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From n-alkane to polyacetylene on Cu(110):Linkage modulation in chain growth

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Science China Chemistry 2022年第4期65卷 733-739页

作者： Zhengming Hao Junjie Zhang Miao Xie Xuechao Li Lina Wang Ye Liu Kaifeng Niu Junbo Wang Luying Song Tao Cheng Haiming Zhang Lifeng Chi Institute of Functional Nano and Soft Materials(FUNSOM)and Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices Soochow UniversitySuzhou 215123China Department of Physics Chemistry and BiologyLinköping UniversityLinköping 58183Sweden

Direct coupling or transformation of inert alkanes based on the selective C-H activation is of great importance for both chemistry and chemical engineering.Here,we report the coupling of polyenes that are transformed from n-dotriacontane(n-C_(22)H_(66))through on-surface cascade dehydrogenation on Cu(110)surface,leading to the formation of polyacetylene(PA).Three distinct Linkages have been resolved by scanning tunneling microscope(STM)and noncontact atomic force microscope(nc-AFM).Apart from the α-type Linkage which is the stemless coupling of the terminal C-C double bond in trans-configuration,β-and γ-type Linkages appear as knots or defects which are,in fact,the C-C couplings in cis-configurations.Interestingly,the“defects”can be effectively suppressed by adjusting the surface coverage,thus making it of general interest for uniform structure modulation.

关键词： on-surface chemistry scanning tunneling microscope all-trans polyacetylene Linkage chain growth

A genetic Linkage map of the threatened catfish Lophiosilurus alexandri:Inferences on effective population size

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Aquaculture and Fisheries 2023年第6期8卷 689-694页

作者： M.Raquel M.Coimbra Renata da S.Farias Bruno C.N.Rda Silva Andres Blanco Miguel Hermida Armando Caballero Michael Bekaert Paulino Martinez Department of Fisheries and Aquaculture Federal Rural University of PernambucoRua Dom Manuel de MedeirosS/nDois IrmaosRecifePE52171-900Brazil Department of Zoology Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversity of Santiago de Compostel1Campus of LugoLugo27002Spain Center of Marine Research University of VigoFaculty of BiologyVigo36310Spain Institute of Aquaculture University of StirlingScotlandFK94LAUnited Kingdom

We report the first genetic Linkage map of the catfish Lophiosilurus alexandri,a South American threatened and promising aquaculture catfish species.Using the progeny of three full-sib families,with 141,74,and 49 offspring,respectively,we could genotype 2351 SNP markers using the ddRAD technology,shared by the male and the female maps constructed.The averaged,female and male maps spanned a total length of 2201.3 cM,2481.9 cM,and 1872.8 cM,respectively,and comprehended the expected 27 Linkage groups according to the karyotype information of the species(2n=54).The recombination rate was nearly twice higher in the female than in the male map.The average map was used to estimate the historical effective population size(Ne)of the species from Linkage disequilibrium between pairs of SNPs using parental individuals and revealed a remarkable drop in Ne about 20-25 generations in the past.The construction of the biggest artificial reservoir in Latin America and associated nutrient retention is pointed as a possible reason for such a reduction and suggests a reevaluation of the conservation status of the species.The current map lays the groundwork for understanding the genetic basis of economically important traits in breeding programs and will be useful for the genome assembly of this important commercial species.

关键词： breeding Linkage size

A pentaploid-based Linkage map of the ancestral octoploid strawberry Fragaria virginiana reveals instances of sporadic hyper-recombination

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Horticulture Research 2020年第1期7卷 1796-1810页

作者： Thomas M.Davis Yilong Yang Lise L.Mahoney Daniel C.Frailey Department of Agriculture Nutritionand Food SystemsUniversity of New HampshireDurhamNH 03824USA

