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1.  Fabrication and Characterization of Monodisperse Magnetic Porous Nickel Microspheres as Novel Catalysts 
A facile and efficient hard-templating strategy is reported for the preparation of porous nickel microspheres with excellent uniformity and strong magnetism. The strategy involves impregnation of porous polymer microspheres with nickel precursors, calcination to remove the template, followed by thermal reduction. The morphology, structure, and the property of the Ni microspheres were characterized by scanning electron microscopy, X-ray powder diffraction, N2 adsorption-desorption isotherms, thermogravimetric analysis, and magnetic hysteresis measurement. The obtained porous nickel microspheres were monodispersed with a particle size of 0.91 μm and crystallite size of 52 nm. Their saturation magnetization was much higher than that of Ni nanoparticles. The unique porous nanostructured Ni microspheres possess catalytic activity and excellent recyclability, as demonstrated in the catalytic reduction of 4-nitrophenol to 4-aminophenol. The micropherical Ni catalysts could be easily separated either by an external magnetic field or by simple filtration.
Electronic supplementary material
The online version of this article (doi:10.1186/s11671-015-1088-8) contains supplementary material, which is available to authorized users.
PMCID: PMC4593984  PMID: 26437654
Magnetic microspheres; Porous nickel microspheres; Separable catalysts; 61.46.Hk; 75.75.-c; 81.07.-b
2.  Re-annotation of presumed noncoding disease/trait-associated genetic variants by integrative analyses 
Scientific Reports  2015;5:9453.
Using RefSeq annotations, most disease/trait-associated genetic variants identified by genome-wide association studies (GWAS) appear to be located within intronic or intergenic regions, which makes it difficult to interpret their functions. We reassessed GWAS-Associated single-nucleotide polymorphisms (herein termed as GASs) for their potential functionalities using integrative approaches. 8834 of 9184 RefSeq “noncoding” GASs were reassessed to have potential regulatory functionalities. As examples, 3 variants (rs3130320, rs3806932 and rs6890853) were shown to have regulatory properties in HepG2, A549 and 293T cells. Except rs3130320 as a known expression quantitative trait loci (eQTL), rs3806932 and rs6890853 were not reported as eQTLs in previous reports. 1999 of 9184 “noncoding” GASs were re-annotated to the promoters or intragenic regions using Ensembl, UCSC and AceView gene annotations but they were not annotated into corresponding regions in RefSeq database. Moreover, these GAS-harboring genes were broadly expressed across different tissues and a portion of them was expressed in a tissue-specific manner, suggesting that they could be functional. Collectively, our study demonstrates the benefits of using integrative analyses to interpret genetic variants and may help to predict or explain disease susceptibility more accurately and comprehensively.
PMCID: PMC4377585  PMID: 25819875
3.  hSulf-1 inhibits cell proliferation and migration and promotes apoptosis by suppressing stat3 signaling in hepatocellular carcinoma 
Oncology Letters  2014;7(4):963-969.
Human sulfatase-1 (hSulf-1) has been shown to desulfate cellular heparin sulfate proteoglycans and modulate several growth factors and cytokines. However, hSulf-1 has not been previously shown to mediate the signal transducer and activator of transcription 3 (stat3) signaling pathway, which is known to regulate cell proliferation, motility and apoptosis. The present study investigated the role of hSulf-1 in stat3 signaling in hepatocellular cancer. hSulf-1 expression vector and stat3 small interfering RNA (siRNA) were constructed to control the expression of hSulf-1 and stat3 in HepG2 cells. hSulf-1 was found to inhibit the phosphorylation of stat3 and downregulate its targeted protein. MTT and Transwell chamber assays, as well as Annexin V/propidium iodide double-staining methods, were used to examine the effects of hSulf-1 on stat3-mediated motility, proliferation and apoptosis in HepG2 cells. Transfection with hSulf-1 cDNA and/or stat3 siRNA inhibited cell proliferation and motility, concurrent with G0/G1 and G2/M phase cell cycle arrest and apoptosis. Overall, the results of the current study suggested that hSulf-1 functions as a negative regulator of proliferation and migration and as a positive regulator of apoptosis in hepatocellular carcinoma, at least partly via the downregulation of stat3 signaling.
PMCID: PMC3961425  PMID: 24944651
human sulfatase-1; hepatocellular carcinoma; stat3 signaling
4.  TRV–GFP: a modified Tobacco rattle virus vector for efficient and visualizable analysis of gene function 
Journal of Experimental Botany  2013;65(1):311-322.
