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Post-J test inference in non-nested linear regression models

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Science China Mathematics 2015年第6期58卷 1203-1216页

作者： chen xinjie FAN YanQin WAN Alan ZOU GuoHua Academy of Mathematics and Systems Science Chinese Academy of Sciences Department of Economics Vanderbilt University Department of Management Sciences City University of Hong Kong School of Mathematical Sciences Capital Normal University

This paper considers the post-J test inference in non-nested linear regression models. Post-J test inference means that the inference problem is considered by taking the first stage J test into account. We first propose a post-J test estimator and derive its asymptotic distribution. We then consider the test problem of the unknown parameters, and a Wald statistic based on the post-J test estimator is proposed. A simulation study shows that the proposed Wald statistic works perfectly as well as the two-stage test from the view of the empirical size and power in large-sample cases, and when the sample size is small, it is even better. As a result,the new Wald statistic can be used directly to test the hypotheses on the unknown parameters in non-nested linear regression models.

关键词： non-nested linear regression post-J test Wald statistic

A linear DNA template-based framework for site-specific unnatural amino acid incorporation

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Synthetic and Systems Biotechnology 2021年第3期6卷 192-199页

作者： xinjie chen Yingying Liu Jiaqi Hou Yuan Lu Key Laboratory of Industrial Biocatalysis Ministry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China

Site-specific incorporation of unnatural amino acids(UNAAs)into proteins using an orthogonal translation system(OTS)has expanded the scope of protein-coding *** key factor affecting UNAA embedding efficiency is the orthogonality of the *** to traditional cell systems,cell-free systems are more convenient to control the reaction process and improve the utilization rate of *** this study,a linear DNA template-based cell-free unnatural protein synthesis system for rapid high-throughput screening and evolution was proposed.A total of 14 cell extracts were selected for screening out cell extract with high expression *** result showed that EcAR7ΔAΔSer cell extract was optimal for the cell-free *** addition,the screening results of four UNAAs,p-propargyloxy-l-phenylalanine(pPaF),p-azyl-phenylalanine(pAzF),p-acetyl-l-phenylalanine(pAcF),and p-benzoyl-l-phenylalanine(pBpF),showed that o-aaRS and o-tRNA of pPaF had good orthogonality.A new pair of corresponding o-aaRS and o-tRNA for pBpF was screened *** results proved that this method could speed up the screening of optimal OTS components for UNAAs with versatile functions.

关键词： Cell-free protein synthesis Linear PCR product Rapid screening Unnatural amino acids

Structural Characterization of Chloroplast Genome in Alpinia japonica(Thunb.)Miq.,a Medicinal Plant of the Genus Alpinia

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Phyton-International Journal of Experimental Botany 2024年第8期93卷 1897-1911页

作者： Wentao Sheng Xi Lei xinjie chen Quan Kuang Department of Biological Technology Nanchang Normal UniversityNanchang330032China

The analysis of chloroplast gene characteristics in Alpinia japonica(Thunb.)*** of great significance for developing relevant genetic *** high-throughput sequencing and bioinformatic research were performed to analyze the chloroplast genome characteristics of *** total chloroplast genome length of *** was 161,906 bp,with a typical circular tetrameric *** 133 genes were annotated,comprising 87 protein-coding,38 tRNA,and 8 rRNA ***,22 genes contained two copies,and 18 genes owned *** sequence analysis showed that it contains 321 simple sequence repeats(SSRs)and 37 long segment *** with the chloroplast genomes of eight representative plants in the genus Alpinia,the gene structure,type,and quantity were relatively ***12 was the highest variation site in the entire chloroplast gene.A phylogenetic tree showed that the genus Alpinia was the most closely related to the genus ***,*** is the most closely related to Alpinia chinensis belonging to the genus ***,the chloroplast genome of a new species was reported in the genus Alpinia,and a basis was provided for the utilization of Alpinia plants as a medical resource.

关键词： The genus Alpinia Alpinia japonica(Thunb.)Miq chloroplast genome phylogenetic tree

Cell-Free PURE System:Evolution and Achievements

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BioDesign Research 2022年第1期2022卷 166-176页

作者： Yi Cui xinjie chen Ze Wang Yuan Lu Key Laboratory of Industrial Biocatalysis Ministry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing 100084China College of Life Sciences Shenyang Normal UniversityShenyang 110034LiaoningChina

The cell-free protein synthesis (CFPS) system, as a technical core of synthetic biology, can simulate the transcription andtranslation process in an in vitro open environment without a complete living cell. It has been widely used in basic and appliedresearch fields because of its advanced engineering features in flexibility and controllability. Compared to a typical crudeextract-based CFPS system, due to defined and customizable components and lacking protein-degrading enzymes, the proteinsynthesis using recombinant elements (PURE) system draws great attention. This review first discusses the elementalcomposition of the PURE system. Then, the design and preparation of functional proteins for the PURE system, especially thecritical ribosome, were examined. Furthermore, we trace the evolving development of the PURE system in versatile areas,including prototyping, synthesis of unnatural proteins, peptides and complex proteins, and biosensors. Finally, as a state-ofthe-art engineering strategy, this review analyzes the opportunities and challenges faced by the PURE system in futurescientific research and diverse applications.

