578 Works

Integrated metabolomics and 16S rRNA sequencing to investigate the regulation of Chinese yam on antibiotic-induced intestinal dysbiosis in rats

Yaping Sun, Tong Liu, Yanpo Si, Bing Cao, Yanli Zhang, Xiaoke Zheng & Weisheng Feng
Antibiotics have saved hundreds of millions of patient’s lives, but there are also many side effects. This paper mainly studies the regulation of Chinese yam on antibiotic-induced gut dysbiosis in rats. Male Wistar rats were divided into three groups, normal control group, antibiotic group, and Chinese yam group. In the antibiotic group and the yam group, a rat model of intestinal dysfunction was established by intragastric administration of imipenem/cilastatin sodium (antibiotic) for 21 days. The...

PtdIns4P restriction by hydrolase SAC1 decides specific fusion of autophagosomes with lysosomes

Hongjun Zhang, Jiao Zhou, Peng Xiao, Yong Lin, Xin Gong, Shiyan Liu, Qingjia Xu, Minjin Wang, Haiyan Ren, Mengji Lu, Yuan Wang, Jing Zhu, Zhiping Xie, Huihui Li & Kefeng Lu
Biogenesis of autophagosomes is the early step of macroautophagy/autophagy and requires membrane acquisition mainly from ER-Golgi-sourced precursor vesicles. Matured autophagosomes fuse with lysosomes for final degradation. However, how this selective fusion is determined remains elusive. Here, we identified Sac1 by a high throughput screen in Saccharomyces cerevisiae to show it was critical for autophagosome-lysosome fusion through its PtdIns4P phosphatase activity. Sac1 deficiency caused a dramatic increase of PtdIns4P at early Golgi apparatus and abnormal incorporation...

The novel outer membrane protein from OprD/Occ family is associated with hypervirulence of carbapenem resistant Acinetobacter baumannii ST2/KL22

Mingxi Hua, Jingyuan Liu, Pengcheng Du, Xinzhe Liu, Min Li, Huizhu Wang, Chen Chen, Xinmin Xu, Yu Jiang, Yajie Wang, Hui Zeng & Ang Li
Acinetobacter baumannii has become a major healthcare threat that causes nosocomial infections, especially in critically ill patients. The spread of carbapenem-resistant A. baumannii (CRAB) strains has long been a clinical concern. It is important to study the epidemiology and virulence characteristics of different CRAB isolates in order to tailor infection prevention and antibiotic prescribing. In this study, a total of 71 CRAB isolates were collected in the hospital, and clinical characteristics of infections were analyzed....

Oxidative stress and NF-κB signaling are involved in LPS induced pulmonary dysplasia in chick embryos

Yun Long, Guang Wang, Ke Li, Zongyi Zhang, Ping Zhang, Jing Zhang, Xiaotan Zhang, Yongping Bao, Xuesong Yang & Pengcheng Wang
Inflammation or dysbacteriosis-derived lipopolysaccharides (LPS) adversely influence the embryonic development of respiratory system. However, the precise pathological mechanisms still remain to be elucidated. In this study, we demonstrated that LPS exposure caused lung maldevelopment in chick embryos, including higher embryo mortality, increased thickness of alveolar gas exchange zone, and accumulation of PAS+ immature pulmonary cells, accompanied with reduced expression of alveolar epithelial cell markers and lamellar body count. Upon LPS exposure, pulmonary cell proliferation was...

Long non-coding RNA VCAN-AS1 promotes the malignant behaviors of breast cancer by regulating the miR-106a-5p-mediated STAT3/HIF-1α pathway

Peng Du, Kaifeng Luo, Guoyong Li, Jisheng Zhu, Qi Xiao, Yong Li & Xingjian Zhang
An accumulating number of studies have found that long noncoding RNAs (lncRNAs) participate in breast cancer (BC) development. LncRNA VCAN-AS1, a novel lncRNA, has been confirmed to regulate the progression of gastric cancer, while its role in BC is elusive. Here, our results illustrate that VCAN-AS1 is overexpressed in BC tissues and cells, while miR-106a-5p was downregulated and negatively correlated with VCAN-AS1. In addition, high VCAN-AS1 expression and low miR-106a-5p expression were closely correlated with...

