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1.  Novel Numerical Characterization of Protein Sequences Based on Individual Amino Acid and Its Application 
BioMed Research International  2015;2015:909567.
The hydrophobicity and hydrophilicity of amino acids play a very important role in protein folding and its interaction with the environment and other molecules, as well as its catalytic mechanism. Based on the two physicochemical indexes, a 2D graphical representation of protein sequences is introduced; meanwhile, a new numerical characteristic has been proposed to compute the distance of different sequences for analysis of sequence similarity/dissimilarity on the basis of this graphical representation. Furthermore, we apply the new distance in the similarities/dissimilarities of ND5 proteins of nine species and predict the four major classes based on the dataset containing 639 domains. The results show that the method is simple and effective.
doi:10.1155/2015/909567
PMCID: PMC4332462
2.  Enhancing Astrocytic Lysosome Biogenesis Facilitates Aβ Clearance and Attenuates Amyloid Plaque Pathogenesis 
The Journal of Neuroscience  2014;34(29):9607-9620.
In sporadic Alzheimer's disease (AD), impaired Aβ removal contributes to elevated extracellular Aβ levels that drive amyloid plaque pathogenesis. Extracellular proteolysis, export across the blood–brain barrier, and cellular uptake facilitate physiologic Aβ clearance. Astrocytes can take up and degrade Aβ, but it remains unclear whether this function is insufficient in AD or can be enhanced to accelerate Aβ removal. Additionally, age-related dysfunction of lysosomes, the major degradative organelles wherein Aβ localizes after uptake, has been implicated in amyloid plaque pathogenesis. We tested the hypothesis that enhancing lysosomal function in astrocytes with transcription factor EB (TFEB), a master regulator of lysosome biogenesis, would promote Aβ uptake and catabolism and attenuate plaque pathogenesis. Exogenous TFEB localized to the nucleus with transcriptional induction of lysosomal biogenesis and function in vitro. This resulted in significantly accelerated uptake of exogenously applied Aβ42, with increased localization to and degradation within lysosomes in C17.2 cells and primary astrocytes, indicating that TFEB is sufficient to coordinately enhance uptake, trafficking, and degradation of Aβ. Stereotactic injection of adeno-associated viral particles carrying TFEB driven by a glial fibrillary acidic protein promoter was used to achieve astrocyte-specific expression in the hippocampus of APP/PS1 transgenic mice. Exogenous TFEB localized to astrocyte nuclei and enhanced lysosome function, resulting in reduced Aβ levels and shortened half-life in the brain interstitial fluid and reduced amyloid plaque load in the hippocampus compared with control virus-injected mice. Therefore, activation of TFEB in astrocytes is an effective strategy to restore adequate Aβ removal and counter amyloid plaque pathogenesis in AD.
doi:10.1523/JNEUROSCI.3788-13.2014
PMCID: PMC4099542  PMID: 25031402
Alzheimer's disease; amyloid; astrocytes; lysosomes; TFEB
3.  An analysis of the association between a polymorphism of KCNJ11 and diabetic retinopathy in a Chinese Han population 
Background
Genome-wide association studies (GWAS) have reported that the polymorphism rs5219 of the potassium inwardly rectifying channel, subfamily J, member 11 (KCNJ11) is associated with type 2 diabetes mellitus (T2DM). Given that diabetic retinopathy (DR) is one of the most common microvascular complications of T2DM, GWAS have identified a number of potential susceptibility genes for DR. However, only a fraction of them have been replicated in different studies and show consistent genetic associations with the occurrence of DR. The aim of the present study was to investigate whether common variants of KCNJ11 confer DR in a cohort of the Chinese Han population.
Methods
A case–control study of 580 T2DM patients, including 105 T2DM with DR and 475 T2DM without DR was performed. A single nucleotide polymorphism (SNP) of KCNJ11 (rs5219) was genotyped, and its association with DR was explored using a dominant genetic model. Genotyping was performed by iPLEX technology. Univariate and multivariate logistic regression (MLR) analysis controlling for confounders was conducted to evaluate the association between rs5219 and DR.
Results
The A allele frequency of rs5219 was significantly higher in DR patients than that in the patients without DR (49.01% versus 38.68%, P <0.05). We found the minor A allele could increase the risk to develop DR (ORint = 1.58, 95% CI: 1.139 to 2.192 for allele and P = 0.006, ORint = 1.607, 95% CI: 1.267 to 2.038 for genotype and P <0.001) in the Chinese Han population.
Conclusions
Our findings provided evidence that KCNJ11 was associated with DR in Chinese Han patients with T2DM.
doi:10.1186/s40001-014-0075-3
PMCID: PMC4301311  PMID: 25573672
KCNJ11; Polymorphism; Diabetic retinopathy; Chinese Han population
4.  Analysis of Potato virus Y Coat Protein Epitopes Recognized by Three Commercial Monoclonal Antibodies 
PLoS ONE  2014;9(12):e115766.
Background
Potato virus Y (PVY, genus Potyvirus) causes substantial economic losses in solanaceous plants. Routine screening for PVY is an essential part of seed potato certification, and serological assays are often used. The commercial, commonly used monoclonal antibodies, MAb1128, MAb1129, and MAb1130, recognize the viral coat protein (CP) of PVY and distinguish PVYN strains from PVYO and PVYC strains, or detect all PVY strains, respectively. However, the minimal epitopes recognized by these antibodies have not been identified.
