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Comparative plastomic analysis and insights into the phylogeny of Salvia (Lamiaceae)

Plant Diversity 2021年第1期43卷 15-26页

作者： Hong Wu peng-fei ma Hong-Tao Li Guo-Xiong Hu De-Zhu Li Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201China University of Chinese Academy of Sciences Beijing100049China College of Life Sciences Guizhou UniversityGuiyangGuizhou550025China

Salvia is the largest genus of Lamiaceae,with almost 1000 species,and has been divided into 11 *** ***,native to East Asia,is particularly important because of its potential medicinal ***,the interspecific relationships of this subgenus have not been resolved and the plastomes of Salvia have rarely been *** the current study,we compared plastid genome structure and organization of 19 species of Salvia(14 newly sequenced and 5 previously published).Our comparative analysis showed that all Salvia plastomes examined have a quadripartite structure typical of most angiosperms and contain an identical set of 114 unique genes(80 protein-coding genes,4 rRNA genes,and 30 tRNA genes).The plastome structure of all Salvia species is highly conserved like other Lamiaceae *** content,gene order,and GC content were highly similar in these *** inverted repeats/single copy region(IR/SC)boundaries of Salvia are highly conserved,and IR contraction only occurred in two species(Salvia mekongensis and ***).In Salvia,sequence divergence was higher in non-coding regions than in coding *** found that using large single copy(LSC)and small single copy regions(SSC)with exclusion of the rapidly evolving sites produced the highest resolution in phylogenetic analysis of Salvia,suggesting that using suitable informative sites to build trees is more conducive in phylogenetic *** study assembled a powerful matrix data set for studying the phylogeny of Salvia,resolving the interspecific relationship of Salvia *** newly sequenced plastid genomes will also enrich the plastome database of Salvia,providing the scientific basis for the development and utilization of germplasm resources of this large and important genus.

关键词： Lamiaceae Salvia subg.Glutinaria Plastome Phylogeny

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Function of chloride intracellular channel 1 in gastric cancer cells

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World Journal of Gastroenterology 2012年第24期18卷 3070-3080页

作者： peng-fei ma Jun-Qiang Chen Zhen Wang Jin-Lu Liu Bo-Pei Li Department of Gastrointestinal Surgery the First Affili- ated Hospital of Guangxi Medical University Nanning 530021 Guangxi Zhuang Autonomous Region China

AIM:To investigate the effect of chloride intracellular channel 1(CLIC1) on the cell proliferation,apoptosis,migration and invasion of gastric cancer ***:CLIC1 expression was evaluated in human gastric cancer cell lines SGC-7901 and MGC-803 by real time polymerase chain reaction(RT-PCR).Four segments of small interference RNA(siRNA) targeting CLIC1 mRNA and a no-sense control segment were designed by bioinformatics ***1 siRNA was selected using Lipofectamine 2000 and transfected transiently into human gastric cancer SGC-7901 and MGC-803 *** transfected efficiency was observed under fluorescence *** transfection,mRNA expression of CLIC1 was detected with RT-PCR and Western blotting was used to detect the protein *** was examined by methyl thiazolyl tetrazolium and apoptosis was detected with flow *** membrane transwell chamber and matrigel were used for the detection of the changes of invasion and migration of the two cell ***:In gastric cancer cell lines SGC-7901 and MGC-803,CLIC1 was obviously expressed and CLIC1 siRNA could effectively suppress the expression of CLIC1 protein and *** of cells transfected with CLIC1 siRNA3 was enhanced notably,and the highest proliferation rate was 23.3%(P = 0.002) in SGC-7901 and 35.55%(P = 0.001) in MGC-803 cells at 48 *** G2/M phase proportion increased,while G0/G1 and S phase proportions *** apoptotic rate of the CLIC1 siRNA3 group obviously decreased in both SGC-7901 cells(62.24%,P = 0.000) and MGC-803 cells(52.67%,P = 0.004).Down-regulation of CLIC1 led to the inhibition of invasion and migration by 54.31%(P = 0.000) and 33.62%(P = 0.001) in SGC-7901 and 40.74%(P = 0.000) and 29.26%(P = 0.002) in ***,there was no significant difference between the mock group cells and the negative control group cells.

