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1.  CD147 modulates autophagy through the PI3K/Akt/mTOR pathway in human prostate cancer PC-3 cells 
Oncology Letters  2015;9(3):1439-1443.
The multifunctional glycoprotein cluster of differentiation (CD)147 is highly expressed on the cell surface of the majority of cancer cells, and promotes tumor invasion, metastasis and growth. However, the role of CD147 in autophagy has not yet been explored in prostrate cancer cells. In the present study, prostate cancer PC-3 cells were cultured under starvation conditions, and the expression level of CD147 gradually increased. Therefore, RNA interference was used to inhibit CD147 expression, in order to investigate the biological role of this glycoprotein in autophagy progression. Autophagic activity was monitored by the changes in green fluorescent protein-light chain 3 (GFP-LC3) location and the expression of the autophagy-associated protein LC3-II. It was found that downregulation of CD147 significantly promoted GFP-LC3 puncta formation and the expression of LC3-II. Furthermore, the levels of phosphorylated serine/threonine protein kinase B (p-Akt) and phosphorylated mammalian target of rapamycin (p-mTOR) were significantly decreased, and the level of LC3-II was inversely associated with levels of p-Akt and p-mTOR in cells with downregulated expression of CD147. The results of a trypan blue exclusion assay revealed that starvation-induced cell death was increased in PC-3/shCD147 cells compared with control PC-3/Scramble cells (37.7±6.4 vs. 21.7±5.5%). Together, these results indicate that CD147 may be important in the inhibition of autophagy via the PI3K/Akt/mTOR pathway, which prevents cell death from unrestrained autophagy.
doi:10.3892/ol.2015.2849
PMCID: PMC4315002  PMID: 25663928
cluster of differentiation 147; autophagy; prostate cancer; PI3K/Akt/mTOR pathway
2.  HIV-1 immunopathogenesis in humanized mouse models 
Science China. Life sciences  2010;53(2):195-203.
In recent years, the technology of constructing chimeric mice with humanized immune systems has markedly improved. Multiple lineages of human immune cells develop in immunodeficient mice that have been transplanted with human hematopoietic stem cells. More importantly, these mice mount functional humoral and cellular immune responses upon immunization and microbial infection. Human immunodeficiency virus type I (HIV-1) can establish an infection in humanized mice, resulting in CD4+ T-cell depletion and an accompanying nonspecific immune activation, which mimics the immunopathology in HIV-1-infected human patients. This makes humanized mice an optimal model for studying the mechanisms of HIV-1 immunopathogenesis and for developing novel immune-based therapies.
doi:10.1007/s11427-010-0059-7
PMCID: PMC4224686  PMID: 20596827
3.  Activation of p53 Transcriptional Activity by SMRT: a Histone Deacetylase 3-Independent Function of a Transcriptional Corepressor 
Molecular and Cellular Biology  2014;34(7):1246-1261.
The silencing mediator of retinoic acid and thyroid hormone receptors (SMRT) is an established histone deacetylase 3 (HDAC3)-dependent transcriptional corepressor. Microarray analyses of MCF-7 cells transfected with control or SMRT small interfering RNA revealed SMRT regulation of genes involved in DNA damage responses, and the levels of the DNA damage marker γH2AX as well as poly(ADP-ribose) polymerase cleavage were elevated in SMRT-depleted cells treated with doxorubicin. A number of these genes are established p53 targets. SMRT knockdown decreased the activity of two p53-dependent reporter genes as well as the expression of p53 target genes, such as CDKN1A (which encodes p21). SMRT bound directly to p53 and was recruited to p53 binding sites within the p21 promoter. Depletion of GPS2 and TBL1, components of the SMRT corepressor complex, but not histone deacetylase 3 (HDAC3) decreased p21-luciferase activity. p53 bound to the SMRT deacetylase activation domain (DAD), which mediates HDAC3 binding and activation, and HDAC3 could attenuate p53 binding to the DAD region of SMRT. Moreover, an HDAC3 binding-deficient SMRT DAD mutant coactivated p53 transcriptional activity. Collectively, these data highlight a biological role for SMRT in mediating DNA damage responses and suggest a model where p53 binding to the DAD limits HDAC3 interaction with this coregulator, thereby facilitating SMRT coactivation of p53-dependent gene expression.
