PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (411)
 

Clipboard (0)
None

Select a Filter Below

Journals
more »
Year of Publication
more »
1.  Lanthionine synthetase C–like protein 2 (LanCL2) is a novel regulator of Akt 
Molecular Biology of the Cell  2014;25(24):3954-3961.
Lanthionine synthetase C-like 2 (LanCL2) is a novel regulator of Akt, promoting maximum Akt activation and cell survival in liver cells. LanCL2 regulates Akt activation by directly facilitating mTORC2 phosphorylation of Akt.
The serine/threonine protein kinase Akt controls a wide range of biochemical and cellular processes under the modulation of a variety of regulators. In this study, we identify the lanthionine synthetase C–like 2 (LanCL2) protein as a positive regulator of Akt activation in human liver cells. LanCL2 knockdown dampens serum- and insulin-stimulated Akt phosphorylation, whereas LanCL2 overexpression enhances these processes. Neither insulin receptor phosphorylation nor the interaction between insulin receptor substrate and phosphatidylinositide 3-kinase (PI3K) is affected by LanCL2 knockdown. LanCL2 also does not function through PP2A, a phosphatase of Akt. Instead, LanCL2 directly interacts with Akt, with a preference for inactive Akt. Moreover, we show that LanCL2 also binds to the Akt kinase mTORC2, but not phosphoinositide-dependent kinase 1. Whereas LanCL2 is not required for the Akt-mTORC2 interaction, recombinant LanCL2 enhances Akt phosphorylation by target of rapamycin complex 2 (mTORC2) in vitro. Finally, consistent with a function of Akt in regulating cell survival, LanCL2 knockdown increases the rate of apoptosis, which is reversed by the expression of a constitutively active Akt. Taken together, our findings reveal LanCL2 as a novel regulator of Akt and suggest that LanCL2 facilitates optimal phosphorylation of Akt by mTORC2 via direct physical interactions with both the kinase and the substrate.
doi:10.1091/mbc.E14-01-0004
PMCID: PMC4244203  PMID: 25273559
2.  Preoperative Evaluation of the Histological Grade of Hepatocellular Carcinoma with Diffusion-Weighted Imaging: A Meta-Analysis 
PLoS ONE  2015;10(2):e0117661.
Objective
To evaluate the diagnostic performance of diffusion-weighted imaging (DWI) in the preoperative prediction of the histological grade of hepatocellular carcinoma (HCC).
Materials and Methods
A comprehensive literature search was performed in several authoritative databases to identify relevant articles. QUADAS-2 was used to assess the quality of included studies. Data were extracted to calculate the pooled sensitivity, specificity, positive likelihood ratio (PLR) and negative likelihood ratio (NLR). Summary receiver operating characteristic (SROC) curves were derived and areas under the SROC curve (AUC) were computed to indicate the diagnostic accuracy. Heterogeneity test, meta-regression analysis and sensitivity analysis were performed to identify factors and studies contributed to the heterogeneity.
Results
A total of 11 studies with 912 HCCs were included in this meta-analysis. The pooled sensitivity, specificity, PLR and NLR with corresponding 95% confidence intervals (CI) were 0.54(0.47–0.61), 0.90(0.87–0.93), 4.88(2.99–7.97) and 0.46(0.27–0.77) for the prediction of well-differentiated HCC (w-HCC), 0.84(0.78–0.89), 0.48(0.43–0.52), 2.29(1.43–3.69) and 0.30(0.22–0.41) for the prediction of poorly-differentiated HCC (p-HCC). The AUC were 0.9311 and 0.8513 in predicting w-HCC and p-HCC, respectively. Results were further evaluated according to the method of image interpretation. Significant heterogeneity was observed.
Conclusion
DWI had excellent and moderately high diagnostic accuracy for the detection of w-HCC and p-HCC, respectively. Nonetheless, further studies in larger populations and an optimized image acquisition and interpretation are required before DWI-derived parameters can be used as a useful image biomarker for the prediction of the histological grade of HCC.
doi:10.1371/journal.pone.0117661
PMCID: PMC4320049  PMID: 25658359
3.  Construction of a high-density genetic map and QTLs mapping for sugars and acids in grape berries 
BMC Plant Biology  2015;15:28.
Background
QTLs controlling individual sugars and acids (fructose, glucose, malic acid and tartaric acid) in grape berries have not yet been identified. The present study aimed to construct a high-density, high-quality genetic map of a winemaking grape cross with a complex parentage (V. vinifera × V. amurensis) × ((V. labrusca × V. riparia) × V. vinifera), using next-generation restriction site-associated DNA sequencing, and then to identify loci related to phenotypic variability over three years.
Results
In total, 1 826 SNP-based markers were developed. Of these, 621 markers were assembled into 19 linkage groups (LGs) for the maternal map, 696 for the paternal map, and 1 254 for the integrated map. Markers showed good linear agreement on most chromosomes between our genetic maps and the previously published V. vinifera reference sequence. However marker order was different in some chromosome regions, indicating both conservation and variation within the genome. Despite the identification of a range of QTLs controlling the traits of interest, these QTLs explained a relatively small percentage of the observed phenotypic variance. Although they exhibited a large degree of instability from year to year, QTLs were identified for all traits but tartaric acid and titratable acidity in the three years of the study; however only the QTLs for malic acid and β ratio (tartaric acid-to-malic acid ratio) were stable in two years. QTLs related to sugars were located within ten LGs (01, 02, 03, 04, 07, 09, 11, 14, 17, 18), and those related to acids within three LGs (06, 13, 18). Overlapping QTLs in LG14 were observed for fructose, glucose and total sugar. Malic acid, total acid and β ratio each had several QTLs in LG18, and malic acid also had a QTL in LG06. A set of 10 genes underlying these QTLs may be involved in determining the malic acid content of berries.
