Publications by authors named "Xiaoyue Yang"

34 Publications

Characterization of Four Novel H5N6 Avian Influenza Viruses with the Internal Genes from H5N1 and H9N2 Viruses and Experimental Challenge of Chickens Vaccinated with Current Commercially Available H5 Vaccines.

Transbound Emerg Dis 2021 Apr 19. Epub 2021 Apr 19.

Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Since 2014, highly pathogenic avian influenza H5N6 viruses have been responsible for outbreaks in poultry. In this study, four H5N6 virus strains were isolated from fecal samples of sick white ducks and dead chickens in Shandong in 2019. These H5N6 viruses were triple-reassortant viruses that have not been previously characterized. Their HA genes were derived from the H5 viruses and were closely related to the vaccine strain Re-11. Their NA genes all fell into the N6-like lineage and the internal gene were derived from H5N1 and H9N2 viruses. They all showed high pathogenicity in mice and caused lethal infection with high rates of transmission in chickens. Moreover, the SPF chickens inoculated with the current used H5 (Re-11 and Re-12 strains)/H7 (H7-Re-2 strain) trivalent inactivated vaccines in China were completely protected from these four H5N6 viruses. Our study indicated the necessity of continued surveillance for H5 Influenza A viruses and the importance of timely update of vaccine strains in poultry industry.
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http://dx.doi.org/10.1111/tbed.14110DOI Listing
April 2021

Walnut green husk polysaccharides prevent obesity, chronic inflammatory responses, nonalcoholic fatty liver disease and colonic tissue damage in high-fat diet fed rats.

Int J Biol Macromol 2021 Apr 19;182:879-898. Epub 2021 Apr 19.

College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China. Electronic address:

High-fat (HF) diets cause obesity, gut microbial dysbiosis and associated disorders and inflammatory bowel disease (IBD) due to increased intestinal permeability, which is an important reason for chronic inflammation and oxidative stress. This study was to investigate the effects and mechanism by which walnut green husk polysaccharides (WGHP) prevents obesity, oxidative stress, inflammation, liver and colon damage in HF diet induced rats. We found that WGHP alleviated HF-induced abnormal weight gain, disordered lipid metabolism, inflammation, oxidative stress, colonic tissue injury and up-regulate the expression level of colonic tight junction protein in the rats. Besides, the administration of WGHP promoted browning of iWAT and thermogenesis in BAT of HF-fed rats, and improved gut microbiota dysbiosis by increasing the bacterial diversity and reducing the relative abundance of potential pathogenic bacteria in the colon of the rats. Furthermore, WGHP consumption not only increased the SCFAs content but also improved the relative abundance of Prevotellaceae and Allobaculum in the gut of rats. Our results suggest that the protective effect of WGHP on metabolic inflammation caused by HF may be due to the regulation of gut microbiota and SCFAs.
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http://dx.doi.org/10.1016/j.ijbiomac.2021.04.047DOI Listing
April 2021

Hybrid speciation via inheritance of alternate alleles of parental isolating genes.

Mol Plant 2021 02 18;14(2):208-222. Epub 2020 Nov 18.

Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China; State Key Laboratory of Grassland Agro-Ecosystem, Innovation Institute of Ecology and Life Sciences, Lanzhou University, Lanzhou 730000, China. Electronic address:

It is increasingly realized that homoploid hybrid speciation (HHS), which involves no change in chromosome number, is an important mechanism of speciation. HHS will likely increase in frequency as ecological and geographical barriers between species are continuing to be disrupted by human activities. HHS requires the establishment of reproductive isolation between a hybrid and its parents, but the underlying genes and genetic mechanisms remain largely unknown. In this study, we reveal by integrated approaches that reproductive isolation originates in one homoploid hybrid plant species through the inheritance of alternate alleles at genes that determine parental premating isolation. The parent species of this hybrid species are reproductively isolated by differences in flowering time and survivorship on soils containing high concentrations of iron. We found that the hybrid species inherits alleles of parental isolating major genes related to flowering time from one parent and alleles of major genes related to iron tolerance from the other parent. In this way, it became reproductively isolated from one parent by the difference in flowering time and from the other by habitat adaptation (iron tolerance). These findings and further modeling results suggest that HHS may occur relatively easily via the inheritance of alternate parental premating isolating genes and barriers.
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http://dx.doi.org/10.1016/j.molp.2020.11.008DOI Listing
February 2021

Mapping Complex Disulfide Bonds via Implementing Photochemical Reduction Online with Liquid Chromatography-Mass Spectrometry.

Authors:
Xiaoyue Yang Yu Xia

J Am Soc Mass Spectrom 2021 Jan 2;32(1):307-314. Epub 2020 Nov 2.

MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China.

