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1.  Engineered Holliday Junctions as Single-Molecule Reporters for Protein-DNA Interactions with Application to a MerR-family Regulator 
Journal of the American Chemical Society  2007;129(41):12461-12467.
Protein-DNA interactions are essential for gene maintenance, replication and expression. Characterizing how proteins interact with and change the structure of DNA is crucial in elucidating the mechanisms of protein function. Here we present a novel and generalizable method of using engineered DNA Holliday junctions (HJs) that contain specific protein-recognition sequences to report protein-DNA interactions in single-molecule FRET measurements, utilizing the intrinsic structural dynamics of HJs. Since the effects of protein binding are converted to the changes in the structure and dynamics of HJs, protein-DNA interactions that involve small structural changes of DNA can be studied. We apply this method to investigate how the MerR-family regulator PbrR691 interacts with DNA for transcriptional regulation. Both apo- and holo-PbrR691 bind the stacked conformers of the engineered HJ, change their structures, constrain their conformational distributions, alter the kinetics and shift the equilibrium of their structural dynamics. The information obtained maps the potential energy surfaces of HJ before and after PbrR691 binding and reveals the protein actions that force DNA structural changes for transcriptional regulation. The ability of PbrR691 to bind both HJ conformers and still allow HJ structural dynamics also informs about its conformational flexibility that may have significance for its regulatory function. This method of using engineered HJs offers quantification of the changes both in structure and dynamics of DNA upon protein binding and thus provides a new tool to elucidate the correlation of structure, dynamics, and function of DNA-binding proteins.
doi:10.1021/ja072485y
PMCID: PMC2528078  PMID: 17880214
2.  A meta-analysis of genome-wide association studies for adiponectin levels in East Asians identifies a novel locus near WDR11-FGFR2 
Human Molecular Genetics  2013;23(4):1108-1119.
Blood levels of adiponectin, an adipocyte-secreted protein correlated with metabolic and cardiovascular risks, are highly heritable. Genome-wide association (GWA) studies for adiponectin levels have identified 14 loci harboring variants associated with blood levels of adiponectin. To identify novel adiponectin-associated loci, particularly those of importance in East Asians, we conducted a meta-analysis of GWA studies for adiponectin in 7827 individuals, followed by two stages of replications in 4298 and 5954 additional individuals. We identified a novel adiponectin-associated locus on chromosome 10 near WDR11-FGFR2 (P = 3.0 × 10−14) and provided suggestive evidence for a locus on chromosome 12 near OR8S1-LALBA (P = 1.2 × 10−7). Of the adiponectin-associated loci previously described, we confirmed the association at CDH13 (P = 6.8 × 10−165), ADIPOQ (P = 1.8 × 10−22), PEPD (P = 3.6 × 10−12), CMIP (P = 2.1 × 10−10), ZNF664 (P = 2.3 × 10−7) and GPR109A (P = 7.4 × 10−6). Conditional analysis at ADIPOQ revealed a second signal with suggestive evidence of association only after conditioning on the lead SNP (Pinitial = 0.020; Pconditional = 7.0 × 10−7). We further confirmed the independence of two pairs of closely located loci (<2 Mb) on chromosome 16 at CMIP and CDH13, and on chromosome 12 at GPR109A and ZNF664. In addition, the newly identified signal near WDR11-FGFR2 exhibited evidence of association with triglycerides (P = 3.3 × 10−4), high density lipoprotein cholesterol (HDL-C, P = 4.9 × 10−4) and body mass index (BMI)-adjusted waist–hip ratio (P = 9.8 × 10−3). These findings improve our knowledge of the genetic basis of adiponectin variation, demonstrate the shared allelic architecture for adiponectin with lipids and central obesity and motivate further studies of underlying mechanisms.
doi:10.1093/hmg/ddt488
PMCID: PMC3900106  PMID: 24105470
3.  Effects of Pulsed 2.856 GHz Microwave Exposure on BM-MSCs Isolated from C57BL/6 Mice 
PLoS ONE  2015;10(2):e0117550.
The increasing use of microwave devices over recent years has meant the bioeffects of microwave exposure have been widely investigated and reported. However the exact biological fate of bone marrow MSCs (BM-MSCs) after microwave radiation remains unknown. In this study, the potential cytotoxicity on MSC proliferation, apoptosis, cell cycle, and in vitro differentiation were assayed following 2.856 GHz microwave exposure at a specific absorption rate (SAR) of 4 W/kg. Importantly, our findings indicated no significant changes in cell viability, cell division and apoptosis after microwave treatment. Furthermore, we detected no significant effects on the differentiation ability of these cells in vitro, with the exception of reduction in mRNA expression levels of osteopontin (OPN) and osteocalcin (OCN). These findings suggest that microwave treatment at a SAR of 4 W/kg has undefined adverse effects on BM-MSCs. However, the reduced-expression of proteins related to osteogenic differentiation suggests that microwave can the influence at the mRNA expression genetic level.
doi:10.1371/journal.pone.0117550
PMCID: PMC4319787  PMID: 25658708
4.  Utility of the diffusion-weighted imaging for activity evaluation in Crohn’s disease patients underwent magnetic resonance enterography 
BMC Gastroenterology  2015;15:12.