doi:10.1128/MCB.01216-13
PMCID: PMC3993559  PMID: 24449765
4.  Dielectrophoresis for Bioparticle Manipulation 
As an ideal method to manipulate biological particles, the dielectrophoresis (DEP) technique has been widely used in clinical diagnosis, disease treatment, drug development, immunoassays, cell sorting, etc. This review summarizes the research in the field of bioparticle manipulation based on DEP techniques. Firstly, the basic principle of DEP and its classical theories are introduced in brief; Secondly, a detailed introduction on the DEP technique used for bioparticle manipulation is presented, in which the applications are classified into five fields: capturing bioparticles to specific regions, focusing bioparticles in the sample, characterizing biomolecular interaction and detecting microorganism, pairing cells for electrofusion and separating different kinds of bioparticles; Thirdly, the effect of DEP on bioparticle viability is analyzed; Finally, the DEP techniques are summarized and future trends in bioparticle manipulation are suggested.
doi:10.3390/ijms151018281
PMCID: PMC4227216  PMID: 25310652
dielectrophoresis; lab-on-a-chip; bioparticle; trapping; detection; focusing; pairing; separation
5.  MACE: model based analysis of ChIP-exo 
Nucleic Acids Research  2014;42(20):e156.
Understanding the role of a given transcription factor (TF) in regulating gene expression requires precise mapping of its binding sites in the genome. Chromatin immunoprecipitation-exo, an emerging technique using λ exonuclease to digest TF unbound DNA after ChIP, is designed to reveal transcription factor binding site (TFBS) boundaries with near-single nucleotide resolution. Although ChIP-exo promises deeper insights into transcription regulation, no dedicated bioinformatics tool exists to leverage its advantages. Most ChIP-seq and ChIP-chip analytic methods are not tailored for ChIP-exo, and thus cannot take full advantage of high-resolution ChIP-exo data. Here we describe a novel analysis framework, termed MACE (model-based analysis of ChIP-exo) dedicated to ChIP-exo data analysis. The MACE workflow consists of four steps: (i) sequencing data normalization and bias correction; (ii) signal consolidation and noise reduction; (iii) single-nucleotide resolution border peak detection using the Chebyshev Inequality and (iv) border matching using the Gale-Shapley stable matching algorithm. When applied to published human CTCF, yeast Reb1 and our own mouse ONECUT1/HNF6 ChIP-exo data, MACE is able to define TFBSs with high sensitivity, specificity and spatial resolution, as evidenced by multiple criteria including motif enrichment, sequence conservation, direct sequence pileup, nucleosome positioning and open chromatin states. In addition, we show that the fundamental advance of MACE is the identification of two boundaries of a TFBS with high resolution, whereas other methods only report a single location of the same event. The two boundaries help elucidate the in vivo binding structure of a given TF, e.g. whether the TF may bind as dimers or in a complex with other co-factors.
doi:10.1093/nar/gku846
PMCID: PMC4227761  PMID: 25249628
6.  Expression and Antibody Preparation of GP5a Gene of Porcine Reproductive and Respiratory Syndrome Virus 
Indian Journal of Microbiology  2013;53(3):370-375.
Porcine reproductive and respiratory syndrome (PRRS) is considered one of the most important infectious diseases to affect the swine industry and characterized by reproductive failure in late term gestation in sows and respiratory disease in pigs of all ages. The GP5a gene, encoding RNA-dependent RNA polymerase, is generally regarded as fairly conserved when compared to other viral proteins. It plays an important role in the process of duplication and transcription carried out by Porcine reproductive and respiratory syndrome virus (PRRSV). We firstly expressed and purified the GP5a protein of PRRSV. This provides a good method for the purification of expressed proteins and the preparation of the corresponding antibodies.
doi:10.1007/s12088-013-0368-1
PMCID: PMC3689410  PMID: 24426138
Porcine reproductive and respiratory syndrome virus; GP5a; Purification; Expression
7.  HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data 
BMC Bioinformatics  2014;15(1):280.
Background
Chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (ChIP-Seq) has been widely used to identify genomic loci of transcription factor (TF) binding and histone modifications. ChIP-Seq data analysis involves multiple steps from read mapping and peak calling to data integration and interpretation. It remains challenging and time-consuming to process large amounts of ChIP-Seq data derived from different antibodies or experimental designs using the same approach. To address this challenge, there is a need for a comprehensive analysis pipeline with flexible settings to accelerate the utilization of this powerful technology in epigenetics research.
