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Biological monitoring using environmental DNA (eDNA) technology has expanded from micro- to macro-organisms. In aquatic eDNA studies, large volumes of water need to be filtered rapidly in the field, which requires development of effective eDNA collection devices. In this study, we introduce a novel portable eDNA collection system containing a GM dual-channel water filter and a DNA extraction kit adapted to large filter membranes (ø 100 mm). The water filter is powered by a high-capacity lithium battery (9,000 mA), which operates two peristaltic pumps and maintains a continuous filtration rate of up to 1 L/min for 5 h in outdoor settings. For sample collection, the optimum conditions are still water and turbidity below 8 nephelometric turbidity units. This allows for the filtration of 10 L of water within 10 min by use of a 0.22-µm filter. Metagenomic and 12S metabarcoding sequencing showed that the DNA extraction quality and species annotation accuracy of our custom DNA extraction kit, which was tailored for this system, rivaled the performance of established kits. The GM water filter's enrichment mode gave consistent results with vacuum filtration, which greatly reduced the filtration time for large water samples, while accurately reproducing species annotations. This innovation streamlines the eDNA collection and annotation process and offers substantial benefits for biodiversity monitoring and conservation efforts. [ABSTRACT FROM AUTHOR]

IgG4-related disease (IgG4-RD) has complex clinical manifestations ranging from fibrosis and inflammation to deregulated metabolism. The molecular mechanisms underpinning these phenotypes are unclear. In this study, by using IgG4-RD patient peripheral blood mononuclear cells (PBMCs), IgG4-RD cell lines and Usp25 knockout mice, we show that ubiquitin-specific protease 25 (USP25) engages in multiple pathways to regulate fibrotic and inflammatory pathways that are characteristic to IgG4-RD. Reduced USP25 expression in IgG4-RD leads to increased SMAD3 activation, which contributes to fibrosis and induces inflammation through the IL-1β inflammatory axis. Mechanistically, USP25 prevents ubiquitination of RAC1, thus, downregulation of USP25 leads to ubiquitination and degradation of RAC1. Decreased RAC1 levels result in reduced aldolase A release from the actin cytoskeleton, which then lowers glycolysis. The expression of LYN, a component of the B cell receptor signalosome is also reduced in USP25-deficient B cells, which might result in B cell activation deficiency. Altogether, our results indicate a potential anti-inflammatory and anti-fibrotic role for USP25 and make USP25 a promising diagnostic marker and potential therapeutic target in IgG4-RD. [ABSTRACT FROM AUTHOR]

Targeted genomic sequencing (TS) greatly benefits precision oncology by rapidly detecting genetic variations with better accuracy and sensitivity owing to its high sequencing depth. Multiple sequencing platforms and variant calling tools are available for TS, making it excruciating for researchers to choose. Therefore, benchmarking study across different platforms and pipelines available for TS is imperative. In this study, we performed a TS of Reference OncoSpan FFPE (HD832) sample enriched by TSO500 panel using four commercially available sequencers, and analyzed the output 50 datasets using five commonly-used bioinformatics pipelines. We systematically investigated the sequencing quality and variant detection sensitivity, expecting to provide optimal recommendations for future research. Four sequencing platforms returned highly concordant results in terms of base quality (Q20 > 94%), sequencing coverage (>97%) and depth (>2000×). Benchmarking revealed good concordance of variant calling across different platforms and pipelines, among which, FASTASeq 300 platform showed the highest sensitivity (100%) and precision (100%) in high-confidence variants calling when analyzed by SNVer and VarScan 2 algorithms. Furthermore, this sequencer demonstrated the shortest sequencing time (~21 h) at the sequencing mode PE150. Through the intersection of 50 datasets generated in this study, we recommended a novel set of variant genes outside the truth set published by HD832, expecting to replenish HD832 for future research on tumor variant diagnosis. Besides, we applied these five tools to another panel (TargetSeq One) for Twist cfDNA Pan-cancer Reference Standard, comprehensive consideration of SNP and InDel sensitivity, SNVer and VarScan 2 performed best among them. Furthermore, SNVer and VarScan 2 also performed best for six cancer cell lines samples regarding SNP and InDel sensitivity. Considering the dissimilarity of variant calls across different pipelines for datasets from the same platform, we recommended an integration of multiple tools to improve variant calling sensitivity and accuracy for the cancer genome. Illumina and GeneMind technologies can be used independently or together by public health laboratories performing tumor TS. SNVer and VarScan 2 perform better regarding variant detection sensitivity for three typical tumor samples. Our study provides a standardized target sequencing resource to benchmark new bioinformatics protocols and sequencing platforms. [ABSTRACT FROM AUTHOR]