Conclusion
The genetic map constructed in this study is potentially a high-density, high-quality map, which could be used for QTL detection, genome comparison, and sequence assembly. It may also serve to broaden our understanding of the grape genome.
Electronic supplementary material
The online version of this article (doi:10.1186/s12870-015-0428-2) contains supplementary material, which is available to authorized users.
doi:10.1186/s12870-015-0428-2
PMCID: PMC4329212  PMID: 25644551
Berry quality; Genetic map; Next-generation sequencing (NGS); QTL analysis; Quantitative trait loci; Restriction-site associated DNA (RAD); Vitis
4.  Distribution of Virulence-Associated Genes and Genetic Relationships in Non-O1/O139 Vibrio cholerae Aquatic Isolates from China 
Applied and Environmental Microbiology  2014;80(16):4987-4992.
Non-O1/O139 Vibrio cholerae is naturally present in aquatic ecosystems and has been linked with cholera-like diarrhea and local outbreaks. The distribution of virulence-associated genes and genetic relationships among aquatic isolates from China are largely unknown. In this study, 295 aquatic isolates of V. cholerae non-O1/O139 serogroups from different regions in China were investigated. Only one isolate was positive for ctxB and harbored a rare genotype; 10 (3.4%) isolates carried several types of rstR sequences, eight of which carried rare types of toxin-coregulated pili (tcpA). Furthermore, 16 (5.4%) isolates carried incomplete (with partial open reading frames [ORFs]) vibrio seventh pandemic island I (VSP-I) or VSP-II clusters, which were further classified as 11 novel types. PCR-based analyses revealed remarkable variations in the distribution of putative virulence genes, including mshA (95.6%), hlyA (95.3%), rtxC (89.8%), rtxA (82.7%), IS1004 (52.9%), chxA (30.2%), SXT (15.3%), type III secretion system (18.0%), and NAG-ST (3.7%) genes. There was no correlation between the prevalence of putative virulence genes and that of CTX prophage or TCP genes, whereas there were correlations among the putative virulence genes. Further multilocus sequence typing (MLST) placed selected isolates (n = 70) into 69 unique sequence types (STs), which were different from those of the toxigenic O1 and O139 counterparts, and each isolate occupied a different position in the MLST tree. The V. cholerae non-O1/O139 aquatic isolates predominant in China have high genotypic diversity; these strains constitute a reservoir of potential virulence genes, which may contribute to evolution of pathogenic isolates.
doi:10.1128/AEM.01021-14
PMCID: PMC4135755  PMID: 24907334
5.  Analytic and Clinical Performance of cobas HPV Testing in Anal Specimens from HIV-Positive Men Who Have Sex with Men 
Journal of Clinical Microbiology  2014;52(8):2892-2897.
Anal human papillomavirus (HPV) infections are common, and the incidence of anal cancer is high in HIV-infected men who have sex with men (MSM). To evaluate the performance of HPV assays in anal samples, we compared the cobas HPV test (cobas) to the Roche Linear Array HPV genotyping assay (LA) and cytology in HIV-infected MSM. Cytology and cobas and LA HPV testing were conducted for 342 subjects. We calculated agreement between the HPV assays and the clinical performance of HPV testing and HPV genotyping alone and in combination with anal cytology. We observed high agreement between cobas and LA, with cobas more likely than LA to show positive results for HPV16, HPV18, and other carcinogenic types. Specimens testing positive in cobas but not in LA were more likely to be positive for other markers of HPV-related disease compared to those testing negative in both assays, suggesting that at least some of these were true positives for HPV. cobas and LA showed high sensitivities but low specificities for the detection of anal intraepithelial neoplasia grade 2/3 (AIN2/3) in this population (100% sensitivity and 26% specificity for cobas versus 98.4% sensitivity and 28.9% specificity for LA). A combination of anal cytology and HPV genotyping provided the highest accuracy for detecting anal precancer. A higher HPV load was associated with a higher risk of AIN2/3 with HPV16 (Ptrend < 0.001), HPV18 (Ptrend = 0.07), and other carcinogenic types (Ptrend < 0.001). We demonstrate that cobas can be used for HPV detection in anal cytology specimens. Additional tests are necessary to identify men at the highest risk of anal cancer among those infected with high-risk HPV.
doi:10.1128/JCM.03517-13
PMCID: PMC4136172  PMID: 24899025
6.  Circulating vitamin D binding protein, total, free and bioavailable 25-hydroxyvitamin D and risk of colorectal cancer 
Scientific Reports  2015;5:7956.
Epidemiological investigation have suggested that there is a significantly inverse association between circulating 25-hydroxyvitamin D (25(OH)D) and the risk for developing colorectal cancer (CRC) in humans. However, little is known about the role of vitamin D binding protein (VDBP) in colorectal carcinogenesis. Blood samples were collected from 212 CRC patients and 212 controls matched with age, gender and blood collection time. We used logistic regression to calculate the odds ratios and 95% confidence intervals for further estimation of the association of the quartiles of VDBP, total, free and bioavailable 25(OH)D with CRC risk. The results revealed that there was no significant association between circulating VDBP concentrations and CRC in the present study, and that a negative association existed between total 25(OH)D and the risk of CRC, which was unchanged after adjustment for VDBP. Higher levels of free and bioavailable 25(OH)D were significantly associated with decreased risk of CRC. After stratifying by VDBP, high levels of total, free and bioavailable 25(OH)D were associated significantly with decreased CRC risk among participants with circulating VDBP below the median. These findings indicate that VDBP is not directly associated with the risk of CRC, but it modulates circulating free and bioavailable 25(OH)D concentration.
doi:10.1038/srep07956
PMCID: PMC4302314  PMID: 25609140
7.  Cell death pathway induced by resveratrol-bovine serum albumin nanoparticles in a human ovarian cell line 
Oncology Letters  2015;9(3):1359-1363.
