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molecular Plant 2013年第2期6卷 570-573页

作者： Xuewei Chen Miguel E. Vega-Sanchez Yves Verhertbruggenb Dawn Chiniquy Patrick E. Canlas Alexandra Fagerstrom Lina Prak Ulla Christensen Ai Oikawa Mawsheng Chern Shimin Zuo Fan Lin Manfred Auer William G.T. Willats Laura Bartley Jesper Harholt Henrik V. Scheller Pamela C. Ronald Department of Plant Pathology and The Genome Center University of California Davis CA 95616 USA Joint BioEnergy Institute Emeryville CA 94608 USA Rice Research Institute Sichuan Agricultural University at Wenjiang Wenjiang Chengdu 611130 China Physical Biosciences division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA Department of Plant and Environmental Sciences Faculty of Science University of Copenhagen DK-1871 Frederiksberg Denmark Department of Botany and Microbiology University of Oklahoma Norman OK 73019 USA Department of Plant and Microbial Biology University of California Berkeley CA 94720 USA

Dear Editor, Xylan polysaccharides constitute the major non-cellulosic components in secondary cell walls of dicots and in both primary and secondary cell walls of grasses （Scheller and Ulvskov, 2010）. Xylan is composed of a linear backbone of 13（1-4）-linked xylose （Xyl）. In grasses, the xylan backbone is substituted with 03-1inked and 02-1inked arabinose residues and, to a lesser extent, a（1-3）-Iinked glucuronic acid residues.

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Insights into the architecture of human-induced polygenic selection in Duroc pigs

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Journal of Animal Science and Biotechnology 2023年第1期14卷 60-71页

作者： Zitao Chen Jinyan Teng Shuqi Diao Zhiting Xu Shaopan Ye Dingjie Qiu Zhe Zhang Yuchun Pan Jiaqi Li Qin Zhang Zhe Zhang National Engineering Research Center for Breeding Swine Industry Guangdong Provincial Key Lab of Agro‑Animal Genomics and Molecular BreedingCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou 510642P.R.China. Department of Animal Science College of Animal ScienceZhejiang University866#Yuhangtang RoadHangzhou 310058P.R.China. Guangdong Provincial Key Laboratory of Marine Biotechnology Shantou University243 Daxue RoadShantou 515063P.R.China Fujian Yongcheng Agricultural&Animal Husbandry Sci-Tech Group Co. Ltd.Fuqing 350399P.R.China. Department of Animal Genetics and Breeding College of Animal Science and TechnologyShandong Agricultural UniversityTai’an 271018P.R.China.

Background:As one of the most utilized commercial composite boar lines,Duroc pigs have been introduced to China and undergone strongly human-induced selection over the past ***,the efficiencies and limitations of previous breeding of Chinese Duroc pigs are largely *** objective of this study was to uncover directional polygenic selection in the Duroc pig genome,and investigate points overlooked in the past breeding ***:Here,we utilized the Generation Proxy Selection Mapping(GPSM)on a dataset of 1067 Duroc pigs with 8,766,074 imputed *** detected a total of 5649 putative SNPs actively under selection in the Chinese Duroc pig population,and the potential functions of the selection regions were mainly related to production,meat and carcass ***,we observed that the allele frequency of variants related to teat number(NT)relevant traits was also changed,which might be influenced by genes that had pleiotropic ***,we identified the direction of selection on NT traits by G,and further pinpointed large-effect genomic regions associated with NT relevant traits by selection signature and *** results of NT relevant traits-specific selection signatures and GWAS,we found three common genome regions,which were overlapped with QTLs related to production,meat and carcass traits besides“teat number”*** implied that there were some pleiotropic variants underlying NT and economic *** further found that rs346331089 has pleiotropic effects on NT and economic traits,e.g.,litter size at weaning(LSW),litter weight at weaning(LWW),days to 100 kg(D100),backfat thickness at 100 kg(B100),and loin muscle area at 100 kg(L100)***:The selected loci that we identified across methods displayed the past breeding process of Chinese Duroc pigs,and our findings could be used to inform future breeding decision.