Assigning disulfide linkage is a crucial task for protein identification. The current bottom-up proteomics workflow has limitations in characterizing peptide digests containing multiple disulfide bonds due to the difficulty of controlling partial reduction via conventional chemical reduction methods. Previously, our lab reported the development of an acetone/2-propanol (IPA) photoinitiating system for rapid (on second time scale) and tunable disulfide bond reduction. Herein, we incorporated this reaction system onto a liquid chromatography-mass spectrometry (LC-MS) system for bottom-up protein analysis applications. The photochemical reduction reaction was implemented in a flow microreactor which allowed for up to 15 s 254 nm UV irradiation. The microreactor was installed post LC separation and right before electrospray ionization, while a T-junction was used to introduce the photoinitiating solution to the LC eluent before entering the microreactor. The degree of disulfide reduction was tunable from partial reduction to complete reduction for peptides containing one or multiple disulfide bonds. Significantly improved sequence coverage was obtained from complete disulfide reduction, while assignment of the disulfide connectivity was facilitated from partial disulfide reduction when coupled with tandem mass spectrometry via collision-induced dissociation. As a proof-of-concept test, trypsin digests of lysozyme (four disulfide bonds) and bovine serum albumin (BSA, 17 disulfide bonds) were analyzed by the LC-MS system coupled with online reduction. Sequence coverage was improved from 35% to 100% and 13% to 87% for lysozyme and BSA, respectively. All four disulfide bonds of lysozyme were determined. For BSA, nine disulfide bonds were characterized and eight adjacent disulfide bonds were narrowed down.
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http://dx.doi.org/10.1021/jasms.0c00324DOI Listing
January 2021

Exogenous Hydrogen Sulfide Within the Nucleus Ambiguus Inhibits Gastrointestinal Motility in Rats.

Front Physiol 2020 11;11:545184. Epub 2020 Sep 11.

Key Laboratory of Animal Resistance, School of Life Sciences, Shandong Normal University, Jinan, China.

Hydrogen sulfide (HS) is a neuromodulator in the central nervous system. However, the physiological role of HS in the nucleus ambiguus (NA) has rarely been reported. This research aimed to elucidate the role of HS in the regulation of gastrointestinal motility in rats. Male Wistar rats were randomly assigned to sodium hydrosulfide (NaHS; 4 and 8 nmol) groups, physiological saline (PS) group, capsazepine (10 pmol) + NaHS (4 nmol) group, L703606 (4 nmol) + NaHS (4 nmol) group, and pyrrolidine dithiocarbamate (PDTC, 4 nmol) + NaHS (4 nmol) group. Gastrointestinal motility curves before and after the injection were recorded using a latex balloon attached with a pressure transducer, which was introduced into the pylorus through gastric fundus. The results demonstrated that NaHS (4 and 8 nmol), an exogenous HS donor, remarkably suppressed gastrointestinal motility in the NA of rats ( < 0.01). The suppressive effect of NaHS on gastrointestinal motility could be prevented by capsazepine, a transient receptor potential vanilloid 1 (TRPV1) antagonist, and PDTC, a NF-κB inhibitor. However, the same amount of PS did not induce significant changes in gastrointestinal motility ( > 0.05). Our findings indicate that NaHS within the NA can remarkably suppress gastrointestinal motility in rats, possibly through TRPV1 channels and NF-κB-dependent mechanism.
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http://dx.doi.org/10.3389/fphys.2020.545184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7516268PMC
September 2020

The protective effects of walnut green husk polysaccharide on liver injury, vascular endothelial dysfunction and disorder of gut microbiota in high fructose-induced mice.

Int J Biol Macromol 2020 Nov 10;162:92-106. Epub 2020 Jun 10.

College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China.

This study aimed to investigate the protective effects of walnut green husk polysaccharide (WGHP) on liver injury, vascular endothelial dysfunction and disorder of gut microbiota in mice induced by high fructose (HF) diet. The chemical analysis results show that the walnut green husk polysaccharide is a low molecular weight acidic heteropolysaccharide, composed mainly of glucuronic acid, arabinose and galactose. Biochemical analysis showed that WGHP significantly improved glucose metabolism and lipid metabolism and decreased oxidative stress in HF-diet induced obesity mice. Histopathological observation of liver and cardiovascular aorta confirmed the protective effects of WGHP on hepatic steatosis and vascular endothelial dysfunction. Furthermore, 16S rRNA sequencing results demonstrated that WGHP reversed the disorders of gut microbiota caused by HF, decreased the relative abundance of Verrucomicrobia and increased the relative abundance of Deferribacteres at the phylum level, decreased the relative abundance of Akkermansia, Lachnoclostridium and norank_f__Muribaculaceae and increased the relative abundance of Prevotellaceae_UCG-001, Helicobacter, Alloprevotella and Allobaculum at the genus levels. Our results indicate that WGHP may act as a functional polysaccharide for protecting liver and cardiovascular in HF-fed mice.
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http://dx.doi.org/10.1016/j.ijbiomac.2020.06.055DOI Listing
November 2020

Transient fault diagnosis for traction control system based on optimal fractional-order method.

ISA Trans 2020 Jul 12;102:365-375. Epub 2020 Mar 12.

School of Automation, Central South University, Changsha, 410083, PR China.

Efficient fault diagnosis of traction control system (TCS) has always been a vital technology for high speed train. Transient fault (TF) derives in harsh operation conditions and manufacturing defect, and its timely diagnosis can prevent catastrophic consequences of TCS or provide degradation information of components. However, TF is easily swallowed by background noise, especially at early stage of failure. This problem brings hardship into feature extraction. Aiming at overcoming the noise problem confronted in weak fault feature extraction, the typical TFs of traction control system are described, and feasibility of speed-based fault diagnosis is demonstrated. Then, an optimal fractional-order method is proposed for TF diagnosis, which suppresses background noise and amplifies the faulty part of the signal. Afterwards, kurtosis and fault duration time are applied to locate the fault component. Three fault diagnosis cases are investigated to validate the application of this methodology.
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http://dx.doi.org/10.1016/j.isatra.2020.03.006DOI Listing
July 2020

Anti-tumor immune response varies among individuals: A gene expression profiling of mouse melanoma.