We developed an easy-traceable TRV vector, TRV2-GFP, by tagging a GFP to the coat protein. TRV2-GFP-infected plants could be identified efficiently by GFP monitoring. TRV2-GFP is useful for functional genomics in many plants, especially for non-Solanaceae plants, like rose
Virus-induced gene silencing (VIGS) is a useful tool for functional characterization of genes in plants. Unfortunately, the efficiency of infection by Tobacco rattle virus (TRV) is relatively low for some non-Solanaceae plants, which are economically important, such as rose (Rosa sp.). Here, to generate an easy traceable TRV vector, a green fluorescent protein (GFP) gene was tagged to the 3’ terminus of the coat protein gene in the original TRV2 vector, and the silencing efficiency of the modified TRV–GFP vector was tested in several plants, including Nicotiana benthamiana, Arabidopsis thaliana, rose, strawberry (Fragaria ananassa), and chrysanthemum (Dendranthema grandiflorum). The results showed that the efficiency of infection by TRV–GFP was equal to that of the original TRV vector in each tested plant. Spread of the modified TRV virus was easy to monitor by using fluorescent microscopy and a hand-held UV lamp. When TRV–GFP was used to silence the endogenous phytoene desaturase (PDS) gene in rose cuttings and seedlings, the typical photobleached phenotype was observed in 75–80% plants which were identified as GFP positive by UV lamp. In addition, the abundance of GFP protein, which represented the concentration of TRV virus, was proved to correlate negatively with the level of the PDS gene, suggesting that GFP could be used as an indicator of the degree of silencing of a target gene. Taken together, this work provides a visualizable and efficient tool to predict positive gene silencing plants, which is valuable for research into gene function in plants, especially for non-Solanaceae plants.
PMCID: PMC3883300  PMID: 24218330
Arabidopsis thaliana; gene silencing; Nicotiana benthamiana; Rosa sp.; TRV–GFP; VIGS.
5.  A DELLA gene, RhGAI1, is a direct target of EIN3 and mediates ethylene-regulated rose petal cell expansion via repressing the expression of RhCesA2  
Journal of Experimental Botany  2013;64(16):5075-5084.
Ethylene plays an important role in organ growth. In Arabidopsis, ethylene can inhibit root elongation by stabilizing DELLA proteins. In previous work, it was found that ethylene suppressed cell expansion in rose petals, and five unisequences of DELLA genes are induced by ethylene. However, the mechanism of transcriptional regulation of DELLA genes by ethylene is still not clear. The results showed that the expression of RhGAI1 was induced in both ethylene-treated and ETR gene-silenced rose petals, and the promoter activity of RhGAI1 was strongly induced by RhEIN3-3 in Arabidopsis protoplasts. What is more, RhEIN3-3 could bind to the promoter of RhGAI1 directly in an electrophoretic mobility shift assay (EMSA). Cell expansion was suppressed in RhGAI1-Δ17-overexpressed Arabidopsis petals and promoted in RhGAI1-silenced rose petals. Moreover, in RhGAI1-silenced petals, the expression of nine cell expansion-related genes was clearly changed, and RhGAI1 can bind to the promoter of RhCesA2 in an EMSA. These results suggested that RhGAI1 was regulated by ethylene at the transcriptional level, and RhGAI1 was a direct target of RhEIN3-3. Also, RhGAI1 was shown to be involved in cell expansion partially through regulating the expression of cell expansion-related genes. Furthermore, RhCesA2 was a direct target of RhGAI1. This work uncovers the transcriptional regulation of RhGAI1 by ethylene and provides a better understanding of how ethylene regulates petal expansion in roses.
PMCID: PMC3830487  PMID: 24014864
Cell expansion; ethylene; petal; RhGAI1; rose; transcriptional regulation.
6.  Dissecting the Characteristics and Dynamics of Human Protein Complexes at Transcriptome Cascade Using RNA-Seq Data 
PLoS ONE  2013;8(6):e66521.
