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| 1 | Distinct gut microbiota profiles in patients with primary sclerosing cholangitis and ulcerative colitis显示文摘AIM To characterize the gut bacterial microbiota of patients with primary sclerosing cholangitis(PSC) and ulcerative colitis(UC).METHODS Stool samples were collected and relevant clinical data obtained from 106 study participants, 43 PSC patients with(n = 32) or without(n = 11) concomitant inflammatory bowel disease, 32 UC patients, and 31 healthy controls. The V3 and V4 regions of the 16 S ribosomal RNA gene were sequenced on Illumina Mi Seq platform to cover low taxonomic levels. Data were further processed in QIIME employing Ma As Lin and LEf Se tools for analysis of the output data.RESULTS Microbial profiles in both PSC and UC were characterized by low bacterial diversity and significant change in global microbial composition. Rothia, Enterococcus, Streptococcus, Veillonella, and three other genera were markedly overrepresented in PSC regardless of concomitant inflammatory bowel disease(IBD). Rothia, Veillonella and Streptococcus were tracked to the species level to identify Rothia mucilaginosa, Streptococcus infantus, S. alactolyticus, and S. equi along with Veillonella parvula and V. dispar. PSC was further characterized by decreased abundance of Adlercreutzia equolifaciens and Prevotella copri. Decrease in genus Phascolarctobacterium was linked to presence of colonic inflammation regardless of IBD phenotype. Akkermansia muciniphila, Butyricicoccus pullicaecorum and Clostridium colinum were decreased in UC along with genus Roseburia. Low levels of serum albumin were significantly correlated with enrichment of order Actinomycetales.CONCLUSION PSC is associated with specific gut microbes independently of concomitant IBD and several bacterial taxa clearly distinguish IBD phenotypes(PSC-IBD and UC). | Lukas Bajer Miloslav Kverka Martin Kostovcik Peter Macinga Jiri Dvorak Zuzana Stehlikova Jan Brezina Pavel Wohl Julius Spicak Pavel Drastich | 2017 | World Journal of Gastroenterology2017，23，25： | 22 |
| 2 | Sequencing a Juglans regia×J.microcarpa hybrid yields high-quality genome assemblies of parental species显示文摘Members of the genus Juglans are monecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes,which greatly complicates genome sequence assembly.The genomes of interspecific hybrids are usually comprised of haploid genomes of parental species.We exploited this attribute of interspecific hybrids to avoid heterozygosity and sequenced an interspecific hybrid Juglans microcarpa×J.regia using a novel combination of single-molecule sequencing and optical genome mapping technologies.The resulting assemblies of both genomes were remarkably complete including chromosome termini and centromere regions.Chromosome termini consisted of arrays of telomeric repeats about 8 kb long and heterochromatic subtelomeric regions about 10 kb long.The centromeres consisted of arrays of a centromere-specific Gypsy retrotransposon and most contained genes,many of them transcribed.Juglans genomes evolved by a whole-genome-duplication dating back to the Cretaceous-Paleogene boundary and consist of two subgenomes,which were fractionated by numerous short gene deletions evenly distributed along the length of the chromosomes.Fractionation was shown to be asymmetric with one subgenome exhibiting greater gene loss than the other.The asymmetry of the process is ongoing and mirrors an asymmetry in gene expression between the subgenomes.Given the importance of J.microcarpa×J.regia hybrids as potential walnut rootstocks,we catalogued disease resistance genes in the parental genomes and studied their chromosomal distribution.We also estimated the molecular clock rates for woody perennials and deployed them in estimating divergence times of Juglans genomes and those of other woody perennials. | Tingting Zhu Le Wang Frank M.You Juan C.Rodriguez Karin R.Deal Limin Chen Jie Li Sandeep Chakraborty Bipin Balan Cai-Zhong Jiang Patrick J.Brown Charles ALeslie Mallikarjuna KAradhya Abhaya M.Dandekar Patrick E.McGuire Daniel Kluepfel Jan Dvorak Ming-Cheng Luo | 2019 | Horticulture Research2019，6，1： | 7 |
| 3 | Pneumatic Measurements Downstream of a Radial Turbine Nozzle Cascade显示文摘This paper deals mainly with pneumatic measurements on a radial turbine nozzle cascade.The full radial cascade guarantees the exit flow field periodicity downstream of it.A special traversing mechanism with a five -hole conical probe moving along a circular path behind the cascade was used for flow field investigation in this type of cascade with very low aspect ratio.The analyses of results of 2D and 3D pneumatic measurements including loss coefficient values are presented. | Martin LUXA Rudolf DVORAK David SIMURDA Jan VIMMR | 2010 | Journal of Thermal Science2010，19，1： | 3 |
| 4 | Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D‐genome genetic diversity and pinpoint the geographic origin of hexaploid wheat显示文摘 | Jirui Wang Ming‐Cheng Luo Zhongxu Chen Frank M. You Yuming Wei Youliang Zheng Jan Dvorak | 2013 | New Phytol2013，，3： | 2 |
| 5 | Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay显示文摘 | Eduard Akhunov Charles Nicolet Jan Dvorak | 2009 | Theor Appl Genet2009，119，3： | 1 |
