327 Works

HIF-1α promotes the keloid development through the activation of TGF-β/Smad and TLR4/MyD88/NF-κB pathways

Rui Lei, Jian Li, Feng Liu, Weihan Li, Shizhen Zhang, Yang Wang, Xi Chu & Jinghong Xu
A keloid is defined as an overgrowth of the dense fibrous tissues that form around a wound. Since they destroy the vascular network, keloid tissues often exhibit anoxic conditions. Hypoxia-inducible factor-1α (HIF-1α) is a core factor that mediates hypoxia stress responses and regulates the hypoxic cellular and biological behaviors. In this study, we found that the expression level of HIF-1α in keloid tissue was significantly higher than that in the normal skin tissue. Hypoxia-induced HIF-1α...

Myotubularin related protein 7 is essential for the spermatogonial stem cell homeostasis via PI3K/AKT signaling

Dan Zhao, Cong Shen, Tingting Gao, Hong Li, Yueshuai Guo, Feng Li, Chenchen Liu, Yuanyuan Liu, Xia Chen, Xi Zhang, Yangyang Wu, Yi Yu, Meng Lin, Yan Yuan, Xiaofang Chen, Xiaoyan Huang, Shenmin Yang, Jun Yu, Jun Zhang & Bo Zheng
Myotubularin related protein 7 (MTMR7), a key member of the MTMR family, depicts phosphatase activity and is involved in myogenesis and tumor growth. We have previously identified MTMR7 in the proteomic profile of mouse spermatogonial stem cell (SSC) maturation and differentiation, implying that MTMR7 is associated with neonatal testicular development. In this study, to further explore the distribution and function of MTMR7 in mouse testis, we studied the effect of Mtmr7 knockdown on neonatal testicular...

Data from: Dynamically prognosticating patients with hepatocellular carcinoma through survival paths mapping based on time-series data

Lujun Shen, Qi Zeng, Pi Guo, Jingjun Huang, Chaofeng Li, Tao Pan, Boyang Chang, Nan Wu, Lewei Yang, Qifeng Chen, Tao Huang, Wang Li & Peihong Wu
Patients with hepatocellular carcinoma (HCC) always require routine surveillance and repeated treatment, which leads to accumulation of huge amount of clinical data. A predictive model utilizes the time-series data to facilitate dynamic prognosis prediction and treatment planning is warranted. Here we introduced an analytical approach, which converts the time-series data into a cascading survival map, in which each survival path bifurcates at fixed time interval depending on selected prognostic features by the Cox-based feature selection....

Data from: The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies

Yang Liu, Simin Liu, Chia-Fen Yeh, Nan Zhang, Guoling Chen, Pinjia Que, Lu Dong & Shou-Hsien Li
Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red...

Paeoniflorin reduce luxS/AI-2 system-controlled biofilm formation and virulence in Streptococcus suis

Jinpeng Li, Qingying Fan, Manyu Jin, Chenlong Mao, Hui Zhang, Xiaoling Zhang, Liyun Sun, Daniel Grenier, Li Yi, Xiaogai Hou & Yang Wang
Streptococcus suis (S. suis), more specifically serotype 2, is a bacterial pathogen that threatens the lives of pigs and humans. Like many other pathogens, S. suis exhibits quorum sensing (QS) system-controlled virulence factors, such as biofilm formation that complicates treatment. Therefore, impairing the QS involving LuxS/AI-2 cycle in S. suis, may be a promising alternative strategy for overcoming S. suis infections. In this study, we investigated paeoniflorin (PF), a monoterpenoid glycoside compound extracted from peony,...

