273 Works

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’...

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...

Suppressed inflammation in obese children induced by a high-fiber diet is associated with the attenuation of gut microbial virulence factor genes

Hui Li, Guojun Wu, Liping Zhao & Menghui Zhang
In our previous study, a gut microbiota-targeted dietary intervention with a high-fiber diet improved the immune status of both genetically obese (Prader-Willi Syndrome, PWS) and simple obese (SO) children. However, PWS children had higher inflammation levels than SO children throughout the trial, the gut microbiota of the two cohorts was similar. As some virulence factors (VFs) produced by the gut microbiota play a role in triggering host inflammation, this study compared the characteristics and changes...

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...

Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity

Feng Yang, Jinghao Zhang, Su Wang, Zhaoyang Sun, Jun Zhou, Feng Li, Yue Liu, Li Ding, Yixin Liu, Wenjing Chi, Tao Liu, Yongqun He, Ping Xiang, Zhijun Bao, Michal A. Olszewski, Hu Zhao & Yanmei Zhang
Severe Helicobacter pylori-linked gastric disorders are especially prevalent in the East Asia region. The ability of H. pylori to cause different clinical outcomes is thought to be associated with unique sets of its genetic features. However, only few genetic features have been definitively linked to specific gastrointestinal pathologies. Genome heterogeneity of clinical H. pylori strains from patients with four different gastric disorders was studied to explore the population structure and molecular genomic features and their...

Genome-wide identification and expression analysis of calmodulin and calmodulin-like genes in wheat (Triticum aestivum L.)

Yongwei Liu, Wenye Chen, Linbin Liu, Yuhuan Su, Yuan Li, Weizhe Jia, Bo Jiao, Jiao Wang, Fan Yang, Fushuang Dong, Jianfang Chai, He Zhao, Mengyu Lv, Yanyi Li & Shuo Zhou
Calmodulin (CaM) and calmodulin-like (CML) genes are widely involved in plant growth and development and mediating plant stress tolerance. However, the whole genome scale studies about CaM and CML gene families have not been done in wheat, and the possible functions of most wheat CaM/CML gene members are still unknown. In this study, a total of 18 TaCaM and 230 TaCML gene members were identified in wheat genome. Among these genes, 28 TaCaM/CML gene members...

Genome-wide identification and expression analysis of calmodulin and calmodulin-like genes in wheat (Triticum aestivum L.)

Yongwei Liu, Wenye Chen, Linbin Liu, Yuhuan Su, Yuan Li, Weizhe Jia, Bo Jiao, Jiao Wang, Fan Yang, Fushuang Dong, Jianfang Chai, He Zhao, Mengyu Lv, Yanyi Li & Shuo Zhou
Calmodulin (CaM) and calmodulin-like (CML) genes are widely involved in plant growth and development and mediating plant stress tolerance. However, the whole genome scale studies about CaM and CML gene families have not been done in wheat, and the possible functions of most wheat CaM/CML gene members are still unknown. In this study, a total of 18 TaCaM and 230 TaCML gene members were identified in wheat genome. Among these genes, 28 TaCaM/CML gene members...

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...

Eukaryotic translation initiation factor 3 subunit B could serve as a potential prognostic predictor for breast cancer

Shaoran Song, Jie Liu, Miao Zhang, Xiaoqian Gao, Wei Sun, Peijun Liu, Yaochun Wang & Juan Li
The EIF3 gene family is essential in controlling translation initiation during the cell cycle. The significance of the EIF3 subunits as prognostic markers and therapeutic targets in breast cancer is not yet clear. We analyzed the expression of EIF3 subunits in breast cancer on the GEPIA and Oncomine databases and compared their expression in breast cancer and normal tissues using BRCA data downloaded from TCGA. Then we performed clinical survival analysis on the Kaplan–Meier Plotter...

Eukaryotic translation initiation factor 3 subunit B could serve as a potential prognostic predictor for breast cancer

Shaoran Song, Jie Liu, Miao Zhang, Xiaoqian Gao, Wei Sun, Peijun Liu, Yaochun Wang & Juan Li
The EIF3 gene family is essential in controlling translation initiation during the cell cycle. The significance of the EIF3 subunits as prognostic markers and therapeutic targets in breast cancer is not yet clear. We analyzed the expression of EIF3 subunits in breast cancer on the GEPIA and Oncomine databases and compared their expression in breast cancer and normal tissues using BRCA data downloaded from TCGA. Then we performed clinical survival analysis on the Kaplan–Meier Plotter...

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...

