647 Works

Data from: The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

Alvaro Martinez Barrio, Sangeet Lamichhaney, Guangyi Fan, Nima Rafati, Mats Pettersson, He Zhang, Jacques Dainat, Diana Ekman, Marc Höppner, Patric Jern, Marcel Martin, Björn Nystedt, Xin Liu, Wenbin Chen, Xinming Liang, Chengcheng Shi, Yuanyuan Fu, Kailong Ma, Xiao Zhan, Chungang Feng, Ulla Gustafson, Carl-Johan Rubin, Markus Sällman Almén, Martina Blass, Michele Casini … & Leif Andersson
Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of...

The type I-E CRISPR-Cas system influences the acquisition of blaKPC-IncF plasmid in Klebsiella pneumonia

Ying Zhou, Yu Tang, Pan Fu, Dongxing Tian, Lianhua Yu, Yunkun Huang, Gang Li, Meng Li, Yong Wang, Zehua Yang, Xiaogang Xu, Zhe Yin, Dongsheng Zhou, Laurent Poirel & Xiaofei Jiang
Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-KP) have disseminated worldwide and emerged as major threats to public health. Of epidemiological significance, the international pandemic of KPC-KP is primarily associated with CG258 isolates and blaKPC-IncF plasmids. CRISPR-Cas system is an adaptive immune system that can hinder gene expansion driven by horizontal gene transfer. Because of blaKPC-IncF plasmids are favored by CG258 K. pneumoniae, it was of interest to examine the co-distribution of CRISPR and blaKPC-IncF plasmids...

β-Sitosterol-loaded solid lipid nanoparticles ameliorate complete Freund’s adjuvant-induced arthritis in rats: involvement of NF-кB and HO-1/Nrf-2 pathway

Feng Zhang, Zhiyu Liu, Xijing He, Zhanqi Li, Bin Shi & Fengmei Cai
Rheumatoid arthritis (RA), autoimmune disease that is categorized via chronic inflammation manifestation, obesity, cardiovascular risk and even enhanced the mortality and affect the 0.3 and 1% of population worldwide. The current experimental study was scrutinize the anti-arthritic effect of β-sitosterol loaded solid lipid nanoparticles (SLN) against complete Fruend adjuvant (CFA)-induced arthritis via dual pathway. Double emulsion solvent displacement method was used for the preparation of β-sitosterol solid lipid nanoparticles (SLN). CFA was used to induce...

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...

Identification of novel tetracycline resistance gene tet(X14) and its co-occurrence with tet(X2) in a tigecycline-resistant and colistin-resistant Empedobacter stercoris

Yingying Cheng, Yong Chen, Yang Liu, Yuqi Guo, Yanzi Zhou, Tingting Xiao, Shuntian Zhang, Hao Xu, Yunbo Chen, Tongling Shan, Yonghong Xiao & Kai Zhou
Tigecycline is one of the last-resort antibiotics to treat severe infections. Recently, tigecycline resistance has sporadically emerged with an increasing trend, and Tet(X) family represents a new resistance mechanism of tigecycline. In this study, a novel chromosome-encoded tigecycline resistance gene, tet(X14), was identified in a tigecycline-resistant and colistin-resistant Empedobacter stercoris strain ES183 recovered from a pig fecal sample in China. Tet(X14) shows 67.14-96.39% sequence identity to the other variants [Tet(X) to Tet(X13)]. Overexpression of Tet(X14)...

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....

Genome-wide identification and functional prediction of circular RNAs in response to heat stress in Chinese Holstein cows

Ying Qi, Lin Zhang, Yuemei Guo, Jing Wang, Mingxing Chu, Yiming Zhang, Junfei Guo & Qiuling Li
Heat stress (HS) leads to substantial economic loss of dairy industry each year. The negative effect of HS in dairy cows is becoming one of the more urgent issue due to accelerating side-effects of global warming. Various genes are involved in HS response but the information about the role of noncoding RNAs, especially circular RNAs (circRNAs) is largely unknown. In our study, we aimed to investigate the different expression profile of circRNAs between HS and...

Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

Rongsui Gao, Wenhong Zu, Yang Liu, Junhua Li, Zeyao Li, Yanling Wen, Haiyan Wang, Jing Yuan, Lin Cheng, Shengyuan Zhang, Yu Zhang, Shuye Zhang, Weilong Liu, Xun Lan, Lei Liu, Feng Li & Zheng Zhang
New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies’...

MiR-30a-5p frequently downregulated in prostate cancer inhibits cell proliferation via targeting PCLAF

Hu Zhao, Xiaofeng Lai, Wei Zhang, Hehuan Zhu, Shenhang Zhang, Weizhen Wu, Shuiliang Wang, Minying Tang, Zhen Deng & Jianming Tan
MicroRNAs (miRNAs) have vastly expanded our view of RNA world in intracellular signal regulating networks. Here, we functionally characterized a normally highly expressed miRNA, miR-30a-5p (MIMAT0000087), which exhibits downregulated expression profiles in prostate cancer samples. MiR-30a-5p knockdown and overexpression in PC-3 cell line alters cell proliferation supporting a tumour suppressor role. We also discovered that PCLAF is the direct target of miR-30a-5p. Notably, PC-3 cell proliferation is inhibited by miR-30a-5p/PCLAF axis. miR-30a-5p represents a novel...

A novel ferroptosis-related gene signature for predicting outcomes in cervical cancer

Xingling Qi, Yipeng Fu, Jia Sheng, Meng Zhang, Mingxing Zhang, Yumeng Wang & Guiling Li
Ferroptosis, a newly discovered iron-dependent form of cell death, contributes to various pathologies; however, the prognostic value of ferroptosis-related genes (FRGs) in cervical cancer (CC) remains unclear. Herein, we identified 15 differentially expressed FRGs based on data from The Cancer Genome Atlas database. Ten FRGs that correlated with prognosis were screened by univariate Cox regression analysis. The least absolute shrinkage and selection operator regression model was performed to develop a novel prognostic signature. A four-gene...

Identification of significant genes and therapeutic agents for breast cancer by integrated genomics

Xiao Sun, Zhenzhen Luo, Liuyun Gong, Xinyue Tan, Jie Chen, Xin Liang & Mengjiao Cai
Breast cancer is the most commonly diagnosed malignancy in women; thus, more cancer prevention research is urgently needed. The aim of this study was to predict potential therapeutic agents for breast cancer and determine their molecular mechanisms using integrated bioinformatics. Summary data from a large genome-wide association study of breast cancer was derived from the UK Biobank. The gene expression profile of breast cancer was from the Oncomine database. We performed a network-wide association study...

Long non-coding RNA RP11-283G6.5 confines breast cancer development through modulating miR-188-3p/TMED3/Wnt/β-catenin signaling

Jing Pei, Shengquan Zhang, Xiaowei Yang, Chunguang Han, Yubo Pan, Jun Li, Zhaorui Wang, Chenyu Sun & Jing Zhang
The contributions of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) to breast cancer are critical areas of investigation. In this study, we identified a novel lncRNA RP11-283G6.5 which was lowly expressed in breast cancer and whose low expression was correlated with poor overall survival and disease-free survival of breast cancer patients. Functional experiments revealed that ectopic expression of RP11-283G6.5 confined breast cancer cellular growth, migration, and invasion, and promoted cellular apoptosis. Conversely, RP11-283G6.5 silencing facilitated...

Fat mass and obesity-associated protein (FTO) mediates signal transducer and activator of transcription 3 (STAT3)-drived resistance of breast cancer to doxorubicin

Yan Wang, Zhiqiang Cheng, Jing Xu, Meina Lai, Liming Liu, Min Zuo & Lin Dang
Excessive activation of signal transducer and activator of transcription 3 (STAT3) is implicated in breast cancer (BC) chemoresistance, but its underlying mechanism is not fully understood. There are STAT3 binding sites in fat mass and obesity-associated protein (FTO) promoter region, thus STAT3 may regulate the transcription of FTO. This study aimed to investigate the correlation between FTO and STAT3 in BC chemoresistance. Herein, FTO and STAT3 were highly expressed in doxorubicin-resistant BC (BC-DoxR) cells. CHIP...

