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1.  Rad50-CARD9 interactions link cytosolic DNA sensing to IL-1β production 
Nature immunology  2014;15(6):538-545.
Double-stranded DNA (dsDNA) in the cytoplasm triggers interleukin-1β (IL-1β) production as an anti-viral host response, and deregulation of the pathways involved can promote inflammatory disease. Here we report a direct cytosolic interaction between the DNA-damage sensor Rad50 and the innate immune adapter CARD9. Dendritic cell transfection with dsDNA or infection with a DNA virus induces the formation of dsDNA-Rad50-CARD9 signaling complexes for NF-κB activation and pro-IL-1β generation. Primary cells conditionally deficient for Rad50 or lacking CARD9 consequently exhibit defective DNA-induced IL-1β production, and Card9−/− mice have impaired inflammatory responses upon DNA virus infection in vivo. These results define a cytosolic DNA recognition pathway for inflammation and a physical and functional connection between a conserved DNA-damage sensor and the innate immune response to pathogens.
doi:10.1038/ni.2888
PMCID: PMC4309842  PMID: 24777530
2.  Evaluation of Immune Responses in Mice after DNA Immunization with Putative Toxoplasma gondii Calcium-Dependent Protein Kinase 5 
Toxoplasma gondii can cause serious public health problems and economic losses worldwide. Calcium-dependent protein kinases (CDPKs) are key mediators of T. gondii signaling pathways and are implicated as important virulence factors. In the present study, we cloned a novel T. gondii CDPK gene, named TgCDPK5, and constructed the eukaryotic expression vector pVAX-CDPK5. Then, we evaluated the immune protection induced by pVAX-CDPK5 in Kunming mice. After injection of pVAX-CDPK5 intramuscularly, immune responses, determined with lymphoproliferative assays and cytokine and antibody measurements, were monitored, and mouse survival times and brain cyst formation were evaluated following challenges with the T. gondii RH strain (genotype I) and the PRU strain (genotype II). pVAX-CDPK5 effectively induced immune responses with increased specific antibodies, a predominance of IgG2a production, and a strong lymphocyte proliferative response. The levels of gamma interferon (IFN-γ), interleukin 2 (IL-2), and IL-12(p70) and the percentages of CD3+ CD4+ and CD3+ CD8+ cells in mice vaccinated with pVAX-CDPK5 were significantly increased. However, IL-4 and IL-10 were not produced in the vaccinated mice. These results demonstrate that pVAX-CDPK5 can elicit strong humoral and cellular Th1 immune responses. The survival time of immunized mice challenged with the T. gondii RH strain (8.67 ± 4.34 days) was slightly, but not significantly, longer than that in the control groups within 7 days (P > 0.05). The numbers of brain cysts in the mice in the pVAX-CDPK5 group were reduced by ∼40% compared with those in the control groups (P < 0.05), which provides a foundation for the further development of effective subunit vaccines against T. gondii.
doi:10.1128/CVI.00059-14
PMCID: PMC4097438  PMID: 24789795
3.  Polarity continuation and frustration in ZnSe nanospirals 
Scientific Reports  2014;4:7447.
ZnSe nanospirals including structures with polarity continuation and polarity frustration are simultaneously observed at atomic resolution. Through careful analysis of polarity within each dumbbell based on aberration-corrected high-angle annular-dark-field imaging, polarity continuation across parallel polytype interfaces as well as the surrounding Z-shape faulted dipoles is verified. Moreover, polarity frustration across regions with different stacking sequence, which would lead to accumulations of boundary interface charges in the triangular-shaped mixed regions with potential optoelectronic applications, is carefully studied.
doi:10.1038/srep07447
PMCID: PMC4265773  PMID: 25502957
4.  Mechanistic Studies of the Genetically Encoded Fluorescent Protein Voltage Probe ArcLight 
PLoS ONE  2014;9(11):e113873.
ArcLight, a genetically encoded fluorescent protein voltage probe with a large ΔF/ΔV, is a fusion between the voltage sensing domain of the Ciona instestinalis voltage sensitive phosphatase and super ecliptic pHluorin carrying a single mutation (A227D in the fluorescent protein). Without this mutation the probe produces only a very small change in fluorescence in response to voltage deflections (∼1%). The large signal afforded by this mutation allows optical detection of action potentials and sub-threshold electrical events in single-trials in vitro and in vivo. However, it is unclear how this single mutation produces a probe with such a large modulation of its fluorescence output with changes in membrane potential. In this study, we identified which residues in super ecliptic pHluorin (vs eGFP) are critical for the ArcLight response, as a similarly constructed probe based on eGFP also exhibits large response amplitude if it carries these critical residues. We found that D147 is responsible for determining the pH sensitivity of the fluorescent protein used in these probes but by itself does not result in a voltage probe with a large signal. We also provide evidence that the voltage dependent signal of ArcLight is not simply sensing environmental pH changes. A two-photon polarization microscopy study showed that ArcLight's response to changes in membrane potential includes a reorientation of the super ecliptic pHluorin. We also explored different changes including modification of linker length, deletion of non-essential amino acids in the super ecliptic pHluorin, adding a farnesylation site, using tandem fluorescent proteins and other pH sensitive fluorescent proteins.
doi:10.1371/journal.pone.0113873
PMCID: PMC4242678  PMID: 25419571
5.  The Ratio of Circulating Regulatory T Cells (Tregs)/Th17 Cells Is Associated with Acute Allograft Rejection in Liver Transplantation 
PLoS ONE  2014;9(11):e112135.
