822 Works

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...

Development of an automatic integrated gene detection system for novel severe acute respiratory syndrome-related coronavirus (SARS-CoV2)

Yuchang Li, Jing Li, Ying Zhang, Lizhong Dai, Lin Li, Juan Liu, Sen Zhang, Xiaoyan Wu, Yi Hu, Chengfeng Qin, Tao Jiang & Xiaoping Kang
In December 2019, Wuhan, China suffered a serious outbreak of a novel coronavirus infectious disease (COVID) caused by novel severe acute respiratory syndrome-related coronavirus (SARS-CoV 2). To quickly identify the pathogen, we designed and screened primer sets, and established a sensitive and specific qRT-PCR assay for SARS-CoV 2; the lower limit of detection (LOD) was 15 (95% CI: 9.8–21) copies per reaction. We combined this qRT-PCR assay with an automatic integration system for nucleic acid...

Burkholderia pseudomallei interferes with host lipid metabolism via NR1D2-mediated PNPLA2/ATGL suppression to block autophagy-dependent inhibition of infection

Mengling Tang, Zhiqiang Hu, Chenglong Rao, Jiangao Chen, Siqi Yuan, Jiangang Zhang, Chan Mao, Jingmin Yan, Yupei Xia, Meijuan Zhang, Juanjuan Yue, Yang Xiang, Jianping Xie, Xuhu Mao & Qian Li
Burkholderia pseudomallei: which causes melioidosis with high mortality in humans, has become a global public health concern. Recently, infection-driven lipid droplet accumulation has been related to the progression of host-pathogen interactions, and its contribution to the pathogenesis of infectious disease has been investigated. Here, we demonstrated that B. pseudomallei infection actively induced a time-dependent increase in the number and size of lipid droplets in human lung epithelial cells and macrophages. We also found that lipid...

Data from: The relationship between substrate morphology and biological performances of nano-silver-loaded dopamine coatings on the titanium surfaces

Weibo Zhang, Shuang Wang, Shaohua Ge, Jialong Chen & Ping Ji
Biomedical device-associated infection(BAI) and lack of osseointegration are the main causes of implant failure. Therefore, it is imperative for implant not only to depress microbial activity and biofilm colonization but also to prompt osteoblast functions and osseointegration. As part of the coating development for implants, the interest of in vitro studies on the interaction between implant substrate morphology and biological performances is growing. In this study, by harnessing the adhesion and reactivity of bioinspired polydopamine,...

Data from: A concise review on antimicrobial peptides for prevention and treatment of dental caries

John Yun Niu, Iris Xiaoxue Yin, William Ka Kei Wu, Quan-Li Li, May Lei Mei & Chun Hung Chu
Antimicrobial peptides have become promising candidates for the development of antimicrobial therapeutics. This paper describes the collection and analysis of data performed for a published concise review on the application of antimicrobial peptides for the management of dental caries. A literature search was performed to locate journal articles published in the English language up to 2019. The search was performed through six common databases. The search term was (Antimicrobial peptide OR AMP OR Cathelicidin OR...

sj-xlsx-2-tam-10.1177_1758835920977117 – Supplemental material for Low intratumor heterogeneity correlates with increased response to PD-1 blockade in renal cell carcinoma

Xia Ran, Jinyuan Xiao, Yi Zhang, Huajing Teng, Fang Cheng, Huiqian Chen, Kaifan Zhang & Zhongsheng Sun
Supplemental material, sj-xlsx-2-tam-10.1177_1758835920977117 for Low intratumor heterogeneity correlates with increased response to PD-1 blockade in renal cell carcinoma by Xia Ran, Jinyuan Xiao, Yi Zhang, Huajing Teng, Fang Cheng, Huiqian Chen, Kaifan Zhang and Zhongsheng Sun in Therapeutic Advances in Medical Oncology

The lipoprotein NlpD in Cronobacter sakazakii responds to acid stress and regulates macrophage resistance and virulence by maintaining membrane integrity

