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Histone Lysine Methyltransferase SDG8 Is Involved in Brassinosteroid-Regulated Gene Expression in Arabidopsis thaliana

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Molecular Plant 2014年第8期7卷 1303-1315页

作者： Xiaolei Wang Jiani Chen Zhouli Xie Sanzhen Liu Trevor Nolan Huaxun Ye Mingcai Zhang Hongqing Guo Patrick S. Schnable Zhaohu Li Yanhai Yin State Key Laboratory of Plant Physiology and Biochemistry Department of Agronomy College of Agronomy and Biotechnology ChinaAgricultural University Beijing 100193 PR China department of genetics Development and Cell Biology Iowa State University Ames IA 50011 USA department of Agronomy Iowa State University Ames IA 50011 USA Present address: department of Plant Pathology Kansas State University Manhattan KS 66506-5502 USA Present address: Du Pont Pioneer Inc. Johnston IA USA Data2Bio LLC Ames IA 50011-3650 USA

The plant steroid hormones, brassinosteroids （BRs）, play important roles in plant growth, development, and responses to environmental stresses. BRs signal through receptors localized to the plasma membrane and other signaling components to regulate the BES1/BZR1 family of transcription factors, which modulates the expression of thousands of genes. How BESl/BZR1 and their interacting proteins function to regulate the large number of genes are not com- pletely understood. Here we report that histone lysine methyltransferase SDG8, implicated in histone 3 lysine 36 diand trimethylation （H3K36me2 and me3）, is involved in BR-regulated gene expression. BES1 interacts with SDG8, directly or indirectly through IWSl, a transcription elongation factor involved in BR-regulated gene expression. The knockout mutant sdg8 displays a reduced growth phenotype with compromised BR responses. Global gene expression studies demonstrated that, while BR regulates about 5000 genes in wild-type plants, the hormone regulates fewer than 700 genes in sdg8 mutant. In addition, more than half of BR-regulated genes are differentially affected in sdg8 mutant. A Chromatin Immunoprecipitation （CHIP） experiment showed that H3K36me3 is reduced in BR-regulated genes in the sdg8 mutant. Based on these results, we propose that SDG8 plays an essential role in mediating BR-regulated gene expression. Our results thus reveal a major mechanism by which histone modifications dictate hormonal regulation of gene expression.

关键词： brassinosteroid histone modifications gene regulation.

CYP1A1,CYP2E1 and EPHX1 polymorphisms in sporadic colorectal neoplasms

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World Journal of Gastroenterology 2016年第45期22卷 9974-9983页

作者： Glaucia Maria M Fernandes Anelise Russo Marcela Alcantara Proenca Nathalia Fernanda Gazola Gabriela Helena Rodrigues Patrícia Matos Biselli-Chicote Ana Elizabete Silva Joao Gomes Netinho érika Cristina Pavarino Eny Maria Goloni-Bertollo genetics and Molecular Biology Research Unit-UPGEM Department of Molecular Biology Sao José do Rio Preto Medical School FAMERP Departament of Biology UNESP-Sao Paulo State University Departament of Surgery and Coloproctology Service Sao José do Rio Preto Medical School FAMERP

AIM To investigate the contribution of polymorphisms in the CYP1A1, CYP2E1 and EPHX1 genes on sporadic colorectal cancer(SCRC) risk. METHODS Six hundred forty-one individuals(227 patients with SCRC and 400 controls) were enrolled in the study. The variables analyzed were age, gender, tobacco and alcohol consumption, and clinical and histopathological tumor parameters. The CYP1A1 *2A, CYP1A1 *2C CYP2E1 *5B and CYP2E1 *6 polymorphisms were analyzed by polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP). The EPHX1 Tyr113 His, EPHX1 His139 Arg and CYP1A1 *2C polymorphisms were detected by real-time PCR. Chisquared test and binary logistic regression were used in the statistical analysis. Haplotype analysis was conducted using the Haploview program, version *** Age over 6 2 years was a risk factor for SCRC development(OR = 7.54, 95%CI: 4.94-11.50, P < 0.01). Male individuals were less susceptible to SCRC(OR = 0.55, 95%CI: 0.35-0.85, P < 0.01). The CYP2E1*5B polymorphism was associated with SCRC in the codominant(heterozygous genotype: OR = 2.66, 95%CI: 1.64-4.32, P < 0.01), dominant(OR = 2.82, 95%CI: 1.74-4.55, P < 0.01), overdominant(OR = 2.58, 95%CI: 1.59-4.19, P < 0.01), and log-additive models(OR = 2.84, 95%CI: 1.78-4.52, P < 0.01). The CYP2E1*6 polymorphism was associated with an increased SCRC risk in codominant(heterozygous genotype: OR = 2.81, 95%CI: 1.84-4.28, P < 0.01; homozygous polymorphic : OR = 7. 3 2, 9 5 % C I : 1.85-28.96, P < 0.01), dominant(OR = 2.97, 95%CI: 1.97-4.50, P < 0.01), recessive(OR = 5.26, 95%CI: 1.35-20.50, P = 0.016), overdominant(OR = 2.64, 95%CI: 1.74-4.01, P < 0.01), and log-additive models(OR = 2.78, 95%CI: 1.91-4.06, P < 0.01). The haplotype formed by the minor alleles of the CYP2E1*5B(C) and CYP2E1*6(A) polymorphisms was associated with SCRC(P = 0.002). However, the CYP1A1 *2A, CYP1A1 *2C, EPHX1 Tyr113 His and EPHX1 His139 Arg polymorphisms were not associated with *** In conclusion, the

