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| 1 | Characteristics of distribution of Mycobacterium tuberculosis lineages in China显示文摘The genotyping methods of Mycobacterium tuberculosis would dramatically improve our understanding of the molecular epidemiology of tuberculosis. 3,929 isolates, from a National Survey of Drug-Resistant Tuberculosis in 2007 in China, were successfully genotyped by large sequence polymorphisms and 15 loci variable number tandem repeats. We found that 2,905(2,905/3,929, 73.9%) cases belonged to Lineage 2, dominated in the east and central regions, 975 cases(975/3,929, 24.8%) were Lineage 4, highly prevailed in the west regions, and 36 and 13 cases were Lineage 3 and Lineage 1, respectively. We also explored the associations between lineages(Lineage 2 vs. Lineage 4) and clinical characteristics by logistic regression. For Lineage 2, the risk factors were Han-ethnicity population and fever. However, for Lineage 4, they were occupation(farmer), and degree of education(non-literate). Fully understanding of the distribution of Mycobacterium tuberculosis lineage and its risk factors would play a critical role in tuberculosis prevention, control, and treatment. | Haixia Chen Li He Chao Cai Jingyi Liu Junnan Jia Liang Ma Hairong Huang Lixia Wang Xumin Ni Jimin Gao Weimin Li | 2018 | Science China(Life Sciences)2018，61，6： | 7 |
| 2 | Abrogation of Hn RNP L enhances anti-PD-1 therapy efficacy via diminishing PD-L1 and promoting CD8^(+) T cell-mediated ferroptosis in castration-resistant prostate cancer显示文摘Owing to incurable castration-resistant prostate cancer(CRPC)ultimately developing after treating with androgen deprivation therapy(ADT),it is vital to devise new therapeutic strategies to treat CRPC.Treatments that target programmed cell death protein 1(PD-1)and programmed death ligand-1(PD-L1)have been approved for human cancers with clinical benefit.However,many patients,especially prostate cancer,fail to respond to anti-PD-1/PD-L1 treatment,so it is an urgent need to seek a support strategy for improving the traditional PD-1/PD-L1 targeting immunotherapy.In the present study,analyzing the data from our prostate cancer tissue microarray,we found that PD-L1 expression was positively correlated with the expression of heterogeneous nuclear ribonucleoprotein L(Hn RNP L).Hence,we further investigated the potential role of Hn RNP L on the PD-L1 expression,the sensitivity of cancer cells to T-cell killing and the synergistic effect with anti-PD-1 therapy in CRPC.Indeed,Hn RNP L knockdown effectively decreased PD-L1 expression and recovered the sensitivity of cancer cells to T-cell killing in vitro and in vivo,on the contrary,Hn RNP L overexpression led to the opposite effect in CRPC cells.In addition,consistent with the previous study,we revealed that ferroptosis played a critical role in T-cell-induced cancer cell death,and Hn RNP L promoted the cancer immune escape partly through targeting YY1/PD-L1 axis and inhibiting ferroptosis in CRPC cells.Furthermore,Hn RNP L knockdown enhanced antitumor immunity by recruiting infiltrating CD8^(+)T cells and synergized with anti-PD-1 therapy in CRPC tumors.This study provided biological evidence that Hn RNP L knockdown might be a novel therapeutic agent in PD-L1/PD-1 blockade strategy that enhanced anti-tumor immune response in CRPC. | Xumin Zhou Libin Zou Hangyu Liao Junqi Luo Taowei Yang Jun Wu Wenbin Chen Kaihui Wu Shengren Cen Daojun Lv Fangpeng Shu Yu Yang Chun Li Bingkun Li Xiangming Mao | 2022 | Acta Pharmaceutica Sinica B2022，12，2： | 4 |
| 3 | Transcriptome characterization of Ishige okamurae(Phaeophyceae)shows strong environmental acclimation显示文摘Ishige okamurae,with leathery branched narrow fronds consisting of cylindrical hairs,is the typical species of the genus Ishige,which is considered as one of the most basal genera in the phylogeny of the Phaeophyceae.Apart from great public interest from the evolutionary respect,more attention has been brought on the abundant bioactive compounds in I.okamurae for therapeutic or economic considerations,such as diphlorethohydroxycarmalol and ishigoside.Yet little is known about related key genes or metabolic pathways involved in I.okamurae,which calls upon us to carry out global analyses of transcriptome by next generation sequencing.Altogether,we obtained 78 583 assembled scaffolds with N50 of 1 709 nucleotides,and 25 357 unigenes with significant BLAST matches(E-value cutoff of 10-5).In terms of characterization of the transcriptome of I.okamurae,we