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1.  Protocol for the China PEACE (Patient-centered Evaluative Assessment of Cardiac Events) retrospective study of coronary catheterisation and percutaneous coronary intervention 
BMJ Open  2014;4(3):e004595.
Introduction
During the past decade, the volume of percutaneous coronary intervention (PCI) in China has risen by more than 20-fold. Yet little is known about patterns of care and outcomes across hospitals, regions and time during this period of rising cardiovascular disease and dynamic change in the Chinese healthcare system.
Methods and analysis
Using the China PEACE (Patient-centered Evaluative Assessment of Cardiac Events) research network, the Retrospective Study of Coronary Catheterisation and Percutaneous Coronary Intervention (China PEACE-Retrospective CathPCI Study) will examine a nationally representative sample of 11 900 patients who underwent coronary catheterisation or PCI at 55 Chinese hospitals during 2001, 2006 and 2011. We selected patients and study sites using a two-stage cluster sampling design with simple random sampling stratified within economical-geographical strata. A central coordinating centre will monitor data quality at the stages of case ascertainment, medical record abstraction and data management. We will examine patient characteristics, diagnostic testing patterns, procedural treatments and in-hospital outcomes, including death, complications of treatment and costs of hospitalisation. We will additionally characterise variation in treatments and outcomes by patient characteristics, hospital, region and study year.
Ethics and dissemination
The China PEACE collaboration is designed to translate research into improved care for patients. The study protocol was approved by the central ethics committee at the China National Center for Cardiovascular Diseases (NCCD) and collaborating hospitals. Findings will be shared with participating hospitals, policymakers and the academic community to promote quality monitoring, quality improvement and the efficient allocation and use of coronary catheterisation and PCI in China.
Registration details
http://www.clinicaltrials.gov (NCT01624896).
doi:10.1136/bmjopen-2013-004595
PMCID: PMC3948460  PMID: 24607563
Catheterization; Angiography; Angioplasty; China
2.  The Pro-Apoptotic Role of the Regulatory Feedback Loop between miR-124 and PKM1/HNF4α in Colorectal Cancer Cells 
Accumulating evidence indicates that miRNA regulatory circuits play important roles in tumorigenesis. We previously reported that miR-124 is correlated with prognosis of colorectal cancer due to PKM-dependent regulation of glycolysis. However, the mechanism by which miR-124 regulates apoptosis in colorectal cancer remains largely elusive. Here, we show that miR-124 induced significant apoptosis in a panel of colorectal cancer cell lines. The mitochondrial apoptosis pathway was activated by miR-124. Furthermore, the pro-apoptotic role of miR-124 was dependent on the status of PKM1/2 level. PKM1 was required for miR-124-induced apoptosis. Via direct protein-protein interaction, PKM1 promoted HNF4α binding to the promoter region of miR-124 and transcribing miR-124. Moreover, HNF4α or PKM1 had a more dramatic effect on colorectal cancer cell apoptosis in the presence of miR-124. However, inhibition of miR-124 blocked cell apoptosis induced by HNF4α or PKM1. These data indicate that miR-124 not only alters the expression of genes involved in glucose metabolism but also stimulates cancer cell apoptosis. In addition, the positive feedback loop between miR-124 and PKM1/HNF4α plays an important role in colorectal cancer cell apoptosis; it suggests that disrupting this regulatory circuit might be a potential therapeutic tool for colorectal cancer treatment.
doi:10.3390/ijms15034318
PMCID: PMC3975400  PMID: 24619225
PKM; HNF4α; miR-124; colorectal cancer
3.  Tetramethylpyrazine Ameliorates High Glucose-Induced Endothelial Dysfunction by Increasing Mitochondrial Biogenesis 
PLoS ONE  2014;9(2):e88243.
Tetramethylpyrazine (TMP) is an active compound isolated from a Chinese herbal prescription that is widely used in traditional Chinese medicine for the treatment of inflammatory and cardiovascular diseases. We have previously reported that TMP acts as a potent antioxidant protecting endothelial cells against high glucose-induced damages. However, the molecular mechanism responsible for the antioxidant effect of TMP remains to be elucidated. In this study, we show that TMP increases nitric oxide production in endothelial cells and promotes endothelium-dependent relaxation in rate aortic rings. The antioxidant effect of TMP appears attributable to its ability to activate the mitochondrial biogenesis, as reflected in an up-regulation of complex III and amelioration of mitochondrial membrane potential. Furthermore, TMP is able to reverse high glucose-induced suppression of SIRT1 and the biogenesis-related factors, including PGC-1α, NRF1 and TFAM, suggesting a new molecular mechanism underlying the protective effect of TMP on the endothelium.
doi:10.1371/journal.pone.0088243
PMCID: PMC3914961  PMID: 24505445
4.  Transactivation of Atg4b by C/EBPβ Promotes Autophagy To Facilitate Adipogenesis 
Molecular and Cellular Biology  2013;33(16):3180-3190.
