375 Works

The synaptic marker neurogranin as a disease state biomarker in Alzheimer’s disease: a systematic review and meta-analysis

Zhibin Wang, Jianwei Yang, Wei Zhu, Yi Tang & Jianping Jia
Objective: Synaptic degeneration is the pathologic foundation of cognitive decline in the Alzheimer’s disease (AD) continuum. We aimed to determine whether cerebrospinal fluid (CSF) synaptic marker neurogranin (Ng) is a disease state or a disease stage biomarker in the AD continuum. Methods: Studies comparing CSF Ng levels among AD, mild cognitive impairment (MCI) and healthy participants were included. Studies were eligible if the correlation between CSF Ng levels and Mini-Mental Status Examination (MMSE) scores was...

Identification of hepatocellular carcinoma-related genes associated with macrophage differentiation based on bioinformatics analyses

Jun Cao, Chi Zhang, Guo-Qing Jiang, Sheng-Jie Jin, Qian Wang, Ao-Qing Wang & Dou-Sheng Bai
Macrophage differentiation is associated with tumorigenesis, including the tumorigenesis of hepatocellular carcinoma (HCC). Herein, we explored the value of macrophage differentiation-associated genes (MDGs) in the prognosis of HCC using data from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) databases. We performed multivariate Cox regression analyses to identify the hub genes affecting HCC patient prognoses. The correlations between hub genes and macrophage differentiation and immune checkpoint inhibitors (PD-1, PD-L1, and CTLA4)...

Distribution characteristics of microbial community structure in atmospheric particulates of the typical industrial city in Jiangsu province, China

Xingcheng Yuan, Guangchao Li, Weihua Yang & Dan Li
In this study, Xuzhou, a typical industrial city in the north of Jiangsu Province, was chosen to investigate the pollution level of atmospheric particulates. The proportion of fine particles (PM2.5) in PM10 is larger than that of coarse particles (about 58%). The physicochemical properties of PM2.5 were analyzed by SEM and EDS. DGGE was used to study the distribution characteristics of bacterial community structure on atmospheric particulates (TSP, PM2.5 and PM10) in different functional areas...

Multi-locus identification of Psilocybe cubensis by high-resolution melting (HRM)

Xiaochun Zhang, Huan Yu, Ziwei Wang, Qi Yang, Ruocheng Xia, Yiling Qu, Ruiyang Tao, Yan Shi, Ping Xiang, Suhua Zhang & Chengtao Li
Hallucinogenic mushroom is a kind of toxic strain containing psychoactive tryptamine substances such as psilocybin, psilocin and ibotenic acid, etc. The mushrooms containing hallucinogenic components are various, widely distributed and lack of standard to define, which made a great challenge to identification. Traditional identification methods, such as morphology and toxicology analysis, showed shortcomings in old or processed samples, while the DNA-based identification of hallucinogenic mushrooms would allow to identify these samples due to the stability...

Long non-coding RNA DUXAP8 promotes the cell proliferation, migration, and invasion of papillary thyroid carcinoma via miR-223-3p mediated regulation of CXCR4

Yan Liu, Hejia Zhang, Hui Wang, Jiarui Du, Peng Dong, Meihan Liu & Yuanqiang Lin
Papillary thyroid carcinoma (PTC) is a differentiated type of thyroid malignancy with a high incidence. Long non-coding RNA (lncRNA) DUXAP8 has been reported to participate in the proliferation, migration, and invasion of several cancer types. However, its association with PTC has not yet been reported. The current study aimed to investigate the role of DUXAP8 in PTC and revealed the underlying mechanisms. The expression of DUXAP8 was knocked down in two PTC cell lines and...

Additional file 1 of Transcriptional dynamics of transposable elements when converting fibroblast cells of Macaca mulatta to neuroepithelial stem cells

Dahai Liu, Li Liu, Kui Duan, Junqiang Guo, Shipeng Li, Zhigang Zhao, Xiaotuo Zhang, Nan Zhou & Yun Zheng
Additional file 1 Supplementary Table S1. The expression levels of 1627 dynamically expressed genes in the reprogramming procedure of rhesus monkey fibroblast cells toward neuroephithelia stem cells. Supplementary Table S2 to S17. The enriched GO terms of genes in Cluster G0 to G15 of Figure 1A, respectively. Supplementary Table S18. The expression levels of 495 dynamically expressed TEs in the reprogramming procedure of rhesus monkey fibroblast cells toward neuroephithelia stem cells. Supplementary Table S19. The...