Int Immunopharmacol 2020 Mar 20;80:106211. Epub 2020 Jan 20.

Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China. Electronic address:

Melanoma is amongst the most aggressive malignant tumors. The purpose of this study is to detect the tumor microenvironment systematically using multi-omics analyses and to propose strategies for precision medicine. Multiple factors of tumor microenvironment contribute to the drug resistance and immune surveillance failure. Here we analyzed genome mutations and characterized the immune state of tumor microenvironments in mouse melanoma by whole exome sequencing (WES) and RNA sequencing (RNA-Seq) approaches. Somatic mutation analysis revealed 35.1% novel mutations in mouse tumors when compared with B16F10 cell line, provided a basis for multi-site sequencing for accurate neoantigen selection. Mutation cluster, gene expression comparison, and gene ontology (GO) analyses by R packages proved DNA repair damage, inflammation, slower cell division, and metabolic change in tumor microenvironment. Further analyses of T-cell receptor (TCR) sequences, immune signaling pathway activation, tumor infiltrated immune cells and chemokine expression revealed extensive difference of antitumor immune response among individuals. Our study revealed the characteristics of tumor microenvironment with mouse melanoma model, suggested the need of comprehensive genome mutations and personal immune state analyses for cancer precision medicine.
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http://dx.doi.org/10.1016/j.intimp.2020.106211DOI Listing
March 2020

A chromosome-level reference genome of the hornbeam, Carpinus fangiana.

Sci Data 2020 01 21;7(1):24. Epub 2020 Jan 21.

Stat Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000, Lanzhou, China.

Betulaceae, the birch family, comprises six living genera and over 160 species, many of which are economically valuable. To deepen our knowledge of Betulaceae species, we have sequenced the genome of a hornbeam, Carpinus fangiana, which belongs to the most species-rich genus of the Betulaceae subfamily Coryloideae. Based on over 75 Gb (~200x) of high-quality next-generation sequencing data, we assembled a 386.19 Mb C. fangiana genome with contig N50 and scaffold N50 sizes of 35.32 kb and 1.91 Mb, respectively. Furthermore, 357.84 Mb of the genome was anchored to eight chromosomes using over 50 Gb (~130x) Hi-C sequencing data. Transcriptomes representing six tissues were sequenced to facilitate gene annotation, and over 5.50 Gb high-quality data were generated for each tissue. The structural annotation identified a total of 27,381 protein-coding genes in the assembled genome, of which 94.36% were functionally annotated. Additionally, 4,440 non-coding genes were predicted.
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http://dx.doi.org/10.1038/s41597-020-0370-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6972722PMC
January 2020

Identification of an Activating Mutation in the Extracellular Domain of HER2 Conferring Resistance to Pertuzumab.

Onco Targets Ther 2019 30;12:11597-11608. Epub 2019 Dec 30.

Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China.

Background: The aberrant expression of HER2 is highly associated with tumour occurrence and metastasis, therefore HER2 is extensively targeted for tumour immunotherapy. For example, trastuzumab and pertuzumab are FDA-approved monoclonal antibodies that target HER2-positive tumour cells. Despite their advances in clinical applications, emerging resistance to these two HER2-targeting antibodies has hindered their further application. Somatic mutations in HER2 receptor have been identified as one of the major reasons for resistance to anti-HER2 antibodies.

Methods: We analysed the frequency of somatic mutations in various tumour types based on TCGA and COSMIC databases. Then, the effect of the most frequent mutation (S310F) on the interaction between pertuzumab and HER2 was analysed by molecular modelling analysis. The effect of the S310F mutation was further evaluated through multiple in vitro binding experiments and antitumour activity assays.

Results: We found through bioinformatics analysis that S310F, an activating mutation in the HER2 extracellular domain, was the most frequent mutation in HER2. The S310F mutation was shown to confer resistance of HER2-positive tumour cells to pertuzumab treatment. With molecular modelling analysis, we confirmed the possibility that the S310F mutation might disrupt the interaction between pertuzumab and HER2 as a result of a significant change in the critical residue S310. Further functional analyses revealed that the S310F mutation completely abolished pertuzumab binding to HER2 receptor and inhibited pertuzumab antitumour efficacy.

Conclusion: We demonstrated the loss-of-function mechanism underlying pertuzumab resistance in HER2-positive tumour cells bearing the S310F mutation.
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http://dx.doi.org/10.2147/OTT.S232912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6941612PMC
December 2019

[Function of tumor infiltrating lymphocytes in solid tumors - a review].

Sheng Wu Gong Cheng Xue Bao 2019 Dec;35(12):2308-2325

College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.