Autophagy is a highly conserved self-digestion pathway involved in various physiological and pathophysiological processes. Recent studies have implicated a pivotal role of autophagy in adipocyte differentiation, but the molecular mechanism for its role and how it is regulated during this process are not clear. Here, we show that CCAAT /enhancer-binding protein β (C/EBPβ), an important adipogenic factor, is required for the activation of autophagy during 3T3-L1 adipocyte differentiation. An autophagy-related gene, Atg4b, is identified as a de novo target gene of C/EBPβ and is shown to play an important role in 3T3-L1 adipocyte differentiation. Furthermore, autophagy is required for the degradation of Klf2 and Klf3, two negative regulators of adipocyte differentiation, which is mediated by the adaptor protein p62/SQSTM1. Importantly, the regulation of autophagy by C/EBPβ and the role of autophagy in Klf2/3 degradation and in adipogenesis are further confirmed in mouse models. Our data describe a novel function of C/EBPβ in regulating autophagy and reveal the mechanism of autophagy during adipocyte differentiation. These new insights into the molecular mechanism of adipose tissue development provide a functional pathway with therapeutic potential against obesity and its related metabolic disorders.
doi:10.1128/MCB.00193-13
PMCID: PMC3753907  PMID: 23754749
5.  Response of seed tocopherols in oilseed rape to nitrogen fertilizer sources and application rates* #  
Tocopherols (Tocs) are vital scavengers of reactive oxygen species (ROS) and important seed oil quality indicators. Nitrogen (N) is one of the most important fertilizers in promoting biomass and grain yield in crop production. However, the effect of different sources and application rates of N on seed Toc contents in oilseed rape is poorly understood. In this study, pot trials were conducted to evaluate the effect of two sources of N fertilizer (urea and ammonium nitrate). Each source was applied to five oilseed rape genotypes (Zheshuang 72, Jiu-Er-1358, Zheshuang 758, Shiralee, and Pakola) at three different application rates (0.41 g/pot (N1), 0.81 g/pot (N2), and 1.20 g/pot (N3)). Results indicated that urea increased α-, γ-, and total Toc (T-Toc) more than did ammonium nitrate. N3 was proven as the most efficient application rate, which yielded high contents of γ-Toc and T-Toc. Highly significant correlations were observed between Toc isomers, T-Toc, and α-/γ-Toc ratio. These results clearly demonstrate that N sources and application rates significantly affect seed Toc contents in oilseed rape.
doi:10.1631/jzus.B1300036
PMCID: PMC3924394  PMID: 24510711
Oilseed rape (Brassica napus L.); Nitrogen rate; Urea; Ammonium nitrate; Tocopherol
6.  Identification of a Novel Haemophilus parasuis-Specific B Cell Epitope Using Monoclonal Antibody against the OppA Protein 
PLoS ONE  2014;9(1):e84516.
Monoclonal antibody (MAb) 1B3 against Haemophilus parasuis (H. parasuis) was generated by fusing SP2/0 murine myeloma cells and spleen cells from BALB/c mice immunized with the whole-bacterial-cell suspension of H. parasuis HS80 (serotype 5). The MAb 1B3 showed strong reactivity with 15 serotype reference strains of H. parasuis using Dot blot and Western blot analysis. Immunoprecipitation and protein spectral analysis indicated that MAb 1B3 recognized by Oligopeptide permease A (OppA) belongs to the ATP binding cassette transporter family. In addition, a linear B-cell epitope recognized by MAb 1B3 was identified by the screening of a phage-displayed 12-mer random peptide library. Sequence analysis showed that MAb 1B3 was recognized by phages-displaying peptides with the consensus motif KTPSEXR (X means variable amino acids). Its amino acid sequence matched 469KTPAEAR475 of H. parasuis OppA protein. A series of progressively truncated peptides were synthesized to define the minimal region that was required for MAb 1B3 binding. The epitope was highly conserved in OppA protein sequences from the isolated H. parasuis strains, which was confirmed by alignment analysis. Furthermore, the minimal linear epitope was highly specific among 75 different bacterial strains as shown in sequence alignments. These results indicated MAb 1B3 might be potentially used to develop serological diagnostic tools for H. parasuis.
doi:10.1371/journal.pone.0084516
PMCID: PMC3887010  PMID: 24416241
7.  Ki-67 expression reveals strong, transient influenza specific CD4 T cell responses after adult vaccination 
Vaccine  2012;30(31):10.1016/j.vaccine.2012.04.059.
Although previous studies have found minimal changes in CD4 T cell responses after vaccination of adults with trivalent inactivated influenza vaccine, daily sampling and monitoring of the proliferation marker Ki-67 have now been used to reveal that a substantial fraction of influenza-specific CD4 T cells respond to vaccination. At 4–6 days after vaccination, there is a sharp rise in the numbers of Ki-67-expressing PBMC that produce IFNγ, IL-2 and/or TNFα in vitro in response to influenza vaccine or peptide. Ki-67+ cell numbers then decline rapidly, and ten days after vaccination, both Ki-67+ and overall influenza-specific cell numbers are similar to pre-vaccination levels. These results provide a tool for assessing the quality and quantity of CD4 T cell responses to different influenza vaccines, and raise the possibility that the anti-influenza T cell memory response may be substantially reshaped by vaccination, even if the overall memory cell numbers do not change significantly.
doi:10.1016/j.vaccine.2012.04.059
PMCID: PMC3858959  PMID: 22554464
Ki-67; influenza vaccine; CD4 T cell
8.  Prevalence and Trends of the Abdominal Aortic Aneurysms Epidemic in General Population - A Meta-Analysis 
PLoS ONE  2013;8(12):e81260.
