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1.  Complete Genome Sequence of the Grouper Iridovirus and Comparison of Genomic Organization with Those of Other Iridoviruses 
Journal of Virology  2005;79(4):2010-2023.
The complete DNA sequence of grouper iridovirus (GIV) was determined using a whole-genome shotgun approach on virion DNA. The circular form genome was 139,793 bp in length with a 49% G+C content. It contained 120 predicted open reading frames (ORFs) with coding capacities ranging from 62 to 1,268 amino acids. A total of 21% (25 of 120) of GIV ORFs are conserved in the other five sequenced iridovirus genomes, including DNA replication, transcription, nucleotide metabolism, protein modification, viral structure, and virus-host interaction genes. The whole-genome nucleotide pairwise comparison showed that GIV virus was partially colinear with counterparts of previously sequenced ranaviruses (ATV and TFV). Besides, sequence analysis revealed that GIV possesses several unique features which are different from those of other complete sequenced iridovirus genomes: (i) GIV is the first ranavirus-like virus which has been sequenced completely and which infects fish other than amphibians, (ii) GIV is the only vertebrate iridovirus without CpG sequence methylation and lacking DNA methyltransferase, (iii) GIV contains a purine nucleoside phosphorylase gene which is not found in other iridoviruses or in any other viruses, (iv) GIV contains 17 sets of repeat sequence, with basic unit sizes ranging from 9 to 63 bp, dispersed throughout the whole genome. These distinctive features of GIV further extend our understanding of molecular events taking place between ranavirus and its hosts and the iridovirus evolution.
PMCID: PMC546566  PMID: 15681403
2.  Estimated Glomerular Filtration Rate Decline Is a Better Risk Factor for Outcomes of Systemic Disease-Related Nephropathy than for Outcomes of Primary Renal Diseases 
PLoS ONE  2014;9(4):e92881.
Currently, the contribution of kidney function decline in renal and patient outcomes is unclear. There are few data on the associations of different etiologies of estimated glomerular filtration rate (eGFR) decline with outcomes in multidisciplinary care. The purpose of this investigation was to establish whether eGFR decline in patients with disease is an important risk factor for developing end-stage renal disease (ESRD) and death.
From December 1, 2001 to December 31, 2011, 5097 adults with chronic kidney disease (CKD) received biochemical tests, physical examinations, a pathological examination, and a comprehensive questionnaire. We used linear regression models and multivariate Cox proportional hazards model to examine the outcome of eGFR decline in renal diseases with different etiologies.
Mean age was 68.1±16.1 (standard deviation, SD) years, and 63.3% patients were male. In the studied cohort, 58.2% of the patients had systemic disease-related nephropathy (SDRN), 29.4% had primary renal diseases (PRDs), and 12.4% had other etiologies. The eGFR decline in SDRN had a significant association with dialysis in the Cox proportional hazards model [crude hazard ratio (HR) = 1.07, 95% confidence interval (CI), 1.04 to 1.10; adjusted HR 1.05, 95% CI, 1.02 to 1.08]. Diabetic nephropathy (DN) had the most severe eGFR decline in CKD stages 3, 4, and 5, and all contributed to the initiation of dialysis and death regardless of whether DN with or without eGFR decline was considered to be the cause. Although hypertensive nephropathy (HN) was related to significant acceleration of eGFR decline, it did not lead to poor outcome. There were still discrepancies between eGFR decline and outcomes in PRDs, hypertensive nephropathy, and lupus nephritis.
eGFR decline and CKD staging provide an informative guide for physicians to make proper clinical judgments in the treatment of CKD, especially SDRN. Poor control of the underlying systemic disease will thus lead to more rapid progression of SDRN.
PMCID: PMC3973643  PMID: 24695125
3.  Association of Esophageal Inflammation, Obesity and Gastroesophageal Reflux Disease: From FDG PET/CT Perspective 
PLoS ONE  2014;9(3):e92001.
Gastroesophageal reflux disease (GERD) is associated with bothersome symptoms and neoplastic progression into Barrett's esophagus and esophageal adenocarcinoma. We aim to determine the correlation between GERD, esophageal inflammation and obesity with 18F-Fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT).
We studied 458 subjects who underwent a comprehensive health check-up, which included an upper gastrointestinal endoscopy, FDG PET/CT and complete anthropometric measures. GERD symptoms were evaluated with Reflux Disease Questionnaire. Endoscopically erosive esophagitis was scored using the Los Angeles classification system. Inflammatory activity, represented by standardized uptake values (SUVmax) of FDG at pre-determined locations of esophagus, stomach and duodenum, were compared. Association between erosive esophagitis, FDG activity and anthropometric evaluation, including body mass index (BMI), waist circumference, visceral and subcutaneous adipose tissue volumes were analyzed.