Analysis of mRNA‑lncRNA and mRNA‑lncRNA-pathway co‑expression networks based on WGCNA in developing pediatric sepsis

Xiaojuan Zhang, Yuqing Cui, Xianfei Ding, Shaohua Liu, Bing Han, Xiaoguang Duan, Haibo Zhang & Tongwen Sun
Pediatric sepsis is a great threat to death worldwide. However, the pathogenesis has not been clearly understood until now in sepsis. This study identified differentially expressed mRNAs and lncRNAs based on Gene Expression Omnibus (GEO) database. And the weighted gene co-expression network analysis (WGCNA) was performed to explore co-expression modules associated with pediatric sepsis. Then, Gene Ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, mRNA‑lncRNA and mRNA‑lncRNA-pathway co-expression network analysis was conducted in...

A virulent Bacillus cereus strain from deep-sea cold seep induces pyroptosis in a manner that involves NLRP3 inflammasome, JNK pathway, and lysosomal rupture

Yan Zhao, Shuai Jiang, Jian Zhang, Xiao-Lu Guan, Bo-Guang Sun & Li Sun
Recent studies indicate that the Bacillus species is distributed in deep-sea environments. However, no specific studies on deep-sea Bacillus cereus have been documented. In the present work, we isolated a B. cereus strain, H2, from the deep-sea cold seep in South China Sea. We characterized the pathogenic potential of H2 and investigated H2-induced death of different types of cells. We found that H2 was capable of tissue dissemination and causing acute mortality in mice and...

Network analysis of PTSD in college students across different areas after the COVID-19 epidemic

Rui Sun, Junjun Qi, Jiali Huang & Xiao Zhou
Background: Various studies have examined the psychological ‘typhoon eye’ and ‘ripple’ effects in mental disorders following COVID-19. However, these studies only considered the disorders as entities and assessed severity, and overlooked the differences in specific symptoms of disorders. Objectives: This aim of the study is to assess the psychological typhoon eye and ripple effects at the symptom-level in posttraumatic stress disorder (PTSD), which is considered as a common psychopathology following the COVID-19 epidemic. Method: In...

MicroRNA-146b-3p regulates the dysfunction of vascular smooth muscle cells via repressing phosphoinositide-3 kinase catalytic subunit gamma

Xijing Zhuang, Feng Gao, Lei Shi, Wei Liu, Wenjun Wang, Xuezhi He & Yang Gao
MicroRNAs are crucial regulators in the phenotype switch of vascular smooth muscle cells (VSMCs). Nonetheless, the role of miR-146b-3p in VSMCs remains unclear. In the present study, platelet-derived growth factor-BB (PDGF-BB) at different concentrations was employed to stimulate VSMCs for different times, to establish the model of VSMC dysfunction. The relative expression of miR-146b-3p was quantified by quantitative real-time polymerase chain reaction (qRT-PCR). The proliferation of VSMCs was measured by BrdU assay. Flow cytometry analysis...

The expression and clinical prognostic value of protein phosphatase 1 catalytic subunit beta in pancreatic cancer

Lingyu Hu, Haokai Xu, Xiaoguang Wang, Bin Wu, Fei Chen, Wei Chen, Yong Gao & Zhengxiang Zhong
Pancreatic cancer (PAAD) is a common malignancy with a poor survival rate. The identification of novel biomarkers could improve clinical outcomes for patients with PAAD. Here we evaluated the expression and clinical significance of PPP1CB in PAAD. PPP1CB expression was higher in PAAD tissue than in matched paracancerous tissue (P < 0.05). We predicted a network of regulatory targets and protein interaction partners of PPP1CB, and identified a PPI network consisting of 39 node genes....

Alleviation of refractory IgA nephropathy by intensive fecal microbiota transplantation: the first case reports

Jin Zhao, Ming Bai, Xiaoxia Yang, Yan Wang, Rong Li & Shiren Sun
Gut dysbiosis may be implicated in the pathogenesis of IgA nephropathy (IgAN) through immune and/or metabolite pathways. Fecal microbiota transplantation (FMT) could reestablish the micro-ecological balance in IgAN, although this has never been attempted before. We explored whether FMT could be efficacious in treating IgAN in two patients with refractory IgAN. Two Chinese female patients with IgAN failed to achieve clinical remission after receiving several rounds of immunosuppressive therapy and suffered from unbearable adverse effects...

