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1.  PHD2 Silencing Enhances the Survival and Paracrine Function of Transplanted Adipose-Derived Stem Cells in Infarcted Myocardium 
Circulation research  2013;113(3):288-300.
Rationale
Transplantation of stem cells into damaged hearts has had modest success as a treatment for ischemic heart disease. One of the limitations is the poor stem cell survival in the diseased microenvironment. Prolyl hydroxylase domain protein 2 (PHD2) is a cellular oxygen sensor that regulates two key transcription factors involved in cell survival and inflammation, hypoxia-inducible factor (HIF) and nuclear factor-κB (NF-κB).
Objective
We studied if and how PHD2 silencing in human adipose-derived stem cells (ADSCs) enhances their cardioprotective effects after transplantation into infarcted hearts.
Methods and Results
ADSCs were transduced with lentiviral shPHD2 to silence PHD2. ADSCs with or without shPHD2 were transplanted after myocardial infarction (MI) in mice. ADSCs reduced cardiomyocyte apoptosis, fibrosis and infarct size and improved cardiac function. shPHD2-ADSCs exerted significantly more protection. PHD2 silencing induced greater ADSCs survival, which was abolished by shHIF-1α. Conditioned medium (CM) from shPHD2-ADSCs decreased cardiomyocyte apoptosis. Insulin-like growth factor 1 (IGF-1) levels were significantly higher in the CM of shPHD2-ADSCs versus ADSCs, and depletion of IGF-1 attenuated the cardioprotective effects of shPHD2-ADSCs-CM. NF-κB activation was induced by shPHD2 to induce IGF-1 secretion via binding to IGF-1 gene promoter.
Conclusions
PHD2 silencing promotes ADSCs survival in MI hearts and enhances their paracrine function to protect cardiomyocytes. The pro-survival effect of shPHD2 on ADSCs is HIF-1α dependent and the enhanced paracrine function of shPHD2-ADSCs is associated with NF-κB-mediated IGF-1 up-regulation. PHD2 silencing in stem cells may be a novel strategy for enhancing the effectiveness of stem cell therapy after MI.
doi:10.1161/CIRCRESAHA.113.300929
PMCID: PMC3744216  PMID: 23694817
Myocardial infarction; stem cell; survival; paracrine effect; cardiomyocyte
2.  The Relative Contribution of Paracine Effect versus Direct Differentiation on Adipose-Derived Stem Cell Transplantation Mediated Cardiac Repair 
PLoS ONE  2013;8(3):e59020.
Background
Recent studies have demonstrated that transplantation of adipose-derived stem cell (ADSC) can improve cardiac function in animal models of myocardial infarction (MI). However, the mechanisms underlying the beneficial effect are not fully understood. In this study, we characterized the paracrine effect of transplanted ADSC and investigated its relative importance versus direct differentiation in ADSC transplantation mediated cardiac repair.
Methodology/Principal Findings
MI was experimentally induced in mice by ligation of the left anterior descending coronary artery. Either human ADSC, conditioned medium (CM) collected from the same amount of ADSC or control medium was injected into the peri-infarct region immediately after MI. Compared with the control group, both ADSC and ADSC-CM significantly reduced myocardial infarct size and improved cardiac function. The therapeutic efficacy of ADSC was moderately superior to ADSC-CM. ADSC-CM significantly reduced cardiomyocyte apoptosis in the infarct border zone, to a similar degree with ADSC treatment. ADSC enhanced angiogenesis in the infarct border zone, but to a stronger degree than that seen in the ADSC-CM treatment. ADSC was able to differentiate to endothelial cell and smooth muscle cell in post-MI heart; these ADSC-derived vascular cells amount to about 9% of the enhanced angiogenesis. No cardiomyocyte differentiated from ADSC was found.
Conclusions
ADSC-CM is sufficient to improve cardiac function of infarcted hearts. The therapeutic function of ADSC transplantation is mainly induced by paracrine-mediated cardioprotection and angiogenesis, while ADSC differentiation contributes a minor benefit by being involved in angiogenesis.
Highlights 1 ADSC-CM is sufficient to exert a therapeutic potential. 2. ADSC was able to differentiate to vascular cells but not cardiomyocyte. 3. ADSC derived vascular cells amount to about 9% of the enhanced angiogenesis. 4. Paracrine effect is the major mechanism of ADSC therapeutic function for MI.
doi:10.1371/journal.pone.0059020
PMCID: PMC3602597  PMID: 23527076
3.  Tonic Glutamatergic Input in The Rostral Ventrolateral Medulla is Increased in Rats With Chronic Heart Failure 
Hypertension  2008;53(2):370-374.
Chronic heart failure (CHF) is characterized by increased sympathetic tone. The glutamatergic input in the rostral ventrolateral medulla (RVLM), which is a key region involved in sympathetic outflow, seems not to be involved in the generation of sympathetic tone in the normal state. The aim of this study was to determine the role of the RVLM glutamate receptors in generation of sympathetic tone in CHF. CHF was produced by left coronary artery ligation. Bilateral microinjection of the glutamate receptor antagonist kynurenic acid (KYN), the N-methyl-D-aspartate (NMDA) receptor antagonist D-AP5, or the non-NMDA receptor antagonist CNQX into the RVLM dose-dependently reduced resting blood pressure and renal sympathetic nerve activity in CHF but not in sham rats. Picoinjection of KYN (100 pmol in 5 nl) significantly decreased the basal discharge by 47% in 25 RVLM presympathetic neurons in CHF rats, In contrast, KYN had no effect on the discharge in all 22 RVLM presympathetic neurons tested in sham rats. These data suggest that upregulated glutamate receptors, including NMDA and non-NMDA, in the RVLM are involved in tonic control of elevated sympathetic tone in CHF.
doi:10.1161/HYPERTENSIONAHA.108.122598
PMCID: PMC3574554  PMID: 19029485
sympathoexcitation; glutamate receptors; micro/picoinjection; extracellular recording; presympathetic neuron
4.  The time interval between hCG priming and oocyte retrieval in ART program: a meta-analysis 
Objective
To evaluate the relationship between different hCG priming-to-oocyte retrieval intervals and assisted reproductive technology (ART) outcome.
