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1.  Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection 
Journal of Clinical Microbiology  2013;51(10):3263-3269.
Cultivation-based assays combined with PCR or enzyme-linked immunosorbent assay (ELISA)-based methods for finding virulence factors are standard methods for detecting bacterial pathogens in stools; however, with emerging molecular technologies, new methods have become available. The aim of this study was to compare four distinct detection technologies for the identification of pathogens in stools from children under 5 years of age in The Gambia, Mali, Kenya, and Bangladesh. The children were identified, using currently accepted clinical protocols, as either controls or cases with moderate to severe diarrhea. A total of 3,610 stool samples were tested by established clinical culture techniques: 3,179 DNA samples by the Universal Biosensor assay (Ibis Biosciences, Inc.), 1,466 DNA samples by the GoldenGate assay (Illumina), and 1,006 DNA samples by sequencing of 16S rRNA genes. Each method detected different proportions of samples testing positive for each of seven enteric pathogens, enteroaggregative Escherichia coli (EAEC), enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), Shigella spp., Campylobacter jejuni, Salmonella enterica, and Aeromonas spp. The comparisons among detection methods included the frequency of positive stool samples and kappa values for making pairwise comparisons. Overall, the standard culture methods detected Shigella spp., EPEC, ETEC, and EAEC in smaller proportions of the samples than either of the methods based on detection of the virulence genes from DNA in whole stools. The GoldenGate method revealed the greatest agreement with the other methods. The agreement among methods was higher in cases than in controls. The new molecular technologies have a high potential for highly sensitive identification of bacterial diarrheal pathogens.
doi:10.1128/JCM.01342-13
PMCID: PMC3811648  PMID: 23884998
2.  Genetic Diversity and Distribution Patterns of Host Insects of Caterpillar Fungus Ophiocordyceps sinensis in the Qinghai-Tibet Plateau 
PLoS ONE  2014;9(3):e92293.
The caterpillar fungus Ophiocordyceps sinensis is one of the most valuable medicinal fungi in the world, and it requires host insects in family Hepialidae (Lepidoptera) to complete its life cycle. However, the genetic diversity and phylogeographic structures of the host insects remain to be explored. We analyzed the genetic diversity and temporal and spatial distribution patterns of genetic variation of the host insects throughout the O. sinensis distribution. Abundant haplotype and nucleotide diversity mainly existed in the areas of Nyingchi, ShangriLa, and around the edge of the Qinghai-Tibet Plateau, where are considered as the diversity center or micro-refuges of the host insects of O. sinensis. However, there was little genetic variation among host insects from 72.1% of all populations, indicating that the host species composition might be relatively simple in large-scale O. sinensis populations. All host insects are monophyletic except for those from four O. sinensis populations around Qinghai Lake. Significant phylogeographic structure (NST>GST, P<0.05) was revealed for the monophyletic host insects, and the three major phylogenetic groups corresponded with specific geographical areas. The divergence of most host insects was estimated to have occurred at ca. 3.7 Ma, shortly before the rapid uplift of the QTP. The geographical distribution and star-like network of the haplotypes implied that most host insects were derived from the relicts of a once-widespread host that subsequently became fragmented. Neutrality tests, mismatch distribution analysis, and expansion time estimation confirmed that most host insects presented recent demographic expansions that began ca. 0.118 Ma in the late Pleistocene. Therefore, the genetic diversity and distribution of the present-day insects should be attributed to effects of the Qinghai-Tibet Plateau uplift and glacial advance/retreat cycles during the Quaternary ice age. These results provide valuable information to guide the protection and sustainable use of these host insects as well as O. sinensis.
doi:10.1371/journal.pone.0092293
PMCID: PMC3965410  PMID: 24667533
3.  Association between Tumor necrosis factor-alpha gene polymorphisms and prostate cancer risk: a meta-analysis 
Diagnostic Pathology  2014;9:74.
Background
Tumor necrosis factor-alpha (TNF-α) is an important inflammatory cytokine that may play a role in controlling the progression of prostate cancer. Two common polymorphisms in the TNF-α gene, −308G/A and −238C/T, have been suggested to alter the risk for prostate cancer, but the results have been inconclusive so far. In order to obtain a better understanding of the effects of these two polymorphisms on prostate cancer risk, all available studies were considered in a meta-analysis.
Methods
We conducted a comprehensive literature search in the Cochrane Library, PubMed, EMBASE, Chinese Biomedical Literature database (CBM), and the China National Knowledge Infrastructure (CNKI). The associations were evaluated by calculating the pooled odds ratio (OR) with 95% confidence interval (95% CI).
Results
In this meta-analysis, we included 14 studies with 5,757 patients and 6,137 control subjects for the TNF-α-308G/A polymorphism and 1,967 patients and 2,004 control subjects for the TNF-α-238C/T polymorphism. A significantly increased prostate cancer risk was found to be associated with the TNF-α-308C/T polymorphism in studies with healthy volunteers (AA + AG vs. GG: OR = 1.531, 95% CI = 1.093–2.145; P = 0.013; AG vs. GG: OR = 1.477, 95% CI = 1.047–2.085; P = 0.026). No significant association was found between the TNF-α-238G/A polymorphism and prostate cancer risk in the overall or subgroup analyses. There was no risk of publication bias in this meta-analysis.
Conclusions
Our results suggest that while the TNF-α-238G/A polymorphism may not be associated with prostate cancer the TNF-α-308C/T polymorphism may significantly contribute to prostate cancer susceptibility in healthy volunteers.
Virtual slides
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1629288120116301
doi:10.1186/1746-1596-9-74
PMCID: PMC3977697  PMID: 24666463
Tumor necrosis factor- alpha; Prostate cancer; Meta-analysis; Polymorphism
4.  Executive Dysfunction Assessed with a Task-Switching Task following Concussion 
PLoS ONE  2014;9(3):e91379.