Results
We have developed a highly integrative pipeline, termed HiChIP for systematic analysis of ChIP-Seq data. HiChIP incorporates several open source software packages selected based on internal assessments and published comparisons. It also includes a set of tools developed in-house. This workflow enables the analysis of both paired-end and single-end ChIP-Seq reads, with or without replicates for the characterization and annotation of both punctate and diffuse binding sites. The main functionality of HiChIP includes: (a) read quality checking; (b) read mapping and filtering; (c) peak calling and peak consistency analysis; and (d) result visualization. In addition, this pipeline contains modules for generating binding profiles over selected genomic features, de novo motif finding from transcription factor (TF) binding sites and functional annotation of peak associated genes.
Conclusions
HiChIP is a comprehensive analysis pipeline that can be configured to analyze ChIP-Seq data derived from varying antibodies and experiment designs. Using public ChIP-Seq data we demonstrate that HiChIP is a fast and reliable pipeline for processing large amounts of ChIP-Seq data.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-280) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2105-15-280
PMCID: PMC4152589  PMID: 25128017
ChIP-Seq; Next-generation sequencing; Peak calling; Duplicate filtering; Irreproducible discovery rate
8.  Pathogenic Fungus Microsporum canis Activates the NLRP3 Inflammasome 
Infection and Immunity  2014;82(2):882-892.
Microsporum canis is a pathogenic fungus with worldwide distribution that causes tinea capitis in animals and humans. M. canis also causes invasive infection in immunocompromised patients. To defy pathogenic fungal infection, the host innate immune system is the first line of defense. As an important arm of innate immunity, the inflammasomes are intracellular multiprotein complexes that control the activation of caspase-1, which cleaves proinflammatory cytokine pro-interleukin-1β (IL-1β) into its mature form. To determine whether the inflammasome is involved in the host defense against M. canis infection, we challenged human monocytic THP-1 cells and mouse dendritic cells with a clinical strain of M. canis isolated from patients with tinea capitis. We found that M. canis infection triggered rapid secretion of IL-1β from both THP-1 cells and mouse dendritic cells. Moreover, by using gene-specific shRNA and competitive inhibitors, we determined that M. canis-induced IL-1β secretion was dependent on NLRP3. The pathways proposed for NLRP3 inflammasome activation, namely, cathepsin B activity, K+ efflux, and reactive oxygen species production, were all required for the inflammasome activation triggered by M. canis. Meanwhile, Syk, Dectin-1, and Card9 were found to be involved in M. canis-induced IL-1β secretion via regulation of pro-IL-1β transcription. More importantly, our data revealed that M. canis-induced production of IL-1β was dependent on the NLRP3 inflammasome in vivo. Together, this study unveils that the NLRP3 inflammasome exerts a critical role in host innate immune responses against M. canis infection, and our data suggest that diseases that result from M. canis infection might be controlled by regulating the activation of inflammasomes.
doi:10.1128/IAI.01097-13
PMCID: PMC3911390  PMID: 24478101
9.  Plasmacytoid Dendritic Cells Suppress HIV-1 Replication but Contribute to HIV-1 Induced Immunopathogenesis in Humanized Mice 
PLoS Pathogens  2014;10(7):e1004291.
The role of plasmacytoid dendritic cells (pDC) in human immunodeficiency virus type 1 (HIV-1) infection and pathogenesis remains unclear. HIV-1 infection in the humanized mouse model leads to persistent HIV-1 infection and immunopathogenesis, including type I interferons (IFN-I) induction, immune-activation and depletion of human leukocytes, including CD4 T cells. We developed a monoclonal antibody that specifically depletes human pDC in all lymphoid organs in humanized mice. When pDC were depleted prior to HIV-1 infection, the induction of IFN-I and interferon-stimulated genes (ISGs) were abolished during acute HIV-1 infection with either a highly pathogenic CCR5/CXCR4-dual tropic HIV-1 or a standard CCR5-tropic HIV-1 isolate. Consistent with the anti-viral role of IFN-I, HIV-1 replication was significantly up-regulated in pDC-depleted mice. Interestingly, the cell death induced by the highly pathogenic HIV-1 isolate was severely reduced in pDC-depleted mice. During chronic HIV-1 infection, depletion of pDC also severely reduced the induction of IFN-I and ISGs, associated with elevated HIV-1 replication. Surprisingly, HIV-1 induced depletion of human immune cells including T cells in lymphoid organs, but not the blood, was reduced in spite of the increased viral replication. The increased cell number in lymphoid organs was associated with a reduced level of HIV-induced cell death in human leukocytes including CD4 T cells. We conclude that pDC play opposing roles in suppressing HIV-1 replication and in promoting HIV-1 induced immunopathogenesis. These findings suggest that pDC-depletion and IFN-I blockade will provide novel strategies for treating those HIV-1 immune non-responsive patients with persistent immune activation despite effective anti-retrovirus treatment.