Resveratrol-bovine serum albumin nanoparticles (RES-BSANP) exhibit chemotherapeutic properties, which trigger apoptosis. The aim of the present study was to investigate the caspase-independent cell death pathway induced by RES-BSANP in human ovarian cancer SKOV3 cells and to analyze its mechanism. Morphological changes were observed by apoptotic body/cell nucleus DNA staining using inverted and fluorescence microscopy. The cell death pathway was determined by phosphatidylserine translocation. Western blot analysis was conducted to detect the activation of apoptosis-inducing factor (AIF), cytochrome c (Cyto c) and B-cell lymphoma 2-associated X protein (Bax). Apoptotic body and nuclear condensation and fragmentation were observed simultaneously following treatment with RES-BSANP. RES-BSANP induced apoptosis in a dose-dependent manner in the human ovarian cancer SKOV3 cells. The translocation of AIF from the mitochondria to the cytoplasm occurred earlier than that of Cyto c. In addition, Bax binding to the mitochondria was required for the release of AIF and Cyto c from the mitochondria. The AIF apoptosis pathway may present an alternative caspase-dependent apoptosis pathway in human ovarian cell death induced by RES-BSANP. Elucidation of this pathway may be critical for the treatment of cancer using high doses of RES-BSANP.
doi:10.3892/ol.2015.2851
PMCID: PMC4315083  PMID: 25663913
resveratrol-bovine serum albumin nanoparticles; apoptosis; programmed cell death; caspase-independent
8.  Numerical investigation of airflow in an idealised human extra-thoracic airway: a comparison study 
Biomechanics and modeling in mechanobiology  2013;13(1):10.1007/s10237-013-0496-x.
Large eddy simulation (LES) technique is employed to numerically investigate the airflow through an idealised human extra-thoracic airway under different breathing conditions, 10 l/min, 30 l/min, and 120 l/min. The computational results are compared with single and cross hot-wire measurements, and with time-averaged flow field computed by standard k-ω and k-ω-SST Reynolds averaged Navier-Stokes (RANS) models and the Lattice-Boltzmann method (LBM). The LES results are also compared to root-mean-square (RMS) flow field computed by the Reynolds stress model (RSM) and LBM. LES generally gives better prediction of the time-averaged flow field than RANS models and LBM. LES also provides better estimation of the RMS flow field than both the RSM and the LBM.
doi:10.1007/s10237-013-0496-x
PMCID: PMC3766393  PMID: 23619907
LES; hot-wire; RANS; LBM; RSM
9.  Vitamin A Supplementation in Early Life Enhances the Intestinal Immune Response of Rats with Gestational Vitamin A Deficiency by Increasing the Number of Immune Cells 
PLoS ONE  2014;9(12):e114934.
Vitamin A is a critical micronutrient for regulating immunity in many organisms. Our previous study demonstrated that gestational or early-life vitamin A deficiency decreases the number of immune cells in offspring. The present study aims to test whether vitamin A supplementation can restore lymphocyte pools in vitamin A-deficient rats and thereby improve the function of their intestinal mucosa; furthermore, the study aimed to identify the best time frame for vitamin A supplementation. Vitamin A-deficient pregnant rats or their offspring were administered a low-dose of vitamin A daily for 7 days starting on gestational day 14 or postnatal day 1, day 14 or day 28. Serum retinol concentrations increased significantly in all four groups that received vitamin A supplementation, as determined by high-performance liquid chromatography. The intestinal levels of secretory immunoglobulin A and polymeric immunoglobulin receptor increased significantly with lipopolysaccharide challenge in the rats that received vitamin A supplementation starting on postnatal day 1. The rats in this group had higher numbers of CD8+ intestinal intraepithelial lymphocytes, CD11C+ dendritic cells in the Peyer's patches and CD4+CD25+ T cells in the spleen compared with the vitamin A-deficient rats; flow cytometric analysis also demonstrated that vitamin A supplementation decreased the number of B cells in the mesenteric lymph nodes. Additionally, vitamin A supplementation during late gestation increased the numbers of CD8+ intestinal intraepithelial lymphocytes and decreased the numbers of B lymphocytes in the mesenteric lymph nodes. However, no significant differences in lymphocyte levels were found between the rats in the other two vitamin A supplement groups and the vitamin A-deficient group. In conclusion, the best recovery of a subset of lymphocytes in the offspring of gestational vitamin A-deficient rats and the greatest improvement in the intestinal mucosal immune response are achieved when vitamin A supplementation occurs during the early postnatal period.
doi:10.1371/journal.pone.0114934
PMCID: PMC4263713  PMID: 25503794
10.  Complete mineralization of perfluorooctanoic acid (PFOA) by γ-irradiation in aqueous solution 
Scientific Reports  2014;4:7418.
Decomposition of perfluorooctanoic acid (C7F15COOH, PFOA) has been gaining increasing interests because it is a ubiquitous environmental contaminant and resistant to the most conventional treatment processes. In this work, the rapid and complete mineralization of PFOA and simultaneous defluorination were achieved by γ-ray irradiation with a 60Co source. The degradation rate of PFOA by γ-ray irradiation would be high, and a pseudo-first-order kinetic rate constant of 0.67 h−1 could be achieved in the N2 satured condition at pH 13.0. The experimental results and quantum chemical calculation confirmed that two radicals, i.e., hydroxyl radical (·OH) and aqueous electrons (eaq−), were responsible for the degradation of PFOA, while only either eaq− or ·OH might not be able to accomplish complete mineralization of PFOA. The synergistic effects of ·OH and eaq− involved in the cleavage of C-C and C-F bonds, and therefore complete mineralization of PFOA were achieved. The intermediate products were identified and the degradation pathway was also proposed. The results of this study may offer a useful, high-efficient approach for complete mineralizing fluorochemicals and other persistent pollutants.
doi:10.1038/srep07418
PMCID: PMC4261166  PMID: 25492109
11.  Evaluation of the 3D Finite Element Method Using a Tantalum Rod for Osteonecrosis of the Femoral Head 
Background
The aim of this study was to contrast the collapse values of the postoperative weight-bearing areas of different tantalum rod implant positions, fibula implantation, and core decompression model and to investigate the advantages and disadvantages of tantalum rod implantation in different ranges of osteonecrosis in comparison with other methods.