Subjects with erosive esophagitis (n = 178, 38.9%) had significantly higher SUVmax at middle esophagus (2.69±0.74 vs. 2.41±0.57, P<.001) and esophagogastric junction (3.10±0.89 vs. 2.38±0.57, P<.001), marginally higher at upper esophageal sphincter (2.29±0.42 vs. 2.21±0.48, P = .062), but not in stomach or duodenum. The severity of erosive esophagitis correlated with SUVmax and subjects with Barrett's esophagus had the highest SUVmax at middle esophagus and esophagogastric junction. Heartburn positively correlated with higher SUVmax at middle oesophagus (r = .262, P = .003). Using multivariate regression analyses, age (P = .027), total cholesterol level (P = .003), alcohol drinking (P = .03), subcutaneous adipose tissue (P<.001), BMI (P<.001) and waist circumference (P<.001) were independently associated with higher SUVmax at respective esophageal locations.
Esophageal inflammation demonstrated by FDG PET/CT correlates with endoscopic findings and symptomatology of GERD. Obesity markers, both visceral and general, are independent determinants of esophageal inflammation.
PMCID: PMC3958434  PMID: 24642729
4.  Crystallized and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates 
Scientific Reports  2014;4:4224.
Vortex is a topological defect with a quantized winding number of the phase in superfluids and superconductors. Here, we investigate the crystallized (triangular, square, honeycomb) and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates (BECs) by using the damped projected Gross-Pitaevskii equation. The amorphous vortices are the result of the considerable deviation induced by the interaction of atomic-molecular vortices. By changing the atom-molecule interaction from attractive to repulsive, the configuration of vortices can change from an overlapped atomic-molecular vortices to carbon-dioxide-type ones, then to atomic vortices with interstitial molecular vortices, and finally into independent separated ones. The Raman detuning can tune the ratio of the atomic vortex to the molecular vortex. We provide a phase diagram of vortices in rotating atomic-molecular BECs as a function of Raman detuning and the strength of atom-molecule interaction.
PMCID: PMC3936233  PMID: 24573303
5.  Cyr61/CTGF/Nov family proteins in gastric carcinogenesis 
Gastric cancer (GC) is the second leading cause of cancer-related death. The poor survival rate may reflect the relatively aggressive tumor biology of GC. Recently, the importance of the tumor microenvironment in carcinogenesis has emerged. In the tumor microenvironment, tumor cells and the surrounding stromal cells aberrantly secrete matricellular proteins capable of modulating carcinogenesis and regulating metastasis. The Cyr61/CTGF/Nov (CCN) proteins are a family of matricellular proteins with variable roles in many physiological and pathological processes. The evidence suggests that CCN family proteins contribute to GC carcinogenic processes. Here, we briefly review recent research on the effects of CCN family proteins in GC carcinogenesis and the development of new targeted agents in this field.
PMCID: PMC3930969  PMID: 24587648
Cyr61/CTGF/Nov proteins; Cysteine-rich angiogenic inducer 61; Connective tissue growth factor; Nephroblastoma over-expressed; Gastric cancer; Gastric carcinogenesis
7.  Addition of Immunosuppressive Treatment to Hemoperfusion Is Associated with Improved Survival after Paraquat Poisoning: A Nationwide Study 
PLoS ONE  2014;9(1):e87568.
Paraquat poisoning associates very high mortality rate. Early treatment with hemoperfusion is strongly suggested by animal and human studies. Although the survival benefit of additional immunosuppressive treatment (IST) in combination with hemoperfusion is also reported since 1971, the large-scale randomized control trials to confirm the effects of IST is difficult to be executed. Therefore, we designed this nationwide large-scale population-based retrospective cohort study to investigate the outcome of paraquat poisoning with hemoperfusion and the additional effects of IST combined with hemoperfusion. This nationwide retrospective cohort study utilized data retrieved from the National Health Insurance Research Database (NHIRD) of Taiwan. A total of 1811 hospitalized patients with a diagnosis of paraquat poisoning who received hemoperfusion between 1997 and 2009 were enrolled. The mean age of all 1811 study subjects was 47.3 years. 70% was male. The overall survival rate was only 26.4%. Respiratory failure and renal failure were diagnosed in 56.2% and 36% patients. The average frequency of hemoperfusion was twice. IST was added in 42.2% patients. IST significantly increases survival rate (from 24.3% to 29.3%, P<0.001). The combined IST with methylprednisolone, cyclophosphamide and dexamethasone associates with the highest survival rate (48%, P<0.001). Moreover, patients younger than 45 years of age in the IST group had the best survival (41.0% vs. 33.7%, p<0.001). Our results support the use of IST with hemoperfusion for paraquat-poisoned patients. The best survival effect of IST is the combination of methylprednisolone, cyclophosphamide and daily dexamethasone, especially in patients with younger age.