Author Summary
Persistent expression of IFN-I is correlated with disease progression in HIV-1 infected humans or SIV-infected monkeys. Thus, persistent pDC activation has been implicated in contributing to AIDS pathogenesis. To define the role of pDC in HIV-1 infection and immunopathogenesis in vivo, we developed a monoclonal antibody that specifically and efficiently depletes human pDC in all lymphoid organs in humanized mice. We discover that pDC are the critical IFN-I producer cells in response to acute HIV-1 infection, because depletion of pDC completely abolished induction of IFN-I or ISG by HIV-1 infection, correlated with elevated level of HIV-1 replication. When pDC were depleted during chronic HIV-1 infection in humanized mice, pDC were still the major IFN-I producing cells in vivo, which contributed to HIV-1 suppression. Despite of higher level of viral replication in pDC-depleted mice, we found that HIV-induced depletion of human T cells and leukocytes was significantly reduced in lymphoid organs, correlated with reduced cell death induction by HIV-1 infection. Our findings demonstrate that pDC play two opposing roles in HIV-1 pathogenesis: they produce IFN-I to suppress HIV-1 replication and induce death of human immune cells to contribute to HIV-induced T cell depletion and immunopathogenesis.
doi:10.1371/journal.ppat.1004291
PMCID: PMC4117636  PMID: 25077616
10.  Definition of a FoxA1 Cistrome that is Crucial for G1-S Phase Cell-Cycle Transit in Castration-Resistant Prostate Cancer 
Cancer research  2011;71(21):6738-6748.
The enhancer pioneer transcription factor FoxA1 is a global mediator of steroid receptor (SR) action in hormone-dependent cancers. In castration-resistant prostate cancer (CRPC), FoxA1 acts as an androgen receptor co-factor to drive G2-M phase cell-cycle transit. Here we describe a mechanistically distinct SR-independent role for FoxA1 in driving G1-S phase cell-cycle transit in CRPC. By comparing FoxA1 binding sites in prostate cancer cell genomes, we defined a co-dependent set of FoxA1-MYBL2 and FoxA1-CREB1 binding sites within the regulatory regions of the Cyclin E2 and E2F1 genes that are critical for CRPC growth. Binding at these sites upregulate the Cyclin E2 and Cyclin A2 genes in CRPC but not in earlier stage androgen-dependent prostate cancer (ADPC), establishing a stage-specific role for this pathway in CRPC growth. Mechanistic investigations indicated that FoxA1, MYBL2 or CREB1 induction of histone H3 acetylation facilitated nucleosome disruption as the basis for co-dependent transcriptional activation and G1-S phase cell-cycle transit. Our findings establish FoxA1 as a pivotal driver of the cell-cycle in CRPC which promotes G1-S phase transit as well as G2-M phase transit through two distinct mechanisms.
doi:10.1158/0008-5472.CAN-11-1882
PMCID: PMC4081454  PMID: 21900400
FoxA1; cistrome; cell-cycle G1-S progression; castration-resistant prostate cancer
11.  Molecular mechanism of SCARB2-mediated attachment and uncoating of EV71 
Protein & Cell  2014;5(9):692-703.
Unlike the well-established picture for the entry of enveloped viruses, the mechanism of cellular entry of non-enveloped eukaryotic viruses remains largely mysterious. Picornaviruses are representative models for such viruses, and initiate this entry process by their functional receptors. Here we present the structural and functional studies of SCARB2, a functional receptor of the important human enterovirus 71 (EV71). SCARB2 is responsible for attachment as well as uncoating of EV71. Differences in the structures of SCARB2 under neutral and acidic conditions reveal that SCARB2 undergoes a pivotal pH-dependent conformational change which opens a lipid-transfer tunnel to mediate the expulsion of a hydrophobic pocket factor from the virion, a pre-requisite for uncoating. We have also identified the key residues essential for attachment to SCARB2, identifying the canyon region of EV71 as mediating the receptor interaction. Together these results provide a clear understanding of cellular attachment and initiation of uncoating for enteroviruses.
Electronic supplementary material
The online version of this article (doi:10.1007/s13238-014-0087-3) contains supplementary material, which is available to authorized users.
doi:10.1007/s13238-014-0087-3
PMCID: PMC4145081  PMID: 24986489
viral entry; uncoating; picornaviruses; receptor binding; SCARB2; EV71; lipid transfer tunnel
12.  Molecular mechanism of SCARB2-mediated attachment and uncoating of EV71 
Protein & Cell  2014;5(9):692-703.