Xuemeng Ji, Ping Lu, Juan Xue, Ning Zhao, Yan Zhang, Lu Dong, Xuejiao Zhang, Ping Li, Yaozhong Hu, Jin Wang, Bowei Zhang, Jingmin Liu, Huan lv & Shuo Wang
Cronobacter sakazakii, an emerging opportunistic pathogen, is implicated in severe foodborne outbreak infections in premature and full-term infants. Generally, acid tolerance is vital for the pathogenesis of foodborne pathogens; however, its role in C. sakazakii virulence remains largely unknown. To screen out acid-tolerance determinants from transposon mutants, anovel counterselection method using gentamicin and acid was developed. Using the counterselection method and growth assay, we screened several acid-sensitive mutants and found that nlpD encodes an acid-resistance...

Alterations of long non-coding RNA and mRNA profiles associated with extracellular matrix homeostasis and vascular aging in rats

Qianqin Li, Zezhou Xiao, Yongsheng Wang, Ximao Liu, Hao Liu, Zhiwen Luo & Shaoyi Zheng
Vascular aging has been closely associated with various cardiovascular disorders; however, its molecular mechanism remains poorly understood. In our study, RNA sequencing was utilized to explore the expression profiles of long non-coding RNAs (lncRNAs) and mRNAs in the thoracic aortas of young (3 weeks) and old (16 weeks) rats. Functional categorization of differentially expressed mRNAs was evaluated using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, and lncRNA–microRNA–mRNA networks was constructed using...

Long non-coding RNA PCAT1 drives clear cell renal cell carcinoma by upregulating YAP via sponging miR-656 and miR-539

Rui Wang, Bin Zheng, Hongyan Liu & Xiuxian Wan
Clear cell renal cell carcinoma (ccRCC) is the most common RCC subtype with high metastasis, poor prognosis and conventional chemotherapy resistance. Prostate cancer associated transcript 1 (PCAT1) is an important lncRNA that was reported to be involved in cell proliferation, migration and invasion of several types of cancer cells. However, its role in ccRCC is still undetermined. This study found that PCAT1 levels were elevated in ccRCC tumors as well as several ccRCC cells, and...

RR3DD: an RNA global structure-based RNA three-dimensional structural classification database

Xu Hong, Jinfang Zheng, Juan Xie, Xiaoxue Tong, Xudong Liu, Qi Song, Sen Liu & Shiyong Liu
The three-dimensional (3D) structure of RNA usually plays an important role in the recognition with RNA-binding protein. Along with the discovering of RNAs, several RNA databases are developed to study the functions of RNA based on sequence, secondary structure, local 3D structural motif and global structure. Based on RNA function and structure, different RNAs are classified and stored in SCOR and DARTS, respectively. The classification of RNA structures is useful in RNA structure prediction and...

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...

Identification of the RP11-21C4.1/SVEP1 gene pair associated with FAT2 mutations as a potential biomarker in gastric cancer

Lingshan Zhou, Yuan Yang, Min Liu, Yuling Gan, Rong Liu, Man Ren, Ya Zheng, Yuping Wang & Yongning Zhou
Gastric cancer (GC) is one of the most common malignancies worldwide. Despite rapid advances in systemic therapy, GC remains the third leading cause of cancer-related deaths. We aimed to identify a novel prognostic signature associated with FAT2 mutations in GC. We analyzed the expression levels of FAT2-mutant and FAT2-wildtype GC samples obtained from The Cancer Genome Atlas (TCGA). The Kaplan–Meier survival curve showed that patients with FAT2 mutations showed better prognosis than those without the...

Derivation and validation of a model to predict acute kidney injury following cardiac surgery in patients with normal renal function

Penghua Hu, Zhiming Mo, Yuanhan Chen, Yanhua Wu, Li Song, Li Zhang, Zhilian Li, Lei Fu, Huaban Liang, Yiming Tao, Shuangxin Liu, Zhiming Ye & Xinling Liang
The study aimed to construct a clinical model based on preoperative data for predicting acute kidney injury (AKI) following cardiac surgery in patients with normal renal function. A total of 22,348 consecutive patients with normal renal function undergoing cardiac surgery were enrolled. Among them, 15,701 were randomly selected for the training group and the remaining for the validation group. To develop a model visualized as a nomogram for predicting AKI, logistic regression was performed with...

