241 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...

Brucella melitensis, a latent “travel bacterium,” continual spread and expansion from Northern to Southern China and its relationship to worldwide lineages

Xiong Zhu, Zhongzhi Zhao, Shuyi Ma, Zhiwei Guo, Miao Wang, Zhenjun Li & Zhiguo Liu
Brucellosis caused by Brucella melitensis is considered to be one of the most important zoonotic diseases in China. In this study, Conventional bio-typing, MLVA (multiple locus variable-number tandem repeat analysis), and WGS (whole-genome sequencing)-SNP (single nucleotide polymorphism) were used to study the genetic similarity of B. melitensis in northern and southern China and analyze its relationship with worldwide lineages. Currently, the distribution of species/biovars of B. melitensis has obviously changed, and B. melitensis has become...

Discovery of a subgenotype of human coronavirus NL63 associated with severe lower respiratory tract infection in China, 2018

Yanqun Wang, Xin Li, Wenkuan Liu, Mian Gan, Lu Zhang, Jin Wang, Zhaoyong Zhang, Airu Zhu, Fang Li, Jing Sun, Guoxian Zhang, Zhen Zhuang, Jiaying Luo, Dehui Chen, Shuyan Qiu, Li Zhang, Duo Xu, Chris Ka Pun Mok, Fuchun Zhang, Jingxian Zhao, Rong Zhou & Jincun Zhao
Human coronavirus NL63 (HCoV-NL63) is primarily associated with common cold in children, elderly and immunocompromised individuals. Outbreaks caused by HCoV-NL63 are rare. Here we report a cluster of HCoV-NL63 cases with severe lower respiratory tract infection that arose in Guangzhou, China, in 2018. Twenty-three hospitalized children were confirmed to be HCoV-NL63 positive, and most of whom were hospitalized with severe pneumonia or acute bronchitis. Whole genomes of HCoV-NL63 were obtained using next-generation sequencing. Phylogenetic and...

Prognostic and immunological significance of metastasis associated lung adenocarcinoma transcript 1 among different kinds of cancers

Lili Guo, Xiuwen Zhang, Hongli Pan, Yang Li, Jing Wang, Lin Li, Yafang Dong, Xinxin Du, Jun Chen & Fengjie Guo
LncRNAs belong to the type of noncoding RNA transcripts, which exceed 200 nucleotides in size. MALAT1 as one of the earlier identified lncRNAs in cancer is investigated by more and more scientific researchers. Expression, clinical significance and function of MALAT1 in pan-cancer exist as big difference. To detect the expression and clinical significance of MALAT1 gene precisely and comprehensively among different kinds of cancers, some classical databases such as GEPIA, TIMER, KM Plotter, and PrognoScan...

Discovery of a subgenotype of human coronavirus NL63 associated with severe lower respiratory tract infection in China, 2018

Yanqun Wang, Xin Li, Wenkuan Liu, Mian Gan, Lu Zhang, Jin Wang, Zhaoyong Zhang, Airu Zhu, Fang Li, Jing Sun, Guoxian Zhang, Zhen Zhuang, Jiaying Luo, Dehui Chen, Shuyan Qiu, Li Zhang, Duo Xu, Chris Ka Pun Mok, Fuchun Zhang, Jingxian Zhao, Rong Zhou & Jincun Zhao
Human coronavirus NL63 (HCoV-NL63) is primarily associated with common cold in children, elderly and immunocompromised individuals. Outbreaks caused by HCoV-NL63 are rare. Here we report a cluster of HCoV-NL63 cases with severe lower respiratory tract infection that arose in Guangzhou, China, in 2018. Twenty-three hospitalized children were confirmed to be HCoV-NL63 positive, and most of whom were hospitalized with severe pneumonia or acute bronchitis. Whole genomes of HCoV-NL63 were obtained using next-generation sequencing. Phylogenetic and...

Glycolysis related gene expression signature in predicting prognosis of laryngeal squamous cell carcinoma

Hui-Ching Lau, Yujie Shen, Qiang Huang, Hui-Ying Huang & Liang Zhou
Researches have suggested that aerobic glycolysis can reflect the development and progression of most carcinomas. We aimed to investigate whether glycolysis-related genes (GRGs) are associated with overall survival in laryngeal squamous cell carcinoma (LSCC). Here, we identified differentially expressed GRGs in TCGA dataset and microarray sample of GSE27020 from GEO database. A set of two glycolytic gene signatures, including DDIT4 and PLOD2 was screened through Cox and Lasso regression. The risk score was calculated using...