CD4+CD25+FoxP3+ regulatory T cells (Tregs) and Th17 cells are known to be involved in the alloreactive responses in organ transplantation, but little is known about the relationship between Tregs and Th17 cells in the context of liver alloresponse. Here, we investigated whether the circulating Tregs/Th17 ratio is associated with acute allograft rejection in liver transplantation. In present study, thirty-eight patients who received liver transplant were enrolled. The patients were divided into two groups: acute allograft rejection group (Gr-AR) (n = 16) and stable allograft liver function group (Gr-SF) (n = 22). The frequencies of circulating Tregs and circulating Th17 cells, as well as Tregs/Th17 ratio were determined using flow cytometry. The association between Tregs/Th17 ratio and acute allograft rejection was then analyzed. Our results showed that the frequency of circulating Tregs was significantly decreased, whereas the frequency of circulating Th17 cells was significantly increased in liver allograft recipients who developed acute rejection. Tregs/Th17 ratio had a negative correlation with liver damage indices and the score of rejection activity index (RAI) after liver transplantation. In addition, the percentages of CTLA-4+, HLA-DR+, Ki67+, and IL-10+ Tregs were higher in Gr-SF group than in Gr-AR group. Our results suggested that the ratio of circulating Tregs/Th17 cells is associated with acute allograft rejection, thus the ratio may serve as an alternative marker for the diagnosis of acute rejection.
doi:10.1371/journal.pone.0112135
PMCID: PMC4221545  PMID: 25372875
6.  Virologic and Immunologic Evidence of Multifocal Genital Herpes Simplex Virus 2 Infection 
Journal of Virology  2014;88(9):4921-4931.
ABSTRACT
Genital herpes simplex virus (HSV) reactivation is thought to be anatomically and temporally localized, coincident with limited ganglionic infection. Short, subclinical shedding episodes are the most common form of HSV-2 reactivation, with host clearance mechanisms leading to rapid containment. The anatomic distribution of shedding episodes has not been characterized. To precisely define patterns of anatomic reactivation, we divided the genital tract into a 22-region grid and obtained daily swabs for 20 days from each region in 28 immunocompetent, HSV-2-seropositive persons. HSV was detected via PCR, and sites of asymptomatic HSV shedding were subjected to a biopsy procedure within 24 h. CD4+ and CD8+ T cells were quantified by immunofluorescence, and HSV-specific CD4+ T cells were identified by intracellular cytokine cytometry. HSV was detected in 868 (7%) of 11,603 genital swabs at a median of 12 sites per person (range, 0 to 22). Bilateral HSV detection occurred on 83 (67%) days with shedding, and the median quantity of virus detected/day was associated with the number of sites positive (P < 0.001). In biopsy specimens of asymptomatic shedding sites, we found increased numbers of CD8+ T cells compared to control tissue (27 versus 13 cells/mm2, P = 0.03) and identified HSV-specific CD4+ T cells. HSV reactivations emanate from widely separated anatomic regions of the genital tract and are associated with a localized cellular infiltrate that was demonstrated to be HSV specific in 3 cases. These data provide evidence that asymptomatic HSV-2 shedding contributes to chronic inflammation throughout the genital tract.
IMPORTANCE This detailed report of the anatomic patterns of genital HSV-2 shedding demonstrates that HSV-2 reactivation can be detected at multiple bilateral sites in the genital tract, suggesting that HSV establishes latency throughout the sacral ganglia. In addition, genital biopsy specimens from sites of asymptomatic HSV shedding have increased numbers of CD8+ T cells compared to control tissue, and HSV-specific CD4+ T cells are found at sites of asymptomatic shedding. These findings suggest that widespread asymptomatic genital HSV-2 shedding is associated with a targeted host immune response and contributes to chronic inflammation throughout the genital tract.
doi:10.1128/JVI.03285-13
PMCID: PMC3993786  PMID: 24554666
7.  HCV-Specific Interleukin-21+CD4+ T Cells Responses Associated with Viral Control through the Modulation of HCV-Specific CD8+ T Cells Function in Chronic Hepatitis C Patients 
Molecules and Cells  2013;36(4):362-367.