Identification of the RP11-21C4.1/SVEP1 gene pair associated with FAT2 mutations as a potential biomarker in gastric cancer

Lingshan Zhou, Yuan Yang, Min Liu, Yuling Gan, Rong Liu, Man Ren, Ya Zheng, Yuping Wang & Yongning Zhou
Gastric cancer (GC) is one of the most common malignancies worldwide. Despite rapid advances in systemic therapy, GC remains the third leading cause of cancer-related deaths. We aimed to identify a novel prognostic signature associated with FAT2 mutations in GC. We analyzed the expression levels of FAT2-mutant and FAT2-wildtype GC samples obtained from The Cancer Genome Atlas (TCGA). The Kaplan–Meier survival curve showed that patients with FAT2 mutations showed better prognosis than those without the...

Cholesterol depletion sensitizes gallbladder cancer to cisplatin by impairing DNA damage response

Yonglong Zhang, Yanfeng Liu, Jinlin Duan, Hui Wang, Yuchen Zhang, Ke Qiao & Jian Wang
Gallbladder cancer (GBC) is the common malignancy of the bile tract system with extremely poor clinical outcomes, owing to its metastatic property and intrinsic resistance to the first-line drugs. Although it is well-established that cholesterol abnormity contributes to gallstone formation, a leading risk factor for GBC, the link of cholesterol homeostasis with GBC has not been investigated. The present study systematically examined the genes implicated in cholesterol homeostasis, and revealed altered gene expressions of de...

Identification of downstream targets and signaling pathways of long non-coding RNA NR_002794 in human trophoblast cells

Yinyao Ma, Hua Wu, Xuxia Liang, Chun Zhang, Yanhua Ma, Yanfen Wei, Jing Li & Hui Chen
Preeclampsia (PE) is a huge threat to pregnant women. Our previous study demonstrated that long non-coding RNA (lncRNA) NR_002794 was highly expressed in placentas of PE patients and could regulate the phenotypes of trophoblast cells. However, the downstream regulatory mechanisms of NR_002794 remain unknown. In this text, some potential downstream targets or signaling pathways of NR_002794 were identified through RNA sequencing (RNA-seq) and bioinformatics analysis in SWAN71 trophoblast cells. Western blot assay demonstrated that NR_002794...

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...

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...

Dominant factors of the phosphorus regulatory network differ under various dietary phosphate loads in healthy individuals

Guoxin Ye, Jiaying Zhang, Zhaori Bi, Weichen Zhang, Minmin Zhang, Qian Zhang, Mengjing Wang & Jing Chen
The purpose of this study was to explore the contribution of each factor of the phosphorus metabolism network following phosphorus diet intervention via Granger causality analysis. In this study, a total of six healthy male volunteers were enrolled. All participants sequentially received regular, low-, and high-phosphorus diets. Consumption of each diet lasted for five days, with a 5-day washout period between different diets. Blood and urinary samples were collected on the fifth day of consumption...

Pyroptosis regulators exert crucial functions in prognosis, progression and immune microenvironment of pancreatic adenocarcinoma: a bioinformatic and in vitro research

Zhenghai Bai, Fangshi Xu, Xiaodan Feng, Yuan Wu, Junhua Lv, Yu Shi & Honghong Pei
Pyroptosis is an inflammatory programmed cell death, showing potentials to be a novel anti-cancer approach. However, the roles of pyroptosis-related (PR) genes (PRGs) in pancreatic adenocarcinoma (PAAD) remain elusive. In the present study, we constructed a novel PR risk signature through the lasso regression analysis. The risk signature was greatly conducive to PAAD prognostic assessment. PR risk score was identified as an independent prognostic factor and could distinguish the prognostic differences of most clinical subgroups....

