924 Works

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...

N(6)-adenosine-methyltransferase-14 promotes glioma tumorigenesis by repressing argininosuccinate synthase 1 expression in an m6A-dependent manner

You-Qing Miao, Wei Chen, Jianfeng Zhou, Qiyang Shen, Ying Sun, Tao Li & Sheng-Chan Wang
Glioma is one of the leading causes of tumor-related deaths worldwide, but its potential mechanism remains unclear. This study aimed to explore the biological role and potential mechanism of argininosuccinate synthase 1 (ASS1) in glioma. The relative expression levels of ASS1 in glioma specimens and cell lines were calculated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and Western blotting. The biological functions of ASS1 were demonstrated using the 5-ethynyl-2ʹ-deoxyuridine (EdU) assay, transwell assay, and in...

Circular RNA hsa_circ_0006091 as a novel biomarker for hepatocellular carcinoma

Yongwei Zhang, Jun Li, Quanwei Cui, Panyi Hu, Shuangjiu Hu & Yeben Qian
Circular RNAs (circRNAs) are stable and extensively distributed non-coding RNA molecules that are differentially expressed in liver cancer tissues in the human body. In this study, we aimed to investigate circRNA as a novel candidate biomarker for hepatocellular carcinoma (HCC). For three groups of HCC and neighboring healthy tissues, the differentially expressed circRNAs were identified through high-throughput sequencing analysis. Reverse transcription PCR (RT-PCR) and quantitative polymerase chain reaction (qPCR) were employed for the evaluation of...

Nuclear receptor 4A1 (NR4A1) silencing protects hepatocyte against hypoxia-reperfusion injury in vitro by activating liver kinase B1 (LKB1)/AMP-activated protein kinase (AMPK) signaling

Yu Zheng, Yingying Tao, Xiaobo Zhan & Qi Wu
The nuclear receptor 4A1 (NR4A1) is widely involved in the regulation of cell survival and is related to ischemic injury in several organs. This research examined the emerging role and mechanism of NR4A1 in hepatocyte ischemia-reperfusion injury (IRI). BRL-3A cells were subjected to hypoxia-reperfusion (H/R) to simulate an IRI model in vitro. The expression of NR4A1 and liver kinase B1 (LKB1)/AMP-activated protein kinase (AMPK) pathway-related proteins (LKB1, AMPK, and ACC) was detected by western blotting...

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...

Mesozoic tectonic transition of the northeastern North China Craton: Evidence from adakitic rocks in southeastern Jilin Province, China

Yu-Song Chen, Zheng-Hong Liu, Qing-Bin Guan, Le Wan, Jin Liu & Tian-Yu Gao
Chronological and geochemical studies of adakites and adakitic rocks are important in understanding the tectonic evolution and geodynamic processes. We present new zircon U–Pb ages, Hf isotope, and geochemical analyses of adakitic rocks exposed in the Baishan area, southeastern Jilin Province, China. These new ages, together with existing age data, indicate that adakitic magmatism in southeastern Jilin Province can be subdivided into four stages: Early–Middle Triassic (251–235 Ma), Late Triassic (221–219 Ma), late Early–early Late...

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...

Prevalence of major morbidities and outcome of all hospitalized neonates. A retrospective cohort study of Huai’an neonatal survivals

Yaling Xu, Xiaoqin Zhu, Hui Wang, Zhaojun Pan, Xiaoqiong Li, Xiaojing Guo, Hongni Yue & Bo Sun
Reliable data for causal implication of neonatal survival in China are lacking. We assumed that by analyzing surviving data of in-hospital neonatal care based on all livebirths in Huai’an, prevalence of neonatal morbidity, mortality and causal relations may be derived comprehensively. Data of all regionally hospitalized neonates were retrospectively linked with corresponding whole livebirths (59,056) in 2015 as a cohort. Diagnoses of diseases and causes of deaths were redefined and categorized. Disease patterns, prevalence of...

Self-reported effects of perceived social support on marital quality in balanced translocation patients and their spouses undergoing preimplantation genetic testing in China: actor–partner interdependence model

Fengyi Mo, Xiaorui Hu, Qing Ma, Li Zhang & Lanfeng Xing
This study aimed to analyse the relationship between perceived social support and marital quality in balanced translocation patients and their spouses undergoing a preimplantation genetic testing (PGT) treatment cycle in China. The authors assessed the actor and partner effects of perceived social support on marital quality in patient–spouse dyads using a dyadic analysis approach. In total, 59 couples were assessed using self-report questionnaires for marital quality and perceived social support. There were significant differences in...