'UK Lipoedema' cohort GWAS data 2021

Sara Dobbins, Dionysios Grigoriadis, Pia Ostergaard, Ege Sackey, Alan Pittman, Katie Riches, Malou van Zanten, Glen Brice, Ruth England, Vaughan Keeley, Kristiana Gordon, Liang Dong, David Savage, Mike Mills, Peter Mortimer & Steve Jeffery
Data from "Investigations of Clinical Characteristics and Genome Associations in the 'UK Lipoedema' Cohort" Grigoriadis et al, Plos One Post QC dataset (in plink format) on 130 GWAS cases from the discovery series. Scripts used to produce this dataset and for its analysis can be found on GitHub (https://github.com/digrigor/SGUL_UK_Lipoedema_GWAS). The full PLOS paper can be accessed at: https://doi.org/10.1371/journal.pone.0274867 or via the references below.

CircCLTH promotes skeletal muscle development and regeneration

Mengjie Chen, Qingyou Liu, Mingming Song, Xingyu Liu, Kongwei Huang, Dandan Zhong, Yaling Chen, Mingsheng Jiang, Junming Sun, Yiqiang Ouyang, Suren R Sooranna, Deshun Shi & Hui Li
Buffalo holds an excellent potential for beef production, and circRNA plays an important role in regulating myogenesis. However, the regulatory mechanism of circRNAs during buffalo skeletal muscle development has not been fully explored. In this study, circRNA expression profiles during the proliferation and differentiation stages of buffalo myoblasts were analysed by RNA-seq. Here, a total of 3,142 circRNAs candidates were identified, and 110 of them were found to be differentially expressed in the proliferation and...

Sevoflurane reduces lipopolysaccharide-induced apoptosis and pulmonary fibrosis in the RAW264.7 cells and mice models to ameliorate acute lung injury by eliminating oxidative damages

Fushuang Zheng, Xiuying Wu, Jin Zhang, Zhiling Fu & Yan Zhang
Sevoflurane is identified as an effective candidate drug for acute lung injury (ALI) treatment, but its curing effects and detailed mechanisms have not been fully disclosed. The present study was designed to resolve this academic issue. The ALI mice models were established, and Hematoxylin-eosin staining assay was performed to examine tissue morphologies. Cell viability was determined by CCK-8 assay, and Annexin V-FITC/PI double staining assay was used to examine cell apoptosis. The expression levels of...

Myostain is involved in ginsenoside Rb1-mediated anti-obesity

Hong-Shi Li, Jiang-Ying Kuang, Gui-Jun Liu, Wei-Jie Wu, Xian-Lun Yin, Hao-Dong Li, Lei Wang, Tao Qin, Wen-Cheng Zhang & Yuan-Yuan Sun
Obesity, one of the major public health problems worldwide, has attracted increasing attention. Ginsenoside Rb1 is the most abundant active component of Panax ginseng C.A.Mey (Araliaceae) and is reported to have beneficial effects on obesity and diabetes. However, the mechanisms by which Rb1 regulates obesity remain to be explored. This paper intends to further explore the mechanism of Rb1 in regulating obesity. The C57BL/6 obese mice were divided into two groups: the control (CTR) and...

NLRC5 restricts dengue virus infection by promoting the autophagic degradation of viral NS3 through E3 ligase CUL2 (cullin 2)

Jiawei Hao, Jinqian Li, Zhenzhen Zhang, Yang Yang, Qing Zhou, Tiantian Wu, Tongling Chen, Zhongdao Wu, Ping Zhang, Jun Cui & Yi-Ping Li
NLRC5 has been reported to be involved in antiviral immunity; however, the underlying mechanism remains poorly understood. Here, we investigated the functional role of NLRC5 in the infection of a flavivirus, dengue virus (DENV). We found that the expression of NLRC5 was strongly induced by virus infection and IFNB or IFNG stimulation in different cell lines. Overexpression of NLRC5 remarkably suppressed DENV infection, whereas knockout of NLRC5 led to a significant increase in DENV infection....

Additional file 3 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 3. Table S3: Performance of three strategies.

NLRC5 Restricts Dengue Virus Infection by Promoting the Autophagic Degradation of Viral NS3 through E3 Ligase CUL2 (cullin 2)

Jiawei Hao, Jinqian Li, Zhenzhen Zhang, Yang Yang, Qing Zhou, Tiantian Wu, Tongling Chen, Zhongdao Wu, Ping Zhang, Jun Cui & Yi-Ping Li
NLRC5 has been reported to be involved in antiviral immunity; however, the underlying mechanism remains poorly understood. Here, we investigated the functional role of NLRC5 in the infection of a flavivirus, dengue virus (DENV). We found that expression of NLRC5 was strongly induced by virus infection and IFNB or IFNG stimulation in different cell lines. Overexpression of NLRC5 remarkably suppressed DENV infection, whereas knockout of NLRC5 led to a significant increase in DENV infection. Mechanistic...