关键词： Single-nucleotide polymorphisms Colorectal neoplasms Cytochrome P-450 CYP2E1 Cytochrome P-450 CYP1A1 Epoxide hydrolases 1

Spectral reflectance response to nitrogen fertilization in field grown corn

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International Journal of Agricultural and Biological Engineering 2018年第4期11卷 118-126页

作者： Chuanqi Xie Ce Yang Alexander Hummel Jr Gregg A Johnson Forrest T Izuno department of Bioproducts and Biosystems Engineering University of MinnesotaSaint PaulMN 55108United States Farm Nutrients Inc. 4949 Hwy 71RembrandtIA 50576United States department of Agronomy and Plant genetics University of MinnesotaSaint PaulMN 55108United States Southern Research and Outreach Center University of MinnesotaWasecaMN 56093United States

This study was carried out to analyze the spectral reflectance response of different nitrogen levels for corn *** different nitrogen treatments of 0%,80%,100%and 120%BMP(best management practice)were *** component analysis-loading(PCA-loading)was used to identify the effective *** least squares(PLS)and multiple linear regression(MLR)models were built to predict different nitrogen *** indices(VIs)were calculated and then used to build more prediction *** full and selected wavelengths-based models showed similar prediction *** overall PLS model obtained the coefficient of determination(R^(2))of 0.6535 with a root mean square error(RMSE)of 0.2681 in the prediction *** selected wavelengths for overall MLR model obtained the R^(2) of 0.6735 and RMSE of 0.3457 in the prediction *** results showed that the wavelengths in visible and near infrared region(350-1000 nm)performed better than the two either spectral regions(1001-1350/1425-1800 nm and 2000-2400 nm).For each data set,the wavelengths around 555 nm and 730 nm were identified to be the most important to predict nitrogen *** vogelmann red edge index 2(VOG 2)performed the best among all *** demonstrated that spectral reflectance has the potential to be used for analyzing nitrogen response in corn.

关键词： spectrum effective wavelengths principal component analysis-loading(PCA-loading) prediction vegetation indices(VIs) corn

MRBLES 2.0: High-throughput generation of chemically functionalized spectrally and magnetically encoded hydrogel beads using a simple single-layer microfluidic device

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Microsystems & Nanoengineering 2020年第1期6卷 145-157页

作者： Yinnian Feng Adam K.White Jamin B.Hein Eric A.Appel Polly M.Fordyce department of genetics Stanford UniversityStanfordCA 94305USA department of Bioengineering Stanford UniversityStanfordCA 94305USA department of Biology Stanford UniversityStanfordCA 94305USA The Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical SciencesUniversity of CopenhagenBlegdamsvej 3b2200 CopenhagenDenmark department of Materials Science&Engineering Stanford UniversityStanfordCA 94305USA Stanford ChEM-H Stanford UniversityStanfordCA 94305USA Chan Zuckerberg Biohub San FranciscoCA 94110USA