Tumor is one of the major diseases threatening human health in the 21st century. Surgical resection, radiotherapy, chemotherapy and targeted therapy are the main clinical treatments for solid tumors. However, these methods are unable to eradicate tumor cells completely, and easily lead to the recurrence and progression of tumor. Tumor immunotherapy is a novel treatment that uses human immune system to control and kill tumor by enhancing or restoring anti-tumor immunity. Tumor immunotherapy has shown to produce long-lasting responses in large numbers of patients, and thereby adoptive immunotherapy and immune checkpoint inhibitors could induce remarkable antigen-specific immune responses. Tumor infiltrating lymphocytes (TILs) are highly heterogeneous lymphocytes existing in tumor tissues and play a crucial role in host antigen-specific tumor immune response. Recent studies show that TILs are closely related to the prognosis of patients during the processes of tumorigenesis and treatment. Adoptive immunotherapy mediated by TILs has displayed favorable curative effect in many solid tumors. This paper reviews the recent progress of TILs in solid tumors.
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http://dx.doi.org/10.13345/j.cjb.190300DOI Listing
December 2019

A method for rapid determination of arsenic species in vegetables using microwave-assisted extraction followed by detection with HPLC hyphenated to inductively coupled plasma-mass spectrometry.

J Sep Sci 2019 Sep 17;42(18):2957-2967. Epub 2019 Jul 17.

MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, P. R. China.

Driven by the significant need for characterization of the chemical speciation of arsenic in food, this work developed a method for rapid determination of four common arsenic species, namely, arsenite, arsenate, monomethyl arsenic acid, and dimethyl arsenic acid, in vegetables using microwave-assisted extraction, followed by detection with high-performance liquid chromatography hyphenated to inductively coupled plasma-mass spectrometry. Initial screening results showed that microwave-assisted extraction using 1% HNO exhibited the highest overall efficiencies for all arsenic species without causing significant degradation of the organic ones. With the aid of response surface methodology, the optimum conditions established for extraction of arsenic species from vegetables were: 500 mg of freeze-dried vegetable sample, extracted by closed vessel microwave-assisted extraction using 10 mL of 2% v/v HNO at 90°C for 17 min. Application of the method in the analysis of 24 market vegetable samples indicates that the extraction efficiencies for total arsenic species were in the range of 91.4-106%. Arsenite and arsenate were found to be the predominant arsenic species in the vegetables, which suggests that vegetable consumption could be an important route of inorganic arsenic exposure for the population with a heavy vegetable diet in arsenic polluted regions.
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http://dx.doi.org/10.1002/jssc.201900282DOI Listing
September 2019

A cross-section study of main determinants of arterial stiffness in Hefei area, China.

Int Angiol 2019 Apr 1;38(2):150-156. Epub 2019 Apr 1.

AnHui Province Key Laboratory of Medical Physics and Technology, Institute of Intelligent Machines, Hefei Institutes of Physical Sciences, Chinese Academy of Sciences, Hefei, China.

Background: Arterial stiffness has emerged as an independent risk factor for adverse cardiovascular disease events and is the consequence of multiple risk factors. The aim of the present study is to explore the main determinants of arterial stiffness in a Chinese population and to study how the arterial stiffness levels affected by different number of risk factors.

Methods: This study included 358 subjects in Hefei area of China. Anthropometric indexes, biochemical indexes, cardiovascular function indexes and lifestyle were achieved. Brachial-ankle pulse wave velocity (baPWV) was used to assess arterial stiffness. Multivariate linear regression model was performed to identify the main determinants of arterial stiffness levels.

Results: baPWV was correlated with age, sex, hypertension, various blood pressure components (systolic blood pressure [SPB], diastolic blood pressure, pulse pressure, and central arterial pressure), serum lipids, fasting blood-glucose and body mass index, subendocardial viability ratio (SEVR) and ejection duration (ED) in bivariate correlation analysis. Moreover, baPWV was only positively correlated with age, hypertension and SBP and inversely correlated with SEVR and ED in multivariable regression model. These five variables explained about 74.8% variances of baPWV and age was the strongest determinant of arterial stiffness. In addition, the levels of arterial stiffness increased with the augmented number of risk factors when the total number of factors was no more than 4.

Conclusions: The main determinants of arterial stiffness were age, hypertension, SBP, SEVR and ED. Furthermore, the number of risk factors had an independent influence on arterial stiffness, it is of great importance to consider the number of risk factors when it comes to cardiovascular risk assessment.
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http://dx.doi.org/10.23736/S0392-9590.19.04078-1DOI Listing
April 2019

Plastic Deformation Behavior of Bi-Crystal Magnesium Nanopillars with a {1012} Twin Boundary under Compression: Molecular Dynamics Simulations.

Materials (Basel) 2019 Mar 5;12(5). Epub 2019 Mar 5.

Hubei Key Laboratory of Theory and Application of Advanced Materials Mechanics, Wuhan University of Technology, Wuhan 430070, China.

In this study, molecular dynamics simulations were performed to study the uniaxial compression deformation of bi-crystal magnesium nanopillars with a { 10 1 ¯ 2 } twin boundary (TB). The generation and evolution process of internal defects of magnesium nanopillars were analyzed in detail. Simulation results showed that the initial deformation mechanism was mainly caused by the migration of the twin boundary, and the transformation of TB into (basal/prismatic) B/P interface was observed. After that, basal slip as well as pyramidal slip nucleated during the plastic deformation process. Moreover, a competition mechanism between twin boundary migration and basal slip was found. Basal slip can inhibit the migration of the twin boundary, and { 10 1 ¯ 1 } ⟨ 10 1 ¯ 2 ⟩ twins appear at a certain high strain level ( ε = 0.104). In addition, Schmid factor (SF) analysis was conducted to understand the activations of deformation modes.
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http://dx.doi.org/10.3390/ma12050750DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6427259PMC
March 2019

Histone demethylase KDM7A reciprocally regulates adipogenic and osteogenic differentiation via regulation of C/EBPα and canonical Wnt signalling.