Background: Mood disorders are very common among adolescents and include mainly bipolar disorder (BD) and major depressive disorder (MDD), with overlapping depressive symptoms that pose a significant challenge to realizing a rapid and accurate differential diagnosis in clinical practice. Misdiagnosis of BD as MDD can lead to inappropriate treatment and detrimental outcomes, including a poorer ultimate clinical and functional prognosis and even an increased risk of suicide. Therefore, it is of great significance for clinical management to identify clinical symptoms or features and biological markers that can accurately distinguish BD from MDD. With the aid of bibliometric analysis, we explore, visualize, and conclude the important directions of differential diagnostic studies of BD and MDD in adolescents. Materials and methods: A literature search was performed for studies on differential diagnostic studies of BD and MDD among adolescents in the Web of Science Core Collection database. All studies considered for this article were published between 2004 and 2023. Bibliometric analysis and visualization were performed using the VOSviewer and CiteSpace software. Results: In total, 148 publications were retrieved. The number of publications on differential diagnostic studies of BD and MDD among adolescents has been generally increasing since 2012, with the United States being an emerging hub with a growing influence in the field. Boris Birmaher is the top author in terms of the number of publications, and the Journal of Affective Disorders is the most published journal in the field. Co-occurrence analysis of keywords showed that clinical characteristics, genetic factors, and neuroimaging are current research hotspots. Ultimately, we comprehensively sorted out the current state of research in this area and proposed possible research directions in future. Conclusion: This is the first-ever study of bibliometric and visual analyses of differential diagnostic studies of BD and MDD in adolescents to reveal the current research status and important directions in the field. Our research and analysis results might provide some practical sources for academic scholars and clinical practice. [ABSTRACT FROM AUTHOR]

Introduction: The seeds of Brucea javanica (L.) Merr. (BJ) have been traditionally used to treat various types of cancers for many years in China. In this study, we systematically investigated a BJ oil emulsion (BJOE) produced from BJ seeds with the purpose of evaluating its antiviral effect against hepatitis B virus (HBV). Methods: HepG2.215 (a wild-type HBV cell line), HepG2, and Huh7, transfected with wildtype (WT) or lamivudine-resistance mutant (LMV-MT) HBV replicon plasmids, were treated with different doses of BJOE and then used for pharmacodynamic evaluation. Cell viability was determined using CCK8 assay. The levels of HBsAg/HBeAg in cell cultured supernatant, HBcAg in cell lysis solution, and HBV DNA in both were evaluated. Results: BJOE at =5 mg/ml was nontoxic to carcinoma cell lines, but could significantly inhibit WT/LMV-MT HBV replication and HBs/e/c antigen expression in a dose-dependent manner by upregulating interleukin-6 (IL-6), demonstrating that it possesses moderate anti-HBV activity. As one of the major components of BJOE, bruceine B was found to play a dominant role in IL-6 induction and HBV inhibition. Discussion: Our results demonstrated that BJOE suppressed HBV replication by stimulating IL-6, indicating that it has promising clinical therapeutic potential for both WT and LMV-MT HBV. [ABSTRACT FROM AUTHOR]

