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Search Results: 1 - 10 of 104182 matches for " Yuanji Zhang "
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The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants
Yuanji Zhang, Liangjiang Wang
BMC Evolutionary Biology , 2005, DOI: 10.1186/1471-2148-5-1
Abstract: We searched all publicly available sequence data for WRKY genes. A single copy of the WRKY gene encoding two WRKY domains was identified from Giardia lamblia, a primitive eukaryote, Dictyostelium discoideum, a slime mold closely related to the lineage of animals and fungi, and the green alga Chlamydomonas reinhardtii, an early branching of plants. This ancestral WRKY gene seems to have duplicated many times during the evolution of plants, resulting in a large family in evolutionarily advanced flowering plants. In rice, the WRKY gene family consists of over 100 members. Analyses suggest that the C-terminal domain of the two-WRKY-domain encoding gene appears to be the ancestor of the single-WRKY-domain encoding genes, and that the WRKY domains may be phylogenetically classified into five groups. We propose a model to explain the WRKY family's origin in eukaryotes and expansion in plants.WRKY genes seem to have originated in early eukaryotes and greatly expanded in plants. The elucidation of the evolution and duplicative expansion of the WRKY genes should provide valuable information on their functions.Transcriptional control is a major mechanism whereby a cell or organism regulates its gene expression. Sequence-specific DNA-binding transcription regulators, one class of transcription factors [1], play an essential role in modulating the rate of transcription of specific target genes. In this way, they direct the temporal and spatial expressions necessary for normal development and proper response to physiological or environmental stimuli. Comparative genome analysis reveals that genes for transcription regulators are abundantly present in plant and animal genomes, and the evolution and diversity of eukaryotes seem to be related to the expansion of lineage-specific transcription regulator families [2].WRKY proteins are recently identified transcriptional regulators comprising a large gene family [3]. The first cDNA encoding a WRKY protein, SPF1, was cloned from sweet p
Analysis of plant-derived miRNAs in animal small RNA datasets
Zhang Yuanji,Wiggins B,Lawrence Christina,Petrick Jay
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-381
Abstract: Background Plants contain significant quantities of small RNAs (sRNAs) derived from various sRNA biogenesis pathways. Many of these sRNAs play regulatory roles in plants. Previous analysis revealed that numerous sRNAs in corn, rice and soybean seeds have high sequence similarity to animal genes. However, exogenous RNA is considered to be unstable within the gastrointestinal tract of many animals, thus limiting potential for any adverse effects from consumption of dietary RNA. A recent paper reported that putative plant miRNAs were detected in animal plasma and serum, presumably acquired through ingestion, and may have a functional impact in the consuming organisms. Results To address the question of how common this phenomenon could be, we searched for plant miRNAs sequences in public sRNA datasets from various tissues of mammals, chicken and insects. Our analyses revealed that plant miRNAs were present in the animal sRNA datasets, and significantly miR168 was extremely over-represented. Furthermore, all or nearly all (>96%) miR168 sequences were monocot derived for most datasets, including datasets for two insects reared on dicot plants in their respective experiments. To investigate if plant-derived miRNAs, including miR168, could accumulate and move systemically in insects, we conducted insect feeding studies for three insects including corn rootworm, which has been shown to be responsive to plant-produced long double-stranded RNAs. Conclusions Our analyses suggest that the observed plant miRNAs in animal sRNA datasets can originate in the process of sequencing, and that accumulation of plant miRNAs via dietary exposure is not universal in animals.
Bifurcation of positive solutions for a semilinear equation with critical Sobolev exponent
Yuanji Cheng
Electronic Journal of Differential Equations , 2006,
Abstract: In this note we consider bifurcation of positive solutions to the semilinear elliptic boundary-value problem with critical Sobolev exponent $$displaylines{ -Delta u = lambda u - alpha u^p+ u^{2^*-1}, quad u >0 , quad hbox{in } Omega,cr u=0, quad hbox{on } partialOmega. }$$ where $Omega subset mathbb{R}^n$, $nge 3 $ is a bounded $C^2$-domain $lambda>lambda_1$, $1 0$ is a bifurcation parameter. Brezis and Nirenberg [2] showed that a lower order (non-negative) perturbation can contribute to regain the compactness and whence yields existence of solutions. We study the equation with an indefinite perturbation and prove a bifurcation result of two solutions for this equation.