The widespread adoption of bead-based multiplexed bioassays requires the ability to easily synthesize encoded microspheres and conjugate analytes of interest to their ***,we present a simple method(MRBLEs 2.0)for the efficient high-throughput generation of microspheres with ratiometric barcode lanthanide encoding(MRBLEs)that bear functional groups for downstream surface *** production in MRBLEs 2.0 relies on the manual mixing of lanthanide/polymer mixtures(each of which comprises a unique spectral code)followed by droplet generation using single-layer,parallel flow-focusing devices and the off-chip batch polymerization of droplets into *** streamline downstream analyte coupling,MRBLEs 2.0 crosslinks copolymers bearing functional groups on the bead surface during bead *** the MRBLEs 2.0 pipeline,we generate monodisperse MRBLEs containing 48 distinct well-resolved spectral codes with high throughput(>150,000/min and can be boosted to 450,000/min).We further demonstrate the efficient conjugation of oligonucleotides and entire proteins to carboxyl MRBLEs and of biotin to amino ***,we show that MRBLEs can also be magnetized via the simultaneous incorporation of magnetic nanoparticles with only a minor decrease in the potential code *** the advantages of dramatically simplified device fabrication,elimination of the need for custom-made equipment,and the ability to produce spectrally and magnetically encoded beads with direct surface functionalization with high throughput,MRBLEs 2.0 can be directly applied by many labs towards a wide variety of downstream assays,from basic biology to diagnostics and other translational research.

关键词： beads spectral functional

Osteocyte Egln1/Phd2 links oxygen sensing and biomineralization via FGF23

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Bone Research 2023年第1期11卷 178-192页

作者： Megan L.Noonan Pu Ni Emmanuel Solis Yamil G.Marambio Rafiou Agoro Xiaona Chu Yue Wang Hongyu Gao Xiaoling Xuei Erica L.Clinkenbeard Guanglong Jiang Sheng Liu Steve Stegen Geert Carmeliet William R.Thompson Yunlong Liu Jun Wan Kenneth E.White department of Medical and Molecular genetics Indiana University School of MedicineIndianapolisIN46202USA Laboratory of Clinical and Experimental Endocrinology Department of Chronic Diseases and MetabolismKU Leuven3000LeuvenBelgium department of Physical Therapy Indiana University School of MedicineIndianapolisIN46202USA department of Anatomy Cell Biologyand PhysiologyIndiana University School of MedicineIndianapolisIN46202USA Center for Computational Biology and Bioinformatics Indiana University School of MedicineIndianapolisIN46202USA departments of Medicine/Division of Nephrology Indiana University School of MedicineIndianapolisIN46202USA

Osteocytes act within a hypoxic environment to control key steps in bone ***23,a critical phosphate-regulating hormone,is stimulated by low oxygen/iron in acute and chronic diseases,however the molecular mechanisms directing this process remain *** goal was to identify the osteocyte factors responsible for FGF23 production driven by changes in oxygen/iron ***-inducible factor-prolyl hydroxylase inhibitors(HIF-PHI)which stabilize HIF transcription factors,increased Fgf23 in normal mice,as well as in osteocyte-like cells;in mice with conditional osteocyte Fgf23 deletion,circulating i FGF23 was *** inducible MSC cell line(‘MPC2’)underwent FG-4592 treatment and ATACseq/RNAseq,and demonstrated that differentiated osteocytes significantly increased HIF genomic accessibility versus progenitor *** genomics also revealed increased prolyl hydroxylase Egln1(Phd2)chromatin accessibility and expression,which was positively associated with osteocyte *** mice with chronic kidney disease(CKD),Phd1-3 enzymes were suppressed,consistent with FGF23 upregulation in this *** loss of Phd2 from osteocytes in vivo resulted in upregulated Fgf23,in line with our findings that the MPC2 cell line lacking Phd2(CRISPR Phd2-KO cells)constitutively activated Fgf23 that was abolished by HIF1α*** vitro,Phd2-KO cells lost iron-mediated suppression of Fgf23 and this activity was not compensated for by Phd1 *** sum,osteocytes become adapted to oxygen/iron sensing during differentiation and are directly sensitive to bioavailable ***,Phd2 is a critical mediator of osteocyte FGF23 production,thus our collective studies may provide new therapeutic targets for skeletal diseases involving disturbed oxygen/iron sensing.