Comparative metabolic profiling of root, leaf, fruit, and stem tissues of Panax notoginseng

Rui Shi, Bingjie Xiong, Shu He, Can Liu, Jiftah Ben-Asher, Abraham Rami Horowitz, Shu Wang & Xiahong He
Panax notoginseng is highly used in traditional Chinese medicine, and its root is valued for ginsenoside contents. However, evidence suggests that other plant parts such as fruit, leaves, and stem are also potential sources of bioactive compounds. Therefore, this study aimed at providing insight into the differential accumulation of metabolites in fruit, leaf, root, and stem tissues collected from P. notoginseng. A total of 808 metabolites from 11 major metabolite classes were identified. Furthermore, 32...

Additional file 6 of Lrpap1 deficiency leads to myopia through TGF-β-induced apoptosis in zebrafish

Shanshan Liu, Ting Chen, Binghao Chen, Yijun Liu, Xiaohe Lu & Jiali Li
Additional file 5. Supplementary Table S4. Gene information of GO analysis.

Additional file 6 of Lrpap1 deficiency leads to myopia through TGF-β-induced apoptosis in zebrafish

Shanshan Liu, Ting Chen, Binghao Chen, Yijun Liu, Xiaohe Lu & Jiali Li
Additional file 5. Supplementary Table S4. Gene information of GO analysis.

miR-140-3p/usp36 axis mediates ubiquitination to regulate PKM2 and suppressed the malignant biological behavior of breast cancer through Warburg effect

Hao Wu, Yile Jiao, Chen Zhou, Xinyi Guo, Zhenru Wu & Qing Lv
Breast cancer is a phenomenon in which breast epithelial cells proliferate out of control under the action of various carcinogenic factors. However, the role of USP36 in breast cancer is unknown. We analyzed the expression of USP36 in breast cancer and its association with poor prognosis in breast cancer patients. The effect of USP36 on malignant biological behavior of breast cancer was verified by cell functional experiments. The upstream regulatory mechanism of USP36 was analyzed...

Additional file 4 of Exploration of the role of Cuproptosis genes and their related long non-coding RNA in clear cell renal cell carcinoma: a comprehensive bioinformatics study

Dian Xia, Qi Liu, Wen Jiao, Longfei Peng, Qi Wang, ZhouTing Tuo & Liangkuan Bi
Additional file 4: Table S2. The names of the 8 cuproptosis-related lncRNAsin the model.

Additional file 5 of Exploration of the role of Cuproptosis genes and their related long non-coding RNA in clear cell renal cell carcinoma: a comprehensive bioinformatics study

Dian Xia, Qi Liu, Wen Jiao, Longfei Peng, Qi Wang, ZhouTing Tuo & Liangkuan Bi
Additional file 5: Table S3. Theclinical features between the entire set, training set and the testing set inthe risk model.

Molasses fermentation to produce low-cost carbon source for denitrification

Chang Liu & Kai Cheng
In the present work, the fermentation of molasses using Saccharomyces cerevisiae was optimized in terms of denitrification efficiency, using the relative total nitrogen (TN) removal ratio and the C/N consumption ratio as the indicators. The denitrification efficiency in different wastewater was also measured in the presence of different carbon sources for denitrification, that is, fermentation broth, unfermented molasses, sodium acetate, ethanol and methanol. The results indicated that the optimal fermentation conditions were as follows: pH...

Molasses fermentation to produce low-cost carbon source for denitrification

Chang Liu & Kai Cheng
In the present work, the fermentation of molasses using Saccharomyces cerevisiae was optimized in terms of denitrification efficiency, using the relative total nitrogen (TN) removal ratio and the C/N consumption ratio as the indicators. The denitrification efficiency in different wastewater was also measured in the presence of different carbon sources for denitrification, that is, fermentation broth, unfermented molasses, sodium acetate, ethanol and methanol. The results indicated that the optimal fermentation conditions were as follows: pH...

Additional file 5 of Genome-wide identification of key enzyme-encoding genes and the catalytic roles of two 2-oxoglutarate-dependent dioxygenase involved in flavonoid biosynthesis in Cannabis sativa L.