Material/Methods
The 3D finite element method was used to establish the 3D finite element model of normal upper femur, 3D finite element model after tantalum rod implantation into different positions of the upper femur in different osteonecrosis ranges, and other 3D finite element models for simulating fibula implant and core decompression.
Results
The collapse values in the weight-bearing area of the femoral head of the tantalum rod implant model inside the osteonecrosis area, implant model in the middle of the osteonecrosis area, fibula implant model, and shortening implant model exhibited no statistically significant differences (p>0.05) when the osteonecrosis range was small (60°). The stress values on the artificial bone surface for the tantalum rod implant model inside the osteonecrosis area and the shortening implant model exhibited statistical significance (p<0.01).
Conclusions
Tantalum rod implantation into the osteonecrosis area can reduce the collapse values in the weight-bearing area when osteonecrosis of the femoral head (ONFH) was in a certain range, thereby obtaining better clinical effects. When ONFH was in a large range (120°), the tantalum rod implantation inside the osteonecrosis area, shortening implant or fibula implant can reduce the collapse values of the femoral head, as assessed by other methods.
doi:10.12659/MSM.890920
PMCID: PMC4266390  PMID: 25479830
Femoral Neoplasms; Finite Element Analysis; Tantalum
12.  Increased expression of melanoma stem cell marker CD271 in metastatic melanoma to the brain 
Human melanoma contains multipotent stem cells that express the neural crest stem cell marker CD271. CD271-expressing melanoma cells in murine xenografts give rise to metastatic tumor. However, a comprehensive clinical investigation of its role in different stages of melanomagenesis has not been well studied. We studied CD271 expression with immunohistochemistry in 11 cases of banal melanocytic nevus, 9 cases of primary cutaneous melanoma, 10 cases of primary mucosal melanoma, 5 cases of metastatic melanoma in regional lymph nodes, and 11 cases of metastatic melanoma in the brain. In addition, 9 cases of metastatic, high-grade adenocarcinomas from breast and lung to the brain were studied as controls. The staining was scored based on the number of positive cells and analyzed by student t-test. All banal melanocytic nevi showed negative to equivocal staining. Primary cutaneous melanomas showed variable patterns, mucosal melanomas were mostly negative, and metastases to lymph nodes ranged from negative to moderate positivity. In contrast, all 11 cases of metastatic melanoma to the brain showed moderate (4 cases) to strong positivity (7 cases). Metastases from lung and breast origin were used as controls and showed negative to weakly positive staining in all but one case. Statistically, CD271 has significantly increased expression in metastatic melanoma to the brain when compared to the other groups studied (P < 0.05). The findings suggest that CD271 expression is specifically increased in metastatic melanoma to the brain. Further prospective study for the role of CD271 in prediction of melanoma brain metastasis as well as prognosis assessment will be of great clinical significance.
PMCID: PMC4313973
Melanoma; metastatic melanoma; CD271; tumor stem cells; melanoma prognosis
13.  Transcript Profiling Reveals Auxin and Cytokinin Signaling Pathways and Transcription Regulation during In Vitro Organogenesis of Ramie (Boehmeria nivea L. Gaud) 
PLoS ONE  2014;9(11):e113768.
In vitro organogenesis, one of the most common pathways leading to in vitro plant regeneration, is widely used in biotechnology and the fundamental study of plant biology. Although previous studies have constructed a complex regulatory network model for Arabidopsis in vitro organogenesis, no related study has been reported in ramie. To generate more complete observations of transcriptome content and dynamics during ramie in vitro organogenesis, we constructed a reference transcriptome library and ten digital gene expression (DGE) libraries for illumina sequencing. Approximately 111.34 million clean reads were obtained for transcriptome and the DGE libraries generated between 13.5 and 18.8 million clean reads. De novo assembly produced 43,222 unigenes and a total of 5,760 differentially expressed genes (DEGs) were filtered. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database, 26 auxin related and 11 cytokinin related DEGs were selected for qRT-PCR validation of two ramie cultivars, which had high (Huazhu No. 5) or extremely low (Dazhuhuangbaima) shoot regeneration abilities. The results revealed differing regulation patterns of auxin and cytokinin in different genotypes. Here we report the first genome-wide gene expression profiling of in vitro organogenesis in ramie and provide an overview of transcription and phytohormone regulation during the process. Furthermore, the auxin and cytokinin related genes have distinct expression patterns in two ramie cultivars with high or extremely low shoot regeneration ability, which has given us a better understanding of the in vitro organogenesis mechanism. This result will provide a foundation for future phytohormone research and lead to improvements of the ramie regeneration system.
doi:10.1371/journal.pone.0113768
PMCID: PMC4240604  PMID: 25415356
14.  Experimental and Theoretical Approaches for the Surface Interaction between Copper and Activated Sludge Microorganisms at Molecular Scale 
Scientific Reports  2014;4:7078.
