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1.  The Rapid Screening of Triazophos Residues in Agricultural Products by Chemiluminescent Enzyme Immunoassay 
PLoS ONE  2015;10(7):e0133839.
A highly sensitive chemiluminescent enzyme immunoassay (CLEIA) method was developed in this study for efficient screening of triazophos residues in a large number of samples. Based on the maximum residue limits (MRLs) set by China and CAC for triazophos in different agro-products, the representative apple, orange, cabbage, zucchini, and rice samples were selected as spiked samples, and the triazophos at the concentrations of the MRL values were spiked to blank samples. Subsequently, the five samples with the spiked triazophos standard were measured by CLEIA 100 times, and the detection results indicated that the correction factors of the apple, orange, cabbage, zucchini, and rice were determined as 0.79, 0.66, 0.85, 0.76, and 0.91, respectively. In this experiment, 1500 real samples were detected by both the CLEIA and the GC-MS methods. With the GC-MS method, 1462 samples were identified as negative samples and 38 samples as positive samples. Based on the correction factors, the false positive rate of the CLEIA method was 0.13%, and false negative rate was 0. The results showed that the established CLEIA method could be used to screen a large number of real samples.
PMCID: PMC4517747  PMID: 26218576
2.  Study on Enhancement Principle and Stabilization for the Luminol-H2O2-HRP Chemiluminescence System 
PLoS ONE  2015;10(7):e0131193.
A luminol-H2O2-HRP chemiluminescence system with high relative luminescent intensity (RLU) and long stabilization time was investigated. First, the comparative study on the enhancement effect of ten compounds as enhancers to the luminol-H2O2-HRP chemiluminescence system was carried out, and the results showed that 4-(imidazol-1-yl)phenol (4-IMP), 4-iodophenol (4-IOP), 4-bromophenol (4-BOP) and 4-hydroxy-4’-iodobiphenyl (HIOP) had the best performance. Based on the experiment, the four enhancers were dissolved in acetone, acetonitrile, methanol, and dimethylformamide (DMF) with various concentrations, the results indicated that 4-IMP, 4-IOP, 4-BOP and HIOP dissolved in DMF with the concentrations of 0.2%, 3.2%, 1.6% and 3.2% could get the highest RLU values. Subsequently, the influences of pH, ionic strength, HRP, 4-IMP, 4-IOP, 4-BOP, HIOP, H2O2 and luminol on the stabilization of the luminol-H2O2-HRP chemiluminescence system were studied, and we found that pH value, ionic strength, 4-IMP, 4-IOP, 4-BOP, HIOP, H2O2 and luminol have little influence on luminescent stabilization, while HRP has a great influence. In different ranges of HRP concentration, different enhancers should be selected. When the concentration is within the range of 0~6 ng/mL, 4-IMP should be selected. When the concentration of HRP ranges from 6 to 25ng/mL, 4-IOP was the best choice. And when the concentration is within the range of 25~80 ng/mL, HIOP should be selected as the enhancer. Finally, the three well-performing chemiluminescent enhanced solutions (CESs) have been further optimized according to the three enhancers (4-IMP, 4-IOP and HIOP) in their utilized HRP concentration ranges.
PMCID: PMC4495922  PMID: 26154162
3.  Neonatal outcome of early rescue ICSI and ICSI with ejaculated sperm 
To evaluate the impact of early rescue ICSI on neonatal outcome.
This retrospective study compared the neonatal outcome of early rescue ICSI and ICSI with ejaculated sperm, including 233 children who were conceived after early rescue ICSI and a control group of 906 children who were conceived after ICSI with ejaculated sperm, and all of the children had a gestational age of 20 weeks or more. The numbers of live and stillbirths, perinatal deaths, prematurity, birthweights and birth defects of the children were compared.
Children in the early rescue ICSI group showed no increased risk of stillbirths, perinatal death or birth defects. Those children also did not differ from those of the ICSI with ejaculated sperm group in gender rate, birthweight, gestational age or prematurity.
Early rescue ICSI did not increase the adverse effect on the neonatal outcome when compared to that of ICSI with ejaculated sperm.
PMCID: PMC4096880  PMID: 24824350
Early rescue ICSI; Total fertilization failure; Children; Outcome; Birth defects
4.  Investigation of Ground-Level Ozone and High-Pollution Episodes in a Megacity of Eastern China 
PLoS ONE  2015;10(6):e0131878.