Background
Cross-sectional imaging techniques as magnetic resonance enterography (MRE) may offer additional information on transmural inflammation, stricturing and fistulising complications in Crohn’s disease (CD). The purpose of our study was to evaluate the diagnostic accuracy of Magnetic Resonance Imaging (MRI) combined with Diffusion-weighted Imaging (DWI) and MRE for determination of inflammation in small bowel CD.
Methods
MR imaging examination was performed with a GE Signa EXCITE 3.0 T MRI scanner. The optimal b value in DWI with a learning cohort of patients was determined. The diagnostic accuracy for active lesions and disease activity were accessed by MRE combined with DWI.
Results
The b value 800 s/mm2 group showed the highest diagnostic sensitivity (74.19%) for diagnostic assessment of active Crohn’s lesions on DWI. MRE combined with DWI showed the highest sensitivity (93.55%), specificity (89.47%) and diagnostic accuracy (92%) compared with MRE or DWI alone. The segmental MR score (MR-score-S) showed a significantly positive correlation with the Capsule Endoscopy Crohn’s Disease Activity Index Score (CECDAI-S) (r = 0.717, p < 0.01). The total MR score (MR-score-T) showed significant association with C-reactive protein (CRP) (r = 0.445, p = 0.019) and erythrocyte sedimentation rate (ESR) (r = 0.688, p < 0.01).
Conclusions
MRE combined with DWI improves the diagnostic accuracy for active lesions and correlates the endoscopic disease activity. MRE with DWI could represent a non-invasive tool in assessing active inflammation in CD.
doi:10.1186/s12876-015-0235-0
PMCID: PMC4323053  PMID: 25653007
5.  Annexin A2 as a target endothelial cell membrane autoantigen in Behçet's disease 
Scientific Reports  2015;5:8162.
Cell membrane proteins are believed to play a critical role in the pathogenesis of autoimmune diseases. However, few membrane autoantigens have been linked with Behçet's disease. Here, a cell-chip was performed to identify autoantibody target cells, and the suspected autoantigens were detected using immunoblotting. The amino acid sequences of the detected proteins were determined using LC-MALDI-TOF/TOF. Putative proteins were recombinantly expressed and purified, and a corresponding ELISA was developed and clinically validated using real clinical samples. It was found that a 36-kDa membrane protein - annexin A2 - was detected in approximately one-third of the patients' blood circulation. The immunohistochemistry results showed that annexin A2 was highly expressed in vascular endothelial cells. Moreover, vascular involvement was significantly higher in the anti-annexin A2 antibody-positive group versus the anti-annexin A2 antibody-negative group among all the clinical samples analyzed, indicating that annexin A2 is a novel endothelial cell membrane antigen involved in Behçet's disease.
doi:10.1038/srep08162
PMCID: PMC4313095  PMID: 25641213
6.  Education influences the association between genetic variants and refractive error: a meta-analysis of five Singapore studies 
Human Molecular Genetics  2013;23(2):546-554.
Refractive error is a complex ocular trait governed by both genetic and environmental factors and possibly their interplay. Thus far, data on the interaction between genetic variants and environmental risk factors for refractive errors are largely lacking. By using findings from recent genome-wide association studies, we investigated whether the main environmental factor, education, modifies the effect of 40 single nucleotide polymorphisms on refractive error among 8461 adults from five studies including ethnic Chinese, Malay and Indian residents of Singapore. Three genetic loci SHISA6-DNAH9, GJD2 and ZMAT4-SFRP1 exhibited a strong association with myopic refractive error in individuals with higher secondary or university education (SHISA6-DNAH9: rs2969180 A allele, β = −0.33 D, P = 3.6 × 10–6; GJD2: rs524952 A allele, β = −0.31 D, P = 1.68 × 10−5; ZMAT4-SFRP1: rs2137277 A allele, β = −0.47 D, P = 1.68 × 10−4), whereas the association at these loci was non-significant or of borderline significance in those with lower secondary education or below (P for interaction: 3.82 × 10−3–4.78 × 10−4). The evidence for interaction was strengthened when combining the genetic effects of these three loci (P for interaction = 4.40 × 10−8), and significant interactions with education were also observed for axial length and myopia. Our study shows that low level of education may attenuate the effect of risk alleles on myopia. These findings further underline the role of gene–environment interactions in the pathophysiology of myopia.
