56 Works

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...

A further look at quantitative trait loci for growth and fatness traits in a White Duroc × Erhualian F3 intercross population

Zheng Deng, Tao Huang, Guorong Yan, Bin Yang, Zhiyan Zhang, Shijun Xiao, Huashui Ai & Lusheng Huang
Genetic analysis of porcine growth and fatness traits is beneficial to the swine industry and provides a reference to understand human obesity. Here, we obtained 29 growth and fatness traits for 473 individuals from a White Duroc × Erhualian F3 intercross population. Basic statistical analyses showed that: (1) Positive correlations between different-stage body weights were detected, the shorter the time interval the stronger the correlation. (2) Strong correlations existed in the paired fatness traits. (3)...

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...

Metabolism-related long non-coding RNAs (lncRNAs) as potential biomarkers for predicting risk of recurrence in breast cancer patients

Jian-ying Ma, Shao-hua Liu, Jie Chen & Qin Liu
Metabolism affects the development, progression, and prognosis of various cancers, including breast cancer (BC). Our aim was to develop a metabolism-related long non-coding RNA (lncRNA) signature to assess the prognosis of BC patients in order to optimize treatment. Metabolism-related genes between breast tumors and normal tissues were screened out, and Pearson correlation analysis was used to investigate metabolism-related lncRNAs. In total, five metabolism-related lncRNAs were enrolled to establish prognostic signatures. Kaplan-Meier plots and the receiver...

Incomplete thermal ablation-induced up-regulation of transcription factor nuclear receptor subfamily 2, group F, member 6 (NR2F6) contributes to the rapid progression of residual liver tumor in hepatoblastoma

Jin-shu Pang, Dong-yue Wen, Rong-quan He, Gang Chen, Peng Lin, Jin-hong Li, Yu-jia Zhao, Lin-Yong Wu, Jun-Hong Chen, Yun He, Li-Ting Qin, Jia-bo Chen, Yong Li & Hong Yang
Hepatoblastoma is a kind of extreme malignancy frequently diagnosed in children. Although surgical resection is considered as the first-line treatment for hepatoblastoma, a relatively large population of patients have lost the preferred opportunity for surgery. Administration of locoregional ablation enables local tumor control but with the deficiency of insufficient ablation, residual tumor, and rapid progression. In this study, we integrated 219 hepatoblastoma and 121 non-cancer liver tissues to evaluate the expression of NR2F6, from which...

Identification of hsa_circ_0002024 as a prognostic competing endogenous RNA (ceRNA) through the hsa_miR_129-5p/Anti-Silencing Function 1B Histone Chaperone (ASF1B) axis in renal cell carcinoma

Zhe Chen, Dehua Ou, Zhuangkai Huang & Peilin Shen
We aimed to identify novel circular RNAs (circRNAs) as prognostic competing endogenous RNAs (ceRNAs) to serve as genetic biomarkers and therapeutic targets for renal cell carcinoma (RCC). High-throughput sequencing data of circRNAs from Gene Expression Omnibus (GEO) and of microRNAs (miRNAs) and messenger RNAs (mRNAs) from The Cancer Genome Atlas (TCGA) were retrieved to identify differentially expressed RNAs (DERNAs). DEmRNAs were subjected to weighted gene coexpression network analysis (WGCNA) to identify prognostic DEmRNA (proDEmRNA) modules....

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’...

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...

Data from: Female developmental environment delays development of male honeybee (Apis mellifera)

Xujiang He, Yi Bo Liu, Yao Yi, Amal Abdelmawla, Yun Lin Zheng & Zhi Jiang Zeng
Background Nutrition and cell size play an important role in the determination of caste differentiation in queen and worker of honeybees (Apis mellifera), whereas the haploid genome dominates the differentiation of drones. However, the effects of female developmental environment on the development of males remain unclear. In this study, young drone larvae were transferred into worker cells (WCs) or remained in drone cells (DCs) to rear drones. The drone larvae were also grafted into queen...

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...

