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Search Results: 1 - 10 of 153684 matches for " Li-zhi Gao "
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Comparisons of mutation rate variation at genome-wide microsatellites: evolutionary insights from two cultivated rice and their wild relatives
Li-zhi Gao, Hongyan Xu
BMC Evolutionary Biology , 2008, DOI: 10.1186/1471-2148-8-11
Abstract: Genome-wide variation of mutation rates was first investigated by means of the composite population parameter θ (θ = 4Nμ, where N is the effective population size and μ is the mutation rate per locus per generation) in four subspecies of Asian cultivated rice O. sativa and its three related species, O. rufipogon, O. glaberrima, and O. officinalis. On the basis of three data sets of microsatellite allele frequencies throughout the genome, population mutation rate (θ) was estimated for each locus. Our results reveal that the variation of population mutation rates at microsatellites within each studied species or subspecies of cultivated rice can be approximated with a gamma distribution. The mean population mutation rates of microsatellites do not significantly differ in motifs of di-, tri-, and tetra-nucleotide repeats for the studied rice species. The shape parameter was also estimated for each subspecies of rice as well as other related rice species. Of them, different subspecies of O. sativa possesses similar shape parameters (α) of the gamma distribution, while other species extensively vary in their population mutation rates.Through the analysis of genome-wide microsatellite data, the population mutation rate can be approximately fitted with a gamma distribution in most of the studied species. In general, different population histories occurred along different lineages may result in the observed variation of population mutation rates at microsatellites among the studied Oryza species.Microsatellites are composed of tandemly repeated, simple DNA sequence motifs of 1–6 nucleotide bases in length. These loci are ubiquitously found throughout both prokaryotic and eukaryotic genomes and typically are highly polymorphic within species and populations. As such, microsatellites have become one of the most popular types of molecular markers and widely employed to study population structure of a diverse range of organisms [1,2], reconstruction of evolutionary history [3],
Evolution of MicroRNA Genes in Oryza sativa and Arabidopsis thaliana: An Update of the Inverted Duplication Model
Yun Zhang, Wen-kai Jiang, Li-zhi Gao
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0028073
Abstract: The origin and evolution of microRNA (miRNA) genes, which are of significance in tuning and buffering gene expressions in a number of critical cellular processes, have long attracted evolutionary biologists. However, genome-wide perspectives on their origins, potential mechanisms of their de novo generation and subsequent evolution remain largely unsolved in flowering plants. Here, genome-wide analyses of Oryza sativa and Arabidopsis thaliana revealed apparently divergent patterns of miRNA gene origins. A large proportion of miRNA genes in O. sativa were TE-related and MITE-related miRNAs in particular, whereas the fraction of these miRNA genes much decreased in A. thaliana. Our results show that the majority of TE-related and pseudogene-related miRNA genes have originated through inverted duplication instead of segmental or tandem duplication events. Based on the presented findings, we hypothesize and illustrate the four likely molecular mechanisms to de novo generate novel miRNA genes from TEs and pseudogenes. Our rice genome analysis demonstrates that non-MITEs and MITEs mediated inverted duplications have played different roles in de novo generating miRNA genes. It is confirmed that the previously proposed inverted duplication model may give explanations for non-MITEs mediated duplication events. However, many other miRNA genes, known from the earlier proposed model, were rather arisen from MITE transpositions into target genes to yield binding sites. We further investigated evolutionary processes spawned from de novo generated to maturely-formed miRNA genes and their regulatory systems. We found that miRNAs increase the tunability of some gene regulatory systems with low gene copy numbers. The results also suggest that gene balance effects may have largely contributed to the evolution of miRNA regulatory systems.