Anti-tumour effects of red blood cell membrane-camouflaged black phosphorous quantum dots combined with chemotherapy and anti-inflammatory therapy

Xueyuan Huang, Bin Wu, Jian Li, Yinghui Shang, Wansong Chen, Xinming Nie & Rong Gui
Conventional anti-tumour chemotherapy is facing the challenges of poor specificity, high toxicity and drug resistance. Tumour microenvironment (TME) plays a critical role in tumour development and drug resistance. To address this problem, we constructed a novel anti-tumour nanoparticle platform RBC@BPQDs-DOX/KIR, black phosphorus nanoparticle quantum dots (BPQDs) with one of the chemotherapeutics (doxorubicin, DOX) and an anti-inflammatory traditional Chinese medicine active component (Kirenol, KIR). Red blood cell membrane (RBCm) vesicles were used as the shell to...

The expression and clinical prognostic value of protein phosphatase 1 catalytic subunit beta in pancreatic cancer

Lingyu Hu, Haokai Xu, Xiaoguang Wang, Bin Wu, Fei Chen, Wei Chen, Yong Gao & Zhengxiang Zhong
Pancreatic cancer (PAAD) is a common malignancy with a poor survival rate. The identification of novel biomarkers could improve clinical outcomes for patients with PAAD. Here we evaluated the expression and clinical significance of PPP1CB in PAAD. PPP1CB expression was higher in PAAD tissue than in matched paracancerous tissue (P < 0.05). We predicted a network of regulatory targets and protein interaction partners of PPP1CB, and identified a PPI network consisting of 39 node genes....

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...

Identification of biomarkers related to Tumor-Infiltrating Lymphocytes (TILs) infiltration with gene co-expression network in colorectal cancer

Rong Liao, Qi-Zhi Ma, Cong-Ya Zhou, Jun-Jun Li, Ning-Na Weng, Yang Yang & Qing Zhu
Colorectal cancer (CRC) is one of the most common tumors, ranking second in the global cause of death from cancer. The prognosis of advanced patients is still very poor. In this study, hub modules with the highest association with tumor-infiltrating immune cells were identified by weighted gene co-expression network analysis based on CRC expression data from the Gene Expression Omnibus database. Next, three hub genes (ADAM8, IL-1A, VAV3) related to infiltrating immune cells were identified...

Morphology and phylogeny of two new Thalassiosiroid taxa (Bacillariophyceae), with two marginal rimoportulae

Biaobiao Niu, Yaqiong Guo, Nina Lundholm & Yang Li
Thalassiosira and related taxa i.e. the taxa within Thalassiosirales are among the most abundant and widespread diatoms. The vast majority have one marginal rimoportula, but very few always have two. The knowledge on Thalassiosiroid taxa in Chinese waters is restricted, and to explore the diversity, monoclonal strains were established from southern Chinese coastal waters. Morphological data were based on light and scanning electron microscopy. The D1‒D3 region of the ribosomal large subunit (LSU) and the...

Transcriptome analysis of adipocytokines and their-related LncRNAs in lung adenocarcinoma revealing the association with prognosis, immune infiltration, and metabolic characteristics

Jie Ren, Hui Zhang, Jinna Wang, Yingsong Xu, Lei Zhao & Qihang Yuan
Lung adenocarcinoma (LUAD) is amongst the major contributors to cancer-related deaths on a global scale. Adipocytokines and long non-coding RNAs (lncRNAs) are indispensable participants in cancer. We performed a pan-cancer analysis of the mRNA expression, single nucleotide variation, copy number variation, and prognostic value of adipocytokines. LUAD samples were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Simultaneously, train, internal and external cohorts were grouped. After a stepwise screening...

Protein disulfide isomerases (PDIs) negatively regulate ebolavirus structural glycoprotein expression in the endoplasmic reticulum (ER) via the autophagy-lysosomal pathway

Bin Wang, Jing Zhang, Xin Liu, Qingqing Chai, Xiaoran Lu, Xiaoyu Yao, Zhichang Yang, Liangliang Sun, Silas F. Johnson, Richard C Schwartz & Yong-Hui Zheng
Zaire ebolavirus (EBOV) causes a severe hemorrhagic fever in humans and non-human primates with high morbidity and mortality. EBOV infection is dependent on its structural glycoprotein (GP), but high levels of GP expression also trigger cell rounding, detachment, and downregulation of many surface molecules that is thought to contribute to its high pathogenicity. Thus, EBOV has evolved an RNA editing mechanism to reduce its GP expression and increase its fitness. We now report that the...