Objectives: This study aimed to characterize the genomic epidemiology of human adenoviruses (HAdVs) in Hubei, China, using metagenomic next-generation sequencing (mNGS). Methods: In total, 25 HAdV-positive samples collected from 21 pediatric patients were sequenced and subjected to mNGS using the NextSeq 550 and GenoLab M sequencing platforms. The metagenomic data were assembled de novo for molecular typing, phylogenetic and recombination analyzes. Results: We assembled 50 HAdV genomes, 88% (22/25) genomes from GenoLab M, and 84% (21/25) genomes from NextSeq 550 have perfect alignments to reference genomes with greater than 90%. The most fully assembled 25 genomes were categorized into 7 HAdV genotypes, the most abundant of which were HAdV-B3 (9/25) and HAdV-C2 (6/25). Phylogenetic analyzes revealed that the newly isolated HAdV-B3 strains diverged into separate clusters according to their genotypes. Vigilance is needed that HAdV-B3 isolates have begun to form new distinct clusters. High nucleotide identity was observed in the whole genome level within the same HAdV genotypes, while marked differences of three capsid genes across HAdV genotypes were noted. The high nucleotide diversity regions were concordant with the reported hypervariable regions. Further, three recombinant strains were identified: S64 and S71 originated from the parental strains HAdV-B14 and HAdV-B11, and S28 originated from HAdV-C1, HAdV-C5, and HAdV-CBJ113. GenoLab M and NextSeq 550 showed comparable performance with respect to data yield, duplication rate, human ratio, and assembly completeness. Conclusion: The sequencing quality and assembly accuracy showed that mNGS assembled genomes can be used for subsequently HAdV genotyping and genomic characterization. The high nucleotide diversity of capsid genes and high frequency of recombination events has highlighted the necessity for HAdV epidemiological surveillance in China. [ABSTRACT FROM AUTHOR]

Background: Neuroinflammatory responses have been recognized as an important aspect in the pathogenesis of Parkinson's disease (PD). Transcriptional regulation plays a critical role in the process of inflammation. Transcription factor myocyte enhancer factor 2D (MEF2D) is identified as a central factor in transmission of extracellular signals and activation of the genetic programs in response to a wide range of stimuli in several cell types, including neurons. But its presence and function in microglia have not been reported. We therefore investigated the effect of MEF2D in activated microglia on the progress of neuroinflammation and the survival of neurons. Methods: BV2 cells and primary cultured glial cells were stimulated with lipopolysaccharide (LPS). Samples from cells were examined for MEF2D expression, interleukin-10 (IL-10), and tumor necrosis factor alpha (TNF-α) by immunoblotting, quantitative real-time PCR (qPCR) or enzyme-linked immunosorbent assay (ELISA). The activity of MEF2D was examined by electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation assay (ChIP). Recombinant lentivirus expressing shRNA specific to MEF2D was used to silence MEF2D expression in BV2 cells. The role of IL-10 transcriptionally induced by MEF2D on neuronal survival was assessed by anti-IL-10 neutralizing antibody. The survival of neurons was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) staining. Male C57bl/6 mice were used to establish an acute PD model. Brain sections and cell slides were tested by immunofluorescence. Results: We demonstrated that MEF2D was present in microglia. Activation of microglia was associated with an increase in MEF2D level and activity in response to different stimuli in vivo and in vitro. MEF2D bound to a MEF2 consensus site in the promoter region of IL-10 gene and stimulated IL-10 transcription. Silencing MEF2D decreased the level of IL-10, increased the TNF-α mRNA, and promoted inflammation-induced cytotoxicity, consistent with the result of inhibiting IL-10 activity with an anti-IL-10 neutralizing antibody. Conclusions: Our study identifies MEF2D as a critical regulator of IL-10 gene expression that negatively controls microglia inflammation response and prevents inflammation-mediated cytotoxicity. [ABSTRACT FROM AUTHOR]