Whole-transcriptome analysis of rat cavernosum and identification of circRNA-miRNA-mRNA networks to investigate nerve injury erectile dysfunction pathogenesis

Jie Huang, Jianxiong Ma, Jie Wang, Ke Ma, Kang Zhou, Wenjie Huang, Fan Zhao, Bodong Lv & Qing Hu
There is growing evidence that circular RNAs (circRNAs) play a vital role in many kinds of diseases, including erectile dysfunction (ED). Nevertheless, the role of circRNAs in cavernous nerve-damaging ED (CNI-ED) is unknown. Here, we aimed to discover novel circRNAs, probed their potential role in the CNI-ED, and construct a ceRNA network of circRNAs. Twelve male Sprague Dawley rats were randomly divided into 2 groups by us: bilateral cavernous nerve crush (BCNC) and control groups....

Long non-coding RNA NEAT1 promotes steatosis via enhancement of estrogen receptor alpha-mediated AQP7 expression in HepG2 cells

Xiaohua Fu, Jing Zhu, Lin Zhang & Jing Shu
Hepatic steatosis is one of the most important features of the pathogenesis for non-alcoholic fatty liver disease. Fat deposition in liver cells can influence hepatic lipogenesis along with other metabolic pathways and further lead to the irreversible liver cirrhosis and injury. However, the underlying mechanism of steatosis remains largely unexplored. Our previous study revealed that AQP7 played an important role in liver steatosis. In this study, we determined that the transcriptional level of AQP7 was...

Long non-coding RNA NEAT1 promotes steatosis via enhancement of estrogen receptor alpha-mediated AQP7 expression in HepG2 cells

Xiaohua Fu, Jing Zhu, Lin Zhang & Jing Shu
Hepatic steatosis is one of the most important features of the pathogenesis for non-alcoholic fatty liver disease. Fat deposition in liver cells can influence hepatic lipogenesis along with other metabolic pathways and further lead to the irreversible liver cirrhosis and injury. However, the underlying mechanism of steatosis remains largely unexplored. Our previous study revealed that AQP7 played an important role in liver steatosis. In this study, we determined that the transcriptional level of AQP7 was...

Using BART to Perform Pareto Optimization and Quantify its Uncertainties

Akira Horiguchi, Thomas J. Santner, Ying Sun & Matthew T. Pratola
Techniques to reduce the energy burden of an industrial ecosystem often require solving a multiobjective optimization problem. However, collecting experimental data can often be either expensive or time-consuming. In such cases, statistical methods can be helpful. This article proposes Pareto Front (PF) and Pareto Set (PS) estimation methods using Bayesian Additive Regression Trees (BART), which is a nonparametric model whose assumptions are typically less restrictive than popular alternatives, such as Gaussian Processes (GPs). These less...

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...

m6A RNA methylation regulators were associated with the malignancy and prognosis of ovarian cancer

Cheng Zhang, JinHui Liu, Hongyu Guo, Dandan Hong, Jing Ji, Qin Zhang, Qun Guan & Qingling Ren
N6-methyladenosine (m6A) RNA methylation regulators play a regulatory role in tumor pathogenesis and development. However, the role of m6A regulator genes in ovarian cancer (OC) has not been fully elucidated. This study aims to investigate the mRNA expressions, clinicopathological features, and prognostic values of m6A regulators in OC. Here, we demonstrate that the 17 m6A RNA methylation regulators are differentially expressed in ovarian cancer and normal tissues. By using consensus clustering, all ovarian cancer patients...

Three periods of gold mineralization in the Liaodong Peninsula, North China Craton

Peng Zhang, Linlin Kou & Yang Zhao
The Liaodong gold province includes voluminous gold deposits, which occur in an Archean gneiss complex, Paleoproterozoic metamorphic rocks, and Mesozoic granite. However, the ore-forming age, the genesis, and the geodynamic setting of the gold deposits are not well constrained. In this study, we have summarized previous geochronology data, H-O-S-Pb isotopes, and He-Ar isotopic compositions of the gold deposits. Based on geochronology data, the gold mineralization was divided into Late Triassic, Early Jurassic, and Early Cretaceous....

MYB proto-oncogene like 2 promotes hepatocellular carcinoma growth and glycolysis via binding to the Optic atrophy 3 promoter and activating its expression

Miao Liu, Qiang Du, Gang Mao, Ning Dai & Fan Zhang
Optic atrophy 3 (OPA3) is an integral protein of the mitochondrial outer membrane. The current study explored the expression of OPA3 in hepatocellular carcinoma (HCC), its association with the prognosis and its involvement in HCC cell proliferation and aerobic glycolysis. In addition, the transcription factors that activate its expression were screened and validated. Gene expression data in normal liver and liver cancer were acquired from the Genotype-Tissue Expression Project (GTEx) and The Cancer Genome Atlas...