focused on anti-stress metabolic pathways and synthetic routes of bioactive compounds in an attempt to obtain a better understanding of the interactive organism-environment regulatory networks.Pathway-based analysis helped us to deepen our comprehension of the interaction between I.okamurae and its surroundings,with MAPK signal pathway as an example.Furthermore,we discovered a wide range of novel putative functional proteins that could be of wide application,such as Rab family,using sequence-based transcriptome.In conclusion,transcriptome characterization of I.okamurae(Phaeophyceae) shows strong environmental acclimation. | QU Jieqiong WANG Xumin CHI Shan WU Shuangxiu SUN Jing LIU Cui CHEN Shengping YU Jun LIU Tao | 2014 | Acta Oceanologica Sinica2014，33，2： | 1 |
| 4 | Analysis of Saccharina japonica transcriptome using the high-throughput DNA sequencing technique and its vanadium-dependent haloperoxidase gene显示文摘Saccharina is one of the most important cold-water living marine brown algal genera.In this study we analyzed the transcriptome of S.japonica,which belongs to the 1 000 Plants(OneKP) Project,by using a nextgeneration high-throughput DNA sequencing technique.About 5.16 GB of raw data were generated,and 65 536 scaffolds with an average length of 454 bp were assembled with SOAP de novo assembly method.In total,19 040 unigenes were identified by BLAST;25 734 scaffolds were clustered into 37 Gene ontology functional groups;6 760 scaffolds were classified into 25 COG categories,as well as 2 665 scaffolds that were assigned to 306 KEGG pathways.Majority of the unigenes exhibited more similarities to algae including brown algae and diatom than other cyanobacteria,marine diatom,and plant.Saccharina japonica has the outstanding capability to accumulate halogen such as Br and I via halogenation processes from seawater.We acquired 42 different vanadium-dependent haloperoxidases(vHPO) in S.japonica transcriptome data,including 5 segments of vanadium-dependent iodoperoxidase(vIPO) and 37 segments of vanadium-dependent bromoperoxidase(vBPO).Complicated analyses of identified fulllength S.japonica vBPO1 and S.japonica vBPO2 revealed the importance of vBPO among species of brown algae and the strong relationship between marine algal vBPOs and vIPOs.This study will enhance our understanding of the biological characteristics and economic values of S.japonica species. | LIANG Xiayuan WANG Xumin CHI Shan WU Shuangxiu SUN Jing LIU Cui CHEN Shengping YU Jun LIU Tao | 2014 | Acta Oceanologica Sinica2014，33，2： | 1 |
| 5 | Origin and evolution of alginate-c5-mannuronan-epimerase gene based on transcriptomic analysis of brown algae显示文摘The coding product of alginate-c5-mannuronan-epimerase gene(algG gene) can catalyze the conversion of mannuronate to guluronate and determine the M/G ratio of alginate.Most of the current knowledge about genes involved in the alginate biosynthesis comes from bacterial systems.In this article,based on some algal and bacterial algG genes registered on GenBank and EMBL databases,we predicted 94 algG genes open reading frame(ORF) sequences of brown algae from the 1 000 Plant Transcriptome Sequencing Project(OneKP).By method of transcriptomic sequence analysis,gene structure and gene localization analysis,multiple sequence alignment and phylogenetic tree construction,we studied the algal algG gene family characteristics,the structure modeling and conserved motifs of AlgG protein,the origin of alginate biosynthesis and the variation incidents that might have happened during evolution in algae.Although there are different members in the algal algG gene family,almost all of them harbor the conserved epimerase region.Based on the phylogenetic analysis of algG genes,we proposed that brown algae acquired the alginate biosynthesis pathway from an ancient bacterium by horizontal gene transfer(HGT).Afterwards,followed by duplications,chromosome disorder,mutation or recombination during evolution,brown algal algG genes were divided into different types. | WANG Ren WANG Xumin ZHANG Yalan YU Jun LIU Tao CHEN Shengping CHI Shan | 2014 | Acta Oceanologica Sinica2014，33，2： | 1 |
