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A bHLH transcription factor,CsSPT,regulates high-temperature resistance in cucumber

Horticultural Plant Journal 2024年第2期10卷 503-514页

作者： Yonggui Liang Chenyu Yang Fangyan Ming Bingwei Yu Zhihua Cheng Yixi Wang Zhengkun Qiu Xiaolan Zhang Bihao Cao Shuangshuang Yan Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(South China) Ministry of Agriculture and Rural AffairsGuangdong Vegetable Engineering and Technology Research CenterCollege of HorticultureSouth China Agricultural UniversityGuangzhouGuangdong 510642China State Key laboratories of Agrobiotechnology Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable CropsMOE Joint Laboratory for International Cooperation in Crop Molecular BreedingChina Agricultural UniversityBeijing 100193China

High-temperature stress threatens the growth and yield of crops. Basic helix-loop-helix(bHLH) transcription factors(TFs) have been shown to play important roles in regulating high-temperature resistance in plants. However, the bHLH TFs responsible for high-temperature tolerance in cucumbers have not been identified. We used transcriptome profiling to screen the high temperature-responsive candidate bHLH TFs in cucumber. Here, we found that the expression of 75 CsbHLH genes was altered under high-temperature stress. The expression of the CsSPT gene was induced by high temperatures in TT(Thermotolerant) cucumber plants. However, the Csspt mutant plants obtained by the CRISPR-Cas9 system showed severe thermosensitive symptoms, including wilted leaves with brown margins and reduced root density and cell *** Csspt mutant plants also exhibited elevated H_(2)O_(2) levels and down-regulated photosystem-related genes under normal ***, there were high relative electrolytic leakage(REC), malondialdehyde(MDA), glutathione(GSH), and superoxide radical(O_(2)^(·-)) levels in the Csspt mutant plants, with decreased Proline content after the high-temperature treatment. Transcriptome analysis showed that the photosystem and chloroplast activities in Csspt mutant plants were extremely disrupted by the high-temperature stress compared with wildtype(WT) plants. Moreover, the plant hormone signal transduction, as well as MAPK and calcium signaling pathways were activated in Csspt mutant plants under high-temperature stress. The HSF and HSP family genes shared the same upregulated expression patterns in Csspt and WT plants under high-temperature conditions. However, most bHLH, NAC, and bZIP family genes were significantly down-regulated by heat in Csspt mutant plants. Thus, these results demonstrated that CsSPT regulated the high-temperature response by recruiting photosynthesis components, signaling pathway molecules, and transcription factors. Our results pro

关键词： Cucumber bHLH CsSPT Photosynthesis High temperature

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Atomic force microscopy correlates antimetastatic potentials of HepG2 cell line with its redox/energy status: effects of curcumin and Khaya senegalensis

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Journal of Integrative Medicine 2017年第3期15卷 214-230页

作者： Jeremiah Olorunjuwon Olugbami Robert Damoiseaux Bryan France Michael A. Gbadegesin Adam Z. Stieg Shivani Sharma Oyeronke A. Odunola James K. Gimzewski Cancer Research and molecular Biology laboratories Department of Biochemistry College of Medicine University of Ibadan Ibadan Oyo 200005 Nigeria Nano and Pico Characterization laboratories California NanoSystems Institute University of California LosAngeles California 90095 USA Department of Chemistry and Biochemistry University of California Los Angeles California 90095 USA molecular screening and shared resources laboratories California NanoSystems Institute University of California Los Angeles California 90095 USA Department of molecular and Medicinal Pharmacology University of California Los Angeles California 90095 USA International Center for Materials Nanoarchitectonics Satellite National Institute for Materials Science Tsukuba 3690114 Japan