Interleukin-21 (IL-21)+CD4+ T cells are involved in the immune response against hepatitis B virus (HBV) by secreting IL-21. However, the role of IL-21+CD4+ T cells in the immune response against chronic hepatitis C (CHC) virus infection is poorly understood. This study aimed to investigate the role of IL-21+CD4+ T cells in CHC patients and the potential mechanisms. The study subjects included nineteen CHC patients who were grouped by viral load (low, < 106 RNA copies/ml, n = 8; high, > 106 RNA copies/ml, n = 11). The peripheral frequency of HCV-specific IL-21+CD4+ T cells was higher in the low viral load group and was negatively correlated with the serum HCV RNA viral load in all CHC patients. Meanwhile, IL-21+ cells accumulated in the liver in the low viral load group. In vitro, IL-21 treatment increased the expression of proliferation markers and cytolytic molecules on HCV-specific CD8+ T cells. In summary, these findings suggest that HCV-specific IL-21+CD4+ T cells might contribute to HCV control by rescuing HCV-specific CD8+ T cells in CHC patients.
doi:10.1007/s10059-013-0181-z
PMCID: PMC3887990  PMID: 24170093
chronic hepatitis C; HCV-specific CD8+ T cells; HCV-specific IL-21+CD4+ T cells; interleukin-21; viral control
9.  Genome-wide sequencing of small RNAs reveals a tissue-specific loss of conserved microRNA families in Echinococcus granulosus 
BMC Genomics  2014;15(1):736.
Background
MicroRNAs (miRNAs) are important post-transcriptional regulators which control growth and development in eukaryotes. The cestode Echinococcus granulosus has a complex life-cycle involving different development stages but the mechanisms underpinning this development, including the involvement of miRNAs, remain unknown.
Results
Using Illumina next generation sequencing technology, we sequenced at the genome-wide level three small RNA populations from the adult, protoscolex and cyst membrane of E. granulosus. A total of 94 pre-miRNA candidates (coding 91 mature miRNAs and 39 miRNA stars) were in silico predicted. Through comparison of expression profiles, we found 42 mature miRNAs and 23 miRNA stars expressed with different patterns in the three life stages examined. Furthermore, considering both the previously reported and newly predicted miRNAs, 25 conserved miRNAs families were identified in the E. granulosus genome. Comparing the presence or absence of these miRNA families with the free-living Schmidtea mediterranea, we found 13 conserved miRNAs are lost in E. granulosus, most of which are tissue-specific and involved in the development of ciliated cells, the gut and sensory organs. Finally, GO enrichment analysis of the differentially expressed miRNAs and their potential targets indicated that they may be involved in bi-directional development, nutrient metabolism and nervous system development in E. granulosus.
Conclusions
This study has, for the first time, provided a comprehensive description of the different expression patterns of miRNAs in three distinct life cycle stages of E. granulosus. The analysis supports earlier suggestions that the loss of miRNAs in the Platyhelminths might be related to morphological simplification. These results may help in the exploration of the mechanism of interaction between this parasitic worm and its definitive and intermediate hosts, providing information that can be used to develop new interventions and therapeutics for the control of cystic echinococcosis.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-736) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-736
PMCID: PMC4156656  PMID: 25168356
Echinococcus granulosus; microRNA; Deep sequencing; Differential expression; Life cycle stage development
10.  Variants in nucleotide excision repair core genes and susceptibility to recurrence of squamous cell carcinoma of the oropharynx 
Genetically determined capacity for NER may modulate both cancer risk and prognosis. Thus, we evaluated associations of seven selected variants in the NER core genes with recurrence risk in 658 SCCOP patients treated principally by radiation. The seven polymorphisms in the core NER genes (XPC-rs2228000, XPC-rs2228001, XPD-rs1799793, XPD-rs13181, XPG-rs17655, ERCC1-rs3212986, and XPA-rs1800975) were genotyped using PCR-RFLP method and log-rank test and multivariable Cox models were used to evaluate the associations in both dominant and recessive genetic models. In a dominant model, we found that polymorphisms of XPC-rs2228000, XPD-rs1799793, and XPG-rs17655 were significantly associated with disease-free survival (log-rank, P = 0.014; P = 0.00008; and P = 0.0007, respectively), and these polymorphisms were significantly associated with recurrence risk of SCCOP (HR = 1.6, 95% CI, 1.1–2.3 for XPC-rs2228000; HR = 0.4, 95%, 0.3–0.6 for XPD-rs1799793; and HR = 0.5, 95% CI, 0.4–0.8 for XPG-rs17655) after multivariable adjustment. Moreover, the borderline significant or significant associations were also found for these three polymorphisms in HPV16/18-positive SCCOP patients (HR= 1.6, 95% CI, 1.0–4.1 for XPC-rs2228000; HR = 0.2, 95%, 0.1–0.5 for XPD-rs1799793; and HR = 0.1, 95% CI, 0.0–0.9 for XPG-rs17655). However, similarly significant associations were not found for these polymorphisms in a recessive model. These findings suggest that polymorphisms of XPC-rs2228000, XPD-rs1799793, and XPG-rs17655 in the NER core genes may contribute to recurrence risk of SCCOP, particularly HPV-positive SCCOP, in a dominant but not in a recessive model. However, validation of these results is warranted.
doi:10.1002/ijc.28051
PMCID: PMC3663873  PMID: 23335232
genetic variants; nucleotide excision repair; human papillomavirus; oropharyngeal cancer; recurrence; DNA repair
11.  Genetic variants in p53-related genes confer susceptibility to second primary malignancy in patients with index squamous cell carcinoma of head and neck 
Carcinogenesis  2013;34(7):1551-1557.