Differential Optical Absorption Spectroscopy (DOAS) was used for the long-term observation of ground-level ozone (O3) from March 2010 to March 2013 over Shanghai, China. The 1-hour average concentration of O3 was 27.2 ± 17.0 ppbv. O3 level increased during spring, reached the peak in late spring and early summer, and then decreased in autumn and finally dropped to the bottom in winter. The highest monthly average O3 concentration in June (41.1 ppbv) was nearly three times as high as the lowest level recorded in December (15.2 ppbv). In terms of pollution episodes, 56 hourly samples (on 14 separate days) in 2010 exceeded the 1-hour ozone limit of 200 μg/m3 specified by the Grade II of the Chinese Ambient Air Quality Standards (CAAQS, revised GB 3095-2012). Utilizing the Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model, the primary contribution to high ozone days (HODs) was identified as the regional transportation of volatile organic compounds (VOC) and high concentrations of O3 from the chemical industrial zone in the Jinshan district of Shanghai. HODs showed higher concentrations of HONO and NO2 than non-episode conditions, implying that HONO at high concentration during HODs was capable of increasing the O3 concentration. The photolysis rate of HONO was estimated, suggesting that the larger number of OH radicals resulting from high concentrations of HONO have a considerable impact on ozone concentrations.
PMCID: PMC4486460  PMID: 26121146
5.  Undersampled MR Image Reconstruction with Data-Driven Tight Frame 
Undersampled magnetic resonance image reconstruction employing sparsity regularization has fascinated many researchers in recent years under the support of compressed sensing theory. Nevertheless, most existing sparsity-regularized reconstruction methods either lack adaptability to capture the structure information or suffer from high computational load. With the aim of further improving image reconstruction accuracy without introducing too much computation, this paper proposes a data-driven tight frame magnetic image reconstruction (DDTF-MRI) method. By taking advantage of the efficiency and effectiveness of data-driven tight frame, DDTF-MRI trains an adaptive tight frame to sparsify the to-be-reconstructed MR image. Furthermore, a two-level Bregman iteration algorithm has been developed to solve the proposed model. The proposed method has been compared to two state-of-the-art methods on four datasets and encouraging performances have been achieved by DDTF-MRI.
PMCID: PMC4495234  PMID: 26199641
6.  Identification, Phylogeny, and Transcript of Chitinase Family Genes in Sugarcane 
Scientific Reports  2015;5:10708.
Chitinases are pathogensis-related proteins, which play an important role in plant defense mechanisms. The role of the sugarcane chitinase family genes remains unclear due to the highly heterozygous and aneuploidy chromosome genetic background of sugarcane. Ten differentially expressed chitinase genes (belonging to class I~VII) were obtained from RNA-seq analysis of both incompatible and compatible sugarcane genotypes during Sporisorium scitamineum challenge. Their structural properties and expression patterns were analyzed. Seven chitinases (ScChiI1, ScChiI2, ScChiI3, ScChiIII1, ScChiIII2, ScChiIV1 and ScChiVI1) showed more positive with early response and maintained increased transcripts in the incompatible interaction than those in the compatible one. Three (ScChiII1, ScChiV1 and ScChiVII1) seemed to have no significant difference in expression patterns between incompatible and compatible interactions. The ten chitinases were expressed differentially in response to hormone treatment as well as having distinct tissue specificity. ScChiI1, ScChiIV1 and ScChiVII1 were induced by various abiotic stresses (NaCl, CuCl2, PEG and 4 °C) and their involvement in plant immunity was demonstrated by over-expression in Nicotiana benthamiana. The results suggest that sugarcane chitinase family exhibit differential responses to biotic and abiotic stress, providing new insights into their function.
PMCID: PMC4451799  PMID: 26035173
7.  Metastasis is regulated via microRNA-200/ZEB1 axis control of tumor cell PD-L1 expression and intratumoral immunosuppression 
Nature communications  2014;5:5241.
Immunosuppression of tumor-infiltrating lymphocytes (TIL) is a common feature of advanced cancer, but its biological basis has remained obscure. We demonstrate here a molecular link between epithelial-to-mesenchymal transition (EMT) and CD8+ TIL immunosuppression, two key drivers of cancer progression. We show that microRNA-200 (miR-200), a cell-autonomous suppressor of EMT and metastasis, targets PD-L1. Moreover, ZEB1, an EMT activator and transcriptional repressor of miR-200, relieves miR-200 repression of PD-L1 on tumor cells, leading to CD8+ T cell immunosuppression and metastasis. These findings are supported by robust correlations between the EMT score, miR-200 levels and PD-L1 expression in multiple human lung cancer datasets. In addition to revealing a link between EMT and T cell dysfunction, these findings also show that ZEB1 promotes metastasis through a heretofore unappreciated cell non-autonomous mechanism, and suggest that subgroups of patients in whom malignant progression is driven by EMT activators may respond to treatment with PD-L1 antagonists.
PMCID: PMC4212319  PMID: 25348003
8.  Genetic polymorphisms of NAMPT related with susceptibility to esophageal Squamous cell carcinoma 
BMC Gastroenterology  2015;15:49.