OBJECTIVE： The fatality of cancer is mostly dependent on the possibility of occurrence of metastasis. Thus, if the development of metastasis can be prevented through novel therapeutic strategies targeted against this process, then the success of cancer treatment will drastically increase. In this study, therefore, we evaluated the antimetastatic potentials of an extract of Khaya senegalensis and curcumin on the metastatic liver cell line HepG2, and also assessed the anticancer property of the extract. METHODS： Cells were cultured and treated with graded concentrations of test substances for 24, 48, or 72 h with provisions made for negative controls. Treated cells were assessed as follows： nanotechnologically--atomic force microscopy （AFM） was used to determine cell stiffness; biochemically--cell cytotoxicity, glutathione level and adenosine triphosphate status, caspase activation and mitochondrial toxicity were considered; and microbiologically--a carrot disk assay was used to assess the anticancer property of the extract of K. senegalensis. RESULTS： Curcumin and K. senegalensis increased the cell stiffness by 2.6- and 4.0-fold respectively, indicating their antimetastatic effects. Corresponding changes in redox （glutathione level） and energy （adenosine triphosphate） status of the cells were also demonstrated. Further mechanistic studies indicated that curcumin was not mitotoxic in HepG2 cells unlike the K. senegalensis extract. In addition the extract potently inhibited the Agrobacterium tumefaciens-induced genetic transformation based on carrot disk assay. CONCLUSION： Cell elasticity measurement data, using AFM, strongly suggested, for the first time, that both curcumin and the extract of K. senegalensis exhibited antimetastatic properties on HepG2 cells.

关键词： Curcumin Khaya senegalensis atomic force microscopy glutathione adenosine triphosphate metasis carcinoma, hepatocellular

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Genome-wide detection of additional fetal chromosomal abnormalities by cell-free DNA testing of 15,626 consecutive pregnant women

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Science China(Life Sciences) 2019年第2期62卷 215-224页

作者： Hong Yao Ya Gao Jia Zhao Rong Zhang Huixin Xu Huamei Hu Yanmei Luo Yuying Yuan Meili Fu Hongyun Zhang Hui Jiang Wei Wang Huanming Yang Jian Wang Zhiqing Liang Fang Chen Department of Gynecology & Obstetrics Southwest Hospital the Third Military Medical University BGI-Shenzhen China National GeneBank BGI-Shenzhen Birth Defect screening Project Lab BGI-Shenzhen Clinical laboratories of BGI Health BGI-Shenzhen James D.Watson Institute of Genome Sciences Laboratory of Genomics and molecular Biomedicine Department of Biology University of Copenhagen

Cell-free DNA(cfDNA) testing for common fetal trisomies(T21, T18, T13) is highly effective. However, the usefulness of cfDNA testing in detecting other chromosomal abnormalities is unclear. We evaluated the performance of cfDNA testing for genome-wide abnormalities, and analyzed the incremental yield by reporting extra abnormalities. We performed genome-wide cfDNA testing in 15,626 consecutive pregnancies prospectively enrolled in this study. cfDNA testing results were reported and counseling was given depending on the presence of extra chromosomal abnormalities. cfDNA testing identified 190 cases(1.2%)of chromosomal abnormalities including 100 common trisomies and 90 additional abnormalities. By expanding the cfDNA reporting range to genome-wide abnormalities, the false positive rate increased to 0.39%(Pscreening findings. cfDNA testing outperformed biochemical screening by showing 60 times higher true positive rate and fewer false negative ***-wide cfDNA testing significantly increased the diagnostic yield by detecting extra abnormalities, especially those without diagnostic indications. Genome-wide cfDNA testing has fewer false positive and false negative results compared with biochemical screening.

关键词： cell-free DNA genome-wide chromosomal abnormalities sensitivity specificity PPV

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Identification of Methylosome Components as Negative Regulators of Plant Immunity Using Chemical Genetics

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molecular Plant 2016年第12期9卷 1620-1633页

作者： Shuai Huang Aruna Balgi Yaping Pan Meng Li Xiaoran Zhang Lilin Du Ming Zhou Michel Roberge Xin Li Michael Smith laboratories Department of Botany University of British Columbia Vancouver BC V6T 1Z4 Canada Department of Biochemistry and molecular Biology University of British Columbia Vancouver BC V6T 1Z3 Canada Verna and Marrs McLean Department of Biochemistry and molecular Biology Baylor College of Medicine Houston TX 77030 USA National Institute of Biological Sciences Beijing 102206 China