Methods
We systematically searched PubMed, EMBASE, the Cochrane Library, Science Citation Index, Chinese biomedicine (CBM) literature database, and Chinese Journal Full-text Database for randomized controlled trials (RCTs) published up to November 2010. Data was extracted from the studies by two independent reviewers. Statistical analysis was performed with Cochrane Collaboration’s Review Manager (RevMan) 5.0.2. From extracted data, Risk Ratio (RR) with 95% confidence interval (CI) was calculated.
Results
5 RCTs totaling 895 participants were included. Oocyte maturation rate was higher in the long interval group compared with short interval group (RR, 0.67; 95% CI, 0.62–0.73). There were no significant difference between the two groups with regard to fertilization rate (RR, 0.99; 95% CI, 0.94–1.04), implantation rate (RR, 0.91; 95% CI, 0.40–2.04), and pregnancy rate (RR, 0.79; 95% CI, 0.58–1.08).
Conclusion
The percentage of mature (MII) oocytes can be increased by prolonging the interval between hCG priming and oocyte retrieval. The prolonged interval could not increase the fertilization rate, implantation rate, and pregnancy rate. Although there was evidence to confirm the results, they still need to be confirmed by large-sample, multicenter, randomized controlled trials. The time interval dependent mechanisms responsible for ART performance need to be elucidated.
doi:10.1007/s10815-011-9613-x
PMCID: PMC3220445  PMID: 21792666
Human chorionic gonadotropin; Oocyte retrieval; Time interval; Infertility; Assisted reproductive technology; Meta-analysis
5.  IMBALANCE OF AT1R AND AT2R IN THE RVLM: POTENTIAL MECHANISM FOR SYMPATHETIC OVERACTIVITY IN HEART FAILURE 
Hypertension  2008;52(4):708-714.
Up-regulation of Angiotensin type 1 receptors (AT1R) in the rostral ventrolateral medulla (RVLM) contributes to the sympatho-excitation in the chronic heart failure (CHF). However, the role of AT2R is not clear. In this study, we measured AT1R and AT2R protein expression in the RVLM and determined their effects on renal sympathetic nerve activity (RSNA), blood pressure (BP), and heart rate (HR) in anaesthetized sham and CHF rats. We found that: (1) while AT1R expression in the RVLM was up-regulated, the AT2R was significantly down-regulated (CHF: 0.06 ± 0.02 vs sham: 0.15 ± 0.02, P < 0.05); (2) simultaneously stimulating RVLM AT1R and AT2R by Ang II evoked sympatho-excitation, hypertension, and tachycardia in both sham and CHF rats, with greater responses in CHF; (3) stimulating RVLM AT1R with Ang II plus the specific AT2R antagonist PD123319 induced a larger sympatho-excitatory response than simultaneously stimulating AT1R and AT2R in sham rats, but not in CHF; (4) activating RVLM AT2R with CGP42112 induced a sympatho-inhibition, hypotension, and bradycardia only in sham rats (RSNA: 36.4 ± 5.1 % of baseline vs 102 ± 3.9 % of baseline in aCSF, P < 0.05); (5) pretreatment with ETYA, a general inhibitor of AA metabolism, into the RVLM attenuates the CGP42112 induced sympatho-inhibition. These results suggest that AT2R in the RVLM exhibits an inhibitory effect on sympathetic outflow, which is, at least partially, mediated by an AA metabolic pathway. These data implicate a down regulation in the AT2R as a contributory factor in the sympatho-excitation in CHF.
doi:10.1161/HYPERTENSIONAHA.108.116228
PMCID: PMC2760297  PMID: 18768398
Angiotensin II type 2 receptor; Angiotensin II type 1 receptor; rostral ventrolateral medulla; sympathetic outflow
6.  2-[3-(Trifluoro­meth­yl)phen­oxy]ethyl 1-oxo-2,6,7-trioxa-1λ5-phosphabicyclo­[2.2.2]octane-4-carboxyl­ate 
In the crystal structure of the title compound, C14H14F3O7P, the central chain, which connects the phosphate bicyclic system and the benzene ring, is made up of an approximately planar C—C(O)—O—C(H2) fragment and a C(H2)—O—C(Ph) link; the mean planes make a dihedral angle of 75.9 (2)°. The F atoms are disordered over two positions; the site occupancy factors are ca 0.6 and 0.4.
doi:10.1107/S1600536808003735
PMCID: PMC2960863  PMID: 21201921
7.  Differential effects of cardiac sympathetic afferent stimulation on neurons in the nucleus tractus solitarius 
Neuroscience letters  2006;409(2):146-150.