Methodology/Principal Findings
SPOT peptide array was used to map the epitopes in CP recognized by MAb1128, MAb1129, and MAb1130. Then alanine replacement as well as N- and C-terminal deletion analysis of the identified peptide epitopes was done to determine critical amino acids for antibody recognition and the respective minimal epitopes. The epitopes of all antibodies were located within the 30 N-terminal-most residues. The minimal epitope of MAb1128 was 25NLNKEK30. Replacement of 25N or 27N with alanine weakened the recognition by MAb1128, and replacement of 26L, 29E, or 30K nearly precluded recognition. The minimal epitope for MAb1129 was 16RPEQGSIQSNP26 and the most critical residues for recognition were 22I and 23Q. The epitope of MAb1130 was defined by residues 5IDAGGS10. Mutation of residue 6D abrogated and mutation of 9G strongly reduced recognition of the peptide by MAb1130. Amino acid sequence alignment demonstrated that these epitopes are relatively conserved among PVY strains. Finally, recombinant CPs were produced to demonstrate that mutations in the variable positions of the epitope regions can affect detection with the MAbs.
Conclusions/Significance
The epitope data acquired can be compared with data on PVY CP-encoding sequences produced by laboratories worldwide and utilized to monitor how widely the new variants of PVY can be detected with current seed potato certification schemes or during the inspection of imported seed potatoes as conducted with these MAbs.
doi:10.1371/journal.pone.0115766
PMCID: PMC4277358  PMID: 25542005
5.  An Antidepressant Decreases CSF Aβ Production in Healthy Individuals and in Transgenic AD Mice 
Science translational medicine  2014;6(236):236re4.
Serotonin signaling suppresses generation of amyloid-β (Aβ) in vitro and in animal models of Alzheimer’s disease (AD). We show that in an aged transgenic AD mouse model (APP/PS1 plaque-bearing mice), the antidepressant citalopram, a selective serotonin reuptake inhibitor (SSRI), decreased Aβ in brain interstitial fluid (ISF) in a dose-dependent manner. Growth of individual amyloid plaques was assessed in plaque-bearing mice that were chronically administered citalopram. Citalopram arrested the growth of pre-existing plaques and reduced the appearance of new plaques by 78%. In healthy human volunteers, citalopram’s effects on Aβ production and Aβ concentrations in cerebrospinal fluid (CSF) were measured prospectively using stable-isotope labeling kinetics (SILK), with CSF sampling during acute dosing of citalopram. Aβ production in CSF was slowed by 37% in the citalopram group compared to placebo. This change was associated with a 38% decrease in total CSF Aβ concentrations in the drug-treated group. The ability to safely decrease Aβ concentrations is potentially important as a preventive strategy for AD. This study demonstrates key target engagement for future AD prevention trials.
doi:10.1126/scitranslmed.3008169
PMCID: PMC4269372  PMID: 24828079
7.  miR-374b-5p suppresses RECK expression and promotes gastric cancer cell invasion and metastasis 
World Journal of Gastroenterology : WJG  2014;20(46):17439-17447.
AIM: To profile expression of microRNAs (miRNAs) in gastric cancer cells and investigate the effect of miR-374b-5p on gastric cancer cell invasion and metastasis.
METHODS: An miRNA microarray assay was performed to identify miRNAs differentially expressed in gastric cancer cell lines (MGC-803 and SGC-7901) compared with a normal gastric epithelial cell line. Upregulation of miR-374b-5p was newly identified and confirmed via quantitative real-time reverse transcription-PCR (qRT-PCR). MGC-803 cells were transfected with a synthesized anti-miR-374b-5p sequence or a control vector using Lipofectamine reagent, or treated with transfection reagent alone or phosphate-buffered saline as controls. Rate of transfection was verified after 48 h by qRT-PCR. Cells were then subjected to transwell migration, wound scratch and cell counting kit-8 assays. A bioinformatic analysis to identify miR-374b-5p target genes was performed using miRanda, PicTar and TargetScan software. A dual luciferase reporter assay was performed to evaluate the influence of miR-374b-5p on target gene activation, and qRT-PCR and Western blot were used to evaluate the levels of target mRNA and protein following transfection with miR-374b-5p antisense oligonucleotides.
RESULTS: The microarray profiling revealed downregulation of 14 (fold change < 0.667; P < 0.05) and upregulation of 12 (fold change > 1.50; P < 0.05) miRNAs in MGC-803 and SGC-7901 cells compared with GES-1 controls. The upregulation of miR-374b-5p (fold change = 1.75 and 1.64 in MGC-803 and SGC-7901, respectively; P < 0.05) was confirmed by qRT-PCR. Compared with the control groups, the restoration of miR-374b-5p expression with anti-miR-374b-5p significantly suppressed the metastasis, invasion and proliferation of MGC-803 cells. The bioinformatic analysis predicted that the 3’ untranslated region (UTR) of reversion-inducing cysteine-rich protein with Kazal motif (RECK) contains three miR-374b-5p target sequences. RECK was verified as a target gene in a dual luciferase reporter assay showing that activation of RECK 3’UTR-pmirGLO was increased by co-transfection with miR-374b-5p. Finally, transfection of miR-374b-5p antisense oligonucleotides increased mRNA and protein levels of RECK in MGC-803 cells (P < 0.05).