Nucleotide-binding leucine-rich repeat （NLR） proteins serve as immune receptors in both plants and animals. To identify components required for NLR-mediated immunity, we designed and carried out a chemical genetics screen to search for small molecules that can alter immune responses in Arabidopsis thaliana. From 13 600 compounds, we identified Ro 8-4304 that was able to specifically suppress the severe autoimmune phenotypes of chs3-2D （chilling sensitive 3, 2D）, including the arrested growth morphology and heightened PR （Pathogenesis Related） gene expression. Further, six Ro 8-4304 insensitive mutants were uncovered from the Ro 8-4304-insensitive mutant （rim） screen using a mutagenized chs3-2D popula- tion. Positional cloning revealed thatriml encodes an allele of AtlCIn （I, currents; CI, chloride; n, nucleotide）. Genetic and biochemical analysis demonstrated that AtlCIn is in the same protein complex with the meth- ylosome components small nuclear ribonucleoprotein D3b （SmD3b） and protein arginine methyltransferase 5 （PRMT5）, which are required for the biogenesis of small nuclear ribonucleoproteins （snRNPs） involved in mRNA splicing. Double mutant analysis revealed that SmD3b is also involved in the sensitivity to Ro 8-4304, and the prmt5-1 chs3-2D double mutant is lethal. Loss of At/C/n, SmD3b, or PRMT5 function results in enhanced disease resistance against the virulent oomycete pathogen Hyaloperonospora arabidopsidis Noco2, suggesting that mRNA splicing plays a previously unknown negative role in plant immunity. The successful implementation of a high-throughput chemical genetic screen and the identification of a small-molecule compound affecting plant immunity indicate that chemical genetics is a powerful tool to study whole-organism plant defense pathways.

关键词： chemical genetics small molecule screening plant immunity TNL autoimmunity methylosome

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Guidelines for application of high-content screening in traditional Chinese medicine:concept,equipment,and troubleshooting

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Acupuncture and Herbal Medicine 2024年第1期4卷 1-15页

作者： Xuechun Chen Lu Li Mingxu Zhang Jian Yang ChunMing Lyu Yizhou Xu Yang Yang Yi Wang Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhouChina Department of Cardiology Hangzhou First People’s HospitalHangzhouChina National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxingChina molecular Devices Shanghai Corporation ShanghaiChina National Key Laboratory of Chinese Medicine Modernization Tianjin University of Traditional Chinese MedicineTianjinChina Science and Technology Experiment Center Shanghai University of Traditional Chinese MedicineShanghaiChina Engineering Research Center of Innovative Anticancer Drugs Ministry of Educationhangzhou China

High-content screening(HCS)technology combines automated high-speed imaging hardware and single-cell quantitative *** can greatly accelerate data acquisition in cellular fluorescence imaging and is a powerful research technique in traditional Chinese medicine(TCM).An increasing number of laboratories and platforms,including TCM laboratories,have begun utilizing HCS ***,this technology is still in its infancy in TCM research and there is a lack of sufficient experience with the associated concepts,instrument configurations,and analysis *** improve the understanding of HCS among researchers in the field of TCM,this paper summarizes the concept of HCS,software and hardware configuration,the overall research process,as well as common problems and related solutions of HCS in TCM research based on our team’s previous research experience,providing several research examples and an outlook on future perspectives,aiming to provide a technical guide for HCS in TCM research.

关键词： High-content imaging High-content screening Traditional Chinese medicine

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Isolation and functional characterization of the C-terminus of rice phos-phatidylinositol 4-kinase in vitro

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Cell Research 2003年第2期13卷 131-139页

作者： XIANG FENG KONG, ZHI HONG XU, HONG WEI XUE, National Laboratory of Plant molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Science (SIBS), The Chinese Academy of Sciences Partner Group of Max-Planck-Institute of molecular Plant Physiology (MPI-MP) on "Plant molecular Physiology and Signal Transduction", 300 Fenglin Road, 200032 Shanghai, China 1National Laboratory of Plant molecular Genetics Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Science (SIBS)The Chinese Academy of Sciences Partner Group el Max-Planck-Institute of molecular Plant Physiology (MPI-MP) on “Plant molecular Physiology and Signal Transduction” 300 Fenglin Road 200032 Shanghai China 1National Laboratory of Plant molecular Genetics Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Science (SIBS)The Chinese Academy of Sciences Partner Group el Max-Planck-Institute of molecular Plant Physiology (MPI-MP) on “Plant molecular Physiology and Signal Transduction” 300 Fenglin Road 200032 Shanghai China 1National Laboratory of Plant molecular Genetics Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Science (SIBS)The Chinese Academy of Sciences Partner Group el Max-Planck-Institute of molecular Plant Physiology (MPI-MP) on “Plant molecular Physiology and Signal Transduction” 300 Fenglin Road 200032 Shanghai China