PMCID: PMC3903773  PMID: 24475310
8.  PPAR α and PPAR γ Polymorphisms as risk factors for Dyslipidemia in a Chinese han population 
The PPAR α and PPAR γ are the key messengers responsible for the translation of nutritional stimuli into changes for the expression of genes, particularly genes involved in lipid metabolism. However, the associations between PPAR α / γ polymorphisms and lipid serum levels in the general population were rarely studied, and the conclusions were conflicting. The objective was to investigate the associations of the PPAR α and PPAR γ polymorphisms with dyslipidemia.
820 subjects were randomly selected from the Prevention of Multiple Metabolic Disorders and MS in Jiangsu Province cohort populations. The logistic regression model was used to examine the association between these polymorphisms and dyslipidemia. SNPstats was used to explore the haplotype association analyses.
In the codominant and log-additive models, rs1800206, rs1805192 and rs3856806 were all associated with dyslipidemia (P < 0.005). When the most common haplotype L-G (established by rs1800206, rs4253778) was treated as the reference group, the V-G haplotype was associated with dyslipidemia (P < 0.001), higher TC and TG levels (P < 0.01). Moreover, when compared to Pro-C haplotype (established by rs1805192, rs3856806), the Pro-T, Ala-C, Ala-T haplotypes were associated with dyslipidemia (p < 0.001). A-T haplotype was associated with higher TC levels, (p < 0.01), and the P-T, A-C, A-T haplotypes were associated with higher TG levels (p < 0.01).
PPAR α and PPAR γ polymorphisms and haplotypes may be the genetic risk factors for dyslipidemia.
PMCID: PMC3905651  PMID: 24460649
PPAR; Polymorphism; Dyslipidemia; Haplotype
9.  Unsafe riding practice among electric bikers in Suzhou, China: an observational study 
BMJ Open  2014;4(1):e003902.
Electric bike (E-bike)-related deaths have been increasing rapidly in China and such injuries may be partly attributable to unsafe riding practice.
To describe potentially unsafe riding behaviours among electric bikers (E-bikers) and to investigate factors influencing these practices in China.
In September 2012, a cross-sectional observation study including a speed measurement component was conducted in Wuzhong (an urban district) and Zhangjiagang (a rural district) of Suzhou, Jiangsu Province, China. Hand-held radar speed metres were used to read travelling speeds of E-bikes and a pro forma observation checklist was used to collect data on road riding practice. Mixed-effect logistic regressions were used to calculate adjusted ORs and 95% CIs for the association between speeding, road rule violations and helmet use and their influencing factors.
Among 800 E-bikes with a speed reading, 70.9% exceeded the designed speed limit of 20 km/h. Among a further 20 647 E-bikers observed, 38.3% did not comply with the road rules when entering intersections; and only 2.2% wore helmets. No regional variation was identified between urban and rural areas. Male E-bikers were associated with more speeding and road rule violations, whereas riding a pedal-equipped E-bike was associated with less road rule violations and less helmet use.
Unsafe riding practices such as speeding, road rule violations and lack of helmet use were commonplace among E-bikers, especially among men. The study findings indicate that measures aimed at improving E-bike safety are required in China.
PMCID: PMC3902425  PMID: 24435891
Electric Bike; Cross Sectional Study; Behavior; Risk Factor Research; Driver
10.  Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data 
BMC Genomics  2014;15:15.
Degradation is essential for RNA maturation, turnover, and quality control. RNA degradome sequencing that integrates a modified 5′-rapid amplification of cDNA ends protocol with next-generation sequencing technologies is a high-throughput approach for profiling the 5′-end of uncapped RNA fragments on a genome-wide scale. The primary application of degradome sequencing has been to identify the truncated transcripts that result from endonucleolytic cleavage guided by microRNAs or small interfering RNAs. As many pathways are involved in RNA degradation, degradome data should contain other RNA species besides the cleavage remnants of small RNA targets. Nevertheless, no systematic approaches have been established to explore the hidden complexity of plant degradome.