Concussion frequently results in executive function deficits that can be specifically probed using task-switching tasks. The current study examined in detail the influence of concussion on task switching performance using both spatial and numerical stimuli. Individuals with concussion (n = 16) were tested within 48 hours of injury and 7, 14, and 28 days later. Healthy sex-, age-, height-, weight- and activity-matched controls (n = 16) were also tested at the same intervals. Switch costs were significantly greater in the participants with concussion than in the controls for both types of stimuli. By contrast, the global costs on non-switching trials were unaffected by concussion. We conclude that concussion has pronounced negative effects on the ability to switch task sets that generalize across task combinations (spatial or numerical) and that persist across at least a month after injury.
doi:10.1371/journal.pone.0091379
PMCID: PMC3950211  PMID: 24618717
5.  A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics 
BioMed Research International  2014;2014:362738.
With the rapid advance in genomics, proteomics, metabolomics, and other types of omics technologies during the past decades, a tremendous amount of data related to molecular biology has been produced. It is becoming a big challenge for the bioinformatists to analyze and interpret these data with conventional intelligent techniques, for example, support vector machines. Recently, the hybrid intelligent methods, which integrate several standard intelligent approaches, are becoming more and more popular due to their robustness and efficiency. Specifically, the hybrid intelligent approaches based on evolutionary algorithms (EAs) are widely used in various fields due to the efficiency and robustness of EAs. In this review, we give an introduction about the applications of hybrid intelligent methods, in particular those based on evolutionary algorithm, in bioinformatics. In particular, we focus on their applications to three common problems that arise in bioinformatics, that is, feature selection, parameter estimation, and reconstruction of biological networks.
doi:10.1155/2014/362738
PMCID: PMC3963368
6.  Over-Expressed Testis-Specific Protein Y-Encoded 1 as a Novel Biomarker for Male Hepatocellular Carcinoma 
PLoS ONE  2014;9(2):e89219.
Hepatocellular carcinoma (HCC) is a male-predominant cancer. Previous studies have focused on the sex-related disparity in HCC, but the underlying mechanism remains unclear. Here, we aimed to discover characteristic biomarkers for male HCC. Clinical samples were subjected to iTRAQ labeling followed by 2DLC-ESI-MS/MS analysis. Seventy-three differential proteins containing 16 up-regulated and 57 down-regulated proteins were screened out in the male HCC group compared to that in female HCC group. Testis-specific Protein Y-encoded 1(TSPY1) is characteristically present in male HCC and was chosen for further investigation. The data from the functional effects of TSPY1 indicated that over-expression of TSPY1 could potentiate HCC cell proliferation, increase soft agar colonization, induce higher cell invasive ability and correlate with the metastatic potential of the HCC cell lines. In addition, TSPY1 and androgen receptor (AR) were co-expressed simultaneously in HCC cell lines as well as in HCC tissue. TSPY1 up- or down-regulation could lead to a high or low level expression of AR. These results implied that TSPY1 may be included in the regulation of AR expression involved in male HCC and it may act as a novel biomarker for male HCC.
doi:10.1371/journal.pone.0089219
PMCID: PMC3930679  PMID: 24586606
7.  CASP8 -652 6N Del Polymorphism Contributes to Colorectal Cancer Susceptibility: Evidence from a Meta-Analysis 
PLoS ONE  2014;9(2):e87925.
Objective
Caspase-8 (CASP8) plays a central role in the apoptotic pathway and aberrant regulation of this pathway may cause cancers. Previous studies investigating the association between CASP8 -652 6N ins/del polymorphism and colorectal cancer (CRC) risk showed inconclusive results. We performed a meta-analysis of all available studies to investigate this association.
Methods
All studies published up to October 2013 on the association between CASP8 -652 6N ins/del polymorphism and CRC risk were identified by searching electronic databases PubMed, EMBASE, and Cochrane library. The association between CASP8 -652 6N ins/del polymorphism and CRC risk was assessed by odds ratios (ORs) together with their 95% confidence intervals (CIs).
Results
Six studies with 6,325 cases and 6,842 controls were included in the meta-analysis. We observed that the CASP8 -652 6N ins/del polymorphism was significantly correlated with CRC risk when all studies were pooled into the meta-analysis (ins/del vs. ins/ins: OR = 0.890, 95%CI 0.821–0.964, P = 0.004; del/del + ins/del vs. ins/ins: OR = 0.899, 95%CI 0.833–0.970, P = 0.006). In stratified analyses by ethnicity, source of control, and quality score, significant association was observed in Asians (ins/del vs. ins/ins: OR = 0.862, 95%CI 0.761–0.977, P = 0.020; del/del + ins/del vs. ins/ins: OR = 0.845, 95%CI 0.749–0.953, P = 0.006), population-based studies (ins/del vs. ins/ins: OR = 0.890, 95%CI 0.813–0.975, P = 0.012; del/del + ins/del vs. ins/ins: OR = 0.901, 95%CI 0.827–0.982, P = 0.018), and high quality studies. However, in subgroup analysis according to cancer location, no significant association was detected.
Conclusions
The present meta-analysis suggests that the CASP8 is a candidate gene for CRC susceptibility. The CASP8 -652 6N ins/del polymorphism may play a protective role in CRC development especially among Asians. Further large and well-designed studies are needed to confirm this association.
doi:10.1371/journal.pone.0087925
PMCID: PMC3912176  PMID: 24498403
8.  Cytotoxicity of Clostridium difficile toxin B does not require cysteine protease-mediated autocleavage and release of the glucosyltransferase domain into the host cell cytosol 
Pathogens and disease  2013;67(1):11-18.