Human protein complexes play crucial roles in various biological processes as the functional module. However, the expression features of human protein complexes at the transcriptome cascade are poorly understood. Here, we used the RNA-Seq data from 16 disparate tissues and four types of human cancers to explore the characteristics and dynamics of human protein complexes. We observed that many individual components of human protein complexes can be generated by multiple distinct transcripts. Similar with yeast, the human protein complex constituents are inclined to co-express in diverse tissues. The dominant isoform of the genes involved in protein complexes tend to encode the complex constituents in each tissue. Our results indicate that the protein complex dynamics not only correlate with the presence or absence of complexes, but may also be related to the major isoform switching for complex subunits. Between any two cancers of breast, colon, lung and prostate, we found that only a few of the differentially expressed transcripts associated with complexes were identical, but 5–10 times more protein complexes involved in differentially expressed transcripts were common. Collectively, our study reveals novel properties and dynamics of human protein complexes at the transcriptome cascade in diverse normal tissues and different cancers.
PMCID: PMC3688907  PMID: 23824284
7.  Integrative Analysis of miRNA and mRNA Profiles in Response to Ethylene in Rose Petals during Flower Opening 
PLoS ONE  2013;8(5):e64290.
MicroRNAs play an important role in plant development and plant responses to various biotic and abiotic stimuli. As one of the most important ornamental crops, rose (Rosa hybrida) possesses several specific morphological and physiological features, including recurrent flowering, highly divergent flower shapes, colors and volatiles. Ethylene plays an important role in regulating petal cell expansion during rose flower opening. Here, we report the population and expression profiles of miRNAs in rose petals during flower opening and in response to ethylene based on high throughput sequencing. We identified a total of 33 conserved miRNAs, as well as 47 putative novel miRNAs were identified from rose petals. The conserved and novel targets to those miRNAs were predicted using the rose floral transcriptome database. Expression profiling revealed that expression of 28 known (84.8% of known miRNAs) and 39 novel (83.0% of novel miRNAs) miRNAs was substantially changed in rose petals during the earlier opening period. We also found that 28 known and 22 novel miRNAs showed expression changes in response to ethylene treatment. Furthermore, we performed integrative analysis of expression profiles of miRNAs and their targets. We found that ethylene-caused expression changes of five miRNAs (miR156, miR164, miR166, miR5139 and rhy-miRC1) were inversely correlated to those of their seven target genes. These results indicate that these miRNA/target modules might be regulated by ethylene and were involved in ethylene-regulated petal growth.
PMCID: PMC3655976  PMID: 23696879
8.  The X Protein of Hepatitis B Virus Inhibits Apoptosis in Hepatoma Cells through Enhancing the Methionine Adenosyltransferase 2A Gene Expression and Reducing S-Adenosylmethionine Production* 
The Journal of Biological Chemistry  2011;286(19):17168-17180.
The X protein (HBx) of hepatitis B virus (HBV) is involved in the development of hepatocellular carcinoma (HCC), and methionine adenosyltransferase 2A (MAT2A) promotes the growth of liver cancer cells through altering S-adenosylmethionine homeostasis. Thus, we speculated that a link between HBx and MAT2A may contribute to HCC development. In this study, the effects of HBx on MAT2A expression and cell apoptosis were investigated, and the molecular mechanism by which HBx and MAT2A regulate tumorigenesis was evaluated. Results from immunohistochemistry analyses of 37 pairs of HBV-associated liver cancer tissues/corresponding peritumor tissues showed that HBx and MAT2A are highly expressed in most liver tumor tissues. Our in vitro results revealed that HBx activates MAT2A expression in a dose-dependent manner in hepatoma cells, and such regulation requires the cis-regulatory elements NF-κB and CREB on the MAT2A gene promoter. Electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) further demonstrated that HBx facilitates the binding of NF-κB and CREB to MAT2A gene promoter. In addition, overexpression of HBx or MAT2A inhibits cell apoptosis, whereas knockdown of MAT2A expression stimulates apoptosis in hepatoma cells. Furthermore, we demonstrated that HBx reduces MAT1A expression and AdoMet production but enhances MAT2β expression. Thus, we proposed that HBx activates MAT2A expression through NF-κB and CREB signaling pathways to reduce AdoMet production, inhibit hepatoma cell apoptosis, and perhaps enhance HCC development. These findings should provide new insights into our understanding how the molecular mechanisms underline the effects of HBV infection on the production of MAT2A and the development of HCC.
PMCID: PMC3089560  PMID: 21247894
Apoptosis; Cancer Tumor Promoter; Chromatin Immunoprecipitation (ChiP); CREB; DNA-Protein Interaction; DNA Viruses; Gene Regulation; Hepatitis Virus; Oncogene; S-Adenosylmethionine (AdoMet)

Results 1-8 (8)