Interactions between metals and activated sludge microorganisms substantially affect the speciation, immobilization, transport, and bioavailability of trace heavy metals in biological wastewater treatment plants. In this study, the interaction of Cu(II), a typical heavy metal, onto activated sludge microorganisms was studied in-depth using a multi-technique approach. The complexing structure of Cu(II) on microbial surface was revealed by X-ray absorption fine structure (XAFS) and electron paramagnetic resonance (EPR) analysis. EPR spectra indicated that Cu(II) was held in inner-sphere surface complexes of octahedral coordination with tetragonal distortion of axial elongation. XAFS analysis further suggested that the surface complexation between Cu(II) and microbial cells was the distorted inner-sphere coordinated octahedra containing four short equatorial bonds and two elongated axial bonds. To further validate the results obtained from the XAFS and EPR analysis, density functional theory calculations were carried out to explore the structural geometry of the Cu complexes. These results are useful to better understand the speciation, immobilization, transport, and bioavailability of metals in biological wastewater treatment plants.
doi:10.1038/srep07078
PMCID: PMC4233339  PMID: 25399801
15.  How Does Domain Replacement Affect Fibril Formation of the Rabbit/Human Prion Proteins 
PLoS ONE  2014;9(11):e113238.
Background
It is known that in vivo human prion protein (PrP) have the tendency to form fibril deposits and are associated with infectious fatal prion diseases, while the rabbit PrP does not readily form fibrils and is unlikely to cause prion diseases. Although we have previously demonstrated that amyloid fibrils formed by the rabbit PrP and the human PrP have different secondary structures and macromolecular crowding has different effects on fibril formation of the rabbit/human PrPs, we do not know which domains of PrPs cause such differences. In this study, we have constructed two PrP chimeras, rabbit chimera and human chimera, and investigated how domain replacement affects fibril formation of the rabbit/human PrPs.
Methodology/Principal Findings
As revealed by thioflavin T binding assays and Sarkosyl-soluble SDS-PAGE, the presence of a strong crowding agent dramatically promotes fibril formation of both chimeras. As evidenced by circular dichroism, Fourier transform infrared spectroscopy, and proteinase K digestion assays, amyloid fibrils formed by human chimera have secondary structures and proteinase K-resistant features similar to those formed by the human PrP. However, amyloid fibrils formed by rabbit chimera have proteinase K-resistant features and secondary structures in crowded physiological environments different from those formed by the rabbit PrP, and secondary structures in dilute solutions similar to the rabbit PrP. The results from transmission electron microscopy show that macromolecular crowding caused human chimera but not rabbit chimera to form short fibrils and non-fibrillar particles.
Conclusions/Significance
We demonstrate for the first time that the domains beyond PrP-H2H3 (β-strand 1, α-helix 1, and β-strand 2) have a remarkable effect on fibrillization of the rabbit PrP but almost no effect on the human PrP. Our findings can help to explain why amyloid fibrils formed by the rabbit PrP and the human PrP have different secondary structures and why macromolecular crowding has different effects on fibrillization of PrPs from different species.
doi:10.1371/journal.pone.0113238
PMCID: PMC4234653  PMID: 25401497
16.  3-Tesla magnetic resonance imaging improves the prostate cancer detection rate in transrectral ultrasound-guided biopsy 
The detection rate of prostate cancer (PCa) using traditional biopsy guided by transrectal ultrasound (TRUS) is not satisfactory. The aim of this study was to determine the utility of 3-Tesla (3-T) magnetic resonance imaging (MRI) prior to TRUS-guided prostate biopsy and to investigate which subgroup of patients had the most evident improvement in PCa detection rate. A total of 420 patients underwent 3-T MRI examination prior to the first prostate biopsy and the positions of suspicious areas were recorded respectively. TRUS-guided biopsy regimes included systematic 12-core biopsy and targeted biopsy identified by MRI. Patients were divided into subgroups according to their serum prostate-specific antigen (PSA) levels, PSA density (PSAD), prostate volume, TRUS findings and digital rectal examination (DRE) findings. The ability of MRI to improve the cancer detection rate was evaluated. The biopsy positive rate of PCa was 41.2% (173/420), and 41 of the 173 (23.7%) patients were detected only by targeted biopsy in the MRI-suspicious area. Compared with the systematic biopsy, the positive rate was significantly improved by the additional targeted biopsy (P=0.0033). The highest improvement of detection rate was observed in patients with a PSA level of 4–10 ng/ml, PSAD of 0.12–0.20 ng/ml2, prostate volume >50 ml, negative TRUS findings and negative DRE findings (P<0.05). Therefore, it is considered that 3-T MRI examination could improve the PCa detection rate on first biopsy, particularly in patients with a PSA level of 4–10 ng/ml, PSAD of 0.12–0.20 ng/ml2, prostate volume of >50 ml, negative TRUS findings and negative DRE findings.
doi:10.3892/etm.2014.2061
PMCID: PMC4247284  PMID: 25452804
prostate cancer; transrectal ultrasound; magnetic resonance imaging; biopsy
17.  Rare Detection of Occult Hepatitis B Virus Infection in Children of Mothers with Positive Hepatitis B Surface Antigen 
PLoS ONE  2014;9(11):e112803.