doi:10.1093/hmg/ddt431
PMCID: PMC3869359  PMID: 24014484
7.  Interaction Relation Ontology Learning 
Abstract
Ontology is widely used in semantic computing and reasoning, and various biomedicine ontologies have become institutionalized to make the heterogeneous knowledge computationally amenable. Relation words, especially verbs, play an important role when describing the interaction between biological entities in molecular function, biological process, and cellular component; however, comprehensive research and analysis are still lacking. In this article, we propose an automatic method to build interaction relation ontology by investigating relation verbs, analyzing the syntactic relation of PubMed abstracts to perform relation vocabulary expansion, and integrating WordNet into our method to construct the hierarchy of relation vocabulary. Five attributes are populated automatically for each word in interaction relation ontology. As a result, the interaction relation ontology is constructed; it contains a total of 963 words and covers the most relation words used in existing methods of proteins interaction relation.
doi:10.1089/cmb.2012.0009
PMCID: PMC3880112  PMID: 24377790
interaction relation; ontology learning; relation words; text mining
8.  Myocardial Repolarization Dispersion and Autonomic Nerve Activity in a Canine Experimental Acute Myocardial Infarction Model 
Background
Evidence from a canine experimental acute myocardial infarction (MI) model shows that until the seventh week after MI the relationship between stellate ganglionic nerve and vagal nerve activities (SGNA/VNA) progressively increases.
Objective
We evaluated how autonomic nervous system activity influences temporal myocardial repolarization dispersion at this period.
Methods
We analyzed autonomic nerve activity as well as QT and RR variability from recordings previously obtained in 9 dogs. From a total 48 short-term electrocardiographic segments, 24 recorded before and 24 seven weeks after experimentally-induced MI, we obtained three indices of temporal myocardial repolarization dispersion: QTe (from q wave T to wave end), QTp (from q wave to T wave peak) and Te (from T wave peak to T wave end) variability index (QTeVI, QTpVI, TeVI). We also performed a heart rate variability power spectral analysis on the same segments.
Results
After MI, all the QT variables increased QTeVI (median [interquartile range]) (from - 1.76[0.82] to −1.32[0.68]), QTeVI (from −1.90[1.01] to −1.45[0.78]) and TeVI (from −0.72[0.67] to −0.22[1.00]), whereas all RR spectral indexes decreased (p<0.001 for all). Distinct circadian rhythms in QTeVI (p<0.05,) QTpVI (p<0.001) and TeVI (p<0.05) appeared after MI with circadian variations resembling that of SGNA/VNA. The morning QTpVI and TeVI acrophases approached the SGNA/VNA acrophase. Conversely, the evening QTeVI acrophase coincided with another SGNA/VNA peak. After MI, regression analysis detected a positive relationship between SGNA/VNA and TeVI (R2: 0.077; β: 0.278; p< 0.001).
Conclusion
Temporal myocardial repolarization dispersion shows a circadian variation after MI reaching its peak at a time when sympathetic is highest and vagal activity lowest.
doi:10.1016/j.hrthm.2013.10.022
PMCID: PMC4078249  PMID: 24120873
9.  Relationship between red cell distribution width and serum uric acid in patients with untreated essential hypertension 
Scientific Reports  2014;4:7291.
We assessed whether red cell distribution width (RDW) is associated with serum uric acid (UA) level in a group of 512 patients with newly diagnosed hypertension, recruited in Beijing. Patients were divided into high uric acid group and low uric acid group according to the median (334.9 μmol/L) of serum uric acid. Compared with the low uric acid group, the patients with high uric acid had higher red blood cell count (P < 0.001) and RDW (P = 0.032). The multiple linear regression analysis showed that RDW (P = 0.001) was positively correlated with uric acid level after the adjustment of related factors. Stepwise multiple logistic regression model confirmed that RDW (odds ratio: OR = 1.75) was independent determinants of high serum uric acid as well as sex (OR = 6.03), triglycerides (OR = 1.84), and Blood Urea Nitrogen (BUN, OR = 1.30). RDW may be independently associated with serum UA level in patients with newly diagnosed hypertension. To firmly establish the causal role of RDW in the incidence of high uric acid level among hypertensive patients, large cohort studies are needed.
doi:10.1038/srep07291
PMCID: PMC4252898  PMID: 25464864
10.  LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone 
BMC Bioinformatics  2014;15(Suppl 15):S4.
Background
Protein-ligand binding is important for some proteins to perform their functions. Protein-ligand binding sites are the residues of proteins that physically bind to ligands. Despite of the recent advances in computational prediction for protein-ligand binding sites, the state-of-the-art methods search for similar, known structures of the query and predict the binding sites based on the solved structures. However, such structural information is not commonly available.
Results
In this paper, we propose a sequence-based approach to identify protein-ligand binding residues. We propose a combination technique to reduce the effects of different sliding residue windows in the process of encoding input feature vectors. Moreover, due to the highly imbalanced samples between the ligand-binding sites and non ligand-binding sites, we construct several balanced data sets, for each of which a random forest (RF)-based classifier is trained. The ensemble of these RF classifiers forms a sequence-based protein-ligand binding site predictor.