| 6 | The discovery of archaea origin phosphomannomutase in algae based on the algal transcriptome显示文摘Phosphomannomutase(PMM;EC 5.4.2.8) is an enzyme that catalyzes the interconversion reaction between mannose-6-phosphate and mannose-1-phosphate.However,its systematic molecular and functional investigations in algae have not hitherto been reported.In this work,with the accomplishment of the 1 000 Plant Project(OneKP) in which more than 218 species of Chromista,including 19 marine phaeophytes,22 marine rhodophytes,171 chlorophytes,5 cryptophytes,4 haptophytes,and 5 glaucophytes were sequenced,we used a gene analysis method to analyze the PMM gene sequences in algae and confirm the existence of the PMM gene in the transcriptomic sequencing data of Rhodophyta and Ochrophyta.Our results showed that only one type of PMM with four conserved motifs exists in Chromista which is similar to human PMM.Moreover,the phylogenetic tree revealed that algae PMM possibly originated from archaea. | FENG Yanjing CHI Shan LIU Cui CHEN Shengping YU Jun WANG Xumin LIU Tao | 2014 | Acta Oceanologica Sinica2014，33，2： | 1 |
| 7 | High-order BesseI-Gaussian beams and its propagation properties显示文摘 | Lu Xuanhui Chen Xumin Zhang Lei | 2003 | Chin Phys Lett2003，20，12： | 1 |
| 8 | High flux filtration medium based on nanot]brous substrate with hydrophilic nanocomposite coating显示文摘 | Wang Xuefen Chen Xumin Kyunghwan Y | 2005 | Environmental Science and Technology2005，39，19： | 1 |
| 9 | High flux filtration medium based on nanofibrous substrate with hydrophilic nanocomposite coating 显示文摘 | WANG Xuefen CHEN Xumin KYUNGHWAN Y | 2005 | Environmental Science and Technology2005，39，19： | 1 |
| 10 | Quantitatively mapping local quality of super-resolution microscopy by rolling Fourier ring correlation显示文摘In fluorescence microscopy,computational algorithms have been developed to suppress noise,enhance contrast,and even enable super-resolution(SR).However,the local quality of the images may vary on multiple scales,and these differences can lead to misconceptions.Current mapping methods fail to finely estimate the local quality,challenging to associate the SR scale content.Here,we develop a rolling Fourier ring correlation(rFRC)method to evaluate the reconstruction uncertainties down to SR scale.To visually pinpoint regions with low reliability,a filtered rFRC is combined with a modified resolution-scaled error map(RSM),offering a comprehensive and concise map for further examination.We demonstrate their performances on various SR imaging modalities,and the resulting quantitative maps enable better SR images integrated from different reconstructions.Overall,we expect that our framework can become a routinely used tool for biologists in assessing their image datasets in general and inspire further advances in the rapidly developing field of computational imaging. | Weisong Zhao Xiaoshuai Huang Jianyu Yang Liying Qu Guohua Qiu Yue Zhao Xinwei Wang Deer Su Xumin Ding Heng Mao Yaming Jiu Ying Hu Jiubin Tan Shiqun Zhao Leiting Pan Liangyi Chen Haoyu Li | 2023 | Light(Science & Applications)2023，12，12： | 0 |
| 11 | Nonlinear vibration analysis of pipeline considering the effects of soft nonlinear clamp显示文摘Soft nonlinear support is a major engineering project,but there are few relevant studies.In this paper,a dynamic pipeline model with soft nonlinear supports at both ends is established.By considering the influence of the Coriolis force and centrifugal force,the dynamical coupling equation of fluid-structure interaction is derived with extended Hamilton’s principle.Then,the approximate analytical solutions are sought via the harmonic balance method.The amplitude-frequency response curves show that different effects can be determined by approximate analysis.It is demonstrated that the increase in the fluid velocity can increase the amplitude of the pipeline system.The frequency range of unstable response increases when the fluid pressure raises.The combination of the soft nonlinear clamp and the large geometrical deformation of the pipeline affects the nonlinear vibration characteristic of the system,and the external excitation force and damping have significant effects on the stability. | Weijiao CHEN Yiming CAO Xumin GUO Hui MA Bangchun WEN Bo WANG | 2022 | Applied Mathematics and Mechanics(English Edition)2022，43，10： | 0 |