Can warnings curb the spread of fake news? The interplay between warning, trust and confirmation bias

Kholekile L. Gwebu, Jing Wang & Ermira Zifla
Despite attempts by social media companies to curb the spread of fake news with warnings flagging news credibility, the effectiveness of such measures remains unclear. Through the lens of the cognitive dissonance theory and individuals’ trust in the news, this study develops a theoretical model that explains why and how warnings affect an individual’s intention to share fake news. The study empirically assesses the predicted relationships using experimental survey data from 382 individuals. The findings...

Can warnings curb the spread of fake news? The interplay between warning, trust and confirmation bias

Kholekile L. Gwebu, Jing Wang & Ermira Zifla
Despite attempts by social media companies to curb the spread of fake news with warnings flagging news credibility, the effectiveness of such measures remains unclear. Through the lens of the cognitive dissonance theory and individuals’ trust in the news, this study develops a theoretical model that explains why and how warnings affect an individual’s intention to share fake news. The study empirically assesses the predicted relationships using experimental survey data from 382 individuals. The findings...

An infectious clone of enterovirus 71(EV71) that is capable of infecting neonatal immune competent mice without adaptive mutations

Huiying Zhang, Zhigang Song, Jingyi Zou, Yanling Feng, Jing Zhang, Lehao Ren, Xiaonan Zhang, Yunwen Hu, Zhenghong Yuan & Zhigang Yi
Enterovirus 71 (EV71) is a major pathogen that causes hand, foot and mouth disease (HFMD), which is a life threatening disease in certain children. The pathogenesis of EV71-caused HFMD is poorly defined due to the lack of simple and robust animal models with severe phenotypes that recapitulate symptoms observed in humans. Here, we generated the infectious clone of a clinical isolate from a severe HFMD patient. Virus rescued from the cDNA clone was infectious in...

A novel fusion circular RNA F-circBA1 derived from the BCR-ABL fusion gene displayed an oncogenic role in chronic myeloid leukemia cells

Yuan Tan, Zhenglan Huang, Xin Wang, Hongdan Dai, Guoyun Jiang & Wenli Feng
The BCR-ABL fusion gene plays a crucial role in the leukemogenesis of chronic myeloid leukemia (CML). The BCR-ABL oncoprotein encoded by this fusion gene has been extensively studied. However, research on whether BCR-ABL also affects circular RNAs (circRNAs) is limited. This study aimed to explore the new fusion circRNAs produced by BCR-ABL and their role in CML cells. In this study, we identified a novel fusion circRNA, named F-circBA1, originating from BCR-ABL in K562 and...

Improving the efficiency of single cell genome sequencing based on overlapping pooling strategy

Jing Tu, Zengyan Yang, Na Lu & Zuhong Lu
Single cell genome sequencing has become a useful tool in medicine and biology studies. However, an independent library is required for each cell in single cell genome sequencing, so that the cost grows in step with the number of cells. In this study, we report a study on efficient single-cell copy number variation (CNV) analysis based on overlapping pooling strategy together with branch and bound (B&B) algorithm. Single cells are overlapped pooled before sequencing, and...

Special electromagnetic field-treated water and far-infrared radiation alleviates lipopolysaccharide-induced acute respiratory distress syndrome in rats by regulating haptoglobin

Changyong Luo, Yan Li, Xu Liang, Yifan Chen, Qiao Zou, Yurong Kong, Zhengguang Guo, Wei Sun & Xin Wang
Special electromagnetic field-treated water (SEW) and far-infrared radiation (FIR) can reduce acute respiratory distress syndrome (ARDS) in rats inflicted by lipopolysaccharides (LPSs). However, little is known about its underlying molecular mechanism. Differentially expressed proteins (DEPs) of SEW and FIR interventions were obtained from a proteomics database. A total of 89 DEPs were identified. Enrichment analysis of DEPs was performed using the Database for Annotation, Visualization, and Integrated Discovery. These DEPs were associated with the responses...