Nicotinamide phosphoribosyl transferase (Nampt) plays a crucial role in tumorigenesis. The present study examines whether genetic polymorphisms of NAMPT are related to the risk of developing esophageal squamous cell carcinoma (ESCC).
A total of 810 subjects were enrolled in this study, including 405 ESCC patients and 405 healthy controls. Using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), genotypes at rs61330082, rs2505568 and rs9034 of NAMPT were identified. Haplotypes were constructed using PHASE software. Multivariate logistic regression models were used to evaluate the potentiating effects of the genotypes, alleles and haplotypes on the development of ESCC.
The presence of genotypes CT and TT and allele T at rs61330082 was less frequent in ESCC cases than in controls (48.89% vs. 53.33%, P < 0.01, 95% CI: 0.33-0.68; 18.52% vs. 30.37%, P < 0.01, 95% CI: 0.22-0.50; 42.96% vs. 57.04%, P < 0.01, 95% CI: 0.38-0.61; respectively). No statistically significant differences existed in the distributions of genotypes or alleles at rs2505568 or rs9034 between ESCC cases and controls. Of five haplotypes constructed, haplotypes CTC, CTT and CAC were higher in ESCC cases (P < 0.01, OR = 1.57, 95% CI: 1.16-2.12; P = 0.04, OR = 1.72, 95% CI: 1.03-2.85; P < 0.01, OR = 3.39, 95% CI: 1.99-5.75; respectively) than in controls.
Genetic polymorphisms of NAMPT, specifically genotype CC and allele C at rs61330082 as well as haplotypes CTC, CTT and CAC, were significantly correlated with ESCC susceptibility.
Electronic supplementary material
The online version of this article (doi:10.1186/s12876-015-0282-6) contains supplementary material, which is available to authorized users.
PMCID: PMC4408598  PMID: 25896907
Nicotinamide phosphoribosyl transferase; Polymorphism; Haplotype; Esophageal squamous cell carcinoma; Susceptibility
9.  Association between aldosterone synthase (CYP11B2) -344C/T polymorphism and atrial fibrillation among Han and Kazak residents of the Xinjiang region 
Objectives: Atrial fibrillation (AF) is one the most common and complex types of clinical arrhythmia syndromes. In recent years, an association between CYP11B2 gene polymorphisms and atrial myocardial fibrosis has received a significant amount of attention. This study explores the relationship between CYP11B2 gene-344C/T polymorphism and AF among Kazak and Han residents in the Xinjiang region and further clarifies the molecular mechanisms of atrial fibrillation. Methods: The study is a case-control study using traditional methods. We selected 156 Kazak and 203 Han patient cases in the Xinjiang region who had non-valvular atrial fibrillation as well as 307 Kazak and 418 Han cases of non-AF patients as a control group. Blood samples were collected, and DNA was extracted from the peripheral blood samples. The presence of the CYP11B2 gene-344C/T polymorphism was determined using polymerase chain reaction-restriction enzyme fragment length polymorphism (PCR-RFLP). Differences in the genotypes and allele distributions among the 2 groups were compared using Statistical Package for Social Science (SPSS) 17.0 statistical software. Student’s t test, the chi-squared test and logistic regression methods were used for the data analysis. Results: The genotypes of both ethnic groups followed a Hardy-Weinberg genetic equilibrium distribution. The 2 patient groups, compared with their respective control groups, showed significant dominant models in CYP11B2 gene-344C/T polymorphism genotype frequency and B1 allele frequency (P<0.05). The frequencies of the CYP11B2 gene-344C/T polymorphism in the Kazak patient group were higher compared with the control groups (P<0.05). The frequencies of the CYP11B2 gene-344C/T polymorphisms in the Han patient group was also higher compared with the control group (P<0.05). Logistic regression analysis showed that the frequencies of the CYP11B2 gene-344C/T genotypes were significantly different between the Kazak and Han patient groups and the control groups. Conclusion: CYP11B2 gene -344C/T polymorphism is associated with AF.
PMCID: PMC4484025  PMID: 26131131
Atrial fibrillation; CYP11B2 gene polymorphism; aldosterone
11.  The Expression and Distributions of ANP32A in the Developing Brain 
BioMed Research International  2015;2015:207347.
Acidic (leucine-rich) nuclear phosphoprotein 32 family, member A (ANP32A), has multiple functions involved in neuritogenesis, transcriptional regulation, and apoptosis. However, whether ANP32A has an effect on the mammalian developing brain is still in question. In this study, it was shown that brain was the organ that expressed the most abundant ANP32A by human multiple tissue expression (MTE) array. The distribution of ANP32A in the different adult brain areas was diverse dramatically, with high expression in cerebellum, temporal lobe, and cerebral cortex and with low expression in pons, medulla oblongata, and spinal cord. The expression of ANP32A was higher in the adult brain than in the fetal brain of not only humans but also mice in a time-dependent manner. ANP32A signals were dispersed accordantly in embryonic mouse brain. However, ANP32A was abundant in the granular layer of the cerebellum and the cerebral cortex when the mice were growing up, as well as in the Purkinje cells of the cerebellum. The variation of expression levels and distribution of ANP32A in the developing brain would imply that ANP32A may play an important role in mammalian brain development, especially in the differentiation and function of neurons in the cerebellum and the cerebral cortex.