Establishing an In Vivo Assay System to Identify Components Involved in Environmental RNA Interference in the Western Corn Rootworm
Keita Miyata, Parthasarathy Ramaseshadri, Yuanji Zhang, Gerrit Segers, Renata Bolognesi, Yoshinori Tomoyasu
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0101661
Abstract: The discovery of environmental RNA interference (RNAi), in which gene expression is suppressed via feeding with double-stranded RNA (dsRNA) molecules, opened the door to the practical application of RNAi-based techniques in crop pest management. The western corn rootworm (WCR, Diabrotica virgifera virgifera) is one of the most devastating corn pests in North America. Interestingly, WCR displays a robust environmental RNAi response, raising the possibility of applying an RNAi-based pest management strategy to this pest. Understanding the molecular mechanisms involved in the WCR environmental RNAi process will allow for determining the rate limiting steps involved with dsRNA toxicity and potential dsRNA resistance mechanisms in WCR. In this study, we have established a two-step in vivo assay system, which allows us to evaluate the involvement of genes in environmental RNAi in WCR. We show that laccase 2 and ebony, critical cuticle pigmentation/tanning genes, can be used as marker genes in our assay system, with ebony being a more stable marker to monitor RNAi activity. In addition, we optimized the dsRNA dose and length for the assay, and confirmed that this assay system is sensitive to detect well-known RNAi components such as Dicer-2 and Argonaute-2. We also evaluated two WCR sid1- like (sil) genes with this assay system. This system will be useful to quickly survey candidate systemic RNAi genes in WCR, and also will be adaptable for a genome-wide RNAi screening to give us an unbiased view of the environmental/systemic RNAi pathway in WCR.
Proteomic Analyses Reveal Common Promiscuous Patterns of Cell Surface Proteins on Human Embryonic Stem Cells and Sperms
Bin Gu,Jiarong Zhang,Ying Wu,Xinzong Zhang,Zhou Tan,Yuanji Lin,Xiao Huang,Liangbiao Chen,Kangshou Yao,Ming Zhang
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0019386
Abstract: It has long been proposed that early embryos and reproductive organs exhibit similar gene expression profiles. However, whether this similarity is propagated to the protein level remains largely unknown. We have previously characterised the promiscuous expression pattern of cell surface proteins on mouse embryonic stem (mES) cells. As cell surface proteins also play critical functions in human embryonic stem (hES) cells and germ cells, it is important to reveal whether a promiscuous pattern of cell surface proteins also exists for these cells.
Characterization of Unique Small RNA Populations from Rice Grain
Sara E. Heisel, Yuanji Zhang, Edwards Allen, Liang Guo, Tracey L. Reynolds, Xiao Yang, David Kovalic, James K. Roberts
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002871
Abstract: Small RNAs (~20 to 24 nucleotides) function as naturally occurring molecules critical in developmental pathways in plants and animals [1], [2]. Here we analyze small RNA populations from mature rice grain and seedlings by pyrosequencing. Using a clustering algorithm to locate regions producing small RNAs, we classified hotspots of small RNA generation within the genome. Hotspots here are defined as 1 kb regions within which small RNAs are significantly overproduced relative to the rest of the genome. Hotspots were identified to facilitate characterization of different categories of small RNA regulatory elements. Included in the hotspots, we found known members of 23 miRNA families representing 92 genes, one trans acting siRNA (ta-siRNA) gene, novel siRNA-generating coding genes and phased siRNA generating genes. Interestingly, over 20% of the small RNA population in grain came from a single foldback structure, which generated eight phased 21-nt siRNAs. This is reminiscent of a newly arising miRNA derived from duplication of progenitor genes [3], [4]. Our results provide data identifying distinct populations of small RNAs, including phased small RNAs, in mature grain to facilitate characterization of small regulatory RNA expression in monocot species.
Regulation of Gene Expression in Plants through miRNA Inactivation
Sergey Ivashuta, Isaac R. Banks, B. Elizabeth Wiggins, Yuanji Zhang, Todd E. Ziegler, James K. Roberts, Gregory R. Heck
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0021330
Abstract: Eukaryotic organisms possess a complex RNA-directed gene expression regulatory network allowing the production of unique gene expression patterns. A recent addition to the repertoire of RNA-based gene regulation is miRNA target decoys, endogenous RNA that can negatively regulate miRNA activity. miRNA decoys have been shown to be a valuable tool for understanding the function of several miRNA families in plants and invertebrates. Engineering and precise manipulation of an endogenous RNA regulatory network through modification of miRNA activity also affords a significant opportunity to achieve a desired outcome of enhanced plant development or response to environmental stresses. Here we report that expression of miRNA decoys as single or heteromeric non-cleavable microRNA (miRNA) sites embedded in either non-protein-coding or within the 3′ untranslated region of protein-coding transcripts can regulate the expression of one or more miRNA targets. By altering the sequence of the miRNA decoy sites, we were able to attenuate miRNA inactivation, which allowed for fine regulation of native miRNA targets and the production of a desirable range of plant phenotypes. Thus, our results demonstrate miRNA decoys are a flexible and robust tool, not only for studying miRNA function, but also for targeted engineering of gene expression in plants. Computational analysis of the Arabidopsis transcriptome revealed a number of potential miRNA decoys, suggesting that endogenous decoys may have an important role in natural modulation of expression in plants.