MYB proto-oncogene like 2 promotes hepatocellular carcinoma growth and glycolysis via binding to the Optic atrophy 3 promoter and activating its expression

Miao Liu, Qiang Du, Gang Mao, Ning Dai & Fan Zhang
Optic atrophy 3 (OPA3) is an integral protein of the mitochondrial outer membrane. The current study explored the expression of OPA3 in hepatocellular carcinoma (HCC), its association with the prognosis and its involvement in HCC cell proliferation and aerobic glycolysis. In addition, the transcription factors that activate its expression were screened and validated. Gene expression data in normal liver and liver cancer were acquired from the Genotype-Tissue Expression Project (GTEx) and The Cancer Genome Atlas...

Genome-wide analysis of the GRF gene family and their expression profiling in peach (Prunus persica)

Li Liu, Xiu-jie Li, Bo Li, Ming-yue Sun & Shao-xuan Li
Growth-regulating factors (GRFs) are plant-specific transcription factors with vital roles in multiple biological processes. Although GRFs have been identified in various plant species, a comprehensive analysis of GRF genes in peach (Prunus persica) has not yet been reported. In this study, 10 PpGRF genes distributed on 6 chromosomes were identified in peach genome and their properties were analyzed systematically. Expression pattern analysis suggested that most PpGRFs were preferentially expressed in young tissues. Multiple types of...

Genome-wide analysis of the GRF gene family their expression profiling in peach (Prunus persica)

Li Liu, Xiu-jie Li, Bo Li, Ming-yue Sun & Shao-xuan Li
Growth-regulating factors (GRFs) are plant-specific transcription factors with vital roles in multiple biological processes. Although GRFs have been identified in various plant species, a comprehensive analysis of GRF genes in peach (Prunus persica) has not yet been reported. In this study, 10 PpGRF genes distributed on 6 chromosomes were identified in peach genome and their properties were analyzed systematically. Expression pattern analysis suggested that most PpGRFs were preferentially expressed in young tissues. Multiple types of...

Cytochrome P450s in plant terpenoid biosynthesis: discovery, characterization and metabolic engineering

Yifeng Zhang, Lin Ma, Ping Su, Luqi Huang & Wei Gao
As the largest family of natural products, terpenoids play valuable roles in medicine, agriculture, cosmetics and food. However, the traditional methods that rely on direct extraction from the original plants not only produce low yields, but also result in waste of resources, and are not applicable at all to endangered species. Modern heterologous biosynthesis is considered a promising, efficient, and sustainable production method, but it relies on the premise of a complete analysis of the...

Gene mining to discover pumpkin response genes to gummy stem blight infection caused by Stagonosporopsis cucurbitacearum

Qian Zhao, Zhenping Gong, Shukun Jiang, Zhugang Li, Liyan Zhang, Lizhi Wang, Xianli Yang, Mingxian Li, Zhongjie Li, Liyong Chi, Rui Li, Chao Yan, Yongcai Lai & Jianzhong Wu
Pumpkin is one of the region’s main cashcrops in northeast China cultivated for its edible seed and sarcocarp. Gummy stem blight (GSB), caused by the main pathogenic fungus of Stagonosporopsis cucurbitacearum (Sc.) which was identified in our previous study, has hampered pumpkin industry development with the affection of its reduced biological yield and edible quality. To clear the plant immune response mechanisms against Sc. infection, RNA-seq technology was employed to sequence pumpkin leaf transcriptome, the...

Comprehensive bioinformatics analysis reveals the hub genes and pathways associated with multiple myeloma

Shengli Zhao, Xiaoyi Mo, Zhenxing Wen, Lijuan Ren, Zhipeng Chen, Wei Lin, Qi Wang, Shaoxiong Min & Bailing Chen
While the prognosis of multiple myeloma (MM) has significantly improved over the last decade because of new treatment options, it remains incurable. Aetiological explanations and biological targets based on genomics may provide additional help for rational disease intervention. Three microarray datasets associated with MM were downloaded from the Gene Expression Omnibus (GEO) database. GSE125364 and GSE39754 were used as the training set, and GSE13591 was used as the verification set. The differentially expressed genes (DEGs)...

