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Appadtion of the NAC Transcription Factors Predates the Emergence of Land Plants

Molecular Plant 2016年第9期9卷 1345-1348页

作者： Aude Maugarny-Cales Beatriz Gonqalves Stefan Jouannic Michael Melkonian gane ka-shu wonge Patrick Laufs Institut Jean-Pierre Bourgin INRA AgroParisTech CNRS Universite ParisSaclay RD10 78026 Versailles Cedex France Univ. Pads-Sud Universite Paris-Saclay 91405 Orsay France IRD UMR DIADE 911 Avenue Agropolis BP6450134394 Mbntpellier Cedex 5 France LMI RICE IRD USTH National Key Laboratory for Plant Cell Biotechnology Agronomical Genetics Institute Pham Van Dong Road Hanoi Vietnam Botany Department Cologne Biocenter University of Cologne 50674 Cologne Germany Beijing Genomics Institute-Shenzhen Shenzhen 518083 China Department of Biological Sciences University of Alberta Edmonton AB T6G 2E9 Canada Department of Medicine University of Alberta Edmonton AB T6G 2E Canada These authors contributed equally to this article.

Dear Editor The NAC （for NO APICAL MERISTEM [NAM], Arabidopsis TRANSCRII^TION ACTIVATOR FACTOR [ATAF] and CUP- SHAPED COTYLEDON [CUC]） proteins are one of the largest families of plant-specific transcription factors （Nagata et aL, 2015）. They are involved in many different biological processes including development and the response to biotic and abiotic stresses. To date, NAC transcription factors have only been identified in land plants （Zhu et al., 2012; Nagata et al., 2015）; and some of them control land-plant-specific processes, such as the formation of specialized water-conducting systems （Xu et al., 2014）. Therefore, it has been suggested that their appearance accompanied the emergence of land plants. Here, we exploited the transcriptomic data generated within the 1000 plants project （***, Wickett et al., 2014） to revisit the origin of NAC proteins. Our careful analysis shows that NAC transcription factors appeared before the ernergence of land plants as we detected their homologs in several groups of streptophyte green algae. The possible significance of this finding is discussed.

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Genome Biology: The Second Modern Synthesis

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Genomics,Proteomics & Bioinformatics 2005年第1期 11-12页

作者： gane ka-shu Wong Beijing 101300 Beijing Genomics Institute China. Chinese Academy of Sciences

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Positive correlation between recombination rate and nucleotide diversity is shown under domestication selection in the chicken genome

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Chinese Science Bulletin 2008年第5期53卷 746-750页

作者： FANG Lin YE Jia LI Ning ZHANG Yong LI SongGang gane ka-shu WONG WANG Jun Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China Beijing Genomics Institute Beijing 101300 China University of Washington Gen0me Center Department of Medicine Fluke Hall M/C 352145 Seattle USA Department of Biochemistry and Molecular Biology University of Southem Denmark DK-5230 Odense M Denmark The Institute of Human Genetics University of Aarhus DK-8000 Aarhus C Denmark

Positive correlation between recombination rate and nucleotide diversity has been observed in a wide variety of eukaryotes on megabase scale. On the basis of genome-wide chicken genetic variation map generated by comparing three domestic breeds with wild ancestor and the positions of markers on the genetic linkage map, we found that SNPs rates were similar for all chromosomes while the recombina-tion rates increased in micro chromosomes. In other words no correlation exists in chromosome size. Nevertheless, when we scanned the genome by calculating the values of each characteristic within non-overlapping windows, instead of single value for each chromosomes, the nucleotide diversity was found to be significantly correlated with the recombination rate (r=0.27, P<0.0005). Furthermore, the significant association not only existed between these two features, but also existed between all 6 pairwise combinations of nucleotide diversity, recombination rate, GC content and average gene length. This co-variation is very meaningful for the studies of sequence evolution.

关键词：小鸡基因组再结合率核苷多样性正相关性

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kaKs_Calculator:Calculating ka and Ks Through Model Selection and Model Averaging

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Genomics, Proteomics & Bioinformatics 2006年第4期4卷 259-263页

作者： Zhang Zhang Jun Li Xiao-Qian Zhao Jun Wang gane ka-shu Wong Jun Yu Institute of Computing Technology Chinese Academy of Sciences Beijing 100080 China Beijing Instituteof Genomics Chinese Academy of Sciences Beijing 101300 China Graduate School of Chinese Academyof Sciences Beijing 100049 China James D. Watson Institute of Genome Sciences Zhejiang UniversityHangzhou 310007 China UW Genome Center University of Washington Seattle WA 98195 USA

kaKs_Calculator is a software package that calculates nonsynonymous （ka） and synonymous （Ks） substitution rates through model selection and model averaging. Since existing methods for this estimation adopt their specific mutation （substitution） models that consider different evolutionary features, leading to diverse estimates, kaKs_Calculator implements a set of candidate models in a maximum likelihood framework and adopts the Akaike information criterion to measure fitness between models and data, aiming to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences. In addition, several existing methods for calculating ka and Ks are also incorporated into this software. kaKs_Calculator, including source codes, compiled executables, and documentation, is freely available for academic use at http：//***/***.