Protective effect of berberine against LPS-induced endothelial cell injury via the JNK signaling pathway and autophagic mechanisms

Junping Guo, Wei Chen, Beibei Bao, Dayong Zhang, Jianping Pan & Mao Zhang
The role of autophagic mechanisms in the protective effect of berberine (BBR) on lipopolysaccharide (LPS)-induced injury in the endothelial cells human umbilical vein endothelial cells (HUVECs) and human pulmonary microvascular endothelial cells (HPMECs) was investigated. Cell viability, proliferation, and apoptosis were detected by the CCK-8 assay, the EdU kit, and flow cytometry, respectively, and autophagy-related protein expression, the number of autophagic vacuoles, and LC3 double-fluorescence were examined using western blot analysis, transmission electron microscopy, and...

STAT3-induced ZBED3-AS1 promotes the malignant phenotypes of melanoma cells by activating PI3K/AKT signaling pathway

Yang Wang, Nan Lou, Min Zuo, Fuqiang Zhu, Yan He, Zhiqiang Cheng & Xiaomei Wang
Melanoma is considered as the most frequent primary malignancy occurring in skin. Accumulating studies have suggested that long non-coding RNAs (lncRNAs) play critical parts in multiple cancers. In this study, we explored the molecular mechanism of ZBED3 antisense RNA 1 (ZBED3-AS1) in melanoma. We observed that ZBED3-AS1 expression was remarkably up-regulated in melanoma tissues, and high ZBED3-AS1 level was linked to unsatisfactory survival of melanoma patients. Then, we discovered that ZBED3-AS1 was overexpressed in melanoma...

Silencing of the chemokine CXC receptor 4 (CXCR4) hampers cancer progression and increases cisplatin (DDP)-sensitivity in clear cell renal cell carcinoma (ccRCC)

Wenguang Wang, Zhilu Gan, Qiang Liu, Shenshen Yan, Rexiti Mulati & Yujie Wang
Aberrant expression of the chemokine CXC receptor 4 (CXCR4) is closely associated with cancer progression and drug-resistance in multiple cancers, and we first investigated the role of CXCR4 in regulating cancer pathogenesis and cisplatin (DDP)-resistance in clear cell renal cell carcinoma (ccRCC) in the present study. Here, we identified that CXCR4 acted as an oncogene to promote cancer progression and genetically silencing of CXCR4 increased cisplatin (DDP)-sensitivity in ccRCC in vitro and in vivo. Functionally,...

Comparative study of bioinformatic tools for the identification of chimeric RNAs from RNA Sequencing

Sandeep Singh & Hui Li
Chimeric RNAs are gaining more and more attention as they have broad implications in both cancer and normal physiology. To date, over 40 chimeric RNA prediction methods have been developed to facilitate their identification from RNA sequencing data. However, a limited number of studies have been conducted to compare the performance of these tools; additionally, previous studies have become outdated as more software tools have been developed within the last three years. In this study,...

Genomics-guided isolation and identification of active secondary metabolites of Bacillus velezensis BA-26

Buqing Wang, Chao Liu, Xuemiao Yang, Yana Wang, Feiyan Zhang, Huicai Cheng, Liping Zhang & Hongwei Liu
Here we report the discovery and identification of antibacterial substances from the secondary metabolites of a new strain Bacillus velezensis BA-26. The whole genome of B. velezensis BA-26 was sequenced. Its genome data were annotated, and four potentially unknown gene clusters and nine known secondary metabolite synthetic gene clusters were analyzed and excavated by antiSMASH software. Based on the predicted secondary metabolites from the genome of strain BA-26, the material identification of isolated and purified...

Prediction of intrahepatic cholestasis of pregnancy in the first 20 weeks of pregnancy

Xinyuan Zhang, Yu Chen, Stephen Salerno, Yi Li, Libin Zhou, Xiaoxi Zeng & Huafeng Li
Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disease associated with a significant risk of fetal complications including pre-term delivery and fetal death. Typically, it was diagnosed in the third trimester of pregnancy. This study utilized characteristics from routine maternal examinations in the first 20 weeks’ gestation to predict ICP in pregnant women. This is a retrospective case-control study. 13,329 medical records were collected on pregnant women presenting to the West China Second University...

Exosomal lncAY927529 enhances prostate cancer cell proliferation and invasion through regulating bone microenvironment

Qi Li, Jinhao Hu, Yibo Shi, Mulun Xiao, Tianxiang Bi, Chaoliang Wang, Liang Yan & Xiaoyan Li
Exosomes mediate the interaction between cancer cells and their microenvironment, and play a key role in tumor development. Although exosomes can package lncRNAs to mediate extracellular communication, the role of exosomal lncRNA AY927529 in prostate cancer (PCa) remains unclear. Exosomes were extracted from normal human prostatic epithelial cell lines (BPH-1 and RWPE-1) and PCa cell lines (VCaP and LNCaP, DU145, PC3) by ultrahigh speed centrifugation. Results of Western blot indicated that Alix, HSC70 and TSGl01...