Conclusions
Experimental results on CASP9 and CASP8 data sets demonstrate that our method compares favorably with the state-of-the-art protein-ligand binding site prediction methods.
doi:10.1186/1471-2105-15-S15-S4
PMCID: PMC4271564  PMID: 25474163
11.  Genetic Variation in CDH13 Is Associated With Lower Plasma Adiponectin Levels but Greater Adiponectin Sensitivity in East Asian Populations 
Diabetes  2013;62(12):4277-4283.
Variants in the CDH13 gene have been identified as determinants of blood levels of adiponectin, an insulin-sensitizing adipokine. However, their association with other metabolic risk factors remains unclear. We examined variants at CDH13 in relation to total and high-molecular-weight (HMW) adiponectin using data from a genome-wide association study performed in 2,434 Singaporean Chinese with replication in up to 3,290 Japanese and 1,610 Koreans. The top signal rs4783244 in CDH13 showed strong associations with total adiponectin (standardized β [β] = −0.34, 95% CI −0.38 to −0.30, P = 2.0 × 10−70), HMW adiponectin (β = −0.40, 95% CI −0.43 to −0.36, P = 1.1 × 10−117), and the HMW-to-total adiponectin ratio (β = −0.44, 95% CI −0.49 to −0.40, P = 3.2 × 10−83). In the replication study, this single nucleotide polymorphism explained 4.1% of total and 6.5% of HMW adiponectin levels. No association was observed between rs4783244 and metabolic traits associated with insulin resistance before adjustment for HMW adiponectin levels. After adjustment for HMW adiponectin levels, the minor allele was associated with lower BMI (β = −0.15, 95% CI −0.19 to −0.11, P = 3.5 × 10−14), homeostasis model assessment-insulin resistance index (β = −0.16, 95% CI −0.20 to −0.12, P = 9.2 × 10−16), and triglycerides (β = −0.16, 95% CI −0.19 to −0.12, P = 1.3 × 10−16) and with higher HDL (β = 0.16, 95% CI 0.12 to 0.19, P = 2.1 × 10−17). CDH13 variants strongly influence plasma total and HMW adiponectin levels in East Asian populations but appear to alter adiponectin sensitivity, resulting in better metabolic health than expected based on circulating adiponectin levels.
doi:10.2337/db13-0129
PMCID: PMC3837060  PMID: 24009259
12.  Factors Influencing Cecal Intubation Time during Retrograde Approach Single-Balloon Enteroscopy 
Background and Aim. The predisposing factors for prolonged cecal intubation time (CIT) during colonoscopy have been well identified. However, the factors influencing CIT during retrograde SBE have not been addressed. The aim of this study was to determine the factors influencing CIT during retrograde SBE. Methods. We investigated patients who underwent retrograde SBE at a medical center from January 2011 to March 2014. The medical charts and SBE reports were reviewed. The patients' characteristics and procedure-associated data were recorded. These data were analyzed with univariate analysis as well as multivariate logistic regression analysis to identify the possible predisposing factors. Results. We enrolled 66 patients into this study. The median CIT was 17.4 minutes. With univariate analysis, there was no statistical difference in age, sex, BMI, or history of abdominal surgery, except for bowel preparation (P = 0.021). Multivariate logistic regression analysis showed that inadequate bowel preparation (odds ratio 30.2, 95% confidence interval 4.63–196.54; P < 0.001) was the independent predisposing factors for prolonged CIT during retrograde SBE. Conclusions. For experienced endoscopist, inadequate bowel preparation was the independent predisposing factor for prolonged CIT during retrograde SBE.
doi:10.1155/2014/212307
PMCID: PMC4258379  PMID: 25505904
13.  Phase-controlled synthesis of α-NiS nanoparticles confined in carbon nanorods for High Performance Supercapacitors 
Scientific Reports  2014;4:7054.
A facile and phase-controlled synthesis of α-NiS nanoparticles (NPs) embedded in carbon nanorods (CRs) is reported by in-situ sulfurating the preformed Ni/CRs. The nanopore confinement by the carbon matrix is essential for the formation of α-NiS and preventing its transition to β-phase, which is in strong contrast to large aggregated β-NiS particles grown freely without the confinement of CRs. When used as electrochemical electrode, the hybrid electrochemical charge storage of the ultrasmall α-NiS nanoparticels dispersed in CRs is benefit for the high capacitor (1092, 946, 835, 740 F g−1 at current densities of 1, 2, 5, 10 A g−1, respectively.). While the high electrochemical stability (approximately 100% retention of specific capacitance after 2000 charge/discharge cycles) is attributed to the supercapacitor-battery electrode, which makes synergistic effect of capacitor (CRs) and battery (NiS NPs) components rather than a merely additive composite. This work not only suggests a general approach for phase-controlled synthesis of nickel sulfide but also opens the door to the rational design and fabrication of novel nickel-based/carbon hybrid supercapacitor-battery electrode materials.
doi:10.1038/srep07054
PMCID: PMC4231331  PMID: 25394517
14.  GENOME-WIDE ASSOCIATION STUDY META-ANALYSIS REVEALS TRANS-ETHNIC REPLICATION OF MEAN ARTERIAL AND PULSE PRESSURE LOCI 
Hypertension  2013;62(5):853-859.