Activation of the cardiac “sympathetic afferent” reflex (CSAR) has been reported to depress the arterial baroreflex and enhance the arterial chemoreflex via a central mechanism. In the present study, we used single-unit extracellular recording techniques to examine the effects of stimulation of cardiac sympathetic afferents on baro- or chemosensitive neurons in the nucleus tractus solitarius (NTS) in anesthetized rats. Of 54 barosensitive NTS neurons tested for their response to epicardial application of capsaicin (0.4 μg), 38 were significantly (P<0.01) inhibited by 38 % while 16 did not respond. Of 42 NTS chemosensitive neurons tested for their response to capsaicin, 33 were significantly (P<0.01) excited by 47 % while 9 did not respond. In addition, of 12 both barosensitive and chemosensitive NTS neurons tested for capsaicin, 2 were excited, 7 were inhibited, and 3 did not respond. In conclusion, this study indicates that CSAR activation inhibited NTS barosensitive neurons and excited NTS chemosensitive neurons, suggesting that the NTS plays an important role in processing the interactions between these cardiovascular reflexes.
doi:10.1016/j.neulet.2006.09.032
PMCID: PMC1904510  PMID: 17014954
cardiovascular reflexes; sympathetic activity; capsaicin; extracellular recording; baro-/chemosensitive neuron
8.  Exercise Training Prevents Arterial Baroreflex Dysfunction in Rats Treated With Central Angiotensin II 
Hypertension  2007;49(3):519-527.
Angiotensin II (Ang II)–induced arterial baroreflex dysfunction is associated with superoxide generation in the brain. Exercise training (EX) improves baroreflex function and decreases oxidative stress in cardiovascular diseases linked to elevated central Ang II. The aim of this study was to determine whether previous EX prevents baroreflex impairment caused by central administration of exogenous Ang II via an Ang II–superoxide mechanism. Four groups of rats were used: non-EX artificial cerebrospinal fluid infused, non-EX Ang II infused, EX artificial cerebrospinal fluid infused, and EX Ang II infused. Rats were treadmill trained for 3 to 4 weeks and subjected to intracerebroventricular infusion of Ang II over the last 3 days of EX. Twenty-four hours after the end of EX, the arterial baroreflex was assessed in anesthetized rats. Compared with non-EX artificial cerebrospinal fluid–infused rats, Ang II significantly decreased baroreflex sensitivity (maximum gain: 3.0 ± 0.2% of maximum per millimeter of mercury versus 1.6 ± 0.1% of maximum per millimeter of mercury; P < 0.01), which was abolished by acute intracerebroventricular infusion of the Ang II type 1 receptor antagonist losartan and the reduced nicotinamide-adenine dinucleotide phosphate oxidase inhibitor apocynin. EX prevented the decrease in baroreflex sensitivity and downregulated Ang II type 1 receptor and NADPH oxidase subunit protein expression in the paraventricular nucleus of Ang II–infused rats. Finally, EX decreased superoxide production in the paraventricular nucleus of Ang II–infused rats. These results indicate that EX improves arterial baroreflex function in conditions of high brain Ang II, which is mediated by the central Ang II type 1 receptor and associated with a reduction in central oxidative stress.
doi:10.1161/01.HYP.0000256955.74461.93
PMCID: PMC1904508  PMID: 17224469
exercise; baroreflex; sympathetic nerve activity; reactive oxygen species; AT1 receptor
9.  Phosphopeptide Enrichment with TiO2-Modified Membranes and Investigation of Tau Protein Phosphorylation 
Analytical chemistry  2013;85(12):5699-5706.
Selective enrichment of phosphopeptides prior to their analysis by mass spectrometry (MS) is vital for identifying protein phosphorylation sites involved in cellular regulation. This study describes modification of porous nylon substrates with TiO2 nanoparticles to create membranes that rapidly enrich phosphopeptides. Membranes with a 22-mm diameter bind 540 nmol of phosphoangiotensin and recover 70% of the phosphopeptides in mixtures with a 15-fold excess of non-phosphorylated proteins. Recovery is 90% for a pure phosphopeptide. Insertion of small membrane disks into HPLC fittings allows rapid enrichment of 5 mL of 1 fmol/μL phosphoprotein digests and concentration into small-volume (10’s of μL) eluates. The combination of membrane enrichment with tandem mass spectrometry reveals seven phosphorylation sites from in vivo phosphorylated tau (p-tau) protein, which is associated with Alzheimer’s disease.
doi:10.1021/ac400198n
PMCID: PMC3721342  PMID: 23638980
10.  New index to predict esophageal variceal bleeding in cirrhotic patients 
AIM: To develop a safe, simple, noninvasive and affordable system to predict esophageal variceal bleeding (EVB) in decompensated cirrhosis patients.
METHODS: Four hundred and eighty-six patients with decompensated cirrhosis (238 males and 248 females), with a mean age of 63.1 ± 11.2 years, were admitted to Changshu Affiliated Hospital of Suzhou University between May 2008 and March 2011. Patients enrolled in this study underwent ultrasound-Doppler (US-Doppler) to assess left gastric vein (LGV) blood flow velocity (LGVV) and blood flow direction (LGVBFD), and were evaluated by the Model For End-Stage Liver Disease (MELD) scoring system. All patients received follow-up evaluations every three months. The resulting data were entered into a database after each time point collection.