关键词： FGF23 collective adapted

Molecular Genetic Analysis of Partial 9p Trisomy in Two Chinese Families with Mental Retardation and Facial Anomaly

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Journal of Huazhong University of Science and Technology(Medical Sciences) 2011年第4期31卷 570-577页

作者：冯爱平代小华王晓然高勇罗瑞丽李雨雷张娜刘静宇 department of Dermatology Union HospitalTongji Medical CollegeHuazhong University of Science and Technology Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and TechnologyCenter for Human Genome ResearchHuazhong University of Science and Technology Laboratory of Human genetics Nanyang Institute of Planned Parenthood

Mental retardation is defined by significant limitations in intellectual function and adaptive behavior that occur before 18 years of *** chromosomal diseases come with mental *** reported two Chinese families with partial trisomy 9p and other chromosome partial monosomy,clinical features of mental retardation and mild facial and pinkie *** the family 1,we showed that the proband carried a trisomy 9p21.3→pter and monosomy 21q22.3→qter by using fluorescence in situ hybridization *** genetic analysis defined the precise breakpoint on chromosome 9p between markers D9S1846 and D9S171,an interval of about 2.9 Mb on 9p21.3,and the breakpoint on chromosome 21q between markers D21S1897 and D21S1446,a region of about 1.5 Mb on *** the family 2,a patient with trisomy 9p21.3→pter and monosomy 5p15.33→pter,and a de novo maternal balanced translocation between chromosomes 5 and 9 was identified in his *** and molecular genetic analysis defined the precise breakpoints on chromosome 9p21.3 and chromosome *** clinical investigation found that any individual had no refractoriness eczema disease except the proband in this *** results further implicate that trisomy 9p is associated with mental retardation,and that there may be key gene duplication on chromosome 9p21.3→9pter responsible for mental retardation and mild facial *** result has been applied successfully in prenatal diagnosis of the second family.

关键词： partial 9p trisomy mental retardation molecular genetic analysis prenatal diagnosis

Possible novel roles of poly(rC)-binding protein 1 in SH-SY5Y neurocytes: an analysis using a dynamic Bayesian network

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Neuroscience Bulletin 2012年第3期28卷 282-290页

作者： Li-Rong Huo Jian-Tao Liang Jun-Hua Zou Lan-Ying Wang Qi Li Xiao-Min Wang department of Physiology Key Laboratory for Neurodegenerative Disorders of the Ministry of Education Capital Medical University Beijing 100069 China Peking University Center of Medical genetics Beijing 100083 China Xuan Wu Hospital of Capital Medical University Beijing 100053 China Genminix Informatics Ltd. Co. Shanghai 201210 China

Objective Poly（rC）-binding protein 1 （PCBP1） belongs to the heterogeneous nuclear ribonucleoprotein family and participates in transcriptional and translational regulation. Previous work has identified transcripts targeted by both knockdown and overexpression of PCBP1 in SH-SY5Y neuroblastoma cells using a microarray or ProteomeLabTM protein fractionation 2-dimensions （PF-2D） and quadrupole time-of-flight mass spectrometer. The present study aimed to further determine whether these altered transcripts from major pathways （such as Wnt signaling, TGF-β signaling, cell cycling, and apoptosis） and two other genes, H2AFX and H2BFS （screened by PF-2D）, have spatial relationships. Methods The genes were studied by qRT-PCR, and dynamic Bayesian network analysis was used to rebuild the coordination network of these transcripts. Results PCBP1 controlled the expression or activity of the seven transcripts. Moreover, PCBP1 indirectly regulated MAP2K2, FOS, FST, TP53 and WNT7B through H2AFX or regulated these genes through SAT. In contrast, TP53 and WNT7B are regulated by other genes. Conclusion The seven transcripts and PCBP1 are closely associated in a spatial interaction network.

关键词： PCBP1 RNA interference overexpression Bayesian network

Association of polymorphic alleles of CTLA4 with inflammatory bowel disease in the Japanese

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World Journal of Gastroenterology 2005年第27期11卷 4188-4193页

作者： Haruhisa Machida Kazuhiro Tsukamoto Chun-Yang Wen Yukiko Narumi Saburou Shikuwa Hajime Isomoto Fuminao Takeshima Yohei Mizuta Norio Niikawa Ikuo Murata Shigeru Kohno Second department of Internal Medicine Nagasaki University School of Medicine 1-7-1 SakamotoNagasaki 852-8501 Japan department of Pharmacotherapeutics Nagasaki University Graduate School of Biomedical Sciences 1-14 Bunkyo-machi Nagasaki 852-8521Japan department of Molecular Pathology Atomic Bomb Disease Institute Nagasaki University Graduate School of Biomedical Sciences 1-12-4 Sakamoto Nagasaki 852-8523Japan department of Human genetics Nagasaki University Graduate School of Biomedical Sciences 1-12-4 Sakamoto Nagasaki 852-8523 Japan