Autophagy Loss Impedes Cancer-Associated Fibroblast Activation via Downregulating Proline Biosynthesis

Jingru Bai, Tong Liu, Bo Tu, Meng Yuan, Zhaoqi Shu, Minghe Fan, Sihan Huo, Yuyao Guo, Lina Wang, Hua Wang & Ying Zhao
Cancer-associated fibroblasts (CAFs) are considered one of the most critical stromal cells that interact with pancreatic ductal adenocarcinoma (PDAC) and promote tumor growth, metastasis, and treatment resistance. Previous studies illustrated macroautophagy/autophagy contributes to CAF activation during tumor progression. Here in our study, we found that autophagy deficiency in CAFs impedes CAF activation by inhibiting proline biosynthesis and collagen production. Furthermore, we uncovered that autophagy promotes proline biosynthesis through mitophagy-mediated regulation of NADK2 (NAD kinase 2,...

Identification of the metabolic remodeling profile in the early-stage of myocardial ischemia and the contributory role of mitochondrion

Jun He, Qian Liu, Jie Wang, Fangjing Xu, Yucheng Fan, Ruhua He, Ru Yan & Li Zhu
Cardiac remodeling is the primary pathological feature of chronic heart failure. Prompt inhibition of remodeling in acute coronary syndrome has been a standard procedure, but the morbidity and mortality are still high. Exploring the characteristics of ischemia in much earlier stages and identifying its biomarkers are essential for introducing novel mechanisms and therapeutic strategies. Metabolic and structural remodeling of mitochondrion is identified to play key roles in ischemic heart disease. The mitochondrial metabolic features in...

A critical review of uranium in the soil-plant system: Distribution, bioavailability, toxicity, and bioremediation strategies

Qingliang Cui, Zhiqin Zhang, Jingzi Beiyuan, Yongxing Cui, Li Chen, Hansong Chen & Linchuan Fang
Increasing uranium (U) content in soils due to anthropogenic U contamination causes accumulation of U in plants, which greatly increases human health risks. This review identified the diverse sources of soil U contamination and their significant spatial variations in surface soils globally based on 789 soil sampling sites collected from 76 studies. The relationships between U biogeochemical transformation and its bioavailability in soil are significantly affected by soil redox potential, pH, metal (hydr)oxides, organic matter,...

LINC00857 regulated by ZNF460 enhances the expression of CLDN12 by sponging miR-150-5p and recruiting SRSF1 for alternative splicing to promote epithelial-mesenchymal transformation of pancreatic adenocarcinoma cells

Yong Zhang, Yuan Fang, Lijie Ma, Jing Xu, Chentao Lv, Li Deng & Guanghui Zhu
Recent research unveiled that LINC00857 plays a regulatory role in multiple human cancers, such as lung adenocarcinoma and gastric cancer. Nevertheless, the function of LINC00857 in pancreatic adenocarcinoma (PAAD) remains unclear. This study concentrates on LINC00857 to discuss the relevant molecular mechanism of this gene in PAAD. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) and western blot were implemented for measuring the expressions of RNAs and proteins. Wound healing and Transwell assays were used to...

Proteotoxic stress disrupts epithelial integrity by inducing MTOR sequestration and autophagy overactivation

Xiaoxiang Cheng, Pei Zhang, Hongyu Zhao, Hui Zheng, Kai Zheng, Hong Zhang & Hongjie Zhang
Macroautophagy/autophagy, an evolutionarily conserved degradation system, serves to clear intracellular components through the lysosomal pathway. Mounting evidence has revealed cytoprotective roles of autophagy; however, the intracellular causes of overactivated autophagy, which has cytotoxic effects, remain elusive. Here we show that sustained proteotoxic stress induced by loss of the RING and Kelch repeat-containing protein C53A5.6/RIKE-1 induces sequestration of LET-363/MTOR complex and overactivation of autophagy, and consequently impairs epithelial integrity in C. elegans. In C53A5.6/RIKE-1-deficient animals, blocking...

Genetic and pathogenic variation of Botrytis cinerea, the causal agent of grey mould on Panax ginseng in China

Rong Wang, Kun Liu, Bingwei Chen, Wanlong Ding & Yong Li
Grey mould, caused by Botrytis cinerea, is an increasingly destructive disease of ginseng (Panax ginseng) in China. However, the extent of variation in the morphological characteristics of fungal colonies, genetic background and pathogenicity of different strains of this pathogen remains unknown. In this study, we isolated and identified 102 isolates of B. cinerea from ginseng. Among these, the sclerotial phenotype was dominant, followed by the mycelial and conidial phenotypes, with the proportion of each phenotype...

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