Through analyzing Arabidopsis and rice RNA degradome data, we recovered 11 short motifs adjacent to predominant and abundant uncapped 5′-ends. Uncapped ends associated with several of these short motifs were more prevalent than those targeted by most miRNA families especially in the 3′ untranslated region of transcripts. Through genome-wide analysis, five motifs showed preferential accumulation of uncapped 5′-ends at the same position in Arabidopsis and rice. Moreover, the association of uncapped 5′-ends with a CA-repeat motif and a motif recognized by Pumilio/Fem-3 mRNA binding factor (PUF) proteins was also found in non-plant species, suggesting that common mechanisms are present across species. Based on these motifs, potential sources of RNA ends that constitute degradome data were proposed and further examined. The 5′-end of small nucleolar RNAs could be precisely captured by degradome sequencing. Position-specific enrichment of uncapped 5′-ends was seen upstream of motifs recognized by several RNA binding proteins especially for the binding site of PUF proteins. False uncapped 5′-ends produced from capped transcripts through non-specific PCR amplification were common artifacts among degradome datasets.
The complexity of plant RNA degradome data revealed in this study may contribute to the alternative applications of degradome in RNA research.
PMCID: PMC3898255  PMID: 24405808
Degradome; RNA degradation; RNA motif; RNA-binding protein; Sequencing artifact
11.  Clear cell carcinoma of the uterine cervix: clinical characteristics and feasibility of fertility-preserving treatment 
OncoTargets and therapy  2014;7:111-116.
The objective of this retrospective study was to analyze the clinical characteristics and prognosis of clear cell adenocarcinoma (CCA) in the post-diethylstilbestrol (DES) era and to evaluate the feasibility of fertility-preserving treatment. The records of 32 patients with CCAs who were treated at Peking Union Medical College Hospital from August 1986 to June 2012 were retrospectively reviewed. Three of the patients had undergone fertility-preserving treatment. The incidence of CCA among cervical adenocarcinomas was 15.2%. The median age was 38 years: 11 patients (34.4%) were diagnosed before 30 years of age and two (6.3%) after 70 years of age. Ten patients (31.2%) were nulliparous. No patient had been exposed to DES. Twenty-nine patients (90.6%) presented with obvious symptoms, and the cervix appeared abnormal in 26 patients (81.3%). Cervical Papanicolaou (Pap) tests were abnormal in all four patients in whom they were performed (three had high-grade squamous intraepithelial lesions and one had atypical squamous cells of undetermined significance). The distribution by stage was 56.3% stage I, 34.4% stage II, 6.3% stage III, and 3.1% stage IV. Treatments mainly included surgery for patients with stage I to IIA CCA and radiochemotherapy for patients with advanced CCA. The overall 5-year progression-free survival was 72.2%. Patients with stage I to IIA CCA had better 5-year progression-free survival than did patients with stage IIB to IV CCA (81.5% versus 40.0%, P=0.003). The three patients who had undergone fertility-preserving treatment had no recurrences. CCA may also affect adolescents and children without prior DES exposure, who are often misdiagnosed as having functional uterine bleeding. Radiotherapy appears to be effective for local control but to have no effect on distant recurrences. In our study, the prognosis of patients with early-stage CCA, including those who had undergone fertility-preserving treatment, was not inferior to that of patients with other types of cervical adenocarcinoma.
PMCID: PMC3891640  PMID: 24470762
clear cell carcinoma; cervix; diagnosis; prognosis; fertility-preserving
12.  Vimentin DNA methylation predicts survival in breast cancer 
Breast cancer research and treatment  2012;137(2):10.1007/s10549-012-2353-5.
The Vimentin gene plays a pivotal role in epithelial-to-mesenchymal transition and is known to be overexpressed in the prognostically poor basal-like breast cancer subtype. Recent studies have reported Vimentin DNA methylation in association with poor clinical outcomes in other solid tumors, but not in breast cancer. We therefore quantified Vimentin DNA methylation using MALDI-TOF mass spectrometry in breast tumors and matched normal pairs in association with gene expression and survival in a hospital-based study of breast cancer patients. Gene expression data via qRT-PCR in cell lines and oligomicroarray data from breast tissues were correlated with percent methylation in the Vimentin promoter. A threshold of 20 percent average methylation compared with matched normal pairs was set for bivariate and multivariate tests of association between methylation and tumor subtype, tumor histopathology, and survival. Vimentin was differentially methylated in luminal breast cancer cell lines, and in luminal A, luminal B, and HER2-enriched breast tumor subtypes, but was rare in basal-like cell lines and tumors. Increased methylation was strongly correlated with decreased mRNA expression in cell lines, and had a moderate inverse correlation in breast tumors. Vimentin methylation predicted poor overall survival independent of race, subtype, stage, nodal status, or metastatic disease and holds promise as a new prognostic biomarker for breast cancer patients.