Clostridium difficile virulence requires secretion of two exotoxins, TcdA and TcdB. The precise mechanism of toxin uptake and delivery is undefined, but current models predict that the cysteine protease domain (CPD) mediated autocleavage and release of glucosyltransferase domain (GTD) is crucial for intoxication. To determine the importance of CPD mediated cleavage to TcdB cytotoxicity, we generated two mutant toxins TcdB-C698S and TcdB-H653A, and assayed their abilities to intoxicate cells. The CPD mutants include an intact GTD but lack the cysteine protease activity. The mutants had reduced potency in that their effect on cells was delayed and required higher concentrations than wild-type TcdB. They did eventually cause cell rounding, glucosylation of Rho GTPases, and apoptosis that was indistinguishable from that caused by TcdB. Although the mutant toxins caused a complete cell rounding, they failed to release their GTD into cytosol, whereas wild-type TcdB displayed significant autocleavage and release of GTD. We conclude that the cysteine protease-mediated autocleavage and release of GTD is not a prerequisite for the cytotoxic activity of TcdB, but rather limits the potency and speed of Rho GTPase glucosylation. Our findings revise and refine the current model for the mode of the action and cellular trafficking of TcdB.
doi:10.1111/2049-632X.12016
PMCID: PMC3742912  PMID: 23620115
Clostridium difficile; toxin B (TcdB); cysteine protease; autocleavage; cytotoxicity
9.  Lack of association between cathepsin D C224T polymorphism and Alzheimer’s disease risk: an update meta-analysis 
BMC Neurology  2014;14:13.
Background
Cathepsin D C224T polymorphism has been reported to associate with AD susceptibility. But the results were inconsistent. This study aimed to assess the relationship between C224T polymorphism and AD risk.
Methods
The relevant studies were identified by searching PubMed, Embase, Web of Science, Google Scholar and Wan fang electronic databases updated on July 2013. The relationship between Cathepsin D C224T polymorphism and AD risk was evaluated by ORs and 95% CIs.
Results
A total of 25 case-control studies including 5,602 cases and 11,049 controls were included in the meta-analysis. There was no association between C224T polymorphism and AD risk with all the studies were pooled in the meta-analysis (CT vs. CC: OR = 1.125, 95% CI = 0.974-1.299, P = 0.109; CT + TT vs. CC: OR = 1.136, 95% CI = 0.978-1.320, P = 0.094). Furthermore, when stratified by ethnicity, age of onset and APOEϵ4 status, significant association did not found in all subgroups.
Conclusion
The present meta-analysis suggested that the Cathepsin D C224T polymorphism was not associated with AD susceptibility.
doi:10.1186/1471-2377-14-13
PMCID: PMC3901763  PMID: 24423188
Cathepsin D; AD; Polymorphism; Meta-analysis
10.  Vascular endothelial growth factor +936C/T polymorphism and breast cancer risk: a meta-analysis of 13 case–control studies 
Tumour Biology  2014;35(3):2687-2692.
The association between vascular endothelial growth factor (VEGF) +936C/T polymorphism and breast cancer risk has been widely reported, but results were inconsistent. In order to derive a more precise estimation of the relationship, a meta-analysis was performed. Eligible articles were identified through search of databases including PubMed, Embase, and Chinese Biomedical Literature Database (CBM). The association between the VEGF +936C/T polymorphism and breast cancer risk was conducted by odds ratios (ORs) and 95 % confidence intervals (95 % CIs). Finally, a total of 13 studies with 6,879 cases and 7,219 controls were included in our meta-analysis. Overall, a significant association was found between VEGF +936C/T polymorphisms and the risk of breast cancer in overall populations under five models (T vs. C: OR = 0.83, 95 % CI = 0.73–0.94, P = 0.002; TT vs. CC: OR = 0.74, 95 % CI = 0.61–0.91, P = 0.004, Fig. 1a; TC vs. CC: OR = 0.83, 95 % CI = 0.71–0.96, P = 0.014; TT vs. CC/CT: OR = 0.77, 95 % CI = 0.62–0.94, P = 0.010; TT/TC vs. CC: OR = 0.82, 95 % CI = 0.72–0.95, P = 0.006). In the subgroup analysis by ethnicity, there were also significant associations found between VEGF +936C/T polymorphism and breast cancer risk in Asians and Caucasians. In conclusion, the results of our meta-analysis suggest that the VEGF +936C/T polymorphism is significantly associated with breast cancer development and the VEGF 936T allele carriers may be associated with decreased breast cancer risk.
doi:10.1007/s13277-013-1354-2
PMCID: PMC3967057  PMID: 24390659
VEGF; Polymorphism; Breast cancer; Meta-analysis
11.  Genetic Variation of Vibrio cholerae during Outbreaks, Bangladesh, 2010–2011 
Emerging Infectious Diseases  2014;20(1):54-60.
Most isolates are closely related, but genetic variation implies accelerated transmission of some lineages.
Cholera remains a major public health problem. To compare the relative contribution of strains from the environment with strains isolated from patients during outbreaks, we performed multilocus variable tandem repeat analyses on samples collected during the 2010 and 2011 outbreak seasons in 2 geographically distinct areas of Bangladesh. A total of 222 environmental and clinical isolates of V. cholerae O1 were systematically collected from Chhatak and Mathbaria. In Chhatak, 75 of 79 isolates were from the same clonal complex, in which extensive differentiation was found in a temporally consistent pattern of successive mutations at single loci. A total of 59 isolates were collected from 6 persons; most isolates from 1 person differed by sequential single-locus mutations. In Mathbaria, 60 of 84 isolates represented 2 separate clonal complexes. The small number of genetic lineages in isolates from patients, compared with those from the environment, is consistent with accelerated transmission of some strains among humans during an outbreak.
doi:10.3201/eid2001.130796
PMCID: PMC3884724  PMID: 24377372
multilocus sequence analysis; infectious disease outbreaks; Vibrio cholerae; bacteria; Bangladesh; cholera; outbreak
12.  Genome-Wide and Differential Proteomic Analysis of Hepatitis B Virus and Aflatoxin B1 Related Hepatocellular Carcinoma in Guangxi, China 
PLoS ONE  2013;8(12):e83465.