Unlike the well-established picture for the entry of enveloped viruses, the mechanism of cellular entry of non-enveloped eukaryotic viruses remains largely mysterious. Picornaviruses are representative models for such viruses, and initiate this entry process by their functional receptors. Here we present the structural and functional studies of SCARB2, a functional receptor of the important human enterovirus 71 (EV71). SCARB2 is responsible for attachment as well as uncoating of EV71. Differences in the structures of SCARB2 under neutral and acidic conditions reveal that SCARB2 undergoes a pivotal pH-dependent conformational change which opens a lipid-transfer tunnel to mediate the expulsion of a hydrophobic pocket factor from the virion, a pre-requisite for uncoating. We have also identified the key residues essential for attachment to SCARB2, identifying the canyon region of EV71 as mediating the receptor interaction. Together these results provide a clear understanding of cellular attachment and initiation of uncoating for enteroviruses.
Electronic supplementary material
The online version of this article (doi:10.1007/s13238-014-0087-3) contains supplementary material, which is available to authorized users.
doi:10.1007/s13238-014-0087-3
PMCID: PMC4145081  PMID: 24986489
viral entry; uncoating; picornaviruses; receptor binding; SCARB2; EV71; lipid transfer tunnel
14.  Evaluation of the Impact of Hepatitis B Vaccination in Adults in Jiangsu Province, China 
PLoS ONE  2014;9(6):e101501.
Hepatitis B immunization programs for newborns, children, and adolescents in China have shown remarkable results. To establish whether there would be any benefit in extending the program to cover older individuals, we examined both the epidemiology of hepatitis B virus (HBV) infection and the coverage of hepatitis B vaccinations among adults born before routine vaccinations were implemented. We then evaluated the impact of hepatitis B vaccination in adults aged 20–59 years. A large-scale cross-sectional epidemiological survey of HBV infection was performed in the province of Jiangsu, south-east China, between September 2009 and March 2010. A total of 86,732 adults aged 20–59 years were included, of which 8,615 (9.9%, 95% CI = 9.7–10.1%) were HBsAg sero-positive. Self-reported vaccination status suggested that the coverage was approximately 23.7% (95% CI = 23.4–24.0%). It was shown that higher HBV vaccination coverage was associated with a lower rate of HBsAg seropositivity among adults. There was a negative correlation between hepatitis B vaccination coverage and HBsAg prevalence (correlation coefficient = −0.805, p = 0.016), which might demonstrate the combined effects of vaccination and pre-vaccination HBsAg screening. In the unvaccinated group, the HBsAg-positive rate had an obvious upward trend with age growing among 20–39 year-olds (Trend χ2 = 22.605, P<0.001), while the vaccinated group showed no such trend (Trend χ2 = 3.462, P = 0.063). Overall, hepatitis B vaccination in adults might reduce the rate of HBsAg positivity. Therefore, routine immunization of adults aged 20–39 years should be seriously considered.
doi:10.1371/journal.pone.0101501
PMCID: PMC4076282  PMID: 24979048
15.  Effect of Thickness of HA-Coating on Microporous Silk Scaffolds Using Alternate Soaking Technology 
BioMed Research International  2014;2014:637821.
Hydroxyapatite (HA) can be coated on various materials surface and has the function of osteogenicity. Microporous silk scaffold has excellent biocompatibility. In this study, alternate soaking technology was used to coat HA on microporous silk scaffolds. However, the cell proliferation was found to decrease with the increasing thickness (cycles of soaking) of HA-coating. This study aims to determine the best thickness (cycles of soaking) of HA-coating on microporous silk scaffolds. The SEM observation showed that group with one cycle of alternate soaking (1C-HA) has the most optimal porosity like non-HA-modified microporous silk scaffolds. The proliferation of osteoblasts has no significant difference between noncoated HA (N-HA) and 1C-HA groups, which are both significantly higher than those in two cycles of soaking (2C-HA) and three cycles of soaking (3C-HA) groups. The transcription levels of specific genes (runx2 and osteonectin) in osteoblasts of 1C-HA group were significantly higher than those of N-HA group. Moreover, the levels showed no significant difference among 1C-HA, 2C-HA, and 3C-HA groups. In conclusion, microporous silk scaffold with 1 cycle of HA-coating can combine the biocompatibility of silk and osteogenicity of HA.
doi:10.1155/2014/637821
PMCID: PMC4100396  PMID: 25093176
16.  Immobilized Lentivirus Vector on Chondroitin Sulfate-Hyaluronate Acid-Silk Fibroin Hybrid Scaffold for Tissue-Engineered Ligament-Bone Junction 
BioMed Research International  2014;2014:816979.