Objective
To conduct a meta-analysis assessing the prevalence and trends of the abdominal aortic aneurysms (AAA) epidemic in general population.
Method
Studies that reported prevalence rates of AAA from the general population were identified through MEDLINE, EMBASE, Web of Science, and reference lists for the period between 1988 and 2013. Studies were included if they reported prevalence rates of AAA in general population from the community. In stratified analyses possible sources of bias, including areas difference, age, gender and diameter of aneurysms were examined. Publication bias was assessed with Egger's test method.
Results
56 studies were identified. The overall pooled prevalence of AAA was 4.8% (4.3%, 5.3%). Stratified analyses showed the following results, areas difference: America 2.2% (2.2%, 2.2%), Europe 2.5% (2.4%, 2.5%), Australia 6.7% (6.5%, 7.0%), Asia 0.5% (0.3%, 0.7%); gender difference: male 6.0% (5.3%, 6.7%), female 1.6% (1.2%, 1.9%); age difference: 55–64years 1.3% (1.2%, 1.5%), 65–74 years 2.8% (2.7%, 2.9%), 75–84 years1.2%(1.1%, 1.3%), ≥85years0.6% (0.4%, 0.7%); aortic diameters difference: 30–39 mm, 3.3% (2.8%, 3.9%), 40–49 mm,0.7% (0.4%,1.0%), ≥50 mm, 0.4% (0.3%, 0.5%). The prevalence of AAA has decreased in Europe from 1988 to 2013. Hypertension, smoking, coronary artery disease, dyslipidemia, respiratory disease, cerebrovascular disease, claudication and renal insufficiency were risk factors for AAA in Europe.
Conclusion
AAA is common in general population. The prevalence of AAA is higher in Australia than America and Europe. The pooled prevalence in western countries is higher than the Asia. Future research requires a larger database on the epidemiology of AAA in general population.
doi:10.1371/journal.pone.0081260
PMCID: PMC3846841  PMID: 24312543
9.  Human Infection with Eurasian Avian-like Influenza A(H1N1) Virus, China 
Emerging Infectious Diseases  2013;19(10):1709-1711.
doi:10.3201/eid1910.130420
PMCID: PMC3810748  PMID: 24050834
influenza; surveillance; serology; avian-like influenza A(H1N1); viruses
10.  Skull metastasis revealing a papillary thyroid carcinoma 
Although thyroid carcinoma is a relatively common form of malignancy, metastatic spread to the skull is rare. Here, we report a case of papillary thyroid carcinoma with frontal and parietal metastasis. A 61-year-old Chinese woman presented with a one year history of a growing mass on the center of the frontal and parietal bone, initially thought to be meningioma. Biopsy of the skull base mass after intracalvarium excision, indicated a tumor of thyroid origin. One month later the patient underwent a total thyroidectomy. Pathological examination confirmed a diagnosis of papillary thyroid carcinoma with frontal and parietal bone metastasis. Based on this experience, the key to successful management of the skull metastasis of thyroid carcinoma is prompt diagnosis and appropriate treatment. Skull metastasis should be considered at the outset of the clinical course of papillary thyroid cancer. To facilitate this, patients should be meticulously investigated by a multidisciplinary team to improve quality of life.
doi:10.3978/j.issn.1000-9604.2013.09.05
PMCID: PMC3828433  PMID: 24255586
Papillary thyroid carcinoma; frontal skull metastasis; diagnosis; treatment
11.  Computational pharmacological comparison of Salvia miltiorrhiza and Panax notoginseng used in the therapy of cardiovascular diseases 
The herb pair comprising Salvia miltiorrhiza (SM) and Panax notoginseng (PN) has been used as a classical formula for cardiovascular diseases (CVDs) in China and in western countries. However, the pharmacology of SM and PN in this herb pair has not been fully elucidated. The aim of this study was to compare the mechanisms of SM and PN at the molecular level for the treatment of CVDs. We used a systems pharmacology approach, integrating ligand clustering, chemical space, docking simulation and network analysis, to investigate these two herbal medicines. The compounds in SM were attached to clusters 2, 3, 5, 6, 8 and 9, while the compounds in PN were attached to clusters 1, 2, 4, 5, 6, 7, 8 and 10. The distributions of chemical space between the compounds from SM and PN were discrete, with the existence of small portions of overlap, and the majority of the compounds did not violate ‘Lipinski’s rule of five’. Docking indicated that the average number of targets correlated with each compound in SM and PN were 5.0 and 3.6, respectively. The minority nodes in the SM and PN drug-target networks possessed common values of betweenness centrality, closeness centrality, topological coefficients and shortest path length. Furthermore, network analyses revealed that SM and PN exerted different modes of action between compounds and targets. These results suggest that the method of computational pharmacology is able to intuitively trace out the similarities and differences of two herbs and their interaction with targets from the molecular level, and that the combination of two herbs may extend their activities in different potential multidrug combination therapies for CVDs.
