91 Works

Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

Bin-Bin Liu, Zhi-Yao Ma, Chen Ren, Richard Hodel, Miao Sun, Xiu-Qun Liu, Guang-Ning Liu, De-Yuan Hong, Elizabeth Zimmer & Jun Wen
With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated the optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and...

Larger males facilitate population expansion in Ophraella communa

Yan Zhang, Zhongshi Zhou, Chenchen Zhao, Weihua Ma, Shaowei Cui, Hongsong Chen, Chao Ma & Jianying Guo
One of the most intriguing concepts in animal ecology is the reproductive advantages offered by larger body size, and the females prefer to mate with larger males in order to gain reproductive advantage. Currently, it is not clear how females recognize signs of male “quality” and what mechanisms are involved in producing offspring with direct or indirect benefits. Our study aims to assess the preferences of females for males in Ophraella communa, determine the reproductive...

Genome and transcriptome assemblies of TIL11

Lin Li, Zhao Li & Linqian Han
Here, we employed single-molecule long-read sequencing of cDNA libraries from five tissues of the teosinte inbred line TIL11 and identified 70,044 non-redundant transcript isoforms. 23,527 predicted genes were identified using our state-of-the-art, machine learning-based bioinformatics pipeline DenovoAS_Finder without a complete reference genome. Additionally, we constructed a draft TIL11 genome based on a Nanopore sequencing dataset with 16,633 high-quality contigs and a N50 of 112 kb.

Tumour suppressor TET2 safeguards enhancers from aberrant DNA methylation and epigenetic reprogramming in ERα-positive breast cancer cells

Ruitu Lyu, Xuguo Zhu, Yinghui Shen, Lijun Xiong, Lu Liu, Hang Liu, Feizhen Wu, Christian Argueta & Li Tan
Aberrant DNA methylation is an epigenetic hallmark of malignant tumours. The DNA methylation level is regulated by not only DNA methyltransferases (DNMTs) but also Ten-Eleven Translocation (TET) family proteins. However, the exact role of TET genes in breast cancer remains controversial. Here, we uncover that the ERα-positive breast cancer patients with high TET2 mRNA expression had better overall survival rates. Consistently, knockout of TET2 promotes the tumorigenesis of ERα-positive MCF7 breast cancer cells. Mechanistically, TET2...

Tumor suppressor TET2 safeguards enhancers from aberrant DNA methylation and epigenetic reprogramming in ERα-positive breast cancer cells

Ruitu Lyu, Xuguo Zhu, Yinghui Shen, Lijun Xiong, Lu Liu, Hang Liu, Feizhen Wu, Christian Argueta & Li Tan
Aberrant DNA methylation is an epigenetic hallmark of malignant tumors. The DNA methylation level is regulated by not only DNA methyltransferases (DNMTs) but also Ten-Eleven Translocation (TET) family proteins. However, the exact role of TET genes in breast cancer remains controversial. Here, we uncover that the ERα-positive breast cancer patients with high TET2 mRNA expression had better overall survival rates. Consistently, knockout of TET2 promotes the tumorigenesis of ERα-positive MCF7 breast cancer cells. Mechanistically, TET2...

Block-Wise Variable Selection for Clustering Via Latent States of Mixture Models

Beomseok Seo, Lin Lin & Jia Li
Mixture modeling is a major paradigm for clustering in statistics. In this article, we develop a new block-wise variable selection method for clustering by exploiting the latent states of the hidden Markov model on variable blocks or the Gaussian mixture model. The variable blocks are formed by depth-first-search on a dendrogram created based on the mutual information between any pair of variables. It is demonstrated that the latent states of the variable blocks together with...

Block-Wise Variable Selection for Clustering Via Latent States of Mixture Models

Beomseok Seo, Lin Lin & Jia Li
Mixture modeling is a major paradigm for clustering in statistics. In this article, we develop a new block-wise variable selection method for clustering by exploiting the latent states of the hidden Markov model on variable blocks or the Gaussian mixture model. The variable blocks are formed by depth-first-search on a dendrogram created based on the mutual information between any pair of variables. It is demonstrated that the latent states of the variable blocks together with...

