Prevalence and characterization of community-associated Staphylococcus aureus isolates from human mastitis in Beijing, China.

OBJECTIVES: Staphylococcus aureus (S. aureus) spreads worldwide and occurrence of mastitis caused by it holds significant implications for public health. We aim to reveal the molecular typing, antibiotic resistance and virulence gene profile of S. aureus causing mastitis through investigation. METHODS: A total of 200 isolates of S. aureus were collected from outpatients infected with mastitis in a hospital in Beijing from 2020.7 to 2021.7. The molecular characteristics were analyzed by MLST and spa typing, virulence genes were screened by PCR, antibiotic susceptible test was performed by VITEK® 2 Compact system and phylogenetic analysis was performed by MEGA11 and iTOL. RESULTS: Nineteen sequence types (STs) belonging to 9 clone complexes (CCs) were identified. ST22 was the most dominant clone (77.0%, 154/200). MRSA accounted for 19.0% (38/200) and 89.5% (34/38) of MRSA isolates belonged to CC22 and CC59. The isolates had relatively low levels of antibiotic resistance, with the exception of ß-lactams and macrolides with resistance rates above 50.0%. The carrying rate of pvl in the ST22-MRSA strains were 84.2% and the detection rates of seb and pvl in the MRSA isolates were significantly higher than those in the MSSA isolates, while the hlg, fnbA and sdrD showed opposite results. Whole genome sequenced specimens of MRSA strains X4 and B5 show the same evolutionary origin as ST22 EMRSA-15 (HE681097), which is popular in Europe. CONCLUSIONS: The method based on molecular epidemiology is an important tool for tracking the spread of S. aureus infections. We need to be alert to the major MRSA clones CC22 and CC59 in the region and be vigilant to the possible pandemic and spread of ST22 EMRSA-15.

Compact high-power 320-nm continuous-wave single-frequency laser based on power scaling of a diode-pumped Pr:LiYF4 ring laser at red.

Single-frequency (SF) lasers in the visible spectral region are usually obtained through an indirect method, i.e., frequency doubling of near-infrared SF lasers. In this work, we report on the direct generation of a high-power continuous-wave (CW) SF laser in red based on a diode-pumped Pr:LiYF4 (YLF) ring cavity technology. A maximum output power is scaled to 3.98 W at 640 nm with a linewidth of about 17.2 MHz and a power stability of 0.6%. Moreover, by inserting a LBO crystal into the ring cavity for intracavity frequency doubling of the 640 nm SF laser, we have also successfully demonstrated an ultraviolet (UV) SF laser at 320 nm, for the first time to the best of our knowledge, with a maximum power of 670 mW. This work provides a promising route for the development of simple, compact, and high-power SF lasers operating in visible and UV spectral regions.

Watt-level and near diffraction-limited Pr3+-doped single-crystal fiber lasers.

Using a CZ-grown a-cut Pr:YLF crystal as laser gain medium after processing it into crystal fiber, we have demonstrated real Pr3+-doped single-crystal fiber lasers for the first time to the best of our knowledge. This Pr3+ crystal fiber has absorbed up to 20.4 W of pump power, which is the highest absorbed power among Pr3+ lasers. For two representative laser emissions at about 639 nm and 607 nm, we have achieved maximum output powers of 5.45 W and 3.04 W, respectively. Output powers of the two lasers show very good linearities, which indicate that the present output powers are only limited by the available pump power. Both laser emissions have exhibited near diffraction-limited beam qualities. This proposal has provided a good and feasible route for the development of compact, high-power, and high-brightness all-solid-state Pr3+ visible lasers via crystal fiber.

The Risk Contagion between Chinese and Mature Stock Markets: Evidence from a Markov-Switching Mixed-Clayton Copula Model.