| 12 | Mass spectrometry analysis of intact protein N-glycosylation signatures of cells and sera in pancreatic adenocarcinomas显示文摘Pancreatic cancer is among the most malignant cancers,and thus early intervention is the key to better survival outcomes.However,no methods have been derived that can reliably identify early precursors of development into malignancy.Therefore,it is urgent to discover early molecular changes during pancreatic tumorigenesis.As aberrant glycosylation is closely associated with cancer progression,numerous efforts have been made to mine glycosylation changes as biomarkers for diagnosis;however,detailed glycoproteomic information,especially site-specific N-glycosylation changes in pancreatic cancer with and without drug treatment,needs to be further explored.Herein,we used comprehensive solid-phase chemoenzymatic glycoproteomics to analyze glycans,glycosites,and intact glycopeptides in pancreatic cancer cells and patient sera.The profiling of N-glycans in cancer cells revealed an increase in the secreted glycoproteins from the primary tumor of MIA PaCa-2 cells,whereas human sera,which contain many secreted glycoproteins,had significant changes of glycans at their specific glycosites.These results indicated the potential role for tumor-specific glycosylation as disease biomarkers.We also found that AMG-510,a small molecule inhibitor against Kirsten rat sarcoma viral oncogene homolog(KRAS)G12C mutation,profoundly reduced the glycosylation level in MIA PaCa-2 cells,suggesting that KRAS plays a role in the cellular glycosylation process,and thus glycosylation inhibition contributes to the anti-tumor effect of AMG-510. | Mingming XU Zhaoliang LIU Wenhua HU Ying HAN Zhen WU Sufeng CHEN Peng XIA Jing DU Xumin ZHANG Piliang HAO Jun XIA Shuang YANG | 2024 | Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)2024，25，1： | 0 |
| 13 | Research progress on three different types of noncoding RNAs related to ionizing radiation显示文摘Non-coding RNAs(ncRNAs)have attracted wide attention in the field of ionizing radiation(IR).They have been found to be involved in cell development,proliferation,differentiation,and apoptosis in both clinical radiotherapy and radiation protection studies.Despite the production of an increasing number of relevant reports in recent years,the molecular mechanisms involved are yet to be clearly understood.In the last few years,ncRNAs have received a lot of research attention,especially microRNAs,long noncoding RNAs,and circular RNAs,which have a well-known association with the development of human disease and are closely related to the biological phenotypic changes caused by IR.With recent developments of research methods,these ncRNAs might play a significant regulatory role in future radiation protection and radiotherapy.This review will summarize the research progress of various types of ncRNAs as biomarkers of IR and potential new targets for radiotherapy,aiming to provide references for future research and the formulation of new strategies. | Jin Gao Xumin Zong Na Chen Tingxi Lan Wentao Yu Huiqiang Long Fengmei Cui Yu Tu | 2021 | Radiation Medicine and Protection2021，2，2： | 0 |
| 14 | Tryptophan synthase of Phaeophyceae originated from the secondary host nucleus显示文摘Tryptophan synthase(TS,EC 4.2.1.20) catalyzes the last two steps of L-tryptophan biosynthesis.In prokaryotes,tryptophan synthase is a multi-enzyme complex,and it consists of α and β subunit which forms an α-ββ-α complex.In fungi and diatoms,TS is a bifunctional enzyme.Because of the limited genomic and transcriptomic data of algae,there are few studies on TS evolution of algae.Here we analyzed the data of the 1000 Plants Project(1KP),and focused on red algae and brown algae.We found out that the TS of Phaeophyceae were fusion genes,which probably originated from the secondary host nucleus,and that the TS of Rhodophyta contained two genes,TSA and TSB,which both display a possible cyanobacterial origin at the time of primary endosymbiosis.In addition,there were two types of TSB genes(TSB1 and TSB2).Through the multiple sequence alignment of TSB proteins,we found several residues conserved in TSB1 but variable in TSB2 which connect with α subunit.The phenomenon may suggest that the TSB2 sequences of Rhodophyta cannot form stable complex with TSA. | ZHANG Yalan CHI Shan WU Shuangxiu LIU Cui YU Jun WANG Xumin CHEN Shengping LIU Tao | 2014 | Acta Oceanologica Sinica2014，33，2： | 0 |
| 15 | Comparative study of the pathogenicity of the mosquito origin strain and duck origin strain of Tembusu virus in ducklings and three-week-old mice显示文摘Dear Editor,Duck Tembusu virus(DTMUV)is the causative agent of a new,acute and severe infectious disease in ducks(Su et al.,2011).TMUV was first isolated from Culex tritaeniorhynchus in Malaysia in 1955(Platt et al.,1975),and this strain is regarded as a reference strain.In our previous study,an infectious clone for the mosquito-derived Tembusu virus prototypical strain MM_1775(GenBank:JX477685.2)was constructed,and the rMM_1775 virus was rescued successfully(Wang et al.,2021).And the TMUV strain rCQW1 was rescued by a reverse genetic system using the viral RNAs of CQW1(GenBank:KM233707.1)(Chen et al.,2018;Guo et al.,2020),which was isolated from ducks in 2013(Zhu et al.,2015). | Xiaoli Wang Yu He Jiaqi Guo Zhen Wu Andres Merits Mingshu Wang Renyong Jia Dekang Zhu Mafeng Liu Xinxin Zhao Qiao Yang Ying Wu Shaqiu Zhang Juan Huang Xumin Ou Qun Gao Di Sun Anchun Cheng Shun Chen | 2023 | Virologica Sinica2023，38，5： | 0 |