Because of their important roles in mediating the stabilization and expression of p53, we hypothesized that high-risk genotypes of polymorphisms in p53-related genes, including p53, p73, p14ARF, MDM2 and MDM4, may be associated with an increased risk of second primary malignancy (SPM) after index squamous cell carcinoma of the head and neck (SCCHN). We analyzed data from a cohort of 1283 patients with index SCCHN who were recruited between 1995 and 2007 at MD Anderson Cancer Center and followed for SPM development. Patients were genotyped for nine polymorphisms of p53-related genes. A log-rank test and Cox models were used to compare SPM-free survival and risk. Our results demonstrated that each p53-related polymorphism had a moderate effect on increased SPM risk, but when we combined risk genotypes of these nine polymorphisms together, we found that SPM-free survival was significantly shorter among risk groups with a greater number of combined risk genotypes. SPM risk increased with increasing number of risk genotypes (P < 0.0001 for trend). Compared with the low-risk group (0–3 combined risk genotypes), both the medium-risk (4–5 combined risk genotypes) and high-risk (6–9 combined risk genotypes) groups had significantly increased SPM risk [hazard ratio (HR): 1.6; 95% confidence interval (CI): 1.0–2.6 and HR: 3.0; 95% CI: 1.8–5.0, respectively]. Moreover, such significant associations were even higher in several subgroups. Our findings suggest that combined risk genotypes of p53-related genes may jointly modify SPM risk, especially in patients who are smokers and those with index non-oropharyngeal cancers. However, larger studies are needed to validate our findings.
doi:10.1093/carcin/bgt096
PMCID: PMC3697893  PMID: 23508638
12.  Effect of Dehydroepiandrosterone Administration in Patients with Poor Ovarian Response According to the Bologna Criteria 
PLoS ONE  2014;9(6):e99858.
Background
Dehydroepiandrosterone (DHEA) is now widely used as an adjuvant to IVF treatment protocols in poor responders. However, clinical evidence for DHEA on improvement of ovarian response and IVF outcome is still limited, the validity of the results of the earlier studies, especially the varied inclusion criteria, is a subject of debate. Recently, the ESHRE Working Group developed a new definition, the Bologna criteria. The aim of the current study was to investigate the potential effect of DHEA treatment on in vitro fertilization (IVF) outcome of poor ovarian responders that fulfill the Bologna criteria.
Methods
This study investigated 386 poor ovarian responders that fulfill the Bologna criteria. Patients underwent IVF-ET treatment with the GnRH antagonist protocol. The study group contained 189 patients, who received 75 mg of DHEA daily (25 mg three times daily) before the IVF cycle. The control group was composed of 197 patients who received infertility treatment, but did not receive DHEA. The IVF outcome parameters in each group were compared.
Results
The study and control groups did not show statistically significant differences in terms of patient demographics characteristics, mean numbers of oocytes retrieved, mature oocytes, fertilization rate, cleavage rate, or embryo availability. While the DHEA group demonstrated significantly higher implantation rates (18.7% vs. 10.1%; P<0.01) and ongoing PRs (26.7% vs. 15.8%; P<0.05) as compared with the control.
Conclusions
DHEA pre-treatment does not significantly increase oocyte yield. However, the ongoing PRs in this subgroup of women are significantly higher after DHEA administration, suggesting that DHEA may increase IVF results by improving oocyte and embryo quality.
doi:10.1371/journal.pone.0099858
PMCID: PMC4059703  PMID: 24932478
13.  Role of miR-146a in human chondrocyte apoptosis in response to mechanical pressure injury in vitro 
MicroRNA (miR)-146a is known to be overexpressed in osteoarthritis (OA). However, the role of miR-146a in OA has not yet been fully elucidated. In the present study, we applied mechanical pressure of 10 MPa to human chondrocytes for 60 min in order to investigate the expression of miR-146a and apoptosis following the mechanical pressure injury. Normal human chondrocytes were transfected with an miR-146a mimic or an inhibitor to regulate miR-146a expression. Potential target genes of miR-146a were predicted using bioinformatics. Moreover, luciferase reporter assay confirmed that Smad4 was a direct target of miR-146a. The expression levels of miR-146a, Smad4 and vascular endothelial growth factor (VEGF) were quantified by quantitative reverse transcription PCR and/or western blot analysis. The effects of miR-146a on apoptosis were detected by Annexin V-fluorescein isothiocyanate (FITC)/propidium iodide (PI) flow cytometry. The results indicated that mechanical pressure affected chondrocyte viability and induced the early apoptosis of chondrocytes. Mechanical pressure injury increased the expression levels of miR-146a and VEGF and decreased the levels of Smad4 in the chondrocytes. In the human chondrocytes, the upregulation of miR-146a induced apoptosis, upregulated VEGF expression and downregulated Smad4 expression. In addition, the knockdown of miR-146a reduced cell apoptosis, upregulated Smad4 expression and downregulated VEGF expression. Smad4 was identified as a direct target of miR-146a by harboring a miR-146a binding sequence in the 3′-untranslated region (3′-UTR) of its mRNA. Furthermore, the upregulation of VEGF induced by miR-146a was mediated by Smad4 in the chondrocytes subjected to mechanical pressure injury. These results demonstrated that miR-146a was overexpressed in our chondrocyte model of experimentally induced human mechanical injury, accompanied by the upregulation of VEGF and the downregulation of Smad4 in vitro. Moreover, our data suggest that miR-146a is involved in human chondrocyte apoptosis in response to mechanical injury, and may contribute to the mechanical injury of chondrocytes, as well as to the pathogenesis of OA by increasing the levels of VEGF and damaging the transforming growth factor (TGF)-β signaling pathway through the targeted inhibition of Smad4 in cartilage.