The lack of a fibrocartilage layer between graft and bone remains the leading cause of graft failure after anterior cruciate ligament (ACL) reconstruction. The objective of this study was to develop a gene-modified silk cable-reinforced chondroitin sulfate-hyaluronate acid-silk fibroin (CHS) hybrid scaffold for reconstructing the fibrocartilage layer. The scaffold was fabricated by lyophilizing the CHS mixture with braided silk cables. The scanning electronic microscopy (SEM) showed that microporous CHS sponges were formed around silk cables. Each end of scaffold was modified with lentiviral-mediated transforming growth factor-β3 (TGF-β3) gene. The cells on scaffold were transfected by bonded lentivirus. In vitro culture demonstrated that mesenchymal stem cells (MSCs) on scaffolds proliferated vigorously and produced abundant collagen. The transcription levels of cartilage-specific genes also increased with culture time. After 2 weeks, the MSCs were distributed uniformly throughout scaffold. Deposited collagen was also found to increase. The chondral differentiation of MSCs was verified by expressions of collagen II and TGF-β3 genes in mRNA and protein level. Histology also confirmed the production of cartilage extracellular matrix (ECM) components. The results demonstrated that gene-modified silk cable-reinforced CHS scaffold was capable of supporting cell proliferation and differentiation to reconstruct the cartilage layer of interface.
doi:10.1155/2014/816979
PMCID: PMC4075190  PMID: 25019087
17.  A Network Biology Approach to Discover the Molecular Biomarker Associated with Hepatocellular Carcinoma 
BioMed Research International  2014;2014:278956.
In recent years, high throughput technologies such as microarray platform have provided a new avenue for hepatocellular carcinoma (HCC) investigation. Traditionally, gene sets enrichment analysis of survival related genes is commonly used to reveal the underlying functional mechanisms. However, this approach usually produces too many candidate genes and cannot discover detailed signaling transduction cascades, which greatly limits their clinical application such as biomarker development. In this study, we have proposed a network biology approach to discover novel biomarkers from multidimensional omics data. This approach effectively combines clinical survival data with topological characteristics of human protein interaction networks and patients expression profiling data. It can produce novel network based biomarkers together with biological understanding of molecular mechanism. We have analyzed eighty HCC expression profiling arrays and identified that extracellular matrix and programmed cell death are the main themes related to HCC progression. Compared with traditional enrichment analysis, this approach can provide concrete and testable hypothesis on functional mechanism. Furthermore, the identified subnetworks can potentially be used as suitable targets for therapeutic intervention in HCC.
doi:10.1155/2014/278956
PMCID: PMC4053081  PMID: 24949431
18.  Class III peroxidases are activated in proanthocyanidin-deficient Arabidopsis thaliana seeds 
Annals of Botany  2013;111(5):839-847.
Background and Aims
It has previously been shown that proanthocyanidins (PAs) in the seed coat of Arabidopsis thaliana have the ability to scavenge superoxide radicals (O2−). However, the physiological processess in PA-deficit seeds are not clear. It is hypothesized that there exist alternative ways in PA-deficient seeds to cope with oxidative stress.
Methods
The content of hydrogen peroxide (H2O2) and its relevance to the activities of superoxide dismutase (SOD), catalase (CAT) and peroxidases was investigated in both wild-type and PA-deficit mutant seeds. A biochemical staining approach was used to detect tissue localizations of peroxidase activities in PA-deficit mutant seeds.
Key Results
PA-deficient mutants possess significantly lower levels of H2O2 than the wild-type, despite their higher accumulation of superoxide radicals. Screening of the key antioxidant enzymes revealed that peroxidase activity was significantly over-activated in mutant seeds. This high peroxidase activity was mainly confined to the seed coat zone. Interestingly, neither ascorbate peroxidase nor glutathione peroxidase, just the guaiacol peroxidases (class III peroxidases), was specifically activated in the seed coat. However, no significant difference in peroxidase activity was observed in embryos of either mutants or the wild-type, although gene expressions of several candidate peroxidases were down-regulated in the embryos of PA-deficient seeds.