| 6 | Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat显示文摘 | Naxin Huo John P. Vogel Gerard R. Lazo Frank M. You Yaqin Ma Stephanie McMahon Jan Dvorak Olin D. Anderson Ming-Cheng Luo Yong Q. Gu | | 0，2009，： | 1 |
| 7 | The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences显示文摘 | Naxin Huo Gerard R. Lazo John P. Vogel Frank M. You Yaqin Ma Daniel M. Hayden Devin Coleman-Derr Theresa A. Hill Jan Dvorak Olin D. Anderson Ming-Cheng Luo Yong Q. Gu | | 0，2008，： | 1 |
| 8 | The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences显示文摘 | Naxin Huo Gerard R. Lazo John P. Vogel Frank M. You Yaqin Ma Daniel M. Hayden Devin Coleman-Derr Theresa A. Hill Jan Dvorak Olin D. Anderson Ming-Cheng Luo Yong Q. Gu | 2008 | Functional & Integrative Genomics2008，，2： | 1 |
| 9 | Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay显示文摘 | Eduard Akhunov Charles Nicolet Jan Dvorak | 2009 | Theor Appl Genet2009，119，3： | 1 |
| 10 | Centromere association is an unlikely mechanism by which the wheat Ph1 locus regulates metaphase I chromosome pairing between homoeologous chromosomes显示文摘 | Jan Dvorak Adam J. Lukaszewski | 2000 | Chromosoma2000，，6： | 1 |
| 11 | Identification of a robust molecular marker for the detection of the stem rust resistance gene Sr45 in common wheat显示文摘 | Sambasivam Periyannan Urmil Bansal Harbans Bariana Karin Deal Ming-Cheng Luo Jan Dvorak Evans Lagudah | 2014 | Theoretical and Applied Genetics2014，，4： | 1 |
| 12 | Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D‐genome genetic diversity and pinpoint the geographic origin of hexaploid wheat显示文摘 | Jirui Wang Ming‐Cheng Luo Zhongxu Chen Frank M. You Yuming Wei Youliang Zheng Jan Dvorak | 2013 | New Phytol2013，，3： | 1 |
| 13 | Fine mapping and epistatic interactions of the vernalization gene VRN - D4 in hexaploid wheat显示文摘 | Nestor Kippes Jie Zhu Andrew Chen Leonardo Vanzetti Adam Lukaszewski Hidetaka Nishida Kenji Kato Jan Dvorak Jorge Dubcovsky | 2014 | Molecular Genetics and Genomics2014，，1： | 1 |
| 14 | Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes显示文摘Bread wheat(Triticum aestivum,AABBDD) is an allohexaploid species derived from two rounds of interspecific hybridizations.A high-quality genome sequence assembly of diploid Aegilops tauschii,the donor of the wheat D genome,will provide a useful platform to study polyploid wheat evolution.A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path(MTP) of 3176 BAC clones from the short arm of Ae.tauschii chromosome 3(At3DS).The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes.Compared with the orthologous regions of rice,Brachypodium,and sorghum,At3 DS contains 38.67%more genes.In comparison to At3 DS,the short arm sequence of wheat chromosome 3B(Ta3BS) is 95-Mb large in size,which is primarily due to the expansion of the non-centromeric region,suggesting that transposable element(TE) bursts in Ta3 B likely occurred there.Also,the size increase is accompanied by a proportional increase in gene number in Ta3 BS.We found that in the sequence of short arm of wheat chromosome 3D(Ta3DS),there was only less than 0.27%gene loss compared to At3 DS.Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome. | Jingzhong Xie Naxin Huo Shenghui Zhou Yi Wang Guanghao Guo Karin R.Deal Shuhong Ouyang Yong Liang Zhenzhong Wang Lichan Xiao Tingting Zhu Tiezhu Hu Vijay Tiwari Jianwei Zhang Hongxia Li Zhongfu Ni Yingyin Yao Huiru Peng Shengli Zhang Olin D.Anderson Patrick E.McGuire Jan Dvorak Ming-Cheng Luo Zhiyong Liu Yong Q.Gu Qixin Sun | 2017 | Journal of Genetics and Genomics2017，44，1： | 1 |
| 15 | Co-located quantitative trait loci mediate resistance to Agrobacterium tumefaciens, Phytophthora cinnamomi,and P.pini in Juglans microcarpa×J.regia hybrids显示文摘Soil-borne plant pathogens represent a serious threat that undermines commercial walnut(Juglans regia)production worldwide.Crown gall,caused by Agrobacterium tumefaciens,and Phytophthora root and crown rots,caused by various Phytophthora spp.,are among the most devastating walnut soil-borne diseases.A recognized strategy to combat soil-borne diseases is adoption of resistant rootstocks.Here,resistance to A.tumefaciens,P.cinnamomi,and P.pini is mapped in the genome of Juglans microcarpa,a North American wild relative of cultivated walnut.Half-sib J.microcarpa mother trees DJUG 31.01 and DJUG 31.09 were crossed with J.regia cv.Serr,producing 353 and 400 hybrids,respectively.Clonally propagated hybrids were genotyped by sequencing to construct genetic maps for the two populations and challenged with the three pathogens.Resistance to each of the three pathogens was mapped as a major QTL on the long arm of J.microcarpa chromosome 4D and was associated with the same haplotype,designated as haplotype b,raising the possibility that the two mother trees were heterozygous for a single Mendelian gene conferring resistance to all three pathogens.The deployment of this haplotype in rootstock breeding will facilitate breeding of a walnut rootstock resistant to both crown gall and Phytophthora root and crown rots. | Ramesh K.Ramasamy Ming-Cheng Luo Charles A.Leslie Dianne Velasco Natalia Ott Ali McClean Abhaya M.Dandekar Mallikarjuna Aradhya Patrick J.Brown Gregory T.Browne Daniel A.Kluepfel Andreas Westphal Jan Dvorak | 2021 | Horticulture Research2021，8，1： | 0 |
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