CONCLUSION: These findings indicate that upregulation of miR-374b-5p contributes to gastric cancer cell metastasis and invasion through inhibition of RECK expression.
doi:10.3748/wjg.v20.i46.17439
PMCID: PMC4265603  PMID: 25516656
Gastric cancer; microRNAs microarray; miR-374b-5p; RECK; Invasion and metastasis
8.  Efficacy of Continuous Positive Airway Pressure on Testosterone in Men with Obstructive Sleep Apnea: A Meta-Analysis 
PLoS ONE  2014;9(12):e115033.
Objective
To evaluate the efficacy of continuous positive airway pressure (CPAP) on serum testosterone in men with obstructive sleep apnea (OSA).
Methods
Two reviewers independently searched PubMed, Cochrane library, Embase and Web of Science before June 2014. Information on characteristics of subjects, study design, pre- and post-CPAP treatment of serum total testosterone, free testosterone and sexual hormone blinding protein (SHBG) was extracted for analysis.
Results
A total of 7 studies with 9 cohorts that included 232 men were pooled into meta-analysis. There was no change of total testosterone levels before and after CPAP treatment in OSA men (standardized mean difference (SMD) = −0.14, 95%CI: −0.63 to 0.34, z = 0.59, p = 0.558), even subdivided by CPAP therapeutic duration (>3 months). Meanwhile, no significant differences in free testosterone and SHBG were detected after CPAP treatment (SMD =  0.16, 95%CI: −0.09 to 0.40, z = 1.25, p = 0.211 and SMD = −0.58, 95%CI: −1.30 to 0.14, z = 1.59, p = 0.112, respectively).
Conclusion
CPAP has no influence on testosterone levels in men with OSA, further large-scale, well-design interventional investigation is needed.
doi:10.1371/journal.pone.0115033
PMCID: PMC4263732  PMID: 25503098
9.  A Meta-Analysis of IL-13 Polymorphisms and Pediatric Asthma Risk 
Background
IL13–1112C/T and +2044A/G polymorphisms have been reported to be correlated with pediatric asthma susceptibility, but study results were still debatable. Thus, a meta-analysis was conducted.
Material/Methods
PubMed and EMBASE databases were searched. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to calculate the strength of association in the random-effects model or fixed-effects model.
Results
Fourteen case-control studies with 4710 asthma cases and 6086 controls were included in this meta-analysis. IL13–1112C/T and +2044A/G polymorphisms were significantly associated with an increased risk of pediatric asthma (OR=1.14, 95% CI 1.01–1.28, P=0.04, I2=0%; OR=1.20, 95% CI 1.09–1.32, P<0.01, I2=0%), respectively. In the subgroup analysis by ethnicity, IL13–1112C/T polymorphism was significantly associated with pediatric asthma risk in whites (OR=1.29, 95% CI 1.02–1.63, P=0.03, I2=16%). IL13 +2044A/G polymorphism was significantly associated with pediatric asthma risk in Asians (OR=1.21, 95% CI 1.10–1.34, P<0.01, I2=24%).
Conclusions
The results of this meta-analysis suggest that IL13–1112C/T and +2044A/G polymorphisms contribute to the development of pediatric asthma.
doi:10.12659/MSM.891017
PMCID: PMC4271802  PMID: 25502839
Asthma; Interleukin-13; Meta-Analysis; Pediatrics; Polymorphism, Genetic
10.  Effect of anterior cervical discectomy and fusion on adjacent segments in rabbits 
This study is to investigate the effect of anterior cervical discectomy with internal fixation and fusion at different levels on adjacent segments in rabbits. Sixty New Zealand rabbits were randomly divided into four groups, one control group and three model groups, with 15 in each group. Each group underwent anterior cervical internal fixation and fusion at C3-4, C4-5, and C5-6 levels respectively. X-ray film was examined three, six and nine months after fusion to observe the changes in intervertebral space and endplate of adjacent segment. Immunohistochemistry was utilized to evaluate the effects of different fusion methods on adjacent segments of spine. As time went by, in model groups, the majority of cartilage endplates were calcified, as examined by X-ray. Immunohistochemical results of the intervertebral disc showed that the expression levels of collagen type II in nucleus pulposus were decreased significantly, while the expression levels collagen type I in annular fibrosus were increased. And collagen type I tends to replace collagen type II gradually in nucleus pulposus as time goes by. The change in collagen between upper and lower adjacent segments at C3-4 and C4-5 showed no statistical significance after fixation and fusion (p > 0.05). But for C5-6, the change showed statistical significance (p < 0.05). Cervical internal fixation and fusion can induce intervertebral disc degeneration of adjacent segment in rabbits, and cervical internal fixation and fusion operated at different levels may result in different effects on adjacent segments of cervical intervertebral disc.
PMCID: PMC4276202  PMID: 25550944
Cervical vertebra; adjacent segment; internal fixation and fusion; intervertebral disc
11.  Diabetes, Prediabetes and the Survival of Nasopharyngeal Carcinoma: A Study of 5,860 Patients 
PLoS ONE  2014;9(10):e111073.