关键词： model selection model averaging AIC approximate method maximum likelihoodmethod

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Genome Biology: The Second Modern Synthesis

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Genomics, Proteomics & Bioinformatics 2005年第1期3卷 3-4页

作者： Jun Yu gane ka-shu Wong Beijing Genomics Institute Chinese Academy of Sciences Beijing 101300 China.

A scientific dream proposed some 20 years ago has been realized-the completion of the DNA sequence for the Human Genome Project （HGP） in 2004. As a result, an entirely new field of biological research has arisen： genome biology or genomics is celebrated for its unprecedented scale, intrinsically digital output, and systematic approach to getting all the data. Its sequel, the HapMap Project, will reach fruition later this year. These projects established new precedents for international collaborations and open data access. Chinese scientists contributed to 1% of the

关键词：基因组学

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Research into a Feature Selection Method for Hyperspectral Imagery Using PSO and SVM

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Journal of China University of Mining and Technology 2007年第4期17卷 473-478页

作者： YANG Hua-chao ZHANG shu-bi DENG ka-zhong DU Pei-jun School of Environment ＆ Spatial Informatics China University of Mining ＆ Technology Xuzhou Jiangsu 221008 China

Classification and recognition of hyperspectral remote sensing images is not the same as that of conventional multi-spectral remote sensing images. We propose,a novel feature selection and classification method for hyperspectral images by combining the global optimization ability of particle swarm optimization (PSO) algorithm and the superior classification performance of a support vector machine (SVM). Global optimal search performance of PSO is improved by using a chaotic optimization search technique. Granularity based grid search strategy is used to optimize the SVM model parameters. Parameter optimization and classification of the SVM are addressed using the training date corre-sponding to the feature subset. A false classification rate is adopted as a fitness function. Tests of feature selection and classification are carried out on a hyperspectral data set. Classification performances are also compared among different feature extraction methods commonly used today. Results indicate that this hybrid method has a higher classification accuracy and can effectively extract optimal bands. A feasible approach is provided for feature selection and classifica-tion of hyperspectral image data.

关键词： hyperspectral remote sensing particle swarm optimization support vector machine feature extraction

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Characterizing the optimal operation of photocatalytic degradation of BDE-209 by nano-sized TiO_2

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Journal of Environmental Sciences 2012年第9期24卷 1670-1678页

作者： ka Lai Chow Yu Bon Man Jin shu Zheng Yan Liang Nora Fung Yee Tam Ming Hung Wong Croucher Institute for Environmental Sciences and Department of Biology Hong Kong Baptist University Hong Kong SAR China Department of Biology and Chemistry City University of Hong Kong Hong Kong SAR China

Brominated flame retardants have been widely used in industry. There is a rapid growing public concern for their availabilities in the environment. Advanced oxidation process （AOP） is a promising and efficient technology which may be used to remove emerging chemicals such as brominated flame retardants. This study aims at investigating optimal operational conditions for the removal of BDE-209 using nano-scaled titanium（IV） oxide. The residual PBDE congeners after photocatalytical degradation of BDE-209 by TiO2 were analysed by gas chromatography-mass spectrometry （GC-MS）. It was found that the degradability of BDE-209 by TiO2 was attributed to its photocatalytic activity but not the small size of the particles. The half-life of removing BDE-209 by TiO2 was 3.05 days under visible light. Tetra- and penta-BDEs were the major degraded products of BDE-209. Optimum conditions for photocatalytical degradation of BDE-209 was found to be at pH 12 （93% ± 1%）, 5, 10, 20 mg/L （93.0% ± 1.70%, 91.6% ± 3.21%, 91.9% ± 0.952%, respectively）, respectively of humic acid and in the form of anatase/rutile TiO2 （82% ± 3%）. Hence, the efficiency of removing BDE-209 can be maximized while being cost effective at the said operating conditions.