RESULTS: Four hundred and sixteen patients completed follow-up evaluations for an average of 31.6 mo (range: 12 to 47 mo). Fifty-one (12.3%) patients experienced EVB. The change in the MELD score over three months (ΔMELD), LGVV and LGVBFD were independently associated with EVB occurrence. MELD-US-Doppler Index (MUI), a new index, was developed and calculated using the following logistic regression equation: MUI = Logit (P) = 1.667 (ΔMELD) + 2.096 (LGVV) - 3.245 (LGVBFD) - 1.697. The area under the receiver operating characteristic curve for prediction of EVB occurrence was significantly higher for the MUI [0.858 (95%CI: 0.774-0.920)] than for ΔMELD [0.734 (95%CI: 0.636-0.817); P < 0.05], LGVV [0.679 (95%CI: 0.578-0.769); P < 0.05] or LGVBFD [0.726 (95%CI: 0.627-0.810); P < 0.05] alone. When the MUI was set at 46, the index had high diagnostic accuracy (85.8%), with high specificity (80%) and sensitivity (87.27%).
CONCLUSION: The MUI, a noninvasive and affordable index, can predict EVB occurrence in decompensated cirrhotic patients and serve as an alternative when conventional endoscopic screening is declined.
doi:10.3748/wjg.v20.i22.6989
PMCID: PMC4051942  PMID: 24944493
Portal hypertension; Ultrasound-Doppler; Esophageal variceal bleeding; Decompensated cirrhosis; Endoscopy
11.  Magnetic Resonance Imaging and Computed Tomography Characteristics of Renal Cell Carcinoma Associated with Xp11.2 Translocation/TFE3 Gene Fusion 
PLoS ONE  2014;9(6):e99990.
Purpose
To characterize Xp11.2 translocation renal cell carcinoma (RCC) using magnetic resonance imaging (MRI) and computed tomography (CT).
Methods
This study retrospectively collected the MRI and CT data of twelve patients with Xp11.2 translocation RCC confirmed by pathology. Nine cases underwent dynamic contrast-enhanced MRI (DCE-MRI) and 6 cases underwent CT, of which 3 cases underwent MRI and CT simultaneously. The MRI and CT findings were analyzed in regard to tumor position, size, hemorrhagic, cystic or necrotic components, calcification, tumor density, signal intensity and enhancement features.
Results
The age of the 12 patients ranged from 13 to 46 years (mean age: 23 years). T2WI revealed heterogeneous intensity, hyper-intensity, and slight hypo-intensity in 6 cases, 2 cases, and 1 case, respectively. On DCE-MR images, mild, moderate, and marked rim enhancement of the tumor in the corticomedullary phase (CMP) were observed in 1, 6, and 2 cases, respectively. The tumor parenchyma showed iso-attenuation (n = 4) or slight hyper-attenuation (n = 1) compared to the normal renal cortex on non-contrast CT images. Imaging findings were suggestive of hemorrhage (n = 4) or necrosis (n = 8) in the tumors, and there was evidence of calcification in 8 cases by CT (n = 3) and pathology (n = 8). On dynamic contrast-enhanced CT images, 3 cases and 1 case manifested moderate and strong CMP enhancement, respectively. Nine tumors by MRI and 4 tumors by CT showed prolonged enhancement. Three neoplasms presented at stage I, 2 at stage II, 3 at stage III, and 4 at stage IV according the 2010 AJCC staging criteria.
Conclusions
XP11.2 translocation RCC should be considered when a child or young adult patient presents with a renal tumor with heterogeneous features such as hemorrhage, necrosis, cystic changes, and calcification on CT and MRI and/or is accompanied by metastatic evidence.
doi:10.1371/journal.pone.0099990
PMCID: PMC4057389  PMID: 24926688
12.  Graph-regularized dual Lasso for robust eQTL mapping 
Bioinformatics  2014;30(12):i139-i148.
Motivation: As a promising tool for dissecting the genetic basis of complex traits, expression quantitative trait loci (eQTL) mapping has attracted increasing research interest. An important issue in eQTL mapping is how to effectively integrate networks representing interactions among genetic markers and genes. Recently, several Lasso-based methods have been proposed to leverage such network information. Despite their success, existing methods have three common limitations: (i) a preprocessing step is usually needed to cluster the networks; (ii) the incompleteness of the networks and the noise in them are not considered; (iii) other available information, such as location of genetic markers and pathway information are not integrated.
Results: To address the limitations of the existing methods, we propose Graph-regularized Dual Lasso (GDL), a robust approach for eQTL mapping. GDL integrates the correlation structures among genetic markers and traits simultaneously. It also takes into account the incompleteness of the networks and is robust to the noise. GDL utilizes graph-based regularizers to model the prior networks and does not require an explicit clustering step. Moreover, it enables further refinement of the partial and noisy networks. We further generalize GDL to incorporate the location of genetic makers and gene-pathway information. We perform extensive experimental evaluations using both simulated and real datasets. Experimental results demonstrate that the proposed methods can effectively integrate various available priori knowledge and significantly outperform the state-of-the-art eQTL mapping methods.
Availability: Software for both C++ version and Matlab version is available at http://www.cs.unc.edu/∼weicheng/.
Contact: weiwang@cs.ucla.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btu293
PMCID: PMC4058913  PMID: 24931977
13.  RNA-Skim: a rapid method for RNA-Seq quantification at transcript level 
Bioinformatics  2014;30(12):i283-i292.
Motivation: RNA-Seq technique has been demonstrated as a revolutionary means for exploring transcriptome because it provides deep coverage and base pair-level resolution. RNA-Seq quantification is proven to be an efficient alternative to Microarray technique in gene expression study, and it is a critical component in RNA-Seq differential expression analysis. Most existing RNA-Seq quantification tools require the alignments of fragments to either a genome or a transcriptome, entailing a time-consuming and intricate alignment step. To improve the performance of RNA-Seq quantification, an alignment-free method, Sailfish, has been recently proposed to quantify transcript abundances using all k-mers in the transcriptome, demonstrating the feasibility of designing an efficient alignment-free method for transcriptome quantification. Even though Sailfish is substantially faster than alternative alignment-dependent methods such as Cufflinks, using all k-mers in the transcriptome quantification impedes the scalability of the method.
