Browsing by Author "Zhu, Hong"

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    Apple miRNAs and tasiRNAs with novel regulatory networks
    Xia, Rui; Zhu, Hong; An, Yong-qiang; Beers, Eric P.; Liu, Zongrang (2012-06-15)
    Background MicroRNAs (miRNAs) and their regulatory functions have been extensively characterized in model species but whether apple has evolved similar or unique regulatory features remains unknown. Results We performed deep small RNA-seq and identified 23 conserved, 10 less-conserved and 42 apple-specific miRNAs or families with distinct expression patterns. The identified miRNAs target 118 genes representing a wide range of enzymatic and regulatory activities. Apple also conserves two TAS gene families with similar but unique trans-acting small interfering RNA (tasiRNA) biogenesis profiles and target specificities. Importantly, we found that miR159, miR828 and miR858 can collectively target up to 81 MYB genes potentially involved in diverse aspects of plant growth and development. These miRNA target sites are differentially conserved among MYBs, which is largely influenced by the location and conservation of the encoded amino acid residues in MYB factors. Finally, we found that 10 of the 19 miR828-targeted MYBs undergo small interfering RNA (siRNA) biogenesis at the 3' cleaved, highly divergent transcript regions, generating over 100 sequence-distinct siRNAs that potentially target over 70 diverse genes as confirmed by degradome analysis. Conclusions Our work identified and characterized apple miRNAs, their expression patterns, targets and regulatory functions. We also discovered that three miRNAs and the ensuing siRNAs exploit both conserved and divergent sequence features of MYB genes to initiate distinct regulatory networks targeting a multitude of genes inside and outside the MYB family.
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    Cohesion and coherence in Chinese ESL writing
    Zhu, Hong (Virginia Tech, 1992)
    Cohesion and coherence are important features for effective writing. Studies in contrastive rhetoric and text linguistics suggest that cohesion and coherence may vary across languages and cultures. This study examined cohesion and coherence features of Chinese ESL writings, explored the similarities and the differences between Chinese and English, and investigated the role of language transfer and interference in Chinese ESL writings. Four Chinese graduate students each composed two expository essays in English and two in Chinese and their writing sessions were videotaped. Essays were scrutinized for cohesion and coherence features, and along with transcripts, interviews and observations, they were examined for evidence of transfers and interferences. Findings indicate that the Chinese language depends more on lexical ties and similarities of structures whereas English employs more connectors. References in Chinese often take the form of lexical repetition and sometimes zero anaphora while English uses more pronouns and deictics. In addition, more ellipses are utilized in Chinese. Coherence features show that Chinese essays are more implicit and general while English writings emphasize explicitness with thesis statements and topic sentences. Chinese writings are writer-centered, and demand more of the reader to make sense of the text. Interferences and transfers were identified. Students were unable to use a variety of connectors that English offers in their own writings and often connections were missing and sometimes misleading. They occasionally failed to mark sentence boundaries; their essays often lacked a clearly defined thesis; and topic sentences were rarely used. The discussion was general, implicit, and writer-centered.
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    In Situ Real-Time Chemiluminescence Imaging of Reactive Oxygen Species Formation from Cardiomyocytes
    Li, Yunbo; Shen, Haiou; Zhu, Hong; Trush, Michael A.; Jiang, Ming; Wang, Ge (Hindawi, 2009-02-25)
    We have applied the highly sensitive chemiluminescence (CL) imagingtechnique to investigate the in situ ROS formation in cultured monolayers of rat H9c2 cardiomyocytes. Photon emission was detected via an innovative imaging system after incubation of H9c2 cells in culture with luminol and horseradish peroxidase (HRP), suggesting constitutive formation of ROS by the cardiomyocytes. Addition of benzo(a)pyrene-1,6-quinone(BPQ) to cultured H9c2 cells resulted in a 4-5-fold increase in the formation of ROS, as detected by the CL imaging. Both constitutive and BPQ-stimulated CL responses in cultured H9c2 cells were sustained for up to 1 hour. The CL responses were completely abolished in the presence of superoxide dismutase and catalase, suggesting the primary involvement of superoxide and hydrogen peroxide (). In contrast to BPQ-mediated redox cycling, blockage of mitochondrial electron transport chain by either antimycin A or rotenone exerted marginal effects on the ROS formation by cultured H9c2 cells. Upregulation of cellular antioxidants fordetoxifying both superoxide and by 3-1,2-dithiole-3-thione resulted in marked inhibition of both constitutive and BPQ-augmented ROS formation in cultured H9c2 cells. Taken together, we demonstrate the sensitive detection of ROS by CL imaging in cultured cardiomyocytes.