关键词： PBDEs TiO2 photocatalysis hydroxyl radicals

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Non-Metric CCD Camera Calibration Algorithm in a Digital Photogrammetry System

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Journal of China University of Mining and Technology 2006年第2期16卷 119-122页

作者： YANG Hua-chao DENG ka-zhong ZHANG shu-bi GUO Guang-li ZHOU Ming School of Environment and Spatial lnformatics China University of Mining ＆ Technology Xuzhou Jiangsu 221008 China

Camera calibration is a critical process in photogrammetry and a necessary step to acquire 3D information from a 2D image. In this paper, a flexible approach for CCD camera calibration using 2D direct linear transformation （DLT） and bundle adjustment is proposed. The proposed approach assumes that the camera interior orientation elements are known, and addresses a new closed form solution in planar object space based on homogenous coordinate representation and matrix factorization. Homogeneous coordinate representation offers a direct matrix correspondence between the parameters of the 2D DLT and the collinearity equation. The matrix factorization starts by recovering the elements of the rotation matrix and then solving for the camera position with the collinearity equation. Camera calibration with high precision is addressed by bundle adjustment using the initial values of the camera orientation elements. The results show that the calibration precision of principal point and focal length is about 0.2 and 0.3 pixels respectivelv, which can meet the requirements of close-range photogrammetry with high accuracy.

关键词： direct linear transformation collinearity equation bundle adjustment camera calibration Hough transformation

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Correlation of effective hepatic blood flow with liver pathology in patients with hepatitis B virus

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Liver Research 2021年第4期5卷 243-250页

作者： Xin shu Haixia Sun Xiaoan Yang Yifan Jia Peiyan Xu Hong Cao ka Zhang Department of Infectious Diseases The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhouChina Department of Infectious Diseases Huadu District People's Hospital of GuangzhouGuangzhouChina

Background and aims:Effective hepatic blood flow(EHBF)decreases with liver disease progression,and identifying liver pathology is critical for patients with liver *** study was designed to elucidate the correlation between EHBF and liver pathology and explore the potential of EHBF for predicting the degree of liver ***:In this study,207 patients with hepatitis B virus(HBV)who underwent liver biopsy and indocyanine green(ICG)clearance tests were *** was measured using the ICG clearance test,and liver tissue was histologically analyzed to determine the pathological stage according to the Scheuer scoring *** data,biochemical indexes,and FibroScan data were collected for statistical ***:EHBF levels decreased as the liver histological stages of inflammation and fibrosis increased(Pkaline phosphatase,aspartate aminotransferase-to-platelet ratio index,fibrosis index based on the four factors,and liver stiffness measurement(P<0.05).The EHBF levels of patients without liver inflammation(G0)were significantly higher than those of patients with liver inflammation(G1e4)(P<0.001).The area under the receiver operating characteristic curve(AUROC)value for discriminating patients without liver inflammation was 0.827,and the optimal cutoff value was 0.936 L/*** EHBF levels of patients with severe liver inflammation(G4)were significantly lower than those of patients with G0e3 liver inflammation(P<0.001).The AUROC value for discriminating patients with severe liver inflammation was 0.792,and the optimal cutoff value was 0.552 L/*** EHBF levels of patients without liver fibrosis(S0)were significantly higher than those of patients with liver fibrosis(S1e4)(P<0.001).The AUROC value for discriminating patients without liver fibrosis was 0.633,and the optimal cutoff val

关键词： Hepatitis B virus(HBV) Liver inflammation Liver fibrosis Effective hepatic blood flow(EHBF) Liver disease

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Evolutionary Transients in the Rice Transcriptome

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Genomics, Proteomics & Bioinformatics 2010年第4期8卷 211-228页

作者： Jun Wang Jianguo Zhang Ruiqiang Li Hongkun Zheng Jun Li Yong Zhang Heng Li Peixiang Ni Songgang Li Shengting Li Jingqiang Wang Dongyuan Liu Jason McDermott Ram Samudrala Siqi Liu Jian Wang Huanming Yang Jun Yu gane ka-shu Wong Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China Beijing Genomics Institute at Shenzhen Shenzhen 518083 China Department of Biochemistry and Molecular Biology University of Southern Denmark DK-5230 Odense M Denmark Theoretical Life Research Center Fudan University Shanghai 200433 China Computational Genomics Group Department of Microbiology University of Washington Seattle WA 98195 USA Computational Biology and Bioinformatics Pacific Northwest National Laboratory Richland WA 99352 USA Department of Biological Sciences and Department of Medicine University of Alberta Edmonton AB T6G 2E9 Canada

In the canonical version of evolution by gene duplication, one copy is kept unaltered while the other is free to evolve. This process of evolutionary experimentation can persist for millions of years. Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may—in principle—be attributable to what we will refer to as ＂evolutionary transients＂, referring here to both the process and the genes that have gone or are undergoing this process. Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsis genes, and why most excess rice genes show low similarity to eudicots.

关键词： evolutionary transients rice gene duplication

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