Xuewen Zhu, Yaolei Mi, Xiangxiao Meng, Yiming Zhang, Weiqiang Chen, Xue Cao, Huihua Wan, Wei Yang, Jun Li, Sifan Wang, Zhichao Xu, Atia Tul Wahab, Shilin Chen & Wei Sun
Additional file 5: Table S4. The list of flavonoid-related genes in the phylogenetic analysis from C. sativa and other plant species.

Additional file 8 of Genome-wide identification of key enzyme-encoding genes and the catalytic roles of two 2-oxoglutarate-dependent dioxygenase involved in flavonoid biosynthesis in Cannabis sativa L.

Xuewen Zhu, Yaolei Mi, Xiangxiao Meng, Yiming Zhang, Weiqiang Chen, Xue Cao, Huihua Wan, Wei Yang, Jun Li, Sifan Wang, Zhichao Xu, Atia Tul Wahab, Shilin Chen & Wei Sun
Additional file 8: Table S5. Cloning primers of CsFLS2 and CsFLS3 in C. sativa.

Comparative transcriptome and proteome analyses of the longissimus dorsi muscle for explaining the difference between donkey meat and other meats

Yan Sun, Yonghui Wang, Yuhua Li, Haijing Li, Changfa Wang & Qin Zhang
Domestic donkeys (Equus asinus) have been maintained mainly for service purposes in the past. Nowadays, there is an increasing interest in donkey milk and meat production in several countries, including China. Donkey meat is highly consumed because of its nutritional value and unique flavor. However, genomic studies on donkey meat are limited. Therefore, in this study, we aimed to examine the molecular difference of longissimus dorsi muscles of donkey, cow, and goat. RNA sequencing and...

CIED-Emission factors, 2015-2018

Ling Tang, Min Jia, Junai Yang, Ling Li, Xin Bo & Zhifu Mi
The Chinese Industrial Emissions Database (CIED) provides inventory of particulate matter (PM), SO2 and NOX from Chinese industries from 2015 to 2018, based on direct measurements from China’s continuous emission monitoring systems (CEMS) network. This document provides emissions factors for China’s different industrial emission sources.

Additional file 2 of Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus

Zengdong Tan, Yan Peng, Yao Xiong, Feng Xiong, Yuting Zhang, Ning Guo, Zhuo Tu, Zhanxiang Zong, Xiaokun Wu, Jiang Ye, Chunjiao Xia, Tao Zhu, Yinmeng Liu, Hongxiang Lou, Dongxu Liu, Shaoping Lu, Xuan Yao, Kede Liu, Rod J. Snowdon, Agnieszka A. Golicz, Weibo Xie, Liang Guo & Hu Zhao
Additional file 2: Table S1. Genome-wide eQTLs identified at 20 DAF. Table S2. Genome-wide eQTLs identified at 40 DAF. Table S3. Genome-wide eGene-eQTLs identified at 20 DAF. Table S4. Genome-wide eGene-eQTLs identified at 40 DAF. Table S5. Results of GO enrichment analysis of specifically identified eGenes at 20 DAF. Table S6. Results of GO enrichment analysis of specifically identified eGenes at 40 DAF. Table S7. Summary of ATAC-Seq data. Table S8. List of homoeologous genes...

VIBRATION CHARACTERISTICS, CHEMICAL BONDS AND WEAK INTERACTIONS OF 4- AND 5-HYDROXYSALICYLIC ACID INVESTIGATED BY TERAHERTZ SPECTROSCOPY AND DENSITY FUNCTIONAL THEORY

Yuan Tang, Zhi Li, Yan Guo, Xianhua Yin, Shan Tu & Dapeng Zhang
The terahertz (THz) absorption spectra of 4- and 5-hydroxysalicylic acid were measured by terahertz time-domain spectroscopy (THz-TDS) in the range of 0.4-2.8 THz. The unit cells of both were calculated by density functional theory (DFT), and the theoretical simulation and experimental data were basically in agreement. To further interpret the origin of the characteristic absorption peaks, vibration characteristics and interactions of the unit cell model were analyzed by using potential energy distribution (PED) and interaction...

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

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

Registration Year

  • 2022
    924

Resource Types

  • Dataset
    924

Affiliations

  • West China Hospital of Sichuan University
    924
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    589
  • Sichuan University
    571
  • Shanghai Jiao Tong University
    525
  • Zhejiang University
    511
  • Fudan University
    503
  • Capital Medical University
    494
  • Nanjing Medical University
    483
  • University of Chinese Academy of Sciences
    467
  • Huazhong University of Science and Technology
    453