating curve (AUC), accuracy, precision, recall, and F1 score. The importance of features was explained using Shapley additive explanations (SHAP). RESULTS: A total of 2561 eyes of 1479 TAO patients were included in this study. The original dataset was randomly divided into a training set (80%, n = 2048) and a test set (20%, n = 513). In the performance evaluation of the test set, the LightGBM model had the best diagnostic performance (AUC 0.9260). According to the SHAP results, features such as conjunctival congestion, swollen caruncles, oedema of the upper eyelid, course of TAO, and intraocular pressure had the most significant impact on the LightGBM model. CONCLUSION: This study used contrast-enhanced MRI as an objective evaluation criterion and constructed a LightGBM model based on readily accessible clinical data. The model had good classification performance, making it a promising artificial intelligence (AI)-assisted tool to help community hospitals evaluate the inflammatory activity of extraocular muscles in TAO patients in a timely manner.

Single-cell transcriptome analysis upon ECM-remodeling meningioma cells.

Meningiomas are the most common tumours that primarily arise in the central nervous system, but their intratumoural heterogeneity has not yet been thoroughly studied. We aimed to investigate the transcriptome characteristics and biological properties of ECM-remodeling meningioma cells. Single-cell RNA sequencing (ScRNA-seq) data from meningioma samples were acquired and used for analyses. We conducted comprehensive bioinformatics analyses, including screening for differentially expressed genes (DEGs), Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway and Gene Ontology (GO) term enrichment analyses, Gene Set Enrichment Analysis (GSEA), protein-protein interaction (PPI) analysis, and copy number variation (CNV) analysis on single-cell sequencing data from meningiomas. Eighteen cell types, including six meningioma subtypes, were identified in the data. ECM-remodeling meningioma cells (MGCs) were mainly distributed in brain-tumour interface tissues. KEGG and GO enrichment analyses revealed that 908 DEGs were mainly related to cell adhesion, extracellular matrix organization, and ECM-receptor interaction. GSEA analysis demonstrated that homophilic cell adhesion via plasma membrane adhesion molecules was significantly enriched (NES = 2.375, P < 0.001). CNV analysis suggested that ECM-remodeling MGCs showed considerably lower average CNV scores. ECM-remodeling MGCs predominantly localized at the brain-tumour interface area and adhere stably to the basement membrane with a lower degree of malignancy. This study provides novel insights into the malignancy of meningiomas.

Genome-wide identification and expression analysis of VQ gene family under abiotic stress in Coix lacryma-jobi L.

BACKGROUND: Valine-glutamine (VQ) proteins are non-specific plant proteins that have a highly conserved motif: FxxhVQxhTG. These proteins are involved in the development of various plant organs such as seeds, hypocotyls, flowers, leaves and also play a role in response to salt, drought and cold stresses. Despite their importance, there is limited information available on the evolutionary and structural characteristics of VQ family genes in Coix lacryma-jobi. RESULTS: In this study, a total of 31 VQ genes were identified from the coix genome and classified into seven subgroups (I-VII) based on phylogenetic analysis. These genes were found to be unevenly distributed on 10 chromosomes. Gene structure analysis revealed that these genes had a similar type of structure within each subfamily. Moreover, 27 of ClVQ genes were found to have no introns. Conserved domain and multiple sequence alignment analysis revealed the presence of a highly conserved sequences in the ClVQ protein. This research utilized quantitative real-time PCR (qRT-PCR) and promoter analysis to investigate the expression of ClVQ genes under different stress conditions. Results showed that most ClVQ genes responded to polyethylene glycol, heat treatment, salt, abscisic acid and methyl jasmonate treatment with varying degrees of expression. Furthermore, some ClVQ genes exhibited significant correlation in expression changes under abiotic stress, indicating that these genes may act synergistically in response to adversarial stress. Additionally, yeast dihybrid verification revealed an interaction between ClVQ4, ClVQ12, and ClVQ26. CONCLUSIONS: This study conducted a genome-wide analysis of the VQ gene family in coix, including an examination of phylogenetic relationships, conserved domains, cis-elements and expression patterns. The goal of the study was to identify potential drought resistance candidate genes, providing a theoretical foundation for molecular resistance breeding.