Both hepatitis B virus (HBV) and aflatoxin B1 (AFB1) exposure can cause liver damage as well as increase the probability of hepatocellular carcinoma (HCC). To investigate the underlying genetic changes that may influence development of HCC associated with HBV infection and AFB1 exposure, HCC patients were subdivided into 4 groups depending upon HBV and AFB1 exposure status: (HBV(+)/AFB1(+), HBV(+)/AFB1(-), HBV(-)/AFB1(+), HBV(-)/AFB1(-)). Genetic abnormalities and protein expression profiles were analyzed by array-based comparative genomic hybridization and isobaric tagging for quantitation. A total of 573 chromosomal aberrations (CNAs) including 184 increased and 389 decreased were detected in our study population. Twenty-five recurrently altered regions (RARs; chromosomal alterations observed in ≥10 patients) in chromosomes were identified. Loss of 4q13.3-q35.2, 13q12.1-q21.2 and gain of 7q11.2-q35 were observed with a higher frequency in the HBV(+)/AFB1(+), HBV(+)/AFB1(-) and HBV(-)/AFB1(+) groups compared to the HBV(-)/AFB(-) group. Loss of 8p12-p23.2 was associated with high TNM stage tumors (P = 0.038) and was an unfavorable prognostic factor for tumor-free survival (P =0.045). A total of 133 differentially expressed proteins were identified in iTRAQ proteomics analysis, 69 (51.8%) of which mapped within identified RARs. The most common biological processes affected by HBV and AFB1 status in HCC tumorigenesis were detoxification and drug metabolism pathways, antigen processing and anti-apoptosis pathways. Expression of AKR1B10 was increased significantly in the HBV(+)/AFB1(+) and HBV(-)/AFB1(+) groups. A significant correlation between the expression of AKR1B10 mRNA and protein levels as well as AKR1B10 copy number was observered, which suggest that AKR1B10 may play a role in AFB1-related hepatocarcinogenesis. In summary, a number of genetic and gene expression alterations were found to be associated with HBV and AFB1- related HCC. The possible synergistic effects of HBV and AFB1 in hepatocarcinogenesis warrant further investigations.
doi:10.1371/journal.pone.0083465
PMCID: PMC3877066  PMID: 24391771
13.  TP53 and MDM2 Gene Polymorphisms, Gene-Gene Interaction, and Hepatocellular Carcinoma Risk: Evidence from an Updated Meta-Analysis 
PLoS ONE  2013;8(12):e82773.
Background
The association between TP53 R72P and/or MDM2 SNP309 polymorphisms and hepatocellular carcinoma (HCC) risk has been widely reported, but results were inconsistent. To clarify the effects of these polymorphisms on HCC risk, an updated meta-analysis of all available studies was conducted.
Methods
Eligible articles were identified by search of databases including PubMed, Cochrane Library, EMBASE and Chinese Biomedical Literature database (CBM) for the period up to July 2013. Data were extracted by two independent authors and pooled odds ratio (OR) with 95% confidence interval (CI) was calculated. Metaregression and subgroup analyses were performed to identify the source of heterogeneity.
Results
Finally, a total of 10 studies including 2,243 cases and 3,615 controls were available for MDM2 SNP309 polymorphism and 14 studies containing 4,855 cases and 6,630 controls were included for TP53 R72P polymorphism. With respect to MDM2 SNP309 polymorphism, significantly increased HCC risk was found in the overall population. In subgroup analysis by ethnicity and hepatitis virus infection status, significantly increased HCC risk was found in Asians, Caucasians, Africans, and HCV positive patients. With respect to TP53 R72P polymorphism, no significant association with HCC risk was observed in the overall and subgroup analyses. In the MDM2 SNP309–TP53 R72P interaction analysis, we found that subjects with MDM2 309TT and TP53 Pro/Pro genotype, MDM2 309 TG and TP53 Arg/Pro genotype, and MDM2 309 GG and TP53 Pro/Pro genotype were associated with significantly increased risk of developing HCC as compared with the reference MDM2 309TT and TP53 Arg/Arg genotype.
Conclusions
We concluded that MDM2 SNP309 polymorphism may play an important role in the carcinogenesis of HCC. In addition, our findings further suggest that the combination of MDM2 SNP 309 and TP53 Arg72Pro genotypes confers higher risk to develop HCC. Further large and well-designed studies are needed to confirm this association.
doi:10.1371/journal.pone.0082773
PMCID: PMC3871586  PMID: 24376578
14.  CYP2D6*4 Allele Polymorphism Increases the Risk of Parkinson’s Disease: Evidence from Meta-Analysis 
PLoS ONE  2013;8(12):e84413.
Background
Many epidemiological studies have been conducted to explore the association between a single CYP2D6 gene polymorphism and Parkinson’s disease (PD) susceptibility. However, the results remain controversial.
Objectives
To clarify the effects of a single CYP2D6 gene polymorphism on the risk of PD, a meta-analysis of all available studies relating to CYP2D6*4 polymorphism and the risk of PD was conducted.
Methods
A comprehensive literature search of PubMed, EMBASE, and the China National Knowledge Infrastructure (CNKI) up to September 1, 2013 was conducted. Data were extracted by two independent authors and pooled odds ratio (OR) with 95% confidence interval (CI) were calculated. Meta-regression, Galbraith plots, subgroup analysis, sensitivity analysis, and publication bias analysis were also performed.