关键词： Artificial selection GWAS Pig Reproductive organ Selection signatures

Association of insertion-deletions polymorphisms with colorectal cancer risk and clinical features

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World Journal of Gastroenterology 2017年第37期23卷 6854-6867页

作者： Diego Marques Layse Raynara Ferreira-Costa Lorenna Larissa Ferreira-Costa Romualdo da Silva Correa Aline Maciel Pinheiro Borges Fernanda Ribeiro Ito Carlos Cesar de Oliveira Ramos Raul Hernandes Bortolin André Ducati Luchessi Andrea Ribeiro-dos-Santos Sidney Santos Vivian Nogueira Silbiger Laboratório de Bioanálise e Biotecnologia molecular Universidade Federal do Rio Grande do Norte Programa de Pós-graduacao em Ciências Farmacêutica Universidade Federal do Rio Grande do Norte Laboratório de Genética Humana e Médica Universidade Federal do Pará Departamento de Cirurgia Oncológica Liga Norte Riograndense Contra o Cancer Laboratório de Patologia eCitopatologia Liga Norte Riograndense Contra o Cancer Depart-amento de Análises Clínicas e Toxicológicas Universidade Federal do Rio Grande do Norte Núcleo de Pesquisas em Oncologia Universidade Federal do Pará

AIM To investigate the association between 16 insertiondeletions(INDEL) polymorphisms, colorectal cancer(CRC) risk and clinical features in an admixed *** O n e h u n d re d a n d fo r ty p a t i e n t s w i t h C R C a n d 140 cancer-free subjects were examined. genomic DNA was extracted from peripheral blood samples. Polymorphisms and genomic ancestry distribution were assayed by Multiplex-PCR reaction, separated by capillary electrophoresis on the ABI 3130 Genetic Analyzer instrument and analyzed on Gene Mapper ID v3.2. Clinicopathological data were obtained by consulting the patients' clinical charts, intra-operative documentation, and pathology *** Logistic regression analysis showed that polymorphism variations in IL4 gene was associated with increased CRC risk, while TYMS and UCP2 genes were associated with decreased risk. Reference to anatomical localization of tumor Del allele of NFKB1 and CASP8 were associated with more colon related incidents than rectosigmoid. In relation to the INDEL association with tumor node metastasis(TNM) stage risk, the Ins alleles of ACE, HLAG and TP53(6 bp INDEL) were associated with higher TNM stage. Furthermore, regarding INDEL association with relapse risk, the Ins alleles of ACE, HLAG, and UGT1A1 were associated with early relapse risk, as well as the Del allele of TYMS. Regarding INDEL association with death risk before 10 years, the Ins allele of SGSM3 and UGT1A1 were associated with death *** The INDEL variations in ACE, UCP2, TYMS, IL4, NFKB1, CASP8, TP53, HLAG, UGT1A1, and SGSM3 were associated with CRC risk and clinical features in an admixed population. These data suggest that this cancer panel might be useful as a complementary tool for better clinical management, and more studies need to be conducted to confirm these findings.

关键词： Colorectal cancer Ins-del polymorphism Admixed population Potential biomarker Diagnostic Risk stratification Prognostic Clinical features

Trans-Gulf of Mexico loop migration of tree swallows revealed by solar geolocation

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Current Zoology 2014年第5期60卷 653-659页

作者： David W. BRADLEY Robert G. CLARK Peter O. DUNN Andrew J. LAUGHLIN Caz M. TAYLOR Carol VLECK Linda A. WHITTINGHAM David W. WINKLER D. Ryan NORRIS Department of Integrative Biology University of Guelph Guelph Ontario N1G 2W 1 Canada Bird Studies Canada Port Rowan Ontario N0E 1M0 Canada Environment Canada. Saskatoon. Saskatchewan S7N 0X4. Canada Behavioral and molecular Ecology Group Department of Biological Sciences University of Wisconsin Milwaukee Wisconsin 53201 USA Department of Ecology and Evolutionary Biology Tulane University New Orleans Louisiana 70118 USA Department of Ecology Evolution and Organismal Biology Iowa State University Ames IA 50011-1020 USA Department of Ecology and Evolutionary Biology Museum of Vertebrates and Lab of Ornithology Comell University Ithaca New York 14853 USA