MMP-9-mediated regulation of hypoxia-reperfusion injury-related neutrophil inflammation in an in vitro proximal tubular cell model

Yan Dong, Hong Zhao, Jiangwei Man, Shengjun Fu & Li Yang
Hypoxia-reperfusion (HR) and inflammation are causes of renal allograft injury. Pathological evidence has indicated that ischemia followed by reperfusion leads to the proteolysis and destruction of the extracellular matrix (ECM) in renal tubular epithelial cells. Matrix metalloproteinases (MMPs), such as MMP-2 and MMP-9, play roles in cleaving and reshaping the ECM. Acute accumulation of MMP-9 secreted from neutrophils promotes the incidence of inflammation and exacerbates graft trauma. Our goal was to investigate the activities of...

Cenozoic rifting and inversion of Beibuwan Basin and its linkage with the strike-slip movement along the Ailao Shan-Red River Shear Zone

Yanjun Cheng, Zhiping Wu, Jie Zhang, Yuqing Liu, Zhengkai Wang & Yining Dai
The Cenozoic Beibuwan Basin is located along the eastern margin of the Ailao Shan Red River Shear Zone (ASRRSZ). The rifting and inversion processes of this basin provide important clues to the mechanism by which extrusion tectonics drive continental rifting and inversion development. However, the rifting and inversion of this basin remain ambiguous. Here, we employ seismic data, information about the time and displacement of faulting, syn-rift fault and isopach maps to analyse the Cenozoic...

Inference on moderation effect with third-variable effect analysis – application to explore the trend of racial disparity in oncotype dx test for breast cancer treatment

Qingzhao Yu, Lu Zhang, Xiaocheng Wu & Bin Li
Third variable effect refers to the effect from a third variable that explains an observed relationship between an exposure and an outcome. Depending on whether there is causal relationship, typically, a third variable takes the format of a mediator or a confounder. A moderation effect is a special case of the third-variable effect, where the moderator and other variables have an interactive effect on the outcome. In this paper, we extend the R package ‘mma’...

Identification of prognostic and bone metastatic alternative splicing signatures in bladder cancer

Runzhi Huang, Zixuan Zheng, Shuyuan Xian, Jiayao Zhang, Jingyi Jia, Dianwen Song, Penghui Yan, Huabin Yin, Peng Hu, Xiaolong Zhu, Zongqiang Huang, Tong Meng & Jie Zhang
Bladder cancer (BLCA), originating from the epithelium of the urinary bladder, was the second most common malignancy in the urinary system with a high metastasis rate and poor post-metastasis prognosis. Alternative splicing events (ASEs) were regarded as important markers of tumor progression and prognosis, however, their roles in bladder cancer bone metastasis have not been recognized. In this study, we constructed a predictive model based on ASEs and explored the molecular mechanism of ASEs in...

Identification of prognostic and bone metastatic alternative splicing signatures in bladder cancer

Runzhi Huang, Zixuan Zheng, Shuyuan Xian, Jiayao Zhang, Jingyi Jia, Dianwen Song, Penghui Yan, Huabin Yin, Peng Hu, Xiaolong Zhu, Zongqiang Huang, Tong Meng & Jie Zhang
Bladder cancer (BLCA), originating from the epithelium of the urinary bladder, was the second most common malignancy in the urinary system with a high metastasis rate and poor post-metastasis prognosis. Alternative splicing events (ASEs) were regarded as important markers of tumor progression and prognosis, however, their roles in bladder cancer bone metastasis have not been recognized. In this study, we constructed a predictive model based on ASEs and explored the molecular mechanism of ASEs in...