doi:10.3892/ijmm.2014.1808
PMCID: PMC4094584  PMID: 24939082
apoptosis; osteoarthritis; mechanical injury; chondrocyte; miR-146a
14.  Selective Killing of Mixed Lineage Leukemia Cells by a Potent Small-Molecule DOT1L Inhibitor 
Cancer cell  2011;20(1):53-65.
SUMMARY
Mislocated enzymatic activity of DOT1L has been proposed as a driver of leukemogenesis in mixed lineage leukemia (MLL). The characterization of EPZ004777, a potent, selective inhibitor of DOT1L is reported. Treatment of MLL cells with the compound selectively inhibits H3K79 methylation and blocks expression of leukemogenic genes. Exposure of leukemic cells to EPZ004777 results in selective killing of those cells bearing the MLL gene translocation, with little effect on non-MLL-translocated cells. Finally, in vivo administration of EPZ004777 leads to extension of survival in a mouse MLL xenograft model. These results provide compelling support for DOT1L inhibition as a basis for targeted therapeutics against MLL.
doi:10.1016/j.ccr.2011.06.009
PMCID: PMC4046888  PMID: 21741596
15.  Levels of PAH-DNA Adducts in Placental Tissue and the Risk of Fetal Neural Tube Defects in a Chinese Population 
We examined the relationship between PAH-DNA adduct levels in the placental tissue, measured by a highly sensitive 32P-postlabeling assay, and the risk of fetal neural tube defects (NTDs). We further explored the interaction between PAH-DNA adducts and placental PAHs with respect to NTD risk. Placental tissues from 80 NTD-affected pregnancies and 50 uncomplicated normal pregnancies were included in this case-control study. Levels of PAH-DNA adducts were lower in the NTD group (8.12 per 108 nucleotides) compared to controls (9.92 per 108 nucleotides). PAH-DNA adduct concentrations below the median was associated with a 3-fold increased NTD risk. Women with a low PAH-DNA adduct level in concert with a high placental PAH level resulted in a 10-fold elevated risk of having an NTD-complicated pregnancy. A low level of placental PAH-DNA adducts was associated with an increased risk of NTDs; this risk increased dramatically when a low adduct level was coupled with a high placental PAH concentration.
doi:10.1016/j.reprotox.2013.01.008
PMCID: PMC4040017  PMID: 23416326
Polycyclic aromatic hydrocarbons (PAHs); DNA adducts; Neural tube defects (NTDs); Placenta; Fetus
16.  Crystallization and preliminary crystallographic study of a trypsin-resistant catalytic domain of human calcineurin 
A trypsin-resistant catalytic domain of human calcineurin α (A subunit, residues 20–347) was crystallized in space group P21212. An X-ray diffraction data set was collected to 2.87 Å resolution and the structure was solved by molecular replacement.
Calcineurin, a Ca2+/calmodulin-dependent serine/threonine protein phosphatase, plays a key role in a number of cellular pathways, including T-cell activation, and is an important molecular target of the immunosuppressive drugs cyclosporin A and FK506. To understand the structural basis underlying the activation of calcineurin by calmodulin, X-ray crystallography was employed to solve the three-dimensional structure of the free calcineurin catalytic domain (residues 20–347 of the A subunit). To accomplish this, a bacterially expressed glutathione S-­transferase (GST) fusion protein of the human calcineurin catalytic domain was first purified by GST-affinity chromatography. After limited digestion by trypsin, the catalytic domain (Cncat) was purified using anion-exchange and size-exclusion chromatography. Crystallization of Cncat was achieved by the hanging-drop vapour-diffusion method at pH 6.5 using PEG 6000 as precipitant. The diffraction results showed that the Cncat crystal belonged to the orthorhombic space group P21212, with unit-cell parameters a = 161.6, b = 87.4, c = 112.0 Å. There are four Cncat molecules in the asymmetric unit, with 49.5% solvent content. An X-ray diffraction data set was collected to 2.87 Å resolution and a clear molecular-replacement solution was obtained. The active site of Cncat is open to the solvent channels in the crystal packing.
doi:10.1107/S1744309112007890
PMCID: PMC3374516  PMID: 22691791
human calcineurin; catalytic domain
17.  Antioxidant capacity of follicular fluid from patients undergoing in vitro fertilization 
This study measured the antioxidant activity of follicular fluid (FF) in infertile patients and assessed its possible correlation between ovarian stimulation and pregnancy outcomes. Samples from 191 infertile patients undergoing in vitro fertilization-embryo transfer (IVF-ET) were determined by α-diphenyl-β-picrylhydrazyl (DPPH) radical scavenging, reducing power, superoxide radical scavenging, β-Carotene bleaching assay, ferrothiocyanate and thiobarbituric acid assays. The comparison between a positive IVF outcome and FF’s antioxidant activity was also studied. The results showed FF had strong antioxidant activity, which equated to common antioxidants Vc and BHT (100 μg/mL). Patients with endometriosis had less efficient antioxidant activity in FF than that of patients with tubal occlusion or polycystic ovary syndrome. In conclusion, this study detected, for the first time, the antioxidant activity of FF from patients undergoing an IVF and the FF exhibited strong antioxidant activity.