The first high-resolution genetic Linkage map of the ancestral octoploid(2n=8x=56)strawberry species,Fragaria virginiana,was constructed using segregation data obtained from a pentaploid progeny population.This novel mapping population of size 178 was generated by crossing highly heterozygous F.virginiana hybrid“LB48”as a paternal parent with diploid(2n=2x=14)Fragaria vesca“Hawaii 4”.The LB48 Linkage map comprises 6055 markers genotyped on the Axiom®IStraw90 strawberry SNP array.The map consists of 28 Linkage groups(LGs)organized into seven homoeology groups of four LGs each,and excludes a small 29th LG of undefined homoeology.One member of each homoeology group was assignable to an“A”subgenome associated with ancestral diploid Fragaria vesca,while no other subgenomes were defined.Despite an intriguing discrepancy within homoeology group VI,synteny comparisons with the previously published Fragaria×ananassa DA×MO Linkage map revealed substantial agreement.Following initial map construction,examination of crossover distributions revealed that six of the total 5162(=29 chromosomes/individual×178 individuals)chromosomes making up the data set exhibited abnormally high crossover counts,ranging from 15 to 48 crossovers per chromosome,as compared with the overall mean of 0.66 crossovers per chromosome.Each of these six hyper-recombinant(HypR)chromosomes occurred in a different LG and in a different individual.When calculated upon exclusion of the six HypR chromosomes,the canonical(i.e.,broadly representative)LB48 map had 1851 loci distributed over a total map length of 1873 cM,while their inclusion increased the number of loci by 130,and the overall map length by 91 cM.Discovery of these hyper-recombinant chromosomes points to the existence of a sporadically acting mechanism that,if identified and manipulable,could be usefully harnessed for multiple purposes by geneticists and breeders.

关键词： Fragaria straw Linkage

Construction of an anchoring SSR marker genetic Linkage map and detection of a sex-linked region in two dioecious populations of red bayberry

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Horticulture Research 2020年第1期7卷 2262-2270页

作者： Yan Wang Hui-Min Jia Yu-Tong Shen Hai-Bo Zhao Qin-Song Yang Chang-Qing Zhu De-Li Sun Guo-Yun Wang Chao-Chao Zhou Yun Jiao Chun-Yan Chai Li-Ju Yan Xiong-Wei Li Hui-Juan Jia Zhong-Shan Gao Fruit Science Institute College of Agriculture and BiotechnologyZhejiang University310058 HangzhouChina Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesChinese Academy of Sciences201602 ShanghaiChina Yuyao Forestry Technology Extension Center 315400 NingboChina Institute of Forestry Ningbo Academy of Agricultural ScienceNingboChina Cixi Forestry Technology Extension Center 315300 CixiChina Linhai Forestry Technology Extension Center 317000 TaizhouChina Forest&Fruit Tree Institute Shanghai Academy of Agricultural Sciences201403 ShanghaiChina

Red bayberry(Morella rubra)is an evergreen fruit tree found in southern China whose whole-genome sequence has recently been published.We updated the Linkage map of the species by adding 118 SSR markers and the femalespecific marker MrFT2_BD-SEX.The integrated map included eight Linkage groups and spanned 491 cM.Eleven sexassociated markers were identified,six of which were located in Linkage group 8,in agreement with the previously reported location of the sex-determining region.The MrFT2_BD-SEX marker was genotyped in 203 cultivated accessions.Among the females of the accessions,we found two female-specific alleles,designated W-b(151 bp)and W-d(129 bp).We previously found that‘Dongkui’,a female cultivar,could produce viable pollen(we refer to such plants‘Dongkui-male’)and serve as the paternal parent in crosses.The genotypes of the MrFT2_BD-SEX marker were W-b/Z in‘Biqi’and W-d/Z in‘Dongkui-male’.The progeny of a cross between these parents produced a 3:1 female(W-)to male(ZZ)ratio and the expected 1:1:1:1 ratio of W-b/W-d:W-b/Z:W-d/Z:Z/Z.In addition,the flowering and fruiting phenotypes of all the F1 progeny fit their genotypes.Our results confirm the existence of ZW sex determination and show that the female phenotype is controlled by a single dominant locus(W)in a small genomic region(59 kb and less than 3.3 cM).Furthermore,we have produced a homozygous“super female”(WW)that should produce all-female offspring in the F2 generation,providing a foundation for commercial use and presenting great potential for use in modern breeding programs.

关键词： breeding cultivar Linkage

Hepatitis C Screening: Barriers to Linkage to Care

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Journal of Clinical and Translational Hepatology 2019年第3期7卷 226-231页

作者： Sammy Saab Youssef PChallita Lisa MNajarian Rong Guo Satvir SSaggi Gina Choi Departments of Surgery University of California at Los AngelesLos AngelesCAUSA Departments of Medicine University of California at Los AngelesLos AngelesCAUSA Departments of Medicine Statistics Core University of California at Los AngelesLos AngelesCAUSA