AIM： To examine an association between the cytotoxic Tlymphocyte antigen 4 （CTLA4） gene that plays a role in downregulation of T-cell activation and inflammatory bowel disease consisting of ulcerative colitis （UC） and Crohn＇s disease （CD） in the ***： We studied 108 patients with UC, 79 patients with CD, and 200 sex-matched healthy controls, with respect to three single nucleotide polymorphisms （SNPs） in CTLA4, such as C-318T in the promoter region, A＋49 Gin exon 1 and G＋6230A in the 3＇ untranslated region （3＇-UTR） by a PCR-restriction fragment length polymorphism method, and to an （AT）, repeat polymorphism in 3＇-UTR by fragment analysis with fluorescence-labeling on denaturing sequence gels. Frequency of alleles and genotypes and their distribution were compared statistically between patients and controls and among subgroups of patients, using X^2 and Fisher exact ***： The frequency of ＂A/A＂ genotype at the G＋6230A SNP site was statistically lower in UC patients than in controls （3.7% vs 11.0%, P = 0.047, odds ratio （OR） = 0.311）. Moreover, the frequency of ＂G/G＂ genotype at the A＋49G SNP site was significantly higher in CD patients with fistula （48.6%） than those without it （26.2%）（P = 0.0388, OR=2.67）.CONCLUSION： The results suggest that CTLA4 located at 2q33 is a determinant of UC and responsible for fistula formation in CD in the Japanese.

关键词： Ulcerative colitis CTLA4 gene Diseasesusceptible gene Crohn's disease Fistula formation

Exposure to trace levels of metals and fluoroquinolones increases inflammation and tumorigenesis risk of zebrafish embryos

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Environmental Science and Ecotechnology 2022年第2期10卷 12-22页

作者： Dantong Jia Ruijie Zhang Jian Shao Wei Zhang Leilei Cai Weiling Sun College of Environmental Sciences and Engineering Peking UniversityThe Key Laboratory of Water and Sediment SciencesMinistry of EducationBeijing100871China State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems International Joint Laboratory for Regional Pollution ControlMinistry of EducationBeijing100871China College of animal Science Guizhou UniversityThe Key Laboratory of Animal GeneticsBreeding and Reproduction in the Plateau Mountainous RegionMinistry of EducationGuiyangGuizhou550025China department of Plant Soil and Microbial SciencesEnvironmental Science and Policy ProgramMichigan State UniversityEast LansingMI48824United States College of Safety and Environmental Engineering Shandong University of Science and TechnologyQingdaoShandong266590China

Exposure to trace-level heavy metals and antibiotics may elicit metabolic disorder,alter protein expression,and then induce pathological changes in zebrafish embryos,despite negligible physiological and developmental *** study investigated the single and combined developmental toxicity of fluoroquinolones(enrofloxacin[ENR]and ciprofloxacin[CIP])(0.5 mM)and heavy metals(Cu and Cd)(0.5 mM)to zebrafish embryos,and molecular responses of zebrafish larvae upon exposure to the single pollutant(0.2 mM)or a binary metal-fluoroquinolone mixture(0.2 mM).In all single and mixture exposure groups,no developmental toxicity was observed,but oxidative stress,inflammation,and lipid depletion were found in zebrafish embryos,which was more severe in the mixture exposure groups than in the single exposure groups,probably due to increased metal bioaccumulation in the presence of ENR or *** analysis revealed the up-regulation of amino acids and down-regulation of fatty acids,corresponding to an active response to oxidative stress and the occurrence of *** up-regulation of antioxidase and immune proteins revealed by proteomics analysis further confirmed the occurrence of oxidative stress and ***,the KEGG pathway enrichment analysis showed a significant disturbance of pathways related to immunity and tumor,indicating the potential risk of tumorigenesis in zebrafish *** findings provide molecular-level insights into the adverse effects of heavy metals and antibiotics(especially in chemical mixtures)on zebrafish embryos,and highlight the potential ecotoxicological risks of trace-level heavy metals and antibiotics in the environment.

关键词： Fluoroquinolone Metal Inflammation Tumor Oxidative stress