Exploring the risk spillover between Chinese and mature stock markets is a promising topic. In this study, we propose a Markov-switching mixed-Clayton (Ms-M-Clayton) copula model that combines a state transition mechanism with a weighted mixed-Clayton copula. It is applied to investigate the dynamic risk dependence between Chinese and mature stock markets in the Americas, Europe, and Asia-Oceania regions. Additionally, the conditional value at risk (CoVaR) is applied to analyze the risk spillovers between these markets. The empirical results demonstrate that there is mainly a time-varying but stable positive risk dependence structure between Chinese and mature stock markets, where the upside and downside risk correlations are asymmetric. Moreover, the risk contagion primarily spills over from mature stock markets to the Chinese stock market, and the downside effect is stronger. Finally, the risk contagion from Asia-Oceania to China is weaker than that from Europe and the Americas. The study provides insights into the risk association between emerging markets, represented by China, and mature stock markets in major regions. It is significant for investors and risk managers, enabling them to avoid investment risks and prevent risk contagion.

The utility of SARS-CoV-2 nucleocapsid protein in laboratory diagnosis.

BACKGROUND: The Coronavirus Disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has now become a global pandemic owing to its high transmissibility. The SARS-CoV-2 nucleocapsid protein tests are playing an important role in screening and diagnosing patients with COVID-19, and studies about the utility of SARS-CoV-2 nucleocapsid protein tests are increasing now. METHODS: In this review, all the relevant original studies were assessed by searching in electronic databases including Scopus, Pubmed, Embase, and Web of Science. "SARS-CoV-2", "COVID-19", "nucleocapsid protein", and "antigen detection" were used as keywords. RESULTS: In this review, we summarized the utility of SARS-CoV-2 nucleocapsid protein in laboratory diagnosis. Among the representative researches, this review analyzed, the sensitivity of SARS-CoV-2 nucleocapsid protein detection varies from 13% to 87.9%, while the specificity could almost reach 100% in most studies. As a matter of fact, the sensitivity is around 50% and could be higher or lower due to the influential factors. CONCLUSION: It is well suggested that SARS-CoV-2 nucleocapsid protein is a convenient method with a short turnaround time of about half an hour, and the presence of N antigen is positively related to viral transmissibility, indicating that SARS-CoV-2 N protein immunoassays contribute to finding out those infected people rapidly and segregating them from the uninfected people.

Candidate Genes and Pathways in Rice Co-Responding to Drought and Salt Identified by gcHap Network.

Drought and salinity stresses are significant abiotic factors that limit rice yield. Exploring the co-response mechanism to drought and salt stress will be conducive to future rice breeding. A total of 1748 drought and salt co-responsive genes were screened, most of which are enriched in plant hormone signal transduction, protein processing in the endoplasmic reticulum, and the MAPK signaling pathways. We performed gene-coding sequence haplotype (gcHap) network analysis on nine important genes out of the total amount, which showed significant differences between the Xian/indica and Geng/japonica population. These genes were combined with related pathways, resulting in an interesting mechanistic draft called the 'gcHap-network pathway'. Meanwhile, we collected a lot of drought and salt breeding varieties, especially the introgression lines (ILs) with HHZ as the parent, which contained the above-mentioned nine genes. This might imply that these ILs have the potential to improve the tolerance to drought and salt. In this paper, we focus on the relationship of drought and salt co-response gene gcHaps and their related pathways using a novel angle. The haplotype network will be helpful to explore the desired haplotypes that can be implemented in haplotype-based breeding programs.

MHC-I in the hippocampus promotes comorbid depressive symptoms in bone cancer pain via the upregulation of microglial TREM2/DAP12 signaling.

Pain and depression comorbidity affects patients' physical and mental health, as well as quality of life. Comorbid depressive symptoms in cancer pain have a severe impact on the recognition and treatment of pain. Similarly, cancer pain patients with depression are inclined towards more despair and greater impairment. The mechanisms responsible for the comorbid depressive symptoms in bone cancer pain (BCP) have not been fully delineated. Here, it was reported that the implantation of carcinoma cells into the femoral cavity of mice led to the upregulation of major histocompatibility complex class I (MHC-I) in the hippocampus. This was associated with the activation of microglial signaling pathway mediated by the triggering receptor expressed on myeloid cells 2 protein (TREM2) and DNAX-activating protein of 12 kDa (DAP12). Pain and depression-like behaviors were reversed by the knockdown of hippocampal MHC-I via a lentiviral vector harboring ribonucleic acid interference (RNAi) sequence. Moreover, MHC-I knockdown exhibited a marked reduction in the expression of TREM2 and DAP12. These results suggested that hippocampal MHC-I was involved in BCP and depression comorbidity via upregulating the signals mediated by TREM2/DAP12 in microglia. The suppression of MHC-I could be a potential therapeutic target for BCP.