Results
Twenty-two separate comparisons consisting of 2,629 patients and 3,601 controls were included in our meta-analysis. The pooled analyses showed a significant association between CYP2D6*4G/A polymorphism and PD risk in all of the comparisons (A vs. G allele: OR = 1.28, 95% CI = 1.14–1.43, P = 0.001; AA vs. GG: OR = 1.43, 95% CI = 1.06–1.93, P = 0.018; AG vs. GG: OR = 1.22, 95% CI = 1.06–1.40, P = 0.006; AG+AA vs. GG: OR = 1.26, 95% CI = 1.10–1.44, P = 0.001; AA vs. AG+GG: OR = 1.37, 95% CI = 1.02–1.83, P = 0.036). In subgroup analysis stratified by ethnicity, significant associations were also demonstrated in Caucasians but not in Asians. No significant association was found in subgroup analysis stratified by age of onset or disease form.
Conclusions
We concluded that the CYP2D6*4G/A polymorphism denotes an increased genetic susceptibility to PD in the overall population, especially in Caucasians. Further large and well-designed studies are needed to confirm this association.
doi:10.1371/journal.pone.0084413
PMCID: PMC3869836  PMID: 24376807
15.  Molecular Characterization of Severin from Clonorchis sinensis Excretory/Secretory Products and Its Potential Anti-apoptotic Role in Hepatocarcinoma PLC Cells 
Background
Clonorchiasis, caused by the infection of Clonorchis sinensis (C. sinensis), is a kind of neglected tropical disease, but it is highly related to cholangiocarcinoma and hepatocellular carcinoma (HCC). It has been well known that the excretory/secretory products of C. sinensis (CsESPs) play key roles in clonorchiasis associated carcinoma. From genome and transcriptome of C. sinensis, we identified one component of CsESPs, severin (Csseverin), which had three putative gelsolin domains. Its homologues are supposed to play a vital role in apoptosis resistance of tumour cell.
Methodology/Principal Findings
There was significant similarity in tertiary structures between human gelsolin and Csseverin by bioinformatics analysis. We identified that Csseverin expressed at life stage of adult worm, metacercaria and egg by the method of quantitative real-time PCR and western blotting. Csseverin distributed in vitellarium and intrauterine eggs of adult worm and tegument of metacercaria by immunofluorence assay. We obtained recombinant Csseverin (rCsseverin) and confirmed that rCsseverin could bind with calciumion in circular dichroism spectrum analysis. It was demonstrated that rCsseverin was of the capability of actin binding by gel overlay assay and immunocytochemistry. Both Annexin V/PI assay and mitochondrial membrane potential assay of human hepatocarcinoma cell line PLC showed apoptosis resistance after incubation with different concentrations of rCsseverin. Morphological analysis, apoptosis-associated changes of mitochondrial membrane potential and Annexin V/PI apoptosis assay showed that co-incubation of PLC cells with rCsseverin in vitro led to an inhibition of apoptosis induced by serum-starved for 24 h.
Conclusions/Significance
Collectively, the molecular properties of Csseverin, a molecule of CsESPs, were characterized in our study. rCsseverin could cause obvious apoptotic inhibition in human HCC cell line. Csseverin might exacerbate the process of HCC patients combined with C. sinensis infection.
Author Summary
Clonorchis sinensis (C. sinensis) has afflicted more than 35 million people in world and approximately 15 million in China, creating a socio-economic burden in epidemic regions. The infection of C. sinensis is highly related to cholangiocarcinoma and hepatocellular carcinoma (HCC). It has been documented that excretory/secretory products of C. sinensis (CsESPs) involved in the pathogenesis of HCC. Csseverin, expressed at life stage of egg, metacercaria and adult worm, was a component of CsESPs. In the current study, we characterized the properties of Csseverin such as sequence signature, actin and calciumion binding activity. In addition, we demonstrated that Csseverin could cause apoptotic inhibition in spontaneously apoptotic human HCC cell line PLC cells by using morphological analysis, detection of the apoptosis-associated change of mitochondrial membrane potential (MMP) as well as Annexin V/PI apoptosis assay. Our study provided an exploratory sight view of mechanism involved in progress of carcinoma associated with the infection of C. sinensis and Csseverin might exacerbate the process of C. sinensis infected HCC patients.
doi:10.1371/journal.pntd.0002606
PMCID: PMC3868641  PMID: 24367717
16.  T Cell Vaccination Inhibits Th1/Th17/Tfh Frequencies and Production of Autoantibodies in Collagen-Induced Arthritis 
The aim of this study is to determine whether the regulatory role of T cell vaccination (TCV) is through inhibition of Th1/Th17/Tfh and production of autoantibodies on collagen-induced arthritis (CIA). First, CIA mice were treated with TCV. After disease onset, the incidence and severity of change in joint histopathology were evaluated. Mice in the TCV-treated group showed less disease severity and less infiltration of inflammatory cells in the joint sections. TCV decreased the frequencies of Th1/Th17/Tfh cells and related cytokines. Reduction of IL-21 may be associated with both Tfh and Th17, which further influence B cell and T cell responses. In addition, inhibition of Th1/Th17/Tfh frequencies led to the reduced expression of T-bet, RORα, RORγt, and Bcl6. Lastly, the proliferation of type-II-collagen-(CII-) specific T cells and the production of anti-CII antibodies were inhibited in the TCV-treated group. The results provide novel evidence that the therapeutic effects of TCV on CIA are associated with the inhibition of Th1/Th17/Tfh frequencies and autoantibodies production.
doi:10.1155/2013/967301
PMCID: PMC3865644  PMID: 24363764
17.  Quantitative PCR for Detection of Shigella Improves Ascertainment of Shigella Burden in Children with Moderate-to-Severe Diarrhea in Low-Income Countries 
Journal of Clinical Microbiology  2013;51(6):1740-1746.