PMCID: PMC4383345  PMID: 25866766
12.  Micheliolide Derivative DMAMCL Inhibits Glioma Cell Growth In Vitro and In Vivo 
PLoS ONE  2015;10(2):e0116202.
There is no highly effective chemotherapy for malignant gliomas to date. We found that dimethylaminomicheliolide (DMAMCL), a selective inhibitor of acute myeloid leukemia (AML) stem/progenitor cells, inhibited the growth of glioma cells.
The distribution of DMAMCL in brain was analyzed by an ultraperformance liquid chromatography-mass spectrometry (UPLC-MS/MS) system. The anti-tumor evaluations of DMAMCL in vitro were performed by MTT, FACS and RT-PCR. In vivo, the mixture of C6 cells and matrigel was injected into caudatum, and the anti-tumor activity of DMAMCL was evaluated by tumor growth and rat survival. The toxicity of DMAMCL was evaluated by body weight, daily food intake, hematological or serum biochemical analyses, and histological appearance of tissues.
The IC50 values of DMAMCL against the C6 and U-87MG cell lines in vitro were 27.18 ± 1.89 μM and 20.58 ± 1.61 μM, respectively. DAMMCL down-regulated the anti-apoptosis gene Bcl-2 and increased apoptosis in C6 and U-87MG cells in a dose-dependent manner. In a C6 rat tumor model, daily administration of DMAMCL for 21 days reduced the burden of C6 tumors by 60% to 88% compared to controls, and more than doubled the mean lifespan of tumor-bearing rats. Distribution analysis showed that the DMAMCL concentration was higher in the brain than in plasma. Evaluations for toxicity revealed that oral administration of DMAMCL at 200 or 300 mg/kg once a day for 21 days did not result in toxicity.
These results suggest that DMAMCL is highly promising for the treatment of glioma.
PMCID: PMC4320118  PMID: 25658946
13.  Molecular Characterization of Three Gonadotropin Subunits and Their Expression Patterns during Ovarian Maturation in Cynoglossus semilaevis 
The endocrine regulation of reproduction in a multiple spawning flatfish with an ovary of asynchronous development remains largely unknown. The objectives of this study were to monitor changes in mRNA expression patterns of three gonadotropin hormone (GTH) subunits (FSHβ, LHβ and CGα) and plasma GTH levels during ovarian maturation of half-smooth tongue sole Cynoglossus semilaevis. Cloning and sequence analysis revealed that the cDNAs of FSHβ, LHβ and CGα were 541, 670 and 685 bp in length, and encode for peptides of 130, 158 and 127 amino acids, respectively. The number of cysteine residues and potential N-linked glycosylation sites of the flatfish GTHs were conserved among teleosts. However, the primary structure of GTHs in Pleuronectiformes appeared to be highly divergent. The FSHβ transcriptional level in the pituitary remained high during the vitellogenic stage while plasma levels of FSH peaked and oocyte development was stimulated. The LHβ expression in the pituitary and ovary reached the maximum level during oocyte maturation stages when the plasma levels of LH peaked. The brain GTHs were expressed at the different ovarian stages. These results suggested that FSH and LH may simultaneously regulate ovarian development and maturation through the brain-pituitary-ovary axis endocrine system in tongue sole.
PMCID: PMC4346864  PMID: 25633101
Cynoglossus semilaevis; multiple spawner; gonadotropin; cDNA cloning; expression patterns; oocyte maturation
14.  Multiple receptor tyrosine kinase activation attenuates therapeutic efficacy of the fibroblast growth factor receptor 2 inhibitor AZD4547 in FGFR2 amplified gastric cancer 
Oncotarget  2014;6(4):2009-2022.