Prevalence of ST1049-KL5 carbapenem-resistant Klebsiella pneumoniae with a blaKPC-2 and blaNDM-1 co-carrying hypertransmissible IncM1 plasmid.

Infection caused by KPC and NDM carbapenemases co-producing Klebsiella pneumoniae (KPC_NDM_CRKP) poses serious public health concerns. Here, we elucidate the prevalence of a hypertransmissible lncM1 plasmid, pKPC_NDM, co-carrying blaKPC-2 and blaNDM-1 genes in sequence type 1049 K_locus 5 (ST1049-KL5) KPC_NDM_CRKP isolates. Genetic and clonal relatedness analyses using pulsed-field gel electrophoresis, single nucleotide polymorphism analysis and core genome multilocus sequence typing suggested clonal dissemination of ST1049-KL5 KPC_NDM_CRKP strains in our hospital. Whole genome sequencing identified an identical 76,517 bp- blaKPC-2 and blaNDM-1 genes co-carrying IncM1 plasmid pKPC_NDM and a pLVPK-like hypervirulent plasmid in all ST1049-KL5 KPC_NDM_CRKP isolates. pKPC_NDM shared 100% identity with a previously sequenced plasmid CRKP35_unnamed4, demonstrating high transferability in conjugation assay, with conjugation frequencies reaching 10-4 and 10-5 in Escherichia coli and K. pneumoniae recipients, respectively. It also maintained favorable stability and flexible compatibility, with retention rates exceeding 80% after 10 days of continuous passage, and could be compatible with pre-existing blaKPC- or blaNDM-carrying plasmids in recipient strains. This study summarizes the characteristics of KPC_NDM_CRKP outbreaks and highlights the importance of ongoing surveillance and infection control strategies to address the challenges posed by ST1049 K. pneumoniae strains.

A prospective study of nanopore-targeted sequencing in the diagnosis of central nervous system infections.

Central nervous system (CNS) infections are a leading cause of death in patients. Nanopore-targeted sequencing (NTS) has begun to be used for pathogenic microbial detection. This study aims to evaluate the ability of NTS in the detection of pathogens in cerebrospinal fluid (CSF) through a prospective study. Fifty CSF specimens collected from 50 patients with suspected CNS infections went through three methods including NTS, metagenomic next-generation sequencing (mNGS), and microbial culture in parallel. When there was an inconsistency between NTS results and the results of the mNGS, the 16S rDNA gene was amplified followed by Sanger sequencing to further verify pathogens detected by NTS. Among 50 CSF specimens, 76% were NTS-positive, which is lower than mNGS (94.0%), yet higher than microbial culture (16.0%). The overall validation rate, diagnostic accordance rate (DAR), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of NTS were 86.7%, 50.0%, 71.0%, 15.8%, 57.9%, and 25.0%, respectively. In the CSF total nucleated cell (TNC) number ≤10 cells/µL, DAR, specificity, and PPV were 20%, 11.1%, and 11.1%, whereas in that with CSF TNC number >10 cells/µL, DAR, sensitivity, specificity, PPV, and NPV were 57.5%, 70.0%, 20.0%, 72.4%, and 18.2%, respectively. Although NTS has a higher microbial detection rate than microbial culture, it should combine CSF TNC result to evaluate the value of NTS for the diagnosis of CNS infections. IMPORTANCE: This study aims to prospectively evaluate the ability of nanopore-targeted sequencing (NTS) in the detection of pathogens in cerebrospinal fluid (CSF). It was the first time combining mNGS and microbial culture to verify the NTS-positive results also using 16S rDNA amplification with Sanger sequencing. Although microbial culture was thought to be the gold standard for pathogens detection and diagnosis of infectious diseases, this study suggested that microbial culture of CSF is not the most appropriate way for diagnosing central nervous system (CNS) infection. NTS should be recommended to be used in CSF for diagnosing CNS infection. When evaluating the value of NTS for diagnosis of CNS infections, the results of CSF TNC should be combined, and NTS-positive result is observed to be more reliable in patients with CSF TNC level >10 cells/µL.