One of the greatest feats of avian migration is the non-stop crossing of extensive areas of inhospitable habitat such as deserts and seas. Differences in spring and autumn migration routes have been reported in species that cross such barriers, and are thought to have evolved in response to seasonal variation in prevailing wind direction. We tested the hypothesis that migration routes vary seasonally with respect to the Gulf of Mexico in the tree swallow Tachycineta bicolor using solar geolocators attached and retrieved at 4 breeding sites in central North America. We found that 100 % of birds （n = 10） made a trans-Gulf flight of 〉850 km from Louisiana south to their wintering grounds in the Yucatan Peninsula in 12-36 hours, achieving minimum ground speeds as high as 32 m/s. Although most days during autumn migration were characterized by unfavorable headwinds blowing to the northwest, migration over the Gulf mostly occurred on days with strong winds blowing to the south. In contrast, in 8 of 9 （88 %） birds on spring migration returned from the wintering grounds towards Louisiana following a clockwise loop pat- tern flying over land to the west around the Gulf. During this spring period there were few days with prevailing winds from the south to assist northward migration. Results suggest that, despite being up to three times further （ca. 2,700 kin）, a coastal circum-Gulf spring migration represents the less risky route when wind conditions are not favorable. These findings also help to resolve a long-standing dispute in the literature concerning migration patterns between the US Gulf coast and Mexico, and provide insight into the factors shaping migration strategies of small songbirds migrating across large bodies of water [Current Zoology 60（5）： 653-559, 2014].

关键词： Ecological Barrier Geolocation Gulf of Mexico Tachycineta bicolor Tree swallow Migration

Kiwifruit Genome Database(KGD):a comprehensive resource for kiwifruit genomics

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Horticulture Research 2020年第1期7卷 1076-1083页

作者： Junyang Yue Jiacheng Liu Wei Tang Ya Qing Wu Xiaofeng Tang Wei Li Ying Yang Lihuan Wang Shengxiong Huang Congbing Fang Kun Zhao Zhangjun Fei Yongsheng Liu Yi Zheng School of Horticulture Anhui Agricultural UniversityHefei 230036China School of Food and Biological Engineering Hefei University of TechnologyHefei 230009China Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA USDA-Agricultural Research Service Robert W.Holley Center for Agriculture and HealthIthacaNY 14853USA Ministry of Education Key Laboratory for Bio-resource and Eco-environment College of Life ScienceState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengdu 610064China Beijing Advanced Innovation Center for Tree Breeding by molecular Design Beijing University of AgricultureBeijing 102206China Plant Science and Technology College Beijing University of AgricultureBeijing 102206China

Kiwifruit(Actinidia spp.)plants produce economically important fruits containing abundant,balanced phytonutrients with extraordinarily high vitamin C *** the release of the first kiwifruit reference genome sequence in 2013,large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit *** efficiently store,analyze,integrate,and disseminate these large-scale datasets to the research community,we constructed the Kiwifruit Genome Database(KGD;http://***/).The database currently contains all publicly available genome and gene sequences,gene annotations,biochemical pathways,transcriptome profiles derived from public RNA-Seq datasets,and comparative genomic analysis results such as syntenic blocks and homologous gene pairs between different kiwifruit genome assemblies.A set of user-friendly query interfaces,analysis tools and visualization modules have been implemented in KGD to facilitate translational and applied research in kiwifruit,which include JBrowse,a popular genome browser,and the NCBI BLAST sequence search *** notable tools developed within KGD include a genome synteny viewer and tools for differential gene expression analysis as well as gene ontology(GO)term and pathway enrichment analysis.

关键词： comprehensive fruit

Bond Length Deviation in CuZr Metallic Glasses

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Bond Length Deviation in CuZr Metallic Glasses

iPlant Systems Biology (iPSB): An International Network Hub in the Plant Community

第十一届中国钢铁年会

作者： Peng Chuanxiao ?opu Daniel Song Kaikai Zhang Zhenting Wang Li Eckert Jürgen School of Mechanical Electrical & Information Engineering Shandong University (Weihai) division of Materials Modeling Institute of Materials Science TU Darmstadt ErichSchmid Institute of Materials Science Austrian Academy of Sciences Department Materials Physics Montanuniversit?t Leoben

We define a structural parameter, called atomic bond length deviation(BLDi), to characterize structural heterogeneity of CuZr melt and metallic glass(MG).molecular dynamics(MD) simulations have been performed to explo... 详细信息

