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Duplication and Divergence of Floral MADS-Box Genes in Grasses： Evidence for the Generation and Modification of Novel Regulators

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Journal of Integrative Plant Biology 2007年第6期49卷 927-939页

作者： Guixia Xu Hongzhi Kong state Key Laboratory of Systematic and Evolutionary Botany Institute of Botany the Chinese Academy of Sciences Beijing 100093 China Graduate university of the Chinese Academy of Sciences Beijing 100039 China

The process of flowering is controlled by a hierarchy of floral genes that act as flowering time genes, inflorescence/floral meristem Identity genes, and/or floral organ-identity genes. The most important and well-characterized floral genes are those that belong to the MADS-box family of transcription factors. Compelling evidence suggests that floral MADS-box genes have experienced a few large-scale duplication events. In particular, the precore eudicot duplication events have been considered to correlate with the emergence and diversification of core eudicots. Duplication of floral MADS-box genes has also been documented in monocots, particularly In grasses, although a systematic study is lacking. In the present study, by conducting extensive phylogenetlc analyses, we identified pre-Poaceae gene duplication events in each of the AP1, P1, AG, AGL11, AGL2/3/4, and AGL9gene lineages. Comparative genomic studies further indicated that some of these duplications actually resulted from the genome doubling event that occurred 66-70 million years ago （MYA）. In addition, we found that after gene duplication, exonization （of intron sequences） and pseudoexonization （of exon sequences） have contributed to the divergence of duplicate genes in sequence structure and, possibly, gene function.

关键词： divergence Oryza sativa gene duplication genome doubling event grasses MADS-box genes.

Regulation of Arabidopsis Early Anther Development by Putative Cell-Cell Signaling Molecules and Transcriptional Regulators

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Journal of Integrative Plant Biology 2007年第1期49卷 60-68页

作者： Yu-Jin Sun Carey LH Hord Chang-Bin Chen Hong Ma Department of Biology and the Huck Institutes of the Life Sciences Pennsylvania State University University Park PA 16802 USA The Integrative Bioscience Graduate Program Pennsylvania State University University Park PA 16802 USA

Anther development in flowering plants involves the formation of several cell types, including the tapetal and pollen mother cells. The use of genetic and molecular tools has led to the identification and characterization of genes that are critical for normal cell division and differentiation in Arabidopsis early anther development. We review here several recent studies on these genes, including the demonstration that the putative receptor protein kinases BAM1 and BAM2 together play essential roles in the control of early cell division and differentiation. In addition, we discuss the hypothesis that BAM1/2 may form a positive-negative feedback regulatory loop with a previously identified key regulator, SPOROCYTELESS （also called NOZZLE）, to control the balance between sporogenous and somatic cell types in the anther. Furthermore, we summarize the isolation and functional analysis of the DYSFUNCTIONAL TAPETUM1 （DYT1） gene in promoting proper tapetal cell differentiation. Our finding that DYT1 encodes a putative transcription factor of the bHLH family, as well as relevant expression analyses, strongly supports a model that DYT1 serves as a critical link between upstream factors and downstream target genes that are critical for normal tapetum development and function. These studies, together with other recently published works, indicate that cell-cell communication and transcriptional control are key processes essential for cell fate specification in anther development.

关键词： anther development Arabidopsis signaling tapetum transcription factor

Molecular Evolution of VEF-Domain-Containing PcG Genes in Plants

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Molecular Plant 2009年第4期2卷 738-754页

作者： Ling-Jing Chen Zhao-Yan Diao Chelsea Specht Z. Renee Sung Department of Plant and Microbial Biology University of California Berkeley CA 94720-3102 USA

Arabidopsis VERNALIZATION2 （VRN2）, EMBRYONIC FLOWER2 （EMF2）, and FERTILIZATION-INDEPENDENT SEED2 （FIS2） are involved in vernalization-mediated flowering, vegetative development, and seed development, respectively. Together with Arabidopsis VEF-L36, they share a VEF domain that is conserved in plants and animals. To investigate the evolution of VEF-domain-containing genes （VEF genes）, we analyzed sequences related to VEF genes across land plants. To date, 24 full-length sequences from 11 angiosperm families and 54 partial sequences from another nine families were identified. The majority of the full-length sequences identified share greatest sequence similarity with and possess the same major domain structure as Arabidopsis EMF2. EMF2-1ike sequences are not only widespread among angiosperms, but are also found in genomic sequences of gymnosperms, lycophyte, and moss. No FIS2- or VEF-L36-1ike sequences were recovered from plants other than Arabidopsis, including from rice and poplar for which whole genomes have been sequenced. Phylogenetic analysis of the full-length sequences showed a high degree of amino acid sequence conservation in EMF2 homologs of closely related taxa. VRN2 homologs are recovered as a clade nested within the larger EMF2 clade. FIS2 and VEF-L36 are recovered in the VRN2 clade. VRN2 clade may have evolved from an EMF2 duplication event that occurred in the rosids prior to the divergence of the eurosid I and eurosid II lineages. We propose that dynamic changes in genome evolution contribute to the generation of the family of VEF-domain-containing genes, Phylogenetic analysis of the VEF domain alone showed that VEF sequences continue to evolve following EM F2NRN2 divergence in accordance with species relationship. Existence of EMF2-1ike sequences in animals and across land plants suggests that a prototype form of EMF2 was present prior to the divergence of the plant and animal lineages. A proposed sequence of events, based on domain organization and