关键词： Chloride intracellular channel 1 Gastric car-cinoma Small interference RNA Apoptosis Invasion Migration

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Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia

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Plant Diversity 2023年第2期45卷 147-155页

作者： Shi-Yu Lv Xia-Ying Ye Zhong-Hu Li peng-fei ma De-Zhu Li School of Life Science Northwest UniversityXi'anShaanxi710069China Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201China Agronomy and Life Science Department Zhaotong UniversityZhaotongYunnan657000China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan650201China

Fargesia,the largest genus within the temperate bamboo tribe Arundinarieae,has more than 90 species mainly distributed in the mountains of Southwest *** Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals,including the giant ***,species-level identification of Fargesia is ***,the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DNA barcoding with standard plant barcodes(rbcL,matK,and ITS) in *** progress in the sequencing technologies,complete plastid genomes(plastomes) and nuclear ribosomal DNA(nrDNA)sequences have been proposed as organelle barcodes for species identification;however,these have not been tested in *** collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastomes and nrDNA sequences compared to standard *** analysis indicates that complete plastomes have substantially higher discriminatory power(28.6%) than standard barcodes(5.7%),whereas nrDNA sequences show a moderate improvement(65.4%) compared to ITS(47.2%).We also found that nuclear markers performed better than plastid markers,and ITS alone had higher discriminatory power than complete *** study also demonstrated that plastomes and nrDNA sequences can contribute to intrageneric phylogenetic resolution in ***,neither of these sequences were able to discriminate all the sampled species,and therefore,more nuclear markers need to be identified.

关键词： Fargesia Genome-skimming DNA barcoding Plastome Ribosomal DNA

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Binder jetting 3D printing process optimization for rapid casting of green parts with high tensile strength

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China Foundry 2021年第4期18卷 335-343页

作者： Zhao-fa Zhang Li Wang Lin-tao Zhang peng-fei ma Bing-heng Lu Chen-wei Du Micro and Nano Technology Research Center State Key Laboratory for Manufacturing Systems EngineeringXi’an Jiaotong UniversityXi’an 710049China National Innovation Institute of Additive manufacturing Xi’an 710065China Beijing Hangxing machinery manufacturing Co. Ltd.Beijing 100013China

Binder jetting 3D printing is a rapid,cost effective,and efficient moulding/core making process,which can be applied to a large variety of ***,it exhibits a relatively low green-part *** may cause the collapse of the printed parts during de-caking and the pick-up procedure,especially in the case of small-scale structures,such as thin walls,tips,and *** this work,polyvinyl alcohol(PVA)was used as the additive in coated sand *** exploiting the binding effect between the two composites(thermoplastic phenolic resin and PVA)triggered by the binder,bonding necks firmly form among the sand particles,improving the green-part strength of the coated sand printed *** based on the Taguchi method were used to investigate the relationship between the process parameters and the green-part tensile *** following set of optimal process parameters was identified:50wt.%alcoholicity of the binder,75%binder saturation,0.36 mm layer thickness and 4.5wt.%PVA ***,the effect of such parameters on the green-part tensile strength was determined via statistical *** green part of an engine cylinder head sand pattern with complex cavity structures was printed,and the green-part tensile strength reached 2.31 ***,the ZL301 aluminum alloy impeller shape casting was prepared using sand molds printed with the optimal process *** results confirm that the proposed binder jetting 3D printing process can guarantee the integrity of the printed green parts and of small-size structures during de-caking and the pick-up ***,the casting made from the printed sand molds exhibits a relatively high quality.

