Publications by authors named "JinRui Xu"

A novel and efficient method for the intermolecular hydroxysulfonylation of vinylarenes using sodium sulfinates has been achieved through aerobic copper catalysis. This transformation proceeded smoothly with green air as the terminal oxidant in the presence of Cu (I)/1,10-phenanthroline as an efficient catalytic system, leading to an array of β-hydroxysulfones in moderate to high yields. The significant advantages of this protocol are the mild reaction conditions, readily available starting materials, good functional-group compatibility, synthetic convenience, and practicability.

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Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, The ENCODE consortium mapped biochemical signals across many cell types and tissues and integrated these data to develop a Registry of 0.9 million human and 300 thousand mouse candidate cis-Regulatory Elements (cCREs) annotated with potential functions.

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Objective: Polycystic ovary syndrome (PCOS) is a metabolic and endocrine disease that entails dysregulated ovulation, hyperandrogenism, and polycystic ovaries. While Wnt5a has been suggested to play key roles in follicular development and female fertility under normal conditions, its functions in the context of PCOS have yet to be established. This study was thus designed to explore the impact of Wnt5a on ovarian granulosa cell autophagy in PCOS, providing in vitro evidence in support of its role in this setting.

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A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms, (fly) and (worm). These data sets comprise 605 TFs identifying 3.

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The pseudorabies virus (PRV) causes severe and fatal acute respiratory disease in pigs. During PRV proliferation, the enzyme deoxyuridine 5'-triphosphate nucleotide hydrolase (dUTPase) plays a pivotal role in maintaining a low dUTP/dTTP ratio, thereby ensuring the accuracy of viral DNA replication. However, its structure and catalytic mechanisms have not been fully elucidated.

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  • * The study analyzed exosomes from bovine serum during early pregnancy, identifying 472 miRNA precursor sequences and 367 mature miRNA sequences, with a focus on differential miRNA expression at specific pregnancy days.
  • * Bioinformatics revealed that certain differentially expressed miRNAs were linked to vital signaling pathways (like VEGF and NF-κB) related to early pregnancy, offering insights for future research on pregnancy markers and improving cattle breeding practices.
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Extracellular vesicles (EVs), characterized by low immunogenicity, high biocompatibility and targeting specificity along with excellent blood-brain barrier permeability, are increasingly recognized as promising drug delivery vehicles for treating a variety of diseases, such as cancer, inflammation and viral infection. However, recent findings demonstrate that the intracellular delivery efficiency of EVs fall short of expectations due to phagocytic clearance mediated by the host mononuclear phagocyte system through Fcγ receptors, complement receptors as well as non-opsonic phagocytic receptors. In this text, we investigate a range of bacterial virulence proteins that antagonize host phagocytic machinery, aiming to explore their potential in engineering EVs to counteract phagocytosis.

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  • - Nanopore direct RNA sequencing (DRS) can directly detect m6A in RNA without needing extra lab techniques, but most current methods don’t fully utilize the raw signal data from DRS reads.
  • - The new deep-learning method, RedNano, leverages both raw signals and basecalling errors, showing improved accuracy over existing methods in detecting m6A across various datasets, including those from Arabidopsis and humans.
  • - RedNano’s implementation is accessible for free, allowing others to use or build upon this more effective approach for RNA m6A detection at the provided GitHub link.
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A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here we present the culmination of the modERN (model organism Encyclopedia of Regulatory Networks) consortium that systematically assayed TF binding events in vivo in two major model organisms, (fly) and (worm). We describe key features of these datasets, comprising 604 TFs identifying 3.

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Numerous statistical methods have emerged for inferring DNA motifs for transcription factors (TFs) from genomic regions. However, the process of selecting informative regions for motif inference remains understudied. Current approaches select regions with strong ChIP-seq signal for a given TF, assuming that such strong signal primarily results from specific interactions between the TF and its motif.

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Tuberculosis (TB) is the leading cause of human death worldwide due to (Mtb) infection. Mtb infection can cause macrophage pyroptosis. PERK, as a signaling pathway protein on the endoplasmic reticulum, plays an important role in infectious diseases.

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Pyroptosis is a host immune strategy to defend against (Mtb) infection. , a calcium-binding protein that plays an important role in promoting cancer progression as well as the pathophysiological development of various non-tumor diseases, has not been explored in Mtb-infected hosts. In this study, transcriptome analysis of the peripheral blood of patients with pulmonary tuberculosis (PTB) revealed that and were significantly up-regulated in PTB patients' peripheral blood.

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Article Synopsis
  • Tuberculosis (TB) is caused by the bacteria Mycobacterium tuberculosis (Mtb), which primarily infects macrophages, leading to programmed cell death known as pyroptosis.
  • The study investigates how endoplasmic reticulum stress (ERS) influences NLRP3 inflammasome activation and pyroptosis in THP-1 macrophages infected with BCG, a vaccine strain of Mtb.
  • Results indicate that BCG infection notably increases ERS, activates the NLRP3 inflammasome, and triggers pyroptosis in macrophages, with inhibitors like TUDCA and MCC950 effectively reducing these effects.
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Long single-molecular sequencing technologies, such as PacBio circular consensus sequencing (CCS) and nanopore sequencing, are advantageous in detecting DNA 5-methylcytosine in CpGs (5mCpGs), especially in repetitive genomic regions. However, existing methods for detecting 5mCpGs using PacBio CCS are less accurate and robust. Here, we present ccsmeth, a deep-learning method to detect DNA 5mCpGs using CCS reads.