关键词： system synthesis versatile

Homoharringtonine synergy with oridonin in treatment of t(8;21) acute myeloid leukemia

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Frontiers of Medicine 2019年第3期13卷 388-397页

作者： Weina Zhang Ying Lu Tao Zhen xinjie chen Ming Zhang Ping Liu Xiangqin Weng Bing chen Yueying Wang State Key Laboratory of Medical Genomics Shanghai Institute of HematologyRuijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200025China

Collaboration of c-KIT mutations with AML1-ETO (AE) has been demonstrated to induce t(8;21) acute myeloid leukemia (AML).Targeted therapies designed to eliminate AE and c-KIT oncoproteins may facilitate effective treatment of t(8;21) *** (HHT) features activity against tumor cells harboring c-KIT mutations,whereas oridonin can induce t(8;21) AML cell apoptosis and AE ***,studies should explore the efficacy of combination therapy with oridonin and HHT in t(8;21) *** this study,we investigated the synergistic effects and mechanism of oridonin combined with HHT in t(8;21) AML cell line and mouse *** two drugs synergistically inhibited cell viability and induced significant mitochondrial membrane potential loss and *** and HHT induced significant downregulation of c-KIT and its downstream signaling pathways and promoted AE *** increased intracellular oridonin concentration by modulating the expressions of MRP1 and MDR1,thus enhancing the effects of *** combination of oridonin and HHT prolonged t(8;21) leukemia mouse *** conclusion,oridonin and HHT exert synergistic effects against t(8;21) leukemia in vivo and in vitro,thereby indicating that their combination may be an effective therapy for t(8;21) leukemia.

关键词： AML1-ETO c-KIT homoharringtonine oridonin t(8 21) AML synergistic effect

Macroscopic superlubricity of potassium hydroxide solution achieved by incorporating in-situ released graphene from friction pairs

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Friction 2023年第4期11卷 567-579页

作者： Hongyu LIANG xinjie chen Yongfeng BU Meijuan XU Gang ZHENG Kaixiong GAO Xijun HUA Yonghong FU Junyan ZHANG Institute of Advanced Manufacturing and Modern Equipment Technology School of Mechanical EngineeringJiangsu UniversityZhenjiang 212013China Institute for Energy Research Jiangsu UniversityZhenjiang 212013China ZhenJiang SiLian Mechatronic Technology Co. Ltd.Zhenjiang 212009China State Key Laboratory of Solid Lubrication Lanzhou Institute of Chemical PhysicsChinese Academy of SciencesLanzhou 730000China

Graphene(G),as a typical two-dimensional material,is often used as an additive for liquid ***,graphene is mostly added to liquid lubricants in a one-time manner in friction;it mainly exists in the form of multilayer agglomerated structures due to theπ–πstacking between graphene sheets,making it unable to fully exert the synergistic lubrication ***,we propose a new macroscopic superlubric system of graphene/potassium hydroxide(G/KOH)solution;and the graphene additive involved is exfoliated in-situ from graphene/epoxy(G/EP)friction pair by friction,continuously providing freshly-peeled graphene into KOH solution and minimizing the adverse effects of graphene ***,the in-situ produced graphene additive has thinner thickness and better anti-aggregation ability,which provide more graphene to accommodate OH−,form more stacked sandwich structures of OH−/graphene/OH−between friction pairs(i.e.,equivalent to a moving pulley block with more wheels),and finally realize *** study develops a new liquid superlubric system suitable for alkaline environments,and at the same time proposes a new way to gradually release graphene additives in situ,rather than adding them all at once,deepening the understanding to liquid superlubricity mechanism,and paving the experimental foundation for the practical application of macroscopic superlubricity.