doi:10.3892/etm.2013.1291
PMCID: PMC3820668  PMID: 24223639
Salvia miltiorrhiza; Panax notoginseng; cardiovascular disease; computational pharmacology
12.  Educational Level, Obesity and Incidence of Diabetes among Chinese Adult Men and Women Aged 18–59 Years Old: An 11-Year Follow-Up Study 
PLoS ONE  2013;8(6):e66479.
Objective
To determine whether educational level and overweight/obesity was associated with the development of diabetes among Chinese adult men and women.
Methods
A cohort (2000–2011) of 10 704 participants aged 18–59 years (8 238 men, 2 466 women) in Qingdao Port Health Study (QPHS) were recruited in this study. The personal lifestyle, height, weight, waist circumference, resting heart rate, blood pressure, fasting blood glucose, total cholesterol, triglycerides and plasma uric acid were collected annually in a comprehensive health checkup program. Cox proportional hazards regression models were used to estimate the association of factors and incidence of diabetes.
Results
During 110 825 person-years of follow-up, 1 056 new onset cases (9.5 per 1 000 person-years) of diabetes were identified. With normal weight as reference, the multiple-adjusted hazard ratio (HR) (95%CI) of diabetes was 1.69(1.38–2.09) for overweight and 2.24(1.66–3.02) for obesity among men, which was 1.81(1.12–2.92) and 2.58(1.37–4.86) among women, respectively. Compared with the participants with high educational level, those with low educational level had a higher risk of diabetes (multiple-adjusted HR (95%CI): 1.43(1.11–1.86)) among men. The association was not found among women and the adjusted HR (95%CI) of diabetes was 1.56(0.89–2.76). The increased risks of low educational level were independent of mediators among men, through normal weight (P for trend = 0.0313) and overweight (P for trend = 0.0212) group but not obesity group (P for trend = 0.0957).
Conclusion
Baseline overweight/obesity was an independent risk factor for diabetes for both men and women. Low educational level was adversely associated with incidence of diabetes through normal weight, overweight and obesity groups, with the association being substantially attenuated by mediating factors only in the obesity group among men. The association was not found among women.
doi:10.1371/journal.pone.0066479
PMCID: PMC3688760  PMID: 23840484
13.  Application of immediate breast reconstruction with silicon prosthetic implantation following bilateral mammary gland excision in treatment of young patients with early breast cancer 
Journal of Thoracic Disease  2013;5(3):278-282.
Objective
To evaluate the application of immediate breast reconstruction (IBR) with silicon prosthetic implantation following bilateral nipple-preserving subcutaneous mammary gland excision in the treatment of young patients with early breast cancer.
Methods
We retrospectively analyzed the clinical data of 21 patients with breast cancer who were performed on IBR following bilateral nipple-preserving subcutaneous mammary gland excision in our hospital from January 2006 to March 2011.
Results
The operations were successful in all the 21 patients. Also, the treatment provided a good cosmetic effect. No local recurrence or distant metastasis was found in these 21 patients during the 6-66-month follow-up.
Conclusions
For the young patients with early breast cancer, mammary gland excision on the affected side along with prophylactic excision of the contralateral side, namely IBR following bilateral nipple-preserving subcutaneous mammary gland excision, provides good clinical effectiveness and cosmetological effects.
doi:10.3978/j.issn.2072-1439.2013.04.09
PMCID: PMC3698255  PMID: 23825759
Breast cancer; prophylactic mastectomy; immediate breast reconstruction
14.  The neuraminidase and matrix genes of the 2009 pandemic influenza H1N1 virus cooperate functionally to facilitate efficient replication and transmissibility in pigs 
The Journal of General Virology  2012;93(Pt 6):1261-1268.
The 2009 pandemic H1N1 virus (pH1N1) contains neuraminidase (NA) and matrix (M) genes from Eurasian avian-like swine influenza viruses (SIVs), with the remaining six genes from North American triple-reassortant SIVs. To characterize the role of the pH1N1 NA and M genes in pathogenesis and transmission, their impact was evaluated in the background of an H1N1 triple-reassortant (tr1930) SIV in which the HA (H3) and NA (N2) of influenza A/swine/Texas/4199-2/98 virus were replaced with those from the classical H1N1 A/swine/Iowa/15/30 (1930) virus. The laboratory-adapted 1930 virus did not shed nor transmit in pigs, but tr1930 was able to shed in infected pigs. The NA, M or both genes of the tr1930 virus were then substituted by those of pH1N1. The resulting virus with both NA and M from pH1N1 grew to significantly higher titre in cell cultures than the viruses with single NA or M from pH1N1. In a pig model, only the virus containing both NA and M from pH1N1 was transmitted to and infected sentinels, whereas the viruses with single NA or M from pH1N1 did not. These results demonstrate that the right combination of NA and M genes is critical for the replication and transmissibility of influenza viruses in pigs.
doi:10.1099/vir.0.040535-0
PMCID: PMC3755515  PMID: 22337640
15.  Endostatin, an angiogenesis inhibitor, ameliorates bleomycin-induced pulmonary fibrosis in rats 
Respiratory Research  2013;14(1):56.