Background
The incidence of diabetes is increasing. But the impact of diabetes and prediabetes on survival of patients with nasopharyngeal carcinoma (NPC) has received little evaluation.
Methods
In a cohort of 5,860 patients, we compared the disease specific survival (DSS), locoregional relapse-free survival (LRFS) and distant metastasis-free survival (DMFS) of patients with diabetes, prediabetes and normoglycemia defined by pretreatment fasting plasma glucose (FPG) using Kaplan–Meier method, log-rank test and Cox proportional hazards model.
Results
Comparing to normoglycemic patients, the diabetic and the prediabetic were generally older, fatter, had hypertension, heart diseases and hyperlipaemia and usually received radiotherapy alone. But both the diabetic and the prediabetic had similar DSS, LRFS and DMFS to normoglycemic patients, even adjusting for such important factors as age, gender, smoking, drinking, hypertension, heart diseases, body mass index, hyperlipaemia, titer of VCA-IgA and EA-IgA, pathology, T-stage, N-stage, chemotherapy and radiotherapy (P>0.05 for all). Additionally, the findings remained unchanged in sensitivity analysis by excluding patients with known diabetes history and in subgroups of the various factors.
Conclusions
The diabetic and prediabetic NPC patients had similar survival to normoglycemic NPC patients. These data, in the largest reported cohort, are the first to evaluate the association between diabetes, prediabetes and the survival in NPC. The findings are relevant to patient management and provided evidence of the effect on this disease exerted by comorbidities.
doi:10.1371/journal.pone.0111073
PMCID: PMC4211733  PMID: 25350747
12.  Comparison of Long-Term Survival and Toxicity of Cisplatin Delivered Weekly versus Every Three Weeks Concurrently with Intensity-Modulated Radiotherapy in Nasopharyngeal Carcinoma 
PLoS ONE  2014;9(10):e110765.
Background
We aimed to compare the long-term survival outcomes and acute toxicity of cisplatin administered weekly versus every three weeks concurrently with intensity-modulated radiotherapy (IMRT) in patients with nasopharyngeal carcinoma (NPC).
Methods
This was a retrospective review of 154 patients with histologically proven, non-disseminated NPC who were treated using IMRT between January 2003 and December 2007. Seventy-three patients (47.4%) received 5–7 weeks of 30–40 mg/m2 cisplatin weekly; 81 patients (52.6%) received two or three cycles of 80 mg/m2 cisplatin every three weeks. IMRT was delivered at 68 Gy/30 fractions to the nasopharyngeal gross target volume and 60–66 Gy to the involved neck area.
Results
The clinical characteristics and treatment factors of the two groups were well-balanced. The median follow-up was 74 months (range, 6–123 months), and the 5-year overall survival, disease-free survival, locoregional relapse-free survival, and distant metastasis–free survival rates were 85.2% vs. 78.9% (P = 0.318), 71.6% vs. 71.0% (P = 0.847), 93.5% vs. 92.6% (P = 0.904), and 80.9% vs. 80.1% (P = 0.925) for the group treated every three weeks and weekly, respectively. Subgroup analyses indicated no significant differences in the survival rates of the two groups among patients with early- or advanced-stage disease. The incidence of acute toxicities was similar between groups.
Conclusion
IMRT with concurrent cisplatin administered weekly or every three weeks leads to similar long-term survival outcomes and acute toxicity in NPC regardless of whether patients have early- or advanced-stage disease.
doi:10.1371/journal.pone.0110765
PMCID: PMC4199726  PMID: 25329593
13.  Association of calpain-10 rs2975760 polymorphism with type 2 diabetes mellitus: a meta-analysis 
Type 2 diabetes mellitus (T2DM) accounts for the majority of diabetes cases and affects a significant proportion of the adult population worldwide. Calpain-10 has been implicated in the development of type 2 diabetes, and some polymorphisms in the CAPN10 gene have been associated with an increased risk of developing this disease. Several molecular epidemiological studies were conducted in recent years to evaluate the association between the CAPN10 rs2975760 polymorphism and T2DM risk in diverse populations. However, the results remain conflicting rather than conclusive. We performed a meta-analysis of 8 case-control studies that included 2758 T2DM cases and 2762 case-free controls. We assessed the strength of the association, using odds ratios (ORs) with 95% confi dence intervals (CIs). Overall, this meta-analysis showed that the CAPN10 rs2975760 polymorphism was not associated with a significantly type 2 diabetes risk in three genetic models. However, after excluding two study for its heterogeneity, a significantly increased risk was found in all comparisons (for C vs T: OR=1.14, 95% CI=1.03-1.27, I 2=0, P heterpgeneity=0.420, P b=0.012; for TC vs TT: OR=1.15, 95% CI=1.01-1.30, I 2=3.8%, P heterpgeneity=0.392, P b=0.030; for CC+TC vs TT: OR=1.16, 95% CI=1.03-1.31, I 2=3.7%, P heterpgeneity=0.393, P b=0.015). No publication bias was found in the present study. This meta-analysis suggests that the C allele of the CAPN10 rs2975760 polymorphism is associated with an increased T2DM risk. Further large and well-designed studies are needed to confi rm this association.
PMCID: PMC4238540  PMID: 25419435
Type 2 diabetes mellitus; calpain-10; polymorphism; meta-analysis
14.  Mitogenic and Oncogenic Stimulation of K433 Acetylation Promotes PKM2 Protein Kinase Activity and Nuclear Localization 
Molecular cell  2013;52(3):340-352.