PMCID: PMC4069891  PMID: 24966936
Antioxidant activity; follicular fluid; in vitro fertilization; endometriosis
18.  High expression of 5-hydroxymethylcytosine and isocitrate dehydrogenase 2 is associated with favorable prognosis after curative resection of hepatocellular carcinoma 
Background
The expression of 5-hydroxymethylcytosine (5-hmC) and isocitrate dehydrogenase 2 (IDH2) is frequently downregulated in numerous cancers. 5-hmC and IDH2 expression in hepatocellular carcinoma (HCC) has yet to be determined.
Methods
The immunohistochemical expression of 5-hmC and IDH2 were analyzed in tissue microarrays containing samples from 646 patients who had undergone hepatectomy for histologically proven HCC. The prognostic value of 5-hmC and IDH2 were evaluated by Cox regression and Kaplan-Meier analyses.
Results
We discovered that low 5-hmC and IDH2 expression was associated with malignant behaviors. Low 5-hmC or IDH2 expression alone and combined 5-hmC and IDH2 expression were associated with lower overall survival (OS) rates and higher cumulative recurrence rates. Multivariate analysis indicated that 5-hmC or IDH2 and 5-hmC/IDH2 were independent prognostic indicators for OS and time to recurrence (TTR), which was confirmed in an independent validation cohort.
Conclusions
5-hmC and IDH2 correlate with less aggressive tumor behavior in HCC. When 5-hmC and IDH2 are considered together, they serve as a prognostic marker in patients with surgically resected HCCs.
doi:10.1186/1756-9966-33-32
PMCID: PMC4081660  PMID: 24716838
5-hydroxymethylcytosine; Isocitrate dehydrogenase 2; Hepatocellular carcinoma; Immunohistochemistry; Prognosis
19.  STING/MPYS Mediates Host Defense against Listeria Monocytogenes Infection by Regulating Ly6Chi Monocyte Migration 
MPYS (a.k.a STING, MITA, TMEM173) is a type I IFN stimulator that is essential for host defense against DNA virus infection and appears important in defense against certain bacteria. The in vivo significance and mechanisms by which MPYS mediates host defense against non-viral pathogens are unknown. Using a MPYS deficient mouse (Tmem173) we determined that, distinct from the IFNRA−/− mice, MPYS deficiency leads to increased bacterial burden in the liver upon Listeria monocytogenes infection. The increase was correlated with the diminished MCP-1 and MCP-3 chemokine production, and decreased blood and liver Ly6Chi monocytes frequency. We further demonstrate that MPYS deficient Ly6Chi monocytes are intrinsically defective in migration to the liver. Lastly, adoptive transfer of WT Ly6Chi monocyte into MPYS deficient mice decreases their liver bacterial burden. Our findings reveal a novel in vivo function of MPYS that is distinct from its role in activating type I IFN production.
doi:10.4049/jimmunol.1201788
PMCID: PMC3593745  PMID: 23378430
20.  The Bioinformatics Analysis of miRNAs Signatures Differentially Expressed in HER2(+) Versus HER2(−) Breast Cancers 
Abstract
Objective
To identify the signatures of miRNAs differentially expressed in HER2(+) versus HER2(−) breast cancers that accurately predict the HER2 status of breast cancer, and to provide further insight into breast cancer therapy.
Methods
By the methods of literature search, aberrant expressed miRNAs were collected. By target prediction algorithm of TargetScan and PicTar and the data enrichment analysis, target gene sets of miRNAs differentially expressed in HER2(+) versus HER2(−) breast cancers were built. Then, using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database, the function modules of Gene Ontology categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) and BIOCARTA pathway, biological functions and signaling pathways that are probably regulated by miRNAs, were analyzed.
Results
We got five sets of miRNAs expressed in different HER2 status of breast cancers finally. The five sets of data contain 22; 32; 3; 38; and 62 miRNAs, respectively. After miRNAs target prediction and data enrichment, 5,734; 22,409; 1,142; 22,293; and 43,460 target genes of five miRNA sets were collected. Gene ontology analysis found these genes may be involved in transcription, protein transport, angiogenesis, and apoptosis. Moreover, certain KEGG and BIOCARTA signaling pathways related toHER2 status were found.