PMCID: PMC3838916  PMID: 23239149
DNA methylation; Breast cancer; Vimentin; Epigenetic; Survival
13.  Effect of Di(2-ethylhexyl)phthalate on Helicobacter pylori-Induced Apoptosis in AGS Cells 
Plastic products are wildly used in human life. Di(2-ethylhexyl)phthalate (DEHP) is an essential additive in plastic manufacturing and is used as plasticizer for many products including plastic food packaging. DEHP is a teratogenic compound and can cause potent reproductive toxicity. DEHP can also cause liver damage, peroxisome proliferation, and carcinogenesis. DEHP is also strongly associated with peptic ulcers and gastric cancer; however, the underlying effect and mechanism of DEHP on the gastrointestinal tract are not entirely clear. The oral infection route of H. pylori parallels the major ingestion route of DEHP into the human body. Therefore, we wanted to study the effect of DEHP and H. pylori exposure on the human gastric epithelial cell line, AGS (gastric adenocarcinoma). The viability of the AGS cell line was significantly lower in 80 μM-DEHP and H. pylori (MOI = 100 : 1) coexposure than DEHP or H. pylori alone. DEHP and H. pylori coexposure also induced caspase-3 activation, and increased Bax/Bcl-2 ratio and DNA fragmentation in AGS cells. These results indicate that DEHP can enhance H. pylori cytotoxicity and induce gastric epithelial cell apoptosis. Therefore, it is possible that DEHP and H. pylori coexposure might enhance the disruption of the gastric mucosa integrity and potentially promote the pathogenesis of gastric carcinogenesis.
PMCID: PMC3876891  PMID: 24454344
14.  Identification of Biomarkers for Esophageal Squamous Cell Carcinoma Using Feature Selection and Decision Tree Methods 
The Scientific World Journal  2013;2013:782031.
Esophageal squamous cell cancer (ESCC) is one of the most common fatal human cancers. The identification of biomarkers for early detection could be a promising strategy to decrease mortality. Previous studies utilized microarray techniques to identify more than one hundred genes; however, it is desirable to identify a small set of biomarkers for clinical use. This study proposes a sequential forward feature selection algorithm to design decision tree models for discriminating ESCC from normal tissues. Two potential biomarkers of RUVBL1 and CNIH were identified and validated based on two public available microarray datasets. To test the discrimination ability of the two biomarkers, 17 pairs of expression profiles of ESCC and normal tissues from Taiwanese male patients were measured by using microarray techniques. The classification accuracies of the two biomarkers in all three datasets were higher than 90%. Interpretable decision tree models were constructed to analyze expression patterns of the two biomarkers. RUVBL1 was consistently overexpressed in all three datasets, although we found inconsistent CNIH expression possibly affected by the diverse major risk factors for ESCC across different areas.
PMCID: PMC3875100  PMID: 24396308
15.  Goldstone and Higgs modes of photons inside a cavity 
Scientific Reports  2013;3:3476.
Goldstone and Higgs modes have been detected in various condensed matter, cold atom and particle physics experiments. Here, we demonstrate that the two modes can also be observed in optical systems with only a few (artificial) atoms inside a cavity. We establish this connection by studying the U(1)/Z2 Dicke model where N qubits (atoms) coupled to a single photon mode. We determine the Goldstone and Higgs modes inside the super-radiant phase and their corresponding spectral weights by performing both 1/J = 2/N expansion and exact diagonalization (ED) study at a finite N. We find nearly perfect agreements between the results achieved by the two approaches when N gets down even to N = 2. The quantum finite size effects at a few qubits make the two modes quite robust against an effectively small counterrotating wave term. We present a few schemes to reduce the critical coupling strength, so the two modes can be observed in several current available experimental systems by just conventional optical measurements.
PMCID: PMC3858793  PMID: 24327105
16.  Use of efficient purse-string stapling technique for esophagogastric anastomosis in minimally invasive Ivor Lewis esophagectomy 
Journal of Thoracic Disease  2013;5(6):898-901.