Background
Recent evidence has demonstrated the role of angiogenesis in the pathogenesis of pulmonary fibrosis. Endostatin, a proteolytic fragment of collagen XVIII, is a potent inhibitor of angiogenesis. The aim of our study was to assess whether endostatin has beneficial effects on bleomycin (BLM)-induced pulmonary fibrosis in rats.
Methods
The rats were randomly divided into five experimental groups: (A) saline only, (B) BLM only, (C) BLM plus early endostatin treatment, (D) BLM plus late endostatin treatment, and (F) BLM plus whole-course endostatin treatment. We investigated the microvascular density (MVD), inflammatory response and alveolar epithelial cell apoptosis in rat lungs in each group at different phases of disease development.
Results
Early endostatin administration attenuated fibrotic changes in BLM-induced pulmonary fibrosis in rats. Endostatin treatment decreased MVD by inhibiting the expression of VEGF/VEGFR-2 (Flk-1) and the activation of extracellular signal-regulated protein kinase 1/2 (ERK1/2). Endostatin treatment also decreased the number of inflammatory cells infiltrating the bronchoalveolar lavage fluid during the early inflammatory phase of BLM-induced pulmonary fibrosis. In addition, the levels of tumour necrosis factor-α (TNF-α) and transforming growth factor β1 (TGF-β1) were reduced by endostatin treatment. Furthermore, endostatin decreased alveolar type II cell apoptosis and had an epithelium-protective effect. These might be the mechanism underlying the preventive effect of endostatin on pulmonary fibrosis.
Conclusions
Our findings suggest that endostatin treatment inhibits the increased MVD, inflammation and alveolar epithelial cell apoptosis, consequently ameliorating BLM-induced pulmonary fibrosis in rats.
doi:10.1186/1465-9921-14-56
PMCID: PMC3668162  PMID: 23688086
Endostatin; Bleomycin; Pulmonary fibrosis; Angiogenesis; Vascular endothelial growth factor; Extracellular signal-regulated protein kinase 1/2; Inflammation; Epithelial cell apoptosis
16.  STRUCTURE-DEPENDENT ACTIVATION OF NR4A2 (Nurr1) BY 1,1-BIS(3′-INDOLYL)-1-(AROMATIC)METHANE ANALOGS IN PANCREATIC CANCER CELLS 
Biochemical pharmacology  2012;83(10):1445-1455.
NR4A2 (Nurr 1) is an orphan nuclear receptor with no known endogenous ligands and is highly expressed in many cancer cell lines including Panc1 and Panc28 pancreatic cancer cells. Structure-dependent activation of NR4A2 by a series of 1,1-bis(3′-indolyl)-1-(aromatic)methane (C-DIM) analogs was determined in pancreatic cancer cells transfected with yeast GAL4-Nurr1 chimeras and a UASx5-luc reporter gene or constructs containing response elements that bind NR4A2. Among 23 different structural analogs, phenyl groups containing p-substituted trifluoromethyl, t-butyl, cyano, bromo, iodo and trifluoromethoxy groups were the most active compounds in transactivation assay. The p-bromophenyl analog (DIM-C-pPhBr) was used as a model for structure-activity studies among a series of ortho-, meta- and para-bromophenyl isomers and the corresponding indole 2- and N-methyl analogs. Results show that NR4A2 activation was maximal with the p-bromophenyl analog and methylation of the indole NH group abrogated activity. Moreover, using GAL4-Nurr1 (full length) or GAL-Nurr1-A/B and GAL4-Nurr1-(C-F) chimeras expressing N- and C-terminal domains of Nurr1, respectively, DIM-C-pPhBr activated all three constructs and these responses were differentially affected by kinase inhibitors. DIM-C-pPhBr also modulated expression of several Nurr1-regulated genes in pancreatic cancer cells including vasoactive intestinal peptide (VIP), and the immunohistochemical and western blot analyses indicated that DIM-C-pPhBr activates nuclear NR4A2.
