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ABSTRACT: Members of the CYCLOIDEA2 (CYC2) clade of the TEOSINTE BRANCHED1, CYCLOIDEA, and PCF transcription factor genes are widely involved in controlling floral zygomorphy, a key innovation in angiosperm evolution, depending on their persistently asymmetric expression in the corresponding floral domains. However, it is unclear how this asymmetric expression is maintained throughout floral development. Selecting Primulina heterotricha as a model, we examined the expression and function of two CYC2 genes, CYC1C and CYC1D. We analyzed the role of their promoters in protein-DNA interactions and transcription activation using electrophoresis mobility shift assays, chromatin immunoprecipitation, and transient gene expression assays. We find that CYC1C and CYC1D positively autoregulate themselves and cross-regulate each other. Our results reveal a double positive autoregulatory feedback loop, evolved for a pair of CYC2 genes to maintain their expression in developing flowers. Further comparative genome analyses, together with the available expression and function data of CYC2 genes in the core eudicots, suggest that this mechanism might have led to the independent origins of floral zygomorphy, which are associated with plant-insect coevolution and the adaptive radiation of angiosperms.
The Plant Cell 05/2012; 24(5):1834-47. · 8.99 Impact Factor
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Xun Xu,
Xin Liu,
Song Ge,
Jeffrey D Jensen,
Fengyi Hu,
Xin Li, Yang Dong,
Ryan N Gutenkunst,
Lin Fang,
Lei Huang, [......],
Yingrui Li,
Chang Yu,
Karsten Kristiansen,
Xiuqing Zhang,
Jian Wang,
Mark Wright,
Susan McCouch,
Rasmus Nielsen,
Jun Wang,
Wen Wang
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ABSTRACT: Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 × raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable for breeding and for identifying agronomically important genes in rice.
Nature Biotechnology 12/2011; 30(1):105-11. · 29.50 Impact Factor
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Hui Xiang,
Jingde Zhu,
Quan Chen,
Fangyin Dai,
Xin Li,
Muwang Li,
Hongyu Zhang,
Guojie Zhang,
Dong Li, Yang Dong, [......],
Ruiqiang Li,
Xiuqing Zhang,
Lijia Ma,
Karsten Kristiansen,
Qiuhong Guo,
Jianhao Jiang,
Stephan Beck,
Qingyou Xia,
Wen Wang,
Jun Wang
Nature Biotechnology 07/2010; 28(7):756. · 29.50 Impact Factor
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Hui Xiang,
Jingde Zhu,
Quan Chen,
Fangyin Dai,
Xin Li,
Muwang Li,
Hongyu Zhang,
Guojie Zhang,
Dong Li, Yang Dong, [......],
Ruiqiang Li,
Xiuqing Zhang,
Lijia Ma,
Karsten Kristiansen,
Qiuhong Guo,
Jianhao Jiang,
Stephan Beck,
Qingyou Xia,
Wen Wang,
Jun Wang
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ABSTRACT: Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis and human, demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.
Nature Biotechnology 05/2010; 28(5):516-20. · 29.50 Impact Factor
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ABSTRACT: Recent transcription profiling studies have revealed an unexpectedly large proportion of antisense transcripts in eukaryotic genomes. These antisense genes seem to regulate gene expression by interacting with sense genes. Previous studies have focused on the non-coding antisense genes, but the possible regulatory role of the antisense protein is poorly understood. In this study, we found that a protein encoded by the antisense gene ADF1 acts as a transcription suppressor, regulating the expression of sense gene MDF1 in Saccharomyces cerevisiae. Based on the evolutionary, genetic, cytological and biochemical evidence, we show that the protein-coding sense gene MDF1 most likely originated de novo from a previously non-coding sequence and can significantly suppress the mating efficiency of baker's yeast in rich medium by binding MATalpha2 and thus promote vegetative growth. These results shed new light on several important issues, including a new sense-antisense interaction mechanism, the de novo origination of a functional gene, and the regulation of yeast mating pathway.
Cell Research 03/2010; 20(4):408-20. · 8.19 Impact Factor
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Yun Ding,
Li Zhao,
Shuang Yang,
Yu Jiang,
Yuan Chen,
Ruoping Zhao,
Yue Zhang,
Guojie Zhang, Yang Dong,
Haijing Yu,
Qi Zhou,
Wen Wang
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ABSTRACT: Gene duplication is supposed to be the major source for genetic innovations. However, how a new duplicate gene acquires functions by integrating into a pathway and results in adaptively important phenotypes has remained largely unknown. Here, we investigated the biological roles and the underlying molecular mechanism of the young kep1 gene family in the Drosophila melanogaster species subgroup to understand the origin and evolution of new genes with new functions. Sequence and expression analysis demonstrates that one of the new duplicates, nsr (novel spermatogenesis regulator), exhibits positive selection signals and novel subcellular localization pattern. Targeted mutagenesis and whole-transcriptome sequencing analysis provide evidence that nsr is required for male reproduction associated with sperm individualization, coiling, and structural integrity of the sperm axoneme via regulation of several Y chromosome fertility genes post-transcriptionally. The absence of nsr-like expression pattern and the presence of the corresponding cis-regulatory elements of the parental gene kep1 in the pre-duplication species Drosophila yakuba indicate that kep1 might not be ancestrally required for male functions and that nsr possibly has experienced the neofunctionalization process, facilitated by changes of trans-regulatory repertories. These findings not only present a comprehensive picture about the evolution of a new duplicate gene but also show that recently originated duplicate genes can acquire multiple biological roles and establish novel functional pathways by regulating essential genes.
PLoS Genetics 01/2010; 6(12):e1001255. · 8.69 Impact Factor
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ABSTRACT: The paper presents the results of an experimental study that was carried out to determine turbulent friction and heat transfer characteristics of four spirally corrugated tubes, which have various geometrical parameters, with water and oil as the working fluids. Experiments were performed under conditions of Reynolds number varying from 6000 to 93,000 for water, and from 3200 to 19,000 for oil, respectively. The results show that the thermal performance of these tubes was superior compared to a smooth tube, but the heat transfer enhancements were not as large as the friction factor increases. Friction factors and heat transfer coefficient in these rough tubes were analyzed on the basis of momentum and heat transfer analogy, and the correlations obtained were compared with the present data and also the results of previous investigators. A mathematical model to evaluate the performance of spirally corrugated tube, which takes account of the large variation of fluid Prandtl number with temperature, was developed by the extension of previous work of Bergles and Webb. The results reported enable practical designs with standard products and optimization of tube geometry for specific conditions.
Experimental Thermal and Fluid Science.
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ABSTRACT: A novel gastro-mucoadhesive delivery system based on ion-exchange fiber has been developed. Rriboflavin-5′-phosphate sodium salt (RF5P), which is site-specifically absorbed from the upper gastrointestinal tract, was used as model drug. A modified dissolution system, which can also be called ‘flow through diffusion cell’ (FTDC), was used to study the drug release from the drug fibers. Gastrointestinal transit studies of the RF5P fiber complexes in rats and gamma imaging study in volunteer was carried out to evaluate the gastro-retentive behavior of the fiber. The pharmacokinetic profile and parameters of riboflavin via analysis of urinary excretion of riboflavin on man were measured. Study on rat and man provide evidence for the validity of the hypothesis that the drug fiber provided good mucoadhesive properties in vivo and should therefore be of considerable interest for the development of future mucoadhesive oral drug delivery dosage forms.
International Journal of Pharmaceutics.