SUMMARY
Alternative splicing of the PKM2 gene produces two isoforms, M1 and M2, which are preferentially expressed in adult and embryonic tissues, respectively. The M2 isoform is reexpressed in human cancer and has nonmetabolic functions in the nucleus as a protein kinase. Here, we report that PKM2 is acetylated by p300 acetyltransferase at K433, which is unique to PKM2 and directly contacts its allosteric activator, fructose 1,6-bisphosphate (FBP). Acetylation prevents PKM2 activation by interfering with FBP binding and promotes the nuclear accumulation and protein kinase activity of PKM2. Acetylationmimetic PKM2(K433) mutant promotes cell proliferation and tumorigenesis. K433 acetylation is decreased by serum starvation and cell-cell contact, increased by cell cycle stimulation, epidermal growth factor (EGF), and oncoprotein E7, and enriched in breast cancers. Hence, K433 acetylation links cell proliferation and transformation to the switch of PKM2 from a cytoplasmic metabolite kinase to a nuclear protein kinase.
doi:10.1016/j.molcel.2013.09.004
PMCID: PMC4183148  PMID: 24120661
15.  Association and interaction analysis of PPARGC1A and serum uric acid on type 2 diabetes mellitus in Chinese Han population 
Background
Peroxisome proliferator-activated receptor gamma coactivator-1α (PPARGC1A/ PGC-1α) is a ligand-activated transcription factor belonging to the nuclear hormone receptor superfamily. The activity of PGC-1α or genetic variations in the gene encoding the enzyme may contribute to individual variations in mitochondrial function and insulin resistance or diabetes. The objective of this study was to assess the extent to which PPARGC1A (rs8192678) and serum uric acid (UA) and its interaction impact on T2DM susceptibility in Chinese Han population.
Method
We conducted a study in a cohort that included 1166 T2DM patients and 1135 controls, and was genotyped for the presence of the PPARGC1A rs8192678 polymorphisms. Genotyping was performed by iPLEX technology. The association between rs8192678 or UA and T2DM was assessed by univariate and multivariate logistic regression (MLR) analysis controlling for confounders. The interaction between rs8192678 and UA for T2DM susceptibility was also assessed by MLR analysis.
Results
The generalized linear regression analysis failed to show an association between the PPARGC1A rs8192678 polymorphisms and T2DM. Interestingly, the present study provided data suggesting that the minor A-allele of PPARGC1A (rs8192678) had a protective effect against T2DM in subjects with higher level of UA (ORint =1.50 95% CI: 1.06-2.12 for allele and P = 0.02, ORint =1.63 95% CI: 1.17-2.26 for genotype and P = 0.004).
Conclusion
The combination of higher level of UA and PPARGC1A (rs8192678) was an independent predictor for T2DM.
doi:10.1186/1758-5996-6-107
PMCID: PMC4190481  PMID: 25302081
PPARGC1A; Serum uric acid; Interaction; Type 2 diabetes mellitus; Chinese Han population
16.  Identifying and describing a cohort effect in the national database of reported cases of hepatitis C virus infection in Canada (1991−2010): an age-period-cohort analysis 
CMAJ Open  2014;2(4):E281-E287.
Background
Hepatitis C virus (HCV) infection has a high likelihood of becoming chronic and lead to a range of conditions with poor health outcomes. Identifying birth groups highly affected by HCV infection may better focus public health interventions and ensure their cost-effectiveness. Our analysis focused on studying the association of the birth year and reporting period with rates of cases of HCV infection reported in Canada over a 20-year period.
Methods
Laboratory-confirmed acute or chronic HCV cases with information on sex, age and year of report from 6 provinces and territories that reported line-listed data to the Canadian Notifiable Diseases Surveillance System from 1991 to 2010 were used. Sex-specific infection rates for 5-year birth groups born between 1921 and 1990 were calculated. Rates of HCV infection were log-logit transformed and underwent mean polish analysis and panel linear regression. Rate ratios of HCV infection in the 5-year age groups and their 95% confidence intervals were calculated, with rates in males and females born in 1941–1945 used as references.
Results
Males born between 1946 and 1970 had 21%−40% higher reported rates of HCV infection, whereas females born between 1946 and 1975 had 12%−43% higher reported rates compared with rates in the respective sexes who were born in 1941–1945.
Interpretation
Individuals born between 1946 and 1965 contributed the most to the rates of HCV infection reported in Canada between 1991 and 2010. The cohort effect was present in male and female cases of HCV infection with birth year up to 1970 and 1975, respectively. Our findings will support the development of HCV prevention programs and policies in Canada.
doi:10.9778/cmajo.20140041
PMCID: PMC4251503  PMID: 25485255
17.  Simultaneous Determination of Polybrominated Diphenyl Ethers and Polychlorinated Biphenyls by Gas Chromatography-Tandem Mass Spectrometry in Human Serum and Plasma 
Talanta  2013;113:41-48.