Minimally invasive esophagectomy (MIE) is increasingly accepted in the treatment of locoregional or advanced esophageal cancer. Laparoscopic-thoracoscopic Ivor-Lewis esophagectomy has been proved to be effective in treating middle and distal esophageal cancer, however, intrathoracic esophagogastric anastomosis is technically complex. When using circular stapler for making intrathoracic anastomosis in MIE, both transoral and transthoracic methods are frequently used for delivering the anvil into the esophageal stump. Herein, we report a new method to construct a thoracoscopic esophagogastric anastomosis by using a circular stapler: efficient purse-string stapling technique (EST). This technique is easy to handle and especially good to be used in patients with distal esophageal cancer or expanded esophageal cavity.
PMCID: PMC3886846  PMID: 24416510
Minimally invasive esophagectomy (MIE); Ivor Lewis esophagectomy; esophageal cancer; esophagogastric anastomosis; efficient purse-string stapling technique (EST)
17.  Interaction of Acupuncture and Electroacupuncture on the Pharmacokinetics of Aspirin and the Effect of Brain Blood Flow in Rats 
Acupuncture and electroacupuncture have been used to improve the brain and motor functions of poststroke patients, and aspirin is used for the prevention of stroke recurrence. Our hypothesis is that acupuncture and electroacupuncture treatments may interact with aspirin in terms of pharmacokinetics via affecting the brain blood flow. The aim of this study is to investigate the potential interactions of acupuncture and electroacupuncture on the pharmacokinetics of aspirin. The effects of acupuncture treatments on brain blood flow were measured by the laser Doppler blood flow imager. The parallel pharmacokinetic study design included three groups: control, acupuncture, and electroacupuncture groups. Two acupoints, namely, Quchi (LI 11) and Zusanli (ST 36), were needled and stimulated electronically in anaesthetized rats. The concentrations of aspirin and its metabolite, salicylic acid were determined by microdialysis and HPLC analysis after aspirin administration (30 mg/kg, i.v.). The brain blood flow responded to electroacupuncture treatments, but the pharmacokinetic parameters of aspirin and salicylic acid in blood and brain were not significantly changed by acupuncture and electroacupuncture treatments. This study may, in part, offer some evidence to support the contention that there is no significant interaction for the combination of aspirin with acupuncture or electroacupuncture.
PMCID: PMC3858995  PMID: 24371465
18.  Zebularine inhibits tumorigenesis and stemness of colorectal cancer via p53-dependent endoplasmic reticulum stress 
Scientific Reports  2013;3:3219.
Aberrant DNA hypermethylation is frequently found in tumor cells and inhibition of DNA methylation is an effective anticancer strategy. In this study, the therapeutic effect of DNA methyltransferase (DNMT) inhibitor zebularine (Zeb) on colorectal cancer (CRC) was investigated. Zeb exhibited anticancer activity in cell cultures, tumor xenografts and mouse colitis-associated CRC model. It stabilizes p53 through ribosomal protein S7 (RPS7)/MDM2 pathways and DNA damage. Zeb-induced cell death was dependent on p53. Microarray analysis revealed that genes related to endoplasmic reticulum (ER) stress and unfolded protein response (UPR) were affected by Zeb. Zeb induced p53-dependent ER stress and autophagy. Pro-survival markers of ER stress/UPR (GRP78) and autophagy (p62) were increased in tumor tissues of CRC patients, AOM/DSS-induced CRC mice and HCT116-derived colonospheres. Zeb downregulates GRP78 and p62, and upregulates a pro-apoptotic CHOP. Our results reveal a novel mechanism for the anticancer activity of Zeb.
PMCID: PMC3827606  PMID: 24225777
19.  Accuracy of faecal occult blood test and Helicobacter pylori stool antigen test for detection of upper gastrointestinal lesions 
BMJ Open  2013;3(10):e003989.
Highly sensitive guaiac-based faecal occult blood (Hemoccult SENSA) and Helicobacter pylori stool antigen testing might help detect upper gastrointestinal lesions when appended to a colorectal cancer screening programme with faecal immunochemical testing. We evaluated the diagnostic accuracies of two stool tests in detecting upper gastrointestinal lesions.
Cross-sectional design.
Hospital-based and community-based screening settings.
A hospital-based deviation cohort of 3172 participants to evaluate test performance and a community-based validation cohort of 3621 to verify the findings.
Three types of stool tests with bidirectional endoscopy as the reference standard.
Sensitivity, specificity and positive and negative likelihood ratios.