关键词： VEF EMF2 FIS2 VRN2 VEF-L36 Arabidopsis PcG phylogeny evolution.

Ikaros isoforms:The saga continues

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World Journal of Biological Chemistry 2011年第6期2卷 140-145页

作者： Laura A Perez-Casellas Aleksandar Savic Sinisa Dovat Department of Pediatrics University of Wisconsin-MadisonMadisonWI 53792United States Clinic of Hematology Clinical Center of VojvodinaFaculty of MedicineUniversity in Novi SadNovi Sad 21000Serbia Department of Pediatrics Pennsylvania State UniversityCollege of MedicineH085Division of Pediatric Hematology/OncologyHersheyPA 17033-0850United States

Through alternate splicing,the Ikaros gene produces multiple *** is essential for normal hematopoiesis and possesses tumor suppressor *** isoforms interact to form dimers and potentially multimeric *** Ikaros complexes produced by the presence of different Ikaros isoforms are hypothesized to confer distinct *** dominantnegative Ikaros isoforms have been shown to inhibit the tumor suppressor activity of full-length ***,we describe how Ikaros activity is regulated by the coordinated expression of the largest Ikaros isoforms IK-1 and *** IK-1 is described as full-length Ikaros,IK-H is the longest Ikaros ***-H,which includes residues coded by exon 3B (60 bp that lie between exons 3 and 4),is abundant in human but not murine hematopoietic *** residues that lie within the 20 amino acids encoded by exon 3B give IK-H DNA-binding characteristics that are distinct from those of ***,IK-H can potentiate or inhibit the ability of IK-1 to bind ***-H binds to the regulatory regions of genes that are upregulated by Ikaros,but not genes that are repressed by *** IK-1 localizes to pericentromeric heterochromatin,IK-H can be found in both pericentromeric and non-pericentromeric ***-silencing activity of gamma satellite DNA has been shown to depend on the binding of IK-H,but not other Ikaros *** unique features of IK-H,its influence on Ikaros activity,and the lack of IK-H expression in mice suggest that Ikaros function in humans may be more complex and possibly distinct from that in mice.

关键词： Ikaros Chromatin,Pericentromeric Transcription IK-H Leukemia γ satellite

Regulation of Ikaros function by casein kinase 2 and protein phosphatase 1

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World Journal of Biological Chemistry 2011年第6期2卷 126-131页

作者： Amy K Erbe Aleksandar Savic Sinisa Dovat Department of Human Oncology University of Wisconsin-MadisonMadisonWI 53792United States Clinic of Hematology Clinical Center of VojvodinaFaculty of MedicineUniversity in Novi SadNovi Sad21000Serbia Department of Pediatrics Pennsylvania State UniversityCollege of MedicineHersheyPA 17033-0850United States

The Ikaros gene encodes a zinc finger,DNA-binding protein that regulates gene transcription and chromatin *** is a master regulator of hematopoiesis and an established tumor *** alteration of Ikaros activity (***) appears to be sufficient to promote malignant transformation in human hematopoietic *** raises questions about the mechanisms that normally regulate Ikaros function and the potential of these mechanisms to contribute to the development of *** focus of this review is the regulation of Ikaros function by phosphorylation/***-specific phosphorylation of Ikaros by casein kinase 2 (CK2) controls Ikaros DNA-binding ability and subcellular *** a consequence,the ability of Ikaros to regulate cell cycle progression,chromatin remodeling,target gene expression,and thymocyte differentiation are controlled by *** addition,hyperphosphorylation of Ikaros by CK2 leads to decreased Ikaros levels due to ubiquitinmediated *** of Ikaros by protein phosphatase 1 (PP1) acts in opposition to CK2 to increase Ikaros stability and restore Ikaros DNA binding ability and pericentromeric ***,the CK2 and PP1 pathways act in concert to regulate Ikaros activity in hematopoiesis and as a tumor *** highlights the importance of these signal transduction pathways as potential mediators of leukemogenesis via their role in regulating the activities of Ikaros.