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...

miR-152-3p aggravates vascular endothelial cell dysfunction by targeting DEAD-box helicase 6 (DDX6) under hypoxia

Zhongyan Zhao, Chanji Wu, Xiangying He, Eryi Zhao, Shijun Hu, Yeguang Han, Ting Wang, Yanquan Chen, Tao Liu & Shixiong Huang
Stroke is a main cause of disability and death worldwide, and ischemic stroke accounts for most stroke cases. Recently, microRNAs (miRNAs) have been verified to play critical roles in the development of stroke. Herein, we explored effects of miR-152-3p on vascular endothelial cell functions under hypoxia. Human umbilical vein endothelial cells (HUVECs) were treated with hypoxia to mimic cell injury in vitro. Reverse transcription quantitative polymerase chain reaction revealed that miR-152-3p exhibited high expression in...

Long non-coding RNA VCAN-AS1 promotes the malignant behaviors of breast cancer by regulating the miR-106a-5p-mediated STAT3/HIF-1α pathway

Peng Du, Kaifeng Luo, Guoyong Li, Jisheng Zhu, Qi Xiao, Yong Li & Xingjian Zhang
An accumulating number of studies have found that long noncoding RNAs (lncRNAs) participate in breast cancer (BC) development. LncRNA VCAN-AS1, a novel lncRNA, has been confirmed to regulate the progression of gastric cancer, while its role in BC is elusive. Here, our results illustrate that VCAN-AS1 is overexpressed in BC tissues and cells, while miR-106a-5p was downregulated and negatively correlated with VCAN-AS1. In addition, high VCAN-AS1 expression and low miR-106a-5p expression were closely correlated with...

miR-342-5p inhibits osteosarcoma cell growth, migration, invasion, and sensitivity to Doxorubicin through targeting Wnt7b

Qing Liu, Zhenting Wang, Xiaohua Zhou, Mingying Tang, Wei Tan, Tianshi Sun & Youwen Deng
Osteosarcoma (OS) accounts for 9 percent of cancer-related deaths in young people. The PI3K/Akt signaling, a well-known carcinogenic signaling pathway in human cancer, cooperates with other signaling pathways such as Wnt signaling to promote cancer progression. Wnt7b, as a transforming member of the Wnt family, could activate mTORC1 through PI3K-AKT signaling and is upregulated in OS. In the present study, we found that miR-342-5p inhibits Wnt7b expression via direct binding to Wnt7b 3′-UTR. miR-342-5p overexpression...

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’...

A ferroptosis-related gene signature for graft loss prediction following renal allograft

Zhenlei Fan, Tao Liu, Hanfei Huang, Jie Lin & Zhong Zeng
Allogeneic kidney transplantation (renal allograft) is the most effective treatment for advanced kidney disease. Previous studies have indicated that ferroptosis participates in the progression of acute kidney injury and renal transplant failure. However, few studies have evaluated the prognostic value of ferroptosis on renal transplantation outcomes. In this study, a total of 22 differentially expressed ferroptosis-related genes (DFGs) were identified, which were mainly enriched in infection-related pathways. Next, a ferroptosis-related gene signature, including GA-binding protein...

S-adenosyl-L-homocysteine hydrolase FgSah1 is required for fungal development and virulence in Fusarium graminearum

Dongya Shi, Yu Zhang, Jin Wang, Weichao Ren, Jie Zhang, Jane Ifunanya Mbadianya, Yuanye Zhu, Changjun Chen & Hongyu Ma
The S-adenosyl-L-homocysteine hydrolase (Sah1) plays a crucial role in methylation and lipid metabolism in yeast and mammals, yet its function remains elusive in filamentous fungi. In this study, we characterized Sah1 in the phytopathogenic fungus F. graminearum by generating knockout and knockout-complemented strains of FgSAH1. We found that the FgSah1-GFP fusion protein was localized to the cytoplasm, and that deletion of FgSAH1 resulted in defects in vegetative growth, asexual and sexual reproduction, stress responses, virulence,...

S-adenosyl-L-homocysteine hydrolase FgSah1 is required for fungal development and virulence in Fusarium graminearum

Dongya Shi, Yu Zhang, Jin Wang, Weichao Ren, Jie Zhang, Jane Ifunanya Mbadianya, Yuanye Zhu, Changjun Chen & Hongyu Ma
The S-adenosyl-L-homocysteine hydrolase (Sah1) plays a crucial role in methylation and lipid metabolism in yeast and mammals, yet its function remains elusive in filamentous fungi. In this study, we characterized Sah1 in the phytopathogenic fungus F. graminearum by generating knockout and knockout-complemented strains of FgSAH1. We found that the FgSah1-GFP fusion protein was localized to the cytoplasm, and that deletion of FgSAH1 resulted in defects in vegetative growth, asexual and sexual reproduction, stress responses, virulence,...