Results: We propose a novel RNA-Seq quantification method, RNA-Skim, which partitions the transcriptome into disjoint transcript clusters based on sequence similarity, and introduces the notion of sig-mers, which are a special type of k-mers uniquely associated with each cluster. We demonstrate that the sig-mer counts within a cluster are sufficient for estimating transcript abundances with accuracy comparable with any state-of-the-art method. This enables RNA-Skim to perform transcript quantification on each cluster independently, reducing a complex optimization problem into smaller optimization tasks that can be run in parallel. As a result, RNA-Skim uses <4% of the k-mers and <10% of the CPU time required by Sailfish. It is able to finish transcriptome quantification in <10 min per sample by using just a single thread on a commodity computer, which represents >100 speedup over the state-of-the-art alignment-based methods, while delivering comparable or higher accuracy.
Availability and implementation: The software is available at http://www.csbio.unc.edu/rs.
Contact: weiwang@cs.ucla.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btu288
PMCID: PMC4058932  PMID: 24931995
14.  Reversible posterior leukoencephalopathy syndrome induced by bevacizumab plus chemotherapy in colorectal cancer 
Reversible posterior leukoencephalopathy syndrome (RPLS) is a rare brain-capillary leak syndrome, characterized by clinical symptoms of headache, visual loss, seizures and altered mental functioning. This syndrome is usually reversible and is associated with hypertension, nephropathy, and use of immunosuppressive medication and cytotoxic agents. We describe two rare cases of RPLS occurring in colorectal cancer, both of which presented with coma, that we believe can be directly attributed to bevacizumab, a monoclonal antibody that inhibits the angiogenesis of tumours by specifically blocking vascular endothelial growth factor. We analysed the clinical features, risk factors and outcomes of RPLS in these two patients, and although no typical finding was identified on imaging examination, we found that inadequate blood pressure control was one of the risk factors leading to RPLS and that supportive treatment including intensive blood pressure control improved outcomes. Due to the increasing use of bevacizumab in colorectal cancer, clinicians should be aware of this potential complication.
doi:10.3748/wjg.v20.i21.6691
PMCID: PMC4047361  PMID: 24914397
Bevacizumab; Reversible posterior leukoencephalopathy syndrome; Colorectal cancer; Hypertension; Coma
15.  Reaction Kinetics for the Biocatalytic Conversion of Phenazine-1-Carboxylic Acid to 2-Hydroxyphenazine 
PLoS ONE  2014;9(6):e98537.
The phenazine derivative 2-hydroxyphenazine (2-OH-PHZ) plays an important role in the biocontrol of plant diseases, and exhibits stronger bacteriostatic and fungistatic activity than phenazine-1-carboxylic acid (PCA) toward some pathogens. PhzO has been shown to be responsible for the conversion of PCA to 2-OH-PHZ, however the kinetics of the reaction have not been systematically studied. Further, the yield of 2-OH-PHZ in fermentation culture is quite low and enhancement in our understanding of the reaction kinetics may contribute to improvements in large-scale, high-yield production of 2-OH-PHZ for biological control and other applications. In this study we confirmed previous reports that free PCA is converted to 2-hydroxy-phenazine-1-carboxylic acid (2-OH-PCA) by the action of a single enzyme PhzO, and particularly demonstrate that this reaction is dependent on NADP(H) and Fe3+. Fe3+ enhanced the conversion from PCA to 2-OH-PHZ and 28°C was a optimum temperature for the conversion. However, PCA added in excess to the culture inhibited the production of 2-OH-PHZ. 2-OH-PCA was extracted and purified from the broth, and it was confirmed that the decarboxylation of 2-OH-PCA could occur without the involvement of any enzyme. A kinetic analysis of the conversion of 2-OH-PCA to 2-OH-PHZ in the absence of enzyme and under different temperatures and pHs in vitro, revealed that the conversion followed first-order reaction kinetics. In the fermentation, the concentration of 2-OH-PCA increased to about 90 mg/L within a red precipitate fraction, as compared to 37 mg/L within the supernatant. The results of this study elucidate the reaction kinetics involved in the biosynthesis of 2-OH-PHZ and provide insights into in vitro methods to enhance yields of 2-OH-PHZ.
doi:10.1371/journal.pone.0098537
PMCID: PMC4048165  PMID: 24905009
16.  The Roles of Ca2+/NFAT Signaling Genes in Kawasaki Disease: Single- and Multiple-Risk Genetic Variants 
Scientific Reports  2014;4:5208.