Sensitive and reliable methods for simultaneous determination of polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) in limited volumes of human serum or plasma need to be further documented especially when they accumulate at low levels that are still capable of disrupting endocrine and immune functions, and affecting neurodevelopment and reproduction. The objective of this study was to develop and validate a sensitive and quantitative method that simultaneously quantifies PBDEs and PCBs in 0.5 ml of human serum or plasma. We optimized a solid-phase extraction (SPE) method and used silica particle purification for the extraction of PBDEs and PCBs. Two multiple reactions monitoring (MRM) transitions were optimized for each congeners. The sum of the transitions was used for quantification, and their abundance ratios were used for identification. The combined method optimization techniques resulted in limits of detection from 3–145 pg/ml for 10 PBDEs and 1–12 pg/ml for 15 PCBs. Method was solidly validated by analyzing serum fortified with a certified PBDE and PCB standard mixture from the National Institute of Standards and Technology (NIST). The accuracy was 88–118% and day-to-day precision was within 19%. The method was successfully applied to quantify native concentrations of PBDE and PCB in commercially available human serum. The sensitivity and selectivity of the GC/EI-MS/MS analysis enables it to be the method of choice for investigations of exposures to PBDE and PCB congeners, especially when sample volume is limited.
doi:10.1016/j.talanta.2013.04.001
PMCID: PMC3698050  PMID: 23708622
gas chromatography-tandem mass spectrometry; polybrominated diphenyl ethers; polychlorinated biphenyls; human plasma; human serum
18.  XPD Asp312Asn polymorphism and esophageal cancer risk: an update meta-analysis based on 3928 cases and 6012 controls 
Background: Although xeroderma pigmentosum group D (XPD) was reported to be related with esophageal cancer (EC) risk, the results remained inconsistent. The aim of this meta-analysis was to make a more precise estimation of the relationship between XPD Asp312Asn polymorphism and EC risk. Methods: We searched PubMed, Web of Science, Embase, Medline, CNKI and Chinese Biomedical database, covering all publications (up to May, 2014). Statistical analyses were performed with Stata software (version 12.0, USA) and RevMan 5.1 (Copenhagen, 2008). The calculation of odds ratios (ORs) with 95% confidence intervals (CI) was calculated to assess the strength of the association. Results: A total of 15 case-control studies from 13 literatures including 3928 cases and 6012 controls described Asp312Asn genotypes and EC risk. A significant association between XPD Asp312Asn polymorphism and EC risk was found when all the eligible studies were pooled into this meta-analysis. It’s also the same result in subgroup analysis of smokers in dominant model (OR=1.63, 95% CI: 1.06-2.50, P=0.03). However, in the stratified analysis by ethnicity and source of population controls, no association between them was discovered. Conclusion: The XPD Asp312Asn polymorphism was proved to contribute to the risk of EC in this meta-analysis. Data showed that tobacco consumption may increase the susceptibility of EC.
PMCID: PMC4211746  PMID: 25356096
XPD polymorphisms; esophageal cancers; ESCC; EADC; meta-analysis
19.  Synergistic effect of puerarin and 5-fluorouracil on hepatocellular carcinoma 
Oncology Letters  2014;8(6):2436-2442.
Hepatocellular carcinoma (HCC) is one of the most common types of human malignancy worldwide, which is becoming increasingly resistant to traditional drug treatments. Puerarin combined with 5-fluorouracil (5-FU) may be a useful treatment for liver cancer. The primary aim of the present study was to determine whether combined treatment with 5-FU and puerarin is more effective against the hepatocellular carcinoma (HCC) cell line, SMMC7721, than treatment with 5-FU or puerarin alone. The growth inhibition of SMMC7721 cells by puerarin or 5-FU alone or in combination was determined by the Cell Counting Kit-8 assay, in vitro. Apoptotic morphological features and the percentage of apoptotic cells were detected using Hoechst 33258 staining and an Annexin V/PI apoptosis kit, respectively. In addition, a tumor xenograft model was established in nude mice using SMMC7721 cells. Puerarin and 5-FU alone or in combination were injected into the mice, and the inhibition of tumor growth was evaluated by monitoring tumor volume and weight. Treatment with 6,400 or 640 μM 5-FU resulted in growth inhibition of 95.56±0.81 and 75.91±3.54%, respectively. The combination index values were <1 when the fraction of affected cells was between 0.2555 and 0.7420. Furthermore, the percentage of apoptotic cells was markedly increased in the combined treatment group when compared with that of the individual treatment groups, in vitro and in vivo. Individual treatment with puerarin resulted in a tumor volume inhibition rate (IR) of 70.58% and a tumor weight IR of 46.20%. Treatment with 5-FU was found to decrease the tumor volume by 76.26% and tumor weight by 49.86%. In the combined treatment group, the tumor volume and weight IRs were 93.11 and 75.21%, respectively. A marked increase in the inhibition of tumor growth and the number of apoptotic cells in response to combined treatment with puerarin and 5-FU was identified with no observed liver or renal toxicity. These results suggest that puerarin and 5-FU exhibit a synergistic treatment effect on the HCC SMMC7721 cell line.
doi:10.3892/ol.2014.2534
PMCID: PMC4214471  PMID: 25364405
chemotherapy; 5-fluorouracil; hepatocellular carcinoma; puerarin
20.  Evaluation of voltage-sensitive fluorescence dyes for monitoring neuronal activity in the embryonic central nervous system 
The Journal of membrane biology  2013;246(9):679-688.