| 16 | Inhibition of MYC suppresses programmed cell death ligand-1 expression and enhances immunotherapy in triple-negative breast cancer显示文摘Background:Cancer immunotherapy has emerged as a promising strategy against triple-negative breast cancer(TNBC).One of the immunosuppressive pathways involves programmed cell death-1(PD-1)and programmed cell death ligand-1(PD-L1),but many patients derived little benefit from PD-1/PD-L1 checkpoint blockades treatment.Prior research has shown that MYC,a master transcription amplifier highly expressed in TNBC cells,can regulate the tumor immune microenvironment and constrain the efficacy of immunotherapy.This study aims to investigate the regulatory relationship between MYC and PD-L1,and whether a cyclin-dependent kinase(CDK)inhibitor that inhibits MYC expression in combination with anti-PD-L1 antibodies can enhance the response to immunotherapy.Methods:Public databases and TNBC tissue microarrays were used to study the correlation between MYC and PD-L1.The expression of MYC and PD-L1 in TNBCs was examined by quantitative real-time polymerase chain reaction and Western blotting.A patient-derived tumor xenograft(PDTX)model was used to evaluate the influence of a CDK7 inhibitor THZ1 on PD-L1 expression.Cell proliferation and migration were detected by 5-ethynyl-2′-deoxyuridine(EdU)cell proliferation and cell migration assays.Tumor xenograft models were established for in vivo verification.Results:A high MYC expression level was associated with a poor prognosis and could alter the proportion of tumor-infiltrating immune cells(TIICs).The positive correlation between MYC and PD-L1 was confirmed by immunostaining samples from 165 TNBC patients.Suppression of MYC in TNBC caused a reduction in the levels of both PD-L1 messenger RNA and protein.In addition,antitumor immune response was enhanced in the TNBC cancer xenograft mouse model with suppression of MYC by CDK7 inhibitor THZ1.Conclusions:The combined therapy of CDK7 inhibitor THZ1 and anti-PD-L1 antibody appeared to have a synergistic effect,which might offer new insight for enhancing immunotherapy in TNBC. | Xintong Li Lin Tang Qin Chen Xumin Cheng Yiqiu Liu Cenzhu Wang Chengjun Zhu Kun Xu Fangyan Gao Jinyi Huang Runtian Wang Xiaoxiang Guan | 2022 | Chinese Medical Journal2022，135，20： | 0 |
| 17 | Na_(2)CO_(3)-responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics显示文摘Alkali-salinity exerts severe osmotic,ionic,and high-p H stresses to plants.To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species(ROS)homeostasis,physiological and diverse quantitative proteomics analyses of alkaligrass(Puccinellia tenuiflora)under Na_(2)CO_(3)stress were conducted.In addition,Western blot,real-time PCR,and transgenic techniques were applied to validate the proteomic results and test the functions of the Na_(2)CO_(3)-responsive proteins.A total of 104 and 102 Na_(2)CO_(3)-responsive proteins were identified in leaves and chloroplasts,respectively.In addition,84 Na_(2)CO_(3)-responsive phosphoproteins were identified,including 56 new phosphorylation sites in 56 phosphoproteins from chloroplasts,which are crucial for the regulation of photosynthesis,ion transport,signal transduction,and energy homeostasis.A full-length Pt FBA encoding an alkaligrass chloroplastic fructosebisphosphate aldolase(FBA)was overexpressed in wild-type cells of cyanobacterium Synechocystis sp.Strain PCC 6803,leading to enhanced Na_(2)CO_(3)tolerance.All these results indicate that thermal dissipation,state transition,cyclic electron transport,photorespiration,repair of photosystem(PS)Ⅱ,PSI activity,and ROS homeostasis were altered in response to Na_(2)CO_(3)stress,which help to improve our understanding of the Na_(2)CO_(3)-responsive mechanisms in halophytes. | Jinwei Suo Heng Zhang Qi Zhao Nan Zhang Yongxue Zhang Ying Li Baohua Song Juanjuan Yu Jianguo Cao Tai Wang Ji Luo Lihai Guo Jun Ma Xumin Zhang Yimin She Lianwei Peng Weimin Ma Siyi Guo Yuchen Miao Sixue Chen Zhi Qin Shaojun Dai | 2020 | Genomics, Proteomics & Bioinformatics2020，18，3： | 0 |
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