198 Works

Alleviative effects of foraging exercise on depressive-like behaviors in chronic mild stress-induced ischemic rat model

Xi Tao, Siyuan Wu, Wenjing Tang, Lu Li, Lijun Huang, Danheng Mo, Chujuan Liu, Tao Song, Shuling Wang, Jia Wang & Juan He
Poststroke depression (PSD) is a common complication that seriously affects the functional recovery and prognosis of an individual. As some patients with PSD fail to respond to drug therapy, it is urgent to find a viable alternative treatment. An active exercise program known as foraging exercise (FE), using food as bait, was designed. First, focal ischemia and chronic unpredictable mild stress (CUMS) were used to establish a PSD model in rats. FE was then performed...

A Gypsy element contributes to the nuclear retention and transcriptional regulation of the resident lncRNA in locusts

Xia Zhang, Ya′Nan Zhu, Bing Chen & Le Kang
The majority of long noncoding RNAs (lncRNAs) contain transposable elements (TEs). PAHAL, a nuclear-retained lncRNA that is inserted by a Gypsy retrotransposon, has been shown to be a vital regulator of phenylalanine hydroxylase (PAH) gene expression that controls dopamine biosynthesis and behavioural aggregation in the migratory locust. However, the role of the Gypsy retrotransposon in the transcriptional regulation of PAHAL remains unknown. Here, we identified a Gypsy retrotransposon (named Gypsy element) as an inverted long...

Integration of transcriptomics and metabolomics to identify key coumarin biosynthetic genes in Bupleurum chinense

Bin Yang, Shi-Hang Liu, Yilian He, Yuchan Li, Liang Feng, Meng Zhang, Jun Zhao, Yiguan Zhang, Xia Yu, Hua Chen, Dabin Hou, Junning Zhao & Ma Yu
Bupleurum chinense DC. is a perennial herb plant belonging to the Umbelliferae family, genus Bupleurum, that is used as a traditional Chinese medicine. Coumarins are characteristic secondary metabolites of the Apiaceous family, which possess anti-inflammatory, anti-cancer and antiviral activities, among others. Few studies on the coumarin biosynthesis pathways in B. Chinese have been reported. In this study, we identified 89 differentially expressed genes belonging to 7 gene families involved in the synthesis of coumarins in...

Integrated bioinformatics and experiments reveal the roles and driving forces for HSF1 in colorectal cancer

Xiaomin Ren, Liyuan Zhang, Xiaolin Ma, Jiaqiu Li & Zhong Lu
Heat shock factor 1 (HSF1) has watershed significance in different tumors. However, the roles and driving forces for HSF1 in colorectal cancer (CRC) are poorly understood. Our study integrally analyzed the roles and driving forces for HSF1 in CRC by bioinformatics and experiments. The expression and prognostic characteristics of HSF1 were analyzed via UALCAN, GEPIA2, TISIDB, Prognoscan and HPA databases. Then, we analyzed the correlation between HSF1 expression and immune features via TIMER2 database. Subsequently,...

KAT7-mediated CANX (calnexin) crotonylation regulates leucine-stimulated MTORC1 activity

Guokai Yan, Xiuzhi Li, Zilong Zheng, Weihua Gao, Changqing Chen, Xinkai Wang, Zhongyi Cheng, Jie Yu, Geng Zou, Muhammad Zahid Farooq, Xiaoyan Zhu, Weiyun Zhu, Qing Zhong & Xianghua Yan
Amino acids play crucial roles in the MTOR (mechanistic target of rapamycin kinase) complex 1 (MTORC1) pathway. However, the underlying mechanisms are not fully understood. Here, we establish a cell-free system to mimic the activation of MTORC1, by which we identify CANX (calnexin) as an essential regulator for leucine-stimulated MTORC1 pathway. CANX translocates to lysosomes after leucine deprivation, and its loss of function renders either the MTORC1 activity or the lysosomal translocation of MTOR insensitive...

ATG7-mediated autophagy facilitates embryonic stem cell exit from naive pluripotency and marks commitment to differentiation

Jilong Zhou, Hainan He, Jing-Jing Zhang, Xin Liu, Wang Yao, Chengyu Li, Tian Xu, Shu-Yuan Yin, Dan-Ya Wu, Cheng-Li Dou, Qiao Li, Jiani Xiang, Wen-Jing Xiong, Li-Yan Wang, Jun-ming Tang, Zhouyiyuan Xue, Xia Zhang & Yi-Liang Miao
Macroautophagy/autophagy is a conserved cellular mechanism to degrade unneeded cytoplasmic proteins and organelles to recycle their components, and it is critical for embryonic stem cell (ESC) self-renewal and somatic cell reprogramming. Whereas autophagy is essential for early development of embryos, no information exists regarding its functions during the transition from naive-to-primed pluripotency. Here, by using an in vitro transition model of ESCs to epiblast-like cells (EpiLCs), we find that dynamic changes in ATG7-dependent autophagy are...