Coptisine-mediated downregulation of E2F7 induces G2/M phase arrest in hepatocellular carcinoma cells through inhibition of E2F4/NFYA/NFYB transcription factors.

Coptisine (COP) has been shown to exhibit a wide range of anticancer properties, including in hepatocellular carcinoma (HCC). Nevertheless, the precise mechanism of COP in the treatment of HCC remains elusive. This study aims to investigate the potential mechanism of action of COP against HCC. By evaluating the anti-HCC activity of COP in different HCC cells lines and in xenografted nude mice, it was found that COP inhibited HCC in vitro and in vivo. Through RNA-Seq analysis, E2F7 was identified as a potential target of COP against HCC, as well as the cell cycle as a possible pathway. The overexpression of E2F7 and the inhibition of CHK1 demonstrated that COP inhibits the activity of HCC and induces G2/M phase arrest of HCC cells by down-regulating E2F7 and influencing the CHK1/CDC25A pathway. Finally, the promoter fragmentation experiments and chromatin immunoprecipitation revealed that COP down-regulated E2F7 by inhibiting the E2F4/NFYA/NFYB transcription factors. In conclusion, our study demonstrated that COP downregulates E2F7 by affecting key transcription factors, thereby inducing cell cycle arrest and inhibits HCC cell growth. This provides further evidence of the efficacy of COP in the treatment of tumors.

Cyberpharmacology uncover the mechanism of the total Rhizoma Coptidis extracts ameliorate chronic atrophic gastritis.

ETHNOPHARMACOLOGICAL RELEVANCE: Characterized by inflammation of the gastric mucosa, atrophy of gastric gland cells, and intestinal metaplasia, Chronic Atrophic Gastritis (CAG) is a precancerous lesion disease. In traditional Chinese medicine, Rhizoma Coptidis (RC) is extensively used for treating gastrointestinal disorders, mainly because RC alkaloids-based extracts are the main active pharmaceutical ingredients. Total Rhizoma Coptidis extracts (TRCE) is a mixture of Rhizoma Coptidis extracts from Rhizoma Coptidis with alkaloids as the main components. However, the efficacy and mechanism of TRCE on CAG need further study. AIM OF THE STUDY: To explore the therapeutic effect and underlying mechanisms of action of TRCE on N-methyl-N'-nitro-N-nitrosoguanidine (MNNG)-induced chronic atrophic gastritis (CAG) using network pharmacological analysis. MATERIALS AND METHODS: The amelioration effect of TRCE on CAG was evaluated in MNNG-induced CAG mice. The pathological severity of the mice was evaluated through H&E staining. Detection of gastric mucosal parietal cell loss was conducted using immunofluorescence staining, and serum indices were measured using ELISA. Additionally, the active compounds and drug targets of Rhizoma Coptidis were curated from the STP, SEA, and TCMSP databases, alongside disease targets of CAG sourced from PharmGkb, OMIM, and GeneCards databases. By mapping drug targets to disease targets, overlapping targets were identified. A shared protein-protein interaction (PPI) and drug target network were constructed for the overlapping targets and analyzed for KEGG enrichment. RESULTS: The results of animal experiments demonstrate that TRCE has the potential to improve the CAG process in mice. In conjunction with disease characteristics, cyberpharmacology analysis has identified nine core compounds, 151 targets, 10 core targets, and five significant inflammatory pathways within the compound-target-pathway network. Furthermore, there is a remarkable coincidence rate of 98% between the core compound targets of TRCE and the targets present in the CAG disease database. The accurate search and calculation of literature reports indicate that the coverage rate for 121 predicted core targets related to CAG reaches 81%. The primary characteristic of CAG lies in its inflammatory process. Both predicted and experimental findings confirm that TRCE can regulate ten key inflammation-associated targets (TP53, STAT3, AKT1, HSP90AA1, TNF, IL-6, MAPK3, SRC, JUN, and HSP90AA1) as well as inflammation-related pathways (MAPK, HIF-1, Toll-Like Receptor, IL-17, TNF, and other signaling pathways). These mechanisms mitigate inflammation and reduce gastric mucosal damage in CAG mice. CONCLUSIONS: In conclusion, TRCE was shown to alleviate CAG by modulating TP53, STAT3, AKT1, HSP90AA1, TNF, IL-6, MAPK3, SRC, JUN, and EGFR, as demonstrated by combined network pharmacology and biological experiments. In conclusion, our study provides a robust foundation for future clinical trials evaluating the efficacy of RC in treating CAG.

