Yuanyuan Jia

Inner Mongolia University

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i-10 index

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Co-Authors

Yu‐Dong Cai

Michigan Technological University

Chang Tian

Shandong Academy of Sciences

Huabing Sun

Tianjin Medical University

Xupei Huang

Florida Atlantic University

Pei Tang

University of Pittsburgh

Zhenhua Dang

Inner Mongolia University

Chi Zhang

McGovern Institute for Brain Research

Junyu Tian

Tianjin Medical University

Jingjing Jiang

Huazhong University of Science and Technology

Dehao Yu

Tianjin Medical University

Cooperative Institutions

Chinese Academy of Sciences

Nanjing Agricultural University

Peking University

Tianjin Medical University General Hospital

Tianjin Medical University

Chinese Academy of Medical Sciences & Peking Union Medical College

Inner Mongolia University

Sun Yat-sen University

Shanghai Jiao Tong University

University of Chinese Academy of Sciences

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A Novel Approach to Multiple Sequence Alignment Using Multiobjective Evolutionary Algorithm Based on Decomposition

IEEE Journal of Biomedical and Health Informatics (2015)

Huazheng Zhu Zhongshi He Yuanyuan Jia

Multiple sequence alignment (MSA) is a fundamental and key step for implementing other tasks in bioinformatics, such as phylogenetic analyses, identification of conserved motifs and domains, structure prediction, etc. Despite the fact that there are many methods to implement MSA, biologically perfect alignment approaches are not found hitherto. This paper proposes a novel idea to perform MSA, where MSA is treated as a multiobjective optimization problem. A famous multiobjective evolutionary algorithm framework based on decomposition is applied for solving MSA, named MOMSA. In the MOMSA algorithm, we develop a new population initialization method and a novel mutation operator. We compare the performance of MOMSA with several alignment methods based on evolutionary algorithms, including VDGA, GAPAM, and IMSA, and also with state-of-the-art progressive alignment approaches, such as MSAprobs, Probalign, MAFFT, Procons, Clustal omega, T-Coffee, Kalign2, MUSCLE, FSA, Dialign, PRANK, and CLUSTALW. These alignment algorithms are tested on benchmark datasets BAliBASE 2.0 and BAliBASE 3.0. Experimental results show that MOMSA can obtain the significantly better alignments than VDGA, GAPAM on the most of test cases by statistical analyses, produce better alignments than IMSA in terms of TC scores, and also indicate that MOMSA is comparable with the leading progressive alignment approaches in terms of quality of alignments.

Multiple sequence alignment

Initialization

Benchmark (surveying)

Sequence (biology)

10.1109/jbhi.2015.2403397

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Citations (37)

PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study

Database (2023)

Jian Hu Baisha Huang Hao Yin Kaijie Qi Yuanyuan Jia

Pear (Pyrus ssp.) belongs to Rosaceae and is an important fruit tree widely cultivated around the world. Currently, challenges to cope with the burgeoning sets of multiomics data are rapidly increasing. Here, we constructed the Pear Multiomics Database (PearMODB) by integrating genome, transcriptome, epigenome and population variation data, and aimed to provide a portal for accessing and analyzing pear multiomics data. A variety of online tools were built including gene search, BLAST, JBrowse, expression heatmap, synteny analysis and primer design. The information of DNA methylation sites and single-nucleotide polymorphisms can be retrieved through the custom JBrowse, providing an opportunity to explore the genetic polymorphisms linked to phenotype variation. Moreover, different gene families involving transcription factors, transcription regulators and disease resistance (nucleotide-binding site leucine-rich repeat) were identified and compiled for quick search. In particular, biosynthetic gene clusters (BGCs) were identified in pear genomes, and specialized webpages were set up to show detailed information of BGCs, laying a foundation for studying metabolic diversity among different pear varieties. Overall, PearMODB provides an important platform for pear genomics, genetics and breeding studies. Database URL http://pearomics.njau.edu.cn.