A partial rice (Oryza sativa L.) cDNA clone. OsPMK1c, was isolated through screening of a cDNA library constructed from tillering materials. OsPI4Klc encoded a peptide of 608 amino acids with a calculated molecular mass of 68.4 kDa. The OsPI4Klc peptide shared high homology and possessed the highly conserved domains present in most isolated cloned PI4-kinases, i.e. a lipid kinase unique (LKU) domain and a catalytic (CAT) domain. A region with similarity to pleckstrin homology (PH) domain was present in OsPI4K1c as well. Further comparison with genomic sequences in databases revealed that OsPI4K1c is located at the 3'-end of a putative rice PI 4-kinase coding gene OsPI4K1, and its coding region corresponded to the C-terminal half of OsPI4Kl protein. Twelve exons (49-562 bp in size) and 11 introns (77-974 bp in size) were identified in OsPI4K1c. The recombinant protein expressed in Escherichia coli phosphorylates phosphatidylinositol at the D4 position of the inositol ring. OsPI4K1 transcript levels were

关键词： Oryza sativa phosphatidylinositol 4-kinase.

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screening and antibacterial efficacy of selected Indian medicinal plants

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Asian Pacific Journal of Tropical Biomedicine 2016年第3期6卷 185-191页

作者： Suresh Mickymaray Mohammad Saleh Al Aboody Pradipta Kumar Rath Panneerselvam Annamalai Thajuddin Nooruddin Department of Medical laboratories College of Science Al-Zulfi Majmaah University Department of Diagnostic Microbiology and molecular Biology Doctors' Diagnostic Centre Post Graduate & Research Department of Botany & Microbiology A. Veeriya Vandayar Memorial Sri Pushpam College(Autonomous) Department of Microbiology School of Life Sciences Bharathidasan University

Objective: To evaluate the antibacterial efficacy of five Indian medicinal plants such as Acalypha indica L.(A. indica), Aerva lanata(L.) Juss. ex Schult.(A. lanata), Clerodendrum inerme(L.) Gaertn., Pergularia daemia(Forsk.) Chiov. and Solanum surattense Burm. f. against opportunistic bacterial pathogens isolated from HIV infected patients for the potential phytoconstituents in plant ***: The opportunistic bacterial pathogens such as Escherichia coli(E. coli),Pseudomonas aeruginosa, Salmonella typhi and Serratia marcescens from Gramnegative group and Staphylococcus aureus from Gram-positive group were isolated from HIV infected patients. The antibacterial efficacy of ethanolic extracts of selected medicinal plants was carried out by disc diffusion method. The potential phytoconstituents of medicinal plant extracts were identified by gas chromatography and mass spectrometry(GC–MS) ***: Among the five medicinal plants tested, A. indica and A. lanata showed the significant antibacterial activity. A. indica showed potential activity against Staphylococcus aureus and E. coli. A. lanata significantly exhibited antibacterial activity against E. coli, Salmonella typhi and Pseudomonas aeruginosa. A total of 19 phytoconstituents were identified in the ethanolic extract of A. indica and A. lanata by GC–MS analysis ***: The results of the present investigation revealed that A. indica and A. lanata, possessed significant antibacterial activity when compared with the other plant extracts tested. The presence of 3-O-methyl-D-glucose by GC–MS analysis in both A. indica and A. lanata extracts has not been reported elsewhere in the literature and the findings in this study could be the first one to report.

关键词： Antibacterial efficacy Medicinal plants Bacterial pathogens Phytoconstituents

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Monodelphis domestica: a new source of mammalian primary neurons in vitro

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Neural Regeneration Research 2022年第8期17卷 1726-1727页

作者： Jelena Ban Miranda Mladinic Laboratory for molecular Neurobiology Department of BiotechnologyUniversity of RijekaRijekaCroatia

In vi t ro mode ls have tremendously revolutionized cell biology and biomedical research,reducing the need for in vivo experiments,as well as offering the simplified models for easier investigations at molecular and cellular level(for example genetic manipulations,electrophysiological measurements,drug screening etc.).However,the major challenge is to develop long-surviving in vitro preparations of post-mitotic cells such as neurons or *** overcome the problem of neuronal inability to proliferate,the immortalized cell lines derived from neuronal tumors have been *** secondary neuronal cultures are restricted to neuroblastoma-like cells,but their biological relevance is often questionable due to genetic drift and lack of mature,differentiated neuronal phenotypes,which makes primary cultures the better *** central nervous system(CNS)in vitro primary cell cultures are mostly prepared from the late embryonic or early postnatal mice and *** mammalian species have been less used,meaning that inter-species diversity is not sufficiently investigated and that the additional comparative analyses are required to avoid misinterpretations in translating the knowledge to humans(Bonfanti and Peretto,2011).