J Cell Mol Med 2019 03 7;23(3):2149-2162. Epub 2019 Jan 7.

NHC Key Lab of Hormones and Development, Tianjin Key Lab of Metabolic Diseases, Metabolic Diseases Hospital & Institute of Endocrinology, Tianjin Medical University, Tianjin, China.

Recent emerging evidences revealed that epigenetic methylation of histone and DNA regulates the lineage commitment of mesenchymal progenitor cells. This study was undertaken to delineate the actions of histone lysine demethylase 7A (KDM7A) on osteogenic and adipogenic differentiation. Kdm7a expression was up-regulated in primary marrow stromal cells and established stromal ST2 line after adipogenic and osteogenic treatment. Silencing of endogenous Kdm7a in the cells blocked adipogenic differentiation whereas promoted osteogenic differentiation. Conversely, overexpression of wild-type Kdm7a in the progenitor cells enhanced adipogenic differentiation whereas inhibited osteogenic differentiation. However, the effect of KDM7A on cell differentiation was largely attenuated when the point mutation was made that abolishes enzymatic activity of KDM7A. Mechanism investigations revealed that silencing of Kdm7a down-regulated the expression of the CCAAT/enhancer binding protein α (C/EBPα) and secreted frizzled-related protein 1 (Sfrp1). Chromatin immunoprecipitation (ChIP) assay revealed that KDM7A directly binds to the promoters of C/EBPα and Sfrp1 and removes the histone methylation marks H3K9me2 and H3K27me2. Furthermore, silencing of Kdm7a activated canonical Wnt signalling. Thereafter, activation of canonical Wnt signalling through silencing of Sfrp1 in ST2 attenuated the stimulation of adipogenic differentiation and inhibition of osteogenic differentiation by KDM7A. Our study suggests that KDM7A balances adipogenic and osteogenic differentiation from progenitor cells through epigenetic control of C/EBPα and canonical Wnt signalling and implicates that control of KDM7A action has an epigenetic perspective of curtailing metabolic disorders like osteoporosis.
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http://dx.doi.org/10.1111/jcmm.14126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6378189PMC
March 2019

RNAm5Cfinder: A Web-server for Predicting RNA 5-methylcytosine (m5C) Sites Based on Random Forest.

Sci Rep 2018 11 23;8(1):17299. Epub 2018 Nov 23.

Department of Biomedical Informatics, School of Basic Medical Sciences, Center for Noncoding RNA Medicine, Peking University, Beijing, China.

5-methylcytosine (m5C) is a common nucleobase modification, and recent investigations have indicated its prevalence in cellular RNAs including mRNA, tRNA and rRNA. With the rapid accumulation of m5C sites data, it becomes not only feasible but also important to build an accurate model to predict m5C sites in silico. For this purpose, here, we developed a web-server named RNAm5Cfinder based on RNA sequence features and machine learning method to predict RNA m5C sites in eight tissue/cell types from mouse and human. We confirmed the accuracy and usefulness of RNAm5Cfinder by independent tests, and the results show that the comprehensive and cell-specific predictors could pinpoint the generic or tissue-specific m5C sites with the Area Under Curve (AUC) no less than 0.77 and 0.87, respectively. RNAm5Cfinder web-server is freely available at http://www.rnanut.net/rnam5cfinder .
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http://dx.doi.org/10.1038/s41598-018-35502-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6251864PMC
November 2018

The complete chloroplast genome of , a Critically Endangered species.

Mitochondrial DNA B Resour 2018 Oct 27;3(2):1167-1168. Epub 2018 Oct 27.

Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China.

(, Sterculiaceae) is a Critically Endangered species. In this study, we reported a complete chloroplast genome of based on high-throughput sequencing data. The size of chloroplast genome was 162,929 bp, including a large single-copy region (LSC: 91,535 bp) and a small single-copy region (SSC: 20,464 bp), separated by a pair of inverted repeats (IRa and IRb: 25,465 bp). The genome encoded 126 genes in total, including 81 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the chloroplast genome is 36.39%. The phylogenetic tree showed clustered together with the family Sterculiaceae.
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http://dx.doi.org/10.1080/23802359.2018.1524271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7801019PMC
October 2018

The complete chloroplast genome of and the phylogenetic analysis of mimosoid species.

Mitochondrial DNA B Resour 2018 Oct 26;3(2):1265-1266. Epub 2018 Oct 26.

Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China.

, a typical sensitive plant, belongs to (Fabaceae). It is well known for the rapid plant movement. In this study, we determined the complete chloroplast genome of using the Illumina reads. The complete chloroplast genome of is 163,237 bp in length, comprising a large single-copy region (LSC) of 92,045 bp, a small single-copy region (SSC) of 18,786 bp, and a pair of inverted repeats (IRs) of 26,203 bp each. The genome contained 129 encoded genes in total, including 84 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the chloroplast genome is 35.53%. We reconstructed the phylogenetic relationships for 19 mimosoid species. It was revealed that was closely related to .
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http://dx.doi.org/10.1080/23802359.2018.1532831DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799972PMC
October 2018

Acetone/Isopropanol Photoinitiating System Enables Tunable Disulfide Reduction and Disulfide Mapping via Tandem Mass Spectrometry.