10.1093/database/baad050

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Citations (9)

Effect of different moisture treatments on photosynthetic characteristics of Rehmannia glutinosa Libosch.

Journal of Northwest A&F University (2009)

Yuanyuan Jia Yujie He Liang Zong-suo Dong Fang Fang Lin

【Objective】 Study on the photosynthetic characteristics of Rehmannia glutinosa Libosch was done under different moisture treatments to provide theoretical basis for their water supply during growing.【Method】 Beijing No.1 as experiments material,the changes of photosynthetic characteristics and chlorophyll content in R.glutinosa Libosch under manmade conditions(the treatments of soil moisture Ⅰ-Ⅲ were 65%,50% and 35% of field capacity) were studied.【Result】 The results were as follows:the net photosynthetic rate of three moisture treatments increased with the increase of photosynthetically active radiation during the seedling,anthesis and root enlargement stage.Under treatmentⅠand treatmentⅡ,light compensation point of the R.glutinosa Libosch was about 1 600 μmol/(m2·s),while under treatment Ⅲ,light compensation point of the R.glutinosa Libosch was about 1 400 μmol/(m2·s).With the growing,the net photosynthetic rate,stomatal conductance,intercellular CO2 concentration,transpiration rate and chlorophyll content increased obviously.The sequence from the hightest to the lowest was treatmentⅠ treatmentⅡtreatment Ⅲ.【Conclusion】 Keeping the soil moisture to 50% of field capacity during the seeding period but 65% during the flowering period and storage root thickening period is the best irrigation arrangement for the leaves of R.glutinosa Libosch to make photosynthesis.

Rehmannia glutinosa

Compensation point

Stomatal Conductance

Photosynthetically active radiation

Photosynthetic capacity

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Citations (1)

Rapid GSH detection and versatile peptide/protein labelling to track cell penetration using coumarin-based probes

The Analyst (2022)

Xue Li Dehao Yu Jing Sun Liangyu Guan Cheng‐Zhi Xie

Biothiols play essential roles in balancing the redox state and modulating cellular functions. Fluorescent probes for monitoring/labelling biothiols often suffer from slow reaction rates, strong background fluorescence and cytotoxic byproduct release. Thus, developing facile and versatile probes to overcome the challenges is still in high demand. Here, we report four coumarin-maleimides as fast responding and fluorogenic probes to detect GSH or label peptides/proteins. The probes quantitatively and selectively react with GSH via Michael addition within 1-2 min, achieving an 11-196-fold increase in fluorescence quantum yield via blockage of the photoinduced electron transfer (PET) process. Optimized probe 4 is applied for the detection of GSH in vitro (A549 cells) and in vivo (zebrafish embryos). Taking advantage of the fast Michael addition between the maleimide moiety and the sulfhydryl group, we expand the application of our method for fluorescent labelling of peptides/proteins and for tracking their cellular uptake process. The labelling strategy works for both Cys-bearing and Cys-free proteins after the introduction of a sulfhydryl group using Traut's reagent. Fluorescence assay reveals that the TAT-peptide can efficiently enter cells, but H3 protein, part of nucleosomes, prefers to bind on the cell membrane by electrostatic interactions, shedding light on the cellular uptake activity of nucleosomes and affording a potential membrane staining strategy. Overall, our study illustrates the broad potential of coumarin-maleimide based dual-functional probes for GSH detection and versatile protein labelling in biochemical research.