Fibroblast growth factor receptor 2 (FGFR2)-targeted therapy has attracted considerable attention as novel anticancer agents in gastric cancer (GC). However, intrinsic or acquired drug resistance has emerged as a major challenge to their clinical use. In this study, we demonstrated that several receptor tyrosine kinase (RTK), including EGFR, HER3 and MET, activations contributed to AZD4547 (a selective FGFR2 inhibitor) hyposensitivity in FGFR2 amplified GC cells. The rescue effect was abrogated by inhibiting these RTKs with their targeted tyrosine kinase inhibitors (TKIs). In addition, synergy in growth inhibition was observed when the GC cells were treated with a combination of AZD4547 and cetuximab (an EGFR monoclonal antibody) both in vitro and in vivo. More importantly, tissue microarray analysis revealed that these resistance-conferring RTKs were highly expressed in FGFR2 positive GC patients. Taken together, these observations demonstrated RTKs including EGFR, HER3 and MET activations as novel mechanisms of hyposensitivity to AZD4547. It will be clinically valuable to investigate the involvement of RTK-mediated signaling in intrinsicor acquired resistance to FGFR2 TKIs in GC. A combination targeted therapeutic strategy may be recommended for treating FGFR2 amplified GC patients with these RTK activations.
PMCID: PMC4385832  PMID: 25576915
drug resistance; gastric cancer; AZD4547; FGFR2
15.  Characterization of the Nucleocytoplasmic Shuttle of the Matrix Protein of Influenza B Virus 
Journal of Virology  2014;88(13):7464-7473.
Influenza B virus is an enveloped negative-strand RNA virus that contributes considerably to annual influenza illnesses in human. The matrix protein of influenza B virus (BM1) acts as a cytoplasmic-nuclear shuttling protein during the early and late stages of infection. The mechanism of this intracellular transport of BM1 was revealed through the identification of two leucine-rich CRM1-dependent nuclear export signals (NESs) (3 to 14 amino acids [aa] and 124 to 133 aa), one bipartite nuclear localization signal (NLS) (76 to 94 aa), and two phosphorylation sites (80T and 84S) in BM1. The biological function of the NLS and NES regions were determined through the observation of the intracellular distribution of enhanced green fluorescent protein (EGFP)-tagged signal peptides, and wild-type, NES-mutant, and NLS-mutant EGFP-BM1. Furthermore, the NLS phosphorylation sites 80T and 84S, were found to be required for the nuclear accumulation of EGFP-NLS and for the efficient binding of EGFP-BM1 to human importin-α1. Moreover, all of these regions/sites were required for the generation of viable influenza B virus in a 12-plasmid virus rescue system.
IMPORTANCE This study expands our understanding of the life cycle of influenza B virus by defining the dynamic mechanism of the nucleocytoplasmic shuttle of BM1 and could provide a scientific basis for the development of antiviral medication.
PMCID: PMC4054458  PMID: 24741102
16.  Characteristics of Nucleocytoplasmic Transport of H1N1 Influenza A Virus Nuclear Export Protein 
Journal of Virology  2014;88(13):7455-7463.
The influenza A virus nuclear export protein (NEP) plays crucial roles in the nuclear export of the viral ribonucleoprotein complex through the chromosome region maintenance 1 (CRM1)-mediated cellular protein transport system. However, the detailed mechanism of NEP nucleocytoplasmic trafficking remains incompletely understood. Here, we investigated the subcellular localization of NEP from two strains of H1N1 influenza A virus and found that 2009 swine-origin H1N1 influenza A virus A/California/04/2009 (CA04) NEP displayed a distinct cellular distribution pattern, forming unique nuclear aggregates, compared to A/WSN/33 (H1N1) (WSN) NEP. Characterization of the nucleocytoplasmic transport pathways of these two NEPs showed that they both enter the nucleus by passive diffusion but are exported through the nuclear export receptor CRM1-mediated pathway with different efficiencies. The two identified nuclear export signals (NESs) on the two NEPs functioned similarly despite differences in their amino acid sequences. Using a two-hybrid assay, we confirmed that the CA04 NEP interacts less efficiently with CRM1 and that a threonine residue at position 48 is responsible for the nuclear aggregation. The present study revealed the dissimilarity in subcellular NEP transport processes between the 2009 pandemic (H1N1) influenza A virus CA04 and the laboratory-adapted H1N1 virus WSN and uncovered the mechanism responsible for this difference.
IMPORTANCE Because the efficiency of the nucleocytoplasmic transport of viral components is often correlated with the viral RNA polymerase activity, propagation, and host range of influenza viruses, the present study investigated the subcellular localization of NEP from two strains of H1N1 influenza virus. We found that the NEPs of both A/California/04/2009 (H1N1) (CA04) and A/WSN/33 (H1N1) (WSN) enter the nucleus by passive diffusion but are exported with different efficiencies, which were caused by weaker binding activity between the CA04 NEP and CRM1. The results of the present study revealed characteristics of the nuclear import and export pathways of NEP and the mechanism responsible for the differences in the cellular distribution of NEP between two H1N1 strains.