Plastid Genome Sequence of a Wild Woody Oil Species, Prinsepia utilis, Provides Insights into Evolutionary and Mutational Patterns of Rosaceae Chloroplast Genomes
Shuo Wang, Chao Shi, Li-Zhi Gao
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0073946
Abstract: Background Prinsepia utilis Royle is a wild woody oil species of Rosaceae that yields edible oil which has been proved to possess particular benefits for human health and medical therapy. However, the lack of bred varieties has largely impeded exploiting immense potentials for high quality of its seed oil. It is urgently needed to enlarge the knowledge of genetic basis of the species and develop genetic markers to enhance modern breeding programs. Results Here we reported the complete chloroplast (cp) genome of 156,328 bp. Comparative cp sequence analyses of P. utilis along with other four Rosaceae species resulted in similar genome structures, gene orders, and gene contents. Contraction/expansion of inverted repeat regions (IRs) explained part of the length variation in the Rosaceae cp genomes. Genome sequence alignments revealed that nucleotide diversity was associated with AT content, and large single copy regions (LSC) and small single copy regions (SSC) harbored higher sequence variations in both coding and non-coding regions than IRs. Simple sequence repeats (SSRs) were detected in the P. utilis and compared with those of the other four Rosaceae cp genomes. Almost all the SSR loci were composed of A or T, therefore it might contribute to the A-T richness of cp genomes and be associated with AT biased sequence variation. Among all the protein-coding genes, ycf1 showed the highest sequence divergence, indicating that it could accomplish the discrimination of species within Rosaceae as well as within angiosperms better than other genes. Conclusions With the addition of this new sequenced cp genome, high nucleotide substitution rate and abundant deletions/insertions were observed, suggesting a greater genomic dynamics than previously explored in Rosaceae. The availability of the complete cp genome of P. utilis will provide chloroplast markers and genetic information to better enhance the conservation and utilization of this woody oil plant.
In Situ Conservation of Wild Rice Populations: A Targeted Study of Common Wild Rice Oryza rufipogon from China  [PDF]
Li-Zhi Gao, Dao-Yuan Li, Xian-Qiang Wu, Wen Chen, Zhen-Man Huang, Xiao-Mei Wei
American Journal of Plant Sciences (AJPS) , 2012, DOI: 10.4236/ajps.2012.37103
Abstract: Although great accomplishments of in situ conservation have been made during the last decade throughout the world, there is an urgent need to conduct more targeted research to explore many basic questions about crop wild relatives (CWR) in situ conservation such as how to better identify and manage the target in situ conservation populations of CWR. In this study, we performed an extensive field investigation of 201 natural populations or habitats of O. rufipogon, a seriously endangered wild progenitor of cultivated rice in China. Our updated information suggests that: 1) the majority of the natural populations have been extinct throughout China, which leads to serious fragmentation of the population system as a whole; and 2) the survived populations have become small in size and thus fragmented within the population as a result of the loss of subpopulations. To assess the relationships between the biodiversity education and conservation of wild rice, we employed participatory approaches in the field investigation. Our data indicate that the continuous rapid decline of biodiversity education seemed closely related to the extinction of wild rice germplasm. These findings imply the potential necessity and huge challenge for making in situ conservation plans in the future. By means of our understanding of ecogeography, sociology and culture, and population genetics of the species, we propose a strategy for selecting in situ conservation locations as well as priority sites for establishing in situ conservation practices in China.
An Improved Chloroplast DNA Extraction Procedure for Whole Plastid Genome Sequencing
Chao Shi, Na Hu, Hui Huang, Ju Gao, You-Jie Zhao, Li-Zhi Gao
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0031468
Abstract: Background Chloroplast genomes supply valuable genetic information for evolutionary and functional studies in plants. The past five years have witnessed a dramatic increase in the number of completely sequenced chloroplast genomes with the application of second-generation sequencing technology in plastid genome sequencing projects. However, cost-effective high-throughput chloroplast DNA (cpDNA) extraction becomes a major bottleneck restricting the application, as conventional methods are difficult to make a balance between the quality and yield of cpDNAs. Methodology/Principal Findings We first tested two traditional methods to isolate cpDNA from the three species, Oryza brachyantha, Leersia japonica and Prinsepia utihis. Both of them failed to obtain properly defined cpDNA bands. However, we developed a simple but efficient method based on sucrose gradients and found that the modified protocol worked efficiently to isolate the cpDNA from the same three plant species. We sequenced the isolated DNA samples with Illumina (Solexa) sequencing technology to test cpDNA purity according to aligning sequence reads to the reference chloroplast genomes, showing that the reference genome was properly covered. We show that 40–50% cpDNA purity is achieved with our method. Conclusion Here we provide an improved method used to isolate cpDNA from angiosperms. The Illumina sequencing results suggest that the isolated cpDNA has reached enough yield and sufficient purity to perform subsequent genome assembly. The cpDNA isolation protocol thus will be widely applicable to the plant chloroplast genome sequencing projects.
Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation
Yang Liu, Shi-xiong Yang, Peng-zhang Ji, Li-zhi Gao
BMC Evolutionary Biology , 2012, DOI: 10.1186/1471-2148-12-92
Abstract: Here, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplast rpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detected at rpl32-trnL (h?=?0.841; π?=?0.00314) were almost as high as at PAL (h?=?0.836; π?=?0.00417). Significant chloroplast DNA population subdivision was detected (GST?=?0.988; NST?=?0.989), suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure in C. taliensis has been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (GST?=?0.222; NST?=?0.301) provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (NST?>?GST; P?<?0.01). The analysis of PAL haplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused by restricted gene flow with isolation by distance, which was also supported by Mantel’s test of nrDNA haplotypes (r?=?0.234, P?<?0.001). We found that chlorotype C1 was fixed in seven populations of Lancang River Region, implying that the Lancang River might have provided a corridor for the long-distance dispersal of the species.We found that C. taliensis showed fairly high genetic differentiation resulting from restricted gene flow and habitat fragmentation. This phylogeographical study gives us deep insights into population structure of the species and conservation strategies for germplasm sampling and developing in situ conservation of natural populations.
Genome Size Variation among and within Camellia Species by Using Flow Cytometric Analysis
Hui Huang, Yan Tong, Qun-Jie Zhang, Li-Zhi Gao
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0064981
Abstract: Background The genus Camellia, belonging to the family Theaceae, is economically important group in flowering plants. Frequent interspecific hybridization together with polyploidization has made them become taxonomically “difficult taxa”. The DNA content is often used to measure genome size variation and has largely advanced our understanding of plant evolution and genome variation. The goals of this study were to investigate patterns of interspecific and intraspecific variation of DNA contents and further explore genome size evolution in a phylogenetic context of the genus. Methodology/Principal Findings The DNA amount in the genus was determined by using propidium iodide flow cytometry analysis for a total of 139 individual plants representing almost all sections of the two subgenera, Camellia and Thea. An improved WPB buffer was proven to be suitable for the Camellia species, which was able to counteract the negative effects of secondary metabolite and generated high-quality results with low coefficient of variation values (CV) <5%. Our results showed trivial effects on different tissues of flowers, leaves and buds as well as cytosolic compounds on the estimation of DNA amount. The DNA content of C. sinensis var. assamica was estimated to be 1C = 3.01 pg by flow cytometric analysis, which is equal to a genome size of about 2940 Mb. Conclusion Intraspecific and interspecific variations were observed in the genus Camellia, and as expected, the latter was larger than the former. Our study suggests a directional trend of increasing genome size in the genus Camellia probably owing to the frequent polyploidization events.