Ca2+/nuclear factor of activated T-cells (Ca2+/NFAT) signaling pathway may play a crucial role in Kawasaki disease (KD). We investigated 16 genetic variants, selected by bioinformatics analyses or previous studies, in 7 key genes involved in this pathway in a Chinese population. We observed a significantly or marginally increased KD risk associated with rs2720378 GC + CC genotypes (OR = 1.39, 95% CI = 1.07–1.80, P = 0.014) or rs2069762 AC + CC genotypes (OR = 1.28, 95% CI = 0.98–1.67, P = 0.066), compared with their wild type counterparts. In classification and regression tree analysis, individuals carrying the combined genotypes of rs2720378 GC or CC genotype, rs2069762 CA or CC genotype and rs1561876 AA genotype exhibited the highest KD risk (OR = 2.12, 95% CI = 1.46–3.07, P < 0.001), compared with the lowest risk carriers of rs2720378 GG genotype. Moreover, a significant dose effect was observed among these three variants (Ptrend < 0.001). In conclusion, this study implicates that single- and multiple-risk genetic variants in this pathway might contribute to KD susceptibility. Further studies on more comprehensive single nucleotide polymorphisms, different ethnicities and larger sample sizes are warranted, and the exact biological mechanisms need to be further clarified.
doi:10.1038/srep05208
PMCID: PMC4047536  PMID: 24903211
17.  A Tetrahedron-Based Endmember Selection Approach for Urban Impervious Surface Mapping 
PLoS ONE  2014;9(6):e93479.
The pixel purity index (PPI) and two-dimensional (2-D) scatter plots are two popular techniques for endmember extraction in remote sensing spectral mixture analysis, yet both suffer from one major drawback, that is, the selection of a final set of endmembers has to endure a cumbersome process of iterative visual inspection and human intervention, especially when a spectrally-complex urban scene is involved. Within the conceptual framework of a V-H-L-S (vegetation-high albedo-low albedo-soil) model, which is expanded from the classic V-I-S (vegetation-impervious surface-soil) model, a tetrahedron-based endmember selection approach combined with a multi-objective optimization genetic algorithm (MOGA) was designed to identify urban endmembers from multispectral imagery. The tetrahedron defining the enclosing volume of MNF-transformed pixels in a three-dimensional (3-D) space was algorithmically sought, so that the tetrahedral vertices can ideally match the four components of the adopted model. A case study with Landsat Enhanced Thematic Mapper Plus (ETM+) satellite imagery in Shanghai, China was conducted to verify the validity of the method. The method performance was compared with those of the traditional PPI and 2-D scatter plots approaches. The results indicated that the tetrahedron-based endmember selection approach performed better in both accuracy and ease of identification for urban surface endmembers owing to the 3-D visualization analysis and use of the MOGA.
doi:10.1371/journal.pone.0093479
PMCID: PMC4043487  PMID: 24892938
18.  High-Avidity and Potently Neutralizing Cross-Reactive Human Monoclonal Antibodies Derived from Secondary Dengue Virus Infection 
Journal of Virology  2013;87(23):12562-12575.
The envelope (E) protein of dengue virus (DENV) is the major target of neutralizing antibodies (Abs) and vaccine development. Previous studies of human dengue-immune sera reported that a significant proportion of anti-E Abs, known as group-reactive (GR) Abs, were cross-reactive to all four DENV serotypes and to one or more other flaviviruses. Based on studies of mouse anti-E monoclonal antibodies (MAbs), GR MAbs were nonneutralizing or weakly neutralizing compared with type-specific MAbs; a GR response was thus not regarded as important for vaccine strategy. We investigated the epitopes, binding avidities, and neutralization potencies of 32 human GR anti-E MAbs. In addition to fusion loop (FL) residues in E protein domain II, human GR MAbs recognized an epitope involving both FL and bc loop residues in domain II. The neutralization potencies and binding avidities of GR MAbs derived from secondary DENV infection were stronger than those derived from primary infection. GR MAbs derived from primary DENV infection primarily blocked attachment, whereas those derived from secondary infection blocked DENV postattachment. Analysis of the repertoire of anti-E MAbs derived from patients with primary DENV infection revealed that the majority were GR, low-avidity, and weakly neutralizing MAbs, whereas those from secondary infection were primarily GR, high-avidity, and potently neutralizing MAbs. Our findings suggest that the weakly neutralizing GR anti-E Abs generated from primary DENV infection become potently neutralizing MAbs against the four serotypes after secondary infection. The observation that the dengue immune status of the host affects the quality of the cross-reactive Abs generated has implications for new strategies for DENV vaccination.
doi:10.1128/JVI.00871-13
PMCID: PMC3838129  PMID: 24027331
19.  Acral myxoinflammatory fibroblastic sarcoma: A case report and literature review 
Acral myxoinflammatory fibroplastic sarcoma is an extremely rare soft-tissue sarcoma. It typically presents as an inflammatory mass in the distal extremities of adult patients. The authors present a review of the available literature as well as a discussion on the surgical management of a patient with acral myxoinflammatory fibroplastic sarcoma who originally requested conservative management but ultimately required a two-digit ray amputation after local recurrence.
PMCID: PMC3891089  PMID: 24431949
Acral; Fibroblastic; Myxoinflammatory; Soft tissue sarcoma
20.  Differential mechanisms underlying neuroprotection of hydrogen sulfide donors against oxidative stress 
Neurochemistry international  2013;62(8):1072-1078.