关键词： binder jetting green-part strength coated sand polyvinyl alcohol rapid casting

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HIV-Specific IL-2^+ and/or IFN-γ^+ CD8^+ T Cell Reponses during Chronic HIV-1 Infection in Former Blood Donors

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Biomedical and Environmental Sciences 2010年第5期23卷 391-401页

作者： YAN-MENG FENG YAN-MIN WAN LIAN-XIN LIU CHAO QIU peng-fei ma HONG peng YU-HUA RUAN LI-FENG HAN KUN-XUE HONG HUI XING YI-MING SHAO State Key Laboratory of Virology Wuhan Institute of VirologyChinese Academy of SciencesWuhan 430071HubeiChina State Key Laboratory for Infectious Diseases Prevention and Control Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China State Key Laboratory for Infectious Diseases Prevention and Control National Center for AIDS/STD Control and PreventionChinese Center for Disease Control and PreventionBeijing 100050China Graduate School of the Chinese Academy of Sciences Beijing 100049China

Objective Conflicting data have been generated from previous studies to determine which kind of relationship exists between HIV-1 specific CD8 Tcell responses and HIV-1 viral load or CD4 count over the course of *** this study,153 HIV-1 infected LTNPs were enrolled to investigate the role of HIV-1 specific CD8 T-cell responses in chronic HIV-1 infection among HIV-1 infected former blood *** The patients were stratified into three groups according to CD4 count：CD4≥500 cells/μL;350 cells/μL≤CD4〈500 cells/μL;CD4〈350 cells/μ*** were isolated from the patients＇ anticoagulated blood ***-2 and IFN-γ secretions of CD 8 T cells against 17 HIV-1 consensus B full peptide pools were analyzed by using ICS *** An overall inverse correlation were observed between CD4 count and plasma viral *** no significant difference was observed during the comparisons of frequency/breadth of HIV-1 specific CD8 T cell responses,CD4 count stratification analysis showed that different correlation pattern existed in three strata：as for patients whose CD4 counts were less than 350 cells/μL,no significant correlations were identified between frequency/breadth of HIV-1 specific CD8 T cell responses and CD4 count/viral load;as for patients whose CD4 counts ranged from 350 cells /μL to 500 cells/μL,significant correlation was only observed between the response breadth of IL-2＋IFN-γ＋ CD8 T cells and CD4 count;however,as for patients whose CD4 counts were more than 500 cells/μL,direct correlations were identified between IL-2＋IFN-γ＋/IL-2＋/IFN-γ＋ CD8 T cells and viral load or CD4 *** Universal consistent inverse correlation was only indentified between CD4 count and viral *** relationship between HIV-1 specific CD8 T cell responses and CD4 count/viral load varied in different CD4 strata,which showed that better preserved CD4 T cells were correlated with better CD8 T cell functions.

关键词： HIV-1 subtype B' CD8 T cell response IFN-γ IL-2 ICS

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The origin and morphological character evolution of the paleotropical woody bamboos

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Journal of Integrative Plant Biology 2024年第10期66卷 2242-2261页

作者： Jing-Xia Liu Cen Guo peng-fei ma Meng-Yuan Zhou Ya-Huang Luo Guang-Fu Zhu Zu-Chang Xu Richard I Milne maria S.Vorontsova De-Zhu Li Germplasm Bank of Wild Species&Yunnan Key Laboratory of Crop Wild Relatives Omics Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China Center for Integrative Conservation&Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglun 666303China State Key Laboratory of Plant Diversity and Specialty Crops Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China Institute of Molecular Plant Sciences School of Biological SciencesUniversity of EdinburghEdinburgh EH93JHUK Royal Botanic Gardens KewRichmond TW93ABUK