DNA repair in lung cancer: a large-scale quantitative analysis for polymorphisms in DNA repairing pathway genes and lung cancer susceptibility

Zexi Liao, Minhan Yi, Jiaxin Li & Yuan Zhang
The results of associations between single nucleotide polymorphisms (SNPs) of genes in DNA repairing pathway and lung cancer (LC) risk are inconsistent. We applied allele, dominant and recessive models to explore the risk of researched variants to LC in total LC and subgroups by ethnicity or LC subtypes with a cutoff point of p < 0.05. A total of 76,935 cases and 88,649 controls from 192 articles were included. Among the analyzed 40 variants from...

Additional file 1 of Relationship between sarcopenia/paravertebral muscles and the incidence of vertebral refractures following percutaneous kyphoplasty: a retrospective study

Qi Chen, Chenyang Lei, Tingxiao Zhao, Zhanqiu Dai, Jun Zhang, Yongming Jin & Chen Xia
Additional file 1.

Table S5.xlsx from Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (Setaria italica (L.) P. Beauv.)

Dan Liu, Yanjiao Cui, Zilong Zhao, Jing Zhang, Suying Li & Zhengli Liu
A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was...

Table S8.xlsx from Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (Setaria italica (L.) P. Beauv.)

Dan Liu, Yanjiao Cui, Zilong Zhao, Jing Zhang, Suying Li & Zhengli Liu
A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was...

Table S2.xlsx from Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (Setaria italica (L.) P. Beauv.)

Dan Liu, Yanjiao Cui, Zilong Zhao, Jing Zhang, Suying Li & Zhengli Liu
A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was...

Additional file 4 of The rhizosphere bacterial community contributes to the nutritional competitive advantage of weedy rice over cultivated rice in paddy soil

Yue Wu, Jian Sun, Pengcheng Yu, Weiliang Zhang, Youze Lin & Dianrong Ma
Additional file 4. Table S2. Node names and their degree in co-occurrence network diagrams of different groups.

DARS-AS1 recruits METTL3/METTL14 to bind and enhance DARS mRNA m6A modification and translation for cytoprotective autophagy in cervical cancer

Weiwei Shen, Miaohua Zhu, Qiming Wang, Xiaoming Zhou, Jiaying Wang, Tingting Wang & Jing Zhang
Cervical cancer (CC) is one of the most prevalent malignancies among females. Cytoprotective autophagy could confer cancer cell tolerance to hypoxic stress, promoting cell survival and adaptation. Aspartyl-tRNA synthetase 1 antisense 1 (DARS-AS1) is an oncogenic long non-coding RNA (lncRNA) in various cancers, but how DARS-AS1 regulates cytoprotective autophagy in hypoxic environment in CC remains unclear. Chromatin immunoprecipitation (ChIP) and luciferase reporter assays were conducted to explore the interaction between hypoxia-inducible factor 1 subunit alpha...

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 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 3 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 3. Differentially expressed protein data.

Additional file 2 of Identification of pyroptosis-related genes and long non-coding RNAs signatures in osteosarcoma

Jian Zhang, Jianjian Deng, Rui Ding, Jinghong Yuan, Jiahao Liu, Xiaokun Zhao, Tianlong Wu, Jingyu Jia & Xigao Cheng
Additional file 2: Table S3. The 57 PRGs

Additional file 10 of TPM1 mediates inflammation downstream of TREM2 via the PKA/CREB signaling pathway

Rong Li, Jing Zhang, Qiong Wang, Meng Cheng & Bin Lin
Additional file 10: Table S1. The sequences for all primers and siRNA.

Additional file 10 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 10: Table S5. GO enrichment analysis by using DAVID.

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