For detecting upper gastrointestinal lesions in cases with negative immunochemical tests, the sensitivity, specificity, and positive and negative likelihood ratios of the guaiac-based and H pylori antigen tests were 16.3% (95% CI 13.3% to 19.8%), 90.1% (88.9% to 91.2%), 1.64 (1.31 to 2.07), and 0.93 (0.89 to 0.97), respectively, and 52.5% (48.1% to 56.9%), 80.6% (79.0% to 82.1%), 2.71 (2.41 to 3.04) and 0.59 (0.54 to 0.65), respectively. For detecting upper gastrointestinal lesions in cases with normal colonoscopy, the results of the guaiac-based and H pylori antigen tests were 17.9% (14.8% to 21.5%), 90.1% (88.9% to 91.2%), 1.81 (1.45 to 2.26) and 0.91 (0.87 to 0.95), respectively, and 53.1% (48.6% to 57.4%), 80.7% (79.1% to 82.2%), 2.75 (2.45 to 3.08) and 0.58 (0.53 to 0.64), respectively. Within the community, positive predictive values of the immunochemical and H pylori antigen tests were 36.0% (26.0% to 46.0%) and 31.9% (28.3% to 35.5%), respectively, for detecting lower and upper gastrointestinal lesions, which were similar to expected values.
The H pylori stool antigen test is more accurate than the guaiac-based test in the screening of upper gastrointestinal lesions in a population with high prevalence of H pylori infection and upper gastrointestinal lesions. It is applicable to add the H pylori antigen test to the immunochemical test for pan detection.
Trial registration
NCT01341197 (
PMCID: PMC3816242  PMID: 24176798
20.  Hepatic Expression of HCV RNA-dependent RNA Polymerase Triggers Innate Immune Signaling and Cytokine Production 
Molecular cell  2012;48(2):313-321.
Innate immunity controls pathogen replication and spread. Yet, certain pathogens, such as Hepatitis C Virus (HCV), escape immune elimination and establish persistent infections that promote chronic inflammation and related diseases. Whereas HCV regulatory proteins that attenuate anti-viral responses are known, those that promote inflammation and liver injury remain to be identified. Here we describe that transient expression of HCV RNA-dependent RNA polymerase (RdRp), NS5B, in mouse liver and human hepatocytes results in production of small RNA species that activate innate immune signaling via TBK1-IRF3 and NF-κB and induce cytokine production including type I interferons (IFN) and IL-6. NS5B-expression also results in liver damage.
PMCID: PMC3483424  PMID: 22959272
21.  Quantum Anomalous Hall Effect and Tunable Topological States in 3d Transition Metals Doped Silicene 
Scientific Reports  2013;3:2908.
Silicene is an intriguing 2D topological material which is closely analogous to graphene but with stronger spin orbit coupling effect and natural compatibility with current silicon-based electronics industry. Here we demonstrate that silicene decorated with certain 3d transition metals (Vanadium) can sustain a stable quantum anomalous Hall effect using both analytical model and first-principles Wannier interpolation. We also predict the quantum valley Hall effect and electrically tunable topological states could be realized in certain transition metal doped silicene where the energy band inversion occurs. Our findings provide new scheme for the realization of quantum anomalous Hall effect and platform for electrically controllable topological states which are highly desirable for future nanoelectronics and spintronics application.
PMCID: PMC3793221  PMID: 24105063
22.  Inhibition of Melanogenesis by Gallic Acid: Possible Involvement of the PI3K/Akt, MEK/ERK and Wnt/β-Catenin Signaling Pathways in B16F10 Cells 
Gallic acid is one of the major flavonoids found in plants. It acts as an antioxidant, and seems to have anti-inflammatory, anti-viral, and anti-cancer properties. In this study, we investigated the effects of gallic acid on melanogenesis, including the activation of melanogenesis signaling pathways. Gallic acid significantly inhibited both melanin synthesis and tyrosinase activity in a dose- and time-dependent manner, and decreased the expression of melanogenesis-related proteins, such as microphthalmia-associated transcription factor (MITF), tyrosinase, tyrosinase-related protein-1 (TRP1), and dopachrome tautomerase (Dct). In addition, gallic acid also acts by phosphorylating and activating melanogenesis inhibitory proteins such as Akt and mitogen-activated protein kinase (MEK)/extracellular signal-regulated kinase (ERK). Using inhibitors against PI3K/Akt (LY294002) or MEK/ERK-specific (PD98059), the hypopigmentation effect was suppressed, and the gallic acid-initiated activation of MEK/ERK and PI3K/Akt was also revoked. Gallic acid also increased GSK3β and p-β-catenin expression but down-regulated p-GSK3β. Moreover, GSK3β-specific inhibitor (SB216763) restored gallic acid-induced melanin reduction. These results suggest that activation of the MEK/ERK, PI3K/Akt, and inhibition of Wnt/β-catenin signaling pathways is involved in the melanogenesis signaling cascade, and that activation by gallic acid reduces melanin synthesis via down-regulation of MITF and its downstream signaling pathway. In conclusion, gallic acid may be a potentially agent for the treatment of certain skin conditions.