doi:10.1016/j.bcp.2012.02.021
PMCID: PMC3408083  PMID: 22405837
DIM analogs; NR4A2/Nurr1; structure-activity
17.  Network pharmacology-based prediction of the multi-target capabilities of the compounds in Taohong Siwu decoction, and their application in osteoarthritis 
Taohong Siwu decoction (THSWD), a formulation prescribed in traditional Chinese medicine (TCM), has been widely used in the treatment of osteoarthritis (OA). TCM has the potential to prevent diseases, such as OA, in an integrative and holistic manner. However, the system-level characterization of the drug-target interactions of THSWD has not been elucidated. In the present study, we constructed a novel modeling system, by integrating chemical space, virtual screening and network pharmacology, to investigate the molecular mechanism of action of THSWD. The chemical distribution of the ligand database and the potential compound prediction demonstrated that THSWD, as a natural combinatorial chemical library, comprises abundant drug-like and lead-like compounds that may act as potential inhibitors for a number of important target proteins associated with OA. Moreover, the results of the ‘compound-target network’ analysis demonstrated that 19 compounds within THSWD were correlated with more than one target, whilst the maximum degree of correlation for the compounds was seven. Furthermore, the ‘target-disease network’ indicated that THSWD may potentially be effective against 69 diseases. These results may aid in the understanding of the use of THSWD as a multi-target therapy in OA. Moreover, they may be useful in establishing other pharmacological effects that may be brought about by THSWD. The in silico method used in this study has the potential to advance the understanding of the molecular mechanisms of TCM.
doi:10.3892/etm.2013.1106
PMCID: PMC3735841  PMID: 23935733
Taohong Siwu decoction; osteoarthritis; multi-target; network pharmacology
18.  Nuclear β-catenin accumulation is associated with increased expression of Nanog protein and predicts poor prognosis of non-small cell lung cancer 
Background
Although the prognostic roles of β-catenin expression in non-small cell lung cancer (NSCLC) have been reported in several immunohistochemical (IHC) studies, the results were not consistent because some studies lack sufficient number of the positive cases or did not evaluate the subcellular localization features of the protein.
Method
In this study, we have evaluated the expression levels and subcellular localization of β-catenin and Nanog proteins IHC staining in tissue specimens from 309 patients with NSCLC, and explored their association with clinicopathological features and patient outcome.
Results
We showed that patients with negative expression of membranous beta-catenin had a trend towards shorter survival (p=0.064) than those with positive expression. In contrast to previous studies, we found that increased expression of either cytoplasmic or nuclear β-catenin was strongly associated with poor prognosis and was an independent prognosticator for overall survival (p <0.01). We further found that NSCLC cells frequently exhibited an abundance of nuclear Nanog protein which was significantly correlated with nuclear β-catenin expression (p <0.01) and poor prognosis (p <0.01). Interestingly, immunofluorescent staining results revealed that increased expression of Nanog and nuclear translocation of β-catenin occurred concomitantly in response to epidermal growth factor receptor(EGFR) signaling in A549 and H23 cells. Furthermore, western blot analysis show that nuclear β-catenin rather than cytoplasmic β-catenin expression in the A549 and H23 cells can be enhanced by adding EGF, Nanog expression in the A549 and H23 cells with knockdown of β-catenin can not be obviously enhanced by adding EGF.
Conclusion
We propose that evaluation of subcellular localization of β-catenin and Nanog expression is of clinical significance for patients with NSCLC.
doi:10.1186/1479-5876-11-114
PMCID: PMC3706347  PMID: 23648139
β-catenin; Nanog; Immunohistochemistry; Prognosis; Lung cancer
19.  The rs1142345 in TPMT Affects the Therapeutic Effect of Traditional Hypoglycemic Herbs in Prediabetes 
Therapeutic interventions in prediabetes are important in the primary prevention of type 2 diabetes (T2D) and its chronic complications. However, little is known about the pharmacogenetic effect of traditional herbs on prediabetes treatment. A total of 194 impaired glucose tolerance (IGT) subjects were treated with traditional hypoglycemic herbs (Tianqi Jiangtang) for 12 months in this study. DNA samples were genotyped for 184 mutations in 34 genes involved in drug metabolism or transportation. Multinomial logistic regression analysis indicated that rs1142345 (A > G) in the thiopurine S-methyltransferase (TPMT) gene was significantly associated with the hypoglycemic effect of the drug (P = 0.001, FDR P = 0.043). The “G” allele frequencies of rs1142345 in the healthy (subjects reverted from IGT to normal glucose tolerance), maintenance (subjects still had IGT), and deterioration (subjects progressed from IGT to T2D) groups were 0.094, 0.214, and 0.542, respectively. Binary logistic regression analysis indicated that rs1142345 was also significantly associated with the hypoglycemic effect of the drug between the healthy and maintenance groups (P = 0.027, OR = 4.828) and between the healthy and deterioration groups (P = 0.001, OR = 7.811). Therefore, rs1142345 was associated with the clinical effect of traditional hypoglycemic herbs. Results also suggested that TPMT was probably involved in the pharmacological mechanisms of T2D.
doi:10.1155/2013/327629
PMCID: PMC3657408  PMID: 23737827
20.  A high-selenium diet induces insulin resistance in gestating rats and their offspring 
Free radical biology & medicine  2012;52(8):1335-1342.