Using an optical imaging technique with voltage-sensitive dyes (VSDs), we have been investigating the functional organization and architecture of the central nervous system (CNS) during embryogenesis. In the embryonic nervous system, a merocyanine-rhodanine dye, NK2761, has proved to be the most useful absorption dye for detecting neuronal activity because of its high signal-to-noise ratio (S/N), low toxicity, and small dye bleaching. In the present study, we evaluated the suitability of voltage-sensitive fluorescence dyes for optical recording in the embryonic CNS. We screened eight styryl (hemicyanine) dyes in isolated brainstem-spinal cord preparations from 7-day old chick embryos. Measurements of voltage-related optical signals were made using a multiple-site optical recording system. The signal size, S/N, photobleaching, effects of perfusion, and recovery of neural responses after staining were compared. We also evaluated optical responses with various magnifications. Although the S/N was lower than with the absorption dye, clear optical responses were detected with several fluorescence dyes, including di-2-ANEPEQ, di-4-ANEPPS, di-3-ANEPPDHQ, di-4-AN(F)EPPTEA, di-2-AN(F)EPPTEA, and di-2-ANEPPTEA. Di-2-ANEPEQ showed the largest S/N, whereas its photobleaching was faster and the recovery of neural responses after staining was slower. Di-4-ANEPPS and di-3-ANEPPDHQ also exhibited a large S/N, but required a relatively long time for recovery of neural activity. Di-4-AN(F)EPPTEA, di-2-AN(F)EPPTEA, and di-2-ANEPPTEA showed smaller S/Ns than di-2-ANEPEQ, di-4-ANEPPS, and di-3-ANEPPDHQ, but the recovery of neural responses after staining was faster. This study demonstrates the potential utility of these styryl dyes in optical monitoring of voltage changes in the embryonic CNS.
doi:10.1007/s00232-013-9584-1
PMCID: PMC4096138  PMID: 23975337
optical recording; voltage-sensitive dye; embryo; nervous system; fluorescence; screening
21.  Mass spectrometry-based, label-free quantitative proteomics of round spermatids in mice 
Molecular Medicine Reports  2014;10(4):2009-2024.
Round haploid spermatids are formed at the completion of meiosis. These spermatids then undergo morphological and cytological changes during spermiogenesis. Although sperm proteomes have been extensively studied, relatively few studies have specifically investigated the proteome of round spermatids. We developed a label-free quantitative method in combination with 2D-nano-LC-ESI-MS/MS to investigate the proteome of round spermatids in mice. Analysis of the proteomic data identified 2,331 proteins in the round spermatids. Functional classification of the proteins based on Gene Ontology terms and enrichment analysis further revealed the following: 504 of the identified proteins are predicted to be involved in the generation of precursor metabolites and energy; 343 proteins in translation and protein targeting; 298 proteins in nucleotide and nucleic acid metabolism; 275 and 289 proteins in transport and cellular component organization, respectively. A number of the identified proteins were associated with cytoskeleton organization (183), protein degradation (116) and response to stimulus (115). KEGG pathway analysis identified 68 proteins that are annotated as components of the ribosomal pathway and 17 proteins were related to aminoacyl-tRNA biosynthesis. The round spermatids also contained 28 proteins involved in the proteasome pathway and 40 proteins in the lysosome pathway. A total of 60 proteins were annotated as parts of the spliceosome pathway, in which heterogeneous nuclear RNA is converted to mRNA. Approximately 94 proteins were identified as actin-binding proteins, involved in the regulation of the actin cytoskeleton. In conclusion, using a label-free shotgun proteomic approach, we identified numerous proteins associated with spermiogenesis in round spermatids.
doi:10.3892/mmr.2014.2460
PMCID: PMC4148364  PMID: 25109358
proteome; round spermatid; label-free quantification; spermatogenesis
22.  Peripheral Type I Interferon Receptor Correlated with Oxidative Stress in Chronic Hepatitis B Virus Infection 
Type I interferon receptor (IFNAR) has been involved in the progression of chronic hepatitis B (CHB). Oxidative stress is also associated with hepatitis B virus (HBV) infection and might contribute to the structure and function of protein synthesis including the IFNAR family. This study was aimed to determine the possible associations between oxidative stress and peripheral IFNAR expression in chronic HBV infection. Fifty-four CHB patients and 31 liver cirrhosis (LC) patients were consecutively collected, as well as 11 healthy subjects as controls. Expression levels of IFNAR1 and IFNAR2 in peripheral blood lymphocytes and monocytes were measured by flow cytometry. IFNAR1 and IFNAR2c mRNA were detected by real-time reverse transcription–polymerase chain reaction. Levels of plasma-soluble IFNAR and oxidative stress parameters, including xanthine oxidase (XOD), malondialdehyde (MDA), glutathione (GSH), glutathione S-transferase (GST), and glutathione peroxidase (GSH-Px) were detected by enzyme linked immunosorbent assay (ELISA). The frequencies of IFNAR1 and IFNAR2 in lymphocytes and monocytes were significantly increased in CHB and LC patients than in healthy controls. Expression levels of IFNAR1 and IFNAR2c mRNA and plasma-soluble IFNAR level in CHB and LC patients were upregulated compared with healthy controls. Mean fluorescence intensity (MFI) of IFNAR2 in monocytes of CHB patients was higher than that in LC patients. Levels of plasma XOD, MDA, and GST were significantly increased in CHB and LC patients compared with healthy controls. Meanwhile, GSH and GSH-Px in CHB and LC patients were decreased than that in healthy controls. Furthermore, plasma MDA, GSH, and GST levels in CHB patients were higher than that in LC patients. In CHB patients, plasma GST level was negatively correlated with MFI of IFNAR2 in lymphocytes. Our results suggested that oxidative stress play an important role in the regulation of IFNAR in chronic HBV infection.
doi:10.1089/jir.2012.0153
PMCID: PMC3741434  PMID: 23663046
23.  Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins 
Nature methods  2013;11(2):149-155.