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    Investigation of Regulatory Mechanisms of Chemical-Mediated Fruit Thinning in Apple (Malus X Domestica Borkh.)
    Zhu, Hong (Virginia Tech, 2010-12-06)
    Fruit thinning is critical to the success of apple industry because most apple trees are prone to biennial bearing characterized by heavy bloom and over-cropping in the "on" year and low or no cropping in the "off" year. Fruit thinning can improve fruit size, increase return bloom, and reduce alternate bearing habit of apple trees. Chemical thinning has been widely used as a horticultural practice by growers for years in apple and other fruit production. However, its thinning results are often variable and very difficult to predict since parameters as well as their interactions (e.g. concentration, environmental condition, cultivar response) that affect thinning effectiveness have been poorly defined and the regulatory mechanisms at molecular level remain to be illustrated. Therefore, the purpose of this study is to characterize the physiological and molecular responses of the apple trees to the thinning treatments, and then use key genes as molecular markers for screening potential thinning agents. The long-term goal is to understand how the applied chemicals and environmental factors interact and regulate key regulatory genes as well as the thinning effectiveness during thinning process, and establish a predictable model for the improvement of fruit thinning consistency and effectiveness in apple and other fruit trees. Effects of naphthaleneacetic acid (NAA), shading, amimoethoxyvinylglycine (AVG) and 1-methylcyclopropene (1-MCP) on young apple fruit abscission, leaf and fruit ethylene production, and the expression of genes related to ethylene biosynthesis, perception and cell wall degradation were examined in "Golden Delicious" apples (Malus x domestica borkh.). NAA at 15 mg·L-1 and shading increased fruit abscission and ethylene production of leaves and fruit when applied at a 12-mm stage of fruit development, whereas AVG, an inhibitor of ethylene biosynthesis, at 250 mg·L-1 reduced NAA-induced fruit abscission and ethylene production of leaves and fruit. 1-MCP at 160 mg·L-1 had no effect on fruit abscission but induced ethylene production by both leaves and fruit. Changes in the gene expression pattern responding to each treatment were analyzed by real-time quantitative PCR. NAA treatment was found to enhance the expression of genes related to ethylene biosynthesis (MdACS5A, MdACS5B and MdACO1) and perception (MdETR1, MdETR1b, MdETR2, MdERS1 and MdERS2). AVG reduced NAA-induced expression of these genes except for MdERS2 in the fruit abscission zone (FAZ). NAA increased the expression of a polygalacturonase gene (MdPG2) in the FAZ but not in the fruit cortex (FC), whereas AVG reduced NAA-enhanced expression of MdPG2 in the FAZ. These results suggest that ethylene biosynthesis, ethylene perception, and MdPG2 gene are involved in young fruit abscission caused by NAA. On the other hand, 1-MCP did not affect the expression of MdACS5A and MdACS5B in the FAZ, although it enhanced the expression of these two genes in the FC from 6 to 24 hours post-treatment. The expression of MdACO1 in both tissues was increased by 1-MCP after 3 or more days post-treatment. 1-MCP had only a small influence on the expression of most ethylene receptor genes, with the exception of MdETR1, which was up-regulated in the FC to a level similar to that observed for NAA treatment. In response to 1-MCP, in the FAZ, the expression of MdCel1 and MdPG2 was up-regulated at the beginning and the end, respectively, of the experiment, but otherwise remained at or below control levels. 1-MCP did not inhibit NAA-induced abscission of young apple fruit, suggesting that abscission does not solely depend on ethylene signal transduction, or that the periods of effectiveness for 1-MCP and ethylene were asynchronous in this study. Gene expression analysis also revealed that both NAA and shading enhanced the expression of gene related to ABA biosynthesis in the FAZ, which suggested the involvement of ABA in young fruit abscission. Global gene expression profile during young fruit abscission was analyzed using an apple oligonucleotide microarray. More than 700 genes were identified with reproducible changes in transcript abundance in the FAZ after NAA treatment. Genes associated with abscission, ethylene, ABA, cell wall degradation, mitochondrial activity, glycolysis, lipid catabolism, secondary metabolism, abiotic stress, and apoptosis were upregulated, while genes involved in regulation of cell cycle, cell wall biosynthesis, photosynthesis, carbon fixation, chromatin assembly, auxin transport/efflux, cytoskeleton function, and flower development were generally downregulated. Comparison of changes in the gene expression patterns during NAA-induced fruit abscission with shading-induced fruit abscission revealed similarities, but also considerable differences. The data suggested that young fruit were shutting down growth and energy production and undergoing a certain kind of programmed cell death (PCD) induced by these different stimuli. Gene expression analysis in abscising young fruit revealed that photosynthesis, carbon utilization, and ABA/ethylene pathways appeared to operate in both NAA- and shading-induced fruit abscission. However, more sugar signaling genes were regulated in shading-induced fruit abscission, compared to NAA-induced fruit abscission.