Penetration (warfare)

10.1039/d2an01510b

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Citations (17)

Targeting Cancer Metabolism Plasticity with JX06 Nanoparticles via Inhibiting PDK1 Combined with Metformin for Endometrial Cancer Patients with Diabetes

Advanced Science (2022)

Xiao Yang Yuan Cheng Jingyi Zhou Lingpu Zhang Xingchen Li

Abstract Diabetes is closely related to the occurrence of endometrial cancer (EC) and its poor prognosis. However, there is no effective clinical treatment for EC patients with diabetes (patient EC+/dia+ ). To explore new therapeutic targets, Ishikawa is cultured with high glucose (Ishikawa HG ) mimicking hyperglycemia in patient EC+/dia+ . Subsequently, it is discovered that Ishikawa HG exhibits glucose metabolic reprogramming characterized by increased glycolysis and decreased oxidative phosphorylation. Further, pyruvate dehydrogenase kinase 1 (PDK1) is identified to promote glycolysis of Ishikawa HG by proteomics. Most importantly, JX06, a novel PDK1 inhibitor combined metformin (Met) significantly inhibits Ishikawa HG proliferation though Ishikawa HG is resistant to Met. Furthermore, a reduction‐sensitive biodegradable polymer is adopted to encapsulate JX06 to form nanoparticles (JX06‐NPs) for drug delivery. It is found that in vitro JX06‐NPs have better inhibitory effect on the growth of Ishikawa HG as well as patient‐derived EC cells (PDC) than JX06. Additionally, it is found that JX06‐NPs can accumulate to the tumor of EC‐bearing mouse with diabetes (mice EC+/dia+ ) after intravenous injection, and JX06‐NPs combined Met can significantly inhibit tumor growth of mice EC+/dia+ . Taken together, the study demonstrates that the combination of JX06‐NPs and Met can target the cancer metabolism plasticity, which significantly inhibits the growth of EC, thereby provides a new adjuvant therapy for patients EC+/dia+ .

Carbohydrate Metabolism

10.1002/advs.202104472

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Citations (24)

Aesthetical Connotation of Kant’s Pre-empirical Sensation

Journal of Harbin Teachers College (2005)

Yuanyuan Jia

The writer believes that Kant’s philosophy comes from pre-empirical sensation, which,however,gives up the sensation idea of 17th century philosophy system, and redefines the power on the subject,or the subject’s inner sensation plays very important role in knowledge acquisition.With the analysis on the synthetic judgment,phenomenon,appearance and pure calculation,the aesthetical connotation of pre-empirical sensation is revealed.

Connotation

Sensation

Phenomenon

Empirical Research

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Citations (0)

Acute glucose fluctuation promotes in vitro intestinal epithelial cell apoptosis and inflammation via the NOX4/ROS/JAK/STAT3 signaling pathway

Experimental and Therapeutic Medicine (2021)

Bingyu Chen Yuanyuan Jia Dongxue Lu Zhiguang Sun

High blood glucose commonly occurs in patients with diabetes mellitus, but little is known of its effects on intestinal epithelial cells, or its associated mechanisms of action therein. In the present study, intestinal epithelial cells were assigned to five groups: i) The normal glucose (NG) group, incubated in 5.0 mmol/l glucose; ii) the constant high glucose (CHG) group, treated with 25.0 mmol/l glucose; iii) the intermittent high glucose (IHG) group, treated with alternating doses of 5.0 and 25.0 mmol/l glucose every 8 h; iv) the mannose group, cultured in 25.0 mmol/l mannose (the osmotic control); and v) the IHG glucose + GKT137831 group, pretreated with 100 nmol/l NADPH oxidase 4 (NOX4) inhibitor, GKT137831, and then exposed to IHG. TNF‑α, IL‑1 and IL‑6 levels were quantified using ELISA kits. Intestinal epithelial cell apoptosis was assessed by flow cytometry and oxidative stress was evaluated by reactive oxygen species (ROS) and malondialdehyde (MDA) detection. The expression levels of proteins associated with apoptosis and involved in the signal transduction of Janus kinase (JAK)/STAT3 pathway were assessed using western blot analysis. The results indicated that NOX4 expression was significantly higher in the CHG group than in the NG group (P<0.01), but lower than in the IHG group (P<0.001). The IHG group exhibited apoptosis and oxidative stress accompanied by the most significant increase in MDA, ROS and inflammatory cytokine levels (P<0.001), which was followed by that of the CHG group. Additionally, the IHG group exhibited reduced Bcl‑2, as well as enhanced Bax and cleaved caspase‑3 levels compared with the CHG group (P<0.001). Furthermore, the level of phosphorylated (p‑)JAK/p‑STAT3 was increased to a greater extent in the IHG group than in the CHG group (P<0.001). In conclusion, the findings of the present study indicated that CHG may trigger intestinal epithelial cell apoptosis and inflammation through the NOX4/ROS/JAK/STAT3 pathway, which may be aggravated by acute glucose fluctuation.