PMCID: PMC4054460  PMID: 24741105
17.  Human mesenchymal stem cells possess different biological characteristics but do not change their therapeutic potential when cultured in serum free medium 
Mesenchymal stem cells (MSCs) are widely investigated in clinical researches to treat various diseases. Classic culture medium for MSCs, even for clinical use, contains fetal bovine serum. The serum-containing medium (SCM) seems a major obstacle for MSCs-related therapies due to the risk of contamination of infectious pathogens. Some studies showed that MSCs could be expanded in serum free medium (SFM); however, whether SFM would change the biological characteristics and safety issues of MSCs has not been well answered.
Human umbilical cord mesenchymal stem cells (hUC-MSCs) were cultured in a chemical defined serum free medium. Growth, multipotency, surface antigen expression, telomerase, immunosuppressive ability, gene expression profile and genomic stability of hUC-MSCs cultured in SFM and SCM were analyzed and compared side by side.
hUC-MSCs propagated more slowly and senesce ultimately in SFM. SFM-expanded hUC-MSCs were different from SCM-expanded hUC-MSCs in growth rate, telomerase, gene expression profile. However, SFM-expanded hUC-MSCs maintained multipotency and the profile of surface antigen which were used to define human MSCs. Both SFM- and SCM-expanded hUC-MSCs gained copy number variation (CNV) in long-term in vitro culture.
hUC-MCSs could be expanded in SFM safely to obtain enough cells for clinical application, meeting the basic criteria for human mesenchymal stem cells. hUC-MSCs cultured in SFM were distinct from hUC-MSCs cultured in SCM, yet they remained therapeutic potentials for future regenerative medicine.
Electronic supplementary material
The online version of this article (doi:10.1186/scrt522) contains supplementary material, which is available to authorized users.
PMCID: PMC4445567  PMID: 25476802
18.  Interferon-Inducible Cholesterol-25-Hydroxylase Inhibits Hepatitis C Virus Replication via Distinct Mechanisms 
Scientific Reports  2014;4:7242.
Cholesterol 25-hydroxylase (CH25H) as an interferon-stimulated gene (ISG) has recently been shown to exert broad antiviral activity through the production of 25-hydroxycholesterol (25HC), which is believed to inhibit the virus-cell membrane fusion during viral entry. However, little is known about the function of CH25H on HCV infection and replication and whether antiviral function of CH25H is exclusively mediated by 25HC. In the present study, we have found that although 25HC produced by CH25H can inhibit HCV replication, CH25H mutants lacking the hydroxylase activity still carry the antiviral activity against HCV but not other viruses such as MHV-68. Further studies have revealed that CH25H can interact with the NS5A protein of HCV and inhibit its dimer formation, which is essential for HCV replication. Thus, our work has uncovered a novel mechanism by which CH25H restricts HCV replication, suggesting that CH25H inhibits viral infection through both 25HC-dependent and independent events.
PMCID: PMC4252895  PMID: 25467815
19.  Genome sequencing of Sporisorium scitamineum provides insights into the pathogenic mechanisms of sugarcane smut 
BMC Genomics  2014;15(1):996.
Sugarcane smut can cause losses in cane yield and sugar content that range from 30% to total crop failure. Losses tend to increase with the passage of years. Sporisorium scitamineum is the fungus that causes sugarcane smut. This fungus has the potential to infect all sugarcane species unless a species is resistant to biotrophic fungal pathogens. However, it remains unclear how the fungus breaks through the cell walls of sugarcane and causes the formation of black or gray whip-like structures on the sugarcane plants.
Here, we report the first high-quality genome sequence of S. scitamineum assembled de novo with a contig N50 of 41 kb, a scaffold N50 of 884 kb and genome size 19.8 Mb, containing an estimated 6,636 genes. This phytopathogen can utilize a wide range of carbon and nitrogen sources. A reduced set of genes encoding plant cell wall hydrolytic enzymes leads to its biotrophic lifestyle, in which damage to the host should be minimized. As a bipolar mating fungus, a and b loci are linked and the mating-type locus segregates as a single locus. The S. scitamineum genome has only 6 G protein-coupled receptors (GPCRs) grouped into five classes, which are responsible for transducing extracellular signals into intracellular responses, however, the genome is without any PTH11-like GPCR. There are 192 virulence associated genes in the genome of S. scitamineum, among which 31 expressed in all the stages, which mainly encode for energy metabolism and redox of short-chain compound related enzymes. Sixty-eight candidates for secreted effector proteins (CSEPs) were found in the genome of S. scitamineum, and 32 of them expressed in the different stages of sugarcane infection, which are probably involved in infection and/or triggering defense responses. There are two non-ribosomal peptide synthetase (NRPS) gene clusters that are involved in the generation of ferrichrome and ferrichrome A, while the terpenes gene cluster is composed of three unknown function genes and seven biosynthesis related genes.
As a destructive pathogen to sugar industry, the S. scitamineum genome will facilitate future research on the genomic basis and the pathogenic mechanisms of sugarcane smut.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-996) contains supplementary material, which is available to authorized users.