Anal Chem 2018 11 24;90(21):13036-13043. Epub 2018 Oct 24.

Department of Chemistry, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Tsinghua University , Beijing 100084 , China.

Herein, we report the development of a new photochemical system which enables rapid and tunable disulfide bond reduction and its application in disulfide mapping via online coupling with mass spectrometry (MS). Acetone, a clean and electrospray ionization (ESI) compatible solvent, is used as the photoinitiator (1% volume) in the solvent system consisting of 1:1 alkyl alcohol and water. Under ultraviolet (UV) irradiation (∼254 nm), the acetone/alcohol system produces hydroxyalkyl radicals, which are responsible for disulfide bond cleavage in peptides. Acetone/isopropanol is most suitable for optimizing the disulfide reduction products, leading to almost complete conversion in less than 5 s when the reaction is conducted in a flow microreactor. The flow microreactor device not only facilitates direct coupling with ESI-MS but also allows fine-tuning of the extent of disulfide reduction by varying the UV exposure time. Near full sequence coverage for peptides consisting of intra- or interchain disulfide bonds has been achieved from complete disulfide reduction and online tandem mass spectrometry (MS/MS) via low energy collision-induced dissociation. Coupling different degrees of partial disulfide reduction with ESI-MS/MS allows disulfide mapping as demonstrated for characterizing the three disulfide bonds in insulin.
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http://dx.doi.org/10.1021/acs.analchem.8b04019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310128PMC
November 2018

The complete chloroplast genome of (Adoxaceae) provides insights into the phylogenetic relationship of Adoxaceae.

Mitochondrial DNA B Resour 2018 Oct 12;3(2):1149-1151. Epub 2018 Oct 12.

Life Science and Engineering College, Northwest Minzu University, Lanzhou, China.

The complete chloroplast genome of , which is endemic and endangered to the Hengduan Mountains, was sequenced and characterized in this study. The chloroplast genome is 157,502 bp in length, and it is consisted of four distinct regions: a large single-copy region (LSC, 86,526 bp), a small single-copy region (SSC, 18,682 bp) and a pair of inverted repeat regions (IRs, 26,147 bp). A total of 134 genes were annotated, including 86 protein-coding genes (80 PCG species), 40 tRNA genes (33 tRNA species) and 8 ribosomal RNA genes (4 rRNA species). We also reconstructed a comprehensive phylogenetic relationship of the family Adoxaceae, which demonstrated that the three Adoxaceae species clustered into two well-supported clades, and is most closely related to the .
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http://dx.doi.org/10.1080/23802359.2018.1493363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7800847PMC
October 2018

The complete chloroplast genome of , a medicinal and extremely toxic species.

Mitochondrial DNA B Resour 2018 Sep 10;3(2):1100-1101. Epub 2018 Sep 10.

Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences, Sichuan University, Chengdu, China.

(, Moraceae) is a medicinal and extremely toxic species. To facilitate species identification and provide genetic information, we determined the complete chloroplast genome of using the Illumina platform. The genome was 161,412 bp in length, comprising a large single-copy region (LSC) of 89,883 bp, a small single-copy region (SSC) of 20,375 bp, and a pair of inverted repeats (IRs) of 25,577 bp each. The genome contained 130 encoded genes in total, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the chloroplast genome is 35.87%. The phylogenetic analysis revealed was closely related to the genus within the family Moraceae.
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http://dx.doi.org/10.1080/23802359.2018.1516121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799485PMC
September 2018

The complete chloroplast genome of , an extremely endangered species.

Mitochondrial DNA B Resour 2018 Sep 10;3(2):974-975. Epub 2018 Sep 10.

College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China.

In this study, we determined the complete chloroplast genome of (Cycadaceae, ) using the Illumina sequencing data. The genome is 162,083 bp in length, including a pair of inverted repeats (IRs) of 25,003 bp each, which are separated by a large single-copy region (LSC) and a small single-copy region (SSC) with the size of 88,970 and 23,108 bp, respectively. The genome comprises 131 encoded genes in total, including 86 protein-coding genes (82 PCG species), 8 ribosomal RNA genes (4 rRNA species), and 37 transfer RNA genes (30 tRNA species). The overall GC content of the chloroplast genome is 39.42%, while the LSC, SSC, and IRs occupy 38.70, 42.03 and 36.52%, respectively. Based on complete chloroplast genome sequences from 13 species, we reconstructed the phylogenetic relationship of the 13 species and found that is closely related to .
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http://dx.doi.org/10.1080/23802359.2018.1507635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7800925PMC
September 2018

Highly Reactive and Tracelessly Cleavable Cysteine-Specific Modification of Proteins via 4-Substituted Cyclopentenone.

Angew Chem Int Ed Engl 2018 09 3;57(36):11598-11602. Epub 2018 Aug 3.

Center of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing, 100084, China.

A rapid and cysteine-specific modification of proteins using 4-substituted cyclopentenone via a Michael addition tandem elimination reaction was developed. Compared to the classical method, this reaction featured fast kinetics with a stable product. More importantly, this conjugation could be tracelessly removed by exchange with a Michael addition donor. The conjugation and regeneration process not only exhibited little change to the structures or conformations of the proteins but also exhibited little disturbance to their biological functions, such as their enzymatic activities.
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http://dx.doi.org/10.1002/anie.201804801DOI Listing
September 2018

(Betulaceae), a new species from southeast Tibet, China.