Background andAims:Hepatitis C(HCV)is a medical and public health concern.Once infected individuals are identified,management includes not only education but also the use of antiviral therapy.Although screening for HCV is readily available,barriers exist which prevent assessment and treatment in individuals potentially infected with HCV.Methods:This is a retrospective study of patients screened for HCV within the University of California,Los Angeles Health Care System between February 22 and July 9,2018.We defined Linkage to care as:1)confirmatory HCV RNA test after screening HCV antibody test found a positive result;and 2)follow-up appointment for treatment was established with a specialist.Demographic and baseline laboratory values were collected.Factors potentially associated with prohibiting Linkage of care were evaluated.Results:During the study period,17,512 individuals were screened for HCV.A total of 238(1.35%)were found to have detectable HCV antibodies.Of the individuals with detectable HCV antibodies,48(20%)did not undergo confirmatory testing with viral levels.Of the 190 individuals who underwent further testing,70 patients were noted to be viremic.Among them,17 of the 70(24%)were not linked to a specialist for further care.Younger patients(p=0.02)and people who inject drugs(p=0.02)were less likely to be referred for specialty care.Conclusions:The results of our study highlight that younger patients and people who inject drugs are less likely to be referred to specialty care for HCV treatment.Efforts are needed to engage these populations.

关键词： Hepatitis C Screening Linkage

User Account Linkage Across Multiple Platforms with Location Data

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Journal of Computer Science & Technology 2020年第4期35卷 751-768页

作者： Wei Chen Weiqing Wang Hongzhi Yin Jun-Hua Fang Lei Zhao Institute of Artificial Intelligence School of Computer Science and TechnologySoochow UniversitySuzhou 215006China Faculty of Information Technology Monash UniversityMelbourne 3000Australia School of Information Technology and Electrical Engineering The University of QueenslandBrisbane 4072Australia

Linking user accounts belonging to the same user across different platforms with location data has received significant attention,due to the popularization of GPS-enabled devices and the wide range of applications benefiting from user account Linkage(e.g.,cross-platform user profiling and recommendation).Different from most existing studies which only focus on user account Linkage across two platforms,we propose a novel model ULMP(i.e.,user account Linkage across multiple platforms),with the goal of effectively and efficiently linking user accounts across multiple platforms with location data.Despite of the practical significance brought by successful user Linkage across multiple platforms,this task is very challenging compared with the ones across two platforms.The major challenge lies in the fact that the number of user combinations shows an explosive growth with the increase of the number of platforms.To tackle the problem,a novel method GTkNN is first proposed to prune the search space by efficiently retrieving top-k candidate user accounts indexed with well-designed spatial and temporal index structures.Then,in the pruned space,a match score based on kernel density estimation combining both spatial and temporal information is designed to retrieve the linked user accounts.The extensive experiments conducted on four real-world datasets demonstrate the superiority of the proposed model ULMP in terms of both effectiveness and efficiency compared with the state-of-art methods.

关键词： user account Linkage multiple platform check-in record

The improved FASTmrEMMA and GCIM algorithms for genome-wide association and Linkage studies in large mapping populations

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The Crop Journal 2020年第5期8卷 723-732页

作者： Yangjun Wen Yawen Zhang Jin Zhang Jianying Feng Yuanming Zhang State Key Laboratory of Crop Genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjing 210095JiangsuChina Crop Information Center College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070HubeiChina

Owing to high power and accuracy and low false positive rate in our multi-locus approaches for genome-wide association studies and Linkage analyses,these approaches have attracted considerable attention in plant and animal genetics.In large mapping population,however,fast multi-locus random-SNP-effect efficient mixed model association(FASTmrEMMA)and genome-wide composite interval mapping(GCIM)run a relatively long time.To address this issue,we proposed the improved FASTmrEMMA and GCIM algorithms in this study.In the new algorithms,some matrix identities,such as the Woodbury matrix identity,were used.In scanning each marker on the entire genome,in other words,the improved algorithms effectively replace the expensive eigenvector solutions in(restricted)maximum likelihood estimations in original algorithms with two(one)updated inner products and one updated vector-matrix-vector multiplication.Simulated and real data analyses showed that their computational efficiencies are increased sharply in large mapping population,although there are no mapping result differences between original and improved algorithms.In addition,the related software packages(mrMLM.GUI and QTL.gCIMapping.GUI)can be downloaded from the R and BioCode websites.