The woody bamboos(Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkable morphological diversity across the subfamily exists within a single hexaploid clade, the paleotropical woody bamboos(PWB), making it ideal to investigate the factors underlying morphological evolution in woody ***, the origin and biogeographical history of PWB remain elusive, as does the effect of environmental factors on the evolution of their morphological characters. We generated a robust and timecalibrated phylogeny of PWB using single nucleotide polymorphisms retrieved from optimized double digest restriction site associated DNA sequencing,and explored the evolutionary trends of habit,inflorescence, and caryopsis type in relation to environmental factors including climate, soil, and topography. We inferred that the PWB started to diversify across the Oligocene–Miocene boundary and formed four major clades, that is, Melocanninae,Racemobambosinae s.l.(comprising Dinochloinae,Greslanlinae, Racemobambosinae ***. and Temburongiinae), Hickeliinae and Bambusinae s.l.(comprising Bambusinae ***. plus Holttumochloinae).The ancestor of PWB was reconstructed as having erect habit, indeterminate inflorescence and basic caryopsis. The characters including climbing/scrambling habit, determinate inflorescence, and nucoid/bacoid caryopsis have since undergone multiple changes and reversals during the diversification of PWB. The evolution of all three traits was correlated with, and hence likely influenced by, aspects of climate, topography, and soil, with climate factors most strongly correlated with morphological traits, and soil factors least so. However, topography had more influence than climate or soil on the evolution of erect habit, whereas both factors had greater effect on the evolution of bacoid caryopsis than did soil. Our results prov

关键词： Bambuseae biogeography ddRAD-seq environmental factors morphological evolution phylogenomics

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Study of HIV-1 Drug Resistance in Patients Receiving Free Antiretroviral Therapy in China

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中国病毒学 2007年第3期22卷 233-240页

作者： Xin-ping LIP　 Hui XING　 Zhe WANG　 Xue-feng SI Lian-en WANG　 Hua CHENG　 Wei-guo CUI　 Shu-lin JIANG　 Ling-jie LIAO　 Hai-wei ZHOU　 Jiang-hong HUANG　 Hong peng　 peng-fei ma　 Yi-ming SHAO State key laboratory of virology Wuhan Institute of Virology Chinese Academy of Science Wuhan 430071 China State key laboratory for Infectious disease prevention and control Division of Research on Virology and Immunology National Center for AIDS/STD Control and Prevention Chinese Center for Disease Control and Prevention Beijing 100050 China Henan Center for Disease Control and Prevention Zhengzhou 450003 China Queshan Center for Disease Control and Prevention Henan 463200 China Graduate University of Chinese Academy of Sciences Beijing 100080 China

To investigate the prevalence of drug-resistance mutations,resistance to antiretroviral drugs,and the subsequent virological response to therapy in treatment-naive and antiretroviral-treated patients infected with HIV/AIDS in Henan,China,a total of 431 plasma samples were collected in Queshan county between 2003 and 2004,from patients undergoing the antiretroviral regimen Zidovudine + Didanosine + Nevirapine(Azt+Ddi+Nvp).Personal information was collected by face to face *** load and genotypic drug resistance were *** resistance mutation data were obtained by analyzing patient-derived sequences through the HIVdb Program(http://***).Overall,38.5% of treatment-naive patients had undetectable plasma viral load(VL),the rate significantly increased to 61.9% in 0 to 6 months treatment patients(mean 3 months)(Pmal viral suppression in patients undergoing treatment for less than 6 months in Queshan,Henan

关键词：艾滋病病毒艾滋病治疗抗药性逆转录酶

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BambooBase:A comprehensive database of bamboo omics and systematics

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Molecular Plant 2024年第5期17卷 682-685页

作者： Yun-Long Liu Shu-Yang Gao Guihua Jin Meng-Yuan Zhou Qijuan Gao Cen Guo Yi-Zhou Yang Liang-Zhong Niu Enhua Xia Zhen-Hua Guo peng-fei ma De-Zhu Li Germplasm Bank of Wild Species&Yunnan Key Laboratory of Crop Wild Relatives Omics Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650201China State Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural UniversityHefeiAnhui 230036China School of Computer and Artificial Intelligence Hefei Normal UniversityHefeiAnhui 230061China Key Laboratory for Plant Diversity and Biogeography in East Asia Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China

Dear Editor,Bamboos(Bambusoideae,Poaceae)are of significant economic and ecological importance,supporting billions of people and contributing to international trade(Wu et al.,2023).They play a crucial role in carbon fixation and support a multitude of other species including the giant panda(Clark et al.,2015).Since the release of the first draft genome of moso bamboo(Phyllostachys edulis)(peng et al.,2013),there has been a notable increase in the sequencing,assembly,and annotation of diverse bamboo genomes(Guo et al.,2019;Zheng et al.,2022;ma et al.,2024).An existing resource for bamboo genomics,BambooGDB(Zhao et al.,2014),provides information based on the individual draft reference genome of moso *** is needed,however,is a resource reinforcing multiple genome assemblies in Bambusoideae to enable researchers to unravel the evolutionary history of chromosomes and genes through cladespecific comparative genomic ***,we present BambooBase(https://***/),a newly developed web-based database designed to provide a seamless user experience for bamboo omics and systematics.