PMCID: PMC3821624  PMID: 24129178
gallic acid; melanogenesis; microphthalmia-associated transcription factor (MITF); tyrosinase; TRP1; Dct; MEK/ERK; PI3K/Akt; Wnt/β-catenin
24.  Hydronephrotic Urine in the Obstructed Kidney Promotes Urothelial Carcinoma Cell Proliferation, Migration, Invasion through the Activation of mTORC2-AKT and ERK Signaling Pathways 
PLoS ONE  2013;8(9):e74300.
Obstructive nephropathy is the most common presentation of urothelial carcinoma. The role of the urine in the obstructed kidney namely “hydronephrotic urine” in urothelial carcinoma has not been extensively explored. This study aims to evaluate whether hydronephrotic urine in the obstructed kidney could promote urothelial carcinoma. The hydronephrotic urine was collected from the obstructed kidneys of Sprague-Dawley rats induced by different periods of unilateral ureteral obstruction (UUO). By the inhibition of LY294002 and PD184352, we confirm that hydronephrotic urine promotes urothelial carcinoma cell (T24) and immortalized normal urothelial cells (E6) proliferation, migration and invasion in a dose-dependent manner through the activation of the mTORC2-AKT and ERK signaling pathways. Hydronephrotic urine also increases the expression of cyclin-D2, cyclin-B and CDK2. It also decreases the expression of p27 and p21 in both urothelial carcinoma cells and normal urothelial cells. By the protein array study, we demonstrate that many growth factors which promote tumor cell survival and metastasis are over-expressed in a time-dependent manner in the hydronephrotic urine, including beta-FGF, IFN-γ, PDGF-BB, PIGF, TGF-β, VEGF-A, VEGF-D and EGF. These results suggest that hydronephrotic urine promotes normal and malignant urothelial cells proliferation, migration and invasion, through the activation of the mTORC2-AKT and ERK signaling pathways. Further investigation using live animal models of tumor growth may be needed to clarify aspects of these statements.
PMCID: PMC3762757  PMID: 24023933
25.  An NKp30-based chimeric antigen receptor promotes T-cell effector functions and anti-tumor efficacy in vivo 
NKp30 is a natural cytotoxicity receptor (NCR) that is expressed on natural killer (NK) cells and recognizes B7-H6, which is expressed on several types of tumors but few normal cells. To target effector T cells against B7-H6-positive tumors, we have developed several chimeric antigen receptors (CAR) based on NKp30, which contain the CD28 and/or CD3ζ signaling domains with the transmembrane domains from CD3ζ, CD28 or CD8α, respectively. The data show that chimeric NKp30-expressing T cells responded to B7-H6-positive tumor cells. The NKp30 CAR expressing T cells produced IFN-γ and killed B7-H6 ligand-expressing tumor cells, and this response was dependent upon ligand expression on target cells but not on MHC expression. PBMC-derived dendritic cells (DCs) also express NKp30 ligands, including immature DCs (iDCs), and they can stimulate NKp30 CAR-bearing T cells to produce IFN-γ, but to a lesser extent. The addition of a CD28 signaling domain significantly enhanced the activity of the NKp30 CAR in a PI3-kinase-dependent manner. Adoptive transfer of T cells expressing a chimeric NKp30 receptor containing a CD28 signaling domain inhibited the growth of a B7-H6-expressing murine lymphoma (RMA/B7-H6) in vivo. Moreover, mice that remained tumor-free were resistant to a subsequent challenge with the wildtype RMA tumor cells, suggesting the generation of immunity against other tumor antigens. Overall, this study demonstrates the specificity and therapeutic potential of adoptive immunotherapy with NKp30 CAR-expressing T cells against B7-H6+ tumor cells in vivo.
PMCID: PMC3633481  PMID: 22851709
Immunotherapy; CD8 T cell; NKp30; lymphoma; B7-H6; CARs; NK cell; NCR

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