Conclusions
The results suggest that enhanced class III peroxidase activity in the seed coat of PA-deficient mutants is an adaptive strategy for seed development and survival.
doi:10.1093/aob/mct045
PMCID: PMC3631330  PMID: 23448691
Proanthocyanidins; peroxidase; seed coat; seed development; seed germination; anti- oxidation; Arabidopsis thaliana
19.  Associations between androgen receptor CAG & GGN repeat polymorphism & recurrent spontaneous abortions in Chinese women 
Background & objectives:
Recurrent spontaneous abortion (RSA) is a reproductive problem that occurs in women in reproductive age with a frequency of 1-3 per cent. Previous studies have reported high levels of serum androgens to be associated with RSAs. At the molecular level, the effect of androgens is mediated through the activation of the androgen receptor (AR). The CAG and GGN repeat polymorphisms of the AR gene are associated with the AR activity. We hypothesize that the AR CAG/GGN repeat polymorphism may be associated with levels of serum androgens. Thus, this study as undertaken to evaluate the relationship between CAG/GGN repeats in exon 1 of the AR gene in women with RSAs.
Methods:
This case-control study was performed in Ningxia, PR China, including 149 women with RSAs and 210 controls. The CAG and GGN repeats of the AR gene were genotyped using a PCR-based assay and were analyzed using Peak Scanner Software v1.0 to determine the CAG/GGN repeat length.
Results:
CAG repeats ranged from 15 to 29 in the RSA patients, compared to 14 to 35 in the control group. The median value of CAG repeats was 22 for the RSA group and 24 for control group. The total AR CAG alleles (≤22 repeats), shorter AR CAG alleles (≤22 repeats), and biallelic means (≤22.5 repeats) were significantly different in the RSA group in comparison to the control group (P<0.001, P<0.01). The median value of the GGN repeats was 23 for the cases and 22 for controls. The total number of AR GGN alleles (≤23 repeats) was significantly different in the RSA group compared to the control group (P<0.5). There was no difference between the RSA group and the control groups in regards to shorter alleles, longer alleles, and biallelic means.
Interpretation & conclusions:
Our observation suggests that the CAG and GGN repeat length is shorter in women with RSAs as compared with controls and that shorter CAG and GGN repeats may be pathogenic for RSAs in Chinese women. Further studies need to be done in different ethnic populations.
PMCID: PMC4140038  PMID: 25027083
Androgen; androgen receptor gene; CAG repeats; GGN repeats; recurrent spontaneous abortion
20.  A mouse model for HBV immunotolerance and immunotherapy 
Lack of an appropriate small animal model remains a major hurdle for studying the immunotolerance and immunopathogenesis induced by hepatitis B virus (HBV) infection. In this study, we report a mouse model with sustained HBV viremia after infection with a recombinant adeno-associated virus (AAV) carrying a replicable HBV genome (AAV/HBV). Similar to the clinical HBV carriers, the mice infected with AAV/HBV were sero-negative for antibodies against HBV surface antigen (HBsAg). Immunization with the conventional HBV vaccine in the presence of aluminum adjuvant failed to elicit an immune response against HBV in these mice. To identify a vaccine that can potentially circumvent this tolerance, the TLR9 agonist CpG was added to HBsAg as an adjuvant. Vaccination of mice with HBsAg/CpG induced not only clearance of viremia, but also strong antibody production and T-cell responses. Furthermore, both the DNA replication and protein expression of HBV were significantly reduced in the livers of AAV/HBV-infected mice. Accordingly, AAV/HBV-infected mice may be used as a robust model for investigating the underlying mechanism(s) of HBV immunotolerance and for developing novel immunotherapies to eradicate HBV infections.
doi:10.1038/cmi.2013.43
PMCID: PMC4002146  PMID: 24076617
AAV vector; HBV; immunotherapy; immunotolerance; mouse model
21.  Generation of a humanized mouse model with both human immune system and liver cells to model hepatitis C virus infection and liver immunopathogenesis 
Nature protocols  2012;7(9):1608-1617.
Establishing a small animal model that accurately recapitulates hepatotropic pathogens, including hepatitis C virus (HCV) infection and immunopathogenesis, is essential for the study of hepatitis virus–induced liver disease and for therapeutics development. This protocol describes our recently developed humanized mouse model for studying HCV and other hepatotropic infections, human immune response and hepatitis and liver fibrosis. The first 5-h stage is the isolation of human liver progenitor and hematopoietic stem cells from fetal liver. Next, AFC8 immunodeficient mice are transplanted with the isolated progenitor/stem cells. This generally takes 2 h. The transplanted mice are then treated for a month with the mouse liver apoptosis–inducing AFC8 dimerizer and left for an additional 2-month period to permit human liver and immune cell growth as well as system reconstitution and development before inoculation with HCV clinical isolates. HCV infection, human immune response and liver disease are observed with high incidence from approximately 2 months after inoculation.
doi:10.1038/nprot.2012.083
PMCID: PMC3979325  PMID: 22899330
22.  HIV-1 immunopathogenesis in humanized mouse models 
Cellular & molecular immunology  2012;9(3):237-244.