Translation and Plurality of Interpretations: A Brief Discussion on Practical Significance in Translation of the
Li-zhi YE
Cross-Cultural Communication , 2005, DOI: 10.3968/1712
Abstract: Based on one of the theories of the modern philosophical hermeneutics---“ fusion of horizon”, the author of this paper is to put forward new perspectives to reconsider the criticism toward the two English versions of Chinese classical work---A Story of Red Mansions. The paper also elaborates the theoretical significance of “ fusion of horizon” in translation practice: It is an unavoidable fact that any target version has translator’s style, so we must have an objective attitude toward the cultural filtering and misunderstanding; translation and plurality of interpretations is the need of history; in order to produce ideal target version, translators should make efforts to enrich and perfect their horizon. Key words: hermeneutics, fusion of horizon, preconceived idea, translation and plurality of interpretations Résumé: Ce texte met en question les critiques sur les deux versions traduites du Rêve du pavillon rouge, et expose la signification de la théorie sur la traduction . Les textes traduits sont marqués plus ou moins de style personnel du traducteur , il faut donc traiter des problèmes de fausses traductions de fa on objective . En meme temps , le pluralisme de traduction et d’explication est devenu nécessaire en raison de l’ouverture du texte . Les traducteurs doivent s’y adapter pour améliorer la qualité de traduction Mots-clés: explicationisme , fusion horizontale , idee preconcu , le pluralisme d'explication 摘要:本文結合現代闡釋學“視域融合”的理論,對≤紅樓夢≥兩個不同譯本的有關批評提出異議,進一步闡述了闡釋學“視域融合”理論對翻譯的借鑒意義:即“先行結構”的影響使譯文不可避免地帶有譯者風格,因而應客觀看待“文化過濾”和誤譯現象。與此同時,文本的開放性使翻譯與闡釋的多元成為必要,作為譯者也應不斷完善自己的先行結構,以提高譯文的品質。 關鍵詞:闡釋學;視域融合;先行結構;闡釋的多元
Social Costs of the Patent System
Li-zhi NING
Canadian Social Science , 2006,
Abstract: The patent system is making progress and incorporating international practice at a tremendous pace in China. However, scholars have been raising doubts to the benefits of the patent system. They believe that the social costs borne by the developing countries for the patent system exceed the overall economic gains in the current international circumstances. China’s current patent system indicates that there is a lack of sufficient understanding of the social costs and of the cost-benefit analysis of the patent system, which causes many controversies. Nowadays the related study is still struggling to quantify the social cost, while the qualitative analysis is highly disputed. However, an anatomy of the social costs is necessary to take specific cost control measures for the purpose of establishing an economically more efficient patent system suitable under China’s current circumstances. Key words: Patent, Social Costs, Patent System Résumé: Pas à pas, la construction sur le système de patente en Chine est bien développé avec les co tumes internationals, relativement, les savants sont suspicieux sur l'éfficacité de ce système parce qu'il a déséquilibré le co t social des pays en développements avec le profit économic du monde entier, les pays en développements sont bien inquiets. Le système de patente chinois a un grand défaut dont l'analyse sur le co t-l'éfficacité n'est pas suffisante,et il provoque pas mal de contestation. Maintenat, l'analyse sur le co t social du système de patente n'a pas encore fait une conclusion précise, mais il est nécessaire de bien analyzer de divers co ts sociaux quand on forge le système de patente, afin qu'on puisse fonder un système qui peut bien contr ler le co t et peut bien adaptable à la situation du pays. Mots-Clés: La patente, le système de patente, le co t social
On the Relation of Exercising of Patent Rights and Antimonopoly Law
Li-zhi NING
Canadian Social Science , 2007,
Abstract: Antimonopoly law provides exemption for the legitimate exercising of patent rights, casts regulation and control over the patent abuse. This article expounds the exemption subject, exemption condition, exemption occasion as well as exemption category, elucidates the relation of abuse behavior and antimonopoly law, puts forward concrete regulating approach on the patent abuse by antimonopoly law. Key words: legitimate exercising of patent rights, patent abuse, antimonopoly law Résumé: le juste exercice du droit de propriété industrielle est immunisé selon la loi antitrust, j’expose dans cette thèse l’objet, la condition, l’occasion et la catégorie de son immunité. Pourtant, l’abus du droit de propriété industrielle est restreint aussi selon la loi antitrust, j’explique la relation entre l’abus du droit de propriété industrielle et la loi antitrust, puis propose mon projet afin de restreindre l’abus du droit de propriété industrielle par la loi antitrust. Mots-Clés: le juste exercice du droit de propriété industrielle, l’abus du droit de propriété industrielle, la loi antitrust
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