关键词： liquid superlubricity concentrated potassium hydroxide(KOH)solution in-situ graphene(G)additives stacked sandwich structure electric double layer(EDL) hydrogen bonds(H-bonds)

Customized synthesis of phosphoprotein bearing phosphoserine or its nonhydrolyzable analog

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Synthetic and Systems Biotechnology 2023年第1期8卷 69-78页

作者： Dong Liu Yingying Liu Hua-Zhen Duan xinjie chen Yanan Wang Ting Wang Qing Yu Yong-Xiang chen Yuan Lu Key Laboratory of Industrial Biocatalysis(Ministry of Education) Department of Chemical EngineeringTsinghua UniversityBeijing100084China Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology(Ministry of Education) Department of ChemistryTsinghua UniversityBeijing100084China

Studies on the mechanism of protein phosphorylation and therapeutic interventions of its related molecular processes are limited by the difficulty in the production of purpose-built phosphoproteins harboring site-specific phosphorylated amino acids or their nonhydrolyzable *** we address this limitation by customizing the cell-free protein synthesis(CFPS)machinery via chassis strain selection and orthogonal translation system(OTS)reconfiguration *** suited chassis strains and reconfigured OTS combinations with high orthogonality were consequently picked out for individualized phosphoprotein ***,we synthesized the sfGFP protein and MEK1 protein with site-specific phosphoserine(O-pSer)or its nonhydrolyzable analog,2-amino-4-phosphonobutyric acid(C-pSer).This study successfully realized building cell-free systems for site-specific incorporation of phosphonate mimics into the target *** work lays the foundation for developing a highly expansible CFPS platform and the streamlined production of user-defined phosphoproteins,which can facilitate research on the physiological mechanism and potential interference tools toward protein phosphorylation.

关键词： Cell-free synthetic biology Phosphoprotein Phosphorylation Orthogonal translation system Nonhydrolyzable analog

Toward efficient multiple-site incorporation of unnatural amino acids using cell-free translation system

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Synthetic and Systems Biotechnology 2022年第1期7卷 522-532页

作者： Jiaqi Hou xinjie chen Nan Jiang Yanan Wang Yi Cui Lianju Ma Ying Lin Yuan Lu College of Life Sciences Shenyang Normal UniversityShenyang110034China Key Laboratory of Industrial Biocatalysis Ministry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China Guangdong Key Laboratory of Fermentation and Enzyme Engineering School of Biology and Biological EngineeringSouth China University of TechnologyGuangzhou510006China

Amber suppression has been widely used to incorporate unnatural amino acids(UNAAs)with unique structures or functional side-chain groups into specific sites of the target protein,which expands the scope of protein-coding ***,this traditional strategy does not allow multiple-site incorporation of different UNAAs into a single protein,which limits the development of unnatural *** address this challenge,the suppression method using multiple termination codons(TAG,TAA or TGA)was proposed,and cell-free unnatural protein synthesis(CFUPS)system was *** the analysis of incorporating 3 different UNAAs(p-propargyloxy-L-phenylalanine,p-azyl-phenylalanine and L-4-Iodophenylalanine)and mass spectrometry,the simultaneous usage of the codons TAG and TAA were suggested for better multiple-site UNAA *** CFUPS conditions were further optimized for better UNAA incorporation efficiency,including the orthogonal translation system(OTS)components,magnesium ions,and the redox *** study established a CFUPS approach based on multiple termination codon suppression to achieve efficient and precise incorporation of different types of UNAAs,thereby synthesizing unnatural proteins with novel physicochemical functions.

关键词： Cell-free protein synthesis Orthogonal translation system Unnatural protein Unnatural amino acid Terminal codon suppression

A cis-eQTL in NSUN2 promotes esophageal squamous-cell carcinoma progression and radiochemotherapy resistance by mRNA-m^(5)C methylation

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Signal Transduction and Targeted Therapy 2022年第9期7卷 3190-3193页

作者： Xiangjie Niu Linna Peng Weiling Liu Chuanwang Miao xinjie chen Jiahui Chu Xinyu Yang Wen Tan chen Wu Dongxin Lin Department of Etiology and Carcinogenesis National Cancer Center/National Clinical Research Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeiingChina CAMS Key Laboratory of Genetics and Genomic Biology Chinese Academy of Medical Sciences and Peking Union Medical CollegeBejingChina Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine Nanjing Medical UniversityNanjingChina

Dear Editor,Esophageal squamous cell carcinoma(ESCC)has poor prognosis because of the difficulty in early detection and low sensitivity of advanced disease to radiochemotherapy.1,2 ESCC presents a high proportion of primary resistance to radiochemotherapy,2which may be due to certain individual genetic *** quantitative trait loci(eQTLs)as proximal and continuous cellular phenotypes have been shown to be helpful to determine how genetic variants may influence phenotype.

关键词： chemotherapy squamous esophageal