Protective effect of berberine against LPS-induced endothelial cell injury via the JNK signaling pathway and autophagic mechanisms

Junping Guo, Wei Chen, Beibei Bao, Dayong Zhang, Jianping Pan & Mao Zhang
The role of autophagic mechanisms in the protective effect of berberine (BBR) on lipopolysaccharide (LPS)-induced injury in the endothelial cells human umbilical vein endothelial cells (HUVECs) and human pulmonary microvascular endothelial cells (HPMECs) was investigated. Cell viability, proliferation, and apoptosis were detected by the CCK-8 assay, the EdU kit, and flow cytometry, respectively, and autophagy-related protein expression, the number of autophagic vacuoles, and LC3 double-fluorescence were examined using western blot analysis, transmission electron microscopy, and...

Hypoxia promotes the proliferation of mouse liver sinusoidal endothelial cells: miRNA–mRNA expression analysis

Zhe Qing, Hanfei Huang, Qun Luo, Jie Lin, Shikun Yang, Tao Liu, Zhong Zeng & Tingfeng Ming
During the initial stage of liver regeneration (LR), hepatocytes and liver sinusoidal endothelial cells (LSECs) initiate regeneration in a hypoxic environment. However, the role of LSECs in liver regeneration in hypoxic environments and their specific molecular mechanism is unknown. Therefore, this study aimed to explore the miRNA–mRNA network that regulates the proliferation of LSECs during hypoxia. In this study, first, we found that the proliferation ability of primary LSECs treated with hypoxia was enhanced compared...

MicroRNA-146b-3p regulates the dysfunction of vascular smooth muscle cells via repressing phosphoinositide-3 kinase catalytic subunit gamma

Xijing Zhuang, Feng Gao, Lei Shi, Wei Liu, Wenjun Wang, Xuezhi He & Yang Gao
MicroRNAs are crucial regulators in the phenotype switch of vascular smooth muscle cells (VSMCs). Nonetheless, the role of miR-146b-3p in VSMCs remains unclear. In the present study, platelet-derived growth factor-BB (PDGF-BB) at different concentrations was employed to stimulate VSMCs for different times, to establish the model of VSMC dysfunction. The relative expression of miR-146b-3p was quantified by quantitative real-time polymerase chain reaction (qRT-PCR). The proliferation of VSMCs was measured by BrdU assay. Flow cytometry analysis...

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....

Study of calcitriol anti-aging effects on human natural killer cells in vitro

Weiran Li, Xu Che, Xuemei Chen, Meiling Zhou, Xiaoping Luo & Tao Liu
Vitamin D is widely considered to have a regulatory effect on the immune system. Some clinical investigations have shown that the demand for vitamin D increases with age. Calcitriol is the biologically active form of vitamin D. However, its effect on human natural killer (NK) cells remains unclear. Therefore, in this study, we investigated the anti-aging and immunomodulatory effects of calcitriol on NK cells using a series of immunological methods to explore its important role...

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...

Identification and verification of vascular cell adhesion protein 1 as an immune-related hub gene associated with the tubulointerstitial injury in diabetic kidney disease

Yan Jia, Hui Xu, Qi Yu, Lishan Tan & Zuying Xiong
Diabetic kidney disease (DKD) is the leading cause of chronic kidney disease (CKD) and end-stage renal disease (ESRD), but the pathogenesis is not completely understood. Tubulointerstitial injury plays critical roles in the development and progression of DKD. The present study aimed to investigate the profile of tubulointerstitial immune cell infiltration and reveal the underlying mechanisms between tubular cell injury and interstitial inflammation in DKD using bioinformatics strategies. First, xCell analysis identified immune cells displaying significant...

A pan-cancer analysis of the prognostic and immunological role of β-actin (ACTB) in human cancers

Yuxi Gu, Shouyi Tang, Zhen Wang, Luyao Cai, Haosen Lian, Yingqiang Shen & Yu Zhou
Beta-actin (ACTB), a highly conserved cytoskeleton structural protein, has been regarded as a common housekeep gene and used as a reference gene for years. However, accumulating evidence indicates that ACTB is abnormally expressed in multiple cancers and hence changes the cytoskeleton to affect the invasiveness and metastasis of tumors. This study aimed to investigate the function and clinical significance of ACTB in pan-cancer. The role of ACTB for prognosis and immune regulation across 33 tumors...