PhytoKeys 2018 2(98):1-13. Epub 2018 May 2.

State Key Laboratory of Grassland Agro-Ecosystem, College of Life Science, Lanzhou University, Lanzhou 730000, China.

A new species Z. Qiang Lu & J. Quan Liu from southeast Tibet is described and illustrated. The specimens of this new species were previously identified and placed under Hand.-Mazz. or Hu. However, the specimens from southeast Tibet differ from those of from other regions with more lateral veins (19-24 vs 14-18) on each side of the midvein and dense pubescence on the abaxial leaf surface, while from those of from other regions differ by nutlet with dense resinous glands and glabrous or sparsely villous at apex. Principal Component Analyses based on morphometric characters recognise the Tibetan populations as a separate group. Nuclear ribosomal ITS sequence variations show stable and distinct genetic divergences between the Tibetan populations and or by two or three fixed nucleotide mutations. Phylogenetic analysis also identified three respective genetic clusters and the cluster diverged early. In addition, the Tibetan populations show a disjunct geographic isolation from the other two species. Therefore, , based on the Tibetan populations, is here erected as a new species, distinctly different from and .
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http://dx.doi.org/10.3897/phytokeys.98.23639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5943419PMC
May 2018

Optimizing Multistep Delivery of PEGylated Tumor-Necrosis-Factor-Related Apoptosis-Inducing Ligand-Toxin Conjugates for Improved Antitumor Activities.

Bioconjug Chem 2017 08 1;28(8):2180-2189. Epub 2017 Aug 1.

Institute of Drug Metabolism and Drug Analysis, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou, 310058, China.

Although TRAIL (tumor-necrosis-factor (TNF)-related apoptosis-inducing ligand) has been considered a promising broad-spectrum antitumor agent, its further application was limited by poor drug delivery and TRAIL-resistant tumors. A three-step drug delivery strategy was applied to TRAIL for solving these two obstacles in the form of PEG-TRAIL-MMAE (Monomethyl Auristatin E). PEGylation of TRAIL in the first step was carried out to improve its in vivo pharmacokinetics, while the interaction between TRAIL conjugates with death receptors in the second step was designed to activate the TRAIL extrinsic apoptosis pathway, and the further release of MMAE from the lysosome was the third step for introducing another apoptosis pathway to overcome TRAIL resistance in some tumors. Herein, in order to reach a balance among the three steps, the PEG/MMAE ratio was optimized for PEG-TRAIL-MMAE conjugates. PEG-TRAIL-MMAE conjugates with various PEG/MMAE ratios were prepared and compared with each other regarding their pharmacokinetics (PK) and pharmacodynamics (PD). As a result, PEG-TRAIL-MMAE conjugates with a PEG/MMAE ratio of 1:2 showed prolonged half-life in rats (6.8 h), and the best antitumor activity in vitro (IC 0.31 nM) and in vivo while no sign of toxicity in xenograft models, suggesting it as a promising multistep drug delivery and antitumor strategy after optimization.
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http://dx.doi.org/10.1021/acs.bioconjchem.7b00327DOI Listing
August 2017

TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection.

R Soc Open Sci 2017 Apr 5;4(4):170050. Epub 2017 Apr 5.

Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China.

Tumour antigens have attracted much attention because of their importance to cancer diagnosis, prognosis and targeted therapy. With the development of cancer genomics, the identification of tumour-specific neoantigens became possible, which is a crucial step for cancer immunotherapy. In this study, we developed software called the tumour-specific neoantigen detector for detecting cancer somatic mutations following the best practices of the genome analysis toolkit and predicting potential tumour-specific neoantigens, which could be either extracellular mutations of membrane proteins or mutated peptides presented by class I major histocompatibility complex molecules. This pipeline was beneficial to the biologist with little programmatic background. We also applied the software to the somatic mutations from the International Cancer Genome Consortium database to predict numerous potential tumour-specific neoantigens. This software is freely available from https://github.com/jiujiezz/tsnad.
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http://dx.doi.org/10.1098/rsos.170050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5414268PMC
April 2017

Nuclear factor I-C reciprocally regulates adipocyte and osteoblast differentiation control of canonical Wnt signaling.

FASEB J 2017 05 25;31(5):1939-1952. Epub 2017 Jan 25.

Key Laboratory of Hormones and Development, Ministry of Health, Tianjin Key Laboratory of Metabolic Diseases, Metabolic Diseases Hospital and Institute of Endocrinology, Tianjin Medical University, Tianjin, China;