We conducted a genome-wide association study meta-analysis of mean arterial pressure and pulse pressure among 26,600 East Asian participants (stage-1) followed by replication study of up to 28,783 participants (stage-2). For novel loci, statistical significance was determined by a P<5.0×10−8 in joint analysis of stage-1 and stage-2 data. For loci reported by the previous mean arterial and pulse pressure genome-wide association study meta-analysis in Europeans, evidence of trans-ethnic replication was determined by consistency in effect direction and a Bonferroni-corrected P<1.4×10−3. No novel loci were identified by the current study. Five independent mean arterial pressure variants demonstrated robust evidence for trans-ethnic replication including rs17249754 at ATP2B1 (P=7.5×10−15), rs2681492 at ATP2B1 (P=3.4×10−7), rs11191593 at NT5C2 (1.1×10−6), rs3824755 at CYP17A1 (P=1.2×10−6), and rs13149993 at FGF5 (P=2.4×10−4). Two additional variants showed suggestive evidence of trans-ethnic replication (consistency in effect direction and P<0.05), including rs319690 at MAP4 (P=0.014) and rs1173771 at NPR3 (P=0.018). For pulse pressure, robust evidence of replication was identified for 2 independent variants, including rs17249754 at ATP2B1 (P=1.2×10−5) and rs11191593 at NT5C2 (P=1.1×10−3), with suggestive evidence of replication among an additional 2 variants including rs3824755 at CYP17A1 (P=6.1×10−3) and rs2681492 at ATP2B1 (P=9.0×10−3). Replicated variants demonstrated consistency in effect sizes between East Asian and European samples, with effect size differences ranging from 0.03 to 0.24 mmHg for mean arterial pressure and from 0.03 to 0.21 mmHg for pulse pressure. In conclusion, we present the first evidence of trans-ethnic replication of several mean arterial and pulse pressure loci in an East Asian population.
doi:10.1161/HYPERTENSIONAHA.113.01148
PMCID: PMC3972802  PMID: 24001895
genetics; polymorphism; single nucleotide; blood pressure; hypertension; genome-wide association study; meta-analysis
15.  Gastrodin Suppresses the Amyloid β-Induced Increase of Spontaneous Discharge in the Entorhinal Cortex of Rats 
Neural Plasticity  2014;2014:320937.
Accumulated soluble amyloid beta- (Aβ-) induced aberrant neuronal network activity may directly contribute to cognitive deficits, which are the most outstanding characteristics of Alzheimer's disease (AD). The entorhinal cortex (EC) is one of the earliest affected brain regions in AD. Impairments of EC neurons are responsible for the cognitive deficits in AD. However, little effort has been made to investigate the effects of soluble Aβ on the discharge properties of EC neurons in vivo. The present study was designed to examine the effects of soluble Aβ1−42 on the discharge properties of EC neurons, using in vivo extracellular single unit recordings. The protective effects of gastrodin (GAS) were also investigated against Aβ1−42-induced alterations in EC neuronal activities. The results showed that the spontaneous discharge of EC neurons was increased by local application of soluble Aβ1−42 and that GAS can effectively reverse Aβ1−42-induced facilitation of spontaneous discharge in a concentration-dependent manner. Moreover, whole-cell patch clamp results indicated that the protective function of GAS on abnormal hyperexcitability may be partially mediated by its inhibitory action on Aβ1−42-elicited inward currents in EC neurons. Our study suggested that GAS may provide neuroprotective effects on Aβ1−42-induced hyperactivity in EC neurons of rats.
doi:10.1155/2014/320937
PMCID: PMC4251795  PMID: 25485157
16.  Apamin-Sensitive Calcium-Activated Potassium Currents in Rabbit Ventricles with Chronic Myocardial Infarction 
Introduction
Apamin-sensitive small-conductance calcium-activated potassium current (IKAS) is increased in heart failure. It is unknown if myocardial infarction (MI) is also associated with an increase of IKAS.