Conclusion
Using TargetScan and PicTar for data enrichment, and DAVID database, Gene Ontology categories, KEGG and BIOCARTA pathway for analysis of miRNAs different expression, we conducted a new method for biological interpretation of miRNA profiling data in HER2(+) versus HER2(−) breast cancers. It may improve understanding the regulatory roles of miRNAs in different molecular subtypes of breast cancers. Therefore, it is beneficial to improve the accuracy of experimental efforts to breast cancer and potential therapeutic targets.
doi:10.1089/cbr.2012.1311
PMCID: PMC3545315  PMID: 23009584
bioinformatics; breast cancer; HER2; miRNAs
21.  Myeloid-Derived Suppressor Cells Are Associated with Viral Persistence and Downregulation of TCR ζ Chain Expression on CD8+ T Cells in Chronic Hepatitis C Patients 
Molecules and Cells  2014;37(1):66-73.
Myeloid-derived suppressor cells (MDSCs) play an important role in impairing the function of T cells. We characterized MDSCs in two chronic hepatitis C (CHC) cohorts: a cross-sectional group that included 61 treatment-naive patients with CHC, 14 rapid virologic response (RVR) cases and 22 early virologic response (EVR) cases; and a longitudinal group of 13 cases of RVR and 10 cases of EVR after pegylated-interferon-α/ribavirin treatment for genotype 1b HCV infection. Liver samples from 32 CHC patients and six healthy controls were subjected to immunohistochemical analysis. MDSCs frequency in treatment-naive CHC was significantly higher than in RVR, EVR, or healthy subjects and was positively correlated with HCV RNA. Patients infected with HCV genotype 2a had a significantly higher frequency of MDSCs than those infected with genotype 1b. Decreased T cell receptor (TCR) ζ expression on CD8+ T cells was significantly associated with an increased frequency of MDSCs in treatment-naive CHC patients and was restored by L-arginine treatment in vitro. Increased numbers of liver arginase-1+ cells were closely associated with the histological activity index in CHC. The TCR ζ chain was significantly downregulated on hepatic CD8+ T cells in CHC. During antiviral follow up, MDSCs frequency in peripheral blood mononuclear cells was directly correlated with the HCV RNA load in the plasma and inversely correlated with TCR ζ chain expression in CD8+ T cells in both RVR and EVR cases. Notably, the RVR group had a higher frequency of MDSCs at baseline than the EVR group. Collectively, this study provides evidence that MDSCs might be associated with HCV persistence and downregulation of CD8 ζ chain expression.
doi:10.14348/molcells.2014.2282
PMCID: PMC3907002  PMID: 24552712
arginase-1; hepatitis C virus; L-arginine; myeloid-derived suppressor cell; TCR ζ chain
22.  A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 Å resolution 
eLife  2013;2:e01299.
Bacteriophage BPP-1 infects and kills Bordetella species that cause whooping cough. Its diversity-generating retroelement (DGR) provides a naturally occurring phage-display system, but engineering efforts are hampered without atomic structures. Here, we report a cryo electron microscopy structure of the BPP-1 head at 3.5 Å resolution. Our atomic model shows two of the three protein folds representing major viral lineages: jellyroll for its cement protein (CP) and HK97-like (‘Johnson’) for its major capsid protein (MCP). Strikingly, the fold topology of MCP is permuted non-circularly from the Johnson fold topology previously seen in viral and cellular proteins. We illustrate that the new topology is likely the only feasible alternative of the old topology. β-sheet augmentation and electrostatic interactions contribute to the formation of non-covalent chainmail in BPP-1, unlike covalent inter-protein linkages of the HK97 chainmail. Despite these complex interactions, the termini of both CP and MCP are ideally positioned for DGR-based phage-display engineering.
DOI: http://dx.doi.org/10.7554/eLife.01299.001
eLife digest
Whooping cough is a respiratory illness caused by bacteria in the Bordetella genus. Among the general public, Bordetella species have become a hot topic in recent years due to the re-emergence of whooping cough in the United States and elsewhere. Scientists, meanwhile have become interested in a virus called BPP-1 that can kill the Bordetella species.
BPP-1 is a double-stranded DNA virus, and such viruses have long been of interest to scientists because they are the most abundant organisms on Earth. These viruses are also noteworthy because their shells (also known as capsids) are capable of withstanding the very high pressures (up to about 40 atmospheres) that are created by packing so much DNA into the very small volume inside the capsid.
BPP-1 is of particular interest because it is capable of making large-scale changes to its own DNA in order to adapt to changes in its hosts and environment. Of all the organism that do not contain nuclei within their cells (collectively known as prokaryotes), BPP-1 is the only one that is capable of making such changes to its DNA. However, efforts to exploit the properties of BPP-1 for bioengineering applications have been hampered because its detailed structure is not known. Now Zhang et al. have used cryo electron microscopy to study the structure of BPP-1 at the atomic level.
Most viruses belong to one of three major lineages, with each lineage having a characteristic fold in its capsid proteins. Zhang et al. found that BPP-1 contains two of these folds, which suggests that it is a hybrid of two of these lineages. This is the first time that such a structure has been observed. Moreover, Zhang et al. found that one of the folds has an unusual topology that has not been seen before. The atomic structure reveals how double-stranded DNA viruses use a variety of non-covalent interactions and a type of protein ‘chainmail’ to form a highly stable capsid that is capable of withstanding very high pressures.