A 3D-Printed Cuttlefish Bone Elastomeric Sponge Rapidly Controlling Noncompressible Hemorrhage.

Developing a self-expanding hemostatic sponge with high blood absorption and rapid shape recovery for noncompressible hemorrhage remains a challenge. In this study, a 3D-printed cuttlefish bone elastomeric sponge (CBES) is fabricated, which combined ordered channels and porous structures, presented tunable mechanical strength, and shape memory potentials. The incorporation of cuttlefish bone powder (CBp) plays key roles in concentrating blood components, promoting aggregation of red blood cells and platelets, and activating platelets, which makes CBES show enhanced hemostatic performance compared with commercial gelatin sponges in vivo. Moreover, CBES promotes more histiocytic infiltration and neovascularization in the early stage of degradation than gelatin sponges, which is conducive to the regeneration and repair of injured tissue. To conclude, CBp loaded 3D-printed elastomeric sponges can promote coagulation, present the potential to guide tissue healing, and broaden the hemostatic application of traditional Chinese medicine.

A Bone-Penetrating Precise Controllable Drug Release System Enables Localized Treatment of Osteoporotic Fracture Prevention via Modulating Osteoblast-Osteoclast Communication.

Improving local bone mineral density (BMD) at fracture-prone sites of bone is a clinical concern for osteoporotic fracture prevention. In this study, a featured radial extracorporeal shock wave (rESW) responsive nano-drug delivery system (NDDS) is developed for local treatment. Based on a mechanic simulation, a sequence of hollow zoledronic acid (ZOL)-contained nanoparticles (HZNs) with controllable shell thickness that predicts various mechanical responsive properties is constructed by controlling the deposition time of ZOL and Ca2+ on liposome templates. Attributed to the controllable shell thickness, the fragmentation of HZNs and the release of ZOL and Ca2+ can be precisely controlled with the intervention of rESW. Furthermore, the distinct effect of HZNs with different shell thicknesses on bone metabolism after fragmentation is verified. In vitro co-culture experiments demonstrate that although HZN2 does not have the strongest osteoclasts inhibitory effect, the best pro-osteoblasts mineralization results are achieved via maintaining osteoblast-osteoclast (OB-OC) communication. In vivo, the HZN2 group also shows the strongest local BMD enhancement after rESW intervention and significantly improves bone-related parameters and mechanical properties in the ovariectomy (OVX)-induced osteoporosis (OP) rats. These findings suggest that an adjustable and precise rESW-responsive NDDS can effectively improve local BMD in OP therapy.

The clinico-pathological characterisation of focal cortical dysplasia type IIb genetically defined by MTOR mosaicism.

AIMS: Focal cortical dysplasia (FCD) is a major cause of drug-resistant paediatric epilepsy and is amenable to successful neurosurgical resection. FCD ILAE Type IIb is the most common FCD subtype, and brain somatic mutations affecting the mTOR pathway play a major pathogenic role. The aim of this study was to comprehensively describe the genotype-phenotype association of 20 patients with histopathologically confirmed FCDIIb using next generation sequencing (NGS) of paired blood-brain samples. METHODS: Clinical and neuropathological data were retrospectively reviewed from the hospital archive. The NGS panel included 11 mTOR-pathway-related genes with maximum coverage of 2000×. The detected variants were validated by digital droplet PCR. RESULTS: Pathogenic MTOR variants were identified in 10 patients (50%). Further comparison with MTOR-wildtype FCDIIb suggested a profound genotype-phenotype association characterised by (1) a non-temporal lobe lesion on MRI, (2) a larger lesion volume occupying grey and white matter (3.032 ± 1.859 cm3 vs 1.110 ± 0.856 cm3 , p = 0.014), (3) more balloon cells (50.20 ± 14.40 BC/mm2 vs 31.64 ± 30.56 BC/mm2 , p = 0.099) and dysmorphic neurons (48.72 ± 19.47DN/mm2 vs 15.28 ± 13.95DN/mm2 , p = 0.000) and (4) a positive correlation between VAF and the lesion volume (r = 0.802, p = 0.017). CONCLUSIONS: Our study identified frequent MTOR mutations in the cell-rich FCDIIb phenotype, clinically characterised by a non-temporal location and large lesion volume. Comprehensive genotype-phenotype associations will help us further explore and define the broad spectrum of FCD lesions to make more targeted therapies available in the realm of epileptology.