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  • * A deep-learning model can predict allele-specific activity using only local nucleotide sequences, emphasizing key transcription-factor-binding motifs affected by genetic variants.
  • * Combining EN-TEx with previous genome annotations shows significant connections between allele-specific loci and GWAS loci, and aids in transferring known eQTLs to challenging tissue types, improving personal functional genomics research.
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  • Premature ovarian insufficiency (POI) affects women under 40, leading to symptoms like amenorrhea and infertility, and has shown potential treatment with exosomes from human pluripotent stem cell-mesenchymal stem cells (hiMSC).
  • In a study using a chemotherapy-induced POI-like mouse model, hiMSC exosomes were tested for their ability to protect ovarian function, with assessments made on hormone levels and follicle count.
  • Results indicated that hiMSC exosomes slowed follicle loss, restored hormone levels, and promoted cell growth while reducing apoptosis in ovarian cells, suggesting a pathway to preserve fertility in female mice.
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Objective To investigate the regulatory effect of wingless gene 7a (Wnt7a) on Bacille Calmette Guerin (BCG) induced autophagy in alveolar epithelial cells. Methods The alveolar epithelial cells of TC-1 mice were treated with interfering Wnt7a lentivirus and BCG alone or together in four groups, namely, small interfering RNA control (si-NC) group, si-NC combined with BCG group, Wnt7a small interfering RNA (si-Wnt7a) group, and si-Wnt7a combined with BCG group. The expressions of Wnt7a, microtubule associated protein 1 light chain 3 (LC3), P62, and autophagy related gene 5 (ATG5) were detected by Western blot analysis, and the distribution of LC3 was detected by immunofluorescence cytochemical staining.

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Objective To investigate the regulation of Wnt5a/receptor tyrosine kinase-like orphan receptor 2 (ROR2) signaling pathway on macrophage autophagy induced by Bacille Calmette Guerin (BCG) infection. Methods RAW264.7 cells were infected with BCG at 0, 2, 6, 12 and 24 hours, and the expressions of Wnt5a, ROR2 and autophagy-related protein microtubule-associated protein 1 light chain 3II (LC3II ) were detected by Western blot analysis.

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Objective: Hyperandrogenemia (HA) is the main pathophysiological change that takes place in polycystic ovary syndrome (PCOS). Cyproterone acetate (CYA) is a drug commonly used to reduce androgen in patients with PCOS. Long-term and continuous exposure to HA can cause ovarian granulosa cells (GCs), pyroptotic death, and follicular dysfunction in PCOS mice.

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Purpose: To investigate the influencing factors of abdominal lymph node metastasis in thoracic esophageal squamous cell carcinoma (TESCC), and to construct its predictive model, in order to analyze the targets for postoperative radiotherapy.

Methods And Materials: From January 2008 to December 2014, the clinicopathological data of 479 patients who underwent radical resection for esophageal cancer in the Fourth Hospital of Hebei Medical University were collected and retrospectively analyzed. The influencing factors of postoperative abdominal lymph node metastasis were analyzed, and a predictive model was constructed based on their independent influencing factors.

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Article Synopsis
  • The study investigates how the Wnt signaling pathway influences early ovarian follicular development using mouse ovaries cultured with inhibitors IWP2 and KN93.
  • Proteomic analysis identified significant changes in protein abundance, with various proteins and pathways linked to ovarian development, specifically highlighting Wnt, Notch, and P53 signaling pathways.
  • The findings enhance understanding of the regulatory mechanisms behind early ovarian development, employing advanced techniques like label-free quantification and liquid chromatography-mass spectrometry for deeper insights.
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Objective To investigate the effect of Wnt5a on autophagy in KGN human granulosa cells. Methods KGN human granulosa cells were treated with DMSO (control group), recombinant Wnt5a protein (rWnt5a), Wnt5a inhibitor IWP2 or BOX5, separately. The expression level of Wnt5a protein was detected by Western blot.

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Autophagy functions as a critical process that can suppress the proliferation of Mycobacterium tuberculosis (Mtb) within infected host cells. Wnt5a is a secreted protein that plays a range of physiological functions, activating several signaling pathways and thereby controlling cellular responses to particular stimuli. The importance of Wnt5a as a regulator of protection against Mtb infection, however, has yet to be fully characterized.

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Purpose: The prognostic effect of postoperative radiotherapy (PORT) on pathological T3N0M0 (pT3N0M0) esophageal squamous cell carcinoma (ESCC) remains inconclusive. This study aimed to retrospectively investigate patterns of failure and whether PORT after R0 resection improves survival in patients with pT3N0M0 ESCC, compared with surgery alone.

Patients And Methods: The clinical data of 256 patients with pT3N0M0 ESCC from January 2007 to December 2010 were retrospectively reviewed.

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