Estimates of the prevalence of Shigella spp. are limited by the suboptimal sensitivity of current diagnostic and surveillance methods. We used a quantitative PCR (qPCR) assay to detect Shigella in the stool samples of 3,533 children aged <59 months from the Gambia, Mali, Kenya, and Bangladesh, with or without moderate-to-severe diarrhea (MSD). We compared the results from conventional culture to those from qPCR for the Shigella ipaH gene. Using MSD as the reference standard, we determined the optimal cutpoint to be 2.9 × 104 ipaH copies per 100 ng of stool DNA for set 1 (n = 877). One hundred fifty-eight (18%) specimens yielded >2.9 × 104 ipaH copies. Ninety (10%) specimens were positive by traditional culture for Shigella. Individuals with ≥2.9 × 104 ipaH copies have 5.6-times-higher odds of having diarrhea than those with <2.9 × 104 ipaH copies (95% confidence interval, 3.7 to 8.5; P < 0.0001). Nearly identical results were found using an independent set of samples. qPCR detected 155 additional MSD cases with high copy numbers of ipaH, a 90% increase from the 172 cases detected by culture in both samples. Among a subset (n = 2,874) comprising MSD cases and their age-, gender-, and location-matched controls, the fraction of MSD cases that were attributable to Shigella infection increased from 9.6% (n = 129) for culture to 17.6% (n = 262) for qPCR when employing our cutpoint. We suggest that qPCR with a cutpoint of approximately 1.4 × 104 ipaH copies be the new reference standard for the detection and diagnosis of shigellosis in children in low-income countries. The acceptance of this new standard would substantially increase the fraction of MSD cases that are attributable to Shigella.
doi:10.1128/JCM.02713-12
PMCID: PMC3716050  PMID: 23536399
18.  XRCC3 Thr241Met polymorphism and ovarian cancer risk: a meta-analysis 
Tumour Biology  2013;35(3):2711-2715.
Genetic polymorphism of X-ray repair crosscomplementing group 3 (XRCC3) Thr241Met has been implicated to alter the risk of ovarian cancer, but the results are controversial. In order to get a more precise result, a meta-analysis was performed. All eligible studies were identified through an extensive search in PubMed, Excerpta Medica Database (Embase), Chinese National Knowledge Infrastructure database, and Chinese Biomedical Literature Database before August 2013. The association between the XRCC3 Thr241Met polymorphism and ovarian cancer risk was conducted by odds ratios (ORs) and 95 % confidence intervals (95 % CIs). Finally, a total of four publications including seven studies with 3,635 cases and 5,473 controls were included in our meta-analysis. Overall, there was no association between XRCC3 Thr241Met polymorphism and risk of ovarian cancer under all five genetic models in overall population (T vs. C: OR = 0.99, 95 % CI = 0.960–1.03, P = 0.752; TT vs. CC: OR = 1.00, 95 % CI = 0.91–1.10, P = 0.943; TC vs. TT: OR = 0.97, 95 % CI = 0.92–1.04, P = 0.396, Fig. 1; TT vs. TC/CC: OR = 1.00, 95 % CI = 0.91–1.12, P = 0.874; TT/TC vs. CC: OR = 0.98, 95 % CI = 0.94–1.03, P = 0.486). In the subgroup analysis according to ethnicity, the results suggested that XRCC3 Thr241Met polymorphism was not associated with the risk of ovarian cancer in Caucasians population. No significant association was found between the XRCC3 Thr241 Met polymorphism and the risk of ovarian cancer. Given the limited sample size and ethnicities included in the meta-analysis, further large scaled and well-designed studies are needed to confirm our results.
doi:10.1007/s13277-013-1357-z
PMCID: PMC3967082  PMID: 24254304
XRCC3; Polymorphism; Ovarian cancer; Meta-analysis
19.  Clinicopathological and prognostic significance of S100A4 overexpression in colorectal cancer: a meta-analysis 
Diagnostic Pathology  2013;8:181.
Background
Accumulated evidence has indicated a correlation between S100A4 expression and colorectal cancer (CRC) progression. However, its prognostic significance for patients with CRC remains inconclusive. To clarify their relationship, a meta-analysis of the relevant published studies was performed.
Method
PubMed, Cochrane Library, and Web of Science databases were electronically searched. All studies evaluating the prognostic value of S100A4 expression in CRC patients regarding survival and a series of clinicopathological parameters were included. The effect of S100A4 expression on the overall survival (OS) and disease-free survival (DFS) were measured by pooled hazard ratios (HRs) and 95% confidence intervals (CIs), while the effect of S100A4 expression on the clinicopathological parameters were measured by the pooled odds ratios (ORs) and their 95% CIs.
Results
Eleven studies (2,824 patients in total) were included in the meta-analysis. Overall, S100A4 overexpression was significantly associated with worse OS (HR = 1.90, 95% CI: 1.58–2.29, P <0.001), and worse DFS (HR = 2.16, 95% CI: 1.53–3.05, P <0.001) in patients with CRC. Subgroup analyses showed that S100A4 overexpression was significantly correlated with poor OS in Asian, European, and Australian patients and patients treated with surgery or chemotherapy. Additionally, there were significant associations between S100A4 expression and several clinicopathological parameters (tumour location, lymph node metastasis, nodal status, TNM stage, and tumour depth).
Conclusions
This meta-analysis indicates that S100A4 overexpression seems to correlate with tumour progression and poor prognosis of CRC patients. It may be a useful marker to predict progression and prognosis of CRC.