ATG7-mediated autophagy facilitates embryonic stem cell exit from naive pluripotency and marks commitment to differentiation

Jilong Zhou, Hainan He, Jing-Jing Zhang, Xin Liu, Wang Yao, Chengyu Li, Tian Xu, Shu-Yuan Yin, Dan-Ya Wu, Cheng-Li Dou, Qiao Li, Jiani Xiang, Wen-Jing Xiong, Li-Yan Wang, Jun-Ming Tang, Zhouyiyuan Xue, Xia Zhang & Yi-Liang Miao
Macroautophagy/autophagy is a conserved cellular mechanism to degrade unneeded cytoplasmic proteins and organelles to recycle their components, and it is critical for embryonic stem cell (ESC) self-renewal and somatic cell reprogramming. Whereas autophagy is essential for early development of embryos, no information exists regarding its functions during the transition from naive-to-primed pluripotency. Here, by using an in vitro transition model of ESCs to epiblast-like cells (EpiLCs), we find that dynamic changes in ATG7-dependent autophagy are...

Selective autophagic degradation of ACLY (ATP citrate lyase) maintains citrate homeostasis and promotes oocyte maturation

Hainan He, Junling Wang, Xingmei Mou, Xin Liu, Qiao Li, Mingyue Zhong, Bingbing Luo, Zhisheng Yu, Jingjing Zhang, Tian Xu, Chengli Dou, Danya Wu, Wei Qing, Linhui Wu, Kai Zhou, Zhengang Fan, Tingting Wang, Taotao Hu, Xia Zhang, Jilong Zhou & Yi-Liang Miao
Macroautophagy/autophagy is a cellular and energy homeostatic mechanism that contributes to maintain the number of primordial follicles, germ cell survival, and anti-ovarian aging. However, it remains unknown whether autophagy in granulosa cells affects oocyte maturation. Here, we show a clear tendency of reduced autophagy level in human granulosa cells from women of advanced maternal age, implying a potential negative correlation between autophagy levels and oocyte quality. We therefore established a co-culture system and show that...

LINC00857 regulated by ZNF460 enhances the expression of CLDN12 by sponging miR-150-5p and recruiting SRSF1 for alternative splicing to promote epithelial-mesenchymal transformation of pancreatic adenocarcinoma cells

Yong Zhang, Yuan Fang, Lijie Ma, Jing Xu, Chentao Lv, Li Deng & Guanghui Zhu
Recent research unveiled that LINC00857 plays a regulatory role in multiple human cancers, such as lung adenocarcinoma and gastric cancer. Nevertheless, the function of LINC00857 in pancreatic adenocarcinoma (PAAD) remains unclear. This study concentrates on LINC00857 to discuss the relevant molecular mechanism of this gene in PAAD. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) and western blot were implemented for measuring the expressions of RNAs and proteins. Wound healing and Transwell assays were used to...

Subspace Estimation with Automatic Dimension and Variable Selection in Sufficient Dimension Reduction

Jing Zeng, Qing Mai & Xin Zhang
Sufficient dimension reduction (SDR) methods target finding lower-dimensional representations of a multivariate predictor to preserve all the information about the conditional distribution of the response given the predictor. The reduction is commonly achieved by projecting the predictor onto a low-dimensional subspace. The smallest such subspace is known as the Central Subspace (CS) and is the key parameter of interest for most SDR methods. In this article, we propose a unified and flexible framework for estimating...

Facile synthesis of magnesium-based metal-organic framework with tailored nanostructure for effective VOCs adsorption

Zhang Xiaotao
A novel Mg(II) metal–organic framework (Mg-MOF) was synthesised based on the ligand of 2,2'-bipyridine-4,4'dicarboxylic acid (Bpdc). Single-crystal X-ray structural analysis confirmed that 3D-nanostructure Mg-MOFs formed a monoclinic system with a channel size of 15.733 Å × 23.736 Å. The N2 adsorption isotherm, Fourier-transform infrared spectroscopy, thermogravimetric analysis and high-resolution transmission electron microscopy were performed to characterise the thermal stability and purity of the Mg-MOFs. The adsorption studies on four typical volatile organic compounds (VOCs) emitted...