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...

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...

A further look at quantitative trait loci for growth and fatness traits in a White Duroc × Erhualian F3 intercross population

Zheng Deng, Tao Huang, Guorong Yan, Bin Yang, Zhiyan Zhang, Shijun Xiao, Huashui Ai & Lusheng Huang
Genetic analysis of porcine growth and fatness traits is beneficial to the swine industry and provides a reference to understand human obesity. Here, we obtained 29 growth and fatness traits for 473 individuals from a White Duroc × Erhualian F3 intercross population. Basic statistical analyses showed that: (1) Positive correlations between different-stage body weights were detected, the shorter the time interval the stronger the correlation. (2) Strong correlations existed in the paired fatness traits. (3)...

Evaluation of cesarean delivery rates in different levels of hospitals in Jiangsu Province, China, using the 10-Group classification system

Ning Gu, Yimin Dai, Dan Lu, Tingmei Chen, Muling Zhang, Tao Huang, Yalan Qi, Xinning Han, Lihua Xie, Jishi Yang, Chengling Fan, Yunhua Yan, Anhong Zhang, Xiaoping Weng, Huiling Zhang, Li Su, Yingyan Li & Yali Hu
To compare cesarean delivery (CD) rates in referral and non-referral hospitals in Maternal Safety Collaboration in Jiangsu province, China. Sixteen participants (4 referral hospitals, 12 non-referral hospitals) from Drum Tower Hospital Collaboration for Maternal Safety reported CD rates in 2019 using ten-group classification system and maternal/neonatal morbidity and mortality. A total of 22,676 CDs were performed among 52,499 deliveries and the average CD rate was 43.2% (range 34.8–69.6%). CD rate in non-referral hospitals (44.7%) was...

Predictive factors associated with disease recurrence in patients with severe intrahepatic cholestasis of pregnancy: a retrospective study of 118 cases

Ting Wang, Weixiao Zhou, Ruoan Jiang, Jianbo Lai, Peiyue Jiang, Xinning Chen & Baohua Li
To compare the clinical characteristics of pregnant women and perinatal outcomes with or without recurrent severe intrahepatic cholestasis of pregnancy (sICP), and identify possible factors associated with disease recurrence. A retrospective study of 164,603 deliveries was performed to identify pregnant women diagnosed with sICP in the previous pregnancy from January 2012 to December 2020. Eligible patients were divided into two subgroups according to the status of disease recurrence in the second pregnancy: recurrent severe ICP...

Metabolism-related long non-coding RNAs (lncRNAs) as potential biomarkers for predicting risk of recurrence in breast cancer patients

Jian-ying Ma, Shao-hua Liu, Jie Chen & Qin Liu
Metabolism affects the development, progression, and prognosis of various cancers, including breast cancer (BC). Our aim was to develop a metabolism-related long non-coding RNA (lncRNA) signature to assess the prognosis of BC patients in order to optimize treatment. Metabolism-related genes between breast tumors and normal tissues were screened out, and Pearson correlation analysis was used to investigate metabolism-related lncRNAs. In total, five metabolism-related lncRNAs were enrolled to establish prognostic signatures. Kaplan-Meier plots and the receiver...

Identification of differentially expressed microRNAs in ovulatory and subordinate follicles in Dazu black goats

Risu Na, Yan Zeng, Yanguo Han, Chengli Liu, Baigao Yang & Yongmeng He
How multiple ovulations happen in prolific goats is still unknown even though studies on ovarian physiology and folliculogenesis have made extensive progress. MicroRNAs (miRNAs) are a class of endogenous regulatory factors and regulate structural gene expression mainly at the post-transcriptional level. In this study, in the follicular phase, six large follicles were collected from prolific Dazu black goat and used to generate RNA libraries for RNA sequencing. Based on the litter size and average number...

Registration Year

  • 2021
    56

Resource Types

  • Dataset
    56

Affiliations

  • Jiangxi Agricultural University
    56
  • Huazhong University of Science and Technology
    36
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    36
  • Zhejiang University
    26
  • Capital Medical University
    26
  • Fudan University
    25
  • West China Hospital of Sichuan University
    23
  • Peking University
    23
  • Southern Medical University
    21
  • Shanghai Jiao Tong University
    21