Nuclear factor I-C (NFIC) has recently been identified as an important player in osteogenesis and bone homeostasis However, the molecular mechanisms involved have yet to be defined. In the current study, Nfic expression was altered in primary marrow stromal cells and established progenitor lines after adipogenic and osteogenic treatment. Overexpression of Nfic in stromal cells ST2, mesenchymal cells C3H10T1/2, and primary marrow stromal cells inhibited adipogenic differentiation, whereas it promoted osteogenic differentiation. Conversely, silencing of endogenous Nfic in the cell lines enhanced adipogenic differentiation, whereas it blocked osteogenic differentiation. Mechanism investigations revealed that Nfic overexpression promoted nuclear translocation of β-catenin and increased nuclear protein levels of β-catenin and transcription factor 7-like 2 (TCF7L2). Promoter studies and the chromatin immunoprecipitation (ChIP) assay revealed that NFIC directly binds to the promoter of low-density lipoprotein receptor-related protein 5 (Lrp5) and thereafter transactivates the promoter. Finally, inactivation of canonical Wnt signaling in ST2 attenuated the inhibition of adipogenic differentiation and stimulation of osteogenic differentiation by NFIC. Our study suggests that NFIC balances adipogenic and osteogenic differentiation from progenitor cells through controlling canonical Wnt signaling and highlights the potential of NFIC as a target for new therapies to control metabolic disorders like osteoporosis and obesity.-Zhou, J., Wang, S., Qi, Q., Yang, X., Zhu, E., Yuan, H., Li, X., Liu, Y., Li, X., Wang, B. Nuclear factor I-C reciprocally regulates adipocyte and osteoblast differentiation control of canonical Wnt signaling.
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http://dx.doi.org/10.1096/fj.201600975RRDOI Listing
May 2017

Sortase A-Generated Highly Potent Anti-CD20-MMAE Conjugates for Efficient Elimination of B-Lineage Lymphomas.

Small 2017 Feb 22;13(6). Epub 2016 Nov 22.

Institute of Drug Metabolism and Drug Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.

Antibody-drug conjugate (ADC) targeting antigens expressed on the surface of tumor cells are an effective approach for delivering drugs into the cells via antigen-mediated endocytosis. One of the well-known tumor antigens, the CD20 of B-lymphocyte, has long been suggested to be noninternalizing epitope, and is thus not considered a desirable target for ADCs. Here, sortase A (srtA)-mediated transpeptidation is used to specifically conjugate triple glycine-modified monomethyl auristatin E (MMAE), a highly toxic antimitotic agent, to anti-CD20 ofatumumab (OFA) equipped with a short C-terminal LPETG (5 amino acids) tag at heavy chain (HL), which generates ADCs that show extremely strong potency in killing CD20 positive cancer cells. One of the srtA-generated ADCs with a cleavable dipeptide linker (valine-citrulline, vc), OFA-HL-vcMMAE, shows IC50 values ranging from 5 pg mL to 4.1 ng mL against CD20+ lymphoma cells. Confocal laser scanning microscopy confirms that OFA-HL-vcMMAE internalization by Ramos cells is significantly improved compared to OFA alone, consistent with the high antitumor activity of the new ADC. OFA-HL-vcMMAE, at 5 mg kg dose, is able to eliminate tumors with mean volume ≈400 mm while no obvious drug-related toxicity is observed. The results show that srtA-generated OFA-MMAE conjugate system provides a viable strategy for targeting CD20+ B lineage lymphomas.
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http://dx.doi.org/10.1002/smll.201602267DOI Listing
February 2017

[Eyes-Brain-Hands Coordination Training System for Mental Retarded Children].

Zhongguo Yi Liao Qi Xie Za Zhi 2016 Sep;40(5):331-5

In order to help improving mental attention and sensory integration ability of mental retarded children, this paper proposes an interactive eyes-brain-hands coordination training system. This system realizes the principle of seeing, thinking and moving of hands by an interactive operation between the computer software custom icons and a touch control panel, so it can improve cognitive function and activity of daily living. The results show this training platform has a high degree of application and acceptance, and provides a portable training method for mental retarded children.
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September 2016

Species delimitation of Chinese hop-hornbeams based on molecular and morphological evidence.

Ecol Evol 2016 07 13;6(14):4731-40. Epub 2016 Jun 13.

State Key Laboratory of Grassland Agro-Ecosystem College of Life Science Lanzhou University Lanzhou China; MOE Key Laboratory for Bio-resources and Eco-environment College of Life Science Sichuan University Chengdu China.

Species delimitation through which infers species boundaries is emerging as a major work in modern systematics. Hop-hornbeam species in Ostrya (Betulaceae) are well known for their hard and heavy woods. Five species were described in China and their interspecific delimitations remain unclear. In this study, we firstly explored their distributions in all recorded field sites distributed in China. We then selected 110 samples from 22 natural populations of five species from this genus and one type specimen of O. yunnanensis, for molecular barcoding analyses. We sequenced four chloroplast (cp) DNA fragments (trnH-psbA, trnL-trnF, rps16, and trnG) and the nuclear internal transcribed spacer (ITS) region for all samples. Sequence variations of Ostrya from four cpDNA fragments identified three groups that showed no correspondence to any morphological delimitation because of the incomplete lineage sorting and/or possible interspecific introgression in the history. However, phylogenetic analyses of ITS sequence variations discerned four species, O. japonica, O. rehderiana, O. trichocarpa, and O. multinervis while O. yunnanensis nested within O. multinervis. Morphological clustering also discerned four species and showed the complete consistency with molecular evidence. Moreover, our phylogenetic analyses-based ITS sequence variations suggested that O. trichocarpa comprised an isolated lineage different from the other Eurasian ones. Based on these results, hop-hornbeams in China should be treated as four separate species. Our results further highlight the importance of ITS sequence variations in delimitating and discerning the closely related species in plants.
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http://dx.doi.org/10.1002/ece3.2251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4979702PMC
July 2016