IL-33 Accelerates Chronic Atrophic Gastritis through AMPK-ULK1 Axis Mediated Autolysosomal Degradation of GKN1.

Chronic atrophic gastritis (CAG) is a complex disease characterized by atrophy and inflammation in gastric mucosal tissue, especially with high expression of interleukins. However, the interaction and mechanisms between interleukins and gastric mucosal epithelial cells in CAG remain largely elusive. Here, we elucidate that IL-33 stands out as the predominant inflammatory factor in CAG, and its expression is induced by H. pylori and MNNG through the ROS-STAT3 signaling pathway. Furthermore, our findings reveal that the IL-33/ST2 axis is intricately involved in the progression of CAG. Utilizing phosphoproteomics mass spectrometry, we demonstrate that IL-33 enhances autophagy in gastric epithelial cells through the phosphorylation of AMPK-ULK1 axis. Notably, inhibiting autophagy alleviates CAG severity, while augmentation of autophagy exacerbates the disease. Additionally, ROS scavenging emerges as a promising strategy to ameliorate CAG by reducing IL-33 expression and inhibiting autophagy. Intriguingly, IL-33 stimulation promotes GKN1 degradation through the autolysosomal pathway. Clinically, the combined measurement of IL-33 and GKN1 in serum shows potential as diagnostic markers. Our findings unveil an IL-33-AMPK-ULK1 regulatory mechanism governing GKN1 protein stability in CAG, presenting potential therapeutic targets for its treatment.

A series of methods incorporating deep learning and computer vision techniques in the study of fruit fly (Diptera: Tephritidae) regurgitation.

In this study, we explored the potential of fruit fly regurgitation as a window to understand complex behaviors, such as predation and defense mechanisms, with implications for species-specific control measures that can enhance fruit quality and yield. We leverage deep learning and computer vision technologies to propose three distinct methodologies that advance the recognition, extraction, and trajectory tracking of fruit fly regurgitation. These methods show promise for broader applications in insect behavioral studies. Our evaluations indicate that the I3D model achieved a Top-1 Accuracy of 96.3% in regurgitation recognition, which is a notable improvement over the C3D and X3D models. The segmentation of the regurgitated substance via a combined U-Net and CBAM framework attains an MIOU of 90.96%, outperforming standard network models. Furthermore, we utilized threshold segmentation and OpenCV for precise quantification of the regurgitation liquid, while the integration of the Yolov5 and DeepSort algorithms provided 99.8% accuracy in fruit fly detection and tracking. The success of these methods suggests their efficacy in fruit fly regurgitation research and their potential as a comprehensive tool for interdisciplinary insect behavior analysis, leading to more efficient and non-destructive insect control strategies in agricultural settings.

Upregulation of Calhm2 in the anterior cingulate cortex contributes to the maintenance of bilateral mechanical allodynia and comorbid anxiety symptoms in inflammatory pain conditions.