This study investigated whether slow-releasing organic hydrogen sulfide donors act through the same mechanisms as those of inorganic donors to protect neurons from oxidative stress. By inducing oxidative stress in a neuronal cell line HT22 with glutamate, we investigated the protective mechanisms of the organic donors: ADT-OH [5-(4-hydroxyphenyl)-3H-1, 2-dithiole-3-thione], the most widely used moiety for synthesizing slow-releasing hydrogen sulfide donors, and ADT, a methyl derivative of ADT-OH. The organic donors were more potent than the inorganic donor sodium hydrogensulfide (NaHS) in protecting HT22 cells against glutamate toxicity. Consistent with previous publications, NaHS partially restored glutamate-depleted glutathione (GSH) levels, protected HT22 from direct free radical damage induced by hydrogen peroxide (H2O2), and NaHS protection was abolished by a KATP channel blocker glibenclamide. However, neither ADT nor ADT-OH enhanced glutamate-depleted GSH levels or protected HT22 from H2O2-induced oxidative stress. Glibenclamide, which abolished NaHS neuroprotection against oxidative stress, did not block ADT and ADT-OH neuroprotection against glutamate-induced oxidative stress. Unexpectedly, we found that glutamate induced AMPK activation and that compound C, a well-established AMPK inhibitor, remarkably protected HT22 from glutamate-induced oxidative stress, suggesting that AMPK activation contributed to oxidative glutamate toxicity. Interestingly, all hydrogen sulfide donors, including NaHS, remarkably attenuated glutamate-induced AMPK activation. However, under oxidative glutamate toxicity, compound C only increased the viability of HT22 cells treated with NaHS, but did not further increase ADT and ADT-OH neuroprotection. Thus, suppressing AMPK activation likely contributed to ADT and ADT-OH neuroprotection. In conclusion, hydrogen sulfide donors acted through differential mechanisms to confer neuroprotection against oxidative toxicity and suppressing AMPK activation was a possible mechanism underlying neuroprotection of organic hydrogen sulfide donors against oxidative toxicity.
doi:10.1016/j.neuint.2013.04.001
PMCID: PMC4040256  PMID: 23587562
hydrogen sulfide donors; neuroprotection; AMPK; oxidative stress
21.  Preoperative pelvic axial rotation: a possible predictor for postoperative coronal decompensation in thoracolumbar/lumbar adolescent idiopathic scoliosis 
European Spine Journal  2013;22(6):1264-1272.
Background
The pelvis as the biomechanical foundation of spine, plays an important role in the balance of the stance and gait through the multi-link spinal-pelvic system. If the pelvic axial rotation (PAR) exists in adolescent idiopathic scoliosis (AIS) patients, it should theoretically have some effects on the body balance.
Purpose
To explore the probable effects of preoperative PAR on the spinal balance in coronal plane in AIS patients with main thoracolumbar/lumbar (TL/L) curve after posterior spinal instrumentation.
Methods
Thirty-eight AIS patients (age: 15 ± 1.5 years) with main TL/L curve (51° ± 6.2°) were recruited retrospectively into this study. The mean follow-up period was 27 months (24–36 months). Standing full spine posteroanterior radiographs were taken preoperatively, 3 month and 1 year postoperatively, and at last follow-up. The convex/concave ratio (CV/CC ratio) of the anterior superior iliac spine laterally and the inferior ilium at the sacroiliac joint medially was measured on posteroanterior radiographs. According to the preoperative CV/CC ratios, the patients were divided into two groups: normal group (N-group: 0.95 ≤ CV/CC ≤ 1.05); and the asymmetrical group (A-group: CV/CC < 0.95, or >1.05).
Results
In all the patients, the 3-month-postoperative CV/CC ratio (1.026 ± 0.087) was significantly different from the preoperative CV/CC ratio (0.969 ± 0.095, P < 0.001), indicating that the pelvis had rotated in the opposite direction of the corrective derotation load applied to the TL/L spine after surgery. No significant change was found in the CV/CC ratio from 3-month-postoperative to the last follow-up (1.013 ± 0.103, P > 0.05). There was no significant difference in the demographic, phenotypic, and treatment variables between the N- (n = 16) and A-groups (n = 22) (P > 0.05). However, more coronal decompensation occurred in the A-group after surgery (36.4 vs. 0.0 %, P = 0.013): two patients having trunk translation, three having lower instrumented vertebra (LIV) translation, and one having LIV tilt; meanwhile, one patient having both LIV translation and LIV tilt, and one having both trunk translation and LIV tilt.
Conclusions
The present study confirmed the existence of PAR in AIS patients, and indicated that the pelvis would experience an active rebalancing in the transverse plane within 3 months after spinal correction, and since then, its position would remain stable. Moreover, TL/L-AIS patients with preoperative asymmetrical PAR probably had greater risk of coronal decompensation postoperatively.
doi:10.1007/s00586-013-2695-7
PMCID: PMC3676562  PMID: 23392555
Idiopathic scoliosis; Pelvis; Rotation; Transverse plane; Decompensation
22.  Involvement of arterial baroreflex in the protective effect of dietary restriction against stroke 
Dietary restriction (DR) protects against neuronal dysfunction and degeneration, and reduces the risk of ischemic stroke. This study examined the role of silent information regulator T1 (SIRT1) and arterial baroreflex in the beneficial effects of DR against stroke, using two distinct stroke models: stroke-prone spontaneously hypertensive rats (SP-SHRs) and Sprague-Dawley (SD) rats with middle cerebral artery occlusion (MCAO). Sirt1 knockout (KO) mice were used to examine the involvement of sirt1. Sinoaortic denervation was used to inactivate arterial baroreflex. Dietary restriction was defined as 40% reduction of dietary intake. Briefly, DR prolonged the life span of SP-SHRs and reduced the infarct size induced by MCAO. Dietary restriction also improved the function arterial baroreflex, decreased the release of proinflammatory cytokines, and reduced end-organ damage. The beneficial effect of DR on stroke was markedly attenuated by blunting arterial baroreflex. Lastly, the infarct area in sirt1 KO mice was significantly larger than in the wild-type mice. However, the beneficial effect of DR against ischemic injury was still apparent in sirt1 KO mice. Accordingly, arterial baroreflex, but not sirt1, is important in the protective effect of DR against stroke.
doi:10.1038/jcbfm.2013.28
PMCID: PMC3677110  PMID: 23443169
arterial baroreflex; dietary restriction; sirt1; stroke
23.  Asymmetrically interacting spreading dynamics on complex layered networks 
Scientific Reports  2014;4:5097.