关键词： Ikaros Leukemia Zinc finger Transcription factor Casein kinase 2 Protein phosphatase 1 Phosphorylation

Ikaros in hematopoiesis and leukemia

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World Journal of Biological Chemistry 2011年第6期2卷 105-107页

作者： Sinisa Dovat Department of Pediatrics Pennsylvania State UniversityCollege of Medicine

Ikaros is a gene whose activity is essential for normal *** acts as a master regulator of lymphoid and myeloid development as well as a tumor *** cells,Ikaros regulates gene expression via chromatin *** the past 15 years tremendous advances have been made in understanding the role of Ikaros in hematopoiesis and *** this Topic Highlights series of reviews,several groups of international experts in this field summarize the experimental data that is shaping the emerging picture of Ikaros function at the biochemical and cellular *** articles provide detailed analyses of recent scientific advancements and present models that will serve as a basis for future studies aimed at developing a better understanding of normal hematopoiesis and hematological malignancies and at accelerating the application of this knowledge in clinical practice.

关键词： Ikaros Hematopoiesis leukemia Chromatin remodeling

OPTIMAL QUADRATIC NITSCHE EXTENDED FINITE ELEMENT METHOD FOR INTERFACE PROBLEM OF DIFFUSION EQUATION

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Journal of Computational Mathematics 2018年第5期36卷 693-717页

作者： Fei Wang Shuo Zhang School of Mathematics and Statistics Xi'an Jiaotong University Xi'an 710049 China Department of Mathematics Pennsylvania State University University Park PA 16802 USA. LSEC ICMSEC NCMIS Academy of Mathematics and System Sciences Chinese Academy of Sciences Beijing 100190 China.

In this paper, we study Nitsche extended finite element method （XFEM） for the inter- face problem of a two dimensional diffusion equation. Specifically, we study the quadratic XFEM scheme on some shape-regular family of grids and prove the optimal convergence rate of the scheme with respect to the mesh size. Main efforts are devoted onto classifying the cases of intersection between the elements and the interface and prove a weighted trace inequality for the extended finite element functions needed, and the general framework of analysing XFEM c^n be implemented then.

关键词： Interface problems Extended finite element methods Error estimates Nitsche's scheme Quadratic element.

一种抽象的稳定化方法及在非线性不可压缩弹性问题上的应用

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计算数学 2020年第3期42卷 298-309页

作者：洪庆国刘春梅许进超宾夕法尼亚州立大学数学系美国宾州PA16802 湖南科技学院理学院永州425199

针对非线性不可压缩弹性力学问题.本文提出了一种抽象的稳定化方法并将其应用于非线性不可压缩弹性问题上.在该框架中,我们证明了只要连续的混合问题是稳定的,则可以修正任何满足离散inf-sup条件的混合有限元方法使其是稳定的且最优收敛... 详细信息

针对非线性不可压缩弹性力学问题.本文提出了一种抽象的稳定化方法并将其应用于非线性不可压缩弹性问题上.在该框架中,我们证明了只要连续的混合问题是稳定的,则可以修正任何满足离散inf-sup条件的混合有限元方法使其是稳定的且最优收敛的.我们将这种抽象的稳定化理论框架应用于非线性不可压缩弹性力学问题,给出了稳定性和收敛性理论结论,并通过数值实验验证了该结论.

关键词：非线性不可压缩弹性问题.混合有限元方法稳定性

面向氢能源、燃料电池和二氧化碳减排的制氢途径的选择(英文)

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燃料化学学报 2005年第6期33卷 641-649页

作者：宋春山 Clean Fuels & Catalysis Program The Energy Instituteand Fuel Science ProgramDepartment of Energy and Geo-Environmental EngineeringPennsylvania State University

对氢气的多种制造途径加以探讨,也涉及到氢能的利用、燃料电池以及二氧化碳的减排。需要指出的是氢气并非能源,而只是能量的载体。所以氢能的发展首先需要制造氢气。对于以化石燃料为基础的制氢过程,如煤的气化和天然气重整,需要开发更... 详细信息

对氢气的多种制造途径加以探讨,也涉及到氢能的利用、燃料电池以及二氧化碳的减排。需要指出的是氢气并非能源,而只是能量的载体。所以氢能的发展首先需要制造氢气。对于以化石燃料为基础的制氢过程,如煤的气化和天然气重整,需要开发更经济和环境友好的新过程,在这些新过程中要同时考虑二氧化碳的有效收集和利用问题。对于煤和生物质,在此提出了一种值得进一步深入研究的富一氧化碳气化制氢的概念。对于以氢为原料的质子交换膜燃料电池系统,必须严格控制制备的氢气中的一氧化碳和硫化氢;对于以烃类为原料的固体氧化物燃料电池,制备的合成气中的硫也需严格控制。然而,传统的脱硫方法并不适宜于这种用于燃料电池的极高深度的氢气和合成气的脱硫。氢能和燃料电池的发展是与控制二氧化碳排放紧密相关的。

关键词：制氢途径的选择氢能利用燃料电池二氧化碳排放