Methods and Results
We performed Langendorff perfusion and optical mapping in 6 normal hearts and 10 hearts with chronic (5 weeks) MI. An additional 6 normal and 10 MI hearts were used for patch clamp studies. The infarct size was 25% [95% confidence interval, 20 to 31] and the left ventricular ejection fraction was 0.5 [0.46 to 0.54]. The rabbits did not have symptoms of heart failure. The action potential duration measured to 80% repolarization (APD80) in the peri-infarct zone (PZ) was150 [142 to 159] ms, significantly (p=0.01) shorter than in the normal ventricles (158 to 177] ms). The intracellular Ca transient duration was also shorter in the PZ (148 [139 to 157] ms) than in normal ventricles (168 [157 to 180] ms; P=0.017). Apamin prolonged the APD80 in PZ by 9.8 [5.5 to 14.1] %, which is greater than in normal ventricles (2.8 [1.3 to 4.3] %, p=0.006). Significant shortening of APD80 was observed at the cessation of rapid pacing in MI but not in normal ventricles. Apamin prevented postpacing APD80 shortening. Patch clamp studies showed that IKAS was significantly higher in the PZ cells (2.51 [1.55 to 3.47] pA/pF, N=17) than in the normal cells (1.08 [0.36 to 1.80] pA/pF, N=15, p=0.019).
Conclusion
We conclude that IKAS is increased in MI ventricles and contributes significantly to ventricular repolarization especially during tachycardia.
doi:10.1111/jce.12176
PMCID: PMC4207647  PMID: 23718850
action potentials; intracellular calcium; ion channels; repolarization reserve; potassium currents; myocardial infarction
17.  Versatile Immunomagnetic Nanocarrier Platform for Capturing Cancer Cells 
ACS nano  2013;7(10):10.1021/nn403281e.
Sensitive and quantitative assessment of changes in circulating tumor cells (CTCs) can help in cancer prognosis and in the evaluation of therapeutics efficacy. However, extremely low occurrence of CTCs in the peripheral blood (approximately one CTC per billion blood cells) and potential changes in molecular biomarkers during the process of epithelial to mesenchymal transition (EMT) create technical hurdles to the enrichment and enumeration CTCs. Recently, efforts have been directed toward development of antibody-capture assays based on the expression of the common biomarker - the epithelial cell adhesion molecule (EpCAM) of epithelium-derived cancer cells. Despite some promising results, the assays relying on EpCAM capture have shown inconsistent sensitivity in clinical settings and often fail to detect CTCs in patients with metastatic cancer. We have addressed this problem by the development of an assay based on hybrid magnetic/plasmonic nanocarriers and a microfluidic channel. In this assay cancer cells are specifically targeted by antibody-conjugated magnetic nanocarriers and are separated from normal blood cells by a magnetic force in a microfluidic chamber. Subsequently, immunofluorescence staining is used to differentiate CTCs from normal blood cells. We demonstrated in cell models of colon, breast and skin cancers that this platform can be easily adapted to a variety of biomarkers, targeting both surface receptor molecules and intracellular biomarkers of epithelial-derived cancer cells. Experiments in whole blood showed capture efficiency greater than 90% when two cancer biomarkers are used for cell capture. Thus, the combination of immunotargeted magnetic nanocarriers with microfluidics provides an important platform that can improve the effectiveness of current CTC assays by overcoming the problem of heterogeneity of tumor cells in the circulation.
doi:10.1021/nn403281e
PMCID: PMC3846426  PMID: 24016305
gold shell/magnetic core nanoparticles; circulating tumor cells; immunomagnetic assay; microfluidic chip
18.  Single-Molecule Dynamics and Mechanisms of Metalloregulators and Metallochaperones 
Biochemistry  2013;52(41):10.1021/bi400597v.
Understanding how cells regulate and transport metal ions is an important goal in the field of bioinorganic chemistry, a frontier research area that resides at the interfaces of chemistry and biology. This Current Topics article reviews recent advances from the authors' group in using single-molecule fluorescence imaging techniques to identify the mechanisms of metal homeostatic proteins, including metalloregulators and metallochaperones. It emphasizes the novel mechanistic insights into how dynamic protein–DNA and protein–protein interactions offer efficient pathways for MerR-family metalloregulators and copper chaperones to fulfill their functions. The article also summarizes other related single-molecule studies of bioinorganic systems, and gives an outlook toward single-molecule imaging of metalloprotein functions in living cells.
doi:10.1021/bi400597v
PMCID: PMC3830456  PMID: 24053279
19.  Apamin Induces Early Afterdepolarizations and Torsades de Pointes Ventricular Arrhythmia From Failing Rabbit Ventricles Exhibiting Secondary Rises in Intracellular Calcium 
Heart rhythm : the official journal of the Heart Rhythm Society  2013;10(10):10.1016/j.hrthm.2013.07.003.
Background
A secondary rise of intracellular Ca2+ (Cai) and an upregulation of IKAS are characteristic findings of failing ventricular myocytes. We hypothesize that apamin, a specific IKAS blocker, may induce torsades de pointes (TdP) ventricular arrhythmia from failing ventricles exhibiting secondary rises of Cai.