关键词： atomic bond length deviation structural heterogeneity of metallic glass shear transformation zones

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molecular Plant 2019年第6期12卷 727-730页

作者： Pascal Falter-Braun Siobhan Brady Rodrigo A.Gutierrez Gloria M.Coruzzi Gabriel Krouk Institute of Network Biology (INET) Helmholtz Zentrum Munchen (HMGU) 85764 Munchen-Neuherberg Germany Microbe-Host Interactions Faculty of Biology. Ludwig-Maximilians-University (LMU) Munich 82152 Planegg-Martinsried Germany Department of Plant Biology and the Genome Center University of California Davis CA 95616 USA Departamento de Genetica molecular y Microbiologia FONDAP Center for Genome Regulation Millennium Institute for Integrative Biology Pontificia Universidad Catolica de Chile Santiago 8331150 Chile Center for genomics and Systems Biology Department of Biology New York University New York NY 10003 USA B&PMP Univ Montpellier CNRS INRA SupAgro Montpellier France

sequenced genome of a multicellular organism (Arabidopsis Genome, 2000) completed just after those of the nematode Caenorhabditis elegans (C. elegans Sequencing Consortium, 1998) and the fruit fly Drosophila melanogaster (Adams et al., 2000). Availability of a full whole-genome sequence for the reference plant opened to plant biologists what is commonly called the post-genomic era.

关键词： Systems Biology International Network Hub Plant Community

Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat

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Plant Communications 2024年第5期5卷 57-74页

作者： Guo Ai Chao He Siteng Bi Ziru Zhou Ankui Liu Xin Hu Yanyan Liu Liujie Jin JiaCheng Zhou Heping Zhang Dengxiang Du Hao Chen Xin Gong Sulaiman Saeed Handong Su Caixia Lan Wei Chen Qiang Li Hailiang Mao Lin Li Hao Liu Dijun Chen Kerstin Kaufmann Khaled FAlazab Wenhao Yan National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 430070China Shenzhen Institute of Nutrition and Health Huazhong Agricultural UniversityWuhan 430070China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenomeAnalysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China State Key Laboratory of Pharmaceutical Biotechnology School of Life SciencesNanjing UniversityNanjing 210023China Department for Plant Cell and molecular Biology Institute for BiologyHumboldt-Universitat Zu Berlin10115 BerlinGermany Plant Research Department Nuclear Research CenterEgyptian Atomic Energy AuthorityCairo 13759Egypt

Spike architecture inﬂuences both grain weight and grain number per spike,which are the two major components of grain yield in bread wheat(Triticum aestivum L.).However,the complex wheat genome and the inﬂuence of various environmental factors pose challenges in mapping the causal genes that affect spike ***,we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in *** identified 170 loci that are responsible for variations in spike length,spikelet number per spike,and grain number per spike through genome-wide association study and meta-QTL *** constructed gene regulatory networks for young inﬂorescences at the double ridge stage and theﬂoret primordium stage,in which the spikelet meristem and theﬂoret meristem are predominant,respec-tively,by integrating transcriptome,histone modification,chromatin accessibility,eQTL,and protein–pro-tein interactome *** these networks,we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike *** functions of TaZF-B1,VRT-B2,and TaSPL15-A/D in establishment of wheat spike architecture were *** study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.

关键词： bread wheat spike traits genetic variation protein–protein interaction gene regulatory network

Diphlorethohydroxycarmalol,a phlorotannin contained in brown edible seaweed Ishige okamurae,prevents AGE-related diabetic nephropathy by suppression of AGE-RAGE interaction

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Food Bioscience 2023年第3期53卷 1541-1550页

作者： Chi Heung Cho Guijae Yoo Mingyeong Kim Chang Jun Lee In-Wook Choi Bomi Ryu Byoung-Mok Kim Sang-Hoon Lee division of Functional Food Research Korea Food Research Institute245 nongsaengmyeong-roIseo-myeonWanju-gunJeollabuk-do55365Republic of Korea Department of Food Biotechnology University of Science and TechnologyDaejeon34113Republic of Korea Department of Food Science and Technology Chonbuk National UniversityJeollabuk-do54896Republic of Korea Major of Food Science and Nutrition Pukyong National UniversityBusan48513Republic of Korea Research Group of Food Processing Korea Food Research Institute245 nongsaengmyeong-roIseo-myeonWanju-gunJeollabuk-do55365Republic of Korea