In recent years, the technology of constructing chimeric mice with humanized immune systems has markedly improved. Multiple lineages of human immune cells develop in immunodeficient mice that have been transplanted with human hematopoietic stem cells. More importantly, these mice mount functional humoral and cellular immune responses upon immunization and microbial infection. Human immunodeficiency virus type I (HIV-1) can establish an infection in humanized mice, resulting in CD4+ T-cell depletion and an accompanying nonspecific immune activation, which mimics the immunopathology in HIV-1-infected human patients. This makes humanized mice an optimal model for studying the mechanisms of HIV-1 immunopathogenesis and for developing novel immune-based therapies.
doi:10.1038/cmi.2012.7
PMCID: PMC3971052  PMID: 22504952
23.  Foxp3 and Treg cells in HIV-1 infection and immuno-pathogenesis 
Immunologic research  2008;41(3):248-266.
FoxP3+CD4+CD25+ regulatory T (Treg) cells are implicated in a number of pathologic processes including elevated levels in cancers and infectious diseases, and reduced levels in autoimmune diseases. Treg cells are activated to modulate immune responses to avoid over-reactive immunity. However, conflicting findings are reported regarding relative levels of Treg cells during HIV-1 infection and disease progression. The role of Treg cells in HIV-1 diseases (aberrant immune activation) is poorly understood due to lack of a robust model. We summarize here the regulation and function of Foxp3 in Treg cells and in modulating HIV-1 replication. Based on recent findings from SIV/monkey and HIV/humanized mouse models, a model of the dual role of Treg cells in HIV-1 infection and immuno-pathogenesis is discussed.
doi:10.1007/s12026-008-8037-x
PMCID: PMC3971055  PMID: 18726715
Regulatory T cells; AIDS; Chromatin; Epigenetic; Humanized mouse; DKO-hu; ONTAK
24.  Bis(μ-nitrato-κ2 O:O)bis­{[1,2-bis­(diiso­propyl­phosphan­yl)-1,2-dicarba-closo-dodeca­borane-κ2 P,P′]silver(I)} di­chloro­methane disolvate 
The title compound, [Ag2(NO3)2(C14H38B10P2)2]·2CH2Cl2, was synthesized by the reaction of 1,2-bis­(diiso­propyl­phosphan­yl)-1,2-dicarba-closo-dodeca­borane with AgNO3. The resulting dinuclear molecule has crystallographically imposed inversion symmetry. The diiso­propyl­phosphanyl-closo-carborane ligand is coordin­ated in a bidentate manner to the AgI atom through the two P atoms. The distorted tetra­hedral coordination of the metal is completed by two O atoms of two bridging nitrate anions. The separation between the two AgI atoms is 3.8913 (5) Å. C—H⋯O hydrogen bonds are observed involving the dichloromethane solvent molecule and the nitrate anion.
doi:10.1107/S1600536814006084
PMCID: PMC3998584  PMID: 24826102
25.  [1,2-Bis(di­cyclo­hexyl­phosphan­yl)-1,2-dicarba-closo-dodeca­borane-2κ2 P,P′]di-μ-chlorido-1:2κ4 Cl:Cl-di­chlorido-1κ2 Cl-dimercury(II) 
The title compound, [Hg2Cl4(C26H54B10P2)], was synthesized by the reaction of 1,2-bis­(di­cyclo­hexyl­phosphan­yl)-1,2-dicarba-closo-dodeca­borane with HgCl2. Both HgII atoms show a distorted tetra­hedral coordination geometry, provided by the two bridging chloride anions and the P atoms of the diphosphanyl ligand for one metal atom, and by two bridging and two terminal chloride anions for the other. The five-membered HgP2C2 chelate ring assumes an envelope conformation, with the HgII atom displaced by 0.1650 (5) Å from the mean plane of the other four atoms (r.m.s. deviation = 0.002 Å). In the crystal, B—H⋯Cl interactions link the molecules, forming a supramolecular chain along the a-axis direction.
doi:10.1107/S1600536814006096
PMCID: PMC3998597  PMID: 24826101

Results 1-25 (96)