Synthesis of 10-Membered Azecines through Pd-Catalyzed Formal [6+4] Cycloaddition and Their Transannular Reaction to Polycyclic Compounds.

Azecine fragments are frequently presented in natural products and bioactive compounds. However, minor efforts have been devoted to these 10-membered N-heterocycles, and their synthesis is still challenging. Reported herein is the first catalytic formal [6+4] cycloaddition for the synthesis of 10-membered azecines. Under palladium catalysis, the reaction of δ-vinylvalerolactones and benzofuran-derived azadienes proceeds smoothly to afford benzofuran-fused azecines with high diastereoselectivity in moderate to good yields. A unique transannular reaction of these 10-membered azecines for the construction of polycyclic compounds is also demonstrated.

Genetic and enzymatic characterization of two novel blaNDM-36, -37 variants in Escherichia coli strains.

The widespread of different NDM variants in clinical Enterobacterales isolates poses a serious public health concern, which requires continuous monitoring. In this study, three E. coli strains carrying two novel blaNDM variants of blaNDM-36, -37 were identified from a patient with refractory urinary tract infection (UTI) in China. We conducted antimicrobial susceptibility testing (AST), enzyme kinetics analysis, conjugation experiment, whole-genome sequencing (WGS), and bioinformatics analysis to characterize the blaNDM-36, -37 enzymes and their carrying strains. The blaNDM-36, -37 harboring E. coli isolates belonged to ST227, O9:H10 serotype and exhibited intermediate or resistance to all ß-lactams tested except aztreonam and aztreonam/avibactam. The genes of blaNDM-36, -37 were located on a conjugative IncHI2-type plasmid. NDM-37 differed from NDM-5 by a single amino acid substitution (His261Tyr). NDM-36 differed from NDM-37 by an additional missense mutation (Ala233Val). NDM-36 had increased hydrolytic activity toward ampicillin and cefotaxime relative to NDM-37 and NDM-5, while NDM-37 and NDM-36 had lower catalytic activity toward imipenem but higher activity against meropenem in comparison to NDM-5. This is the first report of co-occurrence of two novel blaNDM variants in E. coli isolated from the same patient. The work provides insights into the enzymatic function and demonstrates the ongoing evolution of NDM enzymes.

Network meta-analysis of different dosages of esomeprazole and rabeprazole for the treatment of Helicobacter pylori.

BACKGROUND: The optimal dosage of new generation proton pump inhibitors (PPIs) in increasing cure rate of Helicobacter pylori (H. pylori) infection remains unclear. This network meta-analysis aimed to comprehensively evaluate the comparative efficacy and safety of different dosages of esomeprazole and rabeprazole in treating H. pylori infection. MATERIALS AND METHODS: We searched PubMed, Cochrane Central Registry for Controlled Trials (CENTRAL), and EMBASE for randomized controlled trials (RCTs) involving esomeprazole and rabeprazole with different dosages from their inception through 31 March, 2022. After data extraction and risk of bias assessment, network meta-analyses were conducted using STATA 14.0. We calculated the surface under the cumulative ranking (SUCRA) to rank all regimens. RESULTS: Thirteen studies including 14 reports were included. Six dosages including rabeprazole 10 mg (R10bid), 20 mg (R20bid), and 40 mg (R40bid) twice daily and esomeprazole 20 mg (E20bid) and 40 mg (E40bid) twice daily as well as 40 mg once daily (E40qd) were identified. Network meta-analysis suggested that R40bid ranked highest in the cure rate (83.8%), followed by E40bid (82.6%), E20bid (54.5%), R20bid (34.2%), R10bid (22.8%), and E40qd (22.0%); however, E40qd ranked highest in adverse events (91.1%), followed by R20bid (57.8), R10bid (57.6%), E20bid (38.9%), E40bid (34.2%), and R40bid (20.4%). Sensitivity analyses confirmed the robustness of these results. CONCLUSIONS: Based on the available evidence, R40bid and E40bid might be the optimum dosage to increase the cure rate; however, E40qd was superior for adverse events. Nevertheless, future studies should validate the results from this network meta-analysis.