In addition to enabling applications in bioengineering, the new structure might also provide insights into the evolution of prokaryotes.
DOI: http://dx.doi.org/10.7554/eLife.01299.002
doi:10.7554/eLife.01299
PMCID: PMC3863775  PMID: 24347545
CryoEM; atomic resolution; non-covalent chainmail; phage-display; fold topology; Viruses
23.  STAT3-dependent transactivation of miRNA genes following Toxoplasma gondii infection in macrophage 
Parasites & Vectors  2013;6:356.
Background
The apicomplexan parasite Toxoplasma gondii can infect and replicate in virtually any nucleated cell in many species of warm-blooded animals; T. gondii has elaborate mechanisms to counteract host-cell apoptosis in order to maintain survival and breed in the host cells.
Methods
Using microarray profiling and a combination of conventional molecular approaches, we investigated the levels of microRNAs (miRNAs ) in human macrophage during T. gondii infection. We used molecular tools to examine Toxoplasma-upregualted miRNAs to revealed potential signal transducers and activators of transcription 3(STAT3) binding sites in the promoter elements of a subset of miRNA genes. We analysed the apoptosis of human macrophage with the functional inhibition of the STAT3-binding miRNAs by flow cytometry.
Results
Our results demonstrated differential alterations in the mature miRNA expression profile in human macrophage following T. gondii infection. Database analysis of Toxoplasma-upregulated miRNAs revealed potential STAT3 binding sites in the promoter elements of a subset of miRNA genes. We demonstrated that miR-30c-1, miR-125b-2, miR-23b-27b-24-1 and miR-17 ~ 92 cluster genes were transactivated through promoter binding of the STAT3 following T. gondii infection. Importantly, functional inhibition of selected STAT3-binding miRNAs in human macropahges increased apoptosis of host cells.
Conclusions
A panel of miRNAs is regulated through promoter binding of the STAT3 in human macrophage and these miRNAs are involved in anti-apoptosis in response to T. gondii infection.
doi:10.1186/1756-3305-6-356
PMCID: PMC3878672  PMID: 24341525
Toxoplasma; MicroRNA; Apoptosis; STAT3; Macrophage
24.  IL-2 therapy promotes suppressive ICOS+ Treg expansion in melanoma patients  
High-dose (HD) IL-2 therapy in patients with cancer increases the general population of Tregs, which are positive for CD4, CD25, and the Treg-specific marker Foxp3. It is unknown whether specific subsets of Tregs are activated and expanded during HD IL-2 therapy or whether activation of any particular Treg subset correlates with clinical outcome. Here, we evaluated Treg population subsets that were induced in patients with melanoma following HD IL-2 therapy. We identified a Treg population that was positive for CD4, CD25, Foxp3, and the inducible T cell costimulator (ICOS). This Treg population increased more than any other lymphocyte subset during HD IL-2 therapy and had an activated Treg phenotype, as indicated by high levels of CD39, CD73, and TGF-β. ICOS+ Tregs were the most proliferative lymphocyte population in the blood after IL-2 therapy. Patients with melanoma with enhanced expansion of ICOS+ Tregs in blood following the first cycle of HD IL-2 therapy had worse clinical outcomes than patients with fewer ICOS+ Tregs. However, there was no difference in total Treg expansion between HD IL-2 responders and nonresponders. These data suggest that increased expansion of the ICOS+ Treg population following the first cycle of HD IL-2 therapy may be predictive of clinical outcome.
doi:10.1172/JCI46266
PMCID: PMC3871216  PMID: 24292706
25.  Fluorescent Protein Voltage Probes Derived from ArcLight that Respond to Membrane Voltage Changes with Fast Kinetics 
PLoS ONE  2013;8(11):e81295.
We previously reported the discovery of a fluorescent protein voltage probe, ArcLight, and its derivatives that exhibit large changes in fluorescence intensity in response to changes of plasma membrane voltage. ArcLight allows the reliable detection of single action potentials and sub-threshold activities in individual neurons and dendrites. The response kinetics of ArcLight (τ1-on ~10 ms, τ2-on ~ 50 ms) are comparable with most published genetically-encoded voltage probes. However, probes using voltage-sensing domains other than that from the Ciona intestinalis voltage sensitive phosphatase exhibit faster kinetics. Here we report new versions of ArcLight, in which the Ciona voltage-sensing domain was replaced with those from chicken, zebrafish, frog, mouse or human. We found that the chicken and zebrafish-based ArcLight exhibit faster kinetics, with a time constant (τ) less than 6ms for a 100 mV depolarization. Although the response amplitude of these two probes (8-9%) is not as large as the Ciona-based ArcLight (~35%), they are better at reporting action potentials from cultured neurons at higher frequency. In contrast, probes based on frog, mouse and human voltage sensing domains were either slower than the Ciona-based ArcLight or had very small signals.
doi:10.1371/journal.pone.0081295
PMCID: PMC3842285  PMID: 24312287

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