关键词： enable supporting Bamboo

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基于病毒协同遗传算法的自动化立体仓库货位优化模型

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中国管理科学 2017年第5期25卷 70-77页

作者：李鹏飞马航西安邮电大学经济与管理学院陕西西安710121

自动化立体仓库是一个错综复杂的存储系统,货位优化问题直接影响自动化立体仓库的工作效率。针对自动化立体仓库的货位选择问题,本文提出以出入库效率和货架稳定性为优化因素的货位优化模型,并采取病毒协同遗传算法对优化模型进行仿真... 详细信息

自动化立体仓库是一个错综复杂的存储系统,货位优化问题直接影响自动化立体仓库的工作效率。针对自动化立体仓库的货位选择问题,本文提出以出入库效率和货架稳定性为优化因素的货位优化模型,并采取病毒协同遗传算法对优化模型进行仿真。最后对仿真结果及货位优化前,病毒协同遗传算法优化后,传统遗传算法优化后三者的对比结果进行分析,结果说明病毒协同遗传算法(VEGA)能有效实现自动化立体仓库货位优化,是提高货物出入库效率和货架的稳定性的一种有效方法。

关键词：自动化立体仓库货位优化病毒协同遗传算法

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Interaction of major facilitator superfamily domain containing 2A with the blood-brain barrier

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Neural Regeneration Research 2025年第8期20卷 2133-2152页

作者： Yilun ma Taiwei Dong fei Luan Juanjuan Yang Feng Miao Peifeng Wei College of Pharmacy and First Clinical Medical College Shaanxi University of Chinese MedicineXianyangShaanxi ProvinceChina National Drug Clinical Trial Agency The Second Affiliated Hospital of Shaanxi University of Chinese Medicine/Xixian New District Central HospitalXi′anShaanxi ProvinceChina

The functional and structural integrity of the blood-brain barrier is crucial in maintaining homeostasis in the brain microenvironment;however,the molecular mechanisms underlying the formation and function of the blood-brain barrier remain poorly *** major facilitator superfamily domain containing 2A has been identified as a key regulator of blood-brain barrier *** plays a critical role in promoting and maintaining the formation and functional stability of the blood-brain barrier,in addition to the transport of lipids,such as docosahexaenoic acid,across the blood-brain ***,an increasing number of studies have suggested that major facilitator superfamily domain containing 2A is involved in the molecular mechanisms of blood-brain barrier dysfunction in a variety of neurological diseases;however,little is known regarding the mechanisms by which major facilitator superfamily domain containing 2A affects the blood-brain *** paper provides a comprehensive and systematic review of the close relationship between major facilitator superfamily domain containing 2A proteins and the blood-brain barrier,including their basic structures and functions,cross-linking between major facilitator superfamily domain containing 2A and the blood-brain barrier,and the in-depth studies on lipid transport and the regulation of blood-brain barrier *** comprehensive systematic review contributes to an in-depth understanding of the important role of major facilitator superfamily domain containing 2A proteins in maintaining the structure and function of the blood-brain barrier and the research progress to *** will not only help to elucidate the pathogenesis of neurological diseases,improve the accuracy of laboratory diagnosis,and optimize clinical treatment strategies,but it may also play an important role in prognostic *** addition,the effects of major facilitator superfamily domain containing 2A on blood-brain barrier lea

关键词： blood-brain barrier(BBB) caveolin-1 central nervous system docosahexaenoic acid endothelial cells lysophosphatidylcholine major facilitator superfamily domain containing 2A(MFSD2A) transcytosis

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