Difficulties translating antisense-mediated activation of Frataxin expression from cell culture to mice

Audrius Kilikevicius, Jun Wang, Xiulong Shen, Frank Rigo, Thahza P. Prakash, Marek Napierala & David R. Corey
Friedreich’s ataxia (FA) is an inherited neurodegenerative disorder caused by decreased expression of frataxin (FXN) protein. Previous studies have shown that antisense oligonucleotides (ASOs) and single-stranded silencing RNAs can be used to increase expression of frataxin in cultured patient-derived cells. In this study, we investigate the potential for oligonucleotides to increase frataxin expression in a mouse model for FA. After confirming successful in vivo delivery of oligonucleotides using a benchmark gapmer targeting the nuclear noncoding...

miR-199a-3p plays an anti-tumorigenic role in lung adenocarcinoma by suppressing anterior gradient 2

Hui Liu, Yanfeng Wang, Yi Wang, Daoyuan Wu & He Zhang
Previous studies have explored the association between protein-coding genes and microRNAs (miRNAs) in lung adenocarcinoma (LUAD). However, the influence of the miR-199a-3p/anterior gradient 2 (AGR2) axis in LUAD has not yet been fully explored. Therefore, this study aimed to examine the underlying roles of AGR2 and miR-199a-3p in the development of LUAD. The expression levels of miR-199a-3p and AGR2 in LUAD tissues and cells were detected via quantitative reverse transcription-polymerase chain reaction (qRT-PCR). A luciferase...

Impact of hepatocyte-specific deletion of staphylococcal nuclease and tudor domain containing 1 (SND1) on liver insulin resistance and acute liver failure of mice

Chunyan Zhao, Xiaoteng Cui, Yan Zhao, Baoxin Qian, Nan Zhang, Lingbiao Xin, Chuanbo Ha, Jie Yang, Xinting Wang & Xingjie Gao
Although our previous research shows an ameliorated high-fat diet (HFD)-induced hepatic steatosis and insulin resistance in global SND1 transgenic mice, the involvement of SND1 loss-of-function in hepatic metabolism remains elusive. Herein, we aim to explore the potential impact of hepatocyte-specific SND1 deletion on insulin-resistant mice. As SND1 is reported to be linked to inflammatory response, the pathobiological feature of acute liver failure (ALF) is also investigated. Hence, we construct the conditional liver knockout (LKO) mice...

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,...

Additional file 6 of Transcriptional regulation mechanism of wheat varieties with different nitrogen use efficiencies in response to nitrogen deficiency stress

Hanxia Wang, Qiaoyun Ma, Fuhua Shan, Liping Tian, Jie Gong, Wei Quan, Weibing Yang, Qiling Hou, Fengting Zhang & Shengquan Zhang
Additional file 6.

Additional file 1 of Analysis of risk factors related to extremely and very preterm birth: a retrospective study

Xiaohong Ji, Chengqian Wu, Min Chen, Lili Wu, Ting Li, Zhijing Miao, Yan Lv & Hongjuan Ding
Supplementary Material 1

sj-rar-3-tej-10.1177_20417314221132093 – Supplemental material for A new cell-free therapeutic strategy for liver regeneration: Human placental mesenchymal stem cell-derived extracellular vesicles

Ting Li, Yu Fu, Zeyi Guo, Honglei Zhu, Hangyu Liao, Xiaoge Niu, Lin Zhou, Shunjun Fu, Yang Li, Shao Li, Lujia Wang, Yizhou Zheng, Lei Feng, Yi Gao & Guolin He
Supplemental material, sj-rar-3-tej-10.1177_20417314221132093 for A new cell-free therapeutic strategy for liver regeneration: Human placental mesenchymal stem cell-derived extracellular vesicles by Ting Li, Yu Fu, Zeyi Guo, Honglei Zhu, Hangyu Liao, Xiaoge Niu, Lin Zhou, Shunjun Fu, Yang Li, Shao Li, Lujia Wang, Yizhou Zheng, Lei Feng, Yi Gao and Guolin He in Journal of Tissue Engineering

Additional file 2 of Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses

Nadeem Shaikh, Alice Mazzagatti, Simone De Angelis, Sarah C. Johnson, Bjorn Bakker, Diana C. J. Spierings, René Wardenaar, Eleni Maniati, Jun Wang, Michael A. Boemo, Floris Foijer & Sarah E. McClelland
Additional file 2. Contains CNAs for RPE1 after treatment with DMSO, Aphidicolin or siRNA.

Additional file 3 of Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses

Nadeem Shaikh, Alice Mazzagatti, Simone De Angelis, Sarah C. Johnson, Bjorn Bakker, Diana C. J. Spierings, René Wardenaar, Eleni Maniati, Jun Wang, Michael A. Boemo, Floris Foijer & Sarah E. McClelland
Additional file 3. Replication Timing factor derived from RPE1 single cells after treatment with DMSO or aphidicolin.