关键词： overcome offering mostly

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Analysis of Pathway Activity in Primary Tumors and NCI60 Cell Lines Using Gene Expression Profiling Data

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Genomics, Proteomics & Bioinformatics 2007年第1期5卷 15-24页

作者： Xing-Dong Feng Shu-Guang Huang Jian-Yong Shou Bi-Rong Liao Jonathan M. Yingling Xiang Ye Xi Lin Lawrence M. Gelbert Eric W. Su Jude E. Onyia Shu-Yu Li Integrative Biology Lilly Research Laboratories Eli Lilly and Company Lilly Corporate Center Indianapolis IN 46285 USA Global Discovery ＆ Development Statistics Lilly Research Laboratories Eli Lilly and Company Lilly Corporate Center Indianapolis IN 46285 USA Cancer Discovery Research Lilly Research Laboratories Eli Lilly and Company Lilly Corporate Center Indianapolis IN 46285 USA

To determine cancer pathway activities in nine types of primary tumors and NCI60 cell lines, we applied an in silico approach by examining gene signatures reflective of consequent pathway activation using gene expression data. Supervised learning approaches predicted that the Ras pathway is active in -70% of lung adenocarcinomas but inactive in most squamous cell carcinomas, pulmonary carcinoids, and small cell lung carcinomas. In contrast, the TGF-β, TNF-α, Src, Myc, E2F3, and β-catenin pathways are inactive in lung adenocarcinomas. We predicted an active Ras, Myc, Src, and/or E2F3 pathway in significant percentages of breast cancer, colorectal carcinoma, and gliomas. Our results also suggest that Ras may be the most prevailing oncogenic pathway. Additionally, many NCI60 cell lines exhibited a gene signature indicative of an active Ras, Myc, and/or Src, but not E2F3, β-catenin, TNF-α, or TGF-β pathway. To our knowledge, this is the first comprehensive survey of cancer pathway activities in nine major tumor types and the most widely used NCI60 cell lines. The ＂gene expression pathway signatures＂ we have defined could facilitate the understanding of molecular mechanisms in cancer development and provide guidance to the selection of appropriate cell lines for cancer research and pharmaceutical compound screening.

关键词： cancer pathways gene expression profiling supervised learning classification

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A High-Density SNP Genotyping Array for Rice Biology and molecular Breeding

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molecular Plant 2014年第3期7卷 541-553页

作者： Haodong Chen Weibo Xie Hang He Huihui Yu Wei Chen Jing Li Renbo Yu Yue Yao Wenhui Zhang Yuqing He Xiaoyan Tang Fasong Zhou Xing Wang Deng Qifa Zhang Peking-Yale Joint Center for Plant molecular Genetics and Agro-Biotechnology State Key Laboratory of Protein and Plant Gene Research College of LifeSciences Peking University Beijing 100871 China National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University Wuhan430070 China Life Science and Technology Center China National Seed Group Co. Ltd Wuhan 430075 China Shenzhen Institute of molecular Crop Design Shenzhen 518107 China Frontier laboratories of Systems Crop Design Co. Ltd Beijing 100085 China

A high-density single nucleotide polymorphism （SNP） array is critically important for geneticists and molecu- lar breeders. With the accumulation of huge amounts of genomic re-sequencing data and available technologies for accurate SNP detection, it is possible to design high-density and high-quality rice SNP arrays. Here we report the devel- opment of a high-density rice SNP array and its utility. SNP probes were designed by screening more than 10 000 000 SNP loci extracted from the re-sequencing data of 801 rice varieties and an array named RiceSNP50 was produced on the Illumina Infinium platform. The array contained 51 478 evenly distributed markers, 68% of which were within genic regions. Several hundred rice plants with parent/F1 relationships were used to generate a high-quality cluster file for accurate SNP calling. Application tests showed that this array had high genotyping accuracy, and could be used for dif- ferent objectives. For example, a core collection of elite rice varieties was clustered with fine resolution. Genome-wide association studies （GWAS） analysis correctly identified a characterized QTL. Further, this array was successfully used for variety verification and trait introgression. As an accurate high-throughput genotyping tool, RiceSNP50 will play an important role in both functional genomics studies and molecular breeding.

关键词： single nucleotide polymorphisms (SNPs) array rice molecular breeding.

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