PMCID: PMC4246466  PMID: 25406499
Sporisorium scitamineum, Sugarcane smut; Pathogenic mechanisms, G-protein coupled receptors, Carbohydrate degrading enzymes, Biotrophic properties, Candidates for secreted effector proteins, Secondary metabolic pathways
20.  Study on the Traffic Air Pollution inside and outside a Road Tunnel in Shanghai, China 
PLoS ONE  2014;9(11):e112195.
To investigate the vehicle induced air pollution situations both inside and outside the tunnel, the field measurement of the pollutants concentrations and its diurnal variations was performed inside and outside the Xiangyin tunnel in Shanghai from 13:00 on April 24th to 13:00 on April 25th, 2013. The highest hourly average concentrations of pollutants were quantified that CO, NO, NO2 and NOX inside the tunnel were 13.223 mg/m3, 1.829 mg/m3, 0.291 mg/m3 and 3.029 mg/m3, respectively, while the lowest ones were 3.086 mg/m3, 0.344 mg/m3, 0.080 mg/m3 and 0.619 mg/m3. Moreover, the concentrations of pollutants were higher during the daytime, and lower at night, which is relevant to the traffic conditions inside the tunnel. Pollutants concentrations inside the tunnel were much higher than those outside the tunnel. Then in a case of slow wind, the effect of wind is much smaller than the impact of pollution sources. Additionally, the PM2.5 concentrations climbed to the peak sharply (468.45 µg/m3) during the morning rush hours. The concentrations of organic carbon (OC) and elemental carbon (EC) in PM2.5 inside the tunnel were 37.09–99.06 µg/m3 and 22.69–137.99 µg/m3, respectively. Besides, the OC/EC ratio ranged from 0.72 to 2.19 with an average value of 1.34. Compared with the results of other tunnel experiments in Guangzhou and Shenzhen, China, it could be inferred that the proportion of HDVs through the Xiangyin tunnel is relatively lower.
PMCID: PMC4227705  PMID: 25386920
21.  Combined effects of the Pacific Decadal Oscillation and El Niño-Southern Oscillation on Global Land Dry–Wet Changes 
Scientific Reports  2014;4:6651.
The effects of natural variability, especially El Niño-Southern Oscillation (ENSO) effects, have been the focus of several recent studies on the change of drought patterns with climate change. The interannual relationship between ENSO and the global climate is not stationary and can be modulated by the Pacific Decadal Oscillation (PDO). However, the global land distribution of the dry–wet changes associated with the combination of ENSO and the PDO remains unclear. In the present study, this is investigated using a revised Palmer Drought Severity Index dataset (sc_PDSI_pm). We find that the effect of ENSO on dry–wet changes varies with the PDO phase. When in phase with the PDO, ENSO-induced dry–wet changes are magnified with respect to the canonical pattern. When out of phase, these dry–wet variations weaken or even disappear. This remarkable contrast in ENSO's influence between the two phases of the PDO highlights exciting new avenues for obtaining improved global climate predictions. In recent decades, the PDO has turned negative with more La Niña events, implying more rain and flooding over land. La Niña-induced wet areas become wetter and the dry areas become drier and smaller due to the effects of the cold PDO phase.
PMCID: PMC4200402  PMID: 25323549
22.  Temperature Sensing in Seawater Based on Microfiber Knot Resonator 
Sensors (Basel, Switzerland)  2014;14(10):18515-18525.
Ocean internal-wave phenomena occur with the variation in seawater vertical temperature, and most internal-wave detections are dependent on the measurement of seawater vertical temperature. A seawater temperature sensor based on a microfiber knot resonator (MKR) is designed theoretically and demonstrated experimentally in this paper. Especially, the dependences of sensing sensitivity on fiber diameter and probing wavelength are studied. Calculated results show that sensing sensitivity increases with the increasing microfiber diameter with the range of 2.30–3.91 μm and increases with the increasing probing wavelength, which reach good agreement with results obtained by experiments. By choosing the appropriate parameters, the maximum sensitivity measured can reach to be 22.81 pm/°C. The seawater temperature sensor demonstrated here shows advantages of small size, high sensitivity, easy fabrication, and easy integration with fiber systems, which may offer a new optical method to detect temperature of seawater or ocean internal-wave phenomenon and offer valuable reference for assembling micro sensors used for other parameters related to seawater, such as salinity, refractive index, concentration of NO3− and so on.
PMCID: PMC4239933  PMID: 25299951
microfiber; knot resonator; seawater temperature; sensing; ocean internal-wave
23.  Prognostic Value of FGFR Gene Amplification in Patients with Different Types of Cancer: A Systematic Review and Meta-Analysis 
PLoS ONE  2014;9(8):e105524.