Advanced glycation end-products(AGEs)are complex and heterogeneous compounds generated through various steps and are naturally produced during the glycation *** generated AGEs bind to long-lived proteins such as collagen and cause renal dysfunction,leading to AGE-related diabetic nephropathy(DN).In this study,we aimed to confirm the therapeutic potential of marine biological resources by evaluating the role of diphlorethohydroxycarmalol(DPHC),a major phlorotannin compound contained in edible brown algae Ishige okamurae,in the key mechanisms involved in the pathogenesis and progression of AGE-induced *** AGE formation inhibitory and AGE-collagen cross-link inhibiting/breaking ability assay were performed to evaluate the anti-glycation effect of *** AGE-RAGE interaction inhibitory effect was evaluated through molecular docking *** renoprotective effect of DPHC was confirmed in mouse glomerular mesangial *** treatment exhibited anti-glycation ability through suppression of AGE formation and AGE-collagen cross-linking generation,and disruption of cross-links formed between *** addition,DPHC pre-treatment significantly suppressed reactive oxygen species(ROS)production,intracellular methylglyoxal(MGO)/AGEs accumulation,and activation of apoptosis cascade by ***,DPHC suppressed AGE-receptor for AGE(RAGE)interaction by competing with MG-H1 for the binding site of ***,DPHC pre-treatment regulated apoptosis-related protein expression and increased Nrf2,Glo-1,HO-1,CAT,NQO1,and *** findings prove that the chemical structural characteristics of DPHC have the potential to prevent or manage AGE-induced DN by effectively mediating the key mechanisms responsible for its pathogenesis.

关键词： Diphlorethohydroxycarmalol molecular docking RAGE Methylglyoxal Renoprotective effect

Identification of Prognostic Genes for Colon Cancer through Gene Coexpression Network Analysis

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Current Medical Science 2021年第5期41卷 1012-1022页

作者： Dan-wen WANG Zhang-shuo YANG Jian XU Li-jie YANG Tie-cheng YANG Hua-qiao WANG Mao-hui FENG Fei SU Department of Gastrointestinal Surgery Zhongnan Hospital of Wuhan UniversityWuhan 430071China Key Laboratory of Tumor Biological Behavior of Hubei Province Wuhan 430071China Centerfor Clinical medicine of Peritoneal Cancer of Wuhan Wuhan 430071China Clinical Cancer Study Center of Hubei Province Wuhan 430071China Department of Pathology Zhongnan Hospital of Wuhan UniversityWuhan 430071China Department of Oncology the First Hospital of Lanzhou UniversityLanzhou 730000Chin

Objective:The present study was aimed to identify novel key genes,prognostic biomarkers and molecular pathways implicated in tumorigenesis of colon ***:The microarray data GSE41328 containing 10 colon cancer samples and 10 adjacent normal tissues was analyzed to identify 4763 differentially expressed ***,another microarray data GSE17536 was performed for weighted gene co-expression network analysis(WGCNA).Results:In present study,12 co-expressed gene modules associated with tumor progression were identified for further *** red module showed the highest association with pathological stage by Pearson's correlation *** enrichment analysis revealed that genes in red module focused on cell division,cell proliferation,cell cycle and metabolic related ***,a total of 26 key hub genes were identified,and GEPIA database was subsequently selected for *** junction-recognizing protein(HJURP)and cell division cycle 25 homolog C(CDC25C)were identified as effective prognosis biomarkers,which were all detrimental to *** set enrichment analyses(GSEA)found the two hub genes were enriched in“oocyte meiosis”,“oocyte maturation that are progesterone-mediated”,“p53 signaling pathway”,and“cell cycle”.Furthermore,the immunohistochemistry and western blotting showed that HJURP was highly expressed in colon cancer ***:HJURP was identified as a key gene associated with colon cancer progression and prognosis by WGCNA,which might influence the prognosis by regulating cell cycle pathways.

关键词： colon cancer biomarkers weighted gene co-expression network analysis prognosis pathological stage