The spread of disease through a physical-contact network and the spread of information about the disease on a communication network are two intimately related dynamical processes. We investigate the asymmetrical interplay between the two types of spreading dynamics, each occurring on its own layer, by focusing on the two fundamental quantities underlying any spreading process: epidemic threshold and the final infection ratio. We find that an epidemic outbreak on the contact layer can induce an outbreak on the communication layer, and information spreading can effectively raise the epidemic threshold. When structural correlation exists between the two layers, the information threshold remains unchanged but the epidemic threshold can be enhanced, making the contact layer more resilient to epidemic outbreak. We develop a physical theory to understand the intricate interplay between the two types of spreading dynamics.
doi:10.1038/srep05097
PMCID: PMC4037715  PMID: 24872257
24.  Connecting lignin-degradation pathway with pre-treatment inhibitor sensitivity of Cupriavidus necator 
To produce lignocellulosic biofuels economically, the complete release of monomers from the plant cell wall components, cellulose, hemicellulose, and lignin, through pre-treatment and hydrolysis (both enzymatic and chemical), and the efficient utilization of these monomers as carbon sources, is crucial. In addition, the identification and development of robust microbial biofuel production strains that can tolerate the toxic compounds generated during pre-treatment and hydrolysis is also essential. In this work, Cupriavidus necator was selected due to its capabilities for utilizing lignin monomers and producing polyhydroxylbutyrate (PHB), a bioplastic as well as an advanced biofuel intermediate. We characterized the growth kinetics of C. necator in pre-treated corn stover slurry as well as individually in the pre-sence of 11 potentially toxic compounds in the saccharified slurry. We found that C. necator was sensitive to the saccharified slurry produced from dilute acid pre-treated corn stover. Five out of 11 compounds within the slurry were characterized as toxic to C. necator, namely ammonium acetate, furfural, hydroxymethylfurfural (HMF), benzoic acid, and p-coumaric acid. Aldehydes (e.g., furfural and HMF) were more toxic than the acetate and the lignin degradation products benzoic acid and p-coumaric acid; furfural was identified as the most toxic compound. Although toxic to C. necator at high concentration, ammonium acetate, benzoic acid, and p-coumaric acid could be utilized by C. necator with a stimulating effect on C. necator growth. Consequently, the lignin degradation pathway of C. necator was reconstructed based on genomic information and literature. The efficient conversion of intermediate catechol to downstream products of cis,cis-muconate or 2-hydroxymuconate-6-semialdehyde may help improve the robustness of C. necator to benzoic acid and p-coumaric acid as well as improve PHB productivity.
doi:10.3389/fmicb.2014.00247
PMCID: PMC4034039  PMID: 24904560
Cupriavidus necator; pre-treatment inhibitor; saccharified slurry; deacetylation; lignin degradation; biofuel; polyhydroxylbutyrate (PHB); genomics
25.  Elevated Ecto-5’-nucleotidase-Mediated Increased Renal Adenosine Signaling Via A2B Adenosine Receptor Contributes to Chronic Hypertension 
Circulation research  2013;112(11):10.1161/CIRCRESAHA.111.300166.
Rationale
Hypertension is the most prevalent life-threatening disease worldwide and is frequently associated with chronic kidney disease (CKD). However, the molecular basis underlying hypertensive CKD is not fully understood.
Objective
We sought to identify specific factors and signaling pathways that contribute to hypertensive CKD and thereby exacerbate disease progression.
Methods and Results
Using high-throughput quantitative reverse-transcription polymerase chain reaction profiling, we discovered that the expression level of 5′-ectonucleotidase (CD73), a key enzyme that produces extracellular adenosine, was significantly increased in the kidneys of angiotensin II–infused mice, an animal model of hypertensive nephropathy. Genetic and pharmacological studies in mice revealed that elevated CD73-mediated excess renal adenosine preferentially induced A2B adenosine receptor (ADORA2B) production and that enhanced kidney ADORA2B signaling contributes to angiotensin II–induced hypertension. Similarly, in humans, we found that CD73 and ADORA2B levels were significantly elevated in the kidneys of CKD patients compared with normal individuals and were further elevated in hypertensive CKD patients. These findings led us to further discover that elevated renal CD73 contributes to excess adenosine signaling via ADORA2B activation that directly stimulates endothelin-1 production in a hypoxia-inducible factor-α–dependent manner and underlies the pathogenesis of the disease. Finally, we revealed that hypoxia-inducible factor-α is an important factor responsible for angiotensin II–induced CD73 and ADORA2B expression at the transcriptional level.
Conclusions
Overall, our studies reveal that angiotensin II–induced renal CD73 promotes the production of renal adenosine that is a prominent driver of hypertensive CKD by enhanced ADORA2B signaling–mediated endothelin-1 induction in a hypoxia-inducible factor-α–dependent manner. The inhibition of excess adenosine-mediated ADORA2B signaling represents a novel therapeutic target for the disease.
doi:10.1161/CIRCRESAHA.111.300166
PMCID: PMC3886128  PMID: 23584256
adenosine; hypertension; chronic renal disease

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