Clinical phenotypes of euthyroid, hyperthyroid, and hypothyroid thyroid-associated ophthalmopathy.

OBJECTIVE: To compare the demographic and clinical phenotypes of thyroid-associated ophthalmopathy (TAO) with euthyroidism (Eu-TAO), hyperthyroidism (Hr-TAO), and hypothyroidism (Ho-TAO). METHODS: We enrolled 2158 TAO patients in this retrospective study and assessed their demographics, clinical manifestations, activity, and severity. RESULTS: Among the enrolled patients, 526 (24.37%) had Eu-TAO, 1544 (71.55%) had Hr-TAO, and 88 (4.08%) had Ho-TAO. Compared to Hr-TAO (2.02) and Ho-TAO (2.52) patients, Eu-TAO (1.57) patients had the lowest female-to-male ratio (p = 0.026). The mean ages of Eu-TAO, Hr-TAO, and Ho-TAO patients were 43.11 ± 12.05, 42.23 ± 13.63, and 47.39 ± 13.28 years, respectively (p = 0.001). Patients with Eu-TAO had more unilateral involvement (50% vs. 14.38% vs. 21.59%, p < 0.001) than Hr-TAO or Ho-TAO patients. Clinically active TAO patients presented 8.56% in euthyroid vs. 13.86% in hyperthyroid vs. 11.36% in hypothyroid (p = 0.006). Regarding the severity of the European Group on Graves' Orbitopathy (EUGOGO) classification among euthyroid, hyperthyroid, and hypothyroid patients, mild TAO was present in 67.68, 54.27, and 72.72% of participants, moderate-to-severe TAO in 31.18, 42.49, and 26.14%, and sight-threatening TAO in 1.14, 3.24, and 1.14%, respectively. Eu-TAO was positively correlated with unilateral involvement (OR = 5.671, p < 0.001) and age (OR = 1.013, p = 0.003) and negatively correlated with the female-to-male ratio (OR = 0.656, p < 0.001) and TAO severity (OR = 0.742, p < 0.01). CONCLUSIONS: Eu-TAO patients are older and less likely to be female, and show more unilateral and milder clinical phenotypes than hyper/hypothyroid TAO patients.

Orbital solitary fibrous tumours: clinicopathological characteristics and recurrence prediction.

BACKGROUND: SFTs are thought to have an unpredictable clinical course and currently have no recognized prognostic criterion. Our study aimed to determine the relationship between clinicopathological characteristics and the prognosis of patients with orbital SFTs. METHODS: The clinicopathological features of these patients were extracted from clinical records. The relationships between these features and prognosis were analysed. RESULTS: The positive rates of CD34, CD99, Blc2, and STAT6 expression were 90.3%, 90.3%, 83.9%, and 100%, respectively. The tumour recurrence rate was 38.7%. A higher recurrence rate was observed in patients with Ki67 index ≥ 5 (56.25% vs. 20%, P = 0.038). CONCLUSION: A Ki67 index ≥ 5 was an effective parameter for predicting tumour recurrence of orbital SFTs. Close follow-up is needed for these patients.

Clinical characteristics and treatment outcomes of secondary ocular adnexal lymphoma.

BACKGROUND: To describe the clinical characteristics and treatment outcomes of secondary ocular adnexal lymphoma (OAL), and emphasise the impact of timely biopsy and systemic evaluation on the diagnosis and treatment. METHODS: The data of patients with secondary OAL in our hospital from January 2010 to June 2021 were retrospectively reviewed. RESULTS: A total of 54 patients (30 men and 24 women) were included in the study. The mean age at presentation was 60 years (median 62 years; range 37-83 years). The main symptoms included ocular mass (74%), periorbital swelling (43%), and proptosis (39%). The main histopathological types were mucosa-associated lymphoid tissue lymphoma (30%), diffuse large B-cell lymphoma (28%), and natural killer/T-cell lymphoma (18%). In particular, three patients exhibited different pathological types of ocular lymphoma compared to previously diagnosed systemic lymphoma. The most common site of ocular and systemic involvement was the orbit (85%) and lymph nodes (56%), respectively, and 25 (46%) patients had occult extraocular lesions. Additionally, the 5-year overall survival rate of the entire cohort was 56%, and significant differences were observed between the three main pathological types and stages of the disease (all p < 0.001). CONCLUSIONS: Secondary OAL is a rare disease with a poor prognosis. That the disease is associated with a more aggressive pathological type is well established, indolent lymphoma is not uncommon. Furthermore, OAL and previously diagnosed systemic lymphoma may be pathologically distinct in some patients. Therefore, we recommend a prompt excision biopsy and a thorough systemic evaluation of patients with suspected OAL.