Protective effect of Qingre Huoxue decoction against myocardial infarction via PI3K/Akt autophagy pathway based on UPLC-MS, network pharmacology, and in vivo evidence

Zheng Jin, Wenbo Zhang, Yuan Luo, Xiushen Li, Lijin Qing, Qiang Zuo, Junfeng Fang & Wei Wu
Qingre Huoxue (QRHX) decoction, a traditional Chinese medicine, has been widely used to prevent and treat myocardial infarction (MI). This study elucidates the possible mechanisms of QRHX in preventing or treating MI in a rat model. The chemical constituents of QRHX were identified by UPLC-MS. Sprague-Dawley rats were randomly divided into the Sham (normal saline), Model (normal saline), QRHX-L, QRHX-M and QRHX-H group (n = 10 per group). QRHX decoction was administered by gavage to...

A semi-parametric Bayesian approach for detection of gene expression heterosis with RNA-seq data

Ran Bi & Peng Liu
Heterosis refers to the superior performance of a hybrid offspring over its two inbred parents. Although heterosis has been widely observed in agriculture, its molecular mechanism is not well studied. Recent advances in high-throughput genomic technologies such as RNA sequencing (RNA-seq) facilitate the investigation of heterosis at the gene expression level. However, it is challenging to identify genes exhibiting heterosis using RNA-seq data because high-dimension of hypotheses tests are conducted with limited sample size. Furthermore,...

A semi-parametric Bayesian approach for detection of gene expression heterosis with RNA-seq data

Ran Bi & Peng Liu
Heterosis refers to the superior performance of a hybrid offspring over its two inbred parents. Although heterosis has been widely observed in agriculture, its molecular mechanism is not well studied. Recent advances in high-throughput genomic technologies such as RNA sequencing (RNA-seq) facilitate the investigation of heterosis at the gene expression level. However, it is challenging to identify genes exhibiting heterosis using RNA-seq data because high-dimension of hypotheses tests are conducted with limited sample size. Furthermore,...

Establishment of a venovenous extracorporeal membrane oxygenation in a rat model of acute respiratory distress syndrome

Yongnan Li, Jian Huang, Rongzhi Zhang, Shixiong Wang, Xingdong Cheng, Pengbin Zhang, Kerong Zhai, Wei Wang, Debin Liu & Bingren Gao
Introduction:Venovenous extracorporeal membrane oxygenation (VV ECMO) is now considered a reasonable option to salvage acute respiratory distress syndrome (ARDS). However, we lack a rodent model for experimental studies. This study was undertaken to establish an animal model of VV ECMO in ARDS rats.Methods:A total of 18 Sprague-Dawley (SD) rats (350 ± 50 g) were used in this study. Using a rat model of oleic acid (OA)-induced ARDS, VV ECMO was established through cavoatrial cannulation of...

Hepatitis B virus middle surface antigen loss promotes clinical variant persistence in mouse models

Junyu Lin, Jing Li, Peilin Xie, Yue Han, Demin Yu, Jia Chen & Xinxin Zhang
Hepatitis B virus (HBV) middle surface antigen (MHBs) mutation or deletion occurs in patients with chronic HBV infection. However, the functional role of MHBs in HBV infection is still an enigma. Here, we reported that 7.33% (11/150) isolates of CHB patients had MHBs start codon mutations compared with 0.00% (0/146) in acute hepatitis B (AHB) patients. Interestingly, MHBs loss accounted for 11.88% (126/1061) isolates from NCBI GenBank, compared with 0.09% (1/1061) and 0.00% (0/1061) for...

The effects of emotional trait factors on simulated flight performance under an acute psychological stress situation

Jing Dai, Hang Wang, Lin Yang, Xinsheng Cao, Chunchen Wang, Zhijun Gao, Wendong Hu & Zhihong Wen
Objective. Pilots are commonly exposed to some sources of emotional and cognitive stressors, especially for flight cadets, which have an important influence on flight safety. The present study aimed to study the relationship between emotional trait factors, emotional state, mental workload and simulated flight performance (SFP) under an acute psychological stress situation. Methods. Fifty-five undergraduates were included in the study. The Wong and Law emotional intelligence scale (WLEIS), state-trait anxiety inventory (STAI), stress rating questionnaire...

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