Peripheral inflammation-induced chronic pain tends to evoke concomitant anxiety disorders. It's common knowledge that the anterior cingulate cortex (ACC) plays a vital role in maintaining pain modulation and negative emotions. However, the potential mechanisms of chronic inflammation pain and pain-related anxiety remain elusive. Here, it was reported that injecting complete Freund's adjuvant (CFA) unilaterally resulted in bilateral mechanical allodynia and anxiety-like symptoms in mice via behavioral tests. In addition, CFA induced the bilateral upregulation and activation of calcium homeostasis modulator 2 (Calhm2) in ACC pyramidal neurons by quantitative analysis and double immunofluorescence staining. The knockdown of Calhm2 in the bilateral ACC by a lentiviral vector harboring ribonucleic acid (RNA) interference sequence reversed CFA-induced pain behaviors and neuronal sensitization. Furthermore, the modulating of ACC pyramidal neuronal activities via a designer receptor exclusively activated by designer drugs (DREADD)-hM4D(Gi) greatly changed Calhm2 expression, mechanical paw withdrawal thresholds (PWTs) and comorbid anxiety symptoms. Moreover, it was found that Calhm2 regulates inflammation pain promoting the upregulation of N-methyl-D-aspartic acid (NMDA) receptor 2B (NR2B) subunits. Calhm2 knockdown in ACC exhibited a significant decrease in NR2B expression. These results demonstrated that Calhm2 in ACC pyramidal neurons modulates chronic inflammation pain and pain-related anxiety symptoms, which provides a novel underlying mechanism for the development of inflammation pain.

ST7 Becomes One of the Most Common Staphylococcus aureus Clones After the COVID-19 Epidemic in the City of Wuhan, China.

Background: Staphylococcus aureus (S. aureus) was able to rapidly evolve and adapt under the pressure of antibiotics, host immune and environmental change. After Corona Virus Disease 2019 (COVID-19) epidemic in Wuhan, China, a large number of disinfectants were used, which might result in rapid evolution of S. aureus. Methods: A total of 619 S. aureus isolates were collected from Zhongnan Hospital, Wuhan University from 2018 to 2021, including group BEFORE (309 strains collected before COVID-19 pandemic) and group AFTER (310 strains collected after COVID-19 pandemic), for comparing the changes of molecular epidemiology. The molecular characteristics of isolates were analyzed by Multi-locus sequence typing (MLST), spa, chromosomal cassette mec (SCCmec) typing, virulence genes were screened by the PCR, antibiotic susceptibility test was carried out by the VITEK system. Results: Thirty-six sequence types (STs) belonging to 14 clone complexes (CCs) were identified. ST5 was the most prevalent clone in both groups, and ST7, ranking the sixth in group BEFORE, became the second dominant clone in group AFTER (6.5% vs 10.0%), whereas ST239 decreased from the seventh to the fourteenth (5.8% vs 1.9%). ST7 in group AFTER had a higher positive rate of virulence genes, including hlb, fnbB, seb, lukDE, sdrE and the proportion of ST7-t091 MRSA strains increased from 19.1% to 50% compared with group BEFORE. Though no significant difference of MRSA proportion was found between two groups, SCCmec type-III in group AFTER decreased (p<0.01). Though the rate of multidrug-resistance (MDR) decreased, the virulence genes hlb, hlg, fnbB, seb and pvl carrying rates were significantly elevated in MRSA strains of group AFTER. Conclusion: After COVID-19 pandemic, ST7 becomes one of the predominant S. aureus clones in Wuhan and the carrying rate of SCCmec and virulence genes is on the rise. Therefore, it is essential to strengthen the surveillance of ST7 S. aureus clone.

Mining the candidate genes of rice panicle traits via a genome-wide association study.

Panicle traits are important for improving the panicle architecture and grain yield of rice. Therefore, we performed a genome-wide association study (GWAS) to analyze and determine the genetic determinants of five panicle traits. A total of 1.29 million single nucleotide polymorphism (SNP) loci were detected in 162 rice materials. We carried out a GWAS of panicle length (PL), total grain number per panicle (TGP), filled grain number per panicle (FGP), seed setting rate (SSR) and grain weight per panicle (GWP) in 2019, 2020 and 2021. Four quantitative trait loci (QTLs) for PL were detected on chromosomes 1, 6, and 9; one QTL for TGP, FGP, and GWP was detected on chromosome 4; two QTLs for FGP were detected on chromosomes 4 and 7; and one QTL for SSR was detected on chromosome 1. These QTLs were detected via a general linear model (GLM) and mixed linear model (MLM) in both years of the study period. In this study, the genomic best linear unbiased prediction (BLUP) method was used to verify the accuracy of the GWAS results. There are nine QTLs were both detected by the multi-environment GWAS method and the BLUP method. Moreover, further analysis revealed that three candidate genes, LOC_Os01g43700, LOC_Os09g25784, and LOC_Os04g47890, may be significantly related to panicle traits of rice. Haplotype analysis indicated that LOC_Os01g43700 and LOC_Os09g25784 are highly associated with PL and that LOC_Os04g47890 is highly associated with TGP, FGP, and GWP. Our results offer essential genetic information for the molecular improvement of panicle traits. The identified candidate genes and elite haplotypes could be used in marker-assisted selection to improve rice yield through pyramid breeding.

Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis.

Mining salt tolerance genes is significant for breeding high-quality salt-tolerant rice varieties in order to improve the utilization of saline-alkaline land. In this study, 173 rice accessions were measured for their germination potential (GP), germination rate (GR), seedling length (SL), root length (RL), germination potential relative to salt damage rate (GPR), germination rate relative to salt damage rate (GRR), seedling length relative to salt damage rate (SLR), relative salt damage rate at the germination stage (RSD) and comprehensive relative salt damage rate in the early seedling stage (CRS) under normal and salt stress conditions. Genome-wide association analysis was performed with 1,322,884 high-quality SNPs obtained by resequencing. Eight quantitative trait loci (QTLs) related to salt tolerance traits at the germination stage were detected in 2020 and 2021. They were related to the GPR (qGPR2) and SLR (qSLR9), which were newly discovered in this study. Three genes were predicted as salt tolerance candidate genes: LOC_Os02g40664, LOC_Os02g40810, and LOC_Os09g28310. At present, marker-assisted selection (MAS) and gene-edited breeding are becoming more widespread. Our discovery of candidate genes provides a reference for research in this field. The elite alleles identified in this study may provide a molecular basis for cultivating salt-tolerant rice varieties.

Epiberberine regulates lipid synthesis through SHP (NR0B2) to improve non-alcoholic steatohepatitis.

Epiberberine (EPI), extracted from Rhizome Coptidis, has been shown to attenuate hyperlipidemia in vivo. Herein we have studied the mechanism by which EPI is active against non-alcoholic steatohepatitis (NASH) using, mice fed on a methionine- and choline-deficient (MCD) diet and HepG2 cells exposed to free fatty acids (FFA). We show that small heterodimer partner (SHP) protein is key in the regulation of lipid synthesis. In HepG2 cells and in the livers of MCD-fed mice, EPI elevated SHP levels, and this was accompanied by a reduction in sterol regulatory element-binding protein-1c (SREBP-1c) and FASN. Therefore, EPI reduced triglyceride (TG) accumulation in steatotic hepatocytes, even in HepG2 cells treated with siRNA-SHP, and also improved microbiota. Thus, EPI suppresses hepatic TG synthesis and ameliorates liver steatosis by upregulating SHP and inhibiting the SREBP1/FASN pathway, and improves gut microbiome.

Clinical Performance of Nanopore Targeted Sequencing for Diagnosing Infectious Diseases.