Additional file 2 of CASA: a comprehensive database resource for the COVID-19 Alternative Splicing Atlas

Yaxin Chen, Gang Wang, Jingyi Li, Lei Xia, Lin Zhu, Wenxing Li, Qiang Luo, Yinlu Liao, Yao Lin, Liyun Bi, Hubin Chen, Jiemei Chu, Yueqi Li, Jinming Su, Li Ye, Jun-jun Jiang, Hao Liang, Weimin Li & Sanqi An
Additional file 2: Table S2. Summary of alternative splicing records in CASA.

Additional file 4 of Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses

Nadeem Shaikh, Alice Mazzagatti, Simone De Angelis, Sarah C. Johnson, Bjorn Bakker, Diana C. J. Spierings, René Wardenaar, Eleni Maniati, Jun Wang, Michael A. Boemo, Floris Foijer & Sarah E. McClelland
Additional file 4. RNAseq data for BJ and RPE1 cells treated with DMSO or aphidicolin.

Additional file 6 of Transcriptional regulation mechanism of wheat varieties with different nitrogen use efficiencies in response to nitrogen deficiency stress

Hanxia Wang, Qiaoyun Ma, Fuhua Shan, Liping Tian, Jie Gong, Wei Quan, Weibing Yang, Qiling Hou, Fengting Zhang & Shengquan Zhang
Additional file 6.

Additional file 7 of Transcriptional regulation mechanism of wheat varieties with different nitrogen use efficiencies in response to nitrogen deficiency stress

Hanxia Wang, Qiaoyun Ma, Fuhua Shan, Liping Tian, Jie Gong, Wei Quan, Weibing Yang, Qiling Hou, Fengting Zhang & Shengquan Zhang
Additional file 7.

Additional file 8 of Transcriptional regulation mechanism of wheat varieties with different nitrogen use efficiencies in response to nitrogen deficiency stress

Hanxia Wang, Qiaoyun Ma, Fuhua Shan, Liping Tian, Jie Gong, Wei Quan, Weibing Yang, Qiling Hou, Fengting Zhang & Shengquan Zhang
Additional file 8.

Additional file 8 of Transcriptional regulation mechanism of wheat varieties with different nitrogen use efficiencies in response to nitrogen deficiency stress

Hanxia Wang, Qiaoyun Ma, Fuhua Shan, Liping Tian, Jie Gong, Wei Quan, Weibing Yang, Qiling Hou, Fengting Zhang & Shengquan Zhang
Additional file 8.

Additional file 6 of Identification of SSBP1 as a ferroptosis-related biomarker of glioblastoma based on a novel mitochondria-related gene risk model and in vitro experiments

Jun Su, Yue Li, Qing Liu, Gang Peng, Chaoying Qin & Yang Li
Additional file 6: Table S1. The mitochondria-related genes extracted from the uniprot database.

Additional file 9 of Identification of SSBP1 as a ferroptosis-related biomarker of glioblastoma based on a novel mitochondria-related gene risk model and in vitro experiments

Jun Su, Yue Li, Qing Liu, Gang Peng, Chaoying Qin & Yang Li
Additional file 9: Table S4. The 21 prognositc DE-MRGs based on the TCGA GBM cohort.

Protective effects of psoralen polymer lipid nanoparticles on doxorubicin - induced myocardial toxicity

Fansu Meng, Yong Ouyang, Qianqian Ma, Manling Du, Hui Liu, Yong Zhuang, Mujuan Pang, Tiange Cai & Yu Cai
Abstract Doxorubicin (DOX) induced myocardial toxicity may limit its therapeutic use in clinic. Psoralen (PSO), a major active tricyclic furocoumarin extracted from Psoralea corylifolia, is widely used as an antineoplastic agent in treatment of leukemia and other cancers. This study is aim to find the protective effect of psoralen polymer lipid nanoparticles (PSO-PLN) on doxorubicin-induced myocardial toxicity in mice. The model of myocardial toxicity induced by DOX was established. The experiment was divided into 6...

Integrating network pharmacology and experimental validation to decipher the mechanism of the Chinese herbal prescription JieZe-1 in protecting against HSV-2 infection

Tong Liu, Qingqing Shao, Wenjia Wang, Yonggui Ma, Tianli Liu, Ximing Jin, Jianguo Fang, Guangying Huang & Zhuo Chen
The Chinese herbal prescription JieZe-1 (JZ-1) is effective against HSV-2 (Herpes simplex virus type 2) infection. However, its mechanism remains unclear. To explore the mechanism of JZ-1 in protecting against HSV-2 infection. Using the methods of network pharmacology, the hub components and targets were screened and functionally enriched. We established a genital herpes (GH) mouse model and observe the disease characteristics. Then, the GH mice in different groups (10 per/group) were treated with 20 μL...

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