Although supranutrition of selenium (Se) is considered a promising anti-cancer strategy, recent human studies have shown an intriguing association between high body Se status and diabetic risk. This study was done to determine if a prolonged high intake of dietary Se actually induced gestational diabetes in rat dams and insulin resistance in their offspring. Forty-five 67-day-old female Wistar rats (n=15/diet) were fed a Se-deficient (0.01 mg/kg) corn–soy basal diet (BD) or BD+Se (as Se-yeast) at 0.3 or 3.0 mg/kg from 5 weeks before breeding to day 14 postpartum. Offspring (n=8/diet) of the 0.3 and 3.0 mg Se/kg dams were fed with the same respective diet until age 112 days. Compared with the 0.3 mg Se/kg diet, the 3.0 mg/kg diet induced hyperinsulinemia (P<0.01), insulin resistance (P<0.01), and glucose intolerance (P<0.01) in the dams at late gestation and/or day 14 postpartum and in the offspring at age 112 days. These impairments concurred with decreased (P<0.05) mRNA and/or protein levels of six insulin signal proteins in liver and muscle of dams and/or pups. Dietary Se produced dose-dependent increases in Gpx1 mRNA or GPX1 activity in pancreas, liver, and erythrocytes of dams. The 3.0 mg Se/kg diet decreased Selh (P<0.01), Sepp1 (P=0.06), and Sepw1 (P<0.01), but increased Sels (P<0.05) mRNA levels in the liver of the offspring, compared with the 0.3 mg Se/kg diet. In conclusion, supranutrition of Se as a Se-enriched yeast in rats induced gestational diabetes and insulin resistance. Expression of six selenoprotein genes, in particular Gpx1, was linked to this metabolic disorder.
doi:10.1016/j.freeradbiomed.2012.01.017
PMCID: PMC3505681  PMID: 22342560
Gestational diabetes; Insulin resistance; Dietary selenium; Selenoprotein; Free radicals
21.  Formation of Asymmetrical Structured Silica Controlled by a Phase Separation Process and Implication for Biosilicification 
PLoS ONE  2013;8(4):e61164.
Biogenetic silica displays intricate patterns assembling from nano- to microsize level and interesting non-spherical structures differentiating in specific directions. Several model systems have been proposed to explain the formation of biosilica nanostructures. Of them, phase separation based on the physicochemical properties of organic amines was considered to be responsible for the pattern formation of biosilica. In this paper, using tetraethyl orthosilicate (TEOS, Si(OCH2CH3)4) as silica precursor, phospholipid (PL) and dodecylamine (DA) were introduced to initiate phase separation of organic components and influence silica precipitation. Morphology, structure and composition of the mineralized products were characterized using a range of techniques including field emission scanning electron microscopy (FESEM), transmission electron microscope (TEM), X-ray diffraction (XRD), thermogravimetric and differential thermal analysis (TG-DTA), infrared spectra (IR), and nitrogen physisorption. The results demonstrate that the phase separation process of the organic components leads to the formation of asymmetrically non-spherical silica structures, and the aspect ratios of the asymmetrical structures can be well controlled by varying the concentration of PL and DA. On the basis of the time-dependent experiments, a tentative mechanism is also proposed to illustrate the asymmetrical morphogenesis. Therefore, our results imply that in addition to explaining the hierarchical porous nanopatterning of biosilica, the phase separation process may also be responsible for the growth differentiation of siliceous structures in specific directions. Because organic amine (e.g., long-chair polyamines), phospholipids (e.g., silicalemma) and the phase separation process are associated with the biosilicification of diatoms, our results may provide a new insight into the mechanism of biosilicification.
doi:10.1371/journal.pone.0061164
PMCID: PMC3621999  PMID: 23585878
22.  Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia 
Briefings in Bioinformatics  2013;14(5):563-574.
The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There is currently a shortage of cutting-edge bioinformatics training courses in Australia as a consequence of a scarcity of skilled trainers with time and funding to develop and deliver training courses. To address this, a consortium of Australian research organizations, including Bioplatforms Australia, the Commonwealth Scientific and Industrial Research Organisation and the Australian Bioinformatics Network, have been collaborating with EMBL-EBI training team. A group of Australian bioinformaticians attended the train-the-trainer workshop to improve training skills in developing and delivering bioinformatics workshop curriculum. A 2-day NGS workshop was jointly developed to provide hands-on knowledge and understanding of typical NGS data analysis workflows. The road show–style workshop was successfully delivered at five geographically distant venues in Australia using the newly established Australian NeCTAR Research Cloud. We highlight the challenges we had to overcome at different stages from design to delivery, including the establishment of an Australian bioinformatics training network and the computing infrastructure and resource development. A virtual machine image, workshop materials and scripts for configuring a machine with workshop contents have all been made available under a Creative Commons Attribution 3.0 Unported License. This means participants continue to have convenient access to an environment they had become familiar and bioinformatics trainers are able to access and reuse these resources.
doi:10.1093/bib/bbt022
PMCID: PMC3771231  PMID: 23543352
training; next-generation sequencing; NGS; cloud; workshop
23.  Complete Chloroplast Genome Sequence of Holoparasite Cistanche deserticola (Orobanchaceae) Reveals Gene Loss and Horizontal Gene Transfer from Its Host Haloxylon ammodendron (Chenopodiaceae) 
PLoS ONE  2013;8(3):e58747.