Effect of particle sizes of biochar on CO2 emissions in a poplar plantation of ancient Yellow River channel, China.

Forest soil is a vital pool of organic carbon, which is sensitive to management. Biochar addition could change the CO2 emissions from soil, but its effects are still ambiguous. Moreover, the impacts of particle sizes of biochar on CO2 emissions are still unknown. In this study, a series of field experiments were conducted to investigate the effects of biochar addition on CO2 emissions in a poplar plantation (Populus nigra), China. Biochar with two application rates of (10 and 50 t/ha) and three particle sizes (3-1 mm, 1-0.1 mm, and <0.1 mm) was applied into the surface soil (0-10 cm), and the soil without biochar was set as control. The results showed that a high level of fine biochar addition (1-0.1 mm and <0.1 mm) had similar and positive effects on CO2 emissions by increasing the contents of soil ammonium, available phosphorus, easily oxidizable carbon, soil moisture, soil capillary pore, and the activity of ß-glucosidase. However, biochar addition (1-0.1 mm and <0.1 mm) reduced the bioavailability of dissolved organic carbon (DOC), producing a negative relationship between DOC content and CO2 emissions. This investigation highlights the importance of biochar with different particle sizes in adjusting CO2 emissions from temperate soils.

Chaihu Shugan San promotes gastric motility in rats with functional dyspepsia by regulating Drp-1-mediated ICC mitophagy.

CONTEXT: Chaihu Shugan San (CHSGS) was effective in the treatment of functional dyspepsia (FD). OBJECTIVE: To investigate the mechanism of CHSGS in FD through dynamin-related protein 1 (Drp-1)-mediated interstitial cells of cajal (ICC) mitophagy. MATERIALS AND METHODS: Forty Sprague-Dawley (SD) rats were randomly divided into control, model, mdivi-1, mdivi-1 + CHSGS and CHSGS groups. Tail-clamping stimulation was used to establish the FD model. Mdivi-1 + CHSGS and CHSGS groups were given CHSGS aqueous solution (4.8 g/kg) by gavage twice a day. Mdivi-1 (25 mg/kg) was injected intraperitoneally once every other week for 4 w. Mitochondrial damage was observed by corresponding kits and related protein expressions were assessed by Immunofluorescence and (or) Western Blot. RESULTS: Compared with the mean value of the control group, superoxide dismutase (SOD) and citrate synthase (CS) in the model group were decreased by 11% and 35%; malondialdehyde (MDA) and reactive oxygen species (ROS) were increased by 1.2- and 2.8-times; ckit fluorescence and protein expressions were decreased by 85% and 51%, co-localization expression of LC3 and voltage dependent anion channel 1 (VDAC1), Drp-1 and translocase of the outer mitochondrial membrane 20 (Tom20) were increased by 10.1- and 5.4-times; protein expressions of Drp-1, Beclin-1, and LC3 were increased by 0.5-, 1.4-, and 2.5-times whereas p62 was decreased by 43%. After mdivi-1 and (or) CHSGS intervention, the above situation has been improved. DISCUSSION AND CONCLUSION: CHSGS could improve mitochondrial damage and promote gastric motility in FD rats by regulating Drp-1-mediated ICC mitophagy.

Genome assembly of the Chinese maize elite inbred line RP125 and its EMS mutant collection provide new resources for maize genetics research and crop improvement.