The prevalence of occult Hepatitis B virus (HBV) infection in children was considerably varied from 0.1–64% in different reports. In this study we aimed to investigate the prevalence of occult HBV infection among the children born to mothers with positive hepatitis B surface antigen (HBsAg) in Jiangsu, China. Serum samples were collected from 210 children of 207 mothers with positive HBsAg. HBV serological markers were detected by ELISA and HBV DNA was detected by nested PCR. Homology comparison of HBV sequences recovered from the child and mother was used to define the infection. Three children (1.43%) were positive for HBsAg, in whom the HBV pre S and S gene sequence in each child was identical to that in her mother. Of the 207 HBsAg-negative children, nine displayed HBV DNA positive by two nested PCR assays using primers derived from S and C genes. However, the sequence alignment showed that the sequences in each child were considerably different from those in his/her mother. Therefore, the sequences amplified from the children were very likely resultant from the cross-contaminations. Furthermore, the nine children with ‘positive HBV DNA’ were all negative for anti-HBc, and one had anti-HBs 3.42 mIU/ml and eight others had anti-HBs from 72 to >1000 mIU/ml, indicating that the nine children were less likely infected with HBV. Therefore, none of the 207 HBsAg-negative children of HBV-infected mothers was found to have occult HBV infection. We conclude that the prevalence of occult HBV infection in vaccinated children born to HBsAg positive mothers should be extremely low. We recommend that homology comparison of sequences recovered from the child and mother be used to define the occult HBV infection in children born to HBV infected mothers.
doi:10.1371/journal.pone.0112803
PMCID: PMC4226608  PMID: 25383543
18.  Bt Rice Expressing Cry2Aa Does Not Harm Cyrtorhinus lividipennis, a Main Predator of the Nontarget Herbivore Nilapavarta lugens 
PLoS ONE  2014;9(11):e112315.
T2A-1 is a newly developed transgenic rice that expresses a synthesized cry2Aa gene driven by the maize ubiquitin promoter. T2A-1 exhibits high resistance against lepidopteran pests of rice. The brown planthopper, Nilapavarta lugens (Stål), is a main nontarget sap-sucking insect pest of rice, and Cyrtorhinus lividipennis (Reuter) is the major predator of the eggs and young nymphs of planthoppers. As C. lividipennis may expose to the Cry2Aa protein via N. lugens, it is therefore essential to assess the potential effects of transgenic cry2Aa rice on this predator. In the present study, three experiments were conducted to evaluate the ecological risk of transgenic cry2Aa rice to C. lividipennis: (1) a direct feeding experiment in which C. lividipennis was fed an artificial diet containing Cry2Aa at the dose of 10-time higher than that it may encounter in the realistic field condition; (2) a tritrophic experiment in which the Cry2Aa protein was delivered to C. lividipennis indirectly through prey eggs or nymphs; (3) a realistic field experiment in which the population dynamics of C. lividipennis were investigated using vacuum-suction. Both direct exposure to elevated doses of the Cry2Aa protein and prey-mediated exposure to realistic doses of the protein did not result in significant detrimental effects on the development, survival, female ratio and body weight of C. lividipennis. No significant differences in population density and population dynamics were observed between C. lividipennis in transgenic cry2Aa and nontransgenic rice fields. It may be concluded that transgenic cry2Aa rice had no detrimental effects on C. lividipennis. This study represents the first report of an assessment continuum for the effects of transgenic cry2Aa rice on C. lividipennis.
doi:10.1371/journal.pone.0112315
PMCID: PMC4223026  PMID: 25375147
19.  Association of HLA-DP/DQ and STAT4 Polymorphisms with HBV Infection Outcomes and a Mini Meta-Analysis 
PLoS ONE  2014;9(11):e111677.
Background
Though HLA-DP/DQ is regarded to associate with HBV susceptibility and HBV natural clearance, its role in hepatocellular carcinoma (HCC) development is obscure. And the role of STAT4 in HBV susceptibility and clearance as well as HCC development is still contentious. Therefore, we conducted this study, aiming to clarify these obscure relationships.
Methods
We recruited 1312 Chinese Han subjects including healthy controls, HBV carriers and HCC patients in the experiment stage. The meta-analysis included 3467 HCC patients and 5821 HBV carriers to appraise the association with HCC development.
Results
Consistent with previous studies, HLA-DP/DQ associated with HBV susceptibility and HBV natural clearance (p<0.05). However, the experiment showed that HLA-DP rs3077, rs9277535 and rs7453920 did not associate with HCC development (dominant model, rs3077, OR = 0.86, 95%CI = 0.62–1.18; rs9277535, OR = 0.94, 95%CI = 0.68–1.30; rs7453920, OR = 0.75, 95%CI = 0.44–1.27). Meta-analysis again consolidated this conclusion (allele model, rs3077, OR = 0.94, 95%CI = 0.87–1.02; rs9277535, OR = 1.04, 95%CI = 0.97–1.11; rs7453920, OR = 0.89, 95%CI = 0.76–1.02). As for STAT4 rs7574865, we did not find any significant association with HBV susceptibility (OR = 0.91, 95%CI = 0.66–1.26) or HBV natural clearance (OR = 1.13, 95%CI = 0.86–1.49). Moreover, current data failed to acquire positive connection of rs7574865 with HCC development (experiment, OR = 0.86, 95%CI = 0.62–1.19; meta-analysis, OR = 0.87, 95%CI = 0.74–1.03), which may be due to the small sample size.
Conclusions
HLA-DP/DQ polymorphisms (rs3077, rs9277535, rs7453920) did not associate with HCC development, but did correlate with HBV susceptibility and HBV natural clearance. STAT4 rs7574865 seemed not to correlate with HBV susceptibility or natural clearance. And it seemed rather ambiguous in its role on HCC development at present.
doi:10.1371/journal.pone.0111677
PMCID: PMC4218798  PMID: 25365208
20.  High Concentrate Diet Induced Mucosal Injuries by Enhancing Epithelial Apoptosis and Inflammatory Response in the Hindgut of Goats 
PLoS ONE  2014;9(10):e111596.
Purpose
It is widely accepted that lipopolysaccharide and volatile fatty acids (VFA) accumulate in the digestive tract of ruminants fed diets containing high portions of grain. Compared to the ruminal epithelium, the hindgut epithelium is composed of a monolayer structure that is more “leaky” for lipopolysaccharide and susceptible to organic acid-induced damage. The aim of this study was to investigate changes in epithelial structure, apoptosis and inflammatory response in the hindgut of goats fed a high-concentrate diet for 6 weeks.