Background
The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants.
Principal Findings/Significance
Here we report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae. The cp genome of C. deserticola is greatly reduced both in size (102,657 bp) and in gene content, indicating that all genes required for photosynthesis suffer from gene loss and pseudogenization, except for psbM. The striking difference from other holoparasitic plants is that it retains almost a full set of tRNA genes, and it has lower dN/dS for most genes than another close holoparasitic plant, E. virginiana, suggesting that Cistanche deserticola has undergone fewer losses, either due to a reduced level of holoparasitism, or to a recent switch to this life history. We also found that the rpoC2 gene was present in two copies within C. deserticola. Its own copy has much shortened and turned out to be a pseudogene. Another copy, which was not located in its cp genome, was a homolog of the host plant, Haloxylon ammodendron (Chenopodiaceae), suggesting that it was acquired from its host via a horizontal gene transfer.
doi:10.1371/journal.pone.0058747
PMCID: PMC3598846  PMID: 23554920
24.  Ginsenoside Rg1 Decreases Aβ1–42 Level by Upregulating PPARγ and IDE Expression in the Hippocampus of a Rat Model of Alzheimer's Disease 
PLoS ONE  2013;8(3):e59155.
Background and Purpose
The present study was designed to examine the effects of ginsenoside Rg1 on expression of peroxisome proliferator-activated receptor γ (PPARγ) and insulin-degrading enzyme (IDE) in the hippocampus of rat model of Alzheimer's disease (AD) to determine how ginsenoside Rg1 (Rg1) decreases Aβ levels in AD.
Experimental Approach
Experimental AD was induced in rats by a bilateral injection of 10 µg soluble beta-amyloid peptide 1–42 (Aβ1–42) into the CA1 region of the hippocampus, and the rats were treated with Rg1 (10 mg·kg−1, intraperitoneally) for 28 days. The Morris water maze was used to test spatial learning and memory performance. Hematoxylin-eosin staining was performed to analyze the hippocampal histopathological damage. Immunohistochemistry, western blotting, and real-time PCR were used to detect Aβ1–42, PPARγ, and insulin-degrading enzyme (IDE) expression in the hippocampus.
Key Results
Injection of soluble Aβ1–42 into the hippocampus led to significant dysfunction of learning and memory, hippocampal histopathological abnormalities and increased Aβ1–42 levels in the hippocampus. Rg1 treatment significantly improved learning and memory function, attenuated hippocampal histopathological abnormalities, reduced Aβ1–42 levels and increased PPARγ and IDE expression in the hippocampus; these effects of Rg1 could be effectively inhibited by GW9662, a PPARγ antagonist.
Conclusions and Implications
Given that PPARγ can upregulate IDE expression and IDE can degrade Aβ1–42, these results indicate that Rg1 can increase IDE expression in the hippocampus by upregulating PPARγ, leading to decreased Aβ levels, attenuated hippocampal histopathological abnormalities and improved learning and memory in a rat model of AD.
doi:10.1371/journal.pone.0059155
PMCID: PMC3592813  PMID: 23520555
25.  Changes in Nitric Oxide, cGMP, and Nitrotyrosine Concentrations Over Skin Along the Meridians in Obese Subjects 
Obesity (Silver Spring, Md.)  2010;19(8):1560-1567.
The purposes of these studies were to quantify the concentrations of total nitrate and nitrite (NOx−) cyclic guanosine monophosphate (cGMP), and nitrotyrosine over skin surface in normal weight healthy volunteers (n = 64) compared to overweight/obese subjects (n = 54). A semicircular plastic tube was taped to the skin along acupuncture points (acupoints), meridian line without acupoint (MWOP), and nonmeridian control and filled with a 2-Phenyl-4,4,5,5-tetramethylimidazoline-3-oxide-1-oxyl solution for 20 min. The concentrations of NOx−, cGMP, and nitrotyrosine in the samples were quantified in a blinded fashion using chemiluminescence and enzyme-linked immunosorbent assay, respectively. In normal weight healthy volunteers, NOx− and cGMP concentrations were consistently increased over the pericardium meridian (PC) 4–7 compared with nonmeridian areas. NOx− concentration is enhanced over the bladder meridian (BL) 56–57, but cGMP level is similar between the regions. In overweight/obese subjects, NOx− contents were increased or tended to be elevated over PC and BL regions. cGMP is paradoxically decreased over PC acupoints and nonmeridian control on the forearm but the decreases were blunted along BL regions on the leg. Nitrotyrosine concentrations are markedly elevated (five- to sixfold) over both PC and BL in all areas of overweight/obese subjects. This is the first evidence showing that nitrotyrosine level is tremendously elevated over skin accompanied by paradoxical changes in nitric oxide (NO)-cGMP concentrations over PC skin region in overweight/obese subject. The results suggest that NO-related oxidant inflammation is systemically enhanced while cGMP generation is impaired over PC skin region but not over BL region in obesity.
doi:10.1038/oby.2010.294
PMCID: PMC3584154  PMID: 21151015

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