Maize is an important crop worldwide, as well as a valuable model with vast genetic diversity. Accurate genome and annotation information for a wide range of inbred lines would provide valuable resources for crop improvement and pan-genome characterization. In this study, we generated a high-quality de novo genome assembly (contig N50 of 15.43 Mb) of the Chinese elite inbred line RP125 using Nanopore long-read sequencing and Hi-C scaffolding, which yield highly contiguous, chromosome-length scaffolds. Global comparison of the RP125 genome with those of B73, W22, and Mo17 revealed a large number of structural variations. To create new germplasm for maize research and crop improvement, we carried out an EMS mutagenesis screen on RP125. In total, we obtained 5818 independent M2 families, with 946 mutants showing heritable phenotypes. Taking advantage of the high-quality RP125 genome, we successfully cloned 10 mutants from the EMS library, including the novel kernel mutant qk1 (quekou: "missing a small part" in Chinese), which exhibited partial loss of endosperm and a starch accumulation defect. QK1 encodes a predicted metal tolerance protein, which is specifically required for Fe transport. Increased accumulation of Fe and reactive oxygen species as well as ferroptosis-like cell death were detected in qk1 endosperm. Our study provides the community with a high-quality genome sequence and a large collection of mutant germplasm.

Single-cell transcriptomic and chromatin accessibility analyses of dairy cattle peripheral blood mononuclear cells and their responses to lipopolysaccharide.

BACKGROUND: Gram-negative bacteria are important pathogens in cattle, causing severe infectious diseases, including mastitis. Lipopolysaccharides (LPS) are components of the outer membrane of Gram-negative bacteria and crucial mediators of chronic inflammation in cattle. LPS modulations of bovine immune responses have been studied before. However, the single-cell transcriptomic and chromatin accessibility analyses of bovine peripheral blood mononuclear cells (PBMCs) and their responses to LPS stimulation were never reported. RESULTS: We performed single-cell RNA sequencing (scRNA-seq) and single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) in bovine PBMCs before and after LPS treatment and demonstrated that seven major cell types, which included CD4 T cells, CD8 T cells, and B cells, monocytes, natural killer cells, innate lymphoid cells, and dendritic cells. Bioinformatic analyses indicated that LPS could increase PBMC cell cycle progression, cellular differentiation, and chromatin accessibility. Gene analyses further showed significant changes in differential expression, transcription factor binding site, gene ontology, and regulatory interactions during the PBMC responses to LPS. Consistent with the findings of previous studies, LPS induced activation of monocytes and dendritic cells, likely through their upregulated TLR4 receptor. NF-κB was observed to be activated by LPS and an increased transcription of an array of pro-inflammatory cytokines, in agreement that NF-κB is an LPS-responsive regulator of innate immune responses. In addition, by integrating LPS-induced differentially expressed genes (DEGs) with large-scale GWAS of 45 complex traits in Holstein, we detected trait-relevant cell types. We found that selected DEGs were significantly associated with immune-relevant health, milk production, and body conformation traits. CONCLUSION: This study provided the first scRNAseq and scATAC-seq data for cattle PBMCs and their responses to the LPS stimulation to the best of our knowledge. These results should also serve as valuable resources for the future study of the bovine immune system and open the door for discoveries about immune cell roles in complex traits like mastitis at single-cell resolution.

Cryogenic Focused Ion Beam Enables Atomic-Resolution Imaging of Local Structures in Highly Sensitive Bulk Crystals and Devices.

With the development of ultralow-dose (scanning) transmission electron microscopy ((S)TEM) techniques, atomic-resolution imaging of highly sensitive nanomaterials has recently become possible. However, applying these techniques to the study of sensitive bulk materials remains challenging due to the lack of suitable specimen preparation methods. We report that cryogenic focused ion beam (cryo-FIB) can provide a solution to this challenge. We successfully extracted thin specimens from metal-organic framework (MOF) crystals and a hybrid halide perovskite single-crystal film solar cell using cryo-FIB without damaging the inherent structures. The high quality of the specimens enabled the subsequent (S)TEM and electron diffraction studies to reveal complex unknown local structures at an atomic resolution. The obtained structural information allowed us to resolve planar defects in MOF HKUST-1, three-dimensionally reconstruct a concomitant phase in MOF UiO-66, and discover a new CH3NH3PbI3 structure and locate its distribution in a single-crystal film perovskite solar cell. This proof-of-concept study demonstrates that cryo-FIB has a unique ability to handle highly sensitive materials, which can substantially expand the range of applications for electron microscopy.