Experimental Design
Eight local Chinese goats with rumen cannulas were randomly assigned to two groups: one group was fed a high-concentrate diet (65% concentrate of dry matter, HC) and the other group was fed a low-concentrate diet (35% concentrate of dry matter, LC) for 6 wks. Ruminal fluid, plasma, and hindgut mucosa tissues were collected. Histological techniques, real-time PCR and western blotting were used to evaluate the tissues structure, cell apoptosis and local inflammation in the hindguts.
Results
Feeding HC diet for 6 wks resulted in a significant decrease of ruminal pH (p<0.01), and ruminal lipopolysaccharide concentrations were significantly increased in HC goats (p<0.05). Obvious damage was observed to mucosal epithelium of the hindgut and the intercellular tight junctions in HC, but not in LC, goats. The expression of MyD88 and caspase-8 mRNA was increased in colonic epithelium of HC goats compared to LC (p<0.05), and the expression of TLR-4 and caspase-3 showed a tendency to increase. In the cecum, interleukin-1β mRNA expression was decreased (p<0.05), and caspase-3 showed a potential increase (p = 0.07) in HC goats. The level of NF-κB protein was increased in colonic epithelium of HC goats. Caspase-3 activity was elevated in both colon and cecum, whereas caspase-8 activity was statistically increased only in colon.
Conclusions
Feeding a high-concentrate diet to goats for 6 wks led to hindgut mucosal injuries via activating epithelial cells apoptosis and local inflammatory response.
doi:10.1371/journal.pone.0111596
PMCID: PMC4214727  PMID: 25356790
21.  Tremor and clinical fluctuation are related to sleep disorders in Chinese patients with Parkinson’s disease 
Objective
To study the relationship between sleep disturbances and symptoms in patients with Parkinson’s disease (PD).
Methods
The Parkinson’s Disease Sleep Scale-Chinese Version (PDSS-CV) was used to evaluate the sleep disturbances of PD patients in a cross sectional study. The Unified Parkinson’s Disease Rating Scale (UPDRS) parts II-IV, and the Hoehn & Yahr (H&Y) stage were used to determine the level of motor function in PD and the severity of PD. The Spearman correlation and a multiple regression analysis were used to identify the relationship between sleep disturbances and symptoms of PD. The quantities derived from the UPDRS and the H&Y stage and disease duration were compared between groups of patients either with or without sleep disturbances identified by the PDSS. This study was conducted from December 2011 to March 2012 at the First Affiliated Hospital of Sun Yat-sen University, in Guangzhou.
Results
A total of 136 PD patients were included in this study. The overall total PDSS score in PD patients was 107.58 ± 23.35 points (range: 30–146). There were significant differences in the disease duration, the H&Y stage, and the UPDRS section subscores between groups of patients either with or without sleep disturbances (Kruskal-Wallis Test, p <0.05). There were significant negative correlations between PDSS scores and the UPDRS subscores, the H&Y stage and the disease duration (Spearman correlation, p < 0.05). The multiple regression analysis indicated that sleep disturbances identified by the PDSS were only associated with daily life activity, tremor intensity and clinical fluctuation (R2 = 0.22, F(3,132) = 12.4, p < 0.001). The correlations were also significant when the contribution of the other two factors was excluded using partial correlations.
Conclusions
The level of daily life activity and the occurrences of tremor and clinical fluctuation are likely to be important factors that lead to PD patients’ sleep disturbances. This study may elucidate an important clue for the relationship between sleep disturbances and PD symptoms.
doi:10.1186/2047-9158-3-21
PMCID: PMC4209517  PMID: 25349692
Sleep disorders; Parkinson’s disease; Parkinson’s disease sleep scale-Chinese Version(PDSS-CV); Unified Parkinson’s Disease Rating Scale (UPDRS)
22.  Transcriptome profiling using pyrosequencing shows genes associated with bast fiber development in ramie (Boehmeria nivea L.) 
BMC Genomics  2014;15(1):919.
Background
Ramie (Boehmeria nivea L.), popularly known as “China grass”, is one of the oldest crops in China and the second most important fiber crop in terms of area sown. Ramie fiber, extracted from the plant bast, is important in the textile industry. However, the molecular mechanism of ramie fiber development remains unknown.
Results
A whole sequencing run was performed on the 454 GS FLX + platform using four separately pooled parts of ramie bast. This generated 1,030,057 reads with an average length of 457 bp. Among the 58,369 unigenes (13,386 contigs and 44,983 isotigs) that were generated through de novo assembly, 780 were differentially expressed. As a result, 13 genes that belong to the cellulose synthase gene family (four), the expansin gene family (three) and the xyloglucan endotransglucosylase/hydrolase (XTH) gene family (six) were up-regulated in the top part of the bast, which was in contrast to the other three parts. The identification of these 13 concurrently up-regulated unigenes indicated that the early stage (represented by the top part of the bast) might be important for the molecular regulation of ramie fiber development. Further analysis indicated that four of the 13 unigenes from the expansin (two) and XTH (two) families shared a coincident expression pattern during the whole growth season, which implied they were more relevant to ramie fiber development (fiber quality, etc.) during the different seasons than the other genes.
Conclusions
To the best of our knowledge, this study is the first to characterize ramie fiber development at different developmental stages. The identified transcripts will improve our understanding of the molecular mechanisms involved in ramie fiber development. Moreover, the identified differentially expressed genes will accelerate molecular research on ramie fiber growth and the breeding of ramie with better fiber yields and quality.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-919) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-919
PMCID: PMC4326285  PMID: 25339420
Ramie; Bast fiber; Transcriptome; Cellulose synthase; Expansin; Xyloglucan endotransglucosylase/hydrolase
23.  Prognostic Value of Long Non-Coding RNA HOTAIR in Various Cancers 
PLoS ONE  2014;9(10):e110059.