Fibroblast growth factor receptor (FGFR) gene amplification has been reported in different types of cancer. We performed an up-to-date meta-analysis to further characterize the prognostic value of FGFR gene amplification in patients with cancer.
A search of several databases, including MEDLINE (PubMed), EMBASE, Web of Science, and China National Knowledge Infrastructure, was conducted to identify studies examining the association between FGFR gene amplification and cancer. A total of 24 studies met the inclusion criteria, and overall incidence rates, hazard risk (HR), overall survival, disease-free survival, and 95% confidence intervals (CIs) were calculated employing fixed- or random-effects models depending on the heterogeneity of the included studies.
In the meta-analysis of 24 studies, the prevalence of FGFR gene amplification was FGFR1: 0.11 (95% CI: 0.08–0.13) and FGFR2: 0.04 (95% CI: 0.02–0.06). Overall survival was significantly worse among patients with FGFR gene amplification: FGFR1 [HR 1.57 (95% CI: 1.23–1.99); p = 0.0002] and FGFR2 [HR 2.27 (95% CI: 1.73–3.00); p<0.00001].
Current evidence supports the conclusion that the outcomes of patients with FGFR gene amplified cancers is worse than for those with non-FGFR gene amplified cancers.
PMCID: PMC4149366  PMID: 25171497
24.  A Simple Quality Assessment Index for Stereoscopic Images Based on 3D Gradient Magnitude 
The Scientific World Journal  2014;2014:890562.
We present a simple quality assessment index for stereoscopic images based on 3D gradient magnitude. To be more specific, we construct 3D volume from the stereoscopic images across different disparity spaces and calculate pointwise 3D gradient magnitude similarity (3D-GMS) along three horizontal, vertical, and viewpoint directions. Then, the quality score is obtained by averaging the 3D-GMS scores of all points in the 3D volume. Experimental results on four publicly available 3D image quality assessment databases demonstrate that, in comparison with the most related existing methods, the devised algorithm achieves high consistency alignment with subjective assessment.
PMCID: PMC4123633  PMID: 25133265
25.  Molecular mechanism for Rabex-5 GEF activation by Rabaptin-5 
eLife  2014;3:e02687.
Rabex-5 and Rabaptin-5 function together to activate Rab5 and further promote early endosomal fusion in endocytosis. The Rabex-5 GEF activity is autoinhibited by the Rabex-5 CC domain (Rabex-5CC) and activated by the Rabaptin-5 C2-1 domain (Rabaptin-5C21) with yet unknown mechanism. We report here the crystal structures of Rabex-5 in complex with the dimeric Rabaptin-5C21 (Rabaptin-5C212) and in complex with Rabaptin-5C212 and Rab5, along with biophysical and biochemical analyses. We show that Rabex-5CC assumes an amphipathic α-helix which binds weakly to the substrate-binding site of the GEF domain, leading to weak autoinhibition of the GEF activity. Binding of Rabaptin-5C21 to Rabex-5 displaces Rabex-5CC to yield a largely exposed substrate-binding site, leading to release of the GEF activity. In the ternary complex the substrate-binding site of Rabex-5 is completely exposed to bind and activate Rab5. Our results reveal the molecular mechanism for the regulation of the Rabex-5 GEF activity.
eLife digest
Cells need to allow various molecules to pass through the plasma membrane on their surface. Some molecules have to enter the cell, whereas others have to leave. Cells rely on a process called endocytosis to move large molecules into the cell. This involves part of the membrane engulfing the molecule to form a ‘bubble’ around it. This bubble, which is called an endosome, then moves the molecule to final destination inside the cell.
A protein called Rab5 controls how a new endosome is produced. However, before this can happen, various other molecules—including two proteins called Rabex-5 and Rabaptin-5—must activate the Rab5 protein. Exactly how these three proteins interact with each other was unknown.
Zhang et al. used X-ray crystallography to examine the structures of the complexes formed when Rabex-5 and Rabaptin-5 bind to each other, both when Rab5 is present, and also when it is absent. Biochemical and biophysical experiments confirmed that the Rabex-5/Rabaptin-5 complex is able to activate Rab5.
Zhang et al. also found that Rabex-5, on its own, folds so that the site that normally binds to Rab5 instead binds to a different part of Rabex-5, thus preventing endocytosis. However, when Rabaptin-5 forms a complex with Rabex-5, the Rab5 binding site is freed up.
The Rabex-5/Rabaptin-5 complex can switch between a V shape and a linear structure. Binding to Rab5 stabilizes the linear form of the complex, which then helps activate Rab5, and subsequently the activated Rab5 can interact with other downstream molecules, triggering endocytosis.
PMCID: PMC4102244  PMID: 24957337
crystal structure; Rab5; rabex-5; Rabaptin-5; GEF activity; molecular mechanism; E. coli; human

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