关键词： Linkage matrix analyses

Identification of powdery mildew resistance loci in wheat by integrating genome-wide association study(GWAS) and Linkage mapping

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The Crop Journal 2019年第3期7卷 294-306页

作者： Genqiao Li Xiangyang Xu Chengcheng Tan Brett F.Carver Guihua Bai Xuewen Wang J.Michael Bonman Yanqi Wu Robert Hunger Christina Cowger Wheat Peanut and Other Field Crops Research UnitUSDA-ARSStillwaterOK 74075USA Plant and Soil Science Department Oklahoma State UniversityStillwaterOK 74078USA Hard Winter Wheat Genetics Research Unit USDA-ARSManhattanKS 66506USA Department of Genetics University of GeorgiaAthensGA 30602USA Small Grains and Potato Germplasm Research Unit USDA-ARSAberdeenID 83210USA Entomology and Pathology Department Oklahoma State UniversityStillwaterOK 74078USA Plant Science Research Unit USDA-ARSRaleighNC 27695USA

Wheat powdery mildew(Blumeria graminis f.***.tritici, Bgt) is a disease of increasing importance globally due to the adoption of high yielding varieties and modern sustainable farming technologies.Growing resistant cultivars is a preferred approach to managing this disease, and novel powdery mildew resistance genes are urgently needed for new cultivar development.A genome-wide association study was performed on a panel of 1292 wheat landraces and historical cultivars using 5011 single nucleotide polymorphism(SNP)markers.The association panel was evaluated for reactions to three Bgt inoculants, OKS(14)-B-3-1, OKS(14)-C-2-1, and Bgt15.Linkage disequilibrum(LD) analysis indicated that genome-wide LD decayed to 0.1 at 23 Mb, and population structure analysis revealed seven subgroups in the panel.Association analysis using a mixed linear model(MLM) identified three loci for powdery mildew resistance on chromosome 2 B, designated QPm.stars-2BL1,QPm.stars-2BL2, and QPm.stars-2BL3.To evaluate the efficacy of GWAS in gene discovery,QPm.stars-2BL2 was validated using F2 and F2:3 populations derived from PI420646 × OK1059060-126135-3.Linkage analysis delimited the powdery mildew resistance gene in PI 420646 to an interval where QPm.stars-2BL2 was located, lending credence to the GWAS results.QPm.stars-2BL1 and QPm.stars-2BL3, which were associated with four SNPs located at 457.7–461.7 Mb and two SNPs located at 696.6–715.9 Mb in the Chinese Spring reference IWGSC RefSeq v1.0, respectively, are likely novel loci for powdery mildew resistance and can be used in wheat breeding to improve powdery mildew resistance.

关键词： Wheat Powdery mildew GWAS Linkage mapping Genome-wide Linkage disequilibrium

High-density SNP genetic Linkage map construction and quantitative trait locus mapping for resistance to cucumber mosaic virus in tobacco(Nicotiana tabacum L.)

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The Crop Journal 2019年第4期7卷 539-547页

作者： Lirui Cheng Xiaocui Chen Caihong Jiang Bing Ma Min Ren Yazeng Cheng Dan Liu Ruimei Geng Aiguo Yang Key Laboratory of Tobacco Genetic Improvement and Biotechnology Tobacco Research Institute Chinese Academy of Agricultural Sciences Qingdao 266100 Shandong China Key Laboratory of Zunyi Crop Gene Resource and Germplasm Innovation Zunyi Academy of Agricultural Sciences Zunyi 563006 Guizhou China

Genetic Linkage maps are essential for studies of genetics, genomic structure, and genomic evolution, and for mapping quantitative trait loci (QTL). Identification of molecular markers and construction of genetic Linkage maps in tobacco (Nicotiana tabacum L.), a classical model plant and important economic crop, have remained limited. In the present study we identified a large number of single nucleotide polymorphism (SNP) markers and constructed a high-density SNP genetic map for tobacco using restriction site-associated DNA sequencing. In 1216.30 Gb of clean sequence obtained using the Illumina HiSeq 2000 sequencing platform, 99,647,735 SNPs were identified that differed between 203 sequenced plant genomes and the tobacco reference genome. Finally, 13,273 SNP markers were mapped on 24 high-density tobacco genetic Linkage groups. The entire Linkage map spanned 3421.80 cM, with a mean distance of 0.26 cM between adjacent markers. Compared with genetic Linkage maps published previously, this version represents a considerable improvement in the number and density of markers. Seven QTL for resistance to cucumber mosaic virus (CMV) in tobacco were mapped to groups 5 and 8. This high-density genetic map is a promising tool for elucidation of the genetic bases of QTL and for molecular breeding in tobacco.

关键词： Single nucleotide polymorphism Genetic Linkage map Tobacco Cucumber mosaic virus Quantitative trait loci