Virtual slides
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/8643820431072915
doi:10.1186/1746-1596-8-181
PMCID: PMC3833630  PMID: 24188373
Colorectal cancer; Meta-analysis; Progression; Prognosis; S100A4
20.  Association of MDR1 G2677T polymorphism and leukemia risk: evidence from a meta-analysis 
Tumour Biology  2013;35(3):2191-2197.
In the light of the relationship between the MDR1 G2677T polymorphism and the risk of leukemia remains inclusive or controversial. For better understanding of the effect of MDR1 G2677T polymorphism on leukemia risk, we performed a meta-analysis. Eligible studies were identified through a search of electronic databases such as PubMed, Excerpta Medica Database (Embase), Cochrane Library, and Chinese Biomedical Literature Database (CBM). The association between the MDR1 G2677T polymorphism and leukemia risk was conducted by odds ratios (ORs) and 95 % confidence intervals (95 % CI). A total of seven publications including eight studies with 1,229 cases and 1,097 controls were included in the meta-analysis. There was no association between MDR1 G2677T polymorphism and leukemia risk in all of five models in overall populations (T vs. G: OR = 1.00, 95 % CI = 0.88–1.12, P = 0.914; TT vs. GG: OR = 0.97, 95 % CI = 0.75–1.26, P = 0.812; TG vs. GG: OR = 1.00, 95 % CI = 0.92–1.08, P = 0.939; TT vs. TG/GG: OR = 0.98, 95 % CI = 0.67–1.43, P = 0.906; TT/TG vs. GG: OR = 1.00, 95 % CI = 0.95–1.06, P = 0.994). However, the significant association was found in others (Table 2) under the homozygote model (TT vs. GG: OR = 0.68, 95 % CI = 0.48–0.94, P = 0.020) and recessive model (TT vs. TG/GG: OR = 0.63, 95 % CI = 0.43–0.92, P = 0.016). In the subgroup analysis, according to the type of leukemia, significant association was found between MDR1 G2677T polymorphism and myeloid leukemia but not lymphoblastic leukemia (TT vs. GG: OR = 0.66, 95 % CI = 0.46–0.95, P = 0.026; TT vs. TG/GG: OR = 0.56, 95 % CI = 0.38–0.84, P = 0.005). The results suggested that there was no association between MDR1 G2677T polymorphism and leukemia risk in overall populations, but significant association was found in others populations (Asians and Africans), and myeloid leukemia indicated that G2677T polymorphism might be a protective factor in the susceptibility of myeloid leukemia and in Asians and Africans.
doi:10.1007/s13277-013-1291-0
PMCID: PMC3967080  PMID: 24142546
MDR1; Polymorphism; Leukemia; Meta-analysis
21.  Peripapillary retinal nerve fiber layer thickness distribution in Chinese with myopia measured by 3D-optical coherence tomography 
AIM
To assess the effect of myopia on the thickness of retinal nerve fiber layer (RNFL) measured by 3D optical coherence tomography (3D-OCT) in a group of nonglaucomatous Chinese subjects.
METHODS
Two hundred and fifty-eight eyes of 258 healthy Chinese myopic individuals were recruited and four groups were classified according to their spherical equivalent (SE): low myopia (n=42, -0.5D
RESULTS
The overall RNFL parameters shown significant differences between groups excluding 7, 9, 10, 11 o'clock hour thickness. The RNFL thickness of superior, nasal, inferior, average and 1, 2, 3, 4, 5, 6, 12 o'clock sectors were decreased with the increasing axial length and higher degree of myopia. In contrast, as axial length and the degree of myopia increased, the temporal and 8, 9 o'clock sectors thicknesses were increased. A considerable proportion of myopic eyes were classified as outside the normal limits. Six o'clock was the most notable of the total, which 43.4% were outside the normal limits.
CONCLUSION
On the measurement of RNFL, the characteristics of RNFL with the change of the degree of myopia were observed. As the degree of myopia increases, the RNFL thickness measured by 3D-OCT including the average and superior, nasal, inferior sectors decreases. And due to the change of RNFL thickness, it should be considered when using OCT to access for the damage of glaucoma especially people with myopia.
doi:10.3980/j.issn.2222-3959.2013.05.13
PMCID: PMC3808909  PMID: 24195037
optical coherence tomography; myopia; retinal nerve fiber layer
Tumour Biology  2013;35(3):1907-1915.
The association between xeroderma pigmentosum complementation group D (XPD) Asp312Asn and Lys751Gln gene polymorphisms and breast cancer risk has been widely reported, but the results were inconsistent. In order to derive a more precise estimation of the relationship, a meta-analysis was performed. A comprehensive search strategy was conducted towards the electronic databases including Medline, PubMed, Web of Science, Embase, and Chinese Biomedical Literature Database (Chinese). The association between the XPD polymorphism and breast cancer risk was conducted by odds ratios (ORs) and 95 % confidence intervals (95 % CIs). A total of 22 studies with 18,136 cases and 18,351 controls were included in our meta-analysis. Among these, 12 studies with 7,667 cases and 7,480 controls for Asp312Asn polymorphism and 20 studies with 10,469 cases and 10,871 controls for Lys751Gln polymorphism. With regard to Asp312Asn polymorphism, no significantly associated was found with breast cancer risk. However, significant association was found between Lys751Gln polymorphism and breast cancer risk under all genetic models in overall populations (C vs. A—OR = 1.10, 95 % CI = 1.04–1.17, P = 0.002; CC vs. AA—OR = 1.17, 95 % CI = 1.06–1.30, P = 0.003; AC vs. AA—OR = 1.06, 95 % CI = 1.01–1.12, P = 0.032; CC vs. AC/AA—OR = 1.17, 95 % CI = 1.04–1.32, P = 0.009; CC/AC vs. AA—OR = 1.07, 95 % CI = 1.02–1.12, P = 0.005). In subgroup analysis base on ethnicity, significance was found in Caucasians and mix. The results suggest that XPD Asp312Asn polymorphism was not associated with breast cancer. The XPD Lys751Gln polymorphism significantly increased breast cancer risk, especially for Caucasian and mix.