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    Transcriptomics of shading-induced and NAA-induced abscission in apple (Malus domestica) reveals a shared pathway involving reduced photosynthesis, alterations in carbohydrate transport and signaling and hormone crosstalk
    Zhu, Hong; Dardick, Chris D.; Beers, Eric P.; Callahan, Ann M.; Xia, Rui; Yuan, Rongcai (2011-10-17)
    Background Naphthaleneacetic acid (NAA), a synthetic auxin analogue, is widely used as an effective thinner in apple orchards. When applied shortly after fruit set, some fruit abscise leading to improved fruit size and quality. However, the thinning results of NAA are inconsistent and difficult to predict, sometimes leading to excess fruit drop or insufficient thinning which are costly to growers. This unpredictability reflects our incomplete understanding of the mode of action of NAA in promoting fruit abscission. Results Here we compared NAA-induced fruit drop with that caused by shading via gene expression profiling performed on the fruit abscission zone (FAZ), sampled 1, 3, and 5 d after treatment. More than 700 genes with significant changes in transcript abundance were identified from NAA-treated FAZ. Combining results from both treatments, we found that genes associated with photosynthesis, cell cycle and membrane/cellular trafficking were downregulated. On the other hand, there was up-regulation of genes related to ABA, ethylene biosynthesis and signaling, cell wall degradation and programmed cell death. While the differentially expressed gene sets for NAA and shading treatments shared only 25% identity, NAA and shading showed substantial similarity with respect to the classes of genes identified. Specifically, photosynthesis, carbon utilization, ABA and ethylene pathways were affected in both NAA- and shading-induced young fruit abscission. Moreover, we found that NAA, similar to shading, directly interfered with leaf photosynthesis by repressing photosystem II (PSII) efficiency within 10 minutes of treatment, suggesting that NAA and shading induced some of the same early responses due to reduced photosynthesis, which concurred with changes in hormone signaling pathways and triggered fruit abscission. Conclusions This study provides an extensive transcriptome study and a good platform for further investigation of possible regulatory genes involved in the induction of young fruit abscission in apple, which will enable us to better understand the mechanism of fruit thinning and facilitate the selection of potential chemicals for the thinning programs in apple.
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    Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs
    Zhu, Hong; Xia, Rui; Zhao, Bingyu Y.; An, Yong-qiang; Dardick, Chris D.; Callahan, Ann M.; Liu, Zongrang (2012-08-21)
    Background MicroRNAs (miRNAs) have recently emerged as important gene regulators in plants. MiRNAs and their targets have been extensively studied in Arabidopsis and rice. However, relatively little is known about the characterization of miRNAs and their target genes in peach (Prunus persica), which is a complex crop with unique developmental programs. Results We performed small RNA deep sequencing and identified 47 peach-specific and 47 known miRNAs or families with distinct expression patterns. Together, the identified miRNAs targeted 80 genes, many of which have not been reported previously. Like the model plant systems, peach has two of the three conserved trans-acting siRNA biogenesis pathways with similar mechanistic features and target specificity. Unique to peach, three of the miRNAs collectively target 49 MYBs, 19 of which are known to regulate phenylpropanoid metabolism, a key pathway associated with stone hardening and fruit color development, highlighting a critical role of miRNAs in the regulation of peach fruit development and ripening. We also found that the majority of the miRNAs were differentially regulated in different tissues, in part due to differential processing of miRNA precursors. Up to 16% of the peach-specific miRNAs were differentially processed from their precursors in a tissue specific fashion, which has been rarely observed in plant cells. The miRNA precursor processing activity appeared not to be coupled with its transcriptional activity but rather acted independently in peach. Conclusions Collectively, the data characterizes the unique expression pattern and processing regulation of peach miRNAs and demonstrates the presence of a complex, multi-level miRNA regulatory network capable of targeting a wide variety of biological functions, including phenylpropanoid pathways which play a multifaceted spatial-temporal role in peach fruit development.