Celastrol targets mitochondrial respiratory chain complex I to induce reactive oxygen species-dependent cytotoxicity in tumor cells
Guozhu Chen, Xuhui Zhang, Ming Zhao, Yan Wang, Xiang Cheng, Di Wang, Yuanji Xu, Zhiyan Du, Xiaodan Yu
BMC Cancer , 2011, DOI: 10.1186/1471-2407-11-170
Abstract: The downregulation of heat shock protein 90 (HSP90) client proteins, phosphorylation of c-Jun NH2-terminal kinase (JNK), and cleavage of PARP, caspase 9 and caspase 3 were detected by western blotting. The accumulation of reactive oxygen species (ROS) was analyzed by flow cytometry and fluorescence microscopy. Cell cycle progression, mitochondrial membrane potential (MMP) and apoptosis were determined by flow cytometry. Absorption spectroscopy was used to determine the activity of mitochondrial respiratory chain (MRC) complexes.Celastrol induced ROS accumulation, G2-M phase blockage, apoptosis and necrosis in H1299 and HepG2 cells in a dose-dependent manner. N-acetylcysteine (NAC), an antioxidative agent, inhibited celastrol-induced ROS accumulation and cytotoxicity. JNK phosphorylation induced by celastrol was suppressed by NAC and JNK inhibitor SP600125 (SP). Moreover, SP significantly inhibited celastrol-induced loss of MMP, cleavage of PARP, caspase 9 and caspase 3, mitochondrial translocation of Bad, cytoplasmic release of cytochrome c, and cell death. However, SP did not inhibit celastrol-induced ROS accumulation. Celastrol downregulated HSP90 client proteins but did not disrupt the interaction between HSP90 and cdc37. NAC completely inhibited celastrol-induced decrease of HSP90 client proteins, catalase and thioredoxin. The activity of MRC complex I was completely inhibited in H1299 cells treated with 6 μM celastrol in the absence and presence of NAC. Moreover, the inhibition of MRC complex I activity preceded ROS accumulation in H1299 cells after celastrol treatment.We identified ROS as the key intermediate for celastrol-induced cytotoxicity. JNK was activated by celastrol-induced ROS accumulation and then initiated mitochondrial-mediated apoptosis. Celastrol induced the downregulation of HSP90 client proteins through ROS accumulation and facilitated ROS accumulation by inhibiting MRC complex I activity. These results identify a novel target for celastrol-in
Enhancement of Antitumor Immunity Using a DNA-Based Replicon Vaccine Derived from Semliki Forest Virus
Liang Zhang, Yue Wang, Yi Xiao, Yu Wang, JinKai Dong, Kun Gao, Yan Gao, Xi Wang, Wei Zhang, YuanJi Xu, JinQi Yan, JiYun Yu
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0090551
Abstract: A DNA-based replicon vaccine derived from Semliki Forest virus, PSVK-shFcG-GM/B7.1 (Fig. 1a) was designed for tumor immunotherapy as previously constructed. The expression of the fusion tumor antigen (survivin and hCGβ-CTP37) and adjuvant molecular protein (Granulocyte-Macrophage Colony-Stimulating Factor/ GM-CSF/B7.1) genes was confirmed by Immunofluorescence assay in vitro, and immunohistochemistry assay in vivo. In this paper, the immunological effect of this vaccine was determined using immunological assays as well as animal models. The results showed that this DNA vaccine induced both humoral and cellular immune responses in C57BL/6 mice after immunization, as evaluated by the ratio of CD4+/CD8+ cells and the release of IFN-γ. Furthermore, the vaccination of C57BL/6 mice with PSVK-shFcG-GM/B7.1 significantly delayed the in vivo growth of tumors in animal models (survivin+ and hCGβ+ murine melanoma, B16) when compared to vaccination with the empty vector or the other control constructs (Fig. 1b). These data indicate that this type of replicative DNA vaccine could be developed as a promising approach for tumor immunotherapy. Meanwhile, these results provide a basis for further study in vaccine pharmacodynamics and pharmacology, and lay a solid foundation for clinical application.
Logistic approximations and their consequences to bifurcations patterns and long-run dynamics
Torsten Lindstr?m,Yuanji Cheng
Mathematics , 2014,
Abstract: On infinitesimally short time interval various processes contributing to population change tend to operate independently so that we can simply add their contributions (Metz and Diekmann (1986)). This is one of the cornerstones for differential equations modeling in general. Complicated models for processes interacting in a complex manner may be built up, and not only in population dynamics. The principle holds as long as the various contributions are taken into account exactly. In this paper we discuss commonly used approximations that may lead to dependency terms affecting the long run qualitative behavior of the involved equations. We prove that these terms do not produce such effects in the simplest and most interesting biological case, but the general case is left open.
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