MicroRNA miR-188-5p as a mediator of long non-coding RNA MALAT1 regulates cell proliferation and apoptosis in multiple myeloma

Hui Liu, Zuofei Chi, Hong Jin & Wei Yang
Multiple myeloma (MM), a malignancy of plasma cells mainly derived from the bone marrow, has remained incurable generally. LncRNA MALAT1 has been reported to be upregulated in the MM cells and knockdown of MALAT1 inhibited MM cell cycle progression and enhanced cell apoptosis. Online target prediction showed that two target sites for MALAT1 existed in miR-188-5p, which has been identified as a tumor suppressor in other types of cancers. However, the role of miR-188-5p in...

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...

Comprehensive analysis of pivotal biomarkers, immune cell infiltration and therapeutic drugs for steroid-induced osteonecrosis of the femoral head

Bo Wang, Song Gong, Wenkai Shao, Lizhi Han, Zilin Li, Zhichao Zhang, Yang Zheng, Fang Ouyang, Yan Ma, Weihua Xu & Yong Feng
Steroid-induced osteonecrosis of the femoral head (SONFH) is a progressive disease that leads to an increased disability rate. This study aimed to ascertain biomarkers, infiltrating immune cells, and therapeutic drugs for SONFH. The gene expression profile of the GSE123568 dataset was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using the NetworkAnalyst platform. Functional enrichment, protein-protein interaction network (PPI), and module analyses were performed using Metascape tools. An...

MMP-9-mediated regulation of hypoxia-reperfusion injury-related neutrophil inflammation in an in vitro proximal tubular cell model

Yan Dong, Hong Zhao, Jiangwei Man, Shengjun Fu & Li Yang
Hypoxia-reperfusion (HR) and inflammation are causes of renal allograft injury. Pathological evidence has indicated that ischemia followed by reperfusion leads to the proteolysis and destruction of the extracellular matrix (ECM) in renal tubular epithelial cells. Matrix metalloproteinases (MMPs), such as MMP-2 and MMP-9, play roles in cleaving and reshaping the ECM. Acute accumulation of MMP-9 secreted from neutrophils promotes the incidence of inflammation and exacerbates graft trauma. Our goal was to investigate the activities of...

Hypophosphatemia is an independent risk factor for AKI among hospitalized patients with COVID-19 infection

Zijin Chen, Chenni Gao, Haijin Yu, Lin Lu, Jialin Liu, Wei Chen, Xiaogang Xiang, Hafiz Muhammad Jafar Hussain, Benjamin J. Lee, Chuanlei Li, Wenjie Wei, Yuhan Huang, Xiang Li, Zhengying Fang, Shuwen Yu, Qinjie Weng, Yan Ouyang, Xiaofan Hu, Jun Tong, Jian Liu, Li Lin, Mingyu Liu, Xiaoman Xu, Dan Liu, Yuan Song … & Jingyuan Xie
This study sought to investigate incidence and risk factors for acute kidney injury (AKI) in hospitalized COVID-19. In this retrospective study, we enrolled 823 COVID-19 patients with at least two evaluations of renal function during hospitalization from four hospitals in Wuhan, China between February 2020 and April 2020. Clinical and laboratory parameters at the time of admission and follow-up data were recorded. Systemic renal tubular dysfunction was evaluated via 24-h urine collections in a subgroup...

Registration Year

  • 2021
    91

Resource Types

  • Dataset
    91

Affiliations

  • Huazhong Agricultural University
    91
  • Huazhong University of Science and Technology
    54
  • Fudan University
    45
  • Shanghai Jiao Tong University
    45
  • Nanjing Medical University
    45
  • Capital Medical University
    44
  • West China Hospital of Sichuan University
    42
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    41
  • Peking University
    40
  • Chinese Academy of Sciences
    39