Objectives
To test the hypothesis that small conductance Ca2+ activated apamin sensitive K+ current (IKAS) maintains repolarization reserve and prevents ventricular arrhythmia in a rabbit model of heart failure (HF).
Methods
We performed Langendorff perfusion and optical mapping studies in 7 hearts with pacing-induced HF and in 5 normal control rabbit hearts. Atrioventricular (AV) block was created by cryoablation to allow pacing at slow rates.
Results
The left ventricular ejection fraction reduced from 69.1 [95% confidence interval 62.3–76.0]% pre-pacing to 30.4 [26.8–34.0]% (N=7, p<0.001) post-pacing. The QTc in failing ventricles was 337 [313–360] ms at baseline and 410 [381–439] ms after applying 100 nmol/L of apamin (p=0.01). Apamin induced early afterdepolarizations (EADs) in 6 ventricles, premature ventricular beats (PVBs) in 7 ventricles and polymorphic ventricular tachycardia consistent with TdP in 4 ventricles. The earliest activation site of the EADs and PVBs always occurred at the site with long APD and large amplitude of the secondary rises of Cai. Apamin induced secondary rises of Cai in 1 non-failing ventricles, but no EAD or TdP were observed.
Conclusion
In HF ventricles, apamin induces EADs, PVBs and TdP from areas with secondary rises of Cai. IKAS is important in maintaining repolarization reserve and preventing TdP in HF ventricles.
doi:10.1016/j.hrthm.2013.07.003
PMCID: PMC3832504  PMID: 23835258
Action potential duration; apamin; optical mapping; potassium channels; torsades de pointes
20.  Evaluation of Resident Evacuations in Urban Rainstorm Waterlogging Disasters Based on Scenario Simulation: Daoli District (Harbin, China) as an Example 
With the acceleration of urbanization, waterlogging has become an increasingly serious issue. Road waterlogging has a great influence on residents’ travel and traffic safety. Thus, evaluation of residents’ travel difficulties caused by rainstorm waterlogging disasters is of great significance for their travel safety and emergency shelter needs. This study investigated urban rainstorm waterlogging disasters, evaluating the impact of the evolution of such disasters’ evolution on residents’ evacuation, using Daoli District (Harbin, China) as the research demonstration area to perform empirical research using a combination of scenario simulations, questionnaires, GIS spatial technology analysis and a hydrodynamics method to establish an urban rainstorm waterlogging numerical simulation model. The results show that under the conditions of a 10-year frequency rainstorm, there are three street sections in the study area with a high difficulty index, five street sections with medium difficulty index and the index is low at other districts, while under the conditions of a 50-year frequency rainstorm, there are five street sections with a high difficulty index, nine street sections with a medium difficulty index and the other districts all have a low index. These research results can help set the foundation for further small-scale urban rainstorm waterlogging disaster scenario simulations and emergency shelter planning as well as forecasting and warning, and provide a brand-new thought and research method for research on residents’ safe travel.
doi:10.3390/ijerph111009964
PMCID: PMC4210961  PMID: 25264676
scenario simulation; rainstorm waterlogging disasters; evacuation difficulty levels; Daoli District
21.  Prognostic value of serum nicotinamide phosphoribosyltransferase in patients with bladder cancer 
Croatian Medical Journal  2014;55(5):507-513.
Aim
To analyze the serum nicotinamide phosphoribosyltransferase (Nampt) level and its prognostic value in bladder cancer (BC).
Methods
The study included 131 patients with transitional cell BC and 109 healthy controls from the West China Hospital of Sichuan University in the period between 2007 and 2013. Nampt concentration in serum was measured by commercial ELISA kits for human Nampt.
Results
The serum Nampt protein level in patients with BC (mean ± standard deviation, 16.02 ± 7.95 ng/mL) was significantly higher than in the control group (6.46 ± 2.08 ng/mL) (P < 0.001). Serum Nampt level was an independent prognostic marker of non-muscle-invasive BC, with a higher serum Nampt level (>14.74 ng/mL) indicating shorter recurrence-free survival rate (hazard ratio = 2.85, 95% confidence interval, 1.01-8.06; P = 0.048).
Conclusion
Our results suggest that serum Nampt level may serve as a biomarker of BC and an independent prognostic marker of non-muscle-invasive BC.
doi:10.3325/cmj.2014.55.507
PMCID: PMC4228298  PMID: 25358883
22.  Biomass Enzymatic Saccharification Is Determined by the Non-KOH-Extractable Wall Polymer Features That Predominately Affect Cellulose Crystallinity in Corn 
PLoS ONE  2014;9(9):e108449.