Long non-coding RNA has been involved in cancer progression, and high HOX transcript antisense intergenic RNA (HOTAIR) is thought to be a poor prognostic indicator in tumorigenesis of multiple types of cancer. Hence, the present study further reveals its prognostic value in tumor malignancy. A systematic review of PubMed and Web of Science was carried out to select literatures relevant to the correlation between HOTAIR expression levels and clinical outcome of various tumors. Overall survival (OS), metastasis-free survival (MFS), recurrence-free survival (RFS), and disease-free survival (DFS) were subsequently analyzed. Data from studies directly reporting a hazard ratio (HR) and the corresponding 95% confidence interval (CI) or a P value as well as survival curves were pooled in the current meta-analysis. A total of 2255 patients from 19 literatures almost published in 2011 or later were included in the analysis. The results suggest that HOTAIR was highly associated with HR for OS of 2.33 (95%CI = 1.77-3.09, Pheterogeneity = 0.016). Stratified analyses indicate that elevated levels of HOTAIR appears to be a powerful prognostic biomarker for patients with colorectal cancer (HR = 3.02, 95CI% = 1.84-4.95, Pheterogeneity = 0.699) and esophageal squamous cell carcinomas (HR = 2.24, 95CI% = 1.67-3.01, Pheterogeneity = 0.711), a similar effect was also observed in analysis method and specimen, except for ethnicity. In addition, Hazard ratios for up-regulation of HOTAIR for MFS, RFS, and DFS were 2.32 (P<0.001), 1.98 (P = 0.369), and 3.29 (P = 0.001), respectively. In summary, the high level of HOTAIR is intimately associated with an adverse OS in numerous cancers, suggesting that HOTAIR may act as a potential biomarker for the development of malignancies.
doi:10.1371/journal.pone.0110059
PMCID: PMC4193855  PMID: 25303230
24.  Roles of retinoic acid and Tbx1/10 in pharyngeal segmentation: amphioxus and the ancestral chordate condition 
EvoDevo  2014;5(1):36.
Background
Although chordates descend from a segmented ancestor, the evolution of head segmentation has been very controversial for over 150 years. Chordates generally possess a segmented pharynx, but even though anatomical evidence and gene expression analyses suggest homologies between the pharyngeal apparatus of invertebrate chordates, such as the cephalochordate amphioxus, and vertebrates, these homologies remain contested. We, therefore, decided to study the evolution of the chordate head by examining the molecular mechanisms underlying pharyngeal morphogenesis in amphioxus, an animal lacking definitive neural crest.
Results
Focusing on the role of retinoic acid (RA) in post-gastrulation pharyngeal morphogenesis, we found that during gastrulation, RA signaling in the endoderm is required for defining pharyngeal and non-pharyngeal domains and that this process involves active degradation of RA anteriorly in the embryo. Subsequent extension of the pharyngeal territory depends on the creation of a low RA environment and is coupled to body elongation. RA further functions in pharyngeal segmentation in a regulatory network involving the mutual inhibition of RA- and Tbx1/10-dependent signaling.
Conclusions
These results indicate that the involvement of RA signaling and its interactions with Tbx1/10 in head segmentation preceded the evolution of neural crest and were thus likely present in the ancestral chordate. Furthermore, developmental comparisons between different deuterostome models suggest that the genetic mechanisms for pharyngeal segmentation are evolutionary ancient and very likely predate the origin of chordates.
Electronic supplementary material
The online version of this article (doi:10.1186/2041-9139-5-36) contains supplementary material, which is available to authorized users.
doi:10.1186/2041-9139-5-36
PMCID: PMC4320481  PMID: 25664163
Cephalochordate; Cyp26 function; evolution of developmental mechanisms; evolution of the vertebrate head; functional knockdown; pharmacological treatments; pharyngeal patterning; retinoic acid signaling; Tbx1/10
25.  Load System of Segmental T-Loops for Canine Retraction 
Objectives
The orthodontic load system, especially the ideal moment-to-force ratios (M/F), is the commonly used design parameter of segmental T-loops for canine retraction. However, the load system, including M/F, may be affected by the changes in canine angulations and interbracket distance (IBD). Here, we hypothesize that clinical changes in canine position and angulation during canine retraction will significantly affect the load system delivered to the tooth.
Methods
The load systems of two T-loop groups, one for translation (TR) and the other for controlled tipping (CT), from nine bilateral canine retraction patients were made to the targeted values obtained from finite element analyses and validated. Each loop was tested on the corresponding maxillary dental cast obtained in the clinic. The casts were made before and after each treatment interval so that both initial and residual load systems could be obtained. The pre- and post-treatment IBDs were recorded for calculating IBD changes.
Results
As the IBDs decreased, the averaged retraction-force-drop per IBD reduction was 36 cN/mm, a 30% drop per 1 mm IBD decrease. The averaged anti-tipping-moment-drops per IBD reductions were 0.02 N-mm/mm for CT and 1.4 N-mm/mm for TR, ~0.6 % and 17% drop per 1 mm IBD decrease, respectively. Consequently, the average M/F increases per 1 mm IBD reduction were 1.24 mm/mm for CT and 6.34 mm/mm for TR. There was significant residual load left, which could continue to move the tooth if the patient missed the scheduled appointment.
Conclusions
Clinical changes in canine position and angulation during canine retraction significantly affect the load system. The initial planned M/F needs to be lower to reach the expected average ideal value. Patients should be required to follow the office visit schedule closely to avoid negative effects due to significant M/F increases with time.
doi:10.1016/j.ajodo.2013.05.007
PMCID: PMC3829684  PMID: 24075663

Results 1-25 (411)