The gold standard for confirming bacterial infections is culture-positive, which has a long sample-to-result turnaround time and poor sensitivity for unculturable and fastidious pathogens; therefore, it is hard to guide early, targeted antimicrobial therapy and reduce overuse of broad-spectrum antibiotics. Nanopore targeted sequencing (NTS) is reported to be advantageous in detection speed and range over culture in prior published reports. However, investigation of the clinical performance of NTS is deficient at present. Thus, we assessed the feasibility of NTS for the first time with cohort and systematic comparisons with traditional culture assays and PCR followed by Sanger sequencing. This retrospective study was performed on 472 samples, including 6 specimen types from 436 patients, to evaluate the clinical performance of NTS designed for identifying the microbial composition of various infections. Of these samples, 86.7% were found to be NTS positive, which was significantly higher than culture-positive (26.7%). A total of 425 significant human opportunistic bacteria and fungi detected by NTS were selected to go through validation with PCR followed by Sanger sequencing. The average accuracy rate was 85.2% (maximum 100% created by Cryptococcus neoformans, the last one 66.7% provided by both Staphylococcus haemolyticus and Moraxella osloensis, minimum 0% produced by Burkholderia cepacia). The accuracy rate also varied with sample type; the highest accuracy rate was found in pleural and ascites fluid (95.8%) followed by bronchoalveolar lavage fluid (88.7%), urine (86.8%), and wound secretions (85.0%), while the lowest was present in cerebrospinal fluid (58.8%). NTS had a diagnostic sensitivity of 94.5% and specificity of 31.8%. The positive and negative predictive values of NTS were 79.9% and 66.7%, respectively. For diagnosis of infectious diseases, the sensitivity was greatly increased by 56.7% in NTS compared with culture (94.5% vs 37.8%). Therefore, NTS can accurately detect the causative pathogens in infectious samples, particularly in pleural and ascites fluid, bronchoalveolar lavage fluid, urine, and wound secretions, with a short turnaround time of 8-14 h, and might innovatively contribute to personalizing antibiotic treatments for individuals with standardized protocols in clinical practices. IMPORTANCE Nanopore targeted sequencing (NTS) is reported to be advantageous in detection speed and range over culture in prior published reports. Investigation of the clinical performance of NTS is deficient at present. In our study, cohort and systematic comparisons among three assays (culture, NTS, and Sanger sequencing) were analyzed retrospectively for the first time. We found that NTS undoubtedly has incomparable advantages in accurately detecting the causative pathogens in infectious samples, particularly in pleural and ascites fluid, bronchoalveolar lavage fluid, urine, and wound secretions, with a short turnaround time of 8-14 h. For sterile specimens like blood and cerebrospinal fluid (CSF), the NTS outcomes should be validated using other nucleic acid based detection technology. Overall, NTS might innovatively contribute to guiding early, targeted antimicrobial therapy with lower cost and reduce overuse of broad-spectrum antibiotics.

Genomic Analysis of the Unusual Staphylococcus aureus ST630 Isolates Harboring WTA Glycosyltransferase Genes tarM and tagN.

Staphylococcus aureus (S. aureus) can cause a broad spectrum of diseases ranging from skin infections to life-threatening diseases in both community and hospital settings. The surface-exposed wall teichoic acid (WTA) has a strong impact on host interaction, pathogenicity, horizontal gene transfer, and biofilm formation in S. aureus. The unusual S. aureus ST630 strains containing both ribitol-phosphate (RboP) WTA glycosyltransferase gene tarM and glycerol-phosphate (GroP) WTA glycosyltransferase gene tagN have been found recently. Native PAGE analysis showed that the WTA of tagN, tarM-encoding ST630 strains migrated slower than that of non-tagN-encoding ST630 strains, indicating the differences in WTA structure. Some mobile genetic elements (MGEs) such as the unique GroP-WTA biosynthetic gene cluster (SaGroWI), SCCmec element, and prophages that probably originated from the CoNS were identified in tagN, tarM-encoding ST630 strains. The SaGroWI element was first defined in S. aureus ST395 strain, which was refractory to exchange MGEs with typical RboP-WTA expressing S. aureus but could undergo horizontal gene transfer events with other species and genera via the specific bacteriophage Φ187. Overall, our data indicated that this rare ST630 was prone to acquire DNA from CoNS and might serve as a novel hub for the exchange of MGEs between CoNS and S. aureus. IMPORTANCE The structure of wall-anchored glycopolymers wall teichoic acid (WTA) produced by most Gram-positive bacteria is highly variable. While most dominant Staphylococcus aureus lineages produce poly-ribitol-phosphate (RboP) WTA, the tagN, tarM-encoding ST630 lineage probably has a poly-glycerol-phosphate (GroP) WTA backbone like coagulase-negative staphylococci (CoNS). There is growing evidence that staphylococcal horizontal gene transfer depends largely on transducing helper phages via WTA as the receptor. The structural difference of WTA greatly affects the transfer of mobile genetic elements among various bacteria. With the growing advances in sequencing and analysis technologies, genetic analysis has revolutionized research activities in the field of the important pathogen S. aureus. Here, we analyzed the molecular characteristics of ST630 and found an evolutionary link between ST630 and CoNS. Elucidating the genetic information of ST630 lineage will contribute to understanding the emergence and diversification of new pathogenic strains in S. aureus.