doi:10.1007/s13277-013-1256-3
PMCID: PMC3967070  PMID: 24101192
XPD; Polymorphism; Breast cancer; Meta-analysis
Tao-Hong-Si-Wu-Tang (THSWT) is a famous traditional Chinese herbal medicine formula, which has traditionally been used in China for about one thousand years. The present study investigated the effect of THSWT on physical fatigue. 32 male mice were randomly divided into 4 groups with 8 in each group. All were administered orally and daily for 28 days. Group I received isotonic saline solution as control; Group II, III and IV obtained 5, 10 and 20ml/ kg body weight of THSWT solutions, respectively. After 28 days, the anti-physical fatigue effect of THSWT was evaluated by using a forced swimming test, along with the determination of blood lactic acid, blood urea nitrogen (BUN), liver glycogen and muscle glycogen contents. The data showed that THSWT could extend exhaustive swimming time of mice, as well as decrease the BLA and BUN contents and increase the liver glycogen and muscle glycogen contents. The results support that THSWT had anti-physical fatigue effect.
PMCID: PMC3746359  PMID: 24082327
Tao-Hong-Si-Wu-Tang; physical fatigue; forced swimming test; mice
PLoS ONE  2013;8(9):e76031.
Background
The mouse double minute 2 (MDM2) gene encodes a phosphoprotein that interacts with P53 and negatively regulates its activity. The SNP309 polymorphism (T-G) in the promoter of MDM2 gene has been reported to be associated with enhanced MDM2 expression and tumor development. Studies investigating the association between MDM2 SNP309 polymorphism and colorectal cancer (CRC) risk reported conflicting results. We performed a meta-analysis of all available studies to explore the association of this polymorphism with CRC risk.
Methods
All studies published up to July 2013 on the association between MDM2 SNP309 polymorphism and CRC risk were identified by searching electronic databases PubMed, EMBASE, and Chinese Biomedical Literature database (CBM) databases. The association between the MDM2 SNP309 polymorphism and CRC risk was assessed by odds ratios (ORs) together with their 95% confidence intervals (CIs).
Results
A total of 14 case-control studies including 4460 CRC cases and 4828 controls were identified. We did not find a significant association between the MDM2 SNP309 polymorphism and CRC risk in all genetic models in overall population. However, in subgroup analysis by ethnicity, significant associations were found in Asians (TG vs. TT: OR = 1.197, 95% CI = 1.055–1.358, P=0.005; GG+TG vs. TT: OR = 1.246, 95% CI = 1.106–1.404, P=0.000) and Africans. When stratified by HWE in controls, significantly increased risk was also found among the studies consistent with HWE (TG vs. TT: OR = 1.166, 95% CI = 1.037–1.311, P= 0.010). In subgroup analysis according to p53 mutation status, and gender, no any significant association was detected.
Conclusions
The present meta-analysis suggests that the MDM2 is a candidate gene for CRC susceptibility. The MDM2 SNP309 polymorphism may be a risk factor for CRC in Asians.
doi:10.1371/journal.pone.0076031
PMCID: PMC3786895  PMID: 24098760
Tumour Biology  2013;35(2):1695-1701.
The association between methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms and breast cancer risk in the Chinese population has been widely reported, but results were inconsistent. In order to derive a more precise estimation of the relationship, a meta-analysis was performed. Eligible articles were identified through search of databases including Medline, PubMed, Web of Science, Embase, Chinese Biomedical Literature Database (CBM, Chinese), China National Knowledge Infrastructure (CNKI, Chinese), and Wangfang Database (Chinese). The association between the MTHFR polymorphism and breast cancer risk was conducted using odds ratios (ORs) and 95 % confidence intervals (95 % CIs). Finally, a total of 22 studies with 6,103 cases and 7,913 controls were included in our meta-analysis: 13 studies with 3,273 cases and 4,419 controls for C677T polymorphism and 9 studies with 2,830 cases and 3,494 controls for A1298C polymorphism. With regard to C677T polymorphism, significant association was found with breast cancer risk under three models (T vs. C: OR = 1.12, 95 % CI = 1.02–1.23, P = 0.015; TT vs. CC: OR = 1.35, 95 % CI = 1.10–1.67, P = 0.005; TT vs. CC/CT: OR = 1.37, 95 % CI = 1.11–1.70, P = 0.004). There was no significant association found between A1298C polymorphism and breast cancer risk under all genetic models (C vs. A: OR = 0.96, 95 % CI = 0.89–1.03, P = 0.268; CC vs. AA: OR = 0.98, 95 % CI = 0.77–1.26, P = 0.899; AC vs. AA: OR = 0.95, 95 % CI = 0.88–1.02, P = 0.174; CC vs. AC/AA: OR = 1.00, 95 % CI = 0.78–1.28, P = 0.996, CC/AC vs. AA: OR = 0.96, 95 % CI = 0.89–1.02, P = 0.196). In summary, during this meta-analysis, we found that MTHFR C677T polymorphism was significantly associated with breast cancer risk in the Chinese population. Meanwhile, MTHFR A1298C polymorphism was not associated with breast cancer risk in the Chinese population.
doi:10.1007/s13277-013-1234-9
PMCID: PMC3932174  PMID: 24078451
Methylenetetrahydrofolate reductase; Polymorphism; Breast cancer; Meta-analysis

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