Long non-coding RNA TRPM2 antisense RNA as a potential therapeutic target promotes tumorigenesis and metastasis in esophageal cancer

Wei Wang, Yukai Dai, Xin Yang & Xinming Xiong
Esophageal cancer (EC) is one type of aggressive gastrointestinal cancers. The treatment of EC is challenging. Effective therapeutic targets require development. Long non-coding RNA TRPM2 antisense RNA (LncRNA TRPM2-AS) is considering a novel biomarker and therapeutic target for various types of cancer. However, the role of lncRNA TRPM2-AS in EC remains unknown. This study aimed to illustrate effects of LncRNA TRPM2-AS on EC growth and metastasis and potential underlying molecular mechanisms. LncRNA TRPM2-AS expression was...

Identification of a novel circular RNA circZNF652/miR-486-5p/SERPINE1 signaling cascade that regulates cancer aggressiveness in glioblastoma (GBM)

Liang Liu, Shan Xiao, Yan Wang, Zifeng Zhu, Yiyao Cao, Sen Yang, Rongkang Mai & Yong Zheng
Circular RNAs (circRNAs) are closely associated with cancer development in glioblastoma (GBM), and this study aims to explore the molecular mechanisms of a novel circular RNA circZNF652 in regulating GBM aggressiveness. The present study found that CircZNF652 and SERPINE1 were upregulated, while miR-486-5p was downregulated in GBM tissues and cell lines, and GBM patients with high expression of CircZNF652 and SERPINE1, and patients with low expression of miR-486-5p tended to have a worse prognosis. Further...

Downregulation of Smad4 expression confers chemoresistance against imatinib mesylate to chronic myeloid leukemia K562 cells

Jiangzhao Zhang, Min Zhang, Yan Liang, Min Liu & Zhiping Huang
Objective: Imatinib mesylate (IM), a tyrosine kinase inhibitor, exhibits clinically prominent effects against chronic myeloid leukemia (CML); however, a few patients have shown resistance to IM treatment, resulting in disease progression. Smad4 is a tumor inhibitor that transduces TGF-β signaling and modulates genomic stability. Previous studies have indicated that decreased Smad4 expression played a bidirectional role in chemosensitivity in many types of cancers. Therefore, this study aims to evaluate the association between IM sensitivity and...

Establishment of a subcutaneous adipogenesis model and distinct roles of LKB1 regulation on adipocyte lipid accumulation in high-altitude Bos grunniens

Yongqi Yue, Yonglin Hua, Jing Zhang, Yu Guo, Dan Zhao, Wentao Huo, Yan Xiong, Fenfen Chen, Yaqiu Lin, Xianrong Xiong & Jian Li
The domestic yak was regarded as a valuable model to explore the molecular mechanism of high-altitude animal adaptation, including the extreme tolerance of starvation and cold stress, which is closely associated with specifically seasonal deposition and metabolism of subcutaneous adipose tissue. However, the key regulators for these processes remain largely unknown. Here, the yak adipogenesis model in vitro was established and liver kinase b1 (LKB1) was regarded as a key negative regulator involved in yak...

Long intergenic non-protein coding RNA 02570 promotes nasopharyngeal carcinoma progression by adsorbing microRNA miR-4649-3p thereby upregulating both sterol regulatory element binding protein 1, and fatty acid synthase

Fei Liu, Jiazhang Wei, Yanrong Hao, Jiao Lan, Wei Li, Jingjin Weng, Min Li, Cheng Su, Bing Li, Mingzheng Mo, Fengzhu Tang, Yongli Wang, Yong Yang, Wei Jiao & Shenhong Qu
Our previous studies have elucidated a possible connection between long intergenic non-protein coding RNA 2570 (LINC02570) and nasopharyngeal carcinoma (NPC). However, the precise mechanism by which LINC02570 promotes NPC remains unknown. We used quantitative polymerase chain reaction (qPCR) to detect LINC02570 expression in nasopharyngeal cell lines, NPC tissues, and chronic rhinitis tissues. Subcellular LINC02570 localization was confirmed by fluorescence in situ hybridization (FISH). The effects of LINC02570 stable knockdown and overexpression on viabillity, proliferation, migration,...

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...

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