The successful application of MRM in biological specimens raises the exciting possibility that assays can be configured to measure all human proteins, resulting in an assay resource that would promote advances in biomedical research. We report the results of a pilot study designed to test the feasibility of a large-scale, international effort in MRM assay generation. We have configured, validated across three laboratories, and made publicly available as a resource to the community 645 novel MRM assays representing 319 proteins expressed in human breast cancer. Assays were multiplexed in groups of >150 peptides and deployed to quantify endogenous analyte in a panel of breast cancer-related cell lines. Median assay precision was 5.4%, with high inter-laboratory correlation (R2 >0.96). Peptide measurements in breast cancer cell lines were able to discriminate amongst molecular subtypes and identify genome-driven changes in the cancer proteome. These results establish the feasibility of a scaled, international effort.
doi:10.1038/nmeth.2763
PMCID: PMC3922286  PMID: 24317253
24.  Moyamoya syndrome associated with Graves’ disease: a case series study 
Objective
The aim of this study was to describe the clinical and radiological findings of patients with moyamoya syndrome and Graves’ disease. Possible mechanisms predisposing these individuals to ischemic stroke are discussed.
Methods
We retrospectively analyzed 12 consecutive patients with both moyamoya syndrome and Graves’ disease. Moyamoya vasculopathy was diagnosed by digital subtract angiography or magnetic resonance angiography (MRA). The clinical characteristics, laboratory data, vascular radiological characteristics and outcome were reported.
Results
All patients were female and mean age was 33.33±12.65 years. Stenosis or occlusion of bilateral terminal internal carotid artery and/or proximal anterior/middle cerebral arteries was found in nine patients. Among them, three patients displayed asymmetrical stenosis. In addition, there were three patients with probable unilateral moamoya syndrome. Eleven patients presented with ischemic stroke and/or transient ischemic attack (TIA) and one with dizziness. Thyroid function tests demonstrated elevated thyroid hormone levels and suppressed thyroid stimulating hormone levels in all the patients with ischemic events. All patients received anti-thyroid therapy and two had recurrent ischemic attack after drug withdrawal.
Conclusions
Moyamoya syndrome associated Graves’ disease often presented with asymmetric stenosis or occlusion. We hypothesize cerebrovascular hemodynamic changes due to thyrotoxicosis contribute to the ischemic events.
doi:10.3978/j.issn.2305-5839.2014.08.03
PMCID: PMC4200642  PMID: 25333052
Moyamoya syndrome; Graves’ disease; thyrotoxicosis; treatment
25.  Israeli Acute Paralysis Virus: Epidemiology, Pathogenesis and Implications for Honey Bee Health 
PLoS Pathogens  2014;10(7):e1004261.
Israeli acute paralysis virus (IAPV) is a widespread RNA virus of honey bees that has been linked with colony losses. Here we describe the transmission, prevalence, and genetic traits of this virus, along with host transcriptional responses to infections. Further, we present RNAi-based strategies for limiting an important mechanism used by IAPV to subvert host defenses. Our study shows that IAPV is established as a persistent infection in honey bee populations, likely enabled by both horizontal and vertical transmission pathways. The phenotypic differences in pathology among different strains of IAPV found globally may be due to high levels of standing genetic variation. Microarray profiles of host responses to IAPV infection revealed that mitochondrial function is the most significantly affected biological process, suggesting that viral infection causes significant disturbance in energy-related host processes. The expression of genes involved in immune pathways in adult bees indicates that IAPV infection triggers active immune responses. The evidence that silencing an IAPV-encoded putative suppressor of RNAi reduces IAPV replication suggests a functional assignment for a particular genomic region of IAPV and closely related viruses from the Family Dicistroviridae, and indicates a novel therapeutic strategy for limiting multiple honey bee viruses simultaneously and reducing colony losses due to viral diseases. We believe that the knowledge and insights gained from this study will provide a new platform for continuing studies of the IAPV–host interactions and have positive implications for disease management that will lead to mitigation of escalating honey bee colony losses worldwide.
Author Summary
The mysterious outbreak of honey bee Colony Collapse Disorder (CCD) in the US in 2006–2007 has attracted massive media attention and created great concerns over the effects of various risk factors on bee health. Understanding the factors that are linked to the honey bee colony declines may provide insights for managing similar incidents in the future. We conducted this study to elucidate traits of a key honey bee virus, Israeli acute paralysis virus. We then developed an innovative strategy to control virus levels. The knowledge and insights gained from this study will have positive implications for bee disease management, helping to mitigate worldwide colony losses.
doi:10.1371/journal.ppat.1004261
PMCID: PMC4117608  PMID: 25079600

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