Corn is a major food crop with enormous biomass residues for biofuel production. Due to cell wall recalcitrance, it becomes essential to identify the key factors of lignocellulose on biomass saccharification. In this study, we examined total 40 corn accessions that displayed a diverse cell wall composition. Correlation analysis showed that cellulose and lignin levels negatively affected biomass digestibility after NaOH pretreatments at p<0.05 & 0.01, but hemicelluloses did not show any significant impact on hexoses yields. Comparative analysis of five standard pairs of corn samples indicated that cellulose and lignin should not be the major factors on biomass saccharification after pretreatments with NaOH and H2SO4 at three concentrations. Notably, despite that the non-KOH-extractable residues covered 12%–23% hemicelluloses and lignin of total biomass, their wall polymer features exhibited the predominant effects on biomass enzymatic hydrolysis including Ara substitution degree of xylan (reverse Xyl/Ara) and S/G ratio of lignin. Furthermore, the non-KOH-extractable polymer features could significantly affect lignocellulose crystallinity at p<0.05, leading to a high biomass digestibility. Hence, this study could suggest an optimal approach for genetic modification of plant cell walls in bioenergy corn.
doi:10.1371/journal.pone.0108449
PMCID: PMC4177209  PMID: 25251456
23.  Study on the effect of BMSCs-EGFP-tk as mediator of HSV1-tk/GCV suicide gene therapy directed against A549 in vitro 
This study aims to observe the expression of HSV1-tk in mouse bone marrow mesenchymal stem cells (BMSCs-EGFP-tk) and detect the inhibition and killing effects of BMSCs as mediator of HSV1-tk/GCV on A549 cells in vitro, which can provide the experimental basis for gene therapy of lung cancer. We constructed the recombinant plasmid Vector pDON-AI-2 Neo-HSV1-tk-IRES2-EGFP with genetic engineering methods. Then we obtained the virus-like particles with infection ability after packaging the virus. The recombinant plasmid was transfected into mouse bone marrow mesenchymal stem cells in vitro. The expressions of EGFP in cells were observed by fluorescence microscopy and HSV1-tk gene was detected with RT-PCR. At last, the A549 cells and BMSCs-EGFP-tk cells were co-cultured with in vitro contact method, and the effect of BMSCs-EGFP-tk/GCV system was determined by MTT. Results indicated that the biological characteristics of BMSCs-EGFP-tk were consistent with those of BMSCs and fluorescent light expression and HSV1-tk gene expression can persist at least 15 days. The A549 cells and BMSCs-EGFP-tk cells were co-cultured and BMSCs-EGFP-tk:A549 = 2:1, adding 1 μg/mL GCV, the theory mortality is 58.44%, but actually the mortality is 90%. There is almost no difference between BMSCs-EGFP-tk and BMSCs cells in biological characteristics. The growth of A549 cells have an obviously inhibition and the bystander effect is outstanding in vitro after co-culture and this experiment lays solid foundation for the future research.
PMCID: PMC4211835  PMID: 25356185
Lung cancer; BMSCs; HSV1-tk; co-culture; bystander effect
24.  PROBING SINGLE DNA MOLECULE TRANSPORT USING FABRICATED NANOPORES 
Nano letters  2004;4(11):2293-2298.
Nanopores can serve as high throughput, single molecule sensing devices that provide insight into the distribution of static and dynamic molecular activities, properties, or interactions. We have studied double stranded DNA electrophoretic transport dynamics through fabricated nanopores in silicon nitride. A fabricated pore enables us to interrogate a broader range of molecules with a wider range of conditions than can be investigated in a self-assembled protein pore in a lipid membrane.
doi:10.1021/nl048654j
PMCID: PMC4160839  PMID: 25221441
25.  Arsenic trioxide-based therapy in relapsed/refractory multiple myeloma patients: a meta-analysis and systematic review 
OncoTargets and therapy  2014;7:1593-1599.
Multiple myeloma (MM) is a clonal malignancy characterized by the proliferation of malignant plasma cells in the bone marrow and the production of monoclonal immunoglobulin. Although some newly approved drugs (thalidomide, lenalidomide, and bortezomib) demonstrate significant benefit for MM patients with improved survival, all MM patients still relapse. Arsenic trioxide (ATO) is the most active single agent in acute promyelocytic leukemia, the antitumor activity of which is partly dependent on the production of reactive oxygen species. Due to its multifaceted effects observed on MM cell lines and primary myeloma cells, Phase I/II trials have been conducted in heavily pretreated patients with relapsed or refractory MM. Therapy regimens varied dramatically as to the dosage of ATO and monotherapy versus combination therapy with other agents available for the treatment of MM. Although ATO-based combination treatment was well tolerated by most patients, most trials found that ATO has limited effects on MM patients. However, since small numbers of patients were randomized to different treatment arms, trials have not been statistically powered to determine the differences in progression-free survival and overall survival among the experimental arms. Therefore, large Phase III studies of ATO-based randomized controlled trials will be needed to establish whether ATO has any potential beneficial effects in the clinical setting.
doi:10.2147/OTT.S67165
PMCID: PMC4166211  PMID: 25246802
multiple myeloma; arsenic trioxide; clinical trial; therapy; meta-analysis

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