Upregulated miR-322-5p regulates cell cycle and promotes cell proliferation and apoptosis by directly targeting Wee1 in mice liver injury

He Tong, Li Wang, Jing Shi, Haowei Jin, Kefan Zhang, Yulong Bao, Yongshuai Wu, Yipeng Cheng, Pengxia Liu & Changshan Wang
Liver injury from any number of causes (e.g. chemical material, drugs and diet, viral infection) is a global health problem, and its mechanism is not clearly understood. MicroRNAs (miRNAs) expression profiling is gaining popularity because miRNAs, as key regulators in gene expression networks, can influence many biological processes and have also shown promise as biomarkers for disease. Previous studies reported the regulation effects of miRNAs in liver injury, whereas function and molecular mechanisms of miR-322-5p...

The complete chloroplast genome of Primula odontocalyx, a heterostylous species

Yunqi Liu, Li Zhang, Shubao Wang, Rui Li & Yuan Huang
Primula odontocalyx (Franch.) Pax (1905) is a perennial herb of the genus Primula in Primulaceae with heterostyly and ornamental value. Here, the chloroplast genome of P. odontocalyx was sequenced, assembled, and annotated. The complete chloroplast genome was a closed-circular molecule of 151,738 bp in length, containing a large single-copy region (LSC) of 83,817 bp, a small single-copy region (SSC) of 17,529 bp, and two inverted repeat (IR) regions of 25,196 bp. A total of 115...

Supporting data for \"Relative roles of land and ocean cooling in triggering an El Niño following tropical volcanic eruptions\"

Fei Liu, Chen Xing, Lin Chen, Chaochao Gao, Tao Lian, Shangrong Zhou, Hui Wang, Bin Wang & Wenjie Dong
The data include volcanic aerosol forcing over different ocean and land regions, and monthly precipitation, sea surface temperature, sea surface height, and 850hPa zonal wind.

Additional file 1 of Characteristics of oral microbiome of healthcare workers in different clinical scenarios: a cross-sectional analysis

Zhixia Zhang, Wenyi Yu, Guangyao Li, Yukun He, Zhiming Shi, Jing Wu, Xinqian Ma, Yu Zhu, Lili Zhao, Siqin Liu, Yue Wei, Jianbo Xue, Shuming Guo & Zhancheng Gao
Additional File 1: Supplementary Table S1

Additional file 2 of Pseudomonas aeruginosa biofilm dispersion by the mouse antimicrobial peptide CRAMP

Yang Zhang, Peng Cheng, Shiyuan Wang, Xiaofen Li, Lianci Peng, Rendong Fang, Jing Xiong, Hui Li, Cui Mei, Jiye Gao, Zhenhui Song, Dengfeng Xu, Lizhi Fu, Chenghong Li, Xueqing Wu, Yuzhang He & Hongwei Chen
Additional file 2. Differentially expressed gene data.

Additional file 2 of Quantifying substantial carcinogenesis of genetic and environmental factors from measurement error in the number of stem cell divisions

Xinhui Liu, Jifeng Yang, Hongkai Li, Qing Wang, Yuanyuan Yu, Xiaoru Sun, Shucheng Si, Lei Hou, Lu Liu, Fan Yang, Ran Yan, Yifan Yu, Zhentao Fu, Zilong Lu, Dejin Li, Hao Xue, Xiaolei Guo, Fuzhong Xue & Xiaokang Ji
Additional file 2: Table S1. Ranked matrix of LCR in global scope and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S2. Ranked matrix of LCR in national-wide of China and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S3. Ranked matrix of LCR in counties of Shandong province, China and the contribution of the genetic and environmental factors on the...

Eltrombopag modulates the phenotypic evolution and potential immunomodulatory roles of monocytes/macrophages in immune thrombocytopenia

Feifei Yang, Hui Zong, Feng Li, Shulin Luo, Xiuqun Zhang, Yanli Xu & Xuezhong Zhang
Primary immune thrombocytopenia (ITP) is an acquired autoimmune hemorrhagic disease. Loss of immune tolerance plays a crucial role in the pathogenesis of ITP. Monocytes and macrophages play an indispensable role in the pathophysiology of hematopoietic malignancies and have been implicated as key players in platelet destruction. Approximately 80% of adult patients with ITP exhibit corticosteroid treatment failure or become dependent, requiring novel therapy. Thrombopoietin (TPO) receptor agonists (TPO-RAs) have been used clinically to manage ITP...

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