A defective lysophosphatidic acid-autophagy axis increases miscarriage risk by restricting decidual macrophage residence

Hui-Li Yang, Zhen-Zhen Lai, Jia-Wei Shi, Wen-Jie Zhou, Jie Mei, Jiang-Feng Ye, Tao Zhang, Jian Wang, Jian-Yuan Zhao, Da-Jin Li & Ming-Qing Li
Massive infiltrated and enriched decidual macrophages (dMφ) have been widely regarded as important regulators of maternal-fetal immune tolerance and trophoblast invasion, contributing to normal pregnancy. However, the characteristics of metabolic profile and the underlying mechanism of dMφ residence remain largely unknown. Here, we observe that dMφ display an active glycerophospholipid metabolism. The activation of ENPP2-lysophosphatidic acid (LPA) facilitates the adhesion and retention, and M2 differentiation of dMφ during normal pregnancy. Mechanistically, this process is mediated...

A defective lysophosphatidic acid-autophagy axis increases miscarriage risk by restricting decidual macrophage residence

Hui-Li Yang, Zhen-Zhen Lai, Jia-Wei Shi, Wen-Jie Zhou, Jie Mei, Jiang-Feng Ye, Tao Zhang, Jian Wang, Jian-Yuan Zhao, Da-Jin Li & Ming-Qing Li
Massive infiltrated and enriched decidual macrophages (dMφ) have been widely regarded as important regulators of maternal-fetal immune tolerance and trophoblast invasion, contributing to normal pregnancy. However, the characteristics of metabolic profile and the underlying mechanism of dMφ residence remain largely unknown. Here, we observe that dMφ display an active glycerophospholipid metabolism. The activation of ENPP2-lysophosphatidic acid (LPA) facilitates the adhesion and retention, and M2 differentiation of dMφ during normal pregnancy. Mechanistically, this process is mediated...

Prevalence of major morbidities and outcome of all hospitalized neonates. A retrospective cohort study of Huai’an neonatal survivals

Yaling Xu, Xiaoqin Zhu, Hui Wang, Zhaojun Pan, Xiaoqiong Li, Xiaojing Guo, Hongni Yue & Bo Sun
Reliable data for causal implication of neonatal survival in China are lacking. We assumed that by analyzing surviving data of in-hospital neonatal care based on all livebirths in Huai’an, prevalence of neonatal morbidity, mortality and causal relations may be derived comprehensively. Data of all regionally hospitalized neonates were retrospectively linked with corresponding whole livebirths (59,056) in 2015 as a cohort. Diagnoses of diseases and causes of deaths were redefined and categorized. Disease patterns, prevalence of...

Mechanistic insights into non-coding Y RNA processing

Martina Billmeier, Darrell Green, Adam E. Hall, Carly Turnbull, Archana Singh, Ping Xu, Simon Moxon & Tamas Dalmay
Y RNAs (84–112 nt) are non-coding RNAs transcribed by RNA polymerase III and are characterized by a distinctive secondary structure. Human Y RNAs interact with the autoimmune proteins SSB and RO60 that together form a ribonucleoprotein (RNP) complex termed RoRNP and Y RNAs also perform regulatory roles in DNA and RNA replication and stability, which has major implications for diseases including cancer. During cellular stress and apoptosis, Y RNAs are cleaved into 3’ and 5’...

Selective autophagic degradation of ACLY (ATP citrate lyase) maintains citrate homeostasis and promotes oocyte maturation

Hainan He, Junling Wang, Xingmei Mou, Xin Liu, Qiao Li, Mingyue Zhong, Bingbing Luo, Zhisheng Yu, Jingjing Zhang, Tian Xu, Chengli Dou, Danya Wu, Wei Qing, Linhui Wu, Kai Zhou, Zhengang Fan, Tingting Wang, Taotao Hu, Xia Zhang, Jilong Zhou & Yi-Liang Miao
Macroautophagy/autophagy is a cellular and energy homeostatic mechanism that contributes to maintain the number of primordial follicles, germ cell survival, and anti-ovarian aging. However, it remains unknown whether autophagy in granulosa cells affects oocyte maturation. Here, we show a clear tendency of reduced autophagy level in human granulosa cells from women of advanced maternal age, implying a potential negative correlation between autophagy levels and oocyte quality. We therefore established a co-culture system and show that...

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