Even short-term revegetation complicates soil food webs and strengths their links with ecosystem functions

Dima Chen, Bing Wang, Yuhe Zhu, Xiang Chen, Dima Chen, Ying Wu, Liji Wu, Shengen Liu, Linyan Yue, Yang Wang & Yongfei Bai
Degradation of dryland ecosystems is a worldwide problem caused by climate change and human activities. To restore these degraded ecosystems, governments have implemented projects that often include revegetation, but we still lack an understanding of how soil food webs and ecosystem functions are affected by revegetation. By conducting a large-scale revegetation experiment under two degradation intensities (low and high) on the Inner Mongolian degraded grassland, we tested the effects of revegetation on primary producers (plants),...

CTPS1 inhibition suppresses proliferation and migration in colorectal cancer cells

Fahong Wu, Yudong Mao, Tao Ma, Xiaoli Wang, Hangzhi Wei, Tianwei Wang, Jia Wang & Youcheng Zhang
Colorectal cancer (CRC) is now the third most prevalent tumor and one of the deadliest cancers worldwide, with an increasing prevalence every year. Therefore, we urgently need to understand the mechanisms regulating the progression of colorectal cancer and find potential diagnostic biomarkers. In this study, we performed an analysis using the TCGA and GEO databases to find a molecular biomarker for the diagnosis of CRC, namely CTPS1. The results of this analysis revealed that CTPS1...

Gastrochilus wolongensis (Orchidaceae): a new species from Sichuan, China, based on molecular and morphological data

Junyi Zhang, Yuehong Cheng, Min Liao, Senlong Jin, Chunmao Qu, Yingchun Tan, Anđelka Plenković-Moraj & Bo Xu
Gastrochilus wolongensis (Orchidaceae), a new orchid species from Sichuan Province, Southwest China, is described and illustrated. It morphologically resembles G. sinensis, but differs markedly from the latter in having black-purple stripes (vs. purplish-red spots) on the adaxial side of the petals and sepals, a reniform epichile densely covered with long papillate hairs (vs. sparsely pubescent) with purplish-red spots (vs. unspotted), and outside the sac of the hypochile with purplish-red stripes (vs. purplish-red spotted). The molecular...

Additional file 4 of Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

Yongliang Li, Pai Qin, Aolong Sun, Wenjun Xiao, Fenglin Chen, Yang He, Keyao Yu, You Li, Meng Zhang & Xinhong Guo
Additional file 4: Table S1. Detailed information of all 138 TaRING zinc finger genes identified in tomato genome.

Additional file 1 of Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota

Yuan-Guo Xie, Zhen-Hao Luo, Bao-Zhu Fang, Jian-Yu Jiao, Qi-Jun Xie, Xing-Ru Cao, Yan-Ni Qu, Yan-Lin Qi, Yang-Zhi Rao, Yu-Xian Li, Yong-Hong Liu, Andrew Li, Cale Seymour, Marike Palmer, Brian P. Hedlund, Wen-Jun Li & Zheng-Shuang Hua
Additional file 1: Supplementary Table S1-S7. Table S1. The occurrence frequency of 48 single-copy genes and estimated genomic completeness of all Ca. Nanohaloarchaeota genomes. Table S2. Basic genomic features of publicly available Nanohaloarchaeota genome. Table S3. KEGG-based functional annotation of five Nucleotidisoterales MAGs including three from Qijiaojing lake and two from public database. Table S4. Gene counts of carbohydrate metabolism related genes identified by comparing to CAZy database. Table S5. Detected peptidases in Nucleotidisoterales MAGs....

Learning Coefficient Heterogeneity over Networks: A Distributed Spanning-Tree-Based Fused-Lasso Regression

Xin Zhang, Jia Liu & Zhengyuan Zhu
Identifying the latent cluster structure based on model heterogeneity is a fundamental but challenging task arises in many machine learning applications. In this paper, we study the clustered coefficient regression problem in the distributed network systems, where the data are locally collected and held by nodes. Our work aims to improve the regression estimation efficiency by aggregating the neighbors’ information while also identifying the cluster membership for nodes. To achieve efficient estimation and clustering, we...

Different facets of bacterial and fungal communities drive soil multifunctionality in grasslands spanning a 3,500 km transect

Linna Ma, Chaoxue Zhang, Xiaofeng Xu, Congwen Wang, Guofang Liu, Cunzhu Liang, Xiaoan Zuo, Chengjie Wang, Yixia Lv & Renzhong Wang
1. Soil microbial communities are essential in regulating ecosystem functions and services. However, the importance of bacterial and fungal communities as predictors of multiple soil functions (i.e., soil multifunctionality) in grassland ecosystems has not been studied systematically. 2. Here, we measured soil microbial diversity, community composition, biomass, and multiple soil functions of 41 sites in five grassland ecosystems spanning a 3,500 km northeast–southwest transect. The random forest algorithm was adopted to determine the importance of...