NOX4

Malondialdehyde

10.3892/etm.2021.10120

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Citations (14)

Astragaloside IV Inhibits Doxorubicin-Induced Cardiomyocyte Apoptosis Mediated by Mitochondrial Apoptotic Pathway <i>via</i> Activating the PI3K/Akt Pathway

Chemical and Pharmaceutical Bulletin (2013)

Yuanyuan Jia Daiying Zuo Zengqiang Li Hanmo Liu Zhengning Dai

Doxorubicin (DOX) is a widely used antitumor drug whose application is seriously limited by its cardiotoxicity. Mitochondria-mediated cardiomyocyte apoptosis plays a critical role in DOX-induced cardiotoxicity (DIC). The aim of the present study was to investigate the protective effect of astragaloside IV (3-O-beta-D-xylopyranosyl-6-O-beta-D-glucopyranosyl-cycloastragenol, AS-IV), a pure saponin isolated from Astragalus membranaceus, against DOX-induced cardiomyocyte apoptosis in primary cultured neonatal rat cardiomyocytes. Immunocytochemistry and Microculture Tetrazolium (MTT) assays showed that AS-IV significantly reduced DOX-induced cardiomyocyte loss. Additionally, AS-IV markedly ameliorated DOX-caused cardiomyocyte dysfunction via restoring the beating cell ratio and beating rate in cardiomyocytes. Furthermore, AS-IV substantially reduced the mitochondrial reactive oxygen species (ROS) production and lactate dehydrogenase (LDH), creatine kinase-MB isoenzyme (CK-MB) and cytochrome c (CytC) release, and restored the reduced ATP level, succinate dehydrogenase (SDH) and ATP synthase activities induced by DOX, suggesting that AS-IV significantly attenuated DOX-induced mitochondrial damage and dysfunction. It was further observed that DOX-induced cardiomyocyte apoptosis, as qualitatively evaluated by Hoechst 33258 staining and accurately quantified by flow cytometry, was markedly inhibited by AS-IV. Western blot analysis manifested that AS-IV significantly inhibited the activation of mitochondrial apoptotic pathway (MAP) via inducing the phosphorylation of Akt and Bad. Furthermore, phosphatidylinositol 3-kinase (PI3K) inhibitor 2-(4-morpholinyl)-8-phenyl-1(4H)-benzopyran-4-one hydrochloride (LY294002) remarkably inhibited the anti-apoptotic effect of AS-IV. Moreover, AS-IV didn't compromise the antitumor activity of DOX. Taken together, our findings indicate that AS-IV ameliorates DIC, and this beneficial effect appears to be dependent on the activation of the PI3K/Akt pathway. Thus, AS-IV may hold promise as an efficient cardioprotective agent against DIC.

LY294002

Cardiotoxicity

10.1248/cpb.c13-00556

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Citations (68)

A newly emerging HIV-1 circulating recombinant form (CRF110_BC) comprising subtype B and C among intravenous drug users in Yunnan, China

Journal of Infection (2020)

Jianjian Li Qinghua Gao Mi Zhang Jiafa Liu Yuanyuan Jia

10.1016/j.jinf.2020.12.015

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Citations (7)

Characterization of bacteriostatic sausage casing: A composite of bacterial cellulose embedded with ɛ-polylysine