Prevalence and molecular characterization of alpha and beta-Thalassemia mutations among Hakka people in southern China

XiangXing Zeng, ZhiFang Liu, CaiHua He, Jia Wang & LiXiang Yan
Abstract Our aim was to investigate molecular features of thalassemia for proper clinical consultation and prevention in Heyuan. In our research, a total of 25,437 positive screening subjects were further subjected to a genetic analysis of α-thalassemia (α-thal) and β-thalassemia (β-thal). The deletion of α-thal mutation was tested by Gap-PCR, while the non-deletion of α-thal and β-thal mutation were identified by the PCR-reverse dot blot (PCR-RDB) technique. Nested PCR detected Hkαα/-- SEA and Hkαα/αα. Among...

Additional file 9 of Functional structure analysis and genome-wide identification of CNX gene family in cotton

Nan Xu, Hong Zhang, Yuexin Zhang, Yapeng Fan, Jing Wang, Waqar Afzal Malik, Cun Rui, Mingge Han, Xuke Lu, Xiugui Chen, Junjuan Wang, Delong Wang, Shuai Wang, Chao Chen, Lixue Guo, Lanjie Zhao & Wuwei Ye
Additional file 9. Table S9: Relative expression levels of 8 selected genes under four different time treatments of 12% PEG6000.

A global dataset of soil gross nitrogen transformation rates

Ahmed Elrys, Yves Uwiragiye, Yanhui Zhang, Mohamed K. Abdel-Fattah, Zhao-xiong Chen, Hui-min Zhang, Lei Meng, Jing Wang, Tong-bin Zhu, Yi Cheng, Jin-bo Zhang, Zu-cong Cai, Scott X. Chang & Christoph Müller
Source_Data_Figure_2 and 3 R_Codes used in data analysis

Additional file 4 of Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota

Yuan-Guo Xie, Zhen-Hao Luo, Bao-Zhu Fang, Jian-Yu Jiao, Qi-Jun Xie, Xing-Ru Cao, Yan-Ni Qu, Yan-Lin Qi, Yang-Zhi Rao, Yu-Xian Li, Yong-Hong Liu, Andrew Li, Cale Seymour, Marike Palmer, Brian P. Hedlund, Wen-Jun Li & Zheng-Shuang Hua
Additional file 4. All commands, scripts, and R codes are included.

Additional file 11 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 11. Summary statistics for the differential expression analysis. DE: differentially expressed. LS: lateral septum, MPOA: medial preoptic area, NAc: nucleus accumbens.

Integrative analysis of a novel 5 methylated snoRNA genes prognostic signature in patients with glioma

Bing Zhao, Erbao Bian, Deran Zhang, Zhiwei Wang, Yu Wang, Zhigang Cheng, Zhihao Yang, Lianxin Li, Yinfei Zheng & Xiaoyu Yue
Supplementary Table 1 | Genes associated with risk scores.
Supplementary Table 2 | Expression levels and methylation levels of SNORA71B in gliomas (TCGA Database). Supplementary Table 3 | Fold change values of the 5 methylated snoRNA genes (TCGA Database).
Supplementary Table 4 | Methylation levels of five snoRNAs in gliomas (TCGA Database).
Supplementary Table 5 Clinic-pathological characteristics of 13 glioma patients.

Additional file 1 of Genome-wide association study uncovers major genetic loci associated with flowering time in response to active accumulated temperature in wild soybean population

Guang Yang, Wei Li, Chao Fan, Miao Liu, Jianxin Liu, Wenwei Liang, Ling Wang, Shufeng Di, Chao Fang, Haiyang Li, Guohua Ding, Yingdong Bi & Yongcai Lai
Additional file 1: Table S1. Prier used in this study. Table S2. List of 392 Glycine soja accessions and acumulated temperature zones. Table S3. 92 SNPs that significantly associated with flowering time in average across the two-year experiment (2020 and 2021). Table S4. The genes conresponding to the genomic regions surrounding ~50Kb of 92 SNPs that signficantly associated with flowering time in average in 2020 and 2021. Table S5. 28 candidate genes related to flowering...

Registration Year

  • 2022
    198

Resource Types

  • Dataset
    198

Affiliations

  • Inner Mongolia Agricultural University
    198
  • Shanghai Jiao Tong University
    143
  • Chinese Academy of Sciences
    132
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    125
  • Jilin University
    122
  • Zhejiang University
    113
  • University of Chinese Academy of Sciences
    106
  • Capital Medical University
    105
  • Nanjing Medical University
    99
  • Sichuan University
    97